diff omero_get_value.py @ 3:eba4011643dd draft

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

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/omero_get_value.py	Tue Oct 22 11:52:32 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)