Commit 0a8ae8ce authored by Michael Baudis's avatar Michael Baudis
Browse files

typos!

parent 77edbdf2
......@@ -124,6 +124,7 @@ def cli(dbname, collection_src, collection_dst_biosamples, collection_dst_callse
click.echo('Duplicate biosample_name: '+biosample_name, file=log)
else:
# new biosample_name, create new biosample
# TODO: ISO age
biosamples[biosample_name] = {'characteristics': '', 'created': datetime.datetime.utcnow(), 'updated': datetime.datetime.utcnow(), 'individual_id': '',
'name': biosample_name,
'description': get_attribute('DIAGNOSISTEXT',sample),
......@@ -132,12 +133,13 @@ def cli(dbname, collection_src, collection_dst_biosamples, collection_dst_callse
'icdo3_morphology_code': get_attribute('ICDMORPHOLOGYCODE',sample),
'icdo3_topography': get_attribute('ICDTOPOGRAPHY', sample),
'icdo3_topography_code': get_attribute('ICDTOPOGRAPHYCODE', sample),
'tnm': get_attribute('TNM', sample),
'age': get_attribute('AGE', sample),
'city': get_attribute('CITY', sample),
'county': get_attribute('COUNTRY', sample),
'country': get_attribute('COUNTRY', sample),
'death': get_attribute('DEATH',sample),
'geo_lat': get_attribute('GEOLAT', sample),
'get_long': get_attribute('GEOLONG', sample),
'geo_long': get_attribute('GEOLONG', sample),
'sex': get_attribute('SEX', sample),
'redirected_to': ''}}
no_biosamples += 1
......@@ -148,7 +150,7 @@ def cli(dbname, collection_src, collection_dst_biosamples, collection_dst_callse
if log is not None:
click.echo('Duplicate callset_name:'+callset_name, file=log)
else:
callsets[callset_name] = {'name': callset_name, 'bio_sample_name': biosample_name,
callsets[callset_name] = {'name': callset_name, 'biosample_name': biosample_name,
'created': datetime.datetime.utcnow(), 'updated': datetime.datetime.utcnow()}
no_callsets += 1
......
Supports Markdown
0% or .
You are about to add 0 people to the discussion. Proceed with caution.
Finish editing this message first!
Please register or to comment