BasedHardware · liangtovi-debug · May 24, 2026 · May 24, 2026 · May 24, 2026
diff --git a/plugins/omi-pubmed-app/Procfile b/plugins/omi-pubmed-app/Procfile
@@ -0,0 +1 @@
+web: uvicorn main:app --host 0.0.0.0 --port $PORT
diff --git a/plugins/omi-pubmed-app/README.md b/plugins/omi-pubmed-app/README.md
@@ -0,0 +1,20 @@
+# Omi PubMed App
+
+PubMed chat tools integration for Omi. This app uses the public NCBI E-utilities API (no OAuth/API key required).
+
+## Tools
+- `search_pubmed`: Search PubMed by query and return top matches.
+- `get_pubmed_article`: Fetch article details for a PubMed ID.
+- `get_related_pubmed`: Get related articles from a PubMed ID.
+
+## Run locally
+```bash
+pip install -r requirements.txt
+uvicorn main:app --reload --port 8080
+```
+
+## Omi manifest URL
+`/.well-known/omi-tools.json`
+
+## Health check
+`/health`
diff --git a/plugins/omi-pubmed-app/main.py b/plugins/omi-pubmed-app/main.py
@@ -0,0 +1,273 @@
+import html
+from typing import Any
+
+import httpx
+from fastapi import FastAPI, Request
+from fastapi.responses import HTMLResponse
+
+from models import ChatToolResponse
+
+app = FastAPI(
+    title="Omi PubMed App",
+    description="PubMed chat tools for Omi",
+    version="1.0.1",
+)
+
+EUTILS = "https://eutils.ncbi.nlm.nih.gov/entrez/eutils"
+TIMEOUT = 20.0
+
+
+def _safe(value: Any) -> str:
+    return html.unescape(str(value)) if value is not None else ""
+
+
+def _is_valid_pmid(pmid: str) -> bool:
+    return pmid.isdigit() and len(pmid) <= 12
+
+
+def _clamp_max_results(value: Any, default: int = 5) -> int:
+    try:
+        parsed = int(value)
+    except (TypeError, ValueError):
+        return default
+    return max(1, min(parsed, 10))
+
+
+def _extract_article_fields(record: dict) -> dict:
+    title = _safe(record.get("title", "Untitled"))
+    pubdate = _safe(record.get("pubdate", ""))
+    source = _safe(record.get("source", ""))
+    doi = _safe(record.get("elocationid", ""))
+    authors = []
+    for author in record.get("authors", [])[:8]:
+        name = _safe(author.get("name"))
+        if name:
+            authors.append(name)
+
+    abstract = ""
+    if isinstance(record.get("abstract"), list):
+        abstract = " ".join(_safe(x) for x in record["abstract"] if x)
+    elif record.get("abstract"):
+        abstract = _safe(record["abstract"])
+
+    return {
+        "title": title,
+        "pubdate": pubdate,
+        "source": source,
+        "doi": doi,
+        "authors": authors,
+        "abstract": abstract,
+    }
+
+
+async def _fetch_json(client: httpx.AsyncClient, endpoint: str, params: dict) -> dict:
+    resp = await client.get(f"{EUTILS}/{endpoint}", params=params)
+    resp.raise_for_status()
+    return resp.json()
+
+
+async def _search_ids(client: httpx.AsyncClient, query: str, retmax: int = 5) -> list[str]:
+    data = await _fetch_json(
+        client,
+        "esearch.fcgi",
+        {
+            "db": "pubmed",
+            "term": query,
+            "retmode": "json",
+            "retmax": _clamp_max_results(retmax),
+            "sort": "relevance",
+        },
+    )
+    return data.get("esearchresult", {}).get("idlist", [])
+
+
+async def _fetch_summaries(client: httpx.AsyncClient, ids: list[str]) -> dict:
+    if not ids:
+        return {}
+    data = await _fetch_json(
+        client,
+        "esummary.fcgi",
+        {"db": "pubmed", "id": ",".join(ids), "retmode": "json"},
+    )
+    return data.get("result", {})
+
+
+@app.get("/health")
+async def health():
+    return {"status": "ok"}
+
+
+@app.get("/")
+async def home():
+    return HTMLResponse(
+        """
+        <html><body style='font-family:sans-serif;max-width:680px;margin:40px auto;'>
+        <h1>Omi PubMed App</h1>
+        <p>Use PubMed search and article lookup from Omi chat.</p>
+        <p>Manifest: <code>/.well-known/omi-tools.json</code></p>
+        </body></html>
+        """
+    )
+
+
+@app.get("/.well-known/omi-tools.json")
+async def manifest():
+    return {
+        "tools": [
+            {
+                "name": "search_pubmed",
+                "description": "Search PubMed by keywords and return relevant papers.",
+                "endpoint": "/tools/search_pubmed",
+                "method": "POST",
+                "parameters": {
+                    "properties": {
+                        "query": {"type": "string", "description": "Search query"},
+                        "max_results": {"type": "integer", "description": "1-10, default 5"},
+                    },
+                    "required": ["query"],
+                },
+                "auth_required": False,
+                "status_message": "Searching PubMed...",
+            },
+            {
+                "name": "get_pubmed_article",
+                "description": "Get detailed citation and abstract for a PubMed ID.",
+                "endpoint": "/tools/get_pubmed_article",
+                "method": "POST",
+                "parameters": {
+                    "properties": {
+                        "pmid": {"type": "string", "description": "PubMed ID (numeric)"},
+                    },
+                    "required": ["pmid"],
+                },
+                "auth_required": False,
+                "status_message": "Fetching PubMed article...",
+            },
+            {
+                "name": "get_related_pubmed",
+                "description": "Find related PubMed articles from a PubMed ID.",
+                "endpoint": "/tools/get_related_pubmed",
+                "method": "POST",
+                "parameters": {
+                    "properties": {
+                        "pmid": {"type": "string", "description": "PubMed ID (numeric)"},
+                        "max_results": {"type": "integer", "description": "1-10, default 5"},
+                    },
+                    "required": ["pmid"],
+                },
+                "auth_required": False,
+                "status_message": "Finding related PubMed articles...",
+            },
+        ]
+    }
+
+
+@app.get("/manifest.json")
+async def manifest_alias():
+    return await manifest()
+
+
+@app.post("/tools/search_pubmed", response_model=ChatToolResponse, tags=["chat_tools"])
+async def search_pubmed(request: Request):
+    try:
+        body = await request.json()
+        query = (body.get("query") or "").strip()
+        max_results = _clamp_max_results(body.get("max_results", 5))
+        if not query:
+            return ChatToolResponse(error="query is required")
+
+        async with httpx.AsyncClient(timeout=TIMEOUT) as client:
+            ids = await _search_ids(client, query, max_results)
+            if not ids:
+                return ChatToolResponse(result=f"No PubMed results found for: {query}")
+            summaries = await _fetch_summaries(client, ids)
+
+        lines = [f"Top PubMed results for: {query}"]
+        for idx, result_pmid in enumerate(ids, start=1):
+            row = summaries.get(result_pmid, {})
+            title = _safe(row.get("title", "Untitled"))
+            journal = _safe(row.get("fulljournalname", row.get("source", "")))
+            date = _safe(row.get("pubdate", ""))
+            lines.append(f"{idx}. PMID {result_pmid}: {title} ({journal}, {date})")
+        return ChatToolResponse(result="\n".join(lines))
+    except Exception as e:
+        return ChatToolResponse(error=f"PubMed search failed: {e}")
+
+
+@app.post("/tools/get_pubmed_article", response_model=ChatToolResponse, tags=["chat_tools"])
+async def get_pubmed_article(request: Request):
+    try:
+        body = await request.json()
+        pmid = (body.get("pmid") or "").strip()
+        if not pmid:
+            return ChatToolResponse(error="pmid is required")
+        if not _is_valid_pmid(pmid):
+            return ChatToolResponse(error="pmid must be a numeric PubMed ID")
+
+        async with httpx.AsyncClient(timeout=TIMEOUT) as client:
+            summaries = await _fetch_summaries(client, [pmid])
+
+        if pmid not in summaries:
+            return ChatToolResponse(error=f"No PubMed record found for PMID {pmid}")
+
+        record = _extract_article_fields(summaries[pmid])
+        lines = [
+            f"PMID {pmid}",
+            f"Title: {record['title']}",
+            f"Authors: {', '.join(record['authors']) if record['authors'] else 'N/A'}",
+            f"Journal/Date: {record['source']} ({record['pubdate']})",
+            f"DOI/Location: {record['doi'] or 'N/A'}",
+        ]
+        if record["abstract"]:
+            lines.append(f"Abstract: {record['abstract'][:1800]}")
+        return ChatToolResponse(result="\n".join(lines))
+    except Exception as e:
+        return ChatToolResponse(error=f"Failed to fetch PubMed article: {e}")
+
+
+@app.post("/tools/get_related_pubmed", response_model=ChatToolResponse, tags=["chat_tools"])
+async def get_related_pubmed(request: Request):
+    try:
+        body = await request.json()
+        pmid = (body.get("pmid") or "").strip()
+        max_results = _clamp_max_results(body.get("max_results", 5))
+        if not pmid:
+            return ChatToolResponse(error="pmid is required")
+        if not _is_valid_pmid(pmid):
+            return ChatToolResponse(error="pmid must be a numeric PubMed ID")
+
+        async with httpx.AsyncClient(timeout=TIMEOUT) as client:
+            data = await _fetch_json(
+                client,
+                "elink.fcgi",
+                {
+                    "dbfrom": "pubmed",
+                    "db": "pubmed",
+                    "id": pmid,
+                    "linkname": "pubmed_pubmed",
+                    "retmode": "json",
+                },
+            )
+
+            linksets = data.get("linksets", [])
+            related = []
+            if linksets:
+                dbs = linksets[0].get("linksetdbs", [])
+                if dbs:
+                    related = [str(x) for x in dbs[0].get("links", [])[:max_results]]
+
+            if not related:
+                return ChatToolResponse(result=f"No related articles found for PMID {pmid}")
+
+            summaries = await _fetch_summaries(client, related)
+
+        lines = [f"Related PubMed articles for PMID {pmid}:"]
+        for idx, related_pmid in enumerate(related, start=1):
+            row = summaries.get(related_pmid, {})
+            title = _safe(row.get("title", "Untitled"))
+            journal = _safe(row.get("fulljournalname", row.get("source", "")))
+            date = _safe(row.get("pubdate", ""))
+            lines.append(f"{idx}. PMID {related_pmid}: {title} ({journal}, {date})")
+        return ChatToolResponse(result="\n".join(lines))
+    except Exception as e:
+        return ChatToolResponse(error=f"Failed to fetch related PubMed articles: {e}")
diff --git a/plugins/omi-pubmed-app/models.py b/plugins/omi-pubmed-app/models.py
@@ -0,0 +1,7 @@
+from typing import Optional
+from pydantic import BaseModel
+
+
+class ChatToolResponse(BaseModel):
+    result: Optional[str] = None
+    error: Optional[str] = None
diff --git a/plugins/omi-pubmed-app/railway.toml b/plugins/omi-pubmed-app/railway.toml
@@ -0,0 +1,7 @@
+[build]
+builder = "NIXPACKS"
+
+[deploy]
+startCommand = "uvicorn main:app --host 0.0.0.0 --port $PORT"
+restartPolicyType = "ON_FAILURE"
+restartPolicyMaxRetries = 10
diff --git a/plugins/omi-pubmed-app/requirements.txt b/plugins/omi-pubmed-app/requirements.txt
@@ -0,0 +1,4 @@
+fastapi==0.104.1
+uvicorn==0.24.0
+httpx==0.27.2
+pydantic==2.5.2
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		@@ -0,0 +1 @@
		web: uvicorn main:app --host 0.0.0.0 --port $PORT