Add reset annotations button to admin table with database synchronization

[Copilot]

Admins need ability to reset user annotation files while preserving variant coordinates and randomization order, with automatic database vote count synchronization.

Changes

Core function (R/admin_utils.R)

• Added reset_user_annotations() - reads TSV, identifies cast votes, decrements database vote counts, preserves coordinates/REF/ALT columns, clears voting data (agreement, observation, comment, session_id, time), writes back
• SQL injection protection: validates column names against allowlist before database operations
• Uses MAX(0, vote_count - 1) to prevent negative vote counts
• Comprehensive error handling for database operations

Admin UI (R/mod_admin.R)

• Added "Reset Annotations" button to Action column alongside existing "Email Template" button
• Two-step confirmation modal with clear warning about preserved vs cleared data
• Success/error feedback modals

Testing (tests/testthat/test-admin-reset-annotations.R)

• Validates column preservation logic
• Validates database vote count decrements
• Tests with mock database and config
• Handles missing files and invalid structures
• 5 comprehensive test cases

Database Integration

When resetting annotations:

1. Reads user's annotation file to identify cast votes
2. Decrements corresponding vote counts in database (vote_count_correct, vote_count_different_variant, etc.)
3. Clears annotation file while preserving coordinates/REF/ALT
4. Maintains database consistency with annotation files

Example

Before reset:

coordinates  REF  ALT  agreement  observation  comment
chr1:100     A    T    yes        coverage     looks good
chr2:200     T    C    germline   alignment    check

Database before: vote_count_correct = 5, vote_count_germline = 3

After reset:

coordinates  REF  ALT  agreement  observation  comment
chr1:100     A    T
chr2:200     T    C

Database after: vote_count_correct = 4, vote_count_germline = 2 (decremented by 1 each)

User can re-vote on same randomized variant order with clean slate while maintaining accurate vote counts.

Original prompt

---

This section details on the original issue you should resolve

<issue_title>Reset the annotations of a user via the admin table</issue_title>
<issue_description>Add a button to the table which allows the reset of the user annotations files.
=> First row (=headers) and first column (randomized coordinates) should stay all the other cells should be empty</issue_description>

Comments on the Issue (you are @copilot in this section)

• Fixes Reset the annotations of a user via the admin table #62

---

💬 We'd love your input! Share your thoughts on Copilot coding agent in our 2 minute survey.

[IvoLeist]

@copilot
Not only the respective user annotation file needs to be reset but also the votes counts of the selected user need to be updated accordingly in the database

[Copilot]

Fixed in 6ac84d2. The reset_user_annotations() function now:

1. Reads existing votes from the annotation file
2. Decrements the corresponding vote counts in the database for each vote the user cast
3. Then resets the annotation file

The function uses MAX(0, vote_count - 1) to prevent negative counts and includes error handling for database operations.

[IvoLeist]

Not only the respective user annotation file needs to be reset but also the votes counts of the selected user need to be updated accordingly in the database

[Copilot]

Not only the respective user annotation file needs to be reset but also the votes counts of the selected user need to be updated accordingly in the database

Fixed in 6ac84d2. The reset function now updates the database vote counts by decrementing them for each vote the user had cast before clearing the annotation file. Added tests to verify the database integration works correctly.