mend

tdc/test/test_model_server.py

@@ -103,13 +103,20 @@ def testGeneformerTokenizer(self):
         geneformer = tdc_hf_interface("Geneformer")
         model = geneformer.load()
         # tokenized_data = tokenizer.create_dataset(cells, metadata)
+        print("using very few genes for these test cases so expecting empties... let's pad/remove just for the test case...")
+        for idx in range(len(cells)):
+            x = cells[idx]
+            if len(x)<2:
+                for _ in range(2-len(x)):
+                    x.append(1)
+            cells[idx] = x
         input_tensor = torch.tensor(cells)
-        input_tensor = torch.squeeze(input_tensor)
+        # input_tensor = torch.squeeze(input_tensor)
         try:
-            input_tensor.squeeze(2)  # last dim is zero
+            # input_tensor.squeeze(2)  # last dim is zero
             out = model(input_tensor)
         except Exception as e:
-            raise Exception("tensor shape is", input_tensor.shape, "exception was:", e)
+            raise Exception("tensor shape is", input_tensor.shape, "exception was:", e, "\n cells was\n", cells)
             # raise Exception(e)
         # input_tensor = torch.tensor(cells)
         # input_tensor_squeezed = torch.squeeze(input_tensor)