Mercurial > repos > ufz > omero_metadata_import
comparison omero_metadata_upload.py @ 5:4291d37da555 draft
planemo upload for repository https://github.com/Helmholtz-UFZ/galaxy-tools/tree/main/tools/omero commit 636cbb62d59819caca5bc9eab0a8ec31be5bdd46
| author | ufz |
|---|---|
| date | Mon, 16 Dec 2024 20:56:56 +0000 |
| parents | e41f70e69349 |
| children |
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| 4:351c6b43e16c | 5:4291d37da555 |
|---|---|
| 54 result = upload_metadata(conn, "Screen", did, data_dict, df, ann_type, an_name) | 54 result = upload_metadata(conn, "Screen", did, data_dict, df, ann_type, an_name) |
| 55 elif obj_type == "dataset": | 55 elif obj_type == "dataset": |
| 56 if did is None: | 56 if did is None: |
| 57 did = ez.post_dataset(conn, dataset_name=str(datetime.now())) | 57 did = ez.post_dataset(conn, dataset_name=str(datetime.now())) |
| 58 result = upload_metadata(conn, "Dataset", did, data_dict, df, ann_type, an_name) | 58 result = upload_metadata(conn, "Dataset", did, data_dict, df, ann_type, an_name) |
| 59 elif obj_type == "plate": | |
| 60 result = upload_metadata(conn, "Plate", did, data_dict, df, ann_type, an_name) | |
| 61 elif obj_type == "well": | |
| 62 result = upload_metadata(conn, "Well", did, data_dict, df, ann_type, an_name) | |
| 59 elif obj_type == "image": | 63 elif obj_type == "image": |
| 60 result = upload_metadata(conn, "Image", did, data_dict, df, ann_type, an_name) | 64 result = upload_metadata(conn, "Image", did, data_dict, df, ann_type, an_name) |
| 61 else: | 65 else: |
| 62 raise ValueError("Unsupported object type provided: {}".format(obj_type)) | 66 raise ValueError("Unsupported object type provided: {}".format(obj_type)) |
| 63 | 67 |
| 72 log_error(f"Connection error: {str(e)}") | 76 log_error(f"Connection error: {str(e)}") |
| 73 | 77 |
| 74 | 78 |
| 75 if __name__ == "__main__": | 79 if __name__ == "__main__": |
| 76 parser = argparse.ArgumentParser(description='Import metadata into OMERO.') | 80 parser = argparse.ArgumentParser(description='Import metadata into OMERO.') |
| 77 parser.add_argument("--credential-file", dest="credential_file", type=str, required=True, help="Credential file (JSON file with username and password for OMERO)") | 81 parser.add_argument("--credential-file", dest="credential_file", type=str, required=True, |
| 82 help="Credential file (JSON file with username and password for OMERO)") | |
| 78 parser.add_argument('--host', required=True, help='OMERO host') | 83 parser.add_argument('--host', required=True, help='OMERO host') |
| 79 parser.add_argument('--port', required=True, type=int, help='OMERO port') | 84 parser.add_argument('--port', required=True, type=int, help='OMERO port') |
| 80 parser.add_argument('--obj_type', required=True, choices=['project', 'screen', 'dataset', 'image'], | 85 parser.add_argument('--obj_type', required=True, choices=['project', 'screen', 'dataset', 'plate', |
| 86 'well ', 'image'], | |
| 81 help='Type of OMERO object') | 87 help='Type of OMERO object') |
| 82 parser.add_argument('--did', type=int, help='ID of the object (if it exists)') | 88 parser.add_argument('--did', type=int, help='ID of the object (if it exists)') |
| 83 parser.add_argument('--ann_type', required=True, choices=['table', 'KV'], help='Annotation type') | 89 parser.add_argument('--ann_type', required=True, choices=['table', 'KV'], help='Annotation type') |
| 84 parser.add_argument('--ann_file', required=True, help='Path to the annotation file') | 90 parser.add_argument('--ann_file', required=True, help='Path to the annotation file') |
| 85 parser.add_argument('--an_name', required=True, help='Namespace or title for the annotation') | 91 parser.add_argument('--an_name', required=True, help='Namespace or title for the annotation') |