Add GPI option to gpad2gocams for geneontology/gocamgen#83

bin/validate.py

@@ -13,6 +13,7 @@
 import logging
 import sys
 import traceback
+import subprocess
 
 import yamldown
 
@@ -547,10 +548,11 @@ def produce(ctx, group, metadata_dir, gpad, ttl, target, ontology, exclude, base
 @cli.command()
 @click.pass_context
 @click.option("--gpad_path", "-g", type=click.Path(), required=True)
+@click.option("--gpi_path", "-i", type=click.Path(), required=True)
 @click.option("--target", "-t", type=click.Path(), required=True)
 @click.option("--ontology", "-o", type=click.Path(exists=True), required=False)
-# Eventually will need access to GPI as well for getting taxon ID - should exist by now - get path from metadata
-def gpad2gocams(ctx, gpad_path, target, ontology):
+# Eventually will need access to GPI as well for getting taxon ID - should exist by now
+def gpad2gocams(ctx, gpad_path, gpi_path, target, ontology):
     if gpad_path.endswith(".gz"):
         unzipped = os.path.splitext(gpad_path)[0]
         unzip(gpad_path, unzipped)
@@ -562,14 +564,13 @@ def gpad2gocams(ctx, gpad_path, target, ontology):
     absolute_target = os.path.abspath(target)
     gpad_basename = os.path.basename(gpad_path)
     gpad_basename_root, gpad_ext = os.path.splitext(gpad_basename)
-    if gpad_ext in ["gpad", "gpa"]:
+    if gpad_ext in [".gpad", ".gpa"]:
         output_basename = gpad_basename_root + ".nq"
     else:
         output_basename = gpad_basename + ".nq"
     output_path = os.path.join(absolute_target, output_basename)
 
-    ontology_graph = OntologyFactory().create(ontology, ignore_cache=True)
-    builder = GoCamBuilder(ontology_graph)
+    builder = GoCamBuilder(ontology, gpi_file=gpi_path)
 
     for gene, associations in assocs_by_gene.items():
         builder.make_model_and_add_to_store(gene, annotations=associations)

ontobio/rdfgen/gocamgen/gocam_builder.py

@@ -6,6 +6,7 @@
 from ontobio.rdfgen.gocamgen.utils import ShexException
 from ontobio.io.gpadparser import GpadParser
 from ontobio.io.assocparser import AssocParserConfig
+from ontobio.io.entityparser import GpiParser
 from ontobio.ontol_factory import OntologyFactory
 from ontobio.util.go_utils import GoAspector
 import argparse
@@ -16,6 +17,7 @@
 import time
 import click
 from os import path
+from typing import List
 # from abc import ABC, abstractmethod
 from rdflib.graph import ConjunctiveGraph
 from rdflib.store import Store
@@ -40,24 +42,26 @@
 
 
 class GoCamBuilder:
-    def __init__(self, ontology_graph=None):
-        # self.ro_ontology = OntologyFactory().create("http://purl.obolibrary.org/obo/ro.owl")
-        # self.gorel_ontology = OntologyFactory().create("http://release.geneontology.org/2019-03-18/ontology/extensions/gorel.obo")
-        # Can't get logical_definitions w/ ont.create("go"), need to load ontology via PURL
-        # self.ontology = OntologyFactory().create("http://purl.obolibrary.org/obo/go.owl")
-        if ontology_graph is None:
+    def __init__(self, ontology=None, gpi_file=None):
+        if ontology is None:
             ontology_graph = OntologyFactory().create("http://purl.obolibrary.org/obo/go/extensions/go-lego.owl")
+        else:
+            ontology_graph = OntologyFactory().create(ontology, ignore_cache=True)
         self.ontology = ontology_graph
         self.ro_ontology = self.extract_relations_ontology(self.ontology)
+        # self.ontology = OntologyFactory().create("http://purl.obolibrary.org/obo/go.owl")
+        # self.ro_ontology = OntologyFactory().create("http://purl.obolibrary.org/obo/ro.owl")
         self.aspector = GoAspector(self.ontology)
         self.store = plugin.get('IOMemory', Store)()
         self.errors = GeneErrorSet()  # Errors by gene ID
+        self.gpi_entities = self.parse_gpi(gpi_file)
 
     def translate_to_model(self, gene, assocs):
         model = AssocGoCamModel(gene, assocs, store=self.store)
         model.ontology = self.ontology
         model.ro_ontology = self.ro_ontology
         model.go_aspector = self.aspector
+        model.gpi_entities = self.gpi_entities
         model.translate()
 
         return model
@@ -120,6 +124,38 @@ def extract_relations_ontology(ontology_graph):
             ro_terms = ro_terms + ontology_graph.descendants(t, reflexive=True)
         return ontology_graph.subontology(nodes=ro_terms)
 
+    @staticmethod
+    def parse_gpi(gpi_file):
+        # {
+        #    "id":"MGI:MGI:87853",
+        #    "label":"a",
+        #    "full_name":"nonagouti",
+        #    "synonyms":[
+        #       "agouti",
+        #       "As",
+        #       "agouti signal protein",
+        #       "ASP"
+        #    ],
+        #    "type":"gene",
+        #    "parents":[
+        #
+        #    ],
+        #    "xrefs":[
+        #       "UniProtKB:Q03288"
+        #    ],
+        #    "taxon":{
+        #       "id":"NCBITaxon:10090"
+        #    }
+        # }
+        if gpi_file is None:
+            return None
+        parser = GpiParser()
+        gpi_entities = {}
+        entities = parser.parse(gpi_file)
+        for entity in entities:
+            gpi_entities[entity['id']] = entity
+        return gpi_entities
+
 
 class AssocExtractor:
     def __init__(self, gpad_file, parser_config: AssocParserConfig = None):

ontobio/rdfgen/gocamgen/gocamgen.py

@@ -409,10 +409,12 @@ def __init__(self, modeltitle, assocs, connection_relations=None, store=None):
         self.go_aspector = None
         self.default_contributor = "http://orcid.org/0000-0002-6659-0416"
         self.graph.bind("GOREL", GOREL)  # Because GOREL isn't in context.jsonld's
+        self.gpi_entities = None
 
     def translate(self):
 
         self.associations.go_ontology = self.ontology
+        self.associations.gpi_entities = self.gpi_entities
         self.associations.collapse_annotations()
 
         for a in self.associations: