fixed bug: made parseQstatOutput handle domains other than ipr.univ-rennes1.fr properly

before this fix, `parseQstatOutput` created a list of machines with a hardcoded ipr.univ-rennes1.fr domain, resulting in potentatially wrong fqdn

work related to https://bugzilla.ipr.univ-rennes.fr/show_bug.cgi?id=3693

cocluto/ClusterController/QstatParser.py

@@ -54,9 +54,11 @@ class QstatParser:
                 assert False, 'unhandled queue machine state flag :"' + c + '"'
         return queueMachineState
 
-    def parseQstatOutput(self, qstatOutput):
+    def parseQstatOutput(self, qstatOutput, cluster_domain: str = 'ipr.univ-rennes1.fr'):
         """
-        parses result of command 'qstat -f -u \* -pri'
+        parses result of command 'qstat -f -u \\* -pri'
+
+        cluster_domain: network domain of the cluster (eg 'ipr.univ-rennes.fr'). This information is missing from qstat's output and is used to form the fully qualified domain name of the cluster machines.
         """
         logging.debug('qstatOutput type : %s' % type(qstatOutput))
 
@@ -70,25 +72,25 @@ class QstatParser:
             for example, this function would return [1, 2, 3, 4, 6, 7, 8] for the input string "1-4:1,6-8:1"
             """
             task_ids = []
-            astrRanges = re.split(',', task_ranges_sequence)
-            for strRange in astrRanges:
-                singleIndexMatch = re.match('^(?P<elementIndex>[0-9]+)$', strRange)
-                if singleIndexMatch:
-                    iElementIndex = int(singleIndexMatch.group('elementIndex'))
-                    task_ids.extend(range(iElementIndex, iElementIndex + 1))
+            ranges = re.split(',', task_ranges_sequence)
+            for task_range in ranges:
+                single_index_match = re.match('^(?P<elementIndex>[0-9]+)$', task_range)
+                if single_index_match:
+                    element_index = int(single_index_match.group('elementIndex'))
+                    task_ids.extend(range(element_index, element_index + 1))
                 else:
                     # we expect strRange to be of the form "1-4:1", where :
                     # the 1st number is the min element index (sge imposes it to be greater than 0)
                     # the 2nd number is the max element index
                     # the 3rd number is the step between consecutive element indices
-                    rangeMatch = re.match('^(?P<minElementIndex>[0-9]+)-(?P<maxElementIndex>[0-9]+):(?P<stepBetweenIndices>[0-9]+)$', strRange)
-                    if rangeMatch is None:
-                        logError('unexpected format for job array details : "%s" (line="%s"' % (strRange, line))
+                    range_match = re.match('^(?P<minElementIndex>[0-9]+)-(?P<maxElementIndex>[0-9]+):(?P<stepBetweenIndices>[0-9]+)$', task_range)
+                    if range_match is None:
+                        logError('unexpected format for job array details : "%s" (line="%s"' % (task_range, line))
                         assert False
-                    iMinElementIndex = int(rangeMatch.group('minElementIndex'))
-                    iMaxElementIndex = int(rangeMatch.group('maxElementIndex'))
-                    iStepBetweenIndices = int(rangeMatch.group('stepBetweenIndices'))
-                    task_ids.extend(range(iMinElementIndex, iMaxElementIndex + 1, iStepBetweenIndices))
+                    min_element_index = int(range_match.group('minElementIndex'))
+                    min_element_index = int(range_match.group('maxElementIndex'))
+                    step_between_indices = int(range_match.group('stepBetweenIndices'))
+                    task_ids.extend(range(min_element_index, min_element_index + 1, step_between_indices))
             return task_ids
 
         # ugly hack to work around the fact that qstat truncates the fqdn of cluster nodes
@@ -97,7 +99,7 @@ class QstatParser:
         # ---------------------------------------------------------------------------------
         # main.q@physix88.ipr.univ-renne BIP   0/0/36         14.03    lx-amd64
         # TODO: fix this properly by parsing the output of 'qstat -f -u \* -xml' instead of 'qstat -f -u \*'
-        qstatOutput = re.sub(r'\.univ[^ ]*', '.univ-rennes1.fr', qstatOutput)
+        qstatOutput = re.sub(r'\.ipr\.univ[^ ]*', f'.{cluster_domain}', qstatOutput)
 
         jobsState = JobsState()
         f = io.StringIO(qstatOutput)
@@ -209,8 +211,7 @@ class QstatParser:
                             bInPendingJobsSection = True
                             currentQueueMachine = None
                         else:
-                            # print line
-                            None
+                            pass
                 else:
                     # we are in a pending jobs section
                     matchObj = re.match('^[#]+$', line)
@@ -218,7 +219,6 @@ class QstatParser:
                         # unexpected line
                         print('line = "' + line + '"')
                         assert False
-                    None
             line = f.readline()
         f.close()
         return jobsState

cocluto/Util.py

@@ -69,7 +69,7 @@ def executeCommand(command):
     return result
 
 
-def executeCommandOn(target_machine_fqdn, command, user=None):
+def executeCommandOn(target_machine_fqdn: str, command: str, user: str = None):
     """
     execute command on a local or remote machine (using ssh then)
     :param str user: if not None, the user that should be used to execute the command (instead of the current user)

test/test_cocluto.py

@@ -20,7 +20,7 @@ class CoclutoTestCase(unittest.TestCase):
             qstat_output = file.read()
             # qstatParser = ClusterController.QstatParser()
             qstatParser = QstatParser()
-            job_state = qstatParser.parseQstatOutput(qstat_output)
+            job_state = qstatParser.parseQstatOutput(qstat_output, cluster_domain='ipr.univ-rennes1.fr')
 
         self.assertIsInstance(job_state, JobsState)