registry

Author: cmungall

Makefile

@@ -146,8 +146,8 @@ download/reactome-biopax.zip:
 src/semsql/builder/registry/registry_schema.py: src/semsql/builder/registry/registry_schema.yaml
 	$(RUN) gen-python $< > $@
 
-ontologies.Makefile: src/semsql/builder/registry/ontologies.yaml
-	$(RUN) semsql generate-makefile $< > $@.tmp && mv $@.tmp $@
+ontologies.Makefile: src/semsql/builder/registry/ontologies.yaml 
+	$(RUN) semsql generate-makefile -P src/semsql/builder/prefixes/prefixes_local.csv $< > $@.tmp && mv $@.tmp $@
 
 include ontologies.Makefile
 

ontologies.Makefile

@@ -1,3 +1,6 @@
+db/msio.owl: STAMP
+	curl -L -s https://raw.githubusercontent.com/MSI-Metabolomics-Standards-Initiative/MSIO/master/releases/latest_release/MSIO-merged-reasoned.owl > $@.tmp && mv $@.tmp $@
+
 db/phenio.owl: STAMP
 	curl -L -s https://github.com/monarch-initiative/phenio/releases/download/latest/phenio.owl > $@.tmp && mv $@.tmp $@
 
@@ -40,4 +43,4 @@ db/lov.owl: STAMP
 db/schema-dot-org.owl: STAMP
 	curl -L -s https://schema.org/version/latest/schemaorg-current-https.rdf > $@.tmp && mv $@.tmp $@
 
-
+EXTRA_ONTOLOGIES = msio phenio bero aio reacto go-lego bao biolink biopax enanomapper efo edam sweetAll lov schema-dot-org

src/semsql/builder/build.Makefile

@@ -33,7 +33,7 @@ help:
 # All dbs are made from an initial template containing
 # (1) prefixes
 # (2) SQL Schema (primarily views)
-$(TEMPLATE): $(THIS_DIR)/sql_schema/semsql.sql
+$(TEMPLATE): $(THIS_DIR)/sql_schema/semsql.sql build_prefixes
 	cat $< | sqlite3 $@.tmp && \
 	echo .exit | sqlite3 -echo $@.tmp -cmd ".mode csv" -cmd ".import $(THIS_DIR)/prefixes/prefixes.csv prefix" && \
 	mv $@.tmp $@
@@ -96,6 +96,6 @@ $(PREFIX_DIR)/obo_prefixes.db: $(PREFIX_DIR)/obo_prefixes.owl
 $(PREFIX_DIR)/obo_prefixes.csv: $(PREFIX_DIR)/obo_prefixes.db
 	sqlite3 $< -cmd ".separator ','" "SELECT p.value AS prefix, ns.value AS base FROM statements AS p JOIN statements AS ns ON (p.subject=ns.subject) WHERE p.predicate='<http://www.w3.org/ns/shacl#prefix>' AND ns.predicate='<http://www.w3.org/ns/shacl#namespace>'" > $@
 
-$(PREFIX_DIR)/prefixes.csv: $(PREFIX_DIR)/prefixes_curated.csv $(PREFIX_DIR)/obo_prefixes.csv
+$(PREFIX_DIR)/prefixes.csv: $(PREFIX_DIR)/prefixes_curated.csv $(PREFIX_DIR)/prefixes_local.csv $(PREFIX_DIR)/obo_prefixes.csv
 	cat $^ > $@
 

src/semsql/builder/builder.py

@@ -4,7 +4,7 @@
 import shutil
 import subprocess
 from pathlib import Path
-from typing import Optional
+from typing import Optional, TextIO
 
 import requests
 from linkml_runtime.loaders import yaml_loader
@@ -107,17 +107,20 @@ def connect(owl_file: str):
     session = Session()
     return session
 
-def compile_registry(registry_path: str) -> str:
+def compile_registry(registry_path: str, local_prefix_file: TextIO = None) -> str:
     """
     Generate makefile content from registry
 
     :param registry_path:
+    :param local_prefix_file:
     :return:
     """
     registry: registry_schema.Registry
     registry = yaml_loader.load(registry_path, target_class=registry_schema.Registry)
     mkfile = ""
     onts = []
+    if local_prefix_file:
+        local_prefix_file.write("prefix,base\n")
     for ont in registry.ontologies.values():
         target = f"db/{ont.id}.owl"
         dependencies = ["STAMP"]
@@ -128,5 +131,8 @@ def compile_registry(registry_path: str) -> str:
         dependencies_str = " ".join(dependencies)
         mkfile += f"{target}: {dependencies_str}\n\t{command}\n\n"
         onts.append(ont.id)
+        if local_prefix_file:
+            for pn in ont.prefixmap.values():
+                local_prefix_file.write(f"{pn.prefix},{pn.prefix_value}\n")
     mkfile += f"EXTRA_ONTOLOGIES = {' '.join(onts)}"
     return mkfile

src/semsql/builder/cli.py

@@ -51,12 +51,16 @@ 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.argument("registry")
-def generate_makefile(registry):
+def generate_makefile(registry, local_prefixes):
     """
     Generates makefile
     """
-    print(builder.compile_registry(registry))
+    print(builder.compile_registry(registry, local_prefix_file=local_prefixes))
 
 
 @main.command()

src/semsql/builder/prefixes/prefixes.csv

@@ -49,6 +49,11 @@ wikidata,http://www.wikidata.org/entity/
 schema,https://schema.org/
 ICD10CM,http://purl.bioontology.org/ontology/ICD10CM/
 ICD10WHO,https://icd.who.int/browse10/2019/en#/
+prefix,base
+MSIO,http://purl.obolibrary.org/obo/MSIO_
+nmrCV,http://nmrML.org/nmrCV#NMR:
+evs.ncit,http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#
+old.fix,http://purl.org/obo/owl/FIX#
 PSO,http://purl.obolibrary.org/obo/PSO_
 CHIRO,http://purl.obolibrary.org/obo/CHIRO_
 PW,http://purl.obolibrary.org/obo/PW_

src/semsql/builder/prefixes/prefixes_local.csv

@@ -0,0 +1,5 @@
+prefix,base
+MSIO,http://purl.obolibrary.org/obo/MSIO_
+nmrCV,http://nmrML.org/nmrCV#NMR:
+evs.ncit,http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#
+old.fix,http://purl.org/obo/owl/FIX#

src/semsql/builder/registry/ontologies.yaml

@@ -2,6 +2,11 @@ id: semantic-sql-registry
 description: Registry overlap for Semantic-SQL designed to supplement OBO vocabularies
 license: CC0
 ontologies:
+  msio:
+    url: https://raw.githubusercontent.com/MSI-Metabolomics-Standards-Initiative/MSIO/master/releases/latest_release/MSIO-merged-reasoned.owl
+    prefixmap:
+      MSIO: http://purl.obolibrary.org/obo/MSIO_
+      nmrCV: "http://nmrML.org/nmrCV#NMR:"
   phenio:
     description: Monarch Phenomics Integrated Ontology
     url: https://github.com/monarch-initiative/phenio/releases/download/latest/phenio.owl
@@ -28,7 +33,7 @@ ontologies:
     has_imports: true
     prefixmap:
       evs.ncit: http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#
-      fix: http://purl.org/obo/owl/FIX#
+      old.fix: http://purl.org/obo/owl/FIX#
   efo:
     url: http://www.ebi.ac.uk/efo/efo.owl
     has_imports: true

src/semsql/builder/registry/registry_schema.py

@@ -1,5 +1,5 @@
 # Auto generated from registry_schema.yaml by pythongen.py version: 0.9.0
-# Generation date: 2022-09-05T18:53:50
+# Generation date: 2022-09-17T15:44:28
 # Schema: ontology_registry
 #
 # id: https://w3id.org/semsql/registry
@@ -22,7 +22,8 @@
 from linkml_runtime.utils.enumerations import EnumDefinitionImpl
 from rdflib import Namespace, URIRef
 from linkml_runtime.utils.curienamespace import CurieNamespace
-from linkml_runtime.linkml_model.types import Integer, String
+from linkml_runtime.linkml_model.types import Boolean, Integer, String
+from linkml_runtime.utils.metamodelcore import Bool
 
 metamodel_version = "1.7.0"
 version = None
@@ -86,10 +87,11 @@ class Ontology(YAMLRoot):
     url: Optional[Union[str, Identifier]] = None
     has_imports: Optional[int] = None
     jsonld_context: Optional[Union[str, HttpsIdentifier]] = None
-    prefixmap: Optional[Union[Union[str, PrefixMapPrefix], List[Union[str, PrefixMapPrefix]]]] = empty_list()
+    prefixmap: Optional[Union[Dict[Union[str, PrefixMapPrefix], Union[dict, "PrefixMap"]], List[Union[dict, "PrefixMap"]]]] = empty_dict()
     named_prefixmaps: Optional[Union[str, List[str]]] = empty_list()
     format: Optional[str] = None
     compression: Optional[Union[str, "CompressionEnum"]] = None
+    suppress: Optional[Union[bool, Bool]] = None
 
     def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]):
         if self._is_empty(self.id):
@@ -109,9 +111,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]):
         if self.jsonld_context is not None and not isinstance(self.jsonld_context, HttpsIdentifier):
             self.jsonld_context = HttpsIdentifier(self.jsonld_context)
 
-        if not isinstance(self.prefixmap, list):
-            self.prefixmap = [self.prefixmap] if self.prefixmap is not None else []
-        self.prefixmap = [v if isinstance(v, PrefixMapPrefix) else PrefixMapPrefix(v) for v in self.prefixmap]
+        self._normalize_inlined_as_dict(slot_name="prefixmap", slot_type=PrefixMap, key_name="prefix", keyed=True)
 
         if not isinstance(self.named_prefixmaps, list):
             self.named_prefixmaps = [self.named_prefixmaps] if self.named_prefixmaps is not None else []
@@ -123,6 +123,9 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]):
         if self.compression is not None and not isinstance(self.compression, CompressionEnum):
             self.compression = CompressionEnum(self.compression)
 
+        if self.suppress is not None and not isinstance(self.suppress, Bool):
+            self.suppress = Bool(self.suppress)
+
         super().__post_init__(**kwargs)
 
 
@@ -220,7 +223,7 @@ class slots:
                    model_uri=SEMSQL_REGISTRY.jsonld_context, domain=None, range=Optional[Union[str, HttpsIdentifier]])
 
 slots.prefixmap = Slot(uri=SEMSQL_REGISTRY.prefixmap, name="prefixmap", curie=SEMSQL_REGISTRY.curie('prefixmap'),
-                   model_uri=SEMSQL_REGISTRY.prefixmap, domain=None, range=Optional[Union[Union[str, PrefixMapPrefix], List[Union[str, PrefixMapPrefix]]]])
+                   model_uri=SEMSQL_REGISTRY.prefixmap, domain=None, range=Optional[Union[Dict[Union[str, PrefixMapPrefix], Union[dict, PrefixMap]], List[Union[dict, PrefixMap]]]])
 
 slots.named_prefixmaps = Slot(uri=SEMSQL_REGISTRY.named_prefixmaps, name="named_prefixmaps", curie=SEMSQL_REGISTRY.curie('named_prefixmaps'),
                    model_uri=SEMSQL_REGISTRY.named_prefixmaps, domain=None, range=Optional[Union[str, List[str]]])
@@ -242,3 +245,6 @@ class slots:
 
 slots.ontologies = Slot(uri=SEMSQL_REGISTRY.ontologies, name="ontologies", curie=SEMSQL_REGISTRY.curie('ontologies'),
                    model_uri=SEMSQL_REGISTRY.ontologies, domain=None, range=Optional[Union[Dict[Union[str, OntologyId], Union[dict, Ontology]], List[Union[dict, Ontology]]]])
+
+slots.suppress = Slot(uri=SEMSQL_REGISTRY.suppress, name="suppress", curie=SEMSQL_REGISTRY.curie('suppress'),
+                   model_uri=SEMSQL_REGISTRY.suppress, domain=None, range=Optional[Union[bool, Bool]])

src/semsql/builder/registry/registry_schema.yaml

@@ -50,6 +50,7 @@ slots:
     - value: '[''$ref:Prefixmap'', ''$ref:Prefixmap'']'
     multivalued: true
     range: PrefixMap
+    inlined: true
   named_prefixmaps:
     examples:
     - value: '[''sweet'', ''prefixcc'']'