fix: fix conflict

biothings · Jun 15, 2021 · 6cb4767 · 6cb4767
2 parents 56382e3 + 1f7ec7f
commit 6cb4767
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diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -2,6 +2,13 @@
 
 All notable changes to this project will be documented in this file. See [standard-version](https://github.com/conventional-changelog/standard-version) for commit guidelines.
 
+### [1.17.2](https://github.com/kevinxin90/bte_trapi_query_graph_handler/compare/v1.17.1...v1.17.2) (2021-06-15)
+
+
+### Bug Fixes
+
+* :bug: change type to value_type_id in TRAPI response ([4f34d5f](https://github.com/kevinxin90/bte_trapi_query_graph_handler/commit/4f34d5f922c1914d550a1a9a22662f73282424fd))
+
 ### [1.17.1](https://github.com/kevinxin90/bte_trapi_query_graph_handler/compare/v1.17.0...v1.17.1) (2021-06-04)
 
 

diff --git a/package-lock.json b/package-lock.json
diff --git a/package.json b/package.json
@@ -1,62 +1,62 @@
 {
-    "name": "@biothings-explorer/query_graph_handler",
-    "version": "1.17.1",
-    "description": "A nodejs module to query TRAPI Query Graph",
-    "main": "built/index.js",
-    "scripts": {
-        "test": "jest",
-        "test-cov": "jest --coverage",
-        "build": "tsc",
-        "coveralls": "jest --coverage && cat ./coverage/lcov.info | ./node_modules/coveralls/bin/coveralls.js && rm -rf ./coverage",
-        "format": "prettier --write \"src/**/*.*s\" \"built/**/*.js\"",
-        "lint": "tslint -p tsconfig.json",
-        "prepare": "npm run build",
-        "prepublishOnly": "npm test",
-        "version": "npm run format && git add -A src",
-        "postversion": "git push && git push --tags",
-        "release": "npm run format && standard-version",
-        "release:minor": "npm run format && standard-version --release-as minor",
-        "release:patch": "npm run format && standard-version --release-as patch",
-        "release:major": "npm run format && standard-version --release-as major"
-    },
-    "repository": {
-        "type": "git",
-        "url": "git+https://github.com/kevinxin90/bte_trapi_query_graph_handler.git"
-    },
-    "keywords": [
-        "id",
-        "conversion",
-        "biomedical"
-    ],
-    "author": "jiwen xin",
-    "license": "ISC",
-    "bugs": {
-        "url": "https://github.com/kevinxin90/bte_trapi_query_graph_handler/issues"
-    },
-    "homepage": "https://github.com/kevinxin90/bte_trapi_query_graph_handler#readme",
-    "devDependencies": {
-        "@types/debug": "^4.1.5",
-        "@types/jest": "^26.0.22",
-        "@types/node": "^14.14.37",
-        "coveralls": "^3.1.0",
-        "jest": "^26.6.3",
-        "prettier": "^2.2.1",
-        "redis-mock": "^0.56.3",
-        "standard-version": "^9.1.0",
-        "ts-jest": "^26.5.4",
-        "tslint": "^6.1.3",
-        "tslint-config-prettier": "^1.18.0",
-        "typedoc": "^0.20.34",
-        "typescript": "^4.2.3"
-    },
-    "dependencies": {
-        "@biothings-explorer/call-apis": "^1.23.1",
-        "@biothings-explorer/smartapi-kg": "^3.8.1",
-        "biolink-model": "^0.3.0",
-        "biomedical_id_resolver": "^3.9.0",
-        "debug": "^4.3.1",
-        "lodash": "^4.17.21",
-        "ms": "^2.1.3",
-        "redis": "^3.0.2"
-    }
+  "name": "@biothings-explorer/query_graph_handler",
+  "version": "1.17.2",
+  "description": "A nodejs module to query TRAPI Query Graph",
+  "main": "built/index.js",
+  "scripts": {
+    "test": "jest",
+    "test-cov": "jest --coverage",
+    "build": "tsc",
+    "coveralls": "jest --coverage && cat ./coverage/lcov.info | ./node_modules/coveralls/bin/coveralls.js && rm -rf ./coverage",
+    "format": "prettier --write \"src/**/*.*s\" \"built/**/*.js\"",
+    "lint": "tslint -p tsconfig.json",
+    "prepare": "npm run build",
+    "prepublishOnly": "npm test",
+    "version": "npm run format && git add -A src",
+    "postversion": "git push && git push --tags",
+    "release": "npm run format && standard-version",
+    "release:minor": "npm run format && standard-version --release-as minor",
+    "release:patch": "npm run format && standard-version --release-as patch",
+    "release:major": "npm run format && standard-version --release-as major"
+  },
+  "repository": {
+    "type": "git",
+    "url": "git+https://github.com/kevinxin90/bte_trapi_query_graph_handler.git"
+  },
+  "keywords": [
+    "id",
+    "conversion",
+    "biomedical"
+  ],
+  "author": "jiwen xin",
+  "license": "ISC",
+  "bugs": {
+    "url": "https://github.com/kevinxin90/bte_trapi_query_graph_handler/issues"
+  },
+  "homepage": "https://github.com/kevinxin90/bte_trapi_query_graph_handler#readme",
+  "devDependencies": {
+    "@types/debug": "^4.1.5",
+    "@types/jest": "^26.0.22",
+    "@types/node": "^14.14.37",
+    "coveralls": "^3.1.0",
+    "jest": "^26.6.3",
+    "prettier": "^2.2.1",
+    "redis-mock": "^0.56.3",
+    "standard-version": "^9.1.1",
+    "ts-jest": "^26.5.4",
+    "tslint": "^6.1.3",
+    "tslint-config-prettier": "^1.18.0",
+    "typedoc": "^0.20.34",
+    "typescript": "^4.2.3"
+  },
+  "dependencies": {
+    "@biothings-explorer/call-apis": "^1.23.1",
+    "@biothings-explorer/smartapi-kg": "^3.8.1",
+    "biolink-model": "^0.3.1",
+    "biomedical_id_resolver": "^3.9.0",
+    "debug": "^4.3.1",
+    "lodash": "^4.17.21",
+    "ms": "^2.1.3",
+    "redis": "^3.1.1"
+  }
 }
diff --git a/src/batch_edge_query.js b/src/batch_edge_query.js
@@ -32,7 +32,7 @@ module.exports = class BatchEdgeQueryHandler {
    * @private
    */
   _expandBTEEdges(bteEdges) {
-    debug(`BTE EDGE ${JSON.stringify(this.qEdges)}`)
+    debug(`BTE EDGE ${JSON.stringify(this.qEdges)}`);
     return bteEdges;
   }
 
@@ -57,13 +57,13 @@ module.exports = class BatchEdgeQueryHandler {
         //add query predicate to the expanded list
         predicate_filters.concat(item['$edge_metadata']['trapi_qEdge_obj']['qEdge']['predicate'])
         //remove prefix from filter list to match predicate name format
-        predicate_filters = predicate_filters.map(item => utils.removeBioLinkPrefix(item))
+        predicate_filters = predicate_filters.map((item) => utils.removeBioLinkPrefix(item));
         //compare edge predicate to filter list
         this.logs.push(
           new LogEntry('DEBUG', null, `query_graph_handler: Current edge post-query predicate restriction includes: ${JSON.stringify(predicate_filters)}`).getLog()
         );
         if (predicate_filters.includes(edge_predicate)) {
-          return item
+          return item;
         }
       });
       debug(`Filtered results from ${response.length} down to ${filtered.length} results`);
@@ -76,7 +76,7 @@ module.exports = class BatchEdgeQueryHandler {
       return filtered
     } catch (error) {
       debug(`Failed to filter ${response.length} results due to ${error}`);
-      return response
+      return response;
     }
   }
 

diff --git a/src/graph/knowledge_graph.js b/src/graph/knowledge_graph.js
@@ -22,41 +22,41 @@ module.exports = class KnowledgeGraph {
 
   _createNode(kgNode) {
     const res = {
-      category: 'biolink:' + kgNode._semanticType,
+      categories: ['biolink:' + kgNode._semanticType],
       name: kgNode._label,
       attributes: [
         {
           attribute_type_id: 'equivalent_identifiers',
           value: kgNode._curies,
-          type: 'biolink:id',
+          value_type_id: 'biolink:id',
         },
         {
           attribute_type_id: 'num_source_nodes',
           value: kgNode._sourceNodes.size,
-          type: 'bts:num_source_nodes',
+          value_type_id: 'bts:num_source_nodes',
         },
         {
           attribute_type_id: 'num_target_nodes',
           value: kgNode._targetNodes.size,
-          type: 'bts:num_target_nodes',
+          value_type_id: 'bts:num_target_nodes',
         },
         {
           attribute_type_id: 'source_qg_nodes',
           value: Array.from(kgNode._sourceQGNodes),
-          type: 'bts:source_qg_nodes',
+          value_type_id: 'bts:source_qg_nodes',
         },
         {
           attribute_type_id: 'target_qg_nodes',
           value: Array.from(kgNode._targetQGNodes),
-          type: 'bts:target_qg_nodes',
+          value_type_id: 'bts:target_qg_nodes',
         },
       ],
     };
     for (const key in kgNode._nodeAttributes) {
       res.attributes.push({
         attribute_type_id: key,
         value: kgNode._nodeAttributes[key],
-        type: 'bts:' + key,
+        value_type_id: 'bts:' + key,
       });
     }
     return res;
@@ -67,24 +67,24 @@ module.exports = class KnowledgeGraph {
       {
         attribute_type_id: 'provided_by',
         value: Array.from(kgEdge.sources),
-        type: 'biolink:provided_by',
+        value_type_id: 'biolink:provided_by',
       },
       {
         attribute_type_id: 'api',
         value: Array.from(kgEdge.apis),
-        type: 'bts:api',
+        value_type_id: 'bts:api',
       },
       {
         attribute_type_id: 'publications',
         value: Array.from(kgEdge.publications),
-        type: 'biolink:publication',
+        value_type_id: 'biolink:publication',
       },
     ];
     for (const key in kgEdge.attributes) {
       attributes.push({
         attribute_type_id: key,
         value: kgEdge.attributes[key],
-        type: 'bts:' + key,
+        value_type_id: 'bts:' + key,
       });
     }
     return attributes;

diff --git a/src/qedge2bteedge.js b/src/qedge2bteedge.js
@@ -32,9 +32,9 @@ module.exports = class QEdge2BTEEdgeHandler {
       new LogEntry(
         'DEBUG',
         null,
-        `BTE is trying to find SmartAPI edges connecting from ${qEdge
-          .getSubject()
-          .getCategories()} to ${qEdge.getObject().getCategories()} with predicate ${qEdge.getPredicate()}`,
+        `BTE is trying to find SmartAPI edges connecting from ${qEdge.getSubject().getCategories()} to ${qEdge
+          .getObject()
+          .getCategories()} with predicate ${qEdge.getPredicate()}`,
       ).getLog(),
     );
     let filterCriteria = {

diff --git a/src/query_edge.js b/src/query_edge.js
@@ -14,12 +14,12 @@ module.exports = class QEdge {
     this.predicate = info.predicates;
     this.subject = info.subject;
     this.object = info.object;
-    this.expanded_predicates = []
-    this.init()
+    this.expanded_predicates = [];
+    this.init();
   }
 
   init() {
-    this.expanded_predicates = this.getPredicate()
+    this.expanded_predicates = this.getPredicate();
   }
 
   getID() {

diff --git a/src/query_graph.js b/src/query_graph.js
@@ -107,7 +107,7 @@ module.exports = class QueryGraphHandler {
         `BTE identified your query graph as a ${Object.keys(paths).length}-depth query graph`,
       ).getLog(),
     );
-    debug(`ALL PATHS ${JSON.stringify(paths)}`)
+    debug(`ALL PATHS ${JSON.stringify(paths)}`);
     return paths;
   }