Revert "Remove PR import test"

This reverts commit 6d952fe.

Author: shawntanzk

src/ontology/Makefile

@@ -94,7 +94,7 @@ all_main: $(MAIN_FILES)
 ## By default this is the cross-product of IMPORT_MODULES x FORMATS
 
 
-IMPORTS =  go ro uberon pato cl ensmusg ncbitaxon
+IMPORTS =  pr go ro uberon pato cl ensmusg ncbitaxon
 
 IMPORT_ROOTS = $(patsubst %, imports/%_import, $(IMPORTS))
 IMPORT_OWL_FILES = $(foreach n,$(IMPORT_ROOTS), $(n).owl)
@@ -250,6 +250,13 @@ imports/%_import.owl: mirror/merged.owl imports/%_terms_combined.txt
 
 .PRECIOUS: imports/%_import.owl
 
+## Module for ontology: pr
+
+imports/pr_import.owl: mirror/merged.owl imports/pr_terms_combined.txt
+	if [ $(IMP) = true ] && [ $(IMP_LARGE) = true ]; then $(ROBOT) extract -i $< -T imports/pr_terms_combined.txt --force true --individuals exclude --method BOT \
+		query --update ../sparql/inject-subset-declaration.ru --update ../sparql/postprocess-module.ru \
+		annotate --ontology-iri $(ONTBASE)/$@ $(ANNOTATE_ONTOLOGY_VERSION) --output $@.tmp.owl && mv $@.tmp.owl $@; fi
+
 .PHONY: refresh-imports
 refresh-imports:
 	make IMP=true MIR=true PAT=false IMP_LARGE=true all_imports -B
@@ -297,6 +304,16 @@ MIR=true # Global parameter to bypass mirror generation
 IMP_LARGE=true # Global parameter to bypass handling of large imports
 PAT=true # Global parameter to bypass pattern generation
 
+## ONTOLOGY: pr
+## Copy of pr is re-downloaded whenever source changes
+mirror/pr.trigger: $(SRC)
+
+mirror/pr.owl: mirror/pr.trigger
+	if [ $(MIR) = true ] && [ $(IMP) = true ] && [ $(IMP_LARGE) = true ]; then $(ROBOT) convert -I https://raw.githubusercontent.com/obophenotype/pro_obo_slim/master/pr_slim.owl -o $@.tmp.owl && \
+		$(ROBOT) remove -i $@.tmp.owl --base-iri $(URIBASE)/PR --axioms external --preserve-structure false --trim false -o $@.tmp.owl && mv $@.tmp.owl $@; fi
+.PRECIOUS: mirror/pr.owl
+
+
 ## ONTOLOGY: go
 ## Copy of go is re-downloaded whenever source changes
 mirror/go.trigger: $(SRC)

src/ontology/bdso-odk.yaml

@@ -26,6 +26,10 @@ import_group:
     - <http://purl.obolibrary.org/obo/NCBITaxon_Union_*>
     - <http://www.genenames.org/cgi-bin/gene_symbol_report*>
   products:
+    - id: pr
+      make_base: TRUE
+      mirror_from: https://raw.githubusercontent.com/obophenotype/pro_obo_slim/master/pr_slim.owl
+      is_large: TRUE
     - id: go
       use_base: TRUE
       base_iris:

src/ontology/catalog-v001.xml

@@ -2,6 +2,7 @@
 <catalog prefer="public" xmlns="urn:oasis:names:tc:entity:xmlns:xml:catalog">
   <uri id="Imports Wizard Entry" name="http://purl.obolibrary.org/obo/bdscratch/releases/2021-03-08/patterns/definitions.owl" uri="file:/home/huseyin/workspace5/brain_data_standards_ontologies/src/patterns/definitions.owl"/>
   <uri id="User Entered Import Resolution" name="http://purl.obolibrary.org/obo/components/all_templates.owl" uri="components/all_templates.owl"/>
+  <uri id="User Entered Import Resolution" name="http://purl.obolibrary.org/obo/pcl/imports/pr_import.owl" uri="imports/pr_import.owl"/>
   <uri id="User Entered Import Resolution" name="http://purl.obolibrary.org/obo/pcl/imports/go_import.owl" uri="imports/go_import.owl"/>
   <uri id="User Entered Import Resolution" name="http://purl.obolibrary.org/obo/bdscratch/imports/ro_import.owl" uri="imports/ro_import.owl"/>
   <uri id="User Entered Import Resolution" name="http://purl.obolibrary.org/obo/bdscratch/imports/cl_import.obo" uri="imports/cl_import.obo"/>