Merge pull request #40 from rosalindfranklininstitute/v4-datasets

V4 datasets

.github/workflows/integration-testing.yml

@@ -0,0 +1,58 @@
+name: Integration tests V4
+
+on:
+  pull_request:
+    branches:
+      - main
+
+jobs:
+  container_job:
+    runs-on: ubuntu-latest
+
+    services:
+      mongo:
+        image: mongo
+        ports:
+          - 27107:27107
+      scicat-backend:
+        image: ghcr.io/scicatproject/scicat-backend-next:stable
+        ports:
+          - 3000:3000
+        env:
+          MONGODB_URI: mongodb://mongo:27017/scicat
+          EXPRESS_SESSION_SECRET: "${EXPRESS_SESSION_SECRET}"
+          JWT_SECRET: "${JWT_SECRET}"
+          PORT: 3000
+          HTTP_MAX_REDIRECTS: 5
+          HTTP_TIMEOUT: 5000
+          JWT_EXPIRES_IN: 3600
+          SITE: SAMPLE-SITE
+          PID_PREFIX: PID.SAMPLE.PREFIX
+          DOI_PREFIX: DOI.SAMPLE.PREFIX
+          METADATA_KEYS_RETURN_LIMIT: 100
+          METADATA_PARENT_INSTANCES_RETURN_LIMIT: 100
+          ADMIN_GROUPS: admin,ingestor
+
+    steps:
+        - uses: actions/checkout@v2
+        - uses: actions/setup-python@v2
+          with:
+            python-version: ${{ matrix.python-version }}
+
+        - run: source continuous_integration/scripts/install.sh
+
+
+        -  run: |
+            set -vxeuo pipefail
+            python -m pip install .
+            python -m pip install .[dev]
+            python -m pip list
+
+        - run: |
+            set -vxeuo pipefail
+            coverage run -m pytest tests/tests_integration/tests_integration.py
+            coverage report
+          env:
+            BASE_URL: http://localhost:3000/api/v3
+            SCICAT_USER: ingestor
+            SCICAT_PASSWORD: aman

.github/workflows/publish-documentation.yml

@@ -37,7 +37,7 @@ jobs:
       shell: bash -l {0}
       run: |
         set -vxeuo pipefail
-        python -m pip install -r requirements-dev.txt
+        python -m pip install .[dev]
         python -m pip list
     - name: Build Docs
       shell: bash -l {0}

.github/workflows/testing.yml

@@ -32,7 +32,8 @@ jobs:
       shell: bash -l {0}
       run: |
         set -vxeuo pipefail
-        python -m pip install -r requirements-dev.txt
+        python -m pip install .[dev]
+        python -m pip install .[hdf5]
         python -m pip list
     
     - name: Lint with flake8
@@ -45,5 +46,5 @@ jobs:
       shell: bash -l {0}
       run: |
         set -vxeuo pipefail
-        coverage run -m pytest -v
+        coverage run -m pytest --ignore tests_integration -v 
         coverage report