website/.github/workflows/test-website.yml at master · pombase/website · GitHub

1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
# 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:
  pull_request:

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 libyaml-perl libxml-rss-perl
           (cd /tmp/; curl -O -L https://github.com/jgm/pandoc/releases/download/3.1.13/pandoc-3.1.13-1-amd64.deb; sudo dpkg -i pandoc-3.1.13-1-amd64.deb)
           (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 -L https://curation.pombase.org/dumps/latest_build/misc/gocam_model_holes_table.tsv > data_files/gocam_model_holes_table.tsv
           curl -fsSL https://deb.nodesource.com/setup_20.x | sudo -E bash -
           sudo apt-get update
           sudo apt-get install nodejs -y
           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
           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 && \
           curl -L https://curation.pombase.org/dumps/latest_build/pombe-embl/supporting_files/PB_references.txt > PB_references.txt && \
           echo generating doc files: && \
           node ./node_modules/@angular/cli/bin/ng --version && \
           ./etc/update_generated_files.sh main_config.json data_files PB_references.txt && \
           node ./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