diff --git a/requirements.txt b/requirements.txt index ad69ec8..3ef78c4 100644 --- a/requirements.txt +++ b/requirements.txt @@ -1,2 +1,2 @@ requests -cas-tools==0.0.1.dev31 \ No newline at end of file +cas-tools==0.0.1.dev40 \ No newline at end of file diff --git a/setup.py b/setup.py index a4d37c8..51a9533 100644 --- 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 index fbbfcb9..1b5e146 100644 --- 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: