def cases(self, collaborator=None):
self.logger.info("Fetch all cases")
if collaborator:
self.logger.info("Use collaborator {0}".format(collaborator))
return Case.objects(collaborators=collaborator).order_by('-updated_at')
else:
return Case.objects().order_by('-updated_at')
def cases(self, collaborator=None):
self.logger.info("Fetch all cases")
if collaborator:
self.logger.info("Use collaborator {0}".format(collaborator))
return Case.objects(collaborators=collaborator).order_by('-created_at')
else:
return Case.objects().order_by('-created_at')
def cases(self, collaborator=None, query=None, skip_assigned=False):
"""Fetches all cases from the backend.
Args:
collaborator(str): If collaborator should be considered
query(dict): If a specific query is used
Yields:
Cases ordered by date
"""
logger.info("Fetch all cases")
if collaborator:
logger.info("Use collaborator {0}".format(collaborator))
case_query = Case.objects(collaborators=collaborator)
else:
case_query = Case.objects
if query:
# filter if any user names match query
matching_users = User.objects(name__icontains=query)
# filter cases by matching display name of case or individuals
case_query = case_query.filter(
Q(display_name__icontains=query) |
Q(individuals__display_name__icontains=query) |
Q(assignee__in=matching_users)
)
if skip_assigned:
case_query = case_query.filter(assignee__exists=False)
return case_query.order_by('-updated_at')
def get_case(request):
logger.info("setup a case")
case = Case(
case_id="acase",
display_name="acase",
owner='cust000',
collaborators = ['cust000']
)
logger.info("Adding case to database")
case.save()
def teardown():
print('\n')
logger.info('Removing case')
case.delete()
logger.info('Case removed')
request.addfinalizer(teardown)
return case
def add_case(self, case_lines, case_type, owner, scout_configs={}):
"""Add a case to the database
If case exists in database it will be updated.
This method will take information in a ped like format and create
a case object. If the case is already in database it will update
the necessary information.
Args:
case_lines(Iterator): An iterator with the pedigree infromation
case_type(str): The format of the case lines
owner(str): The institute id for owner of the case
"""
logger.info("Setting up a family parser")
case_parser = FamilyParser(case_lines,
family_type=case_type)
if len(case_parser.families) != 1:
raise SyntaxError("Only one case per ped file is allowed")
case_id = list(case_parser.families.keys())[0]
logger.info("Found case {0}".format(case_id))
if not self.institute(institute_id=owner):
logger.warning("Institute {0} does not exist in database".format(
owner))
logger.info("Creating new institute")
self.add_institute(internal_id=owner, display_name=owner)
logger.info("Creating Case with id {0}".format(
'_'.join([owner, case_id])))
case = Case(
case_id='_'.join([owner, case_id]),
display_name=case_id,
owner=owner,
)
collaborators = scout_configs.get('collaborators') or set()
if collaborators:
if isinstance(collaborators, list):
collaborators = set(collaborators)
else:
collaborators = set([collaborators])
collaborators.add(owner)
case['collaborators'] = list(collaborators)
logger.debug("Setting collaborators to: {0}".format(
', '.join(collaborators)))
analysis_type = scout_configs.get('analysis_type', 'unknown').lower()
case['analysis_type'] = analysis_type
logger.debug("Setting analysis type to: {0}".format(analysis_type))
# Get the path of vcf from configs
vcf = scout_configs.get('igv_vcf', '')
case['vcf_file'] = vcf
logger.debug("Setting igv vcf file to: {0}".format(vcf))
# Add the genome build information
genome_build = scout_configs.get('human_genome_build', '')
case['genome_build'] = genome_build
logger.debug("Setting genome build to: {0}".format(genome_build))
# Get the genome version
genome_version = float(scout_configs.get('human_genome_version', '0'))
case['genome_version'] = genome_version
logger.debug("Setting genome version to: {0}".format(genome_version))
# Add the rank model version
rank_model_version = scout_configs.get('rank_model_version', '')
case['rank_model_version'] = rank_model_version
logger.debug("Setting rank model version to: {0}".format(
rank_model_version))
# Check the analysis date
analysis_date = scout_configs.get('analysis_date', '')
case['analysis_date'] = analysis_date
logger.debug("Setting analysis date to: {0}".format(analysis_date))
# Add the pedigree picture, this is a xml file that will be read and
# saved in the mongo database
madeline_path = path(scout_configs.get('madeline', '/__menoexist.tXt'))
if madeline_path.exists():
logger.debug("Found madeline info")
with madeline_path.open('r') as handle:
case['madeline_info'] = handle.read()
logger.debug("Madeline file was read succesfully")
else:
logger.info("No madeline file found. Skipping madeline file.")
# Add the coverage report
coverage_report_path = path(scout_configs.get('coverage_report', '/__menoexist.tXt'))
if coverage_report_path.exists():
logger.debug("Found a coverage report")
with coverage_report_path.open('rb') as handle:
case['coverage_report'] = handle.read()
logger.debug("Coverage was read succesfully")
else:
logger.info("No coverage report found. Skipping coverage report.")
individuals = []
# Add the individuals
for ind_id in case_parser.individuals:
ped_individual = case_parser.individuals[ind_id]
individual = Individual(
individual_id = ind_id,
father = ped_individual.father,
mother = ped_individual.mother,
display_name = ped_individual.extra_info.get(
'display_name', ind_id),
sex = str(ped_individual.sex),
phenotype = ped_individual.phenotype,
)
# Path to the bam file for IGV:
individual['bam_file'] = scout_configs.get(
'individuals',{}).get(
ind_id, {}).get(
'bam_path', '')
individual['capture_kits'] = scout_configs.get(
'individuals',{}).get(
ind_id, {}).get(
'capture_kit', [])
#Add affected individuals first
if ped_individual.affected:
logger.info("Adding individual {0} to case {1}".format(
ind_id, case_id))
case.individuals.append(individual)
else:
individuals.append(individual)
for individual in individuals:
logger.info("Adding individual {0} to case {1}".format(
individual.individual_id, case_id))
case.individuals.append(individual)
clinical_panels = []
research_panels = []
for gene_list in scout_configs.get('gene_lists', {}):
logger.info("Found gene list {0}".format(gene_list))
panel_info = scout_configs['gene_lists'][gene_list]
panel_path = panel_info.get('file')
panel_type = panel_info.get('type', 'clinical')
panel_date = panel_info.get('date')
panel_version = float(panel_info.get('version', '0'))
panel_id = panel_info.get('name')
display_name = panel_info.get('full_name', panel_id)
panel = get_gene_panel(
list_file_name=panel_path,
institute_id=owner,
panel_id=panel_id,
panel_version=panel_version,
display_name=display_name,
panel_date=panel_date)
logger.info("Store gene panel {0} in database".format(
panel.panel_name))
panel.save()
if panel_type == 'clinical':
logger.info("Adding {0} to clinical gene lists".format(
panel.panel_name))
clinical_panels.append(panel)
else:
logger.info("Adding {0} to research gene lists".format(
panel.panel_name))
research_panels.append(panel)
case['clinical_panels'] = clinical_panels
case['research_panels'] = research_panels
default_panels = scout_configs.get('default_panels', [])
logger.info("Adding {0} as default panels to case {1}".format(
', '.join(default_panels), case_id))
case['default_panels'] = list(default_panels)
#If the case exists we need tu update the information
if self.case(institute_id=owner, case_id=case_id):
case = self.update_case(case)
else:
logger.info("Adding case {0} to database".format(case_id))
case.save()
return case
def get_case(scout_configs, family_type):
"""
Take a case file and return the case on the specified format.
Only one case per pedigree file is allowed.
Args:
family_type : A string that describe the format of the ped file
scout_configs (dict): A dictionary scout info.
Returns:
case : A mongo engine object that describe the case
found in the pedigree file.
"""
logger = logging.getLogger(__name__)
# Use ped_parser to get information from the pedigree file
case_parser = FamilyParser(open(scout_configs['ped'], 'r'),
family_type=family_type)
# Check if there is a owner of the case
try:
owner = scout_configs['owner']
except KeyError as e:
logger.error("Scout config must include a owner")
raise e
# Check if there are any collaborators for the case, a case can belong to
# several institutes
collaborators = scout_configs.get('collaborators', None)
if collaborators:
collaborators = set(collaborators)
else:
collaborators = set()
collaborators.add(owner)
logger.info("Collaborators found: {0}".format(','.join(collaborators)))
logger.info("Cases found in ped file: {0}".format(
', '.join(list(case_parser.families.keys()))))
if len(case_parser.families) != 1:
raise SyntaxError("Only one case per ped file is allowed")
for case_id in case_parser.families:
case = case_parser.families[case_id]
# Create a mongo engine case
mongo_case_id = '_'.join([owner, case_id])
mongo_case = Case(case_id=mongo_case_id)
logger.debug("Setting case id to: {0}".format(mongo_case_id))
mongo_case['owner'] = owner
logger.debug("Setting owner to: {0}".format(owner))
mongo_case['collaborators'] = list(collaborators)
logger.debug("Setting collaborators to: {0}".format(
', '.join(collaborators)))
# We use the family id as display name for scout
mongo_case['display_name'] = case_id
logger.debug("Setting display name to: {0}".format(case_id))
# Get the path of vcf from configs
mongo_case['vcf_file'] = scout_configs.get('igv_vcf', '')
logger.debug("Setting igv vcf file to: {0}".format(
scout_configs.get('igv_vcf', '')))
# Add the genome build information
mongo_case['genome_build'] = scout_configs.get('human_genome_build', '')
logger.debug("Setting genome build to: {0}".format(
scout_configs.get('human_genome_build', '')))
# Get the genome version
mongo_case['genome_version'] = float(scout_configs.get('human_genome_version', '0'))
logger.debug("Setting genome version to: {0}".format(
scout_configs.get('human_genome_version', '0')))
# Check the analysis date
mongo_case['analysis_date'] = scout_configs.get('analysis_date', '')
logger.debug("Setting analysis date to: {0}".format(
scout_configs.get('analysis_date', '')))
# Add the pedigree picture, this is a xml file that will be read and
# saved in the mongo database
madeline_path = path(scout_configs.get('madeline', '/__menoexist.tXt'))
if madeline_path.exists():
logger.debug("Found madeline info")
with madeline_path.open('r') as handle:
mongo_case['madeline_info'] = handle.read()
logger.debug("Madeline file was read succesfully")
else:
logger.info("No madeline file found. Skipping madeline file.")
# Add the coverage report
coverage_report_path = path(scout_configs.get('coverage_report', '/__menoexist.tXt'))
if coverage_report_path.exists():
logger.debug("Found a coverage report")
with coverage_report_path.open('rb') as handle:
mongo_case['coverage_report'] = handle.read()
logger.debug("Coverage was read succesfully")
else:
logger.info("No coverage report found. Skipping coverage report.")
clinical_gene_lists = []
research_gene_lists = []
for gene_list in scout_configs.get('gene_lists', {}):
logger.info("Found gene list {0}".format(gene_list))
list_info = scout_configs['gene_lists'][gene_list]
list_type = list_info.get('type', 'clinical')
list_id = list_info.get('name', '')
version = float(list_info.get('version', 0))
date = list_info.get('date', '')
display_name = list_info.get('full_name', list_id)
list_object = GeneList(
list_id=list_id,
version=version,
date=date,
display_name=display_name
)
if list_type == 'clinical':
logger.info("Adding {0} to clinical gene lists".format(list_object))
clinical_gene_lists.append(list_object)
else:
logger.info("Adding {0} to research gene lists".format(list_object))
research_gene_lists.append(list_object)
mongo_case['clinical_gene_lists'] = clinical_gene_lists
mongo_case['research_gene_lists'] = research_gene_lists
default_gene_lists = scout_configs.get('default_gene_lists', [])
mongo_case['default_gene_lists'] = list(default_gene_lists)
individuals = []
for individual_id in case.individuals:
individual = case.individuals[individual_id]
# Get info from configs for the individual
config_info = scout_configs.get(
'individuals', {}
).get(
individual_id, {}
)
ind = Individual()
ind['individual_id'] = individual_id
ind['father'] = individual.father
ind['mother'] = individual.mother
ind['display_name'] = individual.extra_info.get('display_name', individual_id)
ind['sex'] = str(individual.sex)
ind['phenotype'] = individual.phenotype
# Path to the bam file for IGV:
ind['bam_file'] = config_info.get('bam_path', '')
ind['capture_kits'] = config_info.get('capture_kit', [])
individuals.append(ind)
mongo_case['individuals'] = individuals
