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Reduce the chatter of the local QC pipeline #10686

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Aug 13, 2024
Merged

Reduce the chatter of the local QC pipeline #10686

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2 changes: 1 addition & 1 deletion .github/workflows/qc.yml
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Expand Up @@ -19,7 +19,7 @@ jobs:
ontology_qc:
# The type of runner that the job will run on
runs-on: ubuntu-latest
container: obolibrary/odkfull:v1.5
container: obolibrary/odkfull:v1.5.2

# Steps represent a sequence of tasks that will be executed as part of the job
steps:
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4 changes: 2 additions & 2 deletions src/ontology/hp-qc-pipeline.sh
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Expand Up @@ -39,8 +39,8 @@ java -jar $OWL_CHECK_JAR $HP_EDIT

# The ODK QC and build:

sh -e run.sh make IMP=false test #&> log.txt
sh -e run.sh make IMP=false PAT=false MIR=false $HP_OBO
sh -e run.sh make IMP=false PAT=false MIR=false test $HP_OBO -B #&> log.txt

#- tail -n 100 log.txt
# now check hp.obo for duplicated labels, synonyms that are used for different classes
java -jar $OBO_CHECK_JAR $HP_OBO
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2 changes: 1 addition & 1 deletion src/ontology/hp.Makefile
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Expand Up @@ -80,7 +80,7 @@ fastobo: hp.obo
noequivalents:
$(ROBOT) reason --input $(SRC) remove --select imports reason --reasoner ELK --equivalent-classes-allowed asserted-only --output test.owl && rm test.owl && echo "Success"

test: sparql_test all_reports test_obo hp_error consistency noequivalents fastobo
test: sparql_test test_obo hp_error consistency noequivalents fastobo

hp_labels.csv: $(SRC)
robot query --use-graphs true -f csv -i $(SRC) --query ../sparql/term_table.sparql $@
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