task.py: Catch more errors when launching processes

Before something could have failed before launching or when launching the
process but this would not have been properly logged. By expanding the scope
of the try/except we increase the chances of catching such a problem.
The exception is re-raised afterwards

server/web2py/applications/vidjil/models/task.py

@@ -182,6 +182,7 @@ def run_vidjil(id_file, id_config, id_data, grep_reads,
     out_log = out_folder+'/'+output_filename+'.vidjil.log'
     vidjil_log_file = open(out_log, 'w')
 
+    try:
     ## commande complete
     cmd = defs.DIR_VIDJIL + '/vidjil ' + ' -o  ' + out_folder + " -b " + output_filename
     cmd += ' ' + vidjil_cmd + ' '+ seq_file
@@ -209,13 +210,12 @@ def run_vidjil(id_file, id_config, id_data, grep_reads,
     print "===>", out_results
     results_filepath = os.path.abspath(out_results)
 
-    try:
         stream = open(results_filepath, 'rb')
-    except IOError:
+    except:
         print "!!! Vidjil failed, no result file"
         res = {"message": "[%s] c%s: Vidjil FAILED - %s" % (id_data, id_config, out_folder)}
         log.error(res)
-        raise IOError
+        raise
     
     ## Parse some info in .log
     vidjil_log_file.close()
@@ -319,6 +319,7 @@ def run_mixcr(id_file, id_config, id_data, clean_before=False, clean_after=False
         print "! Bad arguments, we expect args_align | args_assemble | args_exportClones"
 
     ## commande complete
+    try:
     mixcr = defs.DIR_MIXCR + 'mixcr'
     cmd = mixcr + ' align --save-reads -t 1 -r ' + align_report + ' ' + args_1 + ' ' + seq_file  + ' ' + out_alignments
     cmd += ' && '
@@ -342,14 +343,13 @@ def run_mixcr(id_file, id_config, id_data, clean_before=False, clean_after=False
     ## Get result file
     print "===>", out_results
     results_filepath = os.path.abspath(out_results)
-    try:
         stream = open(results_filepath, 'rb')
         stream.close()
-    except IOError:
+    except:
         print "!!! MiXCR failed, no result file"
         res = {"message": "[%s] c%s: MiXCR FAILED - %s" % (id_data, id_config, out_folder)}
         log.error(res)
-        raise IOError
+        raise
 
     align_report = get_file_content(align_report)
     assembly_report = get_file_content(assembly_report)
@@ -492,6 +492,7 @@ def run_fuse(id_file, id_config, id_data, sample_set_id, clean_before=True, clea
             files += defs.DIR_RESULTS + row.results_file.data_file + " "
             sequence_file_list += str(row.results_file.sequence_file_id) + "_"
             
+    try:
     fuse_cmd = db.config[id_config].fuse_command
     cmd = "python "+defs.DIR_FUSE+"/fuse.py -o "+ output_file + " " + fuse_cmd + " " + files
 
@@ -507,13 +508,12 @@ def run_fuse(id_file, id_config, id_data, sample_set_id, clean_before=True, clea
 
     fuse_filepath = os.path.abspath(output_file)
 
-    try:
         stream = open(fuse_filepath, 'rb')
-    except IOError:
+    except:
         print "!!! Fuse failed, no .fused file"
         res = {"message": "[%s] c%s: 'fuse' FAILED - %s" % (id_data, id_config, output_file)}
         log.error(res)
-        raise IOError
+        raise
 
     ts = time.time()
 
@@ -576,17 +576,17 @@ def custom_fuse(file_list):
         if db.results_file[id].data_file is not None :
             files += os.path.abspath(defs.DIR_RESULTS + db.results_file[id].data_file) + " "
     
+    try:
     cmd = "python "+ os.path.abspath(defs.DIR_FUSE) +"/fuse.py -o "+output_file+" -t 100 "+files
     proc_srvr = xmlrpclib.ServerProxy("http://%s:%d" % (defs.FUSE_SERVER, defs.PORT_FUSE_SERVER))
     fuse_filepath = proc_srvr.fuse(cmd, out_folder, output_filename)
     
-    try:
         f = open(fuse_filepath, 'rb')
         data = gluon.contrib.simplejson.loads(f.read())
-    except IOError, e:
+    except:
         res = {"message": "'custom fuse' -> IOError"}
         log.error(res)
-        raise e
+        raise
 
     clean_cmd = "rm -rf " + out_folder 
     p = Popen(clean_cmd, shell=True, stdin=PIPE, stdout=PIPE, stderr=STDOUT, close_fds=True)
@@ -687,6 +687,7 @@ def run_pre_process(pre_process_id, sequence_file_id, clean_before=True, clean_a
             
     pre_process = db.pre_process[pre_process_id]
 
+    try:
     cmd = pre_process.command.replace( "&file1&", defs.DIR_SEQUENCES + sequence_file.data_file)
     if sequence_file.data_file2:
         cmd = cmd.replace( "&file2&", defs.DIR_SEQUENCES + sequence_file.data_file2)
@@ -708,15 +709,14 @@ def run_pre_process(pre_process_id, sequence_file_id, clean_before=True, clean_a
 
     filepath = os.path.abspath(output_file)
 
-    try:
         stream = open(filepath, 'rb')
-    except IOError:
+    except:
         print "!!! Pre-process failed, no result file"
         res = {"message": "{%s} p%s: 'pre_process' FAILED - %s" % (sequence_file_id, pre_process_id, output_file)}
         log.error(res)
         db.sequence_file[sequence_file_id] = dict(pre_process_flag = "FAILED")
         db.commit()
-        raise IOError
+        raise