fix python3 string/bytes error when using --printLogs

src/toil/test/cwl/alwaysfails.cwl

@@ -0,0 +1,11 @@
+#!/usr/bin/env cwl-runner
+# Command that will always fail
+cwlVersion: v1.0
+class: CommandLineTool
+baseCommand: invalidcommand
+inputs:
+  message:
+    type: string
+    inputBinding:
+      position: 1
+outputs: []

src/toil/test/utils/utilsTest.py

@@ -40,6 +40,7 @@
 from toil.common import Toil, Config
 from toil.provisioners import clusterFactory
 from toil.version import python
+from mock import patch
 
 logger = logging.getLogger(__name__)
 
@@ -387,6 +388,22 @@ def testGetStatusSuccessfulCWLWF(self):
         wf.wait()
         self.check_status('COMPLETED', status_fn=ToilStatus.getStatus)
 
+    @needs_cwl
+    @needs_docker
+    @patch('builtins.print')
+    def testPrintJobLog(self, mock_print):
+        """Test that ToilStatus.printJobLog() reads the log from a failed command without error."""
+        # Run a workflow that will always fail
+        cmd = ['toil-cwl-runner', '--jobStore', self.toilDir, '--clean=never',
+               'src/toil/test/cwl/alwaysfails.cwl', '--message', 'Testing']
+        wf = subprocess.Popen(cmd)
+        wf.wait()
+        # print log and check output
+        status = ToilStatus(self.toilDir)
+        status.printJobLog()
+        args, kwargs = mock_print.call_args
+        self.assertIn('LOG_FILE_OF_JOB', args[0])
+
 
 def printUnicodeCharacter():
     # We want to get a unicode character to stdout but we can't print it directly because of

src/toil/utils/toilStatus.py

@@ -80,7 +80,7 @@ def printJobLog(self):
             if job.logJobStoreFileID is not None:
                 msg = "LOG_FILE_OF_JOB:%s LOG: =======>\n" % job
                 with job.getLogFileHandle(self.jobStore) as fH:
-                    msg += fH.read()
+                    msg += fH.read().decode('utf-8')
                 msg += "<========="
             else:
                 msg = "LOG_FILE_OF_JOB:%s LOG: Job has no log file" % job