annotate omero_get_id.py @ 3:eba4011643dd draft

planemo upload for repository https://github.com/Helmholtz-UFZ/galaxy-tools/tree/main/tools/omero commit 19d84fd5a372f1428e3e5670144881a56e8af8b2

import argparse
import csv
import json
import sys

import ezomero as ez


def get_ids_ezo(user, pws, host, port, final_obj_type, parent_obj_type, parent_id=None, tsv_file="id_list.tsv"):

    # Function to write tabular file from the ezomero output
    def write_ids_to_tsv(data):
        with open(tsv_file, 'w', newline='') as f:
            writer = csv.writer(f, delimiter='\t')
            for item in data:
                writer.writerow([item])  # Write each ID

    with ez.connect(user, pws, "", host, port, secure=True) as conn:

        if final_obj_type == "Project":
            proj_ids = ez.get_project_ids(conn)
            write_ids_to_tsv(proj_ids)
            return proj_ids

        elif final_obj_type == "Dataset":
            args = {'project': None}
            if parent_obj_type == "Project":
                args['project'] = parent_id
            ds_ids = ez.get_dataset_ids(conn, **args)
            write_ids_to_tsv(ds_ids)
            return ds_ids

        elif final_obj_type == "Image":
            args = {
                'project': None,
                'dataset': None,
                'plate': None,
                'well': None
            }
            if parent_obj_type == "Project":
                args['project'] = parent_id
            elif parent_obj_type == "Dataset":
                args['dataset'] = parent_id
            elif parent_obj_type == "Plate":
                args['plate'] = parent_id
            elif parent_obj_type == "Well":
                args['well'] = parent_id
            elif parent_obj_type != "All":
                raise ValueError("Object set as parent_obj_type is not compatible")

            ds_ims = ez.get_image_ids(conn, **args)
            write_ids_to_tsv(ds_ims)
            return ds_ims

        elif final_obj_type == "Annotation":
            map_annot_ids = ez.get_map_annotation_ids(conn, parent_obj_type, parent_id)
            write_ids_to_tsv(map_annot_ids)
            return map_annot_ids

        elif final_obj_type == "Tag":
            tag_ids = ez.get_tag_ids(conn, parent_obj_type, parent_id)
            write_ids_to_tsv(tag_ids)
            return tag_ids

        elif final_obj_type == "Roi":
            roi_ids = ez.get_roi_ids(conn, parent_id)
            write_ids_to_tsv(roi_ids)
            return roi_ids

        elif final_obj_type == "Table":
            file_ann_ids = ez.get_file_annotation_ids(conn, parent_obj_type, parent_id)
            write_ids_to_tsv(file_ann_ids)
            return file_ann_ids

        else:
            sys.exit(f"Unsupported object type: {filter}")


# Argument parsing
if __name__ == "__main__":
    parser = argparse.ArgumentParser(description="Fetch OMERO object IDs as TSV from parent object.")
    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="Host server address.")
    parser.add_argument('--port', required=True, type=int,
                        help='OMERO port')
    parser.add_argument('--final_obj_type', required=True,
                        help="Type of object to fetch ID: Project, Dataset, Image, Annotation, Tag, Roi, or Table.")
    parser.add_argument('--parent_obj_type', required=True,
                        help="Type of object from which you fetch IDs: Project, Dataset, Plate, Well, Image (or 'All' if you want to get all objects).")
    parser.add_argument('--parent_id', required=False, type=int,
                        help="ID of the OMERO object in `--parent_obj_type`, not required if you used `--parent_obj_type All`.")
    parser.add_argument('--tsv_file', default='id_list.tsv',
                        help="Output TSV file path.")
    args = parser.parse_args()

    if args.parent_id is None and args.parent_obj_type != "All":
        raise ValueError("ID is only optional is you use `--parent_obj_type All`")

    if args.final_obj_type == "Roi" and args.parent_obj_type != "Image":
        raise ValueError("Roi IDs can only be retrived from images, use `--parent_obj_type Image`")

    if args.parent_obj_type == "All" and args.final_obj_type not in ["Image", "Dataset", "Project"]:
        raise ValueError("Only Images, Datasets and Projects is compatible with `--parent_obj_type All`")

    with open(args.credential_file, 'r') as f:
        crds = json.load(f)

    # Call the main function to get the object and save it as a TSV
    get_ids_ezo(user=crds['username'], pws=crds['password'], host=args.host,
                port=args.port,
                final_obj_type=args.final_obj_type,
                parent_obj_type=args.parent_obj_type,
                parent_id=args.parent_id,
                tsv_file=args.tsv_file)