Build

.github/workflows/omero_plugin.yml

@@ -23,7 +23,7 @@ jobs:
     env:
       STAGE: app
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v4
       - name: Checkout omero-test-infra
         uses: actions/checkout@master
         with:

.github/workflows/prettier.yml

@@ -9,7 +9,7 @@ jobs:
 
     steps:
       - name: Checkout
-        uses: actions/checkout@v2
+        uses: actions/checkout@v4
         with:
           # Make sure the actual branch is checked out when running on pull requests
           ref: ${{ github.event.pull_request.head.sha }}

.github/workflows/publish_pypi.yml

@@ -7,14 +7,16 @@ jobs:
     name: Build and publish Python distribution to PyPI
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v2
-      - uses: actions/setup-python@v2
+      - uses: actions/checkout@v4
+      - uses: actions/setup-python@v5
+        with:
+          python-version: '3.10'
       - name: Build a binary wheel and a source tarball
         run: |
-          python -mpip install wheel
-          python setup.py sdist bdist_wheel
+          python -mpip install build
+          python -m build
       - name: Publish distribution to PyPI
         if: startsWith(github.ref, 'refs/tags')
-        uses: pypa/gh-action-pypi-publish@v1.3.0
+        uses: pypa/gh-action-pypi-publish@v1.8.14
         with:
           password: ${{ secrets.PYPI_PASSWORD }}

.omeroci/app-build

@@ -0,0 +1,19 @@
+#!/bin/bash
+
+source /infra/utils
+
+set -e
+set -u
+set -x
+
+cd $TARGET
+DIR=$(setup_dir)
+
+export DJANGO_SETTINGS_MODULE=omeroweb.settings
+export OMERODIR=/opt/omero/web/OMERO.web
+export ICE_CONFIG=${OMERO_DIST}/etc/ice.config
+
+if [ -e test ]; then
+   echo Tests currently disabled
+   exit 1
+fi

idr_gallery/urls.py

@@ -21,7 +21,8 @@
     # handle mapr URLs and redirect to search e.g. /mapr/gene/?value=PAX7
     # First URL is matched by mapr itself, so not used while mapr istalled...
     # we want a regex that matches mapr_key but not favicon
-    re_path(r'^mapr/(?P<mapr_key>(?!favicon)[\w]+)/$', views.mapr, name='mapr'),
+    re_path(r'^mapr/(?P<mapr_key>(?!favicon)[\w]+)/$',
+            views.mapr, name='mapr'),
 ]
 
 for c in SUPER_CATEGORIES:

idr_gallery/views.py

@@ -139,7 +139,8 @@ def find_mapr_key_value(request, mapr_key, mapr_value, exact_match=False):
         # if multiple keys e.g. 'Gene Symbol' or 'Gene Identifier'
         if len(all_keys) > 1:
             # need to check which Key matches the Value...
-            matching_keys = search_engine_keys(request, mapr_value, exact_match)
+            matching_keys = search_engine_keys(request, mapr_value,
+                                               exact_match)
             all_keys = [key for key in all_keys if key in matching_keys]
         if len(all_keys) > 1 and default_key in all_keys:
             mapann_key = default_key
@@ -162,7 +163,8 @@ def search_engine_keys(request, value, exact_match=False):
     url += f"?value={value}"
     json_data = requests.get(url).json().get("data", [])
     if exact_match:
-        json_data = list(filter(lambda x: x.get("Value").lower() == value.lower(), json_data))
+        json_data = list(filter(
+            lambda x: x.get("Value").lower() == value.lower(), json_data))
     keys = [result.get("Key") for result in json_data]
     return keys