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CHECK IF NEEDED: Issue 272 (old branch) #480

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CHECK IF NEEDED: Issue 272 (old branch) #480

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f64f833
Added make targets for integration tests, see #272
cmungall Oct 23, 2018
56bb4ed
fix
cmungall Oct 30, 2018
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47 changes: 47 additions & 0 deletions src/ontology/Makefile
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Original file line number Diff line number Diff line change
Expand Up @@ -116,6 +116,53 @@ subsets/ro-hom.owl: ro.owl
subsets/ro-chado.obo: ro.obo
owltools --use-catalog $< --merge-imports-closure --remove-tbox --remove-annotation-assertions -r -l -s -d --remove-dangling --set-ontology-id $(OBO)/ro/$@ -o -f obo [email protected] && ../tools/translate-to-chado-obo.pl [email protected] > $@

# ========================================
# INTEGRATION TESTS
# ========================================
# See https://github.com/oborel/obo-relations/issues/272

# initial test list, this will be expanded
# Criteria: each ontology must provide a base
INTEGRATED_ONTS = uberon cl go

# All integration tests
it_tests: individual_it_tests it-combined.txt it-diff.obodiff

# Run integration tests on an ontology by ontology basis.
# Note: this will be less complete that running once on the combined
# set. However, this is useful for debugging.
individual_it_tests: $(patsubst %, it-base-%.txt, $(INTEGRATED_ONTS))

# perform integration test on an individual ontology
it-base-%.txt: ro-edit.owl
robot merge -i $< -i $(OBO)/$*/$*-base.owl reason -r elk && touch $@

INTEGRATED_ONTS_I := $(foreach ont,$(INTEGRATED_ONTS),-I $(OBO)/$(ont)/$(ont)-base.owl)

# make a merger of bases of integrated ontologies, plus BFO.
# TODO: build this in advance and distribute it separately, to make
# this fast enough for running in travis.
mirror/ext-combined.owl:
robot merge $(INTEGRATED_ONTS_I) -I $(OBO)/bfo.owl -o $@

# run an integration test on integrated ontologies plus ro-edit
it-combined.txt: mirror/ext-combined.owl ro-edit.owl
robot merge -i ro-edit.owl -i $< reason -r elk && touch $@

# merge integrated onts plus ro-edit
it-inferences-current.obo: mirror/ext-combined.owl ro-edit.owl
robot merge -i ro-edit.owl -i $< reason -n true -r elk -o $@

# merge integrated onts plus last released RO
it-inferences-release.obo: mirror/ext-combined.owl
robot merge -i $(OBO)/ro.owl -i $< reason -n true -r elk -o $@

# How do changes in RO impact downstream ontologies?
# We do this as an obodiff for now for speed and readability;
# Will later switch to markdown diffs when integrated in robot
it-diff.obodiff: it-inferences-release.obo it-inferences-current.obo
diff -u $^ > $@

# ========================================
# REPORTING (EXPERIMENTAL)
# ========================================
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