scripts/build_rag_tree.sh

#!/bin/bash
# build_rag_tree.sh — assemble the curated RAG/ view as SYMLINKS only.
# Physically moves NOTHING: originals stay put, live Qdrant indexes keep working.
# Re-runnable (idempotent): clears only the symlinks it manages, then relinks.
set -uo pipefail
ROOT=/Users/dmpantiu/copernicus_mcp
RAG=$ROOT/RAG
cd "$ROOT"

ln_safe() {  # ln_safe <abs-target> <link-path>
  local tgt="$1" lnk="$2"
  if [ ! -e "$tgt" ]; then echo "  MISS  $tgt (skip $lnk)"; return; fi
  rm -f "$lnk"
  ln -s "$tgt" "$lnk"
  echo "  link  ${lnk#$RAG/}  ->  ${tgt#$ROOT/}"
}

mkdir -p "$RAG"/{originals,chunks,indexes,pipeline,metadata,publications}

echo "== 00 originals (raw parsed / harvested source docs) =="
mkdir -p "$RAG"/originals
ln_safe "$ROOT/marine_parsed"            "$RAG/originals/cmems_marine_parsed"
ln_safe "$ROOT/deep_docs/parsed"         "$RAG/originals/cds_ads_ewds_parsed"
ln_safe "$ROOT/eqc_qa/parsed"            "$RAG/originals/eqc_reports"
ln_safe "$ROOT/eqc_qa/notebooks_code"    "$RAG/originals/notebooks_code"
ln_safe "$ROOT/notebook_harvest"         "$RAG/originals/notebook_harvest"

echo "== 01 chunks (ready text chunks + embedded vectors) =="
mkdir -p "$RAG"/chunks/{marine_docs,cds_docs,cards,eqc_qa,publications}
ln_safe "$ROOT/marine_rag/out/chunks.jsonl"           "$RAG/chunks/marine_docs/chunks.jsonl"
ln_safe "$ROOT/marine_rag/out/chunks_embedded.jsonl"  "$RAG/chunks/marine_docs/chunks_embedded.jsonl"
ln_safe "$ROOT/deep_docs/chunks.jsonl"                "$RAG/chunks/cds_docs/chunks.jsonl"
ln_safe "$ROOT/deep_docs/chunks_embedded.jsonl"       "$RAG/chunks/cds_docs/chunks_embedded.jsonl"
ln_safe "$ROOT/marine_rag/out/cds_cards_chunks.jsonl"   "$RAG/chunks/cards/cds_cards_chunks.jsonl"
ln_safe "$ROOT/marine_rag/out/cds_cards_embedded.jsonl" "$RAG/chunks/cards/cds_cards_embedded.jsonl"
ln_safe "$ROOT/eqc_qa/chunks.jsonl"                   "$RAG/chunks/eqc_qa/chunks.jsonl"
ln_safe "$ROOT/eqc_qa/chunks_embedded.jsonl"          "$RAG/chunks/eqc_qa/chunks_embedded.jsonl"
# publications/chunks -> filled after L3 parse (slot lives under publications/)

echo "== 02 indexes (LIVE Qdrant collections — symlinked, do not move) =="
mkdir -p "$RAG"/indexes
ln_safe "$ROOT/marine_rag/out/qdrant_db"  "$RAG/indexes/marine_docs__copernicus_docs"
ln_safe "$ROOT/deep_docs/qdrant_db"       "$RAG/indexes/cds_docs"
ln_safe "$ROOT/eqc_qa/qdrant_db"          "$RAG/indexes/eqc_qa"
ln_safe "$ROOT/pubs_rag/qdrant_db"        "$RAG/indexes/publications"

echo "== 03 pipeline (build/embed/load scripts, by store) =="
mkdir -p "$RAG"/pipeline/{marine_cmems,cds_ads_ewds,eqc_notebooks,cards,server}
for f in "$ROOT"/marine_rag/*.py;  do ln_safe "$f" "$RAG/pipeline/marine_cmems/$(basename "$f")"; done
for f in "$ROOT"/deep_docs/*.py;   do ln_safe "$f" "$RAG/pipeline/cds_ads_ewds/$(basename "$f")"; done
for f in "$ROOT"/eqc_qa/*.py;      do ln_safe "$f" "$RAG/pipeline/eqc_notebooks/$(basename "$f")"; done
ln_safe "$ROOT/marine_rag/build_cds_cards.py"        "$RAG/pipeline/cards/build_cds_cards.py"
ln_safe "$ROOT/marine_rag/build_missing_cds_cards.py" "$RAG/pipeline/cards/build_missing_cds_cards.py"
ln_safe "$ROOT/marine_rag/embed_cds_cards.py"        "$RAG/pipeline/cards/embed_cds_cards.py"
ln_safe "$ROOT/marine_rag/load_copernicus_docs.py"   "$RAG/pipeline/cards/load_copernicus_docs.py"
ln_safe "$ROOT/marine_rag/rag_server.py"             "$RAG/pipeline/server/rag_server.py"
ln_safe "$ROOT/marine_rag/RAG_SERVER.md"             "$RAG/pipeline/server/RAG_SERVER.md"

echo "== 04 metadata (catalogs, universe, sidecars, manifests) =="
mkdir -p "$RAG"/metadata
ln_safe "$ROOT/meta_harvest/unified_metadata.json"   "$RAG/metadata/unified_metadata.json"
ln_safe "$ROOT/meta_harvest/deep_doc_plan.json"      "$RAG/metadata/deep_doc_plan.json"
ln_safe "$ROOT/marine_rag/out/catalog.json"          "$RAG/metadata/cmems_catalog.json"
ln_safe "$ROOT/marine_rag/out/catalog_summary.json"  "$RAG/metadata/cmems_catalog_summary.json"
ln_safe "$ROOT/eqc_qa/notebooks_by_dataset.json"     "$RAG/metadata/notebooks_by_dataset.json"
ln_safe "$ROOT/deep_docs/manifest.jsonl"             "$RAG/metadata/deep_docs_manifest.jsonl"

echo "== 05 publications (L3 track — the slot articles plug into) =="
mkdir -p "$RAG"/publications/{originals_pdfs,parsed,chunks,pipeline}
ln_safe "$ROOT/publications/pdfs"          "$RAG/publications/originals_pdfs/registry"
ln_safe "$ROOT/publications/pdfs_openalex" "$RAG/publications/originals_pdfs/openalex"
ln_safe "$ROOT/publications/pdfs_extended" "$RAG/publications/originals_pdfs/extended_oa"
ln_safe "$ROOT/publications/extended"      "$RAG/publications/corpus"
ln_safe "$ROOT/pubs_rag/qdrant_db"         "$RAG/publications/index"
for f in "$ROOT"/publications/*.py; do ln_safe "$f" "$RAG/publications/pipeline/$(basename "$f")"; done

echo "DONE. Tree at $RAG (symlinks only; nothing moved)."