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6 Commits

Author SHA1 Message Date
James 20c33d2fb2 Document processing pipeline: OpenRouter OCR + Stepfun extraction 
- Switch OCR from Fireworks Qwen to Gemini 3 Flash via OpenRouter
- Switch extraction/translation to Stepfun Step 3.5 Flash via OpenRouter
- Add CallOpenRouter() to lib/llm.go (OpenAI-compatible API)
- Add OpenRouter API key support to lib/config.go
- Fix extraction preamble causing Stepfun reasoning model to return null content
  (heavy user-message preamble → short system message)
- Fix timestamp fallback: no date = 0, not today
- Fix document type: use file extension instead of hardcoded "pdf"
- Fix findUploadByFilename: Value filter was silently ignored, returning all uploads
- Fix entryQuery: skip category filter when EntryID is specified
- Fix extraction prompt contamination: replace real patient examples with generic ones
- Add reprocess button (↻) for document uploads
- Add delete cascade for upload entries (removes created document/extraction entries)
- Add upload/reprocess/delete logging throughout pipeline
- Consolidated templates, translations, email templates, landing pages
- Portal: defense, genome, dossier sections, MCP, OAuth updates
- Tools: translate pipeline improvements

Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
 2026-03-15 05:28:05 -04:00
James a2141bb5d3 Checkpoint: all pending changes across lib, portal, api, tools 
Extraction prompts refined, dossier sections expanded, MCP tools
enhanced, genome/oauth/upload improvements, health-poller added,
import-genome removed, landing/pricing/dashboard template updates,
carousel images, consent/docs templates, rquery/dbquery tools,
CLAUDE.md and docs updates.

Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
 2026-03-11 23:37:44 -04:00
James cc1dd7690c Lab reference charts, import tracking, DossierFromEntry consolidation 
- Fix lab chart reference bands: parse DOB in DossierFromEntry, generate
  deterministic ref_ids in import-caliper (was collapsing 4363 rows to 1)
- Consolidate DossierFromEntry into lib/dbcore.go (eliminate portal duplicate)
- Add Import field to entries for batch undo (NextImportID, all import paths)
- MyChart direct JSON parsing (skip Gemini for structured lab data)
- Multi-order extraction from markdown/text tables
- Normalize progress callback for UI feedback
- DICOM import, genome import, API, portal, MCP, translation updates
- Remove test DICOM data from repo

Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
 2026-02-24 05:15:03 -05:00
James 75e9ec7722 Refactor: Remove legacy v2, data, roles modules; update auth, queries, translations, portal MCP tools 2026-02-13 15:30:22 -05:00
James e1b40ab872 refactor: unexport raw DB functions, enforce RBAC at data layer 
Rename Query→dbQuery, Save→dbSave, Load→dbLoad, Delete→dbDelete,
Count→dbCount in lib/db_queries.go. Go compiler now prevents any code
outside lib/ from bypassing RBAC checks.

All external callers migrated to RBAC-checked functions:
- EntryCategoryCounts, EntryCount, EntryListByDossier (new)
- LabTestList, LabEntryListForIndex, LabRefLookupAll (new)
- GenomeQuery now requires AccessContext
- EntryDeleteByCategory/EntryDeleteTree now require AccessContext

Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
 2026-02-10 02:34:51 -05:00
Johan 94946baf00 Initial commit 2026-02-01 02:43:27 -05:00