def submit(data_file, id_tracking_file=node_tracking_file):
log.info('Starting submission of %ss.', node_type)
nodes = []
csv_fieldnames = get_field_header(data_file)
write_csv_headers(data_file,fieldnames=csv_fieldnames)
for record in load_data(data_file):
# if record['consented'] == 'YES' \
# and record['visit_number'] != 'UNK':
#if record['visit_number'] != 'UNK':
# use of 'UNK' = hack workaround for unreconciled visit list
log.info('\n...next record...')
try:
log.debug('data record: '+str(record))
# node-specific variables:
load_search_field = 'visit_id'
internal_id = record['DCC_VISIT_IDS']
parent_internal_id = record['rand_patient_id'] ##Text ID to find the parent and get back OSDF ID
grand_parent_internal_id = 'prediabetes'
parent_id = get_parent_node_id(
id_tracking_file, parent_type, parent_internal_id)
# grand_parent_id = get_parent_node_id(
# id_tracking_file, grand_parent_type, grand_parent_internal_id)
if parent_id:
node_is_new = False # set to True if newbie
node = load(internal_id, load_search_field)
if not getattr(node, load_search_field):
log.debug('loaded node newbie...')
node_is_new = True
saved = validate_record(parent_id, node, record,
data_file_name=data_file)
if saved:
header = settings.node_id_tracking.id_fields
saved_name = getattr(saved, load_search_field)
vals = values_to_node_dict(
[[node_type.lower(), saved_name, saved.id,
parent_type.lower(), parent_internal_id, parent_id,
get_cur_datetime()]],
header
)
nodes.append(vals)
if node_is_new:
write_out_csv(id_tracking_file,
fieldnames=get_field_header(id_tracking_file),
values=vals)
else:
log.error('No parent_id found for %s', parent_internal_id)
except Exception, e:
log.exception(e)
raise e
def submit(data_file, id_tracking_file=node_tracking_file):
log.info('Starting submission of %ss.', node_type)
nodes = []
csv_fieldnames = get_field_header(data_file)
for record in load_data(data_file):
# check not 'unknown' jaxid, not missing visit info
if len(record['DCC_VISIT_IDS']) > 0:
log.debug('\n...next record...')
try:
log.debug('data record: '+str(record))
# Node-Specific Variables:
load_search_field = 'name'
internal_id = record['sample_name_id']
parent_internal_id = record['DCC_VISIT_IDS']
grand_parent_internal_id = record['rand_patient_id']
parent_id = get_parent_node_id(
id_tracking_file, parent_type, parent_internal_id)
log.debug('matched parent_id: %s', parent_id)
if parent_id:
node_is_new = False # set to True if newbie
node = load(internal_id, load_search_field)
if not getattr(node, load_search_field):
log.debug('loaded node newbie...')
node_is_new = True
saved = validate_record(parent_id, node, record,
data_file_name=data_file)
if saved:
header = settings.node_id_tracking.id_fields
saved_name = getattr(saved, load_search_field)
vals = values_to_node_dict(
[[node_type.lower(),saved_name,saved.id,
parent_type.lower(),parent_internal_id,parent_id,
get_cur_datetime()]],
header
)
nodes.append(vals)
if node_is_new:
write_out_csv(id_tracking_file,
fieldnames=get_field_header(id_tracking_file),
values=vals)
else:
log.error('No parent_id found for %s', parent_internal_id)
except Exception, e:
log.exception(e)
raise e
else:
write_out_csv(data_file+'_records_no_submit.csv',
fieldnames=record.keys(), values=[record,])
def submit(data_file, id_tracking_file=node_tracking_file):
log.info('Starting submission of %ss.', node_type)
nodes = []
csv_fieldnames = get_field_header(data_file)
write_csv_headers(data_file,fieldnames=csv_fieldnames)
for record in load_data(data_file):
log.info('...next record...')
try:
log.debug('data record: '+str(record))
# node-specific variables:
load_search_field = 'local_file'
internal_id = os.path.basename(record[load_search_field])
parent_internal_id = record['prep_id']
grand_parent_internal_id = record['visit_id']
parent_id = get_parent_node_id(
id_tracking_file, parent_type, parent_internal_id)
log.debug('matched parent_id: %s', parent_id)
if parent_id:
node_is_new = False # set to True if newbie
node = load(internal_id, load_search_field)
if not getattr(node, load_search_field):
log.debug('loaded node newbie...')
node_is_new = True
saved = validate_record(parent_id, node, record,
data_file_name=data_file)
if saved:
# load_search_field = 'urls'
header = settings.node_id_tracking.id_fields
if record['consented'] == 'YES':
saved_name = os.path.basename(getattr(saved, load_search_field))
else:
saved_name = '-'.join([getattr(saved, 'comment'), 'private_file'])
vals = values_to_node_dict(
[[node_type.lower(), saved_name, saved.id,
parent_type.lower(), parent_internal_id, parent_id,
get_cur_datetime()]],
header
)
nodes.append(vals)
if node_is_new:
write_out_csv(id_tracking_file,
fieldnames=get_field_header(id_tracking_file),
values=vals)
else:
log.error('No parent_id found for %s', parent_internal_id)
except Exception, e:
log.exception(e)
raise e
def submit(data_file, id_tracking_file=node_tracking_file):
log.info('Starting submission of %ss.', node_type)
nodes = []
csv_fieldnames = get_field_header(data_file)
write_csv_headers(data_file,fieldnames=csv_fieldnames)
for record in load_data(data_file):
log.info('...next record...')
try:
log.debug('data record: '+str(record))
# node-specific variables:
load_search_field = 'comment'
internal_id = str(record['host_transcriptomics_id']) +'.host_transcriptomics'
parent_internal_id = record['host_seq_prep_name_id'] ##Link to Host_seq_prep ID
grand_parent_internal_id = record['sample_name_id'] ##Link to Sample ID
parent_id = get_parent_node_id(
id_tracking_file, parent_type, parent_internal_id)
log.debug('matched parent_id: %s', parent_id)
if parent_id:
node_is_new = False # set to True if newbie
node = load(internal_id, load_search_field)
if not getattr(node, load_search_field):
log.debug('loaded node newbie...')
node_is_new = True
import pdb ; pdb.set_trace()
saved = validate_record(parent_id, node, record,
data_file_name=data_file)
if saved:
header = settings.node_id_tracking.id_fields
saved_name = getattr(saved, load_search_field)
vals = values_to_node_dict(
[[node_type.lower(),saved_name,saved.id,
parent_type.lower(),parent_internal_id,parent_id]],
header
)
nodes.append(vals)
if node_is_new:
write_out_csv(id_tracking_file,
fieldnames=get_field_header(id_tracking_file),
values=vals)
else:
log.error('No parent_id found for %s', parent_internal_id)
except Exception, e:
log.exception(e)
raise e
def submit(data_file, id_tracking_file=node_tracking_file):
log.info('Starting submission of %ss.', node_type)
nodes = []
csv_fieldnames = get_field_header(data_file)
write_csv_headers(data_file,fieldnames=csv_fieldnames)
for record in load_data(data_file):
log.info('\n...next record...')
try:
log.debug('data record: '+str(record))
# node-specific variables:
load_search_field = 'comment'
internal_id = record['sample_name_id'] + '.proteome'
parent_internal_id = record['sample_name_id'] + '.hostassayprep'
grand_parent_internal_id = record['visit_id']
parent_id = get_parent_node_id(
id_tracking_file, parent_type, parent_internal_id)
node_is_new = False # set to True if newbie
node = load(internal_id, load_search_field)
if not getattr(node, load_search_field):
log.debug('loaded node newbie...')
node_is_new = True
import pdb ; pdb.set_trace()
saved = validate_record(parent_id, node, record,
data_file_name=data_file)
if saved:
header = settings.node_id_tracking.id_fields
saved_name = getattr(saved, load_search_field)
vals = values_to_node_dict(
[[node_type.lower(),saved_name,saved.id,
parent_type.lower(),parent_internal_id,parent_id]],
header
)
nodes.append(vals)
if node_is_new:
write_out_csv(id_tracking_file,
fieldnames=get_field_header(id_tracking_file),
values=vals)
except Exception, e:
log.exception(e)
raise e
def submit(data_file, id_tracking_file=node_tracking_file):
log.info('Starting submission of %ss.', node_type)
nodes = []
csv_fieldnames = get_field_header(data_file)
write_csv_headers(data_file,fieldnames=csv_fieldnames)
for record in load_data(data_file):
log.info('\n...next record...')
try:
log.debug('data record: '+str(record))
if record['local_file'] != '':
load_search_field = 'local_file'
internal_id = os.path.basename(record['local_file'])
parent_internal_id = record['raw_file_id']
grand_parent_internal_id = record['prep_id']
parent_id = get_parent_node_id(
id_tracking_file, parent_type, parent_internal_id)
node_is_new = False # set to True if newbie
node = load(internal_id, load_search_field)
if not getattr(node, load_search_field):
log.debug('loaded node newbie...')
node_is_new = True
saved = validate_record(parent_id, node, record,
data_file_name=data_file)
if saved:
header = settings.node_id_tracking.id_fields
vals = values_to_node_dict(
[[node_type.lower(),saved_name,saved.id,
parent_type.lower(),parent_internal_id,parent_id]],
header
)
nodes.append(vals)
if node_is_new:
write_out_csv(id_tracking_file,
fieldnames=get_field_header(id_tracking_file),
values=vals)
except Exception, e:
log.exception(e)
raise e
