Catch TimeoutExpired error for subprocesses #298

juliema · Feb 19, 2021 · 6c2f3fd · 6c2f3fd
1 parent f250616
commit 6c2f3fd
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Showing 4 changed files with 11 additions and 5 deletions.
diff --git a/lib/assemblers/base.py b/lib/assemblers/base.py
@@ -2,7 +2,7 @@
 
 import datetime
 from os.path import abspath, basename, exists, getsize, join, splitext
-from subprocess import CalledProcessError
+from subprocess import CalledProcessError, TimeoutExpired
 
 from .. import bio, db_atram, util
 
@@ -72,11 +72,11 @@ def run(self):
             self.log.info('Assembling shards with {}: iteration {}'.format(
                 self.args['assembler'], self.state['iteration']))
             self.assemble()
-        except TimeoutError:
+        except (TimeoutExpired, TimeoutError):
             msg = 'Time ran out for the assembler after {} (HH:MM:SS)'.format(
                 datetime.timedelta(seconds=self.args['timeout']))
             self.log.error(msg)
-            raise TimeoutError(msg)
+            raise TimeoutExpired(msg, timeout=self.args['timeout'])
         except CalledProcessError as cpe:
             msg = 'The assembler failed with error: ' + str(cpe)
             self.log.error(msg)

diff --git a/lib/core_atram.py b/lib/core_atram.py
@@ -4,6 +4,7 @@
 import re
 from multiprocessing import Pool
 from os.path import basename, join, split, splitext
+from subprocess import TimeoutExpired
 
 from Bio import SeqIO
 
@@ -34,7 +35,7 @@ def assemble(args):
 
                     try:
                         assembly_loop(args, log, assembler, blast_db, query)
-                    except (TimeoutError, RuntimeError):
+                    except (TimeoutExpired, TimeoutError, RuntimeError):
                         pass
                     except Exception as err:  # pylint: disable=broad-except
                         log.error('Exception: {}'.format(err))

diff --git a/lib/db.py b/lib/db.py
@@ -5,7 +5,7 @@
 import sys
 from os.path import basename, exists, join
 
-ATRAM_VERSION = 'v2.3.4'
+ATRAM_VERSION = 'v2.3.5'
 
 # DB_VERSION != ATRAM_VERSION
 # We don't force DB changes until required.

diff --git a/lib/log.py b/lib/log.py
@@ -49,6 +49,8 @@ def subcommand(self, cmd, temp_dir, timeout=None):
         """
         self.debug(cmd)
 
+        error = None
+
         with tempfile.NamedTemporaryFile(mode='w', dir=temp_dir) as log_output:
             try:
                 subprocess.check_call(
@@ -59,12 +61,15 @@ def subcommand(self, cmd, temp_dir, timeout=None):
                     stderr=log_output)
             except Exception as err:  # pylint: disable=broad-except
                 self.error('Exception: {}'.format(err))
+                error = err
             finally:
                 with open(log_output.name) as log_input:
                     for line in log_input:
                         line = line.strip()
                         if line:
                             self.debug(line)
+                if error:
+                    raise error
 
     def _output(self, msg, level):
         timestamp = datetime.now().strftime('%Y-%m-%d %H:%M:%S')