def combine_mendelian_families(request):
project, family_group = utils.get_project_and_family_group_for_user(request.user, request.GET)
if not project.can_view(request.user):
return PermissionDenied
form = api_forms.CombineMendelianFamiliesForm(request.GET)
if form.is_valid():
search_spec = form.cleaned_data['search_spec']
search_spec.family_group_id = family_group.slug
genes = api_utils.calculate_combine_mendelian_families(family_group, search_spec)
search_hash = cache_utils.save_results_for_spec(project.project_id, search_spec.toJSON(), genes)
api_utils.add_extra_info_to_genes(project, get_reference(), genes)
return JSONResponse({
'is_error': False,
'genes': genes,
'search_hash': search_hash,
})
else:
return JSONResponse({
'is_error': True,
'error': server_utils.form_error_string(form)
})
def mendelian_variant_search(request):
# TODO: how about we move project getter into the form, and just test for authX here?
# esp because error should be described in json, not just 404
project, family = get_project_and_family_for_user(request.user, request.GET)
form = api_forms.MendelianVariantSearchForm(request.GET)
if form.is_valid():
search_spec = form.cleaned_data['search_spec']
search_spec.family_id = family.family_id
variants = api_utils.calculate_mendelian_variant_search(search_spec, family.xfamily())
search_hash = cache_utils.save_results_for_spec(project.project_id, search_spec.toJSON(), [v.toJSON() for v in variants])
add_extra_info_to_variants_family(get_reference(), family, variants)
return_type = request.GET.get('return_type', 'json')
if return_type == 'json':
return JSONResponse({
'is_error': False,
'variants': [v.toJSON() for v in variants],
'search_hash': search_hash,
})
elif return_type == 'csv':
return ''
else:
return HttpResponse("Return type not implemented")
else:
return JSONResponse({
'is_error': True,
'error': server_utils.form_error_string(form)
})
def cohort_variant_search(request):
project, cohort = get_project_and_cohort_for_user(request.user, request.GET)
if not project.can_view(request.user):
return PermissionDenied
form = api_forms.CohortVariantSearchForm(request.GET)
if form.is_valid():
search_spec = form.cleaned_data['search_spec']
search_spec.family_id = cohort.cohort_id
sys.stderr.write("cohort_variant_search - starting: %s %s\n" % (json.dumps(search_spec.toJSON()), cohort.xfamily().family_id))
variants = api_utils.calculate_mendelian_variant_search(search_spec, cohort.xfamily())
list_of_variants = [v.toJSON() for v in variants]
sys.stderr.write("cohort_variant_search - done calculate_mendelian_variant_search: %s %s %s\n" % (json.dumps(search_spec.toJSON()), cohort.xfamily().family_id, len(list_of_variants)))
search_hash = cache_utils.save_results_for_spec(project.project_id, search_spec.toJSON(), list_of_variants)
sys.stderr.write("cohort_variant_search - done save_results_for_spec: %s %s\n" % (json.dumps(search_spec.toJSON()), cohort.xfamily().family_id))
api_utils.add_extra_info_to_variants_cohort(get_reference(), cohort, variants)
sys.stderr.write("cohort_variant_search - done add_extra_info_to_variants_cohort: %s %s\n" % (json.dumps(search_spec.toJSON()), cohort.xfamily().family_id))
return JSONResponse({
'is_error': False,
'variants': [v.toJSON() for v in variants],
'search_hash': search_hash,
})
else:
return JSONResponse({
'is_error': True,
'error': server_utils.form_error_string(form)
})
def cohort_gene_search(request):
project, cohort = get_project_and_cohort_for_user(request.user, request.GET)
sys.stderr.write("cohort_gene_search %s %s: starting ... \n" % (project.project_id, cohort.cohort_id))
form = api_forms.CohortGeneSearchForm(request.GET)
if form.is_valid():
search_spec = form.cleaned_data['search_spec']
search_spec.cohort_id = cohort.cohort_id
sys.stderr.write("cohort_gene_search %s %s: search spec: %s \n" % (project.project_id, cohort.cohort_id, str(search_spec.toJSON())))
genes = api_utils.calculate_cohort_gene_search(cohort, search_spec)
sys.stderr.write("cohort_gene_search %s %s: get %s genes \n" % (project.project_id, cohort.cohort_id, len(genes)))
search_hash = cache_utils.save_results_for_spec(project.project_id, search_spec.toJSON(), genes)
api_utils.add_extra_info_to_genes(project, get_reference(), genes)
sys.stderr.write("cohort_gene_search %s %s: done adding extra info \n" % (project.project_id, cohort.cohort_id))
return JSONResponse({
'is_error': False,
'genes': genes,
'search_hash': search_hash,
})
else:
return JSONResponse({
'is_error': True,
'error': server_utils.form_error_string(form)
})
def cohort_gene_search(request):
project, cohort = get_project_and_cohort_for_user(request.user, request.GET)
sys.stderr.write("cohort_gene_search %s %s: starting ... \n" % (project.project_id, cohort.cohort_id))
form = api_forms.CohortGeneSearchForm(request.GET)
if form.is_valid():
search_spec = form.cleaned_data['search_spec']
search_spec.cohort_id = cohort.cohort_id
sys.stderr.write("cohort_gene_search %s %s: search spec: %s \n" % (project.project_id, cohort.cohort_id, str(search_spec.toJSON())))
genes = api_utils.calculate_cohort_gene_search(cohort, search_spec)
sys.stderr.write("cohort_gene_search %s %s: get %s genes \n" % (project.project_id, cohort.cohort_id, len(genes)))
search_hash = cache_utils.save_results_for_spec(project.project_id, search_spec.toJSON(), genes)
api_utils.add_extra_info_to_genes(project, get_reference(), genes)
sys.stderr.write("cohort_gene_search %s %s: done adding extra info \n" % (project.project_id, cohort.cohort_id))
return JSONResponse({
'is_error': False,
'genes': genes,
'search_hash': search_hash,
})
else:
return JSONResponse({
'is_error': True,
'error': server_utils.form_error_string(form)
})
def combine_mendelian_families(request):
project, family_group = utils.get_project_and_family_group_for_user(request.user, request.GET)
if not project.can_view(request.user):
return PermissionDenied
form = api_forms.CombineMendelianFamiliesForm(request.GET)
if form.is_valid():
search_spec = form.cleaned_data['search_spec']
search_spec.family_group_id = family_group.slug
genes = api_utils.calculate_combine_mendelian_families(family_group, search_spec)
search_hash = cache_utils.save_results_for_spec(project.project_id, search_spec.toJSON(), genes)
api_utils.add_extra_info_to_genes(project, get_reference(), genes)
return JSONResponse({
'is_error': False,
'genes': genes,
'search_hash': search_hash,
})
else:
return JSONResponse({
'is_error': True,
'error': server_utils.form_error_string(form)
})
def cohort_variant_search(request):
project, cohort = get_project_and_cohort_for_user(request.user, request.GET)
if not project.can_view(request.user):
return PermissionDenied
form = api_forms.CohortVariantSearchForm(request.GET)
if form.is_valid():
search_spec = form.cleaned_data['search_spec']
search_spec.family_id = cohort.cohort_id
sys.stderr.write("cohort_variant_search - starting: %s %s\n" % (json.dumps(search_spec.toJSON()), cohort.xfamily().family_id))
variants = api_utils.calculate_mendelian_variant_search(search_spec, cohort.xfamily())
list_of_variants = [v.toJSON() for v in variants]
sys.stderr.write("cohort_variant_search - done calculate_mendelian_variant_search: %s %s %s\n" % (json.dumps(search_spec.toJSON()), cohort.xfamily().family_id, len(list_of_variants)))
search_hash = cache_utils.save_results_for_spec(project.project_id, search_spec.toJSON(), list_of_variants)
sys.stderr.write("cohort_variant_search - done save_results_for_spec: %s %s\n" % (json.dumps(search_spec.toJSON()), cohort.xfamily().family_id))
api_utils.add_extra_info_to_variants_cohort(get_reference(), cohort, variants)
sys.stderr.write("cohort_variant_search - done add_extra_info_to_variants_cohort: %s %s\n" % (json.dumps(search_spec.toJSON()), cohort.xfamily().family_id))
return JSONResponse({
'is_error': False,
'variants': [v.toJSON() for v in variants],
'search_hash': search_hash,
})
else:
return JSONResponse({
'is_error': True,
'error': server_utils.form_error_string(form)
})
def cohort_variant_search(request):
project, cohort = get_project_and_cohort_for_user(request.user, request.GET)
if not project.can_view(request.user):
return HttpResponse('unauthorized')
form = api_forms.CohortVariantSearchForm(request.GET)
if form.is_valid():
search_spec = form.cleaned_data['search_spec']
search_spec.family_id = cohort.cohort_id
variants = api_utils.calculate_mendelian_variant_search(search_spec, cohort.xfamily())
search_hash = cache_utils.save_results_for_spec(project.project_id, search_spec.toJSON(), [v.toJSON() for v in variants])
api_utils.add_extra_info_to_variants_cohort(get_reference(), cohort, variants)
return JSONResponse({
'is_error': False,
'variants': [v.toJSON() for v in variants],
'search_hash': search_hash,
})
else:
return JSONResponse({
'is_error': True,
'error': server_utils.form_error_string(form)
})
def mendelian_variant_search(request):
# TODO: how about we move project getter into the form, and just test for authX here?
# esp because error should be described in json, not just 404
request_dict = request.GET or request.POST
project, family = get_project_and_family_for_user(request.user,
request_dict)
form = api_forms.MendelianVariantSearchForm(request_dict)
if form.is_valid():
search_spec = form.cleaned_data['search_spec']
search_spec.family_id = family.family_id
try:
variants = api_utils.calculate_mendelian_variant_search(
search_spec, family.xfamily())
except Exception as e:
return JSONResponse({
'is_error': True,
'error': str(e.args[0]) if e.args else str(e)
})
sys.stderr.write("done fetching %s variants. Adding extra info..\n" %
len(variants))
hashable_search_params = search_spec.toJSON()
hashable_search_params['family_id'] = family.family_id
search_hash = cache_utils.save_results_for_spec(
project.project_id, hashable_search_params,
[v.toJSON() for v in variants])
add_extra_info_to_variants_family(get_reference(), family, variants)
sys.stderr.write(
"done adding extra info to %s variants. Sending response..\n" %
len(variants))
return_type = request_dict.get('return_type', 'json')
if return_type == 'json':
return JSONResponse({
'is_error': False,
'variants': [v.toJSON() for v in variants],
'search_hash': search_hash,
})
elif return_type == 'csv':
return ''
else:
return HttpResponse("Return type not implemented")
else:
return JSONResponse({
'is_error': True,
'error': server_utils.form_error_string(form)
})
def mendelian_variant_search(request):
# TODO: how about we move project getter into the form, and just test for authX here?
# esp because error should be described in json, not just 404
project, family = get_project_and_family_for_user(request.user,
request.GET)
form = api_forms.MendelianVariantSearchForm(request.GET)
if form.is_valid():
search_spec = form.cleaned_data['search_spec']
search_spec.family_id = family.family_id
variants = api_utils.calculate_mendelian_variant_search(
search_spec, family.xfamily())
search_hash = cache_utils.save_results_for_spec(
project.project_id, search_spec.toJSON(),
[v.toJSON() for v in variants])
add_extra_info_to_variants_family(get_reference(), family, variants)
return_type = request.GET.get('return_type', 'json')
if return_type == 'json':
return JSONResponse({
'is_error': False,
'variants': [v.toJSON() for v in variants],
'search_hash': search_hash,
})
elif return_type == 'csv':
return ''
else:
return HttpResponse("Return type not implemented")
else:
return JSONResponse({
'is_error': True,
'error': server_utils.form_error_string(form)
})
def cohort_gene_search(request):
project, cohort = get_project_and_cohort_for_user(request.user, request.GET)
form = api_forms.CohortGeneSearchForm(request.GET)
if form.is_valid():
search_spec = form.cleaned_data['search_spec']
search_spec.cohort_id = cohort.cohort_id
genes = api_utils.calculate_cohort_gene_search(cohort, search_spec)
search_hash = cache_utils.save_results_for_spec(project.project_id, search_spec.toJSON(), genes)
api_utils.add_extra_info_to_genes(project, get_reference(), genes)
return JSONResponse({
'is_error': False,
'genes': genes,
'search_hash': search_hash,
})
else:
return JSONResponse({
'is_error': True,
'error': server_utils.form_error_string(form)
})
