def handle(self, *args, **options):
project_id = args[0]
project = Project.objects.get(project_id=project_id)
vcf_file_path = os.path.abspath(args[1])
vcf_file = VCFFile.objects.get_or_create(file_path=vcf_file_path)[0]
if options.get('clear'):
for individual in project.individual_set.all():
individual.vcf_files.clear()
if options.get('indiv_id'):
individual = Individual.objects.get(
project=project,
indiv_id=options.get('indiv_id')
)
sample_management.add_vcf_file_to_individual(individual, vcf_file)
else:
sample_management.add_vcf_file_to_project(project, vcf_file)
if options.get('load'):
print("Loading VCF into project store")
xbrowse_controls.load_project(project_id, vcf_files=[vcf_file_path])
print("Loading VCF datastore")
xbrowse_controls.load_project_datastore(project_id, vcf_files=[vcf_file_path])
def handle(self, *args, **options):
project_id = args[0]
project = Project.objects.get(project_id=project_id)
vcf_file_path = os.path.abspath(args[1])
vcf_file = VCFFile.objects.get_or_create(file_path=vcf_file_path)[0]
if options.get('clear'):
for individual in project.individual_set.all():
individual.vcf_files.clear()
if options.get('indiv_id'):
individual = Individual.objects.get(
project=project, indiv_id=options.get('indiv_id'))
sample_management.add_vcf_file_to_individual(individual, vcf_file)
else:
sample_management.add_vcf_file_to_project(project, vcf_file)
if options.get('load'):
print("Loading VCF into project store")
xbrowse_controls.load_project(project_id,
vcf_files=[vcf_file_path])
print("Loading VCF datastore")
xbrowse_controls.load_project_datastore(project_id,
vcf_files=[vcf_file_path])
def transfer_project(self, from_project_id, destination_project_id):
print("From: " + from_project_id)
print("To: " + destination_project_id)
from_project = Project.objects.get(project_id=from_project_id)
destination_project = Project.objects.get(project_id=destination_project_id)
# Make sure individuals are the same
indivs_missing_from_dest_project = (set(
[i.indiv_id for i in Individual.objects.filter(project=from_project)]) - set(
[i.indiv_id for i in Individual.objects.filter(project=destination_project)]))
if indivs_missing_from_dest_project:
raise Exception("Individuals missing from dest project: " + str(indivs_missing_from_dest_project))
# update VCFs
vcfs = from_project.families_by_vcf().keys()
for vcf_file_path in vcfs:
vcf_file = VCFFile.objects.get_or_create(file_path=os.path.abspath(vcf_file_path))[0]
sample_management.add_vcf_file_to_project(destination_project, vcf_file)
print("Added %s to project %s" % (vcf_file, destination_project.project_id))
families_db = get_datastore()._db
projects_db = get_project_datastore()._db
print("==========")
print("Checking 'from' Projects and Families:")
if not check_that_exists(projects_db.projects, {'project_id': from_project_id}, not_more_than_one=True):
raise ValueError("There needs to be 1 project db in %(from_project_id)s" % locals())
if not check_that_exists(families_db.families, {'project_id': from_project_id}, not_more_than_one=False):
raise ValueError("There needs to be atleast 1 family db in %(from_project_id)s" % locals())
print("==========")
print("Make Updates:")
datestamp = datetime.now().strftime("%Y-%m-%d")
if check_that_exists(projects_db.projects, {'project_id': destination_project_id}, not_more_than_one=True):
result = update(projects_db.projects, {'project_id': destination_project_id}, {'project_id': destination_project_id+'_previous', 'version': datestamp})
if check_that_exists(families_db.families, {'project_id': destination_project_id}, not_more_than_one=False):
result = update(families_db.families, {'project_id': destination_project_id}, {'project_id': destination_project_id+'_previous', 'version': datestamp})
result = update(projects_db.projects, {'project_id': from_project_id}, {'project_id': destination_project_id, 'version': '2'})
result = update(families_db.families, {'project_id': from_project_id}, {'project_id': destination_project_id, 'version': '2'})
print("==========")
print("Checking Projects:")
if not check_that_exists(projects_db.projects, {'project_id': destination_project_id}, not_more_than_one=True):
raise ValueError("After: There needs to be 1 project db in %(destination_project_id)s" % locals())
if not check_that_exists(families_db.families, {'project_id': destination_project_id}, not_more_than_one=False):
raise ValueError("After: There needs to be atleast 1 family db in %(destination_project_id)s" % locals())
update_family_analysis_status(destination_project_id)
print("Data transfer finished.")
i = raw_input("Delete the 'from' project: %s? [Y/n] " % from_project_id)
if i.strip() == 'Y':
sample_management.delete_project(from_project_id)
print("Project %s deleted" % from_project_id)
else:
print("Project not deleted")
def handle(self, *args, **options):
project_id = args[0]
project = Project.objects.get(project_id=project_id)
project_dir = os.path.abspath(args[1])
project_yaml_file = os.path.join(project_dir, 'project.yaml')
project_spec = yaml.load(open(project_yaml_file))
# load in sample IDs that we'll use for the project
sample_id_file = os.path.join(project_dir,
project_spec['sample_id_list'])
sample_ids = [l.strip('\n') for l in open(sample_id_file)]
sample_ids = [slugify(s, separator='_') for s in sample_ids]
sample_management.add_indiv_ids_to_project(project, sample_ids)
# set meta info
project.project_name = project_spec['project_name']
project.save()
# nicknames
if 'nicknames' in project_spec:
# todo
pass
# load individuals
if 'ped_files' in project_spec:
for relative_path in project_spec['ped_files']:
ped_file_path = os.path.join(project_dir, relative_path)
sample_management.update_project_from_fam(
project, open(ped_file_path))
# todo: add awesome-slugify to above
# set VCF files
if 'vcf_files' in project_spec:
for relative_path in project_spec['vcf_files']:
vcf_file_path = os.path.join(project_dir, relative_path)
# todo: this should be a fn somewhere that add_vcf_to_project uses too
vcf_file = VCFFile.objects.get_or_create(
file_path=vcf_file_path)[0]
sample_management.add_vcf_file_to_project(project, vcf_file)
def handle(self, *args, **options):
project_id = args[0]
project = Project.objects.get(project_id=project_id)
project_dir = os.path.abspath(args[1])
project_yaml_file = os.path.join(project_dir, 'project.yaml')
project_spec = yaml.load(open(project_yaml_file))
# load in sample IDs that we'll use for the project
sample_id_file = os.path.join(project_dir, project_spec['sample_id_list'])
sample_ids = [l.strip('\n') for l in open(sample_id_file)]
sample_ids = [slugify.slugify(s) for s in sample_ids]
sample_management.add_indiv_ids_to_project(project, sample_ids)
# set meta info
project.project_name = project_spec['project_name']
project.save()
# nicknames
if 'nicknames' in project_spec:
# todo
pass
# load individuals
if 'ped_files' in project_spec:
for relative_path in project_spec['ped_files']:
ped_file_path = os.path.join(project_dir, relative_path)
sample_management.update_project_from_fam(project, open(ped_file_path))
# todo: add awesome-slugify to above
# set VCF files
if 'vcf_files' in project_spec:
for relative_path in project_spec['vcf_files']:
vcf_file_path = os.path.join(project_dir, relative_path)
# todo: this should be a fn somewhere that add_vcf_to_project uses too
vcf_file = VCFFile.objects.get_or_create(file_path=vcf_file_path)[0]
sample_management.add_vcf_file_to_project(project, vcf_file)
def transfer_project(self, from_project_id, destination_project_id):
print("From: " + from_project_id)
print("To: " + destination_project_id)
from_project = Project.objects.get(project_id=from_project_id)
destination_project = Project.objects.get(
project_id=destination_project_id)
# Make sure individuals are the same
indivs_missing_from_dest_project = (set([
i.indiv_id for i in Individual.objects.filter(project=from_project)
]) - set([
i.indiv_id
for i in Individual.objects.filter(project=destination_project)
]))
if indivs_missing_from_dest_project:
raise Exception("Individuals missing from dest project: " +
str(indivs_missing_from_dest_project))
# update VCFs
vcfs = from_project.families_by_vcf().keys()
for vcf_file_path in vcfs:
vcf_file = VCFFile.objects.get_or_create(
file_path=os.path.abspath(vcf_file_path))[0]
sample_management.add_vcf_file_to_project(destination_project,
vcf_file)
print("Added %s to project %s" %
(vcf_file, destination_project.project_id))
families_db = get_datastore(from_project_id)._db
projects_db = get_project_datastore(from_project_id)._db
print("==========")
print("Checking Projects:")
check_that_exists(projects_db.projects,
{'project_id': from_project_id},
not_more_than_one=True)
check_that_exists(projects_db.projects,
{'project_id': destination_project_id},
not_more_than_one=True)
print("==========")
print("Checking Families:")
check_that_exists(families_db.families,
{'project_id': from_project_id},
not_more_than_one=False)
check_that_exists(families_db.families,
{'project_id': destination_project_id},
not_more_than_one=False)
print("==========")
print("Make Updates:")
result = update(
projects_db.projects, {'project_id': destination_project_id}, {
'project_id': destination_project_id + '_previous1',
'version': '1'
})
result = update(projects_db.projects, {'project_id': from_project_id},
{
'project_id': destination_project_id,
'version': '2'
})
result = update(
families_db.families, {'project_id': destination_project_id}, {
'project_id': destination_project_id + '_previous1',
'version': '1'
})
result = update(families_db.families, {'project_id': from_project_id},
{
'project_id': destination_project_id,
'version': '2'
})
print("==========")
print("Checking Projects:")
check_that_exists(projects_db.projects,
{'project_id': destination_project_id},
not_more_than_one=True)
print("==========")
print("Checking Families:")
check_that_exists(families_db.families,
{'project_id': destination_project_id},
not_more_than_one=False)
update_family_analysis_status(destination_project_id)
print("Data transfer finished.")
i = raw_input("Delete the 'from' project: %s? [Y/n] " %
from_project_id)
if i.strip() == 'Y':
sample_management.delete_project(from_project_id)
print("Project %s deleted" % from_project_id)
else:
print("Project not deleted")
def handle(self, *args, **options):
if len(args) < 2:
print("Usage: ./manage.py load_project_dir <project_id> <project_path>")
print("")
sys.exit(1)
project_id = args[0]
try:
project = Project.objects.get(project_id=project_id)
except Project.DoesNotExist:
print("\nError:")
print("\nNo project could be found with id '%s'" % project_id)
print("")
print("Please use the add_project command first to add this project before loading it.")
print("")
sys.exit(1)
project_dir = os.path.abspath(args[1])
project_yaml_file = os.path.join(project_dir, 'project.yaml')
project_spec = yaml.load(open(project_yaml_file))
# load in sample IDs that we'll use for the project
sample_id_file = os.path.join(project_dir, project_spec['sample_id_list'])
sample_ids = [l.strip('\n') for l in open(sample_id_file)]
sample_ids = [slugify(s, separator='_') for s in sample_ids]
sample_management.add_indiv_ids_to_project(project, sample_ids)
# set meta info
project.project_name = project_spec['project_name']
project.save()
# nicknames
if 'nicknames' in project_spec:
# todo
pass
# load individuals
if 'ped_files' in project_spec:
for relative_path in project_spec['ped_files']:
ped_file_path = os.path.join(project_dir, relative_path)
sample_management.update_project_from_fam(project, open(ped_file_path))
# todo: add awesome-slugify to above
# set VCF files
if 'vcf_files' in project_spec:
for relative_path in project_spec['vcf_files']:
vcf_file_path = os.path.join(project_dir, relative_path)
# todo: this should be a fn somewhere that add_vcf_to_project uses too
vcf_file = VCFFile.objects.get_or_create(file_path=vcf_file_path)[0]
sample_management.add_vcf_file_to_project(project, vcf_file)
if 'breakpoint_files' in project_spec:
for relative_path in project_spec['breakpoint_files']:
breakpoint_file = BreakpointFile()
breakpoint_file.project = project
breakpoint_file.file_path = os.path.join(project_dir, relative_path)
breakpoint_file.save()
print("Adding breakpoint file: %s" % breakpoint_file.file_path)
