Mercurial > repos > ufz > omero_roi_import
changeset 3:dfe0aae1495c draft
planemo upload for repository https://github.com/Helmholtz-UFZ/galaxy-tools/tree/main/tools/omero commit 19d84fd5a372f1428e3e5670144881a56e8af8b2
| author | ufz |
|---|---|
| date | Tue, 22 Oct 2024 11:53:15 +0000 |
| parents | 4f4dc352d660 |
| children | 131470834fee |
| files | macros.xml omero_filter.py omero_get_id.py omero_get_value.py omero_roi_import.xml test-data/output_KV_import.txt test-data/output_filter_filename.tsv test-data/output_filter_tag.tsv test-data/output_ids_dataset.tsv test-data/output_ids_image.tsv test-data/output_ids_project.tsv |
| diffstat | 11 files changed, 352 insertions(+), 26 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/macros.xml Tue Oct 22 11:53:15 2024 +0000 @@ -0,0 +1,47 @@ +<macros> + <!-- for historic reasons the omero-py version is used as the version for all tools --> + <token name="@TOOL_VERSION@">5.18.0</token> + <token name="@EZOMERO_VERSION@">3.0.1</token> + <token name="@PROFILE@">23.0</token> + + <xml name="ezomero_requirements"> + <requirements> + <requirement type="package" version="@EZOMERO_VERSION@">ezomero</requirement> + <requirement type="package" version="2.2.2">pandas</requirement> + <yield/> + </requirements> + </xml> + + <xml name="omeropy_requirements"> + <requirements> + <requirement type="package" version="@TOOL_VERSION@">omero-py</requirement> + <!-- openjdk is needed: https://github.com/conda-forge/omero-py-feedstock/pull/16 --> + <requirement type="package" version="21.0.2">openjdk</requirement> + <yield/> + </requirements> + </xml> + + + <xml name="host_port"> + <param name="omero_host" type="text" label="OMERO host URL"> + <validator type="regex" message="Enter a valid host location, for example, your.omero.server">^[a-zA-Z0-9._-]*$</validator> + <validator type="expression" message="No two dots (..) allowed">'..' not in value</validator> + </param> + <param argument="omero_port" type="integer" optional="false" value="4064" label="OMERO port"/> + <param name="test_username" type="hidden" value=""/> + <param name="test_password" type="hidden" value=""/> + </xml> + <token name="@HOST_PORT@"> + --host '$omero_host' + --port $omero_port + </token> + + <xml name="credentials"> + <configfile name="credentials"><![CDATA[ +{ + "username": "$__user__.extra_preferences.get('omero_account|username', $test_username)", + "password": "$__user__.extra_preferences.get('omero_account|password', $test_password)" +} + ]]></configfile> + </xml> +</macros> \ No newline at end of file
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/omero_filter.py Tue Oct 22 11:53:15 2024 +0000 @@ -0,0 +1,77 @@ +import argparse +import csv +import json +import sys + +import ezomero as ez + + +def filter_ids_ezo(user, pws, host, port, filter, id, value1, value2=None, tsv_file="filter_list.tsv"): + + # Transform the id input in a list of integer + id = id.split(',') + id = list(map(int, id)) + + # 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 filter == "filename": + fn_ids = ez.filter_by_filename(conn, id, value1) + write_ids_to_tsv(fn_ids) + return fn_ids + + elif filter == "KP": + kp_ims = ez.filter_by_kv(conn, id, value1, value2) + write_ids_to_tsv(kp_ims) + return kp_ims + + elif filter == "tag": + tg_dict = ez.filter_by_tag_value(conn, id, value1) + write_ids_to_tsv(tg_dict) + return tg_dict + + else: + sys.exit(f"Unsupported object type: {filter}") + + +# Argument parsing +if __name__ == "__main__": + parser = argparse.ArgumentParser(description="Fetch and save data as TSV based on object type.") + 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('--filter', required=True, + help="Filter type - Filename, Key-Value Pairs, Tag") + parser.add_argument('--id', required=True, + help="List of images IDs") + parser.add_argument('--value1', required=True, + help="First searching values - Filename, Key, Tag") + parser.add_argument('--value2', required=False, + help="Second searching values - Value (necessary just for Key-Value Pairs filter") + parser.add_argument('--tsv_file', default='filter_list.tsv', + help="Output TSV file path.") + args = parser.parse_args() + + if args.filter == "KP" and args.value2 is None: + raise ValueError("'--value 2' is necessary to retrieve KP") + + 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 + filter_ids_ezo(user=crds['username'], pws=crds['password'], host=args.host, + port=args.port, + filter=args.filter, + value1=args.value1, + value2=args.value2, + id=args.id, + tsv_file=args.tsv_file)
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/omero_get_id.py Tue Oct 22 11:53:15 2024 +0000 @@ -0,0 +1,116 @@ +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)
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/omero_get_value.py Tue Oct 22 11:53:15 2024 +0000 @@ -0,0 +1,98 @@ +import argparse +import csv +import json +import sys + +import ezomero as ez + + +def get_object_ezo(user, pws, host, port, obj_type, ids, tsv_file): + # Function to write tabular file from the ezomero output + def write_values_to_tsv(data, header): + with open(tsv_file, 'w', newline='') as f: + writer = csv.writer(f, delimiter='\t') + writer.writerow([header]) # Write the header + for item in data: + writer.writerow([item]) # Write each value + + # Function to write tabular file from a dictionary ezomero output + def write_dict_to_tsv(data, headers): + with open(tsv_file, 'w', newline='') as f: + writer = csv.writer(f, delimiter='\t') + writer.writerow(headers) # Write the headers + for key, value in data.items(): + writer.writerow([key, value]) # Write each key-value pair + + # Function to write tabular file from list of list ezomero output + def write_table_to_tsv(data): + with open(tsv_file, 'w') as f: + for row in data: + f.write('\t'.join([str(val) for val in row]) + '\n') + + with ez.connect(user, pws, "", host, port, secure=True) as conn: + if obj_type == "Annotation": + ma_dict = {} + for maid in ids: + current_ma_dict = ez.get_map_annotation(conn, maid) + ma_dict = {**ma_dict, **current_ma_dict} + write_dict_to_tsv(ma_dict, ["Annotation ID", "Annotation Value"]) + return ma_dict + elif obj_type == "Tag": + tags = [] + for tag_id in ids: + tags.append(ez.get_tag(conn, tag_id)) + # Sort the tags for consistency: + tags.sort + write_values_to_tsv(tags, "Tags") + return tags + elif obj_type == "Table": + if len(ids) > 1: + raise ValueError("Only one table can be exported at a time") + table = ez.get_table(conn, ids[0]) + write_table_to_tsv(table) + return table + + else: + sys.exit(f"Unsupported object type: {filter}") + + +# Argument parsing +if __name__ == "__main__": + parser = argparse.ArgumentParser(description="Fetch and save data as TSV based on object type.") + 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('--obj_type', required=True, + help="Type of object to fetch: Annotation, Table or Tag.") + group = parser.add_mutually_exclusive_group() + group.add_argument('--ids', nargs='+', type=int, + help="IDs of the OMERO objects.") + group.add_argument('--ids_path', + help="File with IDs of the OMERO objects (one per line).") + parser.add_argument('--tsv_file', default='id_list.tsv', required=True, + help="Output TSV file path.") + args = parser.parse_args() + + if args.ids_path: + args.ids = [] + with open(args.ids_path, 'r') as f: + for line in f: + try: + args.ids.append(int(line)) + except ValueError: + print(f"{line.strip()} is not a valid ID.") + if len(args.ids) == 0: + raise ValueError("Cound not find a single ID in the file.") + + 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_object_ezo(user=crds['username'], pws=crds['password'], host=args.host, + port=args.port, + obj_type=args.obj_type, + ids=args.ids, + tsv_file=args.tsv_file)
--- a/omero_roi_import.xml Thu Sep 12 16:30:36 2024 +0000 +++ b/omero_roi_import.xml Tue Oct 22 11:53:15 2024 +0000 @@ -1,46 +1,28 @@ -<tool id="omero_roi_import" name="OMERO ROI Import" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" - profile="20.01" license="MIT"> +<tool id="omero_roi_import" name="OMERO ROI Import" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@" license="MIT"> <description> with ezomero </description> <macros> - <token name="@TOOL_VERSION@">5.18.0</token> - <token name="@VERSION_SUFFIX@">3</token> + <import>macros.xml</import> + <token name="@VERSION_SUFFIX@">4</token> </macros> <xrefs> <xref type="bio.tools">omero</xref> </xrefs> - <requirements> - <requirement type="package" version="3.0.1">ezomero</requirement> - <requirement type="package" version="2.2.2">pandas</requirement> - <!-- openjdk is needed: https://github.com/conda-forge/omero-py-feedstock/pull/16 --> - <requirement type="package" version="21.0.2">openjdk</requirement> - </requirements> + <expand macro="ezomero_requirements"/> <command detect_errors="exit_code"><![CDATA[ python '$__tool_directory__/omero_roi_upload.py' --input_file '$input' --image_id $id --credential-file '$credentials' - --host '$omero_host' - --port $omero_port + @HOST_PORT@ --log_file '$log' ]]></command> <configfiles> - <configfile name="credentials"><![CDATA[ -{ - "username": "$__user__.extra_preferences.get('omero_account|username', $test_username)", - "password": "$__user__.extra_preferences.get('omero_account|password', $test_password)" -} - ]]></configfile> + <expand macro="credentials"/> </configfiles> <inputs> + <expand macro="host_port"/> <param argument="input" type="data" format="tabular" optional="false" label="Tab File with ROIs" help="Select ROIs Tabular file"/> <param argument="id" type="integer" value="" optional="false" label="Image ID where annotate the ROIs"/> - <param name="omero_host" type="text" label="OMERO host URL"> - <validator type="regex" message="Enter a valid host location, for example, your.omero.server">^[a-zA-Z0-9._-]*$</validator> - <validator type="expression" message="No two dots (..) allowed">'..' not in value</validator> - </param> - <param argument="omero_port" type="integer" optional="false" value="4064" label="OMERO port"/> - <param name="test_username" type="hidden" value=""/> - <param name="test_password" type="hidden" value=""/> </inputs> <outputs> <data name="log" format="txt"/>
--- a/test-data/output_KV_import.txt Thu Sep 12 16:30:36 2024 +0000 +++ b/test-data/output_KV_import.txt Tue Oct 22 11:53:15 2024 +0000 @@ -1,1 +1,1 @@ -SUCCESS: Successfully uploaded metadata for dataset with ID 2. Result: {'Key1': 'Value1', 'Key2': 'Value2'} +SUCCESS: Successfully uploaded metadata for dataset with ID 3. Result: {'Key1': 'Value1', 'Key2': 'Value2'}
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/output_filter_filename.tsv Tue Oct 22 11:53:15 2024 +0000 @@ -0,0 +1,1 @@ +2
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/output_filter_tag.tsv Tue Oct 22 11:53:15 2024 +0000 @@ -0,0 +1,1 @@ +1
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/output_ids_dataset.tsv Tue Oct 22 11:53:15 2024 +0000 @@ -0,0 +1,1 @@ +1