def delete_subject(genomic_db_id):
try :
subject = Subject.objects.get(genomic_db_id=genomic_db_id)
subject.delete()
data_importer_logger.log_message('delete_subject ----- successfully deleted subject ' + genomic_db_id)
except ObjectDoesNotExist:
data_importer_logger.log_message('delete_subject ----- subject ' + genomic_db_id + ' does not exist')
def delete_affymetrix(name):
try :
affymetrix = Affymetrix.objects.get(name=name)
path = affymetrix.cel_file.path
default_storage.delete(path)
affymetrix.delete()
data_importer_logger.log_message('delete_affymetrix ----- successfully deleted affymetrix ' + name)
except ObjectDoesNotExist:
data_importer_logger.log_message('delete_affymetrix ----- affymetrix ' + name + ' does not exist')
def get_subject(genomic_db_id, site_id, alias, project, owner_site):
try:
subject = Subject(genomic_db_id=genomic_db_id, site_id=site_id, alias=alias, project=project, owner_site=owner_site)
subject.validate_unique()
subject.save()
data_importer_logger.log_message('get_subject ----- successfully created new subject: ' + genomic_db_id)
except ValidationError as e:
subject = Subject.objects.get(genomic_db_id=genomic_db_id)
data_importer_logger.log_message('get_subject ----- get existing subject: ' + genomic_db_id)
return subject
def get_site(name):
try:
site = Site(name=name)
site.validate_unique()
site.save()
data_importer_logger.log_message('get_site ----- successfully created new site: ' + name)
except ValidationError as e:
site = Site.objects.get(name=name)
data_importer_logger.log_message('get_site ----- get existing site: ' + name)
return site
def update_subject(genomic_db_id, site_id, alias, project, owner_site):
try :
subject = Subject.objects.get(genomic_db_id=genomic_db_id)
subject.site_id = site_id
subject.alias = alias
subject.project = project
subject.owner_site = owner_site
subject.save()
data_importer_logger.log_message('update_subject ----- successfully updated subject ' + genomic_db_id)
except ObjectDoesNotExist:
data_importer_logger.log_message('update_subject ----- subject ' + genomic_db_id + ' does not exist')
subject = get_subject(genomic_db_id, site_id, alias, project, owner_site)
return subject
def get_affymetrix(name, subject, affymetrix_file_path_list):
try:
file_path = check_affymetrix(name, affymetrix_file_path_list)
if file_path:
cel_file = open(file_path + '/' + name, 'ro') # open given file
affymetrix = Affymetrix(name=name, subject=subject)
affymetrix.validate_unique()
affymetrix.save()
affymetrix.cel_file.storage.save('affymetrix/'+name, cel_file) # save to media directory
affymetrix.cel_file = 'affymetrix/'+name # save cel_file
affymetrix.save()
cel_file.close()
data_importer_logger.log_message('get_affymetrix ----- successfully created new affymetrix: ' + name)
return affymetrix
data_importer_logger.log_message('get_affymetrix ----- affymetrix ' + name + ' file does not exist')
except ValidationError as e:
data_importer_logger.log_message('get_affymetrix ----- affymetrix ' + name + ' validation error')
