Upgrade gocamgen to its new home in ontobio

geneontology · Jun 18, 2021 · beade49 · beade49
1 parent 755091d
commit beade49
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Showing 4 changed files with 8 additions and 9 deletions.
diff --git a/entity_models.py b/entity_models.py
@@ -1,5 +1,5 @@
 import abc
-from gocamgen.gocamgen import GoCamModel
+from ontobio.rdfgen.gocamgen import gocamgen
 from naming_conventions import NamingConvention
 from rdflib.term import URIRef, Literal
 from rdflib.namespace import RDFS
@@ -35,7 +35,7 @@ def __str__(self):
         return f"{self.id} - {self.name}"
 
     @abc.abstractmethod
-    def declare(self, model: GoCamModel):
+    def declare(self, model: gocamgen.GoCamModel):
         return
 
 

diff --git a/pathway_connections.py b/pathway_connections.py
@@ -9,7 +9,7 @@
 from prefixcommons.curie_util import expand_uri
 from entity_factories import SignorEntityFactory
 from entity_models import SignorEntity
-from gocamgen.gocamgen import GoCamEvidence
+from ontobio.rdfgen.gocamgen import gocamgen
 from util import OntologyTerm
 
 ro = OboRO()
@@ -182,7 +182,7 @@ def gocam_evidence(self, eco_code):
             date = str(datetime.date.today())
         if self.annotator:
             contributors = [self.annotator]
-        return GoCamEvidence(eco_code, ["PMID:" + pmid for pmid in self.references],
+        return gocamgen.GoCamEvidence(eco_code, ["PMID:" + pmid for pmid in self.references],
                                  date=date, contributors=contributors)
 
     def __str__(self):
@@ -191,7 +191,7 @@ def __str__(self):
     def print(self):
         print(self)
 
-    def declare_a_to_mechanism(self, model, eco_code):
+    def declare_a_to_mechanism(self, model: gocamgen.GoCamModel, eco_code):
         # Declare entity A and mechanism
         self.declare_a(model)
         if self.a_is_small_mol():

diff --git a/pathway_importer.py b/pathway_importer.py
@@ -1,4 +1,4 @@
-from gocamgen.gocamgen import GoCamModel, GoCamEvidence
+from ontobio.rdfgen.gocamgen import gocamgen
 from ontobio.vocabulary.relations import OboRO
 from rdflib.term import URIRef
 from rdflib.namespace import Namespace, OWL
@@ -74,7 +74,7 @@ def pathway_connection_filter_protein_binding(p_connections):
 
 
 def generate_model(filename, title):
-    model = GoCamModel(title)
+    model = gocamgen.GoCamModel(title)
 
     p_connections = PathwayConnectionSet.parse_file(filename)
     linenum = 1

diff --git a/requirements.txt b/requirements.txt
@@ -1,2 +1 @@
-gocamgen==0.0.5
-requests==2.18.4
+ontobio==2.7.6