pre-process: improve FAIL

> pear.py > don't produce output file on failure
> don't reschedule run if pre-process has failed

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

@@ -145,7 +145,7 @@ def run_vidjil(id_file, id_config, id_data, id_fuse, grep_reads,
     from datetime import timedelta as timed
     
     ## re schedule if pre_process is still pending
-    if db.sequence_file[id_file].pre_process_flag != "DONE" and db.sequence_file[id_file].pre_process_flag != None :
+    if db.sequence_file[id_file].pre_process_flag == "WAIT" or db.sequence_file[id_file].pre_process_flag == "RUN" :
         
         print "Pre-process is still pending, re-schedule"
     
@@ -160,6 +160,10 @@ def run_vidjil(id_file, id_config, id_data, id_fuse, grep_reads,
         
         return "SUCCESS"
     
+    if db.sequence_file[id_file].pre_process_flag == "FAILED" :
+        print "Pre-process has failed"
+        raise ValueError('pre-process has failed')
+        return "FAIL"
     
     ## les chemins d'acces a vidjil / aux fichiers de sequences
     germline_folder = defs.DIR_VIDJIL + '/germline/'
@@ -702,6 +706,8 @@ def run_pre_process(pre_process_id, sequence_file_id, clean_before=True, clean_a
         db.commit()
         raise IOError
 
+        
+
     # Now we update the sequence file with the result of the pre-process
     # We forget the initial data_file (and possibly data_file2)
     db.sequence_file[sequence_file_id] = dict(data_file = stream,

tools/pear.py

@@ -6,6 +6,7 @@ import gzip
 import subprocess
 import argparse
 import shlex
+import os
 
 parser = argparse.ArgumentParser(description='Use PEAR read merger to make a new fastq file and keep unmerged reads')
 
@@ -32,13 +33,16 @@ subprocess.call(["pear",
 )
 
 
-
-with gzip.open(f_out, 'w') as outFile:
-    with open(f_out+'.assembled.fastq', 'rb') as f1:
-        shutil.copyfileobj(f1, outFile)
-    if (args.keep_r1):
-        with open(f_out+'.unassembled.reverse.fastq', 'rb') as f2:
-            shutil.copyfileobj(f2, outFile)
-    if (args.keep_r2):
-        with open(f_out+'.unassembled.forward.fastq', 'rb') as f3:
-            shutil.copyfileobj(f3, outFile)
+try :
+    with gzip.open(f_out, 'w') as outFile:
+        with open(f_out+'.assembled.fastq', 'rb') as f1:
+            shutil.copyfileobj(f1, outFile)
+        if (args.keep_r1):
+            with open(f_out+'.unassembled.reverse.fastq', 'rb') as f2:
+                shutil.copyfileobj(f2, outFile)
+        if (args.keep_r2):
+            with open(f_out+'.unassembled.forward.fastq', 'rb') as f3:
+                shutil.copyfileobj(f3, outFile)
+except IOError :
+    os.remove(f_out)
+    raise IOError