Convert usage of data_types in codex template to assay_display_name

hubmapconsortium · Sep 19, 2024 · 0bec054 · 0bec054
1 parent debe80f
commit 0bec054
Showing 1 changed file with 7 additions and 7 deletions.
diff --git a/src/user_templates_api/templates/jupyter_lab/templates/codex_clustering/template.txt b/src/user_templates_api/templates/jupyter_lab/templates/codex_clustering/template.txt
@@ -60,7 +60,7 @@
     "uuids = {{ uuids | safe }}\n",
     "\n",
     "# accepted datatypes \n",
-    "accepted_datatypes = ['codex_cytokit']\n",
+    "accepted_datatypes = ['CODEX [Cytokit + SPRM]']\n",
     "\n",
     "# required filetypes\n",
     "required_filetypes = ['sprm_outputs/reg001_expr.ome.tiff-cell_channel_total.csv', 'sprm_outputs/reg001_expr.ome.tiff-cell_channel_mean.csv', 'sprm_outputs/reg001_expr.ome.tiff-cell_centers.csv']\n",
@@ -114,19 +114,19 @@
     "            json={\n",
     "                'size': 10000,\n",
     "                'query': {'ids': {'values': uuids}},\n",
-    "                '_source': ['files', 'data_types']\n",
+    "                '_source': ['files', 'assay_display_name']\n",
     "            }, \n",
     "        ).text\n",
     "    )['hits']['hits']\n",
     "\n",
-    "    # create mapping for uuid to file_types and data_types\n",
+    "    # create mapping for uuid to file_types and assay_display_name\n",
     "    uuid_to_files = {}\n",
     "    uuid_to_datatypes = {}\n",
     "    for hit in hits:\n",
     "        file_paths = [file['rel_path'] for file in hit['_source']['files']]\n",
     "        uuid_to_files[hit['_id']] = file_paths\n",
     "\n",
-    "        hit_data_type = hit['_source']['data_types']\n",
+    "        hit_data_type = hit['_source']['assay_display_name']\n",
     "        uuid_to_datatypes[hit['_id']] = hit_data_type\n",
     "    \n",
     "    # save uuids without warnings\n",
@@ -150,9 +150,9 @@
     "                        accepted_uuids.remove(uuid)\n",
     "\n",
     "        if accepted_datatypes is not None: \n",
-    "            # check if data_types for each uuid are in accepted_datatypes\n",
-    "            data_types = uuid_to_datatypes[uuid]\n",
-    "            for data_type in data_types:\n",
+    "            # check if assay_display_name for each uuid are in accepted_datatypes\n",
+    "            assay_display_name = uuid_to_datatypes[uuid]\n",
+    "            for data_type in assay_display_name:\n",
     "                if data_type not in accepted_datatypes: \n",
     "                    warnings.warn('Dataset with UUID \"' + uuid + '\" has unaccepted data type: ' + data_type)\n",
     "                    if uuid in accepted_uuids:\n",