opencode-bioresearcher 1.8.0 → 1.9.0

package/skills/bioresearcher-deep-research/scripts/ncbi_esummary.py

@@ -0,0 +1,86 @@
+#!/usr/bin/env python3
+"""Shared NCBI PubMed esummary client for the bioresearcher-deep-research scripts.
+
+Extracted verbatim from vet-references.py (DRY): both vet-references.py and
+evidence-ledger.py import fetch_ncbi_summaries from here.
+
+Zero external dependencies (pure Python standard library). Fail-safe: on
+network or API failure, returns whatever was fetched (possibly {}); callers
+treat missing records as "unverified" and never block on network errors.
+"""
+
+import json
+import os
+import sys
+import time
+import urllib.error
+import urllib.parse
+import urllib.request
+
+NCBI_ESUMMARY_URL = "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esummary.fcgi"
+USER_AGENT = "bioresearcher-skills/1.2 (evidence tools; +https://github.com/bioresearcher-agent)"
+
+
+def fetch_ncbi_summaries(pmids: list, timeout: float = 15.0) -> dict:
+    """Fetch esummary JSON for a list of PMIDs with rate-limiting and exponential backoff."""
+    if not pmids:
+        return {}
+
+    api_key = os.environ.get("NCBI_API_KEY", "").strip()
+    email = os.environ.get("NCBI_EMAIL", "bioresearcher-agent@noreply.github.com").strip()
+    min_interval = 0.100 if api_key else 0.334
+
+    results: dict = {}
+    batch_size = 100
+
+    for i in range(0, len(pmids), batch_size):
+        if i > 0:
+            time.sleep(min_interval)
+
+        batch = pmids[i : i + batch_size]
+        params = {
+            "db": "pubmed",
+            "id": ",".join(batch),
+            "retmode": "json",
+            "tool": "bioresearcher",
+            "email": email,
+        }
+        if api_key:
+            params["api_key"] = api_key
+
+        data = urllib.parse.urlencode(params).encode("utf-8")
+        req = urllib.request.Request(
+            NCBI_ESUMMARY_URL,
+            data=data,
+            headers={"User-Agent": USER_AGENT},
+        )
+
+        for attempt in range(4):
+            try:
+                with urllib.request.urlopen(req, timeout=timeout) as resp:
+                    payload = json.loads(resp.read().decode("utf-8"))
+                    result_data = payload.get("result", {})
+                    for uid in batch:
+                        doc = result_data.get(uid)
+                        if doc and isinstance(doc, dict) and "error" not in doc:
+                            results[uid] = doc
+                break
+            except urllib.error.HTTPError as e:
+                if e.code in (429, 500, 502, 503, 504) and attempt < 3:
+                    retry_after_hdr = e.headers.get("Retry-After")
+                    try:
+                        retry_after = float(retry_after_hdr) if retry_after_hdr else float(1.5 * (2**attempt))
+                    except ValueError:
+                        retry_after = float(1.5 * (2**attempt))
+                    time.sleep(retry_after)
+                    continue
+                sys.stderr.write(f"[ncbi-esummary] HTTP {e.code} querying NCBI for batch {i}: {e.reason}\n")
+                break
+            except Exception as e:
+                if attempt < 3:
+                    time.sleep(1.0 * (2**attempt))
+                    continue
+                sys.stderr.write(f"[ncbi-esummary] Network error querying NCBI: {e}\n")
+                break
+
+    return results

package/skills/bioresearcher-deep-research/scripts/vet-references.py

@@ -16,14 +16,10 @@ import json
 import os
 import re
 import sys
-import time
-import urllib.error
-import urllib.parse
-import urllib.request
 from pathlib import Path
 
-NCBI_ESUMMARY_URL = "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esummary.fcgi"
-USER_AGENT = "bioresearcher-skills/1.2 (vet-references; +https://github.com/bioresearcher-agent)"
+sys.path.insert(0, str(Path(__file__).resolve().parent))
+from ncbi_esummary import fetch_ncbi_summaries  # noqa: E402,F401 (shared module, extracted verbatim)
 
 REF_SECTION_RE = re.compile(
     r'(?m)^(#{2,3}\s+(?:\d+[\.\s]+)?(?:References?|Bibliography|Literature Cited|Citations)\b.*?)(?=\n#{1,2}\s+|\Z)',
@@ -37,71 +33,6 @@ PMID_RE = re.compile(r'\bPMID[:\s]+\[?(\d{4,9})\]?', re.IGNORECASE)
 DOI_RE = re.compile(r'(?:DOI[:\s]+|https?://(?:dx\.)?doi\.org/)?\b(10\.\d{4,9}/[^\s\]\)]+)', re.IGNORECASE)
 
 
-def fetch_ncbi_summaries(pmids: list[str], timeout: float = 15.0) -> dict[str, dict]:
-    """Fetch esummary JSON for a list of PMIDs with rate-limiting and exponential backoff."""
-    if not pmids:
-        return {}
-
-    api_key = os.environ.get("NCBI_API_KEY", "").strip()
-    email = os.environ.get("NCBI_EMAIL", "bioresearcher-agent@noreply.github.com").strip()
-    min_interval = 0.100 if api_key else 0.334
-
-    results: dict[str, dict] = {}
-    batch_size = 100
-
-    for i in range(0, len(pmids), batch_size):
-        if i > 0:
-            time.sleep(min_interval)
-
-        batch = pmids[i : i + batch_size]
-        params = {
-            "db": "pubmed",
-            "id": ",".join(batch),
-            "retmode": "json",
-            "tool": "bioresearcher",
-            "email": email,
-        }
-        if api_key:
-            params["api_key"] = api_key
-
-        data = urllib.parse.urlencode(params).encode("utf-8")
-        req = urllib.request.Request(
-            NCBI_ESUMMARY_URL,
-            data=data,
-            headers={"User-Agent": USER_AGENT},
-        )
-
-        for attempt in range(4):
-            try:
-                with urllib.request.urlopen(req, timeout=timeout) as resp:
-                    payload = json.loads(resp.read().decode("utf-8"))
-                    result_data = payload.get("result", {})
-                    for uid in batch:
-                        doc = result_data.get(uid)
-                        if doc and isinstance(doc, dict) and "error" not in doc:
-                            results[uid] = doc
-                break
-            except urllib.error.HTTPError as e:
-                if e.code in (429, 500, 502, 503, 504) and attempt < 3:
-                    retry_after_hdr = e.headers.get("Retry-After")
-                    try:
-                        retry_after = float(retry_after_hdr) if retry_after_hdr else float(1.5 * (2**attempt))
-                    except ValueError:
-                        retry_after = float(1.5 * (2**attempt))
-                    time.sleep(retry_after)
-                    continue
-                sys.stderr.write(f"[vet-references] HTTP {e.code} querying NCBI for batch {i}: {e.reason}\n")
-                break
-            except Exception as e:
-                if attempt < 3:
-                    time.sleep(1.0 * (2**attempt))
-                    continue
-                sys.stderr.write(f"[vet-references] Network error querying NCBI: {e}\n")
-                break
-
-    return results
-
-
 def build_pub_locator(doc: dict) -> str:
     """Build canonical Year;Volume(Issue):Pages string from NCBI esummary."""
     pubdate = doc.get("pubdate", "")