exposing migration again (issues for Josh who was using that), removing webservice from migration, zhuzhing

Author: stitova-idm

emod_api/migration/__init__.py

@@ -0,0 +1 @@
+from .migration import Migration, from_file, from_params, from_demog_and_param_gravity, examine_file, to_csv, from_csv

emod_api/migration/migration.py

@@ -716,44 +716,6 @@ def from_params(demographics_file_path=None,
     migration.MigrationType = migration_type
     return migration
 
-
-def from_demog_and_param_gravity_webservice(demographics_file_path: str, params: str, id_ref: str, migration_type=Migration.LOCAL) -> Migration:
-    """
-    Calls a webservice (running on a GPU) to calculate the migration patterns quickly.
-
-    Args:
-        demographics_file_path: Path to the demographics file.
-        params: Path to the json file with parameters for gravity calculation and server url.
-        id_ref: Metadata tag that needs to match corresponding value in demographics file.
-        migration_type: Migration type.
-
-    Returns:
-        Migration object
-
-    """
-
-    with Path(params).open("r") as f_params:
-        params_url = json.load(f_params)
-
-    # load
-    rates = client.run(Path(demographics_file_path), params_url)
-
-    demog = Demog.from_file(demographics_file_path)
-    migration = Migration()
-    nodes = [node.forced_id for node in demog.nodes]
-
-    # we need a 0-N index for the NumPy array and the node ID for the migration file
-    for i, src in enumerate(nodes):
-        for j, dst in enumerate(nodes):
-            if dst != src:
-                migration[dst][src] = rates[i, j]
-
-    migration.IdReference = id_ref
-    migration.MigrationType = migration_type
-
-    return migration
-
-
 def from_demog_and_param_gravity(demographics_file_path, gravity_params, id_ref, migration_type=Migration.LOCAL):
     demog = Demog.from_file(demographics_file_path)
     return _from_demog_and_param_gravity(demog, gravity_params, id_ref, migration_type)

tests/test_demog.py

@@ -774,10 +774,9 @@ def test_overlay_list_of_nodes(self):
                 'pop': [123, 234, 345, 678],
                 'lon': [10, 11, 12, 13],
                 'lat': [21, 22, 23, 24]}
-        csv_file = pathlib.Path("test_overlay_population.csv")
+        csv_file = os.path.join(self.out_folder, "test_overlay_population.csv")
         pd.DataFrame.from_dict(temp).to_csv(csv_file)
         demo = Demographics.from_csv(csv_file)
-        csv_file.unlink()
 
         overlay_nodes = []  # list of all overlay nodes
         overlay_nodes_id_1 = [1, 2]  # Change susceptibility of nodes with ids 1 and 2
@@ -799,7 +798,7 @@ def test_overlay_list_of_nodes(self):
             overlay_nodes.append(Node.OverlayNode(node_id=node_id, individual_attributes=new_individual_attributes_2))
 
         demo.apply_overlay(overlay_nodes)
-        demo.generate_file("test_overlay_list_of_nodes.json")
+        demo.generate_file( os.path.join(self.out_folder, "test_overlay_list_of_nodes.json"))
 
         self.assertDictEqual(demo.nodes[0].individual_attributes.to_dict(), new_individual_attributes_1.to_dict())
         self.assertDictEqual(demo.nodes[1].individual_attributes.to_dict(), new_individual_attributes_1.to_dict())

tests/test_migration.py

@@ -29,12 +29,17 @@ class MigrationTests(unittest.TestCase):
 
     @classmethod
     def setUpClass(cls):
-
+        cls.output_folder = os.path.join(manifest.output_folder, "migration")
         cls.user = environ["USERNAME"] if system() == "Windows" else environ["USER"]
         filename = os.path.join(manifest.migration_folder, "Kenya_Regional_Migration_from_Census.bin")
         cls.kenya_regional_migration = from_file(filename)
         cls.guinea_pig = Migration()
 
+    @classmethod
+    def tearDownClass(cls):
+        # Class level cleanup after all tests in the class
+        cls.resource = None  # Example cleanup
+
     def test_defaults(self):
         """
         Changing the defaults is a breaking change.
@@ -534,7 +539,6 @@ def test_to_csv(self):
 
     def test_examine_file(self):
         filename = os.path.join(manifest.migration_folder, "Seattle_30arcsec_local_migration.bin")
-        output = os.path.join(manifest.output_folder, "seattle_csv.csv")
 
         expected_output = ["Author:", "DatavalueCount:", "DateCreated:", "GenderDataType:", "IdReference:",
                            "InterpolationType:", "MigrationType:", "NodeCount:", "NodeOffsets:", "Tool:", "Nodes:"]
@@ -795,7 +799,7 @@ def verify_distance(migration_rate_list, node_locations):
         migration_local = from_demog_and_param_gravity(demographics_file, gravity_params=[1, 1, 1, -1],
                                                        id_ref=id_ref, migration_type=Migration.REGIONAL)
 
-        migration_local_file = Path(os.path.join(manifest.output_folder, 'gravity_distance.bin'))
+        migration_local_file = Path(os.path.join(self.output_folder, 'gravity_distance.bin'))
         migration_local.to_file(migration_local_file)
 
         f = io.StringIO()
@@ -812,7 +816,7 @@ def test_from_demog_and_param_gravity_with_reference(self):
                                                  id_ref='from_demog_and_param_gravity_test',
                                                  migration_type=Migration.LOCAL)
 
-        migration_file = Path(os.path.join(manifest.output_folder, 'test_from_demog_and_param_gravity_with_reference.bin'))
+        migration_file = Path(os.path.join(self.output_folder, 'test_from_demog_and_param_gravity_with_reference.bin'))
         migration.to_file(migration_file)
 
         reference_file = Path(os.path.join(manifest.migration_folder, 'migration_gravity_model_reference.bin'))
@@ -823,11 +827,11 @@ def test_from_csv(self):
                 'destination': [2, 3, 4],
                 'rate': [0.1, 0.2, 0.3]}
 
-        csv_file = Path(os.path.join(manifest.output_folder, "test_migration.csv"))
+        csv_file = Path(os.path.join(self.output_folder, "test_migration.csv"))
         pd.DataFrame.from_dict(temp).to_csv(csv_file, index=False)
         migration = from_csv(csv_file, id_ref="testing")
 
-        migration_file = os.path.join(manifest.output_folder, "test_migration.bin")
+        migration_file = os.path.join(self.output_folder, "test_migration.bin")
         migration.to_file(migration_file)
         migration_from_bin = from_file(migration_file)
 

tests/unittests/test_migration_imports.py

@@ -25,7 +25,6 @@ def test_migration_migration_import(self):
             'from_file',
             'examine_file',
             'from_params',
-            'from_demog_and_param_gravity_webservice',
             'from_demog_and_param_gravity',
             'to_csv'
         ]