trying to fix type error on 3.7

bin/ontobio-parse-assocs.py

@@ -34,6 +34,7 @@
 import sys
 import json
 import logging
+from typing import Dict, List
 
 def main():
     """

bin/validate.py

@@ -13,7 +13,7 @@
 import logging
 import sys
 import traceback
-
+from typing import Dict, List
 import yamldown
 
 from functools import wraps
@@ -448,7 +448,7 @@ def produce_gpi(dataset, target_dir, gaf_path, ontology_graph, gpad_gpi_output_v
     gpi_path = os.path.join(os.path.split(gaf_path)[0], "{}.gpi".format(dataset))
     with open(gaf_path) as gf, open(gpi_path, "w") as gpi:
         click.echo("Using {} as the gaf to build gpi with".format(gaf_path))
-        bridge = gafgpibridge.GafGpiBridge()
+        bridge = gafgpibridge
         gpiwriter = entitywriter.GpiWriter(file=gpi, version=gpad_gpi_output_version)
         gpi_cache = set()
 

ontobio/io/gafgpibridge.py

@@ -3,6 +3,7 @@
 
 from ontobio.model.association import GoAssociation, gp_type_label_to_curie
 
+
 class Entity(dict):
 
     def __init__(self, d):
@@ -13,35 +14,36 @@ def __hash__(self):
         return hash(d)
 
 
+def convert_association(association) -> Entity | None:
+    """
+    'id' is already `join`ed in both the Association and the Entity,
+    so we don't have to worry about what that looks like. We assume
+    it's correct.
+    """
+
+    if isinstance(association, GoAssociation):
+        # print(json.dumps(association, indent=4))
+        gpi_obj = {
+            'id': str(association.subject.id),
+            'label': association.subject.label,  # db_object_symbol,
+            'full_name': association.subject.fullname,  # db_object_name,
+            'synonyms': association.subject.synonyms,
+            'type': [gp_type_label_to_curie(association.subject.type[0])], #db_object_type,
+            'parents': "",  # GAF does not have this field, but it's optional in GPI
+            'xrefs': "",  # GAF does not have this field, but it's optional in GPI
+            'taxon': {
+                'id': str(association.subject.taxon)
+            }
+        }
+        return Entity(gpi_obj)
+
+    return None
+
+
 class GafGpiBridge(object):
 
     def __init__(self):
         self.cache = []
 
-    def convert_association(self, association) -> Entity:
-        """
-        'id' is already `join`ed in both the Association and the Entity,
-        so we don't have to worry about what that looks like. We assume
-        it's correct.
-        """
-
-        if isinstance(association, GoAssociation):
-            # print(json.dumps(association, indent=4))
-            gpi_obj = {
-                'id': str(association.subject.id),
-                'label': association.subject.label,  # db_object_symbol,
-                'full_name': association.subject.fullname,  # db_object_name,
-                'synonyms': association.subject.synonyms,
-                'type': [gp_type_label_to_curie(association.subject.type[0])], #db_object_type,
-                'parents': "", # GAF does not have this field, but it's optional in GPI
-                'xrefs': "", # GAF does not have this field, but it's optional in GPI
-                'taxon': {
-                    'id': str(association.subject.taxon)
-                }
-            }
-            return Entity(gpi_obj)
-
-        return None
-
-    def entities(self) -> List[Entity]:
+    def entities(self):
         return list(self.cache)

tests/test_gafparser.py

@@ -580,7 +580,7 @@ def test_gaf_gpi_bridge():
     gaf = ["MGI", "MGI:1923503", "0610006L08Rik", "enables", "GO:0003674", "MGI:MGI:2156816|GO_REF:0000015", "ND", "",
            "F", "RIKEN cDNA 0610006L08 gene", "", "gene", "taxon:10090", "20120430", "MGI", "", ""]
     association = gafparser.to_association(gaf, qualifier_parser=assocparser.Qualifier2_2()).associations[0]
-    bridge = gafgpibridge.GafGpiBridge()
+    bridge = gafgpibridge
     entity = bridge.convert_association(association)
     assert entity.get("type") == ["gene"]
 

tests/test_gpiwriter.py

@@ -5,15 +5,13 @@
 import pytest
 
 
-@pytest.mark.parametrize("gpad_gpi_output_version", ["2.0", "1.2"])
 @pytest.mark.parametrize("gpad_gpi_output_version", ["2.0", "1.2"])
 def test_produce_gpi(gpad_gpi_output_version):
     # Base path relative to this script
     base_path = Path(__file__).parent / "resources"
 
     # Define the paths for the GAF and expected GPI file
     gaf_path = base_path / "mgi.gaf"
-    gpi_path = base_path / "mgi.gpi"
 
     # Ensure the GAF file exists to avoid FileNotFoundError
     if not gaf_path.exists():
@@ -33,15 +31,10 @@ def test_produce_gpi(gpad_gpi_output_version):
     # Verify the contents of the GPI file
     p = entityparser.GpiParser()
     with open(output_gpi_path, "r") as f:
-        assert p.parse(f) is not None, "The GPI file could not be parsed."
+        assert p.parse(f) is not None
         f.seek(0)  # Reset file pointer to the beginning
         results = p.parse(f)
-        assert len(results) > 5, "The GPI file should have about 9 unique genes from ~ 90 associations in the GAF file."
-
-    with open(output_gpi_path, "r") as f:
-        lines = f.readlines()
-
-    assert len(lines) > 0, "The GPI file should not be empty."
+        assert len(results) > 5
 
 
 def test_gpi_2_0_writer():
@@ -52,9 +45,9 @@ def test_gpi_2_0_writer():
         'synonyms': [],
         'type': ["SO:0000000"],  # db_object_type,
         'taxon': {"id": "NCBITaxon:10090"},
-        'encoded_by': "", # encoded_by
+        'encoded_by': "",  # encoded_by
         'parents': "",
-        'protein_containing_complex_members': "", # protein_containing_complex_members
+        'protein_containing_complex_members': "",  # protein_containing_complex_members
         'xrefs': "",
         'properties': ""
     }