Enable to download entire CPTAC dataset

[ypriverol]

Summary by CodeRabbit

• New Features

  • Made --file-type optional for PDC/CPTAC file downloads; omitting it now downloads all available file types for a study.

• Documentation

  • Added comprehensive "Download CPTAC/PDC files" documentation section with usage examples for downloading all types, filtering by file type, batching studies, resuming downloads, and configuring parallel threads and retries.
  • Updated README with new download examples.

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[coderabbitai]

Caution

Review failed

The pull request is closed.

ℹ️ Recent review info

⚙️ Run configuration

Configuration used: defaults

Review profile: CHILL

Plan: Pro

Run ID: 5d24d106-ee0a-474d-ae59-39077b8e3fac

📥 Commits

Reviewing files that changed from the base of the PR and between 6d9dfc8 and 2cb7a90.

📒 Files selected for processing (7)

• README.md
• docs/usage.md
• pridepy/pdc/client.py
• pridepy/pdc/downloader.py
• pridepy/pridepy.py
• pridepy/tests/test_pdc_client.py
• pridepy/tests/test_pdc_downloader.py

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📝 Walkthrough

Walkthrough

This PR enables users to download all file types for a PDC/CPTAC study by making the file_type parameter optional. The change flows through the client API, request parsing, downloader orchestration, and CLI, with updated documentation and comprehensive test coverage.

Changes

Optional file_type support for PDC/CPTAC downloads

Layer / File(s)	Summary
Optional file_type API contract pridepy/pdc/client.py	PDCDownloadRequest.file_type, fetch_study_files(), and refresh_signed_url() now accept Optional[str], allowing callers to omit file-type filtering.
CSV parsing and request generation pridepy/pdc/client.py	parse_download_requests() treats missing or empty file-type values in CSV rows as None instead of raising errors, enabling partial per-row specifications.
Download orchestration and plumbing pridepy/pdc/downloader.py	Type aliases, helper function signatures, and PDCDownloadOptions.file_type all updated to propagate Optional[str]. Failure metadata defaults label to "all" when file_type is unset.
User-facing documentation and CLI help README.md, docs/usage.md, pridepy/pridepy.py	CLI help text clarified; README example and comprehensive docs/usage.md section added covering download patterns, filtering options, resumption, checksums, parallelization, and retries.
Test coverage for optional file_type pridepy/tests/test_pdc_client.py, pridepy/tests/test_pdc_downloader.py	New tests validate plain accessions, CSV without file-type column, mixed file-type rows, and explicit file_type=None behavior; removed assertions that file-type was required.

Estimated code review effort

🎯 3 (Moderate) | ⏱️ ~20 minutes

Possibly related PRs

• PRIDE-Archive/pridepy#110: The main CPTAC/PDC download implementation that this PR extends to support optional file-type filtering.

Suggested labels

Review effort 3/5

Suggested reviewers

• selvaebi
• chakrabandla

Poem

A rabbit hops through files with cheer, 🐰
Optional types now crystal clear!
Download all files, or filter tight—
No file-type means "get every bite!" 🥕
The PDC path shines ever bright.

✨ Finishing Touches

📝 Generate docstrings

• Create stacked PR
• Commit on current branch

🧪 Generate unit tests (beta)

• Create PR with unit tests
• Commit unit tests in branch dev

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