Move ontology downloads from Jenkins to this repository

[marvinm2]

Using GH Actions. Currently, these files are created on Jenkins

The following ontology files:

• PathwayOntology.ttl https://jenkins.bigcat.unimaas.nl/job/Ontology%20conversion%20-%20PW/lastSuccessfulBuild/artifact/pw.ttl
• DiseaseOntology.ttl https://jenkins.bigcat.unimaas.nl/job/Ontology%20conversion%20-%20DOID/lastSuccessfulBuild/artifact/doid.ttl
• CellOntology.ttl https://jenkins.bigcat.unimaas.nl/job/Ontology%20conversion%20-%20CL/lastSuccessfulBuild/artifact/cl.ttl
• chebi-slim.ttl https://jenkins.bigcat.unimaas.nl/job/WikiPathways%20-%20CHEBI/lastSuccessfulBuild/artifact/chebi-slim.ttl

[jmillanacosta]

The task is to turn these shell scripts into separate jobs in a GH Actions workflow.

• Ontology conversion PW:

rm -f *.owl
rm -f *.owl.*
rm -f *.ttl
rm -f *.ttl.*
rm -f *.jar
rm -f *.jar.*

curl -o pw.owl -m 1000 -L http://purl.obolibrary.org/obo/pw.owl

wget https://github.com/ontodev/robot/releases/download/v1.7.0/robot.jar

curl https://raw.githubusercontent.com/ontodev/robot/master/bin/robot > robot
export ROBOT_JAVA_ARGS="-Dhttp.proxyHost=proxy.unimaas.nl -Dhttp.proxyPort=3128 -Dhttps.proxyHost=proxy.unimaas.nl -Dhttps.proxyPort=3128"

sh ./robot convert --input pw.owl --output pw.ttl

• Ontology conversion DOID:

rm -f *.owl
rm -f *.owl.*
rm -f *.ttl
rm -f *.ttl.*
rm -f *.jar
rm -f *.jar.*

curl -o doid.owl -m 420 https://raw.githubusercontent.com/DiseaseOntology/HumanDiseaseOntology/main/src/ontology/doid.owl


wget https://github.com/ontodev/robot/releases/download/v1.7.0/robot.jar

curl https://raw.githubusercontent.com/ontodev/robot/master/bin/robot > robot
export ROBOT_JAVA_ARGS="-Dhttp.proxyHost=proxy.unimaas.nl -Dhttp.proxyPort=3128 -Dhttps.proxyHost=proxy.unimaas.nl -Dhttps.proxyPort=3128"

sh ./robot convert --input doid.owl --output doid.ttl

• Ontology conversion CL:

rm -f *.owl
rm -f *.owl.*
rm -f *.ttl
rm -f *.ttl.*
rm -f *.jar
rm -f *.jar.*

curl -o cl.owl -m 1000 https://raw.githubusercontent.com/obophenotype/cell-ontology/master/cl.owl

wget https://github.com/ontodev/robot/releases/download/v1.7.0/robot.jar

curl https://raw.githubusercontent.com/ontodev/robot/master/bin/robot > robot
export ROBOT_JAVA_ARGS="-Dhttp.proxyHost=proxy.unimaas.nl -Dhttp.proxyPort=3128 -Dhttps.proxyHost=proxy.unimaas.nl -Dhttps.proxyPort=3128"

sh ./robot convert --input cl.owl --output cl.ttl

• Wikipathways-CHEBI slim:

export ONTO=chebi
#rm -f *.owl
#rm -f *.owl.*
rm -f ${ONTO}.props*
rm -f ${ONTO}.iris*
wget https://raw.githubusercontent.com/enanomapper/ontologies/master/config/${ONTO}.props
wget -N `grep "owl=" ${ONTO}.props | cut -d'=' -f2`

echo "SELECT DISTINCT ?chebi WHERE { [] wp:bdbChEBI ?chebi }" > chebi.rq
curl -H "Accept: text/tab-separated-values" --data-urlencode query@chebi.rq -G https://sparql.wikipathways.org/sparql -o chebi.tsv
grep -v "\"chebi\"" chebi.tsv > chebi2.tsv
sed -i 's/"https:\/\/identifiers.org\/chebi\/CHEBI:/+U:http:\/\/purl.obolibrary.org\/obo\/CHEBI_/' chebi2.tsv
sed -i 's/\"//' chebi2.tsv
cp chebi2.tsv ${ONTO}.iris

wget -N https://github.com/enanomapper/slimmer/releases/download/v1.0.1/slimmer-1.0.1-jar-with-dependencies.jar
java -Dhttps.proxyHost=proxy.unimaas.nl -Dhttps.proxyPort=3128 -Dhttp.proxyHost=proxy.unimaas.nl -Dhttp.proxyPort=3128 -cp slimmer-1.0.1-jar-with-dependencies.jar com.github.enanomapper.Slimmer .

rapper -i rdfxml -o turtle chebi-slim.owl > chebi-slim.ttl

@marvinm2 Do you want the files to be pushed to https://github.com/marvinm2/WikiPathwaysLoader/tree/master/data after each run? When should the actions be triggered (manually, scheduled, as a response to an event)?

[marvinm2]

The action failed on the push step. What needs to happen?