def start_qc_analysis(rawfile, storedfile, wf_id, dbfn_id):
analysis = Analysis(user_id=settings.QC_USER_ID,
name='{}_{}_{}'.format(rawfile.producer.name,
rawfile.name, rawfile.date))
analysis.save()
jobutil.create_file_job('run_longit_qc_workflow', storedfile.id,
analysis.id, wf_id, dbfn_id)
def save(self, commit=True):
instance = super().save(commit=False)
instance.user = self.user
if self.analysis:
analysis = self.analysis.clone()
else:
# Create empty analysis for template
user_settings = UserSettings.get_for_user(self.user)
genome_build = user_settings.default_genome_build # Doesn't matter for templates
analysis = Analysis(genome_build=genome_build,
name=f"analysis for template {instance.name}")
analysis.template_type = AnalysisTemplateType.TEMPLATE
analysis.set_defaults_and_save(self.user)
assign_permission_to_user_and_groups(self.user, analysis)
instance.analysis = analysis
if commit:
instance.save()
return instance
def workbook(request, workbook_id=0):
template = 'workbooks/workbook.html'
command = request.path.rsplit('/',1)[1]
if request.method == "POST" :
if command == "create" :
workbook_model = Workbook.createDefault(name="Untitled Workbook", description="", user=request.user)
elif command == "edit" :
workbook_model = Workbook.edit(id=workbook_id, name=request.POST.get('name'), description=request.POST.get('description'))
elif command == "copy" :
workbook_model = Workbook.copy(id=workbook_id, user=request.user)
elif command == "delete" :
Workbook.destroy(id=workbook_id)
if command == "delete":
redirect_url = reverse('workbooks')
return redirect(redirect_url)
else :
redirect_url = reverse('workbook_detail', kwargs={'workbook_id':workbook_model.id})
return redirect(redirect_url)
elif request.method == "GET" :
if workbook_id:
try :
ownedWorkbooks = request.user.workbook_set.all().filter(active=True)
sharedWorkbooks = Workbook.objects.filter(shared__matched_user=request.user, shared__active=True, active=True)
publicWorkbooks = Workbook.objects.all().filter(is_public=True,active=True)
workbooks = ownedWorkbooks | sharedWorkbooks | publicWorkbooks
workbooks = workbooks.distinct()
workbook_model = workbooks.get(id=workbook_id)
workbook_model.worksheets = workbook_model.get_deep_worksheets()
is_shareable = workbook_model.is_shareable(request)
shared = None
if workbook_model.owner.id != request.user.id and not workbook_model.is_public:
shared = request.user.shared_resource_set.get(workbook__id=workbook_id)
plot_types = Analysis.get_types()
return render(request, template, {'workbook' : workbook_model,
'datatypes' : get_gene_datatypes(),
'is_shareable': is_shareable,
'shared' : shared,
'plot_types' : plot_types})
except ObjectDoesNotExist:
redirect_url = reverse('workbooks')
return redirect(redirect_url)
else :
redirect_url = reverse('workbooks')
return redirect(redirect_url)
def create_classification_for_analysis(request, analysis_id):
classification = create_classification_object(request)
analysis = Analysis.get_for_user(request.user, pk=analysis_id)
if analysis.can_write(request.user):
AnalysisClassification.objects.create(analysis=analysis,
classification=classification)
# Remove "Requires classification" tag
VariantTag.objects.filter(
variant=classification.variant,
analysis=analysis,
tag_id=settings.TAG_REQUIRES_CLASSIFICATION).delete()
return redirect(classification)
def workbook_create_with_analysis(request):
analysis_type = request.POST.get('analysis')
allowed_types = Analysis.get_types()
redirect_url = reverse('sample_analyses')
for type in allowed_types :
if analysis_type == type['name'] :
workbook_model = Workbook.create(name="Untitled Workbook", description="this is an untitled workbook with a \"" + analysis_type + "\" plot added to the first worksheet. Click Edit Details to change your workbook title and description.", user=request.user)
worksheet_model = Worksheet.objects.create(name="worksheet 1", description="", workbook=workbook_model)
worksheet_model.set_plot(type=analysis_type)
redirect_url = reverse('workbook_detail', kwargs={'workbook_id':workbook_model.id})
break
return redirect(redirect_url)
def worksheet_display(request, workbook_id=0, worksheet_id=0):
template = 'workbooks/workbook.html'
workbook_model = Workbook.deep_get(workbook_id)
workbook_model.mark_viewed(request)
is_shareable = workbook_model.is_shareable(request)
for worksheet in workbook_model.worksheets:
if str(worksheet.id) == worksheet_id:
display_worksheet = worksheet
plot_types = Analysis.get_types()
return render(request, template, {'workbook' : workbook_model,
'is_shareable' : is_shareable,
'datatypes' : get_gene_datatypes(),
'display_worksheet' : display_worksheet,
'plot_types' : plot_types})
def worksheet_display(request, workbook_id=0, worksheet_id=0):
template = 'workbooks/workbook.html'
workbook_model = Workbook.deep_get(workbook_id)
workbook_model.mark_viewed(request)
is_shareable = workbook_model.is_shareable(request)
for worksheet in workbook_model.worksheets:
if str(worksheet.id) == worksheet_id:
display_worksheet = worksheet
plot_types = Analysis.get_types()
return render(
request, template, {
'workbook': workbook_model,
'is_shareable': is_shareable,
'datatypes': get_gene_datatypes(workbook_model.build),
'display_worksheet': display_worksheet,
'plot_types': plot_types
})
def workbook_create_with_analysis(request):
analysis_type = request.POST.get('analysis')
allowed_types = Analysis.get_types()
redirect_url = reverse('sample_analyses')
for type in allowed_types:
if analysis_type == type['name']:
workbook_model = Workbook.create(
name="Untitled Workbook",
description="this is an untitled workbook with a \"" +
analysis_type +
"\" plot added to the first worksheet. Click Edit Details to change your workbook title and description.",
user=request.user)
worksheet_model = Worksheet.objects.create(name="worksheet 1",
description="",
workbook=workbook_model)
worksheet_model.set_plot(type=analysis_type)
redirect_url = reverse('workbook_detail',
kwargs={'workbook_id': workbook_model.id})
break
return redirect(redirect_url)
def __init__(self, **kwargs):
user = kwargs.get("user")
super().__init__(user)
fields = self.get_field_names()
self.genome_builds = list(GenomeBuild.builds_with_annotation())
if len(self.genome_builds) == 1: # No need to show
genome_build_colmodel = self._overrides.get('genome_build', {})
genome_build_colmodel['hidden'] = True
self._overrides['genome_build'] = genome_build_colmodel
user_grid_config = UserGridConfig.get(user, self.caption)
if user_grid_config.show_group_data:
qs = Analysis.filter_for_user(user)
else:
qs = Analysis.objects.filter(user=user)
qs = qs.filter(genome_build__in=self.genome_builds)
qs = qs.filter(visible=True,
template_type__isnull=True) # Hide templates
q_last_lock = Q(analysislock=F("last_lock")) | Q(
analysislock__isnull=True)
qs = qs.annotate(last_lock=Max("analysislock__pk")).filter(q_last_lock)
self.queryset = qs.values(*fields)
self.extra_config.update({'sortname': 'modified', 'sortorder': 'desc'})
def setUpClass(cls):
super().setUpClass()
user = User.objects.get_or_create(username='******')[0]
cls.grch37 = GenomeBuild.get_name_or_alias("GRCh37")
cls.annotation_version_grch37 = get_fake_annotation_version(cls.grch37)
gene_annotation_release = cls.annotation_version_grch37.gene_annotation_version.gene_annotation_release
cls.transcript_version = create_fake_transcript_version(cls.grch37,
release=gene_annotation_release)
cls.gene_symbol = cls.transcript_version.gene_version.gene_symbol
cls.trio = create_fake_trio(user, cls.grch37)
cls.analysis = Analysis(genome_build=cls.grch37)
cls.analysis.set_defaults_and_save(user)
cls.sample = cls.trio.get_samples()[0]
# Gene List
cls.gene_list = GeneList.objects.get_or_create(name="fake list",
user=cls.analysis.user,
import_status=ImportStatus.SUCCESS)[0]
GeneListGeneSymbol.objects.get_or_create(gene_list=cls.gene_list, gene_symbol=cls.gene_symbol)
# Need some overlapping variants so gene list will work
create_fake_variants(cls.grch37)
# Note: Variant probably doesn't overlap with gene, just want a random one
variant = Variant.objects.filter(Variant.get_no_reference_q()).first()
annotation_run = AnnotationRun.objects.create()
VariantGeneOverlap.objects.create(version=cls.annotation_version_grch37.variant_annotation_version,
annotation_run=annotation_run,
gene=cls.transcript_version.gene,
variant=variant)
# Tag that variant
cls.tag = Tag.objects.get_or_create(pk="foo")[0]
VariantTag.objects.create(genome_build=cls.grch37, analysis=cls.analysis,
variant=variant, tag=cls.tag, user=user)
def get_user_queryset(self, user):
qs = Analysis.filter_for_user(user)
if template_type := self.forwarded.get('template_type', None):
qs = qs.filter(template_type=template_type)
def start_qc_analysis(rawfile, storedfile, wf_id, dbfn_id):
analysis = Analysis(user_id=settings.QC_USER_ID,
name='{}_{}_{}'.format(rawfile.producer.name, rawfile.name, rawfile.date))
analysis.save()
jobutil.create_file_job('run_longit_qc_workflow', storedfile.id,
analysis.id, wf_id, dbfn_id)
def workbook(request, workbook_id=0):
template = 'workbooks/workbook.html'
command = request.path.rsplit('/',1)[1]
if request.method == "POST":
if command == "create":
workbook_model = Workbook.createDefault(name="Untitled Workbook", description="", user=request.user)
elif command == "edit":
workbook_name = request.POST.get('name')
workbook_desc = request.POST.get('description')
whitelist = re.compile(WHITELIST_RE, re.UNICODE)
match_name = whitelist.search(unicode(workbook_name))
match_desc = whitelist.search(unicode(workbook_desc))
if match_name or match_desc:
# XSS risk, log and fail this cohort save
matches = ""
fields = ""
if match_name:
match_name = whitelist.findall(unicode(workbook_name))
logger.error('[ERROR] While saving a workbook, saw a malformed name: ' + workbook_name + ', characters: ' + match_name.__str__())
matches = "name contains"
fields = "name"
if match_desc:
match_desc = whitelist.findall(unicode(workbook_desc))
logger.error('[ERROR] While saving a workbook, saw a malformed description: ' + workbook_desc + ', characters: ' + match_desc.__str__())
matches = "name and description contain" if match_name else "description contains"
fields += (" and description" if match_name else "description")
err_msg = "Your workbook's %s invalid characters; please choose another %s." % (matches, fields,)
messages.error(request, err_msg)
redirect_url = reverse('workbook_detail', kwargs={'workbook_id':workbook_id})
return redirect(redirect_url)
workbook_model = Workbook.edit(id=workbook_id, name=workbook_name, description=workbook_desc)
elif command == "copy":
workbook_model = Workbook.copy(id=workbook_id, user=request.user)
elif command == "delete":
Workbook.destroy(id=workbook_id)
if command == "delete":
redirect_url = reverse('workbooks')
else:
redirect_url = reverse('workbook_detail', kwargs={'workbook_id':workbook_model.id})
return redirect(redirect_url)
elif request.method == "GET" :
if workbook_id:
try :
ownedWorkbooks = request.user.workbook_set.all().filter(active=True)
sharedWorkbooks = Workbook.objects.filter(shared__matched_user=request.user, shared__active=True, active=True)
publicWorkbooks = Workbook.objects.all().filter(is_public=True,active=True)
workbooks = ownedWorkbooks | sharedWorkbooks | publicWorkbooks
workbooks = workbooks.distinct()
workbook_model = workbooks.get(id=workbook_id)
workbook_model.worksheets = workbook_model.get_deep_worksheets()
is_shareable = workbook_model.is_shareable(request)
shared = None
if workbook_model.owner.id != request.user.id and not workbook_model.is_public:
shared = request.user.shared_resource_set.get(workbook__id=workbook_id)
plot_types = Analysis.get_types()
return render(request, template, {'workbook' : workbook_model,
'datatypes' : get_gene_datatypes(),
'is_shareable': is_shareable,
'shared' : shared,
'plot_types' : plot_types})
except ObjectDoesNotExist:
redirect_url = reverse('workbooks')
return redirect(redirect_url)
else :
redirect_url = reverse('workbooks')
return redirect(redirect_url)
def worksheet_plots(request, workbook_id=0, worksheet_id=0, plot_id=0):
command = request.path.rsplit('/', 1)[1]
json_response = False
default_name = "Untitled Workbook"
result = {}
try:
workbook_model = Workbook.objects.get(
id=workbook_id) if workbook_id else None
if request.method == "POST":
workbook_model.save()
if command == "delete":
var = Worksheet_plot.objects.get(id=plot_id).delete()
result['message'] = "This plot has been deleted from workbook."
else:
if "attrs" in request.body:
json_response = True
attrs = json.loads(request.body)['attrs']
settings = json.loads(request.body)['settings']
if plot_id:
plot_model = Worksheet_plot.objects.get(id=plot_id)
plot_model.settings_json = settings
if attrs['cohorts']:
try:
Worksheet_plot_cohort.objects.filter(
plot=plot_model).delete()
for obj in attrs['cohorts']:
wpc = Worksheet_plot_cohort(
plot=plot_model, cohort_id=obj['id'])
wpc.save()
except ObjectDoesNotExist:
None
plot_model.save()
result['updated'] = "success"
elif request.method == "GET":
json_response = True
plot_type = escape(request.GET.get('type', 'default'))
if plot_type not in Analysis.get_types_list():
raise Exception(
"Plot type {} was not found in the allowed list of plot types!"
.format(plot_type))
worksheet_model = Worksheet.objects.get(id=worksheet_id)
plots = worksheet_model.worksheet_plot_set.all()
for p in plots:
p.active = False
p.save()
plots = worksheet_model.worksheet_plot_set.filter(type=plot_type)
if len(plots) == 0:
model = Worksheet_plot(type=plot_type,
worksheet=worksheet_model)
model.save()
else:
model = plots[0]
model.active = True
model.save()
result['data'] = model.toJSON()
else:
result['error'] = "method not correct"
if json_response:
return HttpResponse(json.dumps(result), status=200)
else:
redirect_url = reverse('worksheet_display',
kwargs={
'workbook_id': workbook_model.id,
'worksheet_id': worksheet_model.id
})
return redirect(redirect_url)
except Exception as e:
logger.error("[ERROR] While accessing workbooks/worksheets:")
logger.exception(e)
messages.error(
request,
"An error occurred while trying to process this workbook request.")
return redirect('workbooks')
def workbook(request, workbook_id=0):
template = 'workbooks/workbook.html'
command = request.path.rsplit('/', 1)[1]
workbook_model = None
try:
if request.method == "POST":
if command == "create":
workbook_model = Workbook.createDefault(
name="Untitled Workbook",
description="",
user=request.user)
elif command == "edit":
# Truncate incoming name and desc fields in case someone tried to send ones which were too long
workbook_name = request.POST.get('name')[0:2000]
workbook_desc = request.POST.get('description')[0:2000]
workbook_build = request.POST.get('build')
blacklist = re.compile(BLACKLIST_RE, re.UNICODE)
match_name = blacklist.search(unicode(workbook_name))
match_desc = blacklist.search(unicode(workbook_desc))
if match_name or match_desc:
# XSS risk, log and fail this cohort save
matches = ""
fields = ""
if match_name:
match_name = blacklist.findall(unicode(workbook_name))
logger.error(
'[ERROR] While saving a workbook, saw a malformed name: '
+ workbook_name + ', characters: ' +
str(match_name))
matches = "name contains"
fields = "name"
if match_desc:
match_desc = blacklist.findall(unicode(workbook_desc))
logger.error(
'[ERROR] While saving a workbook, saw a malformed description: '
+ workbook_desc + ', characters: ' +
str(match_desc))
matches = "name and description contain" if match_name else "description contains"
fields += (" and description"
if match_name else "description")
err_msg = "Your workbook's %s invalid characters; please choose another %s." % (
matches,
fields,
)
messages.error(request, err_msg)
redirect_url = reverse('workbook_detail',
kwargs={'workbook_id': workbook_id})
return redirect(redirect_url)
workbook_model = Workbook.edit(id=workbook_id,
name=workbook_name,
description=workbook_desc,
build=workbook_build)
elif command == "copy":
workbook_model = Workbook.copy(id=workbook_id,
user=request.user)
elif command == "delete":
Workbook.destroy(id=workbook_id)
if command == "delete":
redirect_url = reverse('workbooks')
else:
redirect_url = reverse(
'workbook_detail',
kwargs={'workbook_id': workbook_model.id})
return redirect(redirect_url)
elif request.method == "GET":
if workbook_id:
try:
ownedWorkbooks = request.user.workbook_set.filter(
active=True)
sharedWorkbooks = Workbook.objects.filter(
shared__matched_user=request.user,
shared__active=True,
active=True)
publicWorkbooks = Workbook.objects.filter(is_public=True,
active=True)
workbooks = ownedWorkbooks | sharedWorkbooks | publicWorkbooks
workbooks = workbooks.distinct()
workbook_model = workbooks.get(id=workbook_id)
workbook_model.worksheets = workbook_model.get_deep_worksheets(
)
is_shareable = workbook_model.is_shareable(request)
shared = None
if workbook_model.owner.id != request.user.id and not workbook_model.is_public:
shared = request.user.shared_resource_set.get(
workbook__id=workbook_id)
plot_types = Analysis.get_types()
return render(
request, template, {
'workbook': workbook_model,
'datatypes': get_gene_datatypes(
workbook_model.build),
'is_shareable': is_shareable,
'shared': shared,
'plot_types': plot_types
})
except ObjectDoesNotExist:
redirect_url = reverse('workbooks')
return redirect(redirect_url)
else:
redirect_url = reverse('workbooks')
return redirect(redirect_url)
except Exception as e:
logger.error("[ERROR] Exception when viewing a workbook: ")
logger.exception(e)
messages.error(
request,
"An error was encountered while trying to view this workbook.")
finally:
redirect_url = reverse('workbooks')
return redirect(redirect_url)
