Fix an AttributeError raised when a URL is used as a species

dandi/metadata.py

@@ -371,7 +371,9 @@ def extract_species(metadata):
                 f"Cannot interpret species field: {value}. Please "
                 "contact [email protected] to add your species."
             )
-        return models.SpeciesType(identifier=value_id, name=value.capitalize())
+        return models.SpeciesType(
+            identifier=value_id, name=value.capitalize() if value is not None else None
+        )
     else:
         return ...
 

dandi/tests/data/metadata/metadata2asset_3.json

@@ -0,0 +1,92 @@
+{
+  "id": "dandiasset:0b0a1a0b-e3ea-4cf6-be94-e02c830d54be",
+  "schemaKey": "Asset",
+  "schemaVersion": "0.4.1",
+  "keywords": [
+    "test",
+    "sample",
+    "example",
+    "test-case"
+  ],
+  "access": [
+    {
+      "schemaKey": "AccessRequirements",
+      "status": "dandi:OpenAccess"
+    }
+  ],
+  "repository": "https://dandiarchive.org/",
+  "wasGeneratedBy": [
+    {
+      "schemaKey": "Session",
+      "identifier": "XYZ789",
+      "name": "XYZ789",
+      "description": "Some test data",
+      "startDate": "2020-08-31T15:58:28-04:00",
+      "used": [
+        {
+          "schemaKey": "Equipment",
+          "identifier": "probe:probe04",
+          "name": "Ecephys Probe"
+        }
+      ]
+    }
+  ],
+  "contentSize": 69105,
+  "encodingFormat": "application/x-nwb",
+  "digest": {
+    "dandi:dandi-etag": "e455839e5ab2fa659861f58a423fd17f-1"
+  },
+  "path": "/test/path",
+  "wasDerivedFrom": [
+    {
+      "schemaKey": "BioSample",
+      "identifier": "cell01",
+      "sampleType": {
+        "schemaKey": "SampleType",
+        "name": "cell"
+      },
+      "wasDerivedFrom": [
+        {
+          "schemaKey": "BioSample",
+          "identifier": "slice02",
+          "sampleType": {
+            "schemaKey": "SampleType",
+            "name": "slice"
+          },
+          "wasDerivedFrom": [
+            {
+              "schemaKey": "BioSample",
+              "identifier": "tissue03",
+              "sampleType": {
+                "schemaKey": "SampleType",
+                "name": "tissuesample"
+              }
+            }
+          ]
+        }
+      ]
+    }
+  ],
+  "wasAttributedTo": [
+    {
+      "schemaKey": "Participant",
+      "identifier": "a1b2c3",
+      "age": {
+        "unitText": "ISO-8601 duration",
+        "value": "P170DT12212S",
+        "schemaKey": "PropertyValue",
+        "valueReference": {"schemaKey": "PropertyValue", "value": "dandi:BirthReference"}
+      },
+      "sex": {
+        "schemaKey": "SexType",
+        "identifier": "http://purl.obolibrary.org/obo/PATO_0000384",
+        "name": "Male"
+      },
+      "genotype": "Typical",
+      "species": {
+        "schemaKey": "SpeciesType",
+        "identifier": "https://www.example.com/unicorn"
+      }
+    }
+  ]
+}

dandi/tests/test_metadata.py

@@ -202,6 +202,47 @@ def test_timedelta2duration(td, duration):
                 "path": "/test/path",
             },
         ),
+        # Put all corner cases in this test case:
+        (
+            "metadata2asset_3.json",
+            {
+                "contentSize": 69105,
+                "digest": "e455839e5ab2fa659861f58a423fd17f-1",
+                "digest_type": "dandi_etag",
+                "encodingFormat": "application/x-nwb",
+                "experiment_description": "Experiment Description",
+                "experimenter": "Joe Q. Experimenter",
+                "id": "dandiasset:0b0a1a0b-e3ea-4cf6-be94-e02c830d54be",
+                "institution": "University College",
+                "keywords": ["test", "sample", "example", "test-case"],
+                "lab": "Retriever Laboratory",
+                "related_publications": "A Brief History of Test Cases",
+                "session_description": "Some test data",
+                "session_id": "XYZ789",
+                "session_start_time": "2020-08-31T15:58:28-04:00",
+                "age": "23 days",
+                "date_of_birth": "2020-03-14T12:34:56-04:00",
+                "genotype": "Typical",
+                "sex": "M",
+                "species": "https://www.example.com/unicorn",  # Corner case
+                "subject_id": "a1b2c3",
+                "cell_id": "cell01",
+                "slice_id": "slice02",
+                "tissue_sample_id": "tissue03",
+                "probe_ids": "probe04",
+                "number_of_electrodes": 42,
+                "number_of_units": 6,
+                "nwb_version": "2.2.5",
+                "nd_types": [
+                    "Device (2)",
+                    "DynamicTable",
+                    "ElectricalSeries",
+                    "ElectrodeGroup",
+                    "Subject",
+                ],
+                "path": "/test/path",
+            },
+        ),
     ],
 )
 def test_metadata2asset(filename, metadata):