Add ePMC publication URL handling and remove unused DOI DbType branch

Author: suecharo

ddbj_search_converter/jsonl/bp.py

@@ -185,10 +185,17 @@ def parse_publication(project: dict[str, Any], accession: str = "") -> list[Publ
             id_ = item.get("id")
             dbtype = item.get("DbType")
             publication_url = None
-            if dbtype in ("DOI", "eDOI"):
+            if dbtype == "eDOI":
                 publication_url = f"https://doi.org/{id_}"
             elif dbtype == "ePubmed":
                 publication_url = f"https://pubmed.ncbi.nlm.nih.gov/{id_}/"
+            elif dbtype == "ePMC":
+                if id_ is not None and id_.startswith("PMC"):
+                    publication_url = f"https://www.ncbi.nlm.nih.gov/pmc/articles/{id_}/"
+                elif id_ is not None and id_.isdigit():
+                    publication_url = f"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC{id_}/"
+                elif id_ is not None and id_.startswith("10."):
+                    publication_url = f"https://doi.org/{id_}"
             elif dbtype is not None and dbtype.isdigit():
                 dbtype = "ePubmed"
                 publication_url = f"https://pubmed.ncbi.nlm.nih.gov/{id_}/"

tests/py_tests/jsonl/test_bp.py

@@ -205,27 +205,60 @@ def test_single_publication(self) -> None:
         assert pubs[0].url is not None
         assert "pubmed" in pubs[0].url
 
-    def test_publication_doi(self) -> None:
+    def test_publication_edoi(self) -> None:
+        """DbType が eDOI の場合、doi.org の URL を生成する。"""
         project = _make_project()
         project["Project"]["ProjectDescr"]["Publication"] = {
-            "id": "10.1234/test",
-            "DbType": "DOI",
+            "id": "10.1271/bbb.60419",
+            "DbType": "eDOI",
         }
         pubs = parse_publication(project)
         assert len(pubs) == 1
-        assert pubs[0].url is not None
-        assert "doi.org" in pubs[0].url
+        assert pubs[0].url == "https://doi.org/10.1271/bbb.60419"
 
-    def test_publication_edoi(self) -> None:
-        """DbType が eDOI の場合、doi.org の URL を生成する。"""
+    def test_publication_epmc_with_prefix(self) -> None:
+        """DbType が ePMC で PMC プレフィックス付き ID の場合。"""
         project = _make_project()
         project["Project"]["ProjectDescr"]["Publication"] = {
-            "id": "10.1271/bbb.60419",
-            "DbType": "eDOI",
+            "id": "PMC3564981",
+            "DbType": "ePMC",
         }
         pubs = parse_publication(project)
         assert len(pubs) == 1
-        assert pubs[0].url == "https://doi.org/10.1271/bbb.60419"
+        assert pubs[0].url == "https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3564981/"
+
+    def test_publication_epmc_numeric(self) -> None:
+        """DbType が ePMC で数字のみの ID の場合、PMC プレフィックスを付与する。"""
+        project = _make_project()
+        project["Project"]["ProjectDescr"]["Publication"] = {
+            "id": "3594186",
+            "DbType": "ePMC",
+        }
+        pubs = parse_publication(project)
+        assert len(pubs) == 1
+        assert pubs[0].url == "https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3594186/"
+
+    def test_publication_epmc_doi_format(self) -> None:
+        """DbType が ePMC だが ID が DOI 形式の場合、DOI としてリンクする。"""
+        project = _make_project()
+        project["Project"]["ProjectDescr"]["Publication"] = {
+            "id": "10.1007/s10531-014-0684-8",
+            "DbType": "ePMC",
+        }
+        pubs = parse_publication(project)
+        assert len(pubs) == 1
+        assert pubs[0].url == "https://doi.org/10.1007/s10531-014-0684-8"
+
+    def test_publication_not_available(self) -> None:
+        """DbType が eNotAvailable の場合、url は None。"""
+        project = _make_project()
+        project["Project"]["ProjectDescr"]["Publication"] = {
+            "id": "unpublished",
+            "DbType": "eNotAvailable",
+        }
+        pubs = parse_publication(project)
+        assert len(pubs) == 1
+        assert pubs[0].url is None
 
     def test_publication_numeric_dbtype(self) -> None:
         """DbType が数字の場合、ePubmed として扱う。"""