def flowcell_samples(
lims: Lims, flowcell_id: str, bcl_converter: str
) -> Iterable[Union[LimsFlowcellSampleBcl2Fastq, LimsFlowcellSampleDragen]]:
lims_flowcell_sample = {
"bcl2fastq": LimsFlowcellSampleBcl2Fastq,
"dragen": LimsFlowcellSampleDragen,
}
LOG.info("Fetching samples from lims for flowcell %s", flowcell_id)
containers: List[Container] = lims.get_containers(name=flowcell_id)
if not containers:
return []
container: Container = containers[-1] # only take the last one. See ÖA#217.
raw_lanes: List[str] = sorted(container.placements.keys())
for raw_lane in raw_lanes:
lane: int = get_placement_lane(raw_lane)
placement_artifact: Artifact = container.placements[raw_lane]
non_pooled_artifacts: List[Artifact] = get_non_pooled_artifacts(placement_artifact)
for artifact in non_pooled_artifacts:
sample: Sample = artifact.samples[0] # we are assured it only has one sample
label: Optional[str] = get_reagent_label(artifact)
index = get_index(lims=lims, label=label)
yield lims_flowcell_sample[bcl_converter](
flowcell_id=flowcell_id,
lane=lane,
sample_id=sample.id,
index=index,
sample_name=sample.name,
project=sample.project.name,
)
def main(args):
lims = Lims(BASEURI, USERNAME, PASSWORD)
conts = lims.get_containers(name=args.flowcell)
print "found {} containers with name {}".format(len(conts), args.flowcell)
for cont in conts:
if cont.type.name not in args.types:
print "Container {} is a {} and will be renamed".format(cont.id, cont.type.name)
cont.name = args.name
cont.put()
else:
print "Container {} is a {} and will NOT be renamed".format(cont.id, cont.type.name)
def main(args):
lims = Lims(BASEURI, USERNAME, PASSWORD)
conts = lims.get_containers(name=args.flowcell)
print "found {} containers with name {}".format(len(conts), args.flowcell)
for cont in conts:
if cont.type.name not in args.types:
print "Container {} is a {} and will be renamed".format(
cont.id, cont.type.name)
cont.name = args.name
cont.put()
else:
print "Container {} is a {} and will NOT be renamed".format(
cont.id, cont.type.name)
"""
import codecs
from genologics.lims import Lims
# Login parameters for connecting to a LIMS instance.
# NOTE: Modify according to your setup.
from genologics.site_cloud import BASEURI, USERNAME, PASSWORD
# Create the LIMS interface instance, and check the connection and version.
lims = Lims(BASEURI, USERNAME, PASSWORD)
lims.check_version()
# Get the list of all containers.
containers = lims.get_containers()
print len(containers), 'containers in total'
for state in ['Empty', 'Reagent-Only', 'Discarded', 'Populated']:
containers = lims.get_containers(state=state)
print len(containers), state, 'containers'
containers = lims.get_containers(type='96 well plate')
print len(containers)
container = containers[2]
print container, container.occupied_wells
placements = container.get_placements()
for location, artifact in placements.iteritems():
print location, artifact.name
