#328 - Remove annotations in a specified range

[dmnc-grdnr]

This PR adds the following convenience functions to the cas object:

• crop_sofa_string -> replaces the sofa string with a cutout of the original as specified by the index range and removes all annotations in the cas that are outside of that specified range
• remove_annotations_in_range -> removes all annoations (of one specified type) inside of the specified index range of the sofa string

The methods can be called on any cas object directly.

Tests for each function was added to test_cas.py

[reckart]

Thanks for the PR.

"Normally" (i.e. in particular in Java UIMA), the sofa is considered to be immutable once set.

Have you considered generating a new CAS that contains only the cut-out section instead of doing an in-place modification?

[dmnc-grdnr]

I didn't expect such a quick response, thanks :)
Maybe I have overlooked something, but how can you only "partially" read a CAS file or only the section of interest?
Because I don't generate the CAS files I use myself, I am looking for a way to cutout a specific part of it without having to manually modify the original CAS file.

[Copilot]

Pull Request Overview

This PR adds two convenience methods to the Cas class for managing annotations based on their position in the sofa string: cut_sofa_string_to_range and remove_in_range.

Key changes:

• cut_sofa_string_to_range: Cuts the sofa string to a specified range and removes/adjusts annotations accordingly
• remove_in_range: Removes annotations within a specified range, optionally filtered by type
• Comprehensive test coverage for both methods with different scenarios

Reviewed Changes

Copilot reviewed 2 out of 2 changed files in this pull request and generated 7 comments.

File	Description
cassis/cas.py	Adds two new methods: cut_sofa_string_to_range for cutting sofa string with annotation adjustment, and remove_in_range for removing annotations in a range
tests/test_cas.py	Adds four test functions covering different scenarios for both new methods

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[dmnc-grdnr]

I agree with most suggestions, with the exception of the issue iteration/remove (384-398). But I am, again, unsure how to proceed from here on :)

[reckart]

Thanks again :) Same as with the other PR:

• make changes
• make regular commit (no amend, no force push)

This change is a tricky one because you can have annotations that are transitively referenced through a feature of an indexed feature structure, not that themselves are not on the index. That means if you use only select_all(), you would not find them. You would have to use _find_all_fs like in the other PR to actually find those. And then the question is: if you have an annotation that is transitively referenced that would end up being outside of the document, should it be removed entirely and unlinked from its referent - or should it remain but its position be collapsed to the start or end of the sofa? Or possibly something else entirely?

[Copilot]

Pull request overview

Copilot reviewed 2 out of 2 changed files in this pull request and generated 10 comments.

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[reckart]

@zesch Do you have an opinion on this?

if you have an annotation that is transitively referenced that would end up being outside of the document, should it be removed entirely and unlinked from its referent - or should it remain but its position be collapsed to the start or end of the sofa? Or possibly something else entirely?

[zesch]

@zesch Do you have an opinion on this?

if you have an annotation that is transitively referenced that would end up being outside of the document, should it be removed entirely and unlinked from its referent - or should it remain but its position be collapsed to the start or end of the sofa? Or possibly something else entirely?

I would vote for removing it entirely.

[Copilot]

Pull request overview

Copilot reviewed 3 out of 3 changed files in this pull request and generated 7 comments.

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[Copilot]

Pull request overview

Copilot reviewed 3 out of 3 changed files in this pull request and generated 3 comments.

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[reckart]

@dmnc-grdnr ok, I have taken some executive decisions to wrap this up now - otherwise we'll ping pong this forever. Probably I should generally be more proactive of taking over and finishing up PRs.

Thanks for your contribution!