From 5872d941c6c66587eede3e479fa3e3e60690e1f4 Mon Sep 17 00:00:00 2001
From: Martijn Vermaat <martijn@vermaat.name>
Date: Mon, 21 Dec 2015 12:33:58 +0100
Subject: [PATCH] Degrade gracefully on HTTP error from Entrez
---
mutalyzer/ncbi.py | 22 ++++++++++++++++++----
1 file changed, 18 insertions(+), 4 deletions(-)
diff --git a/mutalyzer/ncbi.py b/mutalyzer/ncbi.py
index c4fc77bc..15fcc7c2 100644
--- a/mutalyzer/ncbi.py
+++ b/mutalyzer/ncbi.py
@@ -3,6 +3,8 @@ Communication with the NCBI.
"""
+from urllib2 import HTTPError
+
from Bio import Entrez
from .config import settings
@@ -65,7 +67,11 @@ def _get_link_from_ncbi(source_db, target_db, match_link_name,
source = '%s.%d' % (source_accession, source_version)
# Find source record.
- handle = Entrez.esearch(db=source_db, term=source)
+ try:
+ handle = Entrez.esearch(db=source_db, term=source)
+ except HTTPError:
+ return fail_or_retry()
+
try:
result = Entrez.read(handle)
except Entrez.Parser.ValidationError:
@@ -79,7 +85,11 @@ def _get_link_from_ncbi(source_db, target_db, match_link_name,
return fail_or_retry()
# Find link from source record to target record.
- handle = Entrez.elink(dbfrom=source_db, db=target_db, id=source_gi)
+ try:
+ handle = Entrez.elink(dbfrom=source_db, db=target_db, id=source_gi)
+ except HTTPError:
+ return fail_or_retry()
+
try:
result = Entrez.read(handle)
except Entrez.Parser.ValidationError:
@@ -98,8 +108,12 @@ def _get_link_from_ncbi(source_db, target_db, match_link_name,
return fail_or_retry()
# Get target record.
- handle = Entrez.efetch(
- db=target_db, id=target_gi, rettype='acc', retmode='text')
+ try:
+ handle = Entrez.efetch(
+ db=target_db, id=target_gi, rettype='acc', retmode='text')
+ except HTTPError:
+ return fail_or_retry()
+
target = unicode(handle.read()).strip().split('.')
handle.close()
--
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