diff --git a/.github/workflows/omero_plugin.yml b/.github/workflows/omero_plugin.yml index d14d209a..62f0fb7b 100644 --- a/.github/workflows/omero_plugin.yml +++ b/.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: diff --git a/.github/workflows/prettier.yml b/.github/workflows/prettier.yml index 9208c3f9..c0811bf3 100644 --- a/.github/workflows/prettier.yml +++ b/.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 }} diff --git a/.github/workflows/publish_pypi.yml b/.github/workflows/publish_pypi.yml index 7c4f64d5..a735b04e 100644 --- a/.github/workflows/publish_pypi.yml +++ b/.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 }} diff --git a/.omeroci/app-build b/.omeroci/app-build new file mode 100755 index 00000000..39921935 --- /dev/null +++ b/.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=${OMERO_DIST}/etc/ice.config + +if [ -e test ]; then + echo Tests currently disabled + exit 1 +fi diff --git a/idr_gallery/urls.py b/idr_gallery/urls.py index 034afe72..243ef5fd 100644 --- a/idr_gallery/urls.py +++ b/idr_gallery/urls.py @@ -21,7 +21,8 @@ # handle mapr URLs and redirect to search e.g. /mapr/gene/?value=PAX7 # First URL is matched by mapr itself, so not used while mapr istalled... # we want a regex that matches mapr_key but not favicon - re_path(r'^mapr/(?P(?!favicon)[\w]+)/$', views.mapr, name='mapr'), + re_path(r'^mapr/(?P(?!favicon)[\w]+)/$', + views.mapr, name='mapr'), ] for c in SUPER_CATEGORIES: diff --git a/idr_gallery/views.py b/idr_gallery/views.py index 7180631d..46e7a634 100644 --- a/idr_gallery/views.py +++ b/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