lint

Author: cmungall

ontologies.Makefile

@@ -141,6 +141,17 @@ db/bao.owl: download/bao.owl
 	robot merge -i $< -o $@
 
 
+download/orcid.owl: STAMP
+	curl -L -s https://raw.githubusercontent.com/cthoyt/wikidata-orcid-ontology/main/orcid.owl > $@.tmp
+	sha256sum -b $@.tmp > $@.sha256
+	mv $@.tmp $@
+
+.PRECIOUS: download/orcid.owl
+
+db/orcid.owl: download/orcid.owl
+	cp $< $@
+
+
 download/cpont.owl: STAMP
 	curl -L -s https://w3id.org/cpont/cpont.owl > $@.tmp
 	sha256sum -b $@.tmp > $@.sha256
@@ -305,4 +316,4 @@ download/%.owl: STAMP
 db/%.owl: download/%.owl
 	robot merge -i $< -o $@
 
-EXTRA_ONTOLOGIES = chiro ncit foodon chebiplus msio phenio comploinc bero aio reacto go go-lego bao cpont biolink biopax enanomapper mlo ito reactome-Homo-sapiens efo edam sweetAll lov schema-dot-org cosmo co_324
+EXTRA_ONTOLOGIES = chiro ncit foodon chebiplus msio phenio comploinc bero aio reacto go go-lego bao orcid cpont biolink biopax enanomapper mlo ito reactome-Homo-sapiens efo edam sweetAll lov schema-dot-org cosmo co_324

src/semsql/builder/builder.py

@@ -22,6 +22,7 @@ class DockerConfig:
     """
     Configuration for running ODK Docker image
     """
+
     odk_version: str = None  # not used yet
     memory: str = None
 
@@ -148,13 +149,15 @@ def compile_registry(registry_path: str, local_prefix_file: TextIO = None) -> st
         # main build target
         target = f"db/{ont.id}.owl"
         dependencies = [f"download/{ont.id}.owl"]
-        if ont.has_imports or (ont.format and ont.format != 'rdfxml'):
+        if ont.has_imports or (ont.format and ont.format != "rdfxml"):
             command = f"robot merge -i $< -o $@"
         elif ont.build_command:
             command = ont.build_command.format(ont=ont)
         else:
             command = f"cp $< $@"
-        rule = MakefileRule(target=target, dependencies=dependencies, commands=[command])
+        rule = MakefileRule(
+            target=target, dependencies=dependencies, commands=[command]
+        )
         makefile.rules.append(rule)
         if not ont.suppress:
             onts.append(ont.id)

src/semsql/builder/cli.py

@@ -3,10 +3,10 @@
 import click
 from linkml_runtime import SchemaView
 from linkml_runtime.utils.formatutils import underscore
-from semsql.linkml import path_to_schema
 from sqlalchemy import text
 
 import semsql.builder.builder as builder
+from semsql.linkml import path_to_schema
 from semsql.sqlutils.viewgen import get_viewdef
 
 
@@ -51,10 +51,12 @@ def make(path, docker):
 
 
 @main.command()
-@click.option("--local-prefixes",
-              "-P",
-              type=click.File(mode="w"),
-              help="path to local prefixes file (will be overridden)")
+@click.option(
+    "--local-prefixes",
+    "-P",
+    type=click.File(mode="w"),
+    help="path to local prefixes file (will be overridden)",
+)
 @click.argument("registry")
 def generate_makefile(registry, local_prefixes):
     """
@@ -125,9 +127,7 @@ def view2table(views, schema, index: bool):
                 if index:
                     for sn in sv.class_slots(cn):
                         colname = underscore(sn)
-                        print(
-                            f"CREATE INDEX {tn}_{colname} ON {tn}({colname});"
-                        )
+                        print(f"CREATE INDEX {tn}_{colname} ON {tn}({colname});")
             else:
                 logging.error(f"No view for {cn}")
 

src/semsql/builder/prefixes/prefixes.csv

@@ -54,6 +54,7 @@ prefix,base
 MSIO,http://purl.obolibrary.org/obo/MSIO_
 nmrCV,http://nmrML.org/nmrCV#NMR:
 loinc,https://loinc.org/
+orcid,https://orcid.org/
 evs.ncit,http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#
 old.fix,http://purl.org/obo/owl/FIX#
 mlo,http://www.a2rd.net.br/mlo#

src/semsql/builder/prefixes/prefixes_local.csv

@@ -2,6 +2,7 @@ prefix,base
 MSIO,http://purl.obolibrary.org/obo/MSIO_
 nmrCV,http://nmrML.org/nmrCV#NMR:
 loinc,https://loinc.org/
+orcid,https://orcid.org/
 evs.ncit,http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#
 old.fix,http://purl.org/obo/owl/FIX#
 mlo,http://www.a2rd.net.br/mlo#

src/semsql/builder/registry/__init__.py

@@ -2,6 +2,7 @@
 
 this_path = Path(__file__).parent
 
+
 def path_to_ontology_registry() -> Path:
     """
     Returns path to the registry file