Imdb test case (#34)

* add `imdb` test

* fmt

* fmt?

* fix test name

* cleanup

* fix imdb

* add failing test cases for imdb

* cleanup

* new: `test_imdb_networkx` (failing)

* fix: skip field if null

* fix: `test_imdb_pyg`

* fix lint

* fix lint (again)

* more assertions

* add extra assertion

* temp: raise value error

* temp: panic

* attempt: bump version

Cargo.toml

@@ -1,6 +1,6 @@
 [package]
 name = "phenolrs"
-version = "0.5.5"
+version = "0.5.6"
 edition = "2021"
 
 # See more keys and their definitions at https://doc.rust-lang.org/cargo/reference/manifest.html

pyproject.toml

@@ -4,7 +4,7 @@ build-backend = "maturin"
 
 [project]
 name = "phenolrs"
-version = "0.5.5"
+version = "0.5.6"
 requires-python = ">=3.10"
 classifiers = [
     "Programming Language :: Rust",

python/phenolrs/__init__.py

@@ -1,5 +1,6 @@
 from .phenolrs import *  # noqa: F403
 
+
 __doc__ = phenolrs.__doc__  # type: ignore[name-defined]  # noqa: F405
 if hasattr(phenolrs, "__all__"):  # type: ignore[name-defined]  # noqa: F405
     __all__ = phenolrs.__all__  # type: ignore[name-defined]  # noqa: F405

python/phenolrs/networkx/loader.py

@@ -7,12 +7,12 @@
     DiGraphAdjDict,
     DstIndices,
     EdgeIndices,
+    EdgeValuesDict,
     GraphAdjDict,
     MultiDiGraphAdjDict,
     MultiGraphAdjDict,
     NodeDict,
     SrcIndices,
-    EdgeValuesDict,
 )
 
 

python/phenolrs/numpy/loader.py

@@ -91,15 +91,18 @@ def load_graph_to_numpy(
                 for e_col_name, entries in metagraph["edgeCollections"].items()
             ]
 
-        features_by_col, coo_map, col_to_adb_key_to_ind, col_to_ind_to_adb_key = (
-            graph_to_numpy_format(
-                {
-                    "vertex_collections": vertex_collections,
-                    "edge_collections": edge_collections,
-                    "database_config": db_config_options,
-                    "load_config": load_config_options,
-                }
-            )
+        (
+            features_by_col,
+            coo_map,
+            col_to_adb_key_to_ind,
+            col_to_ind_to_adb_key,
+        ) = graph_to_numpy_format(
+            {
+                "vertex_collections": vertex_collections,
+                "edge_collections": edge_collections,
+                "database_config": db_config_options,
+                "load_config": load_config_options,
+            }
         )
 
         return (

python/phenolrs/phenolrs.pyi

@@ -8,12 +8,12 @@ from .networkx.typings import (
     DiGraphAdjDict,
     DstIndices,
     EdgeIndices,
+    EdgeValuesDict,
     GraphAdjDict,
     MultiDiGraphAdjDict,
     MultiGraphAdjDict,
     NodeDict,
     SrcIndices,
-    EdgeValuesDict,
 )
 from .numpy.typings import (
     ArangoCollectionToArangoKeyToIndex,

python/phenolrs/pyg/loader.py

@@ -49,13 +49,11 @@ def load_into_pyg_data(
             raise PhenolError("edgeCollections must map to non-empty dictionary")
 
         if len(metagraph["vertexCollections"]) > 1:
-            raise PhenolError(
-                "More than one vertex collection specified for homogeneous dataset"
-            )
+            m = "More than one vertex collection specified for homogeneous dataset"
+            raise PhenolError(m)
         if len(metagraph["edgeCollections"]) > 1:
-            raise PhenolError(
-                "More than one edge collection specified for homogeneous dataset"
-            )
+            m = "More than one edge collection specified for homogeneous dataset"
+            raise PhenolError(m)
 
         v_col_spec_name = list(metagraph["vertexCollections"].keys())[0]
         v_col_spec = list(metagraph["vertexCollections"].values())[0]

python/tests/conftest.py

@@ -34,32 +34,47 @@ def connection_information() -> Dict[str, Any]:
     }
 
 
-@pytest.fixture(scope="module")
-def load_abide(abide_db_name: str, connection_information: Dict[str, Any]) -> None:
+def load_dataset(
+    dataset: str, db_name: str, connection_information: Dict[str, Any]
+) -> None:
     client = arango.ArangoClient(connection_information["url"])
     sys_db = client.db(
         "_system",
         username=connection_information["username"],
         password=connection_information["password"],
     )
 
-    if not sys_db.has_database(abide_db_name):
-        sys_db.delete_database(abide_db_name, ignore_missing=True)
-        sys_db.create_database(abide_db_name)
-        abide_db = client.db(
-            abide_db_name,
+    if not sys_db.has_database(db_name):
+        sys_db.create_database(db_name)
+        db = client.db(
+            db_name,
             username=connection_information["username"],
             password=connection_information["password"],
         )
-        dsets = Datasets(abide_db)
-        dsets.load("ABIDE")
+        dsets = Datasets(db)
+        dsets.load(dataset)
+
+
+@pytest.fixture(scope="module")
+def load_abide(abide_db_name: str, connection_information: Dict[str, Any]) -> None:
+    load_dataset("ABIDE", abide_db_name, connection_information)
+
+
+@pytest.fixture(scope="module")
+def load_imdb(imdb_db_name: str, connection_information: Dict[str, Any]) -> None:
+    load_dataset("IMDB_PLATFORM", imdb_db_name, connection_information)
 
 
 @pytest.fixture(scope="module")
 def abide_db_name() -> str:
     return "abide"
 
 
+@pytest.fixture(scope="module")
+def imdb_db_name() -> str:
+    return "imdb"
+
+
 @pytest.fixture(scope="module")
 def custom_graph_db_name() -> str:
     return "custom_graph"
@@ -77,7 +92,6 @@ def load_line_graph(
     )
 
     if not sys_db.has_database(custom_graph_db_name):
-        sys_db.delete_database(custom_graph_db_name, ignore_missing=True)
         sys_db.create_database(custom_graph_db_name)
         custom_graph_db = client.db(
             custom_graph_db_name,
@@ -114,7 +128,6 @@ def load_karate(karate_db_name: str, connection_information: Dict[str, Any]) ->
     )
 
     if not sys_db.has_database(karate_db_name):
-        sys_db.delete_database(karate_db_name, ignore_missing=True)
         sys_db.create_database(karate_db_name)
         karate_db = client.db(
             karate_db_name,
@@ -152,7 +165,6 @@ def load_multigraph(
     )
 
     if not sys_db.has_database(multigraph_db_name):
-        sys_db.delete_database(multigraph_db_name, ignore_missing=True)
         sys_db.create_database(multigraph_db_name)
         multigraph_db = client.db(
             multigraph_db_name,