def pcr_result(sample):
sn = sample.get('pcr', {}).get('sn')
run_well = sample.get('pcr', {}).get('run_well', {}).get('main')
if not sn or not run_well:
return
sql = 'show tag values from pcr_rdml_adp with key = "sample" where sample = \'%(run_well)s\'' % {
'run_well': run_well
}
run_well_set = influxdb_cli.query(sql)
if len(list(run_well_set.get_points())) > 0:
insert_data(
{
'sample_name':
sample.get('name'),
'sn':
sn,
'run_well':
run_well,
'positive_control':
sample.get('pcr', {}).get('run_well', {}).get(
'positive_control', ''),
'negative_control':
sample.get('pcr', {}).get('run_well', {}).get(
'negative_control', '')
}, 'pcr')
def insert_sample(sample_name):
measurement = 'sample_info'
sql = 'show tag values from sample_info with key = "sample_name" where sample_name = \'%(sample_name)s\'' % {
'sample_name': sample_name
}
if len(list(influxdb_cli.query(sql).get_points())) > 0:
return
data = '%s,%s value=true' % (measurement, 'sample_name=%s' % sample_name)
influxdb_cli.write_points(points=[data], protocol='line')
def ont_result(sample):
cell = sample.get('ont', {}).get('cell')
barcode = sample.get('ont', {}).get('barcode')
if not cell or not barcode:
return
sql = 'show tag values from reads_length_stats with key = "cell" where cell = \'%(cell)s\'' % {
'cell': cell
}
cell_set = influxdb_cli.query(sql)
if len(list(cell_set.get_points())) > 0:
sql = 'show tag values from reads_length_stats with key = "barcode" where cell = \'%(cell)s\' and barcode = \'%(barcode)s\'' % {
'cell': cell,
'barcode': barcode
}
barcode_set = influxdb_cli.query(sql)
if len(list(barcode_set.get_points())) > 0:
insert_data(
{
'sample_name': sample.get('name'),
'cell': cell,
'barcode': barcode
}, 'ont')
def insert_data(data, data_type):
insert_sample(data.get('sample_name'))
measurement = 'sample_info_%s' % data_type
sql = 'show tag values from %(measurement)s with key = "sample_name" where sample_name = \'%(sample_name)s\'' % {
'measurement': measurement,
'sample_name': data.get('sample_name')
}
if len(list(influxdb_cli.query(sql).get_points())) > 0:
return
data = '%s,%s value=true' % (
measurement,
','.join(['%s=%s' % (k, v) for k, v in data.items()]),
)
influxdb_cli.write_points(points=[data], protocol='line')
def test_fastq_watch(self):
test_fastq_file = 'test.fastq'
data_dir = conf.get('ont').get('fastq_watch_path')
cell = 'TEST-CELL'
chip = 'TEST-CHIP'
fastq_dir = os.path.join(data_dir, cell, chip, 'fastq_pass')
if not os.path.exists(fastq_dir):
os.makedirs(fastq_dir)
tmp_fastq_file = os.path.join(fastq_dir, '%s.tmp' % test_fastq_file)
fastq_file = tmp_fastq_file[:-4]
shutil.copyfile(test_fastq_file, tmp_fastq_file)
shutil.move(tmp_fastq_file, fastq_file)
time.sleep(1)
sql = "select * from fastq_watch where cell = '%s' and dir = '%s' and path = '%s'" % (
cell, fastq_dir, fastq_file)
res = influxdb_cli.query(sql)
self.assertGreater(len(list(res.get_points())), 0)
def immunochromatography_result(sample):
sample_id = sample.get('immunochromatography', {}).get('sample_id')
report_time = sample.get('immunochromatography', {}).get('report_time')
if not sample_id or not report_time:
return
sql = 'show tag values from immunochromatography with key = "sampleID" where sampleID = \'%(sample_id)s\' and reportTime = \'%(report_time)s\'' % {
'sample_id': sample_id,
'report_time': report_time
}
sample_set = influxdb_cli.query(sql)
if len(list(sample_set.get_points())) > 0:
insert_data(
{
'sample_name': sample.get('name'),
'sample_id': sample_id,
'report_time': report_time
}, 'immunochromatography')