Merge pull request #36 from brain-bican/tdt_sprint_4

Fix issue TDT 155
brain-bican · May 2, 2024 · d6da2e4 · d6da2e4
2 parents fd85db3 + adf5306
commit d6da2e4
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Showing 3 changed files with 10 additions and 3 deletions.
diff --git a/requirements.txt b/requirements.txt
@@ -1,2 +1,2 @@
 requests
-cas-tools==0.0.1.dev31
+cas-tools==0.0.1.dev40
diff --git a/setup.py b/setup.py
@@ -8,7 +8,7 @@
 
 setup(
     name="tdta",
-    version="0.1.0.dev5",
+    version="0.1.0.dev6",
     description="The aim of this project is to provide taxonomy development tools custom actions.",
     long_description=README,
     long_description_content_type="text/markdown",

diff --git a/src/tdta/tdt_export.py b/src/tdta/tdt_export.py
@@ -41,7 +41,14 @@ def export_cas_data(sqlite_db: str, output_file: str, dataset_cache_folder: str
     if "matrix_file_id" in project_config:
         matrix_file_id = str(project_config["matrix_file_id"]).strip()
         anndata = resolve_matrix_file(matrix_file_id, dataset_cache_folder)
-        cas_json = add_cell_ids(cta.to_dict(), anndata)
+        labelsets = cta.labelsets.copy()
+        labelsets.sort(key=lambda x: x.rank)
+        labelset_names = [labelset.name for labelset in labelsets]
+
+        cas_json = add_cell_ids(cta.to_dict(), anndata, labelsets=labelset_names)
+        if cas_json is None:
+            print("WARN: Cell IDs population operation failed, skipping cell_id population")
+            cas_json = cta.to_dict()
         with open(output_file, "w") as json_file:
             json.dump(cas_json, json_file, indent=2)
     else: