Enable custom path also for plates

Author: dominikl

src/omero_zarr/cli.py

@@ -325,10 +325,10 @@ def _configure(self, parser: Parser) -> None:
             help="Set the ExternalInfo path",
         )
         extinfo.add_argument(
-            "--lsid",
+            "--zarrPath",
             default=None,
             help=(
-                "Use a specific lsid (path) (default: Determine from "
+                "Use a specific path (default: Determine from "
                 "clientPath) (only used in combination with --set)"
             ),
         )
@@ -424,7 +424,7 @@ def extinfo(self, args: argparse.Namespace) -> None:
                         img,
                         well,
                         idx,
-                        args.lsid,
+                        args.zarrPath,
                         args.entityType,
                         int(args.entityId),
                     )

src/omero_zarr/extinfo.py

@@ -155,7 +155,7 @@ def set_external_info(
     img: ImageI,
     well: str,
     idx: int,
-    lsid: str,
+    overwrite_path: str,
     entityType: str,
     entityId: int
 ) -> ImageI:
@@ -167,8 +167,8 @@ def set_external_info(
         img (ImageI): OMERO image
         well (str | None): Optional well position (e.g. 'A1')
         idx (int | None): Optional well sample / field index
-        lsid (str | None): Optional custom LSID path. If None, path is
-          derived from image's clientpath
+        overwrite_path (str | None): Optional custom path. If None, path is
+            derived from image's clientpath.
         entityType (str | None): Optional entity type. Defaults to
           'com.glencoesoftware.ngff:multiscales'
         entityId (int | None): Optional entity ID. Defaults to 3
@@ -184,30 +184,36 @@ def set_external_info(
         entityType = "com.glencoesoftware.ngff:multiscales"
     if not entityId:
         entityId = 3
-    if lsid:
-        path = lsid
+
+    img_path = _get_path(conn, img.id)
+    if overwrite_path:
+        if not overwrite_path.endswith("/"):
+            path = f"{overwrite_path}/"
+        else:
+            path = overwrite_path
     else:
-        path = _get_path(conn, img.id)
-        if METADATA_XML_RE.match(path):
-            metadata_xml = METADATA_XML_RE.match(path).group(1)
-            if well:
-                match = WELL_POS_RE.match(well)
-                if match:
-                    col = match.group("col")
-                    row = match.group("row")
-                    path = path.replace(metadata_xml, f"{row}")
-                    path = f"/{path}/{col}/{idx}"
-                else:
-                    raise ValueError(f"Couldn't parse well position: {well}")
-            else:
-                series = img.getSeries()._val
-                path = path.replace(metadata_xml, f"{series}")
-                path = f"/{path}"
+        if METADATA_XML_RE.match(img_path):
+            metadata_xml = METADATA_XML_RE.match(img_path).group(1)
+            path = img_path.replace(metadata_xml,"")
+            path = f"/{path}"
         else:
             raise ValueError(
-                f"Doesn't seem to be an ome.zarr: {path}"
+                f"Doesn't seem to be an ome.zarr: {img_path}"
             )
 
+    if well:
+        match = WELL_POS_RE.match(well)
+        if match:
+            col = match.group("col")
+            row = match.group("row")
+            path = f"{path}{row}/{col}/{idx}"
+        else:
+            raise ValueError(f"Couldn't parse well position: {well}")
+    else:
+        series = img.getSeries()._val
+        path = f"{path}{series}"
+
+
     info = ExternalInfoI()
     info.entityType = rstring(entityType)
     info.entityId = rlong(entityId)