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Fix non-zero exit from riot.
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balhoff committed Sep 16, 2021
1 parent 92ff3e5 commit f5de60b
Showing 1 changed file with 7 additions and 2 deletions.
9 changes: 7 additions & 2 deletions Makefile
Original file line number Diff line number Diff line change
Expand Up @@ -5,7 +5,7 @@ RG=$(RG_ENV) relation-graph
BG_RUNNER=JAVA_OPTS=-Xmx50G blazegraph-runner
JVM_ARGS=JVM_ARGS=-Xmx120G
ARQ=$(JVM_ARGS) arq
BIOLINK=2.1.0
BIOLINK=2.2.4

all: ubergraph.jnl

Expand Down Expand Up @@ -63,9 +63,14 @@ opposites.ttl: antonyms_HP.txt

# This includes a hack to workaround JSON-LD context problems with biolink
# The conversion back to turtle works around a problem with Blazegraph parsing on Java 11
# We need to filter out dateTime values because these are badly formatted in biolink and cause riot to have non-zero exit code
# https://github.com/linkml/linkml/issues/253
biolink-model.ttl:
curl -L 'https://raw.githubusercontent.com/biolink/biolink-model/$(BIOLINK)/biolink-model.ttl' -o $@.tmp
riot --syntax=turtle --output=ntriples $@.tmp | sed -E 's/<https:\/\/w3id.org\/biolink\/vocab\/([^[:space:]][^[:space:]]*):/<http:\/\/purl.obolibrary.org\/obo\/\1_/g' | riot --syntax=ntriples --output=turtle >$@
riot --syntax=turtle --output=ntriples $@.tmp |\
sed -E 's/<https:\/\/w3id.org\/biolink\/vocab\/([^[:space:]][^[:space:]]*):/<http:\/\/purl.obolibrary.org\/obo\/\1_/g' |\
grep -v 'http://www.w3.org/2001/XMLSchema#dateTime' |\
riot --syntax=ntriples --output=turtle >$@

ubergraph.jnl: ontologies-merged.ttl subclass_closure.ttl is_defined_by.ttl properties-nonredundant.nt properties-redundant.nt opposites.ttl lexically-derived-opposites.nt lexically-derived-opposites-inverse.nt biolink-model.ttl
rm -f $@ &&\
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