def set_parents_for_individual(individual):
"""
Sets family for an individual (creating if necessary)
Saves both to db
"""
project = individual.project
if individual.paternal_id and individual.paternal_id != '.':
father = get_or_create_xbrowse_model(Individual, project=project, indiv_id=individual.paternal_id)[0]
update_xbrowse_model(father, family=individual.family)
if individual.maternal_id and individual.maternal_id != '.':
mother = get_or_create_xbrowse_model(Individual, project=project, indiv_id=individual.maternal_id)[0]
update_xbrowse_model(mother, family=individual.family)
def set_parents_for_individual(individual):
"""
Sets family for an individual (creating if necessary)
Saves both to db
"""
project = individual.project
if individual.paternal_id and individual.paternal_id != '.':
father = get_or_create_xbrowse_model(Individual, project=project, indiv_id=individual.paternal_id)[0]
update_xbrowse_model(father, family=individual.family)
if individual.maternal_id and individual.maternal_id != '.':
mother = get_or_create_xbrowse_model(Individual, project=project, indiv_id=individual.maternal_id)[0]
update_xbrowse_model(mother, family=individual.family)
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 update_project_from_individuals(project, xindividuals):
individuals = []
for xindividual in xindividuals:
individual = get_or_create_xbrowse_model(Individual, project=project, indiv_id=xindividual.indiv_id)[0]
individual.from_xindividual(xindividual)
set_family_id_for_individual(individual, xindividual.family_id)
individuals.append(individual)
#set_parents_for_individual(individual)
return individuals
def get_or_create_project_tag(project,
order,
category,
tag_name,
description,
color='#1f78b4',
original_names=None):
"""
Updates or creates a particular ProjectTag in a given project.
Args:
project (object): The project that contains this tag
category (string):
tag_name (string): The name of the new tag (can contain spaces) (eg. "Causal Variant")
description (string): Longer description of the tag
color (string): hex color (eg. "#123456")
original_names (list): if the tag appeaered under one or more different names, remap these to the new tag_name
Returns:
new ProjectTag model object (or an existing one if a match was found)
"""
project_tag = None
if original_names:
for original_name in original_names:
tags = ProjectTag.objects.filter(project=project,
tag__icontains=original_name,
order__isnull=True)
if tags:
project_tag = tags[0]
if project_tag is None:
tags = ProjectTag.objects.filter(project=project, tag__iexact=tag_name)
if tags:
project_tag = tags[0]
if project_tag is None:
tags = ProjectTag.objects.filter(project=project,
tag__icontains=tag_name)
if tags:
project_tag = tags[0]
if project_tag is None:
project_tag, created = get_or_create_xbrowse_model(ProjectTag,
project=project,
tag=tag_name)
if created:
print("Created new tag: %s : %s" % (project, tag_name))
update_xbrowse_model(project_tag,
order=order,
category=category,
tag=tag_name,
title=description,
color=color)
def set_family_id_for_individual(individual, family_id):
"""
Sets family for an individual (creating if necessary)
Saves both to db
"""
project = individual.project
if family_id:
family = get_or_create_xbrowse_model(Family, family_id=family_id, project=project)[0]
else:
family = None
update_xbrowse_model(individual, family=family)
def save_individual_from_json_dict(project, indiv_dict):
individual = get_or_create_xbrowse_model(Individual, indiv_id=indiv_dict['indiv_id'], project=project)[0]
update_xbrowse_model(
individual,
gender = indiv_dict.get('gender'),
affected = indiv_dict.get('affected'),
nickname = indiv_dict.get('nickname', ''),
paternal_id = indiv_dict.get('paternal_id', ''),
maternal_id = indiv_dict.get('maternal_id', ''))
sample_management.set_family_id_for_individual(individual, indiv_dict.get('family_id', ''))
sample_management.set_individual_phenotypes_from_dict(individual, indiv_dict.get('phenotypes', {}))
def update_project_from_individuals(project, xindividuals):
# make sure families exist
families = {}
for family_id in set([xindividual.family_id for xindividual in xindividuals]):
family, _ = get_or_create_xbrowse_model(Family, family_id=family_id, project=project)
families[family_id] = family
individuals = []
for xindividual in xindividuals:
individual, _ = get_or_create_xbrowse_model(
Individual,
project=project,
family=families[xindividual.family_id],
indiv_id=xindividual.indiv_id)
individual.from_xindividual(xindividual)
individuals.append(individual)
#set_parents_for_individual(individual)
return individuals
def save_individual_from_json_dict(project, indiv_dict):
individual = get_or_create_xbrowse_model(Individual, indiv_id=indiv_dict['indiv_id'], project=project)[0]
update_xbrowse_model(
individual,
gender = indiv_dict.get('gender'),
affected = indiv_dict.get('affected'),
nickname = indiv_dict.get('nickname', ''),
paternal_id = indiv_dict.get('paternal_id', ''),
maternal_id = indiv_dict.get('maternal_id', ''))
sample_management.set_family_id_for_individual(individual, indiv_dict.get('family_id', ''))
sample_management.set_individual_phenotypes_from_dict(individual, indiv_dict.get('phenotypes', {}))
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 add_indiv_ids_to_project(project, indiv_id_list):
"""
Add these individuals if they don't already exist
"""
for indiv_id in indiv_id_list:
get_or_create_xbrowse_model(Individual, project=project, indiv_id=indiv_id)
def handle(self, *args, **options):
to_project = BaseProject.objects.get(project_id=options['to_project'])
from_project = BaseProject.objects.get(
project_id=options['from_project'])
to_families = BaseFamily.objects.filter(project=to_project).only(
'family_id').prefetch_related('individual_set')
from_families_map = {
f.family_id: {
'family': f,
'individuals': f.individual_set.all()
}
for f in BaseFamily.objects.filter(
project=from_project,
family_id__in=[f.family_id for f in to_families]).only(
'family_id').prefetch_related('individual_set')
}
print('Transferring individuals from {} to {}:'.format(
from_project.project_name, to_project.project_name))
missing_family_individual_counts = defaultdict(int)
missing_individual_sample_counts = {}
created_vcf_count = 0
for family in to_families:
for from_individual in from_families_map[
family.family_id]['individuals']:
to_individual, individual_created = get_or_create_xbrowse_model(
BaseIndividual,
project=to_project,
family=family,
indiv_id=from_individual.indiv_id,
)
if individual_created:
update_xbrowse_model(
to_individual, **{
field: getattr(from_individual, field)
for field in INDIVIDUAL_FIELDS
})
_update_model(
to_individual, **{
field: getattr(from_individual, field)
for field in INDIVIDUAL_DATA_FIELDS
})
missing_family_individual_counts[family] += (
1 if individual_created else 0)
for from_vcf_file in from_individual.vcf_files.all():
to_vcf_file, vcf_created = VCFFile.objects.get_or_create(
project=to_project,
**{
field: getattr(from_vcf_file, field)
for field in VCF_FILE_FIELDS
})
if vcf_created:
created_vcf_count += 1
to_individual.vcf_files.add(to_vcf_file)
counters = {'samples_created': 0}
create_sample_records(to_individual, None,
to_individual.seqr_individual, counters)
missing_individual_sample_counts[to_individual] = counters[
'samples_created']
missing_individual_counts = defaultdict(int)
updated_families = set()
for family, individual_count in missing_family_individual_counts.items(
):
missing_individual_counts[individual_count] += 1
if individual_count > 0:
updated_families.add(family)
missing_sample_counts = defaultdict(int)
for individual, sample_count in missing_individual_sample_counts.items(
):
missing_sample_counts[sample_count] += 1
if sample_count > 0:
updated_families.add(individual.family)
for family in updated_families:
update_xbrowse_model(
family,
pedigree_image=from_families_map[
family.family_id]['family'].pedigree_image)
print("Done.")
print("----------------------------------------------")
for num_individuals, num_families in missing_individual_counts.items():
print('Added {} individuals to {} families'.format(
num_individuals, num_families))
print("----------------------------------------------")
print('Added {} VCF files'.format(created_vcf_count))
print("----------------------------------------------")
for num_samples, num_individuals in missing_sample_counts.items():
print('Added {} samples to {} individuals'.format(
num_samples, num_individuals))
def handle(self, *args, **options):
to_project = BaseProject.objects.get(project_id=options['to_project'])
from_project = BaseProject.objects.get(project_id=options['from_project'])
to_families = BaseFamily.objects.filter(project=to_project).only('family_id').prefetch_related('individual_set')
from_families_map = {
f.family_id: {'family': f, 'individuals': f.individual_set.all()}
for f in BaseFamily.objects.filter(
project=from_project, family_id__in=[f.family_id for f in to_families]
).only('family_id').prefetch_related('individual_set')
}
print('Transferring individuals from {} to {}:'.format(from_project.project_name, to_project.project_name))
missing_family_individual_counts = defaultdict(int)
missing_individual_sample_counts = {}
created_vcf_count = 0
for family in to_families:
for from_individual in from_families_map[family.family_id]['individuals']:
to_individual, individual_created = get_or_create_xbrowse_model(
BaseIndividual,
project=to_project,
family=family,
indiv_id=from_individual.indiv_id,
)
if individual_created:
update_xbrowse_model(
to_individual,
**{field: getattr(from_individual, field) for field in INDIVIDUAL_FIELDS}
)
_update_model(
to_individual,
**{field: getattr(from_individual, field) for field in INDIVIDUAL_DATA_FIELDS}
)
missing_family_individual_counts[family] += (1 if individual_created else 0)
for from_vcf_file in from_individual.vcf_files.all():
to_vcf_file, vcf_created = VCFFile.objects.get_or_create(
project=to_project,
**{field: getattr(from_vcf_file, field) for field in VCF_FILE_FIELDS}
)
if vcf_created:
created_vcf_count += 1
to_individual.vcf_files.add(to_vcf_file)
counters = {'samples_created': 0}
create_sample_records(to_individual, None, to_individual.seqr_individual, counters)
missing_individual_sample_counts[to_individual] = counters['samples_created']
missing_individual_counts = defaultdict(int)
updated_families = set()
for family, individual_count in missing_family_individual_counts.items():
missing_individual_counts[individual_count] += 1
if individual_count > 0:
updated_families.add(family)
missing_sample_counts = defaultdict(int)
for individual, sample_count in missing_individual_sample_counts.items():
missing_sample_counts[sample_count] += 1
if sample_count > 0:
updated_families.add(individual.family)
for family in updated_families:
update_xbrowse_model(family, pedigree_image=from_families_map[family.family_id]['family'].pedigree_image)
print("Done.")
print("----------------------------------------------")
for num_individuals, num_families in missing_individual_counts.items():
print('Added {} individuals to {} families'.format(num_individuals, num_families))
print("----------------------------------------------")
print('Added {} VCF files'.format(created_vcf_count))
print("----------------------------------------------")
for num_samples, num_individuals in missing_sample_counts.items():
print('Added {} samples to {} individuals'.format(num_samples, num_individuals))
def add_indiv_ids_to_project(project, indiv_id_list):
"""
Add these individuals if they don't already exist
"""
for indiv_id in indiv_id_list:
get_or_create_xbrowse_model(Individual, project=project, indiv_id=indiv_id)
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.")