def add_plot(request):
# TODO: Double check that user owns viz
cohort = Cohort.objects.get_all_tcga_cohort()
# Fetch cohorts list used for autocomplete listing
cohort_perms = Cohort_Perms.objects.filter(user=request.user).values_list('cohort', flat=True)
cohort_listing = Cohort.objects.filter(id__in=cohort_perms, active=True).values('id', 'name')
for cohort_item in cohort_listing:
cohort_item['value'] = int(cohort_item['id'])
cohort_item['label'] = cohort_item['name'].encode('utf8')
del cohort_item['id']
del cohort_item['name']
viz_id = request.GET.get('viz_id', None)
# Filter Options
datatypes = [
{'id': 'CLIN', 'label': 'Clinical'},
{'id': 'GEXP', 'label': 'Gene Expression'},
{'id': 'MIRN', 'label': 'miRNA'},
{'id': 'METH', 'label': 'Methylation'},
{'id': 'CNVR', 'label': 'Copy Number'},
{'id': 'RPPA', 'label': 'Protein'},
{'id': 'GNAB', 'label': 'Mutation'}
]
new_datatypes = SearchableFieldHelper.get_fields_for_all_datatypes()
if viz_id:
viz = SavedViz.objects.get(id=int(viz_id))
plot = Plot.objects.create(visualization=viz,
title='',
x_axis='CLIN:age_at_initial_pathologic_diagnosis',
y_axis='',
color_by='CLIN:Study')
plot.save()
plot_cohort = Plot_Cohorts.objects.create(plot=plot, cohort=cohort)
plot_cohort.save()
return_obj = {'plot': {
'id': int(plot.id),
'title': plot.title.encode('utf-8'),
'cohorts': [{
'id': int(cohort.id),
'name': cohort.name.encode('utf-8')
}],
'x_attr': str(plot.x_axis),
'y_attr': str(plot.y_axis),
'color_by': str(plot.color_by),
'cohort_name': str(cohort.name),
'patient_length': len(cohort.patients_set.all()),
'sample_length': len(cohort.samples_set.all()),
'comments': [],
'viz_perm': 'OWNER'
},
'cohorts': cohort_listing,
'data_types': datatypes,
'new_datatypes': new_datatypes}
return render(request, 'visualizations/plot.html', return_obj, status=200)
return HttpResponse(status=500)
def get_gene_datatypes():
datatype_labels = {'GEXP' : 'Gene Expression',
'METH' : 'Methylation',
'CNVR' : 'Copy Number',
'RPPA' : 'Protein',
'GNAB' : 'Mutation'}
datatype_list = SearchableFieldHelper.get_fields_for_all_datatypes()
if debug: print >> sys.stderr, ' attrs ' + json.dumps(datatype_list)
return_list = []
for type in datatype_list:
if type['datatype'] != 'CLIN' and type['datatype'] != 'MIRN' :
type['label'] = datatype_labels[type['datatype']]
return_list.append(type)
#remove gene in fields as they are set with the variable selection
for index, field in enumerate(type['fields']):
if field['label'] == "Gene":
del type['fields'][index]
return return_list
def initialize_variable_selection_page(request,
variable_list_id=0,
workbook_id=0,
worksheet_id=0,
new_workbook=False):
template = 'variables/variable_edit.html'
context = {'variables' : [] }
workbook_model = None
worksheet_model = None
existing_variable_list = None
if workbook_id != 0 :
try:
workbook_model = Workbook.objects.get(id=workbook_id)
context['workbook'] = workbook_model
worksheet_model = Worksheet.objects.get(id=worksheet_id)
context['worksheet'] = worksheet_model
except ObjectDoesNotExist:
messages.error(request, 'The workbook you were referencing does not exist.')
return redirect('variables')
if variable_list_id != 0:
try:
existing_variable_list = request.user.variablefavorite_set.get(id=variable_list_id)
except ObjectDoesNotExist:
messages.error(request, 'The variable favorite you were looking for does not exist.')
return redirect('variables')
data_attr = [
'DNA_sequencing',
'RNA_sequencing',
'miRNA_sequencing',
'Protein',
'SNP_CN',
'DNA_methylation'
]
# This is a list of specific data classifications which require additional filtering in order to
# Gather categorical or numercial variables for use in the plot
# Filter Options
datatype_labels = {'CLIN' : 'Clinical',
'GEXP' : 'Gene Expression',
'MIRN' : 'miRNA',
'METH' : 'Methylation',
'CNVR' : 'Copy Number',
'RPPA' : 'Protein',
'GNAB' : 'Mutation'}
datatype_list = SearchableFieldHelper.get_fields_for_all_datatypes()
for type in datatype_list:
type['label'] = datatype_labels[type['datatype']]
#remove gene in fields
for index, field in enumerate(type['fields']):
if field['label'] == "Gene":
del type['fields'][index]
#get user programs and variables
ownedPrograms = request.user.program_set.all().filter(active=True)
sharedPrograms = Program.objects.filter(shared__matched_user=request.user, shared__active=True, active=True)
programs = ownedPrograms | sharedPrograms
programs = programs.distinct()
#get user favorites
favorite_list = VariableFavorite.get_list(user=request.user)
for fav in favorite_list :
fav.variables = fav.get_variables()
#TODO common variables need to be refactored into an adaptive list based on common used
displayed_common_variables = [
{'name' : "vital_status", 'code' : 'CLIN:vital_status', 'type' : 'C'},
{'name' : "gender", 'code' : 'CLIN:gender', 'type' : 'C'},
{'name' : "age_at_initial_pathologic_diagnosis", 'code' : 'CLIN:age_at_initial_pathologic_diagnosis', 'type' : 'N'},
{'name' : "tumor_tissue_site", 'code' : 'CLIN:tumor_tissue_site', 'type' : 'C'},
{'name' : "histological_type", 'code' : 'CLIN:histological_type', 'type' : 'C'},
{'name' : "other_diagnosis", 'code' : 'CLIN:other_dx', 'type' : 'C'},
{'name' : "tumor_status", 'code' : 'CLIN:person_neoplasm_cancer_status', 'type' : 'C'},
{'name' : "new_tumor_event_after_initial_treatment", 'code' : 'CLIN:new_tumor_event_after_initial_treatment', 'type' : 'C'},
{'name' : "histological_grade", 'code' : 'CLIN:neoplasm_histologic_grade', 'type' : 'C'},
{'name' : "residual_tumor", 'code' : 'CLIN:residual_tumor', 'type' : 'C'},
{'name' : "tobacco_smoking_history", 'code' : 'CLIN:tobacco_smoking_history', 'type' : 'C'},
{'name' : "icd-10", 'code' : 'CLIN:icd_10', 'type' : 'C'},
{'name' : "icd-o-3_site", 'code' : 'CLIN:icd_o_3_site', 'type' : 'C'},
{'name' : "icd-o-3_histology", 'code' : 'CLIN:icd_o_3_histology', 'type' : 'C'}
]
common_variables = displayed_common_variables
TCGA_program = {"id" : -1, "study" : {"id" :-1, "name" : ""}, "name" : "TCGA"}
common_program = {"id" : -1, "study" : {"id" :-1, "name" : ""}, "name" : "Common", "variables" : common_variables}
# users can select from their saved variable favorites
variable_favorites = VariableFavorite.get_list(request.user)
context = {
'favorite_list' : favorite_list,
'datatype_list' : datatype_list,
'programs' : programs,
'data_attr' : data_attr,
'base_url' : settings.BASE_URL,
'base_api_url' : settings.BASE_API_URL,
'TCGA_program' : TCGA_program,
'common_program' : common_program,
'variable_favorites' : variable_favorites,
'workbook' : workbook_model,
'worksheet' : worksheet_model,
'existing_variable_list' : existing_variable_list,
'new_workbook' : new_workbook
}
return render(request, template, context)
def genericplot(request, id=0):
searches = {}
viz = {}
plots_data = []
plot_render_data = []
viz_perm = None
users = User.objects.filter(is_superuser=0)
# Filter Options
datatypes = [
{'id': 'CLIN', 'label': 'Clinical'},
{'id': 'GEXP', 'label': 'Gene Expression'},
{'id': 'MIRN', 'label': 'miRNA'},
{'id': 'METH', 'label': 'Methylation'},
{'id': 'CNVR', 'label': 'Copy Number'},
{'id': 'RPPA', 'label': 'Protein'},
{'id': 'GNAB', 'label': 'Mutation'}
]
new_datatypes = SearchableFieldHelper.get_fields_for_all_datatypes()
# Fetch cohorts list used for autocomplete listing
cohort_perms = Cohort_Perms.objects.filter(user=request.user).values_list('cohort', flat=True)
cohort_listing = Cohort.objects.filter(id__in=cohort_perms, active=True).values('id', 'name')
for cohort in cohort_listing:
cohort['value'] = int(cohort['id'])
cohort['label'] = cohort['name'].encode('utf8')
del cohort['id']
del cohort['name']
if id != 0:
viz = SavedViz.objects.get(id=id)
plots = Plot.objects.filter(visualization=id)
if viz:
viz_perm = viz.get_perm(request)
for plot in plots:
sample_set, patient_set = union_cohort_samples_patients(plot.plot_cohorts_set.all().values_list('cohort', flat=True))
cohorts = Cohort.objects.filter(id__in=plot.plot_cohorts_set.all().values_list('cohort', flat=True))
# for c in plot.plot_cohorts_set.all():
# cohorts.append(Cohort.objects.filter(id__in=)
cohort_list = []
for cohort in cohorts:
cohort_list.append({
'id': int(cohort.id),
'name': cohort.name.encode('utf-8')
})
item = {
'plot_id': int(plot.id),
'title': plot.title.encode('utf-8'),
'x_attr': str(plot.x_axis),
'y_attr': str(plot.y_axis),
'color_by': str(plot.color_by) if plot.color_by else 'CLIN:Study',
'cohorts': cohort_list,
# 'cohort_name': str(cohort.name),
'patient_length': len(patient_set),
'sample_length': len(sample_set),
# 'notes': str(plot.notes)
}
plots_data.append(item)
plot_render_data.append({
'id': int(plot.id),
'title': plot.title.encode('utf-8'),
'x_attr': str(plot.x_axis),
'y_attr': str(plot.y_axis),
'color_by': str(plot.color_by) if plot.color_by else 'CLIN:Study',
'cohorts': cohort_list,
# 'cohort_name': str(cohort.name),
'patient_length': len(patient_set),
'sample_length': len(sample_set),
'comments': plot.plot_comment.all(),
'viz_perm': viz_perm.perm
})
else:
title = request.POST.get('vis_title', 'Unititled Visualization')
cohort_id = request.POST.get('cohort_id', None)
if not cohort_id:
cohort = Cohort.objects.get_all_tcga_cohort()
else:
cohort = Cohort.objects.get(id=cohort_id)
viz = SavedViz.objects.create(name=title)
viz.save()
perm = Viz_Perms.objects.create(visualization=viz, user=request.user, perm=Viz_Perms.OWNER)
perm.save()
viz_perm = perm
plot = Plot.objects.create(visualization=viz,
title='',
x_axis='CLIN:age_at_initial_pathologic_diagnosis',
y_axis='',
color_by='CLIN:Study')
plot.save()
plot_cohort = Plot_Cohorts.objects.create(plot=plot, cohort=cohort)
plot_cohort.save()
item = {
'plot_id': int(plot.id),
'title': plot.title.encode('utf-8'),
'x_attr': str(plot.x_axis),
'y_attr': str(plot.y_axis),
'color_by': str(plot.color_by),
'cohorts': [{
'id': int(cohort.id),
'name': cohort.name.encode('utf-8')
}],
'cohort_name': str(cohort.name),
'patient_length': len(cohort.patients_set.all()),
'sample_length': len(cohort.samples_set.all()),
}
plots_data.append(item)
plot_render_data.append({
'id': int(plot.id),
'title': plot.title.encode('utf-8'),
'cohorts': [{
'id': int(cohort.id),
'name': cohort.name.encode('utf-8')
}],
'cohort_name': str(cohort.name),
'patient_length': len(cohort.patients_set.all()),
'sample_length': len(cohort.samples_set.all()),
'comments': [],
'viz_perm': perm.perm,
'x_attr': str(plot.x_axis),
'y_attr': str(plot.y_axis),
'color_by': str(plot.color_by),
})
return render(request, 'visualizations/genericplot.html', {'request': request,
'searches': searches,
'viz': viz,
'viz_perm': viz_perm.perm,
'plots_data': plots_data,
'plot_render_data': plot_render_data,
'users': users,
'friendly_name_map': fm_friendly_name_map,
'categorical_attributes': fm_categorical_attributes,
'numerical_attributes': fm_numerical_attributes,
'cohorts': cohort_listing,
'base_url': settings.BASE_URL,
'base_api_url': settings.BASE_API_URL,
'data_types': datatypes,
'new_datatypes': new_datatypes})
