Zarr export tests

.github/workflows/omero_plugin.yml

@@ -0,0 +1,34 @@
+# Install and test and OMERO plugin e.g. a Web app, a CLI plugin or a library
+#
+# This workflow will install omero-test-infra, start an OMERO environment
+# including database, server and web deployment, configure the OMERO plugin
+# and run integration tests.
+#
+# 1. Set up the stage variable depending on the plugin. Supported stages
+# are: app, cli, scripts, lib, srv
+#
+# 2. Adjust the cron schedule as necessary
+
+name: OMERO
+on:
+  push:
+  pull_request:
+  schedule:
+    - cron: '0 0 * * 0'
+
+jobs:
+  test:
+    name: Run integration tests against OMERO
+    runs-on: ubuntu-latest
+    env:
+      STAGE: cli
+    steps:
+      - uses: actions/checkout@v2
+      - name: Checkout omero-test-infra
+        uses: actions/checkout@master
+        with:
+          repository: ome/omero-test-infra
+          path: .omero
+          ref: ${{ secrets.OMERO_TEST_INFRA_REF }}
+      - name: Build and run OMERO tests
+        run: .omero/docker $STAGE

.omeroci/env

@@ -0,0 +1 @@
+PLUGIN=zarr

src/omero_zarr/cli.py

@@ -262,7 +262,9 @@ def export(self, args: argparse.Namespace) -> None:
             if args.bf:
                 self._bf_export(image, args)
             else:
-                image_to_zarr(image, args)
+                target_dir = args.output
+                cache_dir = target_dir if args.cache_numpy else None
+                image_to_zarr(image, target_dir, cache_dir)
         elif isinstance(args.object, PlateI):
             plate = self._lookup(self.gateway, "Plate", args.object.id)
             plate_to_zarr(plate, args)

src/omero_zarr/raw_pixels.py

@@ -16,9 +16,9 @@
 from .util import open_store, print_status
 
 
-def image_to_zarr(image: omero.gateway.ImageWrapper, args: argparse.Namespace) -> None:
-    target_dir = args.output
-    cache_dir = target_dir if args.cache_numpy else None
+def image_to_zarr(
+    image: omero.gateway.ImageWrapper, target_dir: str, cache_dir: str = None
+) -> None:
 
     name = os.path.join(target_dir, "%s.zarr" % image.id)
     print(f"Exporting to {name} ({VERSION})")

test/test_export.py

@@ -0,0 +1,64 @@
+#!/usr/bin/env python
+
+#
+# Copyright (C) 2022 University of Dundee. All Rights Reserved.
+# Use is subject to license terms supplied in LICENSE.txt
+#
+# This program is free software; you can redistribute it and/or modify
+# it under the terms of the GNU General Public License as published by
+# the Free Software Foundation; either version 2 of the License, or
+# (at your option) any later version.
+#
+# This program is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+# GNU General Public License for more details.
+#
+# You should have received a copy of the GNU General Public License along
+# with this program; if not, write to the Free Software Foundation, Inc.,
+# 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
+
+"""
+   Test of the omero zarr export plugin.
+"""
+
+from pathlib import Path
+
+from ome_zarr.io import parse_url
+from ome_zarr.reader import Reader
+from omero.gateway import BlitzGateway
+from omero.testlib import ITest
+from omero_zarr.raw_pixels import image_to_zarr
+
+
+class TestZarrExport(ITest):
+    def test_export(self, tmp_path: Path) -> None:
+        dir_name = "test_export"
+        kwargs = {"sizeX": 50, "sizeY": 25, "sizeZ": 2, "sizeC": 3, "sizeT": 4}
+        export_dir = tmp_path / dir_name
+        export_dir.mkdir()
+        imgs = self.import_fake_file(**kwargs)
+
+        assert imgs is not None
+        image_id = imgs[0].id.val
+        conn = BlitzGateway(client_obj=self.client)
+        image = conn.getObject("Image", image_id)
+
+        # Do the export...
+        image_to_zarr(image, str(export_dir))
+
+        new_dirs = [str(zdir) for zdir in export_dir.iterdir()]
+        print("new_dirs", new_dirs)
+        assert len(new_dirs) == 1
+        zarr_path = new_dirs[0]
+        # Expect a new IMAGE_ID.zarr directory
+        assert zarr_path.endswith(f"{dir_name}/{image_id}.zarr")
+
+        # try to read...
+        reader = Reader(parse_url(zarr_path))
+        nodes = list(reader())
+        assert len(nodes) == 1
+
+        print("data", nodes[0].data)
+        shape = [kwargs.get("size" + dim) for dim in "TCZYX"]
+        assert nodes[0].data[0].shape == tuple(shape)