Merge pull request #121 from HobnobMancer/patch-incomplete-read

Catch incomplete read error
HobnobMancer · Jan 23, 2024 · c8b07ef · c8b07ef
2 parents 0d603a8 + 70e1fba
commit c8b07ef
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Showing 3 changed files with 6 additions and 3 deletions.
diff --git a/cazy_webscraper/__init__.py b/cazy_webscraper/__init__.py
@@ -66,7 +66,7 @@
 from cazy_webscraper.sql import sql_orm
 
 
-__version__ = "2.3.0.1"
+__version__ = "2.3.0.2"
 
 
 VERSION_INFO = f"cazy_webscraper version: {__version__}"

diff --git a/cazy_webscraper/ncbi/taxonomy/multiple_taxa.py b/cazy_webscraper/ncbi/taxonomy/multiple_taxa.py
@@ -42,6 +42,9 @@
 
 import logging
 
+from http.client import IncompleteRead
+
+from Bio.Entrez.Parser import NotXMLError
 from saintBioutils.genbank import entrez_retry
 from saintBioutils.misc import get_chunks_list
 from tqdm import tqdm
@@ -201,7 +204,7 @@ def get_ncbi_tax(epost_results, cazy_data, replaced_taxa_logger, args):
             protein_records = Entrez.read(record_handle, validate=False)
 
     # if no record is returned from call to Entrez
-    except (TypeError, AttributeError) as error:
+    except (TypeError, AttributeError, RuntimeError,  NotXMLError, IncompleteRead) as error:
         logger.error(
             f"Entrez failed to retireve accession numbers."
             "Exiting retrieval of accession numbers, and returning null value 'NA'"

diff --git a/setup.py b/setup.py
@@ -53,7 +53,7 @@
 
 setuptools.setup(
     name="cazy_webscraper",
-    version="2.3.0.1",
+    version="2.3.0.2",
     # Metadata
     author="Emma E. M. Hobbs",
     author_email="eemh1@st-andrews.ac.uk",