Add extinfo command

.isort.cfg

@@ -1,2 +1,2 @@
 [settings]
-known_third_party = dask,numpy,ome_zarr,omero,omero_rois,omero_zarr,pytest,setuptools,skimage,zarr
+known_third_party = dask,numpy,ome_zarr,omero,omero_rois,omero_sys_ParametersI,omero_zarr,pytest,setuptools,skimage,zarr

src/omero_zarr/cli.py

@@ -29,6 +29,7 @@
 from zarr.hierarchy import open_group
 from zarr.storage import FSStore
 
+from .extinfo import external_info_str, get_extinfo, get_images, set_external_info
 from .masks import (
     MASK_DTYPE_SIZE,
     MaskSaver,
@@ -51,6 +52,7 @@
  - masks
 
 """
+
 EXPORT_HELP = """Export an image in zarr format.
 
 Using bioformats2raw
@@ -108,6 +110,12 @@
 
 POLYGONS_HELP = """Export ROI Polygons on the Image or Plate in zarr format"""
 
+EXTINFO_HELP = """Get the ExternalInfo path of an ome.zarr image.
+
+Use --set to set the external info path
+or --reset in order to remove the ExternalInfo from the image.
+"""
+
 
 def gateway_required(func: Callable) -> Callable:
     """
@@ -164,7 +172,7 @@ def _configure(self, parser: Parser) -> None:
             "--style",
             choices=("split", "labeled"),
             default="labeled",
-            help=("Choice of storage for ROIs [breaks ome-zarr]"),
+            help="Choice of storage for ROIs [breaks ome-zarr]",
         )
         polygons.add_argument(
             "--label-path",
@@ -177,8 +185,8 @@ def _configure(self, parser: Parser) -> None:
         polygons.add_argument(
             "--source-image",
             help=(
-                "Path to the multiscales group containing the source image/plate. "
-                "By default, use the output directory"
+                "Path to the multiscales group containing the source "
+                "image/plate. By default, use the output directory"
             ),
             default=None,
         )
@@ -191,7 +199,9 @@ def _configure(self, parser: Parser) -> None:
         )
         polygons.add_argument(
             "--label-name",
-            help=("Name of the array that will be stored. Ignored for --style=split"),
+            help=(
+                "Name of the array that will be stored. Ignored for " "--style=split"
+            ),
             default="0",
         )
 
@@ -204,8 +214,8 @@ def _configure(self, parser: Parser) -> None:
         masks.add_argument(
             "--source-image",
             help=(
-                "Path to the multiscales group containing the source image/plate. "
-                "By default, use the output directory"
+                "Path to the multiscales group containing the source "
+                "image/plate. By default, use the output directory"
             ),
             default=None,
         )
@@ -219,14 +229,16 @@ def _configure(self, parser: Parser) -> None:
         )
         masks.add_argument(
             "--label-name",
-            help=("Name of the array that will be stored. Ignored for --style=split"),
+            help=(
+                "Name of the array that will be stored. Ignored for " "--style=split"
+            ),
             default="0",
         )
         masks.add_argument(
             "--style",
             choices=("split", "labeled"),
             default="labeled",
-            help=("Choice of storage for ROIs [breaks ome-zarr]"),
+            help="Choice of storage for ROIs [breaks ome-zarr]",
         )
         masks.add_argument(
             "--label-bits",
@@ -249,13 +261,18 @@ def _configure(self, parser: Parser) -> None:
         export.add_argument(
             "--bf",
             action="store_true",
-            help="Use bioformats2raw on the server to export images. Requires"
-            " bioformats2raw 0.3.0 or higher and access to the managed repo.",
+            help=(
+                "Use bioformats2raw on the server to export images. Requires "
+                "bioformats2raw 0.3.0 or higher and access to the managed "
+                "repo."
+            ),
         )
         export.add_argument(
             "--bfpath",
-            help="Use bioformats2raw on a local copy of a file. Requires"
-            " bioformats2raw 0.4.0 or higher.",
+            help=(
+                "Use bioformats2raw on a local copy of a file. Requires "
+                "bioformats2raw 0.4.0 or higher."
+            ),
         )
         export.add_argument(
             "--tile_width",
@@ -270,33 +287,82 @@ def _configure(self, parser: Parser) -> None:
         export.add_argument(
             "--resolutions",
             default=None,
-            help="Number of pyramid resolutions to generate"
-            " (only for use with bioformats2raw)",
+            help=(
+                "Number of pyramid resolutions to generate "
+                "(only for use with bioformats2raw)"
+            ),
         )
         export.add_argument(
             "--max_workers",
             default=None,
-            help="Maximum number of workers (only for use with bioformats2raw)",
+            help=("Maximum number of workers (only for " "use with bioformats2raw)"),
         )
         export.add_argument(
             "object",
             type=ProxyStringType("Image"),
             help="The Image to export.",
         )
 
+        extinfo = parser.add(sub, self.extinfo, EXTINFO_HELP)
+        extinfo.add_argument(
+            "object",
+            type=ProxyStringType(),
+            help="Object in Class:ID format",
+        )
+        extinfo.add_argument(
+            "--set",
+            action="store_true",
+            help="Set the ExternalInfo path",
+        )
+        extinfo.add_argument(
+            "--zarrPath",
+            default=None,
+            help=(
+                "Use a specific path (default: Determine from "
+                "clientPath) (only used in combination with --set)"
+            ),
+        )
+        extinfo.add_argument(
+            "--entityType",
+            default="com.glencoesoftware.ngff:multiscales",
+            help=(
+                "Use a specific entityType (default: "
+                "com.glencoesoftware.ngff:multiscales) "
+                "(only used in combination with --set)"
+            ),
+        )
+        extinfo.add_argument(
+            "--entityId",
+            default="3",
+            help=(
+                "Use a specific entityId (default: 3) "
+                "(only used in combination with --set)"
+            ),
+        )
+        extinfo.add_argument(
+            "--reset",
+            action="store_true",
+            help="Removes the ExternalInfo",
+        )
+
         for subcommand in (polygons, masks, export):
             subcommand.add_argument(
-                "--output", type=str, default="", help="The output directory"
+                "--output",
+                type=str,
+                default="",
+                help="The output directory",
             )
         for subcommand in (polygons, masks):
             subcommand.add_argument(
                 "--overlaps",
                 type=str,
                 default=MaskSaver.OVERLAPS[0],
                 choices=MaskSaver.OVERLAPS,
-                help="To allow overlapping shapes, use 'dtype_max':"
-                " All overlapping regions will be set to the"
-                " max value for the dtype",
+                help=(
+                    "To allow overlapping shapes, use 'dtype_max': "
+                    "All overlapping regions will be set to the "
+                    "max value for the dtype"
+                ),
             )
 
     @gateway_required
@@ -335,6 +401,58 @@ def export(self, args: argparse.Namespace) -> None:
             plate = self._lookup(self.gateway, "Plate", args.object.id)
             plate_to_zarr(plate, args)
 
+    @gateway_required
+    def extinfo(self, args: argparse.Namespace) -> None:
+        for img, well, idx in get_images(self.gateway, args.object):
+            img = img._obj
+            group_id = img.getDetails().getGroup().id.val
+            extinfo = get_extinfo(self.gateway, img)
+            if args.set:
+                try:
+                    img = set_external_info(
+                        self.gateway,
+                        img,
+                        well,
+                        idx,
+                        args.zarrPath,
+                        args.entityType,
+                        int(args.entityId),
+                    )
+                    img = self.gateway.getUpdateService().saveAndReturnObject(img)
+                    self.ctx.out(
+                        f"Set ExternalInfo for image ({img.id._val}) "
+                        f"{img.name._val}:\n"
+                        f"{external_info_str(img.details.externalInfo)}"
+                    )
+                except Exception as e:
+                    self.ctx.err(
+                        f"Failed to set external info for image "
+                        f"({img.id._val}) {img.name._val}: {e}"
+                    )
+            elif args.reset:
+                if extinfo:
+                    img.details.externalInfo = None
+                    img = self.gateway.getUpdateService().saveAndReturnObject(img)
+                    self.ctx.out(
+                        f"Removed ExternalInfo from image "
+                        f"({img.id._val}) {img.name._val}"
+                    )
+                else:
+                    self.ctx.out(
+                        f"Image ({img.id._val}) {img.name._val} " "has no ExternalInfo"
+                    )
+            else:
+                if extinfo:
+                    self.ctx.out(
+                        f"ExternalInfo for image ({img.id._val}) "
+                        f"{img.name._val}:\n"
+                        f"{external_info_str(extinfo)}"
+                    )
+                else:
+                    self.ctx.out(
+                        f"Image ({img.id._val}) {img.name._val} has no " "ExternalInfo"
+                    )
+
     def _lookup(
         self, gateway: BlitzGateway, otype: str, oid: int
     ) -> BlitzObjectWrapper: