Add Document Ingestion module for curated docs and web search - #48
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ParamThakkar123 wants to merge 21 commits into
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Add Document Ingestion module for curated docs and web search#48ParamThakkar123 wants to merge 21 commits into
ParamThakkar123 wants to merge 21 commits into
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- Resolved merge conflicts in .gitignore, Project.toml, docs/src/index.md, src/HealthLLM.jl, src/database.jl, src/query.jl, src/utils.jl, test/runtests.jl - Removed src/embedding.jl and src/pgvector.jl (deleted by other branch; functionality inlined into utils.jl and database.jl respectively) - Added missing imports to HealthLLM module - Added docstrings with arguments, returns, and examples to public functions - Updated docs example to show full pipeline
…test/Project.toml
- docs/src/index.md: Full pipeline guide covering file collection, model registration, embedding building/validation/storage, RAG querying, and database query usage - src/utils.jl: Add docstrings to build_index_rag, get_schema, HuggingFaceLoadResult, load_huggingface_model, register_models - test/: Fix UtilsTest, DatabaseTest, QueryTest with proper module imports; remove stale PgvectorTest/EmbeddingTest; add pipeline tests; remove DrWatson dependency; fix test/Project.toml deps - Project.toml: Add DrWatson compat entry for Aqua compliance
Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
Introduces a new Ingestion module that pulls documentation into a RAG index from two kinds of sources: curated docs (JuliaHealth, OMOP CDM, OHDSI, FunSQL.jl) and live web search via a pluggable provider (DuckDuckGo). Includes HTTP/S fetch with HTML-to-text cleaning, a search provider interface, and an orchestration pipeline (ingest/ingest_to_index) that feeds directly into RAGTools for indexing. New files: - src/ingestion.jl — module entry point - src/ingestion/types.jl — SourceDocument, SearchResult - src/ingestion/curated.jl — CURATED_SOURCES registry - src/ingestion/fetch.jl — fetch_url, html_to_text, fetch_curated - src/ingestion/search.jl — AbstractSearchProvider, DuckDuckGoProvider - src/ingestion/pipeline.jl — ingest, ingest_to_index - test/IngestionTest.jl — unit tests for offline logic - docs/src/ingestion.md — full user-facing documentation Dependencies added: HTTP, URIs
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+ Coverage 27.27% 47.64% +20.37%
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Summary
Adds a new
HealthLLM.Ingestionmodule for pulling documentation into a RAG index from curated sources (JuliaHealth, OMOP CDM, OHDSI, FunSQL.jl) and live web search via a pluggable provider (DuckDuckGo).New files
src/ingestion.jl— module entry pointsrc/ingestion/types.jl— SourceDocument, SearchResult typessrc/ingestion/curated.jl— CURATED_SOURCES registrysrc/ingestion/fetch.jl— fetch_url, html_to_text, fetch_curatedsrc/ingestion/search.jl— AbstractSearchProvider, DuckDuckGoProvidersrc/ingestion/pipeline.jl— ingest, ingest_to_index orchestrationtest/IngestionTest.jl— offline unit testsdocs/src/ingestion.md— full documentationDependencies added
Modified files