justin/seed-mcp
1
0
Fork 0
Code Issues Pull Requests Actions Packages Projects Releases Wiki Activity
20 Commits 2 Branches 0 Tags
bd71f30ca72067d8939bcab40ea565397cc8c216
Commit Graph

4 Commits

Author SHA1 Message Date
justin 0e625553e5 gh_plot_reports corpus (4,299 plots) + concurrency + 4-GPU pool 
CORPUS — 4,299 GH plot reports added (3,797 written + 502 from the
earlier slow run + 319 sitemap-listed URLs that 404'd as
discontinued). Combined with prior 760 varieties + 14 AgriPro
trials = 5,073 total chunks now indexed.

scrape/sources/gh_plot_reports.py — concurrency speedup:
- 4 worker threads (ThreadPoolExecutor), each with its own
  requests.Session for connection-pool efficiency.
- Shared class-level rate limiter (0.25 sec between ANY two
  requests across all threads). Net throughput ~4 req/sec —
  well below any rate-limit threshold a public site enforces.
- Diagnosis vs original 1 req/sec: GH had ZERO rate limiting,
  zero 429s, zero retries. The 1 sec self-throttle was just too
  conservative. Bench:
    1 worker  / 1.0 sec throttle:  ~0.4 plots/sec (190 min ETA)
    4 workers / 0.25 sec throttle: ~3 plots/sec  (~25 min actual)

rag/chunk.py — chunk size cap for nomic-embed-text's 2048-token
context window:
- Empirically tested: failure threshold is ~5,250 chars on
  numeric-heavy trial chunks (chars/token ratio 2.4 vs 3.5 for
  prose). Cap at 4,500 chars to be safely under at worst-case
  2.2 chars/token.
- Applied to BOTH variety and trial chunks. Marked truncated
  chunks with metadata.embed_truncated = True; FULL text stays
  in the on-disk .md for get_page to return verbatim.

.gitea/workflows/{refresh,image-only}.yml — OLLAMA_URL pool
restructured for the 4 GPU-pinned endpoints. Bench (50-chunk
batches on nomic-embed-text):

    .0.125:11434  (RTX 40-series)  242 embeds/sec  ← weight ×4
    .0.2:11436    (GPU-pinned)     108 embeds/sec  ← weight ×2
    .0.2:11435    (GPU-pinned)      72 embeds/sec  ← weight ×1
    localhost     (TITAN X)         37 embeds/sec  ← weight ×1

Weighting is done by listing the URL multiple times in
OLLAMA_URL since the embedder uses round-robin. .0.2:11434 is
explicitly EXCLUDED — it isn't pinned to a specific GPU.

Combined index rebuild for 5,073 chunks now finishes in ~3 min
(was 19+ on the single-endpoint pool).

Smoke tests:
✓ list_versions: 5,073 docs across 6 sources, 2 vendors, 6
  brands, 4 crops (corn 2711, soy 2016, silage 223, wheat 123).
✓ search_trials({crop=corn, state=IA, year=2024}): 3 IA 2024
  corn trials surfaced.
✓ search_trials("Phytophthora resistance soybean trial"): NK
  NK43-W1XFS top-1 in LA 2024 trial (cross-vendor result).
✓ search_trials("AP Iliad Idaho wheat"): AgriPro Washington/N
  Idaho 2025 trial surfaced.
✓ search_trials(product=DKC65-95): 3 corn trials containing
  that hybrid in IL/IA 2024.
✓ search_trials(product=NK1701): 3 corn trials in AR/MS 2024.
✓ Product filter correctly returns EMPTY for products that
  aren't in the corpus (DKC65-20 is a 2023 product; 2023 plots
  deferred). Anti-hallucination contract preserved.

Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
 2026-05-25 16:46:35 -04:00
justin c737871c4c Trial-data scrapers: gh_plot_reports + agripro_trials + search_trials tool 
This PR introduces TRIAL data — yield-performance results from real
field trials — as a SEPARATE data type alongside variety identity.
The two are complementary:

  search_docs  → "What's the disease resistance of DKC62-08RIB?"
                  (variety identity — what it IS)
  search_trials → "Which corn hybrid won the IA 2024 trials?"
                  (performance data — how it PERFORMED)

scrape/sources/gh_plot_reports.py — Golden Harvest plot reports
- 4,618 expected (2024+2025; 2023 deferred to a backfill pass).
- URL: /<crop>/plot-report/<state>/<year>/<plot_id>
- Cross-vendor: each plot lists products from multiple brands
  (NK / DEKALB / Golden Harvest / Enogen / Pioneer / Channel) side
  by side at one cooperator's field — the kind of independent
  comparison data Bayer doesn't publish itself.
- Generic per-column metrics dict (Yield/MST/Test Weight/$/Ac for
  corn+soy, Ton/Acre + Milk + Beef columns for silage).
- Politeness: 1 req/sec, retries on 429/5xx, no redirect-follow.

scrape/sources/agripro_trials.py — AgriPro regional trial PDFs
- 14 unique PDFs (38 sitemap links deduped) at /trials-data
- pdfplumber text extraction, region/year detection from filename
- Verbatim PDF text preserved in chunk body so variety + yield
  number adjacency drives retrieval (AP Iliad's Aberdeen ID yield
  matches a query about "AP Iliad Idaho yield")

rag/chunk.py — chunks_from_trial() dispatching by source
- Plot reports: identity preamble + Top-5 by primary metric + full
  ranking table. Metric labels chosen from the data (corn/soy use
  "Yield", silage uses "Ton/Acre").
- AgriPro PDFs: identity preamble + verbatim trial body inline so
  per-location yields surface for region+variety queries.
- Variety chunks get data_type="variety" metadata; trial chunks get
  data_type="trial". Single Chroma collection; the tool router
  filters by data_type rather than maintaining two collections.

rag/index.py — dispatch by sidecar's data_type field
rag/bm25.py — new filter columns (data_type, year, state)

docs_mcp/server.py — sixth MCP tool: search_trials(crop?, state?,
year?, product?, k=10)
- Filters trial chunks via where={"data_type": "trial", ...}
- Optional product substring post-filter for "DKC62-08RIB Iowa 2024"
  style searches
- search_docs now defaults to data_type="variety" so trial chunks
  don't bleed into variety identity queries
- Tool docstring routes the agent: "use lookup_variety to verify
  identity details on any trial winner you surface"

NK trial endpoint (/NKSeeds/wsProxy.asmx/GetPlotResult) is documented
as deferred — the ASMX-SOAP shape returned empty XML on initial
probe. Bayer per-variety yield data is not publicly indexed at all
— documented in the trial-scope note (DEKALB/Asgrow trial data flows
through Channel reps, not the web). AgRevival research books exist
as 10 large annual PDFs but are deferred (low ROI per parse).

Initial corpus shipped in this PR: 14 AgriPro trial PDFs. The 4,618
Golden Harvest plot reports are scraping in background and will be
added in a follow-up corpus-snapshot PR (~70 min ETA).

Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
 2026-05-25 15:19:03 -04:00
justin 9ce920f622 agripro + nk scrapers — 146 Syngenta varieties added (wheat + corn/soy) 
agripro (24 varieties)
- Drupal Views form scrape via /search-agripro-brand-varieties with
  explicit GET params (sidesteps the AJAX-only-on-load default that
  returns an empty form skeleton).
- Per-variety parse: <h1>, .field--node--variety-type--variety,
  .field--node--tag-line--variety, .field--node--body, plus the
  three rated sections (Agronomics / Grain / Disease) with their
  <div class="row"><div class="label">label</div><div>value</div>
  pairs.
- Wheat-class distribution: 12 HRS, 7 SWW, 3 HRW, 1 HWS, 1 Barley
  — provides the Northern Plains HRS coverage WestBred lacks.

nk (122 varieties — recon's "29" was outdated; the current NK seed
finder lists 41 corn + 81 soy)
- ASP.NET WebForms endpoint:
  POST /NKSeeds/{Corn,Soy}ProductFinder.aspx/GetProducts returns
  {"d": "<html>"} where the inner HTML is one <div class="sf-result">
  per variety. BeautifulSoup tokenizes the whole blob.
- Per-card: product code (NK8005, NK008-P8XF), RM/MG from the
  title <span>, "Brands Available" trait variants, marketing
  positioning + bullet strengths, tech-sheet PDF URL.
- pdfplumber text extraction on the tech-sheet PDFs adds:
  * corn disease ratings (Gray Leaf Spot, NCLB, Goss's Wilt,
    Anthracnose, Tar Spot, Fusarium, etc.) where the PDF prints
    "Label N" lines (text-extractable)
  * soybean Phytophthora source genes (Rps1c, Rps3a, ...)
  * soybean SCN race coverage
  * soybean agronomic ratings (Emergence, Standability, Shatter
    Tolerance, Green Stem) with text-extractable 1-9 values
  * soybean soil-type adaptation (Best/Good/Fair/Poor) for drought
    prone / high pH / poorly drained / etc.
- Agronomic rating BARS for corn (Emergence, Stalk Strength,
  Drought) are not text-extractable; we record the labels with an
  explicit "rated in PDF chart, see tech sheet" value so the agent
  can direct the farmer at the source for those numbers.

Scale-direction correction in lessons.md:
- NK and AgriPro both use 1 = best, lower = more resistant — the
  REVERSED convention vs Bayer / Golden Harvest. NK's tech-sheet
  footer literally prints "1-9 Scale: 1 = Best, 9 = Worst".
  AgriPro positioning on stripe-rust-resistant varieties (AP Iliad
  with Stripe Rust 1, Eyespot 2) confirms the same direction.
- sources-not-yet-indexed section trimmed to just Beck's PFR +
  Beck's products — everything else IS now in the corpus.

Cross-vendor coverage after this PR: 760 varieties.
  bayer_seeds     475 (DEKALB 288 / Asgrow 102 / WestBred 85)
  golden_harvest  139
  nk              122  (41 corn / 81 soy)
  agripro          24  (12 HRS / 7 SWW / 3 HRW / 1 HWS / 1 Barley)
Vendors: Bayer, Syngenta. Brands: 6. Crops: corn, soy, wheat (109
wheat now, up from 85).

requirements.txt: pdfplumber>=0.11 for NK tech-sheet parsing.

Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
 2026-05-25 14:16:36 -04:00
justin 75f714b454 Phase 4-5: deployable container + corpus snapshot + CI fixes 
deploy/docker-compose.yml — replace <product>/<registry> placeholders
with concrete values for Drawbar's stack:
- image: git.jpaul.io/justin/seed-mcp:latest (CF tunnel for pulls; CI
  pushes via LAN 192.168.0.2:1234 to avoid 100 MB body cap)
- container_name: seed-mcp
- port 8001:8000 (8001 host-side to not collide with crop-chem-docs
  on 8000)
- PRODUCT_NAME=crop_seed, hybrid search enabled, stateless HTTP
- llama-rerank shared with crop-chem-docs (NOT redefined here —
  expected to already be in Drawbar's parent compose network)
- networks.drawbar-mcp external: true so seed-mcp joins the existing
  cross-MCP shared network

.gitignore — corpus/ is now COMMITTED, not ignored. The monthly
refresh workflow scrapes and commits corpus changes; the image-only
workflow rebuilds indexes from the committed corpus. Allowing the
corpus to flow through git means the :corpus-YYYY.MM.DD image tag
pins to a specific seed-catalog snapshot. chroma/ and bm25/ remain
ignored — those are deterministically derived from corpus.

Initial committed snapshot: 614 varieties.
- bayer_seeds: 475 (DEKALB 288 + Asgrow 102 + WestBred 85)
- golden_harvest: 139 (Syngenta corn + soy; 36 sitemap URLs
  302-redirected = discontinued)

rag/chunk.py — normalize brand and crop to uppercase/lowercase in
Chroma metadata so cross-vendor brand-filter lookups don't break on
casing inconsistency (Bayer stores "DEKALB", Golden Harvest stores
"Golden Harvest"; _build_where uppercases user-supplied brand which
matched the former but not the latter pre-fix). Sidecar JSON keeps
original casing for display.

Stub scrapers (nk, agripro, becks_pfr, becks_products) — change
return code from 2 to 0 so the monthly-refresh CI workflow doesn't
fail on deferred sources. Real implementations will return 0 on
success / 1 on failure when they ship.

Smoke-tested cross-vendor retrieval against the 614-chunk index:
- list_versions shows both vendors with correct facet counts
- broad "corn hybrid 100 RM" query returns both DEKALB and Golden
  Harvest hits in top 5
- brand='Golden Harvest' filter returns 3 GH-only varieties
- variety-code prefilter still works (E085Z5 → top hit on GH)

Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
 2026-05-25 13:40:05 -04:00