Crossref deposit links the author's code and data archive: isSupplementedBy, as a DOI for a doi.org link and a URI otherwise, beside hasPreprint in the relations program; regression suite validates every variant against the 5.4.0 schema

crossref_deposit.py

@@ -335,17 +335,44 @@ def preprint_doi(submission: dict) -> Optional[str]:
     return preprint_check.normalize(ref) if ref else None
 
 
+_DOI_LINK = re.compile(r"^https?://(?:dx\.)?doi\.org/(10\.\d{4,9}/\S+)$", re.IGNORECASE)
+
+
+def code_data_relation(submission: dict) -> Optional[tuple[str, str]]:
+    """(identifier-type, identifier) for the author's code and data archive,
+    or None. A doi.org link is registered as the DOI it resolves; any other
+    public link (GitHub, a lab page) as a URI. ICSAC links to the archive; the
+    author hosts it (policy 2026-09-28)."""
+    import publications
+    url = publications.code_data_url(submission)
+    if not url:
+        return None
+    m = _DOI_LINK.match(url)
+    if m:
+        return ("doi", m.group(1))
+    return ("uri", url)
+
+
 def _relations(parent: ET.Element, submission: dict) -> None:
-    """rel:program with hasPreprint -> the preprint's DOI (schema order: after
-    the licence program, before doi_data)."""
+    """rel:program (schema order: after the licence program, before doi_data)
+    with up to two related items: hasPreprint -> the preprint's DOI, and
+    isSupplementedBy -> the author's code and data archive (2026-09-29), so the
+    archive is found from the article's own Crossref record."""
     pre = preprint_doi(submission)
-    if not pre:
+    sup = code_data_relation(submission)
+    if not pre and not sup:
         return
     prog = ET.SubElement(parent, _q("program", REL_NS))
-    item = ET.SubElement(prog, _q("related_item", REL_NS))
-    rel = ET.SubElement(item, _q("intra_work_relation", REL_NS),
-                        {"relationship-type": "hasPreprint", "identifier-type": "doi"})
-    rel.text = pre
+    if pre:
+        item = ET.SubElement(prog, _q("related_item", REL_NS))
+        rel = ET.SubElement(item, _q("intra_work_relation", REL_NS),
+                            {"relationship-type": "hasPreprint", "identifier-type": "doi"})
+        rel.text = pre
+    if sup:
+        item = ET.SubElement(prog, _q("related_item", REL_NS))
+        rel = ET.SubElement(item, _q("inter_work_relation", REL_NS),
+                            {"relationship-type": "isSupplementedBy", "identifier-type": sup[0]})
+        rel.text = sup[1]
 
 
 def _doi_data(parent: ET.Element, doi: str, landing: str, pdf_url: Optional[str]) -> None:

intake/scripts/test_crossref_supplement.py

@@ -0,0 +1,95 @@
+#!/usr/bin/env python3
+"""Checks for the code and data relation in the Crossref deposit (2026-09-29):
+an article whose author gave a public code and data link carries
+isSupplementedBy in its Crossref record, as a DOI when the link is a doi.org
+link and as a URI otherwise; every variant validates against the Crossref
+5.4.0 schema. Offline and pure: no network, no files written.
+Run from the repo root with the venv:
+    .venv/bin/python intake/scripts/test_crossref_supplement.py
+"""
+from __future__ import annotations
+
+import sys
+from pathlib import Path
+
+ROOT = Path(__file__).resolve().parents[2]
+sys.path.insert(0, str(ROOT))
+
+failures: list[str] = []
+
+
+def check(cond: bool, name: str) -> None:
+    print(("  ok   " if cond else "  FAIL ") + name)
+    if not cond:
+        failures.append(name)
+
+
+import crossref_deposit as cd  # noqa: E402
+
+BASE = {"sub_id": "ICSAC-SUB-00099", "title": "A test paper", "abstract": "An abstract.",
+        "license": "cc-by-4.0", "source": "upload",
+        "creators": [{"name": "Test, Author", "orcid": "0000-0002-1825-0097"}]}
+ZEN = "https://doi.org/10.5281/zenodo.23042786"
+
+
+def build(sub: dict, content_type: str = "journal-article") -> str:
+    xml = cd.build_deposit_xml(sub, doi="10.67697/icsac.2026.099",
+                               landing_url="https://icsacinstitute.org/publications/a-test-paper",
+                               pdf_url="https://icsacinstitute.org/papers/ICSAC-SUB-00099.pdf",
+                               content_type=content_type)
+    try:
+        cd.validate_xml(xml)
+        ok = True
+    except Exception as exc:  # noqa: BLE001
+        print(f"       schema: {exc}")
+        ok = False
+    return xml.decode() if ok else ""
+
+
+print("1. which identifier")
+rel = cd.code_data_relation
+check(rel(dict(BASE, code_data={"available": True, "url": ZEN})) == ("doi", "10.5281/zenodo.23042786"),
+      "a doi.org link is registered as its DOI")
+check(rel(dict(BASE, code_data={"available": True, "url": "https://dx.doi.org/10.5061/dryad.abc123"})) == ("doi", "10.5061/dryad.abc123"),
+      "a dx.doi.org link too")
+check(rel(dict(BASE, code_data={"available": True, "url": "https://github.com/someone/repo"})) == ("uri", "https://github.com/someone/repo"),
+      "any other public link is registered as a URI")
+check(rel(dict(BASE, code_data={"available": False, "url": None})) is None, "no link, no relation")
+check(rel(dict(BASE)) is None, "a submission from before the field existed has no relation")
+check(rel(dict(BASE, code_data={"available": True, "url": "  "})) is None, "a blank link is no link")
+
+print("2. the deposit")
+x = build(dict(BASE, code_data={"available": True, "url": ZEN}))
+check(bool(x), "an article with a DOI archive validates against the Crossref 5.4.0 schema")
+check('<rel:inter_work_relation relationship-type="isSupplementedBy" identifier-type="doi">10.5281/zenodo.23042786</rel:inter_work_relation>' in x,
+      "it carries isSupplementedBy -> the archive DOI")
+check(x.find("<rel:program") < x.find("<doi_data") and x.find("<rel:program") > 0, "the relation sits before doi_data")
+check("hasPreprint" not in x, "an upload with no preprint carries no preprint relation")
+
+x = build(dict(BASE, code_data={"available": True, "url": "https://github.com/someone/repo"}))
+check(bool(x) and 'identifier-type="uri">https://github.com/someone/repo<' in x,
+      "a GitHub link validates and is registered as a URI")
+
+x = build(dict(BASE, source="doi", doi="10.5281/zenodo.123456",
+               code_data={"available": True, "url": ZEN}))
+check(bool(x) and x.count("<rel:program") == 1 and x.count("<rel:related_item>") == 2,
+      "a preprint and an archive share one relations program, two related items")
+check('relationship-type="hasPreprint"' in x and 'relationship-type="isSupplementedBy"' in x,
+      "both relations present")
+
+x = build(dict(BASE))
+check(bool(x) and "<rel:program" not in x, "no preprint and no archive: no relations program at all")
+
+x = build(dict(BASE, code_data={"available": True, "url": ZEN}), content_type="report-paper")
+check(bool(x) and "isSupplementedBy" in x, "report-paper deposits carry the relation and validate too")
+
+x = build(dict(BASE, code_data={"available": True, "url": "https://example.org/data?x=1&y=2"}))
+check(bool(x) and "x=1&amp;y=2" in x, "a link with an ampersand is escaped and still validates")
+
+print()
+if failures:
+    print(f"FAILED: {len(failures)}")
+    for f in failures:
+        print("  - " + f)
+    sys.exit(1)
+print("ALL GREEN")