zotkit 0.4.1__tar.gz → 0.4.2__tar.gz

{zotkit-0.4.1/zotkit.egg-info → zotkit-0.4.2}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: zotkit
-Version: 0.4.1
+Version: 0.4.2
 Summary: Headless Zotero library management: Web API CRUD plus direct WebDAV attachment upload/download — no desktop app required
 Author: Shawn
 License-Expression: MIT
@@ -125,9 +125,20 @@ zotkit lint field:physics topic:new-idea    # offline tag check
 ```
 
 `--arxiv` takes ids or abs/pdf URLs (several, space- or comma-separated) and maps
-the full record (all authors, abstract, date, DOI, `preprint` item type); `--doi`
+the full record (all authors, abstract, date, DOI); `--doi`
 maps CrossRef records (journal articles, conference papers, books, chapters, …)
-and refuses to guess on CrossRef types it doesn't know. Both accept `--collection`
+and refuses to guess on CrossRef types it doesn't know.
+
+**Version of record**: when arXiv reports a *journal* DOI (the paper was formally
+published — as opposed to arXiv's own `10.48550/*` DataCite DOI), `--arxiv`
+builds the journal record from CrossRef instead of a `preprint`: proper item
+type, venue, volume/pages, formal date. The arXiv identity is kept — `arXiv: <id>`
+goes in Extra, the `url` stays the open-access abs page (the journal link lives in
+the DOI field), the arXiv abstract fills in when CrossRef has none, and the PDF
+still comes from arXiv. If the CrossRef lookup fails, the item falls back to the
+preprint record with a warning rather than failing. Items whose abstract zotkit
+wrote also carry an `abstract-source: arxiv|crossref` line in Extra, naming where
+it actually came from. Both accept `--collection`
 and `--tags`, and `--no-pdf` skips the arXiv PDFs. Rate limiting is built into the
 request layer — batches use one arXiv metadata request and space PDF downloads
 per arXiv's terms of use, so callers (humans or agents) never pace themselves. A

{zotkit-0.4.1 → zotkit-0.4.2}/README.md

@@ -105,9 +105,20 @@ zotkit lint field:physics topic:new-idea    # offline tag check
 ```
 
 `--arxiv` takes ids or abs/pdf URLs (several, space- or comma-separated) and maps
-the full record (all authors, abstract, date, DOI, `preprint` item type); `--doi`
+the full record (all authors, abstract, date, DOI); `--doi`
 maps CrossRef records (journal articles, conference papers, books, chapters, …)
-and refuses to guess on CrossRef types it doesn't know. Both accept `--collection`
+and refuses to guess on CrossRef types it doesn't know.
+
+**Version of record**: when arXiv reports a *journal* DOI (the paper was formally
+published — as opposed to arXiv's own `10.48550/*` DataCite DOI), `--arxiv`
+builds the journal record from CrossRef instead of a `preprint`: proper item
+type, venue, volume/pages, formal date. The arXiv identity is kept — `arXiv: <id>`
+goes in Extra, the `url` stays the open-access abs page (the journal link lives in
+the DOI field), the arXiv abstract fills in when CrossRef has none, and the PDF
+still comes from arXiv. If the CrossRef lookup fails, the item falls back to the
+preprint record with a warning rather than failing. Items whose abstract zotkit
+wrote also carry an `abstract-source: arxiv|crossref` line in Extra, naming where
+it actually came from. Both accept `--collection`
 and `--tags`, and `--no-pdf` skips the arXiv PDFs. Rate limiting is built into the
 request layer — batches use one arXiv metadata request and space PDF downloads
 per arXiv's terms of use, so callers (humans or agents) never pace themselves. A

{zotkit-0.4.1 → zotkit-0.4.2}/pyproject.toml

@@ -4,7 +4,7 @@ build-backend = "setuptools.build_meta"
 
 [project]
 name = "zotkit"
-version = "0.4.1"
+version = "0.4.2"
 description = "Headless Zotero library management: Web API CRUD plus direct WebDAV attachment upload/download — no desktop app required"
 readme = "README.md"
 license = "MIT"

{zotkit-0.4.1 → zotkit-0.4.2}/zotkit/__init__.py

@@ -2,4 +2,4 @@
 from .core import Conventions, TagConventionError, Zot, lint_tags, load_conventions
 
 __all__ = ["Zot", "lint_tags", "load_conventions", "Conventions", "TagConventionError"]
-__version__ = "0.4.1"
+__version__ = "0.4.2"

{zotkit-0.4.1 → zotkit-0.4.2}/zotkit/cli.py

@@ -158,9 +158,13 @@ def main(argv=None):
                     for r in fetch_arxiv_batch(wanted):
                         if r.get("error"):
                             failures.append((r["id"], r["error"]))
-                        else:
-                            items.append(r["item"])
-                            pdfs[r["item"]["title"]] = (r["id"], r["pdf_url"])
+                            continue
+                        if r.get("note"):  # version-of-record upgrade happened
+                            print(r["note"])
+                        if r.get("warning"):
+                            print(f"warning: {r['warning']}", file=sys.stderr)
+                        items.append(r["item"])
+                        pdfs[r["item"]["title"]] = (r["id"], r["pdf_url"])
                 else:
                     for d in wanted:
                         try:

{zotkit-0.4.1 → zotkit-0.4.2}/zotkit/metadata.py

@@ -95,6 +95,11 @@ def _squash(s: str) -> str:
     return re.sub(r"\s+", " ", s or "").strip()
 
 
+def _add_extra(item: dict, line: str) -> None:
+    """Append a line to the item's Extra field, never overwriting what's there."""
+    item["extra"] = f"{item['extra']}\n{line}" if item.get("extra") else line
+
+
 def _person(name: str) -> dict:
     """Split a display name into first/last on the final space; single-token
     names go in lastName alone (matches Zotero's single-field mode)."""
@@ -145,14 +150,39 @@ def _arxiv_item(entry, aid: str) -> tuple[dict, str]:
         "archiveID": f"arXiv:{aid}",
         "libraryCatalog": "arXiv.org",
     }
+    if item["abstractNote"]:
+        _add_extra(item, "abstract-source: arxiv")
     return item, f"https://arxiv.org/pdf/{aid}"
 
 
+_DATACITE_PREFIX = "10.48550/"  # arXiv's own DOIs; anything else is a journal DOI
+
+
+def _journal_record(pre: dict, aid: str) -> dict:
+    """Version-of-record upgrade: the arXiv record carries a journal DOI, so
+    build the item from CrossRef instead (venue/volume/pages/formal date),
+    keeping the arXiv identity: abstract fallback when CrossRef has none,
+    `arXiv: <id>` in Extra, and the open-access abs page as url (the journal
+    link is carried by the DOI field). Raises MetadataError on lookup failure —
+    the caller falls back to the preprint record."""
+    j = fetch_doi(pre["DOI"])
+    if not j.get("abstractNote") and pre.get("abstractNote"):
+        j["abstractNote"] = pre["abstractNote"]
+        _add_extra(j, "abstract-source: arxiv")
+    j["url"] = pre["url"]
+    _add_extra(j, f"arXiv: {aid}")
+    return j
+
+
 def fetch_arxiv_batch(ids_or_urls: list[str]) -> list[dict]:
     """arXiv export API, one id_list request per ≤50 ids → results in input
     order, each {"id", "item", "pdf_url"} or {"id", "error"}. A bad id never
     fails the batch; only transport-level trouble raises MetadataError.
 
+    Version of record: when arXiv reports a journal DOI (not its own
+    10.48550/* DataCite DOI) the item is rebuilt from CrossRef ("note" key
+    says so); if that lookup fails the preprint record stands ("warning" key).
+
     The response can't be trusted positionally: entries come back in arbitrary
     order (and with resolved version numbers), so they are mapped back to the
     requested ids by version-stripped id.
@@ -191,8 +221,17 @@ def fetch_arxiv_batch(ids_or_urls: list[str]) -> list[dict]:
             entry = emap.get(_bare(c["id"]))
             if entry is None:
                 c["error"] = f"arXiv has no record for '{c['id']}' — check the id"
-            else:
-                c["item"], c["pdf_url"] = _arxiv_item(entry, c["id"])
+                continue
+            c["item"], c["pdf_url"] = _arxiv_item(entry, c["id"])
+            doi = c["item"]["DOI"]
+            if not doi.startswith(_DATACITE_PREFIX):
+                try:
+                    c["item"] = _journal_record(c["item"], c["id"])
+                    c["note"] = (f"{c['id']} → journal DOI {doi}, "
+                                 "building journal record")
+                except MetadataError as e:
+                    c["warning"] = (f"{c['id']}: journal DOI {doi} lookup failed "
+                                    f"({e}) — keeping preprint record")
     return results
 
 
@@ -268,7 +307,7 @@ def fetch_doi(doi: str) -> dict:
         "url": msg.get("URL") or f"https://doi.org/{doi}",
         "volume": msg.get("volume", ""),
         "issue": msg.get("issue", ""),
-        "pages": msg.get("page", ""),
+        "pages": msg.get("page") or msg.get("article-number", ""),
         "publisher": _squash(msg.get("publisher", "")),
         "language": msg.get("language", ""),
         "ISSN": (msg.get("ISSN") or [""])[0],
@@ -282,4 +321,7 @@ def fetch_doi(doi: str) -> dict:
     if not item["title"]:
         raise MetadataError(f"CrossRef record for '{doi}' has no title — refusing to "
                             "create an empty item")
-    return {k: v for k, v in item.items() if v not in ("", [])}
+    item = {k: v for k, v in item.items() if v not in ("", [])}
+    if item.get("abstractNote"):
+        _add_extra(item, "abstract-source: crossref")
+    return item

{zotkit-0.4.1 → zotkit-0.4.2/zotkit.egg-info}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: zotkit
-Version: 0.4.1
+Version: 0.4.2
 Summary: Headless Zotero library management: Web API CRUD plus direct WebDAV attachment upload/download — no desktop app required
 Author: Shawn
 License-Expression: MIT
@@ -125,9 +125,20 @@ zotkit lint field:physics topic:new-idea    # offline tag check
 ```
 
 `--arxiv` takes ids or abs/pdf URLs (several, space- or comma-separated) and maps
-the full record (all authors, abstract, date, DOI, `preprint` item type); `--doi`
+the full record (all authors, abstract, date, DOI); `--doi`
 maps CrossRef records (journal articles, conference papers, books, chapters, …)
-and refuses to guess on CrossRef types it doesn't know. Both accept `--collection`
+and refuses to guess on CrossRef types it doesn't know.
+
+**Version of record**: when arXiv reports a *journal* DOI (the paper was formally
+published — as opposed to arXiv's own `10.48550/*` DataCite DOI), `--arxiv`
+builds the journal record from CrossRef instead of a `preprint`: proper item
+type, venue, volume/pages, formal date. The arXiv identity is kept — `arXiv: <id>`
+goes in Extra, the `url` stays the open-access abs page (the journal link lives in
+the DOI field), the arXiv abstract fills in when CrossRef has none, and the PDF
+still comes from arXiv. If the CrossRef lookup fails, the item falls back to the
+preprint record with a warning rather than failing. Items whose abstract zotkit
+wrote also carry an `abstract-source: arxiv|crossref` line in Extra, naming where
+it actually came from. Both accept `--collection`
 and `--tags`, and `--no-pdf` skips the arXiv PDFs. Rate limiting is built into the
 request layer — batches use one arXiv metadata request and space PDF downloads
 per arXiv's terms of use, so callers (humans or agents) never pace themselves. A