def save_individual_from_json_dict(project, indiv_dict):
individual = Individual.objects.get_or_create(
indiv_id=indiv_dict['indiv_id'], project=project)[0]
individual.gender = indiv_dict.get('gender')
individual.affected = indiv_dict.get('affected')
individual.nickname = indiv_dict.get('nickname', '')
individual.paternal_id = indiv_dict.get('paternal_id', '')
individual.maternal_id = indiv_dict.get('maternal_id', '')
individual.save()
try:
seqr_individual = get_seqr_individual_from_base_individual(individual)
seqr_individual.sex = individual.gender
seqr_individual.affected = individual.affected
seqr_individual.display_name = individual.nickname
seqr_individual.paternal_id = individual.paternal_id
seqr_individual.maternal_id = individual.maternal_id
seqr_individual.save()
except Exception as e:
print("Exception when updating SeqrIndividual: " + str(e))
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 save_individual_from_json_dict(project, indiv_dict):
individual = Individual.objects.get_or_create(indiv_id=indiv_dict['indiv_id'], project=project)[0]
individual.gender = indiv_dict.get('gender')
individual.affected = indiv_dict.get('affected')
individual.nickname = indiv_dict.get('nickname', '')
individual.paternal_id = indiv_dict.get('paternal_id', '')
individual.maternal_id = indiv_dict.get('maternal_id', '')
individual.save()
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 save_individual_from_json_dict(project, indiv_dict):
individual = Individual.objects.get_or_create(indiv_id=indiv_dict['indiv_id'], project=project)[0]
individual.gender = indiv_dict.get('gender')
individual.affected = indiv_dict.get('affected')
individual.nickname = indiv_dict.get('nickname', '')
individual.paternal_id = indiv_dict.get('paternal_id', '')
individual.maternal_id = indiv_dict.get('maternal_id', '')
individual.save()
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 save_individual_from_json_dict(project, indiv_dict):
individual = Individual.objects.get_or_create(indiv_id=indiv_dict["indiv_id"], project=project)[0]
individual.gender = indiv_dict.get("gender")
individual.affected = indiv_dict.get("affected")
individual.nickname = indiv_dict.get("nickname", "")
individual.paternal_id = indiv_dict.get("paternal_id", "")
individual.maternal_id = indiv_dict.get("maternal_id", "")
individual.save()
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 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 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 handle(self, *args, **options):
project = Project.objects.get(project_id=args[0])
d = json.load(open(args[1]))
# create families
for family_d in d['families']:
family = Family.objects.get_or_create(
project=project, family_id=family_d['family_id'])[0]
family.family_name = family_d['family_name']
family.analysis_status = family_d['analysis_status']
family.save()
# individuals
for indiv_d in d['individuals']:
individual = Individual.objects.get_or_create(
project=project, indiv_id=indiv_d['indiv_id'])[0]
individual.nickname = indiv_d['nickname']
individual.gender = indiv_d['gender']
individual.affected = indiv_d['affected']
individual.maternal_id = indiv_d['maternal_id']
individual.paternal_id = indiv_d['paternal_id']
individual.other_notes = indiv_d['other_notes']
individual.save()
sample_management.set_family_id_for_individual(
individual, indiv_d['family_id'])
# phenotypes
for pheno_d in d['project_phenotypes']:
pheno = ProjectPhenotype.objects.get_or_create(
slug=pheno_d['slug'], project=project)[0]
pheno.name = pheno_d['name']
pheno.category = pheno_d['category']
pheno.datatype = pheno_d['datatype']
pheno.save()
for ipheno_d in d['indiv_phenotypes']:
indiv = Individual.objects.get(project=project,
indiv_id=ipheno_d['indiv_id'])
phenotype = ProjectPhenotype.objects.get(project=project,
slug=ipheno_d['slug'])
ipheno = IndividualPhenotype.objects.get_or_create(
phenotype=phenotype, individual=indiv)[0]
ipheno.boolean_val = None
ipheno.float_val = None
if phenotype.datatype == 'bool':
ipheno.boolean_val = ipheno_d['val']
ipheno.save()
def handle(self, *args, **options):
project = Project.objects.get(project_id=args[0])
d = json.load(open(args[1]))
# create families
for family_d in d['families']:
family = Family.objects.get_or_create(project=project, family_id=family_d['family_id'])[0]
family.family_name = family_d['family_name']
family.analysis_status = family_d['analysis_status']
family.save()
# individuals
for indiv_d in d['individuals']:
individual = Individual.objects.get_or_create(project=project, indiv_id=indiv_d['indiv_id'])[0]
individual.nickname = indiv_d['nickname']
individual.gender = indiv_d['gender']
individual.affected = indiv_d['affected']
individual.maternal_id = indiv_d['maternal_id']
individual.paternal_id = indiv_d['paternal_id']
individual.other_notes = indiv_d['other_notes']
individual.save()
sample_management.set_family_id_for_individual(individual, indiv_d['family_id'])
# phenotypes
for pheno_d in d['project_phenotypes']:
pheno = ProjectPhenotype.objects.get_or_create(slug=pheno_d['slug'], project=project)[0]
pheno.name = pheno_d['name']
pheno.category = pheno_d['category']
pheno.datatype = pheno_d['datatype']
pheno.save()
for ipheno_d in d['indiv_phenotypes']:
indiv = Individual.objects.get(project=project, indiv_id=ipheno_d['indiv_id'])
phenotype = ProjectPhenotype.objects.get(project=project, slug=ipheno_d['slug'])
ipheno = IndividualPhenotype.objects.get_or_create(phenotype=phenotype, individual=indiv)[0]
ipheno.boolean_val = None
ipheno.float_val = None
if phenotype.datatype == 'bool':
ipheno.boolean_val = ipheno_d['val']
ipheno.save()
def copy_project(from_project,
to_project,
samples=False,
settings=False,
upsert=False,
users=False,
saved_variants=False,
data=False):
"""
This is idempotent
:param from_project:
:param to_project:
:param settings:
:param upsert:
:param users:
:param saved_variants:
:param data:
:return:
"""
# todo: put all the data copying (vcf, bam, coverage) in one section
#
# project settings
#
if settings:
# gene lists
for d in from_project.get_gene_lists():
ProjectGeneList.objects.create(gene_list=d, project=to_project)
# reference populations
for r in from_project.get_private_reference_populations():
to_project.private_reference_populations.add(r)
# phenotypes
for from_p in from_project.get_phenotypes():
to_p = ProjectPhenotype.objects.get_or_create(
project=to_project,
slug=from_p.slug,
category=from_p.category,
datatype=from_p.datatype,
name=from_p.name,
)[0]
# collaborators
if users:
managers = from_project.get_managers()
for m in managers:
to_project.set_as_manager(m)
collaborators = from_project.get_collaborators()
for u in collaborators:
to_project.set_as_collaborator(u)
#
# sample data
#
if samples:
# individuals with phenotypes
for from_individual in from_project.individual_set.all():
if upsert:
to_individual = Individual.objects.get_or_create(
indiv_id=from_individual.indiv_id, project=to_project)[0]
else:
try:
to_individual = Individual.objects.get(
indiv_id=from_individual.indiv_id, project=to_project)
except ObjectDoesNotExist:
continue
to_individual.nickname = from_individual.nickname
to_individual.gender = from_individual.gender
to_individual.affected = from_individual.affected
to_individual.paternal_id = from_individual.paternal_id
to_individual.maternal_id = from_individual.maternal_id
to_individual.other_notes = from_individual.other_notes
if data:
to_individual.coverage_file = from_individual.coverage_file
to_individual.save()
if data:
for vcf in from_individual.vcf_files.all():
to_individual.vcf_files.add(vcf)
# individual phenotypes
for from_phenotype in from_individual.get_phenotypes():
# project phenotype should already exist
project_phenotype = ProjectPhenotype.objects.get(
project=to_project,
slug=from_phenotype.phenotype.slug,
category=from_phenotype.phenotype.category,
datatype=from_phenotype.phenotype.datatype)
individual_phenotype = IndividualPhenotype.objects.get_or_create(
phenotype=project_phenotype, individual=to_individual)[0]
individual_phenotype.boolean_val = from_phenotype.boolean_val
individual_phenotype.float_val = from_phenotype.float_val
individual_phenotype.save()
if from_individual.family:
sample_management.set_family_id_for_individual(
to_individual, from_individual.family.family_id)
# families
for from_family in from_project.family_set.all():
try:
to_family = Family.objects.get(project=to_project,
family_id=from_family.family_id)
except ObjectDoesNotExist:
continue
to_family.family_name = from_family.family_name
to_family.short_description = from_family.short_description
to_family.about_family_content = from_family.about_family_content
to_family.analysis_status = from_family.analysis_status
to_family.save()
def can_copy_cohort_into_project(cohort, to_project):
for individual in cohort.individuals.all():
if not Individual.objects.filter(
project=to_project,
indiv_id=individual.indiv_id).exists():
return False
return True
# cohorts
for from_cohort in from_project.cohort_set.all():
if not can_copy_cohort_into_project(from_cohort, to_project):
print "Warning: could not load cohort %s" % from_cohort.cohort_id
continue
to_cohort = Cohort.objects.get_or_create(
project=to_project, cohort_id=from_cohort.cohort_id)[0]
to_cohort.display_name = from_cohort.display_name
to_cohort.short_description = from_cohort.short_description
to_cohort.save()
for from_i in from_cohort.individuals.all():
to_i = Individual.objects.get(project=to_project,
indiv_id=from_i.indiv_id)
to_cohort.individuals.add(to_i)
# flags
if saved_variants:
# variant notes
for from_note in VariantNote.objects.filter(project=from_project):
to_note = VariantNote.objects.get_or_create(
user=from_note.user,
date_saved=from_note.date_saved,
project=to_project,
note=from_note.note,
xpos=from_note.xpos,
ref=from_note.ref,
alt=from_note.alt,
)[0]
if from_note.family:
to_note.family = Family.objects.get(
project=to_project, family_id=from_note.family.family_id)
if from_note.individual:
to_note.individual = Individual.objects.get(
project=to_project, indiv_id=from_note.individual.indiv_id)
# variant tags
# start with project tags
# should these be in the --settings or --saved_variants parameters?
for from_tag in ProjectTag.objects.filter(project=from_project):
to_tag = ProjectTag.objects.get_or_create(
project=to_project,
tag=from_tag.tag,
title=from_tag.title,
color=from_tag.color,
)[0]
# now variant tags
for from_tag in VariantTag.objects.filter(
project_tag__project=from_project):
to_project_tag = ProjectTag.objects.get(
project=to_project, tag=from_tag.project_tag.tag)
to_family = None
if from_tag.family:
to_family = Family.objects.get(
project=to_project, family_id=from_tag.family.family_id)
to_tag = VariantTag.objects.get_or_create(
project_tag=to_project_tag,
family=to_family,
xpos=from_tag.xpos,
ref=from_tag.ref,
alt=from_tag.alt,
)[0]
def copy_project(from_project, to_project, samples=False, settings=False, upsert=False, users=False, saved_variants=False, data=False):
"""
This is idempotent
:param from_project:
:param to_project:
:param settings:
:param upsert:
:param users:
:param saved_variants:
:param data:
:return:
"""
# todo: put all the data copying (vcf, bam, coverage) in one section
#
# project settings
#
if settings:
# gene lists
for d in from_project.get_gene_lists():
ProjectGeneList.objects.create(gene_list=d, project=to_project)
# reference populations
for r in from_project.get_private_reference_populations():
to_project.private_reference_populations.add(r)
# phenotypes
for from_p in from_project.get_phenotypes():
to_p = ProjectPhenotype.objects.get_or_create(
project=to_project,
slug=from_p.slug,
category=from_p.category,
datatype=from_p.datatype,
name=from_p.name,
)[0]
# collaborators
if users:
managers = from_project.get_managers()
for m in managers:
to_project.set_as_manager(m)
collaborators = from_project.get_collaborators()
for u in collaborators:
to_project.set_as_collaborator(u)
#
# sample data
#
if samples:
# individuals with phenotypes
for from_individual in from_project.individual_set.all():
if upsert:
to_individual = Individual.objects.get_or_create(indiv_id=from_individual.indiv_id, project=to_project)[0]
else:
try:
to_individual = Individual.objects.get(indiv_id=from_individual.indiv_id, project=to_project)
except ObjectDoesNotExist:
continue
to_individual.nickname = from_individual.nickname
to_individual.gender = from_individual.gender
to_individual.affected = from_individual.affected
to_individual.paternal_id = from_individual.paternal_id
to_individual.maternal_id = from_individual.maternal_id
to_individual.other_notes = from_individual.other_notes
if data:
to_individual.coverage_file = from_individual.coverage_file
to_individual.save()
if data:
for vcf in from_individual.vcf_files.all():
to_individual.vcf_files.add(vcf)
# individual phenotypes
for from_phenotype in from_individual.get_phenotypes():
# project phenotype should already exist
project_phenotype = ProjectPhenotype.objects.get(project=to_project,
slug=from_phenotype.phenotype.slug,
category=from_phenotype.phenotype.category,
datatype=from_phenotype.phenotype.datatype
)
individual_phenotype = IndividualPhenotype.objects.get_or_create(
phenotype=project_phenotype,
individual=to_individual
)[0]
individual_phenotype.boolean_val = from_phenotype.boolean_val
individual_phenotype.float_val = from_phenotype.float_val
individual_phenotype.save()
if from_individual.family:
sample_management.set_family_id_for_individual(to_individual, from_individual.family.family_id)
# families
for from_family in from_project.family_set.all():
try:
to_family = Family.objects.get(project=to_project, family_id=from_family.family_id)
except ObjectDoesNotExist:
continue
to_family.family_name = from_family.family_name
to_family.short_description = from_family.short_description
to_family.about_family_content = from_family.about_family_content
to_family.analysis_status = from_family.analysis_status
to_family.save()
def can_copy_cohort_into_project(cohort, to_project):
for individual in cohort.individuals.all():
if not Individual.objects.filter(project=to_project, indiv_id=individual.indiv_id).exists():
return False
return True
# cohorts
for from_cohort in from_project.cohort_set.all():
if not can_copy_cohort_into_project(from_cohort, to_project):
print "Warning: could not load cohort %s" % from_cohort.cohort_id
continue
to_cohort = Cohort.objects.get_or_create(project=to_project, cohort_id=from_cohort.cohort_id)[0]
to_cohort.display_name = from_cohort.display_name
to_cohort.short_description = from_cohort.short_description
to_cohort.save()
for from_i in from_cohort.individuals.all():
to_i = Individual.objects.get(project=to_project, indiv_id=from_i.indiv_id)
to_cohort.individuals.add(to_i)
# flags
if saved_variants:
# variant notes
for from_note in VariantNote.objects.filter(project=from_project):
to_note = VariantNote.objects.get_or_create(
user=from_note.user,
date_saved=from_note.date_saved,
project=to_project,
note=from_note.note,
xpos=from_note.xpos,
ref=from_note.ref,
alt=from_note.alt,
)[0]
if from_note.family:
to_note.family = Family.objects.get(project=to_project, family_id=from_note.family.family_id)
if from_note.individual:
to_note.individual = Individual.objects.get(project=to_project, indiv_id=from_note.individual.indiv_id)
# variant tags
# start with project tags
# should these be in the --settings or --saved_variants parameters?
for from_tag in ProjectTag.objects.filter(project=from_project):
to_tag = ProjectTag.objects.get_or_create(
project=to_project,
tag=from_tag.tag,
title=from_tag.title,
color=from_tag.color,
)[0]
# now variant tags
for from_tag in VariantTag.objects.filter(project_tag__project=from_project):
to_project_tag = ProjectTag.objects.get(project=to_project, tag=from_tag.project_tag.tag)
to_family = None
if from_tag.family:
to_family = Family.objects.get(project=to_project, family_id=from_tag.family.family_id)
to_tag = VariantTag.objects.get_or_create(
project_tag=to_project_tag,
family=to_family,
xpos=from_tag.xpos,
ref=from_tag.ref,
alt=from_tag.alt,
)[0]
