Add swap_filesets.py

scripts/swap_filesets.py

@@ -0,0 +1,147 @@
+import argparse
+import sys
+
+import omero.clients
+from omero.cli import cli_login
+from omero.gateway import BlitzGateway
+
+# Swap Images between 2 Filesets. Input is Fileset, Image, Plate or Screen
+# Usage: $ python swap_filesets.py Image:1 Image:2 --report --dry-run
+
+def swap_fileset(conn, old_fileset, new_fileset, sql_filename, report = False, dryrun = False):
+
+    if report:
+        print("Swapping images between Fileset %s and Fileset %s" %
+              (old_fileset.id, new_fileset.id))
+    first_file = new_fileset.listFiles()[0]
+    file_path = first_file.getPath()
+    # remove any path after .zarr
+    if ".zarr" in file_path:
+        file_path = file_path.split(".zarr")[0] + ".zarr"
+
+    new_images = new_fileset.copyImages()
+    old_images = old_fileset.copyImages()
+
+    # link all OLD Images to the NEW Fileset
+    for image in old_images:
+        if report:
+            print("Moving Image: %s to Fileset: %s" % (image.id, new_fileset.id))
+        if dryrun:
+            continue
+        img = image._obj
+        img.fileset = omero.model.FilesetI(new_fileset.id, False)
+        conn.getUpdateService().saveObject(img, conn.SERVICE_OPTS)
+
+    # unlink all NEW Images (to be deleted)
+    for image in new_images:
+        if report:
+            print("Unlinking Image: %s" % (image.id))
+        if dryrun:
+            continue
+        img = image._obj
+        img.fileset = None
+        conn.getUpdateService().saveObject(img, conn.SERVICE_OPTS)
+
+    # Print the HQL updates we need to update each Pixels to new Fileset file
+    # Set it to dataset.zarr/OME/METADATA.ome.xml since this works for Plates (Images???)
+    cmd = f"UPDATE pixels SET name = 'METADATA.ome.xml', path = '{file_path}/OME' where image in (select id from Image where fileset = {new_fileset.id});"
+    with open(sql_filename, 'a') as f:
+        f.write(cmd)
+        f.write("\n")
+    if report:
+        print(cmd)
+
+
+def get_object(conn, obj_string):
+    for dtype in ["Screen", "Plate", "Dataset", "Image", "Fileset"]:
+        if obj_string.startswith(dtype):
+            obj_id = int(obj_string.replace(dtype + ":", ""))
+            obj = conn.getObject(dtype, obj_id)
+            if obj is None:
+                print(obj_string, "not found!")
+            return obj
+
+
+def get_fileset(conn, obj_string):
+    """obj_string is Image:123 or Fileset:123 or Plate:123"""
+
+    obj = get_object(conn, obj_string)
+    if obj_string.startswith("Fileset:"):
+        return obj
+    if obj_string.startswith("Image:"):
+        return obj.getFileset()
+    if obj_string.startswith("Plate:"):
+        for well in obj.listChildren():
+            for ws in well.listChildren():
+                image = ws.getImage()
+                return image.getFileset()
+
+
+def main(argv):
+    """
+    Swaps Fileset from 'Old Object' to 'New Object'.
+    For all the Images in the 'Old Object' (Screen, Plate, Dataset, Image or Fileset), we swap the
+    Fileset to use the Fileset in the 'New Object'. Images in the `New Object` are left
+    unlinked to any Fileset, and can then be deleted.
+    Also prints an sql command(s) to update the pixels in the NEW Images only.
+    For Screens containing multiple Plates (Filesets), we match the Plates by Name
+    """
+    parser = argparse.ArgumentParser()
+    parser.add_argument('old_object', help='Object:ID where Object is Screen, Plate, Dataset, Image, Fileset')
+    parser.add_argument('new_object', help='Object:ID where Object is Screen, Plate, Dataset, Image, Fileset')
+    parser.add_argument('sql_output', help='File path to output sql commands')
+    parser.add_argument("--report", action="store_true", help="Print logs")
+    parser.add_argument("--dry-run", action="store_true", help="Don't save any changes")
+    args = parser.parse_args(argv)
+    old_object = args.old_object
+    new_object = args.new_object
+
+    sql_filename = args.sql_output
+    print("SQL writing to " + sql_filename)
+
+    with cli_login() as cli:
+        conn = BlitzGateway(client_obj=cli._client)
+        if ":" not in old_object or ":" not in new_object:
+            print("Use e.g. $ python swap_fileset Plate:123 Plate:456")
+        # make sure we are dealing with same types:
+        assert (old_object.split(":")[0] == new_object.split(":")[0])
+
+        if "Screen" in old_object:
+            old_screen = get_object(conn, old_object)
+            new_screen = get_object(conn, new_object)
+            old_plates_by_name = {}
+            for plate in old_screen.listChildren():
+                old_plates_by_name[plate.getName()] = plate
+
+            for new_plate in new_screen.listChildren():
+                name = new_plate.getName()
+                if name not in old_plates_by_name:
+                    print(f"No Plate named {name} in {old_object}")
+                old_fileset = get_fileset(conn, f"Plate:{old_plates_by_name[name].id}")
+                new_fileset = get_fileset(conn, f"Plate:{new_plate.id}")
+                swap_fileset(conn, old_fileset, new_fileset, sql_filename, args.report, args.dry_run)
+
+        if "Dataset" in old_object:
+            old_dataset = get_object(conn, old_object)
+            new_dataset = get_object(conn, new_object)
+            old_images_by_name = {}
+            for image in old_dataset.listChildren():
+                old_images_by_name[image.getName()] = image
+
+            for new_image in new_dataset.listChildren():
+                name = new_image.getName()
+                if name not in old_images_by_name:
+                    print(f"No Image named {name} in {old_object}")
+                old_fileset = get_fileset(conn, f"Image:{old_images_by_name[name].id}")
+                new_fileset = get_fileset(conn, f"Image:{new_image.id}")
+                swap_fileset(conn, old_fileset, new_fileset, sql_filename, args.report, args.dry_run)
+
+        else:
+            old_fileset = get_fileset(conn, old_object)
+            new_fileset = get_fileset(conn, new_object)
+            swap_fileset(conn, old_fileset, new_fileset, sql_filename, args.report, args.dry_run)
+
+    print("SQL output added to " + sql_filename)
+
+if __name__ == '__main__':
+    main(sys.argv[1:])