def transfer_individual_info(source_individual, destination_individual):
"""Transfers the given Individual and returns the new Individual"""
assert source_individual.individual_id == destination_individual.individual_id
destination_individual.maternal_id = choose_one(destination_individual, 'maternal_id', source_individual.maternal_id, destination_individual.maternal_id)
destination_individual.paternal_id = choose_one(destination_individual, 'paternal_id', source_individual.paternal_id, destination_individual.paternal_id)
destination_individual.sex = choose_one(destination_individual, 'sex', source_individual.sex, destination_individual.sex)
destination_individual.affected = choose_one(destination_individual, 'affected', source_individual.affected, destination_individual.affected)
destination_individual.display_name = choose_one(destination_individual, 'display_name', source_individual.display_name, destination_individual.display_name)
destination_individual.case_review_status = choose_one(destination_individual, 'case_review_status', source_individual.case_review_status, destination_individual.case_review_status)
# if PhenoTips HPO terms entered for both individuals, prompt user to choose
destination_individual.phenotips_data = choose_one(
destination_individual,
'phenotips_data',
source_individual.phenotips_data,
destination_individual.phenotips_data
)
destination_individual.mme_id = choose_one(destination_individual, 'mme_id', source_individual.mme_id, destination_individual.mme_id)
destination_individual.mme_submitted_data = choose_one(destination_individual, 'mme_submitted_data', source_individual.mme_submitted_data, destination_individual.mme_submitted_data)
destination_individual.save()
def transfer_project_info(source_project, destination_project):
"""Transfers the given project"""
# destination_project.name - keep project name as is
# destination_project.deprecated_project_id - keep as is
destination_project.description = choose_one(
destination_project, "description", source_project.description,
destination_project.description)
# update permissions - transfer source project users
for user in source_project.can_edit_group.user_set.all():
destination_project.can_edit_group.user_set.add(user)
for user in source_project.can_view_group.user_set.all():
destination_project.can_view_group.user_set.add(user)
# update permissions - transfer source project gene lists
for locus_list in get_objects_for_group(source_project.can_view_group,
CAN_VIEW, LocusList):
assign_perm(user_or_group=destination_project.can_view_group,
perm=CAN_VIEW,
obj=locus_list)
# update permissions - transfer SampleBatches
for sample_batch in SampleBatch.objects.filter(
sample__individual__family__project=source_project):
assign_perm(user_or_group=destination_project.can_edit_group,
perm=CAN_EDIT,
obj=sample_batch)
assign_perm(user_or_group=destination_project.can_view_group,
perm=CAN_VIEW,
obj=sample_batch)
# transfer custom reference populations
for p in source_project.custom_reference_populations.all():
destination_project.custom_reference_populations.add(p)
# phenotips and MME
destination_project.is_phenotips_enabled = True
# TODO check for each individual whether the source project has phenotips data
destination_project.phenotips_user_id = source_project.phenotips_user_id
destination_project.is_mme_enabled = source_project.is_mme_enabled or destination_project.is_mme_enabled
destination_project.mme_primary_data_owner = choose_one(
destination_project, "mme_primary_data_owner",
source_project.mme_primary_data_owner,
destination_project.mme_primary_data_owner)
destination_project.save()
def transfer_family_info(source_family, destination_family):
"""Transfers the given family and returns the new family"""
print("Transferring " + str(source_family) + " to " +
str(destination_family))
assert source_family.family_id == destination_family.family_id
destination_family.description = choose_one(destination_family,
'description',
source_family.description,
destination_family.description)
#destination_family.project - keep this since source_family.project will be deleted
destination_family.display_name = choose_one(
destination_family, "display_name", source_family.display_name,
destination_family.display_name)
#new_family.pedigree_image - keep this as is, it will need to be regenerated anyway
destination_family.analysis_notes = choose_one(
destination_family, 'analysis_notes', source_family.analysis_notes,
destination_family.analysis_notes)
destination_family.analysis_summary = choose_one(
destination_family, 'analysis_summary', source_family.analysis_summary,
destination_family.analysis_summary)
destination_family.causal_inheritance_mode = choose_one(
destination_family, 'causal_inheritance_mode',
source_family.causal_inheritance_mode,
destination_family.causal_inheritance_mode)
destination_family.analysis_status = choose_one(
destination_family, 'analysis_status', source_family.analysis_status,
destination_family.analysis_status)
destination_family.internal_case_review_notes = choose_one(
destination_family, 'internal_case_review_notes',
source_family.internal_case_review_notes,
destination_family.internal_case_review_notes)
destination_family.internal_case_review_summary = choose_one(
destination_family, 'internal_case_review_summary',
source_family.internal_case_review_summary,
destination_family.internal_case_review_summary)
destination_family.internal_analysis_status = choose_one(
destination_family, 'internal_analysis_status',
source_family.internal_analysis_status,
destination_family.internal_analysis_status)
destination_family.save()
def handle(self, *args, **options):
to_project_id = options["to_project"]
from_project_id = options["from_project"]
from_project_datatype = options["from_project_datatype"]
assert from_project_id
assert to_project_id
print("=============================")
print("Transferring metadata from project %s to %s" % (from_project_id, to_project_id))
if not ask_yes_no_question("Continue?"):
return
"""
The following models are transfered between projects.
ProjectCollaborator => user = models.ForeignKey(User), project = models.ForeignKey('base.Project'), collaborator_type = models.CharField(max_length=20, choices=COLLABORATOR_TYPES, default="collaborator")
Project => (private_reference_populations = models.ManyToManyField(ReferencePopulation), gene_lists = models.ManyToManyField('gene_lists.GeneList', through='ProjectGeneList'))
Family => Project,
FamilyGroup => Project (families = models.ManyToManyField(Family))
FamilyImageSlide => Family
Cohort => Project (individuals = models.ManyToManyField('base.Individual'), vcf_files, bam_file)
Individual => Project, Family # vcf_files = models.ManyToManyField(VCFFile, null=True, blank=True), bam_file = models.ForeignKey('datasets.BAMFile', null=True, blank=True)
FamilySearchFlag => User, Family
CausalVariant => Family
ProjectTag => Project
VariantTag => ProjectTag, Family
VariantNote => User, Project
IndividualPhenotype => Individual, ProjectPhenotype
ProjectPhenotype => Project
"""
# Project
to_project, created = Project.objects.get_or_create(project_id=to_project_id)
if created:
print("--> Created project: " + str(to_project))
to_project.created_date = timezone.now()
else:
print("--> Transferring into existing project: " + str(to_project))
from_project = Project.objects.get(project_id=from_project_id)
to_project.project_name = choose_one(to_project, 'project_name', from_project.project_name, to_project.project_name)
to_project.description = choose_one(to_project, 'description', from_project.description, to_project.description)
# set combined_projects_info
if to_project.combined_projects_info:
combined_projects_info = json.loads(to_project.combined_projects_info)
else:
combined_projects_info = {}
combined_projects_info.update({from_project_datatype: {'project_id': from_project.project_id}})
to_project.combined_projects_info = json.dumps(combined_projects_info)
# TODO update collaborators?
# Copy gene list
for project_gene_list in ProjectGeneList.objects.filter(project=from_project):
print("--> Adding gene list: " + project_gene_list.gene_list.slug)
ProjectGeneList.objects.get_or_create(project=to_project, gene_list=project_gene_list.gene_list)
# Reference Populations
for reference_population in from_project.private_reference_populations.all():
if not to_project.private_reference_populations.filter(pk=reference_population.pk).exists():
print("--> Adding private reference population: " + reference_population.slug)
to_project.private_reference_populations.add(reference_population)
to_project.save()
# ProjectCollaborator
collaborators = ProjectCollaborator.objects.filter(project=from_project)
if len(collaborators) > 0 and ask_yes_no_question("Transfer the %s collaborators?" % len(collaborators)):
print("Transferring the %s collaborators" % len(collaborators))
for c in collaborators:
_, created = ProjectCollaborator.objects.get_or_create(project=to_project, user=c.user, collaborator_type=c.collaborator_type)
if created:
print("-----> Added %s %s" % (c.collaborator_type, c.user.email))
# --- SeqrProject - update new schema
seqr_project, seqr_project_created = transfer_project(to_project)
to_project.seqr_project = seqr_project
to_project.save()
print("--> Set project.combined_projects_info to %s" % (to_project.combined_projects_info, ))
# Family
to_family_id_to_family = {} # maps family_id to the to_family object
from_families = Family.objects.filter(project=from_project)
print("----> Transferring %s families" % len(from_families))
for from_f in from_families:
to_f, created = Family.objects.get_or_create(project=to_project, family_id=from_f.family_id)
if created:
print("----> Created family %s" % to_f.family_id)
else:
print("----> Transferring into existing family %s (%s)" % (to_f.family_id, to_f.short_description))
to_family_id_to_family[to_f.family_id] = to_f
to_f.family_name = choose_one(to_f, 'family_name', from_f.family_name, to_f.family_name)
to_f.short_description = choose_one(to_f, 'short_description', from_f.short_description, to_f.short_description)
to_f.about_family_content = choose_one(to_f, 'about_family_content', from_f.about_family_content, to_f.about_family_content)
to_f.analysis_summary_content = choose_one(to_f, 'analysis_summary_content', from_f.analysis_summary_content, to_f.analysis_summary_content)
to_f.pedigree_image = None # choose_one(to_f, 'pedigree_image', from_f.pedigree_image, to_f.pedigree_image)
to_f.pedigree_image_height = None # choose_one(to_f, 'pedigree_image_height', from_f.pedigree_image_height, to_f.pedigree_image_height)
to_f.pedigree_image_width = None # choose_one(to_f, 'pedigree_image_width', from_f.pedigree_image_width, to_f.pedigree_image_width)
to_f.analysis_status = choose_one(to_f, 'analysis_status', from_f.analysis_status, to_f.analysis_status, default_value='Q')
to_f.analysis_status_date_saved = choose_one(to_f, 'analysis_status_date_saved', from_f.analysis_status_date_saved, to_f.analysis_status_date_saved)
to_f.analysis_status_saved_by = choose_one(to_f, 'analysis_status_saved_by', from_f.analysis_status_saved_by, to_f.analysis_status_saved_by)
to_f.causal_inheritance_mode = choose_one(to_f, 'causal_inheritance_mode', from_f.causal_inheritance_mode, to_f.causal_inheritance_mode)
to_f.internal_case_review_notes = choose_one(to_f, 'internal_case_review_notes', from_f.internal_case_review_notes, to_f.internal_case_review_notes)
to_f.internal_case_review_summary = choose_one(to_f, 'internal_case_review_summary', from_f.internal_case_review_summary, to_f.internal_case_review_summary)
to_f.coded_phenotype = choose_one(to_f, 'coded_phenotype', from_f.coded_phenotype, to_f.coded_phenotype)
to_f.post_discovery_omim_number = choose_one(to_f, 'post_discovery_omim_number', from_f.post_discovery_omim_number, to_f.post_discovery_omim_number)
# combined families info
if to_f.combined_families_info:
combined_families_info = json.loads(to_f.combined_families_info)
else:
combined_families_info = {}
combined_families_info.update({from_project_datatype: {'project_id': from_project.project_id, 'family_id': from_f.family_id}})
to_f.combined_families_info = json.dumps(combined_families_info)
to_f.save()
# --- SeqrProject - update new schema
seqr_family, seqr_family_created = transfer_family(to_f, seqr_project)
to_f.seqr_family = seqr_family
to_f.save()
print("----> Set family.combined_families_info to %s" % (to_f.combined_families_info, ))
# FamilyGroup
for from_fg in FamilyGroup.objects.filter(project=from_project):
FamilyGroup.objects.get_or_create(project=to_project, slug=from_fg.slug, name=from_fg.name, description=from_fg.description)
# FamilyImageSlide
#for from_family in Family.objects.filter(project=from_project):
# TODO - need to iterate over image slides of from_family, and link to image slides of to_family
# FamilyImageSlide.objects.get_or_create(family=to_family, )
# Cohort
#cohorts = list(Cohort.objects.filter(project=project))
#output_obj += cohorts
# Individual
print("-------> Transferring %s individuals" % len(Individual.objects.filter(project=from_project)))
for from_family in Family.objects.filter(project=from_project):
to_family = to_family_id_to_family[from_family.family_id]
for from_i in Individual.objects.filter(project=from_project, family=from_family):
to_i, created = Individual.objects.get_or_create(project=to_project, family=to_family, indiv_id=from_i.indiv_id)
if created:
print("-------> Created individual %s" % to_i.indiv_id)
else:
print("-------> Transferring into existing individual %s" % (to_i.indiv_id))
to_i.created_date = choose_one(to_i, 'created_date', from_i.created_date, to_i.created_date, use_lower_value=True)
to_i.maternal_id = choose_one(to_i, 'maternal_id', from_i.maternal_id, to_i.maternal_id)
to_i.paternal_id = choose_one(to_i, 'paternal_id', from_i.paternal_id, to_i.paternal_id)
to_i.gender = choose_one(to_i, 'gender', from_i.gender, to_i.gender, default_value='U')
to_i.affected = choose_one(to_i, 'affected', from_i.affected, to_i.affected, default_value='U')
to_i.nickname = choose_one(to_i, 'nickname', from_i.nickname, to_i.nickname)
to_i.other_notes = choose_one(to_i, 'other_notes', from_i.other_notes, to_i.other_notes)
to_i.case_review_status = choose_one(to_i, 'case_review_status', from_i.case_review_status, to_i.case_review_status)
to_i.phenotips_id = choose_one(to_i, 'phenotips_id', from_i.phenotips_id, to_i.phenotips_id)
to_i.phenotips_data = choose_one(to_i, 'phenotips_data', from_i.phenotips_data, to_i.phenotips_data)
# create phenotips patients and upload data
to_i.mean_target_coverage = None
to_i.coverage_status = choose_one(to_i, 'coverage_status', from_i.coverage_status, to_i.coverage_status, default_value='S')
if from_i.bam_file_path:
if to_i.bam_file_path:
to_i.bam_file_path = to_i.bam_file_path + "," + from_i.bam_file_path
else:
to_i.bam_file_path = from_i.bam_file_path
to_i.vcf_id = '' # VCF ids will now be stored at the Sample not the Individual level
for vcf_file in from_i.vcf_files.all():
if vcf_file not in to_i.vcf_files.all():
to_i.vcf_files.add(vcf_file)
to_i.in_case_review = choose_one(to_i, 'in_case_review', from_i.in_case_review, to_i.in_case_review)
# combined individuals info
if to_i.combined_individuals_info:
combined_individuals_info = json.loads(to_i.combined_individuals_info)
else:
combined_individuals_info = {}
combined_individuals_info.update({from_project_datatype: {
'project_id': from_project.project_id,
'family_id': from_f.family_id,
'indiv_id': from_i.indiv_id}
})
to_i.combined_individuals_info = json.dumps(combined_individuals_info)
to_i.save()
seqr_individual, seqr_individual_created, phenotips_data_retrieved = transfer_individual(to_i, seqr_family, seqr_project, connect_to_phenotips=True)
seqr_individual.seqr_individual = seqr_individual
seqr_individual.save()
print("-------> Set individual.combined_individuals_info to %s" % (to_i.combined_individuals_info, ))
for from_v in CausalVariant.objects.filter(family=from_family):
CausalVariant.objects.get_or_create(
family = to_family,
variant_type=from_v.variant_type,
xpos=from_v.xpos,
ref=from_v.ref,
alt=from_v.alt)
# add this project to phenotips
print("--> PHENOTIPS")
create_user_in_phenotips(to_project.project_id, to_project.project_name)
individuals_to_add = Individual.objects.filter(project=to_project, family=to_family)
add_individuals_to_phenotips(to_project.project_id, [i.indiv_id for i in individuals_to_add])
for i in individuals_to_add:
if i.phenotips_data:
to_project.phenotips_user_id = to_project.project_id
try:
json_obj = json.loads(i.phenotips_data)
update_patient_data(to_project, i, patient_json=json_obj)
except Exception as e:
logger.error("%s - error while updating phenotips for %s: %s", e, i.phenotips_id, json_obj)
# TODO: merge MME?
from_variant_notes = VariantNote.objects.filter(project=from_project)
print("--> Transferring %s VariantNotes:" % len(from_variant_notes))
for from_vn in from_variant_notes:
if from_vn.family and from_vn.family.family_id:
to_family = to_family_id_to_family.get(from_vn.family.family_id)
else:
to_family = None
_, created = VariantNote.objects.get_or_create(
project=to_project,
family=to_family,
user=from_vn.user,
date_saved=from_vn.date_saved,
note=from_vn.note,
xpos=from_vn.xpos,
ref=from_vn.ref,
alt=from_vn.alt)
if created:
print("-----> Created variant note %s:%s>%s" % (from_vn.xpos, from_vn.ref, from_vn.alt))
from_project_tags = ProjectTag.objects.filter(project=from_project)
print("--> Transferring %s ProjectTags" % len(from_project_tags))
for from_ptag in from_project_tags:
to_ptag, created = ProjectTag.objects.get_or_create(project=to_project, tag=from_ptag.tag)
to_ptag.title = choose_one(to_ptag, 'title', from_ptag.title, to_ptag.title)
to_ptag.category = choose_one(to_ptag, 'category', from_ptag.category, to_ptag.category)
to_ptag.color = choose_one(to_ptag, 'color', from_ptag.color, to_ptag.color)
to_ptag.order = choose_one(to_ptag, 'order', from_ptag.order, to_ptag.order)
to_ptag.save()
from_variant_tags = VariantTag.objects.filter(project_tag=from_ptag)
print("-----> Transferring %s VariantTags for %s" % (len(from_variant_tags), from_ptag.tag))
for from_vtag in from_variant_tags:
if from_vtag.family and from_vtag.family.family_id:
to_family = to_family_id_to_family.get(from_vtag.family.family_id)
else:
to_family = None
_, created = VariantTag.objects.get_or_create(
family=to_family,
project_tag=to_ptag,
xpos=from_vtag.xpos,
ref=from_vtag.ref,
alt=from_vtag.alt)
if created:
print("-----> Created variant tag %s:%s>%s" % (from_vtag.xpos, from_vtag.ref, from_vtag.alt))
def handle(self, *args, **options):
to_project_id = options["to_project"]
from_project_id = options["from_project"]
from_project_datatype = options["from_project_datatype"]
assert from_project_id
assert to_project_id
print("=============================")
print("Transferring metadata from project %s to %s" % (from_project_id, to_project_id))
if not ask_yes_no_question("Continue?"):
return
"""
The following models are transfered between projects.
ProjectCollaborator => user = models.ForeignKey(User), project = models.ForeignKey('base.Project'), collaborator_type = models.CharField(max_length=20, choices=COLLABORATOR_TYPES, default="collaborator")
Project => (private_reference_populations = models.ManyToManyField(ReferencePopulation), gene_lists = models.ManyToManyField('gene_lists.GeneList', through='ProjectGeneList'))
Family => Project,
FamilyGroup => Project (families = models.ManyToManyField(Family))
FamilyImageSlide => Family
Cohort => Project (individuals = models.ManyToManyField('base.Individual'), vcf_files, bam_file)
Individual => Project, Family # vcf_files = models.ManyToManyField(VCFFile, null=True, blank=True), bam_file = models.ForeignKey('datasets.BAMFile', null=True, blank=True)
FamilySearchFlag => User, Family
CausalVariant => Family
ProjectTag => Project
VariantTag => ProjectTag, Family
VariantNote => User, Project
IndividualPhenotype => Individual, ProjectPhenotype
ProjectPhenotype => Project
"""
# Project
to_project, created = Project.objects.get_or_create(project_id=to_project_id)
if created:
print("--> Created project: " + str(to_project))
to_project.created_date = timezone.now()
else:
print("--> Transferring into existing project: " + str(to_project))
from_project = Project.objects.get(project_id=from_project_id)
to_project.project_name = choose_one(to_project, 'project_name', from_project.project_name, to_project.project_name)
to_project.description = choose_one(to_project, 'description', from_project.description, to_project.description)
# set combined_projects_info
if to_project.combined_projects_info:
combined_projects_info = json.loads(to_project.combined_projects_info)
else:
combined_projects_info = {}
combined_projects_info.update({from_project_datatype: {'project_id': from_project.project_id}})
to_project.combined_projects_info = json.dumps(combined_projects_info)
# TODO update collaborators?
# Copy gene list
for project_gene_list in ProjectGeneList.objects.filter(project=from_project):
print("--> Adding gene list: " + project_gene_list.gene_list.slug)
ProjectGeneList.objects.get_or_create(project=to_project, gene_list=project_gene_list.gene_list)
# Reference Populations
for reference_population in from_project.private_reference_populations.all():
if not to_project.private_reference_populations.filter(pk=reference_population.pk).exists():
print("--> Adding private reference population: " + reference_population.slug)
to_project.private_reference_populations.add(reference_population)
to_project.save()
# ProjectCollaborator
collaborators = ProjectCollaborator.objects.filter(project=from_project)
if len(collaborators) > 0 and ask_yes_no_question("Transfer the %s collaborators?" % len(collaborators)):
print("Transferring the %s collaborators" % len(collaborators))
for c in collaborators:
_, created = ProjectCollaborator.objects.get_or_create(project=to_project, user=c.user, collaborator_type=c.collaborator_type)
if created:
print("-----> Added %s %s" % (c.collaborator_type, c.user.email))
# --- SeqrProject - update new schema
seqr_project, seqr_project_created = transfer_project(to_project)
to_project.seqr_project = seqr_project
to_project.save()
print("--> Set project.combined_projects_info to %s" % (to_project.combined_projects_info, ))
# Family
to_family_id_to_family = {} # maps family_id to the to_family object
from_families = Family.objects.filter(project=from_project)
print("----> Transferring %s families" % len(from_families))
for from_f in from_families:
to_f, created = Family.objects.get_or_create(project=to_project, family_id=from_f.family_id)
if created:
print("----> Created family %s" % to_f.family_id)
else:
print("----> Transferring into existing family %s (%s)" % (to_f.family_id, to_f.short_description))
to_family_id_to_family[to_f.family_id] = to_f
to_f.family_name = choose_one(to_f, 'family_name', from_f.family_name, to_f.family_name)
to_f.short_description = choose_one(to_f, 'short_description', from_f.short_description, to_f.short_description)
to_f.about_family_content = choose_one(to_f, 'about_family_content', from_f.about_family_content, to_f.about_family_content)
to_f.analysis_summary_content = choose_one(to_f, 'analysis_summary_content', from_f.analysis_summary_content, to_f.analysis_summary_content)
to_f.pedigree_image = None # choose_one(to_f, 'pedigree_image', from_f.pedigree_image, to_f.pedigree_image)
to_f.pedigree_image_height = None # choose_one(to_f, 'pedigree_image_height', from_f.pedigree_image_height, to_f.pedigree_image_height)
to_f.pedigree_image_width = None # choose_one(to_f, 'pedigree_image_width', from_f.pedigree_image_width, to_f.pedigree_image_width)
to_f.analysis_status = choose_one(to_f, 'analysis_status', from_f.analysis_status, to_f.analysis_status, default_value='Q')
to_f.analysis_status_date_saved = choose_one(to_f, 'analysis_status_date_saved', from_f.analysis_status_date_saved, to_f.analysis_status_date_saved)
to_f.analysis_status_saved_by = choose_one(to_f, 'analysis_status_saved_by', from_f.analysis_status_saved_by, to_f.analysis_status_saved_by)
to_f.causal_inheritance_mode = choose_one(to_f, 'causal_inheritance_mode', from_f.causal_inheritance_mode, to_f.causal_inheritance_mode)
to_f.internal_case_review_notes = choose_one(to_f, 'internal_case_review_notes', from_f.internal_case_review_notes, to_f.internal_case_review_notes)
to_f.internal_case_review_summary = choose_one(to_f, 'internal_case_review_summary', from_f.internal_case_review_summary, to_f.internal_case_review_summary)
to_f.coded_phenotype = choose_one(to_f, 'coded_phenotype', from_f.coded_phenotype, to_f.coded_phenotype)
to_f.post_discovery_omim_number = choose_one(to_f, 'post_discovery_omim_number', from_f.post_discovery_omim_number, to_f.post_discovery_omim_number)
# combined families info
if to_f.combined_families_info:
combined_families_info = json.loads(to_f.combined_families_info)
else:
combined_families_info = {}
combined_families_info.update({from_project_datatype: {'project_id': from_project.project_id, 'family_id': from_f.family_id}})
to_f.combined_families_info = json.dumps(combined_families_info)
to_f.save()
# --- SeqrProject - update new schema
seqr_family, seqr_family_created = transfer_family(to_f, seqr_project)
to_f.seqr_family = seqr_family
to_f.save()
print("----> Set family.combined_families_info to %s" % (to_f.combined_families_info, ))
# FamilyGroup
for from_fg in FamilyGroup.objects.filter(project=from_project):
FamilyGroup.objects.get_or_create(project=to_project, slug=from_fg.slug, name=from_fg.name, description=from_fg.description)
# FamilyImageSlide
#for from_family in Family.objects.filter(project=from_project):
# TODO - need to iterate over image slides of from_family, and link to image slides of to_family
# FamilyImageSlide.objects.get_or_create(family=to_family, )
# Cohort
#cohorts = list(Cohort.objects.filter(project=project))
#output_obj += cohorts
# Individual
print("-------> Transferring %s individuals" % len(Individual.objects.filter(project=from_project)))
for from_family in Family.objects.filter(project=from_project):
to_family = to_family_id_to_family[from_family.family_id]
for from_i in Individual.objects.filter(project=from_project, family=from_family):
to_i, created = Individual.objects.get_or_create(project=to_project, family=to_family, indiv_id=from_i.indiv_id)
if created:
print("-------> Created individual %s" % to_i.indiv_id)
else:
print("-------> Transferring into existing individual %s" % (to_i.indiv_id))
to_i.created_date = choose_one(to_i, 'created_date', from_i.created_date, to_i.created_date, use_lower_value=True)
to_i.maternal_id = choose_one(to_i, 'maternal_id', from_i.maternal_id, to_i.maternal_id)
to_i.paternal_id = choose_one(to_i, 'paternal_id', from_i.paternal_id, to_i.paternal_id)
to_i.gender = choose_one(to_i, 'gender', from_i.gender, to_i.gender, default_value='U')
to_i.affected = choose_one(to_i, 'affected', from_i.affected, to_i.affected, default_value='U')
to_i.nickname = choose_one(to_i, 'nickname', from_i.nickname, to_i.nickname)
to_i.other_notes = choose_one(to_i, 'other_notes', from_i.other_notes, to_i.other_notes)
to_i.case_review_status = choose_one(to_i, 'case_review_status', from_i.case_review_status, to_i.case_review_status)
to_i.case_review_status_accepted_for = choose_one(to_i, 'case_review_status_accepted_for', from_i.case_review_status_accepted_for, to_i.case_review_status_accepted_for)
to_i.phenotips_id = choose_one(to_i, 'phenotips_id', from_i.phenotips_id, to_i.phenotips_id)
to_i.phenotips_data = choose_one(to_i, 'phenotips_data', from_i.phenotips_data, to_i.phenotips_data)
# create phenotips patients and upload data
to_i.mean_target_coverage = None
to_i.coverage_status = choose_one(to_i, 'coverage_status', from_i.coverage_status, to_i.coverage_status, default_value='S')
if from_i.bam_file_path:
if to_i.bam_file_path:
to_i.bam_file_path = to_i.bam_file_path + "," + from_i.bam_file_path
else:
to_i.bam_file_path = from_i.bam_file_path
to_i.vcf_id = '' # VCF ids will now be stored at the Sample not the Individual level
for vcf_file in from_i.vcf_files.all():
if vcf_file not in to_i.vcf_files.all():
to_i.vcf_files.add(vcf_file)
to_i.in_case_review = choose_one(to_i, 'in_case_review', from_i.in_case_review, to_i.in_case_review)
# combined individuals info
if to_i.combined_individuals_info:
combined_individuals_info = json.loads(to_i.combined_individuals_info)
else:
combined_individuals_info = {}
combined_individuals_info.update({from_project_datatype: {
'project_id': from_project.project_id,
'family_id': from_f.family_id,
'indiv_id': from_i.indiv_id}
})
to_i.combined_individuals_info = json.dumps(combined_individuals_info)
to_i.save()
seqr_individual, seqr_individual_created, phenotips_data_retrieved = transfer_individual(to_i, seqr_family, seqr_project, connect_to_phenotips=True)
seqr_individual.seqr_individual = seqr_individual
seqr_individual.save()
print("-------> Set individual.combined_individuals_info to %s" % (to_i.combined_individuals_info, ))
for from_v in CausalVariant.objects.filter(family=from_family):
CausalVariant.objects.get_or_create(
family = to_family,
variant_type=from_v.variant_type,
xpos=from_v.xpos,
ref=from_v.ref,
alt=from_v.alt)
# add this project to phenotips
print("--> PHENOTIPS")
create_user_in_phenotips(to_project.project_id, to_project.project_name)
individuals_to_add = Individual.objects.filter(project=to_project, family=to_family)
add_individuals_to_phenotips(to_project.project_id, [i.indiv_id for i in individuals_to_add])
for i in individuals_to_add:
if i.phenotips_data:
to_project.phenotips_user_id = to_project.project_id
try:
json_obj = json.loads(i.phenotips_data)
update_patient_data(to_project, i.phenotips_id, patient_json=json_obj, is_external_id=True)
except Exception as e:
logger.error("%s - error while updating phenotips for %s: %s", e, i.phenotips_id, json_obj)
# TODO: merge MME?
from_variant_notes = VariantNote.objects.filter(project=from_project)
print("--> Transferring %s VariantNotes:" % len(from_variant_notes))
for from_vn in from_variant_notes:
if from_vn.family and from_vn.family.family_id:
to_family = to_family_id_to_family.get(from_vn.family.family_id)
else:
to_family = None
_, created = VariantNote.objects.get_or_create(
project=to_project,
family=to_family,
user=from_vn.user,
date_saved=from_vn.date_saved,
note=from_vn.note,
xpos=from_vn.xpos,
ref=from_vn.ref,
alt=from_vn.alt)
if created:
print("-----> Created variant note %s:%s>%s" % (from_vn.xpos, from_vn.ref, from_vn.alt))
from_project_tags = ProjectTag.objects.filter(project=from_project)
print("--> Transferring %s ProjectTags" % len(from_project_tags))
for from_ptag in from_project_tags:
to_ptag, created = ProjectTag.objects.get_or_create(project=to_project, tag=from_ptag.tag)
to_ptag.title = choose_one(to_ptag, 'title', from_ptag.title, to_ptag.title)
to_ptag.category = choose_one(to_ptag, 'category', from_ptag.category, to_ptag.category)
to_ptag.color = choose_one(to_ptag, 'color', from_ptag.color, to_ptag.color)
to_ptag.order = choose_one(to_ptag, 'order', from_ptag.order, to_ptag.order)
to_ptag.save()
from_variant_tags = VariantTag.objects.filter(project_tag=from_ptag)
print("-----> Transferring %s VariantTags for %s" % (len(from_variant_tags), from_ptag.tag))
for from_vtag in from_variant_tags:
if from_vtag.family and from_vtag.family.family_id:
to_family = to_family_id_to_family.get(from_vtag.family.family_id)
else:
to_family = None
_, created = VariantTag.objects.get_or_create(
family=to_family,
project_tag=to_ptag,
xpos=from_vtag.xpos,
ref=from_vtag.ref,
alt=from_vtag.alt)
if created:
print("-----> Created variant tag %s:%s>%s" % (from_vtag.xpos, from_vtag.ref, from_vtag.alt))
def handle(self, *args, **options):
"""transfer project"""
raise NotImplementedError("This script is not complete. combine_base_projects.py and update_projects_in_new_schema.py are being used instead - likely until the transition to the new schema is complete")
print("Starting")
counter = defaultdict(int)
destination_project, created = Project.objects.get_or_create(deprecated_project_id=options['project_id_a'])
source_project = Project.objects.get(deprecated_project_id=options['project_id_b'])
if created:
print("Destination project created: " + str(destination_project))
# transfer Project metadata
transfer_project_info(source_project, destination_project)
if options['project_name']:
destination_project.name = options['project_name']
if options['project_description']:
destination_project.description = options['project_description']
destination_project.save()
# transfer Families and Individuals
for source_family in Family.objects.filter(project=source_project):
destination_families = Family.objects.filter(
project=destination_project,
family_id=source_family.family_id
)
if not destination_families:
# just move the family to the destination project. Its descendent individuals, samples and sample batches will move along with it.
source_family.project = destination_project
source_family.save()
counter['reparented source_family'] += 1
continue
# the destination project contains a family with the same family_id as the source_family
destination_family = destination_families[0]
transfer_family_info(source_family, destination_family)
counter['copied attributes from source_family'] += 1
for source_individual in Individual.objects.filter(family=source_family):
destination_individuals = Individual.objects.filter(
family=destination_family,
individual_id=source_individual.individual_id
)
if not destination_individuals:
# just move the individual to the destination family. Its descendent samples and sample batches will move along with it.
source_individual.family = destination_family
source_individual.save()
counter['reparented source_individual'] += 1
continue
# the destination family contains an individual with the same individual_id as the source project
destination_individual = destination_individuals[0]
transfer_individual_info(source_individual, destination_individual)
counter['copied attributes from source_individual'] += 1
# Assume samples and sample batches are not duplicated between the 2 projects
for source_variant_tag_type in VariantTagType.objects.filter(project=source_project):
# if the same VariantTagType doesn't already exist in the destination project,
# move the tag type to the destination project. Its descendent VariantTags will move along with it.
destination_variant_tag_types = VariantTagType.objects.filter(
project=destination_project,
name=source_variant_tag_type.name
)
if not destination_variant_tag_types:
source_variant_tag_type.project = destination_project
counter['reparented variant_tag_type'] += 1
source_variant_tag_type.save()
continue
destination_variant_tag_type = destination_variant_tag_types[0]
destination_variant_tag_type.description = choose_one(destination_variant_tag_type, 'description', source_variant_tag_type.description, destination_variant_tag_type.description)
destination_variant_tag_type.color = choose_one(destination_variant_tag_type, 'color', source_variant_tag_type.color, destination_variant_tag_type.color)
destination_variant_tag_type.save()
counter['copied attributes from variant_tag_type'] += 1
for source_variant_tag in VariantTag.objects.filter(variant_tag_type=source_variant_tag_type):
destination_variant_tag, created = VariantTag.objects.get_or_create(
variant_tag_type=destination_variant_tag_type,
xpos_start=source_variant_tag.xpos_start,
xpos_end=source_variant_tag.xpos_end,
ref=source_variant_tag.ref,
alt=source_variant_tag.alt,
)
if created:
counter['VariantTag created'] += 1
if source_variant_tag.family and not destination_variant_tag.family:
destination_variant_tag.family = source_variant_tag.family
destination_variant_tag.search_parameters = choose_one(destination_variant_tag, 'search_parameters', source_variant_tag.search_parameters, destination_variant_tag.search_parameters)
counter['updated VariantTag'] += 1
destination_variant_tag.save()
for source_variant_note in VariantNote.objects.filter(project=source_project):
# if the same VariantNote doesn't already exist in the destination project,
# move the note to the destination project
if not VariantNote.objects.filter(
project=destination_project,
note=source_variant_note.note,
created_by=source_variant_note.created_by):
source_variant_note.project = destination_project
counter['saved VariantNote'] += 1
source_variant_note.save()
# all data has been transferred to the destination so delete the source project
print("Deleting project " + str(source_project) )
for source_family in Family.objects.filter(project=source_project):
for source_individual in Individual.objects.filter(family=source_family):
source_individual.delete()
source_family.delete()
source_project.delete()
for source_variant_tag_type in VariantTagType.objects.filter(project=source_project):
for source_variant_tag in VariantTag.objects.filter(variant_tag_type=source_variant_tag_type):
source_variant_tag.delete()
source_variant_tag_type.delete()
for source_variant_note in VariantNote.objects.filter(project=source_project):
source_variant_note.delete()
for key, value in counter.items():
print("%15s: %s" % (key, value))