Consolidated v4 fixes

.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

@@ -7,6 +7,7 @@ on:
       - cron: '00 4 * * *'  # daily at 4AM
 
 jobs:
+
   build:
 
     runs-on: ubuntu-latest
@@ -31,11 +32,19 @@ 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
+      shell: bash -l {0}
+      run: |
+        set -vxeuo pipefail
+        python -m flake8
+
     - name: Test with pytest
       shell: bash -l {0}
       run: |
         set -vxeuo pipefail
-        coverage run -m pytest -v
+        coverage run -m pytest --ignore tests_integration -v 
         coverage report

docs/source/conf.py

@@ -90,7 +90,7 @@
 #
 # This is also used if you do content translation via gettext catalogs.
 # Usually you set "language" from the command line for these cases.
-language = None
+language = "en"
 
 # List of patterns, relative to source directory, that match files and
 # directories to ignore when looking for source files.

docs/source/howto/ingest.md

@@ -13,6 +13,7 @@ from pyscicat.model import (
     Datablock,
     DataFile,
     Dataset,
+    Sample,
     Ownable
 )
 
@@ -61,6 +62,19 @@ Note that we store the provided dataset_id in a variable for later use.
 
 Also note the `sourceFolder`. This is a folder on the file system that SciCat has access to, and will contain the files for this `Dataset`.
 
+Proposals and instruments have to be created by an administrator. A sample with `sampleId="gargleblaster"` can be created like this:
+```python
+sample = Sample(
+    sampleId="gargleblaster",
+    owner="Chamber of Commerce",
+    description="A legendary drink.",
+    sampleCharacteristics={"Flavour": "Unknown, but potent"},
+    isPublished=False,
+    **ownable.dict()
+)
+sample_id = client.upload_sample(sample)  # sample_id == "gargleblaster"
+```
+
 ## Upload a Datablock
 
 ```python