Bugfix in replicate_zarr_structure_mip (omero metadata were only written for last well) [ref #61 #62]

tcompa · tcompa · commit 2bd5c6a4efd6 · 2022-06-21T07:11:16.000Z
diff --git a/fractal/tasks/replicate_zarr_structure_mip.py b/fractal/tasks/replicate_zarr_structure_mip.py
@@ -98,11 +98,11 @@ def replicate_zarr_structure_mip(zarrurl):
             }
         ]
 
-    # Copy .zattrs file at the COL/ROW/SITE level
-    path_zattrs = zarrurl + f"{row}/{column}/0/.zattrs"
-    with open(path_zattrs) as zattrs_file:
-        zattrs = json.load(zattrs_file)
-        group_field.attrs["omero"] = zattrs["omero"]
+        # Copy .zattrs file at the COL/ROW/SITE level
+        path_zattrs = zarrurl + f"{row}/{column}/0/.zattrs"
+        with open(path_zattrs) as zattrs_file:
+            zattrs = json.load(zattrs_file)
+            group_field.attrs["omero"] = zattrs["omero"]
 
 
 if __name__ == "__main__":

Original file line number	Diff line number	Diff line change
`@@ -98,11 +98,11 @@ def replicate_zarr_structure_mip(zarrurl):`
`98`	`98`	`}`
`99`	`99`	`]`
`100`	`100`
`101`		`- # Copy .zattrs file at the COL/ROW/SITE level`
`102`		`- path_zattrs = zarrurl + f"{row}/{column}/0/.zattrs"`
`103`		`- with open(path_zattrs) as zattrs_file:`
`104`		`- zattrs = json.load(zattrs_file)`
`105`		`- group_field.attrs["omero"] = zattrs["omero"]`
	`101`	`+ # Copy .zattrs file at the COL/ROW/SITE level`
	`102`	`+ path_zattrs = zarrurl + f"{row}/{column}/0/.zattrs"`
	`103`	`+ with open(path_zattrs) as zattrs_file:`
	`104`	`+ zattrs = json.load(zattrs_file)`
	`105`	`+ group_field.attrs["omero"] = zattrs["omero"]`
`106`	`106`
`107`	`107`
`108`	`108`	`if __name__ == "__main__":`