Add plugin plant-public

plugins/Presisitence/plant-public/LICENSE

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+MIT License
+
+Copyright (c) 2026 Presisitence
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.

plugins/Presisitence/plant-public/README.md

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+# plant-public
+
+Public plant-pathology bioinformatics for MiniMax Code: UniProt, NCBI, InterProScan, PDB,
+AlphaFold DB, Ensembl Plants, Sol Genomics (Solanaceae), and Arabidopsis BAR / ATTED / STRING.
+
+This Plugin ships a stdio MCP server. It does not bundle any local genomes or RNA-seq matrices.
+All sequence and annotation data come from public APIs. Web-only tools (SignalP, PlantCARE, …)
+return submission guidance rather than invented results.
+
+## Try it
+
+```text
+Look up tomato WRKY transcription factors in UniProt and NCBI. Then get InterProScan domains
+for one protein and fetch its AlphaFold model if a UniProt accession exists.
+```
+
+```text
+用 Ensembl Plants 查 solanum_lycopersicum 的 NPR1 同源基因，再给出 Sol Genomics BLAST 该怎么提交。
+```
+
+Expected result: the agent calls `uniprot_search` / `ncbi_search` / `ensembl_plants_gene` (or
+`plant_resource_guide("solgenomics")` for the SGN web path), returns accessions, FASTA or domain
+tables from the live APIs, and marks any web-only step as a guide rather than fake data.
+
+## Requirements
+
+- Python 3.10+ and [uv](https://docs.astral.sh/uv/) on PATH (`mcp.json` starts the server with `uv run server.py`).
+- Optional `NCBI_API_KEY` environment variable to raise NCBI rate limits. No key is required.
+- Windows, macOS, and Linux.
+
+## Data and network
+
+The MCP server contacts public scholarly APIs only:
+
+- `rest.uniprot.org`
+- `eutils.ncbi.nlm.nih.gov`
+- `www.ebi.ac.uk` (InterProScan)
+- `data.rcsb.org` / RCSB PDB search
+- `alphafold.ebi.ac.uk`
+- `rest.ensembl.org` (Ensembl Plants)
+- `bar.utoronto.ca`, `atted.jp`, `string-db.org` (Arabidopsis)
+
+No telemetry. No credentials in the package. Optional `NCBI_API_KEY` stays in the user's environment.
+
+## License
+
+MIT. See [LICENSE](LICENSE). Upstream databases have their own terms; respect rate limits.

plugins/Presisitence/plant-public/bio_toolkit/__init__.py

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+"""植物抗病生物信息学公共接口工具集（不含本地基因组/转录组）。
+
+- uniprot   : 蛋白序列与功能注释 (UniProt REST)
+- ncbi      : 序列/基因/文献检索 (NCBI E-utilities)
+- interpro  : 结构域/家族注释 (EBI InterProScan REST)
+- structure : 蛋白结构 (RCSB PDB + AlphaFold DB)
+- plant     : 植物垂直资源指引 + Ensembl Plants / Sol Genomics
+- bar       : 拟南芥 BAR/ThaleMine
+- atted     : 拟南芥 ATTED-II 共表达
+- stringdb  : 拟南芥 STRING 蛋白互作 + 功能富集 (species=3702)
+"""
+
+__version__ = "0.1.0"

plugins/Presisitence/plant-public/bio_toolkit/atted.py

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+"""ATTED-II (atted.jp) 共表达数据库 API v5 封装。
+
+拟南芥共表达网络：给定基因返回共表达基因及 z 分数（找共调控基因/候选上游 TF）。
+公开 REST API（GET，JSON）。
+"""
+from __future__ import annotations
+
+from typing import Any
+
+from .http import get_json
+
+ATTED_API5 = "https://atted.jp/api5/"
+# 平台→当前数据库 id（版本随 ATTED 更新，可用 db 参数覆盖；截至 2026-07）。
+# 注意：ATTED 只认带版本号的库 id，裸 'Ath-r' 会被静默当成统一库。
+_PLATFORM_DB = {"u": None, "r": "Ath-r.c5-0", "m": "Ath-m.c8-0"}
+
+
+def coexpression(
+    gene_id: str,
+    top_n: int = 100,
+    cutoff: float | None = None,
+    platform: str = "u",
+    db: str | None = None,
+) -> dict[str, Any]:
+    """拟南芥共表达基因（AGI + z 分数）。gene_id: AGI(如 At3g26440) 或 Entrez ID。
+    platform: u/m/r（统一/微阵列/RNA-seq）；db 显式指定完整 ATTED 库 id(如 Ath-r.c5-0)时优先于 platform。"""
+    pf = platform.lower()
+    if db is None and pf not in _PLATFORM_DB:
+        return {"error": f"platform 须为 u/m/r，收到 {platform!r}", "platforms": list(_PLATFORM_DB)}
+    resolved_db = db if db is not None else _PLATFORM_DB.get(pf)
+    params: dict[str, Any] = {"gene": gene_id.strip(), "topN": top_n}
+    if cutoff is not None:
+        params["value"] = cutoff
+    if resolved_db:
+        params["db"] = resolved_db
+    return {
+        "gene_id": gene_id.strip(),
+        "platform": pf if db is None else None,
+        "db": resolved_db,
+        "top_n": top_n,
+        "cutoff": cutoff,
+        "result": get_json(ATTED_API5, params=params),
+    }

plugins/Presisitence/plant-public/bio_toolkit/bar.py

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+"""BAR (Bio-Analytic Resource, bar.utoronto.ca) API 封装。
+
+拟南芥模式参考数据：基因信息、ThaleMine 功能注释/GeneRIF/文献、
+eFP 表达数值与 eFP 图像（含 Biotic Stress 生物胁迫）。
+全部为公开 REST API（GET，JSON）。绝不编造返回数据：失败时返回错误与可选项。
+"""
+from __future__ import annotations
+
+from typing import Any
+
+from .http import BioHTTPError, get, get_json
+
+BAR_API = "https://bar.utoronto.ca/api"
+
+
+def _unwrap(resp: Any) -> Any:
+    """BAR 多数端点包一层 {"wasSuccessful":true,"data":...}；成功则取 data，否则原样返回。"""
+    if isinstance(resp, dict) and resp.get("wasSuccessful") and "data" in resp:
+        return resp["data"]
+    return resp
+
+
+def _intermine_rows(resp: Any) -> list[dict[str, Any]]:
+    """把 ThaleMine(InterMine) 的 {views/columnHeaders, results:[[...]]} 转成按列名归键的字典列表。"""
+    if not isinstance(resp, dict):
+        return []
+    cols = resp.get("views") or resp.get("columnHeaders") or []
+    out: list[dict[str, Any]] = []
+    for row in resp.get("results") or []:
+        out.append({c: v for c, v in zip(cols, row)} if isinstance(row, list) else row)
+    return out
+
+
+def gene_info(gene_id: str, species: str = "arabidopsis") -> dict[str, Any]:
+    """BAR 基因信息（位点/链向/别名/注释）。gene_id 如 AT3G26440。"""
+    gid = gene_id.strip()
+    resp = get_json(f"{BAR_API}/gene_information/single_gene_query/{species}/{gid}")
+    return {"gene_id": gid, "species": species, "data": _unwrap(resp)}
+
+
+def gene_function(gene_id: str) -> dict[str, Any]:
+    """ThaleMine 拟南芥基因功能注释 + GeneRIF。gene_id 为 AGI（如 At3g26440）。"""
+    gid = gene_id.strip()
+    info = get_json(f"{BAR_API}/thalemine/gene_information/{gid}")
+    rifs = get_json(f"{BAR_API}/thalemine/gene_rifs/{gid}")
+    return {"gene_id": gid, "gene_information": _intermine_rows(info), "gene_rifs": _intermine_rows(rifs)}
+
+
+def publications(gene_id: str) -> dict[str, Any]:
+    """ThaleMine 拟南芥基因相关文献。gene_id 为 AGI。"""
+    gid = gene_id.strip()
+    pubs = get_json(f"{BAR_API}/thalemine/publications/{gid}")
+    return {"gene_id": gid, "publications": _intermine_rows(pubs)}
+
+
+def efp_views(species: str = "arabidopsis", view: str | None = None) -> dict[str, Any]:
+    """eFP 发现工具。view 缺省：列出全部 view→database 映射；
+    给定 view（如 Biotic_Stress）：返回该视图对照/处理样本分组（病原实验设计）。"""
+    if view:
+        resp = get_json(f"{BAR_API}/microarray_gene_expression/{species}/{view}/samples")
+        return _unwrap(resp)  # 已含 {species, view, groups}
+    resp = get_json(f"{BAR_API}/microarray_gene_expression/{species}/databases")
+    return _unwrap(resp)  # 已含 {species, databases}
+
+
+def efp_expression(gene_id: str, database: str = "klepikova", species: str = "arabidopsis") -> dict[str, Any]:
+    """取基因在指定 eFP database 的表达数值（RNA-seq 类库如 klepikova 可用）。
+    注：微阵列库(atgenexp_*/生物胁迫)此端点暂不支持数值——生物胁迫请用 efp_image 取图、efp_views 取实验设计。"""
+    gid = gene_id.strip()
+    url = f"{BAR_API}/gene_expression/expression/{database}/{gid}"
+    try:
+        resp = get_json(url)
+    except BioHTTPError as exc:
+        return {
+            "gene_id": gid,
+            "database": database,
+            "error": f"该 database 在表达值端点不可用（{exc}）。RNA-seq 库(如 klepikova)可用；"
+                     "微阵列库/生物胁迫请用 bar_efp_image 取图或 bar_efp_views 查实验设计。",
+        }
+    return {"gene_id": gid, "database": database, "species": species, "data": _unwrap(resp)}
+
+
+def efp_image_url(
+    gene_id: str,
+    view: str = "Biotic_Stress",
+    mode: str = "Absolute",
+    species: str = "arabidopsis",
+    check: bool = False,
+) -> dict[str, Any]:
+    """拟南芥基因 eFP 图像 URL（含 Biotic_Stress 生物胁迫；默认只返回 URL，不下载/不落盘）。
+    view 如 Biotic_Stress/Abiotic_Stress/Developmental_Map；mode Absolute/Relative/Compare。
+    check=True 时做一次状态探测（会请求但不保存）。"""
+    gid = gene_id.strip()
+    url = f"{BAR_API}/efp_image/efp_{species}/{view}/{mode}/{gid}"
+    reachable: bool | None = None
+    if check:
+        try:
+            reachable = get(url).status_code == 200
+        except BioHTTPError:
+            reachable = False
+    return {"gene_id": gid, "view": view, "mode": mode, "url": url, "reachable": reachable}

plugins/Presisitence/plant-public/bio_toolkit/cli.py

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+"""独立命令行入口：不启动 MCP 也能直接调度公共数据库。
+
+用法示例:
+    uv run plant-cli uniprot summary P0DP23
+    uv run plant-cli ncbi search protein "Solanum lycopersicum[Organism] AND WRKY[Gene]"
+    uv run plant-cli alphafold P0DP23
+    uv run plant-cli plant list
+    uv run plant-cli plant guide solgenomics
+"""
+from __future__ import annotations
+
+import argparse
+import json
+import sys
+from pathlib import Path
+from typing import Any
+
+from . import (
+    atted,
+    bar,
+    interpro,
+    ncbi,
+    plant,
+    stringdb,
+    structure,
+    uniprot,
+)
+
+
+def _out(obj: Any) -> None:
+    if isinstance(obj, str):
+        print(obj)
+    else:
+        print(json.dumps(obj, ensure_ascii=False, indent=2))
+
+
+def build_parser() -> argparse.ArgumentParser:
+    p = argparse.ArgumentParser(prog="plant-cli", description="植物抗病生信公共接口 CLI")
+    sub = p.add_subparsers(dest="cmd", required=True)
+
+    up = sub.add_parser("uniprot", help="UniProt")
+    up.add_argument("action", choices=["summary", "fasta", "search"])
+    up.add_argument("value")
+    up.add_argument("--size", type=int, default=25)
+
+    nc = sub.add_parser("ncbi", help="NCBI E-utilities")
+    nc.add_argument("action", choices=["search", "fetch", "search-fetch"])
+    nc.add_argument("db")
+    nc.add_argument("value")
+    nc.add_argument("--rettype", default="fasta")
+    nc.add_argument("--retmax", type=int, default=10)
+
+    af = sub.add_parser("alphafold", help="AlphaFold DB")
+    af.add_argument("uniprot")
+
+    pdb = sub.add_parser("pdb", help="RCSB PDB 条目")
+    pdb.add_argument("pdb_id")
+
+    ip = sub.add_parser("interpro", help="InterProScan")
+    ip.add_argument("action", choices=["run", "status", "result"])
+    ip.add_argument("arg1", help="run: fasta文件; status/result: job_id")
+    ip.add_argument("email_or_type", nargs="?", default="tsv")
+
+    pl = sub.add_parser("plant", help="植物垂直资源")
+    pl.add_argument("action", choices=["list", "guide", "ensembl", "taxid"])
+    pl.add_argument("arg1", nargs="?")
+    pl.add_argument("arg2", nargs="?")
+
+    ba = sub.add_parser("bar", help="BAR/ThaleMine 拟南芥资源")
+    ba.add_argument("action", choices=["info", "function", "pubs", "views", "expr", "image"])
+    ba.add_argument("arg1", nargs="?", help="基因ID (AGI)；views 时为 view 名(可选)")
+    ba.add_argument("arg2", nargs="?", help="expr: database；image: view")
+
+    at = sub.add_parser("atted", help="ATTED-II 拟南芥共表达")
+    at.add_argument("gene", help="基因ID (AGI)")
+    at.add_argument("--top", type=int, default=100)
+    at.add_argument("--platform", default="u", help="u/m/r")
+
+    st = sub.add_parser("string", help="STRING 拟南芥互作/富集 (species=3702)")
+    st.add_argument("action", choices=["partners", "enrichment"])
+    st.add_argument("genes")
+    st.add_argument("--score", type=int, default=400)
+    return p
+
+
+def main(argv: list[str] | None = None) -> int:
+    try:
+        sys.stdout.reconfigure(encoding="utf-8")
+    except (AttributeError, ValueError):
+        pass
+    args = build_parser().parse_args(argv)
+
+    if args.cmd == "uniprot":
+        if args.action == "summary":
+            _out(uniprot.summarize(args.value))
+        elif args.action == "fasta":
+            _out(uniprot.get_fasta(args.value))
+        else:
+            _out(uniprot.search(args.value, size=args.size))
+
+    elif args.cmd == "ncbi":
+        if args.action == "search":
+            _out(ncbi.esearch(args.db, args.value, retmax=args.retmax))
+        elif args.action == "fetch":
+            _out(ncbi.efetch(args.db, args.value, rettype=args.rettype))
+        else:
+            _out(ncbi.search_and_fetch(args.db, args.value, rettype=args.rettype, retmax=args.retmax))
+
+    elif args.cmd == "alphafold":
+        _out(structure.alphafold_summary(args.uniprot))
+
+    elif args.cmd == "pdb":
+        _out(structure.pdb_entry(args.pdb_id))
+
+    elif args.cmd == "interpro":
+        if args.action == "run":
+            seq = Path(args.arg1).read_text(encoding="utf-8") if Path(args.arg1).exists() else args.arg1
+            _out(interpro.run_and_wait(seq, args.email_or_type))
+        elif args.action == "status":
+            _out({"job_id": args.arg1, "status": interpro.status(args.arg1)})
+        else:
+            _out(interpro.result(args.arg1, args.email_or_type))
+
+    elif args.cmd == "plant":
+        if args.action == "list":
+            _out(plant.list_resources())
+        elif args.action == "guide":
+            _out(plant.get_resource(args.arg1 or ""))
+        elif args.action == "ensembl":
+            _out(plant.ensembl_lookup_symbol(args.arg1, args.arg2))
+        else:
+            key = (args.arg1 or "").lower()
+            _out({"species": key, "taxid": plant.TAXIDS.get(key), "known": list(plant.TAXIDS)})
+
+    elif args.cmd == "bar":
+        if args.action == "info":
+            _out(bar.gene_info(args.arg1))
+        elif args.action == "function":
+            _out(bar.gene_function(args.arg1))
+        elif args.action == "pubs":
+            _out(bar.publications(args.arg1))
+        elif args.action == "views":
+            _out(bar.efp_views(view=args.arg1 or None))
+        elif args.action == "expr":
+            _out(bar.efp_expression(args.arg1, database=args.arg2 or "klepikova"))
+        else:
+            _out(bar.efp_image_url(args.arg1, view=args.arg2 or "Biotic_Stress"))
+
+    elif args.cmd == "atted":
+        _out(atted.coexpression(args.gene, top_n=args.top, platform=args.platform))
+
+    elif args.cmd == "string":
+        if args.action == "partners":
+            _out(stringdb.interaction_partners(args.genes, required_score=args.score))
+        else:
+            _out(stringdb.enrichment(args.genes))
+
+    return 0
+
+
+if __name__ == "__main__":
+    sys.exit(main())