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Merged
ypriverol merged 1 commit into from
Oct 16, 2025
Merged

add to README #68

ypriverol merged 1 commit into from
Oct 16, 2025

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@ypriverol
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@ypriverol ypriverol commented Oct 16, 2025 •
edited by coderabbitai bot
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PR Type

Documentation

Description

  • Added documentation for downloading raw files from ProteomeXchange datasets

  • Included usage example with command-line syntax and output directory

  • Documented FTP/HTTP(S) download resolution and resume capabilities

Diagram Walkthrough

flowchart LR
  A["ProteomeXchange Dataset"] --> B["pridepy download-px-raw-files"]
  B --> C["Resolve PX XML"]
  C --> D["Download via FTP/HTTP(S)"]
  D --> E["Local Files with Resume Support"]
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File Walkthrough
Relevant files
Documentation
README.md
Document ProteomeXchange raw file download feature             

README.md

  • Added new section documenting ProteomeXchange raw file download
    functionality
  • Included command-line example with -a and -o flags
  • Documented automatic protocol resolution (FTP/HTTP) and resume support
 +11/-0   

Summary by CodeRabbit

Release Notes

  • Documentation
    • Added new documentation section describing how to download all raw files from a ProteomeXchange accession, including protocol handling details (FTP with HTTP(S) fallback), resume and skip-if-already-downloaded support, and example CLI commands.

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coderabbitai bot commented Oct 16, 2025 •
edited
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Walkthrough

README.md is updated with a new documentation subsection explaining how to download all raw files from a ProteomeXchange accession using a dedicated command, including details on protocol selection (FTP preferred, HTTP(S) fallback) and support for resuming or skipping already-downloaded files.

Changes

Cohort / File(s) Summary
Documentation addition
README.md		 Added new subsection "Downloading raw files from ProteomeXchange (PX)" describing command usage, protocol handling, and resume/skip behavior for bulk raw file downloads.

Estimated code review effort

🎯 1 (Trivial) | ⏱️ ~5 minutes

Poem

🐰 A tale of raw files now told,
In README's pages of gold,
ProteomeXchange downloads with grace,
FTP first in this helpful new place! 📥✨

Pre-merge checks and finishing touches

❌ Failed checks (1 inconclusive)
Check name Status Explanation Resolution
Title Check ❓ Inconclusive The title “add to README” is too vague and generic to convey the key change, which is adding a new ProteomeXchange raw file download subsection. It does not clearly summarize the main content of the pull request. Please update the title to a concise but specific description of the change, for example “Add ProteomeXchange raw file download instructions to README” so that it clearly reflects the main addition.
✅ Passed checks (2 passed)
Check name Status Explanation
Description Check ✅ Passed Check skipped - CodeRabbit’s high-level summary is enabled.
Docstring Coverage ✅ Passed No functions found in the changes. Docstring coverage check skipped.
✨ Finishing touches
🧪 Generate unit tests (beta)
  • Create PR with unit tests
  • Post copyable unit tests in a comment
  • Commit unit tests in branch dev
📜 Recent review details

Configuration used: CodeRabbit UI

Review profile: CHILL

Plan: Pro

📥 Commits

Reviewing files that changed from the base of the PR and between 03fd460 and 1b37309.

📒 Files selected for processing (1)
  • README.md (1 hunks)
🧰 Additional context used
🪛 markdownlint-cli2 (0.18.1)
README.md

92-92: Dollar signs used before commands without showing output

(MD014, commands-show-output)

⏰ Context from checks skipped due to timeout of 90000ms. You can increase the timeout in your CodeRabbit configuration to a maximum of 15 minutes (900000ms). (2)
  • GitHub Check: build
  • GitHub Check: build
🔇 Additional comments (1)
README.md (1)

87-97: Clear and helpful addition.

Nice job outlining the PX command flow and defaults—it mirrors the CLI behaviour and gives users exactly what they need.

Thanks for using CodeRabbit! It's free for OSS, and your support helps us grow. If you like it, consider giving us a shout-out.

❤️ Share

Comment @coderabbitai help to get the list of available commands and usage tips.

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qodo-code-review bot commented Oct 16, 2025

PR Compliance Guide 🔍

Below is a summary of compliance checks for this PR:

Security Compliance
🟢
No security concerns identified No security vulnerabilities detected by AI analysis. Human verification advised for critical code.
Ticket Compliance
⚪
🎫 No ticket provided 
- [ ] Create ticket/issue <!-- /create_ticket --create_ticket=true -->

</details></td></tr>
Codebase Duplication Compliance
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Codebase context is not defined

Follow the guide to enable codebase context checks.

Custom Compliance
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No custom compliance provided

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Compliance status legend 🟢 - Fully Compliant
🟡 - Partial Compliant
🔴 - Not Compliant
⚪ - Requires Further Human Verification
🏷️ - Compliance label

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qodo-code-review bot commented Oct 16, 2025

PR Code Suggestions ✨

Explore these optional code suggestions:

CategorySuggestion                                                                                                                                    Impact
General
Document how to force file re-downloads

Document how a user can force a re-download of a file, since skipping
already-downloaded files is the default behavior.

README.md [96]

-- Resume and skip-if-already-downloaded are supported by default.
+- Resume and skip-if-already-downloaded are supported by default. To force a re-download, you must first delete the local file.
  • Apply / Chat
Suggestion importance[1-10]: 6

__

Why: This suggestion improves the documentation's completeness by addressing a common user scenario (forcing a re-download), which is important given the default "skip if exists" behavior.

Low
Clarify contradictory command usage documentation

Clarify the documentation for the download-px-raw-files command, as it states
only an accession is needed while the example command includes an additional -o
flag.

README.md [89-93]

-You can download all raw files referenced by a ProteomeXchange dataset by passing only the accession:
+You can download all raw files referenced by a ProteomeXchange dataset by providing its accession:
 
 ```bash
 $ pridepy download-px-raw-files -a PXD039236 -o /Users/yourname/Downloads/foldername/


- [ ] **Apply / Chat** <!-- /improve --apply_suggestion=1 -->


<details><summary>Suggestion importance[1-10]: 5</summary>

__

Why: The suggestion correctly identifies a contradiction in the documentation that could confuse users, improving the clarity and usability of the instructions.


</details></details></td><td align=center>Low

</td></tr>
<tr><td align="center" colspan="2">

- [ ] More <!-- /improve --more_suggestions=true -->

</td><td></td></tr></tbody></table>

@ypriverol ypriverol merged commit 8410afe into master Oct 16, 2025
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@ypriverol