Merge pull request #673 from dougli1sqrd/make_uses_dosdp

fixing the yamls, csvs, and make target to use dosdp-tools in odk docker

src/envo/Makefile

@@ -1,6 +1,6 @@
 # This Makefile is for use by the ENVO Release Manager (currently cjm)
 # Also used by Jenkins: http://build.berkeleybop.org/job/build-envo
-# 
+#
 # requirements: Oort (http://code.google.com/p/owltools/wiki/OortIntro)
 #
 # To make a release, type 'make release' in this directory
@@ -26,7 +26,7 @@ full_test: test envo.check-obo subsets/EnvO-Lite-GSC.check-obo
 test_python:
 	python3 --version
 
-build: base all_modules all_imports envo.owl envo.obo envo.json subsets/envo-basic.obo subsets/envo-basic.json subsets/EnvO-Lite-GSC.obo 
+build: base all_modules all_imports envo.owl envo.obo envo.json subsets/envo-basic.obo subsets/envo-basic.json subsets/EnvO-Lite-GSC.obo
 
 prepare_release: build  copy-release
 
@@ -84,9 +84,9 @@ subsets/envo-basic.obo: envo-simple.owl
 #envo-mireot.obo: envo-edit.owl chebi-lite.obo pato-lite.obo
 #	ontology-release-runner --no-subsets --skip-format owx --run-obo-basic-dag-check --no-reasoner --allow-overwrite --asserted --outdir build $< chebi-lite.obo pato-lite.obo && cp build/envo-merged.obo $@
 
-#chebi-lite.obo: 
+#chebi-lite.obo:
 #	owltools $(OBO)/chebi.obo --make-subset-by-properties -o -f obo $@
-#pato-lite.obo: 
+#pato-lite.obo:
 #	owltools $(OBO)/pato.obo --make-subset-by-properties -o -f obo $@
 
 release-diffs:
@@ -137,7 +137,7 @@ imports/%_combined_seed.tsv: imports/%_terms.txt imports/seed.tsv
 
 # Create an import module using the OWLAPI module extraction code via OWLTools.
 # We use the standard catalog, but rewrite the import to X to be a local mirror of ALL of X.
-# After extraction, we further reduce the ontology by creating a "mingraph" (removes all annotations except label) and by 
+# After extraction, we further reduce the ontology by creating a "mingraph" (removes all annotations except label) and by
 imports/%_import.owl: mirror/%.owl envo-edit.owl imports/%_combined_seed.tsv
 	robot extract -i $< -T imports/$*_combined_seed.tsv -m BOT -O $(ENVO_IMPORTS_BASE_URI)/$@ -o $@.tmp.owl && mv $@.tmp.owl $@
 
@@ -342,12 +342,13 @@ mappings/gold-mapping.txt: envo.owl
 # ----------------------------------------
 
 
-all_modules: all_modules_owl all_modules_obo 
+all_modules: all_modules_owl all_modules_obo
 all_modules_owl: $(ALL_MODS_OWL)
 all_modules_obo: $(patsubst %, modules/%.obo, $(MODS))
 
 modules/%.owl: modules/%.csv patterns/%.yaml curie_map.yaml
-	apply-pattern.py -P curie_map.yaml -b http://purl.obolibrary.org/obo/ -i $< -p patterns/$*.yaml  > modules/$*.omn && owltools modules/$*.omn --set-ontology-id $(OBO)/envo/modules/$*.owl -o $@
+	./run.sh dosdp-tools --table-format=csv --template=./patterns/$*.yaml --outfile=modules/$*.tmp.owl --obo-prefixes=true generate --infile=modules/$*.csv
+	./run.sh robot annotate --input modules/$*.tmp.owl -O http://purl.obolibrary.org/obo/envo/modules/$*.owl --output modules/$*.owl && rm modules/$*.tmp.owl
 
 modules/%.obo: modules/%.owl
 	owltools $< -o -f obo $@.tmp && grep -v ^owl-axioms $@.tmp > $@

src/envo/modules/entity_attribute.csv

@@ -1,4 +1,4 @@
-iri,class iri,attribute,attribute label,entity,entity label
+defined_class,defined_class_label,attribute,attribute label,entity,entity label
 ENVO:09200000,quality of an environmental material,PATO:0000146,temperature,ENVO:00010483,environmental material
 ENVO:09200001,,PATO:0000146,temperature,ENVO:00002005,air
 ENVO:09200004,,PATO:0000973,porosity,ENVO:00001998,soil

src/envo/modules/entity_attribute.obo

@@ -3,105 +3,121 @@ ontology: envo/modules/entity_attribute
 
 [Term]
 id: ENVO:09200000
-name: temperature of environmental material
-def: "The temperature of some environmental material." []
-synonym: "environmental material temperature" EXACT []
+name: http://purl.obolibrary.org/obo/PATO_0000146 of http://purl.obolibrary.org/obo/ENVO_00010483
+def: "The http://purl.obolibrary.org/obo/PATO_0000146 of some http://purl.obolibrary.org/obo/ENVO_00010483." []
+synonym: "http://purl.obolibrary.org/obo/ENVO_00010483 http://purl.obolibrary.org/obo/PATO_0000146" EXACT []
 intersection_of: PATO:0000146
 intersection_of: RO:0000052 ENVO:00010483
 
 [Term]
 id: ENVO:09200001
-name: temperature of air
-def: "The temperature of some air." []
-synonym: "air temperature" EXACT []
+name: http://purl.obolibrary.org/obo/PATO_0000146 of http://purl.obolibrary.org/obo/ENVO_00002005
+def: "The http://purl.obolibrary.org/obo/PATO_0000146 of some http://purl.obolibrary.org/obo/ENVO_00002005." []
+synonym: "http://purl.obolibrary.org/obo/ENVO_00002005 http://purl.obolibrary.org/obo/PATO_0000146" EXACT []
 intersection_of: PATO:0000146
 intersection_of: RO:0000052 ENVO:00002005
 
 [Term]
 id: ENVO:09200004
-name: porosity of soil
-def: "The porosity of some soil." []
-synonym: "soil porosity" EXACT []
+name: http://purl.obolibrary.org/obo/PATO_0000973 of http://purl.obolibrary.org/obo/ENVO_00001998
+def: "The http://purl.obolibrary.org/obo/PATO_0000973 of some http://purl.obolibrary.org/obo/ENVO_00001998." []
+synonym: "http://purl.obolibrary.org/obo/ENVO_00001998 http://purl.obolibrary.org/obo/PATO_0000973" EXACT []
 intersection_of: PATO:0000973
 intersection_of: RO:0000052 ENVO:00001998
 
 [Term]
 id: ENVO:09200005
-name: mass density of soil
-def: "The mass density of some soil." []
-synonym: "soil mass density" EXACT []
+name: http://purl.obolibrary.org/obo/PATO_0001019 of http://purl.obolibrary.org/obo/ENVO_00001998
+def: "The http://purl.obolibrary.org/obo/PATO_0001019 of some http://purl.obolibrary.org/obo/ENVO_00001998." []
+synonym: "http://purl.obolibrary.org/obo/ENVO_00001998 http://purl.obolibrary.org/obo/PATO_0001019" EXACT []
 intersection_of: PATO:0001019
 intersection_of: RO:0000052 ENVO:00001998
 
 [Term]
 id: ENVO:09200008
-name: composition of soil
-def: "The composition of some soil." []
-synonym: "soil composition" EXACT []
+name: http://purl.obolibrary.org/obo/PATO_0000025 of http://purl.obolibrary.org/obo/ENVO_00001998
+def: "The http://purl.obolibrary.org/obo/PATO_0000025 of some http://purl.obolibrary.org/obo/ENVO_00001998." []
+synonym: "http://purl.obolibrary.org/obo/ENVO_00001998 http://purl.obolibrary.org/obo/PATO_0000025" EXACT []
 intersection_of: PATO:0000025
 intersection_of: RO:0000052 ENVO:00001998
 
 [Term]
 id: ENVO:09200009
-name: structure of soil
-def: "The structure of some soil." []
-synonym: "soil structure" EXACT []
+name: http://purl.obolibrary.org/obo/PATO_0000141 of http://purl.obolibrary.org/obo/ENVO_00001998
+def: "The http://purl.obolibrary.org/obo/PATO_0000141 of some http://purl.obolibrary.org/obo/ENVO_00001998." []
+synonym: "http://purl.obolibrary.org/obo/ENVO_00001998 http://purl.obolibrary.org/obo/PATO_0000141" EXACT []
 intersection_of: PATO:0000141
 intersection_of: RO:0000052 ENVO:00001998
 
 [Term]
 id: ENVO:09200010
-name: acidity of soil
-def: "The acidity of some soil." []
-synonym: "soil acidity" EXACT []
+name: http://purl.obolibrary.org/obo/PATO_0001842 of http://purl.obolibrary.org/obo/ENVO_00001998
+def: "The http://purl.obolibrary.org/obo/PATO_0001842 of some http://purl.obolibrary.org/obo/ENVO_00001998." []
+synonym: "http://purl.obolibrary.org/obo/ENVO_00001998 http://purl.obolibrary.org/obo/PATO_0001842" EXACT []
 intersection_of: PATO:0001842
 intersection_of: RO:0000052 ENVO:00001998
 
 [Term]
 id: ENVO:09200011
-name: pressure of air
-def: "The pressure of some air." []
-synonym: "air pressure" EXACT []
+name: http://purl.obolibrary.org/obo/PATO_0001025 of http://purl.obolibrary.org/obo/ENVO_00002005
+def: "The http://purl.obolibrary.org/obo/PATO_0001025 of some http://purl.obolibrary.org/obo/ENVO_00002005." []
+synonym: "http://purl.obolibrary.org/obo/ENVO_00002005 http://purl.obolibrary.org/obo/PATO_0001025" EXACT []
 intersection_of: PATO:0001025
 intersection_of: RO:0000052 ENVO:00002005
 
 [Term]
 id: ENVO:09200012
-name: temperature of soil
-def: "The temperature of some soil." []
-synonym: "soil temperature" EXACT []
+name: http://purl.obolibrary.org/obo/PATO_0000146 of http://purl.obolibrary.org/obo/ENVO_00001998
+def: "The http://purl.obolibrary.org/obo/PATO_0000146 of some http://purl.obolibrary.org/obo/ENVO_00001998." []
+synonym: "http://purl.obolibrary.org/obo/ENVO_00001998 http://purl.obolibrary.org/obo/PATO_0000146" EXACT []
 intersection_of: PATO:0000146
 intersection_of: RO:0000052 ENVO:00001998
 
 [Term]
 id: ENVO:09200013
-name: wetness of soil
-def: "The wetness of some soil." []
-synonym: "soil wetness" EXACT []
+name: http://purl.obolibrary.org/obo/PATO_0001822 of http://purl.obolibrary.org/obo/ENVO_00001998
+def: "The http://purl.obolibrary.org/obo/PATO_0001822 of some http://purl.obolibrary.org/obo/ENVO_00001998." []
+synonym: "http://purl.obolibrary.org/obo/ENVO_00001998 http://purl.obolibrary.org/obo/PATO_0001822" EXACT []
 intersection_of: PATO:0001822
 intersection_of: RO:0000052 ENVO:00001998
 
 [Term]
 id: ENVO:09200014
-name: temperature of water
-def: "The temperature of some water." []
-synonym: "water temperature" EXACT []
+name: http://purl.obolibrary.org/obo/PATO_0000146 of http://purl.obolibrary.org/obo/ENVO_00002006
+def: "The http://purl.obolibrary.org/obo/PATO_0000146 of some http://purl.obolibrary.org/obo/ENVO_00002006." []
+synonym: "http://purl.obolibrary.org/obo/ENVO_00002006 http://purl.obolibrary.org/obo/PATO_0000146" EXACT []
 intersection_of: PATO:0000146
 intersection_of: RO:0000052 ENVO:00002006
 
 [Term]
 id: ENVO:09200015
-name: humidity of soil
-def: "The humidity of some soil." []
-synonym: "soil humidity" EXACT []
+name: http://purl.obolibrary.org/obo/PATO_0015009 of http://purl.obolibrary.org/obo/ENVO_00001998
+def: "The http://purl.obolibrary.org/obo/PATO_0015009 of some http://purl.obolibrary.org/obo/ENVO_00001998." []
+synonym: "http://purl.obolibrary.org/obo/ENVO_00001998 http://purl.obolibrary.org/obo/PATO_0015009" EXACT []
 intersection_of: PATO:0015009
 intersection_of: RO:0000052 ENVO:00001998
 
 [Term]
 id: ENVO:09200016
-name: conductivity of soil
-def: "The conductivity of some soil." []
-synonym: "soil conductivity" EXACT []
+name: http://purl.obolibrary.org/obo/PATO_0001757 of http://purl.obolibrary.org/obo/ENVO_00001998
+def: "The http://purl.obolibrary.org/obo/PATO_0001757 of some http://purl.obolibrary.org/obo/ENVO_00001998." []
+synonym: "http://purl.obolibrary.org/obo/ENVO_00001998 http://purl.obolibrary.org/obo/PATO_0001757" EXACT []
 intersection_of: PATO:0001757
 intersection_of: RO:0000052 ENVO:00001998
 
+[Term]
+id: ENVO:09200017
+name: http://purl.obolibrary.org/obo/PATO_0000025 of http://purl.obolibrary.org/obo/ENVO_00002006
+def: "The http://purl.obolibrary.org/obo/PATO_0000025 of some http://purl.obolibrary.org/obo/ENVO_00002006." []
+synonym: "http://purl.obolibrary.org/obo/ENVO_00002006 http://purl.obolibrary.org/obo/PATO_0000025" EXACT []
+intersection_of: PATO:0000025
+intersection_of: RO:0000052 ENVO:00002006
+
+[Term]
+id: ENVO:09200018
+name: http://purl.obolibrary.org/obo/PATO_0001757 of http://purl.obolibrary.org/obo/ENVO_00002006
+def: "The http://purl.obolibrary.org/obo/PATO_0001757 of some http://purl.obolibrary.org/obo/ENVO_00002006." []
+synonym: "http://purl.obolibrary.org/obo/ENVO_00002006 http://purl.obolibrary.org/obo/PATO_0001757" EXACT []
+intersection_of: PATO:0001757
+intersection_of: RO:0000052 ENVO:00002006
+