More remote CRUD

[normanrz]

Description:

• Added RemoteDataset.add_layer_as_ref, RemoteLayer.add_mag_as_ref, RemoteAttachments.add_attachment_as_ref, RemoteAttachments.delete_attachment, RemoteAttachment.rename_attachment, Attachments.rename_attachments.

Issues:

• implements Allow more dataset CRUD via API webknossos#9375

Todos:

Make sure to delete unnecessary points or to check all before merging:

• Updated Changelog
• Updated Documentation
• Added / Updated Tests

[gemini-code-assist]

Summary of Changes

Hello, I'm Gemini Code Assist¹! I'm currently reviewing this pull request and will post my feedback shortly. In the meantime, here's a summary to help you and other reviewers quickly get up to speed!

This pull request significantly expands the remote data management capabilities of the WEBKNOSSOS CLI and underlying libraries. It streamlines workflows by allowing direct conversion and upload of image data, as well as remote downsampling and upsampling of datasets. These changes reduce the need for manual data transfers and local processing, making it easier to work with WEBKNOSSOS datasets hosted on remote servers.

Highlights

• Enhanced CLI for Remote Operations: The webknossos convert, webknossos downsample, and webknossos upsample CLI commands now support direct interaction with remote WEBKNOSSOS servers, allowing for conversion and processing of datasets directly on the platform.
• Direct Upload during Conversion: A new --upload flag has been added to the webknossos convert command, enabling users to convert local image stacks into WEBKNOSSOS datasets and upload them directly to a specified server in a single step.
• Remote Dataset Composition: New API endpoints and client methods were introduced to allow for composing remote layers, magnifications, and attachments by reference, facilitating more flexible remote data management.
• Improved Documentation and Error Handling: The documentation for CLI commands has been updated to reflect the new remote capabilities and options. Internal error handling for dataset and layer operations, particularly around magnification existence and renaming, has been refined.

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Changelog

• webknossos/Changelog.md
  • The webknossos convert command now accepts a --upload flag, to upload the converted dataset to WEBKNOSSOS. In that case, the target path is not required anymore. [Remote convert cli #1433]
  • The webknossos downsample and webknossos upsample commands now work with remote datasets on WEBKNOSSOS. [Remote convert cli #1433]

Activity

• The pull request description indicates initial development and standard checks, including an unspecified 'abc' task and a fix for an issue.
• The author has listed several standard tasks to be completed before merging, such as updating the changelog, documentation, and tests, and considering adding examples.

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[gemini-code-assist]

Code Review

This pull request significantly enhances the remote CRUD capabilities of the library, allowing users to convert and upload datasets in one step, and to downsample/upsample remote datasets directly. The documentation has been updated accordingly, which is great for usability. The refactoring to use a common open_dataset utility is a good improvement for code maintainability.

I've found a couple of potential issues:

• A likely copy-paste error in an API client route for adding a magnification.
• A redundant API call after renaming an attachment, which could impact performance.

Overall, this is a solid contribution with valuable new features. Addressing the mentioned points will make it even better.

[github-actions]

☂️ Python Coverage

current status: ✅

Overall Coverage

Lines	Covered	Coverage	Threshold	Status
11342	9590	85%	80%	🟢

New Files

No new covered files...

Modified Files

File	Coverage	Status
webknossos/webknossos/client/api_client/_abstract_api_client.py	91%	🟢
webknossos/webknossos/client/api_client/models.py	100%	🟢
webknossos/webknossos/client/api_client/wk_api_client.py	87%	🟢
webknossos/webknossos/dataset/abstract_dataset.py	93%	🟢
webknossos/webknossos/dataset/dataset.py	78%	🟢
webknossos/webknossos/dataset/layer/_init_.py	100%	🟢
webknossos/webknossos/dataset/layer/abstract_layer.py	94%	🟢
webknossos/webknossos/dataset/layer/remote_layer.py	87%	🟢
webknossos/webknossos/dataset/layer/segmentation_layer/init.py	100%	🟢
webknossos/webknossos/dataset/layer/segmentation_layer/attachments/attachments.py	85%	🟢
webknossos/webknossos/dataset/remote_dataset.py	82%	🟢
TOTAL	91%	🟢

updated for commit: fa20bef by action🐍