merged makefiles #9

obophenotype · Mar 8, 2022 · 63f883f · 63f883f
1 parent cc1d342
commit 63f883f
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Showing 13 changed files with 21 additions and 163,484 deletions.
diff --git a/src/ontology/Makefile b/src/ontology/Makefile
@@ -1,13 +1,21 @@
+JOBS = 1 17 10 16 8
+
 ROBOT = robot
 URIBASE = http://purl.obolibrary.org/obo
 
-all: dependencies aba_uberon.owl report.xlsx
+LINKML = linkml-data2owl
+
+STRUCTURE_GRAPHS = $(patsubst %, sources/%.json, $(JOBS))
+ALL_GRAPH_ONTOLOGIES = $(patsubst sources/%.json,sources/%.ofn,$(STRUCTURE_GRAPHS))
+#ALL_TEMPLATES = $(patsubst sources/%.json,../linkml/data/template_%.tsv,$(STRUCTURE_GRAPHS))
+
+all: dependencies $(ALL_GRAPH_ONTOLOGIES) aba_uberon.owl report.xlsx
 
 # Installing depedencies so it can run in ODK container
 
 .PHONY: dependencies
 dependencies:
-	pip install openpyxl
+	pip install -r ../../requirements.txt
 
 IMP=true # Global parameter to bypass import generation
 MIR=true # Global parameter to bypass mirror generation
@@ -18,6 +26,16 @@ mirror/uberon.owl:
 
 # TODO: move to making uberon slice.
 
+sources/%.json:
+	curl -o $@ $(subst %,$(subst sources/,,$@),"http://api.brain-map.org/api/v2/structure_graph_download/%")
+
+../linkml/data/template_%.tsv: sources/%.json
+	python ../scripts/structure_graph_template.py -i $< -o $@
+
+sources/%.ofn: ../linkml/data/template_%.tsv
+	$(LINKML) -C Class -s ../linkml/structure_graph_schema.yaml $< -o $@
+.PRECIOUS: sources/%.ofn
+
 #Convert to obo format
 
 sources/allen-mba.obo: 

diff --git a/src/ontology/sources/1.ofn b/src/ontology/sources/1.ofn
diff --git a/src/ontology/sources/10.ofn b/src/ontology/sources/10.ofn
diff --git a/src/ontology/sources/16.ofn b/src/ontology/sources/16.ofn
diff --git a/src/ontology/sources/17.ofn b/src/ontology/sources/17.ofn
diff --git a/src/ontology/sources/8.ofn b/src/ontology/sources/8.ofn
diff --git a/src/scripts/structure_graph_template.py b/src/scripts/structure_graph_template.py
@@ -9,7 +9,7 @@
               "17.json": "http://purl.obolibrary.org/obo/DMBA_",
               "10.json": "http://purl.obolibrary.org/obo/HBA_",
               "16.json": "http://purl.obolibrary.org/obo/DHBA_",
-              "8.json": "http://purl.obolibrary.org/obo/PHA_"}
+              "8.json": "http://purl.obolibrary.org/obo/PBA_"}
 
 
 def generate_template(graph_json, output):