diff omero_get_children_ids.py @ 0:b0876c73076b draft

planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/omero_get_children_ids commit 8ac44b0341c70ce330fc0f24712b6f9b59b14731

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/omero_get_children_ids.py	Fri Dec 22 12:55:40 2023 +0000
@@ -0,0 +1,77 @@
+import argparse
+import json
+
+from omero.gateway import BlitzGateway
+
+
+def get_omero_credentials(config_file):
+    if config_file is None:  # IDR connection
+        omero_username = "public"
+        omero_password = "public"
+    else:  # other omero instance
+        with open(config_file) as f:
+            cfg = json.load(f)
+            omero_username = cfg["username"]
+            omero_password = cfg["password"]
+
+            if omero_username == "" or omero_password == "":
+                omero_username = "public"
+                omero_password = "public"
+    return (omero_username, omero_password)
+
+
+def recursive_get_children_id(parent_object, final_object_type):
+    output = []
+    if parent_object.OMERO_CLASS == 'WellSample':
+        return [parent_object.getImage().id]
+    for children in parent_object.listChildren():
+        if children.OMERO_CLASS == final_object_type.title():
+            output.append(children.id)
+        else:
+            # We need to go one step further
+            output += recursive_get_children_id(children, final_object_type)
+    return output
+
+
+def get_children_ids(parent_object_type,
+                     omero_id,
+                     final_object_type,
+                     omero_username,
+                     omero_password,
+                     omero_host="idr.openmicroscopy.org",
+                     omero_secured=False):
+    # Connect to omero:
+    with BlitzGateway(
+        omero_username, omero_password, host=omero_host, secure=omero_secured
+    ) as conn:
+        # Retrieve omero object
+        parent_object = conn.getObject(parent_object_type.title(), omero_id)
+        return recursive_get_children_id(parent_object, final_object_type)
+
+
+if __name__ == "__main__":
+    p = argparse.ArgumentParser()
+    p.add_argument("-oh", "--omero-host", type=str,
+                   default="idr.openmicroscopy.org")
+    p.add_argument("--omero-secured", action="store_true", default=True)
+    p.add_argument("-cf", "--config-file", dest="config_file",
+                   default=None)
+    p.add_argument("--parent-object-type", dest="parent_object_type",
+                   type=str, default=None, required=True)
+    p.add_argument("--omero-id", dest="omero_id",
+                   type=int, default=None, required=True)
+    p.add_argument("--final-object-type", dest="final_object_type",
+                   type=str, default=None, required=True)
+    p.add_argument("--output", type=str, default=None, required=True)
+    args = p.parse_args()
+    children_ids = get_children_ids(
+        args.parent_object_type,
+        args.omero_id,
+        args.final_object_type,
+        *get_omero_credentials(args.config_file),
+        omero_host=args.omero_host,
+        omero_secured=args.omero_secured,
+    )
+    with open(args.output, 'w') as fo:
+        fo.write('\n'.join([str(id) for id in children_ids]))
+        fo.write('\n')