def add_case(self, case_obj, vtype='snv', mode='vcf', ped_svg=None):
"""Load a case with individuals.
Args:
case_obj (puzzle.models.Case): initialized case model
"""
new_case = Case(case_id=case_obj['case_id'],
name=case_obj['name'],
variant_source=case_obj['variant_source'],
variant_type=vtype,
variant_mode=mode,
pedigree=ped_svg)
# build individuals
inds = [Individual(
ind_id=ind['ind_id'],
mother=ind['mother'],
father=ind['father'],
sex=ind['sex'],
phenotype=ind['phenotype'],
ind_index=ind['index'],
variant_source=ind['variant_source'],
bam_path=ind['bam_path'],
) for ind in case_obj['individuals']]
new_case.individuals = inds
self.session.add(new_case)
self.save()
return new_case
def add_case(self, case_obj, vtype='snv', mode='vcf', ped_svg=None):
"""Load a case with individuals.
Args:
case_obj (puzzle.models.Case): initialized case model
"""
new_case = Case(case_id=case_obj.case_id,
name=case_obj.name,
variant_source=case_obj.variant_source,
variant_type=vtype,
variant_mode=mode,
pedigree=ped_svg)
# build individuals
inds = [Individual(
ind_id=ind.ind_id,
name=ind.name,
mother=ind.mother,
father=ind.father,
sex=ind.sex,
phenotype=ind.phenotype,
ind_index=ind.ind_index,
variant_source=ind.variant_source,
bam_path=ind.bam_path,
) for ind in case_obj.individuals]
new_case.individuals = inds
self.session.add(new_case)
self.save()
return new_case
def add_case(self, case_obj, vtype="snv", mode="vcf", ped_svg=None):
"""Load a case with individuals.
Args:
case_obj (puzzle.models.Case): initialized case model
"""
new_case = Case(
case_id=case_obj["case_id"],
name=case_obj["name"],
variant_source=case_obj["variant_source"],
variant_type=vtype,
variant_mode=mode,
pedigree=ped_svg,
)
# build individuals
inds = [
Individual(
ind_id=ind["ind_id"],
mother=ind["mother"],
father=ind["father"],
sex=ind["sex"],
phenotype=ind["phenotype"],
ind_index=ind["index"],
variant_source=ind["variant_source"],
bam_path=ind["bam_path"],
)
for ind in case_obj["individuals"]
]
new_case.individuals = inds
self.session.add(new_case)
self.save()
return new_case
def add_case(self, case_obj, vtype='snv', mode='vcf', ped_svg=None):
"""Load a case with individuals.
Args:
case_obj (puzzle.models.Case): initialized case model
"""
new_case = Case(case_id=case_obj.case_id,
name=case_obj.name,
variant_source=case_obj.variant_source,
variant_type=vtype,
variant_mode=mode,
pedigree=ped_svg,
compressed=case_obj.compressed,
tabix_index=case_obj.tabix_index)
# build individuals
inds = [Individual(
ind_id=ind.ind_id,
name=ind.name,
mother=ind.mother,
father=ind.father,
sex=ind.sex,
phenotype=ind.phenotype,
ind_index=ind.ind_index,
variant_source=ind.variant_source,
bam_path=ind.bam_path,
) for ind in case_obj.individuals]
new_case.individuals = inds
if self.case(new_case.case_id):
logger.warning("Case already exists in database!")
else:
self.session.add(new_case)
self.save()
return new_case
def add_case():
"""Make a new case out of a list of individuals."""
ind_ids = request.form.getlist('ind_id')
case_id = request.form['case_id']
source = request.form['source']
variant_type = request.form['type']
if len(ind_ids) == 0:
return abort(400, "must add at least one member of case")
# only GEMINI supported
new_case = Case(case_id=case_id,
name=case_id,
variant_source=source,
variant_type=variant_type,
variant_mode='gemini')
# Add individuals to the correct case
for ind_id in ind_ids:
ind_obj = app.db.individual(ind_id)
new_case.individuals.append(ind_obj)
app.db.session.add(new_case)
app.db.save()
return redirect(url_for('.case', case_id=new_case.name))
def test_case(session):
"""Test to add a case to the session"""
# proband = Individual(ind_id="Proband")
family = Case(case_id="afamily")
# proband.case = family
session.add(family)
session.commit()
fam = session.query(Case).filter(Case.case_id == "afamily").one()
assert fam.id == 1
def test_individual(session):
"""Test to add a case to the session"""
# proband = Individual(ind_id="Proband")
family = Case(case_id="2")
proband = Individual(ind_id="Proband")
proband.cases.append(family)
session.add(proband)
session.add(family)
session.commit()
fam = session.query(Case).filter(Case.case_id == "2").one()
assert fam.individuals[0].ind_id == "Proband"
def add_case(self, case_obj, vtype='snv', mode='vcf', ped_svg=None):
"""Load a case with individuals.
Args:
case_obj (puzzle.models.Case): initialized case model
"""
new_case = Case(case_id=case_obj.case_id,
name=case_obj.name,
variant_source=case_obj.variant_source,
variant_type=vtype,
variant_mode=mode,
pedigree=ped_svg,
compressed=case_obj.compressed,
tabix_index=case_obj.tabix_index)
# build individuals
inds = [
Individual(
ind_id=ind.ind_id,
name=ind.name,
mother=ind.mother,
father=ind.father,
sex=ind.sex,
phenotype=ind.phenotype,
ind_index=ind.ind_index,
variant_source=ind.variant_source,
bam_path=ind.bam_path,
) for ind in case_obj.individuals
]
new_case.individuals = inds
if self.case(new_case.case_id):
logger.warning("Case already exists in database!")
else:
self.session.add(new_case)
self.save()
return new_case
