diff --git a/.eslintignore b/.eslintignore new file mode 100644 index 00000000..a9ba028c --- /dev/null +++ b/.eslintignore @@ -0,0 +1 @@ +.eslintrc.js diff --git a/.eslintrc.js b/.eslintrc.js index c6974d7e..dc44580c 100644 --- a/.eslintrc.js +++ b/.eslintrc.js @@ -1,4 +1,5 @@ module.exports = { + root: true, env: { browser: true, jest: true, @@ -6,9 +7,16 @@ module.exports = { commonjs: true, es2021: true, }, - extends: ["eslint:recommended", "plugin:@typescript-eslint/recommended", "prettier"], + extends: [ + "eslint:recommended", + "plugin:@typescript-eslint/recommended", + "plugin:@typescript-eslint/recommended-requiring-type-checking", + "prettier", + ], parser: "@typescript-eslint/parser", parserOptions: { + tsconfigRootDir: __dirname, + project: ["./tsconfig.json", "./packages/*/tsconfig.json"], ecmaVersion: 12, }, plugins: ["@typescript-eslint", "prettier"], diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml deleted file mode 100644 index b6227c12..00000000 --- a/.github/workflows/test.yml +++ /dev/null @@ -1,43 +0,0 @@ -# This workflow will do a clean install of node dependencies, build the source code and run tests across different versions of node -# For more information see: https://help.github.com/actions/language-and-framework-guides/using-nodejs-with-github-actions - -on: - push: - branches: - - "**" - pull_request: - branches: [ main ] - -name: Test Coveralls - -jobs: - - test-coverage: - name: Generate coverage report - runs-on: ubuntu-latest - steps: - - - uses: actions/checkout@v1 - - - name: Use Node.js 14.x - uses: actions/setup-node@v1 - with: - node-version: 14.x - - - name: npm install, generate coverage report - run: | - npm ci - npm run test-cov - - name: Send coverage report to coveralls for visualization - uses: coverallsapp/github-action@master - with: - github-token: ${{ secrets.GITHUB_TOKEN }} - finish: - needs: test-coverage - runs-on: ubuntu-latest - steps: - - name: Coveralls Finished - uses: coverallsapp/github-action@master - with: - github-token: ${{ secrets.github_token }} - parallel-finished: true \ No newline at end of file diff --git a/.github/workflows/test_ws_codecov.yml b/.github/workflows/test_ws_codecov.yml index 84aafd68..2fdcbe37 100644 --- a/.github/workflows/test_ws_codecov.yml +++ b/.github/workflows/test_ws_codecov.yml @@ -16,18 +16,24 @@ jobs: - uses: actions/checkout@v3 with: repository: biothings/biothings_explorer + ref: ${{ steps.branch-name.outputs.current_branch }} - - name: Use Node.js 16.x - uses: actions/setup-node@v1 + - name: Use Node.js 18.x + uses: actions/setup-node@v3 with: - node-version: 16.x + node-version: 18.x - - name: npm install, generate coverage report + - name: Use pnpm + uses: pnpm/action-setup@v2 + with: + version: 8 + + - name: pnpm install, generate coverage report run: | - npm run clone - npm run git checkout ${{ steps.branch-name.outputs.current_branch }} - npm i || true && npm i - npm run test-cov + pnpm run clone + pnpm run git checkout ${{ steps.branch-name.outputs.current_branch }} + pnpm i + pnpm run test-cov - name: Send coverage report to codecov for visualization uses: codecov/codecov-action@v3 diff --git a/.github/workflows/test_ws_cov.yml b/.github/workflows/test_ws_cov.yml deleted file mode 100644 index 5700f1a1..00000000 --- a/.github/workflows/test_ws_cov.yml +++ /dev/null @@ -1,32 +0,0 @@ -on: ["push", "pull_request"] - -name: Test Coveralls with workspace - -jobs: - - test-coverage: - name: Generate coverage report - runs-on: ubuntu-latest - steps: - - - uses: actions/checkout@v3 - with: - repository: biothings/bte-trapi-workspace - - - name: Use Node.js 16.x - uses: actions/setup-node@v1 - with: - node-version: 16.x - - - name: npm install, generate coverage report - run: | - npm run clone - npm i || true && npm i - npm run test-cov --workspace=@biothings-explorer/bte-trapi - - - name: Send coverage report to coveralls for visualization - uses: coverallsapp/github-action@v1.1.1 - with: - github-token: ${{ secrets.GITHUB_TOKEN }} - base-path: ./packages/@biothings-explorer/bte-trapi - path-to-lcov: ./packages/@biothings-explorer/bte-trapi/coverage/lcov.info diff --git a/.gitignore b/.gitignore index ba80b108..498ea28b 100644 --- a/.gitignore +++ b/.gitignore @@ -47,6 +47,9 @@ typings/ # TypeScript cache *.tsbuildinfo +# Turbo cache +.turbo + # Optional npm cache directory .npm @@ -121,7 +124,13 @@ built /.idea .idea/ -packages +packages/* + +# Explicit allow packages.txt +!packages/packages.txt + +# Temporary: allow web-app until new web-app integrated +!packages/web-app # .vscode generally .vscode/* diff --git a/.node-version b/.node-version index 6f7f377b..3f430af8 100644 --- a/.node-version +++ b/.node-version @@ -1 +1 @@ -v16 +v18 diff --git a/.vscode/launch.json b/.vscode/launch.json index 126178fd..f7a94254 100644 --- a/.vscode/launch.json +++ b/.vscode/launch.json @@ -10,7 +10,7 @@ "smartapi_sync" ], "cwd": "${workspaceFolder}", - "runtimeExecutable": "npm", + "runtimeExecutable": "pnpm", "restart": false, "env": { "DEBUG": "biomedical-id-resolver,bte*" @@ -31,7 +31,7 @@ "smartapi_sync" ], "cwd": "${workspaceFolder}", - "runtimeExecutable": "npm", + "runtimeExecutable": "pnpm", "restart": false, "env": { "DEBUG": "biomedical-id-resolver,bte*", @@ -50,10 +50,10 @@ "preLaunchTask": "build", "runtimeArgs": [ "run", - "debug", + "debug" ], "cwd": "${workspaceFolder}", - "runtimeExecutable": "npm", + "runtimeExecutable": "pnpm", "restart": false, "env": { "DEBUG": "biomedical-id-resolver,bte*", @@ -72,10 +72,10 @@ "preLaunchTask": "build and start redis", "runtimeArgs": [ "run", - "debug", + "debug" ], "cwd": "${workspaceFolder}", - "runtimeExecutable": "npm", + "runtimeExecutable": "pnpm", "restart": false, "env": { "REDIS_HOST": "localhost", @@ -97,10 +97,10 @@ "preLaunchTask": "build and start redis", "runtimeArgs": [ "run", - "debug", + "debug" ], "cwd": "${workspaceFolder}", - "runtimeExecutable": "npm", + "runtimeExecutable": "pnpm", "restart": false, "env": { "REDIS_HOST": "localhost", @@ -123,10 +123,10 @@ "preLaunchTask": "build", "runtimeArgs": [ "run", - "debug", + "debug" ], "cwd": "${workspaceFolder}", - "runtimeExecutable": "npm", + "runtimeExecutable": "pnpm", "restart": false, "env": { "REDIS_HOST": "localhost", @@ -149,10 +149,10 @@ "preLaunchTask": "build and start redis cluster", "runtimeArgs": [ "run", - "debug", + "debug" ], "cwd": "${workspaceFolder}", - "runtimeExecutable": "npm", + "runtimeExecutable": "pnpm", "restart": false, "env": { "REDIS_HOST": "localhost", @@ -175,10 +175,10 @@ "preLaunchTask": "build", "runtimeArgs": [ "run", - "debug", + "debug" ], "cwd": "${workspaceFolder}", - "runtimeExecutable": "npm", + "runtimeExecutable": "pnpm", "restart": false, "env": { "REDIS_HOST": "localhost", @@ -194,6 +194,6 @@ ], "stopOnEntry": true, "console": "integratedTerminal" - }, + } ] } diff --git a/.vscode/tasks.json b/.vscode/tasks.json index 8d70d916..1c305d24 100644 --- a/.vscode/tasks.json +++ b/.vscode/tasks.json @@ -6,7 +6,7 @@ { "label": "build", "type": "shell", - "command": "npm run compile", + "command": "pnpm run build", "presentation": { "echo": true, "reveal": "never", diff --git a/__test__/data/api_results/big_sri_input.json b/__test__/data/api_results/big_sri_input.json deleted file mode 100644 index 95a46f3b..00000000 --- a/__test__/data/api_results/big_sri_input.json +++ /dev/null @@ -1 +0,0 @@ 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\ No newline at end of file diff --git a/__test__/data/api_results/big_sri_input_2.json b/__test__/data/api_results/big_sri_input_2.json deleted file mode 100644 index 90ee4ed1..00000000 --- a/__test__/data/api_results/big_sri_input_2.json +++ /dev/null @@ -1 +0,0 @@ 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\ No newline at end of file diff --git a/__test__/data/api_results/big_sri_input_3.json b/__test__/data/api_results/big_sri_input_3.json deleted file mode 100644 index da63630b..00000000 --- a/__test__/data/api_results/big_sri_input_3.json +++ /dev/null @@ -1 +0,0 @@ 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Example 33"},"equivalent_identifiers":[{"identifier":"PUBCHEM.COMPOUND:134253059","label":"US10233188, Example 33"},{"identifier":"INCHIKEY:SIQQWLHTEDFPMX-IRXDYDNUSA-N"}],"type":["biolink:SmallMolecule","biolink:MolecularEntity","biolink:ChemicalEntity","biolink:PhysicalEssence","biolink:ChemicalOrDrugOrTreatment","biolink:ChemicalEntityOrGeneOrGeneProduct","biolink:ChemicalEntityOrProteinOrPolypeptide","biolink:NamedThing","biolink:Entity","biolink:PhysicalEssenceOrOccurrent"]},"PUBCHEM.COMPOUND:134253060":{"id":{"identifier":"PUBCHEM.COMPOUND:134253060","label":"US10233188, Example 35"},"equivalent_identifiers":[{"identifier":"PUBCHEM.COMPOUND:134253060","label":"US10233188, Example 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6-({4-[(3,4-difluorophenyl)carbamoyl]-3-methyl-1,2-thiazol-5-yl}amino)-pyrazine-2-carboxylate"},{"identifier":"INCHIKEY:DAYBHSYGYSCAAV-UHFFFAOYSA-N"}],"type":["biolink:SmallMolecule","biolink:MolecularEntity","biolink:ChemicalEntity","biolink:PhysicalEssence","biolink:ChemicalOrDrugOrTreatment","biolink:ChemicalEntityOrGeneOrGeneProduct","biolink:ChemicalEntityOrProteinOrPolypeptide","biolink:NamedThing","biolink:Entity","biolink:PhysicalEssenceOrOccurrent"]},"PUBCHEM.COMPOUND:134253066":{"id":{"identifier":"PUBCHEM.COMPOUND:134253066","label":"US10233188, Example 41"},"equivalent_identifiers":[{"identifier":"PUBCHEM.COMPOUND:134253066","label":"US10233188, Example 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Example 49"},"equivalent_identifiers":[{"identifier":"PUBCHEM.COMPOUND:134253069","label":"US10233188, Example 49"},{"identifier":"INCHIKEY:KQYUHJHGUAHQIZ-KDOFPFPSSA-N"}],"type":["biolink:SmallMolecule","biolink:MolecularEntity","biolink:ChemicalEntity","biolink:PhysicalEssence","biolink:ChemicalOrDrugOrTreatment","biolink:ChemicalEntityOrGeneOrGeneProduct","biolink:ChemicalEntityOrProteinOrPolypeptide","biolink:NamedThing","biolink:Entity","biolink:PhysicalEssenceOrOccurrent"]},"PUBCHEM.COMPOUND:134253070":{"id":{"identifier":"PUBCHEM.COMPOUND:134253070","label":"US10233188, Example 51"},"equivalent_identifiers":[{"identifier":"PUBCHEM.COMPOUND:134253070","label":"US10233188, Example 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OMPOUND:49840306","label":"N-[5-[4-(Dimethylamino)piperidin-1-yl]pyridin-2-yl]-4-[5-propan-2-yl-3-(trifluoromethyl)-1H-pyrazol-4-yl]pyrimidin-2-amine"},{"identifier":"CHEMBL.COMPOUND:CHEMBL1272171","label":"CHEMBL1272171"},{"identifier":"CAS:1256963-03-7"},{"identifier":"INCHIKEY:DBZXYASRLGQZEQ-UHFFFAOYSA-N"}],"type":["biolink:SmallMolecule","biolink:MolecularEntity","biolink:ChemicalEntity","biolink:PhysicalEssence","biolink:ChemicalOrDrugOrTreatment","biolink:ChemicalEntityOrGeneOrGeneProduct","biolink:ChemicalEntityOrProteinOrPolypeptide","biolink:NamedThing","biolink:Entity","biolink:PhysicalEssenceOrOccurrent"]},"PUBCHEM.COMPOUND:49840175":{"id":{"identifier":"PUBCHEM.COMPOUND:49840175","label":"4-(3-Chloro-5-propan-2-yl-1H-pyrazol-4-yl)-N-(5-piperidin-4-ylpyridin-2-yl)pyrimidin-2-amine"},"equivalent_identifiers":[{"identifier":"PUBCHEM.COMPOUND:49840175","label":"4-(3-Chloro-5-propan-2-yl-1H-pyrazol-4-yl)-N-(5-piperidin-4-ylpyridin-2-yl)pyrimidin-2-amine"},{"identifier":"CHEMBL.COMPOUND:CHEMBL1271898","label":"CHEMBL1271898"},{"identifier":"INCHIKEY:KGEGZSPPABUDIC-UHFFFAOYSA-N"}],"type":["biolink:SmallMolecule","biolink:MolecularEntity","biolink:ChemicalEntity","biolink:PhysicalEssence","biolink:ChemicalOrDrugOrTreatment","biolink:ChemicalEntityOrGeneOrGeneProduct","biolink:ChemicalEntityOrProteinOrPolypeptide","biolink:NamedThing","biolink:Entity","biolink:PhysicalEssenceOrOccurrent"]},"PUBCHEM.COMPOUND:49840108":{"id":{"identifier":"PUBCHEM.COMPOUND:49840108","label":"{4-[3-(4-Fluoro-phenyl)-1H-pyrazol-4-yl]-pyrimidin-2-yl}-(5-piperazin-1-yl-pyridin-2-yl)-amine"},"equivalent_identifiers":[{"identifier":"PUBCHEM.COMPOUND:49840108","label":"{4-[3-(4-Fluoro-phenyl)-1H-pyrazol-4-yl]-pyrimidin-2-yl}-(5-piperazin-1-yl-pyridin-2-yl)-amine"},{"identifier":"CHEMBL.COMPOUND:CHEMBL1271725","label":"CHEMBL1271725"},{"identifier":"INCHIKEY:CTYBGHPMUGCYIR-UHFFFAOYSA-N"}],"type":["biolink:SmallMolecule","biolink:MolecularEntity","biolink:ChemicalEntity","biolink:PhysicalEssence","biolink:ChemicalOrDrugOrTreatment","biolink:ChemicalEntityOrGeneOrGeneProduct","biolink:ChemicalEntityOrProteinOrPolypeptide","biolink:NamedThing","biolink:Entity","biolink:PhysicalEssenceOrOccurrent"]},"PUBCHEM.COMPOUND:49840172":{"id":{"identifier":"PUBCHEM.COMPOUND:49840172","label":"[4-(5-Isopropyl-3-methyl-1H-pyrazol-4-yl)-pyrimidin-2-yl]-(5-piperazin-1-yl-pyridin-2-yl)-amine"},"equivalent_identifiers":[{"identifier":"PUBCHEM.COMPOUND:49840172","label":"[4-(5-Isopropyl-3-methyl-1H-pyrazol-4-yl)-pyrimidin-2-yl]-(5-piperazin-1-yl-pyridin-2-yl)-amine"},{"identifier":"CHEMBL.COMPOUND:CHEMBL1271784","label":"CHEMBL1271784"},{"identifier":"INCHIKEY:CHCNFXZXNLWZAK-UHFFFAOYSA-N"}],"type":["biolink:SmallMolecule","biolink:MolecularEntity","biolink:ChemicalEntity","biolink:PhysicalEssence","biolink:ChemicalOrDrugOrTreatment","biolink:ChemicalEntityOrGeneOrGeneProduct","biolink:ChemicalEntityOrProteinOrPolypeptide","biolink:NamedThing","biolink:Entity","biolink:PhysicalEssenceOrOccurrent"]},"PUBCHEM.COMPOUND:49840173":{"id":{"identifier":"PUBCHEM.COMPOUND:49840173","label":"[4-(5-Chloro-3-isopropyl-1H-pyrazol-4-yl)-pyrimidin-2-yl]-(6-piperazin-1-yl-pyridazin-3-yl)-amine"},"equivalent_identifiers":[{"identifier":"PUBCHEM.COMPOUND:49840173","label":"[4-(5-Chloro-3-isopropyl-1H-pyrazol-4-yl)-pyrimidin-2-yl]-(6-piperazin-1-yl-pyridazin-3-yl)-amine"},{"identifier":"CHEMBL.COMPOUND:CHEMBL1271842","label":"CHEMBL1271842"},{"identifier":"INCHIKEY:KHGITEBUGKISDS-UHFFFAOYSA-N"}],"type":["biolink:SmallMolecule","biolink:MolecularEntity","biolink:ChemicalEntity","biolink:PhysicalEssence","biolink:ChemicalOrDrugOrTreatment","biolink:ChemicalEntityOrGeneOrGeneProduct","biolink:ChemicalEntityOrProteinOrPolypeptide","biolink:NamedThing","biolink:Entity","biolink:PhysicalEssenceOrOccurrent"]},"PUBCHEM.COMPOUND:49840239":{"id":{"identifier":"PUBCHEM.COMPOUND:49840239","label":"[4-(5-Chloro-3-isopropyl-1H-pyrazol-4-yl)-pyrimidin-2-yl]-[5-(3,5-dimethyl-piperazin-1-yl)-pyridin-2-yl]-amine"},"equivalent_identifiers":[{"identifier":"PUBCHEM.COMPOUND:49840239","label":"[4-(5-Chloro-3-isopropyl-1H-pyrazol-4-yl)-pyrimidin-2-yl]-[5-(3,5-dimethyl-piperazin-1-yl)-pyridin-2-yl]-amine"},{"identifier":"CHEMBL.COMPOUND:CHEMBL1272065","label":"CHEMBL1272065"},{"identifier":"INCHIKEY:RRMMUFLOCMXAIP-UHFFFAOYSA-N"}],"type":["biolink:SmallMolecule","biolink:MolecularEntity","biolink:ChemicalEntity","biolink:PhysicalEssence","biolink:ChemicalOrDrugOrTreatment","biolink:ChemicalEntityOrGeneOrGeneProduct","biolink:ChemicalEntityOrProteinOrPolypeptide","biolink:NamedThing","biolink:Entity","biolink:PhysicalEssenceOrOccurrent"]},"PUBCHEM.COMPOUND:49839967":{"id":{"identifier":"PUBCHEM.COMPOUND:49839967","label":"Cyclohexyl-[4-(3-methyl-1H-pyrazol-4-yl)-pyrimidin-2-yl]-amine"},"equivalent_identifiers":[{"identifier":"PUBCHEM.COMPOUND:49839967","label":"Cyclohexyl-[4-(3-methyl-1H-pyrazol-4-yl)-pyrimidin-2-yl]-amine"},{"identifier":"CHEMBL.COMPOUND:CHEMBL1269113","label":"CHEMBL1269113"},{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olecularEntity","biolink:ChemicalEntity","biolink:PhysicalEssence","biolink:ChemicalOrDrugOrTreatment","biolink:ChemicalEntityOrGeneOrGeneProduct","biolink:ChemicalEntityOrProteinOrPolypeptide","biolink:NamedThing","biolink:Entity","biolink:PhysicalEssenceOrOccurrent"]},"PUBCHEM.COMPOUND:118735338":{"id":{"identifier":"PUBCHEM.COMPOUND:118735338","label":"AZ-Dyrk1B-33"},"equivalent_identifiers":[{"identifier":"PUBCHEM.COMPOUND:118735338","label":"AZ-Dyrk1B-33"},{"identifier":"CHEMBL.COMPOUND:CHEMBL3421980","label":"CHEMBL3421980"},{"identifier":"CAS:1679330-37-0"},{"identifier":"INCHIKEY:CZCUSHJQJWKYTD-UHFFFAOYSA-N"}],"type":["biolink:SmallMolecule","biolink:MolecularEntity","biolink:ChemicalEntity","biolink:PhysicalEssence","biolink:ChemicalOrDrugOrTreatment","biolink:ChemicalEntityOrGeneOrGeneProduct","biolink:ChemicalEntityOrProteinOrPolypeptide","biolink:NamedThing","biolink:Entity","biolink:PhysicalEssenceOrOccurrent"]},"PUBCHEM.COMPOUND:118735337":{"id":{"identifier":"PUBCHEM.COMPOUND:118735337","label":"3-(2-Methylpyrimidin-4-yl)-1H-pyrrolo[2,3-c]pyridine"},"equivalent_identifiers":[{"identifier":"PUBCHEM.COMPOUND:118735337","label":"3-(2-Methylpyrimidin-4-yl)-1H-pyrrolo[2,3-c]pyridine"},{"identifier":"CHEMBL.COMPOUND:CHEMBL3421979","label":"CHEMBL3421979"},{"identifier":"INCHIKEY:VAXXXDBEUYQWBN-UHFFFAOYSA-N"}],"type":["biolink:SmallMolecule","biolink:MolecularEntity","biolink:ChemicalEntity","biolink:PhysicalEssence","biolink:ChemicalOrDrugOrTreatment","biolink:ChemicalEntityOrGeneOrGeneProduct","biolink:ChemicalEntityOrProteinOrPolypeptide","biolink:NamedThing","biolink:Entity","biolink:PhysicalEssenceOrOccurrent"]},"PUBCHEM.COMPOUND:118735336":{"id":{"identifier":"PUBCHEM.COMPOUND:118735336","label":"3-[2-[(E)-2-Phenylethenyl]-4-pyrimidinyl]-1H-pyrrolo[2,3-c]pyridine"},"equivalent_identifiers":[{"identifier":"PUBCHEM.COMPOUND:118735336","label":"3-[2-[(E)-2-Phenylethenyl]-4-pyrimidinyl]-1H-pyrrolo[2,3-c]pyridine"},{"identifier":"CHEMBL.COMPOUND:CHEMBL3421978","label":"CHEMBL3421978"},{"identifier":"INCHIKEY:SSUYSUSCBUXMBR-VOTSOKGWSA-N"}],"type":["biolink:SmallMolecule","biolink:MolecularEntity","biolink:ChemicalEntity","biolink:PhysicalEssence","biolink:ChemicalOrDrugOrTreatment","biolink:ChemicalEntityOrGeneOrGeneProduct","biolink:ChemicalEntityOrProteinOrPolypeptide","biolink:NamedThing","biolink:Entity","biolink:PhysicalEssenceOrOccurrent"]},"PUBCHEM.COMPOUND:118735335":{"id":{"identifier":"PUBCHEM.COMPOUND:118735335","label":"7-Methyl-3-[2-(4-methylsulfonylphenyl)pyrimidin-4-yl]-1H-pyrrolo[2,3-c]pyridine"},"equivalent_identifiers":[{"identifier":"PUBCHEM.COMPOUND:118735335","label":"7-Methyl-3-[2-(4-methylsulfonylphenyl)pyrimidin-4-yl]-1H-pyrrolo[2,3-c]pyridine"},{"identifier":"CHEMBL.COMPOUND:CHEMBL3421977","label":"CHEMBL3421977"},{"identifier":"INCHIKEY:WDJPGJTYVFXRTA-UHFFFAOYSA-N"}],"type":["biolink:SmallMolecule","biolink:MolecularEntity","biolink:ChemicalEntity","biolink:PhysicalEssence","biolink:ChemicalOrDrugOrTreatment","biolink:ChemicalEntityOrGeneOrGeneProduct","biolink:ChemicalEntityOrProteinOrPolypeptide","biolink:NamedThing","biolink:Entity","biolink:PhysicalEssenceOrOccurrent"]},"PUBCHEM.COMPOUND:118735334":{"id":{"identifier":"PUBCHEM.COMPOUND:118735334","label":"1-Methyl-3-[2-(4-methylsulfonylphenyl)pyrimidin-4-yl]pyrrolo[2,3-c]pyridine"},"equivalent_identifiers":[{"identifier":"PUBCHEM.COMPOUND:118735334","label":"1-Methyl-3-[2-(4-methylsulfonylphenyl)pyrimidin-4-yl]pyrrolo[2,3-c]pyridine"},{"identifier":"CHEMBL.COMPOUND:CHEMBL3421976","label":"CHEMBL3421976"},{"identifier":"INCHIKEY:UTJIEBWCJRJUNS-UHFFFAOYSA-N"}],"type":["biolink:SmallMolecule","biolink:MolecularEntity","biolink:ChemicalEntity","biolink:PhysicalEssence","biolink:ChemicalOrDrugOrTreatment","biolink:ChemicalEntityOrGeneOrGeneProduct","biolink:ChemicalEntityOrProteinOrPolypeptide","biolink:NamedThing","biolink:Entity","biolink:PhysicalEssenceOrOccurrent"]},"PUBCHEM.COMPOUND:3103157":{"id":{"identifier":"PUBCHEM.COMPOUND:3103157","label":"Cyclohexyl 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-butyloxazol-2-yl)methylthio)thiazol-2-yl)-2-methylpiperidine-4-carboxamide"},"equivalent_identifiers":[{"identifier":"PUBCHEM.COMPOUND:44563119","label":"N-(5-((5-Tert-butyloxazol-2-yl)methylthio)thiazol-2-yl)-2-methylpiperidine-4-carboxamide"},{"identifier":"CHEMBL.COMPOUND:CHEMBL455194","label":"CHEMBL455194"},{"identifier":"INCHIKEY:WDVFSNIVMZTNHY-UHFFFAOYSA-N"}],"type":["biolink:SmallMolecule","biolink:MolecularEntity","biolink:ChemicalEntity","biolink:PhysicalEssence","biolink:ChemicalOrDrugOrTreatment","biolink:ChemicalEntityOrGeneOrGeneProduct","biolink:ChemicalEntityOrProteinOrPolypeptide","biolink:NamedThing","biolink:Entity","biolink:PhysicalEssenceOrOccurrent"]},"PUBCHEM.COMPOUND:9943464":{"id":{"identifier":"PUBCHEM.COMPOUND:9943464","label":"3-(1-Methyl-1H-indol-3-ylmethylene)-1,3-dihydro-pyrrolo[2,3-b]pyridin-2-one"},"equivalent_identifiers":[{"identifier":"PUBCHEM.COMPOUND:9943464","label":"3-(1-Methyl-1H-indol-3-ylmethylene)-1,3-dihydro-pyrrolo[2,3-b]pyridin-2-one"},{"identifier":"CHEMBL.COMPOUND:CHEMBL172179","label":"CHEMBL172179"},{"identifier":"INCHIKEY:RJBBKRZRJMHITR-ZROIWOOFSA-N"}],"type":["biolink:SmallMolecule","biolink:MolecularEntity","biolink:ChemicalEntity","biolink:PhysicalEssence","biolink:ChemicalOrDrugOrTreatment","biolink:ChemicalEntityOrGeneOrGeneProduct","biolink:ChemicalEntityOrProteinOrPolypeptide","biolink:NamedThing","biolink:Entity","biolink:PhysicalEssenceOrOccurrent"]},"PUBCHEM.COMPOUND:4155347":{"id":{"identifier":"PUBCHEM.COMPOUND:4155347","label":"2-Hydroxybohemine"},"equivalent_identifiers":[{"identifier":"PUBCHEM.COMPOUND:4155347","label":"2-Hydroxybohemine"},{"identifier":"CHEMBL.COMPOUND:CHEMBL419931","label":"CHEMBL419931"},{"identifier":"CAS:471270-60-7"},{"identifier":"INCHIKEY:HFIXLXXNEZMSGH-UHFFFAOYSA-N"}],"type":["biolink:SmallMolecule","biolink:MolecularEntity","biolink:ChemicalEntity","biolink:PhysicalEssence","biolink:ChemicalOrDrugOrTreatment","biolink:ChemicalEntityOrGeneOrGeneProduct","biolink:ChemicalEntityOrProteinOrPolypeptide","biolink:NamedThing","biolink:Entity","biolink:PhysicalEssenceOrOccurrent"]},"PUBCHEM.COMPOUND:11669987":{"id":{"identifier":"PUBCHEM.COMPOUND:11669987","label":"2-Fluoro-4-(5-fluoro-4-(1-isopropyl-2-methyl-1H-imidazol-5-yl)pyrimidin-2-ylamino)-N-(1-methylpiperidin-4-yl)benzamide"},"equivalent_identifiers":[{"identifier":"PUBCHEM.COMPOUND:11669987","label":"2-Fluoro-4-(5-fluoro-4-(1-isopropyl-2-methyl-1H-imidazol-5-yl)pyrimidin-2-ylamino)-N-(1-methylpiperidin-4-yl)benzamide"},{"identifier":"CHEMBL.COMPOUND:CHEMBL509406","label":"CHEMBL509406"},{"identifier":"INCHIKEY:SEKBBOWCTFTKRL-UHFFFAOYSA-N"}],"type":["biolink:SmallMolecule","biolink:MolecularEntity","biolink:ChemicalEntity","biolink:PhysicalEssence","biolink:ChemicalOrDrugOrTreatment","biolink:ChemicalEntityOrGeneOrGeneProduct","biolink:ChemicalEntityOrProteinOrPolypeptide","biolink:NamedThing","biolink:Entity","biolink:PhysicalEssenceOrOccurrent"]},"PUBCHEM.COMPOUND:44563157":{"id":{"identifier":"PUBCHEM.COMPOUND:44563157","label":"N-(5-((5-Tert-butyloxazol-2-yl)methylthio)thiazol-2-yl)-6-methylpiperidine-3-carboxamide"},"equivalent_identifiers":[{"identifier":"PUBCHEM.COMPOUND:44563157","label":"N-(5-((5-Tert-butyloxazol-2-yl)methylthio)thiazol-2-yl)-6-methylpiperidine-3-carboxamide"},{"identifier":"CHEMBL.COMPOUND:CHEMBL454645","label":"CHEMBL454645"},{"identifier":"INCHIKEY:QALGDBRHRSNPSF-UHFFFAOYSA-N"}],"type":["biolink:SmallMolecule","biolink:MolecularEntity","biolink:ChemicalEntity","biolink:PhysicalEssence","biolink:ChemicalOrDrugOrTreatment","biolink:ChemicalEntityOrGeneOrGeneProduct","biolink:ChemicalEntityOrProteinOrPolypeptide","biolink:NamedThing","biolink:Entity","biolink:PhysicalEssenceOrOccurrent"]},"PUBCHEM.COMPOUND:44563177":{"id":{"identifier":"PUBCHEM.COMPOUND:44563177","label":"2-Fluoro-4-(5-fluoro-4-(1-isopropyl-2-methyl-1H-imidazol-5-yl)pyrimidin-2-ylamino)-N,N-dimethylbenzamide"},"equivalent_identifiers":[{"identifier":"PUBCHEM.COMPOUND:44563177","label":"2-Fluoro-4-(5-fluoro-4-(1-isopropyl-2-methyl-1H-imidazol-5-yl)pyrimidin-2-ylamino)-N,N-dimethylbenzamide"},{"identifier":"CHEMBL.COMPOUND:CHEMBL454648","label":"CHEMBL454648"},{"identifier":"INCHIKEY:TYRDCYYKRYFRKP-UHFFFAOYSA-N"}],"type":["biolink:SmallMolecule","biolink:MolecularEntity","biolink:ChemicalEntity","biolink:PhysicalEssence","biolink:ChemicalOrDrugOrTreatment","biolink:ChemicalEntityOrGeneOrGeneProduct","biolink:ChemicalEntityOrProteinOrPolypeptide","biolink:NamedThing","biolink:Entity","biolink:PhysicalEssenceOrOccurrent"]},"PUBCHEM.COMPOUND:60200408":{"id":{"identifier":"PUBCHEM.COMPOUND:60200408","label":"7-N-(4-Ethoxyphenyl)-6-methyl-5-N-[(3R)-piperidin-3-yl]pyrazolo[1,5-a]pyrimidine-5,7-diamine"},"equivalent_identifiers":[{"identifier":"PUBCHEM.COMPOUND:60200408","label":"7-N-(4-Ethoxyphenyl)-6-methyl-5-N-[(3R)-piperidin-3-yl]pyrazolo[1,5-a]pyrimidine-5,7-diamine"},{"identifier":"CHEMBL.COMPOUND:CHEMBL2163604","label":"CHEMBL2163604"},{"identifier":"INCHIKEY:WJOUGMPFYANZMI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OMPOUND:70685615":{"id":{"identifier":"PUBCHEM.COMPOUND:70685615","label":"N-[3-[[6-(3,4-Dimethoxyphenyl)-7H-purin-2-yl]amino]phenyl]piperidine-4-carboxamide"},"equivalent_identifiers":[{"identifier":"PUBCHEM.COMPOUND:70685615","label":"N-[3-[[6-(3,4-Dimethoxyphenyl)-7H-purin-2-yl]amino]phenyl]piperidine-4-carboxamide"},{"identifier":"CHEMBL.COMPOUND:CHEMBL2023418","label":"CHEMBL2023418"},{"identifier":"INCHIKEY:KSGQCBIEDABXGB-UHFFFAOYSA-N"}],"type":["biolink:SmallMolecule","biolink:MolecularEntity","biolink:ChemicalEntity","biolink:PhysicalEssence","biolink:ChemicalOrDrugOrTreatment","biolink:ChemicalEntityOrGeneOrGeneProduct","biolink:ChemicalEntityOrProteinOrPolypeptide","biolink:NamedThing","biolink:Entity","biolink:PhysicalEssenceOrOccurrent"]},"PUBCHEM.COMPOUND:70683509":{"id":{"identifier":"PUBCHEM.COMPOUND:70683509","label":"1-[3-[[6-(3,4-Dimethoxyphenyl)-7H-purin-2-yl]amino]phenyl]-3-(2-morpholin-4-ylethyl)urea"},"equivalent_identifiers":[{"identifier":"PUBCHEM.COMPOUND:70683509","label":"1-[3-[[6-(3,4-Dimethoxyphenyl)-7H-purin-2-yl]amino]phenyl]-3-(2-morpholin-4-ylethyl)urea"},{"identifier":"CHEMBL.COMPOUND:CHEMBL2023414","label":"CHEMBL2023414"},{"identifier":"INCHIKEY:DVILUUWSIUVTCY-UHFFFAOYSA-N"}],"type":["biolink:SmallMolecule","biolink:MolecularEntity","biolink:ChemicalEntity","biolink:PhysicalEssence","biolink:ChemicalOrDrugOrTreatment","biolink:ChemicalEntityOrGeneOrGeneProduct","biolink:ChemicalEntityOrProteinOrPolypeptide","biolink:NamedThing","biolink:Entity","biolink:PhysicalEssenceOrOccurrent"]},"PUBCHEM.COMPOUND:70683494":{"id":{"identifier":"PUBCHEM.COMPOUND:70683494","label":"N-(3-Chlorophenyl)-6-(3,4-dimethoxyphenyl)-7H-purin-2-amine"},"equivalent_identifiers":[{"identifier":"PUBCHEM.COMPOUND:70683494","label":"N-(3-Chlorophenyl)-6-(3,4-dimethoxyphenyl)-7H-purin-2-amine"},{"identifier":"CHEMBL.COMPOUND:CHEMBL2023194","label":"CHEMBL2023194"},{"identifier":"INCHIKEY:NXPRGHRSTVWAIH-UHFFFAOYSA-N"}],"type":["biolink:SmallMolecule","biolink:MolecularEntity","biolink:ChemicalEntity","biolink:PhysicalEssence","biolink:ChemicalOrDrugOrTreatment","biolink:ChemicalEntityOrGeneOrGeneProduct","biolink:ChemicalEntityOrProteinOrPolypeptide","biolink:NamedThing","biolink:Entity","biolink:PhysicalEssenceOrOccurrent"]},"PUBCHEM.COMPOUND:46929748":{"id":{"identifier":"PUBCHEM.COMPOUND:46929748","label":"2-Anilino-N-[4-[3-[2-(methylamino)pyrimidin-4-yl]pyridin-2-yl]oxyphenyl]benzamide"},"equivalent_identifiers":[{"identifier":"PUBCHEM.COMPOUND:46929748","label":"2-Anilino-N-[4-[3-[2-(methylamino)pyrimidin-4-yl]pyridin-2-yl]oxyphenyl]benzamide"},{"identifier":"CHEMBL.COMPOUND:CHEMBL1243200","label":"CHEMBL1243200"},{"identifier":"INCHIKEY:YRIZEPGWRQGUBO-UHFFFAOYSA-N"}],"type":["biolink:SmallMolecule","biolink:MolecularEntity","biolink:ChemicalEntity","biolink:PhysicalEssence","biolink:ChemicalOrDrugOrTreatment","biolink:ChemicalEntityOrGeneOrGeneProduct","biolink:ChemicalEntityOrProteinOrPolypeptide","biolink:NamedThing","biolink:Entity","biolink:PhysicalEssenceOrOccurrent"]},"PUBCHEM.COMPOUND:20609848":{"id":{"identifier":"PUBCHEM.COMPOUND:20609848","label":"2-N-(4-Aminocyclohexyl)-6-N-[[4-(3,5-dimethylphenyl)phenyl]methyl]-9-propan-2-ylpurine-2,6-diamine"},"equivalent_identifiers":[{"identifier":"PUBCHEM.COMPOUND:20609848","label":"2-N-(4-Aminocyclohexyl)-6-N-[[4-(3,5-dimethylphenyl)phenyl]methyl]-9-propan-2-ylpurine-2,6-diamine"},{"identifier":"INCHIKEY:NZJXOACOFBXWDC-UHFFFAOYSA-N"}],"type":["biolink:SmallMolecule","biolink:MolecularEntity","biolink:ChemicalEntity","biolink:PhysicalEssence","biolink:ChemicalOrDrugOrTreatment","biolink:ChemicalEntityOrGeneOrGeneProduct","biolink:ChemicalEntityOrProteinOrPolypeptide","biolink:NamedThing","biolink:Entity","biolink:PhysicalEssenceOrOccurrent"]},"PUBCHEM.COMPOUND:21362586":{"id":{"identifier":"PUBCHEM.COMPOUND:21362586","label":"3-[4-[[[2-[(4-Aminocyclohexyl)amino]-9-propan-2-ylpurin-6-yl]amino]methyl]phenyl]benzoic 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end of file diff --git a/__test__/data/api_results/mychem_query_2.json b/__test__/data/api_results/mychem_query_2.json deleted file mode 100644 index 37319fab..00000000 --- a/__test__/data/api_results/mychem_query_2.json +++ /dev/null @@ -1 +0,0 @@ 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\ No newline at end of file diff --git a/__test__/data/api_results/mychem_query_3.json b/__test__/data/api_results/mychem_query_3.json deleted file mode 100644 index 21d79d47..00000000 --- a/__test__/data/api_results/mychem_query_3.json +++ /dev/null @@ -1 +0,0 @@ -[{"query":"16739650","_id":"VXBAJLGYBMTJCY-NSCUHMNNSA-N","_score":17.28317,"chembl._license":"http://bit.ly/2KAUCAm","chembl.inchi":"InChI=1S/C23H24N4O/c1-27-13-3-2-4-14-28-21-10-6-8-19(16-21)22-11-12-24-23(26-22)25-20-9-5-7-18(15-20)17-27/h2-3,5-12,15-16H,4,13-14,17H2,1H3,(H,24,25,26)/b3-2+","chembl.inchi_key":"VXBAJLGYBMTJCY-NSCUHMNNSA-N","chembl.max_phase":1,"chembl.molecule_chembl_id":"CHEMBL1944698","chembl.molecule_type":"Small 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a/__test__/data/api_results/mychem_query_5_input.json b/__test__/data/api_results/mychem_query_5_input.json deleted file mode 100644 index 1bd474c7..00000000 --- a/__test__/data/api_results/mychem_query_5_input.json +++ /dev/null @@ -1 +0,0 @@ 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\ No newline at end of file diff --git a/__test__/data/api_results/mychem_query_6.json b/__test__/data/api_results/mychem_query_6.json deleted file mode 100644 index 47cc1f8c..00000000 --- a/__test__/data/api_results/mychem_query_6.json +++ /dev/null @@ -1 +0,0 @@ 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\ No newline at end of file diff --git a/__test__/data/api_results/mychem_query_6_input.json b/__test__/data/api_results/mychem_query_6_input.json deleted file mode 100644 index 5093a78d..00000000 --- a/__test__/data/api_results/mychem_query_6_input.json +++ /dev/null @@ -1 +0,0 @@ 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if (arr1.length !== arr2.length) { - return false; - } - arr1.sort((a, b) => (a > b ? -1 : 1)); - arr2.sort((a, b) => (a > b ? -1 : 1)); - for (var i = 0; i < arr1.length; i++) { - if (!arrEquals(arr1[i], arr2[i])) return false; - } - return true; -}; - -describe("Testing v1.1 endpoints", () => { - const example_folder = path.resolve(__dirname, "../../examples/v1.1"); - const clinical_risk_kp_folder = path.resolve(__dirname, "../../examples/v1.1/multiomics/clinical_risk_kp"); - const old_spec_folder = path.resolve(__dirname, "../../examples/v0.9.2"); - const invalid_example_folder = path.resolve(__dirname, "../../examples/v1.1/invalid"); - const drug2disease_query = JSON.parse( - fs.readFileSync(path.join(clinical_risk_kp_folder, "query_drug_to_disease.json")), - ); - const gene2chemical_query = JSON.parse( - fs.readFileSync(path.join(example_folder, "query_chemicals_physically_interacts_with_genes.json")), - ); - const disease2gene_query = JSON.parse( - fs.readFileSync(path.join(example_folder, "query_genes_relate_to_disease.json")), - ); - const query_using_earlier_trapi_spec = JSON.parse( - fs.readFileSync(path.join(old_spec_folder, "query_genes_relate_to_disease.json")), - ); - const query_without_category = JSON.parse( - fs.readFileSync(path.join(example_folder, "query_without_input_category.json")), - ); - const expand_node = JSON.parse(fs.readFileSync(path.join(example_folder, "query_with_node_to_be_expanded.json"))); - - test("GET /v1/meta_knowledge_graph", async () => { - await request(app) - .get("/v1/meta_knowledge_graph") - .expect(200) - .expect("Content-Type", /json/) - .then(response => { - expect(response.body).toHaveProperty("nodes"); - expect(response.body).toHaveProperty("nodes.biolink:Gene"); - expect(response.body).toHaveProperty("nodes.biolink:Gene.id_prefixes"); - - expect(response.body).toHaveProperty("edges"); - expect(response.body.edges).toEqual( - expect.arrayContaining([ - expect.objectContaining({ - subject: "biolink:SmallMolecule", - predicate: "biolink:affects", - object: "biolink:Gene", - }), - ]), - ); - }); - }); - - test("GET /v1/team/{team_name}/meta_knowledge_graph", async () => { - await request(app) - .get("/v1/team/Service Provider/meta_knowledge_graph") - .expect(200) - .expect("Content-Type", /json/) - .then(response => { - expect(response.body).toHaveProperty("nodes"); - expect(response.body).toHaveProperty("nodes.biolink:Gene"); - expect(response.body).toHaveProperty("nodes.biolink:Gene.id_prefixes"); - - expect(response.body).toHaveProperty("edges"); - expect(response.body.edges).toEqual( - expect.arrayContaining([ - expect.objectContaining({ - subject: "biolink:SequenceVariant", - predicate: "biolink:is_sequence_variant_of", - object: "biolink:Gene", - }), - ]), - ); - }); - }); - - test("Query to Text Mining team Should return 200 with valid response", async () => { - await request(app) - .get("/v1/team/Text Mining Provider/meta_knowledge_graph") - .expect(200) - .expect("Content-Type", /json/) - .then(response => { - expect(response.body).toHaveProperty("nodes.biolink:Gene"); - expect(response.body.edges).toEqual( - expect.arrayContaining([ - expect.objectContaining({ - subject: "biolink:SmallMolecule", - predicate: "biolink:treats", - object: "biolink:Disease", - }), - ]), - ); - }); - }); - - test("Query to Invalid team Should return 200 with empty response", async () => { - await request(app) - .get("/v1/team/wrong team/meta_knowledge_graph") - .expect(404) - .expect("Content-Type", /json/) - .then(response => { - expect(response.body).toEqual({ - status: "KPsNotAvailable", - description: - "Unable to load predicates: Failed to Load MetaKG: PredicatesLoadingError: Not Found - 0 operations", - }); - }); - }); - - test("GET /v1/smartapi/{smartapi_id}/meta_knowledge_graph", async () => { - await request(app) - // testing with "Text Mining Targeted Association API" - .get("/v1/smartapi/978fe380a147a8641caf72320862697b/meta_knowledge_graph") - .expect(200) - .expect("Content-Type", /json/) - .then(response => { - expect(response.body).toHaveProperty("nodes.biolink:Disease"); - expect(response.body.edges).toEqual( - expect.arrayContaining([ - expect.objectContaining({ - subject: "biolink:SmallMolecule", - predicate: "biolink:treats", - object: "biolink:Disease", - }), - ]), - ); - }); - }); - - test("Query to Invalid API Should return 404 with error message included", async () => { - await request(app) - .get("/v1/smartapi/78fe380a147a8641caf72320862697b/meta_knowledge_graph") - .expect(404) - .expect("Content-Type", /json/) - .then(response => { - expect(response.body).toHaveProperty("status", "KPsNotAvailable"); - expect(response.body).toHaveProperty( - "description", - "Unable to load predicates: Failed to Load MetaKG: PredicatesLoadingError: Not Found - 0 operations", - ); - }); - }); - - test("POST /v1/query with gene2chemical query", async () => { - const mychem_query_3_input = JSON.parse( - fs.readFileSync(path.resolve(__dirname, "../data/api_results/mychem_query_3_input.json")), - ); - const mychem_query_4_input = JSON.parse( - fs.readFileSync(path.resolve(__dirname, "../data/api_results/mychem_query_4_input.json")), - ); - const mychem_query_5_input = JSON.parse( - fs.readFileSync(path.resolve(__dirname, "../data/api_results/mychem_query_5_input.json")), - ); - const mychem_query_6_input = JSON.parse( - fs.readFileSync(path.resolve(__dirname, "../data/api_results/mychem_query_6_input.json")), - ); - const mychem_query_7_input = JSON.parse( - fs.readFileSync(path.resolve(__dirname, "../data/api_results/mychem_query_7_input.json")), - ); - const mychem_query_8_input = JSON.parse( - fs.readFileSync(path.resolve(__dirname, "../data/api_results/mychem_query_8_input.json")), - ); - const mychem_query_9_input = JSON.parse( - fs.readFileSync(path.resolve(__dirname, "../data/api_results/mychem_query_9_input.json")), - ); - const big_sri_input = JSON.parse( - fs.readFileSync(path.resolve(__dirname, "../data/api_results/big_sri_input.json")), - ); - const big_sri_input_2 = JSON.parse( - fs.readFileSync(path.resolve(__dirname, "../data/api_results/big_sri_input_2.json")), - ); - const ngd_input = JSON.parse(fs.readFileSync(path.resolve(__dirname, "../data/api_results/ngd_input.json"))); - - axios.default.mockImplementation(async qData => { - let res = undefined; - if ( - qData.url === "https://mychem.info/v1/query" && - qData.data === - "q=A0A024RB10,A0A024RB77,B4DDL9,E7ESI2,G3V5T9,P24941&scopes=drugcentral.bioactivity.uniprot.uniprot_id" - ) { - res = [ - { query: "A0A024RB10", notfound: true }, - { query: "A0A024RB77", notfound: true }, - { query: "B4DDL9", notfound: true }, - { query: "E7ESI2", notfound: true }, - { query: "G3V5T9", notfound: true }, - { - query: "P24941", - _id: "XZXHXSATPCNXJR-ZIADKAODSA-N", - _score: 9.885763, - drugcentral: { _license: "http://bit.ly/2SeEhUy", xrefs: { chembl_id: ["CHEMBL502835", "CHEMBL3039504"] } }, - }, - { - query: "P24941", - _id: "BCFGMOOMADDAQU-UHFFFAOYSA-N", - _score: 9.098851, - drugcentral: { _license: "http://bit.ly/2SeEhUy", xrefs: { chembl_id: ["CHEMBL1201179", "CHEMBL554"] } }, - }, - { - query: "P24941", - _id: "MLDQJTXFUGDVEO-UHFFFAOYSA-N", - _score: 9.098851, - drugcentral: { _license: "http://bit.ly/2SeEhUy", xrefs: { chembl_id: ["CHEMBL1336", "CHEMBL1200485"] } }, - }, - { - query: "P24941", - _id: "REFJWTPEDVJJIY-UHFFFAOYSA-N", - _score: 8.601126, - drugcentral: { _license: "http://bit.ly/2SeEhUy", xrefs: { chembl_id: "CHEMBL50" } }, - }, - { - query: "P24941", - _id: "AHJRHEGDXFFMBM-UHFFFAOYSA-N", - _score: 8.601126, - drugcentral: { _license: "http://bit.ly/2SeEhUy", xrefs: { chembl_id: ["CHEMBL189963", "CHEMBL2364621"] } }, - }, - { - query: "P24941", - _id: "VERWOWGGCGHDQE-UHFFFAOYSA-N", - _score: 8.601126, - drugcentral: { _license: "http://bit.ly/2SeEhUy", xrefs: { chembl_id: "CHEMBL2403108" } }, - }, - ]; - } - if (qData.url === "https://automat.transltr.io/ctd/1.3/query") { - res = { - message: { - query_graph: { - nodes: { - n0: { ids: ["NCBIGene:1017"], categories: ["biolink:Gene"], is_set: false, constraints: [] }, - n1: { ids: null, categories: ["biolink:SmallMolecule"], is_set: false, constraints: [] }, - }, - edges: { - e01: { - subject: "n0", - object: "n1", - knowledge_type: null, - predicates: ["biolink:decreases_molecular_interaction"], - attribute_constraints: [], - qualifier_constraints: [], - }, - }, - }, - knowledge_graph: { nodes: {}, edges: {} }, - results: [], - }, - log_level: null, - workflow: [{ runner_parameters: null, id: "lookup", parameters: null }], - submitter: "infores:bte", - }; - } - if ( - qData.url === "https://biothings.ncats.io/bindingdb/query" && - qData.data === "q=A0A024RB10,A0A024RB77,B4DDL9,E7ESI2,G3V5T9,P24941&scopes=subject.uniprot.accession" - ) { - res = JSON.parse(fs.readFileSync(path.resolve(__dirname, "../data/api_results/bindingdb_query_0.json"))); - } - if ( - qData.url === "https://biothings.ncats.io/bindingdb/query" && - qData.data === "q=A0A024RB10,A0A024RB77,B4DDL9,E7ESI2,G3V5T9,P24941&scopes=subject.uniprot.accession" && - qData.params?.from - ) { - res = JSON.parse( - fs.readFileSync(path.resolve(__dirname, `../data/api_results/bindingdb_query_${qData.params.from}.json`)), - ); - } - if ( - qData.url === "https://mychem.info/v1/query" && - arrEquals(qData.data?.q, [ - "CHEMBL502835", - "CHEMBL3039504", - "CHEMBL1201179", - "CHEMBL554", - "CHEMBL1336", - "CHEMBL1200485", - "CHEMBL50", - "CHEMBL189963", - "CHEMBL2364621", - "CHEMBL2403108", - ]) - ) { - res = JSON.parse(fs.readFileSync(path.resolve(__dirname, "../data/api_results/mychem_query_2.json"))); - } - if (qData.url === "https://mychem.info/v1/query" && arrEquals(qData.data?.q, mychem_query_3_input)) { - res = JSON.parse(fs.readFileSync(path.resolve(__dirname, "../data/api_results/mychem_query_3.json"))); - } - if (qData.url === "https://mychem.info/v1/query" && arrEquals(qData.data?.q, mychem_query_4_input)) { - res = JSON.parse(fs.readFileSync(path.resolve(__dirname, "../data/api_results/mychem_query_4.json"))); - } - if (qData.url === "https://mychem.info/v1/query" && arrEquals(qData.data?.q, mychem_query_5_input)) { - res = JSON.parse(fs.readFileSync(path.resolve(__dirname, "../data/api_results/mychem_query_5.json"))); - } - if (qData.url === "https://mychem.info/v1/query" && arrEquals(qData.data?.q, mychem_query_6_input)) { - res = JSON.parse(fs.readFileSync(path.resolve(__dirname, "../data/api_results/mychem_query_6.json"))); - } - if (qData.url === "https://mychem.info/v1/query" && arrEquals(qData.data?.q, mychem_query_7_input)) { - res = JSON.parse(fs.readFileSync(path.resolve(__dirname, "../data/api_results/mychem_query_7.json"))); - } - if (qData.url === "https://mychem.info/v1/query" && arrEquals(qData.data?.q, mychem_query_8_input)) { - res = JSON.parse(fs.readFileSync(path.resolve(__dirname, "../data/api_results/mychem_query_8.json"))); - } - if (qData.url === "https://mychem.info/v1/query" && arrEquals(qData.data?.q, mychem_query_9_input)) { - res = JSON.parse(fs.readFileSync(path.resolve(__dirname, "../data/api_results/mychem_query_9.json"))); - } - return { data: res }; - }); - - axios.default.post.mockImplementation(async (...q) => { - const [url, qData] = q; - let res = undefined; - if (arrEquals(qData?.curies, ["NCBIGene:1017"])) { - res = { - "NCBIGene:1017": { - id: { identifier: "NCBIGene:1017", label: "CDK2" }, - equivalent_identifiers: [ - { identifier: "NCBIGene:1017", label: "CDK2" }, - { identifier: "ENSEMBL:ENSG00000123374" }, - { identifier: "HGNC:1771", label: "CDK2" }, - { identifier: "OMIM:116953" }, - { identifier: "UMLS:C1332733", label: "CDK2 gene" }, - { - identifier: "UniProtKB:A0A024RB10", - label: "A0A024RB10_HUMAN Cyclin-dependent kinase 2, isoform CRA_a (trembl)", - }, - { - identifier: "UniProtKB:A0A024RB77", - label: "A0A024RB77_HUMAN Cyclin-dependent kinase 2, isoform CRA_b (trembl)", - }, - { - identifier: "UniProtKB:B4DDL9", - label: - "B4DDL9_HUMAN cDNA FLJ54979, highly similar to Homo sapiens cyclin-dependent kinase 2 (CDK2), transcript variant 2, mRNA (trembl)", - }, - { identifier: "UniProtKB:E7ESI2", label: "E7ESI2_HUMAN Cyclin-dependent kinase 2 (trembl)" }, - { identifier: "ENSEMBL:ENSP00000393605" }, - { identifier: "UniProtKB:G3V5T9", label: "G3V5T9_HUMAN Cyclin-dependent kinase 2 (trembl)" }, - { identifier: "ENSEMBL:ENSP00000452514" }, - { identifier: "UniProtKB:P24941", label: "CDK2_HUMAN Cyclin-dependent kinase 2 (sprot)" }, - { identifier: "PR:P24941", label: "cyclin-dependent kinase 2 (human)" }, - { identifier: "UMLS:C0108855", label: "CDK2 protein, human" }, - ], - type: [ - "biolink:Gene", - "biolink:GeneOrGeneProduct", - "biolink:GenomicEntity", - "biolink:ChemicalEntityOrGeneOrGeneProduct", - "biolink:PhysicalEssence", - "biolink:OntologyClass", - "biolink:BiologicalEntity", - "biolink:NamedThing", - "biolink:Entity", - "biolink:PhysicalEssenceOrOccurrent", - "biolink:ThingWithTaxon", - "biolink:MacromolecularMachineMixin", - "biolink:Protein", - "biolink:GeneProductMixin", - "biolink:Polypeptide", - "biolink:ChemicalEntityOrProteinOrPolypeptide", - ], - information_content: 100, - }, - }; - } - if (arrEquals(qData?.curies, big_sri_input)) { - res = JSON.parse(fs.readFileSync(path.resolve(__dirname, "../data/api_results/big_sri_query.json"))); - } - if (arrEquals(qData?.curies, big_sri_input_2)) { - res = JSON.parse(fs.readFileSync(path.resolve(__dirname, "../data/api_results/big_sri_query_2.json"))); - } - if (arrEquals(qData?.umls, ngd_input)) { - res = JSON.parse(fs.readFileSync(path.resolve(__dirname, "../data/api_results/ngd_query.json"))); - } - if (res === undefined) { - res = (await og_axios.post(...q)).data; - } - return { data: res }; - }); - - await request(app) - .post("/v1/query") - .send(gene2chemical_query) - .set("Accept", "application/json") - .expect(200) - .expect("Content-Type", /json/) - .then(response => { - expect(response.body.message).toHaveProperty("query_graph"); - expect(response.body.message).toHaveProperty("knowledge_graph"); - expect(response.body.message.knowledge_graph).toHaveProperty("nodes"); - expect(response.body.message.knowledge_graph).toHaveProperty("edges"); - expect(response.body.message.knowledge_graph.nodes).toHaveProperty("NCBIGene:1017"); - }); - }); - - //Skip this test for now, need to check the actual API data - test.skip("POST /v1/query with clinical risk kp query", async () => { - await request(app) - .post("/v1/query") - .send(drug2disease_query) - .set("Accept", "application/json") - .expect(200) - .expect("Content-Type", /json/) - .then(response => { - expect(response.body.message).toHaveProperty("query_graph"); - expect(response.body.message).toHaveProperty("knowledge_graph"); - expect(response.body.message.knowledge_graph).toHaveProperty("nodes"); - expect(response.body.message.knowledge_graph).toHaveProperty("edges"); - expect(response.body.message.knowledge_graph.nodes).toHaveProperty("MONDO:0001583"); - }); - }); - - test("POST /v1/query with query graph defined in old trapi standard", async () => { - await request(app) - .post("/v1/query") - .send(query_using_earlier_trapi_spec) - .set("Accept", "application/json") - .expect(400) - .expect("Content-Type", /json/) - .then(response => { - expect(response.body).toHaveProperty("description"); - expect(response.body.description).toContain("Your input query graph is invalid"); - }); - }); - - test("POST /v1/query with disease2gene query", async () => { - const big_sri_input_3 = JSON.parse( - fs.readFileSync(path.resolve(__dirname, "../data/api_results/big_sri_input_3.json")), - ); - const ngd_input_2 = JSON.parse(fs.readFileSync(path.resolve(__dirname, "../data/api_results/ngd_input_2.json"))); - - axios.default.mockImplementation(qData => { - let res = undefined; - - if ( - qData.url === "https://mygene.info/v3/query" && - qData.data === "q=MONDO:0005737&scopes=clingen.clinical_validity.mondo" - ) { - res = [{ query: "MONDO:0005737", notfound: true }]; - } - if (qData.url === "https://api.monarchinitiative.org/api/bioentity/disease/MONDO:0005737/genes") { - res = { - associations: [], - compact_associations: null, - objects: null, - numFound: 0, - docs: null, - facet_counts: {}, - highlighting: null, - }; - } - if ( - qData.url === "https://biothings.ncats.io/semmeddb/query" && - arrEquals(qData.data?.q?.[0], ["C0282687", "CAUSES", "gngm", 1, 1]) - ) { - res = { max_total: 0, hits: [{ query: ["C0282687", "CAUSES", "gngm", 1, 1], notfound: true }] }; - } - if ( - qData.url === "https://biothings.ncats.io/semmeddb/query" && - arrEquals(qData.data?.q?.[0], ["C0282687", "PART_OF", "gngm", 1, 1]) - ) { - res = { max_total: 0, hits: [{ query: ["C0282687", "PART_OF", "gngm", 1, 1], notfound: true }] }; - } - if ( - qData.url === "https://biothings.ncats.io/semmeddb/query" && - arrEquals(qData.data?.q?.[0], ["C0282687", "ASSOCIATED_WITH", "gngm", 1, 1]) - ) { - res = { - max_total: 8, - hits: [ - { - query: ["C0282687", "ASSOCIATED_WITH", "gngm", 1, 1], - _id: "118612906", - _score: 19.9111, - object: { name: "Hemorrhagic Fever, Ebola", umls: "C0282687" }, - pmid: 11752702, - predicate: "ASSOCIATED_WITH", - subject: { name: "Genetic Structures", umls: "C1136352" }, - }, - { - query: ["C0282687", "ASSOCIATED_WITH", "gngm", 1, 1], - _id: "142375549", - _score: 19.9111, - object: { name: "Hemorrhagic Fever, Ebola", umls: "C0282687" }, - pmid: 26376249, - predicate: "ASSOCIATED_WITH", - subject: { name: "TIE1 gene", umls: "C1539965" }, - }, - { - query: ["C0282687", "ASSOCIATED_WITH", "gngm", 1, 1], - _id: "185194271", - _score: 19.9111, - object: { name: "Hemorrhagic Fever, Ebola", umls: "C0282687" }, - pmid: 32161708, - predicate: "ASSOCIATED_WITH", - subject: { name: "IMPACT gene", umls: "C1825598" }, - }, - { - query: ["C0282687", "ASSOCIATED_WITH", "gngm", 1, 1], - _id: "149589561", - _score: 19.9111, - object: { name: "Hemorrhagic Fever, Ebola", umls: "C0282687" }, - pmid: 20878400, - predicate: "ASSOCIATED_WITH", - subject: { name: "KIR2DS1" }, - }, - { - query: ["C0282687", "ASSOCIATED_WITH", "gngm", 1, 1], - _id: "149589562", - _score: 19.9111, - object: { name: "Hemorrhagic Fever, Ebola", umls: "C0282687" }, - pmid: 20878400, - predicate: "ASSOCIATED_WITH", - subject: { name: "KIR2DS3" }, - }, - { - query: ["C0282687", "ASSOCIATED_WITH", "gngm", 1, 1], - _id: "144337438", - _score: 19.9111, - object: { name: "Hemorrhagic Fever, Ebola", umls: "C0282687" }, - pmid: 17940958, - predicate: "ASSOCIATED_WITH", - subject: { name: "AXL gene", umls: "C0812237" }, - }, - { - query: ["C0282687", "ASSOCIATED_WITH", "gngm", 1, 1], - _id: "187446981", - _score: 19.9111, - object: { name: "Hemorrhagic Fever, Ebola", umls: "C0282687" }, - pmid: 32625555, - predicate: "ASSOCIATED_WITH", - subject: { name: "IMPACT gene", umls: "C1825598" }, - }, - { - query: ["C0282687", "ASSOCIATED_WITH", "gngm", 1, 1], - _id: "194568803", - _score: 19.9111, - object: { name: "Hemorrhagic Fever, Ebola", umls: "C0282687" }, - pmid: 34166464, - predicate: "ASSOCIATED_WITH", - subject: { name: "STAT3 gene", umls: "C1367307" }, - }, - ], - }; - } - if ( - qData.url === "https://biothings.ncats.io/pfocr/query" && - qData.data === "q=D019142&scopes=associatedWith.mentions.diseases.mesh" - ) { - res = { - max_total: 1, - hits: [ - { - query: "D019142", - _id: "PMC7725765__fpubh-08-596944-g0001.jpg", - _score: 10.558324, - associatedWith: { - figureUrl: "https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7725765/bin/fpubh-08-596944-g0001.jpg", - mentions: { genes: { ncbigene: ["6301"] } }, - pmc: "PMC7725765", - title: - "Pathway diagram for pathogen spill-over to humans from animals describes three distinct processes", - }, - }, - ], - }; - } - if ( - qData.url === "https://myvariant.info/v1/query" && - qData.data === "q=DOID:4325&scopes=civic.evidence_items.disease.doid" - ) { - res = { max_total: 0, hits: [{ query: ["C0282687", "PART_OF", "gngm", 1, 1], notfound: true }] }; - } - if (qData.url === "https://myvariant.info/v1/query" && qData.data === "q=DOID:4325&scopes=docm.doid") { - res = { - message: { - query_graph: { - nodes: { - n0: { ids: ["MONDO:0005737"], categories: ["biolink:Disease"], constraints: [] }, - n1: { ids: null, categories: ["biolink:Gene"], constraints: [] }, - }, - edges: { - e01: { predicates: ["biolink:increases_expression_of"], subject: "n0", object: "n1", constraints: [] }, - }, - }, - knowledge_graph: { nodes: {}, edges: {} }, - results: [], - }, - max_results: 10, - trapi_version: "1.2", - biolink_version: "2.2.3", - logs: [ - { - timestamp: "2023-01-27T02:54:54.360512", - level: "INFO", - message: "Normalized curie: MONDO:0005737 to UMLS:C0282687", - code: null, - }, - { - timestamp: "2023-01-27T02:54:54.490870", - level: "INFO", - message: "Converted category biolink:Disease to biolink:Disease using Biolink semantic operations.", - code: null, - }, - { - timestamp: "2023-01-27T02:54:54.490891", - level: "INFO", - message: "Converted category biolink:Gene to biolink:Gene using Biolink semantic operations.", - code: null, - }, - { - timestamp: "2023-01-27T02:54:54.499238", - level: "INFO", - message: - "Converted predicate biolink:increases_expression_of to biolink:increases_expression_of using Biolink semantic operations.", - code: null, - }, - { - timestamp: "2023-01-27T02:54:54.697830", - level: "INFO", - message: "Disease with curie UMLS:C0282687 does not exist in the database.", - code: null, - }, - { - timestamp: "2023-01-27T02:54:54.698874", - level: "INFO", - message: "Disease with curie UMLS:C0282687 does not exist in the database.", - code: null, - }, - { timestamp: "2023-01-27T02:54:54.708116", level: "INFO", message: "No results found.", code: null }, - ], - id: "5a9c6638-3a5c-44f6-b368-046caa28fa10", - status: "Success", - description: null, - workflow: [{ id: "lookup" }], - }; - } - if ( - qData.url === "https://biothings.ncats.io/mgigene2phenotype/query" && - qData.data === "q=DOID:4325&scopes=mgi.associated_with_disease.doid" - ) { - res = { max_total: 0, hits: [{ query: "DOID:4325", notfound: true }] }; - } - if (qData.url === "https://biothings.ncats.io/biggim_drugresponse_kp/query") { - res = { max_total: 0, hits: [{ query: ["MONDO:0005737", "biolink:has_biomarker"], notfound: true }] }; - } - if ( - qData.url === "https://biothings.ncats.io/DISEASES/query" && - qData.data === "q=DOID:4325&scopes=DISEASES.doid" - ) { - res = JSON.parse(fs.readFileSync(path.resolve(__dirname, "../data/api_results/biothings_disease_query.json"))); - } - if (qData.url === "https://biothings.ncats.io/text_mining_targeted_association/query") { - res = JSON.parse(fs.readFileSync(path.resolve(__dirname, "../../data/api_results/textmining_query.json"))); - } - if (qData.url === "https://mydisease.info/v1/query" && qData.data === "q=C0282687&scopes=disgenet.xrefs.umls") { - res = JSON.parse(fs.readFileSync(path.resolve(__dirname, "../data/api_results/mydisease_query.json"))); - } - if (qData.url === "https://automat.transltr.io/biolink/1.3/query") { - res = { - message: { - query_graph: { - nodes: { - n0: { ids: ["MONDO:0005737"], categories: ["biolink:Disease"], is_set: false, constraints: [] }, - n1: { ids: null, categories: ["biolink:Gene"], is_set: false, constraints: [] }, - }, - edges: { - e01: { - subject: "n0", - object: "n1", - knowledge_type: null, - predicates: ["biolink:contribution_from"], - attribute_constraints: [], - qualifier_constraints: [], - }, - }, - }, - knowledge_graph: { nodes: {}, edges: {} }, - results: [], - }, - log_level: null, - workflow: [{ runner_parameters: null, id: "lookup", parameters: null }], - submitter: "infores:bte", - }; - } - if (qData.url === "https://chp-api.transltr.io/query") { - res = { - message: { - query_graph: { - nodes: { - n0: { ids: ["MONDO:0005737"], categories: ["biolink:Disease"], constraints: [] }, - n1: { ids: null, categories: ["biolink:Gene"], constraints: [] }, - }, - edges: { - e01: { predicates: ["biolink:decreases_expression_of"], subject: "n0", object: "n1", constraints: [] }, - }, - }, - knowledge_graph: { nodes: {}, edges: {} }, - results: [], - }, - max_results: 10, - trapi_version: "1.2", - biolink_version: "2.2.3", - logs: [ - { - timestamp: "2023-01-27T02:54:54.923048", - level: "INFO", - message: "Normalized curie: MONDO:0005737 to UMLS:C0282687", - code: null, - }, - { - timestamp: "2023-01-27T02:54:55.042431", - level: "INFO", - message: "Converted category biolink:Disease to biolink:Disease using Biolink semantic operations.", - code: null, - }, - { - timestamp: "2023-01-27T02:54:55.042452", - level: "INFO", - message: "Converted category biolink:Gene to biolink:Gene using Biolink semantic operations.", - code: null, - }, - { - timestamp: "2023-01-27T02:54:55.050923", - level: "INFO", - message: - "Converted predicate biolink:decreases_expression_of to biolink:decreases_expression_of using Biolink semantic operations.", - code: null, - }, - { - timestamp: "2023-01-27T02:54:55.254680", - level: "INFO", - message: "Disease with curie UMLS:C0282687 does not exist in the database.", - code: null, - }, - { - timestamp: "2023-01-27T02:54:55.255578", - level: "INFO", - message: "Disease with curie UMLS:C0282687 does not exist in the database.", - code: null, - }, - { timestamp: "2023-01-27T02:54:55.264499", level: "INFO", message: "No results found.", code: null }, - ], - id: "cfc39f7e-5398-422c-a200-e9561ca9dc45", - status: "Success", - description: null, - workflow: [{ id: "lookup" }], - }; - } - if (qData.url === "https://automat.transltr.io/pharos/1.3/query") { - res = JSON.parse(fs.readFileSync(path.resolve(__dirname, "../data/api_results/pharos_query.json"))); - } - if (qData.url === "https://automat.transltr.io/uberongraph/1.3/query") { - res = { - message: { - query_graph: { - nodes: { - n0: { ids: ["MONDO:0005737"], categories: ["biolink:Disease"], is_set: false, constraints: [] }, - n1: { ids: null, categories: ["biolink:Gene"], is_set: false, constraints: [] }, - }, - edges: { - e01: { - subject: "n0", - object: "n1", - knowledge_type: null, - predicates: ["biolink:related_to"], - attribute_constraints: [], - qualifier_constraints: [], - }, - }, - }, - knowledge_graph: { nodes: {}, edges: {} }, - results: [], - }, - log_level: null, - workflow: [{ runner_parameters: null, id: "lookup", parameters: null }], - submitter: "infores:bte", - }; - } - if (qData.url === "https://automat.transltr.io/hetio/1.3/query") { - res = { - message: { - query_graph: { - nodes: { - n0: { ids: ["MONDO:0005737"], categories: ["biolink:Disease"], is_set: false, constraints: [] }, - n1: { ids: null, categories: ["biolink:Gene"], is_set: false, constraints: [] }, - }, - edges: { - e01: { - subject: "n0", - object: "n1", - knowledge_type: null, - predicates: ["biolink:entity_negatively_regulates_entity"], - attribute_constraints: [], - qualifier_constraints: [], - }, - }, - }, - knowledge_graph: { nodes: {}, edges: {} }, - results: [], - }, - log_level: null, - workflow: [{ runner_parameters: null, id: "lookup", parameters: null }], - submitter: "infores:bte", - }; - } - if ( - qData.url === "https://biothings.ncats.io/semmeddb/query" && - arrEquals(qData.data?.q?.[0], ["C0282687", "DISRUPTS", "gngm", 1, 1]) - ) { - res = { max_total: 0, hits: [{ query: ["C0282687", "DISRUPTS", "gngm", 1, 1], notfound: true }] }; - } - if ( - qData.url === "https://biothings.ncats.io/semmeddb/query" && - arrEquals(qData.data?.q?.[0], ["C0282687", "AFFECTS", "gngm", 1, 1]) - ) { - res = { - max_total: 7, - hits: [ - { - query: ["C0282687", "AFFECTS", "gngm", 1, 1], - _id: "129653976", - _score: 19.361662, - object: { name: "Hemorrhagic Fever, Ebola", umls: "C0282687" }, - pmid: 19683682, - predicate: "AFFECTS", - subject: { name: "PTPRC gene", umls: "C1335285" }, - }, - { - query: ["C0282687", "AFFECTS", "gngm", 1, 1], - _id: "136992331", - _score: 19.361662, - object: { name: "Hemorrhagic Fever, Ebola", umls: "C0282687" }, - pmid: 25722412, - predicate: "AFFECTS", - subject: { name: "CCDC6 gene", umls: "C1425774" }, - }, - { - query: ["C0282687", "AFFECTS", "gngm", 1, 1], - _id: "135827604", - _score: 19.361662, - object: { name: "Hemorrhagic Fever, Ebola", umls: "C0282687" }, - pmid: 26698106, - predicate: "AFFECTS", - subject: { name: "NPC1" }, - }, - { - query: ["C0282687", "AFFECTS", "gngm", 1, 1], - _id: "144337294", - _score: 19.361662, - object: { name: "Hemorrhagic Fever, Ebola", umls: "C0282687" }, - pmid: 17940958, - predicate: "AFFECTS", - subject: { name: "AXL gene", umls: "C0812237" }, - }, - { - query: ["C0282687", "AFFECTS", "gngm", 1, 1], - _id: "147460221-1", - _score: 19.361662, - object: { name: "Hemorrhagic Fever, Ebola", umls: "C0282687" }, - pmid: 29717011, - predicate: "AFFECTS", - subject: { name: "Genes", umls: "C0017337" }, - }, - { - query: ["C0282687", "AFFECTS", "gngm", 1, 1], - _id: "147460221-2", - _score: 19.361662, - object: { name: "Hemorrhagic Fever, Ebola", umls: "C0282687" }, - pmid: 29717011, - predicate: "AFFECTS", - subject: { name: "EEF1A2" }, - }, - { - query: ["C0282687", "AFFECTS", "gngm", 1, 1], - _id: "194542488", - _score: 19.361662, - object: { name: "Hemorrhagic Fever, Ebola", umls: "C0282687" }, - pmid: 34160256, - predicate: "AFFECTS", - subject: { name: "Viral Genome", umls: "C0042720" }, - }, - ], - }; - } - if ( - qData.url === "https://biothings.ncats.io/semmeddb/query" && - arrEquals(qData.data?.q?.[0], ["C0282687", "PREDISPOSES", "gngm", 1, 1]) - ) { - res = { max_total: 0, hits: [{ query: ["C0282687", "PREDISPOSES", "gngm", 1, 1], notfound: true }] }; - } - if ( - qData.url === "https://biothings.ncats.io/semmeddb/query" && - arrEquals(qData.data?.q?.[0], ["C0282687", "PRODUCES", "gngm", 1, 1]) - ) { - res = { max_total: 0, hits: [{ query: ["C0282687", "PRODUCES", "gngm", 1, 1], notfound: true }] }; - } - if ( - qData.url === "https://biothings.ncats.io/semmeddb/query" && - arrEquals(qData.data?.q?.[0], ["C0282687", "AUGMENTS", "gngm", 1, 1]) - ) { - res = { max_total: 0, hits: [{ query: ["C0282687", "AUGMENTS", "gngm", 1, 1], notfound: true }] }; - } - if ( - qData.url === "https://biothings.ncats.io/semmeddb/query" && - arrEquals(qData.data?.q?.[0], ["C0282687", "PREVENTS", "gngm", 1, 1]) - ) { - res = { max_total: 0, hits: [{ query: ["C0282687", "PREVENTS", "gngm", 1, 1], notfound: true }] }; - } - if ( - qData.url === "https://biothings.ncats.io/semmeddb/query" && - arrEquals(qData.data?.q?.[0], ["C0282687", "TREATS", "gngm", 1, 1]) - ) { - res = { max_total: 0, hits: [{ query: ["C0282687", "TREATS", "gngm", 1, 1], notfound: true }] }; - } - if ( - qData.url === "https://biothings.ncats.io/semmeddb/query" && - arrEquals(qData.data?.q?.[0], ["C0282687", "ASSOCIATED_WITH", "gngm", 1, 1]) - ) { - res = { max_total: 0, hits: [{ query: ["C0282687", "ASSOCIATED_WITH", "gngm", 1, 1], notfound: true }] }; - } - if ( - qData.url === "https://biothings.ncats.io/semmeddb/query" && - arrEquals(qData.data?.q?.[0], ["C0751434", "CAUSES", "gngm", 1, 1]) - ) { - res = { - max_total: 3, - hits: [ - { - query: ["C0751434", "CAUSES", "gngm", 1, 1], - _id: "108764506", - _score: 20.859911, - object: { name: "Classical phenylketonuria", umls: "C0751434" }, - pmid: 10495930, - predicate: "CAUSES", - subject: { name: "PAH gene", umls: "C1418251" }, - }, - { - query: ["C0751434", "CAUSES", "gngm", 1, 1], - _id: "164232103", - _score: 20.859911, - object: { name: "Classical phenylketonuria", umls: "C0751434" }, - pmid: 28706611, - predicate: "CAUSES", - subject: { name: "PAH gene", umls: "C1418251" }, - }, - { - query: ["C0751434", "CAUSES", "gngm", 1, 1], - _id: "164232106", - _score: 20.859911, - object: { name: "Classical phenylketonuria", umls: "C0751434" }, - pmid: 28706611, - predicate: "CAUSES", - subject: { name: "PAH gene", umls: "C1418251" }, - }, - { query: ["C4025094", "CAUSES", "gngm", 1, 1], notfound: true }, - ], - }; - } - return { data: res }; - }); - - axios.default.post.mockImplementation(async (...q) => { - const [url, qData] = q; - let res = undefined; - if (arrEquals(qData?.curies, ["MONDO:0005737"])) { - res = { - "MONDO:0005737": { - id: { identifier: "MONDO:0005737", label: "Ebola hemorrhagic fever" }, - equivalent_identifiers: [ - { identifier: "MONDO:0005737", label: "Ebola hemorrhagic fever" }, - { identifier: "DOID:4325", label: "Ebola hemorrhagic fever" }, - { identifier: "ORPHANET:319218" }, - { identifier: "UMLS:C0282687", label: "Hemorrhagic Fever, Ebola" }, - { identifier: "MESH:D019142", label: "Hemorrhagic Fever, Ebola" }, - { identifier: "MEDDRA:10014071" }, - { identifier: "MEDDRA:10014072" }, - { identifier: "MEDDRA:10014074" }, - { identifier: "MEDDRA:10055245" }, - { identifier: "NCIT:C36171", label: "Ebola Hemorrhagic Fever" }, - { identifier: "SNOMEDCT:37109004" }, - { identifier: "ICD10:A98.4" }, - ], - type: [ - "biolink:Disease", - "biolink:DiseaseOrPhenotypicFeature", - "biolink:ThingWithTaxon", - "biolink:BiologicalEntity", - "biolink:NamedThing", - "biolink:Entity", - ], - information_content: 100, - }, - }; - } - if (arrEquals(qData?.curies, big_sri_input_3)) { - res = JSON.parse(fs.readFileSync(path.resolve(__dirname, "../data/api_results/big_sri_query_3.json"))); - } - if (arrEquals(qData?.umls, ngd_input_2)) { - res = JSON.parse(fs.readFileSync(path.resolve(__dirname, "../data/api_results/ngd_query_2.json"))); - } - if (res === undefined) { - res = (await og_axios.post(...q)).data; - } - return { data: res }; - }); - - await request(app) - .post("/v1/query") - .send(disease2gene_query) - .set("Accept", "application/json") - .expect(200) - .expect("Content-Type", /json/) - .then(response => { - expect(response.body).toHaveProperty("message"); - expect(response.body.message).toHaveProperty("query_graph"); - expect(response.body.message).toHaveProperty("knowledge_graph"); - expect(response.body.message.knowledge_graph).toHaveProperty("nodes"); - expect(response.body.message.knowledge_graph).toHaveProperty("edges"); - expect(response.body.message.knowledge_graph.nodes).toHaveProperty("MONDO:0005737"); - }); - }); - - test("POST /v1/query with query that doesn't provide input category", async () => { - axios.default.mockImplementation(async qData => { - let res = undefined; - if (qData.url === "https://api.monarchinitiative.org/api/bioentity/disease/MONDO:0019259/genes") { - res = { - associations: [ - { - id: "29f0376e-6945-4252-8348-7be7e1562dc3", - type: null, - subject: { - taxon: { id: null, label: null }, - id: "MONDO:0019259", - label: "classic phenylketonuria", - iri: "http://purl.obolibrary.org/obo/MONDO_0019259", - category: ["disease"], - }, - subject_eq: null, - subject_extensions: null, - object: { - taxon: { id: "NCBITaxon:9606", label: "Homo sapiens" }, - id: "HGNC:8582", - label: "PAH", - iri: "https://www.genenames.org/data/gene-symbol-report/#!/hgnc_id/HGNC:8582", - category: ["gene"], - }, - object_eq: null, - object_extensions: null, - relation: { - inverse: true, - id: "RO:0004012", - label: "is causal loss of function germline mutation of in", - iri: "http://purl.obolibrary.org/obo/RO_0004012", - category: null, - }, - slim: null, - negated: false, - qualifiers: null, - evidence_graph: { nodes: null, edges: null }, - evidence_types: [ - { id: "ECO:0000322", label: "imported manually asserted information used in automatic assertion" }, - ], - provided_by: ["https://archive.monarchinitiative.org/#orphanet"], - publications: [], - }, - ], - compact_associations: null, - objects: null, - numFound: 1, - docs: null, - facet_counts: {}, - highlighting: null, - }; - } - if (qData.url === "https://biothings.ncats.io/semmeddb/query") { - res = { - max_total: 3, - hits: [ - { - query: ["C0751434", "CAUSES", "gngm", 1, 1], - _id: "108764506", - _score: 20.859911, - object: { name: "Classical phenylketonuria", umls: "C0751434" }, - pmid: 10495930, - predicate: "CAUSES", - subject: { name: "PAH gene", umls: "C1418251" }, - }, - { - query: ["C0751434", "CAUSES", "gngm", 1, 1], - _id: "164232103", - _score: 20.859911, - object: { name: "Classical phenylketonuria", umls: "C0751434" }, - pmid: 28706611, - predicate: "CAUSES", - subject: { name: "PAH gene", umls: "C1418251" }, - }, - { - query: ["C0751434", "CAUSES", "gngm", 1, 1], - _id: "164232106", - _score: 20.859911, - object: { name: "Classical phenylketonuria", umls: "C0751434" }, - pmid: 28706611, - predicate: "CAUSES", - subject: { name: "PAH gene", umls: "C1418251" }, - }, - { query: ["C4025094", "CAUSES", "gngm", 1, 1], notfound: true }, - ], - }; - } - if (qData.url === "https://automat.transltr.io/uberongraph/1.3/query") { - res = { - message: { - query_graph: { - nodes: { - n0: { ids: ["MONDO:0005737"], categories: ["biolink:Disease"], is_set: false, constraints: [] }, - n1: { ids: null, categories: ["biolink:Gene"], is_set: false, constraints: [] }, - }, - edges: { - e01: { - subject: "n0", - object: "n1", - knowledge_type: null, - predicates: ["biolink:related_to"], - attribute_constraints: [], - qualifier_constraints: [], - }, - }, - }, - knowledge_graph: { nodes: {}, edges: {} }, - results: [], - }, - log_level: null, - workflow: [{ runner_parameters: null, id: "lookup", parameters: null }], - submitter: "infores:bte", - }; - } - return { data: res }; - }); - - axios.default.post.mockImplementation(async (...q) => { - const [url, qData] = q; - let res = undefined; - if (arrEquals(qData?.curies, ["UMLS:C0751434"])) { - res = { - "UMLS:C0751434": { - id: { identifier: "MONDO:0019259", label: "classic phenylketonuria" }, - equivalent_identifiers: [ - { identifier: "MONDO:0019259", label: "classic phenylketonuria" }, - { identifier: "ORPHANET:79254" }, - { identifier: "UMLS:C0751434", label: "Classical phenylketonuria" }, - { identifier: "UMLS:C4025094", label: "Reduced phenylalanine hydroxylase activity" }, - { identifier: "MEDDRA:10034875" }, - { identifier: "NCIT:C117117", label: "Classical Phenylketonuria" }, - { identifier: "HP:0005982", label: "Reduced phenylalanine hydroxylase level" }, - ], - type: [ - "biolink:Disease", - "biolink:DiseaseOrPhenotypicFeature", - "biolink:ThingWithTaxon", - "biolink:BiologicalEntity", - "biolink:NamedThing", - "biolink:Entity", - ], - information_content: 100, - }, - }; - } - if (arrEquals(qData?.curies, ["UMLS:C0751434", "HGNC:8582", "UMLS:C1418251"])) { - res = { - "UMLS:C0751434": { - id: { identifier: "MONDO:0019259", label: "classic phenylketonuria" }, - equivalent_identifiers: [ - { identifier: "MONDO:0019259", label: "classic phenylketonuria" }, - { identifier: "ORPHANET:79254" }, - { identifier: "UMLS:C0751434", label: "Classical phenylketonuria" }, - { identifier: "UMLS:C4025094", label: "Reduced phenylalanine hydroxylase activity" }, - { identifier: "MEDDRA:10034875" }, - { identifier: "NCIT:C117117", label: "Classical Phenylketonuria" }, - { identifier: "HP:0005982", label: "Reduced phenylalanine hydroxylase level" }, - ], - type: [ - "biolink:Disease", - "biolink:DiseaseOrPhenotypicFeature", - "biolink:ThingWithTaxon", - "biolink:BiologicalEntity", - "biolink:NamedThing", - "biolink:Entity", - ], - information_content: 100, - }, - "HGNC:8582": { - id: { identifier: "NCBIGene:5053", label: "PAH" }, - equivalent_identifiers: [ - { identifier: "NCBIGene:5053", label: "PAH" }, - { identifier: "ENSEMBL:ENSG00000171759" }, - { identifier: "HGNC:8582", label: "PAH" }, - { identifier: "OMIM:612349" }, - { identifier: "UMLS:C1418251", label: "PAH gene" }, - { identifier: "UniProtKB:A0A024RBG4", label: "A0A024RBG4_HUMAN Phe-4-monooxygenase (trembl)" }, - { identifier: "UniProtKB:P00439", label: "PH4H_HUMAN Phenylalanine-4-hydroxylase (sprot)" }, - { identifier: "PR:P00439", label: "phenylalanine-4-hydroxylase (human)" }, - { identifier: "ENSEMBL:ENSP00000448059" }, - ], - type: [ - "biolink:Gene", - "biolink:GeneOrGeneProduct", - "biolink:GenomicEntity", - "biolink:ChemicalEntityOrGeneOrGeneProduct", - "biolink:PhysicalEssence", - "biolink:OntologyClass", - "biolink:BiologicalEntity", - "biolink:NamedThing", - "biolink:Entity", - "biolink:PhysicalEssenceOrOccurrent", - "biolink:ThingWithTaxon", - "biolink:MacromolecularMachineMixin", - "biolink:Protein", - "biolink:GeneProductMixin", - "biolink:Polypeptide", - "biolink:ChemicalEntityOrProteinOrPolypeptide", - ], - information_content: 100, - }, - "UMLS:C1418251": { - id: { identifier: "NCBIGene:5053", label: "PAH" }, - equivalent_identifiers: [ - { identifier: "NCBIGene:5053", label: "PAH" }, - { identifier: "ENSEMBL:ENSG00000171759" }, - { identifier: "HGNC:8582", label: "PAH" }, - { identifier: "OMIM:612349" }, - { identifier: "UMLS:C1418251", label: "PAH gene" }, - { identifier: "UniProtKB:A0A024RBG4", label: "A0A024RBG4_HUMAN Phe-4-monooxygenase (trembl)" }, - { identifier: "UniProtKB:P00439", label: "PH4H_HUMAN Phenylalanine-4-hydroxylase (sprot)" }, - { identifier: "PR:P00439", label: "phenylalanine-4-hydroxylase (human)" }, - { identifier: "ENSEMBL:ENSP00000448059" }, - ], - type: [ - "biolink:Gene", - "biolink:GeneOrGeneProduct", - "biolink:GenomicEntity", - "biolink:ChemicalEntityOrGeneOrGeneProduct", - "biolink:PhysicalEssence", - "biolink:OntologyClass", - "biolink:BiologicalEntity", - "biolink:NamedThing", - "biolink:Entity", - "biolink:PhysicalEssenceOrOccurrent", - "biolink:ThingWithTaxon", - "biolink:MacromolecularMachineMixin", - "biolink:Protein", - "biolink:GeneProductMixin", - "biolink:Polypeptide", - "biolink:ChemicalEntityOrProteinOrPolypeptide", - ], - information_content: 100, - }, - }; - } - - return { data: res }; - }); - - await request(app) - .post("/v1/query") - .send(query_without_category) - .set("Accept", "application/json") - // .expect(200) - // .expect('Content-Type', /json/) - .then(response => { - // console.log(response); - expect(response.body).toHaveProperty("message"); - expect(response.body.message).toHaveProperty("query_graph"); - expect(response.body.message).toHaveProperty("knowledge_graph"); - expect(response.body.message.knowledge_graph).toHaveProperty("nodes"); - expect(response.body.message.knowledge_graph).toHaveProperty("edges"); - expect(response.body.message.knowledge_graph.nodes).toHaveProperty("NCBIGene:5053"); - expect(response.body.message.knowledge_graph.nodes["NCBIGene:5053"]).toHaveProperty("categories", [ - "biolink:Gene", - ]); - }); - }); - - // test("POST /v1/query with query that needs to expand node", async () => { - // console.log("expanded node", expand_node); - // await request(app) - // .post("/v1/query") - // .send(expand_node) - // .set('Accept', 'application/json') - // .expect(200) - // .expect('Content-Type', /json/) - // .then(response => { - // console.log(response.body.message.knowledge_graph); - // expect(response.body).toHaveProperty("message"); - // expect(response.body.message).toHaveProperty("query_graph"); - // expect(response.body.message).toHaveProperty("knowledge_graph"); - // expect(response.body.message.knowledge_graph).toHaveProperty("nodes"); - // expect(response.body.message.knowledge_graph).toHaveProperty("edges"); - // expect(response.body.message.knowledge_graph.nodes).toHaveProperty("REACT:R-HSA-109582"); - // expect(response.body.message.knowledge_graph.nodes).toHaveProperty("GO:0000082"); - // }) - // }) -}); diff --git a/__test__/integration/TRAPIv1.test.js b/__test__/integration/TRAPIv1.test.js deleted file mode 100644 index 12aef368..00000000 --- a/__test__/integration/TRAPIv1.test.js +++ /dev/null @@ -1,142 +0,0 @@ -const app = require("../../src/app"); -const request = require('supertest'); -const fs = require("fs"); -var path = require('path'); - -//V1 tests are now skipped. -describe.skip("Testing v1 endpoints", () => { - const example_folder = path.resolve(__dirname, '../../examples/v1'); - const clinical_risk_kp_folder = path.resolve(__dirname, '../../examples/v1/multiomics/clinical_risk_kp'); - const old_spec_folder = path.resolve(__dirname, "../../examples/v0.9.2"); - const invalid_example_folder = path.resolve(__dirname, "../../examples/v1/invalid"); - const drug2disease_query = JSON.parse(fs.readFileSync(path.join(clinical_risk_kp_folder, 'query_drug_to_disease.json'))); - const gene2chemical_query = JSON.parse(fs.readFileSync(path.join(example_folder, 'query_chemicals_physically_interacts_with_genes.json'))); - const disease2gene_query = JSON.parse(fs.readFileSync(path.join(example_folder, 'query_genes_relate_to_disease.json'))); - const query_using_earlier_trapi_spec = JSON.parse(fs.readFileSync(path.join(old_spec_folder, 'query_genes_relate_to_disease.json'))); - const query_without_category = JSON.parse(fs.readFileSync(path.join(example_folder, 'query_without_input_category.json'))) - const expand_node = JSON.parse(fs.readFileSync(path.join(example_folder, 'query_with_node_to_be_expanded.json'))) - - test("GET /v1/predicates", async () => { - await request(app) - .get("/v1/predicates") - .expect(200) - .expect('Content-Type', /json/) - .then((response) => { - expect(response.body).toHaveProperty("biolink:Gene"); - expect(response.body["biolink:Gene"]).toHaveProperty("biolink:SmallMolecule"); - expect(response.body["biolink:Gene"]["biolink:SmallMolecule"]).toContain("biolink:related_to"); - }) - }) - - test("GET /v1/smartapi/{smartapi_id}/predicates", async () => { - await request(app) - .get("/v1/smartapi/978fe380a147a8641caf72320862697b/predicates") - .expect(200) - .expect('Content-Type', /json/) - .then((response) => { - expect(response.body).toHaveProperty("biolink:Gene"); - expect(response.body["biolink:Gene"]).toHaveProperty("biolink:SmallMolecule"); - }) - }) - - test("POST /v1/query with gene2chemical query", async () => { - await request(app) - .post("/v1/query") - .send(gene2chemical_query) - .set('Accept', 'application/json') - .expect(200) - .expect('Content-Type', /json/) - .then(response => { - expect(response.body.message).toHaveProperty("query_graph"); - expect(response.body.message).toHaveProperty("knowledge_graph"); - expect(response.body.message.knowledge_graph).toHaveProperty("nodes"); - expect(response.body.message.knowledge_graph).toHaveProperty("edges"); - expect(response.body.message.knowledge_graph.nodes).toHaveProperty("NCBIGene:1017") - }) - }) - - test("POST /v1/query with clinical risk kp query", async () => { - await request(app) - .post("/v1/query") - .send(drug2disease_query) - .set('Accept', 'application/json') - .expect(200) - .expect('Content-Type', /json/) - .then(response => { - expect(response.body.message).toHaveProperty("query_graph"); - expect(response.body.message).toHaveProperty("knowledge_graph"); - expect(response.body.message.knowledge_graph).toHaveProperty("nodes"); - expect(response.body.message.knowledge_graph).toHaveProperty("edges"); - expect(response.body.message.knowledge_graph.nodes).toHaveProperty("MONDO:0001583") - }) - }) - - test("POST /v1/query with query graph defined in old trapi standard", async () => { - await request(app) - .post("/v1/query") - .send(query_using_earlier_trapi_spec) - .set('Accept', 'application/json') - .expect(400) - .expect('Content-Type', /json/) - .then(response => { - expect(response.body).toHaveProperty("error", "Your input query graph is invalid"); - }) - }) - - test("POST /v1/query with disease2gene query", async () => { - await request(app) - .post("/v1/query") - .send(disease2gene_query) - .set('Accept', 'application/json') - .expect(200) - .expect('Content-Type', /json/) - .then(response => { - expect(response.body).toHaveProperty("message"); - expect(response.body.message).toHaveProperty("query_graph"); - expect(response.body.message).toHaveProperty("knowledge_graph"); - expect(response.body.message.knowledge_graph).toHaveProperty("nodes"); - expect(response.body.message.knowledge_graph).toHaveProperty("edges"); - expect(response.body.message.knowledge_graph.nodes).toHaveProperty("MONDO:0005737"); - }) - }) - - test("POST /v1/query with query that doesn't provide input category", async () => { - await request(app) - .post("/v1/query") - .send(query_without_category) - .set('Accept', 'application/json') - .expect(200) - .expect('Content-Type', /json/) - .then(response => { - expect(response.body).toHaveProperty("message"); - expect(response.body.message).toHaveProperty("query_graph"); - expect(response.body.message).toHaveProperty("knowledge_graph"); - expect(response.body.message.knowledge_graph).toHaveProperty("nodes"); - expect(response.body.message.knowledge_graph).toHaveProperty("edges"); - expect(response.body.message.knowledge_graph.nodes).toHaveProperty("MONDO:0016575"); - expect(response.body.message.knowledge_graph.nodes).toHaveProperty("UMLS:C0008780"); - expect(response.body.message.knowledge_graph.nodes["UMLS:C0008780"]).toHaveProperty("category", "biolink:PhenotypicFeature"); - }) - }) - - // test("POST /v1/query with query that needs to expand node", async () => { - // console.log("expanded node", expand_node); - // await request(app) - // .post("/v1/query") - // .send(expand_node) - // .set('Accept', 'application/json') - // .expect(200) - // .expect('Content-Type', /json/) - // .then(response => { - // console.log(response.body.message.knowledge_graph); - // expect(response.body).toHaveProperty("message"); - // expect(response.body.message).toHaveProperty("query_graph"); - // expect(response.body.message).toHaveProperty("knowledge_graph"); - // expect(response.body.message.knowledge_graph).toHaveProperty("nodes"); - // expect(response.body.message.knowledge_graph).toHaveProperty("edges"); - // expect(response.body.message.knowledge_graph.nodes).toHaveProperty("REACT:R-HSA-109582"); - // expect(response.body.message.knowledge_graph.nodes).toHaveProperty("GO:0000082"); - // }) - // }) - -}) diff --git a/__test__/integration/controllers/association.test.js b/__test__/integration/controllers/association.test.js deleted file mode 100644 index b75bd9bf..00000000 --- a/__test__/integration/controllers/association.test.js +++ /dev/null @@ -1,68 +0,0 @@ -const assoc = require("../../../src/controllers/association"); - -describe("Test association module", () => { - test("By default, should return all associations", async () => { - const res = await assoc(); - expect(res.length).toBeGreaterThan(10); - expect(res[0]).toHaveProperty("subject"); - expect(res[0]).toHaveProperty("api"); - }) - - test("If sub specified, should only return associations related to the sub", async () => { - const res = await assoc('Gene'); - const inputTypes = new Set(res.map(item => item.subject)); - expect(Array.from(inputTypes)).toHaveLength(1); - expect(Array.from(inputTypes)).toEqual(['Gene']) - }) - - test("If invalid sub specified, should only empty list", async () => { - const res = await assoc('Gene1'); - expect(res).toEqual([]); - }) - - test("If obj specified, should only return associations related to the obj", async () => { - const res = await assoc(undefined, 'SmallMolecule'); - const outputTypes = new Set(res.map(item => item.object)); - const inputTypes = new Set(res.map(item => item.subject)); - expect(inputTypes.size).toBeGreaterThan(1); - expect(Array.from(outputTypes)).toHaveLength(1); - expect(Array.from(outputTypes)).toEqual(['SmallMolecule']) - }) - - test("If pred specified, should only return associations related to the pred", async () => { - const res = await assoc(undefined, undefined, "treats"); - const preds = new Set(res.map(item => item.predicate)); - const inputTypes = new Set(res.map(item => item.subject)); - expect(inputTypes.size).toBeGreaterThan(1); - expect(Array.from(preds)).toHaveLength(1); - expect(Array.from(preds)).toEqual(['treats']) - }) - - test("If api specified, should only return associations related to the api", async () => { - const res = await assoc(undefined, undefined, undefined, undefined, "MyGene.info API"); - const apis = new Set(res.map(item => item.api.name)); - const inputTypes = new Set(res.map(item => item.subject)); - expect(inputTypes.size).toBeGreaterThan(1); - expect(Array.from(apis)).toHaveLength(1); - expect(Array.from(apis)).toEqual(['MyGene.info API']) - }) - - test("If source specified, should only return associations related to the source", async () => { - const res = await assoc(undefined, undefined, undefined, undefined, undefined, "infores:disgenet"); - const sources = new Set(res.map(item => item.provided_by)); - const inputTypes = new Set(res.map(item => item.subject)); - expect(inputTypes.size).toBeGreaterThan(1); - expect(Array.from(sources)).toHaveLength(1); - expect(Array.from(sources)).toEqual(['infores:disgenet']) - }) - - test("If both sub and obj specified, should only return associations related to both sub and obj", async () => { - const res = await assoc('Gene', 'SmallMolecule'); - const outputTypes = new Set(res.map(item => item.object)); - const inputTypes = new Set(res.map(item => item.subject)); - expect(Array.from(inputTypes)).toHaveLength(1); - expect(Array.from(outputTypes)).toHaveLength(1); - expect(Array.from(inputTypes)).toEqual(['Gene']); - expect(Array.from(outputTypes)).toEqual(['SmallMolecule']); - }) -}) diff --git a/__test__/integration/routes/entry.test.js b/__test__/integration/routes/entry.test.js deleted file mode 100644 index 61b5b426..00000000 --- a/__test__/integration/routes/entry.test.js +++ /dev/null @@ -1,13 +0,0 @@ -const app = require("../../../src/app"); -const request = require('supertest'); - -describe("Test entry point", () => { - test("query / should display frontpage", async () => { - await request(app) - .get("/") - .expect(200) - .then((response) => { - expect(response.text).toContain("BioThings Explorer"); - }) - }) -}) diff --git a/__test__/integration/routes/metakg.test.js b/__test__/integration/routes/metakg.test.js deleted file mode 100644 index f987f70d..00000000 --- a/__test__/integration/routes/metakg.test.js +++ /dev/null @@ -1,101 +0,0 @@ -const app = require("../../../src/app"); -const request = require('supertest'); - -// no one is really using the BTE /metakg endpoint and it is not publically advertised in its SmartAPI registration... -describe("Test /metakg endpoint", () => { - test("Should return 200 with valid response using default values", async () => { - await request(app) - .get("/metakg") - .expect(200) - .expect('Content-Type', /json/) - .then((response) => { - expect(response.body).toHaveProperty("associations"); - expect(response.body.associations.length).toBeGreaterThan(100); - }) - }) - - test("Should return 200 with valid response when user specify api", async () => { - await request(app) - .get("/metakg?api=MyGene.info API") - .expect(200) - .expect('Content-Type', /json/) - .then((response) => { - expect(response.body).toHaveProperty("associations"); - const apis = Array.from(new Set(response.body.associations.map(item => item.api.name))); - expect(apis).toEqual(['MyGene.info API']); - }) - }) - - test("Should return 200 with valid response when user specify provided by", async () => { - await request(app) - .get("/metakg?provided_by=infores:disgenet") - .expect(200) - .expect('Content-Type', /json/) - .then((response) => { - expect(response.body).toHaveProperty("associations"); - const res = Array.from(new Set(response.body.associations.map(item => item.provided_by))); - expect(res).toEqual(['infores:disgenet']); - }) - }) - - test("Should return 200 with valid response when user specify subject", async () => { - await request(app) - .get("/metakg?subject=Gene") - .expect(200) - .expect('Content-Type', /json/) - .then((response) => { - expect(response.body).toHaveProperty("associations"); - const res = Array.from(new Set(response.body.associations.map(item => item.subject))); - expect(res).toEqual(['Gene']); - }) - }) - - test("Should return 200 with valid response when user specify object", async () => { - await request(app) - .get("/metakg?object=Gene") - .expect(200) - .expect('Content-Type', /json/) - .then((response) => { - expect(response.body).toHaveProperty("associations"); - const res = Array.from(new Set(response.body.associations.map(item => item.object))); - expect(res).toEqual(['Gene']); - }) - }) - - test("Should return 200 with empty response when user specify invalid object", async () => { - await request(app) - .get("/metakg?object=Gene1") - .expect(200) - .expect('Content-Type', /json/) - .then((response) => { - expect(response.body).toHaveProperty("associations"); - expect(response.body.associations).toEqual([]); - }) - }) - - test("Should return 200 with valid response when user specify both subject and object", async () => { - await request(app) - .get("/metakg?object=Gene&subject=SmallMolecule") - .expect(200) - .expect('Content-Type', /json/) - .then((response) => { - expect(response.body).toHaveProperty("associations"); - const objs = Array.from(new Set(response.body.associations.map(item => item.object))); - const subjs = Array.from(new Set(response.body.associations.map(item => item.subject))); - expect(objs).toEqual(['Gene']); - expect(subjs).toEqual(['SmallMolecule']); - }) - }) - - test("Should return info from TRAPI /meta_knowledge_graph endpoint", async () => { - await request(app) - .get("/metakg") - .expect(200) - .expect('Content-Type', /json/) - .then((response) => { - expect(response.body).toHaveProperty("associations"); - const apis = Array.from(new Set(response.body.associations.map(item => item.api.name))); - expect(apis).toContain("BioLink API"); - }) - }) -}) \ No newline at end of file diff --git a/__test__/integration/routes/performance.test.js b/__test__/integration/routes/performance.test.js deleted file mode 100644 index b19a4945..00000000 --- a/__test__/integration/routes/performance.test.js +++ /dev/null @@ -1,11 +0,0 @@ -const app = require("../../../src/app"); -const request = require('supertest'); - -describe("Test /performance endpoint", () => { - test("Should return 200 with valid response", async () => { - await request(app) - .get("/performance") - .expect(200) - .expect('Content-Type', /html/) - }) -}) \ No newline at end of file diff --git a/__test__/integration/routes/v1query.test.js b/__test__/integration/routes/v1query.test.js deleted file mode 100644 index e7a836c0..00000000 --- a/__test__/integration/routes/v1query.test.js +++ /dev/null @@ -1,88 +0,0 @@ -const app = require("../../../src/app"); -const request = require("supertest"); -const fs = require("fs"); -var path = require("path"); - -// Reason: Takes too long as predict, missing smartapi.yaml for validation -describe("Testing /v1/query endpoints", () => { - const invalid_example_folder = path.resolve(__dirname, "../../../examples/v1.1/invalid"); - const example_folder = path.resolve(__dirname, "../../../examples/v1.1"); - test("Input query graph that doesn't pass Swagger Validation should return 400 error", async () => { - const InvalidInputQueryGraph = { - message1: 1, - }; - await request(app) - .post("/v1/query") - .send(InvalidInputQueryGraph) - .set("Accept", "application/json") - .expect(400) - .expect("Content-Type", /json/) - .then(response => { - expect(response.body).toHaveProperty("description"); - expect(response.body.description).toContain("Your input query graph is invalid"); - }); - }); - - test("Input query graph missing nodes definition should return 400", async () => { - const query_with_nodes_undefined = JSON.parse( - fs.readFileSync(path.join(invalid_example_folder, "query_graph_with_nodes_not_specified.json")), - ); - await request(app) - .post("/v1/query") - .send(query_with_nodes_undefined) - .set("Accept", "application/json") - .expect(400) - .expect("Content-Type", /json/) - .then(response => { - expect(response.body).toHaveProperty("description"); - expect(response.body.description).toContain("Your input query graph is invalid"); - }); - }); - - test("Input query graph missing edges definition should return 400 error", async () => { - const query_with_edges_undefined = JSON.parse( - fs.readFileSync(path.join(invalid_example_folder, "query_graph_with_edges_not_specified.json")), - ); - await request(app) - .post("/v1/query") - .send(query_with_edges_undefined) - .set("Accept", "application/json") - .expect(400) - .expect("Content-Type", /json/) - .then(response => { - expect(response.body).toHaveProperty("description"); - expect(response.body.description).toContain("Your input query graph is invalid"); - }); - }); - - test("Input query graph with nodes and edges mismatch should return 400 error", async () => { - const query_with_nodes_and_edges_not_match = JSON.parse( - fs.readFileSync(path.join(invalid_example_folder, "query_graph_with_nodes_and_edges_not_match.json")), - ); - await request(app) - .post("/v1/query") - .send(query_with_nodes_and_edges_not_match) - .set("Accept", "application/json") - .expect(400) - .expect("Content-Type", /json/) - .then(response => { - expect(response.body).toHaveProperty("description"); - expect(response.body.description).toContain("Your input query graph is invalid"); - }); - }); - - test.skip("Multi-hop query results should have combined edges", async () => { - const query = JSON.parse(fs.readFileSync(path.join(example_folder, "query_multihop_gene_gene_chemical.json"))); - await request(app) - .post("/v1/query") - .send(query) - .set("Accept", "application/json") - .expect(200) - .expect("Content-Type", /json/) - .then(response => { - expect(Object.keys(response.body.message.results[0].node_bindings).sort()).toEqual(["n0", "n1", "n2"].sort()); - - expect(Object.keys(response.body.message.results[0].edge_bindings).sort()).toEqual(["e01", "e02"].sort()); - }); - }); -}); diff --git a/__test__/integration/routes/v1query_by_api.test.js b/__test__/integration/routes/v1query_by_api.test.js deleted file mode 100644 index 5a5a5f6c..00000000 --- a/__test__/integration/routes/v1query_by_api.test.js +++ /dev/null @@ -1,145 +0,0 @@ -const app = require("../../../src/app"); -const request = require("supertest"); -const fs = require("fs"); -const axios = require("axios"); -var path = require("path"); - -//API IDs used in the tests -const myChemAPI = "8f08d1446e0bb9c2b323713ce83e2bd3"; -const textMiningAPI = "978fe380a147a8641caf72320862697b"; - -// if needed -const og_axios = jest.requireActual("axios"); - -jest.mock("axios"); - -describe("Testing /v1/smartapi/{smartapi_id}/query endpoints", () => { - const invalid_example_folder = path.resolve(__dirname, "../../../examples/v1.1/invalid"); - const example_folder = path.resolve(__dirname, "../../../examples/v1.1"); - test("Input query graph that doesn't pass Swagger Validation should return 400 error", async () => { - const InvalidInputQueryGraph = { - message1: 1, - }; - await request(app) - .post(`/v1/smartapi/${myChemAPI}/query/`) - .send(InvalidInputQueryGraph) - .set("Accept", "application/json") - .expect(400) - .expect("Content-Type", /json/) - .then(response => { - expect(response.body).toHaveProperty("description"); - expect(response.body.description).toContain("Your input query graph is invalid"); - }); - }); - - test("Input query graph missing nodes definition should return 400", async () => { - const query_with_nodes_undefined = JSON.parse( - fs.readFileSync(path.join(invalid_example_folder, "query_graph_with_nodes_not_specified.json")), - ); - await request(app) - .post(`/v1/smartapi/${myChemAPI}/query/`) - .send(query_with_nodes_undefined) - .set("Accept", "application/json") - .expect(400) - .expect("Content-Type", /json/) - .then(response => { - expect(response.body).toHaveProperty("description"); - expect(response.body.description).toContain("Your input query graph is invalid"); - }); - }); - - test("Input query graph missing edges definition should return 400 error", async () => { - const query_with_edges_undefined = JSON.parse( - fs.readFileSync(path.join(invalid_example_folder, "query_graph_with_edges_not_specified.json")), - ); - await request(app) - .post(`/v1/smartapi/${myChemAPI}/query/`) - .send(query_with_edges_undefined) - .set("Accept", "application/json") - .expect(400) - .expect("Content-Type", /json/) - .then(response => { - expect(response.body).toHaveProperty("description"); - expect(response.body.description).toContain("Your input query graph is invalid"); - }); - }); - - test("Input query graph with nodes and edges mismatch should return 400 error", async () => { - const query_with_nodes_and_edges_not_match = JSON.parse( - fs.readFileSync(path.join(invalid_example_folder, "query_graph_with_nodes_and_edges_not_match.json")), - ); - await request(app) - .post(`/v1/smartapi/${myChemAPI}/query/`) - .send(query_with_nodes_and_edges_not_match) - .set("Accept", "application/json") - .expect(400) - .expect("Content-Type", /json/) - .then(response => { - expect(response.body).toHaveProperty("description"); - expect(response.body.description).toContain("Your input query graph is invalid"); - }); - }); - // 2021-09-09: need to update the example query - // also skipping because this API and its x-bte annotation will soon change. - // Once both are updated, can review this test and its desired behavior again... - test.skip("Query to Text Mining Targeted Association KP should have id resolution turned off", async () => { - const query = JSON.parse( - fs.readFileSync(path.join(example_folder, "textmining/query_chemicals_related_to_gene_or_gene_product.json")), - ); - await request(app) - .post(`/v1/smartapi/${textMiningAPI}/query/`) - .send(query) - .set("Accept", "application/json") - .expect(200) - .expect("Content-Type", /json/) - .then(response => { - expect(response.body.message.knowledge_graph.nodes).toHaveProperty("CHEBI:32677"); - expect(response.body.message.knowledge_graph.nodes["CHEBI:32677"].attributes[0].value).toEqual(["CHEBI:32677"]); - }); - }); - - // 2023-03-14: id resolution has been disable on by-team and by-api endpoints for a while - // so this test doesn't make a lot of sense anymor... - test.skip("Query to non-Text Mining KPs should have id resolution turned on", async () => { - const sri_path = path.resolve(__dirname, "../../data/api_results/chembl_sri.json"); - axios.default.post.mockResolvedValue({ data: JSON.parse(fs.readFileSync(sri_path)) }); - const mychem_path = path.resolve(__dirname, "../../data/api_results/mychem_query.json"); - axios.default.mockResolvedValue({ data: JSON.parse(fs.readFileSync(mychem_path)) }); - // axios.default.post.mockImplementation(async (...q) => { - // const res = await og_axios.default.post(...q) - // console.log(JSON.stringify(res.data)) - // return res - // }) - const query = JSON.parse(fs.readFileSync(path.join(example_folder, "serviceprovider/mychem.json"))); - await request(app) - .post(`/v1/smartapi/${myChemAPI}/query`) - .send(query) - .set("Accept", "application/json") - .expect(200) - .expect("Content-Type", /json/) - .then(response => { - expect(Object.keys(response.body.message.knowledge_graph.nodes)).toContain("PUBCHEM.COMPOUND:5070"); - }); - }); - - // Reason: TypeError: Cannot set property attributes of # which has only a getter - test.skip("Query to Text Mining Co-occurrence KP should be correctly paginated", async () => { - const query = JSON.parse( - fs.readFileSync(path.join(example_folder, "textmining/query_chemicals_related_to_disease.json")), - ); - const apiResponse = await axios.get( - "https://biothings.ncats.io/text_mining_co_occurrence_kp/query?q=object.id:%22MONDO:0005252%22%20AND%20subject.type:%22SmallMolecule%22", - ); - const hits = apiResponse.data.total; - await request(app) - .post("/v1/smartapi/5be0f321a829792e934545998b9c6afe/query/") - .send(query) - .set("Accept", "application/json") - .expect(200) - .expect("Content-Type", /json/) - .then(response => { - expect(response.body.message.knowledge_graph.nodes["CHEBI:26404"].attributes[0].value).toEqual(["CHEBI:26404"]); - expect(Object.keys(response.body.message.knowledge_graph.nodes)).toHaveLength(hits + 1); - }); - }); -}); diff --git a/__test__/integration/routes/v1query_by_team.test.js b/__test__/integration/routes/v1query_by_team.test.js deleted file mode 100644 index 5304e18c..00000000 --- a/__test__/integration/routes/v1query_by_team.test.js +++ /dev/null @@ -1,132 +0,0 @@ -const app = require("../../../src/app"); -const request = require("supertest"); -const fs = require("fs"); -const axios = require("axios"); -var path = require("path"); - -describe("Testing /v1/team/{team_name}/query endpoints", () => { - const invalid_example_folder = path.resolve(__dirname, "../../../examples/v1.1/invalid"); - const example_folder = path.resolve(__dirname, "../../../examples/v1.1"); - test("Input query graph that doesn't pass Swagger Validation should return 400 error", async () => { - const InvalidInputQueryGraph = { - message1: 1, - }; - await request(app) - .post("/v1/team/Text Mining Provider/query/") - .send(InvalidInputQueryGraph) - .set("Accept", "application/json") - .expect(400) - .expect("Content-Type", /json/) - .then(response => { - expect(response.body).toHaveProperty("description"); - expect(response.body.description).toContain("Your input query graph is invalid"); - }); - }); - - test("Input query graph missing nodes definition should return 400", async () => { - const query_with_nodes_undefined = JSON.parse( - fs.readFileSync(path.join(invalid_example_folder, "query_graph_with_nodes_not_specified.json")), - ); - await request(app) - .post("/v1/team/Text Mining Provider/query/") - .send(query_with_nodes_undefined) - .set("Accept", "application/json") - .expect(400) - .expect("Content-Type", /json/) - .then(response => { - expect(response.body).toHaveProperty("description"); - expect(response.body.description).toContain("Your input query graph is invalid"); - }); - }); - - test("Input query graph missing edges definition should return 400 error", async () => { - const query_with_edges_undefined = JSON.parse( - fs.readFileSync(path.join(invalid_example_folder, "query_graph_with_edges_not_specified.json")), - ); - await request(app) - .post("/v1/team/Text Mining Provider/query/") - .send(query_with_edges_undefined) - .set("Accept", "application/json") - .expect(400) - .expect("Content-Type", /json/) - .then(response => { - expect(response.body).toHaveProperty("description"); - expect(response.body.description).toContain("Your input query graph is invalid"); - }); - }); - - test("Input query graph with nodes and edges mismatch should return 400 error", async () => { - const query_with_nodes_and_edges_not_match = JSON.parse( - fs.readFileSync(path.join(invalid_example_folder, "query_graph_with_nodes_and_edges_not_match.json")), - ); - await request(app) - .post("/v1/team/Text Mining Provider/query/") - .send(query_with_nodes_and_edges_not_match) - .set("Accept", "application/json") - .expect(400) - .expect("Content-Type", /json/) - .then(response => { - expect(response.body).toHaveProperty("description"); - expect(response.body.description).toContain("Your input query graph is invalid"); - }); - }); - // 2021-09-09: need to update the example query - // also skipping because this API and its x-bte annotation will soon change. - // Once both are updated, can review this test and its desired behavior again... - test.skip("Query to Text Mining KPs should have id resolution turned off", async () => { - const query = JSON.parse( - fs.readFileSync(path.join(example_folder, "textmining/query_chemicals_related_to_gene_or_gene_product.json")), - ); - await request(app) - .post("/v1/team/Text Mining Provider/query/") - .send(query) - .set("Accept", "application/json") - .expect(200) - .expect("Content-Type", /json/) - .then(response => { - expect(response.body.message.knowledge_graph.nodes).toHaveProperty("CHEBI:32677"); - expect(response.body.message.knowledge_graph.nodes["CHEBI:32677"].attributes[0].value).toEqual(["CHEBI:32677"]); - }); - }); - - // 2021-09-09: need to update the example query, and keep in mind the use of the new SRI-ID-resolver, and the way node attributes are structured... - test.skip("Query to Service Provider KPs should have id resolution turned on", async () => { - const query = JSON.parse( - fs.readFileSync(path.join(example_folder, "textmining/query_chemicals_related_to_gene_or_gene_product.json")), - ); - await request(app) - .post("/v1/team/Service Provider/query/") - .send(query) - .set("Accept", "application/json") - .expect(200) - .expect("Content-Type", /json/) - .then(response => { - expect(response.body.message.knowledge_graph.nodes).toHaveProperty("CHEBI:32677"); - expect(response.body.message.knowledge_graph.nodes["CHEBI:32677"].attributes[0].value).toEqual([ - "CHEBI:32677", - "name:glutamine residue", - ]); - }); - }); - - // Reason: TypeError: Cannot set property attributes of # which has only a getter - test.skip("Query to Text Mining Co-occurrence KP should be correctly paginated", async () => { - const query = JSON.parse( - fs.readFileSync(path.join(example_folder, "textmining/query_chemicals_related_to_disease.json")), - ); - const apiResponse = await axios.get( - "https://biothings.ncats.io/text_mining_co_occurrence_kp/query?q=object.id:%22MONDO:0005252%22%20AND%20subject.type:%22SmallMolecule%22", - ); - const hits = apiResponse.data.total; - await request(app) - .post("/v1/team/Text Mining Provider/query/") - .send(query) - .set("Accept", "application/json") - .expect(200) - .expect("Content-Type", /json/) - .then(response => { - expect(response.body.message.knowledge_graph.nodes["CHEBI:26404"].attributes[0].value).toEqual(["CHEBI:26404"]); - expect(Object.keys(response.body.message.knowledge_graph.nodes)).toHaveLength(hits + 1); - }); - }); -}); diff --git a/__test__/unittest/routes/metakg.test.js b/__test__/unittest/routes/metakg.test.js deleted file mode 100644 index 54eafb5f..00000000 --- a/__test__/unittest/routes/metakg.test.js +++ /dev/null @@ -1,19 +0,0 @@ -const app = require("../../../src/app"); -const request = require("supertest"); -const assoc = require("../../../src/controllers/association"); -jest.mock("../../../src/controllers/association"); - -describe("Test /performance endpoint", () => { - test("Should return 404 when loading metakg failed", async () => { - assoc.mockImplementation(() => { - throw new Error("Error"); - }); - await request(app) - .get("/metakg") - .expect(404) - .expect("Content-Type", /json/) - .then(res => { - expect(res.body).toHaveProperty("description", "Unable to load metakg: Failed to load metakg"); - }); - }); -}); diff --git a/__test__/unittest/routes/performance.test.js b/__test__/unittest/routes/performance.test.js deleted file mode 100644 index 41a9a65f..00000000 --- a/__test__/unittest/routes/performance.test.js +++ /dev/null @@ -1,15 +0,0 @@ -const app = require("../../../src/app"); -const request = require('supertest'); -const fs = require("fs"); - - -describe("Test /performance endpoint", () => { - test("Should return 404 with valid response", async () => { - const spy = jest.spyOn(fs, 'access').mockImplementation(() => { throw new Error() }); - await request(app) - .get("/performance") - .expect(404) - .expect('Content-Type', /json/) - spy.mockRestore(); - }) -}) \ No newline at end of file diff --git a/__test__/unittest/routes/predicates.test.js b/__test__/unittest/routes/predicates.test.js deleted file mode 100644 index 198c7b5e..00000000 --- a/__test__/unittest/routes/predicates.test.js +++ /dev/null @@ -1,21 +0,0 @@ -const app = require("../../../src/app"); -const request = require("supertest"); -const pred = require("../../../src/controllers/meta_knowledge_graph"); -const PredicateLoadingError = require("../../../src/utils/errors/predicates_error"); -const PredicatesLoadingError = require("../../../src/utils/errors/predicates_error"); -jest.mock("../../../src/controllers/meta_knowledge_graph"); - -describe("Test /v1/meta_knowledge_graph endpoint", () => { - test("Should return 404 with valid response", async () => { - pred.mockImplementation(() => { - throw new PredicatesLoadingError(); - }); - await request(app) - .get("/v1/meta_knowledge_graph") - .expect(404) - .expect("Content-Type", /json/) - .then(res => { - expect(res.body).toHaveProperty("description", "Unable to load predicates: Failed to load metakg"); - }); - }); -}); diff --git a/__test__/unittest/routes/predicates_team.test.js b/__test__/unittest/routes/predicates_team.test.js deleted file mode 100644 index 37af061b..00000000 --- a/__test__/unittest/routes/predicates_team.test.js +++ /dev/null @@ -1,21 +0,0 @@ -const app = require("../../../src/app"); -const request = require("supertest"); -const pred = require("../../../src/controllers/meta_knowledge_graph"); -const PredicateLoadingError = require("../../../src/utils/errors/predicates_error"); -const PredicatesLoadingError = require("../../../src/utils/errors/predicates_error"); -jest.mock("../../../src/controllers/meta_knowledge_graph"); - -describe("Test /v1/meta_knowledge_graph endpoint", () => { - test("Should return 404 with valid response", async () => { - pred.mockImplementation(() => { - throw new PredicatesLoadingError(); - }); - await request(app) - .get("/v1/team/Text Mining Provider/meta_knowledge_graph") - .expect(404) - .expect("Content-Type", /json/) - .then(res => { - expect(res.body).toHaveProperty("description", "Unable to load predicates: Failed to load metakg"); - }); - }); -}); diff --git a/__test__/unittest/utils.test.js b/__test__/unittest/utils.test.js deleted file mode 100644 index 9908c724..00000000 --- a/__test__/unittest/utils.test.js +++ /dev/null @@ -1,62 +0,0 @@ -const { expectCt } = require("helmet"); -const utils = require("../../src/utils/common"); -const WorkflowError = require("../../src/utils/errors/workflow_error"); - -describe("Test utility functions", () => { - describe("Test removeQuotesFromQuery function", () => { - test("single quotes should be removed", () => { - const input = "'kevin'"; - const res = utils.removeQuotesFromQuery(input); - expect(res).toEqual('kevin'); - }) - - test("double quotes should be removed", () => { - const input = '"kevin"'; - const res = utils.removeQuotesFromQuery(input); - expect(res).toEqual('kevin'); - }) - - test("unquoted string should return itself", () => { - const input = 'kevin'; - const res = utils.removeQuotesFromQuery(input); - expect(res).toEqual('kevin'); - }) - - test("string with only quotes in the middle should also return itself", () => { - const input = 'ke"vin'; - const res = utils.removeQuotesFromQuery(input); - expect(res).toEqual('ke"vin'); - }) - }) - - describe("Test workflow validator", () => { - test("undefined workflow", () => { - let workflow; - expect(utils.validateWorkflow(workflow)).toEqual(undefined); - }) - - test("Workflow not in right shape", () => { - const workflow = {}; - expect(() => utils.validateWorkflow(workflow)).toThrow(WorkflowError); - }) - - test("Workflow wrong legnth", () => { - let workflow = []; - expect(() => utils.validateWorkflow(workflow)).toThrow(WorkflowError); - workflow = [{id: 'lookup'}, {id: 'lookup'}]; - expect(() => utils.validateWorkflow(workflow)).toThrow(WorkflowError); - }) - - test("Workflow unsupported value", () => { - let workflow = [{id: 'abcde'}]; - expect(() => utils.validateWorkflow(workflow)).toThrow(WorkflowError); - workflow = ["abcde"]; - expect(() => utils.validateWorkflow(workflow)).toThrow(WorkflowError); - }) - - test("No error when value is id:lookup", () => { - const workflow = [{id: 'lookup'}]; - expect(utils.validateWorkflow(workflow)).toEqual(undefined); - }) - }) -}) \ No newline at end of file diff --git a/bte-pm2.json b/bte-pm2.json index 5cdd8afd..3b286188 100644 --- a/bte-pm2.json +++ b/bte-pm2.json @@ -3,7 +3,7 @@ { "name": "bte-trapi", "cwd": ".", - "script": "./src/server.js", + "script": "./packages/bte-server/built/server.js", "exec_mode": "cluster", "instances": 4, "autorestart": true, diff --git a/data/predicates.json b/data/predicates.json deleted file mode 100644 index 4ed249f4..00000000 --- a/data/predicates.json +++ /dev/null @@ -1 +0,0 @@ -[{"association":{"api_name":"Text Mined Cooccurrence 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RUPTS-orgf-rev"},{"$ref":"#/components/x-bte-kgs-operations/orch-PREDISPOSES-inpo"},{"$ref":"#/components/x-bte-kgs-operations/eico-INHIBITS-gngm-rev"},{"$ref":"#/components/x-bte-kgs-operations/gngm-INTERACTS_WITH-imft"},{"$ref":"#/components/x-bte-kgs-operations/gngm-INTERACTS_WITH-imft-rev"},{"$ref":"#/components/x-bte-kgs-operations/lipd-ASSOCIATED_WITH-patf-rev"},{"$ref":"#/components/x-bte-kgs-operations/antb-COEXISTS_WITH-aapp-rev"},{"$ref":"#/components/x-bte-kgs-operations/aapp-PREVENTS-dsyn"},{"$ref":"#/components/x-bte-kgs-operations/cgab-LOCATION_OF-neop-rev"},{"$ref":"#/components/x-bte-kgs-operations/gngm-INTERACTS_WITH-carb"},{"$ref":"#/components/x-bte-kgs-operations/phsf-PRODUCES-bacs-rev"},{"$ref":"#/components/x-bte-kgs-operations/eico-ASSOCIATED_WITH-dsyn-rev"},{"$ref":"#/components/x-bte-kgs-operations/topp-TREATS-comd"},{"$ref":"#/components/x-bte-kgs-operations/hops-ASSOCIATED_WITH-patf-rev"},{"$ref":"#/components/x-bte-kgs-operations/cell-PRODUCES-horm"},{"$ref":"#/components/x-bte-kgs-operations/inch-AUGMENTS-bpoc-rev"},{"$ref":"#/components/x-bte-kgs-operations/gngm-PREDISPOSES-mobd"},{"$ref":"#/components/x-bte-kgs-operations/lipd-INTERACTS_WITH-gngm-rev"},{"$ref":"#/components/x-bte-kgs-operations/celc-AFFECTS-phsf"},{"$ref":"#/components/x-bte-kgs-operations/gngm-AFFECTS-sosy"},{"$ref":"#/components/x-bte-kgs-operations/gngm-AFFECTS-sosy-rev"},{"$ref":"#/components/x-bte-kgs-operations/bacs-AFFECTS-sosy-rev"},{"$ref":"#/components/x-bte-kgs-operations/gngm-STIMULATES-moft"},{"$ref":"#/components/x-bte-kgs-operations/gngm-STIMULATES-moft-rev"},{"$ref":"#/components/x-bte-kgs-operations/phsu-PREDISPOSES-patf-rev"},{"$ref":"#/components/x-bte-kgs-operations/imft-COEXISTS_WITH-imft"},{"$ref":"#/components/x-bte-kgs-operations/imft-COEXISTS_WITH-imft-rev"},{"$ref":"#/components/x-bte-kgs-operations/aapp-PRODUCES-hops"},{"$ref":"#/components/x-bte-kgs-operations/orch-PREVENTS-sosy-rev"},{"$ref":"#/components/x-bte-kgs-operations/horm-DISRUPTS-celf-rev"},{"$ref":"#/components/x-bte-kgs-operations/inch-COEXISTS_WITH-gngm-rev"},{"$ref":"#/components/x-bte-kgs-operations/hops-COEXISTS_WITH-gngm-rev"},{"$ref":"#/components/x-bte-kgs-operations/bpoc-PRODUCES-orch"},{"$ref":"#/components/x-bte-kgs-operations/dsyn-AFFECTS-comd"},{"$ref":"#/components/x-bte-kgs-operations/carb-AUGMENTS-bpoc-rev"},{"$ref":"#/components/x-bte-kgs-operations/hops-PREDISPOSES-neop-rev"},{"$ref":"#/components/x-bte-kgs-operations/aapp-DISRUPTS-inpo"},{"$ref":"#/components/x-bte-kgs-operations/lipd-DISRUPTS-celf-rev"},{"$ref":"#/components/x-bte-kgs-operations/gngm-PRODUCES-gngm"},{"$ref":"#/components/x-bte-kgs-operations/gngm-PRODUCES-gngm-rev"},{"$ref":"#/components/x-bte-kgs-operations/food-AFFECTS-ortf"},{"$ref":"#/components/x-bte-kgs-operations/orch-AUGMENTS-sosy"},{"$ref":"#/components/x-bte-kgs-operations/orch-AUGMENTS-sosy-rev"},{"$ref":"#/components/x-bte-kgs-operations/comd-PRODUCES-bacs-rev"},{"$ref":"#/components/x-bte-kgs-operations/aapp-PREDISPOSES-sosy"},{"$ref":"#/components/x-bte-kgs-operations/aapp-PREDISPOSES-sosy-rev"},{"$ref":"#/components/x-bte-kgs-operations/gngm-PRODUCES-imft"},{"$ref":"#/components/x-bte-kgs-operations/gngm-PRODUCES-imft-rev"},{"$ref":"#/components/x-bte-kgs-operations/gngm-COEXISTS_WITH-hops"},{"$ref":"#/components/x-bte-kgs-operations/imft-INTERACTS_WITH-gngm"},{"$ref":"#/components/x-bte-kgs-operations/imft-INTERACTS_WITH-gngm-rev"},{"$ref":"#/components/x-bte-kgs-operations/dsyn-COMPLICATES-neop"},{"$ref":"#/components/x-bte-kgs-operations/nsba-COEXISTS_WITH-aapp-rev"},{"$ref":"#/components/x-bte-kgs-operations/phsu-DISRUPTS-cell-rev"},{"$ref":"#/components/x-bte-kgs-operations/gngm-AUGMENTS-cell"},{"$ref":"#/components/x-bte-kgs-operations/gngm-AUGMENTS-cell-rev"},{"$ref":"#/components/x-bte-kgs-operations/strd-INHIBITS-gngm-rev"},{"$ref":"#/components/x-bte-kgs-operations/aapp-INHIBITS-antb"},{"$ref":"#/components/x-bte-kgs-operations/orch-CAUSES-cgab"},{"$ref":"#/components/x-bte-kgs-operations/cgab-COEXISTS_WITH-patf-rev"},{"$ref":"#/components/x-bte-kgs-operations/horm-AUGMENTS-ortf-rev"},{"$ref":"#/components/x-bte-kgs-operations/bacs-DISRUPTS-celc-rev"},{"$ref":"#/components/x-bte-kgs-operations/antb-TREATS-sosy-rev"},{"$ref":"#/components/x-bte-kgs-operations/phsu-DISRUPTS-dsyn-rev"},{"$ref":"#/components/x-bte-kgs-operations/topp-PREDISPOSES-sosy"},{"$ref":"#/components/x-bte-kgs-operations/topp-PREDISPOSES-sosy-rev"},{"$ref":"#/components/x-bte-kgs-operations/inch-CAUSES-sosy-rev"},{"$ref":"#/components/x-bte-kgs-operations/orch-DISRUPTS-inpo"},{"$ref":"#/components/x-bte-kgs-operations/strd-STIMULATES-gngm-rev"},{"$ref":"#/components/x-bte-kgs-operations/gngm-INTERACTS_WITH-antb"},{"$ref":"#/components/x-bte-kgs-operations/aapp-PREVENTS-acab"},{"$ref":"#/components/x-bte-kgs-operations/diap-DIAGNOSES-comd"},{"$ref":"#/components/x-bte-kgs-operations/inch-AFFECTS-bpoc-rev"},{"$ref":"#/components/x-bte-kgs-operations/gngm-CONVERTS_TO-gngm"},{"$ref":"#/componen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RUPTS-orgf-rev"},{"$ref":"#/components/x-bte-kgs-operations/orch-PREDISPOSES-inpo"},{"$ref":"#/components/x-bte-kgs-operations/eico-INHIBITS-gngm-rev"},{"$ref":"#/components/x-bte-kgs-operations/gngm-INTERACTS_WITH-imft"},{"$ref":"#/components/x-bte-kgs-operations/gngm-INTERACTS_WITH-imft-rev"},{"$ref":"#/components/x-bte-kgs-operations/lipd-ASSOCIATED_WITH-patf-rev"},{"$ref":"#/components/x-bte-kgs-operations/antb-COEXISTS_WITH-aapp-rev"},{"$ref":"#/components/x-bte-kgs-operations/aapp-PREVENTS-dsyn"},{"$ref":"#/components/x-bte-kgs-operations/cgab-LOCATION_OF-neop-rev"},{"$ref":"#/components/x-bte-kgs-operations/gngm-INTERACTS_WITH-carb"},{"$ref":"#/components/x-bte-kgs-operations/phsf-PRODUCES-bacs-rev"},{"$ref":"#/components/x-bte-kgs-operations/eico-ASSOCIATED_WITH-dsyn-rev"},{"$ref":"#/components/x-bte-kgs-operations/topp-TREATS-comd"},{"$ref":"#/components/x-bte-kgs-operations/hops-ASSOCIATED_WITH-patf-rev"},{"$ref":"#/components/x-bte-kgs-operations/cell-PRODUCES-horm"},{"$ref":"#/components/x-bte-kgs-operations/inch-AUGMENTS-bpoc-rev"},{"$ref":"#/components/x-bte-kgs-operations/gngm-PREDISPOSES-mobd"},{"$ref":"#/components/x-bte-kgs-operations/lipd-INTERACTS_WITH-gngm-rev"},{"$ref":"#/components/x-bte-kgs-operations/celc-AFFECTS-phsf"},{"$ref":"#/components/x-bte-kgs-operations/gngm-AFFECTS-sosy"},{"$ref":"#/components/x-bte-kgs-operations/gngm-AFFECTS-sosy-rev"},{"$ref":"#/components/x-bte-kgs-operations/bacs-AFFECTS-sosy-rev"},{"$ref":"#/components/x-bte-kgs-operations/gngm-STIMULATES-moft"},{"$ref":"#/components/x-bte-kgs-operations/gngm-STIMULATES-moft-rev"},{"$ref":"#/components/x-bte-kgs-operations/phsu-PREDISPOSES-patf-rev"},{"$ref":"#/components/x-bte-kgs-operations/imft-COEXISTS_WITH-imft"},{"$ref":"#/components/x-bte-kgs-operations/imft-COEXISTS_WITH-imft-rev"},{"$ref":"#/components/x-bte-kgs-operations/aapp-PRODUCES-hops"},{"$ref":"#/components/x-bte-kgs-operations/orch-PREVENTS-sosy-rev"},{"$ref":"#/components/x-bte-kgs-operations/horm-DISRUPTS-celf-rev"},{"$ref":"#/components/x-bte-kgs-operations/inch-COEXISTS_WITH-gngm-rev"},{"$ref":"#/components/x-bte-kgs-operations/hops-COEXISTS_WITH-gngm-rev"},{"$ref":"#/components/x-bte-kgs-operations/bpoc-PRODUCES-orch"},{"$ref":"#/components/x-bte-kgs-operations/dsyn-AFFECTS-comd"},{"$ref":"#/components/x-bte-kgs-operations/carb-AUGMENTS-bpoc-rev"},{"$ref":"#/components/x-bte-kgs-operations/hops-PREDISPOSES-neop-rev"},{"$ref":"#/components/x-bte-kgs-operations/aapp-DISRUPTS-inpo"},{"$ref":"#/components/x-bte-kgs-operations/lipd-DISRUPTS-celf-rev"},{"$ref":"#/components/x-bte-kgs-operations/gngm-PRODUCES-gngm"},{"$ref":"#/components/x-bte-kgs-operations/gngm-PRODUCES-gngm-rev"},{"$ref":"#/components/x-bte-kgs-operations/food-AFFECTS-ortf"},{"$ref":"#/components/x-bte-kgs-operations/orch-AUGMENTS-sosy"},{"$ref":"#/components/x-bte-kgs-operations/orch-AUGMENTS-sosy-rev"},{"$ref":"#/components/x-bte-kgs-operations/comd-PRODUCES-bacs-rev"},{"$ref":"#/components/x-bte-kgs-operations/aapp-PREDISPOSES-sosy"},{"$ref":"#/components/x-bte-kgs-operations/aapp-PREDISPOSES-sosy-rev"},{"$ref":"#/components/x-bte-kgs-operations/gngm-PRODUCES-imft"},{"$ref":"#/components/x-bte-kgs-operations/gngm-PRODUCES-imft-rev"},{"$ref":"#/components/x-bte-kgs-operations/gngm-COEXISTS_WITH-hops"},{"$ref":"#/components/x-bte-kgs-operations/imft-INTERACTS_WITH-gngm"},{"$ref":"#/components/x-bte-kgs-operations/imft-INTERACTS_WITH-gngm-rev"},{"$ref":"#/components/x-bte-kgs-operations/dsyn-COMPLICATES-neop"},{"$ref":"#/components/x-bte-kgs-operations/nsba-COEXISTS_WITH-aapp-rev"},{"$ref":"#/components/x-bte-kgs-operations/phsu-DISRUPTS-cell-rev"},{"$ref":"#/components/x-bte-kgs-operations/gngm-AUGMENTS-cell"},{"$ref":"#/components/x-bte-kgs-operations/gngm-AUGMENTS-cell-rev"},{"$ref":"#/components/x-bte-kgs-operations/strd-INHIBITS-gngm-rev"},{"$ref":"#/components/x-bte-kgs-operations/aapp-INHIBITS-antb"},{"$ref":"#/components/x-bte-kgs-operations/orch-CAUSES-cgab"},{"$ref":"#/components/x-bte-kgs-operations/cgab-COEXISTS_WITH-patf-rev"},{"$ref":"#/components/x-bte-kgs-operations/horm-AUGMENTS-ortf-rev"},{"$ref":"#/components/x-bte-kgs-operations/bacs-DISRUPTS-celc-rev"},{"$ref":"#/components/x-bte-kgs-operations/antb-TREATS-sosy-rev"},{"$ref":"#/components/x-bte-kgs-operations/phsu-DISRUPTS-dsyn-rev"},{"$ref":"#/components/x-bte-kgs-operations/topp-PREDISPOSES-sosy"},{"$ref":"#/components/x-bte-kgs-operations/topp-PREDISPOSES-sosy-rev"},{"$ref":"#/components/x-bte-kgs-operations/inch-CAUSES-sosy-rev"},{"$ref":"#/components/x-bte-kgs-operations/orch-DISRUPTS-inpo"},{"$ref":"#/components/x-bte-kgs-operations/strd-STIMULATES-gngm-rev"},{"$ref":"#/components/x-bte-kgs-operations/gngm-INTERACTS_WITH-antb"},{"$ref":"#/components/x-bte-kgs-operations/aapp-PREVENTS-acab"},{"$ref":"#/components/x-bte-kgs-operations/diap-DIAGNOSES-comd"},{"$ref":"#/components/x-bte-kgs-operations/inch-AFFECTS-bpoc-rev"},{"$ref":"#/components/x-bte-kgs-operations/gngm-CONVERTS_TO-gngm"},{"$ref":"#/componen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server","url":"https://cam-kp-api.transltr.io/1.3.0","x-location":"RENCI","x-maturity":"production"}],"tags":[{"name":"maturity"},{"name":"translator"},{"name":"trapi"}]},{"_id":"dc91716f44207d2e1287c727f281d339","_ignored":["paths.pathitem.post.summary.raw"],"_meta":{"date_created":"2021-03-11T18:52:08.763346+00:00","last_updated":"2023-05-22T07:05:46.676193+00:00","url":"https://raw.githubusercontent.com/NCATS-Tangerine/translator-api-registry/master/biothings_explorer/smartapi.yaml","username":"andrewsu"},"info":{"contact":{"email":"asu@scripps.edu","name":"Andrew Su","url":"https://github.com/andrewsu"},"description":"A TRAPI/Reasoner Standard API for BioThings Explorer (BTE)","termsOfService":"https://biothings.io/about","title":"BioThings Explorer (BTE) TRAPI","version":"2.8.1","x-translator":{"biolink-version":"3.1.1","component":"ARA","infores":"infores:biothings-explorer","team":["Exploring Agent"]},"x-trapi":{"asyncquery":true,"operations":["lookup"],"rate_limit":15,"test_data_location":{"default":{"url":"https://raw.githubusercontent.com/NCATS-Tangerine/translator-api-registry/master/biothings_explorer/sri-test-bte-ara.json"}},"version":"1.3.0"}},"paths":{"/meta_knowledge_graph":{"get":{"responses":{"200":{"content":{"application/json":{"schema":{"$ref":"#/components/schemas/MetaKnowledgeGraph"}}},"description":"Returns meta knowledge graph representation of this TRAPI web service."}},"summary":"Meta knowledge graph representation of this TRAPI web service.","tags":["meta_knowledge_graph"]}},"/smartapi/{smartapi_id}/meta_knowledge_graph":{"get":{"parameters":[{"description":"SmartAPI ID of an API with x-bte annotation. The easiest way to find these is to read the list of APIs BTE uses https://github.com/biothings/biothings_explorer/blob/main/src/config/apis.js","example":"09c8782d9f4027712e65b95424adba79","in":"path","name":"smartapi_id","required":true,"schema":{"type":"string"}}],"responses":{"200":{"content":{"application/json":{"schema":{"$ref":"#/components/schemas/MetaKnowledgeGraph"}}},"description":"Returns a TRAPI-compliant meta-knowledge-graph representation for an individual SmartAPI KP API (that has x-bte annotation)"}},"summary":"TRAPI-compliant meta-knowledge-graph representation for an individual SmartAPI KP API (that has x-bte annotation)","tags":["meta_knowledge_graph"]}},"/team/{team_name}/meta_knowledge_graph":{"get":{"parameters":[{"description":"Translator Team Name. Current options: Service Provider, Multiomics Provider, Text Mining Provider. The easiest way to find what KP APIs would be included under these teams is to read the list of APIs BTE uses https://github.com/biothings/biothings_explorer/blob/main/src/config/apis.js. Note that Service Provider endpoints are also advertised separately as a KP http://smart-api.info/registry?q=36f82f05705c317bac17ddae3a0ea2f0 ","example":"Service Provider","in":"path","name":"team_name","required":true,"schema":{"enum":["Multiomics Provider","Text Mining Provider","Service Provider"],"type":"string"}}],"responses":{"200":{"content":{"application/json":{"schema":{"$ref":"#/components/schemas/MetaKnowledgeGraph"}}},"description":"Returns a TRAPI-compliant meta-knowledge-graph representation for one KP team's SmartAPI KP APIs (that have x-bte annotation)"}},"summary":"TRAPI-compliant meta-knowledge-graph representation for one KP team's SmartAPI KP APIs (that have x-bte annotation)","tags":["meta_knowledge_graph"]}},"/query":{"post":{"parameters":[{"description":"option to choose whether or not to enable caching","in":"query","name":"caching","required":false,"schema":{"type":"boolean"}},{"description":"dryrun a query (logs the queries BTE will make)","in":"query","name":"dryrun","required":false,"schema":{"type":"boolean"}}],"requestBody":{"content":{"application/json":{"example":{"message":{"query_graph":{"edges":{"e1":{"object":"n1","subject":"n0"}},"nodes":{"n0":{"categories":["biolink:SequenceVariant"],"ids":["DBSNP:rs121913521"]},"n1":{"categories":["biolink:Disease"]}}}}},"schema":{"$ref":"#/components/schemas/Query"}}},"description":"Query information to be submitted","required":true},"responses":{"200":{"content":{"application/json":{"schema":{"$ref":"#/components/schemas/Response"}}},"description":"OK. There may or may not be results. Note that some of the provided identifiers may not have been recognized."},"400":{"content":{"application/json":{"schema":{"type":"string"}}},"description":"Bad request. The request is invalid according to this OpenAPI schema OR a specific identifier is believed to be invalid somehow (not just unrecognized)."},"413":{"content":{"application/json":{"schema":{"type":"string"}}},"description":"Payload too large. Indicates that batch size was over the limit specified in x-trapi."},"429":{"content":{"application/json":{"schema":{"type":"string"}}},"description":"Too many requests. Indicates that the client issued requests that exceed the rate limit specified in x-trapi."},"500":{"content":{"application/json":{"schema":{"type":"string"}}},"description":"Internal server error."},"501":{"content":{"application/json":{"schema":{"type":"string"}}},"description":"Not implemented."}},"summary":"Initiate a TRAPI-format query to BTE (operating as an ARA) and wait to receive a Response","tags":["query"]}},"/smartapi/{smartapi_id}/query":{"post":{"parameters":[{"description":"SmartAPI ID of an API with x-bte annotation. The easiest way to find these is to read the list of APIs BTE uses https://github.com/biothings/biothings_explorer/blob/main/src/config/apis.js","example":"09c8782d9f4027712e65b95424adba79","in":"path","name":"smartapi_id","required":true,"schema":{"type":"string"}},{"description":"option to choose whether or not to enable caching","in":"query","name":"caching","required":false,"schema":{"type":"boolean"}},{"description":"dryrun a query (logs the queries BTE will make)","in":"query","name":"dryrun","required":false,"schema":{"type":"boolean"}}],"requestBody":{"content":{"application/json":{"example":{"message":{"query_graph":{"edges":{"e1":{"object":"n1","subject":"n0"}},"nodes":{"n0":{"categories":["biolink:SequenceVariant"],"ids":["DBSNP:rs121913521"]},"n1":{"categories":["biolink:Disease"]}}}}},"schema":{"$ref":"#/components/schemas/Query"}}},"description":"Query information to be submitted","required":true},"responses":{"200":{"content":{"application/json":{"schema":{"$ref":"#/components/schemas/Response"}}},"description":"OK. There may or may not be results. Note that some of the provided identifiers may not have been recognized."},"400":{"content":{"application/json":{"schema":{"type":"string"}}},"description":"Bad request. The request is invalid according to this OpenAPI schema OR a specific identifier is believed to be invalid somehow (not just unrecognized)."},"413":{"content":{"application/json":{"schema":{"type":"string"}}},"description":"Payload too large. Indicates that batch size was over the limit specified in x-trapi."},"429":{"content":{"application/json":{"schema":{"type":"string"}}},"description":"Too many requests. Indicates that the client issued requests that exceed the rate limit specified in x-trapi."},"500":{"content":{"application/json":{"schema":{"type":"string"}}},"description":"Internal server error."},"501":{"content":{"application/json":{"schema":{"type":"string"}}},"description":"Not implemented."}},"summary":"Query individual SmartAPI KP API (that has x-bte annotation) as a TRAPI KP API","tags":["query"]}},"/team/{team_name}/query":{"post":{"parameters":[{"description":"Translator Team Name. Current options: Service Provider, Multiomics Provider, Text Mining Provider. The easiest way to find what KP APIs would be included under these teams is to read the list of APIs BTE uses https://github.com/biothings/biothings_explorer/blob/main/src/config/apis.js. Note that Service Provider endpoints are also advertised separately as a KP http://smart-api.info/registry?q=36f82f05705c317bac17ddae3a0ea2f0 ","example":"Service Provider","in":"path","name":"team_name","required":true,"schema":{"enum":["Multiomics Provider","Text Mining Provider","Service Provider"],"type":"string"}},{"description":"option to choose whether or not to enable caching","in":"query","name":"caching","required":false,"schema":{"type":"boolean"}},{"description":"dryrun a query (logs the queries BTE will make)","in":"query","name":"dryrun","required":false,"schema":{"type":"boolean"}}],"requestBody":{"content":{"application/json":{"example":{"message":{"query_graph":{"edges":{"e1":{"object":"n1","subject":"n0"}},"nodes":{"n0":{"categories":["biolink:SequenceVariant"],"ids":["DBSNP:rs121913521"]},"n1":{"categories":["biolink:Disease"]}}}}},"schema":{"$ref":"#/components/schemas/Query"}}},"description":"Query information to be submitted","required":true},"responses":{"200":{"content":{"application/json":{"schema":{"$ref":"#/components/schemas/Response"}}},"description":"OK. There may or may not be results. Note that some of the provided identifiers may not have been recognized."},"400":{"content":{"application/json":{"schema":{"type":"string"}}},"description":"Bad request. The request is invalid according to this OpenAPI schema OR a specific identifier is believed to be invalid somehow (not just unrecognized)."},"413":{"content":{"application/json":{"schema":{"type":"string"}}},"description":"Payload too large. Indicates that batch size was over the limit specified in x-trapi."},"429":{"content":{"application/json":{"schema":{"type":"string"}}},"description":"Too many requests. Indicates that the client issued requests that exceed the rate limit specified in x-trapi."},"500":{"content":{"application/json":{"schema":{"type":"string"}}},"description":"Internal server error."},"501":{"content":{"application/json":{"schema":{"type":"string"}}},"description":"Not implemented."}},"summary":"Query an individual Translator team's SMARTAPI KP APIs (that have x-bte annotation) as an individual TRAPI service by specifying the team name","tags":["query"]}},"/check_query_status/{id}":{"get":{"parameters":[{"description":"option to override original query log level","in":"query","name":"log_level","required":false,"schema":{"description":"Logging level. The order of priority is ERROR, WARNING, INFO, DEBUG. BTE will return all logs at the specified level and those at higher priority levels","enum":["ERROR","WARNING","INFO","DEBUG"],"type":"string"}}],"responses":{"200":{"content":{"application/json":{"schema":{"properties":{"id":{"description":"the job-id","type":"string"},"reason":{"description":"when the state is 'failed', this field states a reason for the failure","type":"string"},"returnvalue":{"description":"When the state is 'completed', this will contain the TRAPI Response object. Note that BTE might return an error, no results, etc as a Response...","properties":{"response":{"$ref":"#/components/schemas/Response"}},"type":"object"},"state":{"description":"the status of the job"}},"required":["id","state"],"type":"object"}}},"description":"Returns status. If successfully completed, it will return a TRAPI Response object under the field returnvalue"}},"summary":"This endpoint should be used when a Query was sent to BTE through an /asyncquery endpoint without a callback property: BTE then handled it in a polling manner and provided a job id. The job id can be used here to check the status or retrieve the Response.","tags":["asyncquery"]},"parameters":[{"description":"job-id","in":"path","name":"id","required":true,"schema":{"type":"string"}}]},"/asyncquery":{"post":{"parameters":[{"description":"option to choose whether or not to enable caching","in":"query","name":"caching","required":false,"schema":{"type":"boolean"}},{"description":"dryrun a query (logs the queries BTE will make)","in":"query","name":"dryrun","required":false,"schema":{"type":"boolean"}}],"requestBody":{"content":{"application/json":{"example":{"message":{"query_graph":{"edges":{"e1":{"object":"n1","subject":"n0"}},"nodes":{"n0":{"categories":["biolink:SequenceVariant"],"ids":["DBSNP:rs121913521"]},"n1":{"categories":["biolink:Disease"]}}}}},"schema":{"$ref":"#/components/schemas/AsyncQuery"}}},"description":"Query information to be submitted","required":true},"responses":{"200":{"content":{"application/json":{"schema":{"type":"string"}}},"description":"The query is accepted for processing. The behavior will depend on whether the callback property is included. If the callback property is included, the Response will be sent to the callback url when complete. If the callback property is not included, BTE will handle the query in a polling manner: it will provide a job-id that can be used to check the status or retrieve the Response using BTE's /v1/check_query_status/{id} endpoint."},"400":{"content":{"application/json":{"schema":{"type":"string"}}},"description":"Bad request. The request is invalid according to this OpenAPI schema OR a specific identifier is believed to be invalid somehow (not just unrecognized)."},"413":{"content":{"application/json":{"schema":{"type":"string"}}},"description":"Payload too large. Indicates that batch size was over the limit specified in x-trapi."},"429":{"content":{"application/json":{"schema":{"type":"string"}}},"description":"Too many requests. Indicates that the client issued requests that exceed the rate limit specified in x-trapi."},"500":{"content":{"application/json":{"schema":{"type":"string"}}},"description":"Internal server error."},"501":{"content":{"application/json":{"schema":{"type":"string"}}},"description":"Not implemented."}},"summary":"Initiate a query that will be handled in an asynchronous manner (there is a queue and queries will be executed in the order that they enter the queue). For BTE, it is optional to have a callback property in the request-body. If the callback property is not included, BTE will handle the query in a polling manner: it will provide a job-id that can be used to check the status or retrieve the Response using BTE's /v1/check_query_status/{id} endpoint.","tags":["asyncquery"]}},"/smartapi/{smartapi_id}/asyncquery":{"post":{"parameters":[{"description":"SmartAPI ID of an API with x-bte annotation. The easiest way to find these is to read the list of APIs BTE uses https://github.com/biothings/biothings_explorer/blob/main/src/config/apis.js","example":"09c8782d9f4027712e65b95424adba79","in":"path","name":"smartapi_id","required":true,"schema":{"type":"string"}},{"description":"option to choose whether or not to enable caching","in":"query","name":"caching","required":false,"schema":{"type":"boolean"}},{"description":"dryrun a query (logs the queries BTE will make)","in":"query","name":"dryrun","required":false,"schema":{"type":"boolean"}}],"requestBody":{"content":{"application/json":{"example":{"message":{"query_graph":{"edges":{"e1":{"object":"n1","subject":"n0"}},"nodes":{"n0":{"categories":["biolink:SequenceVariant"],"ids":["DBSNP:rs121913521"]},"n1":{"categories":["biolink:Disease"]}}}}},"schema":{"$ref":"#/components/schemas/AsyncQuery"}}},"description":"Query information to be submitted","required":true},"responses":{"200":{"content":{"application/json":{"schema":{"type":"string"}}},"description":"The query is accepted for processing. The behavior will depend on whether the callback property is included. If the callback property is included, the Response will be sent to the callback url when complete. If the callback property is not included, BTE will handle the query in a polling manner: it will provide a job-id that can be used to check the status or retrieve the Response using BTE's /v1/check_query_status/{id} endpoint."},"400":{"content":{"application/json":{"schema":{"type":"string"}}},"description":"Bad request. The request is invalid according to this OpenAPI schema OR a specific identifier is believed to be invalid somehow (not just unrecognized)."},"413":{"content":{"application/json":{"schema":{"type":"string"}}},"description":"Payload too large. Indicates that batch size was over the limit specified in x-trapi."},"429":{"content":{"application/json":{"schema":{"type":"string"}}},"description":"Too many requests. Indicates that the client issued requests that exceed the rate limit specified in x-trapi."},"500":{"content":{"application/json":{"schema":{"type":"string"}}},"description":"Internal server error."},"501":{"content":{"application/json":{"schema":{"type":"string"}}},"description":"Not implemented."}},"summary":"This endpoint is for asynchronously querying an individual SmartAPI KP API (that has x-bte annotation) as a TRAPI KP API.\nInitiate a query that will be handled in an asynchronous manner (there is a queue and queries will be executed in the order that they enter the queue). For BTE, it is optional to have a callback property in the request-body. If the callback property is not included, BTE will handle the query in a polling manner: it will provide a job-id that can be used to check the status or retrieve the Response using BTE's /v1/check_query_status/{id} endpoint.","tags":["asyncquery"]}},"/team/{team_name}/asyncquery":{"post":{"parameters":[{"description":"Translator Team Name. Current options: Service Provider, Multiomics Provider, Text Mining Provider. The easiest way to find what KP APIs would be included under these teams is to read the list of APIs BTE uses https://github.com/biothings/biothings_explorer/blob/main/src/config/apis.js. Note that Service Provider endpoints are also advertised separately as a KP http://smart-api.info/registry?q=36f82f05705c317bac17ddae3a0ea2f0 ","example":"Service Provider","in":"path","name":"team_name","required":true,"schema":{"enum":["Multiomics Provider","Text Mining Provider","Service Provider"],"type":"string"}},{"description":"option to choose whether or not to enable caching","in":"query","name":"caching","required":false,"schema":{"type":"boolean"}},{"description":"dryrun a query (logs the queries BTE will make)","in":"query","name":"dryrun","required":false,"schema":{"type":"boolean"}}],"requestBody":{"content":{"application/json":{"example":{"message":{"query_graph":{"edges":{"e1":{"object":"n1","subject":"n0"}},"nodes":{"n0":{"categories":["biolink:SequenceVariant"],"ids":["DBSNP:rs121913521"]},"n1":{"categories":["biolink:Disease"]}}}}},"schema":{"$ref":"#/components/schemas/AsyncQuery"}}},"description":"Query information to be submitted","required":true},"responses":{"200":{"content":{"application/json":{"schema":{"type":"string"}}},"description":"The query is accepted for processing. The behavior will depend on whether the callback property is included. If the callback property is included, the Response will be sent to the callback url when complete. If the callback property is not included, BTE will handle the query in a polling manner: it will provide a job-id that can be used to check the status or retrieve the Response using BTE's /v1/check_query_status/{id} endpoint."},"400":{"content":{"application/json":{"schema":{"type":"string"}}},"description":"Bad request. The request is invalid according to this OpenAPI schema OR a specific identifier is believed to be invalid somehow (not just unrecognized)."},"413":{"content":{"application/json":{"schema":{"type":"string"}}},"description":"Payload too large. Indicates that batch size was over the limit specified in x-trapi."},"429":{"content":{"application/json":{"schema":{"type":"string"}}},"description":"Too many requests. Indicates that the client issued requests that exceed the rate limit specified in x-trapi."},"500":{"content":{"application/json":{"schema":{"type":"string"}}},"description":"Internal server error."},"501":{"content":{"application/json":{"schema":{"type":"string"}}},"description":"Not implemented."}},"summary":"This endpoint is for asynchronously querying an individual Translator team's SMARTAPI KP APIs (that have x-bte annotation) as an individual TRAPI service by specifying the team name.\nInitiate a query that will be handled in an asynchronous manner (there is a queue and queries will be executed in the order that they enter the queue). For BTE, it is optional to have a callback property in the request-body. If the callback property is not included, BTE will handle the query in a polling manner: it will provide a job-id that can be used to check the status or retrieve the Response using BTE's /v1/check_query_status/{id} endpoint.","tags":["asyncquery"]}}},"servers":[{"description":"ITRB Production server","url":"https://bte.transltr.io/v1","x-maturity":"production"},{"description":"ITRB Test server","url":"https://bte.test.transltr.io/v1","x-maturity":"testing"},{"description":"ITRB CI server","url":"https://bte.ci.transltr.io/v1","x-maturity":"staging"}],"tags":[{"name":"1.3.0"},{"name":"meta_knowledge_graph"},{"name":"query"},{"name":"asyncquery"},{"name":"translator"},{"name":"trapi"},{"name":"biothings"}]},{"_id":"00fb85fc776279163199e6c50f6ddfc6","_ignored":["paths.pathitem.get.description.raw"],"_meta":{"date_created":"2023-01-06T22:18:30.729725+00:00","last_updated":"2023-05-22T07:05:45.564647+00:00","url":"https://raw.githubusercontent.com/NCATS-Tangerine/translator-api-registry/master/ddinter/ddinter.yaml","username":"colleenXu"},"components":{"x-bte-kgs-operations":{"drugA-to-drugB":[{"inputs":[{"id":"DRUGBANK","semantic":"SmallMolecule"}],"outputs":[{"id":"DRUGBANK","semantic":"SmallMolecule"}],"parameters":{"fields":"drug_b.drugbank,level","size":1000},"predicate":"interacts_with","requestBody":{"body":{"q":"{{ queryInputs }}","scopes":"drug_a.drugbank"}},"response_mapping":{"$ref":"#/components/x-bte-response-mapping/drugB"},"source":"infores:ddinter","supportBatch":true,"useTemplating":true}],"drugB-to-drugA":[{"inputs":[{"id":"DRUGBANK","semantic":"SmallMolecule"}],"outputs":[{"id":"DRUGBANK","semantic":"SmallMolecule"}],"parameters":{"fields":"drug_a.drugbank,level","size":1000},"predicate":"interacts_with","requestBody":{"body":{"q":"{{ queryInputs }}","scopes":"drug_b.drugbank"}},"response_mapping":{"$ref":"#/components/x-bte-response-mapping/drugA"},"source":"infores:ddinter","supportBatch":true,"useTemplating":true}]},"x-bte-response-mapping":{"drugA":{"DRUGBANK":"drug_a.drugbank","drug_interaction_severity_level":"level"},"drugB":{"DRUGBANK":"drug_b.drugbank","drug_interaction_severity_level":"level"}}},"info":{"contact":{"email":"help@biothings.io","name":"BioThings Team","x-id":"https://github.com/biothings","x-role":"responsible developers"},"description":"Documentation of the BioThings API for [DDInter](http://ddinter.scbdd.com/) data.","termsOfService":"https://biothings.io/about","title":"BioThings DDInter API","version":"1.0","x-translator":{"biolink-version":"3.1.1","component":"KP","infores":"infores:biothings-ddinter","team":["Service Provider"]}},"paths":{"/interaction/{id}":{"get":{"description":"By default, this will return the complete association in JSON format. If the input is not valid, 404 (NOT FOUND) will be returned.\n\nOptionally, you can pass a \"fields\" parameter to return only the annotation you want (by filtering returned object fields). \"fields\" accepts any attributes (a.k.a fields) available from the association. Multiple attributes should be separated by commas. If an attribute is not available for a specific association, it will be ignored. Note that the attribute names are case-sensitive.\n\nJust like the query service, you can also pass a \"callback\" parameter to make a JSONP call.","parameters":[{"example":"DDInter1414_DDInter1004_Moderate","in":"path","name":"id","required":true,"schema":{"type":"string"}},{"$ref":"#/components/parameters/fields"},{"$ref":"#/components/parameters/callback"},{"$ref":"#/components/parameters/email"},{"$ref":"#/components/parameters/size"}],"responses":{"200":{"description":"A 200 status code indicates a successful query, and is accompanied by the query response payload."}},"tags":["interaction"]}},"/interaction":{"post":{"description":"Although making simple GET requests above to our service is sufficient in most use cases, there are some times you might find it easier to batch query (e.g., retrieving multiple associations). Fortunately, you can also make batch queries via POST requests when you need to.","parameters":[{"description":"Accepts multiple association ids separated by commas. Note that currently we only take ids up to 1000 maximum, the rest will be omitted.\n\nThe request body can also be used to provide these ids.","in":"query","name":"ids","required":false,"schema":{"type":"string"}},{"$ref":"#/components/parameters/fields"},{"$ref":"#/components/parameters/email"},{"$ref":"#/components/parameters/size"}],"requestBody":{"content":{"application/json":{"example":{"ids":["DDInter1214_DDInter100_Moderate","DDInter1214_DDInter1017_Moderate"]},"schema":{"properties":{"ids":{"description":"Accepts multiple association ids. Note that currently we only take the input ids up to 1000 maximum, the rest will be omitted.","items":{"type":"string"},"type":"array"}},"type":"object"}}}},"responses":{"200":{"description":"A 200 status code indicates a successful query, and is accompanied by the query response payload."}},"tags":["interaction"]}},"/metadata":{"get":{"description":"Get metadata about the data available from the API","responses":{"200":{"description":"A 200 status code indicates a successful query, and is accompanied by the query response payload."}},"tags":["metadata"]}},"/metadata/fields":{"get":{"description":"Get metadata about the data fields available from the API","responses":{"200":{"description":"A 200 status code indicates a successful query, and is accompanied by the query response payload."}},"tags":["metadata"]}},"/query":{"get":{"description":"Query service. In the output, \"total\" in the output gives the total number of matching hits, while the actual hits are returned under \"hits\" field.","parameters":[{"description":"Required, passing user query. The detailed query syntax for parameter is explained [here for a core BioThings API](https://docs.mychem.info/en/latest/doc/chem_query_service.html#query-syntax).","example":"drug_a.drugbank:DB08880","in":"query","name":"q","required":true,"schema":{"type":"string"}},{"$ref":"#/components/parameters/fields"},{"$ref":"#/components/parameters/size"},{"$ref":"#/components/parameters/from"},{"$ref":"#/components/parameters/fetch_all"},{"$ref":"#/components/parameters/scroll_id"},{"$ref":"#/components/parameters/sort"},{"$ref":"#/components/parameters/facets"},{"$ref":"#/components/parameters/facet_size"},{"$ref":"#/components/parameters/callback"},{"$ref":"#/components/parameters/dotfield"},{"$ref":"#/components/parameters/email"}],"responses":{"200":{"description":"A 200 status code indicates a successful query, and is accompanied by the query response payload."}},"tags":["query"]},"post":{"description":"Although making simple GET requests above to our query service is sufficient for most use cases, there are times you might find it more efficient to make batch queries (e.g., retrieving data for multiple inputs). 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The easiest way to find these is to read the list of APIs BTE uses https://github.com/biothings/biothings_explorer/blob/main/src/config/apis.js","example":"09c8782d9f4027712e65b95424adba79","in":"path","name":"smartapi_id","required":true,"schema":{"type":"string"}},{"description":"option to choose whether or not to enable caching","in":"query","name":"caching","required":false,"schema":{"type":"boolean"}},{"description":"dryrun a query (logs the queries BTE will make)","in":"query","name":"dryrun","required":false,"schema":{"type":"boolean"}}],"requestBody":{"content":{"application/json":{"example":{"message":{"query_graph":{"edges":{"e1":{"object":"n1","subject":"n0"}},"nodes":{"n0":{"categories":["biolink:SequenceVariant"],"ids":["DBSNP:rs121913521"]},"n1":{"categories":["biolink:Disease"]}}}}},"schema":{"$ref":"#/components/schemas/AsyncQuery"}}},"description":"Query information to be submitted","required":true},"responses":{"200":{"content":{"application/json":{"schema":{"$ref":"#/components/schemas/AsyncQueryResponse"}}},"description":"The query is accepted for processing. 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Indicates that the client issued requests that exceed the rate limit specified in x-trapi."},"500":{"content":{"application/json":{"schema":{"type":"string"}}},"description":"Internal server error."},"501":{"content":{"application/json":{"schema":{"type":"string"}}},"description":"Not implemented."}},"summary":"This endpoint is for asynchronously querying an individual SmartAPI KP API (that has x-bte annotation) as a TRAPI KP API.\nInitiate a query that will be handled in an asynchronous manner (there is a queue and queries will be executed in the order that they enter the queue). For BTE, it is optional to have a callback property in the request-body. If the callback property is not included, BTE will handle the query in a polling manner: it will provide a job-id that can be used to check the status or retrieve the Response.","tags":["asyncquery"]}},"/team/{team_name}/asyncquery":{"post":{"parameters":[{"description":"Translator Team Name. Current options: Service Provider, Multiomics Provider, Text Mining Provider. The easiest way to find what KP APIs would be included under these teams is to read the list of APIs BTE uses https://github.com/biothings/biothings_explorer/blob/main/src/config/apis.js. Note that Service Provider endpoints are also registered separately as a KP in the SmartAPI Registry","example":"Service Provider","in":"path","name":"team_name","required":true,"schema":{"enum":["Multiomics Provider","Text Mining Provider","Service Provider"],"type":"string"}},{"description":"option to choose whether or not to enable caching","in":"query","name":"caching","required":false,"schema":{"type":"boolean"}},{"description":"dryrun a query (logs the queries BTE will make)","in":"query","name":"dryrun","required":false,"schema":{"type":"boolean"}}],"requestBody":{"content":{"application/json":{"example":{"message":{"query_graph":{"edges":{"e1":{"object":"n1","subject":"n0"}},"nodes":{"n0":{"categories":["biolink:SequenceVariant"],"ids":["DBSNP:rs121913521"]},"n1":{"categories":["biolink:Disease"]}}}}},"schema":{"$ref":"#/components/schemas/AsyncQuery"}}},"description":"Query information to be submitted","required":true},"responses":{"200":{"content":{"application/json":{"schema":{"$ref":"#/components/schemas/AsyncQueryResponse"}}},"description":"The query is accepted for processing. 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Indicates that the client issued requests that exceed the rate limit specified in x-trapi."},"500":{"content":{"application/json":{"schema":{"type":"string"}}},"description":"Internal server error."},"501":{"content":{"application/json":{"schema":{"type":"string"}}},"description":"Not implemented."}},"summary":"This endpoint is for asynchronously querying an individual Translator team's SMARTAPI KP APIs (that have x-bte annotation) as an individual TRAPI service by specifying the team name.\nInitiate a query that will be handled in an asynchronous manner (there is a queue and queries will be executed in the order that they enter the queue). For BTE, it is optional to have a callback property in the request-body. If the callback property is not included, BTE will handle the query in a polling manner: it will provide a job-id that can be used to check the status or retrieve the Response.","tags":["asyncquery"]}},"/asyncquery_status/{job_id}":{"get":{"operationId":"asyncquery_status","parameters":[{"description":"Identifier of the job for status request","in":"path","name":"job_id","required":true,"schema":{"type":"string"}}],"responses":{"200":{"content":{"application/json":{"schema":{"$ref":"#/components/schemas/AsyncQueryStatusResponse"}}},"description":"Returns the status and current logs of a previously submitted asyncquery."},"404":{"description":"job_id not found"},"501":{"content":{"application/json":{"schema":{"type":"string"}}},"description":"Return code 501 indicates that this endpoint has not been implemented at this site. 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If the input is not valid, 404 (NOT FOUND) will be returned.\n\nOptionally, you can pass a \"fields\" parameter to return only the annotation you want (by filtering returned object fields). \"fields\" accepts any attributes (a.k.a fields) available from the association. Multiple attributes should be separated by commas. If an attribute is not available for a specific ontology term, it will be ignored. Note that the attribute names are case-sensitive.\n\nJust like the query service, you can also pass a \"callback\" parameter to make a JSONP call.","parameters":[{"example":"GO:0008613","in":"path","name":"id","required":true,"schema":{"type":"string"}},{"$ref":"#/components/parameters/fields"},{"$ref":"#/components/parameters/callback"},{"$ref":"#/components/parameters/email"},{"$ref":"#/components/parameters/size"}],"responses":{"200":{"description":"A 200 status code indicates a successful query, and is accompanied by the query response payload."}},"tags":["ontology"]}},"/geneset":{"post":{"description":"Although making simple GET requests above to our service is sufficient in most use cases, there are some times you might find it easier to batch query (e.g., retrieving multiple ontology terms). Fortunately, you can also make batch queries via POST requests when you need to.","parameters":[{"description":"Accepts multiple ontology term ids separated by commas. Note that currently we only take ids up to 1000 maximum, the rest will be omitted.\n\nThe request body can also be used to provide these ids.","in":"query","name":"ids","required":false,"schema":{"type":"string"}},{"$ref":"#/components/parameters/fields"},{"$ref":"#/components/parameters/email"},{"$ref":"#/components/parameters/size"}],"requestBody":{"content":{"application/json":{"example":{"ids":["GO:0008613","GO:0008510"]},"schema":{"properties":{"ids":{"description":"Accepts multiple ontology term ids. Note that currently we only take the input ids up to 1000 maximum, the rest will be omitted.","items":{"type":"string"},"type":"array"}},"type":"object"}}}},"responses":{"200":{"description":"A 200 status code indicates a successful query, and is accompanied by the query response payload."}},"tags":["ontology"]}},"/metadata":{"get":{"description":"Get metadata about the data available from the API","responses":{"200":{"description":"A 200 status code indicates a successful query, and is accompanied by the query response payload."}},"tags":["metadata"]}},"/metadata/fields":{"get":{"description":"Get metadata about the data fields available from the API","responses":{"200":{"description":"A 200 status code indicates a successful query, and is accompanied by the query response payload."}},"tags":["metadata"]}},"/query":{"get":{"description":"Query service. In the output, \"total\" in the output gives the total number of matching hits, while the actual hits are returned under \"hits\" field.","parameters":[{"description":"Required, passing user query. The detailed query syntax for parameter is explained [here for a core BioThings API](https://docs.mychem.info/en/latest/doc/chem_query_service.html#query-syntax).","example":"go:\"GO:0008613\"","in":"query","name":"q","required":true,"schema":{"type":"string"}},{"$ref":"#/components/parameters/fields"},{"$ref":"#/components/parameters/size"},{"$ref":"#/components/parameters/from"},{"$ref":"#/components/parameters/fetch_all"},{"$ref":"#/components/parameters/scroll_id"},{"$ref":"#/components/parameters/sort"},{"$ref":"#/components/parameters/facets"},{"$ref":"#/components/parameters/facet_size"},{"$ref":"#/components/parameters/callback"},{"$ref":"#/components/parameters/dotfield"},{"$ref":"#/components/parameters/email"}],"responses":{"200":{"description":"A 200 status code indicates a successful query, and is accompanied by the query response payload."}},"tags":["query"]},"post":{"description":"Although making simple GET requests above to our query service is sufficient for most use cases, there are times you might find it more efficient to make batch queries (e.g., retrieving data for multiple inputs). Fortunately, you can also make batch queries via POST requests when you need to.\n\nThe \"query” field in the returned object indicates the matching query term. If a query term has no match, it will return with a “notfound” field with the value “true”.","parameters":[{"description":"Accepts multiple values separated by commas. Note that currently we only take the input values up to 1000 maximum, the rest will be omitted.\n\nThe request body can also be used to provide these ids.","in":"query","name":"q","required":false,"schema":{"items":{"type":"string"},"type":"array"}},{"description":"Optional, specify one or more fields (separated by commas) to search. Default: _id\n\nThe request body can also be used to provide this information.","in":"query","name":"scopes","required":false,"schema":{"type":"string"}},{"$ref":"#/components/parameters/fields"},{"$ref":"#/components/parameters/email"},{"$ref":"#/components/parameters/size"},{"$ref":"#/components/parameters/from"},{"$ref":"#/components/parameters/fetch_all"},{"$ref":"#/components/parameters/scroll_id"}],"requestBody":{"content":{"application/json":{"example":{"q":["GO:0008613","GO:0008510"],"scopes":["go"]},"schema":{"properties":{"q":{"description":"Accepts multiple values separated by commas. Note that currently we only take the input values up to 1000 maximum, the rest will be omitted.","items":{"type":"string"},"type":"array"},"scopes":{"description":"Specify one or more fields (separated by commas) to search. Default: _id","items":{"type":"string"},"type":"array"}},"type":"object"}}}},"responses":{"200":{"description":"A 200 status code indicates a successful query, and is accompanied by the query response payload."}},"tags":["query"],"x-bte-kgs-operations":[{"$ref":"#/components/x-bte-kgs-operations/has_subclass"},{"$ref":"#/components/x-bte-kgs-operations/subclass_of"},{"$ref":"#/components/x-bte-kgs-operations/part_of"},{"$ref":"#/components/x-bte-kgs-operations/has_part"}]}}},"servers":[{"description":"Encrypted Production server","url":"https://biothings.ncats.io/go_mf","x-maturity":"production"},{"description":"Production server","url":"http://biothings.ncats.io/go_mf","x-maturity":"production"}],"tags":[{"name":"ontology"},{"name":"molecular activity"},{"name":"query"},{"name":"translator"},{"name":"biothings"}]},{"_id":"7f70cdfaeb801501da08dacc294e8b9f","_meta":{"date_created":"2023-05-08T23:59:06.007881+00:00","last_updated":"2023-05-22T07:06:12.952126+00:00","url":"https://raw.githubusercontent.com/suihuanglab/spoke-kp/main/spoke-kp.yaml","username":"brettasmi"},"info":{"contact":{"email":"brett.smith@isbscience.org"},"description":"SPOKE KP for TRAPI 1.4 - an NIH NCATS Knowledge Provider exposing UCSF's SPOKE","license":{"name":"Apache 2.0","url":"http://www.apache.org/licenses/LICENSE-2.0.html"},"termsOfService":"https://spoke.rbvi.ucsf.edu/license.html","title":"SPOKE KP for TRAPI 1.4","version":"1.4.0","x-translator":{"biolink-version":"3.2.5","component":"KP","externalDocs":{"description":"Repository","url":"https://github.com/suihuanglab/spoke-kp"},"infores":"infores:spoke","team":["imProving Agent"]},"x-trapi":{"asyncquery":false,"batch_size_limit":200,"operations":["lookup"],"rate_limit":20,"test_data_location":{"default":{"url":"https://github.com/suihuanglab/spoke-kp/tree/main/test-data"}},"version":"1.4.0-beta2"}},"paths":{"/meta_knowledge_graph":{"get":{"responses":{"200":{"content":{"application/json":{"schema":{"$ref":"#/components/schemas/MetaKnowledgeGraph"}}},"description":"Returns meta knowledge graph representation of this TRAPI web service."}},"summary":"Meta knowledge graph representation of this TRAPI web service.","tags":["meta_knowledge_graph"]}},"/query":{"post":{"description":"","requestBody":{"content":{"application/json":{"example":"{\n \"message\": {\n \"query_graph\": {\n \"nodes\": {\n \"n00\": {\n \"ids\": [\"DOID:1681\"],\n \"categories\": [\"biolink:Disease\"]\n },\n \"n01\": {\n \"categories\": [\"biolink:Gene\"]\n }\n },\n \"edges\": {\n \"e00\": {\n \"subject\": \"n00\",\n \"object\": \"n01\"\n }\n }\n }\n },\n}","schema":{"$ref":"#/components/schemas/Query"}}},"description":"Query information to be submitted","required":true},"responses":{"200":{"content":{"application/json":{"schema":{"$ref":"#/components/schemas/Response"}}},"description":"OK. There may or may not be results. Note that some of the provided identifiers may not have been recognized."},"400":{"content":{"application/json":{"schema":{"type":"string"}}},"description":"Bad request. The request is invalid according to this OpenAPI schema OR a specific identifier is believed to be invalid somehow (not just unrecognized)."},"413":{"content":{"application/json":{"schema":{"type":"string"}}},"description":"Payload too large. Indicates that batch size was over the limit specified in x-trapi."},"429":{"content":{"application/json":{"schema":{"type":"string"}}},"description":"Too many requests. Indicates that the client issued requests that exceed the rate limit specified in x-trapi."},"500":{"content":{"application/json":{"schema":{"type":"string"}}},"description":"Internal server error."},"501":{"content":{"application/json":{"schema":{"type":"string"}}},"description":"Not implemented."}},"summary":"Initiate a query and wait to receive a Response","tags":["query"]}},"/asyncquery":{"post":{"description":"","requestBody":{"content":{"application/json":{"example":"{\n \"message\": {\n \"query_graph\": {\n \"nodes\": {\n \"n00\": {\n \"ids\": [\"DOID:1681\"],\n \"categories\": [\"biolink:Disease\"]\n },\n \"n01\": {\n \"categories\": [\"biolink:Gene\"]\n }\n },\n \"edges\": {\n \"e00\": {\n \"subject\": \"n00\",\n \"object\": \"n01\"\n }\n }\n }\n },\n \"callback\": \"https://example.com/notimplemented\"\n}","schema":{"$ref":"#/components/schemas/AsyncQuery"}}},"description":"Query information to be submitted","required":true},"responses":{"200":{"content":{"application/json":{"schema":{"$ref":"#/components/schemas/AsyncQueryResponse"}}},"description":"The query is accepted for processing and the Response will be sent to the callback url when complete."},"400":{"content":{"application/json":{"schema":{"type":"string"}}},"description":"Bad request. The request is invalid according to this OpenAPI schema OR a specific identifier is believed to be invalid somehow (not just unrecognized)."},"413":{"content":{"application/json":{"schema":{"type":"string"}}},"description":"Payload too large. Indicates that batch size was over the limit specified in x-trapi."},"429":{"content":{"application/json":{"schema":{"type":"string"}}},"description":"Too many requests. Indicates that the client issued requests that exceed the rate limit specified in x-trapi."},"500":{"content":{"application/json":{"schema":{"type":"string"}}},"description":"Internal server error."},"501":{"content":{"application/json":{"schema":{"type":"string"}}},"description":"Not implemented."}},"summary":"Initiate a query with a callback to receive the response","tags":["asyncquery"]}},"/asyncquery_status/{job_id}":{"get":{"operationId":"asyncquery_status","parameters":[{"description":"Identifier of the job for status request","example":"rXEOAosN3L","in":"path","name":"job_id","required":true,"schema":{"type":"string"}}],"responses":{"200":{"content":{"application/json":{"schema":{"$ref":"#/components/schemas/AsyncQueryStatusResponse"}}},"description":"Returns the status and current logs of a previously submitted asyncquery."},"404":{"description":"job_id not found"},"501":{"content":{"application/json":{"schema":{"type":"string"}}},"description":"Return code 501 indicates that this endpoint has not been implemented at this site. Sites that implement /asyncquery MUST implement /asyncquery_status/{job_id}, but those that do not implement /asyncquery SHOULD NOT implement /asyncquery_status."}},"summary":"Retrieve the current status of a previously submitted asyncquery given its job_id","tags":["asyncquery_status"]}}},"servers":[{"description":"ITRB CI server","url":"https://spokekp.ci.transltr.io/api/v1.4/","x-maturity":"staging"},{"description":"dev","url":"https://spokekp.healthdatascience.cloud/api/v1.4/","x-maturity":"development"}],"tags":[{"description":"Retrieve the meta knowledge graph representation of this TRAPI web service. KPs MUST provide all subject category - predicate - object category triplets that are supported by the service, NOT including all implied ancestor relationships. ARAs SHOULD provide the union of all meta knowledge graphs of all the KPs that they can consult.","name":"meta_knowledge_graph"},{"description":"Initiate a query and wait to receive the response","name":"query"},{"description":"Initiate a query with a callback to receive the response","name":"asyncquery"},{"description":"Retrieve the current status of a previously submitted asyncquery given its job_id","name":"asyncquery_status"},{"description":"Required for SmartAPI validation of x-translator","name":"translator"},{"description":"Required for SmartAPI validation of x-trapi","name":"trapi"}]},{"_id":"671b45c0301c8624abbd26ae78449ca2","_ignored":["paths.pathitem.get.description.raw"],"_meta":{"date_created":"2021-02-10T05:26:25.703523+00:00","last_updated":"2023-05-22T07:06:13.463136+00:00","url":"https://raw.githubusercontent.com/NCATS-Tangerine/translator-api-registry/master/mydisease.info/smartapi.yaml","username":"newgene"},"components":{"x-bte-kgs-operations":{"chemical-disease":[{"inputs":[{"id":"MESH","semantic":"SmallMolecule"}],"outputs":[{"id":"MESH","semantic":"Disease"}],"parameters":{"fields":"ctd.mesh","size":1000},"predicate":"related_to","requestBody":{"body":{"q":"{{ queryInputs 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Your Node version must be higher than v12. +For development, you will need Node.js the pnpm package manager installed in your environment. Your Node version must be higher than v12. -#### Node.js and NPM +#### Node.js and pnpm -It's recommended to manage Node and NPM using the Node Version Manager (NVM). [You can find the install script for NVM here](https://github.com/nvm-sh/nvm#installing-and-updating). After installing NVM, you'll want to ensure you're using at least version 18, which is the current recommended version of Node for BTE. +It's recommended to manage Node using the Node Version Manager (NVM). [You can find the install script for NVM here](https://github.com/nvm-sh/nvm#installing-and-updating). After installing NVM, you'll want to ensure you're using at least version 18, which is the current recommended version of Node for BTE. ```bash nvm install 18 @@ -103,7 +103,10 @@ nvm use 18 > On Windows, ensure that you're doing this from within WSL. To install WSL, see the [instructions in the Docker section](#docker). -This will install the latest version of Node v18, and the appropriate version of NPM as well. +This will install the latest version of Node v18. It'll also install npm, which we forgoing in favor of pnpm -- don't get the two confused! + +This workspace uses pnpm instead of npm for its speed and better workspace support. To get pnpm installed, see the [instructions on pnpm's website](https://pnpm.io/installation). + #### Dependencies: @@ -143,24 +146,24 @@ The following commands will clone the repository and install it ``` git clone https://github.com/biothings/biothings_explorer.git cd biothings_explorer -npm run setup +pnpm run setup ``` > If you ever change Node versions, you'll probably encounter some problems re-running the project. To fix this: > ```bash -> npm install && npm rebuild +> pnpm install && pnpm rebuild > ``` ### Syncing SmartAPI Specifications -By default, this package does not automatically sync the latest SmartAPI Specifications. You may set it to do so by setting either `NODE_ENV=production` or `SMARTAPI_SYNC=true` as environment variables (e.g. `SMARTAPI_SYNC=true npm start`). `SMARTAPI_SYNC` overrides the behavior of `NODE_ENV`. +By default, this package does not automatically sync the latest SmartAPI Specifications. You may set it to do so by setting either `NODE_ENV=production` or `SMARTAPI_SYNC=true` as environment variables (e.g. `SMARTAPI_SYNC=true pnpm start`). `SMARTAPI_SYNC` overrides the behavior of `NODE_ENV`. You may additionally manually trigger a one-time sync by using the following command: ```bash -npm run smartapi_sync +pnpm run smartapi_sync ``` Note that this is only required for a local workspace, in a container syncing is handled automatically. @@ -172,13 +175,13 @@ Note that this is only required for a local workspace, in a container syncing is To start the server with debug logging, which outputs logging statements to the terminal in real time: ``` -npm start +pnpm start ``` To run the server without debug logging: ``` -npm run basic-start +pnpm run basic-start ``` #### Running the project with Redis @@ -186,7 +189,7 @@ npm run basic-start If you have a native installation or Docker image of Redis, the workspace provides a means of automatically starting the server alongside redis with default host/port configurations: ``` -npm start redis +pnpm start redis ``` This will automatically start Redis (preferring a Docker container, and falling back to native installation), and then start the server ready to connect to redis. If an existing Redis container is running, or the native Redis is running, they will be reset (all keys dropped) before starting. @@ -196,7 +199,7 @@ This will automatically start Redis (preferring a Docker container, and falling After stopping BTE (or in order to stop it if it's running detached from the terminal), if you want to ensure related Redis instances are stopped: ``` -npm stop +pnpm stop ``` This will ensure the server and its subprocesses are killed, and will stop any Redis containers and native Redis servers. diff --git a/docs/README-useful-info-for-devs.md b/docs/README-useful-info-for-devs.md index 903a5965..92353350 100644 --- a/docs/README-useful-info-for-devs.md +++ b/docs/README-useful-info-for-devs.md @@ -10,7 +10,7 @@ ### Running BTE -* To get console logs in close-to-real-time, you can use `USE_THREADING=false npm start` to run your local instance +* To get console logs in close-to-real-time, you can use `USE_THREADING=false pnpm start` to run your local instance ## BTE links diff --git a/docs/README-writing-x-bte.md b/docs/README-writing-x-bte.md index e3eb8d3d..949acd62 100644 --- a/docs/README-writing-x-bte.md +++ b/docs/README-writing-x-bte.md @@ -675,7 +675,7 @@ It can be helpful to paste the yaml into the SmartAPI [editor](https://smart-api To test that the yaml can be used properly by BTE, you can install a local version of BTE (using [bte-trapi-workspace](https://github.com/biothings/bte-trapi-workspace)). If you have any issues installing BTE, contact a member of the BTE team. Then you can: * modify the `packages/@biothings-explorer/bte-trapi/src/config/smartapi_overrides.json` file. Set `only_overrides` to `true`, and put a key-value pair into the `apis` section. The key can be arbitrary, and the value can be a file path (starting with file:/// for absolute paths) or a link to a raw yaml file. See the instructions [here](https://github.com/biothings/biothings_explorer#using-api_overridetrue) for details on this. -* run `API_OVERRIDE=true npm run smartapi_sync --workspace='@biothings-explorer/bte-trapi'` to set BTE to only use the API yaml you're testing +* run `API_OVERRIDE=true pnpm run smartapi_sync --workspace='@biothings-explorer/bte-trapi'` to set BTE to only use the API yaml you're testing * start up BTE `npm run debug --workspace='@biothings-explorer/bte-trapi'` and set up a `POST` request to `http://localhost:3000/v1/smartapi/your-id-here/query` where `your-id-here` is replaced with the key you set in the `apis` section. * put a TRAPI query into the `POST` request's request-body section. One can test each operation, or only a few. For testing an operation, you can set the example subject ID (from the testExamples notes) and semantic type and the object-semantic type (and sometimes the predicate). Then run the `POST` query, and look for the object-ID (from the testExamples notes) in BTE's response. You can also look at the corresponding edge to see if the edge-attributes match what you'd expect from the response-mapping (aka all info is there and is formatted correctly). diff --git a/docs/RELEASE.md b/docs/RELEASE.md index d594956a..a121018f 100644 --- a/docs/RELEASE.md +++ b/docs/RELEASE.md @@ -35,7 +35,7 @@ 2. Run one of these commands to make a new release: ```bash - npm run release:patch + pnpm run release:patch (use "release:patch", "release:minor" or "release:major" based on the release types) ``` diff --git a/docs/USAGE.md b/docs/USAGE.md index 03ac6bf5..1a36e135 100644 --- a/docs/USAGE.md +++ b/docs/USAGE.md @@ -100,13 +100,13 @@ If the environment variable `API_OVERRIDE=true` is set (see example below), then Starting BTE with API Overrides and automatic syncing enabled: ```bash -SMARTAPI_SYNC=true API_OVERRIDE=true npm run start +SMARTAPI_SYNC=true API_OVERRIDE=true pnpm run start ``` Alternatively, you may choose to only get `smartapi_specs.json` and apply overrides once, removing the requirement of enabling `SMARTAPI_SYNC` while running the server: ```bash -API_OVERRIDE=true npm run smartapi_sync +API_OVERRIDE=true pnpm run smartapi_sync ``` Override files may be specified as a URL which returns the expected yaml file or a `file:///` URI or arbitrary filepath, either of which must contain the absolute path to your override file. Override files are expected to be in yaml format. If overrides are specified with IDs not in the current SmartAPI spec, they will be appended as new API hits with a log warning. diff --git a/docs/smartapi.yaml b/docs/smartapi.yaml deleted file mode 100644 index abc4952e..00000000 --- a/docs/smartapi.yaml +++ /dev/null @@ -1,2098 +0,0 @@ -openapi: 3.0.3 -info: - description: A TRAPI/Reasoner Standard API for BioThings Explorer (BTE) - version: 3.0.0 - title: BioThings Explorer (BTE) TRAPI - contact: - email: asu@scripps.edu - name: Andrew Su - url: https://github.com/andrewsu - termsOfService: https://biothings.io/about - x-translator: - component: ARA - team: - - Exploring Agent - biolink-version: "3.5.0" - infores: "infores:biothings-explorer" - x-trapi: - version: 1.4.0 - asyncquery: true - operations: - ## look at https://standards.ncats.io/operation.json for details. - ## could use lookup_and_score in the future? - - lookup - ## no batch_size_limit (BTE manages IDs for QNodes and sub-queries internally) - ## /query endpoints have a limit of 15 requests/client/min - ## /meta_knowledge_graph endpoints have a limit of 30 requests/client/min - ## other endpoints don't have rate limits - rate_limit: 15 - test_data_location: - default: - url: "https://raw.githubusercontent.com/NCATS-Tangerine/translator-api-registry/master/biothings_explorer/sri-test-bte-ara.json" -servers: -## ITRB Production and Test deployments are made by ITRB, based on the staging instance -## ITRB CI / staging deployments are made by our team (will add details later) -## non-ITRB dev: deployments are made by our team -## we have full control on when / what branches for modules are used -- url: https://bte.transltr.io/v1 - description: ITRB Production server - x-maturity: production -- url: https://bte.test.transltr.io/v1 - description: ITRB Test server - x-maturity: testing -- url: https://bte.ci.transltr.io/v1 - description: ITRB CI server - x-maturity: staging -- url: https://api.bte.ncats.io/v1 - description: Non-ITRB dev (internal use) - x-maturity: development -tags: -- name: 1.4.0 -- name: meta_knowledge_graph -- name: query -- name: asyncquery -- name: asyncquery_status -- name: translator -- name: trapi -- name: biothings -## Note: BTE has custom behavior so DO NOT blindly copy-paste the TRAPI specs / schemas into the document below -## instead go through it and copy-paste in sections as-needed -## examples are using MyVariant-specific query -paths: - ## copied directly from TRAPI spec - /meta_knowledge_graph: - get: - tags: - - meta_knowledge_graph - summary: Meta knowledge graph representation of this TRAPI web service. - responses: - '200': - description: >- - Returns meta knowledge graph representation of this TRAPI web - service. - content: - application/json: - schema: - $ref: '#/components/schemas/MetaKnowledgeGraph' - ## copied from /meta_knowledge_graph above and modified: BTE-specific endpoint - /smartapi/{smartapi_id}/meta_knowledge_graph: - get: - tags: - - meta_knowledge_graph - summary: TRAPI-compliant meta-knowledge-graph representation for an individual SmartAPI KP API (that has x-bte annotation) - parameters: - - description: >- - SmartAPI ID of an API with x-bte annotation. The easiest way to find these is to read the list of APIs BTE uses - https://github.com/biothings/biothings_explorer/blob/main/src/config/apis.js - in: path - name: smartapi_id - required: true - example: 09c8782d9f4027712e65b95424adba79 ## MyVariant - schema: - type: string - responses: - '200': - description: >- - Returns a TRAPI-compliant meta-knowledge-graph representation for an individual SmartAPI KP API (that has x-bte annotation) - content: - application/json: - schema: - $ref: '#/components/schemas/MetaKnowledgeGraph' - ## copied from /meta_knowledge_graph above and modified: BTE-specific endpoint - /team/{team_name}/meta_knowledge_graph: - get: - tags: - - meta_knowledge_graph - summary: TRAPI-compliant meta-knowledge-graph representation for one KP team's SmartAPI KP APIs (that have x-bte annotation) - parameters: - - description: >- - Translator Team Name. Current options: Service Provider, Multiomics Provider, Text Mining Provider. - The easiest way to find what KP APIs would be included under these teams is to read the list of APIs BTE uses - https://github.com/biothings/biothings_explorer/blob/main/src/config/apis.js. - Note that Service Provider endpoints are also registered separately as a KP in the SmartAPI Registry - in: path - name: team_name - required: true - example: "Service Provider" - schema: - type: string - enum: - - Multiomics Provider - - Text Mining Provider - - Service Provider - responses: - '200': - description: >- - Returns a TRAPI-compliant meta-knowledge-graph representation for one KP team's SmartAPI KP APIs (that have x-bte annotation) - content: - application/json: - schema: - $ref: '#/components/schemas/MetaKnowledgeGraph' - ## modified TRAPI spec: example and BTE-specific parameters, used by developers running local instances of BTE - /query: - post: - tags: - - query - summary: Initiate a TRAPI-format query to BTE (operating as an ARA) and wait to receive a Response - parameters: - - description: option to choose whether or not to enable caching - in: query - name: caching - required: false - schema: - type: boolean - - description: dryrun a query (logs the queries BTE will make) - in: query - name: dryrun - required: false - schema: - type: boolean - requestBody: - description: Query information to be submitted - required: true - content: - application/json: - schema: - $ref: '#/components/schemas/Query' - ## should use MyVariant to answer this - example: - message: - query_graph: - nodes: - n0: - ids: - - "DBSNP:rs121913521" - categories: - - "biolink:SequenceVariant" - n1: - categories: - - "biolink:Disease" - edges: - e1: - subject: "n0" - object: "n1" - responses: - '200': - description: >- - OK. There may or may not be results. Note that some of the provided - identifiers may not have been recognized. - content: - application/json: - schema: - $ref: '#/components/schemas/Response' - '400': - description: >- - Bad request. The request is invalid according to this OpenAPI - schema OR a specific identifier is believed to be invalid somehow - (not just unrecognized). - content: - application/json: - schema: - type: string - '413': - description: >- - Payload too large. Indicates that batch size was over the limit - specified in x-trapi. - content: - application/json: - schema: - type: string - '429': - description: >- - Too many requests. Indicates that the client issued requests that - exceed the rate limit specified in x-trapi. - content: - application/json: - schema: - type: string - '500': - description: >- - Internal server error. - content: - application/json: - schema: - type: string - '501': - description: >- - Not implemented. - content: - application/json: - schema: - type: string - ## copied from /query above and modified: BTE-specific endpoint - /smartapi/{smartapi_id}/query: - post: - tags: - - query - summary: Query individual SmartAPI KP API (that has x-bte annotation) as a TRAPI KP API - parameters: - - description: >- - SmartAPI ID of an API with x-bte annotation. The easiest way to find these is to read the list of APIs BTE uses - https://github.com/biothings/biothings_explorer/blob/main/src/config/apis.js - in: path - name: smartapi_id - required: true - example: 09c8782d9f4027712e65b95424adba79 ## MyVariant - schema: - type: string - - description: option to choose whether or not to enable caching - in: query - name: caching - required: false - schema: - type: boolean - - description: dryrun a query (logs the queries BTE will make) - in: query - name: dryrun - required: false - schema: - type: boolean - requestBody: - description: Query information to be submitted - required: true - content: - application/json: - schema: - $ref: '#/components/schemas/Query' - ## should use MyVariant to answer this - example: - message: - query_graph: - nodes: - n0: - ids: - - "DBSNP:rs121913521" - categories: - - "biolink:SequenceVariant" - n1: - categories: - - "biolink:Disease" - edges: - e1: - subject: "n0" - object: "n1" - responses: - '200': - description: >- - OK. There may or may not be results. Note that some of the provided - identifiers may not have been recognized. - content: - application/json: - schema: - $ref: '#/components/schemas/Response' - '400': - description: >- - Bad request. The request is invalid according to this OpenAPI - schema OR a specific identifier is believed to be invalid somehow - (not just unrecognized). - content: - application/json: - schema: - type: string - '413': - description: >- - Payload too large. Indicates that batch size was over the limit - specified in x-trapi. - content: - application/json: - schema: - type: string - '429': - description: >- - Too many requests. Indicates that the client issued requests that - exceed the rate limit specified in x-trapi. - content: - application/json: - schema: - type: string - '500': - description: >- - Internal server error. - content: - application/json: - schema: - type: string - '501': - description: >- - Not implemented. - content: - application/json: - schema: - type: string - ## copied from /query above and modified: BTE-specific endpoint - /team/{team_name}/query: - post: - tags: - - query - summary: >- - Query an individual Translator team's SMARTAPI KP APIs (that have x-bte annotation) as an individual TRAPI - service by specifying the team name - parameters: - - description: >- - Translator Team Name. Current options: Service Provider, Multiomics Provider, Text Mining Provider. - The easiest way to find what KP APIs would be included under these teams is to read the list of APIs BTE uses - https://github.com/biothings/biothings_explorer/blob/main/src/config/apis.js. - Note that Service Provider endpoints are also registered separately as a KP in the SmartAPI Registry - in: path - name: team_name - required: true - example: "Service Provider" - schema: - type: string - enum: - - Multiomics Provider - - Text Mining Provider - - Service Provider - - description: option to choose whether or not to enable caching - in: query - name: caching - required: false - schema: - type: boolean - - description: dryrun a query (logs the queries BTE will make) - in: query - name: dryrun - required: false - schema: - type: boolean - requestBody: - description: Query information to be submitted - required: true - content: - application/json: - schema: - $ref: '#/components/schemas/Query' - ## should use MyVariant to answer this - example: - message: - query_graph: - nodes: - n0: - ids: - - "DBSNP:rs121913521" - categories: - - "biolink:SequenceVariant" - n1: - categories: - - "biolink:Disease" - edges: - e1: - subject: "n0" - object: "n1" - responses: - '200': - description: >- - OK. There may or may not be results. Note that some of the provided - identifiers may not have been recognized. - content: - application/json: - schema: - $ref: '#/components/schemas/Response' - '400': - description: >- - Bad request. The request is invalid according to this OpenAPI - schema OR a specific identifier is believed to be invalid somehow - (not just unrecognized). - content: - application/json: - schema: - type: string - '413': - description: >- - Payload too large. Indicates that batch size was over the limit - specified in x-trapi. - content: - application/json: - schema: - type: string - '429': - description: >- - Too many requests. Indicates that the client issued requests that - exceed the rate limit specified in x-trapi. - content: - application/json: - schema: - type: string - '500': - description: >- - Internal server error. - content: - application/json: - schema: - type: string - '501': - description: >- - Not implemented. - content: - application/json: - schema: - type: string - ## modified TRAPI spec: summary sections tell users that AsyncQuery schema was changed to make callback optional - /asyncquery: - post: - tags: - - asyncquery - summary: >- - Initiate a query that will be handled in an asynchronous manner (there is a - queue and queries will be executed in the order that they enter the queue). - For BTE, it is optional to have a callback property in the request-body. If - the callback property is not included, BTE will handle the query in a polling - manner: it will provide a job-id that can be used to check the status or retrieve - the Response. - parameters: - - description: option to choose whether or not to enable caching - in: query - name: caching - required: false - schema: - type: boolean - - description: dryrun a query (logs the queries BTE will make) - in: query - name: dryrun - required: false - schema: - type: boolean - requestBody: - description: Query information to be submitted - required: true - content: - application/json: - schema: - $ref: '#/components/schemas/AsyncQuery' - ## should use MyVariant to answer this - example: - message: - query_graph: - nodes: - n0: - ids: - - "DBSNP:rs121913521" - categories: - - "biolink:SequenceVariant" - n1: - categories: - - "biolink:Disease" - edges: - e1: - subject: "n0" - object: "n1" - responses: - '200': - description: >- - The query is accepted for processing. The behavior will depend on whether - the callback property is included. If the callback property is included, - the Response will be sent to the callback url when complete. If the callback - property is not included, BTE will handle the query in a polling manner: it - will provide a job-id that can be used to check the status or retrieve - the Response. - content: - application/json: - schema: - $ref: '#/components/schemas/AsyncQueryResponse' - '400': - description: >- - Bad request. The request is invalid according to this OpenAPI - schema OR a specific identifier is believed to be invalid somehow - (not just unrecognized). - content: - application/json: - schema: - type: string - '413': - description: >- - Payload too large. Indicates that batch size was over the limit - specified in x-trapi. - content: - application/json: - schema: - type: string - '429': - description: >- - Too many requests. Indicates that the client issued requests that - exceed the rate limit specified in x-trapi. - content: - application/json: - schema: - type: string - '500': - description: >- - Internal server error. - content: - application/json: - schema: - type: string - '501': - description: >- - Not implemented. - content: - application/json: - schema: - type: string - ## copied from /asyncquery above and modified: BTE-specific endpoint - /smartapi/{smartapi_id}/asyncquery: - post: - tags: - - asyncquery - summary: >- - This endpoint is for asynchronously querying an individual SmartAPI KP API (that has x-bte annotation) - as a TRAPI KP API. - - Initiate a query that will be handled in an asynchronous manner (there is a - queue and queries will be executed in the order that they enter the queue). - For BTE, it is optional to have a callback property in the request-body. If - the callback property is not included, BTE will handle the query in a polling - manner: it will provide a job-id that can be used to check the status or retrieve - the Response. - parameters: - - description: >- - SmartAPI ID of an API with x-bte annotation. The easiest way to find these is to read the list of APIs BTE uses - https://github.com/biothings/biothings_explorer/blob/main/src/config/apis.js - in: path - name: smartapi_id - required: true - example: 09c8782d9f4027712e65b95424adba79 ## MyVariant - schema: - type: string - - description: option to choose whether or not to enable caching - in: query - name: caching - required: false - schema: - type: boolean - - description: dryrun a query (logs the queries BTE will make) - in: query - name: dryrun - required: false - schema: - type: boolean - requestBody: - description: Query information to be submitted - required: true - content: - application/json: - schema: - $ref: '#/components/schemas/AsyncQuery' - ## should use MyVariant to answer this - example: - message: - query_graph: - nodes: - n0: - ids: - - "DBSNP:rs121913521" - categories: - - "biolink:SequenceVariant" - n1: - categories: - - "biolink:Disease" - edges: - e1: - subject: "n0" - object: "n1" - responses: - '200': - description: >- - The query is accepted for processing. The behavior will depend on whether - the callback property is included. If the callback property is included, - the Response will be sent to the callback url when complete. If the callback - property is not included, BTE will handle the query in a polling manner: it - will provide a job-id that can be used to check the status or retrieve - the Response. - content: - application/json: - schema: - $ref: '#/components/schemas/AsyncQueryResponse' - '400': - description: >- - Bad request. The request is invalid according to this OpenAPI - schema OR a specific identifier is believed to be invalid somehow - (not just unrecognized). - content: - application/json: - schema: - type: string - '413': - description: >- - Payload too large. Indicates that batch size was over the limit - specified in x-trapi. - content: - application/json: - schema: - type: string - '429': - description: >- - Too many requests. Indicates that the client issued requests that - exceed the rate limit specified in x-trapi. - content: - application/json: - schema: - type: string - '500': - description: >- - Internal server error. - content: - application/json: - schema: - type: string - '501': - description: >- - Not implemented. - content: - application/json: - schema: - type: string - ## copied from /asyncquery above and modified: BTE-specific endpoint - /team/{team_name}/asyncquery: - post: - tags: - - asyncquery - summary: >- - This endpoint is for asynchronously querying an individual Translator team's SMARTAPI KP APIs (that have x-bte annotation) - as an individual TRAPI service by specifying the team name. - - Initiate a query that will be handled in an asynchronous manner (there is a - queue and queries will be executed in the order that they enter the queue). - For BTE, it is optional to have a callback property in the request-body. If - the callback property is not included, BTE will handle the query in a polling - manner: it will provide a job-id that can be used to check the status or retrieve - the Response. - parameters: - - description: >- - Translator Team Name. Current options: Service Provider, Multiomics Provider, Text Mining Provider. - The easiest way to find what KP APIs would be included under these teams is to read the list of APIs BTE uses - https://github.com/biothings/biothings_explorer/blob/main/src/config/apis.js. - Note that Service Provider endpoints are also registered separately as a KP in the SmartAPI Registry - in: path - name: team_name - required: true - example: "Service Provider" - schema: - type: string - enum: - - Multiomics Provider - - Text Mining Provider - - Service Provider - - description: option to choose whether or not to enable caching - in: query - name: caching - required: false - schema: - type: boolean - - description: dryrun a query (logs the queries BTE will make) - in: query - name: dryrun - required: false - schema: - type: boolean - requestBody: - description: Query information to be submitted - required: true - content: - application/json: - schema: - $ref: '#/components/schemas/AsyncQuery' - ## should use MyVariant to answer this - example: - message: - query_graph: - nodes: - n0: - ids: - - "DBSNP:rs121913521" - categories: - - "biolink:SequenceVariant" - n1: - categories: - - "biolink:Disease" - edges: - e1: - subject: "n0" - object: "n1" - responses: - '200': - description: >- - The query is accepted for processing. The behavior will depend on whether - the callback property is included. If the callback property is included, - the Response will be sent to the callback url when complete. If the callback - property is not included, BTE will handle the query in a polling manner: it - will provide a job-id that can be used to check the status or retrieve - the Response. - content: - application/json: - schema: - $ref: '#/components/schemas/AsyncQueryResponse' - '400': - description: >- - Bad request. The request is invalid according to this OpenAPI - schema OR a specific identifier is believed to be invalid somehow - (not just unrecognized). - content: - application/json: - schema: - type: string - '413': - description: >- - Payload too large. Indicates that batch size was over the limit - specified in x-trapi. - content: - application/json: - schema: - type: string - '429': - description: >- - Too many requests. Indicates that the client issued requests that - exceed the rate limit specified in x-trapi. - content: - application/json: - schema: - type: string - '500': - description: >- - Internal server error. - content: - application/json: - schema: - type: string - '501': - description: >- - Not implemented. - content: - application/json: - schema: - type: string - ## custom: removed example so SmartAPI registry uptime check won't fail - /asyncquery_status/{job_id}: - get: - tags: - - asyncquery_status - summary: >- - Retrieve the current status of a previously submitted - asyncquery given its job_id - operationId: asyncquery_status - parameters: - - in: path - name: job_id - description: Identifier of the job for status request - # example: rXEOAosN3L - required: true - schema: - type: string - responses: - '200': - description: >- - Returns the status and current logs of a previously - submitted asyncquery. - content: - application/json: - schema: - $ref: '#/components/schemas/AsyncQueryStatusResponse' - '404': - description: job_id not found - '501': - description: >- - Return code 501 indicates that this endpoint has not been - implemented at this site. Sites that implement /asyncquery - MUST implement /asyncquery_status/{job_id}, but those that - do not implement /asyncquery SHOULD NOT implement - /asyncquery_status. - content: - application/json: - schema: - type: string -components: - ## look for comments to see parts that have been modified for BTE - ## also, many sections have additionalProperties: true - ## - Query: comment out workflow.oneOf section since the $ref breaks execution of BTE's api-schema-builder/openapi-validator-middleware - ## - AsyncQuery: callback property not required (commented it out of the 'required' field), - ## comment out workflow.oneOf section - ## - Response: comment out workflow.oneOf section - ## - Attribute: comment out properties.attributes.items since the self-$ref breaks execution of - ## BTE's api-schema-builder/openapi-validator-middleware - schemas: - Query: - description: >- - The Query class is used to package a user request for information. A - Query object consists of a required Message object with optional - additional properties. Additional properties are intended to convey - implementation-specific or query-independent parameters. For example, - an additional property specifying a log level could allow a user to - override the default log level in order to receive more fine-grained - log information when debugging an issue. - x-body-name: request_body - type: object - properties: - message: - $ref: '#/components/schemas/Message' - description: >- - The query Message is a serialization of the user request. Content - of the Message object depends on the intended TRAPI operation. For - example, the fill operation requires a non-empty query_graph field - as part of the Message, whereas other operations, e.g. overlay, - require non-empty results and knowledge_graph fields. - log_level: - description: The least critical level of logs to return - oneOf: - - $ref: '#/components/schemas/LogLevel' - nullable: true - workflow: - description: List of workflow steps to be executed. - # oneOf: - # - $ref: http://standards.ncats.io/workflow/1.3.4/schema - nullable: true - submitter: - type: string - description: >- - Any string for self-identifying the submitter of a query. The - purpose of this optional field is to aid in the tracking of - the source of queries for development and issue resolution. - nullable: true - additionalProperties: true - required: - - message - AsyncQuery: - description: >- - The AsyncQuery class is effectively the same as the Query class but - it requires a callback property. - x-body-name: request_body - type: object - properties: - callback: - type: string - format: uri - pattern: ^https?:// - description: >- - Upon completion, this server will send a POST request to the - callback URL with `Content-Type: application/json` header and - request body containing a JSON-encoded `Response` object. - The server MAY POST `Response` objects before work is fully - complete to provide interim results with a Response.status - value of 'Running'. If a POST operation to the callback URL - does not succeed, the server SHOULD retry the POST at least - once. - message: - $ref: '#/components/schemas/Message' - description: >- - The query Message is a serialization of the user request. Content - of the Message object depends on the intended TRAPI operation. For - example, the fill operation requires a non-empty query_graph field - as part of the Message, whereas other operations, e.g. overlay, - require non-empty results and knowledge_graph fields. - log_level: - description: The least critical level of logs to return - oneOf: - - $ref: '#/components/schemas/LogLevel' - nullable: true - workflow: - description: List of workflow steps to be executed. - # oneOf: - # - $ref: http://standards.ncats.io/workflow/1.3.4/schema - nullable: true - submitter: - type: string - description: >- - Any string for self-identifying the submitter of a query. The - purpose of this optional field is to aid in the tracking of - the source of queries for development and issue resolution. - nullable: true - additionalProperties: true - required: - ## BTE does not require the callback property, see the asyncquery - ## endpoint summary and 200 response description - # - callback - - message - AsyncQueryResponse: - type: object - description: >- - The AsyncQueryResponse object contains a payload that must be - returned from a submitted async_query. - properties: - status: - description: >- - One of a standardized set of short codes: - e.g. Accepted, QueryNotTraversable, KPsNotAvailable - type: string - example: Accepted - nullable: true - description: - description: >- - A brief human-readable description of the result of the - async_query submission. - type: string - example: Async_query has been queued - nullable: true - job_id: - description: >- - An identifier for the submitted job that can be used with - /async_query_status to receive an update on the status of - the job. - type: string - example: rXEOAosN3L - nullable: false - additionalProperties: true - required: - - job_id - AsyncQueryStatusResponse: - type: object - description: >- - The AsyncQueryStatusResponse object contains a payload that describes - the current status of a previously submitted async_query. - properties: - status: - description: >- - One of a standardized set of short codes: - Queued, Running, Completed, Failed - type: string - example: Running - nullable: false - description: - description: >- - A brief human-readable description of the current state - or summary of the problem if the status is Failed. - type: string - example: Callback URL returned 500 - nullable: false - logs: - description: >- - A list of LogEntry items, containing errors, warnings, debugging - information, etc. List items MUST be in chronological order with - earliest first. The most recent entry should be last. Its timestamp - will be compared against the current time to see if there is - still activity. - type: array - items: - $ref: '#/components/schemas/LogEntry' - nullable: false - response_url: - description: >- - Optional URL that can be queried to restrieve the full TRAPI - Response. - type: string - example: https://arax.ncats.io/api/arax/v1.3/response/116481 - nullable: true - additionalProperties: true - required: - - status - - description - - logs - Response: - type: object - description: >- - The Response object contains the main payload when a TRAPI query - endpoint interprets and responds to the submitted query successfully - (i.e., HTTP Status Code 200). The message property contains the - knowledge of the response (query graph, knowledge graph, and results). - The status, description, and logs properties provide additional details - about the response. - properties: - message: - description: >- - Contains the knowledge of the response (query graph, knowledge - graph, and results). - $ref: '#/components/schemas/Message' - status: - description: >- - One of a standardized set of short codes, - e.g. Success, QueryNotTraversable, KPsNotAvailable - type: string - example: Success - nullable: true - description: - description: A brief human-readable description of the outcome - type: string - example: Success. 42 results found. - nullable: true - logs: - description: >- - A list of LogEntry items, containing errors, warnings, debugging - information, etc. List items MUST be in chronological order with - earliest first. - type: array - items: - $ref: '#/components/schemas/LogEntry' - nullable: true - workflow: - description: List of workflow steps that were executed. - # oneOf: - # - $ref: http://standards.ncats.io/workflow/1.3.4/schema - nullable: true - schema_version: - type: string - example: 1.4.0 - description: Version label of the TRAPI schema used in this document - biolink_version: - type: string - example: 3.1.2 - description: Version label of the Biolink model used in this document - additionalProperties: true - required: - - message - Message: - description: >- - The message object holds the main content of a Query or a Response in - three properties: query_graph, results, and knowledge_graph. - The query_graph property contains the query configuration, the results - property contains any answers that are returned by the service, - and knowledge_graph property contains lists of edges and nodes in the - thought graph corresponding to this message. The content of these - properties is context-dependent to the encompassing object and - the TRAPI operation requested. - type: object - properties: - results: - description: >- - List of all returned Result objects for the query posed. - The list SHOULD NOT be assumed to be ordered. The 'score' property, - if present, MAY be used to infer result rankings. - type: array - items: - $ref: '#/components/schemas/Result' - nullable: true - query_graph: - description: >- - QueryGraph object that contains a serialization of a query in the - form of a graph - oneOf: - - $ref: '#/components/schemas/QueryGraph' - nullable: true - knowledge_graph: - description: >- - KnowledgeGraph object that contains lists of nodes and edges - in the thought graph corresponding to the message - oneOf: - - $ref: '#/components/schemas/KnowledgeGraph' - nullable: true - auxiliary_graphs: - type: object - description: >- - Dictionary of AuxiliaryGraph instances that are used by Knowledge - Graph Edges and Result Analyses. These are referenced elsewhere by - the dictionary key. - additionalProperties: - $ref: '#/components/schemas/AuxiliaryGraph' - nullable: true - additionalProperties: false - LogEntry: - description: >- - The LogEntry object contains information useful for tracing - and debugging across Translator components. Although an - individual component (for example, an ARA or KP) may have its - own logging and debugging infrastructure, this internal - information is not, in general, available to other components. - In addition to a timestamp and logging level, LogEntry - includes a string intended to be read by a human, along with - one of a standardized set of codes describing the condition of - the component sending the message. - type: object - properties: - timestamp: - type: string - format: date-time - description: >- - Timestamp in ISO 8601 format, providing the LogEntry time - either in univeral coordinated time (UTC) using the 'Z' tag - (e.g 2020-09-03T18:13:49Z), or, if local time is provided, - the timezone offset must be provided - (e.g. 2020-09-03T18:13:49-04:00). - example: '2020-09-03T18:13:49+00:00' - nullable: false - level: - oneOf: - - $ref: '#/components/schemas/LogLevel' - nullable: true - code: - type: string - description: >- - One of a standardized set of short codes - e.g. QueryNotTraversable, KPNotAvailable, KPResponseMalformed - nullable: true - message: - type: string - description: A human-readable log message - nullable: true - additionalProperties: true - required: - - timestamp - - message - LogLevel: - type: string - description: Logging level - enum: - - ERROR - - WARNING - - INFO - - DEBUG - Result: - type: object - description: >- - A Result object specifies the nodes and edges in the knowledge graph - that satisfy the structure or conditions of a user-submitted query - graph. It must contain a NodeBindings object (list of query graph node - to knowledge graph node mappings) and a list of Analysis objects. - properties: - node_bindings: - type: object - description: >- - The dictionary of Input Query Graph to Result Knowledge Graph node - bindings where the dictionary keys are the key identifiers of the - Query Graph nodes and the associated values of those keys are - instances of NodeBinding schema type (see below). This value is an - array of NodeBindings since a given query node may have multiple - knowledge graph Node bindings in the result. - additionalProperties: - type: array - items: - $ref: '#/components/schemas/NodeBinding' - analyses: - type: array - description: >- - The list of all Analysis components that contribute to the result. - See below for Analysis components. - items: - $ref: '#/components/schemas/Analysis' - additionalProperties: true - required: - - node_bindings - - analyses - NodeBinding: - type: object - description: >- - An instance of NodeBinding is a single KnowledgeGraph Node mapping, - identified by the corresponding 'id' object key identifier of the - Node within the Knowledge Graph. Instances of NodeBinding may - include extra annotation in the form of additional properties. - (such annotation is not yet fully standardized). Each Node - Binding must bind directly to node in the original Query Graph. - properties: - id: - $ref: '#/components/schemas/CURIE' - description: >- - The CURIE of a Node within the Knowledge Graph. - query_id: - oneOf: - - $ref: '#/components/schemas/CURIE' - description: >- - An optional property to provide the CURIE in the QueryGraph to - which this binding applies. If the bound QNode does not have an - an 'id' property or if it is empty, then this query_id MUST be - null or absent. If the bound QNode has one or more CURIEs - as an 'id' and this NodeBinding's 'id' refers to a QNode 'id' - in a manner where the CURIEs are different (typically due to - the NodeBinding.id being a descendant of a QNode.id), then - this query_id MUST be provided. In other cases, there is no - ambiguity, and this query_id SHOULD NOT be provided. - nullable: true - attributes: - type: array - description: >- - A list of attributes providing further information about the - node binding. This is not intended for capturing node attributes - and should only be used for properties that vary from result to - result. - items: - $ref: '#/components/schemas/Attribute' - nullable: true - additionalProperties: true - required: - - id - Analysis: - type: object - description: >- - An analysis is a dictionary that contains information about - the result tied to a particular service. Each Analysis is - generated by a single reasoning service, and describes the - outputs of analyses performed by the reasoner on a particular - Result (e.g. a result score), along with provenance information - supporting the analysis (e.g. method or data that supported - generation of the score). - properties: - resource_id: - $ref: '#/components/schemas/CURIE' - description: The id of the resource generating this Analysis - score: - type: number - format: float - example: 163.233 - description: >- - A numerical score associated with this result indicating the - relevance or confidence of this result relative to others in the - returned set. Higher MUST be better. - nullable: true - edge_bindings: - type: object - description: >- - The dictionary of input Query Graph to Knowledge Graph edge - bindings where the dictionary keys are the key identifiers of the - Query Graph edges and the associated values of those keys are - instances of EdgeBinding schema type (see below). This value is an - array of EdgeBindings since a given query edge may resolve to - multiple Knowledge Graph Edges. - additionalProperties: - type: array - items: - $ref: '#/components/schemas/EdgeBinding' - support_graphs: - type: array - description: >- - This is a list of references to Auxiliary Graph instances - that supported the analysis of a Result as performed by the - reasoning service. Each item in the list is the key of a - single Auxiliary Graph. - nullable: true - items: - type: string - scoring_method: - type: string - description: >- - An identifier and link to an explanation for the method used - to generate the score - nullable: true - attributes: - type: array - description: >- - The attributes of this particular Analysis. - items: - $ref: '#/components/schemas/Attribute' - nullable: true - additionalProperties: true - required: - - resource_id - - edge_bindings - EdgeBinding: - type: object - description: >- - A instance of EdgeBinding is a single KnowledgeGraph Edge mapping, - identified by the corresponding 'id' object key identifier of the - Edge within the Knowledge Graph. Instances of EdgeBinding may include - extra annotation (such annotation is not yet fully standardized). - Edge bindings are captured within a specific reasoner's Analysis - object because the Edges in the Knowledge Graph that get bound to - the input Query Graph may differ between reasoners. - properties: - id: - type: string - description: The key identifier of a specific KnowledgeGraph Edge. - attributes: - type: array - description: >- - A list of attributes providing further information about the - edge binding. This is not intended for capturing edge attributes - and should only be used for properties that vary from result to - result. - items: - $ref: '#/components/schemas/Attribute' - nullable: true - additionalProperties: true - required: - - id - AuxiliaryGraph: - type: object - description: >- - A single AuxiliaryGraph instance that is used by Knowledge Graph - Edges and Result Analyses. Edges comprising an Auxiliary Graph - are a subset of the Knowledge Graph in the message. Data creators - can create an AuxiliaryGraph to assemble a specific collections - of edges from the Knowledge Graph into a named graph that can be - referenced from an Edge as evidence/explanation supporting that Edge, - or from a Result Analysis as information used to generate a score. - properties: - edges: - type: array - description: >- - List of edges that form the Auxiliary Graph. Each item is a - reference to a single Knowledge Graph edge - items: - type: string - nullable: false - minItems: 1 - attributes: - type: array - description: >- - Attributes of the Auxiliary Graph - items: - $ref: '#/components/schemas/Attribute' - nullable: true - additionalProperties: true - required: - - edges - KnowledgeGraph: - type: object - description: >- - The knowledge graph associated with a set of results. The instances - of Node and Edge defining this graph represent instances of - biolink:NamedThing (concept nodes) and biolink:Association - (relationship edges) representing (Attribute) annotated knowledge - returned from the knowledge sources and inference agents wrapped by - the given TRAPI implementation. - properties: - nodes: - type: object - description: >- - Dictionary of Node instances used in the KnowledgeGraph, - referenced elsewhere in the TRAPI output by the dictionary key. - additionalProperties: - $ref: '#/components/schemas/Node' - edges: - type: object - description: >- - Dictionary of Edge instances used in the KnowledgeGraph, - referenced elsewhere in the TRAPI output by the dictionary key. - additionalProperties: - $ref: '#/components/schemas/Edge' - additionalProperties: true - required: - - nodes - - edges - QueryGraph: - type: object - description: >- - A graph representing a biomedical question. It serves as a template for - each result (answer), where each bound knowledge graph node/edge is - expected to obey the constraints of the associated query graph element. - properties: - nodes: - type: object - description: >- - The node specifications. The keys of this map are unique node - identifiers and the corresponding values include the constraints - on bound nodes. - additionalProperties: - $ref: '#/components/schemas/QNode' - edges: - type: object - description: >- - The edge specifications. The keys of this map are unique edge - identifiers and the corresponding values include the constraints - on bound edges, in addition to specifying the subject and object - QNodes. - additionalProperties: - $ref: '#/components/schemas/QEdge' - additionalProperties: true - required: - - nodes - - edges - QNode: - type: object - description: A node in the QueryGraph used to represent an entity in a - query. If a CURIE is not specified, any nodes matching the category - of the QNode will be returned in the Results. - properties: - ids: - type: array - items: - $ref: '#/components/schemas/CURIE' - minItems: 1 - example: [OMIM:603903] - description: CURIE identifier for this node - nullable: true - categories: - type: array - description: >- - These should be Biolink Model categories and are allowed - to be of type 'abstract' or 'mixin' (only in QGraphs!). - Use of 'deprecated' categories should be avoided. - items: - $ref: '#/components/schemas/BiolinkEntity' - minItems: 1 - nullable: true - is_set: - type: boolean - description: >- - Boolean that if set to true, indicates that this QNode MAY have - multiple KnowledgeGraph Nodes bound to it within each Result. - The nodes in a set should be considered as a set of independent - nodes, rather than a set of dependent nodes, i.e., the answer - would still be valid if the nodes in the set were instead returned - individually. Multiple QNodes may have is_set=True. If a QNode - (n1) with is_set=True is connected to a QNode (n2) with - is_set=False, each n1 must be connected to n2. If a QNode (n1) - with is_set=True is connected to a QNode (n2) with is_set=True, - each n1 must be connected to at least one n2. - default: false - constraints: - type: array - description: >- - A list of constraints applied to a query node. - If there are multiple items, they must all be true (equivalent - to AND) - items: - $ref: '#/components/schemas/AttributeConstraint' - default: [] - additionalProperties: true - QEdge: - type: object - description: >- - An edge in the QueryGraph used as a filter pattern specification in a - query. If the optional predicate property is not specified, - it is assumed to be a wildcard match to the target knowledge space. - If specified, the ontological inheritance hierarchy associated with - the term provided is assumed, such that edge bindings returned may be - an exact match to the given QEdge predicate term, - or to a term that is a descendant of the QEdge predicate term. - properties: - knowledge_type: - description: >- - Indicates the type of knowledge that the client wants from the - server between the subject and object. If the value is - 'lookup', then the client wants direct lookup information from - knowledge sources. If the value is 'inferred', then the client - wants the server to get creative and connect the subject and - object in more speculative and non-direct-lookup ways. If this - property is absent or null, it MUST be assumed to mean - 'lookup'. This feature is currently experimental and may be - further extended in the future. - example: lookup - nullable: true - type: string - predicates: - type: array - description: >- - These should be Biolink Model predicates and are allowed to be of - type 'abstract' or 'mixin' (only in QGraphs!). Use of 'deprecated' - predicates should be avoided. - items: - $ref: '#/components/schemas/BiolinkPredicate' - minItems: 1 - nullable: true - subject: - type: string - example: https://omim.org/entry/603903 - description: >- - Corresponds to the map key identifier of the - subject concept node anchoring the query filter - pattern for the query relationship edge. - object: - type: string - example: https://www.uniprot.org/uniprot/P00738 - description: >- - Corresponds to the map key identifier of the - object concept node anchoring the query filter - pattern for the query relationship edge. - attribute_constraints: - type: array - description: >- - A list of attribute constraints applied to a query edge. - If there are multiple items, they must all be true (equivalent - to AND) - items: - $ref: '#/components/schemas/AttributeConstraint' - default: [] - qualifier_constraints: - type: array - description: >- - A list of QualifierConstraints that provide nuance to the QEdge. - If multiple QualifierConstraints are provided, there is an OR - relationship between them. If the QEdge has multiple - predicates or if the QNodes that correspond to the subject or - object of this QEdge have multiple categories or multiple - curies, then qualifier_constraints MUST NOT be specified - because these complex use cases are not supported at this time. - items: - $ref: '#/components/schemas/QualifierConstraint' - default: [] - additionalProperties: true - required: - - subject - - object - Node: - type: object - description: >- - A node in the KnowledgeGraph which represents some biomedical - concept. Nodes are identified by the keys in the KnowledgeGraph - Node mapping. - properties: - name: - type: string - example: Haptoglobin - description: Formal name of the entity - nullable: true - categories: - type: array - description: >- - These should be Biolink Model categories and are NOT allowed - to be of type 'abstract' or 'mixin'. Returning 'deprecated' - categories should also be avoided. - items: - $ref: '#/components/schemas/BiolinkEntity' - nullable: true - attributes: - type: array - description: A list of attributes describing the node - items: - $ref: '#/components/schemas/Attribute' - nullable: true - additionalProperties: false - Attribute: - type: object - description: >- - Generic attribute for a node or an edge that expands the key-value - pair concept by including fields for additional metadata. These fields - can be used to describe the source of the statement made in a key-value - pair of the attribute object, or describe the attribute's value itself - including its semantic type, or a url providing additional information - about it. An attribute may be further qualified with sub-attributes - (for example to provide confidence intervals on a value). - properties: - attribute_type_id: - $ref: '#/components/schemas/CURIE' - description: >- - The 'key' of the attribute object, holding a CURIE of an ontology - property defining the attribute (preferably the CURIE of a - Biolink association slot). This property captures the relationship - asserted to hold between the value of the attribute, and the node - or edge from which it hangs. For example, that a value of - '0.000153' represents a p-value supporting an edge, or that - a value of 'ChEMBL' represents the original source of the knowledge - expressed in the edge. - example: biolink:synonym - original_attribute_name: - type: string - description: >- - The term used by the original source of an attribute to describe - the meaning or significance of the value it captures. This may be - a column name in a source tsv file, or a key in a source json - document for the field in the data that held the attribute's - value. Capturing this information where possible lets us preserve - what the original source said. Note that the data type is string' - but the contents of the field could also be a CURIE of a third - party ontology term. - example: p-value - nullable: true - value: - description: >- - Value of the attribute. May be any data type, including a list. - example: 0.000153 - value_type_id: - oneOf: - - $ref: '#/components/schemas/CURIE' - description: >- - CURIE describing the semantic type of an attribute's value. Use - a Biolink class if possible, otherwise a term from an external - ontology. If a suitable CURIE/identifier does not exist, enter a - descriptive phrase here and submit the new type for consideration - by the appropriate authority. - example: EDAM:data_1187 - nullable: true - attribute_source: - type: string - description: >- - The source of the core assertion made by the key-value pair of an - attribute object. Use a CURIE or namespace designator for this - resource where possible. - example: UniProtKB - nullable: true - value_url: - type: string - description: >- - Human-consumable URL linking to a web document that provides - additional information about an attribute's value (not the node - or the edge fom which it hangs). - example: https://pubmed.ncbi.nlm.nih.gov/32529952 - nullable: true - description: - type: string - description: >- - Human-readable description for the attribute and its value. - example: Assertion Authored By Dr. Trans L. Ator - nullable: true - attributes: - type: array - description: >- - A list of attributes providing further information about the - parent attribute (for example to provide provenance - information about the parent attribute). - # items: - # $ref: '#/components/schemas/Attribute' - nullable: true - required: - - attribute_type_id - - value - additionalProperties: false - Edge: - type: object - description: >- - A specification of the semantic relationship linking two concepts - that are expressed as nodes in the knowledge "thought" graph - resulting from a query upon the underlying knowledge source. - properties: - predicate: - description: >- - The type of relationship between the subject and object - for the statement expressed in an Edge. These should be - Biolink Model predicate terms and are NOT allowed - to be of type 'abstract' or 'mixin'. Returning 'deprecated' - predicate terms should also be avoided. - example: biolink:gene_associated_with_condition - oneOf: - - $ref: '#/components/schemas/BiolinkPredicate' - nullable: false - subject: - description: >- - Corresponds to the map key CURIE of the - subject concept node of this relationship edge. - example: MONDO:0011382 - oneOf: - - $ref: '#/components/schemas/CURIE' - nullable: false - object: - description: >- - Corresponds to the map key CURIE of the - object concept node of this relationship edge. - example: UniProtKB:P00738 - oneOf: - - $ref: '#/components/schemas/CURIE' - nullable: false - attributes: - description: A list of additional attributes for this edge - items: - $ref: '#/components/schemas/Attribute' - nullable: true - type: array - qualifiers: - description: >- - A set of Qualifiers that act together to add nuance - or detail to the statement expressed in an Edge. - items: - $ref: '#/components/schemas/Qualifier' - nullable: true - type: array - sources: - type: array - description: >- - A list of RetrievalSource objects that provide information - about how a particular Information Resource served - as a source from which the knowledge expressed in an Edge, - or data used to generate this knowledge, was retrieved. - items: - $ref: '#/components/schemas/RetrievalSource' - minItems: 1 - nullable: false - additionalProperties: false - required: - - object - - predicate - - subject - - sources - Qualifier: - additionalProperties: false - description: >- - An additional nuance attached to an assertion - type: object - properties: - qualifier_type_id: - $ref: '#/components/schemas/CURIE' - description: >- - CURIE for a Biolink 'qualifier' association slot, generally taken - from Biolink association slots designated for this purpose - (that is, association slots with names ending in 'qualifier') - e.g. biolink:subject_aspect_qualifier, - biolink:subject_direction_qualifier, - biolink:object_aspect_qualifier, etc. Such qualifiers are used - to elaborate a second layer of meaning of a knowledge graph edge. - Available qualifiers are edge properties in the Biolink Model (see - https://biolink.github.io/biolink-model/docs/edge_properties.html) - which have slot names with the suffix string 'qualifier'. - pattern: ^biolink:[a-z][a-z_]*$ - example: biolink:subject_aspect_qualifier - nullable: false - qualifier_value: - type: string - description: >- - The value associated with the type of the qualifier, drawn from - a set of controlled values by the type as specified in - the Biolink model (e.g. 'expression' or 'abundance' for the - qualifier type 'biolink:subject_aspect_qualifier', etc). - The enumeration of qualifier values for a given qualifier - type is generally going to be constrained by the category - of edge (i.e. biolink:Association subtype) of the (Q)Edge. - example: expression - nullable: false - required: - - qualifier_type_id - - qualifier_value - QualifierConstraint: - additionalProperties: false - description: >- - Defines a query constraint based on the - qualifier_types and qualifier_values of a set of - Qualifiers attached to an edge. For example, it can constrain a - "ChemicalX - affects - ?Gene" query to return only edges where - ChemicalX specifically affects the 'expression' of the Gene, by - constraining on the qualifier_type "biolink:object_aspect_qualifier" - with a qualifier_value of "expression". - properties: - qualifier_set: - type: array - description: >- - A set of Qualifiers that serves to add nuance to a query, - by constraining allowed values held by Qualifiers - on queried Edges. - items: - $ref: '#/components/schemas/Qualifier' - nullable: false - required: - - qualifier_set - type: object - BiolinkEntity: - description: >- - Compact URI (CURIE) for a Biolink class, biolink:NamedThing - or a child thereof. The CURIE must use the prefix 'biolink:' - followed by the PascalCase class name. - type: string - pattern: ^biolink:[A-Z][a-zA-Z]*$ - externalDocs: - description: Biolink model entities - url: https://biolink.github.io/biolink-model/docs/NamedThing.html - example: biolink:PhenotypicFeature - BiolinkPredicate: - description: >- - CURIE for a Biolink 'predicate' slot, taken from the Biolink slot - ('is_a') hierarchy rooted in biolink:related_to (snake_case). This - predicate defines the Biolink relationship between the subject and - object nodes of a biolink:Association defining a knowledge graph edge. - type: string - pattern: ^biolink:[a-z][a-z_]*$ - externalDocs: - description: Biolink model predicates - url: https://biolink.github.io/biolink-model/docs/related_to.html - example: biolink:interacts_with - CURIE: - type: string - description: >- - A Compact URI, consisting of a prefix and a reference separated - by a colon, such as UniProtKB:P00738. Via an external context - definition, the CURIE prefix and colon may be replaced by a URI - prefix, such as http://identifiers.org/uniprot/, to form a full - URI. - externalDocs: - url: https://www.w3.org/TR/2010/NOTE-curie-20101216/ - MetaKnowledgeGraph: - type: object - description: >- - Knowledge-map representation of this TRAPI web service. The meta - knowledge graph is composed of the union of most specific categories - and predicates for each node and edge. - properties: - nodes: - type: object - description: >- - Collection of the most specific node categories provided by - this TRAPI web service, indexed by Biolink class CURIEs. - A node category is only exposed here if there is - node for which that is the most specific category available. - additionalProperties: - $ref: '#/components/schemas/MetaNode' - edges: - type: array - description: >- - List of the most specific edges/predicates provided by this TRAPI - web service. A predicate is only exposed here if there is an edge - for which the predicate is the most specific available. - items: - $ref: '#/components/schemas/MetaEdge' - required: - - nodes - - edges - MetaNode: - type: object - description: >- - Description of a node category provided by this TRAPI web service. - properties: - id_prefixes: - type: array - description: >- - List of CURIE prefixes for the node category that this TRAPI web - service understands and accepts on the input. - items: - type: string - minItems: 1 - example: [CHEMBL.COMPOUND, INCHIKEY] - attributes: - type: array - description: >- - Node attributes provided by this TRAPI web service. - items: - $ref: '#/components/schemas/MetaAttribute' - nullable: true - required: - - id_prefixes - additionalProperties: false - MetaEdge: - type: object - description: >- - Edge in a meta knowledge map describing relationship between a subject - Biolink class and an object Biolink class. - properties: - subject: - $ref: '#/components/schemas/BiolinkEntity' - description: >- - Subject node category of this relationship edge. - example: biolink:ChemicalEntity - predicate: - $ref: '#/components/schemas/BiolinkPredicate' - description: >- - Biolink relationship between the subject and object categories. - example: biolink:affects - object: - $ref: '#/components/schemas/BiolinkEntity' - description: >- - Object node category of this relationship edge. - example: biolink:Protein - knowledge_types: - description: >- - A list of knowledge_types that are supported by the service. - If the knowledge_types is null, this means that only 'lookup' - is supported. Currently allowed values are 'lookup' or 'inferred'. - items: - type: string - minItems: 1 - nullable: true - type: array - attributes: - type: array - description: >- - Edge attributes provided by this TRAPI web service. - items: - $ref: '#/components/schemas/MetaAttribute' - nullable: true - qualifiers: - description: >- - Qualifiers that are possible to be found on this edge type. - items: - $ref: '#/components/schemas/MetaQualifier' - nullable: true - type: array - association: - description: >- - The Biolink association type (entity) that this edge represents. - Associations are classes in Biolink - that represent a relationship between two entities. - For example, the association 'gene interacts with gene' - is represented by the Biolink class, - 'biolink:GeneToGeneAssociation'. If association - is filled out, then the testing harness can - help validate that the qualifiers are being used - correctly. - example: 'biolink:ChemicalToGeneAssociation' - $ref: '#/components/schemas/BiolinkEntity' - required: - - subject - - predicate - - object - additionalProperties: false - MetaQualifier: - type: object - properties: - qualifier_type_id: - $ref: '#/components/schemas/CURIE' - description: >- - The CURIE of the qualifier type. - example: biolink:subject_aspect_qualifier - nullable: false - applicable_values: - type: array - description: >- - The list of values that are possible for this qualifier. - items: - type: string - example: [expression, activity, abundance, degradation] - required: - - qualifier_type_id - MetaAttribute: - type: object - properties: - attribute_type_id: - $ref: '#/components/schemas/CURIE' - description: >- - Type of an attribute provided by this TRAPI web service - (preferably the CURIE of a Biolink association slot) - example: biolink:p_value - attribute_source: - type: string - description: >- - Source of an attribute provided by this TRAPI web service. - example: infores:chembl - nullable: true - original_attribute_names: - type: array - items: - type: string - description: >- - Names of an the attribute as provided by the source. - nullable: true - minItems: 1 - constraint_use: - type: boolean - description: >- - Indicates whether this attribute can be used as a query - constraint. - default: false - constraint_name: - type: string - description: >- - Human-readable name or label for the constraint concept. - Required whenever constraint_use is true. - example: p-value - nullable: true - required: - - attribute_type_id - AttributeConstraint: - type: object - description: >- - Generic query constraint for a query node or query edge - properties: - id: - oneOf: - - $ref: '#/components/schemas/CURIE' - description: >- - CURIE of the concept being constrained. For properties - defined by the Biolink model this SHOULD be a biolink CURIE. - otherwise, if possible, from the EDAM ontology. If a suitable - CURIE does not exist, enter a descriptive phrase here and - submit the new type for consideration by the appropriate - authority. - example: EDAM:data_0844 - name: - type: string - description: >- - Human-readable name or label for the constraint concept. - If appropriate, it SHOULD be the term name of the CURIE used - as the 'id'. This is redundant but required for human - readability. - example: molecular mass - not: - type: boolean - default: false - operator: - type: string - description: >- - Relationship between the database value and the constraint value - for the specified id. The operators ==, >, and < mean - is equal to, is greater than, and is less than, - respectively. The 'matches' operator indicates that the value - is a regular expression to be evaluated. If value is a list type, - then at least one evaluation must be true (equivalent to OR). - This means that the == operator with a list acts like a SQL 'IN' - clause. If the value of the compared attribute is a list, then - comparisons are performed between each of the constraint values - and each of the attribute values, and any one true evaluation - counts as an overall true (e.g., [1,2,3] == [6,7,2] is true). - The == operator is therefore a broad interpretation of inclusion. - The '===' operator requires that the constraint value and - the attribute value be the same data type, length, - content, and order (e.g. only [1,2,3] === [1,2,3]). - The 'not' property negates the operator such that not - and == means 'not equal to' (or 'not in' for a list), and not > - means <=, and not < means >=, not matches means does not - match, and not === means the match between the constraint - and attribute values are not exact. - The '==' operator SHOULD NOT be used in a manner that - describes an "is a" subclass relationship for the parent QNode. - enum: - - == - - '>' - - < - - matches - - === - value: - example: 57.0 - description: >- - Value of the attribute. May be any data type, including a list. - If the value is a list and there are multiple items, at least one - comparison must be true (equivalent to OR) unless the '===' - operator is used. If 'value' is of data - type 'object', the keys of the object MAY be treated as a list. - A 'list' data type paired with the '>' or '<' operators will - encode extraneous comparisons, but this is permitted as it is in - SQL and other languages. - unit_id: - example: UO:0000222 - description: >- - CURIE of the units of the value or list of values in the 'value' - property. The Units of Measurement Ontology (UO) should be used - if possible. The unit_id MUST be provided for (lists of) - numerical values that correspond to a quantity that has units. - nullable: true - unit_name: - example: kilodalton - description: >- - Term name that is associated with the CURIE of the units - of the value or list of values in the 'value' - property. The Units of Measurement Ontology (UO) SHOULD be used - if possible. This property SHOULD be provided if a unit_id is - provided. This is redundant but recommended for human readability. - nullable: true - required: - - name - - id - - operator - - value - additionalProperties: false - RetrievalSource: - type: object - description: >- - Provides information about how a particular InformationResource - served as a source from which knowledge expressed in an Edge, or - data used to generate this knowledge, was retrieved. - properties: - resource_id: - $ref: '#/components/schemas/CURIE' - description: >- - The CURIE for an Information Resource that served as a source - of knowledge expressed in an Edge, or a source of data used to - generate this knowledge. - example: infores:drugbank - nullable: false - resource_role: - $ref: '#/components/schemas/ResourceRoleEnum' - description: >- - The role played by the InformationResource in serving as a - source for an Edge. Note that a given Edge should have one - and only one 'primary' source, and may have any number of - 'aggregator' or 'supporting data' sources. - upstream_resource_ids: - type: array - nullable: true - items: - $ref: '#/components/schemas/CURIE' - description: >- - An upstream InformationResource from which the resource - being described directly retrieved a record of the knowledge - expressed in the Edge, or data used to generate this knowledge. - This is an array because there are cases where a merged Edge - holds knowledge that was retrieved from multiple sources. e.g. - an Edge provided by the ARAGORN ARA can expressing knowledge it - retrieved from both the automat-mychem-info and molepro KPs, - which both provided it with records of this single fact. - example: [infores:automat-mychem-info, infores:molepro] - source_record_urls: - type: array - nullable: true - items: - type: string - description: >- - A URL linking to a specific web page or document provided by the - source, that contains a record of the knowledge expressed in the - Edge. If the knowledge is contained in more than one web page on - an Information Resource's site, urls MAY be provided for each. - For example, Therapeutic Targets Database (TTD) has separate web - pages for 'Imatinib' and its protein target KIT, both of which hold - the claim that 'the KIT protein is a therapeutic target for Imatinib'. - example: >- - [https://db.idrblab.net/ttd/data/drug/details/d0az3c, - https://db.idrblab.net/ttd/data/target/details/t57700] - required: - - resource_id - - resource_role - additionalProperties: true - ResourceRoleEnum: - type: string - description: >- - The role played by the InformationResource in serving as a - source for an Edge. Note that a given Edge should have one - and only one 'primary' source, and may have any number of - 'aggregator' or 'supporting data' sources. This enumeration - is found in Biolink Model, but is repeated here for convenience. - enum: - - primary_knowledge_source - - aggregator_knowledge_source - - supporting_data_source diff --git a/package-lock.json b/package-lock.json deleted file mode 100644 index 1a82ef2c..00000000 --- a/package-lock.json +++ /dev/null @@ -1,104712 +0,0 @@ -{ - "name": "@biothings-explorer/bte-trapi", - "version": "2.8.1", - "lockfileVersion": 2, - "requires": true, - "packages": { - "": { - "name": "@biothings-explorer/bte-trapi", - "version": "2.8.1", - "license": "ISC", - "workspaces": [ - "./packages/@biothings-explorer/api-response-transform", - "./packages/@biothings-explorer/call-apis", - "./packages/@biothings-explorer/query_graph_handler", - "./packages/@biothings-explorer/smartapi-kg", - "./packages/biolink-model", - "./packages/biomedical_id_resolver", - "./src/web-app", - ".", - "./packages/@biothings-explorer/node-expansion" - ], - "dependencies": { - "@biothings-explorer/query_graph_handler": "file:packages/@biothings-explorer/query_graph_handler", - 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"commander": "^2.7.1", - "lodash.get": "^4.4.2", - "lodash.isequal": "^4.5.0", - "validator": "^13.6.0" - } - }, - "zdog": { - "version": "1.1.3", - "resolved": "https://registry.npmjs.org/zdog/-/zdog-1.1.3.tgz", - "integrity": "sha512-raRj6r0gPzopFm5XWBJZr/NuV4EEnT4iE+U3dp5FV5pCb588Gmm3zLIp/j9yqqcMiHH8VNQlerLTgOqL7krh6w==" - } - } -} diff --git a/package.json b/package.json index 9cbdd1d4..7f46edd3 100644 --- a/package.json +++ b/package.json @@ -1,39 +1,34 @@ { "name": "@biothings-explorer/bte-trapi", - "version": "2.8.1", + "version": "3.0.0", "description": "BioThings Explorer's TRAPI Knowledgebase Query API", - "main": "src/server.js", + "main": "packages/bte-server/built/server.js", "scripts": { - "setup": "npm run clone && (npm i || true) && npm i", + "setup": "pnpm run clone && pnpm i", "clone": "./scripts/clone_packages.sh", - "pull": "./scripts/pull_packages.sh", + "pull": "pnpm run git pull", "git": "./scripts/run_git_packages.sh", - "compile": "tsc -b tsconfig.build.json", - "prepare": "npm run compile", - "build": "npm run compile", + "prepare": "pnpm run build", + "build": "turbo run build", + "clean": "turbo run clean", + "build:clean": "pnpm run clean && pnpm run build", + "format": "prettier --check .", + "format:fix": "prettier --write .", + "lint": "eslint . --ext .ts,.js", + "lint:fix": "pnpm lint --fix", + "test": "turbo run --parallel test", + "test-cov": "turbo run --parallel test-cov", + "siege-local": "artillery run -e local --output report_local.json --config performance-test/config.yaml performance-test/scenarios/query.yaml", + "smartapi_sync": "DEBUG=bte* SYNC_AND_EXIT=true node ./scripts/smartapi_sync.js", "get_rev": "./scripts/get_rev.sh", - "watch": "tsc -b tsconfig.build.json --watch", - "watch2": "nodemon -e js,mjs,json,ts --watch packages --exec npm run compile", + "basic-start": "node .", "start": "./scripts/start_server.sh", "stop": "./scripts/stop_server.sh", - "basic-start": "nodemon --ignore './data/' src/server.js", - "debug": "DEBUG=biomedical-id-resolver,bte* npm run basic-start", - "debug-all": "DEBUG=* nodemon --ignore './data/' src/server.js", - "clean": "rimraf \"packages/**/built\" \"packages/**/*.tsbuildinfo\"", - "clean_on_prod": "rimraf \"packages/**/__test__\" \"packages/**/.git\" \"packages/**/node_modules\"", - "prettier": "prettier \"*.{js,json,yml,md}\" \"packages/**/*\"", - "format": "npm run prettier -- --write", - "format:check": "npm run prettier -- --check", - "lint": "npm run format:check", - "test": "jest --forceExit --env node", - "test-all": "jest --", - "test-cov": "jest --coverage --env node", - "release": "standard-version", - "release:minor": "standard-version --release-as minor", - "release:patch": "standard-version --release-as patch", - "release:major": "standard-version --release-as major", - "siege-local": "artillery run -e local --output report_local.json --config performance-test/config.yaml performance-test/scenarios/query.yaml", - "smartapi_sync": "DEBUG=bte* SYNC_AND_EXIT=true node ./scripts/smartapi_sync.js" + "watch": "nodemon -e js,mjs,json,ts --watch './packages/**/src/*' './packages/**/data/*' --exec 'pnpm run build && node .'", + "debug": "DEBUG=biomedical-id-resolver,bte* pnpm run watch" + }, + "engines": { + "pnpm": ">=8.9.2" }, "repository": { "type": "git", @@ -53,77 +48,66 @@ }, "homepage": "https://github.com/biothings/biothings_explorer#readme", "devDependencies": { - "@typescript-eslint/eslint-plugin": "^4.29.3", - "@typescript-eslint/parser": "^4.29.3", - "artillery": "^1.6.2", - "cookie-parser": "~1.4.4", - "coveralls": "^3.1.0", + "@types/node": "^20.8.7", + "@typescript-eslint/eslint-plugin": "^6.8.0", + "@typescript-eslint/parser": "^6.8.0", + "artillery": "^1.7.9", + "cookie-parser": "~1.4.6", + "coveralls": "^3.1.1", "eslint": "^7.32.0", - "eslint-config-prettier": "^8.3.0", + "eslint-config-prettier": "^8.10.0", "eslint-plugin-prettier": "^3.4.1", "http-errors": "~1.6.3", - "jest": "^29.5.0", - "lerna": "^6.6.1", + "jest": "^29.7.0", + "lerna": "^6.6.2", "morgan": "~1.9.1", - "nodemon": "^2.0.20", - "prettier": "^2.3.1", + "nodemon": "^2.0.22", + "prettier": "^2.8.8", "pug": "^3.0.2", "rimraf": "^3.0.2", - "standard-version": "^9.1.1", - "supertest": "^6.1.3", + "supertest": "^6.3.3", "supports-color": "^7.2.0", - "typescript": "4.3.4" + "typescript": "5.2.2" }, "dependencies": { - "@biothings-explorer/query_graph_handler": "file:packages/@biothings-explorer/query_graph_handler", - "@biothings-explorer/smartapi-kg": "file:packages/@biothings-explorer/", - "@bull-board/express": "^5.0.0", - "@sentry/node": "^7.57.0", - "@sentry/profiling-node": "^1.0.8", + "@biothings-explorer/query_graph_handler": "file:packages/query_graph_handler", + "@biothings-explorer/smartapi-kg": "file:packages/smartapi-kg", + "@bull-board/express": "^5.9.1", + "@sentry/node": "^7.74.1", + "@sentry/profiling-node": "^1.2.1", "axios": "^0.27.2", - "body-parser": "^1.19.0", - "bull": "^4.10.4", + "body-parser": "^1.20.2", + "bull": "^4.11.4", "compression": "^1.7.4", "connect-history-api-fallback": "^2.0.0", "cors": "^2.8.5", - "debug": "^4.3.1", - "dotenv": "^8.2.0", - "express": "^4.17.3", - "express-rate-limit": "^5.2.6", - "express-winston": "^4.1.0", - "helmet": "^4.4.1", + "debug": "^4.3.4", + "dotenv": "^8.6.0", + "express": "^4.18.2", + "express-rate-limit": "^5.5.1", + "express-winston": "^4.2.0", + "helmet": "^4.6.0", "husky": "^4.3.8", - "ioredis": "^5.0.6", + "ioredis": "^5.3.2", "js-yaml": "^4.1.0", "lodash": "^4.17.21", "lz4": "^0.6.5", - "nanoid": "^3.1.31", + "nanoid": "^3.3.6", "node-cron": "^2.0.3", - "npm": "^9.4.1", - "openapi-validator-middleware": "^3.2.2", + "openapi-validator-middleware": "^3.2.6", "piscina": "^3.2.0", "ps-node": "^0.1.6", "snake-case": "^3.0.4", "stream-chunker": "^1.2.8", - "stream-json": "^1.7.3", + "stream-json": "^1.8.0", + "turbo": "^1.10.16", "valid-url": "^1.0.9", - "winston": "^3.3.3", - "winston-daily-rotate-file": "^4.5.1" + "winston": "^3.11.0", + "winston-daily-rotate-file": "^4.7.1" }, "husky": { "hooks": { "commit-msg": "commitlint -E HUSKY_GIT_PARAMS" } - }, - "workspaces": [ - "./packages/@biothings-explorer/api-response-transform", - "./packages/@biothings-explorer/call-apis", - "./packages/@biothings-explorer/query_graph_handler", - "./packages/@biothings-explorer/smartapi-kg", - "./packages/biolink-model", - "./packages/biomedical_id_resolver", - "./src/web-app", - ".", - "./packages/@biothings-explorer/node-expansion" - ] + } } diff --git a/packages/packages.txt b/packages/packages.txt new file mode 100644 index 00000000..89e4947b --- /dev/null +++ b/packages/packages.txt @@ -0,0 +1,8 @@ +biothings/bte-server.git bte-server +biothings/api-respone-transform.js.git api-response-transform +biothings/call-apis.js.git call-apis +biothings/smartapi-kg.js.git smartapi-kg +biothings/bte_trapi_query_graph_handler.git query_graph_handler +biothings/node-expansion.git node-expansion +biothings/biolink-model.js.git biolink-model +biothings/biomedical_id_resolver.js.git biomedical_id_resolver diff --git a/src/web-app/.eslintrc.cjs b/packages/web-app/.eslintrc.cjs similarity index 100% rename from src/web-app/.eslintrc.cjs rename to packages/web-app/.eslintrc.cjs diff --git a/src/web-app/.gitignore b/packages/web-app/.gitignore similarity index 100% rename from src/web-app/.gitignore rename to packages/web-app/.gitignore diff --git a/src/web-app/.vscode/extensions.json b/packages/web-app/.vscode/extensions.json similarity index 100% rename from src/web-app/.vscode/extensions.json rename to packages/web-app/.vscode/extensions.json diff --git a/src/web-app/README.md b/packages/web-app/README.md similarity index 87% rename from src/web-app/README.md rename to packages/web-app/README.md index d1062030..520ed4f5 100644 --- a/src/web-app/README.md +++ b/packages/web-app/README.md @@ -16,14 +16,14 @@ Additionally I added [vite-svg-loader](https://github.com/jpkleemans/vite-svg-lo Node v.17>= ``` -npm i +pnpm i ``` ## Run / Develop ``` -npm run dev +pnpm run dev ``` @@ -31,7 +31,7 @@ npm run dev ``` -npm run build +pnpm run build ``` @@ -39,7 +39,7 @@ npm run build ``` -npm run preview +pnpm run preview ``` @@ -47,6 +47,6 @@ npm run preview ``` -npm run lint +pnpm run lint ``` diff --git a/src/web-app/index.html b/packages/web-app/index.html similarity index 100% rename from src/web-app/index.html rename to packages/web-app/index.html diff --git a/packages/web-app/package.json b/packages/web-app/package.json new file mode 100644 index 00000000..25d6fc82 --- /dev/null +++ b/packages/web-app/package.json @@ -0,0 +1,68 @@ +{ + "name": "@marcodarko/btewebapp", + "description": "Vite, Vuex, Vue Router & Tailwind CSS.", + "version": "1.0.8", + "scripts": { + "dev": "vite", + "postinstall": "pnpm run build", + "build": "vite build", + "preview": "vite preview --port 4173", + "lint": "eslint . --ext .vue,.js,.jsx,.cjs,.mjs --fix --ignore-path .gitignore" + }, + "dependencies": { + "@codemirror/autocomplete": "^6.10.2", + "@codemirror/commands": "^6.3.0", + "@codemirror/lang-json": "^6.0.1", + "@codemirror/language": "^6.9.1", + "@codemirror/state": "^6.3.1", + "@codemirror/view": "^6.21.3", + "@tailwindcss/forms": "^0.5.6", + "axios": "^1.5.1", + "codemirror": "^6.0.1", + "cytoscape": "^3.26.0", + "cytoscape-popper": "^2.0.0", + "moment": "^2.29.4", + "pinia": "^2.1.7", + "renderjson": "^1.4.0", + "tippy.js": "^6.3.7", + "vue": "^3.3.6", + "vue-router": "^4.2.5", + "zdog": "^1.1.3" + }, + "devDependencies": { + "@rushstack/eslint-patch": "^1.5.1", + "@types/debug": "^4.1.10", + "@types/lodash": "^4.14.200", + "@types/node": "^20.8.7", + "@vitejs/plugin-vue": "^3.2.0", + "@vue/eslint-config-prettier": "^7.1.0", + "autoprefixer": "^10.4.16", + "cssnano": "^5.1.15", + "eslint": "^8.52.0", + "eslint-plugin-vue": "^9.17.0", + "jest": "^29.7.0", + "postcss": "^8.4.31", + "postcss-import": "^15.1.0", + "prettier": "^2.8.8", + "sass": "^1.69.4", + "tailwindcss": "^3.3.3", + "ts-jest": "^29.1.1", + "vite": "^3.2.7", + "vite-svg-loader": "^3.6.0" + }, + "keywords": [ + "vue", + "vue3", + "vuejs", + "vue3js", + "template", + "router", + "vuerouter", + "vue-router", + "tailwind", + "tailwindcss", + "tailwind-css", + "pinia", + "svg" + ] +} diff --git a/src/web-app/postcss.config.js b/packages/web-app/postcss.config.js similarity index 100% rename from src/web-app/postcss.config.js rename to packages/web-app/postcss.config.js diff --git a/src/web-app/public/bte.svg b/packages/web-app/public/bte.svg similarity index 100% rename from src/web-app/public/bte.svg rename to packages/web-app/public/bte.svg diff --git a/src/web-app/src/App.vue b/packages/web-app/src/App.vue similarity index 100% rename from src/web-app/src/App.vue rename to packages/web-app/src/App.vue diff --git a/src/web-app/src/assets/img/biothings-explorer-128.png b/packages/web-app/src/assets/img/biothings-explorer-128.png similarity index 100% rename from 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a/src/web-app/src/assets/img/biothings-explorer-text-2.svg b/packages/web-app/src/assets/img/biothings-explorer-text-2.svg similarity index 100% rename from src/web-app/src/assets/img/biothings-explorer-text-2.svg rename to packages/web-app/src/assets/img/biothings-explorer-text-2.svg diff --git a/src/web-app/src/assets/img/biothings-explorer-text.png b/packages/web-app/src/assets/img/biothings-explorer-text.png similarity index 100% rename from src/web-app/src/assets/img/biothings-explorer-text.png rename to packages/web-app/src/assets/img/biothings-explorer-text.png diff --git a/src/web-app/src/assets/img/biothings-explorer-text.svg b/packages/web-app/src/assets/img/biothings-explorer-text.svg similarity index 100% rename from src/web-app/src/assets/img/biothings-explorer-text.svg rename to packages/web-app/src/assets/img/biothings-explorer-text.svg diff --git a/src/web-app/src/assets/img/biothings-explorer-xl.png b/packages/web-app/src/assets/img/biothings-explorer-xl.png similarity 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b/packages/web-app/src/assets/img/network-01.svg similarity index 100% rename from src/web-app/src/assets/img/network-01.svg rename to packages/web-app/src/assets/img/network-01.svg diff --git a/src/web-app/src/assets/img/network-2-01.svg b/packages/web-app/src/assets/img/network-2-01.svg similarity index 100% rename from src/web-app/src/assets/img/network-2-01.svg rename to packages/web-app/src/assets/img/network-2-01.svg diff --git a/src/web-app/src/assets/img/nih-logo.png b/packages/web-app/src/assets/img/nih-logo.png similarity index 100% rename from src/web-app/src/assets/img/nih-logo.png rename to packages/web-app/src/assets/img/nih-logo.png diff --git a/src/web-app/src/assets/img/scripps-logo.png b/packages/web-app/src/assets/img/scripps-logo.png similarity index 100% rename from src/web-app/src/assets/img/scripps-logo.png rename to packages/web-app/src/assets/img/scripps-logo.png diff --git a/src/web-app/src/assets/tailwind.css b/packages/web-app/src/assets/tailwind.css similarity index 100% rename from src/web-app/src/assets/tailwind.css rename to packages/web-app/src/assets/tailwind.css diff --git a/src/web-app/src/components/BTE.vue b/packages/web-app/src/components/BTE.vue similarity index 100% rename from src/web-app/src/components/BTE.vue rename to packages/web-app/src/components/BTE.vue diff --git a/src/web-app/src/components/BTELogoVertical.vue b/packages/web-app/src/components/BTELogoVertical.vue similarity index 100% rename from src/web-app/src/components/BTELogoVertical.vue rename to packages/web-app/src/components/BTELogoVertical.vue diff --git a/src/web-app/src/components/CodeEditor.vue b/packages/web-app/src/components/CodeEditor.vue similarity index 100% rename from src/web-app/src/components/CodeEditor.vue rename to packages/web-app/src/components/CodeEditor.vue diff --git a/src/web-app/src/components/CytoNetwork.vue b/packages/web-app/src/components/CytoNetwork.vue similarity index 100% rename from src/web-app/src/components/CytoNetwork.vue rename to packages/web-app/src/components/CytoNetwork.vue diff --git a/src/web-app/src/components/LinkOutIcon.vue b/packages/web-app/src/components/LinkOutIcon.vue similarity index 100% rename from src/web-app/src/components/LinkOutIcon.vue rename to packages/web-app/src/components/LinkOutIcon.vue diff --git a/src/web-app/src/components/LoadingLogo.vue b/packages/web-app/src/components/LoadingLogo.vue similarity index 100% rename from src/web-app/src/components/LoadingLogo.vue rename to packages/web-app/src/components/LoadingLogo.vue diff --git a/src/web-app/src/components/Logo.vue b/packages/web-app/src/components/Logo.vue similarity index 100% rename from src/web-app/src/components/Logo.vue rename to packages/web-app/src/components/Logo.vue diff --git a/src/web-app/src/components/Nav.vue b/packages/web-app/src/components/Nav.vue similarity index 100% rename from src/web-app/src/components/Nav.vue rename to packages/web-app/src/components/Nav.vue diff --git a/src/web-app/src/components/QueryBox.vue b/packages/web-app/src/components/QueryBox.vue similarity index 100% rename from src/web-app/src/components/QueryBox.vue rename to packages/web-app/src/components/QueryBox.vue diff --git a/src/web-app/src/main.js b/packages/web-app/src/main.js similarity index 88% rename from src/web-app/src/main.js rename to packages/web-app/src/main.js index da82c661..47bfc7ad 100644 --- a/src/web-app/src/main.js +++ b/packages/web-app/src/main.js @@ -5,7 +5,7 @@ import App from "./App.vue"; import router from "./router"; import "./assets/tailwind.css"; -import 'tippy.js/dist/tippy.css'; +import "tippy.js/dist/tippy.css"; const app = createApp(App); diff --git a/src/web-app/src/router/index.js b/packages/web-app/src/router/index.js similarity index 100% rename from src/web-app/src/router/index.js rename to packages/web-app/src/router/index.js diff --git a/packages/web-app/src/stores/examples.js b/packages/web-app/src/stores/examples.js new file mode 100644 index 00000000..8abb39b3 --- /dev/null +++ b/packages/web-app/src/stores/examples.js @@ -0,0 +1,225 @@ +import moment from "moment"; +import { defineStore } from "pinia"; +import axios from "axios"; +import { useMainStore } from "./general"; + +export const useExamplesStore = defineStore({ + id: "examples", + state: () => ({ + queries: [ + { + selected: false, + name: "Disease (Kartagener syndrome) has phenotypic feature", + id: 423423, + elements: { + nodes: [ + { data: { id: "dis", name: "⭐Disease\n(MONDO:0016575)", color: "#8d5bd4" } }, + { data: { id: "ph", name: "PhenotypicFeature", color: "#2abcbd" } }, + ], + edges: [{ data: { source: "dis", target: "ph", name: "⭐biolink:has_phenotype" } }], + }, + query: { + message: { + query_graph: { + nodes: { + n0: { + categories: ["biolink:Disease"], + ids: ["MONDO:0016575"], + }, + n1: { + categories: ["biolink:PhenotypicFeature"], + }, + }, + edges: { + e01: { + subject: "n0", + object: "n1", + predicates: ["biolink:has_phenotype"], + }, + }, + }, + }, + }, + }, + { + selected: false, + name: "Disease (Kartagener syndrome) relation to genes", + id: 428423, + elements: { + nodes: [ + { data: { id: "dis", name: "⭐Disease\n(MONDO:0016575)", color: "#8d5bd4" } }, + { data: { id: "gene", name: "Gene", color: "#369ac1" } }, + ], + edges: [{ data: { source: "dis", target: "gene", name: "" } }], + }, + query: { + message: { + query_graph: { + nodes: { + n0: { + categories: ["biolink:Disease"], + ids: ["MONDO:0005737"], + }, + n1: { + categories: ["biolink:Gene"], + }, + }, + edges: { + e01: { + subject: "n0", + object: "n1", + }, + }, + }, + }, + }, + }, + { + selected: false, + name: "Disease (Ebola hemorrhagic fever) gene relation to small molecules", + id: 426654, + elements: { + nodes: [ + { data: { id: "dis", name: "⭐Disease\n(MONDO:0005737)", color: "#8d5bd4" } }, + { data: { id: "gene", name: "Gene", color: "#369ac1" } }, + { data: { id: "sm", name: "SmallMolecule", color: "hotpink" } }, + ], + edges: [ + { data: { source: "dis", target: "gene", name: "" } }, + { data: { source: "gene", target: "sm", name: "" } }, + ], + }, + query: { + message: { + query_graph: { + nodes: { + n0: { + categories: ["biolink:Disease"], + ids: ["MONDO:0005737"], + }, + n1: { + categories: ["biolink:Gene"], + }, + n2: { + categories: ["biolink:SmallMolecule"], + }, + }, + edges: { + e01: { + subject: "n0", + object: "n1", + }, + e02: { + subject: "n1", + object: "n2", + }, + }, + }, + }, + }, + }, + { + selected: false, + name: "Gene (NCBIGene:3778) relation to small molecules via other genes", + id: 453423, + elements: { + nodes: [ + { data: { id: "gene", name: "⭐Gene\n(NCBIGene:3778)", color: "#369ac1" } }, + { data: { id: "gene2", name: "Gene", color: "#369ac1" } }, + { data: { id: "sm", name: "SmallMolecule", color: "hotpink" } }, + ], + edges: [ + { data: { source: "gene", target: "gene2", name: "" } }, + { data: { source: "gene2", target: "sm", name: "" } }, + ], + }, + query: { + message: { + query_graph: { + nodes: { + n0: { + categories: ["biolink:Gene"], + ids: ["NCBIGene:3778"], + }, + n1: { + categories: ["biolink:Gene"], + }, + n2: { + categories: ["biolink:SmallMolecule"], + }, + }, + edges: { + e01: { + subject: "n0", + object: "n1", + }, + e02: { + subject: "n1", + object: "n2", + }, + }, + }, + }, + }, + }, + ], + message: "", + jobs: [], + jobPicked: "", + }), + getters: { + selectedQuery: state => state.queries.find(q => q.selected), + }, + actions: { + select(id) { + this.queries.forEach(q => { + if (q.id == id) { + q.selected = !q.selected; + } else { + q.selected = false; + } + }); + }, + async sendRequest(query, description) { + let self = this; + let store = useMainStore(); + store.loading = true; + axios + .post("/v1/asyncquery", JSON.parse(query)) + .then(res => { + store.loading = false; + console.log(res.data); + self.jobs.unshift({ + id: res.data.job_id, + date: this.getDateRightNow(), + url: res.data.job_url, + description: description, + }); + self.message = `A new job ID has been created: ${res.data.job_id} `; + self.updateJobs(); + }) + .catch(err => { + store.loading = false; + console.log(err); + self.message = `Oh no: ${err} `; + throw err; + }); + }, + updateJobs() { + localStorage.setItem("bte-jobs", JSON.stringify(this.jobs)); + }, + getJobs() { + let j = JSON.parse(localStorage.getItem("bte-jobs")); + if (j && j.length) { + this.jobs = j; + } + }, + deleteJobs() { + localStorage.removeItem("bte-jobs"); + this.jobs = []; + }, + getDateRightNow() { + return moment().format("MMMM Do YYYY, h:mm:ss"); + }, + }, +}); diff --git a/src/web-app/src/stores/general.js b/packages/web-app/src/stores/general.js similarity index 90% rename from src/web-app/src/stores/general.js rename to packages/web-app/src/stores/general.js index 8fb01b6a..aa066352 100644 --- a/src/web-app/src/stores/general.js +++ b/packages/web-app/src/stores/general.js @@ -5,9 +5,7 @@ export const useMainStore = defineStore({ state: () => ({ loading: false, }), - getters: { - - }, + getters: {}, actions: { setLoading(v) { this.loading = v; diff --git a/src/web-app/src/views/AboutView.vue b/packages/web-app/src/views/AboutView.vue similarity index 100% rename from src/web-app/src/views/AboutView.vue rename to packages/web-app/src/views/AboutView.vue diff --git a/src/web-app/src/views/HomeView.vue b/packages/web-app/src/views/HomeView.vue similarity index 100% rename from src/web-app/src/views/HomeView.vue rename to packages/web-app/src/views/HomeView.vue diff --git a/src/web-app/src/views/Try.vue b/packages/web-app/src/views/Try.vue similarity index 100% rename from src/web-app/src/views/Try.vue rename to packages/web-app/src/views/Try.vue diff --git a/src/web-app/tailwind.config.js b/packages/web-app/tailwind.config.js similarity index 75% rename from src/web-app/tailwind.config.js rename to packages/web-app/tailwind.config.js index 95288c68..e367de9e 100644 --- a/src/web-app/tailwind.config.js +++ b/packages/web-app/tailwind.config.js @@ -4,7 +4,5 @@ module.exports = { theme: { extend: {}, }, - plugins: [ - require('@tailwindcss/forms'), - ], + plugins: [require("@tailwindcss/forms")], }; diff --git a/src/web-app/vite.config.js b/packages/web-app/vite.config.js similarity index 100% rename from src/web-app/vite.config.js rename to packages/web-app/vite.config.js diff --git a/pnpm-lock.yaml b/pnpm-lock.yaml new file mode 100644 index 00000000..a3e8160e --- /dev/null +++ b/pnpm-lock.yaml @@ -0,0 +1,16265 @@ +lockfileVersion: '6.0' + +settings: + autoInstallPeers: true + excludeLinksFromLockfile: false + +importers: + + .: + dependencies: + '@biothings-explorer/query_graph_handler': + specifier: file:packages/query_graph_handler + version: file:packages/query_graph_handler(supports-color@7.2.0) + '@biothings-explorer/smartapi-kg': + specifier: file:packages/smartapi-kg + version: file:packages/smartapi-kg(supports-color@7.2.0) + '@bull-board/express': + specifier: ^5.9.1 + version: 5.9.1(supports-color@7.2.0) + '@sentry/node': + specifier: ^7.74.1 + version: 7.74.1(supports-color@7.2.0) + '@sentry/profiling-node': + specifier: ^1.2.1 + version: 1.2.1(supports-color@7.2.0) + axios: + specifier: ^0.27.2 + version: 0.27.2(debug@4.3.4) + body-parser: + specifier: ^1.20.2 + version: 1.20.2(supports-color@7.2.0) + bull: + specifier: ^4.11.4 + version: 4.11.4(supports-color@7.2.0) + compression: + specifier: ^1.7.4 + version: 1.7.4(supports-color@7.2.0) + connect-history-api-fallback: + specifier: ^2.0.0 + version: 2.0.0 + cors: + specifier: ^2.8.5 + version: 2.8.5 + debug: + specifier: ^4.3.4 + version: 4.3.4(supports-color@7.2.0) + dotenv: + specifier: ^8.6.0 + version: 8.6.0 + express: + specifier: ^4.18.2 + version: 4.18.2(supports-color@7.2.0) + express-rate-limit: + specifier: ^5.5.1 + version: 5.5.1 + express-winston: + specifier: ^4.2.0 + version: 4.2.0(winston@3.11.0) + helmet: + specifier: ^4.6.0 + version: 4.6.0 + husky: + specifier: ^4.3.8 + version: 4.3.8 + ioredis: + specifier: ^5.3.2 + version: 5.3.2(supports-color@7.2.0) + js-yaml: + specifier: ^4.1.0 + version: 4.1.0 + lodash: + specifier: ^4.17.21 + version: 4.17.21 + lz4: + specifier: ^0.6.5 + version: 0.6.5 + nanoid: + specifier: ^3.3.6 + version: 3.3.6 + node-cron: + specifier: ^2.0.3 + version: 2.0.3 + openapi-validator-middleware: + specifier: ^3.2.6 + version: 3.2.6(openapi-types@12.1.3) + piscina: + specifier: ^3.2.0 + version: 3.2.0 + ps-node: + specifier: ^0.1.6 + version: 0.1.6 + snake-case: + specifier: ^3.0.4 + version: 3.0.4 + stream-chunker: + specifier: ^1.2.8 + version: 1.2.8 + stream-json: + specifier: ^1.8.0 + version: 1.8.0 + turbo: + specifier: ^1.10.16 + version: 1.10.16 + valid-url: + specifier: ^1.0.9 + version: 1.0.9 + winston: + specifier: ^3.11.0 + version: 3.11.0 + winston-daily-rotate-file: + specifier: ^4.7.1 + version: 4.7.1(winston@3.11.0) + devDependencies: + '@types/node': + specifier: ^20.8.7 + version: 20.8.7 + '@typescript-eslint/eslint-plugin': + specifier: ^6.8.0 + version: 6.8.0(@typescript-eslint/parser@6.8.0)(eslint@7.32.0)(supports-color@7.2.0)(typescript@5.2.2) + '@typescript-eslint/parser': + specifier: ^6.8.0 + version: 6.8.0(eslint@7.32.0)(supports-color@7.2.0)(typescript@5.2.2) + artillery: + specifier: ^1.7.9 + version: 1.7.9(supports-color@7.2.0) + cookie-parser: + specifier: ~1.4.6 + version: 1.4.6 + coveralls: + specifier: ^3.1.1 + version: 3.1.1 + eslint: + specifier: ^7.32.0 + version: 7.32.0(supports-color@7.2.0) + eslint-config-prettier: + specifier: ^8.10.0 + version: 8.10.0(eslint@7.32.0) + eslint-plugin-prettier: + specifier: ^3.4.1 + version: 3.4.1(eslint-config-prettier@8.10.0)(eslint@7.32.0)(prettier@2.8.8) + http-errors: + specifier: ~1.6.3 + version: 1.6.3 + jest: + specifier: ^29.7.0 + version: 29.7.0(@types/node@20.8.7)(supports-color@7.2.0)(ts-node@10.9.1) + lerna: + specifier: ^6.6.2 + version: 6.6.2(debug@4.3.4)(supports-color@7.2.0) + morgan: + specifier: ~1.9.1 + version: 1.9.1(supports-color@7.2.0) + nodemon: + specifier: ^2.0.22 + version: 2.0.22 + prettier: + specifier: ^2.8.8 + version: 2.8.8 + pug: + specifier: ^3.0.2 + version: 3.0.2 + rimraf: + specifier: ^3.0.2 + version: 3.0.2 + supertest: + specifier: ^6.3.3 + version: 6.3.3(supports-color@7.2.0) + supports-color: + specifier: ^7.2.0 + version: 7.2.0 + typescript: + specifier: 5.2.2 + version: 5.2.2 + + packages/api-response-transform: + dependencies: + '@commitlint/cli': + specifier: ^17.8.1 + version: 17.8.1 + '@commitlint/config-conventional': + specifier: ^11.0.0 + version: 11.0.0 + async: + specifier: ^3.2.4 + version: 3.2.4 + axios: + specifier: ^0.21.4 + version: 0.21.4(debug@4.3.4) + common-path-prefix: + specifier: ^3.0.0 + version: 3.0.0 + husky: + specifier: ^8.0.3 + version: 8.0.3 + jsonata: + specifier: ^1.8.6 + version: 1.8.6 + lodash: + specifier: ^4.17.21 + version: 4.17.21 + devDependencies: + '@babel/core': + specifier: ^7.23.2 + 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false + + file:packages/node-expansion(debug@4.3.4): + resolution: {directory: packages/node-expansion, type: directory} + id: file:packages/node-expansion + name: '@biothings-explorer/node-expansion' + dependencies: + axios: 0.27.2(debug@4.3.4) + lodash: 4.17.21 + transitivePeerDependencies: + - debug + dev: false + + file:packages/query_graph_handler(supports-color@7.2.0): + resolution: {directory: packages/query_graph_handler, type: directory} + id: file:packages/query_graph_handler + name: '@biothings-explorer/query_graph_handler' + dependencies: + '@biothings-explorer/api-response-transform': file:packages/api-response-transform(debug@4.3.4) + '@biothings-explorer/call-apis': file:packages/call-apis(supports-color@7.2.0) + '@biothings-explorer/node-expansion': file:packages/node-expansion(debug@4.3.4) + '@biothings-explorer/smartapi-kg': file:packages/smartapi-kg(supports-color@7.2.0) + '@sentry/node': 7.74.1(supports-color@7.2.0) + '@types/axios': 0.14.0(debug@4.3.4) + async: 3.2.4 + biolink-model: file:packages/biolink-model(supports-color@7.2.0) + biomedical_id_resolver: file:packages/biomedical_id_resolver(supports-color@7.2.0) + chi-square-p-value: 1.0.5 + debug: 4.3.4(supports-color@7.2.0) + eslint: 7.32.0(supports-color@7.2.0) + ioredis: 5.3.2(supports-color@7.2.0) + lodash: 4.17.21 + redlock: 5.0.0-beta.2 + rimraf: 3.0.2 + transitivePeerDependencies: + - '@swc/core' + - '@swc/wasm' + - chokidar + - supports-color + dev: false + + file:packages/smartapi-kg(supports-color@7.2.0): + resolution: {directory: packages/smartapi-kg, type: directory} + id: file:packages/smartapi-kg + name: '@biothings-explorer/smartapi-kg' + dependencies: + '@babel/runtime': 7.23.2 + '@commitlint/cli': 17.8.1 + '@commitlint/config-conventional': 11.0.0 + '@types/jest': 26.0.24 + '@types/lodash': 4.14.200 + axios: 0.21.4(debug@4.3.4) + camelcase: 6.3.0 + core-js: 3.33.1 + debug: 4.3.4(supports-color@7.2.0) + eslint: 7.32.0(supports-color@7.2.0) + husky: 8.0.3 + load-json-file: 7.0.1 + lodash: 4.17.21 + rimraf: 3.0.2 + transitivePeerDependencies: + - '@swc/core' + - '@swc/wasm' + - supports-color + dev: false diff --git a/pnpm-workspace.yaml b/pnpm-workspace.yaml new file mode 100644 index 00000000..affcf0f6 --- /dev/null +++ b/pnpm-workspace.yaml @@ -0,0 +1,3 @@ +packages: + - "./packages/**" + - "./packages/bte-server/web-app" diff --git a/process.yml b/process.yml index 60f5276b..7b83f6d5 100644 --- a/process.yml +++ b/process.yml @@ -1,6 +1,6 @@ apps: - name: bte_reasoner_api - script: ./src/server.js + script: ./packages/bte-server/built/server.js exec_mode: cluster instances: max - \ No newline at end of file + diff --git a/scripts/clone_packages.sh b/scripts/clone_packages.sh index ee88cc68..98b15c8d 100755 --- a/scripts/clone_packages.sh +++ b/scripts/clone_packages.sh @@ -22,22 +22,9 @@ set -x while read line || [ -n "$line" ]; do read -r url module_dir <<< $line - git clone $base_url"$url" "$module_dir" -done < scripts/packages.txt + git clone $base_url"$url" "./packages/$module_dir" +done < packages/packages.txt -cd "./packages/@biothings-explorer/call-apis" -ln -s ../../../scripts/tsconfig.json_call-apis ./tsconfig.json -cd $current_folder - -cd "./packages/@biothings-explorer/node-expansion" -ln -s ../../../scripts/tsconfig.json_node-expansion ./tsconfig.json -# # no need to do this after we commit the package name change to the repo -# if [ "$(uname)" = "Darwin" ]; then -# # sed on mac has a workaround to make it work -# sed -i '' 's/single-hop-app/bte-trapi/g' package.json -# else -# sed -i 's/single-hop-app/bte-trapi/g' package.json -# fi cd $current_folder set +x diff --git a/scripts/get_rev.sh b/scripts/get_rev.sh index 354fc92a..a6c1396d 100755 --- a/scripts/get_rev.sh +++ b/scripts/get_rev.sh @@ -7,7 +7,7 @@ echo '# Generated from "npm run get_rev" on ' $(date) while read line || [ -n "$line" ]; do read -r url module_dir <<< $line - cd "$module_dir" + cd "./packages/$module_dir" echo `git ls-remote --get-url` `git rev-parse --short HEAD` `git rev-parse HEAD` cd $current_folder -done < scripts/packages.txt +done < packages/packages.txt diff --git a/scripts/packages.txt b/scripts/packages.txt deleted file mode 100644 index 38e724bd..00000000 --- a/scripts/packages.txt +++ /dev/null @@ -1,8 +0,0 @@ -biothings/biothings_explorer . -biothings/api-respone-transform.js.git ./packages/@biothings-explorer/api-response-transform -biothings/call-apis.js.git ./packages/@biothings-explorer/call-apis -biothings/smartapi-kg.js.git ./packages/@biothings-explorer/smartapi-kg -biothings/bte_trapi_query_graph_handler.git ./packages/@biothings-explorer/query_graph_handler -biothings/node-expansion.git ./packages/@biothings-explorer/node-expansion -biothings/biolink-model.js.git ./packages/biolink-model -biothings/biomedical_id_resolver.js.git ./packages/biomedical_id_resolver diff --git a/scripts/pull_packages.sh b/scripts/pull_packages.sh deleted file mode 100755 index d9b7ed36..00000000 --- a/scripts/pull_packages.sh +++ /dev/null @@ -1,14 +0,0 @@ -#!/bin/bash - -current_folder=`pwd` - -while read line || [ -n "$line" ]; -do - read -r url module_dir <<< $line - cd "$module_dir" - echo - basename "$module_dir" - echo "-----" - git pull - cd $current_folder -done < scripts/packages.txt diff --git a/scripts/run_git_packages.sh b/scripts/run_git_packages.sh index 150addeb..ae23c3fa 100755 --- a/scripts/run_git_packages.sh +++ b/scripts/run_git_packages.sh @@ -2,13 +2,17 @@ current_folder=`pwd` +echo ". (workspace)" +echo "-----" +git $* + while read line || [ -n "$line" ]; do read -r url module_dir <<< $line - cd "$module_dir" + cd "./packages/$module_dir" echo basename "$module_dir" echo "-----" git $* cd $current_folder -done < scripts/packages.txt +done < packages/packages.txt diff --git a/scripts/start_server.sh b/scripts/start_server.sh index 2eb7db42..4c751146 100755 --- a/scripts/start_server.sh +++ b/scripts/start_server.sh @@ -3,7 +3,6 @@ current_folder=`pwd` redis_available=false -npm run compile if [ "$1" = "redis" ] then { @@ -23,12 +22,12 @@ then } if [ "$redis_available" ] ; then - REDIS_HOST=localhost REDIS_PORT=6379 npm run debug + REDIS_HOST=localhost REDIS_PORT=6379 pnpm run debug else - npm run debug + pnpm run debug fi else - npm run debug + pnpm run debug fi cd $current_folder diff --git a/scripts/tsconfig.json_call-apis b/scripts/tsconfig.json_call-apis deleted file mode 100644 index 7a367ebd..00000000 --- a/scripts/tsconfig.json_call-apis +++ /dev/null @@ -1,25 +0,0 @@ -{ - "extends": "../../../tsconfig.opts.json", - "compilerOptions": { - "rootDir": "src", - "outDir": "built" - }, - "include": [ - "./src/**/*" - ], - "exclude": [ - "node_modules", - "__test__/" - ], - "references": [ - { - "path": "../api-response-transform" - }, - { - "path": "../../biomedical_id_resolver" - }, - { - "path": "../smartapi-kg" - } - ] -} diff --git a/scripts/tsconfig.json_node-expansion b/scripts/tsconfig.json_node-expansion deleted file mode 100644 index 30c4f5d2..00000000 --- a/scripts/tsconfig.json_node-expansion +++ /dev/null @@ -1,16 +0,0 @@ -{ - "extends": "../../../tsconfig.opts.json", - "compilerOptions": { - "rootDir": "src", - "outDir": "built" - }, - "include": [ - "./src/**/*" - ], - "exclude": [ - "node_modules", - "__test__/" - ], - "references": [ - ] -} diff --git a/src/app.js b/src/app.js deleted file mode 100644 index 454e7b7c..00000000 --- a/src/app.js +++ /dev/null @@ -1,15 +0,0 @@ -const express = require('express'); -const Config = require("./config/index"); -const { routes } = require("./routes/index"); - - -class App { - constructor() { - this.app = express(); - this.config = new Config(this.app); - this.app = this.config.setConfig(); - routes.setRoutes(this.app); - } -} - -module.exports = new App().app; diff --git a/src/config/apis.js b/src/config/apis.js deleted file mode 100644 index 59813cd7..00000000 --- a/src/config/apis.js +++ /dev/null @@ -1,248 +0,0 @@ -// APIs in this list are accessible by the main endpoints v1/query and v1/asyncquery -exports.API_LIST = { - include: [ // enabled for use in general and by_team endpoints - // external (not Su / Wu Lab), non-TRAPI APIs - // annotated with SmartAPI x-bte - // also accessible by v1/team/Service Provider/ endpoints and by api-specific endpoints - { - id: 'd22b657426375a5295e7da8a303b9893', - name: 'BioLink API' - // also known as Monarch: https://monarchinitiative.org/ - // NOT the same as the Biolink-model - }, - { - id: '0212611d1c670f9107baf00b77f0889a', - name: 'CTD API', - primarySource: true - }, - { - id: '43af91b3d7cae43591083bff9d75c6dd', - name: 'EBI Proteins API' - }, - { - id: 'dca415f2d792976af9d642b7e73f7a41', - name: 'LitVar API' - }, - { - id: '1f277e1563fcfd124bfae2cc3c4bcdec', - name: 'QuickGO API' - }, - { - id: '1c056ffc7ed0dd1229e71c4752239465', - name: 'Ontology Lookup Service API' - }, - // internal (Su / Wu Lab), non-TRAPI: "pending" BioThings APIs - // annotated with SmartAPI x-bte - // also accessible by v1/team/Service Provider/ endpoints and by api-specific endpoints - { - id: '38e9e5169a72aee3659c9ddba956790d', - name: 'BioThings BindingDB API' - }, - { - id: '55a223c6c6e0291dbd05f2faf27d16f4', - name: 'BioThings BioPlanet Pathway-Disease API' - }, - { - id: 'b99c6dd64abcefe87dcd0a51c249ee6d', - name: 'BioThings BioPlanet Pathway-Gene API' - }, - { - id: '00fb85fc776279163199e6c50f6ddfc6', - name: 'BioThings DDInter API' - }, - { - id: 'e3edd325c76f2992a111b43a907a4870', - name: 'BioThings DGIdb API' - }, - { - id: 'a7f784626a426d054885a5f33f17d3f8', - name: 'BioThings DISEASES API' - }, - { - id: '1f47552dabd67351d4c625adb0a10d00', - name: 'BioThings EBIgene2phenotype API' - }, - { - id: 'cc857d5b7c8b7609b5bbb38ff990bfff', - name: 'BioThings GO Biological Process API' - }, - { - id: 'f339b28426e7bf72028f60feefcd7465', - name: 'BioThings GO Cellular Component API' - }, - { - id: '34bad236d77bea0a0ee6c6cba5be54a6', - name: 'BioThings GO Molecular Function API' - }, - { - id: '316eab811fd9ef1097df98bcaa9f7361', - name: 'BioThings GTRx API' - }, - { - id: 'a5b0ec6bfde5008984d4b6cde402d61f', - name: 'BioThings HPO API' - }, - { - id: '32f36164fabed5d3abe6c2fd899c9418', - name: 'BioThings IDISK API' - }, - { - id: '77ed27f111262d0289ed4f4071faa619', - name: 'BioThings MGIgene2phenotype API' - }, - { - id: 'edeb26858bd27d0322af93e7a9e08761', - name: 'BioThings PFOCR API' - }, - { - id: 'b772ebfbfa536bba37764d7fddb11d6f', - name: 'BioThings RARe-SOURCE API' - }, - { - id: '03283cc2b21c077be6794e1704b1d230', - name: 'BioThings Rhea API' - }, - { - id: '1d288b3a3caf75d541ffaae3aab386c8', - name: 'BioThings SEMMEDDB API' - }, - { - id: 'ec6d76016ef40f284359d17fbf78df20', - name: 'BioThings UBERON API' - }, - // internal (Su / Wu Lab), non-TRAPI: Core BioThings APIs - // annotated with SmartAPI x-bte - // also accessible by v1/team/Service Provider/ endpoints and by api-specific endpoints - { - id: '8f08d1446e0bb9c2b323713ce83e2bd3', - name: 'MyChem.info API' - }, - { - id: '671b45c0301c8624abbd26ae78449ca2', - name: 'MyDisease.info API' - }, - { - id: '59dce17363dce279d389100834e43648', - name: 'MyGene.info API' - }, - { - id: '09c8782d9f4027712e65b95424adba79', - name: 'MyVariant.info API' - }, - // non-TRAPI: pending BioThings APIs made in collab with Multiomics Provider - // annotated with SmartAPI x-bte - // also accessible by v1/team/Service Provider/ and v1/team/Multiomics Provider endpoints, and by api-specific endpoints - { - id: 'adf20dd6ff23dfe18e8e012bde686e31', - name: 'Multiomics BigGIM-DrugResponse KP API' - }, - { - id: '08a5ddcde71b4bf838327ef469076acd', - name: 'Multiomics ClinicalTrials KP' - }, - { - id: 'd86a24f6027ffe778f84ba10a7a1861a', - name: 'Multiomics EHR Risk KP API' - }, - { - id: '02af7d098ab304e80d6f4806c3527027', - name: 'Multiomics Wellness KP API' - }, - // non-TRAPI: pending BioThings APIs made in collab with Text Mining Provider - // annotated with SmartAPI x-bte - // also accessible by v1/team/Service Provider/ and v1/team/Text Mining Provider endpoints, and by api-specific endpoints - { - id: '978fe380a147a8641caf72320862697b', - name: 'Text Mining Targeted Association API' - }, - // TRAPI (Translator standard) APIs: Automat - // not accessible by team or api-specific endpoints - // Notes: We don't ingest the following: - // - Automat-robokop: seems to repeat a lot of data that is in the other APIs - { - // this API overlaps with our Biolink API registration, but we have bugs with our api-response-transform - // this may have been updated more recently / transformed data into TRAPI format - id: 'ef0656900ff73f861611bcad87a94bce', - name: 'Automat-biolink(Trapi v1.4.0)' - }, - { - // this may overlap with info we have in MyDisease, MyChem, and other APIs... - id: '97da45e75266b021fae885735befad07', - name: 'Automat-ctd(Trapi v1.4.0)' - }, - { - id: 'a80b9c70e756453d1ce8971b59fe1778', - name: 'Automat-drug-central(Trapi v1.4.0)' - }, - { - id: '2575e053d0a631433b447995e1bc9602', - name: 'Automat-gtex(Trapi v1.4.0)' - }, - { - id: '387f7a2c21656ddfcce5ccf9ea459049', - name: 'Automat-gtopdb(Trapi v1.4.0)' - }, - { - id: 'cd9fc0ca8cc6d9f56bd56a34766de791', - name: 'Automat-gwas-catalog(Trapi v1.4.0)' - }, - { - id: '8a1e2c2eade9fe3a932ba1dbb7f85688', - name: 'Automat-hetio(Trapi v1.4.0)' - }, - { - id: '067d3a847117c6f42896cc8cd140a704', - name: 'Automat-hgnc(Trapi v1.4.0)' - }, - { - id: '0658e8749b9601a5faba5157ba12eb06', - name: 'Automat-hmdb(Trapi v1.4.0)' - }, - { - // this API overlaps with our BioThings GO APIs, but - // may have been updated more recently / transformed data into TRAPI format - id: '43cf256c660cc5bdeac23fdd3063d474', - name: 'Automat-human-goa(Trapi v1.4.0)' - }, - { - id: '76a164ff43e7ab39a5b98a782f6361bf', - name: 'Automat-icees-kg(Trapi v1.4.0)' - }, - { - id: '0b0a4d48ccd9ad2fd34ee53c34f87e94', - name: 'Automat-intact(Trapi v1.4.0)' - }, - { - id: '26ca4939d437c411bcb65b85a9dc2b99', - name: 'Automat-panther(Trapi v1.4.0)' - }, - { - id: '1c71f68839a44b1b857e79ae7f7e3381', - name: 'Automat-pharos(Trapi v1.4.0)' - }, - { - id: '465ff6de7ddf35ca8b2df6c0b01e6554', - name: 'Automat-viral-proteome(Trapi v1.4.0)' - }, - // TRAPI (Translator standard) APIs: COHD - // not accessible by team or api-specific endpoints - // notes on COHD: - // - DON'T INGEST 'Columbia Open Health Data (COHD)'/70117385218edc9bc01633829011dfcf - // IT IS NOT TRAPI (and may be outdated?) - // - COHD for COVID-19 should work but BTE gets a 500 when retrieving meta_knowledge_graph... - // smartapi ID fc8245e92c970298449294fc04211869 - { - id: 'af364143267ad5235bf78c1511223875', - name: 'COHD TRAPI' - }, - // TRAPI (Translator standard) APIs: CHP - // not accessible by team or api-specific endpoints - { - id: '23f770568b92b7a82063989b3ddd9706', - name: 'Connections Hypothesis Provider API' - }, - ], - exclude: [ // explicitly disabled for use even in by_api endpoint. for TRAPI and APIs annotated with SmartAPI x-bte - - ] -}; diff --git a/src/config/index.js b/src/config/index.js deleted file mode 100644 index 5d142b19..00000000 --- a/src/config/index.js +++ /dev/null @@ -1,117 +0,0 @@ -const compression = require("compression"); -const cors = require("cors"); -var bodyParser = require("body-parser"); -const rateLimit = require("express-rate-limit"); -const helmet = require("helmet"); -const dotenv = require("dotenv"); -const Sentry = require("@sentry/node"); - -module.exports = class Config { - constructor(app) { - this.app = app; - } - - setConfig() { - this.setSentry(); - this.setTrustProxy(); - this.setDotEnv(); - this.setNodeEnv(); - this.setBodyParser(); - this.setCors(); - this.setCompression(); - this.setHttpHeaders(); - this.setLimiter(); - return this.app; - } - - setDotEnv() { - dotenv.config(); - } - - setNodeEnv() { - process.env.NODE_ENV = process.env.NODE_ENV || "development"; - } - - setTrustProxy() { - this.app.set("trust proxy", ["loopback", "linklocal", "uniquelocal"]); - } - - setBodyParser() { - // support application/json type post data - this.app.use(bodyParser.json({ limit: "50mb" })); - //support application/x-www-form-urlencoded post data - this.app.use(bodyParser.urlencoded({ limit: "50mb", extended: true })); - return this.app; - } - - setCors() { - const options = { - allowedHeaders: ["Origin", "X-Requested-With", "Content-Type", "Accept", "X-Access-Token", "Authorization"], - credentials: true, - methods: "GET,HEAD,OPTIONS,PUT,PATCH,POST,DELETE", - origin: "*", - preflightContinue: false, - }; - this.app.use(cors(options)); - } - - setCompression() { - this.app.use(compression()); - } - - setHttpHeaders() { - this.app.use( - helmet({ - contentSecurityPolicy: false, - }), - ); - } - - setLimiter() { - const slowLimiter = rateLimit({ - windowMs: 1 * 60 * 1000, //1min - max: process.env.MAX_QUERIES_PER_MIN || 15, - }); - const medLimiter = rateLimit({ - windowMs: 1 * 60 * 1000, //1min - max: process.env.MAX_QUERIES_PER_MIN || 30, - }); - const fastLimiter = rateLimit({ - windowMs: 1 * 60 * 1000, //1min - max: process.env.MAX_QUERIES_PER_MIN || 60, - }); - this.app.use("/v1/query", slowLimiter); - this.app.use("/v1/team/:team_name/query", slowLimiter); - this.app.use("/v1/team/:team_name/query", slowLimiter); - this.app.use("/v1/meta_knowledge_graph", medLimiter); - this.app.use("/v1/team/:teamName/meta_knowledge_graph", medLimiter); - this.app.use("/v1/smartapi/:smartapiID/meta_knowledge_graph", medLimiter); - } - - setSentry() { - // use SENTRY_DSN environment variable - Sentry.init({ - // dsn: "https://5297933ef0f6487c9fd66532bb1fcefe@o4505444772806656.ingest.sentry.io/4505449737420800", - integrations: [ - // enable HTTP calls tracing - new Sentry.Integrations.Http({ tracing: true }), - // enable Express.js middleware tracing - new Sentry.Integrations.Express({ app: this.app }), - // Automatically instrument Node.js libraries and frameworks - ...Sentry.autoDiscoverNodePerformanceMonitoringIntegrations(), - ], - - // Set tracesSampleRate to 1.0 to capture 100% - // of transactions for performance monitoring. - // We recommend adjusting this value in production - tracesSampleRate: process.env.EXPRESS_SAMPLE_RATE ? parseFloat(process.env.EXPRESS_SAMPLE_RATE) : 1.0, - environment: process.env.INSTANCE_ENV - }); - - // RequestHandler creates a separate execution context, so that all - // transactions/spans/breadcrumbs are isolated across requests - this.app.use(Sentry.Handlers.requestHandler({ user: false })); - // TracingHandler creates a trace for every incoming request - this.app.use(Sentry.Handlers.tracingHandler()); - } -}; diff --git a/src/config/smartapi_exclusions.js b/src/config/smartapi_exclusions.js deleted file mode 100644 index b9d3b22d..00000000 --- a/src/config/smartapi_exclusions.js +++ /dev/null @@ -1,11 +0,0 @@ -exports.EXCLUDE_LIST = [ - // List of TRAPI APIs to be excluded from cron job update. Used specifically so BTE doesn't retrieve itself - { - id: 'dc91716f44207d2e1287c727f281d339', - name: 'BioThings Explorer (BTE) TRAPI' - }, - { - id: '36f82f05705c317bac17ddae3a0ea2f0', - name: 'Service Provider TRAPI' - }, -] diff --git a/src/config/smartapi_overrides.json b/src/config/smartapi_overrides.json deleted file mode 100644 index 36ee72e1..00000000 --- a/src/config/smartapi_overrides.json +++ /dev/null @@ -1,6 +0,0 @@ -{ - "conf": { - "only_overrides": false - }, - "apis": {} -} diff --git a/src/controllers/annotate.js b/src/controllers/annotate.js deleted file mode 100644 index d2de14d2..00000000 --- a/src/controllers/annotate.js +++ /dev/null @@ -1,110 +0,0 @@ -const axios = require("axios"); - -const TYPE_TO_ID_MAPPING = { - "Gene": "NCBIGene", - "SmallMolecule": "CHEBI", - "AnatomicalEntity": "UBERON", - "BiologicalProcess": "GO", - "MolecularActivity": "GO", - "Cell": "CL", - "SequenceVariant": "SO", - "Disease": "MONDO", - "PhenotypicFeature": "HP", -} - -module.exports = class NGDFilter { - constructor(queryResult, criteria) { - this.queryResult = queryResult; - this.criteria = criteria; - } - - extractInputID(resolvedIDs, semanticType) { - if (resolvedIDs === undefined) { - return undefined - } - if (!(semanticType in TYPE_TO_ID_MAPPING)) { - return undefined; - } - if (!("db_ids" in resolvedIDs)) { - return undefined; - } - let prefix = TYPE_TO_ID_MAPPING[semanticType]; - if (!(prefix in resolvedIDs["db_ids"])) { - return undefined; - } - return resolvedIDs.db_ids[prefix][0] - } - - async queryNGD(inputs) { - let result = []; - let i, j, tmp; - for (i = 0, j = inputs.length; i < j; i += 1000) { - let query = { - "q": inputs.slice(i, i + 1000).map(item => item.split('-')), - "scopes": [["subject.id", "object.id"], ["object.id", "subject.id"]], - "fields": "association.ngd", - "dotfield": true - } - const userAgent = `BTE/${process.env.NODE_ENV === 'production' ? 'prod' : 'dev'} Node/${process.version} ${process.platform}`; - tmp = await axios.post("https://biothings.ncats.io/text_mining_co_occurrence_kp/query", - JSON.stringify(query), - { - headers: { - 'Content-Type': 'application/json', - 'User-Agent': userAgent, - } - }) - result = [...result, ...tmp.data]; - } - return result; - } - - parseResponse(res) { - let result = {}; - res.map(rec => { - if ("association.ngd" in rec) { - result[rec["query"].join("-")] = rec["association.ngd"]; - } - }); - return result; - } - - async annotateNGD() { - let ngd_inputs = new Set(); - let id_dict = {}; - if (Array.isArray(this.queryResult) && this.queryResult.length > 0) { - this.queryResult.map((record, i) => { - if ("$association" in record) { - let input_type = record["$association"]["input_type"]; - let output_type = record["$association"]["output_type"]; - let input_resolved_ids = record["$input_resolved_identifiers"][record["$original_input"][record["$input"]]]; - if (!("resolved" in record["$output_id_mapping"])) { - return; - } - let output_resolved_ids = record["$output_id_mapping"]["resolved"]; - let input_id = this.extractInputID(input_resolved_ids, input_type); - let output_id = this.extractInputID(output_resolved_ids, output_type); - if (input_id !== undefined && output_id !== undefined) { - let s_id = String(input_id); - let o_id = String(output_id); - if (input_type === "Gene") { - s_id = 'NCBIGene:' + s_id; - } - if (output_type === "Gene") { - o_id = 'NCBIGene:' + o_id; - } - ngd_inputs.add(s_id + '-' + o_id); - id_dict[i] = s_id + '-' + o_id; - } - } - }); - let ngd_results = await this.queryNGD(Array.from(ngd_inputs)); - let parsed_ngd_results = this.parseResponse(ngd_results); - this.queryResult.map((rec, i) => { - if (i in id_dict) { - rec["$ngd"] = parsed_ngd_results[id_dict[i]]; - } - }) - } - } -} diff --git a/src/controllers/association.js b/src/controllers/association.js deleted file mode 100644 index 9ef7abb7..00000000 --- a/src/controllers/association.js +++ /dev/null @@ -1,44 +0,0 @@ -const meta_kg = require("@biothings-explorer/smartapi-kg"); -const fs = require("fs"); -var path = require('path'); -const util = require('util'); -const readFile = util.promisify(fs.readFile); -const debug = require("debug")("bte:biothings-explorer-trapi:metakg"); - -module.exports = async (sub = undefined, obj = undefined, pred = undefined, component = undefined, api = undefined, source = undefined) => { - const smartapi_specs = path.resolve(__dirname, '../../data/smartapi_specs.json'); - debug(`smartapi specs loaded: ${smartapi_specs}`) - const predicates = path.resolve(__dirname, '../../data/predicates.json'); - debug(`predicates endpoints loaded, ${predicates}`) - const kg = new meta_kg.default(smartapi_specs, predicates); - debug("metakg initialized") - kg.constructMetaKGSync(true, {}); - debug(`metakg loaded: ${kg.ops.length} ops`) - const associations = []; - const filtered_res = kg.filter({ - input_type: sub, - output_type: obj, - predicate: pred, - api_name: api, - source: source, - component: component - }) - filtered_res.map(op => { - associations.push({ - subject: op.association.input_type, - object: op.association.output_type, - predicate: op.association.predicate, - provided_by: op.association.source, - api: { - name: op.association.api_name, - smartapi: { - metadata: op.association.smartapi.meta.url, - id: op.association.smartapi.id, - ui: "https://smart-api.info/ui/" + op.association.smartapi.id - }, - "x-translator": op.association["x-translator"] - } - }); - }) - return associations; -} // test comment please ignore diff --git a/src/controllers/async/asyncquery.js b/src/controllers/async/asyncquery.js deleted file mode 100644 index 84160e53..00000000 --- a/src/controllers/async/asyncquery.js +++ /dev/null @@ -1,225 +0,0 @@ -const axios = require("axios"); -const { customAlphabet } = require("nanoid"); -const utils = require("../../utils/common"); -const { redisClient } = require("@biothings-explorer/query_graph_handler"); -const { LogEntry } = require("@biothings-explorer/query_graph_handler"); -const lz4 = require("lz4"); -const { Readable } = require("stream"); -const chunker = require("stream-chunker"); -const { parser } = require("stream-json"); -const Assembler = require("stream-json/Assembler"); -const Sentry = require("@sentry/node"); -const ErrorHandler = require("../../middlewares/error.js"); - -exports.asyncquery = async (req, res, next, queueData, queryQueue) => { - try { - if (queryQueue) { - const nanoid = customAlphabet("0123456789abcdefghijklmnopqrstuvwxyzABCDEFGHIJKLMNOPQRSTUVWXYZ", 10); - - let jobId = nanoid(); - - // add job to the queue - let url; - if (queryQueue.name === "bte_query_queue_by_api") { - jobId = `BA_${jobId}`; - } - if (queryQueue.name === "bte_query_queue_by_team") { - jobId = `BT_${jobId}`; - } - url = `${req.protocol}://${req.header("host")}/v1/asyncquery_status/${jobId}`; - - let job = await queryQueue.add( - { ...queueData, url: url.replace('status', 'response') }, - { - jobId: jobId, - url: url, - timeout: parseInt(process.env.JOB_TIMEOUT ?? (1000 * 60 * 5).toString()), - removeOnFail: { - age: 24 * 60 * 60, // keep failed jobs for a day (in case user needs to review fail reason) - count: 2000, - }, - removeOnComplete: { - age: 90 * 24 * 60 * 60, // keep completed jobs for 90 days - count: 2000, - }, - }, - ); - res.setHeader("Content-Type", "application/json"); - // return the job id so the user can check on it later - res.end(JSON.stringify({ status: "Accepted", description: "Async query queued", job_id: job.id, job_url: url })); - } else { - res.setHeader("Content-Type", "application/json"); - res.status(503).end(JSON.stringify({ error: "Redis service is unavailable" })); - } - } catch (error) { - next(error); - } -}; - -async function storeQueryResponse(jobID, response, logLevel = null) { - // const lock = await redisClient.client.lock(); - return await redisClient.client.usingLock([`asyncQueryResult:lock:${jobID}`], 600000, async signal => { - const defaultExpirySeconds = String(30 * 24 * 60 * 60); // 30 days - const entries = []; - if (typeof response === "undefined") { - return; - } - // encode each property separately (accessible separately) - await Promise.all( - Object.entries(response).map(async ([key, value]) => { - if (typeof value === "undefined") { - return; - } - const input = Readable.from(JSON.stringify(value)); - await new Promise(resolve => { - let i = 0; - input - // .pipe(encoder) - .pipe(chunker(10000000, { flush: true })) - .on("data", async chunk => { - await redisClient.client.hsetTimeout( - `asyncQueryResult:${jobID}:${key}`, - String(i++), - lz4.encode(chunk).toString("base64url"), - ); - }) - .on("end", () => { - resolve(); - }); - }); - await redisClient.client.expireTimeout( - `asyncQueryResult:${jobID}:${key}`, - process.env.ASYNC_COMPLETED_EXPIRE_TIME || defaultExpirySeconds, - ); - entries.push(key); - }), - ); - // register all keys so they can be properly retrieved - await redisClient.client.setTimeout(`asyncQueryResult:entries:${jobID}`, JSON.stringify(entries)); - await redisClient.client.expireTimeout( - `asyncQueryResult:entries:${jobID}`, - process.env.ASYNC_COMPLETED_EXPIRE_TIME || defaultExpirySeconds, - ); - // remember log_level setting from original query - await redisClient.client.setTimeout(`asyncQueryResult:logLevel:${jobID}`, JSON.stringify(logLevel)); - await redisClient.client.expireTimeout( - `asyncQueryResult:logLevel:${jobID}`, - process.env.ASYNC_COMPLETED_EXPIRE_TIME || defaultExpirySeconds, - ); - }); -} - -exports.getQueryResponse = async (jobID, logLevel = null) => { - return await redisClient.client.usingLock([`asyncQueryResult:lock:${jobID}`], 600000, async signal => { - const entries = await redisClient.client.getTimeout(`asyncQueryResult:entries:${jobID}`); - if (!entries) { - return null; - } - const originalLogLevel = JSON.parse(await redisClient.client.getTimeout(`asyncQueryResult:logLevel:${jobID}`)); - const values = await Promise.all( - JSON.parse(entries).map(async key => { - const value = await new Promise(async resolve => { - const msgDecoded = Object.entries(await redisClient.client.hgetallTimeout(`asyncQueryResult:${jobID}:${key}`)) - .sort(([key1], [key2]) => parseInt(key1) - parseInt(key2)) - .map(([key, val]) => lz4.decode(Buffer.from(val, "base64url")).toString(), ""); - - const msgStream = Readable.from(msgDecoded); - const pipeline = msgStream.pipe(parser()); - const asm = Assembler.connectTo(pipeline); - asm.on("done", asm => resolve(asm.current)); - }); - return [key, value]; - }), - ); - const response = Object.fromEntries(values); - if (response.logs && logLevel) { - utils.filterForLogLevel(response, logLevel); - } else if (response.logs && originalLogLevel) { - utils.filterForLogLevel(response, originalLogLevel); - } - return response ? response : undefined; - }); -}; - -exports.asyncqueryResponse = async (handler, callback_url, jobID = null, jobURL = null, queryGraph = null) => { - let response; - let callback_response; - try { - await handler.query(); - response = handler.getResponse(); - if (jobURL) { - response.logs.unshift(new LogEntry("INFO", null, `job results available at: ${jobURL}`).getLog()); - } - if (jobID) { - await storeQueryResponse(jobID, response, handler.options.logLevel); - } - } catch (e) { - console.error(e); - - if (ErrorHandler.shouldHandleError(e)) { - Sentry.captureException(e); - } - - //shape error > will be handled below - response = { - message: { - query_graph: queryGraph, - knowledge_graph: { nodes: {}, edges: {} }, - results: [], - }, - status: "Failed", - schema_version: global.SCHEMA_VERSION, - biolink_version: global.BIOLINK_VERSION, - workflow: [{ id: 'lookup' }], - description: e.toString(), - trace: process.env.NODE_ENV === "production" ? undefined : e.stack, - }; - - if (jobID) { - await storeQueryResponse(jobID, response); - } - - throw e; - } - - if (callback_url) { - if (!utils.stringIsAValidUrl(callback_url)) { - return { - response: "TRAPI Execution complete", - status: 200, - callback: "The callback url must be a valid url", - }; - } - try { - const userAgent = `BTE/${process.env.NODE_ENV === "production" ? "prod" : "dev"} Node/${process.version} ${ - process.platform - }`; - callback_response = await axios.post(callback_url, JSON.stringify(response), { - headers: { - "Content-Type": "application/json", - "User-Agent": userAgent, - }, - timeout: 300000, // 5min - maxBodyLength: 2 * 1000 * 1000 * 1000, // 2GB - }); - //console.log(res) - } catch (e) { - return { - response: "TRAPI Execution complete", - status: e.response?.status, - callback: `Request failed, received code ${e.response?.status}`, - }; - } - } else { - return { - response: "TRAPI Execution complete", - status: 200, - callback: "Callback url was not provided", - }; - } - return { - response: "TRAPI Execution complete", - status: callback_response?.status, - callback: "Data sent to callback_url", - }; -}; diff --git a/src/controllers/async/asyncquery_queue.js b/src/controllers/async/asyncquery_queue.js deleted file mode 100644 index 54620bdd..00000000 --- a/src/controllers/async/asyncquery_queue.js +++ /dev/null @@ -1,88 +0,0 @@ -const Queue = require("bull"); -const axios = require("axios"); -const { redisClient, getNewRedisClient } = require("@biothings-explorer/query_graph_handler"); -const debug = require("debug")("bte:biothings-explorer-trapi:asyncquery_queue"); -const Redis = require("ioredis"); -const ps = require("ps-node"); - -global.queryQueue = {}; - -exports.getQueryQueue = name => { - let queryQueue = null; - if (!redisClient.clientEnabled || process.env.INTERNAL_DISABLE_REDIS) { - return queryQueue; - } - debug( - `Getting queue ${name} using redis in ${process.env.REDIS_CLUSTER === "true" ? "cluster" : "non-cluster"} mode`, - ); - if (global.queryQueue[name]) { - return global.queryQueue[name]; - } - debug(`Initializing queue ${name} for first time...`); - let details = { - createClient: () => { - const client = getNewRedisClient(); - client.internalClient.options.enableReadyCheck = false; - client.internalClient.options.maxRetriesPerRequest = null; - return client.internalClient; - }, - // createClient: () => redis.createCluster({ - // }), - prefix: `{BTE:bull}`, - }; - global.queryQueue[name] = new Queue(name, process.env.REDIS_HOST ? details : "redis://127.0.0.1:6379", { - defaultJobOptions: { - removeOnFail: { - age: 24 * 60 * 60, // keep failed jobs for a day (in case user needs to review fail reason) - count: 2000 - }, - removeOnComplete: { - age: 90 * 24 * 60 * 60, // keep completed jobs for 90 days - count: 2000 - }, - }, - settings: { - maxStalledCount: 1, - //lockDuration: 300000 - lockDuration: 3600000, // 60min - }, - }) - .on("error", function (error) { - console.log("err", error); - }) - .on("failed", async function (job, error) { - debug(`Async job ${job.id} failed with error ${error.message}`); - try { - job.data.abortController.abort(); - } catch (error) { - debug(error); - } - if (job.data.callback_url) { - const logs = await global.queryQueue[name]?.getJobLogs(job.id)?.logs?.map(log => JSON.parse(log)); - try { - await axios({ - method: "post", - url: job.data.callback_url, - schema_version: global.SCHEMA_VERSION, - biolink_version: global.BIOLINK_VERSION, - workflow: [{ id: 'lookup' }], - logs: logs, - data: { - message: { - query_graph: job.data.queryGraph, - knowledge_graph: { nodes: {}, edges: {} }, - results: [], - }, - status: "Failed", - description: error.toString(), - trace: process.env.NODE_ENV === "production" ? undefined : error.stack, - } - }); - } catch (error) { - debug(`Callback failed with error ${error.message}`); - } - } - }); - - return global.queryQueue[name]; -}; diff --git a/src/controllers/cron/index.js b/src/controllers/cron/index.js deleted file mode 100644 index 3c7f045d..00000000 --- a/src/controllers/cron/index.js +++ /dev/null @@ -1,5 +0,0 @@ -const smartapiCron = require("./update_local_smartapi"); - -module.exports = () => { - smartapiCron(); -} \ No newline at end of file diff --git a/src/controllers/cron/update_local_smartapi.js b/src/controllers/cron/update_local_smartapi.js deleted file mode 100644 index 10f57c2c..00000000 --- a/src/controllers/cron/update_local_smartapi.js +++ /dev/null @@ -1,379 +0,0 @@ -const debug = require("debug")("bte:biothings-explorer-trapi:cron"); -const axios = require("axios"); -const fs = require("fs"); -var path = require("path"); -const cron = require("node-cron"); -const util = require("util"); -const readFile = util.promisify(fs.readFile); -const yaml = require("js-yaml"); -var url = require("url"); -const validUrl = require("valid-url"); -const config = require("../../config/smartapi_exclusions"); - -const userAgent = `BTE/${process.env.NODE_ENV === "production" ? "prod" : "dev"} Node/${process.version} ${ - process.platform -}`; - -const getServerFromSpec = spec => { - const productionLevel = process.env.INSTANCE_ENV ?? ""; - - const getLevel = maturity => { - switch (productionLevel) { - case "test": - if (maturity == "testing") return 0; - if (maturity == "production") return 1; - return 10000; - case "ci": - if (maturity == "staging") return 0; - if (maturity == "testing") return 1; - if (maturity == "production") return 2; - return 10000; - case "dev": - if (maturity == "development") return 0; - if (maturity == "staging") return 1; - if (maturity == "testing") return 2; - if (maturity == "production") return 3; - return 10000; - default: - if (maturity == "production") return 0; - return 10000; - } - }; - - const servers = spec.servers.map(server => ({ - url: server.url, - level: getLevel(server["x-maturity"] ?? "production"), - maturity: server["x-maturity"] ?? "production", - https: server.url.includes("https"), - })); - - const sorted_servers = servers.sort((a, b) => { - if (a.level != b.level) return a.level - b.level; - if (a.https != b.https) return a.https ? -1 : 1; - return 0; - }); - - if (sorted_servers[0].level == 10000) { - throw new Error( - `Server ${sorted_servers[0].url} skipped due to insufficient maturity level ${sorted_servers[0].maturity}`, - ); - } - return sorted_servers[0].url; -}; - -const getTRAPIWithPredicatesEndpoint = specs => { - const trapi = []; - let excluded_list = config.EXCLUDE_LIST.map(api => api.id); - specs.map(spec => { - try { - if ( - "info" in spec && - "x-translator" in spec.info && - spec.info["x-translator"].component === "KP" && - "paths" in spec && - "/query" in spec.paths && - "x-trapi" in spec.info && - spec.servers.length && - "/meta_knowledge_graph" in spec.paths && - !excluded_list.includes(spec._id) && - getServerFromSpec(spec) - ) { - let api = { - association: { - api_name: spec.info.title, - smartapi: { - id: spec._id, - meta: spec._meta, - }, - "x-translator": { - component: "KP", - team: spec.info["x-translator"].team, - infores: spec.info["x-translator"].infores - }, - "x-trapi": { - batch_size_limit: spec.info["x-trapi"].batch_size_limit, - rate_limit: spec.info["x-trapi"].rate_limit, - }, - }, - tags: spec.tags.map(item => item.name), - query_operation: { - path: "/query", - server: getServerFromSpec(spec), - method: "post", - }, - }; - // check TRAPI latest accepted version - if ("/meta_knowledge_graph" in spec.paths) { - if ( - (Object.prototype.hasOwnProperty.call(spec.info["x-trapi"], "version") && - spec.info["x-trapi"].version.includes("1.4")) - ) { - api["predicates_path"] = "/meta_knowledge_graph"; - trapi.push(api); - } - } else { - debug(`[error]: Unable to parse spec, ${spec ? spec.info.title : spec}. Endpoint required not found.`); - } - } - } catch (err) { - debug(`[error]: Unable to parse spec, ${spec ? spec.info.title : spec}. Error message is ${err.toString()}`); - } - }); - return trapi; -}; - -const constructQueryUrl = (serverUrl, path) => { - if (serverUrl.endsWith("/")) { - serverUrl = serverUrl.slice(0, -1); - } - return serverUrl + path; -}; - -const getPredicatesFromGraphData = (predicate_endpoint, data) => { - //if /predicates just return normal response - if (predicate_endpoint !== "/meta_knowledge_graph") { - return data; - } - // transform graph data to legacy format > object.subject : predicates - const predicates = {}; - - const addNewPredicates = edge => { - if (edge.knowledge_types && Array.isArray(edge.knowledge_types)) { - if (!edge.knowledge_types.includes("lookup")) { - return; - } - } - if (!Object.prototype.hasOwnProperty.call(predicates, edge.object)) { - predicates[edge.object] = {}; - } - if (Array.isArray(predicates[edge.object][edge.subject])) { - predicates[edge.object][edge.subject].push({predicate: edge.predicate, qualifiers: edge.qualifiers}); - } else { - predicates[edge.object][edge.subject] = [{predicate: edge.predicate, qualifiers: edge.qualifiers}]; - } - }; - - if (Object.prototype.hasOwnProperty.call(data, "edges")) { - data.edges.forEach(edge => addNewPredicates(edge)); - } else { - //some apis still redirect to previous format - return data; - } - return predicates; -}; - -const getOpsFromEndpoint = async metadata => { - return axios - .get(constructQueryUrl(metadata.query_operation.server, metadata.predicates_path), { timeout: 10000 }) - .then(res => { - if (res.status === 200) { - debug(`Successfully got ${metadata.predicates_path} for ${metadata.query_operation.server}`); - return { - ...metadata, - ...{ predicates: getPredicatesFromGraphData(metadata.predicates_path, res.data) }, - nodes: res.data.nodes, - }; - } - debug( - `[error]: API "${metadata.association.api_name}" Unable to get ${metadata.predicates_path}` + - ` for ${metadata.query_operation.server} due to query failure with status code ${res.status}`, - ); - return false; - }) - .catch(err => { - debug( - `[error]: API "${metadata.association.api_name}" failed to get ${metadata.predicates_path} for ${ - metadata.query_operation.server - } due to error ${err.toString()}`, - ); - return false; - }); -}; - -const getOpsFromPredicatesEndpoints = async specs => { - const metadatas = getTRAPIWithPredicatesEndpoint(specs); - let res = []; - debug(`Now caching predicates from ${metadatas.length} TRAPI APIs`); - await Promise.allSettled(metadatas.map(metadata => getOpsFromEndpoint(metadata))).then(results => { - results.map(rec => { - if (rec.status === "fulfilled" && rec.value) { - res.push(rec.value); - } - }); - }); - debug(`Got ${res.length} successful requests`); - return res; -}; - -const updateSmartAPISpecs = async () => { - const SMARTAPI_URL = - "https://smart-api.info/api/query?q=tags.name:translator&size=1000&sort=_seq_no&raw=1&fields=paths,servers,tags,components.x-bte*,info,_meta"; - const overridesPath = path.resolve(__dirname, "../../config/smartapi_overrides.json"); - let overrides; - try { - overrides = JSON.parse(await readFile(overridesPath)); - } catch (error) { - debug(`ERROR getting API Overrides file because ${error}`); - return; - } - let res = await axios.get(SMARTAPI_URL, { headers: { "User-Agent": userAgent } }).catch(err => { - if (process.env.API_OVERRIDE === "true" && overrides.conf.only_overrides === true) { - debug(`SmartAPI request failed, creating specs from overrides config.`); - return { data: [] }; - } else { - debug(`SmartAPI request failed.`); - throw err.message; - } - }); - const localFilePath = path.resolve(__dirname, "../../../data/smartapi_specs.json"); - const predicatesFilePath = path.resolve(__dirname, "../../../data/predicates.json"); - const writeFunc = process.env.SYNC_AND_EXIT === "true" ? fs.writeFileSync : fs.writeFile; - if (process.env.API_OVERRIDE === "true") { - await getAPIOverrides(res.data); - } - debug(`Retrieved ${res.data.total} SmartAPI records`); - //clean _score fields - const hits = res.data.hits; - hits.forEach(function (obj) { - delete obj._score; - }); - writeFunc(localFilePath, JSON.stringify({ hits: hits }), err => { - if (err) throw err; - }); - const predicatesInfo = await getOpsFromPredicatesEndpoints(res.data.hits); - writeFunc(predicatesFilePath, JSON.stringify(predicatesInfo), err => { - if (err) throw err; - }); -}; - -const getAPIOverrides = async data => { - const overridesPath = path.resolve(__dirname, "../../config/smartapi_overrides.json"); - let overrides; - try { - overrides = JSON.parse(await readFile(overridesPath)); - } catch (error) { - debug(`ERROR getting API Overrides file because ${error}`); - return; - } - // if only_overrides is enabled, only overridden apis are used - if (overrides.conf.only_overrides) { - debug("Override specifies removal of undeclared APIs"); - data.hits = []; - } - await Promise.all( - Object.keys(overrides.apis).map(async id => { - let override; - try { - const filepath = path.resolve(url.fileURLToPath(overrides.apis[id])); - override = yaml.load(await readFile(filepath)); - } catch (e1) { - if (e1 instanceof TypeError) { - if (validUrl.isWebUri(overrides.apis[id])) { - try { - override = yaml.load((await axios.get(overrides.apis[id])).data, { - headers: { "User-Agent": userAgent }, - }); - } catch (weberror) { - debug(`ERROR getting URL-hosted override for API ID ${id} because ${weberror}`); - return; - } - } else { - try { - const filepath = path.resolve(overrides.apis[id]); - override = yaml.load(await readFile(filepath)); - } catch (filerror) { - debug(`ERROR getting local file override for API ID ${id} because ${filerror}`); - return; - } - } - } else { - debug(`ERROR getting 'file:///' override for API ID ${id} because ${e1}`); - return; - } - } - debug(`Successfully got override ${id} from ${overrides.apis[id]}`); - override._id = id; - override._meta = { - date_created: undefined, - last_updated: undefined, - url: overrides.apis[id], - username: undefined, - }; - const index = overrides.conf.only_overrides ? -1 : data.hits.findIndex(hit => hit._id === id); - if (index === -1) { - debug(`[warning] Overridden API ID ${id} not recognized, appending as new API hit.`); - data.hits.push(override); - } else { - data.hits[index] = override; - } - return; - }), - ); -}; - -module.exports = () => { - // not meant to be used with server started - // rather, if just this function is imported and run (e.g. using workspace script) - let sync_and_exit = process.env.SYNC_AND_EXIT === "true"; - if (sync_and_exit) { - console.log("Syncing SmartAPI specs with subsequent exit..."); - updateSmartAPISpecs() - .then(() => { - console.log("SmartAPI sync successful."); - process.exit(0); - }) - .catch(err => { - debug(`Updating local copy of SmartAPI specs failed! The error message is ${err.toString()}`); - }); - return; - } - - let schedule_sync = process.env.NODE_ENV === "production"; - let manual_sync = - process.env.SMARTAPI_SYNC === "true" ? true : process.env.SMARTAPI_SYNC === "false" ? false : undefined; - let api_override = process.env.API_OVERRIDE === "true"; - let disable_smartapi_sync = !(manual_sync || (schedule_sync && typeof manual_sync === "undefined")); - if (disable_smartapi_sync) { - debug(`SmartAPI sync disabled, server process ${process.pid} disabling smartapi updates.`); - } else { - if (process.env.INSTANCE_ID) { - // check if it's a PM2 cluster node and in this case, - // only instance #0 will sync from SmartAPI - disable_smartapi_sync = process.env.INSTANCE_ID !== "0"; - if (disable_smartapi_sync) { - debug(`Running as a children process, server process ${process.pid} disabling smartapi updates.`); - } - } - } - - if (!disable_smartapi_sync) { - cron.schedule("*/10 * * * *", async () => { - debug(`Updating local copy of SmartAPI specs now at ${new Date().toUTCString()}!`); - try { - await updateSmartAPISpecs(); - debug("Successfully updated the local copy of SmartAPI specs."); - } catch (err) { - debug(`Updating local copy of SmartAPI specs failed! The error message is ${err.toString()}`); - } - }); - - if (api_override) { - const overridesPath = path.resolve(__dirname, "../../config/smartapi_overrides.json"); - let overrides; - try { - overrides = JSON.parse(fs.readFileSync(overridesPath)); - } catch (error) { - debug(`ERROR getting API Overrides file because ${error}`); - return; - } - if (Object.keys(overrides.apis).length > 0) { - debug(`API Override(s) set. Updating local SmartAPI specs with overrides now at ${new Date().toUTCString()}!`); - try { - updateSmartAPISpecs(); - } catch (error) { - debug(`Updating local copy of SmartAPI specs failed! The error message is ${error.toString()}`); - } - } - } - } -}; diff --git a/src/controllers/ids.js b/src/controllers/ids.js deleted file mode 100644 index 880715f4..00000000 --- a/src/controllers/ids.js +++ /dev/null @@ -1,277 +0,0 @@ -module.exports = { - Gene: { - id_ranks: ['NCBIGene', 'ENSEMBL', 'HGNC', 'SYMBOL', 'OMIM', 'UniProtKB', 'UMLS', 'MGI', 'name'], - semantic: 'Gene', - api_name: 'mygene.info', - url: 'https://mygene.info/v3/query', - mapping: { - NCBIGene: ['entrezgene'], - name: ['name'], - SYMBOL: ['symbol'], - UMLS: ['umls.cui', 'umls.protein_cui'], - HGNC: ['HGNC'], - UniProtKB: ['uniprot.Swiss-Prot'], - ENSEMBL: ['ensembl.gene'], - OMIM: ['MIM'], - MGI: ['MGI'], - }, - additional_attributes_mapping: { - interpro: ['interpro.desc'], - type_of_gene: ['type_of_gene'], - }, - }, - Transcript: { - id_ranks: ['ENSEMBL', 'SYMBOL', 'name'], - semantic: 'Transcript', - api_name: 'mygene.info', - url: 'https://mygene.info/v3/query', - mapping: { - ENSEMBL: ['ensembl.transcript'], - SYMBOL: ['symbol'], - name: ['name'], - }, - additional_attributes_mapping: { - interpro: ['interpro.desc'], - }, - }, - Protein: { - id_ranks: ['UniProtKB', 'ENSEMBL', 'SYMBOL', 'UMLS', 'name'], - semantic: 'Protein', - api_name: 'mygene.info', - url: 'https://mygene.info/v3/query', - mapping: { - name: ['name'], - SYMBOL: ['symbol'], - UMLS: ['umls.cui', 'umls.protein_cui'], - UniProtKB: ['uniprot.Swiss-Prot'], - ENSEMBL: ['ensembl.protein'], - }, - additional_attributes_mapping: { - interpro: ['interpro.desc'], - }, - }, - SequenceVariant: { - id_ranks: ['HGVS', 'DBSNP', 'MYVARIANT_HG19', 'CLINVAR'], - api_name: 'myvariant.info', - semantic: 'SequenceVariant', - url: 'https://myvariant.info/v1/query', - mapping: { - MYVARIANT_HG19: ['_id'], - DBSNP: ['dbsnp.rsid', 'clinvar.rsid', 'dbnsfp.rsid'], - HGVS: ['clinvar.hgvs.genomic', 'clinvar.hgvs.protein', 'clinvar.hgvs.coding', 'dbnsfp.clinvar.hgvs'], - ClINVAR: ['clinvar.rcv.accession'], - }, - additional_attributes_mapping: { - cadd_consequence: ['cadd.consequence'], - cadd_variant_type: ['cadd.type'], - dbsnp_variant_type: ['dbsnp.vartype'], - clinvar_clinical_significance: ['clinvar.rcv.clinical_significance'], - sift_category: ['cadd.sift.cat'], - }, - }, - SmallMolecule: { - id_ranks: ['CHEBI', 'CHEMBL.COMPOUND', 'DRUGBANK', 'PUBCHEM.COMPOUND', 'MESH', 'INCHI', 'INCHIKEY', 'UNII', 'KEGG.COMPOUND', 'UMLS', 'LINCS', 'CAS', 'HMDB', 'name'], - semantic: 'SmallMolecule', - api_name: 'mychem.info', - url: 'https://mychem.info/v1/query', - mapping: { - 'CHEMBL.COMPOUND': ['chembl.molecule_chembl_id', 'drugbank.xrefs.chembl', 'drugcentral.xrefs.chembl_id', 'unichem.chembl'], - DRUGBANK: ['drugcentral.xrefs.drugbank_id', 'pharmgkb.xrefs.drugbank', 'chebi.xrefs.drugbank', 'drugbank.id', 'unichem.drugbank'], - 'PUBCHEM.COMPOUND': ['pubchem.cid', 'drugbank.xrefs.pubchem.cid', 'drugcentral.xrefs.pubchem_cid', 'pharmgkb.xrefs.pubchem.cid', 'chebi.xrefs.pubchem.cid', 'unichem.pubchem'], - CHEBI: ['chebi.id', 'chembl.chebi_par_id', 'drugbank.xrefs.chebi', 'drugcentral.xrefs.chebi', 'pharmgkb.xrefs.chebi', 'unichem.chebi'], - UMLS: ['drugcentral.xrefs.umlscui', 'pharmgkb.xrefs.umls', 'umls.cui'], - MESH: ['umls.mesh', 'drugcentral.xrefs.mesh_descriptor_ui', 'ginas.xrefs.MESH', 'pharmgkb.xrefs.mesh'], - UNII: ['drugcentral.xrefs.unii', 'unii.unii', 'aeolus.unii', 'ginas.unii'], - INCHIKEY: ['drugbank.inchi_key', 'ginas.inchikey', 'unii.inchikey', 'chebi.inchikey', 'chembl.inchi_key', 'pubchem.inchi_key'], - INCHI: ['drugbank.inchi', 'chebi.inchi', 'chembl.inchi', 'pharmgkb.inchi', 'pubchem.inchi'], - 'KEGG.COMPOUND': ['drugbank.xrefs.kegg.cid', 'chebi.xrefs.kegg_compound', 'pharmgkb.xrefs.kegg_compound'], - LINCS: ['unichem.lincs', 'chebi.xrefs.lincs'], - CAS: ['chebi.xrefs.cas', 'ginas.cas_primary', 'pharmgkb.xrefs.cas'], - HMDB: ['chebi.xrefs.hmdb', 'pharmgkb.xrefs.hmdb'], - name: ['chembl.pref_name', 'drugbank.name', 'umls.name', 'ginas.preferred_name', 'pharmgkb.name', 'chebi.name'], - }, - additional_attributes_mapping: { - chembl_max_phase: ['chembl.max_phase'], - chembl_molecule_type: ['chembl.molecule_type'], - drugbank_drug_category: ['drugbank.categories.category'], - drugbank_taxonomy_class: ['drugbank.taxonomy.class'], - drugbank_groups: ['drugbank.groups'], - drugbank_kingdom: ['drugbank.taxonomy.kingdom'], - drugbank_superclass: ['drugbank.taxonomy.superclass'], - contraindications: ['drugcentral.drug_use.contraindication.concept_name'], - indications: ['drugcentral.drug_use.indication.concept_name'], - mesh_pharmacology_class: ['drugcentral.pharmacology_class.mesh_pa.description'], - fda_epc_pharmacology_class: ['drugcentral.pharmacology_class.fda_epc.description'], - }, - }, - Drug: { - id_ranks: ['CHEBI', 'CHEMBL.COMPOUND', 'DRUGBANK', 'PUBCHEM.COMPOUND', 'MESH', 'INCHI', 'INCHIKEY', 'UNII', 'KEGG.COMPOUND', 'UMLS', 'LINCS', 'CAS', 'HMDB', 'RXCUI', 'NDC', 'name'], - semantic: 'Drug', - api_name: 'mychem.info', - url: 'https://mychem.info/v1/query', - mapping: { - 'CHEMBL.COMPOUND': ['chembl.molecule_chembl_id', 'drugbank.xrefs.chembl', 'drugcentral.xrefs.chembl_id', 'unichem.chembl'], - DRUGBANK: ['drugcentral.xrefs.drugbank_id', 'pharmgkb.xrefs.drugbank', 'chebi.xrefs.drugbank', 'drugbank.id', 'unichem.drugbank'], - 'PUBCHEM.COMPOUND': ['pubchem.cid', 'drugbank.xrefs.pubchem.cid', 'drugcentral.xrefs.pubchem_cid', 'pharmgkb.xrefs.pubchem.cid', 'chebi.xrefs.pubchem.cid', 'unichem.pubchem'], - CHEBI: ['chebi.id', 'chembl.chebi_par_id', 'drugbank.xrefs.chebi', 'drugcentral.xrefs.chebi', 'pharmgkb.xrefs.chebi', 'unichem.chebi'], - UMLS: ['drugcentral.xrefs.umlscui', 'pharmgkb.xrefs.umls', 'umls.cui'], - MESH: ['umls.mesh', 'drugcentral.xrefs.mesh_descriptor_ui', 'ginas.xrefs.MESH', 'pharmgkb.xrefs.mesh'], - UNII: ['drugcentral.xrefs.unii', 'unii.unii', 'aeolus.unii', 'ginas.unii'], - INCHIKEY: ['drugbank.inchi_key', 'ginas.inchikey', 'unii.inchikey', 'chebi.inchikey', 'chembl.inchi_key', 'pubchem.inchi_key'], - INCHI: ['drugbank.inchi', 'chebi.inchi', 'chembl.inchi', 'pharmgkb.inchi', 'pubchem.inchi'], - 'KEGG.COMPOUND': ['drugbank.xrefs.kegg.cid', 'chebi.xrefs.kegg_compound', 'pharmgkb.xrefs.kegg_compound'], - LINCS: ['unichem.lincs', 'chebi.xrefs.lincs'], - CAS: ['chebi.xrefs.cas', 'ginas.cas_primary', 'pharmgkb.xrefs.cas'], - HMDB: ['chebi.xrefs.hmdb', 'pharmgkb.xrefs.hmdb'], - RXCUI: ['ginas.xrefs.RXCUI', 'unii.rxcui', 'aeolus.rxcui'], - NDC: ['pharmgkb.xrefs.ndc'], - name: ['chembl.pref_name', 'drugbank.name', 'umls.name', 'ginas.preferred_name', 'pharmgkb.name', 'chebi.name'], - }, - additional_attributes_mapping: { - chembl_max_phase: ['chembl.max_phase'], - chembl_molecule_type: ['chembl.molecule_type'], - drugbank_drug_category: ['drugbank.categories.category'], - drugbank_taxonomy_class: ['drugbank.taxonomy.class'], - drugbank_groups: ['drugbank.groups'], - drugbank_kingdom: ['drugbank.taxonomy.kingdom'], - drugbank_superclass: ['drugbank.taxonomy.superclass'], - contraindications: ['drugcentral.drug_use.contraindication.concept_name'], - indications: ['drugcentral.drug_use.indication.concept_name'], - mesh_pharmacology_class: ['drugcentral.pharmacology_class.mesh_pa.description'], - fda_epc_pharmacology_class: ['drugcentral.pharmacology_class.fda_epc.description'], - }, - }, - PhenotypicFeature: { - id_ranks: ['UMLS', 'SNOMEDCT', 'HP', 'MEDDRA', 'EFO', 'NCIT', 'MESH', 'MP', 'name'], - semantic: 'PhenotypicFeature', - api_name: 'HPO API', - url: 'https://biothings.ncats.io/hpo/query', - mapping: { - UMLS: ['xrefs.umls'], - SNOMEDCT: ['xrefs.snomed_ct', 'xrefs.snomedct_us'], - HP: ['_id'], - MEDDRA: ['xrefs.meddra'], - EFO: ['xrefs.efo'], - NCIT: ['xrefs.ncit'], - MESH: ['xrefs.mesh'], - MP: ['xrefs.mp'], - name: ['name'], - }, - }, - Disease: { - id_ranks: ['MONDO', 'DOID', 'OMIM', 'ORPHANET', 'SNOMEDCT', 'NCIT', 'EFO', 'UMLS', 'MESH', 'HP', 'GARD', 'MEDDRA', 'name'], - semantic: 'Disease', - api_name: 'mydisease.info', - url: 'https://mydisease.info/v1/query', - mapping: { - MONDO: ['mondo.mondo', 'disgenet.xrefs.mondo'], - DOID: ['mondo.xrefs.doid', 'disease_ontology.doid', 'disgenet.xrefs.doid'], - UMLS: ['mondo.xrefs.umls', 'mondo.xrefs.umls_cui', 'disgenet.xrefs.umls', 'umls.umls', 'disease_ontology.xrefs.umls_cui'], - name: ['mondo.label', 'disgenet.xrefs.disease_name', 'disease_ontology.name'], - MESH: ['mondo.xrefs.mesh', 'disease_ontology.xrefs.mesh', 'ctd.mesh'], - OMIM: ['mondo.xrefs.omim', 'hpo.omim', 'disgenet.xrefs.omim', 'disease_ontology.xrefs.omim'], - EFO: ['mondo.xrefs.efo', 'disgenet.xrefs.efo', 'disease_ontology.xrefs.efo'], - ORPHANET: ['hpo.orphanet', 'mondo.xrefs.orphanet'], - GARD: ['mondo.xrefs.gard', 'disease_ontology.xrefs.gard'], - HP: ['mondo.xrefs.hp', 'disgenet.xrefs.hp'], - SNOMEDCT: ['mondo.xrefs.sctid', 'umls.snomed.preferred', 'umls.snomed.non-preferred'], - NCIT: ['mondo.xrefs.ncit', 'disease_ontology.xrefs.ncit'], - MEDDRA: ['mondo.xrefs.meddra', 'disease_ontology.xrefs.meddra'], - }, - }, - ClinicalFinding: { - id_ranks: ['LOINC', 'NCIT', 'EFO', 'name'], - semantic: 'Disease', - api_name: 'mydisease.info', - url: 'https://mydisease.info/v1/query', - mapping: { - LOINC: ['mondo.xrefs.loinc'], - NCIT: ['mondo.xrefs.ncit', 'disease_ontology.xrefs.ncit'], - EFO: ['mondo.xrefs.efo', 'disgenet.xrefs.efo', 'disease_ontology.xrefs.efo'], - name: ['mondo.label', 'disgenet.xrefs.disease_name', 'disease_ontology.name'], - }, - }, - MolecularActivity: { - id_ranks: ['GO', 'MetaCyc', 'RHEA', 'KEGG.REACTION', 'REACT', 'name'], - semantic: 'MolecularActivity', - api_name: 'Gene Ontology Molecular Function API', - url: 'https://biothings.ncats.io/go_mf/query', - mapping: { - GO: ['_id'], - MetaCyc: ['xrefs.metacyc'], - RHEA: ['xrefs.rhea'], - 'KEGG.REACTION': ['xrefs.kegg_reaction'], - REACT: ['xrefs.reactome'], - name: ['name'], - }, - }, - BiologicalProcess: { - id_ranks: ['GO', 'MetaCyc', 'REACT', 'KEGG', 'name'], - semantic: 'BiologicalProcess', - api_name: 'Gene Ontology Biological Process API', - url: 'https://biothings.ncats.io/go_bp/query', - mapping: { - GO: ['_id'], - MetaCyc: ['xrefs.metacyc'], - KEGG: ['xrefs.kegg_pathway'], - REACT: ['xrefs.reactome'], - name: ['name'], - }, - }, - CellularComponent: { - id_ranks: ['GO', 'MetaCyc', 'name'], - semantic: 'CellularComponent', - api_name: 'Gene Ontology Cellular Component API', - url: 'https://biothings.ncats.io/go_cc/query', - mapping: { - GO: ['_id'], - MetaCyc: ['xrefs.metacyc'], // field missing in the API? - name: ['name'], - }, - }, - Pathway: { - id_ranks: ['REACT', 'KEGG', 'PHARMGKB.PATHWAYS', 'WIKIPATHWAYS', 'BIOCARTA', 'GO', 'SMPDB', 'name'], - semantic: 'Pathway', - api_name: 'Geneset API', - url: 'https://biothings.ncats.io/geneset/query', - mapping: { - REACT: ['reactome'], - WIKIPATHWAYS: ['wikipathways'], - KEGG: ['kegg'], - BIOCARTA: ['biocarta'], - 'PHARMGKB.PATHWAYS': ['pharmgkb'], - GO: ['go'], - SMPDB: ['smpdb'], - name: ['name'], - }, - additional_attributes_mapping: { - num_of_participants: ['num_of_participants'], - }, - }, - AnatomicalEntity: { - id_ranks: ['UBERON', 'UMLS', 'MESH', 'NCIT', 'name'], - semantic: 'AnatomicalEntity', - api_name: 'UBERON API', - url: 'https://biothings.ncats.io/uberon/query', - mapping: { - UBERON: ['_id'], - UMLS: ['xrefs.umls'], - MESH: ['xrefs.mesh'], - NCIT: ['xrefs.ncit'], // field missing in the API? - name: ['name'], - }, - }, - Cell: { - id_ranks: ['CL', 'NCIT', 'MESH', 'EFO', 'name'], - semantic: 'Cell', - api_name: 'Cell Ontology API', - url: 'https://biothings.ncats.io/cell_ontology/query', - mapping: { - CL: ['_id'], - NCIT: ['xrefs.ncit'], - MESH: ['xrefs.mesh'], - EFO: ['xrefs.efo'], // field missing in the API? - name: ['name'], - }, - }, -}; diff --git a/src/controllers/meta_knowledge_graph.js b/src/controllers/meta_knowledge_graph.js deleted file mode 100644 index d920e1db..00000000 --- a/src/controllers/meta_knowledge_graph.js +++ /dev/null @@ -1,206 +0,0 @@ -const meta_kg = require("@biothings-explorer/smartapi-kg"); -const snakeCase = require("snake-case"); -const fs = require("fs"); -var path = require("path"); -const util = require("util"); -const PredicatesLoadingError = require("../utils/errors/predicates_error"); -const readFile = util.promisify(fs.readFile); -const debug = require("debug")("bte:biothings-explorer-trapi:metakg"); -const { API_LIST: apiList } = require("../config/apis"); -const { supportedLookups } = require("@biothings-explorer/query_graph_handler"); - -module.exports = class MetaKnowledgeGraphHandler { - constructor(smartAPIID = undefined, teamName = undefined) { - this.smartAPIID = smartAPIID; - this.teamName = teamName; - } - - async _loadMetaKG(smartAPIID = undefined, teamName = undefined) { - const smartapi_specs = path.resolve(__dirname, "../../data/smartapi_specs.json"); - const predicates = path.resolve(__dirname, "../../data/predicates.json"); - const kg = new meta_kg.default(smartapi_specs, predicates); - try { - if (smartAPIID !== undefined) { - debug(`Constructing with SmartAPI ID ${smartAPIID}`); - kg.constructMetaKGSync(false, { apiList, smartAPIID: smartAPIID }); - } else if (teamName !== undefined) { - debug(`Constructing with team ${teamName}`); - kg.constructMetaKGSync(false, { apiList, teamName: teamName }); - } else { - debug(`Constructing with default`); - kg.constructMetaKGSync(true, { apiList }); - } - if (kg.ops.length === 0) { - debug(`Found 0 operations`); - throw new PredicatesLoadingError("Not Found - 0 operations"); - } - return kg; - } catch (error) { - debug(`ERROR getting graph with ID:${smartAPIID} team:${teamName} because ${error}`); - throw new PredicatesLoadingError(`Failed to Load MetaKG: ${error}`); - } - } - - _modifyCategory(category) { - if (category.startsWith("biolink:")) { - return "biolink:" + category.charAt(8).toUpperCase() + category.slice(9); - } else { - return "biolink:" + category.charAt(0).toUpperCase() + category.slice(1); - } - } - - _modifyPredicate(predicate) { - if (predicate.startsWith("biolink:")) { - return "biolink:" + snakeCase.snakeCase(predicate.slice(8)); - } else { - return "biolink:" + snakeCase.snakeCase(predicate); - } - } - - _modifyQualifierData(type_id, value) { - type_id = this._modifyPredicate(type_id); - - if (type_id.includes("predicate")) { - if (!value.startsWith("biolink:")) { - value = "biolink:" + value; - } - } else { - if (value.startsWith("biolink:")) { - value = value.slice(8); - } - } - - return [type_id, value]; - } - - async getKG(smartAPIID = this.smartAPIID, teamName = this.teamName) { - const kg = await this._loadMetaKG(smartAPIID, teamName); - let knowledge_graph = { - nodes: {}, - edges: [], - }; - let predicates = {}; - let node_sets = {}; - kg.ops.map(op => { - let input = this._modifyCategory(op.association.input_type); - let inputIDs = Array.isArray(op.association.input_id) ? op.association.input_id : [op.association.input_id]; - let output = this._modifyCategory(op.association.output_type); - let outputIDs = Array.isArray(op.association.output_id) ? op.association.output_id : [op.association.output_id]; - let pred = this._modifyPredicate(op.association.predicate); - let qualifiers = op.association.qualifiers; - - //edges - if (!(input in predicates)) { - predicates[input] = {}; - } - if (!(output in predicates[input])) { - predicates[input][output] = []; - } - if (predicates[input][output].every(obj => JSON.stringify(obj) !== JSON.stringify({predicate: pred, qualifiers}))) { - predicates[input][output].push({predicate: pred, qualifiers}); - } - - //nodes - if (!(input in node_sets)) { - node_sets[input] = new Set(); - } - inputIDs.forEach(id => id && node_sets[input].add(id)); - - if (!(output in node_sets)) { - node_sets[output] = new Set(); - } - outputIDs.forEach(id => id && node_sets[output].add(id)); - }); - const edges = {}; - Object.keys(predicates).map(input => { - Object.keys(predicates[input]).map(output => { - predicates[input][output].map(pred => { - if (edges[`${input}-${pred.predicate}-${output}`]) { - const cur_edge = edges[`${input}-${pred.predicate}-${output}`]; - if (pred.qualifiers) { - Object.entries(pred.qualifiers).forEach(([qual, val]) => { - let values = Array.isArray(val) ? val : [val]; - values.forEach(curVal => { - console.log(curVal) - const [type_id, value] = this._modifyQualifierData(qual, curVal); - const existing_qualifier = cur_edge.qualifiers?.find(q => q.qualifier_type_id === type_id); - if (existing_qualifier) { - if (!existing_qualifier.applicable_values.includes(value)) existing_qualifier.applicable_values.push(value); - } else { - if (!cur_edge.qualifiers) cur_edge.qualifiers = []; - cur_edge.qualifiers.push({ qualifier_type_id: type_id, applicable_values: [value] }); - } - }) - }) - } - return; - } - - const edge = { - subject: input, - predicate: pred.predicate, - object: output, - qualifiers: pred.qualifiers ? Object.entries(pred.qualifiers).map(([qual, val]) => { - if (!Array.isArray(val)) { - const [type_id, value] = this._modifyQualifierData(qual, val); - return { qualifier_type_id: type_id, applicable_values: [value] }; - } else { - let type_id = this._modifyPredicate(qual); - let values = []; - val.forEach(curVal => { - const [_, value] = this._modifyQualifierData(qual, curVal); - values.push(value); - }) - return { qualifier_type_id: type_id, applicable_values: values }; - } - }) : undefined, - knowledge_types: ["lookup"], - }; - knowledge_graph.edges.push(edge); - edges[`${input}-${pred.predicate}-${output}`] = edge; - }); - }); - }); - if (!smartAPIID && !teamName) { - const has_inferred = {}; - (await supportedLookups()).forEach(edge => { - const {subject, predicate, object, qualifiers} = edge; - if (Object.keys(edges).includes(`${subject}-${predicate}-${object}`)) { - if (!has_inferred[`${subject}-${predicate}-${object}`]) edges[`${subject}-${predicate}-${object}`].knowledge_types.push("inferred"); - has_inferred[`${subject}-${predicate}-${object}`] = true; - - const cur_edge = edges[`${subject}-${predicate}-${object}`]; - if (qualifiers) { - Object.entries(qualifiers).forEach(([qual, val]) => { - const [type_id, value] = this._modifyQualifierData(qual, val); - const existing_qualifier = cur_edge.qualifiers?.find(q => q.qualifier_type_id === type_id); - if (existing_qualifier) { - if (!existing_qualifier.applicable_values.includes(value)) existing_qualifier.applicable_values.push(value); - } else { - if (!cur_edge.qualifiers) cur_edge.qualifiers = []; - cur_edge.qualifiers.push({ qualifier_type_id: type_id, applicable_values: [value] }); - } - }) - } - } else { - edges[`${subject}-${predicate}-${object}`] = { - subject, - predicate, - object, - qualifiers: qualifiers ? Object.entries(qualifiers).map(([qual, val]) => { - const [type_id, value] = this._modifyQualifierData(qual, val); - return { qualifier_type_id: type_id, applicable_values: [value] }; - }) : undefined, - knowledge_types: ["inferred"], - }; - knowledge_graph.edges.push(edges[`${subject}-${predicate}-${object}`]); - has_inferred[`${subject}-${predicate}-${object}`] = true; - } - }); - } - Object.keys(node_sets).map(node => { - knowledge_graph.nodes[node] = { id_prefixes: Array.from(node_sets[node]) }; - }); - return knowledge_graph; - } -}; diff --git a/src/controllers/threading/taskHandler.js b/src/controllers/threading/taskHandler.js deleted file mode 100644 index 71cae982..00000000 --- a/src/controllers/threading/taskHandler.js +++ /dev/null @@ -1,71 +0,0 @@ -const { isMainThread, threadId } = require("worker_threads"); -const debug = require("debug")(`bte:biothings-explorer-trapi:worker${threadId}`); - -if (!isMainThread) { - // Log thread start before BioLink model loads - debug(`Worker thread ${threadId} is ready to accept tasks.`); -} - -const { tasks } = require("../../routes/index"); -const { getQueryQueue } = require("../async/asyncquery_queue"); -const Sentry = require('@sentry/node'); -const { ProfilingIntegration } = require('@sentry/profiling-node'); - -// use SENTRY_DSN environment variable -Sentry.init({ - // dsn: "https://5297933ef0f6487c9fd66532bb1fcefe@o4505444772806656.ingest.sentry.io/4505449737420800", - integrations: [ - // Automatically instrument Node.js libraries and frameworks - ...Sentry.autoDiscoverNodePerformanceMonitoringIntegrations(), - new ProfilingIntegration() - ], - environment: process.env.INSTANCE_ENV, - debug: true, - normalizeDepth: 6, - maxBreadcrumbs: 500, - // Set tracesSampleRate to 1.0 to capture 100% - // of transactions for performance monitoring. - // We recommend adjusting this value in production - tracesSampleRate: process.env.THREAD_SAMPLE_RATE ? parseFloat(process.env.THREAD_SAMPLE_RATE) : 1.0, - profilesSampleRate: process.env.THREAD_PROFILE_RATE ? parseFloat(process.env.THREAD_PROFILE_RATE) : 1.0, // Profiling sample rate is relative to tracesSampleRate, - _experiments: { - maxProfileDurationMs: 6 * 60 * 1000 // max profiling duration of 6 minutes (technically "beta" feature) - } -}); - -const runTask = async ({ req, route, port, job: { jobId, queueName } = {} }) => { - debug(`Worker thread ${threadId} beginning task.`); - - global.SCHEMA_VERSION = "1.4.0" - - global.parentPort = port; - port.postMessage({ threadId, registerId: true }); - global.cachingTasks = []; - - global.queryInformation = { - queryGraph: req?.body?.message?.query_graph, - }; - - if (queueName) { - const queue = await getQueryQueue(queueName); - global.job = await queue.getJob(jobId); - } - - const transaction = Sentry.startTransaction({ name: route }); - transaction.setData("request", req.data.queryGraph); - Sentry.getCurrentHub().configureScope((scope) => { - scope.clearBreadcrumbs(); - scope.setSpan(transaction); - }); - - const completedTask = await tasks[route](req); - await Promise.all(global.cachingTasks); - - transaction.finish(); - - debug(`Worker thread ${threadId} completed task.`); - - return completedTask; -}; - -module.exports = runTask; diff --git a/src/controllers/threading/threadHandler.js b/src/controllers/threading/threadHandler.js deleted file mode 100644 index 582fd813..00000000 --- a/src/controllers/threading/threadHandler.js +++ /dev/null @@ -1,365 +0,0 @@ -const { MessageChannel, threadId } = require("worker_threads"); -const debug = require("debug")("bte:biothings-explorer-trapi:threading"); -const path = require("path"); -// const taskHandler = require("./taskHandler"); -const { redisClient } = require("@biothings-explorer/query_graph_handler"); -const Piscina = require("piscina"); -const { isWorkerThread } = require("piscina"); -const EventEmitter = require("events"); -const os = require("os"); -const ServerOverloadedError = require("../../utils/errors/server_overloaded_error"); -const { customAlphabet } = require("nanoid"); -const { getQueryQueue } = require("../async/asyncquery_queue"); - -const Sentry = require("@sentry/node"); -const ErrorHandler = require("../../middlewares/error.js"); - -const SYNC_MIN_CONCURRENCY = 2; -const ASYNC_MIN_CONCURRENCY = 3; - -// On Prod: 0.25 ratio * 16 cores * 4 instances = 16 threads -const SYNC_CONCURRENCY_RATIO = 0.25; -/** On Prod: 0.25 ratio * 16 cores * 4 instances = 16 threads - * Async has 3 queues: - * - general - * - by api - * - by team - * - * Distribution between those is seen below. - * */ -const ASYNC_CONCURRENCY_RATIO = 0.25; - -let SYNC_CONCURRENCY = Math.ceil(os.cpus().length * SYNC_CONCURRENCY_RATIO); -if (SYNC_CONCURRENCY < SYNC_MIN_CONCURRENCY) SYNC_CONCURRENCY = SYNC_MIN_CONCURRENCY; -let ASYNC_CONCURRENCY = Math.ceil(os.cpus().length * ASYNC_CONCURRENCY_RATIO); -if (ASYNC_CONCURRENCY < ASYNC_MIN_CONCURRENCY) ASYNC_CONCURRENCY = ASYNC_MIN_CONCURRENCY; - -const ASYNC_MAIN_CONCURRENCY = ASYNC_CONCURRENCY <= 9 ? Math.ceil(ASYNC_CONCURRENCY / 3) : ASYNC_CONCURRENCY - 6; -const ASYNC_BY_API_CONCURRENCY = ASYNC_CONCURRENCY <= 9 ? Math.floor(ASYNC_CONCURRENCY / 3) : 3; -const ASYNC_BY_TEAM_CONCURRENCY = ASYNC_CONCURRENCY <= 9 ? Math.floor(ASYNC_CONCURRENCY / 3) : 3; - -if (!global.threadpool && !isWorkerThread && !(process.env.USE_THREADING === "false")) { - const env = { - ...process.env, - DEBUG_COLORS: true, - }; - global.threadpool = { - /**Medium-volume, medium-intensity requests - * Maximum threads equal to 1/4 CPUs as BTE usually runs 4 intances - * Maximum queue set, so if the queue if full, requests will be dropped - * Usually, queuing will be handled by Bull, but if Bull is unavailable - * (e.g. local debugging w/o a Redis instance), queuing falls back to Piscina - */ - sync: new Piscina({ - filename: path.resolve(__dirname, "./taskHandler.js"), - minThreads: 2, - maxThreads: SYNC_CONCURRENCY, - maxQueue: 600, - idleTimeout: 10 * 60 * 1000, // 10 minutes - env, - }), - /**Low-volume, high-intensity requests - * No other settings since this queue is handled externally with Bull - * High timeout because we expect near-constant use, so rather not kill the thread - */ - async: new Piscina({ - filename: path.resolve(__dirname, "./taskHandler.js"), - // e.g. 8 cores * - maxThreads: ASYNC_CONCURRENCY, - minThreads: 1, - idleTimeout: 60 * 60 * 1000, // 1 hour - env, - }), - /**High-volume, low-intensity requests - * Expecting frequent use, so timeout is high - */ - misc: new Piscina({ - filename: path.resolve(__dirname, "./taskHandler.js"), - idleTimeout: 60 * 60 * 1000, // 1 hour - minThreads: 2, - maxQueue: 600, - env, - }), - }; -} - -const queueTaskToWorkers = async (pool, req, route, job) => { - return new Promise(async (resolve, reject) => { - let WorkerThreadID; - const abortController = new AbortController(); - const { port1: toWorker, port2: fromWorker } = new MessageChannel(); - const taskData = { req, route, port: toWorker }; - if (job) taskData.job = { jobId: job.id, queueName: job.queue.name }; - const task = pool.run(taskData, { signal: abortController.signal, transferList: [toWorker] }); - if (job) { - job.update({ ...job.data, abortController }); - } - - // catch failures that cause the worker to outright fail - task.catch(error => { - if (error.name === "AbortError") { - debug(`Worker thread ${WorkerThreadID} terminated successfully.`); - } else if (error.message === "Task queue is at limit") { - debug( - [pool === global.threadpool.sync ? "Synchronous" : "Misc", "server queue is at limit, job rejected."].join( - " ", - ), - ); - const expectedWaitTime = Math.ceil(pool.waitTime.p99 / 1000) + 1; - const message = [ - "The server is currently under heavy load.", - ` Please try again after about ${expectedWaitTime}s`, - pool === global.threadpool.sync ? ", or try using the asynchronous endpoints." : ".", - ].join(""); - error = new ServerOverloadedError(message, expectedWaitTime); - } else { - debug(`Caught error in worker thread ${WorkerThreadID}, error below:`); - debug(error); - } - reject(error); - }); - let reqDone = false; - let cacheInProgress = 0; - let cacheKeys = {}; - const timeout = parseInt(process.env.REQUEST_TIMEOUT ?? (60 * 5).toString()) * 1000; - fromWorker.on("message", ({ threadId, ...msg }) => { - if (msg.cacheInProgress) { - // cache handler has started caching - cacheInProgress += 1; - } else if (msg.addCacheKey) { - // hashed edge id cache in progress - cacheKeys[msg.cacheKey] = false; - } else if (msg.completeCacheKey) { - // hashed edge id cache complete - cacheKeys[msg.cacheKey] = true; - } else if (msg.registerId) { - if (job) { - WorkerThreadID = threadId; - job.update({ ...job.data, threadId }); - } - } else if (typeof msg.cacheDone !== "undefined") { - cacheInProgress = msg.cacheDone - ? cacheInProgress - 1 // a caching handler has finished caching - : 0; // caching has been entirely cancelled - } else if (typeof msg.result !== "undefined") { - // request has finished with a message - reqDone = true; - resolve(msg); - } else if (msg.err) { - // request has resulted in a catchable error - reqDone = true; - reject(msg.err); - } - if (reqDone && cacheInProgress <= 0 && job) { - job.progress(100); - } - }); - - if (timeout && pool !== global.threadpool.async) { - setTimeout(() => { - // clean up any incompletely cached hashes to avoid issues pulling from cache - const activeKeys = Object.entries(cacheKeys).filter(([key, complete]) => !complete); - if (activeKeys.length) { - try { - redisClient.client.delTimeout(activeKeys); - } catch (error) { - null; - } - } - abortController.abort(); - reject( - new Error( - `Request timed out (exceeded time limit of ${ - timeout / 1000 - }s). Please use the asynchronous endpoint (/v1/asyncquery) for long-running queries.`, - ), - ); - }, timeout); - } - }); -}; - -async function runTask(req, task, route, res, useBullSync = true) { - const queryQueue = global.queryQueue.bte_sync_query_queue; - req = { - data: { - route, - queryGraph: req.body.message?.query_graph, - workflow: req.body.workflow, - options: { - logLevel: req.body.log_level, - submitter: req.body.submitter, - smartAPIID: req.params.smartapi_id, - teamName: req.params.team_name, - ...req.query, - }, - }, - params: req.params, - endpoint: req.originalUrl, - }; - if (queryQueue && useBullSync) { - const nanoid = customAlphabet("0123456789abcdefghijklmnopqrstuvwxyzABCDEFGHIJKLMNOPQRSTUVWXYZ", 10); - const jobId = nanoid(); - const jobOpts = { - jobId, - attempts: 1, - timeout: undefined, - removeOnFail: { - age: 24 * 60 * 60, // keep failed jobs for a day (in case user needs to review fail reason) - count: 2000, - }, - removeOnComplete: { - age: 90 * 24 * 60 * 60, // keep completed jobs for 90 days - count: 2000, - }, - }; - - if ((await queryQueue.count()) >= 600) { - const pool = global.threadpool.sync; - const expectedWaitTime = Math.ceil(pool.waitTime.p99 / 1000) + 1; - const message = [ - "The server is currently under heavy load.", - ` Please try again after about ${expectedWaitTime}s`, - ", or try using the asynchronous endpoints.", - ].join(""); - throw new ServerOverloadedError(message, expectedWaitTime); - } - - return new Promise(async (resolve, reject) => { - const job = await queryQueue.add(req.data, jobOpts); - try { - const response = await job.finished(); - resolve(response); - } catch (error) { - // Have to reconstruct the error because Bull does some weirdness - const jobLatest = await queryQueue.getJob(jobOpts.jobId); - const reconstructedError = new Error(); - try { - reconstructedError.name = jobLatest.stacktrace[0].split(":")[0]; - reconstructedError.message = jobLatest.stacktrace[0].split("\n")[0]; - reconstructedError.stack = jobLatest.stacktrace[0]; - } catch (constructionError) { - reconstructedError.name = 'ThreadingError'; - reconstructedError.message = JSON.stringify(jobLatest.stacktrace); - } - reject(reconstructedError); - } - }); - } - // redis unavailable or query not to sync queue such as asyncquery_status - if (!(process.env.USE_THREADING === "false")) { - const response = await queueTaskToWorkers( - useBullSync ? global.threadpool.sync : global.threadpool.misc, - req, - route, - ); - if (typeof response.result !== "undefined") { - if (response.status) { - res?.status(response.status); - } - return response.result ? response.result : undefined; // null msg means keep response body empty - } else if (response.err) { - throw new response.err(); - } else { - throw new Error("Threading Error: Task resolved without message"); - } - } - // threading disabled - try { - const response = await task(req); - return response; - } catch (error) { - throw error; - } -} - -async function runBullTask(job, route, async = true) { - const req = { id: job.id, data: { ...job.data } }; - return new Promise(async (resolve, reject) => { - try { - const response = await queueTaskToWorkers( - async ? global.threadpool.async : global.threadpool.sync, - req, - route, - job, - ); - if (typeof response.result !== "undefined") { - resolve(response.result ? response.result : undefined); // null result means keep response body empty - } else if (response.err) { - reject(response.err); - } else { - reject(new Error("Threading Error: Task resolved without message")); - } - } catch (error) { - reject(error); - } - }); -} - -function taskResponse(response, status = undefined) { - if (global.parentPort) { - global.parentPort.postMessage({ threadId, result: response, status: status }); - return undefined; - } else { - return response; - } -} - -function taskError(error) { - if (global.parentPort) { - if (ErrorHandler.shouldHandleError(error)) { - Sentry.captureException(error); - } - global.parentPort.postMessage({ threadId, err: error }); - return undefined; - } else { - throw error; - } -} - -if (!global.queryQueue.bte_sync_query_queue && !isWorkerThread) { - getQueryQueue("bte_sync_query_queue"); - if (global.queryQueue.bte_sync_query_queue) { - global.queryQueue.bte_sync_query_queue.process(SYNC_CONCURRENCY, async job => { - try { - return await runBullTask(job, job.data.route, false); - } catch (error) { - throw error; - } - }); - } -} - -if (!global.queryQueue.bte_query_queue && !isWorkerThread) { - getQueryQueue("bte_query_queue"); - if (global.queryQueue.bte_query_queue) { - global.queryQueue.bte_query_queue.process(ASYNC_MAIN_CONCURRENCY, async job => { - return await runBullTask(job, "asyncquery_v1"); - }); - } -} - -if (!global.queryQueue.bte_query_queue_by_api && !isWorkerThread) { - getQueryQueue("bte_query_queue_by_api"); - if (global.queryQueue.bte_query_queue_by_api) { - global.queryQueue.bte_query_queue_by_api.process(ASYNC_BY_API_CONCURRENCY, async job => { - return await runBullTask(job, "asyncquery_v1_by_api"); - }); - } -} - -if (!global.queryQueue.bte_query_queue_by_team && !isWorkerThread) { - getQueryQueue("bte_query_queue_by_team"); - if (global.queryQueue.bte_query_queue_by_team) { - global.queryQueue.bte_query_queue_by_team.process(ASYNC_BY_TEAM_CONCURRENCY, async job => { - return await runBullTask(job, "asyncquery_v1_by_team"); - }); - } -} - -module.exports = { - runTask, - runBullTask, - taskResponse, - taskError, -}; diff --git a/src/controllers/utils.js b/src/controllers/utils.js deleted file mode 100644 index 147549d3..00000000 --- a/src/controllers/utils.js +++ /dev/null @@ -1,19 +0,0 @@ -const { set } = require("lodash"); - -exports.toArray = (input) => { - if (Array.isArray(input)) { - return input; - } - return [input]; -} - -exports.getUnique = (input) => { - return Array.from(new Set(input)); -} - -exports.removeBioLinkPrefix = (input) => { - if (input && input.startsWith("biolink:")) { - return input.slice(8); - } - return input; -} diff --git a/src/middlewares/error.js b/src/middlewares/error.js deleted file mode 100644 index b6222de7..00000000 --- a/src/middlewares/error.js +++ /dev/null @@ -1,113 +0,0 @@ -const swaggerValidation = require("./validate"); -const QueryGraphHandler = require("@biothings-explorer/query_graph_handler"); -const PredicatesLoadingError = require("../utils/errors/predicates_error"); -const MetaKGLoadingError = require("../utils/errors/metakg_error"); -const ServerOverloadedError = require("../utils/errors/server_overloaded_error"); -const debug = require("debug")("bte:biothings-explorer-trapi:error_handler"); -const Sentry = require('@sentry/node'); - -class ErrorHandler { - shouldHandleError(error) { - // Capture all 404 and 500 errors - if (error instanceof swaggerValidation.InputValidationError || error.name === "InputValidationError") { - return false; - } - if ( - error instanceof QueryGraphHandler.InvalidQueryGraphError || - error.stack.includes("InvalidQueryGraphError") || - error.name === "InvalidQueryGraphError" - ) { - return false; - } - if (error.name === "QueryAborted") { - return false; - } - return true; - } - - setRoutes(app) { - // first pass through sentry - app.use(Sentry.Handlers.errorHandler({ - shouldHandleError(error) { - // Do not capture non-server errors - if (error.status && error.status < 500) { - return false; - } - if (error instanceof swaggerValidation.InputValidationError || error.name === "InputValidationError") { - return false; - } - if ( - error instanceof QueryGraphHandler.InvalidQueryGraphError || - error.stack.includes("InvalidQueryGraphError") || - error.name === "InvalidQueryGraphError" - ) { - return false; - } - if (error.name === "QueryAborted") { - return false; - } - return true; - } - })); - - app.use((error, req, res, next) => { - const json = { - status: "QueryNotTraversable", - description: error.message, - }; - if (error instanceof swaggerValidation.InputValidationError || error.name === "InputValidationError") { - json.description = `Your input query graph is invalid. Errors: ${error.errors.join("\n")}`; - return res.status(400).json(json); - } - // read stack when instance or err is broken - if ( - error instanceof QueryGraphHandler.InvalidQueryGraphError || - error.stack.includes("InvalidQueryGraphError") || - error.name === "InvalidQueryGraphError" - ) { - json.description = `Your input query graph is invalid: ${error.message}`; - return res.status(400).json(json); - } - if (error instanceof PredicatesLoadingError || error.name === "PredicatesLoadingError") { - json.status = 'KPsNotAvailable'; - json.description = `Unable to load predicates: ${error.message}` - return res.status(404).json(json); - } - - if (error instanceof MetaKGLoadingError || error.name === "MetaKGLoadingError") { - json.status = 'KPsNotAvailable'; - json.description = `Unable to load metakg: ${error.message}`; - return res.status(404).json(json); - } - - if (error instanceof ServerOverloadedError || error.name === "ServerOverloadedError") { - return res.status(503).set("Retry-After", error.retryAfter).json(json); - } - if (!error.statusCode) error.statusCode = 500; - - if (error.statusCode === 301) { - return res.status(301).redirect("/"); - } - debug(error); - if (req.originalUrl.includes('asyncquery')) { - return res.status(error.statusCode).json({ - status: error.statusCode, - description: error.toString(), - trace: process.env.NODE_ENV === "production" ? undefined : error.stack, - }) - } - return res.status(error.statusCode).json({ - message: { - query_graph: req.body?.message?.query_graph, - knowledge_graph: { nodes: {}, edges: {} }, - results: [], - }, - status: error.statusCode, - description: error.toString(), - trace: process.env.NODE_ENV === "production" ? undefined : error.stack, - }); - }); - } -} - -module.exports = new ErrorHandler(); diff --git a/src/middlewares/logging.js b/src/middlewares/logging.js deleted file mode 100644 index 34bec648..00000000 --- a/src/middlewares/logging.js +++ /dev/null @@ -1,46 +0,0 @@ -const winston = require('winston'); -const expressWinston = require('express-winston'); -require('winston-daily-rotate-file'); - - -class LoggingHandler { - setRoutes(app) { - const transport = new (winston.transports.DailyRotateFile)({ - filename: 'BioThings-Explorer-TRAPI-%DATE%.log', - dirname: process.env.LOG || './log', - datePattern: 'YYYY-MM-DD', - zippedArchive: true, - maxSize: '20m', - maxFiles: '14d' - }); - app.use(expressWinston.logger({ - format: winston.format.combine( - winston.format.timestamp({ format: 'YYYY-MM-DD HH:mm:ss' }), - winston.format.colorize(), - winston.format.json(), - - ), - transports: [ - transport - ], - requestWhitelist: ['headers', 'body'], - meta: true, // optional: control whether you want to log the meta data about the request (default to true) - expressFormat: true, // Use the default Express/morgan request formatting. Enabling this will override any msg if true. Will only output colors with colorize set to true - colorize: false, // Color the text and status code, using the Express/morgan color palette (text: gray, status: default green, 3XX cyan, 4XX yellow, 5XX red). - ignoreRoute: function (req, res) { return false; }, // optional: allows to skip some log messages based on request and/or response - statusLevels: false, - level: (req, res) => { - let level = ""; - if (res.statusCode >= 100) { level = "info"; } - if (res.statusCode >= 400) { level = "warn"; } - if (res.statusCode >= 500) { level = "error"; } - // Ops is worried about hacking attempts so make Unauthorized and Forbidden critical - if (res.statusCode == 401 || res.statusCode == 403) { level = "critical"; } - // No one should be using the old path, so always warn for those - return level; - } - })); - } -} - -module.exports = new LoggingHandler(); \ No newline at end of file diff --git a/src/middlewares/validate.js b/src/middlewares/validate.js deleted file mode 100644 index 285a76aa..00000000 --- a/src/middlewares/validate.js +++ /dev/null @@ -1,24 +0,0 @@ -const swaggerValidation = require('openapi-validator-middleware'); -const path = require('path'); - -const schema = path.join(__dirname, '../../docs/smartapi.yaml'); - -const inputValidationOptions = { - formats: [ - { name: 'double', pattern: /\d+(\.\d+)?/ }, - { name: 'int64', pattern: /^\d{1,19}$/ }, - { name: 'int32', pattern: /^\d{1,10}$/ }, - { - name: 'file', - validate: () => { - return true; - } - } - ], - beautifyErrors: true, - //firstError: true, - expectFormFieldsInBody: true -}; -swaggerValidation.init(schema, inputValidationOptions); - -module.exports = swaggerValidation; \ No newline at end of file diff --git a/src/routes/bullboard.js b/src/routes/bullboard.js deleted file mode 100644 index 584f30bd..00000000 --- a/src/routes/bullboard.js +++ /dev/null @@ -1,65 +0,0 @@ -const { getQueryQueue } = require("../controllers/async/asyncquery_queue"); -const { createBullBoard } = require("@bull-board/api"); -const { BullAdapter } = require("@bull-board/api/bullAdapter"); -const { ExpressAdapter } = require("@bull-board/express"); -const path = require("path"); -const debug = require("debug")("bte:biothings-explorer-trapi:bullboard"); -const { redisClient } = require("@biothings-explorer/query_graph_handler"); - -class RouteBullBoardPage { - setRoutes(app) { - debug("Initializing Bull Dashboard"); - if (!redisClient.clientEnabled || process.env.INTERNAL_DISABLE_REDIS) { - debug("Redis is not enabled, disabling Bull Dashboard"); - app.use("/queues", async (req, res, next) => { - res - .status(503) - .set("Retry-After", 600) - .set("Content-Type", "application/json") - .end(JSON.stringify({ error: "Redis service is unavailable, so async job queuing is disabled." })); - }); - return; - } - const queues = { - "/v1/asynquery": getQueryQueue("bte_query_queue"), - "/v1/smartapi/{smartapi_id}/asyncquery": getQueryQueue("bte_query_queue_by_api"), - "/v1/team/{team_name}/asyncquery": getQueryQueue("bte_query_queue_by_team"), - "/v1/query": getQueryQueue("bte_sync_query_queue"), - }; - - const serverAdapter = new ExpressAdapter(); - serverAdapter.setBasePath("/queues"); - - const instance = { - prod: "Prod", - test: "Test", - ci: "Staging", - dev: "Dev", - }[process.env.INSTANCE_ENV ?? "dev"]; - - const { addQueue, removeQueue, setQueues, replaceQueues } = createBullBoard({ - queues: Object.entries(queues).map(([name, queue]) => { - const adapter = new BullAdapter(queue, { - readOnlyMode: true, - description: name, - }); - adapter.setFormatter( - "name", - job => `${name === "/v1/query" ? "Synchronous" : "Asynchronous"} Request #${job.id}`, - ); - adapter.setFormatter("data", ({ abortController, threadId, route, ...rest }) => rest); - return adapter; - }), - serverAdapter, - options: { - uiConfig: { - boardTitle: `BTE ${instance}`, - }, - }, - }); - - app.use("/queues", serverAdapter.getRouter()); - } -} - -module.exports = new RouteBullBoardPage(); diff --git a/src/routes/frontpage.js b/src/routes/frontpage.js deleted file mode 100644 index a73cb6c7..00000000 --- a/src/routes/frontpage.js +++ /dev/null @@ -1,19 +0,0 @@ -const utils = require("../utils/common"); -const history = require("connect-history-api-fallback"); -const express = require("express"); -const path = require("path"); - -class RouteFrontPage { - setRoutes(app) { - const staticFileMiddleware = express.static(path.resolve(__dirname, "../web-app/dist")); - app.use(staticFileMiddleware); - app.use( - history({ - disableDotRule: true, - }), - ); - app.use(staticFileMiddleware); - } -} - -module.exports = new RouteFrontPage(); diff --git a/src/routes/index.js b/src/routes/index.js deleted file mode 100644 index f8c045b3..00000000 --- a/src/routes/index.js +++ /dev/null @@ -1,58 +0,0 @@ -const routesMetaKG = require("./metakg"); -const routesFrontPage = require("./frontpage"); -const routesPerformance = require("./performance"); -const routesV1QueryByAPI = require("./v1/query_v1_by_api"); -const routesV1QueryByTeam = require("./v1/query_v1_by_team"); -const routesV1Query = require("./v1/query_v1"); -const routesV1AsyncQuery = require('./v1/asyncquery_v1'); -const routesV1AsyncQueryByAPI = require("./v1/asyncquery_v1_by_api"); -const routesV1AsyncQueryByTeam = require("./v1/asyncquery_v1_by_team"); -const routesV1CheckQueryStatus = require('./v1/asyncquery_status'); -const routesV1MetaKG = require("./v1/meta_knowledge_graph_v1") -const routesV1MetaKGByAPI = require("./v1/meta_knowledge_graph_v1_by_api"); -const routesV1MetaKGByTeam = require("./v1/meta_knowledge_graph_v1_by_team"); -const ErrorHandler = require("../middlewares/error"); -const LoggingHandler = require("../middlewares/logging"); -const routesBullBoardPage = require("./bullboard"); - -class Routes { - setRoutes(app) { - routesMetaKG.setRoutes(app); - routesV1MetaKG.setRoutes(app); - routesV1AsyncQuery.setRoutes(app); - routesV1AsyncQueryByAPI.setRoutes(app); - routesV1AsyncQueryByTeam.setRoutes(app); - routesV1MetaKGByAPI.setRoutes(app); - routesV1MetaKGByTeam.setRoutes(app); - routesV1CheckQueryStatus.setRoutes(app); - routesBullBoardPage.setRoutes(app); - routesPerformance.setRoutes(app); - routesV1QueryByAPI.setRoutes(app); - routesV1QueryByTeam.setRoutes(app); - LoggingHandler.setRoutes(app); - routesV1Query.setRoutes(app); - ErrorHandler.setRoutes(app); - routesFrontPage.setRoutes(app); - } - -} - -module.exports = { - routes: new Routes(), - tasks: { - query_v1: routesV1Query.task, - query_v1_by_api: routesV1QueryByAPI.task, - query_v1_by_team: routesV1QueryByTeam.task, - asyncquery_status: routesV1CheckQueryStatus.task, - // async processor uses thread - asyncquery_v1: routesV1AsyncQuery.task, - asyncquery_v1_by_api: routesV1AsyncQueryByAPI.task, - asyncquery_v1_by_team: routesV1AsyncQueryByTeam.task, - // Not threaded due to being lightweight/speed being higher priority - performance: routesPerformance.task, - metakg: routesMetaKG.task, - meta_knowledge_graph_v1: routesV1MetaKG.task, - meta_knowledge_graph_v1_by_api: routesV1MetaKGByAPI.task, - meta_knowledge_graph_v1_by_team: routesV1MetaKGByTeam.task, - } -} diff --git a/src/routes/metakg.js b/src/routes/metakg.js deleted file mode 100644 index c226c7d9..00000000 --- a/src/routes/metakg.js +++ /dev/null @@ -1,37 +0,0 @@ -const utils = require("../utils/common"); -const assoc = require("../controllers/association"); -const MetaKGLoadingError = require("../utils/errors/metakg_error"); - -class RouteMetaKG { - setRoutes(app) { - app - .route("/metakg") - .get(async (req, res, next) => { - try { - res.setHeader("Content-Type", "application/json"); - let api = undefined, - source = undefined; - if (req.query.api !== undefined) { - api = utils.removeQuotesFromQuery(req.query.api); - } - if (req.query.provided_by !== undefined) { - source = utils.removeQuotesFromQuery(req.query.provided_by); - } - let assocs = await assoc( - req.query.subject, - req.query.object, - req.query.predicate, - req.query.component, - api, - source, - ); - res.end(JSON.stringify({ associations: assocs })); - } catch (error) { - next(new MetaKGLoadingError()); - } - }) - .all(utils.methodNotAllowed); - } -} - -module.exports = new RouteMetaKG(); diff --git a/src/routes/performance.js b/src/routes/performance.js deleted file mode 100644 index b837cd92..00000000 --- a/src/routes/performance.js +++ /dev/null @@ -1,33 +0,0 @@ -var path = require("path"); -const fs = require("fs"); -const debug = require("debug")("bte:biothings-explorer-trapi:performance"); -const utils = require("../utils/common"); - -class RoutePerformance { - setRoutes(app) { - app - .route("/performance") - .get((req, res) => { - debug("start to retrieve performance log."); - const file_path = path.resolve(__dirname, "../../performance-test/report.html"); - debug(`file path is ${file_path}`); - try { - fs.access(file_path, fs.constants.R_OK, err => { - debug("performance file exists!"); - res.sendFile(file_path); - }); - // if (fs.existsSync(file_path)) { - // debug("performance file exists!") - // res.sendFile(file_path) - // } - } catch (err) { - res.setHeader("Content-Type", "application/json"); - res.status(404); - res.end(JSON.stringify({ error: err.toString() })); - } - }) - .all(utils.methodNotAllowed); - } -} - -module.exports = new RoutePerformance(); diff --git a/src/routes/v1/asyncquery_status.js b/src/routes/v1/asyncquery_status.js deleted file mode 100644 index ee4de9ce..00000000 --- a/src/routes/v1/asyncquery_status.js +++ /dev/null @@ -1,110 +0,0 @@ -const path = require("path"); -const { redisClient } = require("@biothings-explorer/query_graph_handler"); -const { getQueryQueue } = require("../../controllers/async/asyncquery_queue"); -const { getQueryResponse } = require("../../controllers/async/asyncquery"); -const lz4 = require("lz4"); -const utils = require("../../utils/common"); - -let queryQueue; - -const swaggerValidation = require("../../middlewares/validate"); -const { runTask, taskResponse, taskError } = require("../../controllers/threading/threadHandler"); -const debug = require("debug")("bte:biothings-explorer-trapi:async"); - -class VCheckQueryStatus { - setRoutes(app) { - app - .route(["/v1/asyncquery_status/:id", "/v1/asyncquery_response/:id"]) - .get(swaggerValidation.validate, async (req, res, next) => { - try { - const response = await runTask(req, this.task, path.parse(__filename).name, res, false); - res.setHeader("Content-Type", "application/json"); - res.end(JSON.stringify(response)); - } catch (err) { - next(err); - } - }) - .all(utils.methodNotAllowed); - } - - async task(req) { - //logger.info("query /query endpoint") - try { - debug(`checking query status of job ${req.params.id}`); - let by = req.data.options.by; - let job_id = req.params.id; - let queryQueue; - if (redisClient.clientEnabled) { - if (job_id.startsWith("BT_")) { - queryQueue = getQueryQueue("bte_query_queue_by_team"); - } else if (job_id.startsWith("BA_")) { - queryQueue = getQueryQueue("bte_query_queue_by_api"); - } else { - queryQueue = getQueryQueue("bte_query_queue"); - } - } - if (queryQueue) { - let job = await queryQueue.getJobFromId(job_id); - - if (job === null) { - return taskResponse(null, 404); - } - await queryQueue.isReady(); - const state = await job.getState(); - let logs = await queryQueue.getJobLogs(job_id); - logs = logs.logs.map(log => JSON.parse(log)); - let [status, description] = { - // convert to TRAPI states - completed: ["Completed", "The query has finished executing."], - failed: ["Failed", job.failedReason], - delayed: ["Queued", "The query is queued, but has been delayed."], - active: ["Running", "The query is currently being processed."], - waiting: ["Queued", "The query is waiting in the queue."], - paused: ["Queued", "The query is queued, but the queue is temporarily paused."], - stuck: ["Failed", "The query is stuck (if you see this, raise an issue)."], - null: ["Failed", "The query status is unknown, presumed failed (if you see this, raise an issue)."], - }[state]; - let progress = job._progress; - if (status === "Failed" && !req.endpoint.includes("asyncquery_response")) { - if (description.includes("Promise timed out")) { - // something might break when calculating process.env.JOB_TIMEOUT so wrap it in try catch - try { - return taskResponse({ - job_id, - status, - description: `Job was stopped after exceeding time limit of ${ - parseInt(process.env.JOB_TIMEOUT ?? (1000 * 60 * 5).toString()) / 1000 - }s`, - logs, - }); - } catch (e) { - return taskResponse({ job_id, status, description, logs }); - } - } - return taskResponse({ job_id, status, description, logs }); - } - - // If done, just give response if using the response_url - if ((state === "completed" || state === "failed") && req.endpoint.includes("asyncquery_response")) { - let returnValue; - const storedResponse = await getQueryResponse(job_id, req.data.options.logLevel); - - if (!storedResponse.logs && logs) { - storedResponse.logs = logs; - } - - returnValue = storedResponse ? storedResponse : { error: "Response expired. Responses are kept 30 days." }; - return taskResponse(returnValue, returnValue.statusCode || 200); - } - - taskResponse({ job_id, status, progress, description, response_url: job.data.url, logs }, 200); - } else { - taskResponse({ error: "Redis service is unavailable" }, 503); - } - } catch (error) { - taskError(error); - } - } -} - -module.exports = new VCheckQueryStatus(); diff --git a/src/routes/v1/asyncquery_v1.js b/src/routes/v1/asyncquery_v1.js deleted file mode 100644 index 2be62dfc..00000000 --- a/src/routes/v1/asyncquery_v1.js +++ /dev/null @@ -1,61 +0,0 @@ -const path = require("path"); -const swaggerValidation = require("../../middlewares/validate"); -const { asyncquery, asyncqueryResponse } = require("../../controllers/async/asyncquery"); -const { getQueryQueue } = require("../../controllers/async/asyncquery_queue"); -const utils = require("../../utils/common"); -const { isMainThread } = require("worker_threads"); -const { TRAPIQueryHandler } = require("@biothings-explorer/query_graph_handler"); -const { API_LIST: apiList } = require("../../config/apis"); -const { taskResponse, runBullTask } = require("../../controllers/threading/threadHandler"); -const smartAPIPath = path.resolve( - __dirname, - process.env.STATIC_PATH ? `${process.env.STATIC_PATH}/data/smartapi_specs.json` : "../../../data/smartapi_specs.json", -); -const predicatesPath = path.resolve( - __dirname, - process.env.STATIC_PATH ? `${process.env.STATIC_PATH}/data/predicates.json` : "../../../data/predicates.json", -); - -class V1RouteAsyncQuery { - setRoutes(app) { - app - .route("/v1/asyncquery") - .post(swaggerValidation.validate, async (req, res, next) => { - let queueData = { - queryGraph: req.body.message.query_graph, - workflow: req.body.workflow, - callback_url: req.body.callback_url || req.body["callback"], - options: { - logLevel: req.body.log_level, - submitter: req.body.submitter, - ...req.query, - }, - }; - await asyncquery(req, res, next, queueData, global.queryQueue["bte_query_queue"]); - }) - .all(utils.methodNotAllowed); - } - - async task(job) { - const jobID = job.id, - queryGraph = job.data.queryGraph, - workflow = job.data.workflow, - callback_url = job.data.callback_url, - options = { ...job.data.options, schema: await utils.getSchema() }, - jobURL = job.data.url ?? null; - - global.queryInformation = { - jobID, - queryGraph, - callback_url, - }; - - utils.validateWorkflow(workflow); - const handler = new TRAPIQueryHandler({ apiList, ...options }, smartAPIPath, predicatesPath); - handler.setQueryGraph(queryGraph); - const result = await asyncqueryResponse(handler, callback_url, jobID, jobURL, queryGraph); - taskResponse(result); - } -} - -module.exports = new V1RouteAsyncQuery(); diff --git a/src/routes/v1/asyncquery_v1_by_api.js b/src/routes/v1/asyncquery_v1_by_api.js deleted file mode 100644 index f40b428f..00000000 --- a/src/routes/v1/asyncquery_v1_by_api.js +++ /dev/null @@ -1,70 +0,0 @@ -const path = require("path"); -const swaggerValidation = require("../../middlewares/validate"); -const { asyncquery, asyncqueryResponse } = require("../../controllers/async/asyncquery"); -const { getQueryQueue } = require("../../controllers/async/asyncquery_queue"); -const utils = require("../../utils/common"); -const { isMainThread } = require("worker_threads"); -const { TRAPIQueryHandler } = require("@biothings-explorer/query_graph_handler"); -const { API_LIST: apiList } = require("../../config/apis"); -const { taskResponse, runBullTask } = require("../../controllers/threading/threadHandler"); -const smartAPIPath = path.resolve( - __dirname, - process.env.STATIC_PATH ? `${process.env.STATIC_PATH}/data/smartapi_specs.json` : "../../../data/smartapi_specs.json", -); -const predicatesPath = path.resolve( - __dirname, - process.env.STATIC_PATH ? `${process.env.STATIC_PATH}/data/predicates.json` : "../../../data/predicates.json", -); - -class V1RouteAsyncQueryByAPI { - setRoutes(app) { - app - .route("/v1/smartapi/:smartapi_id/asyncquery") - .post(swaggerValidation.validate, async (req, res, next) => { - let queueData = { - queryGraph: req.body.message.query_graph, - smartAPIID: req.params.smartapi_id, - workflow: req.body.workflow, - callback_url: req.body.callback_url || req.body["callback"], - options: { - logLevel: req.body.log_level, - submitter: req.body.submitter, - ...req.query, - }, - // enableIDResolution - }; - await asyncquery(req, res, next, queueData, global.queryQueue["bte_query_queue_by_api"]); - }) - .all(utils.methodNotAllowed); - } - - async task(job) { - const jobID = job.id, - queryGraph = job.data.queryGraph, - workflow = job.data.workflow, - callback_url = job.data.callback_url, - options = { ...job.data.options, schema: await utils.getSchema() }, - smartAPIID = job.data.smartAPIID, - enableIDResolution = job.data.enableIDResolution, - jobURL = job.data.url ?? null; - - global.queryInformation = { - jobID, - queryGraph, - callback_url, - }; - - utils.validateWorkflow(workflow); - const handler = new TRAPIQueryHandler( - { apiList, smartAPIID, enableIDResolution, ...options }, - smartAPIPath, - predicatesPath, - false, - ); - handler.setQueryGraph(queryGraph); - const result = await asyncqueryResponse(handler, callback_url, jobID, jobURL, queryGraph); - taskResponse(result); - } -} - -module.exports = new V1RouteAsyncQueryByAPI(); diff --git a/src/routes/v1/asyncquery_v1_by_team.js b/src/routes/v1/asyncquery_v1_by_team.js deleted file mode 100644 index e93d1dc0..00000000 --- a/src/routes/v1/asyncquery_v1_by_team.js +++ /dev/null @@ -1,72 +0,0 @@ -const path = require("path"); -const swaggerValidation = require("../../middlewares/validate"); -const { asyncquery, asyncqueryResponse } = require("../../controllers/async/asyncquery"); -const { getQueryQueue } = require("../../controllers/async/asyncquery_queue"); -const utils = require("../../utils/common"); -const { isMainThread } = require("worker_threads"); -const { TRAPIQueryHandler } = require("@biothings-explorer/query_graph_handler"); -const { API_LIST: apiList } = require("../../config/apis"); -const { taskResponse, runBullTask } = require("../../controllers/threading/threadHandler"); -const smartAPIPath = path.resolve( - __dirname, - process.env.STATIC_PATH ? `${process.env.STATIC_PATH}/data/smartapi_specs.json` : "../../../data/smartapi_specs.json", -); -const predicatesPath = path.resolve( - __dirname, - process.env.STATIC_PATH ? `${process.env.STATIC_PATH}/data/predicates.json` : "../../../data/predicates.json", -); - -class V1RouteAsyncQueryByTeam { - setRoutes(app) { - app - .route("/v1/team/:team_name/asyncquery") - .post(swaggerValidation.validate, async (req, res, next) => { - const queryGraph = req.body.message.query_graph; - let queueData = { - queryGraph: queryGraph, - teamName: req.params.team_name, - logLevel: req.body.log_level, - workflow: req.body.workflow, - callback_url: req.body.callback_url || req.body["callback"], - options: { - logLevel: req.body.log_level, - submitter: req.body.submitter, - ...req.query, - }, - enableIDResolution: true, - }; - await asyncquery(req, res, next, queueData, global.queryQueue["bte_query_queue_by_team"]); - }) - .all(utils.methodNotAllowed); - } - - async task(job) { - const jobID = job.id, - queryGraph = job.data.queryGraph, - workflow = job.data.workflow, - callback_url = job.data.callback_url, - options = { ...job.data.options, schema: await utils.getSchema() }, - teamName = job.data.teamName, - enableIDResolution = job.data.enableIDResolution, - jobURL = job.data.url ?? null; - - global.queryInformation = { - jobID, - queryGraph, - callback_url, - }; - - utils.validateWorkflow(workflow); - const handler = new TRAPIQueryHandler( - { apiList, teamName, enableIDResolution, ...options }, - smartAPIPath, - predicatesPath, - false - ); - handler.setQueryGraph(queryGraph); - const result = await asyncqueryResponse(handler, callback_url, jobID, jobURL, queryGraph); - taskResponse(result); - } -} - -module.exports = new V1RouteAsyncQueryByTeam(); diff --git a/src/routes/v1/meta_knowledge_graph_v1.js b/src/routes/v1/meta_knowledge_graph_v1.js deleted file mode 100644 index 67932a00..00000000 --- a/src/routes/v1/meta_knowledge_graph_v1.js +++ /dev/null @@ -1,22 +0,0 @@ -const handler = require("../../controllers/meta_knowledge_graph"); -const utils = require("../../utils/common"); - -class RouteMetaKG { - setRoutes(app) { - app - .route("/v1/meta_knowledge_graph") - .get(async (req, res, next) => { - try { - const metaKGHandler = new handler(undefined); - const kg = await metaKGHandler.getKG(); - res.setHeader("Content-Type", "application/json"); - res.end(JSON.stringify(kg)); - } catch (error) { - next(error); - } - }) - .all(utils.methodNotAllowed); - } -} - -module.exports = new RouteMetaKG(); diff --git a/src/routes/v1/meta_knowledge_graph_v1_by_api.js b/src/routes/v1/meta_knowledge_graph_v1_by_api.js deleted file mode 100644 index d15324c0..00000000 --- a/src/routes/v1/meta_knowledge_graph_v1_by_api.js +++ /dev/null @@ -1,22 +0,0 @@ -const handler = require("../../controllers/meta_knowledge_graph"); -const utils = require("../../utils/common"); - -class RouteMetaKGByAPI { - setRoutes(app) { - app - .route("/v1/smartapi/:smartapiID/meta_knowledge_graph") - .get(async (req, res, next) => { - try { - const metaKGHandler = new handler(req.params.smartapiID); - const kg = await metaKGHandler.getKG(); - res.setHeader("Content-Type", "application/json"); - res.end(JSON.stringify(kg)); - } catch (error) { - next(error); - } - }) - .all(utils.methodNotAllowed); - } -} - -module.exports = new RouteMetaKGByAPI(); diff --git a/src/routes/v1/meta_knowledge_graph_v1_by_team.js b/src/routes/v1/meta_knowledge_graph_v1_by_team.js deleted file mode 100644 index 3ab41ea9..00000000 --- a/src/routes/v1/meta_knowledge_graph_v1_by_team.js +++ /dev/null @@ -1,22 +0,0 @@ -const handler = require("../../controllers/meta_knowledge_graph"); -const utils = require("../../utils/common"); - -class RouteMetaKGByTeam { - setRoutes(app) { - app - .route("/v1/team/:teamName/meta_knowledge_graph") - .get(async (req, res, next) => { - try { - const metaKGHandler = new handler(undefined, req.params.teamName); - const kg = await metaKGHandler.getKG(); - res.setHeader("Content-Type", "application/json"); - res.end(JSON.stringify(kg)); - } catch (error) { - next(error); - } - }) - .all(utils.methodNotAllowed); - } -} - -module.exports = new RouteMetaKGByTeam(); diff --git a/src/routes/v1/query_v1.js b/src/routes/v1/query_v1.js deleted file mode 100644 index 3c78f412..00000000 --- a/src/routes/v1/query_v1.js +++ /dev/null @@ -1,54 +0,0 @@ -const path = require("path"); -const { API_LIST: apiList } = require("../../config/apis"); -const TRAPIGraphHandler = require("@biothings-explorer/query_graph_handler"); -const swaggerValidation = require("../../middlewares/validate"); -const smartAPIPath = path.resolve( - __dirname, - process.env.STATIC_PATH ? `${process.env.STATIC_PATH}/data/smartapi_specs.json` : "../../../data/smartapi_specs.json", -); -const predicatesPath = path.resolve( - __dirname, - process.env.STATIC_PATH ? `${process.env.STATIC_PATH}/data/predicates.json` : "../../../data/predicates.json", -); -const utils = require("../../utils/common"); -const { runTask, taskResponse, taskError } = require("../../controllers/threading/threadHandler"); -const { isMainThread } = require("worker_threads"); -const { getQueryQueue } = require("../../controllers/async/asyncquery_queue"); - -class V1RouteQuery { - setRoutes(app) { - app - .route("/v1/query") - .post(swaggerValidation.validate, async (req, res, next) => { - try { - // req.schema = await utils.getSchema(); - const response = await runTask(req, this.task, path.parse(__filename).name, res); - res.setHeader("Content-Type", "application/json"); - res.end(JSON.stringify(response)); - } catch (err) { - next(err); - } - }) - .all(utils.methodNotAllowed); - } - - async task(job) { - const queryGraph = job.data.queryGraph, - workflow = job.data.workflow, - options = { ...job.data.options, schema: await utils.getSchema() }; - try { - utils.validateWorkflow(workflow); - const handler = new TRAPIGraphHandler.TRAPIQueryHandler({ apiList, ...options }, smartAPIPath, predicatesPath); - handler.setQueryGraph(queryGraph); - await handler.query(); - - const response = handler.getResponse(); - utils.filterForLogLevel(response, options.logLevel); - return taskResponse(response); - } catch (error) { - return taskError(error); - } - } -} - -module.exports = new V1RouteQuery(); diff --git a/src/routes/v1/query_v1_by_api.js b/src/routes/v1/query_v1_by_api.js deleted file mode 100644 index 529653dd..00000000 --- a/src/routes/v1/query_v1_by_api.js +++ /dev/null @@ -1,62 +0,0 @@ -const TRAPIGraphHandler = require("@biothings-explorer/query_graph_handler"); -const swaggerValidation = require("../../middlewares/validate"); -const path = require("path"); -const smartAPIPath = path.resolve( - __dirname, - process.env.STATIC_PATH ? `${process.env.STATIC_PATH}/data/smartapi_specs.json` : "../../../data/smartapi_specs.json", -); -const predicatesPath = path.resolve( - __dirname, - process.env.STATIC_PATH ? `${process.env.STATIC_PATH}/data/predicates.json` : "../../../data/predicates.json", -); -const utils = require("../../utils/common"); -const { runTask, taskResponse, taskError } = require("../../controllers/threading/threadHandler"); -const { API_LIST: apiList } = require("../../config/apis"); - -class RouteQueryV1ByAPI { - setRoutes(app) { - app - .route("/v1/smartapi/:smartapi_id/query") - .post(swaggerValidation.validate, async (req, res, next) => { - try { - req.schema = await utils.getSchema(); - const response = await runTask(req, this.task, path.parse(__filename).name); - res.setHeader("Content-Type", "application/json"); - res.end(JSON.stringify(response)); - } catch (error) { - next(error); - } - }) - .all(utils.methodNotAllowed); - } - - async task(job) { - try { - const queryGraph = job.data.queryGraph, - workflow = job.data.workflow, - options = { ...job.data.options, schema: await utils.getSchema() }; - utils.validateWorkflow(workflow); - // Disabled the disabling of text-mining / multiomics provider APIs -- we're not sure why they were disabled in the first place... - // const enableIDResolution = (['5be0f321a829792e934545998b9c6afe', '978fe380a147a8641caf72320862697b'].includes(req.params.smartapi_id)) ? false : true; - const handler = new TRAPIGraphHandler.TRAPIQueryHandler( - { - apiList, - ...options, - // enableIDResolution - }, - smartAPIPath, - predicatesPath, - false, - ); - handler.setQueryGraph(queryGraph); - await handler.query(); - const response = handler.getResponse(); - utils.filterForLogLevel(response, options.logLevel); - return taskResponse(response); - } catch (error) { - return taskError(error); - } - } -} - -module.exports = new RouteQueryV1ByAPI(); diff --git a/src/routes/v1/query_v1_by_team.js b/src/routes/v1/query_v1_by_team.js deleted file mode 100644 index 14dd761a..00000000 --- a/src/routes/v1/query_v1_by_team.js +++ /dev/null @@ -1,61 +0,0 @@ -const TRAPIGraphHandler = require("@biothings-explorer/query_graph_handler"); -const swaggerValidation = require("../../middlewares/validate"); -const path = require("path"); -const smartAPIPath = path.resolve( - __dirname, - process.env.STATIC_PATH ? `${process.env.STATIC_PATH}/data/smartapi_specs.json` : "../../../data/smartapi_specs.json", -); -const predicatesPath = path.resolve( - __dirname, - process.env.STATIC_PATH ? `${process.env.STATIC_PATH}/data/predicates.json` : "../../../data/predicates.json", -); -const utils = require("../../utils/common"); -const { runTask, taskResponse, taskError } = require("../../controllers/threading/threadHandler"); -const { API_LIST: apiList } = require("../../config/apis"); - -class RouteQueryV1ByTeam { - setRoutes(app) { - app - .route("/v1/team/:team_name/query") - .post(swaggerValidation.validate, async (req, res, next) => { - try { - req.schema = await utils.getSchema(); - const response = await runTask(req, this.task, path.parse(__filename).name); - res.setHeader("Content-Type", "application/json"); - res.end(JSON.stringify(response)); - } catch (error) { - next(error); - } - }) - .all(utils.methodNotAllowed); - } - - async task(job) { - const queryGraph = job.data.queryGraph, - workflow = job.data.workflow, - options = { ...job.data.options, schema: await utils.getSchema() }; - try { - utils.validateWorkflow(workflow); - // const enableIDResolution = (req.params.team_name === "Text Mining Provider") ? false : true; - const handler = new TRAPIGraphHandler.TRAPIQueryHandler( - { - apiList, - ...options, - enableIDResolution: true, - }, - smartAPIPath, - predicatesPath, - false, - ); - handler.setQueryGraph(queryGraph); - await handler.query(); - const response = handler.getResponse(); - utils.filterForLogLevel(response, options.logLevel); - return taskResponse(response); - } catch (error) { - return taskError(error); - } - } -} - -module.exports = new RouteQueryV1ByTeam(); diff --git a/src/server.js b/src/server.js deleted file mode 100644 index 7e785418..00000000 --- a/src/server.js +++ /dev/null @@ -1,32 +0,0 @@ -const debug = require("debug")("bte:biothings-explorer-trapi:server-start"); - -async function main() { - await testRedisConnection(); // must happen before app to avoid issues - const app = require("./app"); - const cron = require("./controllers/cron/index"); - const PORT = Number.parseInt(process.env.PORT) || 3000; - cron(); - app.listen(PORT, () => { - // console.log(`App listening at http://localhost:${PORT}`); - console.log(`⭐⭐⭐ BioThings Explorer is ready! ⭐ Try it now @ http://localhost:${PORT} ✨`) - }); - process.env.DEBUG_COLORS = 'true'; -} - -async function testRedisConnection() { - const { redisClient } = require("@biothings-explorer/query_graph_handler"); - - if (redisClient.clientEnabled) { // redis enabled - debug('Checking connection to redis...'); - try { - await redisClient.client.pingTimeout(); - debug('Redis connection successful.'); - } catch (error) { - debug(`Redis connection failed due to error ${error}`); - debug(`Disabling redis for current server runtime...`); - process.env.INTERNAL_DISABLE_REDIS = true; - } - } -} - -main(); diff --git a/src/utils/checkIfZombified.js b/src/utils/checkIfZombified.js deleted file mode 100644 index caac4a57..00000000 --- a/src/utils/checkIfZombified.js +++ /dev/null @@ -1,10 +0,0 @@ -const checkIfZombified = () => { - if (process.ppid === 1) { - console.log("Bull processor zombified, exiting..."); - throw new Error("Bull processor zombified, exiting..."); - } else { - setTimeout(checkIfZombified, 1000); - } -} - -exports.checkIfZombified = checkIfZombified; diff --git a/src/utils/common.js b/src/utils/common.js deleted file mode 100644 index 6665b05d..00000000 --- a/src/utils/common.js +++ /dev/null @@ -1,58 +0,0 @@ -const WorkflowError = require("./errors/workflow_error"); -const URL = require("url").URL; -const yaml2json = require('js-yaml'); -const fs = require('fs/promises'); -const path = require('path'); - -const schema = []; - -exports.getSchema = async () => { - if (schema.length !== 0) return schema[0]; - schema.push(yaml2json.load(await fs.readFile(path.join(__dirname, '../../docs/smartapi.yaml'), { encoding: 'utf8' }))); -// console.log(schema); - return schema[0]; -}; - -exports.removeQuotesFromQuery = (queryString) => { - if (queryString.startsWith('"') && queryString.endsWith('"')) { - return queryString.slice(1, -1); - } else if (queryString.startsWith("'") && queryString.endsWith("'")) { - return queryString.slice(1, -1); - } else { - return queryString; - } -} - -exports.validateWorkflow = (workflow) => { - if (workflow === undefined) { - return; - } - if (!Array.isArray(workflow) || workflow.length !== 1 || workflow[0].id !== 'lookup') { - throw new WorkflowError("BTE doesn't handle the operations specified in the workflow field."); - } -} - -exports.stringIsAValidUrl = (s) => { - try { - new URL(s); - return true; - } catch (err) { - return false; - } -}; - -exports.filterForLogLevel = (response, logLevel) => { - const logLevels = { - ERROR: 3, - WARNING: 2, - INFO: 1, - DEBUG: 0 - } - if (logLevel && Object.keys(logLevels).includes(logLevel)) { - response.logs = response.logs.filter(log => { - return logLevels[log.level] >= logLevels[logLevel] - }); - } -} - -exports.methodNotAllowed = (req, res, next) => res.status(405).send(); diff --git a/src/utils/errors/metakg_error.js b/src/utils/errors/metakg_error.js deleted file mode 100644 index f40681cd..00000000 --- a/src/utils/errors/metakg_error.js +++ /dev/null @@ -1,11 +0,0 @@ -class MetaKGLoadingError extends Error { - constructor(message = "Failed to load metakg", ...params) { - super(...params); - - this.name = 'MetaKGLoadingError'; - this.message = message; - this.statusCode = 400; - } -} - -module.exports = MetaKGLoadingError; \ No newline at end of file diff --git a/src/utils/errors/predicates_error.js b/src/utils/errors/predicates_error.js deleted file mode 100644 index f340f00c..00000000 --- a/src/utils/errors/predicates_error.js +++ /dev/null @@ -1,11 +0,0 @@ -class PredicatesLoadingError extends Error { - constructor(message = "Failed to load metakg", ...params) { - super(...params); - - this.name = 'PredicatesLoadingError'; - this.message = message; - this.statusCode = 400; - } -} - -module.exports = PredicatesLoadingError; \ No newline at end of file diff --git a/src/utils/errors/server_overloaded_error.js b/src/utils/errors/server_overloaded_error.js deleted file mode 100644 index d78aa73f..00000000 --- a/src/utils/errors/server_overloaded_error.js +++ /dev/null @@ -1,11 +0,0 @@ -class ServerOverloadedError extends Error { - constructor(message, retryAfter, ...params) { - super(params); - this.name = "ServerOverloadedError"; - this.message = message ?? "Server is overloaded, please try again later."; - this.status = 503; - this.retryAfter = retryAfter ?? 60; - } -} - -module.exports = ServerOverloadedError; diff --git a/src/utils/errors/workflow_error.js b/src/utils/errors/workflow_error.js deleted file mode 100644 index 6bc77969..00000000 --- a/src/utils/errors/workflow_error.js +++ /dev/null @@ -1,11 +0,0 @@ -class WorkflowError extends Error { - constructor(message = "BTE doesn't handle the operations specified in the workflow field", ...params) { - super(...params); - - this.name = 'WorkflowError'; - this.message = message; - this.statusCode = 400; - } -} - -module.exports = WorkflowError; diff --git a/src/web-app/package-lock.json b/src/web-app/package-lock.json deleted file mode 100644 index f36fe8ae..00000000 --- a/src/web-app/package-lock.json +++ /dev/null @@ -1,6511 +0,0 @@ -{ - "name": "@marcodarko/btewebapp", - "version": "1.0.8", - "lockfileVersion": 2, - "requires": true, - "packages": { - "": { - "name": "@marcodarko/btewebapp", - 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"vue": "^3.2.39", - "vue-router": "^4.1.5", - "zdog": "^1.1.3" - }, - "devDependencies": { - "@rushstack/eslint-patch": "^1.2.0", - "@vitejs/plugin-vue": "^3.1.0", - "@vue/eslint-config-prettier": "^7.0.0", - "autoprefixer": "^10.4.11", - "cssnano": "^5.1.13", - "eslint": "^8.23.1", - "eslint-plugin-vue": "^9.5.1", - "postcss": "^8.4.16", - "postcss-import": "^15.0.0", - "prettier": "^2.7.1", - "sass": "^1.54.9", - "tailwindcss": "^3.1.8", - "vite": "^3.2.7", - "vite-svg-loader": "^3.6.0" - }, - "keywords": [ - "vue", - "vue3", - "vuejs", - "vue3js", - "template", - "router", - "vuerouter", - "vue-router", - "tailwind", - "tailwindcss", - "tailwind-css", - "pinia", - "svg" - ] -} diff --git a/src/web-app/src/stores/examples.js b/src/web-app/src/stores/examples.js deleted file mode 100644 index 0f574884..00000000 --- a/src/web-app/src/stores/examples.js +++ /dev/null @@ -1,228 +0,0 @@ -import moment from 'moment' -import { defineStore } from "pinia"; -import axios from 'axios'; -import { useMainStore } from './general' - -export const useExamplesStore = defineStore({ - id: "examples", - state: () => ({ - queries: [ - { - 'selected': false, - 'name' :'Disease (Kartagener syndrome) has phenotypic feature', - 'id': 423423, - 'elements': { - 'nodes': [ - { data: { id: 'dis', name: '⭐Disease\n(MONDO:0016575)', color: '#8d5bd4' } }, - { data: { id: 'ph', name: 'PhenotypicFeature', color: '#2abcbd' } }, - ], - 'edges': [ - { data: { source: 'dis', target: 'ph', name:'⭐biolink:has_phenotype' } } - ] - }, - 'query': - { - "message": { - "query_graph": { - "nodes": { - "n0": { - "categories": ["biolink:Disease"], - "ids": ["MONDO:0016575"] - }, - "n1": { - "categories": ["biolink:PhenotypicFeature"] - } - }, - "edges": { - "e01": { - "subject": "n0", - "object": "n1", - "predicates": ["biolink:has_phenotype"] - } - } - } - } - } - }, - { - 'selected': false, - 'name' :'Disease (Kartagener syndrome) relation to genes', - 'id': 428423, - 'elements': { - 'nodes': [ - { data: { id: 'dis', name: '⭐Disease\n(MONDO:0016575)', color: '#8d5bd4' } }, - { data: { id: 'gene', name: 'Gene', color: '#369ac1' } }, - ], - 'edges': [ - { data: { source: 'dis', target: 'gene', name:'' } } - ] - }, - "query":{ - "message": { - "query_graph": { - "nodes": { - "n0": { - "categories": ["biolink:Disease"], - "ids": ["MONDO:0005737"] - }, - "n1": { - "categories": ["biolink:Gene"] - } - }, - "edges": { - "e01": { - "subject": "n0", - "object": "n1" - } - } - } - } - } - }, - { - 'selected': false, - 'name' :'Disease (Ebola hemorrhagic fever) gene relation to small molecules', - 'id': 426654, - 'elements': { - 'nodes': [ - - { data: { id: 'dis', name: '⭐Disease\n(MONDO:0005737)', color: '#8d5bd4' } }, - { data: { id: 'gene', name: 'Gene', color: '#369ac1' } }, - { data: { id: 'sm', name: 'SmallMolecule', color: 'hotpink' } }, - ], - 'edges': [ - { data: { source: 'dis', target: 'gene', name:'' } }, - { data: { source: 'gene', target: 'sm', name:'' } }, - ] - }, - "query": { - "message": { - "query_graph": { - "nodes": { - "n0": { - "categories": ["biolink:Disease"], - "ids": ["MONDO:0005737"] - }, - "n1": { - "categories": ["biolink:Gene"] - }, - "n2": { - "categories": ["biolink:SmallMolecule"] - } - }, - "edges": { - "e01": { - "subject": "n0", - "object": "n1" - }, - "e02": { - "subject": "n1", - "object": "n2" - } - } - } - } - } - }, - { - 'selected': false, - 'name' :'Gene (NCBIGene:3778) relation to small molecules via other genes', - 'id': 453423, - 'elements': { - 'nodes': [ - { data: { id: 'gene', name: '⭐Gene\n(NCBIGene:3778)', color: '#369ac1' } }, - { data: { id: 'gene2', name: 'Gene', color: '#369ac1' } }, - { data: { id: 'sm', name: 'SmallMolecule', color: 'hotpink' } }, - ], - 'edges': [ - { data: { source: 'gene', target: 'gene2', name:'' } }, - { data: { source: 'gene2', target: 'sm', name:'' } }, - ] - }, - "query": { - "message": { - "query_graph": { - "nodes": { - "n0": { - "categories": ["biolink:Gene"], - "ids": ["NCBIGene:3778"] - }, - "n1": { - "categories": ["biolink:Gene"] - }, - "n2": { - "categories": ["biolink:SmallMolecule"] - } - }, - "edges": { - "e01": { - "subject": "n0", - "object": "n1" - }, - "e02": { - "subject": "n1", - "object": "n2" - } - } - } - } - } - }, - ], - message: '', - jobs: [], - jobPicked: '' - }), - getters: { - selectedQuery: (state) => state.queries.find((q) => q.selected), - }, - actions: { - select(id) { - this.queries.forEach((q) => { - if ( q.id == id) { - q.selected = !q.selected - }else{ - q.selected = false; - } - }) - }, - async sendRequest(query, description) { - let self = this; - let store = useMainStore(); - store.loading = true; - axios.post('/v1/asyncquery', JSON.parse(query)).then(res=>{ - store.loading = false; - console.log(res.data) - self.jobs.unshift({ - 'id': res.data.job_id, - 'date': this.getDateRightNow(), - 'url': res.data.job_url, - 'description': description - }); - self.message = `A new job ID has been created: ${res.data.job_id} ` - self.updateJobs(); - }).catch(err=>{ - store.loading = false; - console.log(err); - self.message = `Oh no: ${err} ` - throw err; - }); - }, - updateJobs(){ - localStorage.setItem('bte-jobs', JSON.stringify(this.jobs)); - }, - getJobs(){ - let j = JSON.parse(localStorage.getItem('bte-jobs')); - if (j && j.length) { - this.jobs = j; - } - }, - deleteJobs(){ - localStorage.removeItem('bte-jobs'); - this.jobs = []; - }, - getDateRightNow(){ - return moment().format('MMMM Do YYYY, h:mm:ss'); - } - }, -}); diff --git a/tsconfig.opts.json b/tsconfig.base.json similarity index 100% rename from tsconfig.opts.json rename to tsconfig.base.json diff --git a/tsconfig.build.json b/tsconfig.build.json index aff4341d..207733bf 100644 --- a/tsconfig.build.json +++ b/tsconfig.build.json @@ -1,8 +1,23 @@ { + "compilerOptions": { + "paths": { + "@biothings-explorer/api-response-transform": ["packages/api-response-transform"], + "biolink-model": ["packages/biolink-model"], + "biomedical_id_resolver": ["packages/biomedical_id_resolver"], + "@biothings-explorer/call-apis": ["packages/biomedical_id_resolver"], + "@biothings-explorer/node-expansion": ["packages/node-expansion"], + "@biothings-explorer/query_graph_handler": ["packages/query_graph_handler"], + "@biothings-explorer/smartapi-kg": ["packages/smartapi-kg"], + "@biothings-explorer/bte-server": ["packages/bte-server"] + } + }, "files": [], "references": [ { - "path": "." + "path": "packages/bte-server" + }, + { + "paths": "packages/bte-server/web-app" }, { "path": "packages/biolink-model" @@ -11,19 +26,19 @@ "path": "packages/biomedical_id_resolver" }, { - "path": "packages/@biothings-explorer/smartapi-kg" + "path": "packages/smartapi-kg" }, { - "path": "packages/@biothings-explorer/api-response-transform" + "path": "packages/api-response-transform" }, { - "path": "packages/@biothings-explorer/call-apis" + "path": "packages/call-apis" }, { - "path": "packages/@biothings-explorer/query_graph_handler" + "path": "packages/query_graph_handler" }, { - "path": "packages/@biothings-explorer/node-expansion" + "path": "packages/node-expansion" } ] } diff --git a/tsconfig.json b/tsconfig.json index 1816db24..5cdbf83c 100644 --- a/tsconfig.json +++ b/tsconfig.json @@ -1,5 +1,5 @@ { - "extends": "./tsconfig.opts.json", + "extends": "./tsconfig.base.json", "compilerOptions": { "rootDir": "src", "outDir": "built" @@ -10,17 +10,10 @@ "./data/predicates.json" ], "exclude": [ - "node_modules", - "__test__/", - "packages", - "./src/web-app/dist/*" + "**/node_modules/**", + "**/__test__/**", + "**/packages/**", + "./packages/server/src/web-app/dist/*" ], - "references": [ - { - "path": "./packages/@biothings-explorer/smartapi-kg" - }, - { - "path": "./packages/@biothings-explorer/query_graph_handler" - } - ] + "references": [] } diff --git a/turbo.json b/turbo.json new file mode 100644 index 00000000..3d8ac536 --- /dev/null +++ b/turbo.json @@ -0,0 +1,67 @@ +{ + "$schema": "https://turbo.build/schema.json", + "pipeline": { + "build": { + "dependsOn": [ + "^build" + ], + "outputs": [ + "./built/**", + "./dist/**" + ] + }, + "clean": {}, + "build:clean": {}, + "test": { + "dependsOn": [ + "build" + ] + }, + "test-cov": { + "dependsOn": [ + "build" + ] + }, + "//:lint": { + "inputs": [ + "!.git/**", + "!node_modules/**", + "!packages/**" + ] + }, + "//:lint:fix": { + "inputs": [ + "!.git/**", + "!node_modules/**", + "!packages/**" + ] + }, + "//:format": { + "inputs": [ + "!.git/**", + "!node_modules/**", + "!packages/**" + ] + }, + "//:format:fix": { + "inputs": [ + "!.git/**", + "!node_modules/**", + "!packages/**" + ] + }, + "lint": {}, + "lint:fix": {}, + "format": {}, + "format:fix": {} + }, + "globalDependencies": [ + ".eslintrc.js", + ".eslintignore", + ".lintstagedrc.js", + ".prettierrc.yaml", + "tsconfig.base.json", + "tsconfig.build.json", + "tsconfig.json" + ] +}