def create_template_prep(self, exp):
# handle Template Prep stage
self.name = exp.plan.planDisplayedName
self.date = exp.chefStartTime
self.last_updated = exp.chefLastUpdate
self.instrumentName = exp.chefInstrumentName
# if run aborted only last update date is available
if not self.date:
self.date = self.last_updated
if exp.plan.planStatus == "voided":
self.state = ERROR
self.error_string = exp.chefStatus
elif exp.chefProgress < 100:
self.state = IN_PROGRESS
self.progress_string = "%d%%" % exp.chefProgress
self.status_string = exp.chefStatus
estimated_end_time = utils.convert_seconds_to_datetime_string(
exp.chefLastUpdate, exp.chefRemainingSeconds)
if estimated_end_time:
self.status_string += (
" Until " + estimated_end_time.strftime("%I:%M%p").lower())
else:
self.state = DONE
self.update_application_and_samples(exp.plan)
def create_library_prep(self, sampleSet):
# handle Library Prep stage
self.name = sampleSet.displayedName
self.date = sampleSet.libraryPrepInstrumentData.startTime
self.last_updated = sampleSet.libraryPrepInstrumentData.lastUpdate
self.instrumentName = sampleSet.libraryPrepInstrumentData.instrumentName
if not self.date:
self.date = self.last_updated
if sampleSet.status == "voided":
self.state = ERROR
self.error_string = sampleSet.libraryPrepInstrumentData.instrumentStatus
elif sampleSet.libraryPrepInstrumentData.progress < 100:
self.state = IN_PROGRESS
self.progress_string = "%d%%" % sampleSet.libraryPrepInstrumentData.progress
self.status_string = sampleSet.libraryPrepInstrumentData.instrumentStatus
estimated_end_time = utils.convert_seconds_to_datetime_string(
sampleSet.libraryPrepInstrumentData.lastUpdate,
sampleSet.libraryPrepInstrumentData.remainingSeconds,
)
if estimated_end_time:
self.status_string += (
" Until " +
estimated_end_time.strftime("%I:%M %p").lower())
else:
self.state = DONE
# application icon for Chef library prep - don't show, it's visually distinct from run type icons
# self.runType = sampleSet.libraryPrepType
# self.applicationCategoryDisplayedName = sampleSet.get_libraryPrepType_display()
# samples
sampleSetItems = sampleSet.samples.order_by(
"dnabarcode__id_str").values_list("sample__displayedName",
"dnabarcode__id_str")
samples = {}
if len(sampleSetItems) == 1 and not sampleSetItems[0][1]:
self.sampleDisplayedName = sampleSetItems[0][0]
elif len(sampleSetItems) > 0:
for sampleName, barcode in sampleSetItems:
if sampleName not in samples:
samples[sampleName] = {
"sampleName": sampleName,
"barcodes": barcode or "",
}
elif barcode:
samples[sampleName]["barcodes"] += " " + barcode
self.barcodedSamples = sorted(
list(samples.values()),
key=lambda x: (x["barcodes"], x["sampleName"].lower()),
)
def create_library_prep(self, sampleSet):
# handle Library Prep stage
self.name = sampleSet.displayedName
self.date = sampleSet.libraryPrepInstrumentData.startTime
self.last_updated = sampleSet.libraryPrepInstrumentData.lastUpdate
self.instrumentName = sampleSet.libraryPrepInstrumentData.instrumentName
if not self.date:
self.date = self.last_updated
if sampleSet.status == "voided":
self.state = ERROR
self.error_string = sampleSet.libraryPrepInstrumentData.instrumentStatus
elif sampleSet.libraryPrepInstrumentData.progress < 100:
self.state = IN_PROGRESS
self.progress_string = "%d%%" % sampleSet.libraryPrepInstrumentData.progress
self.status_string = sampleSet.libraryPrepInstrumentData.instrumentStatus
estimated_end_time = utils.convert_seconds_to_datetime_string(sampleSet.libraryPrepInstrumentData.lastUpdate,
sampleSet.libraryPrepInstrumentData.remainingSeconds)
if estimated_end_time:
self.status_string += ' Until ' + estimated_end_time.strftime('%I:%M %p').lower()
else:
self.state = DONE
# application icon for Chef library prep - don't show, it's visually distinct from run type icons
#self.runType = sampleSet.libraryPrepType
#self.applicationCategoryDisplayedName = sampleSet.get_libraryPrepType_display()
# samples
sampleSetItems = sampleSet.samples.order_by('dnabarcode__id_str').values_list('sample__displayedName', 'dnabarcode__id_str')
samples = {}
if len(sampleSetItems) == 1 and not sampleSetItems[0][1]:
self.sampleDisplayedName = sampleSetItems[0][0]
elif len(sampleSetItems) > 0:
for sampleName, barcode in sampleSetItems:
if sampleName not in samples:
samples[sampleName] = {
"sampleName": sampleName,
"barcodes": barcode or ""
}
elif barcode:
samples[sampleName]["barcodes"] += " " + barcode
self.barcodedSamples = sorted( samples.values(), key=lambda x:(x['barcodes'],x['sampleName'].lower()) )
def create_template_prep(self, exp):
# handle Template Prep stage
self.name = exp.plan.planDisplayedName
self.date = exp.chefStartTime
self.last_updated = exp.chefLastUpdate
self.instrumentName = exp.chefInstrumentName
# if run aborted only last update date is available
if not self.date:
self.date = self.last_updated
if exp.plan.planStatus == "voided":
self.state = ERROR
self.error_string = exp.chefStatus
elif exp.chefProgress < 100:
self.state = IN_PROGRESS
self.progress_string = "%d%%" % exp.chefProgress
self.status_string = exp.chefStatus
estimated_end_time = utils.convert_seconds_to_datetime_string(exp.chefLastUpdate, exp.chefRemainingSeconds)
if estimated_end_time:
self.status_string += ' Until ' + estimated_end_time.strftime('%I:%M%p').lower()
else:
self.state = DONE
self.update_application_and_samples(exp.plan)
def chef(request):
querydict = request.GET
days = get_int(querydict, "days", 7)
size = get_int(querydict, "size", 10)
page = get_int(querydict, "page", 1)
days_ago = datetime.datetime.now() - datetime.timedelta(days=days)
# monitoring page should show Chef plans that are currently in progress or have recently finished Chef processing,
# regardless if they are being or have been sequenced
plans = models.PlannedExperiment.objects.filter(
experiment__chefLastUpdate__gte=days_ago)
sampleSets = models.SampleSet.objects.filter(
libraryPrepInstrumentData__lastUpdate__gte=days_ago)
libprep_done = []
chef_table = []
# planned runs may have both Template and Library prep data
for plan in plans:
data = {
"planName":
plan.planDisplayedName,
"sampleSetName":
", ".join(
plan.sampleSets.order_by("displayedName").values_list(
"displayedName", flat=True)),
"last_updated":
plan.experiment.chefLastUpdate,
"instrumentName":
plan.experiment.chefInstrumentName,
"template_prep_progress":
plan.experiment.chefProgress,
"template_prep_status":
plan.experiment.chefStatus,
"template_prep_operation_mode":
plan.experiment.chefOperationMode,
"template_prep_remaining_time":
utils.convert_seconds_to_hhmmss_string(
plan.experiment.chefRemainingSeconds),
"template_prep_estimated_end_time":
utils.convert_seconds_to_datetime_string(
plan.experiment.chefLastUpdate,
plan.experiment.chefRemainingSeconds),
}
samplesets_w_libprep = plan.sampleSets.filter(
libraryPrepInstrumentData__isnull=False)
if samplesets_w_libprep:
libprep_done.extend(
list(samplesets_w_libprep.values_list("pk", flat=True)))
data.update({
"lib_prep_progress":
samplesets_w_libprep[0].libraryPrepInstrumentData.progress,
"lib_prep_status":
samplesets_w_libprep[0].libraryPrepInstrumentData.
instrumentStatus,
})
chef_table.append(data)
# add sample sets with Library prep only
for sampleSet in sampleSets:
if sampleSet.pk not in libprep_done:
chef_table.append({
"planName":
"",
"sampleSetName":
sampleSet.displayedName,
"sample_prep_type":
"Library Prep", # TODO: i18n - not used by UI
"last_updated":
sampleSet.libraryPrepInstrumentData.lastUpdate,
"instrumentName":
sampleSet.libraryPrepInstrumentData.instrumentName,
"lib_prep_progress":
sampleSet.libraryPrepInstrumentData.progress,
"lib_prep_status":
sampleSet.libraryPrepInstrumentData.instrumentStatus,
"operation_mode":
sampleSet.libraryPrepInstrumentData.operationMode,
"remaining_time":
utils.convert_seconds_to_hhmmss_string(
sampleSet.libraryPrepInstrumentData.remainingSeconds),
"estimated_end_time":
utils.convert_seconds_to_datetime_string(
sampleSet.libraryPrepInstrumentData.lastUpdate,
sampleSet.libraryPrepInstrumentData.remainingSeconds,
),
})
chef_table = sorted(chef_table,
key=lambda plan: plan["last_updated"],
reverse=True)
chef_pager = Paginator(chef_table, size, 0)
try:
chef_page = chef_pager.page(page)
except InvalidPage:
chef_page = chef_pager.page(1)
context = {"plans": chef_page}
return render(request, "rundb/monitor/chef.html", context)
def chef(request):
querydict = request.GET
days = get_int(querydict, "days", 7)
size = get_int(querydict, "size", 10)
page = get_int(querydict, "page", 1)
days_ago = datetime.datetime.now() - datetime.timedelta(days=days)
# monitoring page should show Chef plans that are currently in progress or have recently finished Chef processing,
# regardless if they are being or have been sequenced
plans = models.PlannedExperiment.objects.filter(experiment__chefLastUpdate__gte=days_ago)
sampleSets = models.SampleSet.objects.filter(libraryPrepInstrumentData__lastUpdate__gte=days_ago)
libprep_done = []
chef_table = []
# planned runs may have both Template and Library prep data
for plan in plans:
data = {
'planName': plan.planDisplayedName,
'sampleSetName': ', '.join(plan.sampleSets.order_by('displayedName').values_list('displayedName', flat=True)),
'last_updated' : plan.experiment.chefLastUpdate,
'instrumentName': plan.experiment.chefInstrumentName,
'template_prep_progress': plan.experiment.chefProgress,
'template_prep_status': plan.experiment.chefStatus,
'template_prep_operation_mode': plan.experiment.chefOperationMode,
'template_prep_remaining_time': utils.convert_seconds_to_hhmmss_string(plan.experiment.chefRemainingSeconds),
'template_prep_estimated_end_time': utils.convert_seconds_to_datetime_string(plan.experiment.chefLastUpdate, plan.experiment.chefRemainingSeconds)
}
samplesets_w_libprep = plan.sampleSets.filter(libraryPrepInstrumentData__isnull=False)
if samplesets_w_libprep:
libprep_done.extend(list(samplesets_w_libprep.values_list('pk', flat=True)))
data.update({
'lib_prep_progress': samplesets_w_libprep[0].libraryPrepInstrumentData.progress,
'lib_prep_status': samplesets_w_libprep[0].libraryPrepInstrumentData.instrumentStatus
})
chef_table.append(data)
# add sample sets with Library prep only
for sampleSet in sampleSets:
if sampleSet.pk not in libprep_done:
chef_table.append({
'planName': '',
'sampleSetName': sampleSet.displayedName,
'sample_prep_type': 'Library Prep',
'last_updated' : sampleSet.libraryPrepInstrumentData.lastUpdate,
'instrumentName': sampleSet.libraryPrepInstrumentData.instrumentName,
'lib_prep_progress': sampleSet.libraryPrepInstrumentData.progress,
'lib_prep_status': sampleSet.libraryPrepInstrumentData.instrumentStatus,
'operation_mode': sampleSet.libraryPrepInstrumentData.operationMode,
'remaining_time': utils.convert_seconds_to_hhmmss_string(sampleSet.libraryPrepInstrumentData.remainingSeconds),
'estimated_end_time': utils.convert_seconds_to_datetime_string(sampleSet.libraryPrepInstrumentData.lastUpdate, sampleSet.libraryPrepInstrumentData.remainingSeconds)
})
chef_table = sorted(chef_table, key=lambda plan: plan['last_updated'], reverse=True)
chef_pager = Paginator(chef_table, size, 0)
try:
chef_page = chef_pager.page(page)
except InvalidPage:
chef_page = chef_pager.page(1)
context = {
"plans": chef_page
}
return render(request, "rundb/monitor/chef.html", context)