Merge pull request #17 from will-moore/alt_store_bfoptions

Alt store bfoptions

README.rst

@@ -21,17 +21,21 @@ To create sql containing required functions and run it:
 
 To generate sql and create the symlinks from the ManagedRepository to the NGFF data for a
 specified Fileset ID:
+The clientpath is used as the basis for the clientpath for each file in the Fileset. If omitted then
+the clientpath is 'unknown'. When writing .zarr.bfoptions into the ManagedRepository alongside the
+symlink to fileset.zarr, the clientpath will be added to bfoptions as `omezarr.alt_store`, allowing
+ZarrReader to read directly from that source.
 
 ::
 
-    $ omero mkngff sql --symlink_repo /OMERO/ManagedRepository --secret=secret --bfoptions 1234 /path/to/fileset.zarr > myNgff.sql
+    $ omero mkngff sql --symlink_repo /OMERO/ManagedRepository --secret=secret --bfoptions --clientpath=https://url/to/fileset.zarr 1234 /path/to/fileset.zarr > myNgff.sql
     $ psql -U omero -d idr -h $DBHOST -f myNgff.sql
 
-To ONLY perform the symlink creation (and optionally create fileset.zarr.bfoptions)
+To ONLY perform the symlink creation (and optionally create fileset.zarr.bfoptions with clientpath as above)
 
 ::
 
-    $ omero mkngff symlink /OMERO/ManagedRepository 1234 /path/to/fileset.zarr --bfoptions
+    $ omero mkngff symlink /OMERO/ManagedRepository 1234 /path/to/fileset.zarr --bfoptions --clientpath=https://url/to/fileset.zarr
 
 
 To ONLY create fileset.zarr.bfoptions

src/omero_mkngff/__init__.py

@@ -197,6 +197,10 @@ def _configure(self, parser: Parser) -> None:
             "--bfoptions", action="store_true", help="Create data.zarr.bfoptions file"
         )
         symlink.add_argument("--fs_suffix", default="_mkngff", help=FS_SUFFIX_HELP)
+        symlink.add_argument(
+            "--clientpath",
+            help=("Adds omezarr.alt_store=clientpath/path/to/img.zarr to bfoptions"),
+        )
         symlink.set_defaults(func=self.symlink)
 
         bfoptions = sub.add_parser(
@@ -290,22 +294,27 @@ def sql(self, args: Namespace) -> None:
         if args.symlink_repo:
             self.create_symlink(args.symlink_repo, prefix, args.symlink_target)
             if args.bfoptions:
-                self.write_bfoptions(args.symlink_repo, prefix, args.symlink_target)
+                self.write_bfoptions(
+                    args.symlink_repo, prefix, args.symlink_target, args.clientpath
+                )
 
     def bfoptions(self, args: Namespace) -> None:
         self.suffix = "" if args.fs_suffix == "None" else args.fs_suffix
         prefix = self.get_prefix(args)
-        self.write_bfoptions(args.symlink_repo, prefix, args.symlink_target)
+        self.write_bfoptions(
+            args.symlink_repo, prefix, args.symlink_target, args.clientpath
+        )
 
     def symlink(self, args: Namespace) -> None:
         self.suffix = "" if args.fs_suffix == "None" else args.fs_suffix
         prefix = self.get_prefix(args)
         self.create_symlink(args.symlink_repo, prefix, args.symlink_target)
         if args.bfoptions:
-            self.write_bfoptions(args.symlink_repo, prefix, args.symlink_target)
+            self.write_bfoptions(
+                args.symlink_repo, prefix, args.symlink_target, args.clientpath
+            )
 
     def get_prefix(self, args):  # type: ignore
-
         conn = self.ctx.conn(args)  # noqa
         q = conn.sf.getQueryService()
         rv = q.findAllByQuery(
@@ -334,15 +343,18 @@ def get_symlink_dir(self, symlink_repo, prefix):  # type: ignore
         symlink_dir = f"{prefix_dir}{self.suffix}"
         return symlink_dir
 
-    def write_bfoptions(self, managed_repo, fsprefix, symlink_target):  # type: ignore # noqa
+    def write_bfoptions(self, managed_repo, fsprefix, symlink_target, clientpath=None):  # type: ignore # noqa
         file_path = Path(symlink_target)
         mkngff_dir = self.get_symlink_dir(managed_repo, fsprefix)
         # os.makedirs(mkngff_dir, exist_ok=True)
         zarr_path = os.path.join(mkngff_dir, file_path.name)
         bfoptions_path = f"{zarr_path}.bfoptions"
         self.ctx.err("write bfoptions to: %s" % bfoptions_path)
+        lines = ["omezarr.list_pixels=false\n", "omezarr.quick_read=true\n"]
+        if clientpath is not None:
+            lines.append("omezarr.alt_store=%s\n" % clientpath)
         with open(bfoptions_path, "w") as f:
-            f.writelines(["omezarr.list_pixels=false", "\nomezarr.quick_read=true"])
+            f.writelines(lines)
 
     def create_symlink(self, symlink_repo, prefix, symlink_target):  # type: ignore # noqa
         symlink_path = Path(symlink_target)