1. On Pull Request #68

Workflow file for this run

.github/workflows/1_on_pull_request.yml at a51b2b8

	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)

	# 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/^+//')

	echo "Deleted nodes:"
	echo "$deleted_nodes"

	echo "Added/modified nodes:"
	echo "$added_or_modified_nodes"

	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"

	# Remove modified nodes from the deleted nodes list
	actual_deleted_nodes=$(echo "$deleted_nodes" \| grep -v -f <(echo "$modified_nodes"))

	# Output the results
	if [ -z "$actual_deleted_nodes" ] && [ -z "$modified_nodes" ]; then
	echo "No nodes were deleted or modified."
	else
	if [ -n "$actual_deleted_nodes" ]; then
	echo "Deleted nodes:"
	echo "$actual_deleted_nodes"
	echo "Note: Review required for deleted nodes."
	fi

	if [ -n "$modified_nodes" ]; then
	echo "Modified nodes:"
	echo "$modified_nodes"
	echo "Note: Review required for modified nodes."
	fi
	fi

	# Store the deleted nodes as an environment variable for later use
	echo "deleted_nodes=$deleted_nodes" >> $GITHUB_ENV


	- name: Report on testing
	id: report
	run: \|
	# Update PR description
	NEW_DESCRIPTION='
	---
	## Automated Testing
	As table
	\| # \| 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 }}}\$\$ \|
	\| 3 \| Test three \| \| \$\${\color{green}PASS}\$\$ \|

	As checklist
	- [ ] Interactions are connected
	- [ ] Datanodes are annotated with database references
	- [ ] Decription, consisting of 2-3 sentence overview of processes described in the pathway
	- [ ] At least one literature reference
	- [ ] At least one pathway ontology term
	- [ ] Pathway title conforms to the [guidelines](https://github.com/wikipathways/wikipathways-faq/discussions/24)
	---
	'

	# 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

	commit-outputs:
	needs: [get-pr,get-gpml,metadata,authors,pubmed,frontmatter,json-svg,testing]
	runs-on: ubuntu-latest
	steps:
	- name: Download all output files from artifacts
	uses: actions/download-artifact@v4

	- name: Checkout jekyll repo
	# TESTING: change repo and ssh-key from sandbox to real
	uses: actions/checkout@v4
	with:
	repository: wikipathways/sandbox-wp.gh.io
	path: wikipathways.github.io
	fetch-depth: 1
	ref: main
	ssh-key: ${{ secrets.ACTIONS_SANDBOX_DEPLOY_KEY }}

	- name: Commit report
	env:
	GPML_FILE: ${{ needs.get-gpml.outputs.gpml-file }}
	PR_NUMBER: ${{ needs.get-pr.outputs.pr-number }}
	run: \|
	wpid="$(echo "$GPML_FILE" \| sed 's/.gpml//')"

	## Copy to draft_assets
	mkdir -p wikipathways.github.io/draft_assets/"$wpid"
	cp gpml-file/"$wpid".gpml wikipathways.github.io/draft_assets/"$wpid"/.
	cp metadata/"$wpid". wikipathways.github.io/draft_assets/"$wpid"/.
	cp pubmed/"$wpid"-bibliography.tsv wikipathways.github.io/draft_assets/"$wpid"/.
	cp json-svg/"$wpid".json wikipathways.github.io/draft_assets/"$wpid"/.
	cp json-svg/"$wpid".png wikipathways.github.io/draft_assets/"$wpid"/.
	cp json-svg/"$wpid".svg wikipathways.github.io/draft_assets/"$wpid"/.
	cp json-svg/"$wpid"-thumb.png wikipathways.github.io/draft_assets/"$wpid"/.

	## Copy to _data/drafts
	cp metadata/"$wpid"-datanodes.tsv wikipathways.github.io/_data/drafts/.
	cp pubmed/"$wpid"-bibliography.tsv wikipathways.github.io/_data/drafts/.

	## Copy to _drafts
	cp frontmatter/"$wpid".md wikipathways.github.io/_drafts/.

	## Copy to _authors
	if [ -d "authors" ]; then
	cp authors/*.md wikipathways.github.io/_authors/.
	cp author_list.csv wikipathways.github.io/scripts/.
	fi

	## Commit, pull and push
	cd "${{ github.workspace }}/wikipathways.github.io"
	git config --global user.name 'GitHub Action'
	git config --global user.email '[email protected]'
	git add .
	if git diff --exit-code --staged; then
	echo "No changes"
	else
	git commit -m 'Adds outputs from PR processing'
	git pull --rebase
	git push
	fi

	update-pr-desc:
	needs: [get-pr,get-gpml,metadata,authors,pubmed,frontmatter,testing] #json-svg add once that step is resolved
	runs-on: ubuntu-latest
	steps:
	- name: Check out code
	uses: actions/checkout@v4
	with:
	ref: refs/pull/${{ needs.get-pr.outputs.pr-number }}/head

	- name: Compile and update PR description
	env:
	GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
	PR_NUMBER: ${{ needs.get-pr.outputs.pr-number }}
	GPML_FILE: ${{ needs.get-gpml.outputs.gpml-file }}
	STATUS: ${{ needs.get-gpml.outputs.status }}
	run: \|
	wpid="$(echo "$GPML_FILE" \| sed 's/.gpml//')"

	NEW_DESCRIPTION="${{ needs.get-gpml.outputs.pr-desc }}

	## Pathway Page Links
	* [Pending pathway page](https://sandbox.wikipathways.org/drafts/$wpid)
	"

	if [ "$STATUS" = "Edit" ]; then
	wpid_root="${wpid%%__*}"
	NEW_DESCRIPTION="$NEW_DESCRIPTION
	* [Current pathway page](https://sandbox.wikipathways.org/pathways/$wpid_root)
	"
	fi

	NEW_DESCRIPTION="$NEW_DESCRIPTION
	Note: The above URLs will activate after ~5 min.

	---
	"

	NEW_DESCRIPTION="$NEW_DESCRIPTION
	${{ needs.metadata.outputs.pr-desc }}
	${{ needs.authors.outputs.pr-desc }}
	${{ needs.pubmed.outputs.pr-desc }}
	${{ needs.frontmatter.outputs.pr-desc }}
	${{ needs.json-svg.outputs.pr-desc }}
	${{ needs.testing.outputs.pr-desc }}
	"

	# Edit PR description
	gh pr edit $PR_NUMBER --body "$NEW_DESCRIPTION"

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