diff --git a/src/linkml_reference_validator/etl/sources/pmid.py b/src/linkml_reference_validator/etl/sources/pmid.py
index fe1d7d5..d6933a7 100644
--- a/src/linkml_reference_validator/etl/sources/pmid.py
+++ b/src/linkml_reference_validator/etl/sources/pmid.py
@@ -13,7 +13,7 @@
import logging
import re
import time
-from typing import Optional
+from typing import Any, Optional
from Bio import Entrez # type: ignore
from bs4 import BeautifulSoup # type: ignore
@@ -118,13 +118,20 @@ def fetch(
record = records[0] if isinstance(records, list) else records
+ if not isinstance(record, dict):
+ logger.warning(
+ "Unexpected record format for PMID:%s: %s", pmid, type(record))
+ return None
+
+ record_dict: dict[str, Any] = record
+
# Convert Entrez StringElement objects to plain strings
- title = str(record.get("Title", ""))
- authors = self._parse_authors(record.get("AuthorList", []))
- journal = str(record.get("Source", ""))
- pub_date = record.get("PubDate", "")
+ title = str(record_dict.get("Title", ""))
+ authors = self._parse_authors(record_dict.get("AuthorList", []))
+ journal = str(record_dict.get("Source", ""))
+ pub_date = record_dict.get("PubDate", "")
year = str(pub_date)[:4] if pub_date else ""
- doi = str(record.get("DOI", "")) if record.get("DOI") else ""
+ doi = str(record_dict.get("DOI", "")) if record_dict.get("DOI") else ""
abstract = self._fetch_abstract(pmid, config)
full_text, content_type = self._fetch_pmc_fulltext(pmid, config)
@@ -178,7 +185,8 @@ def _fetch_abstract(
"""
time.sleep(config.rate_limit_delay)
- handle = Entrez.efetch(db="pubmed", id=pmid, rettype="abstract", retmode="text")
+ handle = Entrez.efetch(db="pubmed", id=pmid,
+ rettype="abstract", retmode="text")
abstract_text = handle.read()
handle.close()
@@ -206,7 +214,8 @@ def _fetch_mesh_terms(
"""
time.sleep(config.rate_limit_delay)
- handle = Entrez.efetch(db="pubmed", id=pmid, rettype="xml", retmode="xml")
+ handle = Entrez.efetch(db="pubmed", id=pmid,
+ rettype="xml", retmode="xml")
xml_content = handle.read()
handle.close()
@@ -271,14 +280,31 @@ def _get_pmcid(self, pmid: str, config: ReferenceValidationConfig) -> Optional[s
"""
time.sleep(config.rate_limit_delay)
- handle = Entrez.elink(dbfrom="pubmed", db="pmc", id=pmid, linkname="pubmed_pmc")
- result = Entrez.read(handle)
- handle.close()
+ 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 result and result[0].get("LinkSetDb"):
- links = result[0]["LinkSetDb"][0].get("Link", [])
- if links:
- return links[0]["Id"]
+ 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
@@ -296,7 +322,8 @@ def _fetch_pmc_xml(
"""
time.sleep(config.rate_limit_delay)
- handle = Entrez.efetch(db="pmc", id=pmcid, rettype="xml", retmode="xml")
+ handle = Entrez.efetch(
+ db="pmc", id=pmcid, rettype="xml", retmode="xml")
xml_content = handle.read()
handle.close()
diff --git a/src/linkml_reference_validator/plugins/reference_validation_plugin.py b/src/linkml_reference_validator/plugins/reference_validation_plugin.py
index 1b07570..bcf8477 100644
--- a/src/linkml_reference_validator/plugins/reference_validation_plugin.py
+++ b/src/linkml_reference_validator/plugins/reference_validation_plugin.py
@@ -94,6 +94,16 @@ def __init__(
self.validator = SupportingTextValidator(config)
self.schema_view: Optional[SchemaView] = None
+ @property
+ def cache_dir(self) -> Path:
+ """Return the cache directory for this plugin."""
+ return self.config.cache_dir
+
+ @cache_dir.setter
+ def cache_dir(self, value: Path) -> None:
+ """Update the cache directory for this plugin."""
+ self.config.cache_dir = value
+
def pre_process(self, context: ValidationContext) -> None:
"""Pre-process hook called before validation.
@@ -293,17 +303,16 @@ def _get_converter(self) -> Optional[Converter]:
return None
schema = self.schema_view.schema
if schema and schema.prefixes:
- # schema.prefixes is a dict of prefix name -> Prefix object
- # The Prefix object has a prefix_reference attribute with the URI
- prefix_map = {
- name: (
- prefix.prefix_reference
- if hasattr(prefix, "prefix_reference")
- else str(prefix)
- )
- for name, prefix in schema.prefixes.items()
- }
- return Converter.from_prefix_map(prefix_map)
+ # schema.prefixes is a list of Prefix objects
+ # Each Prefix object has a prefix_name and prefix_reference attribute
+ prefix_map: dict[str, str] = {}
+ for prefix in schema.prefixes:
+ prefix_name = getattr(prefix, "prefix_name", None)
+ prefix_reference = getattr(prefix, "prefix_reference", None)
+ if isinstance(prefix_name, str) and prefix_reference is not None:
+ prefix_map[prefix_name] = str(prefix_reference)
+ if prefix_map:
+ return Converter.from_prefix_map(prefix_map)
return None
# type: ignore
diff --git a/tests/test_plugin_integration.py b/tests/test_plugin_integration.py
index 2183b02..12b13ec 100644
--- a/tests/test_plugin_integration.py
+++ b/tests/test_plugin_integration.py
@@ -38,7 +38,8 @@ def test_plugin_initialization_with_params():
plugin = ReferenceValidationPlugin(
cache_dir="/tmp/cache",
)
- assert plugin.config.cache_dir.as_posix() == "/tmp/cache"
+ # Access the cache_dir attribute directly if config is not exposed
+ assert plugin.cache_dir.as_posix() == "/tmp/cache"
def test_extract_reference_id_string(plugin):
diff --git a/tests/test_sources.py b/tests/test_sources.py
index 95abb3c..750a46e 100644
--- a/tests/test_sources.py
+++ b/tests/test_sources.py
@@ -130,6 +130,7 @@ def test_fetch_relative_path_with_base_dir(self, tmp_path):
result = source.fetch("notes.md", config)
assert result is not None
+ assert result.content is not None
assert "Some notes here." in result.content
def test_fetch_relative_path_cwd_fallback(self, source, config, tmp_path, monkeypatch):
@@ -154,7 +155,8 @@ def test_fetch_nonexistent_file(self, source, config):
def test_extract_title_from_markdown(self, source, config, tmp_path):
"""Should extract title from first heading."""
test_file = tmp_path / "titled.md"
- test_file.write_text("Some preamble\n\n# The Real Title\n\nContent here.")
+ test_file.write_text(
+ "Some preamble\n\n# The Real Title\n\nContent here.")
result = source.fetch(str(test_file), config)
@@ -164,7 +166,8 @@ def test_extract_title_from_markdown(self, source, config, tmp_path):
def test_html_content_preserved(self, source, config, tmp_path):
"""HTML content should be preserved as-is."""
test_file = tmp_path / "test.html"
- test_file.write_text("Test & content
")
+ test_file.write_text(
+ "Test & content
")
result = source.fetch(str(test_file), config)
@@ -280,6 +283,27 @@ 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()
+
class TestDOISource:
"""Tests for DOISource (refactored from ReferenceFetcher)."""
@@ -470,7 +494,8 @@ def config(self, tmp_path):
"Project_Description",
"bioproject",
),
- (BioSampleSource, "biosample:SAMN00000001", "Title", "Description", "biosample"),
+ (BioSampleSource, "biosample:SAMN00000001",
+ "Title", "Description", "biosample"),
],
)
@patch("linkml_reference_validator.etl.sources.entrez.Entrez.read")
@@ -505,7 +530,8 @@ def test_fetch_entrez_summary(
assert result.content == "Example content summary."
assert result.content_type == "summary"
assert result.metadata["entrez_db"] == db_name
- mock_esummary.assert_called_once_with(db=db_name, id=reference_id.split(":", 1)[1])
+ mock_esummary.assert_called_once_with(
+ db=db_name, id=reference_id.split(":", 1)[1])
mock_handle.close.assert_called_once()
@pytest.mark.parametrize(
@@ -578,7 +604,8 @@ def test_fetch_geo_converts_accession_to_uid(
# Configure mock_read to return different values for esearch vs esummary
mock_read.side_effect = [
{"IdList": ["200067472"]}, # esearch result
- [{"title": "GEO Dataset Title", "summary": "GEO dataset summary."}], # esummary result
+ # esummary result
+ [{"title": "GEO Dataset Title", "summary": "GEO dataset summary."}],
]
result = source.fetch("GSE67472", config)
@@ -592,7 +619,8 @@ def test_fetch_geo_converts_accession_to_uid(
assert result.metadata["entrez_uid"] == "200067472"
# Verify esearch was called with accession
- mock_esearch.assert_called_once_with(db="gds", term="GSE67472[Accession]")
+ mock_esearch.assert_called_once_with(
+ db="gds", term="GSE67472[Accession]")
# Verify esummary was called with UID, not accession
mock_esummary.assert_called_once_with(db="gds", id="200067472")