PR suggestion: Remove graph_data_model parameter in create_manifests to simplify the code

.github/workflows/test.yml

@@ -151,7 +151,7 @@ jobs:
 
 
       - name: Upload pytest test results
-        uses: actions/upload-artifact@v2
+        uses: actions/upload-artifact@v4
         with:
           name: pytest-results-${{ matrix.python-version }}
           path: htmlcov

schematic/manifest/generator.py

@@ -28,12 +28,11 @@
     execute_google_api_requests,
     export_manifest_drive_service,
 )
+from schematic.utils.io_utils import read_pickle
 from schematic.utils.schema_utils import (
     DisplayLabelType,
     extract_component_validation_rules,
 )
-from schematic.utils.df_utils import update_df, load_df
-from schematic.utils.io_utils import read_pickle
 from schematic.utils.validate_utils import rule_in_rule_list
 
 logger = logging.getLogger(__name__)
@@ -1662,13 +1661,11 @@ def create_manifests(
         title: Optional[str] = None,
         strict: Optional[bool] = True,
         use_annotations: Optional[bool] = False,
-        graph_data_model: Optional[nx.MultiDiGraph] = None,
         data_model_graph_pickle: Optional[str] = None,
     ) -> Union[List[str], List[pd.DataFrame]]:
         """Create multiple manifests
 
         Args:
-            path_to_data_model (str): str path to data model
             data_model_graph_pickle (str, optional): path to pickled networkx MultiDiGraph object. Defaults to None.
             graph_data_model (str, optional): An networkx MultiDiGraph object. Defaults to None.
             data_types (list): a list of data types
@@ -1728,25 +1725,20 @@ def create_manifests(
                     "Please check your submission and try again."
                 )
 
-        if graph_data_model is None:
-            if data_model_graph_pickle:
-                """What if pickle file does not fit in memory?"""
-                graph_data_model = read_pickle(data_model_graph_pickle)
-            else:
-                data_model_parser = DataModelParser(
-                    path_to_data_model=path_to_data_model
-                )
+        if data_model_graph_pickle:
+            """What if pickle file does not fit in memory?"""
+            graph_data_model = read_pickle(data_model_graph_pickle)
+        else:
+            data_model_parser = DataModelParser(path_to_data_model=path_to_data_model)
 
-                # Parse Model
-                parsed_data_model = data_model_parser.parse_model()
+            # Parse Model
+            parsed_data_model = data_model_parser.parse_model()
 
-                # Instantiate DataModelGraph
-                data_model_grapher = DataModelGraph(
-                    parsed_data_model, data_model_labels
-                )
+            # Instantiate DataModelGraph
+            data_model_grapher = DataModelGraph(parsed_data_model, data_model_labels)
 
-                # Generate graph
-                graph_data_model = data_model_grapher.graph
+            # Generate graph
+            graph_data_model = data_model_grapher.graph
 
         # Gather all returned result urls
         all_results = []

schematic_api/api/routes.py

@@ -33,11 +33,11 @@
 from schematic.schemas.data_model_parser import DataModelParser
 from schematic.store.synapse import ManifestDownload, SynapseStorage
 from schematic.utils.general import entity_type_mapping
+from schematic.utils.io_utils import read_pickle
 from schematic.utils.schema_utils import (
     DisplayLabelType,
     get_property_label_from_display_name,
 )
-from schematic.utils.io_utils import read_pickle
 from schematic.visualization.attributes_explorer import AttributesExplorer
 from schematic.visualization.tangled_tree import TangledTree
 
@@ -292,10 +292,8 @@ def initalize_metadata_model(schema_url, data_model_labels):
     )
     return metadata_model
 
-def get_temp_file(
-        url: str,
-        suffix: str
-) -> str:
+
+def get_temp_file(url: str, suffix: str) -> str:
     """
     Retrieve a file via URL and store it in a temporary location
     :param url str: URL to the file
@@ -308,6 +306,7 @@ def get_temp_file(
 
     return tmp_file.name
 
+
 def get_temp_model_path(schema_url):
     # Get model type:
     model_extension = pathlib.Path(schema_url).suffix.replace(".", "").upper()
@@ -357,10 +356,8 @@ def get_manifest_route(
 
     config_handler(asset_view=asset_view)
 
-    graph_data_model = None
     if graph_url is not None:
         graph_path = get_temp_model_path(graph_url)
-        graph_data_model = read_pickle(graph_path)
 
     all_results = ManifestGenerator.create_manifests(
         path_to_data_model=schema_url,
@@ -372,7 +369,7 @@ def get_manifest_route(
         strict=strict_validation,
         use_annotations=use_annotations,
         data_model_labels=data_model_labels,
-        graph_data_model=graph_data_model,
+        data_model_graph_pickle=graph_path,
     )
 
     # return an excel file if output_format is set to "excel"

tests/test_cli.py

@@ -1,16 +1,15 @@
+import json
 import os
-
-import pytest
 import pickle
-import json
 from unittest.mock import patch
 
+import pytest
 from click.testing import CliRunner
 
-from schematic.schemas.commands import schema
+from schematic.configuration.configuration import Configuration
 from schematic.manifest.commands import manifest
 from schematic.models.commands import model
-from schematic.configuration.configuration import Configuration
+from schematic.schemas.commands import schema
 from tests.conftest import Helpers
 
 
@@ -52,9 +51,10 @@ def assert_expected_file(self, result, output_path):
         "output_path",
         [
             # Test case 1: pickle file passed to output_path
-            "tests/data/example.model.pickle", 
+            "tests/data/example.model.pickle",
             # Test case 2: jsonld file passed to output_path
-            "tests/data/example.model.jsonld"],
+            "tests/data/example.model.jsonld",
+        ],
         ids=["output_path_pickle", "output_path_jsonld"],
     )
     @pytest.mark.parametrize(
@@ -65,7 +65,8 @@ def assert_expected_file(self, result, output_path):
             # Test case 2: graph passed to output_type
             "graph",
             # Test case 3: both jsonld and graph are created
-            "all"],
+            "all",
+        ],
         ids=["output_type_jsonld", "output_type_graph", "output_type_all"],
     )
     def test_schema_convert_cli(self, runner, output_path, output_type):