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1_on_pull_request.yml
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name: 1. On Pull Request
# This is the primary workflow to process pathway edits coming in as GPML files from
# PathVisio. A new pull request should be create per pathway. Subsequent edits to the
# same GPML can accumulate in the same pull request while in review.
#
# The outputs of this workflow will be temporarily stored as PR artifacts to allow access
# by subsequent jobs and to allow parallelization. At the end of the worflow, the outputs
# will be pushed to the main website (wikipathways.github.io repo) for transparent review.
#
# The acceptance/merge of a processed pull request will trigger a secondary workflow to
# migrate output files to published folders in main website repo, as well as the assets
# and homology repos.
#
# Inputs: Each pull request should have one and only one GPML file attached.
#
# Outputs:
# - info.json
# - datanodes.tsv
# - bibliography.tsv (via refs.tsv)
# - .json .svg and .png files
# - .md file
# - TODO: test results?
#
on:
workflow_dispatch:
inputs:
manual-pr-number:
description: 'PR Number'
required: true
default: '10'
#pull_request:
#paths:
# - '**/*.gpml'
concurrency:
group: ${{ github.workflow }}-${{ github.head_ref || github.ref }}
cancel-in-progress: false # to allow multiple runs to queue up rather than clobber
jobs:
get-pr:
# This job determines the PR number and stores it as a GITHUB_OUTPUT environment variable
# that can accessed by subsequent jobs.
runs-on: ubuntu-latest
outputs:
pr-number: ${{ steps.get-pr.outputs.pr-number }}
steps:
- name: Get PR
id: get-pr
# Get PR from triggering event, unless provided via manual workflow run
run: |
if [ -z "${{ inputs.manual-pr-number }}" ]; then
echo "pr-number=${{ github.event.pull_request.number }}" >> $GITHUB_OUTPUT
else
echo "pr-number=${{ inputs.manual-pr-number }}" >> $GITHUB_OUTPUT
fi
get-gpml:
# This job gets the GPML file, renames it (if new), and uploads it as an artifact
# that can accessed by subsequent jobs. The GPML filename is also stored as a
# GITHUB_OUTPUT environment variable. The job also extracts key information from
# the GPML file and starts a new PR description to let reviewers know the processing status.
#
# A markdown text report is stored as pr-desc to be compiled and written to the PR description.
#
# The branch name from the submitter's fork is also extracted and stored (if needed).
needs: [get-pr]
#if: ${{ needs.get-pr.outputs.pr-number }}
runs-on: ubuntu-latest
outputs:
gpml-filepath: ${{ steps.get-gpml.outputs.gpml-filepath }}
gpml-file: ${{ steps.get-gpml.outputs.gpml-file }}
status: ${{ steps.get-gpml.outputs.status }}
pr-desc: ${{ steps.get-gpml.outputs.pr-desc }}
branch-name: ${{ steps.get-branch.outputs.branch-name }}
gpml-name: ${{ steps.get-gpml.outputs.gpml-name }}
gpml-desc: ${{ steps.get-gpml.outputs.gpml-desc }}
env:
PR_NUMBER: ${{ needs.get-pr.outputs.pr-number }}
steps:
- name: Checkout repository
uses: actions/checkout@v4
with:
ref: refs/pull/${{ needs.get-pr.outputs.pr-number }}/head
- name: Install XML processing tools
# Used to parse XML values from GPML
run: sudo apt-get install -y libxml2-utils
- name: Get GPML
id: get-gpml
env:
GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
run: |
GPML_FILEPATH=$(gh pr view $PR_NUMBER --json files --jq '.files.[].path' | grep '.gpml$')
echo "Found GPML file at: $GPML_FILEPATH"
GPML_FILE="$(basename ""$GPML_FILEPATH"")"
# TEMPORARY: Rename previously processed test GPMLs
if [[ $GPML_FILE == *__* ]]; then
# Split on '__' and take the first part, then append '.gpml'
GPML_FILE="${GPML_FILE%%__*}.gpml"
fi
# Rename GPMLs with unique PR number
STATUS="New"
if [[ $GPML_FILE =~ ^WP[1-9][0-9]{0,4}\.gpml$ ]]; then
echo "Appending PR number to existing WPID."
STATUS="Edit"
#TODO: add label to PR
wpid="$(echo "$GPML_FILE" | sed 's/.gpml//')"
echo "$wpid"
GPML_FILE="${wpid}__PR${PR_NUMBER}.gpml"
echo "$GPML_FILE"
else
echo "Assigning temporary WPID and appending PR number."
#TODO: add label to PR
GPML_FILE="WP0__PR${PR_NUMBER}.gpml"
fi
echo "status=$STATUS" >> $GITHUB_OUTPUT
cp "$GPML_FILEPATH" ./"$GPML_FILE"
GPML_FILEPATH="./${GPML_FILE}"
echo "gpml-file=$GPML_FILE" >> $GITHUB_OUTPUT
echo "gpml-filepath=$GPML_FILEPATH" >> $GITHUB_OUTPUT #for subsequent jobs
# Extract information from GPML
wpid="$(echo "$GPML_FILE" | sed 's/.gpml//')"
org="$(xmllint --xpath 'string(//*[local-name()="Pathway"]/@Organism)' "$GPML_FILEPATH")"
name="$(xmllint --xpath 'string(//*[local-name()="Pathway"]/@Name)' "$GPML_FILEPATH")"
desc="$(xmllint --xpath 'string(//*[local-name()="Comment" and @Source="WikiPathways-description"])' "$GPML_FILEPATH")"
echo "gpml-name=$name"
echo "gpml-name=$name" >> $GITHUB_OUTPUT #for subsequent jobs
echo "gpml-desc=$desc"
echo "gpml-desc=$desc" >> $GITHUB_OUTPUT #for subsequent jobs
# Start PR description (newlines are important in NEW_DESCRIPTION string)
NEW_DESCRIPTION="
## Pathway Information
**WPID**: $wpid
**TITLE**: $name
**ORGANISM**: $org
**DESCRIPTION**: $desc
"
if [ "$STATUS" = "Edit" ]; then
wpid_root="${wpid%%__*}"
NEW_DESCRIPTION="$NEW_DESCRIPTION
*Note: This is an edit to an existing pathway.*
"
else
NEW_DESCRIPTION="$NEW_DESCRIPTION
*Note: This is a new pathway submission.*
"
fi
NEW_DESCRIPTION="$NEW_DESCRIPTION
---
"
# Store PR description for compilation in final job
# EOF base64 needed for storing multi-line strings as output variables
EOF=$(dd if=/dev/urandom bs=15 count=1 status=none | base64)
echo "pr-desc<<$EOF" >> $GITHUB_OUTPUT
echo "$NEW_DESCRIPTION" >> $GITHUB_OUTPUT
echo "$EOF" >> $GITHUB_OUTPUT
# Temporarily append PR description
NEW_DESCRIPTION="$NEW_DESCRIPTION
Processing...
"
# Edit PR description
gh pr edit $PR_NUMBER --body "$NEW_DESCRIPTION"
- name: Upload GPML file as artifact
uses: actions/upload-artifact@v4
with:
name: gpml-file
path: ${{ steps.get-gpml.outputs.gpml-filepath }}
retention-days: 1
if-no-files-found: error # 'warn' or 'ignore' are also available, defaults to `warn`
- name: Get branch name
id: get-branch
# Determine PR branch from submitter's fork, if needed #TODO: prune if not needed
run: |
BRANCH_NAME=$(curl -s -H "Authorization: token ${{ secrets.GITHUB_TOKEN }}" \
https://api.github.com/repos/${{ github.repository }}/pulls/${{needs.get-pr.outputs.pr-number}} \
| jq -r .head.ref)
echo "branch-name=$BRANCH_NAME"
echo "branch-name=$BRANCH_NAME" >> $GITHUB_OUTPUT
if ! git ls-remote --heads origin $BRANCH_NAME; then
git push origin HEAD:refs/heads/$BRANCH_NAME
fi
metadata:
# This job generates files dervied from the GPML, including info.json, datanodes.tsv and refs.tsv.
# The meta-data-action Java application performs the bulk of the work:
# https://github.com/wikipathways/meta-data-action
#
# The generated files are uploaded as artifacts to be downloaded and pushed together with other files
# to another repo in a final sync job. This strategy allows for parallel job processing!
#
# A markdown text report is stored as pr-desc to be compiled and written to the PR description.
needs: [get-pr,get-gpml]
runs-on: ubuntu-latest
outputs:
pr-desc: ${{ steps.report.outputs.pr-desc }}
env:
GPML_FILE: ${{ needs.get-gpml.outputs.gpml-file }}
steps:
- name: Checkout repository for scripts
# TODO: impl more efficient way to get scripts
uses: actions/checkout@v4
- name: Download GPML artifact
# Downloads gpml-file artifact to working dir
# Note: Automatically unzips as folders containing files with original filenames
uses: actions/download-artifact@v4
with:
name: gpml-file
- name: Setup Java
uses: actions/setup-java@v4
with:
distribution: 'temurin'
java-version: '11'
- name: Cache meta-data-action with dependencies
uses: actions/cache@v4
id: cacheMetaJar
with:
path: ./meta-data-action-1.1.2-jar-with-dependencies.jar
key: cached-meta-data-action-${{ hashFiles('meta-data-action-1.1.2-jar-with-dependencies.jar') }}
restore-keys: |
cached-meta-data-action-${{ hashFiles('meta-data-action-1.1.2-jar-with-dependencies.jar') }}
cached-meta-data-action-
- name: Install deps
run: |
echo "Refreshing cached-meta-data-action"
if [ ! -e ./meta-data-action-1.1.2-jar-with-dependencies.jar ]; then
wget -O meta-data-action-1.1.2-jar-with-dependencies.jar https://github.com/wikipathways/meta-data-action/releases/download/v1.1.2/meta-data-action-1.1.2-jar-with-dependencies.jar
fi
- name: Cache and install dependencies
uses: actions/cache@v4
id: cache
with:
path: ${{ github.workspace }}/Hs_Derby_Ensembl_108.bridge
key: ${{ runner.os }}-java-Hs_Derby_Ensembl_108
restore-keys: |
${{ runner.os }}-java-Hs_Derby_Ensembl_108
${{ runner.os }}-java-Hs_Derby_Ensembl_
- if: steps.cache.outputs.cache-hit != 'true'
name: Install deps
run: |
cd "${{ github.workspace }}"
if [ ! -e ./Hs_Derby_Ensembl_108.bridge ]; then
wget -O Hs_Derby_Ensembl_108.bridge https://zenodo.org/record/7781913/files/Hs_Derby_Ensembl_108.bridge?download=1
fi
- name: Generate gdb.config, fileNames.config, and fileDownloads.config
run: scripts/meta-data-action/configGenerator.sh ./$GPML_FILE
- name: Cache all bridge files
uses: actions/cache@v4
id: cacheAllBridge
with:
path: |
./metabolites*.bridge
./Ag*.bridge
./An*.bridge
./At*.bridge
./Bs*.bridge
./Bt*.bridge
./Ce*.bridge
./Cf*.bridge
./Ci*.bridge
./Dr*.bridge
./Da*.bridge
./Dp*.bridge
./Dm*.bridge
./Ec*.bridge
./Gg*.bridge
./Fg*.bridge
./Gm*.bridge
./Hs*.bridge
./Hv*.bridge
./Ml*.bridge
./Mm*.bridge
./Mx*.bridge
./Oa*.bridge
./Ova*.bridge
./Oi*.bridge
./Oj*.bridge
./Pi*.bridge
./Pt*.bridge
./Qc*.bridge
./Rn*.bridge
./Sc*.bridge
./Sl*.bridge
./Ss*.bridge
./Vv*.bridge
./Xt*.bridge
./Zm*.bridge
key: cached-bridge-files
restore-keys: |
cached-bridge-files
- if: steps.cacheAllBridge.outputs.cache-hit != 'true'
name: Install all bridge files
run: |
echo "Cache not found: cached-bridge-files"
declare -a OrganismNames=("Metabolites" "Anopheles gambiae" "Aspergillus niger" "Arabidopsis thaliana" "Bacillus subtilis" "Bos taurus" "Caenorhabditis elegans" "Canis familiaris" "Ciona intestinalis" "Danio rerio" "Daphnia magna" "Daphnia pulex" "Drosophila melanogaster" "Escherichia coli" "Gallus gallus" "Fusarium graminearum" "Glycine max" "Homo sapiens" "Hordeum vulgare" "Macaca mulatta" "Mus musculus" "Mycobacterium tuberculosis" "Ornithorhynchus anatinus" "Ovis aries" "Oryza indica" "Oryza japonica" "Populus trichocarpa" "Pan troglodytes" "Equus caballus" "Rattus norvegicus" "Saccharomyces cerevisiae" "Solanum lycopersicum" "Sus scrofa" "Vitis vinifera" "Xenopus tropicalis" "Zea mays")
for org in "${OrganismNames[@]}"; do
echo "generating configuration files for "$org""
scripts/meta-data-action/configGenerator.sh "$org"
echo "installing bridgedb files for "$org""
scripts/meta-data-action/installDependencies.sh "$org"
done
- name: Generate configs, install bridgeDb, generate info and tsv files
run: |
chmod 777 meta-data-action-1.1.2-jar-with-dependencies.jar
f=./$GPML_FILE
org="$(sed -n '/<Pathway /s/.*Organism=\(.*\)[^\n]*/\1/p' $f | tr -d '"' | tr -d '>' | tr -d '\r')"
echo "generating configuration files for "$org""
scripts/meta-data-action/configGenerator.sh "$org"
wpid="$(echo "$GPML_FILE" | sed 's/.gpml//')"
cat gdb.config
echo "generating info and datanode files for $wpid, organism "$org""
java -jar meta-data-action-1.1.2-jar-with-dependencies.jar local "$f" $(date --utc +%F) gdb.config "$org"
# generated files are placed in "pathways" dir
#ls -R
mkdir ./metadata
mv pathways/"$wpid"-info.json metadata/.
mv pathways/"$wpid"*.tsv metadata/.
- name: Upload metadata files as artifacts
uses: actions/upload-artifact@v4
with:
name: metadata
path: metadata/
retention-days: 1
if-no-files-found: error # 'warn' or 'ignore' are also available, defaults to `warn`
- name: Report on meta-data-action
id: report
run: |
# Verify generated files
infojson=$(find . -path "./metadata/WP*info.json" -print -quit)
dntsv=$(find . -path "./metadata/WP*datanodes.tsv" -print -quit)
refstsv=$(find . -path "./metadata/WP*refs.tsv" -print -quit)
# Update PR description
NEW_DESCRIPTION="
## Generate Metadata Files
"
if [[ -n $infojson ]]; then
NEW_DESCRIPTION="$NEW_DESCRIPTION
- [x] info.json generated"
else
NEW_DESCRIPTION="$NEW_DESCRIPTION
- [] info.json generated"
fi
if [[ -n $dntsv ]]; then
NEW_DESCRIPTION="$NEW_DESCRIPTION
- [x] datanodes.tsv generated"
else
NEW_DESCRIPTION="$NEW_DESCRIPTION
- [] datanodes.tsv generated"
fi
if [[ -n $refstsv ]]; then
NEW_DESCRIPTION="$NEW_DESCRIPTION
- [x] refs.tsv generated"
else
NEW_DESCRIPTION="$NEW_DESCRIPTION
- [] refs.tsv generated"
fi
# Store PR description for compilation in final job
EOF=$(dd if=/dev/urandom bs=15 count=1 status=none | base64)
echo "pr-desc<<$EOF" >> $GITHUB_OUTPUT
echo "$NEW_DESCRIPTION" >> $GITHUB_OUTPUT
echo "$EOF" >> $GITHUB_OUTPUT
authors:
# This job generates new author profiles if needed. It checks the list of authors from the GPML file
# against the list of prior authors in scripts/authors-list.csv and updates the list accordingly.
#
# An artifact is created and uploaded only if new author profiles are generated. A later job will
# check to see if an "authors" artifact is present and commit files at that time.
#
# A markdown text report is stored as pr-desc to be compiled and written to the PR description.
if: true
needs: [get-pr,get-gpml,metadata]
runs-on: ubuntu-latest
outputs:
pr-desc: ${{ steps.report.outputs.pr-desc }}
env:
GPML_FILE: ${{ needs.get-gpml.outputs.gpml-file }}
steps:
- name: Checkout repository for scripts
uses: actions/checkout@v4
- name: Download GPML artifact
# Downloads gpml-file artifact to working dir
# Note: Automatically unzips file with original filename
uses: actions/download-artifact@v4
with:
name: gpml-file
- name: Update author list and create md profiles
run: |
# Read list of previous authors
authorList=()
{
read #skip header line
while IFS=, read -r username realname orcid wikidata github; do
authorList+=("$username")
done
}< scripts/author_list.csv
echo ${#authorList[@]}
# Generate unique list of authors from this GPML
uniqueAuthors=()
auth="$(sed -n '/<Pathway /s/.*Author=\"\[\(.*\)\]\".*/\1/p' $GPML_FILE )"
IFS=',' read -r -a curAuthors <<< "$auth"
echo $curAuthors
echo ${#curAuthors[@]}
for i in "${curAuthors[@]}"; do
skip=
for j in "${uniqueAuthors[@]}"; do
[[ $i == $j ]] && { skip=1; break; }
done
[[ -n $skip ]] || uniqueAuthors+=("$i")
done
echo ${uniqueAuthors[@]}
echo ${#uniqueAuthors[@]}
# For any new authors, generate a profile and add them to the list
mkdir ./authors
k=0
for a in "${uniqueAuthors[@]}"; do
a=$(echo "$a" | sed -e 's/^[[:space:]]*//' -e 's/[[:space:]]*$//')
a1=${a//AAR&Co/AARandCo}
a1=${a//Önder/Onder}
a2=$(echo "$a" | tr ' ' '_')
if [[ ! " ${authorList[*]} " =~ " ${a} " ]]; then
echo "Adding $a"
echo $a","$a",,," >> scripts/author_list.csv
echo "---" > "authors/$a1.md"
echo "username: $a1" >> "authors/$a1.md"
echo "realname: $a" >> "authors/$a1.md"
echo "website: " >> "authors/$a1.md"
echo "affiliation: " >> "authors/$a1.md"
echo "bio: " >> "authors/$a1.md"
echo "github: " >> "authors/$a1.md"
echo "orcid: " >> "authors/$a1.md"
echo "linkedin: " >> "authors/$a1.md"
echo "googlescholar: " >> "authors/$a1.md"
echo "wikidata: " >> "authors/$a1.md"
echo "twitter: " >> "authors/$a1.md"
echo "mastodon-url: " >> "authors/$a1.md"
echo "meta:" >> "authors/$a1.md"
echo "instagram:" >> "authors/$a1.md"
echo "email:" >> "authors/$a1.md"
echo "redirect_from:" >> "authors/$a1.md"
echo "- /index.php/User:$a2" >> "authors/$a1.md"
echo "- /index.php/Special:Contributions/$a2" >> "authors/$a1.md"
echo "---" >> "authors/$a1.md"
$k=$k + 1
fi
done
if [ $k -gt 0 ]; then
mv scripts/author_list.csv authors/.
fi
echo "NEW_AUTHORS=$k" >> $GITHUB_ENV
- name: Upload author files as artifacts
uses: actions/upload-artifact@v4
with:
name: authors
path: authors/
retention-days: 1
if-no-files-found: ignore # 'warn' or 'ignore' are also available, defaults to `warn`
- name: Report on authors
id: report
run: |
# Update PR description
if [ ${{ env.NEW_AUTHORS }} -eq 0 ]; then
NEW_DESCRIPTION="- [x] No new author profiles needed"
elif [ ${{ env.NEW_AUTHORS }} -eq 1 ]; then
NEW_DESCRIPTION="- [x] 1 author profile generated"
else
NEW_DESCRIPTION="- [x] ${{ env.NEW_AUTHORS }} author profiles generated"
fi
# Store PR description for compilation in final job
EOF=$(dd if=/dev/urandom bs=15 count=1 status=none | base64)
echo "pr-desc<<$EOF" >> $GITHUB_OUTPUT
echo "$NEW_DESCRIPTION" >> $GITHUB_OUTPUT
echo "$EOF" >> $GITHUB_OUTPUT
pubmed:
# This job generates a bibliography.tsv file based on the refs.tsv generated by the metadata job.
#
# A "pubmed" artifact is created and uploaded containing this new tsv file. A later job will
# commit the file to appropriate draft folders in the website repo.
#
# A markdown text report is stored as pr-desc to be compiled and written to the PR description.
if: true
needs: [get-pr,get-gpml,metadata]
runs-on: ubuntu-latest
outputs:
pr-desc: ${{ steps.report.outputs.pr-desc }}
env:
GPML_FILE: ${{ needs.get-gpml.outputs.gpml-file }}
steps:
- name: Checkout repository for scripts
uses: actions/checkout@v4
- name: Download Metadata artifact
# Downloads metadata artifact to working dir
# Note: Automatically unzips as a folder containing files with original filenames
uses: actions/download-artifact@v4
with:
name: metadata
- name: Setup Node
uses: actions/setup-node@v4
with:
node-version: 16
- name: Cache dependencies
uses: actions/cache@v4
with:
path: ~/.npm
key: ${{ runner.os }}-node-${{ hashFiles('**/package-lock.json') }}
restore-keys: |
${{ runner.os }}-node-
- name: Install dependencies
working-directory: scripts/generate-references
run: npm install
- name: Generate references
working-directory: scripts/generate-references
run: |
mkdir -p ../../pubmed
cp ../../*-refs.tsv ../../pubmed/.
node index.js
# where are generated files placed
rm ../../*-refs.tsv
- name: Upload pubmed file as artifact
uses: actions/upload-artifact@v4
with:
name: pubmed
path: pubmed/
retention-days: 1
if-no-files-found: error # 'warn' or 'ignore' are also available, defaults to `warn`
- name: Report on pubmed
id: report
run: |
# Update PR description
NEW_DESCRIPTION="- [x] bibliography.tsv generated"
# Store PR description for compilation in final job
EOF=$(dd if=/dev/urandom bs=15 count=1 status=none | base64)
echo "pr-desc<<$EOF" >> $GITHUB_OUTPUT
echo "$NEW_DESCRIPTION" >> $GITHUB_OUTPUT
echo "$EOF" >> $GITHUB_OUTPUT
frontmatter:
# This job generates a wpid.md file based on the wpid-info.json file generated by the metadata job.
#
# A "frontmatter" artifact is created and uploaded containing this .md file. A later job will
# commit the file to the appropriate draft folder in the website repo.
#
# A markdown text report is stored as pr-desc to be compiled and written to the PR description.
if: true
needs: [get-pr,get-gpml,metadata]
runs-on: ubuntu-latest
outputs:
pr-desc: ${{ steps.report.outputs.pr-desc }}
env:
GPML_FILE: ${{ needs.get-gpml.outputs.gpml-file }}
steps:
- name: Checkout repository for scripts
uses: actions/checkout@v4
- name: Download Metadata artifact
# Downloads metadata artifacts to working dir
# Note: Automatically unzips as folders containing files with original filenames
uses: actions/download-artifact@v4
with:
name: metadata
- name: Setup Python
uses: actions/setup-python@v5
with:
python-version: '3.x'
- name: Install deps
run: |
pip install python-frontmatter
- name: Run create_pathway_frontmatter.py
run: |
wpid="$(echo "$GPML_FILE" | sed 's/.gpml//')"
echo "generating frontmatter file for $wpid"
json_info_f=./"$wpid"-info.json
echo "*****input for python script : $json_info_f"
if [ -e "$json_info_f" ]; then
python scripts/create_pathway_frontmatter.py "$json_info_f"
sed -i 's/&/and/g' ./"$wpid".md
sed -i 's/AAR&Co/AARandCo/g' ./"$wpid".md
sed -i 's/Önder/Onder/g' ./"$wpid".md
else
echo "info.json file missing for $wpid" >2
fi
#move the generated file to the frontmatter folder
mkdir ./frontmatter
mv ./"$wpid".md frontmatter/.
- name: Upload frontmatter file as artifact
uses: actions/upload-artifact@v4
with:
name: frontmatter
path: frontmatter/
retention-days: 1
if-no-files-found: error # 'warn' or 'ignore' are also available, defaults to `warn`
- name: Report on frontmatter
id: report
run: |
# Update PR description
NEW_DESCRIPTION="- [x] .md generated"
# Store PR description for compilation in final job
EOF=$(dd if=/dev/urandom bs=15 count=1 status=none | base64)
echo "pr-desc<<$EOF" >> $GITHUB_OUTPUT
echo "$NEW_DESCRIPTION" >> $GITHUB_OUTPUT
echo "$EOF" >> $GITHUB_OUTPUT
json-svg:
# This job generates json, svg and png files based on the GPML file.
#
# A "json-svg" artifact is created and uploaded containing the JSON, SVG and PNG files. A later job will
# commit the file to the appropriate draft folder in the website repo.
#
# A markdown text report is stored as pr-desc to be compiled and written to the PR description.
if: false
needs: [get-pr,get-gpml,metadata]
runs-on: ubuntu-latest
outputs:
pr-desc: ${{ steps.report.outputs.pr-desc }}
env:
GPML_FILE: ${{ needs.get-gpml.outputs.gpml-file }}
steps:
- name: Checkout repository for scripts
uses: actions/checkout@v4
- name: Download GPML and Metadata artifacts
# Downloads gpml-file and metadata artifacts to working dir
# Note: Automatically unzips as folders containing files with original filenames
uses: actions/download-artifact@v4
- name: Setup Node
uses: actions/setup-node@v4
with:
node-version: 16
- name: Cache NPM dependencies
uses: actions/cache@v4
with:
path: ~/.npm
key: ${{ runner.os }}-node-${{ hashFiles('**/package-lock.json') }}
restore-keys: |
${{ runner.os }}-node-
- name: Install deps
working-directory: scripts/generate-svgs
run: |
npm install
sudo apt-get update
sudo apt-get install -y xmlstarlet
- name: Run generate-svgs to convert GPML to JSON and SVG
run: |
echo "SANDBOX: Adapted to produce JSON and SVG files in sandbox-wp-db repo only"
DB_PATH="${{ github.workspace }}"
wpid="$(echo "$GPML_FILE" | sed 's/.gpml//')"
echo "generating JSON and SVG files for $wpid"
cd "$DB_PATH"
mkdir -p pathways/"$wpid"
for old_f in pathways/"$wpid"/"$wpid".{json,svg}; do
if [ -e "$old_f" ]; then
rm "$old_f"
fi
done
cd "scripts/generate-svgs"
./gpmlconverter --id "$wpid" -i $DB_PATH/gpml-file/"$wpid".gpml -o $DB_PATH/pathways/"$wpid"/"$wpid".svg
# delete intermediate JSON files
rm $DB_PATH/pathways/"$wpid"/"$wpid".json.b4bridgedb.json || true
rm $DB_PATH/pathways/"$wpid"/"$wpid".b4wd.json || true
rm $DB_PATH/pathways/"$wpid"/"$wpid".b4hgnc.json || true
# pretty print the JSON
for json_f in $DB_PATH/pathways/"$wpid"/"$wpid".json; do
mv "$json_f" "$json_f".tmp.json
jq -S . "$json_f".tmp.json >"$json_f"
rm "$json_f".tmp.json
done
#move the generated files to the json-svg folder
mkdir ../../json-svg
mv $DB_PATH/pathways/"$wpid"/"$wpid".json ../../json-svg/.
mv $DB_PATH/pathways/"$wpid"/"$wpid".png ../../json-svg/.
mv $DB_PATH/pathways/"$wpid"/"$wpid".svg ../../json-svg/.
mv $DB_PATH/pathways/"$wpid"/"$wpid"-thumb.png ../../json-svg/.
- name: Upload json-svg file as artifact
uses: actions/upload-artifact@v4
with:
name: json-svg
path: json-svg/
retention-days: 1
if-no-files-found: error # 'warn' or 'ignore' are also available, defaults to `warn`
- name: Report on json-svg
id: report
run: |
# Update PR description
NEW_DESCRIPTION="- [x] .json generated
- [x] .svg generated
- [x] .png generated
"
# Store PR description for compilation in final job
EOF=$(dd if=/dev/urandom bs=15 count=1 status=none | base64)
echo "pr-desc<<$EOF" >> $GITHUB_OUTPUT
echo "$NEW_DESCRIPTION" >> $GITHUB_OUTPUT
echo "$EOF" >> $GITHUB_OUTPUT
testing:
if: true
needs: [get-pr, get-gpml, metadata]
runs-on: ubuntu-latest
outputs:
pr-desc: ${{ steps.report.outputs.pr-desc }}
env:
GPML_FILE: ${{ needs.get-gpml.outputs.gpml-file }}
GPML_NAME: ${{ needs.get-gpml.outputs.gpml-name }}
GPML_DESC: ${{ needs.get-gpml.outputs.gpml-desc }}
STATUS: ${{ needs.get-gpml.outputs.status }}
GH_TOKEN: ${{ github.token }}
steps:
- name: Checkout repository for scripts
uses: actions/checkout@v4
- name: Download GPML and Metadata artifacts
# Downloads gpml-file and metadata artifacts to working dir
# Note: Automatically unzips as folders containing files with original filenames
uses: actions/download-artifact@v4
- name: Install tools
run: sudo apt-get install -y jq
- name: Fetch PR Diff
id: fetch_diff
run: |
PR_NUMBER="${{ needs.get-pr.outputs.pr-number }}"
# Fetch the entire diff for the PR
diff_output=$(gh pr diff "$PR_NUMBER")
echo "$diff_output" > diff_output.txt # Save the diff to a file for processing later
echo "Diff fetched successfully"
- name: Test for characters in title
run: |
title=$GPML_NAME
echo "The length of the title is ${#title}"
title_length=${#title}
if [ "$title_length" -ge 10 ]; then
echo "Title has at least 10 characters."
echo "note_test_title=Title has at least 10 characters." >> $GITHUB_ENV
echo "status_test_title=PASS" >> $GITHUB_ENV
echo "color_test_title=green" >> $GITHUB_ENV
else
echo "Title has less than 10 characters."
echo "note_test_title=Title has less than 10 characters." >> $GITHUB_ENV
echo "status_test_title=REVIEW REQUIRED" >> $GITHUB_ENV
echo "color_test_title=red" >> $GITHUB_ENV
fi
- name: Test for number of words in description
run: |
# Read the diff output from the file
diff_output=$(cat diff_output.txt)
# Extract relevant changes (for example, only looking for Comment changes)
old_desc=$(echo "$diff_output" | grep -E '^[-]' | grep 'WikiPathways-description' | sed 's/^-//')
new_desc=$(echo "$diff_output" | grep -E '^[+]' | grep 'WikiPathways-description' | sed 's/^+//')
# Function to count words and characters in a string
word_count() {
echo "$1" | wc -w
}
char_count() {
echo "$1" | wc -c
}
# Calculate word and character differences
old_word_count=$(word_count "$old_desc")
new_word_count=$(word_count "$new_desc")
word_diff=$((new_word_count - old_word_count))
old_char_count=$(char_count "$old_desc")
new_char_count=$(char_count "$new_desc")
char_diff=$((new_char_count - old_char_count))
echo "Old description word count: $old_word_count"
echo "New description word count: $new_word_count"
echo "Word difference: $word_diff"
echo "Character difference: $char_diff"
# Check if description change is significant
status="${{ env.STATUS }}"
if [ "$status" = "New" ]; then
if [ "$new_word_count" -ge 15 ]; then
echo "Description for new pathway has at least 15 words."
echo "note_test_desc=Description has at least 15 words." >> $GITHUB_ENV
echo "status_test_desc=PASS" >> $GITHUB_ENV
echo "color_test_desc=green" >> $GITHUB_ENV
else
echo "Description for new pathway has fewer than 15 words."
echo "note_test_desc=Description has fewer than 15 words." >> $GITHUB_ENV
echo "status_test_desc=REVIEW REQUIRED" >> $GITHUB_ENV
echo "color_test_desc=red" >> $GITHUB_ENV
fi
else
if [ "$word_diff" -gt 3 ] || [ "$char_diff" -gt 10 ]; then
echo "Description changed significantly. Review required."
echo "note_test_desc=Description change exceeds 3 words or 10 characters." >> $GITHUB_ENV
echo "status_test_desc=REVIEW REQUIRED" >> $GITHUB_ENV
echo "color_test_desc=red" >> $GITHUB_ENV
else
echo "Description change is minor."
echo "note_test_desc=Minor description change." >> $GITHUB_ENV
echo "status_test_desc=PASS" >> $GITHUB_ENV
echo "color_test_desc=green" >> $GITHUB_ENV
fi
fi
- name: Check for deleted, added, and modified nodes
run: |
# Read the diff output from the file
diff_output=$(cat diff_output.txt)
# Check if the GPML file is new
status="${{ env.STATUS }}"
if [ "$status" = "New" ]; then
# For new GPML files, treat all nodes as added nodes
added_nodes=$(grep '<DataNode' "$GPML_FILE" | sed 's/^+//')
num_added_nodes=$(echo "$added_nodes" | sed '/^$/d' | wc -l)
# Output the results for a new GPML file
echo "New GPML submission detected."
echo "All nodes are considered as added nodes."
echo "Added nodes: $num_added_nodes"
# Set the environment variables for new GPML files
echo "note_test_nodes=All nodes are new, as this is a new GPML file." >> $GITHUB_ENV
echo "status_test_nodes=PASS" >> $GITHUB_ENV
echo "color_test_nodes=green" >> $GITHUB_ENV
else
# For modified GPML files, proceed with checking deleted, added, and modified nodes
# Extract nodes that were removed from the GPML file (lines starting with '-')
deleted_nodes=$(echo "$diff_output" | grep "^-" | grep '<DataNode' | sed 's/^-//')
# Extract nodes that were added or changed in the GPML file (lines starting with '+')
added_or_modified_nodes=$(echo "$diff_output" | grep "^+" | grep '<DataNode' | sed 's/^+//')
modified_nodes=""
# Use while loop to iterate through deleted nodes safely
while IFS= read -r deleted_node; do
if [ -n "$deleted_node" ]; then
graph_id=$(echo "$deleted_node" | grep -o 'GraphId="[^"]*"' | sed 's/GraphId="//;s/"//')
# Check if the same GraphId exists in the added/modified nodes
matching_added_node=$(echo "$added_or_modified_nodes" | grep "GraphId=\"$graph_id\"")
if [ -n "$matching_added_node" ]; then
modified_nodes="$modified_nodes\n$deleted_node"
fi
fi
done <<< "$deleted_nodes"
# Safely remove modified nodes from deleted nodes
if [ -n "$modified_nodes" ]; then
safe_modified_nodes=$(echo "$modified_nodes" | sed '/^$/d' | sed 's/[\/&]/\\&/g')
actual_deleted_nodes=$(echo "$deleted_nodes" | grep -vF "$safe_modified_nodes")
else
actual_deleted_nodes="$deleted_nodes"
fi
# Count the number of nodes
num_deleted_nodes=$(echo "$actual_deleted_nodes" | sed '/^$/d' | wc -l)
num_modified_nodes=$(echo "$modified_nodes" | sed '/^$/d' | wc -l)
num_added_nodes=$(echo "$added_or_modified_nodes" | grep -vF "$modified_nodes" | sed '/^$/d' | wc -l)
# Output the results for modified GPML file
echo "Summary:"
echo "Deleted nodes: $num_deleted_nodes"
echo "Modified nodes: $num_modified_nodes"
echo "Added nodes: $num_added_nodes"
# Determine pass or review required and report
if [ "$num_deleted_nodes" -eq 0 ] && [ "$num_modified_nodes" -eq 0 ] && [ "$num_added_nodes" -eq 0 ]; then
# No changes, pass
echo "No nodes were deleted, modified, or added."
echo "note_test_nodes=No nodes were deleted, modified, or added." >> $GITHUB_ENV
echo "status_test_nodes=PASS" >> $GITHUB_ENV
echo "color_test_nodes=green" >> $GITHUB_ENV
else
# Nodes were changed, review required
echo "Review required."
[ "$num_deleted_nodes" -gt 0 ] && echo "Deleted nodes: $num_deleted_nodes"
[ "$num_modified_nodes" -gt 0 ] && echo "Modified nodes: $num_modified_nodes"
[ "$num_added_nodes" -gt 0 ] && echo "Added nodes: $num_added_nodes"
review_note=""
[ "$num_deleted_nodes" -gt 0 ] && review_note+="Deleted nodes: $num_deleted_nodes\n"
[ "$num_modified_nodes" -gt 0 ] && review_note+="Modified nodes: $num_modified_nodes\n"
[ "$num_added_nodes" -gt 0 ] && review_note+="Added nodes: $num_added_nodes\n"
echo "note_test_nodes=$review_note" >> $GITHUB_ENV
echo "status_test_nodes=REVIEW REQUIRED" >> $GITHUB_ENV
echo "color_test_nodes=red" >> $GITHUB_ENV
fi
fi
# Store the deleted, modified, and added nodes as environment variables for later use
echo "deleted_nodes=${deleted_nodes}" >> $GITHUB_ENV
echo "modified_nodes=${modified_nodes}" >> $GITHUB_ENV
echo "added_nodes=${added_or_modified_nodes}" >> $GITHUB_ENV
- name: Report on testing
id: report
run: |
# Fixing newline characters for the Data nodes notes
note_test_nodes_formatted=$(echo "${{ env.note_test_nodes }}" | tr '\n' '<br>')
# Initialize the review tasks based on the automated test results
review_tasks=""
if [ "${{ env.status_test_title }}" = "REVIEW REQUIRED" ]; then
review_tasks="${review_tasks}- [ ] Title length review required\n"
fi
if [ "${{ env.status_test_desc }}" = "REVIEW REQUIRED" ]; then
review_tasks="${review_tasks}- [ ] Description review required\n"
fi
if [ "${{ env.status_test_nodes }}" = "REVIEW REQUIRED" ]; then
review_tasks="${review_tasks}- [ ] Data nodes review required\n"
fi
# Update PR description
NEW_DESCRIPTION='
---
## Automated Testing
| # | Test name | Notes | Result |
|---|---|---|---|
| 1 | Title Length | ${{ env.note_test_title }} | \$\${\color{${{ env.color_test_title }}}${{ env.status_test_title }}}\$\$ |
| 2 | Description Length | ${{ env.note_test_desc }} | \$\${\color{${{ env.color_test_desc }}}${{ env.status_test_desc }}}\$\$ |