def main(lims, args, epp_logger):
d_elts = []
no_updated = 0
incorrect_udfs = 0
project_names = ''
source_udfs = args.source_udf
dest_udfs = args.dest_udf
s_elt = Process(lims, id=args.pid)
analytes, inf = s_elt.analytes()
for analyte in analytes:
for samp in analyte.samples:
d_elts.append(samp.project)
d_elts = list(set(d_elts))
if args.status_changelog:
epp_logger.prepend_old_log(args.status_changelog)
if not dest_udfs:
dest_udfs = source_udfs
elif len(dest_udfs) != len(source_udfs):
logging.error(
"source_udfs and dest_udfs lists of arguments are uneven.")
sys.exit(-1)
for d_elt in d_elts:
project_names = ' '.join([project_names, d_elt.name])
for i in range(len(source_udfs)):
source_udf = source_udfs[i]
dest_udf = dest_udfs[i]
with open(args.status_changelog, 'a') as changelog_f:
if source_udf in s_elt.udf:
copy_sesion = CopyField(s_elt, d_elt, source_udf, dest_udf)
test = copy_sesion.copy_udf(changelog_f)
if test:
no_updated = no_updated + 1
else:
logging.warning(
("Udf: {1} in Process {0} is undefined/blank, exiting"
).format(s_elt.id, source_udf))
incorrect_udfs = incorrect_udfs + 1
if incorrect_udfs > 0:
warn = "Failed to update %s udf(s) due to missing/wrong source udf info." % incorrect_udfs
else:
warn = ''
d = {'up': no_updated, 'ap': len(d_elts), 'w': warn, 'pr': project_names}
abstract = ("Updated {up} udf(s). Handeled project(s): {pr} {w}").format(
**d)
print >> sys.stderr, abstract
def main(lims, args, epp_logger):
d_elts = []
no_updated = 0
incorrect_udfs = 0
project_names = ''
source_udfs = args.source_udf
dest_udfs = args.dest_udf
s_elt = Process(lims,id = args.pid)
analytes, inf = s_elt.analytes()
for analyte in analytes:
for samp in analyte.samples:
d_elts.append(samp.project)
d_elts = list(set(d_elts))
if args.status_changelog:
epp_logger.prepend_old_log(args.status_changelog)
if not dest_udfs:
dest_udfs = source_udfs
elif len(dest_udfs) != len(source_udfs):
logging.error("source_udfs and dest_udfs lists of arguments are uneven.")
sys.exit(-1)
for d_elt in d_elts:
project_names = ' '.join([project_names, d_elt.name])
for i in range(len(source_udfs)):
source_udf = source_udfs[i]
dest_udf = dest_udfs[i]
with open(args.status_changelog, 'a') as changelog_f:
if source_udf in s_elt.udf:
copy_sesion = CopyField(s_elt, d_elt, source_udf, dest_udf)
test = copy_sesion.copy_udf(changelog_f)
if test:
no_updated = no_updated + 1
else:
logging.warning(("Udf: {1} in Process {0} is undefined/blank, exiting").format(s_elt.id, source_udf))
incorrect_udfs = incorrect_udfs + 1
if incorrect_udfs > 0:
warn = "Failed to update %s udf(s) due to missing/wrong source udf info." %incorrect_udfs
else:
warn = ''
d = {'up': no_updated,
'ap': len(d_elts),
'w' : warn,
'pr': project_names}
abstract = ("Updated {up} udf(s). Handeled project(s): {pr} {w}").format(**d)
print >> sys.stderr, abstract
def main(lims, args, epp_logger):
source_udfs = args.source_udf
dest_udfs = args.dest_udf
correct_artifacts = 0
incorrect_artifacts = 0
no_updated = 0
p = Process(lims, id=args.pid)
artifacts, inf = p.analytes()
if args.status_changelog:
epp_logger.prepend_old_log(args.status_changelog)
if not dest_udfs:
dest_udfs = source_udfs
elif len(dest_udfs) != len(source_udfs):
logging.error(
"source_udfs and dest_udfs lists of arguments are uneven.")
sys.exit(-1)
for i in range(len(source_udfs)):
source_udf = source_udfs[i]
dest_udf = dest_udfs[i]
with open(args.status_changelog, 'a') as changelog_f:
for artifact in artifacts:
if source_udf in artifact.udf:
correct_artifacts = correct_artifacts + 1
copy_sesion = CopyField(artifact, artifact.samples[0],
source_udf, dest_udf)
test = copy_sesion.copy_udf(changelog_f)
if test:
no_updated = no_updated + 1
else:
incorrect_artifacts = incorrect_artifacts + 1
logging.warning(("Found artifact for sample {0} with {1} "
"undefined/blank, exiting").format(
artifact.samples[0].name, source_udf))
if incorrect_artifacts == 0:
warning = "no artifacts"
else:
warning = "WARNING: skipped {0} udfs(s)".format(incorrect_artifacts)
d = {
'ua': no_updated,
'ca': correct_artifacts,
'ia': incorrect_artifacts,
'warning': warning
}
abstract = ("Updated {ua} udf(s), out of {ca} in total, "
"{warning} with incorrect udf info.").format(**d)
print >> sys.stderr, abstract # stderr will be logged and printed in GUI
def main(lims, args, epp_logger):
source_udfs = args.source_udf
dest_udfs = args.dest_udf
correct_artifacts = 0
incorrect_artifacts = 0
no_updated = 0
p = Process(lims,id = args.pid)
artifacts, inf = p.analytes()
if args.status_changelog:
epp_logger.prepend_old_log(args.status_changelog)
if not dest_udfs:
dest_udfs = source_udfs
elif len(dest_udfs) != len(source_udfs):
logging.error("source_udfs and dest_udfs lists of arguments are uneven.")
sys.exit(-1)
for i in range(len(source_udfs)):
source_udf = source_udfs[i]
dest_udf = dest_udfs[i]
with open(args.status_changelog, 'a') as changelog_f:
for artifact in artifacts:
if source_udf in artifact.udf:
correct_artifacts = correct_artifacts +1
copy_sesion = CopyField(artifact, artifact.samples[0], source_udf, dest_udf)
test = copy_sesion.copy_udf(changelog_f)
if test:
no_updated = no_updated + 1
else:
incorrect_artifacts = incorrect_artifacts + 1
logging.warning(("Found artifact for sample {0} with {1} "
"undefined/blank, exiting").format(artifact.samples[0].name, source_udf))
if incorrect_artifacts == 0:
warning = "no artifacts"
else:
warning = "WARNING: skipped {0} udfs(s)".format(incorrect_artifacts)
d = {'ua': no_updated,
'ca': correct_artifacts,
'ia': incorrect_artifacts,
'warning' : warning}
abstract = ("Updated {ua} udf(s), out of {ca} in total, "
"{warning} with incorrect udf info.").format(**d)
print >> sys.stderr, abstract # stderr will be logged and printed in GUI
