LOGGER = logging.getLogger(__name__)
class GEOSubmission(Submission):
- def __init__(self, name, model):
- super(GEOSubmission, self).__init__(name, model)
+ def __init__(self, name, model, host):
+ super(GEOSubmission, self).__init__(name, model, host)
def make_soft(self, result_map):
samples = []
for lib_id, result_dir in result_map.items():
an_analysis = self.get_submission_node(result_dir)
metadata = self.get_sample_metadata(an_analysis)
- if len(metadata) > 1:
- errmsg = 'Confused there are more than one samples for %s'
- LOGGER.debug(errmsg % (str(an_analysis,)))
+ if len(metadata) == 0:
+ errmsg = 'No metadata found for {0}'
+ LOGGER.error(errmsg.format(str(an_analysis),))
+ continue
+ elif len(metadata) > 1:
+ errmsg = 'Confused there are more than one sample for %s'
+ LOGGER.debug(errmsg % (str(an_analysis),))
metadata = metadata[0]
metadata['raw'] = self.get_raw_files(an_analysis)
metadata['supplimental'] = self.get_sample_files(an_analysis)
context = Context({
'submission': str(analysis_node.uri),
- 'file_class': str(geoSoftNS['supplemental'])
+ 'file_class': str(geoSoftNS['supplemental'].uri)
})
return self.execute_query(query_template, context)
context = Context({
'submission': str(analysis_node.uri),
- 'file_class': str(geoSoftNS['raw']),
+ 'file_class': str(geoSoftNS['raw'].uri),
})
lanes = {}