Update from master branch (#426)

.github/workflows/integration_tests.yaml

@@ -0,0 +1,27 @@
+name: Integration Tests
+
+on: pull_request
+
+concurrency:
+  group: ${{ github.workflow }}-${{ github.event.pull_request.number || github.ref }}
+  cancel-in-progress: true
+
+jobs:
+  integration_tests:
+    name: Integration tests
+    uses: uc-cdis/.github/.github/workflows/integration_tests.yaml@master
+    with:
+      SERVICE_TO_TEST: graph_submission
+    secrets:
+      CI_AWS_ACCESS_KEY_ID: ${{ secrets.CI_AWS_ACCESS_KEY_ID }}
+      CI_AWS_SECRET_ACCESS_KEY: ${{ secrets.CI_AWS_SECRET_ACCESS_KEY }}
+      JENKINS_API_TOKEN: ${{ secrets.JENKINS_API_TOKEN }}
+      QA_DASHBOARD_S3_PATH: ${{ secrets.QA_DASHBOARD_S3_PATH }}
+      CI_TEST_ORCID_USERID: ${{ secrets.CI_TEST_ORCID_USERID }}
+      CI_TEST_ORCID_PASSWORD: ${{ secrets.CI_TEST_ORCID_PASSWORD }}
+      CI_TEST_RAS_USERID: ${{ secrets.CI_TEST_RAS_USERID }}
+      CI_TEST_RAS_PASSWORD: ${{ secrets.CI_TEST_RAS_PASSWORD }}
+      CI_TEST_RAS_2_USERID: ${{ secrets.CI_TEST_RAS_2_USERID }}
+      CI_TEST_RAS_2_PASSWORD: ${{ secrets.CI_TEST_RAS_2_PASSWORD }}
+      CI_SLACK_BOT_TOKEN: ${{ secrets.CI_SLACK_BOT_TOKEN }}
+      CI_SLACK_CHANNEL_ID: ${{ secrets.CI_SLACK_CHANNEL_ID }}

.pre-commit-config.yaml

@@ -11,6 +11,6 @@ repos:
     -   id: no-commit-to-branch
         args: [--branch, develop, --branch, master, --pattern, release/.*]
 -   repo: https://github.com/psf/black
-    rev: 22.12.0
+    rev: 24.4.0
     hooks:
     -   id: black

.secrets.baseline

@@ -75,6 +75,10 @@
     {
       "path": "detect_secrets.filters.allowlist.is_line_allowlisted"
     },
+    {
+      "path": "detect_secrets.filters.common.is_baseline_file",
+      "filename": ".secrets.baseline"
+    },
     {
       "path": "detect_secrets.filters.common.is_ignored_due_to_verification_policies",
       "min_level": 2
@@ -123,7 +127,7 @@
         "filename": "README.md",
         "hashed_secret": "a94a8fe5ccb19ba61c4c0873d391e987982fbbd3",
         "is_verified": false,
-        "line_number": 72
+        "line_number": 74
       }
     ],
     "bin/settings.py": [
@@ -350,5 +354,5 @@
       }
     ]
   },
-  "generated_at": "2024-02-08T23:30:59Z"
+  "generated_at": "2024-04-22T20:07:28Z"
 }

Dockerfile

@@ -42,7 +42,7 @@ WORKDIR /$appname
 # this will make sure than the dependencies is cached
 COPY poetry.lock pyproject.toml /$appname/
 RUN poetry config virtualenvs.create false \
-    && poetry install -vv --no-root --no-dev --no-interaction \
+    && poetry install -vv --no-root --without dev --no-interaction \
     && poetry show -v
 
 # copy source code ONLY after installing dependencies
@@ -53,7 +53,7 @@ COPY ./bin/confighelper.py /var/www/$appname/confighelper.py
 
 # install sheepdog
 RUN poetry config virtualenvs.create false \
-    && poetry install -vv --no-dev --no-interaction \
+    && poetry install -vv --without dev --no-interaction \
     && poetry show -v
 
 RUN COMMIT=`git rev-parse HEAD` && echo "COMMIT=\"${COMMIT}\"" >$appname/version_data.py \

README.md

@@ -68,7 +68,7 @@ Ensure you've run `poetry install`.
 
 Ensure you have Postgresql 13 set up and running.
 
-Ensure there is a postgres user `postgres` *and* `test` setup with password `test`:
+Ensure there are 2 postgres users `postgres` and `test`, both set up with password `test`:
 
 ```
 CREATE USER postgres WITH PASSWORD 'test';