Change CRISPResso_status.txt format to JSON

CRISPResso2/CRISPRessoAggregateCORE.py

@@ -85,7 +85,7 @@ def main():
 
         log_filename=_jp('CRISPRessoAggregate_RUNNING_LOG.txt')
         logger.addHandler(logging.FileHandler(log_filename))
-        logger.addHandler(CRISPRessoShared.StatusHandler(_jp('CRISPRessoAggregate_status.txt')))
+        logger.addHandler(CRISPRessoShared.StatusHandler(_jp('CRISPRessoAggregate_status.json')))
 
         with open(log_filename, 'w+') as outfile:
               outfile.write('[Command used]:\n%s\n\n[Execution log]:\n' % ' '.join(sys.argv))

CRISPResso2/CRISPRessoBatchCORE.py

@@ -124,7 +124,7 @@ def main():
 
         log_filename = _jp('CRISPRessoBatch_RUNNING_LOG.txt')
         logger.addHandler(logging.FileHandler(log_filename))
-        status_handler = CRISPRessoShared.StatusHandler(_jp('CRISPRessoBatch_status.txt'))
+        status_handler = CRISPRessoShared.StatusHandler(_jp('CRISPRessoBatch_status.json'))
         logger.addHandler(status_handler)
 
         with open(log_filename, 'w+') as outfile:

CRISPResso2/CRISPRessoCORE.py

@@ -1125,7 +1125,7 @@ def print_stacktrace_if_debug():
             with open(log_filename, 'w+') as outfile:
                 outfile.write('CRISPResso version %s\n[Command used]:\n%s\n\n[Execution log]:\n' %(CRISPRessoShared.__version__, crispresso_cmd_to_write))
 
-        logger.addHandler(CRISPRessoShared.StatusHandler(_jp('CRISPResso_status.txt')))
+        logger.addHandler(CRISPRessoShared.StatusHandler(_jp('CRISPResso_status.json')))
 
         aln_matrix_loc = os.path.join(_ROOT, "EDNAFULL")
         CRISPRessoShared.check_file(aln_matrix_loc)

CRISPResso2/CRISPRessoCompareCORE.py

@@ -154,7 +154,7 @@ def main():
 
         log_filename = _jp('CRISPRessoCompare_RUNNING_LOG.txt')
         logger.addHandler(logging.FileHandler(log_filename))
-        logger.addHandler(CRISPRessoShared.StatusHandler(_jp('CRISPRessoCompare_status.txt')))
+        logger.addHandler(CRISPRessoShared.StatusHandler(_jp('CRISPRessoCompare_status.json')))
 
         with open(log_filename, 'w+') as outfile:
             outfile.write('[Command used]:\nCRISPRessoCompare %s\n\n[Execution log]:\n' % ' '.join(sys.argv))

CRISPResso2/CRISPRessoMetaCORE.py

@@ -229,7 +229,7 @@ def main():
 
         log_filename=_jp('CRISPRessoMeta_RUNNING_LOG.txt')
         logger.addHandler(logging.FileHandler(log_filename))
-        logger.addHandler(CRISPRessoShared.StatusHandler(_jp('CRISPRessoMeta_status.txt')))
+        logger.addHandler(CRISPRessoShared.StatusHandler(_jp('CRISPRessoMeta_status.json')))
 
         with open(log_filename, 'w+') as outfile:
             outfile.write('[Command used]:\n%s\n\n[Execution log]:\n' % ' '.join(sys.argv))

CRISPResso2/CRISPRessoPooledCORE.py

@@ -359,7 +359,7 @@ def main():
 
         log_filename = _jp('CRISPRessoPooled_RUNNING_LOG.txt')
         logger.addHandler(logging.FileHandler(log_filename))
-        logger.addHandler(CRISPRessoShared.StatusHandler(_jp('CRISPRessoPooled_status.txt')))
+        logger.addHandler(CRISPRessoShared.StatusHandler(_jp('CRISPRessoPooled_status.json')))
 
         if args.zip_output and not args.place_report_in_output_folder:
             logger.warn('Invalid arguement combination: If zip_output is True then place_report_in_output_folder must also be True. Setting place_report_in_output_folder to True.')

CRISPResso2/CRISPRessoPooledWGSCompareCORE.py

@@ -231,7 +231,7 @@ def main():
 
         log_filename = _jp('CRISPRessoPooledWGSCompare_RUNNING_LOG.txt')
         logger.addHandler(logging.FileHandler(log_filename))
-        logger.addHandler(CRISPRessoShared.StatusHandler(_jp('CRISPRessoPooledWGSCompare_status.txt')))
+        logger.addHandler(CRISPRessoShared.StatusHandler(_jp('CRISPRessoPooledWGSCompare_status.json')))
 
         with open(log_filename, 'w+') as outfile:
             outfile.write(

CRISPResso2/CRISPRessoShared.py

@@ -91,7 +91,7 @@ class StatusFormatter(logging.Formatter):
     def format(self, record):
         record.percent_complete = ''
         if record.args and 'percent_complete' in record.args:
-            record.percent_complete = '{0:.2f}% '.format(record.args['percent_complete'])
+            record.percent_complete = float(record.args['percent_complete'])
             self.last_percent_complete = record.percent_complete
         elif hasattr(self, 'last_percent_complete'): # if we don't have a percent complete, use the last one
             record.percent_complete = self.last_percent_complete
@@ -101,7 +101,7 @@ def format(self, record):
 class StatusHandler(logging.FileHandler):
     def __init__(self, filename):
         super().__init__(filename, 'w')
-        self.setFormatter(StatusFormatter('%(percent_complete)s%(message)s'))
+        self.setFormatter(StatusFormatter('{\n  "message": "%(message)s",\n  "percent_complete": %(percent_complete)s\n}'))
 
     def emit(self, record):
         """Overwrite the existing file and write the new log."""
@@ -896,7 +896,7 @@ def write_crispresso_info(crispresso_output_file, crispresso2_info):
 
     """
     with open(crispresso_output_file, 'w') as fh:
-        json.dump(crispresso2_info, fh, cls=CRISPRessoJSONEncoder)
+        json.dump(crispresso2_info, fh, cls=CRISPRessoJSONEncoder, indent=2)
 
 
 def get_command_output(command):
@@ -1045,7 +1045,7 @@ def check_if_failed_run(folder_name, info):
     """
 
     run_data_file = os.path.join(folder_name, 'CRISPResso2_info.json')
-    status_info = os.path.join(folder_name, 'CRISPResso_status.txt')
+    status_info = os.path.join(folder_name, 'CRISPResso_status.json')
     if not os.path.isfile(run_data_file) or not os.path.isfile(status_info):
         info("Skipping folder '%s'. Cannot find run data status file at '%s'."%(folder_name, run_data_file))
         if "CRISPRessoPooled" in folder_name:
@@ -1059,20 +1059,31 @@ def check_if_failed_run(folder_name, info):
     else:
         with open(status_info) as fh:
             try:
-                file_contents = fh.read()
-                search_result = re.search(r'(\d+\.\d+)% (.+)', file_contents)
-                if search_result:
-                    percent_complete, status = search_result.groups()
-                    if percent_complete != '100.00':
-                        info("Skipping folder '%s'. Run is not complete (%s)." % (folder_name, status))
-                        return True, status
+                status_dict = json.load(fh)
+                if status_dict['percent_complete'] != 100.0:
+                    info("Skipping folder '%s'. Run is not complete (%s)." % (folder_name, status_dict['status']))
+                    return True, str(status_dict['message'])
                 else:
-                    return True, file_contents
-            except Exception as e:
-                print(e)
-                info("Skipping folder '%s'. Cannot parse status file '%s'." % (folder_name, status_info))
-                return True, "Cannot parse status file '%s'." % (status_info)
-    return False, ""
+                    return False, ""
+            except:
+                pass
+
+        with open(status_info) as fh:
+                try:
+                    file_contents = fh.read()
+                    search_result = re.search(r'(\d+\.\d+)% (.+)', file_contents)
+                    if search_result:
+                        percent_complete, status = search_result.groups()
+                        if percent_complete != '100.00':
+                            info("Skipping folder '%s'. Run is not complete (%s)." % (folder_name, status))
+                            return True, status
+                    else:
+                        return True, file_contents
+                except Exception as e:
+                    print(e)
+                    info("Skipping folder '%s'. Cannot parse status file '%s'." % (folder_name, status_info))
+                    return True, "Cannot parse status file '%s'." % (status_info)
+        return False, ""
 
 
 def guess_amplicons(fastq_r1,fastq_r2,number_of_reads_to_consider,flash_command,max_paired_end_reads_overlap,min_paired_end_reads_overlap,aln_matrix,needleman_wunsch_gap_open,needleman_wunsch_gap_extend,split_interleaved_input=False,min_freq_to_consider=0.2,amplicon_similarity_cutoff=0.95):

CRISPResso2/CRISPRessoWGSCORE.py

@@ -364,7 +364,7 @@ def print_stacktrace_if_debug():
         except:
             warn('Folder %s already exists.' % OUTPUT_DIRECTORY)
 
-        logger.addHandler(CRISPRessoShared.StatusHandler(_jp('CRISPRessoWGS_status.txt')))
+        logger.addHandler(CRISPRessoShared.StatusHandler(_jp('CRISPRessoWGS_status.json')))
 
         info('Checking dependencies...')