refactor: decompose Methods.java into focused utility classes - #90
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maxulysse wants to merge 12 commits into
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refactor: decompose Methods.java into focused utility classes#90maxulysse wants to merge 12 commits into
maxulysse wants to merge 12 commits into
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Methods.java was 1,790 lines mixing 7+ concerns. Extract 5 new classes: - HashUtils: consolidate 3 duplicate MD5 implementations - YamlUtils: YAML reading and manipulation - ArchiveDownloader: curl/zip/tar extraction and S3 downloads - FileTraversalUtils: directory walking and file collection - NextflowOutputFilter: output line filtering and sanitization Methods.java is now a 488-line thin delegation facade. Delete duplicate filterNextflowOutput Groovy adapter. Update NfCoreUtils and CsvUtils to use HashUtils.
The sanitizeOutput method was ~100 lines with 9 getOrDefault calls and inline validation. Extract a SanitizeOptions inner class to centralize option parsing and validation.
- Fix raw types: List -> List<?> / List<String> in FileTraversalUtils and Methods public API - Fix silent exception swallowing: ArchiveDownloader.curlAndUntar, curlAndUnzip, and NfCoreUtils.installModule now throw IOException on failure instead of logging and returning silently - Consolidate DEFAULT_CSV_DOUBLE_DIGITS: single source of truth in CsvUtils.DEFAULT_DOUBLE_DIGITS, referenced by Methods and OutputSanitizer
- Implement missing additionalPatterns filtering in NextflowOutputFilter (was lost during refactoring, now properly applies regex patterns to output) - Consolidate MD5 implementations in HashUtils: - Extract shared byteToHex(byte) helper method - Use consistent hex conversion in both md5Hex() and listToMD5() - Change listToMD5 parameter from ArrayList<Object> to List<?> for type safety - Align exception handling (NoSuchAlgorithmException instead of UnsupportedEncodingException) - Update Methods.java delegation to match new HashUtils signature Generated by Mistral Vibe. Co-Authored-By: Mistral Vibe <vibe@mistral.ai>
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Summary
Methods.java was 1,790 lines mixing 7+ concerns. This PR breaks it into 5 utility classes, extracts a typed options model from OutputSanitizer, and fixes three code-quality blockers from review.
New classes
HashUtilsYamlUtilsArchiveDownloaderFileTraversalUtilsNextflowOutputFilterChanges to existing files
SanitizeOptionsinner class. Moves 9getOrDefaultcalls and validation out of the 100-linesanitizeOutputmethod.HashUtils.md5Hex().installModulenow throwsIOExceptionon failure instead of swallowing it.HashUtils.md5Hex(). OwnsDEFAULT_DOUBLE_DIGITSas single source of truth.curlAndUntarandcurlAndUnzipnow throwIOExceptionon failure instead of logging and returning silently.Also fixed
filterNextflowOutput(Object, Map)adapter (identical to theLinkedHashMapvariant)List→List<?>/List<String>) in public API signaturesDEFAULT_CSV_DOUBLE_DIGITS(was duplicated in Methods and OutputSanitizer)Deferred
HashUtilsNextflowOutputFilter.filterNextflowOutput127-line methodbuildMatchers(List<String>)helper (duplicated 3x)Verification
Generated via opencode and mistral-ai
Verified by @maxulysse