Mercurial > repos > ufz > omero_filter
changeset 5:a70140649a13 draft default tip
planemo upload for repository https://github.com/Helmholtz-UFZ/galaxy-tools/tree/main/tools/omero commit 3f4e79a4e8350481f3c8d70bc64f01b4cb0a4bf0
| author | ufz |
|---|---|
| date | Fri, 13 Jun 2025 20:47:26 +0000 |
| parents | 9d04b28b8dc8 |
| children | |
| files | omero_filter.xml omero_metadata_upload.py test-data/output_attachement_import.txt |
| diffstat | 3 files changed, 8 insertions(+), 2 deletions(-) [+] |
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--- a/omero_filter.xml Tue Apr 08 15:12:55 2025 +0000 +++ b/omero_filter.xml Fri Jun 13 20:47:26 2025 +0000 @@ -72,7 +72,7 @@ <param name="omero_port" value="6064"/> <conditional name="filter_type"> <param name="filter" value="filename"/> - <param name="value1" value="sample_image_2.jpg"/> + <param name="value1" value="sample_image.jpg"/> <param name="did" value="1,2"/> </conditional> <param name="test_username" value="root"/>
--- a/omero_metadata_upload.py Tue Apr 08 15:12:55 2025 +0000 +++ b/omero_metadata_upload.py Fri Jun 13 20:47:26 2025 +0000 @@ -19,6 +19,9 @@ headers=True) tb_dict = ez.get_table(conn, id_tb_ann) return tb_dict + elif ann_type == "attachement": + id_file_attach = ez.post_file_annotation(conn, file_path=data_dict, ns=an_name, object_type=obj_type, object_id=int(did)) + return id_file_attach except Exception as e: log_error(f"Error uploading metadata for {obj_type} with ID {did}: {str(e)}") return None @@ -41,6 +44,8 @@ data_dict = df.to_dict(orient='records') elif ann_type == "KV": data_dict = {col: df[col].iloc[0] for col in df.columns} + elif ann_type == "attachement": + data_dict = ann_file try: with ez.connect(user, pws, "", host, port, secure=True) as conn: @@ -86,7 +91,7 @@ 'well ', 'image'], help='Type of OMERO object') parser.add_argument('--did', type=int, help='ID of the object (if it exists)') - parser.add_argument('--ann_type', required=True, choices=['table', 'KV'], help='Annotation type') + parser.add_argument('--ann_type', required=True, choices=['table', 'KV', "attachement"], help='Annotation type') parser.add_argument('--ann_file', required=True, help='Path to the annotation file') parser.add_argument('--an_name', required=True, help='Namespace or title for the annotation') parser.add_argument('--log_file', default='metadata_import_log.txt', help='Path to the log file')