Search box: cope with weird PMID formatting #1683
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| # This is a basic workflow to help you get started with Actions | |
| name: Tests | |
| # Controls when the action will run. Triggers the workflow on push or pull request | |
| # events but only for the master branch | |
| on: | |
| push: | |
| branches: [ master ] | |
| pull_request: | |
| branches: [ master ] | |
| jobs: | |
| test-website: | |
| runs-on: ubuntu-latest | |
| steps: | |
| - uses: actions/checkout@v3 | |
| - name: Prerequisites | |
| run: | | |
| sudo apt-get update | |
| sudo apt-get -y install libjson-perl libperlio-gzip-perl libgd-perl libjson-perl pandoc libyaml-perl | |
| (curl -L http://cpanmin.us | sudo perl - --self-upgrade) && sudo cpanm --notest Pandoc Text::CSV | |
| git clone https://github.com/pombase/curation.git pombase-curation | |
| git clone https://github.com/pombase/genome_changelog.git genome_changelog | |
| cp -r genome_changelog/results/pombase_tables data_files | |
| curl -OL http://current.geneontology.org/metadata/GO.xrf_abbs | |
| curl -OL https://raw.githubusercontent.com/pombase/pombase-config/master/website/trackListTemplate.json | |
| curl -OL https://raw.githubusercontent.com/pombase/pombase-config/master/website/pombase_jbrowse_track_metadata.csv | |
| curl -OL https://raw.githubusercontent.com/pombase/pombase-chado/master/etc/create_jbrowse_track_list.pl && chmod a+x create_jbrowse_track_list.pl | |
| curl -OL https://raw.githubusercontent.com/japonicusdb/japonicus-config/main/japonicus_site_config.json | |
| (cd /tmp/; curl -O -L https://github.com/jgm/pandoc/releases/download/2.8/pandoc-2.8-1-amd64.deb; sudo dpkg -i pandoc-2.8-1-amd64.deb) | |
| yarn | |
| - name: Test | |
| run: | | |
| cp src/pombase/index.html src/index.html # usually copied by pombase-chado/etc/build_container.sh | |
| echo generating JBrowse JSON: | |
| ./create_jbrowse_track_list.pl trackListTemplate.json pombase_jbrowse_track_metadata.csv /dev/null /dev/null ./minimal_jbrowse_track_list.json && \ | |
| curl -L https://raw.githubusercontent.com/pombase/pombase-config/master/website/pombase_v2_config.json > main_config.json && \ | |
| echo generating doc files: && \ | |
| ./etc/update_generated_files.sh main_config.json data_files && node --max_old_space_size=8000 ./node_modules/@angular/cli/bin/ng build --no-progress && \ | |
| echo checking for broken links in PomBase docs: && \ | |
| ./etc/check_docs_broken_links.pl main_config.json src/docs src/assets && \ | |
| echo checking for broken links in JaponicusDB docs: && \ | |
| ./etc/check_docs_broken_links.pl japonicus_site_config.json src/docs src/assets && \ | |
| echo all checks passed |