merge: #723 — prisma fetch tiers: every Unpaywall location, Semantic Scholar openAccessPdf, idconv PMCID resolution (refs #723)

docs/docs/cli/bib-fetch-pfs-comments.md

@@ -12,7 +12,10 @@ Usage: stack bib fetch-pfs-comments [OPTIONS]
  docket from its stored watermark.                                              
                                                                                 
  Sealed dockets (comment period closed + quiet period + an empty pull)          
- cost nothing: no rule-metadata fetch, no resolve call, no walk.                
+ cost nothing: no rule-metadata fetch, no resolve call, no walk. The            
+ same is true for a docket already known via `--docket` that resolves           
+ to a different id. A CMS id with no `dockets` row at all is not free           
+ even under `--docket`: see that option's help.                                 
                                                                                 
 ╭─ Options ────────────────────────────────────────────────────────────────────╮
 │ --since                   TEXT     [default: 2017-01-01]                     │
@@ -23,8 +26,15 @@ Usage: stack bib fetch-pfs-comments [OPTIONS]
 │                                    [default: 0]                              │
 │ --sleep                   FLOAT    [default: 1.3]                            │
 │ --docket                  TEXT     Only pull this reg.gov docket (e.g.       │
-│                                    CMS-2026-2377); other dockets are skipped │
-│                                    before any API call once known.           │
+│                                    CMS-2026-2377). Filtered before any API   │
+│                                    call ONLY once the docket is known (a     │
+│                                    `dockets` row already exists for its CMS  │
+│                                    id) — a CMS id with no `dockets` row yet  │
+│                                    still costs one Federal Register          │
+│                                    rule-metadata fetch plus one              │
+│                                    resolve_docket call, because the reg.gov  │
+│                                    docket id isn't known until those calls   │
+│                                    resolve it.                               │
 │ --force                            Walk every docket from page 1, sealed or  │
 │                                    not. Never unseals.                       │
 │ --help                             Show this message and exit.               │

docs/docs/cli/pfs-elements.md

@@ -14,9 +14,8 @@ Usage: stack pfs elements [OPTIONS]
 │ --code               TEXT  HCPCS/CPT code (repeatable).                      │
 │ --family             TEXT  Expand a registered family (CCM, APCM, …);        │
 │                            repeatable.                                       │
-│ --all-payable              Every A/R/T code in the newest RVU year           │
-│                            (experimental: ~20 min of SQL before any model    │
-│                            call).                                            │
+│ --all-payable              Every A/R/T code in the newest RVU year, one      │
+│                            inverted pass over fr_anchors.                    │
 │ --no-llm                   Skip the local-model classifier (unknown lines go │
 │                            to review).                                       │
 │ --dry-run                  Extract and report; write nothing.                │

docs/docs/cli/prisma-fetch.md

@@ -10,7 +10,9 @@ Usage: stack prisma fetch [OPTIONS] NAME
                                                                                 
  Fetch PDFs for every non-excluded item lacking an attachment.                  
                                                                                 
- Source cascade: Unpaywall → PMC → fallback (via the VPN droplet).              
+ Source cascade: Unpaywall (every OA location) → Semantic Scholar → PMC         
+ → fallback (via the VPN droplet). PMIDs lacking a PMCID are resolved           
+ through NCBI idconv before the PMC tiers run.                                  
  Items excluded at stage 2 are untouched — the queue filter only                
  passes `screen:include` and `screen:uncertain` through.                        
                                                                                 

src/cli/prisma.py

@@ -342,7 +342,9 @@ def fetch(
 ) -> None:
     """Fetch PDFs for every non-excluded item lacking an attachment.
 
-    Source cascade: Unpaywall → PMC → fallback (via the VPN droplet).
+    Source cascade: Unpaywall (every OA location) → Semantic Scholar → PMC
+    → fallback (via the VPN droplet). PMIDs lacking a PMCID are resolved
+    through NCBI idconv before the PMC tiers run.
     Items excluded at stage 2 are untouched — the queue filter only
     passes `screen:include` and `screen:uncertain` through.
 

src/prisma/fetch.py

@@ -1,11 +1,15 @@
-"""PDF retrieval for PRISMA screening — Unpaywall → PMC → fallback proxy.
+"""PDF retrieval for PRISMA screening — Unpaywall → Semantic Scholar → PMC
+→ fallback proxy.
 
 Call graph::
 
-    pending_queue(db, project)
-        → list of (zot_id, doi, pmid, pmcid) needing a PDF
+    pending_queue(db, project, client=...)
+        → list of (zot_id, doi, pmid, pmcid) needing a PDF; with a client,
+          PMIDs lacking a PMCID are resolved through NCBI idconv (#723)
     fetch_one(item, *, proxy=None)
         → tries each source in order, returns (source, path_on_disk) | None
+          (every Unpaywall oa_location, then Semantic Scholar's
+          openAccessPdf — which also lends a PMCID to the PMC tiers)
     attach_pdf(db, zot_parent_id, path)
         → creates a Zotero attachment row and copies the file into
           the Zotero storage directory
@@ -71,7 +75,14 @@ class PendingItem:
 # ── Queue ────────────────────────────────────────────────────────
 
 
-def pending_queue(db: Db, project: str, limit: int | None = None) -> list[PendingItem]:
+def pending_queue(
+    db: Db,
+    project: str,
+    limit: int | None = None,
+    *,
+    client: httpx.Client | None = None,
+    email: str = "",
+) -> list[PendingItem]:
     """Items in *project* that passed or deferred stage-2 screening and
     don't yet have a PDF attached.
 
@@ -80,6 +91,12 @@ def pending_queue(db: Db, project: str, limit: int | None = None) -> list[Pendin
       - tagged ``screen:include`` OR ``screen:uncertain``
       - NOT tagged ``module:prisma`` (anchor guard)
       - no child attachment with an existing PDF path
+
+    With *client*, items that carry a PMID but no PMCID are resolved in
+    one NCBI idconv batch and the answer is written back to ``extra`` as
+    a ``PMCID:`` line, so the PMC tiers get their chance and the next
+    run asks no question twice (#723). Without a client the queue is
+    built from the stored fields only — no network.
     """
     rows = db.con.execute(
         """
@@ -120,16 +137,87 @@ def pending_queue(db: Db, project: str, limit: int | None = None) -> list[Pendin
                 title=_field(db, zot_id, "title"),
             )
         )
+    if client is not None:
+        _resolve_queue_pmcids(db, out, client, email)
+    return out
+
+
+def _resolve_queue_pmcids(
+    db: Db, items: list[PendingItem], client: httpx.Client, email: str
+) -> None:
+    missing = [it for it in items if it.pmid and not it.pmcid]
+    if not missing:
+        return
+    found = resolve_pmcids(client, [it.pmid for it in missing], email)
+    if not found:
+        return
+    for it in missing:
+        pmcid = found.get(it.pmid.strip())
+        if not pmcid:
+            continue
+        it.pmcid = pmcid
+        extra = _field(db, it.zot_id, "extra")
+        db.set_fields(
+            it.zot_id,
+            {"extra": f"{extra}\nPMCID: {pmcid}" if extra else f"PMCID: {pmcid}"},
+        )
+    db.commit()
+
+
+_IDCONV = "https://pmc.ncbi.nlm.nih.gov/tools/idconv/api/v1/articles/"
+_IDCONV_BATCH = 200
+
+
+def resolve_pmcids(
+    client: httpx.Client, pmids: list[str], email: str
+) -> dict[str, str]:
+    """PMID → PMCID via NCBI's idconv service, 200 ids per call (#723).
+
+    Only records idconv actually found are returned; ``status: error``
+    rows ("Identifier not found in PMC") and transport failures drop out.
+    """
+    ids = [p for p in dict.fromkeys((p or "").strip() for p in pmids) if p.isdigit()]
+    out: dict[str, str] = {}
+    for i in range(0, len(ids), _IDCONV_BATCH):
+        chunk = ids[i : i + _IDCONV_BATCH]
+        try:
+            r = client.get(
+                _IDCONV,
+                params={
+                    "ids": ",".join(chunk),
+                    "idtype": "pmid",
+                    "format": "json",
+                    "tool": "stack-prisma",
+                    "email": email,
+                },
+                timeout=30,
+            )
+            if r.status_code != 200:
+                continue
+            records = r.json().get("records") or []
+        except (httpx.HTTPError, ValueError):
+            continue
+        for rec in records:
+            pmcid = rec.get("pmcid")
+            if not pmcid or rec.get("status") == "error":
+                continue
+            out[str(rec.get("requested-id") or rec.get("pmid"))] = pmcid
     return out
 
 
 # ── Source fetchers ─────────────────────────────────────────────
 
 
-def fetch_unpaywall(client: httpx.Client, doi: str, email: str) -> str | None:
-    """Unpaywall → PDF URL (or None)."""
+def unpaywall_urls(client: httpx.Client, doi: str, email: str) -> list[str]:
+    """Every OA URL Unpaywall knows for *doi*, best location first.
+
+    ``best_oa_location`` is a ranking, not a guarantee — on the #650
+    pass it pointed at dead publisher links while a later
+    ``oa_locations`` entry served the PDF (#723). Direct PDF URLs come
+    before landing pages across all locations; duplicates dropped.
+    """
     if not doi:
-        return None
+        return []
     try:
         r = client.get(
             f"https://api.unpaywall.org/v2/{doi}",
@@ -137,11 +225,78 @@ def fetch_unpaywall(client: httpx.Client, doi: str, email: str) -> str | None:
             timeout=15,
         )
         if r.status_code != 200:
-            return None
-        best = r.json().get("best_oa_location") or {}
-        return best.get("url_for_pdf") or best.get("url")
-    except httpx.HTTPError:
+            return []
+        data = r.json()
+    except (httpx.HTTPError, ValueError):
+        return []
+    locs = [data.get("best_oa_location") or {}, *(data.get("oa_locations") or [])]
+    out: list[str] = []
+    for key in ("url_for_pdf", "url"):
+        for loc in locs:
+            u = loc.get(key)
+            if u and u not in out:
+                out.append(u)
+    return out
+
+
+def fetch_unpaywall(client: httpx.Client, doi: str, email: str) -> str | None:
+    """Unpaywall → best PDF URL (or None). See :func:`unpaywall_urls`."""
+    urls = unpaywall_urls(client, doi, email)
+    return urls[0] if urls else None
+
+
+_S2_BASE = "https://api.semanticscholar.org/graph/v1/paper"
+_S2_MIN_INTERVAL = 1.0  # unauthenticated graph API: ~1 req/s shared pool
+_S2_LAST = [0.0]
+_s2_lock = threading.Lock()
+
+
+@dataclass
+class S2Hit:
+    """What Semantic Scholar knows that helps the cascade."""
+
+    pdf_url: str
+    pmcid: str
+
+
+def fetch_semantic_scholar(client: httpx.Client, doi: str) -> S2Hit | None:
+    """Semantic Scholar graph API → ``openAccessPdf`` URL and/or a PMCID.
+
+    Found 4 of 30 items the rest of the cascade missed on the #650 pass
+    (#723). Its ``externalIds.PubMedCentral`` also fills in a PMCID the
+    Zotero record lacks, so the PMC tiers run for items Unpaywall only
+    knows by landing page. Rate-limited to ``_S2_MIN_INTERVAL`` across
+    threads; no API key needed.
+    """
+    if not doi:
         return None
+    with _s2_lock:
+        wait = _S2_MIN_INTERVAL - (time.monotonic() - _S2_LAST[0])
+        if wait > 0:
+            time.sleep(wait)
+        try:
+            r = client.get(
+                f"{_S2_BASE}/DOI:{doi}",
+                params={"fields": "openAccessPdf,externalIds"},
+                timeout=15,
+            )
+        except httpx.HTTPError:
+            return None
+        finally:
+            _S2_LAST[0] = time.monotonic()
+    if r.status_code != 200:
+        return None
+    try:
+        data = r.json()
+    except ValueError:
+        return None
+    pdf = (data.get("openAccessPdf") or {}).get("url") or ""
+    pmc = str((data.get("externalIds") or {}).get("PubMedCentral") or "")
+    if pmc and not pmc.startswith("PMC"):
+        pmc = f"PMC{pmc}"
+    if not pdf and not pmc:
+        return None
+    return S2Hit(pdf_url=pdf, pmcid=pmc)
 
 
 def fetch_pmc(client: httpx.Client, pmcid: str) -> str | None:
@@ -469,34 +624,47 @@ def fetch_one(
 ) -> tuple[str, Path] | None:
     """Run one item through the source cascade.
 
-    ``client`` is the unproxied httpx client (for Unpaywall + PMC).
-    ``client_proxied`` (optional) routes the fallback tier through the
-    VPN; if None, the fallback is skipped.
+    ``client`` is the unproxied httpx client (Unpaywall, Semantic
+    Scholar, PMC). ``client_proxied`` (optional) routes the fallback
+    tier through the VPN; if None, the fallback is skipped.
+
+    Order: every Unpaywall location → Semantic Scholar openAccessPdf →
+    PMC S3 → PMC OA service → Europe PMC → fallback. A PMCID the item
+    lacks may arrive from Semantic Scholar before the PMC tiers run.
     """
     filename = scratch / f"{item.zot_id}-{_hash(item.doi or item.title)}.pdf"
     doi = item.doi
     if not doi and item.title:
         doi = resolve_doi_from_title(client, item.title) or ""
 
-    url = fetch_unpaywall(client, doi, email)
-    if url:
+    for url in unpaywall_urls(client, doi, email):
         path = download(client, url, filename)
         if path:
             return "unpaywall", path
 
-    url = fetch_pmc_s3(client, item.pmcid)
+    pmcid = item.pmcid
+    s2 = fetch_semantic_scholar(client, doi)
+    if s2:
+        if s2.pdf_url:
+            path = download(client, s2.pdf_url, filename)
+            if path:
+                return "s2", path
+        if not pmcid:
+            pmcid = s2.pmcid
+
+    url = fetch_pmc_s3(client, pmcid)
     if url:
         path = download(client, url, filename)
         if path:
             return "pmc", path
 
-    url = fetch_pmc(client, item.pmcid)
+    url = fetch_pmc(client, pmcid)
     if url:
         path = download(client, url, filename)
         if path:
             return "pmc", path
 
-    path = fetch_europepmc_download(client, item.pmcid, filename)
+    path = fetch_europepmc_download(client, pmcid, filename)
     if path:
         return "pmc", path
 
@@ -563,13 +731,13 @@ def run(
     as `screen:reason:unavailable-fulltext`.
     """
     scratch_dir.mkdir(parents=True, exist_ok=True)
-    pending = pending_queue(db, project, limit=limit)
-    stats = {"unpaywall": 0, "pmc": 0, "fallback": 0, "missed": 0, "errors": 0}
+    stats = {"unpaywall": 0, "s2": 0, "pmc": 0, "fallback": 0, "missed": 0, "errors": 0}
 
     client = httpx.Client(
         headers={"User-Agent": USER_AGENT.format(email)},
         follow_redirects=True,
     )
+    pending = pending_queue(db, project, limit=limit, client=client, email=email)
     client_proxied: httpx.Client | None = None
     if fetch_proxy:
         # Mirrors behind altcha treat our generic UA as a bot; a real
@@ -626,8 +794,9 @@ def run(
                 if progress and done % 25 == 0:
                     print(
                         f"  fetched {done}/{len(pending)}  "
-                        f"(up={stats['unpaywall']} pmc={stats['pmc']} "
-                        f"fb={stats['fallback']} miss={stats['missed']})"
+                        f"(up={stats['unpaywall']} s2={stats['s2']} "
+                        f"pmc={stats['pmc']} fb={stats['fallback']} "
+                        f"miss={stats['missed']})"
                     )
     finally:
         client.close()

tests/prisma/test_fetch_deep.py

@@ -55,7 +55,8 @@ class TestFallbackSerialized:
             return None  # miss → cascade ends, no download
 
         # direct tiers all miss so every call reaches the fallback tier
-        monkeypatch.setattr(fetch_mod, "fetch_unpaywall", lambda c, d, e: None)
+        monkeypatch.setattr(fetch_mod, "unpaywall_urls", lambda c, d, e: [])
+        monkeypatch.setattr(fetch_mod, "fetch_semantic_scholar", lambda c, d: None)
         monkeypatch.setattr(fetch_mod, "fetch_pmc", lambda c, p: None)
         monkeypatch.setattr(fetch_mod, "fetch_fallback", fake_fallback)
 

tests/prisma/test_fetch_exercise.py

@@ -184,7 +184,7 @@ class TestFetchOne:
         )
         with (
             patch(
-                "prisma.fetch.fetch_unpaywall", return_value="https://ex.com/paper.pdf"
+                "prisma.fetch.unpaywall_urls", return_value=["https://ex.com/paper.pdf"]
             ),
             patch("prisma.fetch.download", return_value=tmp_path / "paper.pdf"),
         ):
@@ -196,7 +196,8 @@ class TestFetchOne:
     def test_pmc_hit(self, tmp_path):
         item = PendingItem(zot_id=1, doi="", title="Paper", pmcid="PMC123", pmid="")
         with (
-            patch("prisma.fetch.fetch_unpaywall", return_value=None),
+            patch("prisma.fetch.unpaywall_urls", return_value=[]),
+            patch("prisma.fetch.fetch_semantic_scholar", return_value=None),
             patch("prisma.fetch.fetch_pmc", return_value="https://pmc/pdf.pdf"),
             patch("prisma.fetch.download", return_value=tmp_path / "paper.pdf"),
         ):
@@ -211,7 +212,8 @@ class TestFetchOne:
         )
         proxied = MagicMock()
         with (
-            patch("prisma.fetch.fetch_unpaywall", return_value=None),
+            patch("prisma.fetch.unpaywall_urls", return_value=[]),
+            patch("prisma.fetch.fetch_semantic_scholar", return_value=None),
             patch("prisma.fetch.fetch_pmc", return_value=None),
             patch(
                 "prisma.fetch.fetch_fallback", return_value="https://mirror/paper.pdf"
@@ -232,7 +234,8 @@ class TestFetchOne:
             zot_id=1, doi="10.1234/test", title="Paper", pmcid="", pmid=""
         )
         with (
-            patch("prisma.fetch.fetch_unpaywall", return_value=None),
+            patch("prisma.fetch.unpaywall_urls", return_value=[]),
+            patch("prisma.fetch.fetch_semantic_scholar", return_value=None),
             patch("prisma.fetch.fetch_pmc", return_value=None),
         ):
             result = fetch_one(
@@ -246,7 +249,7 @@ class TestFetchOne:
             patch(
                 "prisma.fetch.resolve_doi_from_title", return_value="10.1234/resolved"
             ),
-            patch("prisma.fetch.fetch_unpaywall", return_value="https://ex.com/p.pdf"),
+            patch("prisma.fetch.unpaywall_urls", return_value=["https://ex.com/p.pdf"]),
             patch("prisma.fetch.download", return_value=tmp_path / "p.pdf"),
         ):
             result = fetch_one(

tests/prisma/test_fetch_tiers.py

@@ -0,0 +1,312 @@
+"""Tests for the #723 fetch tiers — Unpaywall all-locations, Semantic
+Scholar openAccessPdf, and idconv PMCID resolution in the queue."""
+
+from __future__ import annotations
+
+from unittest.mock import MagicMock
+
+import httpx
+import pytest
+
+from prisma import fetch as fetch_mod
+from prisma.fetch import (
+    PendingItem,
+    fetch_one,
+    fetch_semantic_scholar,
+    pending_queue,
+    resolve_pmcids,
+    unpaywall_urls,
+)
+from zot.db import TYPE_MAP, Db
+from zot.schema import create_db
+
+
+@pytest.fixture(autouse=True)
+def _no_s2_throttle(monkeypatch):
+    monkeypatch.setattr(fetch_mod, "_S2_MIN_INTERVAL", 0.0)
+
+
+def _json_client(routes: dict[str, object], seen: list[str] | None = None):
+    """MockTransport client: substring of URL → JSON body (or status int)."""
+
+    def handler(request):
+        url = str(request.url)
+        if seen is not None:
+            seen.append(url)
+        for needle, body in routes.items():
+            if needle in url:
+                if isinstance(body, int):
+                    return httpx.Response(body)
+                return httpx.Response(200, json=body)
+        return httpx.Response(404)
+
+    return httpx.Client(transport=httpx.MockTransport(handler))
+
+
+# ── unpaywall_urls ────────────────────────────────────────────────
+
+
+class TestUnpaywallUrls:
+    def test_all_locations_pdf_first(self):
+        body = {
+            "best_oa_location": {"url_for_pdf": None, "url": "https://a/landing"},
+            "oa_locations": [
+                {"url_for_pdf": None, "url": "https://a/landing"},
+                {"url_for_pdf": "https://b/paper.pdf", "url": "https://b/landing"},
+                {"url_for_pdf": "https://c/paper.pdf", "url": None},
+            ],
+        }
+        urls = unpaywall_urls(_json_client({"unpaywall": body}), "10.1/x", "e@x")
+        # every PDF URL before any landing page; no duplicates
+        assert urls == [
+            "https://b/paper.pdf",
+            "https://c/paper.pdf",
+            "https://a/landing",
+            "https://b/landing",
+        ]
+
+    def test_best_location_only_legacy_shape(self):
+        body = {"best_oa_location": {"url_for_pdf": "https://oa/p.pdf"}}
+        assert unpaywall_urls(_json_client({"unpaywall": body}), "10.1/x", "e@x") == [
+            "https://oa/p.pdf"
+        ]
+
+    def test_no_doi(self):
+        assert unpaywall_urls(MagicMock(), "", "e@x") == []
+
+    def test_404(self):
+        assert unpaywall_urls(_json_client({"unpaywall": 404}), "10.1/x", "e@x") == []
+
+    def test_no_locations(self):
+        body = {"best_oa_location": None, "oa_locations": []}
+        assert unpaywall_urls(_json_client({"unpaywall": body}), "10.1/x", "e@x") == []
+
+
+# ── fetch_semantic_scholar ────────────────────────────────────────
+
+
+class TestFetchSemanticScholar:
+    def test_pdf_and_pmcid(self):
+        seen: list[str] = []
+        body = {
+            "openAccessPdf": {"url": "https://s2/p.pdf", "status": "GREEN"},
+            "externalIds": {"PubMedCentral": "5226373", "DOI": "10.1/x"},
+        }
+        hit = fetch_semantic_scholar(
+            _json_client({"semanticscholar": body}, seen), "10.1/x"
+        )
+        assert hit is not None
+        assert hit.pdf_url == "https://s2/p.pdf"
+        assert hit.pmcid == "PMC5226373"
+        assert "paper/DOI:10.1/x" in seen[0] and "openAccessPdf" in seen[0]
+
+    def test_pmcid_only(self):
+        body = {"openAccessPdf": None, "externalIds": {"PubMedCentral": "PMC42"}}
+        hit = fetch_semantic_scholar(_json_client({"semanticscholar": body}), "10.1/x")
+        assert hit is not None
+        assert hit.pdf_url == ""
+        assert hit.pmcid == "PMC42"
+
+    def test_nothing_useful(self):
+        body = {"openAccessPdf": None, "externalIds": {"DOI": "10.1/x"}}
+        assert (
+            fetch_semantic_scholar(_json_client({"semanticscholar": body}), "10.1/x")
+            is None
+        )
+
+    def test_404(self):
+        assert (
+            fetch_semantic_scholar(_json_client({"semanticscholar": 404}), "10.1/x")
+            is None
+        )
+
+    def test_no_doi(self):
+        assert fetch_semantic_scholar(MagicMock(), "") is None
+
+    def test_throttled(self, monkeypatch):
+        """Calls are spaced by _S2_MIN_INTERVAL even from a cold start."""
+        monkeypatch.setattr(fetch_mod, "_S2_MIN_INTERVAL", 0.2)
+        monkeypatch.setattr(fetch_mod, "_S2_LAST", [0.0])
+        client = _json_client({"semanticscholar": 404})
+        import time
+
+        t0 = time.monotonic()
+        fetch_semantic_scholar(client, "10.1/a")
+        fetch_semantic_scholar(client, "10.1/b")
+        assert time.monotonic() - t0 >= 0.2
+
+
+# ── resolve_pmcids ────────────────────────────────────────────────
+
+
+class TestResolvePmcids:
+    _RECORDS = {
+        "status": "ok",
+        "records": [
+            {
+                "doi": "10.1/x",
+                "pmcid": "PMC5226373",
+                "pmid": 27893131,
+                "requested-id": "27893131",
+            },
+            {
+                "pmid": 28679817,
+                "requested-id": "28679817",
+                "status": "error",
+                "errmsg": "Identifier not found in PMC",
+            },
+        ],
+    }
+
+    def test_maps_found_only(self):
+        seen: list[str] = []
+        out = resolve_pmcids(
+            _json_client({"idconv": self._RECORDS}, seen),
+            ["27893131", "28679817"],
+            "e@x",
+        )
+        assert out == {"27893131": "PMC5226373"}
+        assert "idtype=pmid" in seen[0] and "ids=27893131%2C28679817" in seen[0]
+        assert "email=e%40x" in seen[0]
+
+    def test_batches_of_200(self):
+        seen: list[str] = []
+        client = _json_client({"idconv": {"status": "ok", "records": []}}, seen)
+        resolve_pmcids(client, [str(i) for i in range(1, 402)], "e@x")
+        assert len(seen) == 3
+
+    def test_skips_non_numeric_and_dupes(self):
+        seen: list[str] = []
+        client = _json_client({"idconv": {"status": "ok", "records": []}}, seen)
+        resolve_pmcids(client, ["", "abc", "12", "12"], "e@x")
+        assert len(seen) == 1 and "ids=12&" in seen[0]
+
+    def test_empty(self):
+        assert resolve_pmcids(MagicMock(), [], "e@x") == {}
+
+    def test_http_error(self):
+        assert resolve_pmcids(_json_client({"idconv": 500}), ["1"], "e@x") == {}
+
+
+# ── pending_queue PMCID resolution ────────────────────────────────
+
+
+def _db(tmp_path):
+    path = str(tmp_path / "z.sqlite")
+    create_db(path).close()
+    return path
+
+
+def _item(db, project, extra, doi="10.1/x"):
+    iid = db.create_item(TYPE_MAP["journalArticle"])
+    db.set_fields(iid, {"title": "Test Item", "DOI": doi, "extra": extra})
+    db.sync_tags(iid, [f"project:{project}", "screen:include"])
+    db.commit()
+    return iid
+
+
+class TestPendingQueueIdconv:
+    def test_resolves_and_persists(self, tmp_path):
+        path = _db(tmp_path)
+        recs = {
+            "status": "ok",
+            "records": [
+                {"pmcid": "PMC777", "pmid": 111, "requested-id": "111"},
+            ],
+        }
+        seen: list[str] = []
+        client = _json_client({"idconv": recs}, seen)
+        with Db(path) as db:
+            a = _item(db, "p", "PMID: 111")
+            b = _item(db, "p", "PMID: 222\nPMCID: PMC222", doi="10.1/y")
+            c = _item(db, "p", "", doi="10.1/z")
+            items = pending_queue(db, "p", client=client, email="e@x")
+            by_id = {it.zot_id: it for it in items}
+            assert by_id[a].pmcid == "PMC777"
+            assert by_id[b].pmcid == "PMC222"
+            assert by_id[c].pmcid == ""
+            # only the one PMID lacking a PMCID was sent
+            assert len(seen) == 1 and "ids=111&" in seen[0]
+            # persisted into extra, existing lines kept
+            assert fetch_mod._field(db, a, "extra") == "PMID: 111\nPMCID: PMC777"
+            # second call: nothing left to resolve
+            pending_queue(db, "p", client=client, email="e@x")
+            assert len(seen) == 1
+
+    def test_no_client_no_network(self, tmp_path):
+        path = _db(tmp_path)
+        with Db(path) as db:
+            a = _item(db, "p", "PMID: 111")
+            items = pending_queue(db, "p")
+            assert items[0].zot_id == a and items[0].pmcid == ""
+
+
+# ── fetch_one cascade order ───────────────────────────────────────
+
+
+def _pdf_client(routes_json: dict[str, object], pdf_urls: set[str], seen: list[str]):
+    def handler(request):
+        url = str(request.url)
+        seen.append(url)
+        if url in pdf_urls:
+            return httpx.Response(
+                200,
+                content=b"%PDF-1.7\n" + b"x" * 2000,
+                headers={"content-type": "application/pdf"},
+            )
+        for needle, body in routes_json.items():
+            if needle in url:
+                return (
+                    httpx.Response(200, json=body)
+                    if not isinstance(body, int)
+                    else httpx.Response(body)
+                )
+        return httpx.Response(404)
+
+    return httpx.Client(transport=httpx.MockTransport(handler))
+
+
+class TestFetchOneTiers:
+    def test_second_unpaywall_location_wins(self, tmp_path):
+        seen: list[str] = []
+        up = {
+            "best_oa_location": {"url_for_pdf": "https://dead/p.pdf"},
+            "oa_locations": [
+                {"url_for_pdf": "https://dead/p.pdf"},
+                {"url_for_pdf": "https://alive/p.pdf"},
+            ],
+        }
+        client = _pdf_client({"unpaywall": up}, {"https://alive/p.pdf"}, seen)
+        item = PendingItem(zot_id=1, doi="10.1/x", pmid="", pmcid="", title="T")
+        res = fetch_one(item, email="e@x", scratch=tmp_path, client=client)
+        assert res is not None and res[0] == "unpaywall"
+        assert "https://dead/p.pdf" in seen and "https://alive/p.pdf" in seen
+        assert not any("semanticscholar" in u for u in seen)
+
+    def test_s2_pdf_after_unpaywall_miss(self, tmp_path):
+        seen: list[str] = []
+        s2 = {"openAccessPdf": {"url": "https://s2/p.pdf"}, "externalIds": {}}
+        client = _pdf_client(
+            {"unpaywall": 404, "semanticscholar": s2}, {"https://s2/p.pdf"}, seen
+        )
+        item = PendingItem(zot_id=1, doi="10.1/x", pmid="", pmcid="", title="T")
+        res = fetch_one(item, email="e@x", scratch=tmp_path, client=client)
+        assert res is not None and res[0] == "s2"
+
+    def test_s2_pmcid_feeds_pmc_tiers(self, tmp_path):
+        seen: list[str] = []
+        s2 = {"openAccessPdf": None, "externalIds": {"PubMedCentral": "99"}}
+        client = _pdf_client({"unpaywall": 404, "semanticscholar": s2}, set(), seen)
+        item = PendingItem(zot_id=1, doi="10.1/x", pmid="", pmcid="", title="T")
+        assert fetch_one(item, email="e@x", scratch=tmp_path, client=client) is None
+        assert any("prefix=PMC99." in u for u in seen), seen  # S3 listing tried
+        assert any("id=PMC99" in u for u in seen), seen  # OA service tried
+
+    def test_item_pmcid_not_overridden(self, tmp_path):
+        seen: list[str] = []
+        s2 = {"openAccessPdf": None, "externalIds": {"PubMedCentral": "99"}}
+        client = _pdf_client({"unpaywall": 404, "semanticscholar": s2}, set(), seen)
+        item = PendingItem(zot_id=1, doi="10.1/x", pmid="", pmcid="PMC1", title="T")
+        fetch_one(item, email="e@x", scratch=tmp_path, client=client)
+        assert not any("PMC99" in u for u in seen)
+        assert any("prefix=PMC1." in u for u in seen)