Add script to fix antibody map annotation

scripts/fix_abmaps.py

@@ -0,0 +1,36 @@
+import omero
+from omero.cli import cli_login
+from omero.gateway import BlitzGateway
+
+# This script will add an empty "Antibody Name" key-value pair
+# to every MapAnnotation which doesn't have one. Additionally it
+# will rename all "Antibody" keys to "Antibody Name"
+
+with cli_login() as c:
+    conn = BlitzGateway(client_obj=c.get_client())
+    queryService = conn.getQueryService()
+    params = omero.sys.Parameters()
+    query = "select m from MapAnnotation m join m.mapValue mv where m.ns='openmicroscopy.org/mapr/antibody'"
+    maps = conn.getQueryService().findAllByQuery(query, params)
+    for i, map in enumerate(maps):
+        nvs = map.getMapValue()
+        id = None
+        names = []
+        update = False
+        for nv in nvs:
+            if nv.name == "Antibody Identifier":
+                id = nv.value
+            elif nv.name == "Antibody Name":
+                names.append(nv.value)
+            elif nv.name == "Antibody":
+                nv.name = "Antibody Name"
+                update = True
+                names.append(nv.value)
+        if len(names) == 0:
+            nvs.append(omero.model.NamedValue("Antibody Name", ""))
+            map.setMapValue(nvs)
+            update = True
+        if update:
+            conn.getUpdateService().saveAndReturnObject(map)
+        print(f"{i} - {id}")
+