Merge pull request #386 from dandi/gh-385

Populate wasDerivedFrom
dandi · Feb 19, 2021 · 543e11b · 543e11b
2 parents d138c6f + 10d2c21
commit 543e11b
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Showing 2 changed files with 48 additions and 8 deletions.
diff --git a/dandi/metadata.py b/dandi/metadata.py
@@ -231,8 +231,6 @@ def extract_anatomy(metadata):
 def extract_model(modelcls, metadata, **kwargs):
     m = modelcls.unvalidated()
     for field in m.__fields__.keys():
-        if modelcls == models.BioSample and field == "wasDerivedFrom":
-            continue
         value = kwargs.get(field, extract_field(field, metadata))
         if value is not Ellipsis:
             setattr(m, field, value)
@@ -253,9 +251,23 @@ def func(metadata):
     return func
 
 
-extract_wasDerivedFrom = extract_model_list(
-    models.BioSample, "identifier", "tissue_sample_id"
-)
+def extract_wasDerivedFrom(metadata):
+    derived_from = None
+    for field, sample_name in [
+        ("tissue_sample_id", "tissuesample"),
+        ("slice_id", "slice"),
+        ("cell_id", "cell"),
+    ]:
+        if metadata.get(field) is not None:
+            derived_from = [
+                models.BioSample(
+                    identifier=metadata[field],
+                    wasDerivedFrom=derived_from,
+                    sampleType=models.SampleType(name=sample_name),
+                )
+            ]
+    return derived_from
+
 
 extract_wasAttributedTo = extract_model_list(
     models.Participant, "identifier", "subject_id"

diff --git a/dandi/tests/test_metadata.py b/dandi/tests/test_metadata.py
@@ -132,8 +132,32 @@ def test_metadata2asset(schema_dir):
   },
   "wasDerivedFrom": [
     {
-      "identifier": "tissue03",
-      "schemaKey": "BioSample"
+      "identifier": "cell01",
+      "schemaKey": "BioSample",
+      "sampleType": {
+        "name": "cell",
+        "schemaKey": "SampleType"
+      },
+      "wasDerivedFrom": [
+        {
+          "identifier": "slice02",
+          "schemaKey": "BioSample",
+          "sampleType": {
+            "name": "slice",
+            "schemaKey": "SampleType"
+          },
+          "wasDerivedFrom": [
+            {
+              "identifier": "tissue03",
+              "schemaKey": "BioSample",
+              "sampleType": {
+                "name": "tissuesample",
+                "schemaKey": "SampleType"
+              }
+            }
+          ]
+        }
+      ]
     }
   ],
   "wasAttributedTo": [
@@ -213,7 +237,11 @@ def test_metadata2asset_simple1(schema_dir):
   },
   "wasDerivedFrom": [
     {
-      "identifier": "tissue42"
+      "identifier": "tissue42",
+      "sampleType": {
+        "name": "tissuesample",
+        "schemaKey": "SampleType"
+      }
     }
   ],
   "wasGeneratedBy": [