def phenotypes():
"""Add phenotype(s) to the case model."""
ind_id = request.form['ind_id']
phenotype_id = request.form['phenotype_id']
if not phenotype_id:
return abort(500, 'no phenotype_id submitted')
ind_obj = app.db.individual(ind_id)
terms_added = app.db.add_phenotype(ind_obj, phenotype_id)
if len(terms_added) > 0:
# update the HPO gene list for the case
hpo_list = app.db.case_genelist(ind_obj.case)
hpo_results = hpo_genes(ind_obj.case.phenotype_ids())
if hpo_results is None:
return abort(500, "couldn't link to genes, try again"
.format(phenotype_id))
gene_ids = [result['gene_id'] for result in hpo_results
if result['gene_id']]
hpo_list.gene_ids = gene_ids
app.db.save()
return redirect(request.referrer)
def update_hpolist(self, case_obj):
"""Update the HPO gene list for a case based on current terms."""
hpo_list = self.case_genelist(case_obj)
hpo_results = hpo_genes(case_obj.phenotype_ids(),
*self.phenomizer_auth)
if hpo_results is None:
pass
# Why raise here?
# raise RuntimeError("couldn't link to genes, try again")
else:
gene_ids = [result['gene_id'] for result in hpo_results
if result['gene_id']]
hpo_list.gene_ids = gene_ids
self.save()
def update_hpolist(self, ind_id):
"""Update the HPO gene list for a case based on current terms."""
ind_obj = self.individual(ind_id)
# update the HPO gene list for the case
hpo_list = self.case_genelist(ind_obj.case)
hpo_results = hpo_genes(ind_obj.case.phenotype_ids())
if hpo_results is None:
pass
#Why raise here?
# raise RuntimeError("couldn't link to genes, try again")
else:
gene_ids = [result['gene_id'] for result in hpo_results
if result['gene_id']]
hpo_list.gene_ids = gene_ids
self.save()
def update_hpolist(self, case_obj):
"""Update the HPO gene list for a case based on current terms."""
hpo_list = self.case_genelist(case_obj)
hpo_results = hpo_genes(case_obj.phenotype_ids(),
*self.phenomizer_auth)
if hpo_results is None:
pass
# Why raise here?
# raise RuntimeError("couldn't link to genes, try again")
else:
gene_ids = [
result['gene_id'] for result in hpo_results
if result['gene_id']
]
hpo_list.gene_ids = gene_ids
self.save()