[DAR-6239][External] Fix nifti export for multi slotted items

[vvihorev]

Problem

When a multi-slot item containing multiple DICOM slots is exported as a nifti volume, only the first slot is exported.

Solution

Iterate over all slots when exporting a file. If there are more than one slot, create a separate AnnotationFile for each slot, thus generating a separate output volume for each mask in each slot.

Changelog

Fix nifti export broken for multi-slotted items

[linear]

DAR-6239 BUG: Nifti export is broken for multi-slotted items

[Copilot]

Pull Request Overview

This PR fixes the issue with nifti export for multi-slotted items by iterating over all DICOM slots and generating a separate output volume for each mask.

• Updated test fixtures to include a multi-slotted dicom payload in e2e_tests/objects.py.
• Added proper error handling for export responses in e2e_tests/helpers.py and new tests for multi-slotted items in the CLI tests.
• Modified JSON parsing (_parse_darwin_v2) in darwin/utils/utils.py to support an additional slot_index parameter and adjust filenames accordingly.

Reviewed Changes

Copilot reviewed 11 out of 12 changed files in this pull request and generated no comments.

Show a summary per file

File	Description
e2e_tests/objects.py	Added multi_slotted_dicom payload with two DICOM slots for testing.
e2e_tests/helpers.py	Added response.raise_for_status() to ensure export errors are caught immediately.
e2e_tests/cli/test_import.py	Added a new test for importing annotations from multi-slotted DICOM items.
e2e_tests/cli/test_convert.py	Extended test cases to cover new nifti multislot conversion.
darwin/utils/utils.py	Modified parse_darwin_json and _parse_darwin_v2 to support per-slot parsing and adjusted filename generation.

Files not reviewed (1)

• e2e_tests/data/import/multi_slotted_annotations_with_dicom_slots/multi_slotted_dicom_item.json: Language not supported

Comments suppressed due to low confidence (1)

darwin/utils/utils.py:612

• [nitpick] In _parse_darwin_v2, annotations are filtered by checking if annotation.slot_names[0] equals the current slot's name. This may unintentionally omit annotations that are associated with multiple slots; please verify that this behavior is intentional.

annotations = [

[umbertoDifa]

LGTM!