Use fastobo to load ontologies from OBO files

ontobio/ontol_factory.py

@@ -13,6 +13,7 @@
 import os
 import subprocess
 import hashlib
+import fastobo
 
 
 # TODO
@@ -155,6 +156,13 @@ def translate_file_to_ontology(handle, **args):
         logging.info("RdfMapper: {}".format(args))
         m = RdfMapper(**args)
         return m.convert(handle,'ttl')
+    elif handle.endswith(".obo"):
+        doc = fastobo.load(handle)
+        with tempfile.TemporaryFile() as tmp:
+            fastobo.dump_graph(doc, tmp)
+            tmp.seek(0)
+            g = obograph_util.convert_json_object(json.load(tmp), **args)
+        return Ontology(handle=handle, payload=g)
     else:
         if not (handle.endswith(".obo") or handle.endswith(".owl")):
             logging.info("Attempting to parse non obo or owl file with owltools: "+handle)

requirements.txt

@@ -19,4 +19,5 @@ pydotplus>=0.0
 plotly==2.0.7
 pyyaml
 yamldown>=0.1.7
-click
+fastobo~=0.3.1
+click

setup.py

@@ -56,7 +56,8 @@
         'pandas==0.24.2',
         'click==7.0',
         'yamldown',
-        'dataclasses'
+        'dataclasses',
+        'fastobo~=0.3.1',
     ],
 
     # List additional groups of dependencies here (e.g. development