adding Marker to parse effectively pdf

specs/002-image-aware-embedding/tasks.md

@@ -48,12 +48,13 @@
 
 **Independent Test**: Upload a PDF containing at least one page with a labelled anatomical diagram. After status shows `READY`, call `GET /api/v1/books/{id}/figures` — response must contain at least one entry with `figureType`, `caption`, `page`, and `imageUrl` populated. Verify the PNG file exists at the path in `imagePath`.
 
-- [X] T013 [US2] Create `PdfStructureParser` service in `backend/src/main/java/com/aiteacher/document/PdfStructureParser.java` — uses Spring AI's `PagePdfDocumentReader` to extract per-page text; groups pages into `SectionEntity` records using heading-detection heuristics (lines matching `^\d+(\.\d+)*\s+[A-Z]`); groups sections into `ChapterEntity` records; persists both to Postgres via `ChapterRepository` and `SectionRepository`; returns `List<SectionEntity>` for the book
-- [X] T014 [US2] Create `FigureExtractionService` in `backend/src/main/java/com/aiteacher/document/FigureExtractionService.java` — opens PDF with PDFBox `PDDocument`; iterates pages; extracts `PDImageXObject` instances; skips images whose width or height are below `min-image-size-px`; classifies `FigureType` using the keyword-matching table from data-model.md §FigureType; parses caption from the nearest text line matching `CAPTION_PATTERN`; saves PNG via `FigureStorageService`; persists `FigureEntity` to `FigureRepository`; returns `List<FigureEntity>` per book
+- [X] T013 [US2] ~~Create `PdfStructureParser`~~ → **SUPERSEDED**: PDF parsing is handled by `MarkerPageParser` (see T013b). `PdfStructureParser` exists but is not wired into the pipeline.
+- [X] T013b [US2] Create `MarkerPageParser` in `backend/src/main/java/com/aiteacher/document/MarkerPageParser.java` — POSTs PDF to `http://localhost:8000/marker/upload?output_format=json` via Spring `RestClient`; parses JSON response into `List<PageResult>` (one per page block); extracts heading, ordered text, and pre-cropped figure PNG bytes per page
+- [X] T014 [US2] Update `FigureExtractionService` in `backend/src/main/java/com/aiteacher/document/FigureExtractionService.java` — **Marker migration**: removed PDFBox rendering + bbox-crop loop; decodes PNG bytes from `PageResult.FigureData` via `ImageIO.read()`; skips images below `min-image-size-px`; classifies `FigureType`; saves via `FigureStorageService`; persists `FigureEntity`
 - [X] T015 [US2] Create `VisionDescriptionService` in `backend/src/main/java/com/aiteacher/document/VisionDescriptionService.java` — accepts a `Path` to a PNG and a caption String; calls the OpenAI vision model (via Spring AI `ChatClient` with image media type) to generate a 2–4 sentence clinical description; returns the generated description string; handles API failures by returning the caption as fallback
 - [X] T016 [US2] Create `TextChunkingService` in `backend/src/main/java/com/aiteacher/document/TextChunkingService.java` — accepts a `SectionEntity`; splits `fullText` into overlapping 400–600 token windows (20-token overlap); wraps each window in a Spring AI `Document` with the flat metadata map defined in data-model.md §Text chunk document; returns `List<Document>`
 - [X] T017 [US2] Create `ChunkFigureRefService` in `backend/src/main/java/com/aiteacher/document/ChunkFigureRefService.java` — accepts a Spring AI `Document` (with its `id` as `chunkId`) and a `List<FigureEntity>` for the book; scans chunk text for patterns `Fig\.\s*\d+[\-\.]\d+` and `Figure\s+\d+[\-\.]\d+`; matches against figure labels; persists `ChunkFigureRefEntity` rows via `ChunkFigureRefRepository`
-- [X] T018 [US2] Rewrite `BookEmbeddingService.embedBook()` in `backend/src/main/java/com/aiteacher/book/BookEmbeddingService.java` to orchestrate the full pipeline: (1) `PdfStructureParser` → sections; (2) parallel: `FigureExtractionService` + `TextChunkingService` for each section; (3) `VisionDescriptionService` for each figure; (4) embed figure captions+descriptions as `Document`s (metadata per data-model.md §Figure caption document) into `vectorStore`; (5) embed text chunks into `vectorStore`; (6) `ChunkFigureRefService` for each chunk; update `captionEmbeddingId` on `FigureEntity` after embedding
+- [X] T018 [US2] Update `BookEmbeddingService.embedBook()` — **Marker migration**: injected `MarkerPageParser` replacing `DocumentAiPageParser`; updated `figureExtractionService.extract()` call (removed `pdfPath` arg); updated log message. Pipeline: (1) `MarkerPageParser` → `List<PageResult>`; (2) `buildAndSaveSections()` → sections; (3) `TextChunkingService` → chunks → embed; (4) `FigureExtractionService.extract()` → figures; (5) `VisionDescriptionService` → embed figure chunks; (6) `ChunkFigureRefService` → refs
 - [X] T019 [US2] Extend `BookEmbeddingService.deleteBookChunks()` to also delete: all `ChunkFigureRefEntity` rows (via `findByFigureIdIn`), all `FigureEntity` rows (via `deleteAllByBookId`), all figure PNG files (via `FigureStorageService.delete(bookId)`), all `SectionEntity` and `ChapterEntity` rows for the book
 - [X] T020 [US2] Add `POST /api/v1/books/{id}/reembed` endpoint to `BookController` in `backend/src/main/java/com/aiteacher/book/BookController.java` — returns `202` with `{ bookId, status: "PROCESSING" }`; returns `404` if not found; returns `409` if already `PROCESSING`; calls `deleteBookChunks()` then `embedBook()` asynchronously