def add_family_group_submit(request, project_id):
project = get_object_or_404(Project, project_id=project_id)
if not project.can_admin(request.user):
raise PermissionDenied
error = None
form = AddFamilyGroupForm(project, request.POST)
if form.is_valid():
# todo: move to sample_anagement
family_group, created = get_or_create_xbrowse_model(
FamilyGroup,
project=project,
slug=form.cleaned_data['family_group_slug'],
)
update_xbrowse_model(family_group, name=form.cleaned_data['name'], description=form.cleaned_data['description'])
seqr_analysis_group = find_matching_seqr_model(family_group)
for family in form.cleaned_data['families']:
family_group.families.add(family)
seqr_analysis_group.families.add(find_matching_seqr_model(family))
else:
error = server_utils.form_error_string(form)
if error:
return server_utils.JSONResponse({'is_error': True, 'error': error})
else:
return server_utils.JSONResponse({'is_error': False, 'new_url': reverse('family_group_home', args=(project.project_id, family_group.slug))})
def handle(self, *args, **options):
"""For each xbrowse_server.base.models.FamilyGroup, create a corresponding seqr.models.AnalysisGroup
"""
counters = collections.defaultdict(int)
errors = []
for source_group in tqdm(
FamilyGroup.objects.filter(seqr_analysis_group__isnull=True),
unit=" family groups"):
counters['FamilyGroups processed'] += 1
analysis_group = _create_seqr_model(
source_group,
name=source_group.name,
description=source_group.description,
project=source_group.project,
)
if analysis_group:
analysis_group.families.add(*[
find_matching_seqr_model(family)
for family in source_group.families.all()
])
counters['AnalysisGroups created'] += 1
else:
counters['Errors'] += 1
errors.append(
'Error: unable to transfer "{}" (Project: "{}")'.format(
source_group.name, source_group.project.project_name))
logger.info("Done")
logger.info("Stats: ")
for k, v in counters.items():
logger.info(" %s: %s" % (k, v))
for error in errors:
logger.info(error)
def handle(self, *args, **options):
"""For each xbrowse_server.base.models.FamilyGroup, create a corresponding seqr.models.AnalysisGroup
"""
counters = collections.defaultdict(int)
errors = []
for source_group in tqdm(FamilyGroup.objects.filter(seqr_analysis_group__isnull=True), unit=" family groups"):
counters['FamilyGroups processed'] += 1
analysis_group = _create_seqr_model(
source_group,
name=source_group.name,
description=source_group.description,
project=source_group.project,
)
if analysis_group:
analysis_group.families.add(*[find_matching_seqr_model(family) for family in source_group.families.all()])
counters['AnalysisGroups created'] += 1
else:
counters['Errors'] += 1
errors.append('Error: unable to transfer "{}" (Project: "{}")'.format(source_group.name, source_group.project.project_name))
logger.info("Done")
logger.info("Stats: ")
for k, v in counters.items():
logger.info(" %s: %s" % (k, v))
for error in errors:
logger.info(error)
def add_family_group_submit(request, project_id):
project = get_object_or_404(Project, project_id=project_id)
if not project.can_admin(request.user):
raise PermissionDenied
error = None
form = AddFamilyGroupForm(project, request.POST)
if form.is_valid():
# todo: move to sample_anagement
family_group, created = get_or_create_xbrowse_model(
FamilyGroup,
project=project,
slug=form.cleaned_data['family_group_slug'],
)
update_xbrowse_model(family_group,
name=form.cleaned_data['name'],
description=form.cleaned_data['description'])
seqr_analysis_group = find_matching_seqr_model(family_group)
for family in form.cleaned_data['families']:
family_group.families.add(family)
seqr_analysis_group.families.add(find_matching_seqr_model(family))
else:
error = server_utils.form_error_string(form)
if error:
return server_utils.JSONResponse({'is_error': True, 'error': error})
else:
return server_utils.JSONResponse({
'is_error':
False,
'new_url':
reverse('family_group_home',
args=(project.project_id, family_group.slug))
})
def remove_gene_list(request, project_id, gene_list_slug):
"""
Manager can edit project settings
"""
project = get_object_or_404(Project, project_id=project_id)
gene_list = get_object_or_404(GeneList, slug=gene_list_slug)
if not project.can_admin(request.user):
raise PermissionDenied
if request.method == 'POST':
ProjectGeneList.objects.filter(project=project, gene_list=gene_list).delete()
if project.seqr_project:
seqr_locus_list = find_matching_seqr_model(gene_list)
remove_perm(user_or_group=project.seqr_project.can_view_group, perm=CAN_VIEW, obj=seqr_locus_list)
return redirect('project_gene_list_settings', project.project_id)
return render(request, 'project/remove_gene_list.html', {
'project': project,
'gene_list': gene_list,
'new_page_url': '/project/{}/project_page'.format(project.seqr_project.guid) if project.seqr_project else None,
})
def remove_gene_list(request, project_id, gene_list_slug):
"""
Manager can edit project settings
"""
project = get_object_or_404(Project, project_id=project_id)
gene_list = get_object_or_404(GeneList, slug=gene_list_slug)
if not project.can_admin(request.user):
raise PermissionDenied
if request.method == 'POST':
ProjectGeneList.objects.filter(project=project, gene_list=gene_list).delete()
if project.seqr_project:
seqr_locus_list = find_matching_seqr_model(gene_list)
remove_perm(user_or_group=project.seqr_project.can_view_group, perm=CAN_VIEW, obj=seqr_locus_list)
return redirect('project_gene_list_settings', project.project_id)
return render(request, 'project/remove_gene_list.html', {
'project': project,
'gene_list': gene_list,
'new_page_url': '/project/{}/project_page'.format(project.seqr_project.guid) if project.seqr_project else None,
})
def add_gene_list(request, project_id):
"""
Manager can edit project settings
"""
project = get_object_or_404(Project, project_id=project_id)
if not project.can_admin(request.user):
raise PermissionDenied
error = None
if request.method == 'POST':
for slug in request.POST.getlist('gene_list_slug'):
try:
genelist = GeneList.objects.get(slug=slug)
except ObjectDoesNotExist:
error = 'Invalid gene list'
break
if not genelist.is_public and genelist.owner != request.user:
error = 'Unauthorized'
break
ProjectGeneList.objects.get_or_create(project=project, gene_list=genelist)
if project.seqr_project:
seqr_locus_list = find_matching_seqr_model(genelist)
assign_perm(user_or_group=project.seqr_project.can_view_group, perm=CAN_VIEW, obj=seqr_locus_list)
if not error:
return redirect('project_gene_list_settings', project_id=project_id)
public_lists = GeneList.objects.filter(is_public=True)
return render(request, 'project/add_gene_list.html', {
'project': project,
'my_lists': GeneList.objects.filter(owner=request.user),
'public_lists': public_lists,
'error': error,
'new_page_url': '/project/{}/project_page'.format(project.seqr_project.guid) if project.seqr_project else None,
})
def add_gene_list(request, project_id):
"""
Manager can edit project settings
"""
project = get_object_or_404(Project, project_id=project_id)
if not project.can_admin(request.user):
raise PermissionDenied
error = None
if request.method == 'POST':
for slug in request.POST.getlist('gene_list_slug'):
try:
genelist = GeneList.objects.get(slug=slug)
except ObjectDoesNotExist:
error = 'Invalid gene list'
break
if not genelist.is_public and genelist.owner != request.user:
error = 'Unauthorized'
break
ProjectGeneList.objects.get_or_create(project=project, gene_list=genelist)
if project.seqr_project:
seqr_locus_list = find_matching_seqr_model(genelist)
assign_perm(user_or_group=project.seqr_project.can_view_group, perm=CAN_VIEW, obj=seqr_locus_list)
if not error:
return redirect('project_gene_list_settings', project_id=project_id)
public_lists = GeneList.objects.filter(is_public=True)
return render(request, 'project/add_gene_list.html', {
'project': project,
'my_lists': GeneList.objects.filter(owner=request.user),
'public_lists': public_lists,
'error': error,
'new_page_url': '/project/{}/project_page'.format(project.seqr_project.guid) if project.seqr_project else None,
})
def safe_get_or_create(xbrowse_model):
seqr_model = find_matching_seqr_model(xbrowse_model)
if seqr_model:
return seqr_model, False
else:
return _create_seqr_model(xbrowse_model), True
def handle(self, *args, **options):
from_project = BaseProject.objects.get(project_id=options['from_project'])
to_project = BaseProject.objects.get(project_id=options['to_project'])
to_seqr_project = find_matching_seqr_model(to_project)
family_ids = options['family_ids']
families = BaseFamily.objects.filter(project=from_project, family_id__in=family_ids)
print('Found {} out of {} families. No match for: {}.'.format(len(families), len(set(family_ids)), set(family_ids) - set([f.family_id for f in families])))
for f in families:
print("==> Moving {}".format(f))
for individual in f.individual_set.all():
individual.project = to_project
individual.save()
# Update individuals in phenotips
if _phenotips_patient_exists(individual.seqr_individual):
# make sure phenotips_patient_id is up to date
seqr_individual = individual.seqr_individual
data_json = _get_patient_data(
from_project.seqr_project,
seqr_individual,
)
seqr_individual.phenotips_patient_id = data_json["id"]
seqr_individual.save()
# update permissions
phenotips_readonly_username, _ = _get_phenotips_uname_and_pwd_for_project(to_project.seqr_project.phenotips_user_id, read_only=True)
_add_user_to_patient(phenotips_readonly_username, seqr_individual.phenotips_patient_id, allow_edit=False)
phenotips_readwrite_username, _ = _get_phenotips_uname_and_pwd_for_project(to_project.seqr_project.phenotips_user_id, read_only=False)
_add_user_to_patient(phenotips_readwrite_username, seqr_individual.phenotips_patient_id, allow_edit=True)
# Update individuals samples/ VCFs
for from_vcf_file in individual.vcf_files.all():
to_vcf_file, _ = VCFFile.objects.get_or_create(
project=to_project,
elasticsearch_index=from_vcf_file.elasticsearch_index,
file_path=from_vcf_file.file_path,
dataset_type=from_vcf_file.dataset_type,
sample_type=from_vcf_file.sample_type,
loaded_date=from_vcf_file.loaded_date,
)
individual.vcf_files.add(to_vcf_file)
individual.vcf_files.remove(from_vcf_file)
# Update variant tags/ notes
saved_variants = set()
for note in BaseVariantNote.objects.filter(family=f):
seqr_note = find_matching_seqr_model(note)
if seqr_note:
saved_variants.add(seqr_note.saved_variant)
note.project = to_project
note.save()
for variant_tag in BaseVariantTag.objects.filter(family=f):
to_project_tag, created = get_or_create_xbrowse_model(
ProjectTag, project=to_project, tag=variant_tag.project_tag.tag
)
if created:
update_xbrowse_model(
to_project_tag,
category=variant_tag.project_tag.category,
title=variant_tag.project_tag.title,
color=variant_tag.project_tag.color,
order=variant_tag.project_tag.order,
)
update_xbrowse_model(variant_tag, project_tag=to_project_tag)
seqr_variant_tag = find_matching_seqr_model(variant_tag)
if seqr_variant_tag:
saved_variants.add(seqr_variant_tag.saved_variant)
for saved_variant in saved_variants:
saved_variant.project = to_seqr_project
saved_variant.save()
# Update families
update_xbrowse_model(f, project=to_project)
print("Done.")
def safe_get_or_create(xbrowse_model):
seqr_model = find_matching_seqr_model(xbrowse_model)
if seqr_model:
return seqr_model, False
else:
return _create_seqr_model(xbrowse_model), True
