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Seems like src/envo/Makefile would benefit from a clean target #1602

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turbomam opened this issue Jan 16, 2025 · 8 comments · May be fixed by #1603
Open

Seems like src/envo/Makefile would benefit from a clean target #1602

turbomam opened this issue Jan 16, 2025 · 8 comments · May be fixed by #1603
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@turbomam

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@turbomam
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turbomam commented Jan 16, 2025 •
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I find it challenging to debug the EnvO build process. I would expect that I can return to a known good state at any time by running a cleanup target followed by an all target, even if that means the build will take more time the next time around. I do not see any cleanup target in any of the EnvO makefiles at this time.

ChatGPT suggests

.PHONY: clean

clean:
	# Remove temporary and intermediate files
	rm -rf $(TMPDIR)/
	rm -rf tmp/
	rm -rf reports/
	rm -rf modules/*.tmp.owl
	rm -rf modules/*.obo
	rm -rf modules/*.owl
	rm -rf mirror/*.owl
	rm -rf imports/*.owl
	rm -rf imports/*.obo
	rm -rf patterns/matches/logical/
	rm -rf patterns/matches/annotations/

	# Remove generated ontology files
	rm -f $(ONT).owl $(ONT).obo $(ONT).json
	rm -f $(ONT)-full.owl $(ONT)-full.obo $(ONT)-full.json
	rm -f $(ONT)-base.owl $(ONT)-base.obo $(ONT)-base.json
	rm -f $(SRC) $(PRE_SRC)

	# Remove subset files
	rm -f subsets/*.owl subsets/*.obo subsets/*.json subsets/*.tsv

	# Remove downloaded or mirrored external ontologies
	rm -rf mirror/
	rm -f GO.xrf_abbs

	# Remove any temporary downloads or caches
	rm -rf diffs/
	rm -f *.tmp
	rm -f *.log

	# Optional: Remove release artifacts if generated
	rm -rf $(RELEASEDIR)/$(ONT).owl $(RELEASEDIR)/$(ONT).obo $(RELEASEDIR)/$(ONT).json
	rm -rf $(RELEASEDIR)/subsets/
	rm -rf $(RELEASEDIR)/mappings/
	rm -rf $(RELEASEDIR)/imports/
@turbomam turbomam self-assigned this Jan 16, 2025
@turbomam
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turbomam commented Jan 16, 2025 •
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make: *** No rule to make target 'envo-edit.owl', needed by 'mirror/pato.owl'. Stop.

re-checked-out

  • envo-edit.owl
  • imports/bfo_import.owl
  • imports/chebi_import.owl
  • imports/envo_bridge.owl
  • imports/fao_import.owl
  • imports/foodon_import.owl
  • imports/go_import.owl
  • imports/iao_import.owl
  • imports/ncbitaxon_import.owl
  • imports/obi_import.owl
  • imports/pato_import.owl
  • imports/pco_import.owl
  • imports/po_import.owl
  • imports/ro_import.owl
  • imports/uberon_import.owl
  • modules/chemical_concentration.owl
  • modules/entity_attribute.owl
  • modules/entity_attribute_location.owl
  • modules/entity_quality_location.owl
  • modules/process_attribute.owl

how are these regenerated?

@turbomam
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robot query -f tsv -i envo.owl -q  sparql/edges.sparql reports/envo-edges.tsv.tmp && mv reports/envo-edges.tsv.tmp reports/envo-edges.tsv

reports/envo-edges.tsv.tmp (No such file or directory)
Use the -vvv option to show the stack trace.
Use the --help option to see usage information.
make: *** [Makefile:508: reports/envo-edges.tsv] Error 1

@turbomam
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OK after

mkdir reports

@turbomam
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robot --catalog catalog-v001.xml report -p reports/report_profile_edit.txt -l true -i envo-edit.owl --fail-on ERROR --print 5 -o reports/envo-edit-robot-report.tsv

reports/report_profile_edit.txt (No such file or directory)
Use the -vvv option to show the stack trace.
Use the --help option to see usage information.
make: *** [Makefile:531: reports/envo-edit-robot-report.tsv] Error 1

@turbomam
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git checkout reports/report_profile_edit.txt

@pbuttigieg
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@turbomam please state the issue clearly and completely in the first post - the stream of consciousness issues that you've recently opened are hard to follow

@turbomam
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make clean
mkdir reports
git checkout reports/report_profile_edit.txt
git checkout envo-edit.owl
./run.sh make all_imports

still complains about missing files like imports/bfo_import.owl, even when trying to create the imports!

./run.sh make imports/bfo_import.owl

@pbuttigieg
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Note this make process was inherited from OBO. I think some sort of dummy import files are needed to initiate. They will be overwritten. No idea why, @cmungall may be able to explain.

@turbomam turbomam linked a pull request Jan 16, 2025 that will close this issue
clean makefile target. make all works after using it. #1603
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clean makefile target. make all works after using it. EnvironmentOntology/envo
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@pbuttigieg @turbomam