def _run(self):
artifacts = None
# Get the output artifacts
if self.source == 'input':
artifacts = self.process.all_inputs(unique=True, resolve=True)
elif self.source == 'output':
artifacts = self.process.all_outputs(unique=True, resolve=True)
elif self.source == 'submitted':
artifacts = list(frozenset([s.artifact for a in self.process.all_inputs() for s in a.samples]))
# Find the workflow stage
s = self.stage_name if self.stage_name else None
stage = get_workflow_stage(self.lims, self.workflow_name, s)
if not stage:
raise ValueError(
'Stage specified by workflow: %s and stage: %s does not exist in %s' % (self.workflow_name, self.stage_name, self.baseuri)
)
# Route the artifacts
self.lims.route_artifacts(artifacts, stage_uri=stage.uri)
def _run(self):
# Find the Discard plate workflow uri
discard_plate_stage = get_workflow_stage(self.lims, workflow_name=discard_wf_name, stage_name=plate_discard_wf_stage_name)
self.info('Found Stage %s uri: %s', plate_discard_wf_stage_name, discard_plate_stage.uri)
# Fetch the artifacts associated with the step
step_artifacts = self.process.all_inputs()
self.lims.get_batch(step_artifacts)
# Fetch the sample associated with these artifacts
samples = [a.samples[0] for a in step_artifacts]
self.lims.get_batch(samples)
self.info('Found %d Samples in the step', len(samples))
# Fetch the all the artifacts associated with these samples
step_associated_artifacts = fetch_all_artifacts_for_samples(self.lims, samples)
self.info('Found %d Analytes (derived samples)', len(step_associated_artifacts))
# List all the containers and retrieve them
containers = list(set([a.container for a in step_associated_artifacts]))
batch_limit(self.lims, containers)
self.info('Found %d containers', len(containers))
# Filter the containers to keep the one that are valid
valid_containers = [c for c in containers if is_valid_container(c)]
self.info('Found %d valid containers to potentially discard', len(valid_containers))
# Get all the artifacts in the valid containers and retrieve the one that were not retrieved already
container_artifacts = set()
for c in valid_containers:
container_artifacts.update(set(c.placements.values()))
non_step_atifacts = container_artifacts.difference(set(step_associated_artifacts))
batch_limit(self.lims, list(non_step_atifacts))
self.info(
'Found %d others associated with the container but not associated with discarded samples',
len(non_step_atifacts)
)
artifacts_to_route = []
container_to_route = []
for container in valid_containers:
route_allowed = True
self.info(
'Test container %s, with %s artifacts',
container.name,
len(container.placements.values())
)
for artifact in list(container.placements.values()):
if artifact in step_associated_artifacts or has_workflow_stage(artifact, sample_discard_wf_stage_name):
self.info(
'Container %s might route because artifact %s in step_associated_artifacts (%s) or has been discarded before (%s)',
container.name, artifact.name, artifact in step_associated_artifacts, has_workflow_stage(artifact, sample_discard_wf_stage_name)
)
else:
# This container will have to wait
route_allowed = False
self.info(
"Container: %s won't route because artifact %s in step_associated_artifacts (%s) or has been discarded before (%s)",
container.name, artifact.name, artifact in step_associated_artifacts, has_workflow_stage(artifact, sample_discard_wf_stage_name)
)
if route_allowed:
artifacts_to_route.extend(list(container.placements.values()))
container_to_route.append(container)
self.info('Will route container: %s', container.name)
self.info('Route %s containers with %s artifacts', len(container_to_route), len(artifacts_to_route))
print('Route %s containers with %s artifacts' % (len(container_to_route), len(artifacts_to_route)))
self.lims.route_artifacts(artifacts_to_route, stage_uri=discard_plate_stage.uri)
