Add extinfo command #167

dominikl · 2025-02-25T11:40:42Z

This command will automatically set the ExternalInfo for ome.zarr images imported using the omero-zarr-pixel-buffer, if the --set option is specified. Default is to just print the ExternalInfo.

I takes the path from the Fileset "usedFiles", which is assumed to only have one entry ..../SOME.ome.zarr/OME/METADATA.ome.xml and then set the ExternalInfo lsid to the full path of the multiscale 5d image; ..../SOME.ome.zarr/0 for an image ..../SOME.ome.zarr/A/1/1 etc. for plates.

Limitations: Only works for ome.zarr imported from the filesystem.

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.

Positional Arguments:
  object                   Object in Class:ID format

Optional Arguments:
  In addition to any higher level options

  -h, --help               show this help message and exit
  --set                    Set the ExternalInfo path
  --lsid LSID              Use a specific lsid (path) (default: Determine from clientPath) (only used in combination with --set)
  --entityType ENTITYTYPE  Use a specific entityType (default: com.glencoesoftware.ngff:multiscales) (only used in combination with --set)
  --entityId ENTITYID      Use a specific entityId (default: 3) (only used in combination with --set)
  --reset                  Removes the ExternalInfo

joshmoore · 2025-02-28T14:10:38Z

💯 As a part of this I can imagine wanting to get and to reset as well.

will-moore · 2025-03-03T14:08:40Z

$ omero login
Error loading: /Users/wmoore/Desktop/ZARR/omero-cli-zarr/src/omero/plugins/zarr.py
Traceback (most recent call last):
  File "/Users/wmoore/Desktop/PY/omero-py/target/omero/cli.py", line 1677, in loadpath
    exec(f.read(), loc)
  File "<string>", line 1, in <module>
  File "/Users/wmoore/Desktop/ZARR/omero-cli-zarr/src/omero_zarr/cli.py", line 32, in <module>
    from .extinfo import external_info_str, get_extinfo, get_images, set_external_info
  File "/Users/wmoore/Desktop/ZARR/omero-cli-zarr/src/omero_zarr/extinfo.py", line 92, in <module>
    ) -> tuple[ImageWrapper, str | None, int | None]:
TypeError: unsupported operand type(s) for |: 'type' and 'NoneType'

dominikl · 2025-03-03T14:32:39Z

Interesting... is this a python version thing? I use 3.12.9.

will-moore · 2025-03-03T14:38:32Z

It could be, I'm on an old env python 3.9.15.

dominikl · 2025-03-03T14:45:32Z

Yes, looks like it's supported from 3.10 on. As we still recommend 3.9 I'll remove that stuff again.

will-moore · 2025-03-03T15:16:39Z

src/omero_zarr/extinfo.py

+            select e from ExternalInfo as e
+            where e.id = :id
+        """
+        extinfo = conn.getQueryService().findByQuery(query, params)


In think this needs to be a cross-group query findByQuery(query, params, conn.SERVICE_OPTS) otherwise you won't see it if the extinfo isn't in your default group.

This is still outstanding. Same for the other conn.getQueryService().findByQuery below too.

But I do that one line above conn.SERVICE_OPTS.setOmeroGroup("-1") , is that not enough?

Ah ok, then you have to pass conn.SERVICE_OPTS that into the function call again. Ok, i'll fix that.

will-moore · 2025-03-03T15:51:37Z

src/omero_zarr/extinfo.py

+        join fetch usedFile.originalFile as f
+        join fetch f.hasher where image.id = :id
+    """
+    fs = conn.getQueryService().findByQuery(query, params)


cross-group query here too

will-moore · 2025-03-07T14:28:56Z

src/omero_zarr/cli.py

@@ -108,6 +109,12 @@

 POLYGONS_HELP = """Export ROI Polygons on the Image or Plate in zarr format"""

+EXTINFO_HELP = """Get the ExternalInfo path of an ome.zarr image.


Get or set...

Get, because that's the default action.

will-moore · 2025-03-07T14:43:45Z

I was trying to test this on a non-zarr image, by specifying the --path but...

$ omero zarr extinfo Image:2856 --set --path test_extinfo_path
Previous session expired for will on localhost:4064
Server: [localhost:4064]
Username: [will]
Password:
Created session for will@localhost:4064. Idle timeout: 10 min. Current group: Swedlow Lab
Failed to set external info for image (2856) 438CTR_01_4_R3D_D3D.dv_1: Doesn't seem to be an ome.zarr: Users/wmoore/Desktop/images/DVs/438CTR_01_4_R3D_D3D.dv

It seems that there's something strange about --path, like it's being swallowed / overwritten somehow so that args.path was always None. Renaming this argument to anything else seemed to fix it. I suggest using lsid since that corresponds to the field in the extInfo.

dominikl · 2025-03-07T15:03:32Z

There's a check if it is a ome.zarr: https://github.com/ome/omero-cli-zarr/pull/167/files#diff-2d64f99479103ff3050c633344ddf895f61491094e9dab65218a3ec17cbfcb59R177 As that's actually only intended to be used with zarr. Otherwise it wouldn't make sense to have it as omero-cli-zarr plugin!?

will-moore · 2025-03-07T15:27:38Z

The point is that you have a --path argument for...

help="Use a specific path (default: Determine from clientPath) (only used in combination with --set)",

but it doesn't work for me. Does it work for you?

for more information, see https://pre-commit.ci

see: pytest-dev/pytest-testinfra#765

joshmoore · 2025-03-11T16:38:48Z

.pre-commit-config.yaml

    hooks:
      - id: flake8
        additional_dependencies: [
-          flake8-blind-except,


Too re-enable, we'll probably need help from @will-moore on knowing what exceptions can be thrown.

joshmoore · 2025-03-11T16:39:30Z

.pre-commit-config.yaml

          flake8-builtins,
          flake8-rst-docstrings,
-          flake8-logging-format,


This looks like it broke in Python 3.12: pytest-dev/pytest-testinfra#765

dominikl · 2025-03-12T09:22:43Z

Thanks Josh for fixing the precommit stuff! So this now suppports single image ome.zarrs, multi-series zarrs, and plates. Did I forget another use case?

will-moore · 2025-03-13T11:45:38Z

src/omero_zarr/extinfo.py

+    """
+    if extinfo is not None:
+        return (
+            f"[entityType={_checkNone(extinfo.entityType)}\n"


Minor: wondering why the [ here and ] on the line below?

ExternalInfo for image (2856) 438CTR_01_4_R3D_D3D.dv_1: [entityType=com.glencoesoftware.ngff:multiscales entityId=3 lsid=test_extinfo_path]

will-moore · 2025-03-13T12:00:04Z

When working with images that are not in your default group, you need to specify the group when saving (and use {"omero.group": "-1"} for querying, which is the default in conn.SERVICE_OPTS.

This is what I have to get --set and --reset working for such images:

+++ b/src/omero_zarr/cli.py
@@ -405,6 +405,7 @@ class ZarrControl(BaseControl):
     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 self.gateway is None:
@@ -424,7 +425,7 @@ class ZarrControl(BaseControl):
                         args.entityType,
                         int(args.entityId),
                     )
-                    img = update_service.saveAndReturnObject(img)
+                    img = update_service.saveAndReturnObject(img, {"omero.group": str(group_id)})
                     self.ctx.out(
                         f"Set ExternalInfo for image ({img.id._val}) "
                         f"{img.name._val}:\n"
@@ -438,7 +439,7 @@ class ZarrControl(BaseControl):
             elif args.reset:
                 if extinfo:
                     img.details.externalInfo = None
-                    img = update_service.saveAndReturnObject(img)
+                    img = update_service.saveAndReturnObject(img, {"omero.group": str(group_id)})
                     self.ctx.out(
                         f"Removed ExternalInfo from image "
                         f"({img.id._val}) {img.name._val}"
diff --git a/src/omero_zarr/extinfo.py b/src/omero_zarr/extinfo.py
index 52aaf1c..7c1feb2 100644
--- a/src/omero_zarr/extinfo.py
+++ b/src/omero_zarr/extinfo.py
@@ -34,7 +34,7 @@ def get_extinfo(conn: BlitzGateway, image: ImageWrapper) -> ExternalInfoI:
             where e.id = :id
         """
         conn.SERVICE_OPTS.setOmeroGroup("-1")
-        extinfo = conn.getQueryService().findByQuery(query, params)
+        extinfo = conn.getQueryService().findByQuery(query, params, conn.SERVICE_OPTS)
         return extinfo
     return None
 
@@ -64,7 +64,7 @@ def _get_path(conn: BlitzGateway, image_id: int) -> str:
         where image.id = :id
     """
     conn.SERVICE_OPTS.setOmeroGroup("-1")
-    fs = conn.getQueryService().findByQuery(query, params)
+    fs = conn.getQueryService().findByQuery(query, params, conn.SERVICE_OPTS)
     path = fs._getUsedFiles()[0]._clientPath._val
     return path

dominikl · 2025-03-13T12:30:02Z

That's odd. You have to explicitely set the omero.group for saveAndReturnObject even if there are no changes with respect to the group? But well, I can add it.

for more information, see https://pre-commit.ci

Add extinfo command

b8ae691

dominikl force-pushed the extinfo branch from d55eb01 to f01f471 Compare February 28, 2025 13:22

Add support for plates

5f3f675

dominikl force-pushed the extinfo branch from 03bde3a to 5f3f675 Compare February 28, 2025 13:30

Add set and reset options

837af45

dominikl force-pushed the extinfo branch from 8b7844d to 837af45 Compare March 3, 2025 13:43

will-moore reviewed Mar 3, 2025

View reviewed changes

Make sure query are cross groups

c7f2252

dominikl force-pushed the extinfo branch from 3ee3cca to c7f2252 Compare March 5, 2025 14:54

will-moore reviewed Mar 7, 2025

View reviewed changes

dominikl force-pushed the extinfo branch 3 times, most recently from ec042a0 to b379cdf Compare March 10, 2025 15:40

Add series support, changed path arg to lsid

e922f47

dominikl force-pushed the extinfo branch 5 times, most recently from a6c74e7 to e922f47 Compare March 11, 2025 09:15

Fix formatting and minor issues

a0e519b

dominikl force-pushed the extinfo branch from 7d4045c to a0e519b Compare March 11, 2025 10:31

Fix imports

ad4a5b2

dominikl force-pushed the extinfo branch 2 times, most recently from 3cc6c05 to ad4a5b2 Compare March 11, 2025 15:56

pre-commit-ci bot and others added 5 commits March 11, 2025 15:56

[pre-commit.ci] auto fixes from pre-commit.com hooks

4ed92ff

for more information, see https://pre-commit.ci

Update pre-commit to match ome-zarr

5900a48

Disable flake8-logging-format

0ff9b48

see: pytest-dev/pytest-testinfra#765

mypy fixes

7bcabd6

Fix flake8 errors

a65b241

joshmoore reviewed Mar 11, 2025

View reviewed changes

dominikl marked this pull request as ready for review March 11, 2025 16:52

dominikl requested a review from will-moore March 12, 2025 09:22

will-moore reviewed Mar 13, 2025

View reviewed changes

dominikl and others added 2 commits March 13, 2025 12:33

Fix group issues

543227a

[pre-commit.ci] auto fixes from pre-commit.com hooks

f862432

for more information, see https://pre-commit.ci

will-moore mentioned this pull request Mar 14, 2025

externalInfo display ome/omero-web#613

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snoopycrimecop mentioned this pull request Apr 2, 2025

Use the release/v1 branch for the PyPA action publishing to PyPI #168

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Add extinfo command #167

Add extinfo command #167

dominikl commented Feb 25, 2025 •

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dominikl commented Mar 13, 2025 •

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		@@ -108,6 +109,12 @@

		POLYGONS_HELP = """Export ROI Polygons on the Image or Plate in zarr format"""

		EXTINFO_HELP = """Get the ExternalInfo path of an ome.zarr image.

Add extinfo command #167

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Add extinfo command #167

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