Merge branch 'feature-s/fix_migrator_script' into 'dev'

Feature s/fix migrator script

See merge request !818

server/web2py/applications/vidjil/scripts/migrator.py

@@ -247,8 +247,11 @@ def copy_files(data, src, dest, log=MigrateLogger()):
     for t in file_fields:
         for entry in data[t]:
             if (data[t][entry][file_fields[t]] is not None):
-                log.debug("Copying %s" % data[t][entry][file_fields[t]])
-                copy(src + '/' + data[t][entry][file_fields[t]], dest + '/' + data[t][entry][file_fields[t]])
+                try:
+                    copy(src + '/' + data[t][entry][file_fields[t]], dest + '/' + data[t][entry][file_fields[t]])
+                    log.debug("Copying %s" % data[t][entry][file_fields[t]])
+                except:
+                    log.error("failed to copy file %s" % data[t][entry][file_fields[t]])
 
 def export_peripheral_data(extractor, data_dict, sample_set_ids, log=MigrateLogger()):
     sequence_rows = extractor.getSequenceFiles(sample_set_ids)
@@ -369,9 +372,9 @@ def import_data(filesrc, filedest, groupid, config=None, pprocess=None, dry_run=
             db.rollback()
             log.info("dry run successful, no data saved")
         else:
-            db.commit()
             log.info("copying files from %s to %s" % (filesrc, filedest))
             copy_files(data, filesrc + '/files', filedest, log=log)
+            db.commit()
             log.info("done")
     except:
         log.error("something went wrong, rolling back")