docs: Update usage_cli.rst

[KuechlerO]

Added to documentation:
After fixing submission errors, one needs to re-import the TSV file before re-submission.

Maybe also:
Update PNG displayed on https://clinvar-this.readthedocs.io/en/latest/usage_cli.html to show circling back from fix file content to clinvar-this batch import.

Summary by CodeRabbit

• Documentation
  • Updated the clinvar-this command line tool documentation for enhanced clarity on usage and workflow.
  • Expanded the error handling section to emphasize the two-step process of fixing variants and re-importing before re-submission.
  • Improved explanations in the workflow section regarding error handling and NCBI ClinVar server processing checks.

[coderabbitai]

Walkthrough

The documentation for the clinvar-this command line tool has been revised to improve clarity regarding its usage and workflow. Key updates include an expanded section on error handling, emphasizing the necessity of fixing variants and re-importing them before re-submission. The document maintains its overall structure while enhancing the workflow section to detail the steps for error resolution and submission processes. Terminology relevant to ClinVar's variant-centric approach has been preserved for user context.

Changes

File	Change Summary
docs/usage_cli.rst	Updated documentation for clinvar-this command line tool; expanded error handling section, clarified two-step process for re-importing and resubmitting variants, and enhanced workflow explanations. Overall structure retained.

Poem

In the garden of code, where changes bloom,
The clinvar-this tool sheds light in the gloom.
Fix your variants, then re-import with care,
A new payload awaits, with status to share.
With clearer paths and guidance anew,
Hop along, dear user, there's much you can do! 🐇✨

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[coderabbitai]

Actionable comments posted: 0

🧹 Outside diff range and nitpick comments (1)

docs/usage_cli.rst (1)

37-37: LGTM! Clear and important workflow clarification.

The added step clearly explains the necessary process after encountering errors, which was a critical missing piece in the workflow documentation. This aligns well with the PR's objective of improving user guidance.

Consider adding a note about potential waiting time between re-import and re-submit, similar to the existing note about server processing time. For example:

- When there are errors, fix the variants to be submitted, re-import (``clinvar-this`` will create a new payload with ``"record_status": "update"`` for each finding) and then re-submit with ``clinvar-this batch submit``.
+ When there are errors, fix the variants to be submitted, re-import (``clinvar-this`` will create a new payload with ``"record_status": "update"`` for each finding), and then re-submit with ``clinvar-this batch submit``. Note that you may need to wait briefly after re-import before re-submitting to ensure the payload is properly processed.

📜 Review details

Configuration used: CodeRabbit UI
Review profile: CHILL

📥 Commits

Files that changed from the base of the PR and between 6e9fdaf and 2594558.

📒 Files selected for processing (1)

• docs/usage_cli.rst (1 hunks)

🧰 Additional context used

🔇 Additional comments (1)

docs/usage_cli.rst (1)

Line range hint 19-21: Verify workflow diagram update.

The PR objectives mention updating the workflow diagram to show the circular path from "fix file content" back to "clinvar-this batch import". Please ensure that the referenced PNG file has been updated accordingly.