From 38e91255c80bfb04b814ef37056b355d692c2c96 Mon Sep 17 00:00:00 2001
From: William Moore <w.moore@dundee.ac.uk>
Date: Fri, 26 Jan 2024 16:24:10 +0000
Subject: [PATCH] Use METADATA.ome.xml to check for bioformats2raw layout

---
 omero_web_zarr/utils.py | 33 ++++++++++++++++++++-------------
 1 file changed, 20 insertions(+), 13 deletions(-)

diff --git a/omero_web_zarr/utils.py b/omero_web_zarr/utils.py
index 5cb4e12..686460c 100644
--- a/omero_web_zarr/utils.py
+++ b/omero_web_zarr/utils.py
@@ -100,28 +100,33 @@ def generate_coordinate_transformations(shapes):
         return transformations
 
 
-def get_zarr_s3_path(conn, image_id):
-    """
-    Check Fileset clientPaths for path ending zarr/.zattrs
-
-    If Image is in a Plate/Well, add eg. /A/1/0/ to path.
-    """
+def get_clientpath_by_endswith(conn, image_id, pathending):
     query_service = conn.getQueryService()
     params = ParametersI()
     params.addId(image_id)
-    params.add("zarr", rstring("%%%s" % "zarr/.zattrs"))
+    params.add("zarr", rstring("%%%s" % pathending))
     query = """ select u.clientPath from Fileset fs
         join fs.usedFiles u
         left outer join fs.images as image
         where image.id=:id
         and u.clientPath like :zarr"""
-
     result = query_service.projection(query, params, conn.SERVICE_OPTS)
     if len(result) == 0:
         return None
+    return result[0][0].val
+
+
+def get_zarr_s3_path(conn, image_id):
+    """
+    Check Fileset clientPaths for path ending zarr/.zattrs
+
+    If Image is in a Plate/Well, add eg. /A/1/0/ to path.
+    """
+    client_path = get_clientpath_by_endswith(conn, image_id, "zarr/.zattrs")
+    if client_path is None:
+        return None
 
     # We also need clientPath to be a publicly-accessible URL
-    client_path = result[0][0].val
     zarr_path = client_path.replace("/.zattrs", "")
 
     # Check if Image is in a Well - need to add /row/col/field/ e.g. /A/1/0
@@ -140,8 +145,10 @@ def get_zarr_s3_path(conn, image_id):
         row_col_field = f"/{row}/{column}/{ws_index}/"
         zarr_path += row_col_field
     else:
-        # assumes bioformats2raw image!!
-        # TODO: need to handle this case - NOT true for all Images
-        zarr_path += "/0/"
+        # Check whether this is a bioformats2raw image
+        metadata_path = get_clientpath_by_endswith(conn, image_id,
+                                                   "OME/METADATA.ome.xml")
+        if metadata_path is not None:
+            zarr_path += "/0/"
 
-    return zarr_path
\ No newline at end of file
+    return zarr_path