diff --git a/tdc/model_server/tokenizers/geneformer.py b/tdc/model_server/tokenizers/geneformer.py index c3a2fa16..3fa338cd 100644 --- a/tdc/model_server/tokenizers/geneformer.py +++ b/tdc/model_server/tokenizers/geneformer.py @@ -102,11 +102,11 @@ def tokenize_cell_vectors(self, X_norm = (X_view / n_counts * target_sum / norm_factor_vector) X_norm = sp.csr_matrix(X_norm) - tokenized_cells += [ + tokenized_cells.append([ self.rank_genes(X_norm[i].data, coding_miRNA_tokens[X_norm[i].indices]) for i in range(X_norm.shape[0]) - ] + ]) # add custom attributes for subview to dict if self.custom_attr_name_dict is not None: diff --git a/tdc/test/test_model_server.py b/tdc/test/test_model_server.py index e54839d0..aa2b070a 100644 --- a/tdc/test/test_model_server.py +++ b/tdc/test/test_model_server.py @@ -103,7 +103,8 @@ def testGeneformerTokenizer(self): geneformer = tdc_hf_interface("Geneformer") model = geneformer.load() input_tensor = torch.tensor(cells) - raise Exception("shape is", input_tensor.shape, "values are\n", input_tensor) + input_tensor = torch.squeeze(input_tensor) + # raise Exception("shape is", input_tensor.shape, "values are\n", input_tensor) out = model(input_tensor) assert out, "FAILURE: Geneformer output is false-like. Value = {}".format(out) assert len(out) == len(cells), "FAILURE: Geneformer output and cells input don't have the same length. {} vs {}".format(len(out), len(cells))