Implement remote table registration calls by DavidStirling · Pull Request #28 · glencoesoftware/omero2pandas

DavidStirling · 2025-04-11T11:37:38Z

This PR adds the second stage of remote table registration intended for use with the omero-plus API.

Changes as follows:

Remote table registration can now be performed with just omero2pandas. Usage docs included.
Registration has been broken up into multiple functions to permit just creating the tiledb and not registering as has been done with some test workflows. This is now accessible at omero2pandas.remote.create_tiledb (was register_table)
Had to fix Refactor handling of existing connection objects #21 to get the new system to play nicely with existing omero client objects
omero-py already requires requests so no new dependencies were needed
Remote registration needed a CSRF token to interact with the API, so we first make a call to get the token and then send our registration request. This is a bit more fragile than I'd like it to be, so I'd be happy to hear of alternative approaches.

kkoz

In the README, we should decide on whether or not we're capitalizing TileDB

README.md

kkoz · 2025-04-15T18:31:46Z

README.md

+validation process to ensure that the table seen by the server is the same one that 
+the user has requested the API to register. This is achieved by writing a "SecretToken" 
+key to the tiledb array metadata. The tiledb file seen by the server must have a key 
+matching the one provided in the registration call managed by omero2pandas.


The point of the SecretToken is not really validation - it's to ensure the client attempting to register a file has read access to that file.

README.md

omero2pandas/remote.py

kkoz · 2025-04-15T18:55:44Z

omero2pandas/remote.py

-    write_path = str(write_path)
+    output_path = str(output_path)
    # Use a default chunk size if not set
    chunk_size = chunk_size or 1000


Is the default chunk_size in the function definition sufficient here?

Functions above this one permit explicitly supplying chunk_size=None which is interpreted as "determine automatically". For most modes this process involves inspecting the input table to figure out how many rows the API can process at once, but this is largely irrelevant for local TileDB conversion.

It'd be possible to resolve this in the calls to create_tiledb by not passing chunk_size at all if it was None, but having to unpack this created more mess than just having a fallback here.

kkoz · 2025-04-15T19:06:40Z

omero2pandas/remote.py

+    content = _check_response(result)
+    ann_id = content["data"]["file_annotation"]
+    LOGGER.info(f"Registered table successfully as FileAnnotation {ann_id}")
+    return ann_id


Is there a reason we return the annotation ID instead of the Original File ID? In most places we use Original File ID for table identification.

We use the annotation ID in omero table register

We also do this elsewhere in the library. This was chosen on the basis that getting an OriginalFile given the FileAnnotation is easier than figuring out the FileAnnotation starting from the OriginalFile.

Co-authored-by: Kevin Kozlowski <kevin@glencoesoftware.com>

kkoz · 2025-04-17T13:36:12Z

Testing:

First I attempted to run the following:

    client = omero.client('localhost', 4064)
    df = pd.read_csv(csv_path)
    res = omero2pandas.upload_table(
        df, 'o2p Test Table',
        local_path='/home/kevin/testdata/tables/o2ptest.tiledb',
        omero_connector=client,
        username='kevin', password='mypass')
    print(res)

And got

Generating TileDB file...:   0%|                                                                                                                      | 6/? rows, 00:00 
Traceback (most recent call last):
  File "/home/kevin/code/scripts/o2ptest.py", line 27, in <module>
    o2ptest()
  File "/home/kevin/omero/server/omerovenv/lib/python3.10/site-packages/click/core.py", line 1161, in __call__
    return self.main(*args, **kwargs)
  File "/home/kevin/omero/server/omerovenv/lib/python3.10/site-packages/click/core.py", line 1082, in main
    rv = self.invoke(ctx)
  File "/home/kevin/omero/server/omerovenv/lib/python3.10/site-packages/click/core.py", line 1697, in invoke
    return _process_result(sub_ctx.command.invoke(sub_ctx))
  File "/home/kevin/omero/server/omerovenv/lib/python3.10/site-packages/click/core.py", line 1443, in invoke
    return ctx.invoke(self.callback, **ctx.params)
  File "/home/kevin/omero/server/omerovenv/lib/python3.10/site-packages/click/core.py", line 788, in invoke
    return __callback(*args, **kwargs)
  File "/home/kevin/code/scripts/o2ptest.py", line 19, in testclient
    res = omero2pandas.upload_table(
  File "/home/kevin/code/omero2pandas/omero2pandas/__init__.py", line 245, in upload_table
    ann_id = create_remote_table(source, table_name, local_path,
  File "/home/kevin/code/omero2pandas/omero2pandas/remote.py", line 47, in create_remote_table
    ann_id = register_table(connector, remote_path, table_name, links, token,
  File "/home/kevin/code/omero2pandas/omero2pandas/remote.py", line 100, in register_table
    raise ValueError("Unknown server? This should never happen!")
ValueError: Unknown server? This should never happen!

Seems supplying your own omero.client is not supported here - should it be?

I then attempted the following:

And got the following error:

requests.exceptions.ConnectionError: HTTPSConnectionPool(host='localhost', port=443): Max retries exceeded with url: /api/v0/token (Caused by NewConnectionError('<urllib3.connection.HTTPSConnection object at 0x74dca0518e50>: Failed to establish a new connection: [Errno 111] Connection refused'))

This is almost certainly because my local install is not configured for https. Do we want to have an option to support this or are we comfortable only supporting https-enabled servers?

I proceeded with my testing by replacing https with http in line 101 or remote.py

However, I then got the following error:

ERROR:omero2pandas.remote:Request returned HTTP code 400: Badly formed request body
Traceback (most recent call last):
  File "/home/kevin/code/scripts/o2ptest.py", line 39, in <module>
    o2ptest()
  File "/home/kevin/omero/server/omerovenv/lib/python3.10/site-packages/click/core.py", line 1161, in __call__
    return self.main(*args, **kwargs)
  File "/home/kevin/omero/server/omerovenv/lib/python3.10/site-packages/click/core.py", line 1082, in main
    rv = self.invoke(ctx)
  File "/home/kevin/omero/server/omerovenv/lib/python3.10/site-packages/click/core.py", line 1697, in invoke
    return _process_result(sub_ctx.command.invoke(sub_ctx))
  File "/home/kevin/omero/server/omerovenv/lib/python3.10/site-packages/click/core.py", line 1443, in invoke
    return ctx.invoke(self.callback, **ctx.params)
  File "/home/kevin/omero/server/omerovenv/lib/python3.10/site-packages/click/core.py", line 788, in invoke
    return __callback(*args, **kwargs)
  File "/home/kevin/code/scripts/o2ptest.py", line 31, in testcreds
    res = omero2pandas.upload_table(
  File "/home/kevin/code/omero2pandas/omero2pandas/__init__.py", line 245, in upload_table
    ann_id = create_remote_table(source, table_name, local_path,
  File "/home/kevin/code/omero2pandas/omero2pandas/remote.py", line 47, in create_remote_table
    ann_id = register_table(connector, remote_path, table_name, links, token,
  File "/home/kevin/code/omero2pandas/omero2pandas/remote.py", line 131, in register_table
    content = _check_response(result)
  File "/home/kevin/code/omero2pandas/omero2pandas/remote.py", line 148, in _check_response
    response.raise_for_status()
  File "/home/kevin/omero/server/omerovenv/lib/python3.10/site-packages/requests/models.py", line 1024, in raise_for_status
    raise HTTPError(http_error_msg, response=self)
requests.exceptions.HTTPError: 400 Client Error: Bad Request for url: http://localhost/omero_plus/api/v0/table?bsession=e5b745c0-aed6-4c5a-b73a-f609e888c7f7

Not sure what's happening here - I'll look into it a bit more.

There was also some unexpected naming behavior I encountered during testing.
The first time you run upload_table as I did above, the TileDB is created at local_path. However, running the exact same command again will result in another TileDB getting written inside the original one, since write_path.is_dir() now evaluates to true.
https://github.com/glencoesoftware/omero2pandas/pull/28/files#diff-66280cb8c4d95664d7c51ed98c0b88b22f42efa4244f1abfe2123a5e3c61f704R36
This is probably not the behavior clients will be expecting - I would guess either the operation should fail if anything is found at local_path or the TileDB should be overwritten.

kkoz · 2025-04-17T14:09:25Z

It looks like the BadRequest error was because there were no targets specified in the request body. There should probably be a better error message from the API, but in the meantime we should require links here.

kkoz · 2025-04-17T14:16:18Z

With a link provided the registration works, however the table headers are not what I was expecting:

kkoz · 2025-04-17T14:17:38Z

With a link provided the registration works, however the table headers are not what I was expecting:

This may be an issue with the csv being formatted for import with omero-metadata. I'll check

kkoz · 2025-04-17T14:22:13Z

Confirmed this was the issue. I don't think most users would expect this tool to work with the omero-metadata stuff in the csv so don't worry about this.

DavidStirling · 2025-04-17T14:24:11Z

Seems supplying your own omero.client is not supported here - should it be?

Should be fixed now, handling the different client objects we may get is tricky so I'm glad I put a check in there 😄

This is almost certainly because my local install is not configured for https. Do we want to have an option to support this or are we comfortable only supporting https-enabled servers?

Path parsing in Python without adding dependencies is more clunky than I'd like, so for now I'd hard-coded in https as a requirement. If we want to support http we could stick in an extra argument or something? Happy to hear ideas, especially those that don't involve urllib.

There was also some unexpected naming behavior I encountered during testing.
The first time you run upload_table as I did above, the TileDB is created at local_path. However, running the exact same command again will result in another TileDB getting written inside the original one, since write_path.is_dir() now evaluates to true.

Nice catch, I missed that TileDBs are seen as directories by the os. For convenience I'd wanted to let the user supply folder names instead of full paths to dump the TileDB based on the table name instead. Pushed a tweak that should catch the TileDB nesting issue, but if that's not sufficient we can require absolute paths to .tiledb files as the inputs.

Support for an overwrite arg is a good idea. IMO this would probably be worth it's own PR as the download methods would benefit here, it's not exclusive to remote mode.

It looks like the BadRequest error was because there were no targets specified in the request body. There should probably be a better error message from the API, but in the meantime we should require links here.

Fixed

Confirmed this was the issue. I don't think most users would expect this tool to work with the omero-metadata stuff in the csv so don't worry about this.

👍

kkoz

Error handling and functionality working as expected.

mabruce · 2025-04-30T19:52:02Z

I'm getting that same Bad Request for url ... error, but can't seem to find a workable combination of parameters.

df = pd.DataFrame({'col1': [1, 2], 'col2': [3, 4]})
omero2pandas.upload_table(df, "Table", parent_type='Image', parent_id=36445,
                          local_path="table.tiledb",
                          remote_path="/data/marc/tables/table1.tiledb")

ERROR:omero2pandas.remote:Request returned HTTP code 400: Failed to open file at given URI
Traceback (most recent call last):
  File "C:\Users\Marc\Desktop\remote_table.py", line 5, in <module>
    omero2pandas.upload_table(df, "Table", parent_type='Image', parent_id=36445,
  File "C:\Users\Marc\Desktop\remote_csv.venv\lib\site-packages\omero2pandas\__init__.py", line 245, in upload_table
    ann_id = create_remote_table(source, table_name, local_path,
  File "C:\Users\Marc\Desktop\remote_csv.venv\lib\site-packages\omero2pandas\remote.py", line 48, in create_remote_table
    ann_id = register_table(connector, remote_path, table_name, links, token,
  File "C:\Users\Marc\Desktop\remote_csv.venv\lib\site-packages\omero2pandas\remote.py", line 132, in register_table
    content = _check_response(result)
  File "C:\Users\Marc\Desktop\remote_csv.venv\lib\site-packages\omero2pandas\remote.py", line 149, in _check_response
    response.raise_for_status()
  File "C:\Users\Marc\Desktop\remote_csv.venv\lib\site-packages\requests\models.py", line 1024, in raise_for_status
    raise HTTPError(http_error_msg, response=self)
requests.exceptions.HTTPError: 400 Client Error: Bad Request for url: https://[url]/omero_plus/api/v0/table?bsession=[uuid]

I've tried adding links=[('Image', 36445)] but get the same error.

Auth here is through omero-user-token.

DavidStirling · 2025-04-30T20:01:57Z

I'm getting that same Bad Request for url ... error, but can't seem to find a workable combination of parameters.

df = pd.DataFrame({'col1': [1, 2], 'col2': [3, 4]})
omero2pandas.upload_table(df, "Table", parent_type='Image', parent_id=36445,
                          local_path="table.tiledb",
                          remote_path="/data/marc/tables/table1.tiledb")

@mabruce It looks like you're trying to save to table.tiledb locally but register table1.tiledb on the server side?

mabruce · 2025-04-30T20:08:04Z

Yes, my assumption was that this would work like with ROI_Converter_NGFF --server_directory where you could run the conversion on your local machine (telling OMERO where to find it later) and then move the data to its final location. Would this approach be expected to work with remote.create_tiledb + remote.register_table?

DavidStirling · 2025-04-30T20:09:36Z

Yes, you'd have to perform the steps individually to achieve that workflow. The wrapper is primarily intended for scenarios where storage is mounted on both the client and server machines.

mabruce

Successfully registered a table "remotely" via symlinks to destination folder on server.

DavidStirling added 2 commits April 11, 2025 11:54

Implement remote table registration calls

57b3d3b

Type check create_tiledb path input

1b24a61

DavidStirling requested review from erindiel, kkoz, mabruce and sbesson and removed request for sbesson April 11, 2025 11:37

kkoz requested changes Apr 15, 2025

View reviewed changes

DavidStirling and others added 4 commits April 16, 2025 08:57

Apply suggestions from code review

334aac3

Co-authored-by: Kevin Kozlowski <kevin@glencoesoftware.com>

Make table_name required and validate in main call

c342667

Drop unnecessary file check

0997433

Clarify SecretToken wording

a517608

Populate server info when constructing connectors from existing clients

8e0d0db

Check target dir is not a tiledb if generating file name automatically

c79cca9

Make OMERO link targets mandatory

7bfb9dd

kkoz approved these changes Apr 17, 2025

View reviewed changes

mabruce approved these changes May 1, 2025

View reviewed changes

sbesson merged commit ef09991 into glencoesoftware:main May 20, 2025
1 check passed

Conversation

DavidStirling commented Apr 11, 2025

Uh oh!

kkoz left a comment

Choose a reason for hiding this comment

Uh oh!

Uh oh!

Uh oh!

Uh oh!

kkoz Apr 15, 2025

Choose a reason for hiding this comment

Uh oh!

Uh oh!

Uh oh!

Uh oh!

Uh oh!

kkoz Apr 15, 2025

Choose a reason for hiding this comment

Uh oh!

DavidStirling Apr 16, 2025

Choose a reason for hiding this comment

Uh oh!

kkoz Apr 15, 2025

Choose a reason for hiding this comment

Uh oh!

mabruce Apr 15, 2025 • edited Loading Uh oh! There was an error while loading. Please reload this page.

Uh oh!

Choose a reason for hiding this comment

Uh oh!

DavidStirling Apr 16, 2025

Choose a reason for hiding this comment

Uh oh!

kkoz commented Apr 17, 2025

Uh oh!

kkoz commented Apr 17, 2025

Uh oh!

kkoz commented Apr 17, 2025

Uh oh!

kkoz commented Apr 17, 2025

Uh oh!

kkoz commented Apr 17, 2025

Uh oh!

DavidStirling commented Apr 17, 2025

Uh oh!

kkoz left a comment

Choose a reason for hiding this comment

Uh oh!

mabruce commented Apr 30, 2025

Uh oh!

DavidStirling commented Apr 30, 2025

Uh oh!

mabruce commented Apr 30, 2025

Uh oh!

DavidStirling commented Apr 30, 2025 • edited Loading Uh oh! There was an error while loading. Please reload this page.

Uh oh!

Uh oh!

mabruce left a comment • edited Loading Uh oh! There was an error while loading. Please reload this page.

Uh oh!

Choose a reason for hiding this comment

Uh oh!

Uh oh!

Reviewers

Assignees

Labels

Projects

Milestone

Development

Uh oh!

4 participants

mabruce Apr 15, 2025 •

edited

Loading

DavidStirling commented Apr 30, 2025 •

edited

Loading

mabruce left a comment •

edited

Loading