Add scripts/get_filesets_to_csv.py

scripts/get_filesets_to_csv.py

@@ -0,0 +1,66 @@
+
+import csv
+import sys
+from omero.cli import cli_login
+from omero.gateway import BlitzGateway
+from omero.sys import ParametersI
+from omero.rtypes import rstring
+
+
+def get_zarr_name_from_fileset(conn, fileset_id):
+
+    query_service = conn.getQueryService()
+    params = ParametersI()
+    params.addId(fileset_id)
+    params.add("zarr", rstring("%%%s" % "zarr/.zattrs"))
+    query = """ select u.clientPath, fs.templatePrefix from Fileset fs
+        join fs.usedFiles u
+        where fs.id=:id
+        and u.clientPath like :zarr"""
+
+    result = query_service.projection(query, params, conn.SERVICE_OPTS)
+    if len(result) == 0:
+        return None
+
+    client_path = result[0][0].val
+    prefix = result[0][1].val
+
+    zarr_name = client_path.split(".zarr")[0] + ".zarr"
+    zarr_name = zarr_name.split("/")[-1]
+
+    print(zarr_name, prefix)
+    return zarr_name, prefix
+
+
+def lookup_filesets(conn, name):
+
+    filesets = []
+    screen = conn.getObject("Screen", attributes={'name': name})
+    for plate in screen.listChildren():
+        image = None
+        for well in plate.listChildren():
+            ws = list(well.listChildren())
+            if len(ws) > 0:
+                image = list(well.listChildren())[0].getImage()
+                if image is not None:
+                    break
+        # don't .getFileset() as it loads all Files and Images
+        zarr_path, prefix = get_zarr_name_from_fileset(conn, image.fileset.id.val)
+        filesets.append((image.fileset.id.val, zarr_path, prefix))
+
+    return filesets
+
+
+def main(argv):
+
+    with cli_login() as cli:
+        conn = BlitzGateway(client_obj=cli._client)
+
+        filesets = lookup_filesets(conn, "idr0125-way-cellpainting/screenA")
+        with open('idr0125_filesets.csv', 'a', newline='') as csvfile:
+            fswriter = csv.writer(csvfile)
+            for (fsid, zarr_name, prefix) in filesets:
+                fswriter.writerow([fsid, zarr_name, prefix])
+
+if __name__ == '__main__':
+    main(sys.argv[1:])