Mercurial > repos > ufz > omero_get_value

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planemo upload for repository https://github.com/Helmholtz-UFZ/galaxy-tools/tree/main/tools/omero commit 233f0e70cb20a02ec8530dbcfd5c7e70eef74476
author ufz
date Mon, 26 Jan 2026 15:04:30 +0000
parents 86428b102388
children
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b3320a1f2120 planemo upload for repository https://github.com/Helmholtz-UFZ/galaxy-tools/tree/main/tools/omero commit 54b50795912de3f2508cfcfc6911d71a94b34c56
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1 import argparse
b3320a1f2120 planemo upload for repository https://github.com/Helmholtz-UFZ/galaxy-tools/tree/main/tools/omero commit 54b50795912de3f2508cfcfc6911d71a94b34c56
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2 import csv
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3 import os
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4 import sys
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5 from typing import Optional
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7 import ezomero as ez
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8 import pandas as pd
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9 from connect_omero import establish_connection
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11 # Import environmental variables
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12 usr = os.getenv("OMERO_USER")
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13 psw = os.getenv("OMERO_PASSWORD")
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14 uuid_key = os.getenv("UUID_SESSION_KEY")
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16
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17 def get_object_ezo(
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18 host: str,
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19 port: int,
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20 obj_type: str,
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21 ids: list,
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22 out_dir: str,
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23 uuid_key: Optional[str] = None,
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24 ses_close: Optional[bool] = True
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25 ) -> str | dict:
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27 """
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28 Fetch OMERO objects (Annotation, Table and Key-Value Pairs list) and save them as TSV based on object type.
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30 Parameters
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31 ----------
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32 host : str
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33 OMERO server host (i.e. OMERO address or domain name)"
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34 port : int
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35 OMERO server port (default:4064)
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36 obj_type : str
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37 Type of object to fetch ID: Project, Dataset, Image, Annotation, Tag, ROI, or Table.
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38 ids : list
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39 IDs of the OMERO objects.
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40 out_dir : str
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41 Output path of the file
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42 uuid_key : str, optional
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43 OMERO UUID session key to connect without password
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44 ses_close : bool
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45 Decide if close or not the section after executing the script. Defaulf value is true, useful when connecting with the UUID session key.
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46 Returns
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47 -------
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48 csv.writer
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49 A CSV writer object configured to write TSV data.
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50 """
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51
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52 conn = establish_connection(uuid_key, usr, psw, host, port)
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53
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54 # Function to write tabular file from the ezomero output
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55 def write_values_to_tsv(data, header):
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56 with open("output.tsv", 'w', newline='') as f:
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57 writer = csv.writer(f, delimiter='\t')
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58 writer.writerow([header]) # Write the header
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59 for item in data:
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60 writer.writerow([item]) # Write each value
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61
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62 # Function to write tabular file from a dictionary ezomero output
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63 def write_dict_to_tsv(data, headers):
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64 with open("output.tsv", 'w', newline='') as f:
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65 writer = csv.writer(f, delimiter='\t')
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66 writer.writerow(headers) # Write the headers
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67 for key, value in data.items():
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68 writer.writerow([key, value]) # Write each key-value pair
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69
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70 # Function to write tabular file from list of list ezomero output
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71 def write_table_to_tsv(data, id):
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72 with open(f"./output/ID_{id}_table.tsv", 'w') as f:
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73 for row in data:
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74 f.write('\t'.join([str(val) for val in row]) + '\n')
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75
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76 try:
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77 # Fetch different object according to the user input
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78 if obj_type == "Annotation":
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79 ma_dict = {}
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80 for maid in ids:
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81 current_ma_dict = ez.get_map_annotation(conn, maid)
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82 ma_dict = {**ma_dict, **current_ma_dict}
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83 print(ma_dict)
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84 write_dict_to_tsv(ma_dict, ["Annotation ID", "Annotation Value"])
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85 elif obj_type == "Tag":
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86 tags = []
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87 for tag_id in ids:
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88 tags.append(ez.get_tag(conn, tag_id))
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89 # Sort the tags for consistency:
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90 tags.sort
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91 write_values_to_tsv(tags, "Tags")
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92 elif obj_type == "Table":
1
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93 for id in ids:
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94 table = ez.get_table(conn, id)
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95 print(table)
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96 write_table_to_tsv(table, id)
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97 elif obj_type == ("Attachment"):
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98 for id in ids:
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99 attch_path = ez.get_file_annotation(conn, id, folder_path='./output/')
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100 base_name = os.path.basename(attch_path)
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101 df = pd.read_csv(attch_path, sep='\t')
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102 df.to_csv(f"./output/ID_{id}_{base_name}", sep='\t', index=False)
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103 os.remove(attch_path)
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104 else:
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105 sys.exit(f"Unsupported object type: {filter}")
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106
3
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107 finally:
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108 if ses_close:
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109 conn.close()
0
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110
3
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111
0
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112 if __name__ == "__main__":
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113 parser = argparse.ArgumentParser(description="Fetch and save data as TSV based on object type.")
3
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114 parser.add_argument('--host', required=True, help="OMERO server host (i.e. OMERO address or domain name)")
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115 parser.add_argument('--port', required=True, type=int, help="OMERO server port (default:4064)")
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116 parser.add_argument('--obj_type', required=True, help="Type of object to fetch: Annotation, Table or Tag.")
0
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117 group = parser.add_mutually_exclusive_group()
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118 group.add_argument('--ids', nargs='+', type=int, help="IDs of the OMERO objects.")
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119 group.add_argument('--ids_path', help="File with IDs of the OMERO objects (one per line).")
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120 parser.add_argument('--session_close', required=False, help='Namespace or title for the annotation')
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121 parser.add_argument('--out_dir', required=True, help="Output path.")
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122
0
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123 args = parser.parse_args()
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124
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125 if args.ids_path:
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126 args.ids = []
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127 with open(args.ids_path, 'r') as f:
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128 for line in f:
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129 try:
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130 args.ids.append(int(line))
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131 except ValueError:
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132 print(f"{line.strip()} is not a valid ID.")
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133 if len(args.ids) == 0:
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134 raise ValueError("Cound not find a single ID in the file.")
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135
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136 # Call the main function to get the object and save it as a TSV
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137 get_object_ezo(host=args.host,
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138 port=args.port,
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139 obj_type=args.obj_type,
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140 ids=args.ids,
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141 ses_close=args.session_close,
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142 out_dir=args.out_dir)