def handle(self, *args, **options):
"""calls the parsing and insertion functions"""
required = ['username', 'title', 'file_name', 'source_column_index',
'data_file_column']
for arg in required:
if not options[arg]:
raise CommandError("%s was not provided" % arg)
source_columns = \
[x.strip() for x in options['source_column_index'].split(",")]
try:
with open(options['file_name']) as metadata_file:
dataset_uuid = process_metadata_table(
username=options['username'], title=options['title'],
metadata_file=metadata_file, source_columns=source_columns,
data_file_column=options['data_file_column'],
auxiliary_file_column=options['auxiliary_file_column'],
base_path=options['base_path'],
data_file_permanent=options['data_file_permanent'],
species_column=options['species_column'],
genome_build_column=options['genome_build_column'],
annotation_column=options['annotation_column'],
slug=options['slug'], is_public=options['is_public'])
except IOError as exc:
raise CommandError("Could not open file '%s': %s" %
options['file_name'], exc)
except ValueError as exc:
raise CommandError(exc)
self.stdout.write("Created dataset with UUID '%s'" % dataset_uuid)
def post(self, request, *args, **kwargs):
# get required params
try:
metadata_file = request.FILES['file']
title = request.POST['title']
data_file_column = request.POST['data_file_column']
except (KeyError, ValueError):
error = {'error_message':
'Import failed because required parameters are missing'}
return render(request, self.template_name, error)
source_column_index = request.POST.getlist('source_column_index')
if not source_column_index:
error = {'error_message':
'Import failed because no source columns were selected'}
return render(request, self.template_name, error)
# workaround for breaking change in Angular
# https://github.com/angular/angular.js/commit/7fda214c4f65a6a06b25cf5d5aff013a364e9cef
source_column_index = [column.replace("string:", "")
for column in source_column_index]
try:
dataset_uuid = process_metadata_table(
username=request.user.username, title=title,
metadata_file=metadata_file,
source_columns=source_column_index,
data_file_column=data_file_column,
auxiliary_file_column=request.POST.get('aux_file_column',
None),
base_path=request.POST.get('base_path', ""),
data_file_permanent=request.POST.get('data_file_permanent',
False),
species_column=request.POST.get('species_column', None),
genome_build_column=request.POST.get('genome_build_column',
None),
annotation_column=request.POST.get('annotation_column', None),
slug=request.POST.get('slug', None),
is_public=request.POST.get('is_public', False))
except ValueError as exc:
error = {'error_message': exc}
return render(request, self.template_name, error)
return HttpResponseRedirect(
reverse(self.success_view_name, args=(dataset_uuid,)))
