Always update pixels

src/omero_mkngff/__init__.py

@@ -27,6 +27,7 @@
 from omero.cli import BaseControl, Parser
 from omero.sys import ParametersI
 
+SUFFIX = "mkngff"
 HELP = """Plugin to swap OMERO filesets with NGFF
 
 CLI plugin used to swap an existing OMERO fileset with
@@ -105,12 +106,6 @@
           values (nextval('seq_filesetentry'), {DETAILS2},
                   new_fileset, new_file, i-1, 'unknown');
 
-      if info[i][2] = 'METADATA.ome.xml' then
-          update pixels set path = trim(trailing '/' from info[i][1]), name = info[i][2]
-            from (select id from image where image.fileset = old_fileset) as subquery
-           where pixels.image = subquery.id;
-      end if;
-
     end loop;
 
     update image set fileset = new_fileset where fileset = old_fileset;
@@ -197,7 +192,7 @@ def sql(self, args: Namespace) -> None:
             self.ctx.die(401, f"Symlink target does not exist: {args.symlink_target}")
             return
 
-        # create *_converted/path/to/zarr directory containing symlink to data
+        # create *_SUFFIX/path/to/zarr directory containing symlink to data
         if args.symlink_repo:
             prefix_dir = os.path.join(args.symlink_repo, prefix)
             self.ctx.err(f"Checking for prefix_dir {prefix_dir}")
@@ -206,7 +201,7 @@ def sql(self, args: Namespace) -> None:
             symlink_container = f"{symlink_path.parent}"
             if symlink_container.startswith("/"):
                 symlink_container = symlink_container[1:]  # remove "/" from start
-            symlink_dir = os.path.join(f"{prefix_dir}_converted", symlink_container)
+            symlink_dir = f"{prefix_dir}_{SUFFIX}"
             self.ctx.err(f"Creating dir at {symlink_dir}")
             os.makedirs(symlink_dir, exist_ok=True)
 
@@ -218,21 +213,34 @@ def sql(self, args: Namespace) -> None:
             os.symlink(args.symlink_target, symlink_source, target_is_directory)
 
         rows = []
+        # Need a file to set path/name on pixels table BioFormats uses for setId()
+        setid_target = None
         for row_path, row_name, row_mime in self.walk(symlink_path):
+            # remove common path to shorten
+            row_path = str(row_path).replace(f"{symlink_path.parent}", "")
             if str(row_path).startswith("/"):
                 row_path = str(row_path)[1:]  # remove "/" from start
+            row_full_path = f"{prefix_path}/{prefix_name}_{SUFFIX}/{row_path}"
+            # pick the first .zattrs file we find, then update to ome.xml if we find it
+            if setid_target is None and row_name == ".zattrs" or row_name == "METADATA.ome.xml":
+                setid_target = [row_full_path, row_name]
             rows.append(
                 ROW.format(
-                    PATH=f"{prefix_path}/{prefix_name}_converted/{row_path}/",
+                    PATH=f"{row_full_path}/",
                     NAME=row_name,
                     MIME=row_mime,
                 )
             )
 
+        # Add a command to update the Pixels table with path/name using old Fileset ID *before* new Fileset is created
+        fpath = setid_target[0]
+        fname = setid_target[1]
+        self.ctx.out(f"UPDATE pixels SET name = '{fname}', path = '{fpath}' where image in (select id from Image where fileset = {args.fileset_id});")
+
         self.ctx.out(
             TEMPLATE.format(
                 OLD_FILESET=args.fileset_id,
-                PREFIX=f"{prefix_path}/{prefix_name}_converted/",
+                PREFIX=f"{prefix_path}/{prefix_name}_{SUFFIX}/",
                 ROWS=",\n".join(rows),
                 REPO=self.get_uuid(args),
                 UUID=args.secret,