Merge pull request #27 from TheJacksonLaboratory/G3-208-batch-upload-…

…database-functions

G3 208 Setup and cleanup before adding batch upload database functions

.github/workflows/_check-coverage-action.yml

@@ -61,4 +61,30 @@ jobs:
         uses: actions/upload-artifact@v3
         with:
           name: coverage-report-html
-          path: htmlcov
+          path: htmlcov
+      - name: Upload coverage to Compass
+        run: |
+          METRIC_VALUE=$(cat coverage_report.txt | grep 'Total coverage:' | awk '{print $NF}' | sed 's/%//')
+          curl --request POST \
+          --url https://jacksonlaboratory.atlassian.net/gateway/api/compass/v1/metrics \
+          --user "${{ vars.ATLASSIAN_COMPASS_EMAIL }}:${{ secrets.ATLASSIAN_COMPASS_KEY }}" \
+          --header "Accept: application/json" \
+          --header "Content-Type: application/json" \
+          --data "{
+            \"metricSourceId\": \"ari:cloud:compass:44257862-6c68-4d47-8211-da38d2bb001b:metric-source/90bb0329-f6c5-429a-abbc-8d174535ad21/a96140ef-9d79-4015-bb9f-68989e182d48\",
+            \"value\": $METRIC_VALUE,
+            \"timestamp\": \"$(date -u +'%Y-%m-%dT%H:%M:%SZ')\"
+          }"
+      - name: Upload complexity to Compass
+        run: |
+          METRIC_VALUE=$(poetry run radon cc src --total-average | grep 'Average complexity:' | awk '{print $NF}' | sed 's/[\(\)]//g')
+          curl --request POST \
+          --url https://jacksonlaboratory.atlassian.net/gateway/api/compass/v1/metrics \
+          --user "${{ vars.ATLASSIAN_COMPASS_EMAIL }}:${{ secrets.ATLASSIAN_COMPASS_KEY }}" \
+          --header "Accept: application/json" \
+          --header "Content-Type: application/json" \
+          --data "{
+            \"metricSourceId\": \"ari:cloud:compass:44257862-6c68-4d47-8211-da38d2bb001b:metric-source/90bb0329-f6c5-429a-abbc-8d174535ad21/6f106703-9bc2-49fc-a65e-4f914b9bf878\",
+            \"value\": $METRIC_VALUE,
+            \"timestamp\": \"$(date -u +'%Y-%m-%dT%H:%M:%SZ')\"
+          }"

.github/workflows/coverage.yml

@@ -9,6 +9,7 @@ on:
 jobs:
   check-coverage:
     uses: ./.github/workflows/_check-coverage-action.yml
+    secrets: inherit
     with:
       required-coverage: ${{ vars.REQUIRED_COVERAGE }}
       coverage-module: "geneweaver.db"

README.md

@@ -7,3 +7,56 @@
 The Geneweaver DB library provides database access functionality for the Geneweaver 
 project. The library contains SQL queries wrapped in standard python functions, as well
 as a database connection manager.
+
+
+## Installation
+
+To install the Geneweaver DB library, run one of the following commands:
+
+#### Using Pip
+```
+pip install geneweaver-db
+```
+
+#### Using Poetry
+```
+poetry add geneweaver-db
+```
+
+## Usage
+The Geneweaver DB library is intended to be used as a dependency for other Geneweaver
+packages, but can also be used as a stand-alone pacakge.
+
+The package has three main sections:
+- `geneweaver.db` - contains non-async database functions.
+- `geneweaver.db.aio` - contains async database functions.
+- `geneweaver.db.query` - contains SQL queries and SQL generation functions.
+
+Database functions _usually_ take a `Cursor` or `AsyncCursor` object as their first
+argument.
+
+### Non-Async Functions
+```python
+import psycopg
+import geneweaver
+from geneweaver.db.core.settings import settings
+
+def get_my_gene():
+    with psycopg.connect(settings.URI) as conn:
+            with conn.cursor() as cur:
+                result = geneweaver.db.gene.get(cur, 'my_gene')
+    return result
+```
+
+### Async Functions
+```python
+import psycopg
+import geneweaver
+from geneweaver.db.core.settings import settings
+
+async def get_my_gene():
+    async with psycopg.AsyncConnection.connect(settings.URI) as conn:
+            async with conn.cursor() as cur:
+                result = await geneweaver.db.aio.gene.get(cur, 'my_gene')
+    return result
+```

pyproject.toml

@@ -1,12 +1,12 @@
 [tool.poetry]
 name = "geneweaver-db"
-version = "0.3.0a13"
+version = "0.3.0a14"
 description = "Database Interaction Services for GeneWeaver"
 authors = ["Jax Computational Sciences <[email protected]>"]
 readme = "README.md"
 license = "Apache-2.0"
-homepage = "https://bergsalex.github.io/geneweaver-docs/"
-repository = "https://bitbucket.org/jacksonlaboratory/geneweaver-db"
+homepage = "https://thejacksonlaboratory.github.io/geneweaver-docs/"
+repository = "https://github.com/TheJacksonLaboratory/geneweaver-db"
 packages = [
     { include = "geneweaver/db", from = "src" },
 ]
@@ -19,7 +19,7 @@ psycopg = {extras = ["binary"], version = "^3.1.13"}
 
 
 [tool.poetry.group.dev.dependencies]
-geneweaver-testing = "^0.0.3"
+geneweaver-testing = "^0.1.2"
 pytest-asyncio = "^0.23.5"
 
 [tool.ruff]

src/geneweaver/db/__init__.py

@@ -1 +1,4 @@
 """The root of the geneweaver database package."""
+
+# ruff: noqa: F401
+from geneweaver.db import aio, exceptions, gene, geneset, publication, species, user