Merge pull request #60 from INCATools/rg-tab

Refactor to use relation-graph TSV output

.github/workflows/main.yaml

@@ -77,30 +77,11 @@ jobs:
       #    install your root project, if required 
       #----------------------------------------------      
       - name: Install library
-        run: poetry install --no-interaction --extras gilda
+        run: poetry install --no-interaction
 
       #----------------------------------------------
       #              run test suite   
       #----------------------------------------------
       - name: Run tests
         run: poetry run python -m unittest discover
 
-      #----------------------------------------------
-      #              coverage report   
-      #----------------------------------------------
-      - name: Generate coverage results
-        run: |
-          poetry run coverage run -m unittest discover
-          poetry run coverage xml
-          poetry run coverage report -m
-
-      #----------------------------------------------
-      #           upload coverage results
-      #----------------------------------------------
-      - name: Upload coverage report
-        uses: codecov/[email protected]
-        with:
-          name: codecov-results-${{ matrix.python-version }}
-          token: ${{ secrets.CODECOV_TOKEN }}
-          file: ./coverage.xml
-          fail_ci_if_error: true

Makefile

@@ -13,18 +13,32 @@ PREFIX_DIR = $(BUILDER_DIR)/prefixes
 ALL_OBO_ONTS := $(shell cat reports/obo.tsv)
 SELECTED_ONTS = obi mondo go envo ro hp mp zfa wbphenotype ecto upheno uberon_cm doid chebi pr wbphenotype fbbt dron
 
+# EXTRA_ONTOLOGIES is defined in ontologies.Makefile
+ALL_ONTS = $(ALL_OBO_ONTS) $(EXTRA_ONTOLOGIES)
+
+STAGED_ONTOLOGIES = $(patsubst %,stage/%.db.gz,$(ALL_ONTS))
+
 TEST_ONTOLOGIES = go-nucleus robot-example
 
+
 all: build_all stage_all
-build_all: $(patsubst %,all-%,$(ALL_OBO_ONTS))
-stage_all: $(patsubst %,stage/%.db.gz,$(ALL_OBO_ONTS))
+build_all: $(patsubst %,all-%,$(ALL_ONTS))
+stage_all: $(STAGED_ONTOLOGIES)
 
 selected: $(patsubst %,all-%,$(SELECTED_ONTS))
 
 all-%: db/%.db
 	sqlite3 $< "SELECT COUNT(*) FROM statements"
 stage/%.db.gz: db/%.db
 	gzip -c $< > $@.tmp && mv $@.tmp $@
+.PRECIOUS: stage/%.db.gz
+
+list-onts:
+	echo $(ALL_ONTS)
+list-extra:
+	echo $(EXTRA_ONTOLOGIES)
+list-staged:
+	ls -alt $(STAGED_ONTOLOGIES)
 
 # INSTALL
 include install.Makefile
@@ -97,10 +111,6 @@ db/obo-ontologies.owl:
 reports/obo.tsv: db/obo-ontologies.db
 	sqlite3 $< "SELECT subject FROM ontology_status_statement WHERE value = 'active'" | perl -npe 's@^obo:@@' > $@
 
-# to test
-list-onts:
-	echo $(ALL_OBO_ONTS)
-
 
 
 
@@ -119,21 +129,6 @@ reports/%.problems.tsv: db/%.db target/%.views
 STAMP:
 	touch $@
 
-# download OWL, ensuring converted to RDF/XML
-db/%.owl: STAMP
-	robot merge -I http://purl.obolibrary.org/obo/$*.owl -o $@
-.PRECIOUS: db/%.owl 
-
-db/foodon.owl: STAMP
-	robot merge -I $(OBO)/foodon.owl relax reduce -c true -o $@
-
-db/go.owl: STAMP
-	curl -L -s http://purl.obolibrary.org/obo/go/extensions/go-plus.owl > $@
-
-db/monarch.owl:
-	robot merge -I http://purl.obolibrary.org/obo/upheno/monarch.owl -o $@
-
-
 db/reactome-Homo-sapiens.owl: download/reactome-biopax.zip db/biopax.owl
 	unzip -p $< Homo_sapiens.owl > $@.tmp &&\
 	robot merge -i $@.tmp  -i db/biopax.owl -o $@

install.Makefile

@@ -17,7 +17,7 @@ bin/rdftab:
 	curl -L -o $@ $(RDFTAB_URL)
 	chmod +x $@
 
-RG_VERSION=2.2.0
+RG_VERSION=2.3.0
 bin/relation-graph:
 	curl -L -s https://github.com/balhoff/relation-graph/releases/download/v$(RG_VERSION)/relation-graph-cli-$(RG_VERSION).tgz | tar -zxv  && mv relation-graph-cli-$(RG_VERSION) relation-graph && (cd bin && ln -s ../relation-graph/bin/relation-graph)