def output():
sample_set_id = get_sample_set_id_from_results_file(
request.vars["results_file_id"])
if (auth.can_view_sample_set(sample_set_id)):
results_id = int(request.vars["results_file_id"])
output_directory = defs.DIR_OUT_VIDJIL_ID % results_id
files = os.listdir(output_directory)
file_dicts = []
for f in files:
file_size = vidjil_utils.format_size(
os.stat(output_directory + f).st_size)
file_dicts.append({'filename': f, 'size': file_size})
log.info("view output files",
extra={
'user_id': auth.user.id,
'record_id': request.vars["results_file_id"],
'table_name': "results_file"
})
return dict(message="output files",
results_file_id=results_id,
files=file_dicts)
return error_message("access denied")
def upload():
session.forget(response)
mes = ""
error = ""
if request.vars['id'] == None :
error += "missing id"
elif db.sequence_file[request.vars["id"]] is None:
error += "no sequence file with this id"
if not error:
mes += " file {%s} " % (request.vars['id'])
res = {"message": mes + "processing uploaded file"}
log.debug(res)
if request.vars.file != None :
f = request.vars.file
try:
if request.vars["file_number"] == "1" :
db.sequence_file[request.vars["id"]] = dict(data_file = db.sequence_file.data_file.store(f.file, f.filename))
else :
db.sequence_file[request.vars["id"]] = dict(data_file2 = db.sequence_file.data_file.store(f.file, f.filename))
mes += "upload finished"
except IOError as e:
if str(e).find("File name too long") > -1:
error += 'Your filename is too long, please shorten it.'
else:
error += "System error during processing of uploaded file."
log.error(str(e))
data_file = db.sequence_file[request.vars["id"]].data_file
data_file2 = db.sequence_file[request.vars["id"]].data_file2
if request.vars["file_number"] == "1" and len(error) == 0 and data_file is None:
error += "no data file"
if request.vars["file_number"] == "2" and len(error) == 0 and data_file2 is None:
error += "no data file"
if data_file is not None and data_file2 is not None and request.vars['pre_process'] != '0':
db.sequence_file[request.vars["id"]] = dict(pre_process_flag = "WAIT")
old_task_id = db.sequence_file[request.vars["id"]].pre_process_scheduler_task_id
if db.scheduler_task[old_task_id] != None:
scheduler.stop_task(old_task_id)
db(db.scheduler_task.id == old_task_id).delete()
db.commit()
schedule_pre_process(int(request.vars['id']), int(request.vars['pre_process']))
mes += " | p%s start pre_process %s " % (request.vars['pre_process'], request.vars['id'] + "-" +request.vars['pre_process'])
if data_file is not None :
seq_file = defs.DIR_SEQUENCES + data_file
# Compute and store file size
size = os.path.getsize(seq_file)
mes += ' (%s)' % vidjil_utils.format_size(size)
db.sequence_file[request.vars["id"]] = dict(size_file = size)
if data_file2 is not None :
seq_file2 = defs.DIR_SEQUENCES + data_file2
#TODO
# Log and exit
res = {"message": error + mes}
if error:
res['success'] = 'false'
res['priority'] = 3
log.error(res)
else:
log.info(res)
return gluon.contrib.simplejson.dumps(res, separators=(',',':'))
def upload():
session.forget(response)
mes = ""
error = ""
if request.vars['id'] == None:
error += "missing id"
elif db.sequence_file[request.vars["id"]] is None:
error += "no sequence file with this id"
if not error:
mes += " file {%s} " % (request.vars['id'])
res = {"message": mes + "processing uploaded file"}
log.debug(res)
if request.vars.file != None:
f = request.vars.file
try:
if request.vars["file_number"] == "1":
db.sequence_file[request.vars["id"]] = dict(
data_file=db.sequence_file.data_file.store(
f.file, f.filename))
else:
db.sequence_file[request.vars["id"]] = dict(
data_file2=db.sequence_file.data_file.store(
f.file, f.filename))
mes += "upload finished (%s)" % (f.filename)
except IOError as e:
if str(e).find("File name too long") > -1:
error += 'Your filename is too long, please shorten it.'
else:
error += "System error during processing of uploaded file."
log.error(str(e))
data_file = db.sequence_file[request.vars["id"]].data_file
data_file2 = db.sequence_file[request.vars["id"]].data_file2
if request.vars["file_number"] == "1" and len(
error) == 0 and data_file is None:
error += "no data file"
if request.vars["file_number"] == "2" and len(
error) == 0 and data_file2 is None:
error += "no data file"
if data_file is not None and data_file2 is not None and request.vars[
'pre_process'] != '0':
db.sequence_file[request.vars["id"]] = dict(
pre_process_flag="WAIT")
old_task_id = db.sequence_file[
request.vars["id"]].pre_process_scheduler_task_id
if db.scheduler_task[old_task_id] != None:
scheduler.stop_task(old_task_id)
db(db.scheduler_task.id == old_task_id).delete()
db.commit()
schedule_pre_process(int(request.vars['id']),
int(request.vars['pre_process']))
mes += " | p%s start pre_process %s " % (
request.vars['pre_process'],
request.vars['id'] + "-" + request.vars['pre_process'])
if data_file is not None:
seq_file = defs.DIR_SEQUENCES + data_file
# Compute and store file size
size = os.path.getsize(seq_file)
mes += ' (%s)' % vidjil_utils.format_size(size)
db.sequence_file[request.vars["id"]] = dict(size_file=size)
if data_file2 is not None:
seq_file2 = defs.DIR_SEQUENCES + data_file2
#TODO
# Log and exit
res = {"message": error + mes}
if error:
res['success'] = 'false'
res['priority'] = 3
log.error(res)
else:
log.info(res)
return gluon.contrib.simplejson.dumps(res, separators=(',', ':'))