diff omero_filter.py @ 0:8a3324018fc5 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_filter.py	Tue Oct 22 11:54:08 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)