Remove dead PMC full-text code from PMIDSource

src/linkml_reference_validator/etl/sources/pmid.py

@@ -17,7 +17,6 @@
 
 from Bio import Entrez  # type: ignore
 from bs4 import BeautifulSoup  # type: ignore
-import requests  # type: ignore
 
 from linkml_reference_validator.models import ReferenceContent, ReferenceValidationConfig
 from linkml_reference_validator.etl.sources.base import ReferenceSource, ReferenceSourceRegistry
@@ -335,138 +334,3 @@ def _parse_publication_types(
         ]
 
         return types if types else None
-
-    def _fetch_pmc_fulltext(
-        self, pmid: str, config: ReferenceValidationConfig
-    ) -> tuple[Optional[str], str]:
-        """Attempt to fetch full text from PMC.
-
-        Args:
-            pmid: PubMed ID
-            config: Configuration for rate limiting
-
-        Returns:
-            Tuple of (full_text, content_type)
-        """
-        pmcid = self._get_pmcid(pmid, config)
-        if not pmcid:
-            return None, "no_pmc"
-
-        full_text = self._fetch_pmc_xml(pmcid, config)
-        if full_text and len(full_text) > 1000:
-            return full_text, "full_text_xml"
-
-        full_text = self._fetch_pmc_html(pmcid, config)
-        if full_text and len(full_text) > 1000:
-            return full_text, "full_text_html"
-
-        return None, "pmc_restricted"
-
-    def _get_pmcid(self, pmid: str, config: ReferenceValidationConfig) -> Optional[str]:
-        """Get PMC ID for a PubMed ID.
-
-        Args:
-            pmid: PubMed ID
-            config: Configuration for rate limiting
-
-        Returns:
-            PMC ID if available
-        """
-        time.sleep(config.rate_limit_delay)
-
-        try:
-            handle = Entrez.elink(
-                dbfrom="pubmed", db="pmc", id=pmid, linkname="pubmed_pmc"
-            )
-        except Exception as exc:
-            logger.warning("Failed to link PMID:%s to PMC: %s", pmid, exc)
-            return None
-
-        try:
-            result = Entrez.read(handle)
-        except Exception as exc:
-            logger.warning(
-                "Failed to read PMC link for PMID:%s: %s", pmid, exc)
-            return None
-        finally:
-            handle.close()
-
-        if isinstance(result, list) and result and isinstance(result[0], dict):
-            link_set_db = result[0].get("LinkSetDb", [])
-            if isinstance(link_set_db, list) and link_set_db:
-                links = link_set_db[0].get("Link", [])
-                if isinstance(links, list) and links:
-                    first_link = links[0]
-                    if isinstance(first_link, dict) and "Id" in first_link:
-                        return str(first_link["Id"])
-
-        return None
-
-    def _fetch_pmc_xml(
-        self, pmcid: str, config: ReferenceValidationConfig
-    ) -> Optional[str]:
-        """Fetch full text from PMC XML API.
-
-        Args:
-            pmcid: PMC ID
-            config: Configuration for rate limiting
-
-        Returns:
-            Extracted text from XML
-        """
-        time.sleep(config.rate_limit_delay)
-
-        handle = Entrez.efetch(
-            db="pmc", id=pmcid, rettype="xml", retmode="xml")
-        xml_content = handle.read()
-        handle.close()
-
-        if isinstance(xml_content, bytes):
-            xml_content = xml_content.decode("utf-8")
-
-        if "cannot be obtained" in xml_content.lower() or "restricted" in xml_content.lower():
-            return None
-
-        soup = BeautifulSoup(xml_content, "xml")
-        body = soup.find("body")
-
-        if body:
-            paragraphs = body.find_all("p")
-            if paragraphs:
-                text = "\n\n".join(p.get_text() for p in paragraphs)
-                return text
-
-        return None
-
-    def _fetch_pmc_html(
-        self, pmcid: str, config: ReferenceValidationConfig
-    ) -> Optional[str]:
-        """Fetch full text from PMC HTML as fallback.
-
-        Args:
-            pmcid: PMC ID
-            config: Configuration for rate limiting
-
-        Returns:
-            Extracted text from HTML
-        """
-        time.sleep(config.rate_limit_delay)
-
-        url = f"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC{pmcid}/"
-
-        response = requests.get(url, timeout=30)
-        if response.status_code != 200:
-            return None
-
-        soup = BeautifulSoup(response.content, "html.parser")
-        article_body = soup.find("div", class_="article-body") or soup.find(
-            "div", class_="tsec"
-        )
-
-        if article_body:
-            paragraphs = article_body.find_all("p")
-            if paragraphs:
-                text = "\n\n".join(p.get_text() for p in paragraphs)
-                return text
-
-        return None

src/linkml_reference_validator/plugins/REVIEW.md

@@ -229,7 +229,7 @@ Comprehensive Repository Review Report
   2. CLI Not Tested:
   Violates: "Always include CLI tests"
   3. Insufficient Doctests for Complex Functions:
-  Some complex functions lack doctests (e.g., _fetch_pmc_fulltext)
+  Some complex functions lack doctests
 
   Architecture Strengths
 
@@ -247,13 +247,8 @@ Comprehensive Repository Review Report
   reference_fetcher.py (68% coverage)
 
   Untested lines (54 total):
-  - Lines 224-232: _fetch_pmc_fulltext logic
-  - Lines 265-286: _fetch_pmc_xml parsing
-  - Lines 297-314: _fetch_pmc_html scraping
   - Lines 139-140, 170-172: Error handling
 
-  Impact: PMC full-text retrieval completely untested
-
   reference_validation_plugin.py (56% coverage)
 
   Untested lines (55 total):

tests/test_fulltext_providers.py

@@ -173,3 +173,14 @@ def test_locate_returns_text_from_xml(self, config):
         assert loc.format_hint == "xml"
         assert loc.provider == "pmc"
         assert "Sentence 0 of the body." in loc.text
+
+    @patch("linkml_reference_validator.etl.fulltext.pmc.Entrez.elink")
+    def test_resolve_pmcid_handles_entrez_error(self, mock_elink, config):
+        """Should return None when the Entrez elink call fails."""
+        from linkml_reference_validator.etl.fulltext.pmc import PMCFullTextProvider
+
+        mock_elink.side_effect = RuntimeError(
+            "Couldn't resolve #exLinkSrv2, the address table is empty."
+        )
+
+        assert PMCFullTextProvider()._resolve_pmcid("12112053", config) is None

tests/test_sources.py

@@ -297,27 +297,6 @@ def test_can_handle_pmid(self, source):
         assert source.can_handle("PMID 12345678")
         assert not source.can_handle("DOI:10.1234/test")
 
-    @patch("linkml_reference_validator.etl.sources.pmid.Entrez.read")
-    @patch("linkml_reference_validator.etl.sources.pmid.Entrez.elink")
-    def test_get_pmcid_handles_entrez_error(
-        self,
-        mock_elink,
-        mock_read,
-        source,
-        config,
-    ):
-        """Should return None when Entrez.read raises an error."""
-        handle = MagicMock()
-        mock_elink.return_value = handle
-        mock_read.side_effect = RuntimeError(
-            "Couldn't resolve #exLinkSrv2, the address table is empty."
-        )
-
-        result = source._get_pmcid("12112053", config)
-
-        assert result is None
-        handle.close.assert_called_once()
-
     # --- Publication types (issue #56) -----------------------------------
 
     _ARTICLE_XML = """<?xml version="1.0"?>