international-complete-owl-conversion.sh

#!/usr/bin/env bash

#
# This script is for use by the SNOMED International team to convert the International Edition to Complete OWL.
# The script provides an automated repeatable process to support testing and production of the technical preview.
# The inputs are the previous release zip and the current release delta zip containing stated relationships and some OWL axioms.
# The output is a delta zip for the current release containing all stated relationships from the previous release as inactive
# and a set of OWL axioms generated from all stated relationships plus those in the current release.
# Note: Previously published OWL axioms will not be in the output delta, those should be picked up from the previous release snapshot.
#


# Make script stop if any line fails
set -e;

echo "--"
echo "-- Checking inputs"
echo "--"
if [ "$#" -ne 2 ]; then
  echo "You must enter exactly 2 command line arguments."
  echo "The path to the previous release snapshot and the path to the current authoring delta."
  exit 1;
fi

owlToolkitJar="`ls target/snomed-owl-toolkit*-executable.jar | tail -n1`"
snapshot=$1
delta=$2
if [ ! -f $owlToolkitJar ]; then
  echo "SNOMED OWL Toolkit jar not found!"
  exit 1;
fi
if [ ! -f $snapshot ]; then
  echo "Snapshot file not found!"
  exit 1;
fi
if [ ! -f $delta ]; then
  echo "Delta file not found!"
  exit 1;
fi

echo "Jar: $owlToolkitJar"
echo "Snapshot: $snapshot"
echo "Delta: $delta"
echo


echo "--"
echo "-- Classifying (before conversion)"
echo "--"
java -jar $owlToolkitJar -classify -rf2-snapshot-archives $snapshot -rf2-authoring-delta-archive $delta;
echo


echo "--"
echo "-- Generating Ontology file (before conversion)"
echo "--"
java -jar $owlToolkitJar -rf2-to-owl -without-annotations -rf2-snapshot-archives $snapshot -rf2-authoring-delta-archive $delta;
ontologyBefore="`ls -rt ontology-* | tail -n1`"
if [ ! -f $ontologyBefore ]; then
  echo "Can not find generated ontology file"
  exit 1;
fi
mv "$ontologyBefore" "ontology-before-conversion.owl"
ontologyBefore="ontology-before-conversion.owl"
echo "Generated $ontologyBefore"
echo


echo "--"
echo "-- Converting to Complete OWL"
echo "--"
java -jar $owlToolkitJar -rf2-stated-to-complete-owl -rf2-snapshot-archives $snapshot -rf2-authoring-delta-archive $delta;
conversionDelta="`ls -rt complete-owl-axiom-delta* | tail -n1`"
echo "- Created $conversionDelta"
echo


echo "--"
echo "-- Merging Complete OWL with Delta archive"
echo "--"
rm -rf work
mkdir work
unzip $delta '**/Delta/*' -d work
cd work
unzip ../$conversionDelta
echo "- Replacing Stated Relationship delta"
cat sct2_StatedRelationship_Delta* > */Delta/Terminology/sct2_StatedRelationship_Delta*
echo "- Replacing OWL delta"
cat sct2_sRefset_OWL* > */Delta/Terminology/sct2_sRefset_OWL*
echo "- Creating zip"
completeOWL=SnomedCT_CompleteOWLDelta.zip
zip -r $completeOWL S*
mv $completeOWL ..
cd ..
echo "- Created $completeOWL"
echo


echo "--"
echo "-- Generating Ontology file (after conversion)"
echo "--"
java -jar $owlToolkitJar -rf2-to-owl -without-annotations -rf2-snapshot-archives $snapshot -rf2-authoring-delta-archive $completeOWL;
ontologyAfter="`ls -rt ontology-* | tail -n1`"
if [ ! -f $ontologyAfter ]; then
  echo "Can not find generated ontology file"
  exit 1;
fi
mv "$ontologyAfter" "ontology-after-conversion.owl"
ontologyAfter="ontology-after-conversion.owl"
echo "- Generated $ontologyAfter"
echo


echo "--"
echo "-- Diffing Ontology files"
echo "--"
diff $ontologyBefore $ontologyAfter > ontology-diff.txt
if [ "`wc -l ontology-diff.txt | sed 's/^ *\([0-9]*\).*/\1/g'`" -eq 0 ]; then
  echo "- Ontology files before and after OWL conversion are identical"
else
  echo "Difference found between Ontology files before and after OWL conversion! Check the contents of ontology-diff.txt"
  exit 1
fi
echo


echo "--"
echo "-- Classifying Complete OWL"
echo "--"
java -jar $owlToolkitJar -classify -rf2-snapshot-archives $snapshot -rf2-authoring-delta-archive $completeOWL;
echo