Mercurial > repos > ufz > omero_metadata_import
changeset 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 | 351c6b43e16c |
| children | 6d8603230e85 |
| files | omero_dataset_to_plate.py omero_metadata_import.xml omero_metadata_upload.py test-data/dataset_conversion_log.txt test-data/mapping.tsv test-data/omero_output.txt test-data/output_KV_import.txt test-data/output_filter_filename.tsv |
| diffstat | 8 files changed, 147 insertions(+), 8 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/omero_dataset_to_plate.py Mon Dec 16 20:56:56 2024 +0000 @@ -0,0 +1,127 @@ +import argparse +import csv +import json +import re +import sys +from collections import defaultdict + + +import omero +from omero.gateway import BlitzGateway +from omero.rtypes import rint, rstring + + +def convert_dataset_to_plate(host, user, pws, port, dataset_id, log_file, mapping_file, delete_dataset): + """ + Connect to OMERO server, convert a dataset to a plate using the specified well mapping file + """ + conn = BlitzGateway(user, pws, host=host, port=port, secure=True) + if not conn.connect(): + sys.exit("ERROR: Failed to connect to OMERO server") + + def log_message(message, status="INFO"): + with open(log_file, 'w') as f: + f.write(f"{message}") + + dataset = conn.getObject("Dataset", dataset_id) + if dataset is None: + conn.close() + sys.exit("ERROR: Dataset not found") + + update_service = conn.getUpdateService() + + # Create a Plate + plate = omero.model.PlateI() + plate.name = rstring(dataset.getName()) + plate = update_service.saveAndReturnObject(plate) + + # Parse the mapping file + image_to_well_mapping = {} + if mapping_file: + with open(mapping_file, 'r') as f: + reader = csv.DictReader(f, delimiter='\t') + for row in reader: + filename = row['Filename'] + well = row['Well'] + match = re.match(r"([A-Z])(\d+)", well) + if match: + row_char, col = match.groups() + row = ord(row_char.upper()) - ord('A') + col = int(col) - 1 + image_to_well_mapping[filename] = (row, col) + else: + conn.close() + sys.exit(f"Invalid well format '{well}' for file '{filename}'") + + # List the dataset children + images = list(dataset.listChildren()) + if not images: + conn.close() + sys.exit("ERROR: No images found in dataset") + + # Compare images in the mapping file and in the dataset + grouped_images = defaultdict(list) + for image in images: + image_name = image.getName() + if image_to_well_mapping: + if image_name in image_to_well_mapping: + row, col = image_to_well_mapping[image_name] + grouped_images[(row, col)].append(image) + else: + conn.close() + sys.exit(f"Image '{image_name}' not found in mapping file.") + + # Assign images to the well based on the mapping file + for (row, col), imgs_in_group in grouped_images.items(): + well = omero.model.WellI() + well.plate = omero.model.PlateI(plate.id.val, False) + well.column = rint(col) + well.row = rint(row) + + for image in imgs_in_group: + ws = omero.model.WellSampleI() + ws.image = omero.model.ImageI(image.id, False) + ws.well = well + well.addWellSample(ws) + + try: + update_service.saveObject(well) + except ValueError as e: + conn.close() + sys.exit("ERROR: Failed to update plate for dataset '{}' due to: {}".format(dataset.getName(), str(e))) + + # Close the connection and, in case, delete the dataset + if delete_dataset is True: + conn.deleteObjects("Dataset", [dataset_id], wait=True) + log_message(f"Images from Dataset {dataset_id} successfully added to Plate {plate.id.val}") + conn.close() + + +if __name__ == "__main__": + parser = argparse.ArgumentParser(description="Convert an OMERO dataset to a plate.") + parser.add_argument("--credential-file", dest="credential_file", type=str, required=True, + help="Credential file (JSON file with username and password for OMERO)") + parser.add_argument('--host', required=True, help='OMERO host') + parser.add_argument('--port', required=True, type=int, help='OMERO port') + parser.add_argument('--dataset_id', type=int, required=True, help="Dataset ID to convert plate") + parser.add_argument('--log_file', default='metadata_import_log.txt', + help='Path to the log file') + parser.add_argument('--mapping_file', + help='Tabular file mapping filenames to well positions (2 columns: filename, Well)') + parser.add_argument('--delete_dataset', action='store_true', + help='Flag to delete the original dataset') + args = parser.parse_args() + + with open(args.credential_file, 'r') as f: + crds = json.load(f) + + convert_dataset_to_plate( + user=crds['username'], + pws=crds['password'], + host=args.host, + port=args.port, + dataset_id=args.dataset_id, + log_file=args.log_file, + mapping_file=args.mapping_file, + delete_dataset=args.delete_dataset + )
--- a/omero_metadata_import.xml Tue Oct 29 06:59:10 2024 +0000 +++ b/omero_metadata_import.xml Mon Dec 16 20:56:56 2024 +0000 @@ -30,16 +30,18 @@ <option value="project">Project</option> <option value="screen">Screen</option> <option value="dataset">Dataset</option> + <option value="plate">Plate</option> + <option value="well">Well</option> <option value="image">Image</option> </param> <conditional name="object_id"> - <param name="object_id_selection" type="select" label="Selection" help="Create a new OMERO object or target an existing one"> + <param name="object_id_selection" type="select" label="Selection" help="Create a new OMERO object or target an existing one"> <option value="new_object">Create new object</option> <option value="existing_object">Target an existing object</option> </param> <when value="new_object"/> <when value="existing_object"> - <param name="did" type="integer" value="" optional="false" label="Object ID"/> + <param name="did" type="integer" min = "1" optional="false" label="Object ID"/> </when> </conditional> <param argument="ann_type" type="select" optional="false" label="Annotation type" help="Select annotation format">
--- a/omero_metadata_upload.py Tue Oct 29 06:59:10 2024 +0000 +++ b/omero_metadata_upload.py Mon Dec 16 20:56:56 2024 +0000 @@ -56,6 +56,10 @@ if did is None: did = ez.post_dataset(conn, dataset_name=str(datetime.now())) result = upload_metadata(conn, "Dataset", did, data_dict, df, ann_type, an_name) + elif obj_type == "plate": + result = upload_metadata(conn, "Plate", did, data_dict, df, ann_type, an_name) + elif obj_type == "well": + result = upload_metadata(conn, "Well", did, data_dict, df, ann_type, an_name) elif obj_type == "image": result = upload_metadata(conn, "Image", did, data_dict, df, ann_type, an_name) else: @@ -74,10 +78,12 @@ if __name__ == "__main__": parser = argparse.ArgumentParser(description='Import metadata into OMERO.') - parser.add_argument("--credential-file", dest="credential_file", type=str, required=True, help="Credential file (JSON file with username and password for OMERO)") + parser.add_argument("--credential-file", dest="credential_file", type=str, required=True, + help="Credential file (JSON file with username and password for OMERO)") parser.add_argument('--host', required=True, help='OMERO host') parser.add_argument('--port', required=True, type=int, help='OMERO port') - parser.add_argument('--obj_type', required=True, choices=['project', 'screen', 'dataset', 'image'], + parser.add_argument('--obj_type', required=True, choices=['project', 'screen', 'dataset', 'plate', + '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')
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/dataset_conversion_log.txt Mon Dec 16 20:56:56 2024 +0000 @@ -0,0 +1,1 @@ +Images from Dataset 2 successfully added to Plate 1 \ No newline at end of file
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/mapping.tsv Mon Dec 16 20:56:56 2024 +0000 @@ -0,0 +1,3 @@ +Filename Well +sample_A03_image.jpg A2 +sample_H11_image.jpg H5
--- a/test-data/omero_output.txt Tue Oct 29 06:59:10 2024 +0000 +++ b/test-data/omero_output.txt Mon Dec 16 20:56:56 2024 +0000 @@ -1,2 +1,2 @@ -Image:3 -Image:4 +Image:5 +Image:6
--- a/test-data/output_KV_import.txt Tue Oct 29 06:59:10 2024 +0000 +++ b/test-data/output_KV_import.txt Mon Dec 16 20:56:56 2024 +0000 @@ -1,1 +1,1 @@ -SUCCESS: Successfully uploaded metadata for dataset with ID 3. Result: {'Key1': 'Value1', 'Key2': 'Value2'} +SUCCESS: Successfully uploaded metadata for dataset with ID 4. Result: {'Key1': 'Value1', 'Key2': 'Value2'}