def __init__(self, lims_sample):
""" Wrapper around the genologics Sample class
Args:
lims_sample (genologics.Sample): the sample instance to extend
"""
self.lims = lims_sample
self._apptag = ApplicationTag(self.lims.udf['Sequencing Analysis'])
def set_missingreads(lims_sample, force=False):
"""Set the 'Reads Missing (M)' UDF base on app tag."""
raw_apptag = lims_sample.udf['Sequencing Analysis']
app_tag = ApplicationTag(raw_apptag)
target_amount = app_tag.reads
missing_reads = lims_sample.udf.get('Reads missing (M)')
if not force and missing_reads is not None:
log.warn("missing reads already set: %s", missing_reads)
else:
lims_sample.udf['Reads missing (M)'] = target_amount
log.info("updating reads missing")
lims_sample.put()
def apptag_wgs():
raw_tag = 'WGSPCFC030'
return ApplicationTag(raw_tag)
def apptag_focused_exome():
raw_tag = 'EFTSXTR020'
return ApplicationTag(raw_tag)
def apptag_rml():
raw_tag = 'RMLP10R150'
return ApplicationTag(raw_tag)
def apptag_metagenome():
raw_tag = 'METPCFR020'
return ApplicationTag(raw_tag)
def apptag_external_wgs():
raw_tag = 'WGXCUSR000'
return ApplicationTag(raw_tag)
def apptag_external():
raw_tag = 'EXXCUSR000'
return ApplicationTag(raw_tag)
def apptag_rna():
raw_tag = 'RNLPOAR030'
return ApplicationTag(raw_tag)
def apptag_microbial():
raw_tag = 'MWGNXTR003'
return ApplicationTag(raw_tag)
def apptag_wes():
raw_tag = 'EXOSXTR100'
return ApplicationTag(raw_tag)