Add Document Ingestion module for curated docs and web search - #48
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ParamThakkar123 wants to merge 19 commits into
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ParamThakkar123 wants to merge 19 commits into
ParamThakkar123 wants to merge 19 commits into
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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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## main #48 +/- ##
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+ Coverage 60.78% 71.66% +10.88%
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Files 4 15 +11
Lines 102 720 +618
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Add embedding generation and vector storage functionality with tests and documentation.
Introduces a Prompt module with: - FUNSQL system prompt and customizable PromptTemplate - Context formatting from retrieved chunks - Build prompts for LLM query construction Includes full test coverage and documentation page.
Introduces an Execution module with: - FUNSQL query execution against DuckDB via RAGTools - Result extraction, formatting, and display - End-to-end query-to-answer pipeline integration Includes tests and documentation updates.
…to response_generation
The Documentation job failed with six unresolvable `@ref` targets, from two separate causes: - `Chunk`, `HeaderChunk` and the rest of the chunking API are defined and exported by the `Ingestion` submodule but were never re-exported from `HealthLLM`, so `[`Chunk`](@ref)` in querying.md (which runs under `CurrentModule = HealthLLM`) had no binding to resolve against. Add them to the `import .Ingestion:` and `export` lists alongside the other ingestion names. - Documenter resolves `@ref`s inside a docstring in that docstring's own module. The `Prompt` docstrings reference `retrieve`, `search` and `Chunk`, none of which `Prompt` imports, so they failed as `HealthLLM.Prompt.retrieve` and friends. Qualify them with the `[`name`](@ref Module.name)` form, which keeps the rendered link text unchanged. `julia --project=docs docs/make.jl` now completes CrossReferences and RenderDocument with no errors. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_01RYi1NAjjGQ848cUMLEbh1x
feat: add Execution module for FUNSQL query execution and answer generation
feat: add Prompt module for grounded RAG query construction
feat: add retrieve() convenience method for text-query-to-search
Add embedding and storage modules
Add document chunking strategies with provenance tracking
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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