def handle(self, *args, **options):
from_project = Project.objects.get(guid=options['from_project'])
to_project = Project.objects.get(guid=options['to_project'])
family_ids = options['family_ids']
families = Family.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 phenotips for {}".format(f))
for seqr_individual in f.individual_set.all():
if phenotips_patient_exists(seqr_individual):
# make sure phenotips_patient_id is up to date
data_json = _get_patient_data(
from_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.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.phenotips_user_id, read_only=False)
_add_user_to_patient(phenotips_readwrite_username,
seqr_individual.phenotips_patient_id,
allow_edit=True)
for variant_tag_type in VariantTagType.objects.filter(
project=from_project):
variant_tags = VariantTag.objects.filter(
saved_variant__family__in=families,
variant_tag_type=variant_tag_type)
if variant_tags:
print('Updating "{}" tags'.format(variant_tag_type.name))
to_tag_type, created = VariantTagType.objects.get_or_create(
project=to_project, name=variant_tag_type.name)
if created:
to_tag_type.category = variant_tag_type.category
to_tag_type.description = variant_tag_type.description
to_tag_type.color = variant_tag_type.color
to_tag_type.order = variant_tag_type.order
to_tag_type.save()
variant_tags.update(variant_tag_type=to_tag_type)
print("Updating families")
families.update(project=to_project)
print("Done.")
def transfer_individual(source_individual, new_project, connect_to_phenotips):
"""Transfers the given Individual and returns the new Individual"""
# get rid of '.' to signify 'unknown'
if source_individual.paternal_id == "." or source_individual.maternal_id == "." or source_individual.gender == "." or source_individual.affected == ".":
if source_individual.paternal_id == ".":
source_individual.paternal_id = ""
if source_individual.maternal_id == ".":
source_individual.maternal_id = ""
if source_individual.affected == ".":
source_individual.affected = ""
if source_individual.gender == ".":
source_individual.gender = ""
source_individual.save()
new_individual, created = safe_get_or_create(source_individual)
if created:
print("Created SeqrSample", new_individual)
update_model_fields(new_individual, source_individual, [
'family',
'indiv_id',
'created_date',
'maternal_id',
'paternal_id',
'gender',
'affected',
'nickname',
'case_review_status',
'phenotips_id',
'phenotips_data',
])
if new_individual.display_name == new_individual.individual_id:
new_individual.display_name = ''
new_individual.save()
# update PhenoTips data
phenotips_data_retrieved = False
if connect_to_phenotips and new_project.is_phenotips_enabled:
try:
data_json = _get_patient_data(
new_project,
new_individual,
)
_update_individual_phenotips_data(new_individual, data_json)
phenotips_data_retrieved = True
except phenotips_api.PhenotipsException as e:
print("Couldn't retrieve latest data from phenotips for %s: %s" %
(new_individual, e))
return new_individual, created, phenotips_data_retrieved
def _retrieve_and_update_individual_phenotips_data(project, individual):
"""Retrieve and update the phenotips_data and phenotips_patient_id fields for the given Individual
Args:
project (Model): Project model
individual (Model): Individual model
"""
try:
latest_phenotips_json = phenotips_api._get_patient_data(
project,
individual,
)
except phenotips_api.PhenotipsException as e:
print("Couldn't retrieve latest data from phenotips for %s: %s" % (individual, e))
return
_update_individual_phenotips_data(individual, latest_phenotips_json)
def transfer_individual(source_individual, new_project, connect_to_phenotips):
"""Transfers the given Individual and returns the new Individual"""
# get rid of '.' to signify 'unknown'
if source_individual.paternal_id == "." or source_individual.maternal_id == "." or source_individual.gender == "." or source_individual.affected == ".":
if source_individual.paternal_id == ".":
source_individual.paternal_id = ""
if source_individual.maternal_id == ".":
source_individual.maternal_id = ""
if source_individual.affected == ".":
source_individual.affected = ""
if source_individual.gender == ".":
source_individual.gender = ""
source_individual.save()
new_individual, created = safe_get_or_create(source_individual)
if created:
print("Created SeqrSample", new_individual)
update_model_fields(new_individual, source_individual, [
'family', 'indiv_id', 'created_date', 'maternal_id', 'paternal_id', 'gender', 'affected', 'nickname',
'case_review_status', 'phenotips_id', 'phenotips_data',
])
if new_individual.display_name == new_individual.individual_id:
new_individual.display_name = ''
new_individual.save()
# update PhenoTips data
phenotips_data_retrieved = False
if connect_to_phenotips and new_project.is_phenotips_enabled:
try:
data_json = _get_patient_data(
new_project,
new_individual,
)
_update_individual_phenotips_data(new_individual, data_json)
phenotips_data_retrieved = True
except phenotips_api.PhenotipsException as e:
print("Couldn't retrieve latest data from phenotips for %s: %s" % (new_individual, e))
return new_individual, created, phenotips_data_retrieved
def transfer_individual(source_individual, new_project, connect_to_phenotips):
"""Transfers the given Individual and returns the new Individual"""
# get rid of '.' to signify 'unknown'
if source_individual.paternal_id == "." or source_individual.maternal_id == "." or source_individual.gender == "." or source_individual.affected == ".":
if source_individual.paternal_id == ".":
source_individual.paternal_id = ""
if source_individual.maternal_id == ".":
source_individual.maternal_id = ""
if source_individual.affected == ".":
source_individual.affected = ""
if source_individual.gender == ".":
source_individual.gender = ""
source_individual.save()
new_individual, created = safe_get_or_create(source_individual)
if created:
print("Created SeqrSample", new_individual)
update_model_fields(new_individual, source_individual, [
'family',
'indiv_id',
'created_date',
'maternal_id',
'paternal_id',
'gender',
'affected',
'nickname',
'case_review_status',
'phenotips_id',
'phenotips_data',
])
if new_individual.display_name == new_individual.individual_id:
new_individual.display_name = ''
new_individual.save()
# update PhenoTips data
phenotips_data_retrieved = False
if connect_to_phenotips and new_project.is_phenotips_enabled:
try:
data_json = _get_patient_data(
new_project,
new_individual,
)
_update_individual_phenotips_data(new_individual, data_json)
phenotips_data_retrieved = True
except phenotips_api.PhenotipsException as e:
print("Couldn't retrieve latest data from phenotips for %s: %s" %
(new_individual, e))
# transfer MME data
if new_project.is_mme_enabled:
mme_data_for_individual = list(
settings.SEQR_ID_TO_MME_ID_MAP.find({
'seqr_id':
new_individual.individual_id
}).sort('insertion_date', pymongo.DESCENDING))
if mme_data_for_individual:
submitted_data = mme_data_for_individual[0]['submitted_data']
if submitted_data:
new_individual.mme_submitted_data = json.dumps(
submitted_data, default=json_util.default)
new_individual.mme_id = submitted_data['patient']['id']
new_individual.save()
return new_individual, created, phenotips_data_retrieved
def handle(self, *args, **options):
from_project = Project.objects.get(guid=options['from_project'])
to_project = Project.objects.get(guid=options['to_project'])
to_base_project = find_matching_xbrowse_model(to_project)
family_ids = options['family_ids']
families = Family.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 seqr_individual in f.individual_set.all():
base_individual = find_matching_xbrowse_model(seqr_individual)
base_individual.project = to_base_project
base_individual.save()
# Update individuals in phenotips
if _phenotips_patient_exists(seqr_individual):
# make sure phenotips_patient_id is up to date
data_json = _get_patient_data(
from_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.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.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 base_individual.vcf_files.all():
to_vcf_file, _ = VCFFile.objects.get_or_create(
project=to_base_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,
)
base_individual.vcf_files.add(to_vcf_file)
base_individual.vcf_files.remove(from_vcf_file)
# Update variant tags/ notes
saved_variants = SavedVariant.objects.filter(family=f)
for variant_tag in VariantTag.objects.filter(
saved_variant__in=saved_variants).select_related(
'variant_tag_type'):
if variant_tag.variant_tag_type.project:
to_tag_type, created = get_or_create_seqr_model(
VariantTagType,
project=to_project,
name=variant_tag.variant_tag_type.name)
if created:
update_seqr_model(
to_tag_type,
category=variant_tag.variant_tag_type.category,
description=variant_tag.variant_tag_type.
description,
color=variant_tag.variant_tag_type.color,
order=variant_tag.variant_tag_type.order,
)
update_seqr_model(variant_tag,
variant_tag_type=to_tag_type)
else:
to_project_tag, created = ProjectTag.objects.get_or_create(
project=to_base_project,
tag=variant_tag.variant_tag_type.name)
if created:
to_project_tag.category = variant_tag.variant_tag_type.category
to_project_tag.title = variant_tag.variant_tag_type.description
to_project_tag.color = variant_tag.variant_tag_type.color
to_project_tag.order = variant_tag.variant_tag_type.order
to_project_tag.save()
variant_tag.project_tag = to_project_tag
variant_tag.save()
base_family = find_matching_xbrowse_model(f)
for note in BaseVariantNote.objects.filter(family=base_family):
note.project = to_base_project
note.save()
# Update families
update_seqr_model(f, project=to_project)
print("Done.")
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.")
