annotate omero_get_value.py @ 3:0ebede62d62d 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 20:47:13 +0000
parents b1f969b7c527
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5ad32d18fe82 planemo upload for repository https://github.com/Helmholtz-UFZ/galaxy-tools/tree/main/tools/omero commit 636cbb62d59819caca5bc9eab0a8ec31be5bdd46
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1 import argparse
5ad32d18fe82 planemo upload for repository https://github.com/Helmholtz-UFZ/galaxy-tools/tree/main/tools/omero commit 636cbb62d59819caca5bc9eab0a8ec31be5bdd46
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2 import csv
5ad32d18fe82 planemo upload for repository https://github.com/Helmholtz-UFZ/galaxy-tools/tree/main/tools/omero commit 636cbb62d59819caca5bc9eab0a8ec31be5bdd46
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3 import json
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4 import os
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5 import sys
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7 import ezomero as ez
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8 import pandas as pd
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10
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11 def get_object_ezo(user, pws, host, port, obj_type, ids, out_dir):
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5ad32d18fe82 planemo upload for repository https://github.com/Helmholtz-UFZ/galaxy-tools/tree/main/tools/omero commit 636cbb62d59819caca5bc9eab0a8ec31be5bdd46
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12 # Function to write tabular file from the ezomero output
5ad32d18fe82 planemo upload for repository https://github.com/Helmholtz-UFZ/galaxy-tools/tree/main/tools/omero commit 636cbb62d59819caca5bc9eab0a8ec31be5bdd46
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13 def write_values_to_tsv(data, header):
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14 with open("output.tsv", 'w', newline='') as f:
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15 writer = csv.writer(f, delimiter='\t')
5ad32d18fe82 planemo upload for repository https://github.com/Helmholtz-UFZ/galaxy-tools/tree/main/tools/omero commit 636cbb62d59819caca5bc9eab0a8ec31be5bdd46
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16 writer.writerow([header]) # Write the header
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17 for item in data:
5ad32d18fe82 planemo upload for repository https://github.com/Helmholtz-UFZ/galaxy-tools/tree/main/tools/omero commit 636cbb62d59819caca5bc9eab0a8ec31be5bdd46
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18 writer.writerow([item]) # Write each value
5ad32d18fe82 planemo upload for repository https://github.com/Helmholtz-UFZ/galaxy-tools/tree/main/tools/omero commit 636cbb62d59819caca5bc9eab0a8ec31be5bdd46
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20 # Function to write tabular file from a dictionary ezomero output
5ad32d18fe82 planemo upload for repository https://github.com/Helmholtz-UFZ/galaxy-tools/tree/main/tools/omero commit 636cbb62d59819caca5bc9eab0a8ec31be5bdd46
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21 def write_dict_to_tsv(data, headers):
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22 with open("output.tsv", 'w', newline='') as f:
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23 writer = csv.writer(f, delimiter='\t')
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24 writer.writerow(headers) # Write the headers
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25 for key, value in data.items():
5ad32d18fe82 planemo upload for repository https://github.com/Helmholtz-UFZ/galaxy-tools/tree/main/tools/omero commit 636cbb62d59819caca5bc9eab0a8ec31be5bdd46
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26 writer.writerow([key, value]) # Write each key-value pair
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28 # Function to write tabular file from list of list ezomero output
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29 def write_table_to_tsv(data, id):
b1f969b7c527 planemo upload for repository https://github.com/Helmholtz-UFZ/galaxy-tools/tree/main/tools/omero commit 6f47dff3775455a8c45d39a3863a2306cd942443
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30 with open(f"./output/ID_{id}_table.tsv", 'w') as f:
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31 for row in data:
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32 f.write('\t'.join([str(val) for val in row]) + '\n')
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34 with ez.connect(user, pws, "", host, port, secure=True) as conn:
5ad32d18fe82 planemo upload for repository https://github.com/Helmholtz-UFZ/galaxy-tools/tree/main/tools/omero commit 636cbb62d59819caca5bc9eab0a8ec31be5bdd46
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35 if obj_type == "Annotation":
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36 ma_dict = {}
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37 for maid in ids:
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38 current_ma_dict = ez.get_map_annotation(conn, maid)
5ad32d18fe82 planemo upload for repository https://github.com/Helmholtz-UFZ/galaxy-tools/tree/main/tools/omero commit 636cbb62d59819caca5bc9eab0a8ec31be5bdd46
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39 ma_dict = {**ma_dict, **current_ma_dict}
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40 print(ma_dict)
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41 write_dict_to_tsv(ma_dict, ["Annotation ID", "Annotation Value"])
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42 elif obj_type == "Tag":
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43 tags = []
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44 for tag_id in ids:
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45 tags.append(ez.get_tag(conn, tag_id))
5ad32d18fe82 planemo upload for repository https://github.com/Helmholtz-UFZ/galaxy-tools/tree/main/tools/omero commit 636cbb62d59819caca5bc9eab0a8ec31be5bdd46
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46 # Sort the tags for consistency:
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47 tags.sort
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48 write_values_to_tsv(tags, "Tags")
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49 elif obj_type == "Table":
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50 for id in ids:
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51 table = ez.get_table(conn, id)
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52 print(table)
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53 write_table_to_tsv(table, id)
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54 elif obj_type == ("Attachment"):
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55 for id in ids:
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56 attch_path = ez.get_file_annotation(conn, id, folder_path='./output/')
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57 base_name = os.path.basename(attch_path)
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58 df = pd.read_csv(attch_path, sep='\t')
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59 df.to_csv(f"./output/ID_{id}_{base_name}", sep='\t', index=False)
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60 os.remove(attch_path)
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61 else:
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62 sys.exit(f"Unsupported object type: {filter}")
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63
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64
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65 # Argument parsing
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66 if __name__ == "__main__":
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67 parser = argparse.ArgumentParser(description="Fetch and save data as TSV based on object type.")
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68 parser.add_argument("--credential-file", dest="credential_file", type=str,
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69 required=True, help="Credential file (JSON file with username and password for OMERO)")
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70 parser.add_argument('--host', required=True,
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71 help="Host server address.")
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72 parser.add_argument('--port', required=True, type=int,
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73 help='OMERO port')
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74 parser.add_argument('--obj_type', required=True,
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75 help="Type of object to fetch: Annotation, Table or Tag.")
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76 group = parser.add_mutually_exclusive_group()
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77 group.add_argument('--ids', nargs='+', type=int,
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78 help="IDs of the OMERO objects.")
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79 group.add_argument('--ids_path',
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80 help="File with IDs of the OMERO objects (one per line).")
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81 parser.add_argument('--out_dir', required=True,
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82 help="Output path.")
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83 args = parser.parse_args()
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84
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85 if args.ids_path:
5ad32d18fe82 planemo upload for repository https://github.com/Helmholtz-UFZ/galaxy-tools/tree/main/tools/omero commit 636cbb62d59819caca5bc9eab0a8ec31be5bdd46
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86 args.ids = []
5ad32d18fe82 planemo upload for repository https://github.com/Helmholtz-UFZ/galaxy-tools/tree/main/tools/omero commit 636cbb62d59819caca5bc9eab0a8ec31be5bdd46
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87 with open(args.ids_path, 'r') as f:
5ad32d18fe82 planemo upload for repository https://github.com/Helmholtz-UFZ/galaxy-tools/tree/main/tools/omero commit 636cbb62d59819caca5bc9eab0a8ec31be5bdd46
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88 for line in f:
5ad32d18fe82 planemo upload for repository https://github.com/Helmholtz-UFZ/galaxy-tools/tree/main/tools/omero commit 636cbb62d59819caca5bc9eab0a8ec31be5bdd46
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89 try:
5ad32d18fe82 planemo upload for repository https://github.com/Helmholtz-UFZ/galaxy-tools/tree/main/tools/omero commit 636cbb62d59819caca5bc9eab0a8ec31be5bdd46
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90 args.ids.append(int(line))
5ad32d18fe82 planemo upload for repository https://github.com/Helmholtz-UFZ/galaxy-tools/tree/main/tools/omero commit 636cbb62d59819caca5bc9eab0a8ec31be5bdd46
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91 except ValueError:
5ad32d18fe82 planemo upload for repository https://github.com/Helmholtz-UFZ/galaxy-tools/tree/main/tools/omero commit 636cbb62d59819caca5bc9eab0a8ec31be5bdd46
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92 print(f"{line.strip()} is not a valid ID.")
5ad32d18fe82 planemo upload for repository https://github.com/Helmholtz-UFZ/galaxy-tools/tree/main/tools/omero commit 636cbb62d59819caca5bc9eab0a8ec31be5bdd46
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93 if len(args.ids) == 0:
5ad32d18fe82 planemo upload for repository https://github.com/Helmholtz-UFZ/galaxy-tools/tree/main/tools/omero commit 636cbb62d59819caca5bc9eab0a8ec31be5bdd46
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94 raise ValueError("Cound not find a single ID in the file.")
5ad32d18fe82 planemo upload for repository https://github.com/Helmholtz-UFZ/galaxy-tools/tree/main/tools/omero commit 636cbb62d59819caca5bc9eab0a8ec31be5bdd46
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95
5ad32d18fe82 planemo upload for repository https://github.com/Helmholtz-UFZ/galaxy-tools/tree/main/tools/omero commit 636cbb62d59819caca5bc9eab0a8ec31be5bdd46
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96 with open(args.credential_file, 'r') as f:
5ad32d18fe82 planemo upload for repository https://github.com/Helmholtz-UFZ/galaxy-tools/tree/main/tools/omero commit 636cbb62d59819caca5bc9eab0a8ec31be5bdd46
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97 crds = json.load(f)
5ad32d18fe82 planemo upload for repository https://github.com/Helmholtz-UFZ/galaxy-tools/tree/main/tools/omero commit 636cbb62d59819caca5bc9eab0a8ec31be5bdd46
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98
5ad32d18fe82 planemo upload for repository https://github.com/Helmholtz-UFZ/galaxy-tools/tree/main/tools/omero commit 636cbb62d59819caca5bc9eab0a8ec31be5bdd46
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99 # Call the main function to get the object and save it as a TSV
5ad32d18fe82 planemo upload for repository https://github.com/Helmholtz-UFZ/galaxy-tools/tree/main/tools/omero commit 636cbb62d59819caca5bc9eab0a8ec31be5bdd46
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100 get_object_ezo(user=crds['username'], pws=crds['password'], host=args.host,
5ad32d18fe82 planemo upload for repository https://github.com/Helmholtz-UFZ/galaxy-tools/tree/main/tools/omero commit 636cbb62d59819caca5bc9eab0a8ec31be5bdd46
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101 port=args.port,
5ad32d18fe82 planemo upload for repository https://github.com/Helmholtz-UFZ/galaxy-tools/tree/main/tools/omero commit 636cbb62d59819caca5bc9eab0a8ec31be5bdd46
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102 obj_type=args.obj_type,
5ad32d18fe82 planemo upload for repository https://github.com/Helmholtz-UFZ/galaxy-tools/tree/main/tools/omero commit 636cbb62d59819caca5bc9eab0a8ec31be5bdd46
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103 ids=args.ids,
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104 out_dir=args.out_dir)