def send_data(self):
headers_barcodes = [ELEMENT_RUN_ELEMENT_ID, ELEMENT_RUN_NAME, ELEMENT_LANE, ELEMENT_PC_PASS_FILTER, ELEMENT_PROJECT,
ELEMENT_LIBRARY_INTERNAL_ID, ELEMENT_SAMPLE_INTERNAL_ID, ELEMENT_BARCODE,
ELEMENT_NB_READS_PASS_FILTER, ELEMENT_PC_READ_IN_LANE, ELEMENT_YIELD,
ELEMENT_PC_Q30_R1, ELEMENT_PC_Q30_R2]
headers_samples = [ELEMENT_PROJECT, ELEMENT_LIBRARY_INTERNAL_ID, ELEMENT_SAMPLE_INTERNAL_ID,
ELEMENT_NB_READS_PASS_FILTER, ELEMENT_YIELD, ELEMENT_PC_Q30_R1, ELEMENT_PC_Q30_R2]
headers_unexpected = [ELEMENT_RUN_ELEMENT_ID, ELEMENT_RUN_NAME, ELEMENT_LANE, ELEMENT_BARCODE, ELEMENT_NB_READS_PASS_FILTER, ELEMENT_PC_READ_IN_LANE]
cfg = Configuration()
#Send run elements
array_json = format_info(self.barcodes_info.values(), headers_barcodes, style='array')
url=cfg.query('rest_api','url') + 'run_elements/'
for payload in array_json:
if not post_entry(url, payload):
id = payload.pop(ELEMENT_RUN_ELEMENT_ID.key)
patch_entry(url, payload, **{ELEMENT_RUN_ELEMENT_ID.key:id})
#Send unexpected barcodes
array_json = format_info(self.unexpected_barcode_info.values(), headers_unexpected, style='array')
url=cfg.query('rest_api','url') + 'unexpected_barcodes/'
for payload in array_json:
if not post_entry(url, payload):
id = payload.pop(ELEMENT_RUN_ELEMENT_ID.key)
patch_entry(url, payload, **{ELEMENT_RUN_ELEMENT_ID.key:id})
#Send samples information
array_json = format_info(self.libraries_info.values(), headers_samples, style='array')
url=cfg.query('rest_api','url') + 'samples/'
for payload in array_json:
lib_id = {ELEMENT_LIBRARY_INTERNAL_ID.key:payload.get(ELEMENT_LIBRARY_INTERNAL_ID.key)}
if not post_entry(url, payload):
patch_entry(url, payload, **lib_id)
def send_data(self):
cfg = Configuration()
headers_samples = [ELEMENT_PROJECT, ELEMENT_LIBRARY_INTERNAL_ID, ELEMENT_SAMPLE_INTERNAL_ID,
ELEMENT_NB_READS_PASS_FILTER, ELEMENT_YIELD, ELEMENT_PC_Q30_R1, ELEMENT_PC_Q30_R2]
array_json = format_info(self.all_info, headers_samples, style='array')
url=cfg.query('rest_api','url') + 'samples/'
for payload in array_json:
if not post_entry(url, payload):
id = payload.pop(ELEMENT_LIBRARY_INTERNAL_ID.key)
patch_entry(url, payload, **{ELEMENT_LIBRARY_INTERNAL_ID.key:id})
from report_generation.formaters import format_info
from report_generation.model import Info, ELEMENT_NB_READS_SEQUENCED, \
ELEMENT_NB_MAPPED_READS, ELEMENT_NB_DUPLICATE_READS, ELEMENT_NB_PROPERLY_MAPPED, \
ELEMENT_MEDIAN_COVERAGE, ELEMENT_PC_DUPLICATE_READS, ELEMENT_PC_PROPERLY_MAPPED, \
ELEMENT_PC_BASES_CALLABLE, ELEMENT_SAMPLE_INTERNAL_ID, ELEMENT_SAMPLE_EXTERNAL_ID, ELEMENT_NB_READS_PASS_FILTER,\
ELEMENT_PC_MAPPED_READS, ELEMENT_PROJECT, ELEMENT_YIELD, \
ELEMENT_LIBRARY_INTERNAL_ID, ELEMENT_PC_Q30_R1, ELEMENT_PC_Q30_R2, ELEMENT_NB_BASE, ELEMENT_NB_READS_IN_BAM, \
ELEMENT_MEAN_COVERAGE, ELEMENT_SAMPLE_PLATE, ELEMENT_SAMPLE_PLATE_WELL, ELEMENT_GENDER, ELEMENT_GENOTYPE_PC_NOCALL, \
ELEMENT_GENOTYPE_PC_MISMATCH
from report_generation.readers.mapping_stats_parsers import parse_bamtools_stats, parse_callable_bed_file, \
parse_highdepth_yaml_file, get_nb_sequence_from_fastqc_html, parse_genotype_concordance
from report_generation.rest_communication import post_entry, patch_entry
__author__ = 'tcezard'
cfg = Configuration()
lims=Lims(**cfg.get('clarity'))
female_alias = ['f', 'female']
male_alias = ['m', 'male']
def match_gender(gender1, gender2):
gender1 = str(gender1).lower()
gender2 = str(gender2).lower()
if gender1.lower() in female_alias and gender2.lower() in female_alias:
return 'female'
elif gender1.lower() in male_alias and gender2.lower() in male_alias:
return 'male'
else:
return 'mismatch (vcf:%s lims:%s)'%(gender1, gender2)
class Bcbio_report: