Ontobot script for GO.

ontobot.sh

#!/bin/bash

#Set ONT_ID
#Set ONT_NAME

ROBOT=1.6.0
DT=0.14
BRANCH_BASE="update-$ONT_ID-import"

#check that ontobot doesn't already have an open PR
if [ ! $(curl 'https://api.github.com/repos/geneontology/go-ontology/pulls?state=open' | jq 'map(select(.user.login == "ontobot")) | .[].head.ref' | grep $BRANCH_BASE) ]; then

  mkdir bin
  echo "-Xmx16G" >bin/owltools.vmoptions
  curl -L -O 'https://github.com/owlcollab/owltools/releases/download/2020-04-06/owltools'
  chmod +x owltools
  mv owltools bin/
  curl -L -O https://github.com/INCATools/dosdp-tools/releases/download/v$DT/dosdp-tools-$DT.tgz
  tar -zxf dosdp-tools-$DT.tgz
  curl -L -O https://github.com/ontodev/robot/releases/download/v$ROBOT/robot.jar
  curl -L -O https://github.com/ontodev/robot/raw/master/bin/robot
  mv robot.jar bin/
  chmod +x robot
  mv robot bin/
  export PATH=$PATH:`pwd`/bin:`pwd`/dosdp-tools-$DT/bin
  export ROBOT_JAVA_ARGS=-Xmx12G

  json_escape () {
    python -c 'import json,sys; print(json.dumps(sys.stdin.read())[1:-1])'
  }

  git clone --depth 2 https://github.com/geneontology/go-ontology.git
  cd go-ontology/src/ontology

  DATE=`date +%Y-%m-%d`
  BRANCH=$BRANCH_BASE-$DATE
  git checkout -b $BRANCH

  make reasoned.owl
  mv reasoned.owl reasoned-prev.owl
  make imports/${ONT_ID}_import.obo
  make reasoned.owl
  robot diff --left reasoned-prev.owl --right reasoned.owl -f markdown -o go-diff.md
  GO_DIFF=`json_escape <go-diff.md`

  # Check if only version line has changed
  if [ $(git diff --numstat imports/${ONT_ID}_import.obo | grep -E '1\s+1' | wc -l) != 1 ]; then
    git add imports/${ONT_ID}_import.owl
    git add imports/${ONT_ID}_import.obo

    q='"'

    if ! $(git diff --cached --quiet) ; then
      git -c "user.name=OntoBot" -c "[email protected]" commit -m "Update $ONT_NAME import."
      git push https://ontobot:[email protected]/ontobot/go-ontology.git $BRANCH
      echo "{${q}title${q}: ${q}Update $ONT_NAME import${q}, ${q}body${q}: ${q}I've updated the $ONT_NAME import. Here's a diff of how this impacts the classified ontology:\n\n$GO_DIFF${q}, ${q}head${q}: ${q}ontobot:$BRANCH${q}, ${q}base${q}: ${q}master${q}}" >json_body.txt
      curl -X POST -d @json_body.txt "https://ontobot:[email protected]/repos/geneontology/go-ontology/pulls"
    fi
  fi
fi