def test_json_for_gene(self):
gene = GeneInfo.objects.get(id=1)
json = get_json_for_gene(gene)
fields = {
'chromGrch37',
'chromGrch38',
'codingRegionSizeGrch37',
'codingRegionSizeGrch38',
'endGrch37',
'endGrch38',
'gencodeGeneType',
'geneId',
'geneSymbol',
'startGrch37',
'startGrch38',
}
self.assertSetEqual(set(json.keys()), fields)
user = User.objects.filter().first()
json = get_json_for_gene(gene,
user=user,
add_dbnsfp=True,
add_omim=True,
add_constraints=True,
add_notes=True,
add_expression=True)
fields.update({
'constraints', 'diseaseDesc', 'expression', 'functionDesc',
'notes', 'omimPhenotypes'
})
self.assertSetEqual(set(json.keys()), fields)
def test_json_for_gene(self):
gene = GeneInfo.objects.get(id=1)
json = get_json_for_gene(gene)
self.assertSetEqual(set(json.keys()), GENE_FIELDS)
user = User.objects.filter().first()
json = get_json_for_gene(gene,
user=user,
add_dbnsfp=True,
add_omim=True,
add_constraints=True,
add_notes=True,
add_primate_ai=True)
fields = {'primateAi'}
fields.update(GENE_DETAIL_FIELDS)
fields.remove('mgiMarkerId')
self.assertSetEqual(set(json.keys()), fields)
def test_json_for_gene(self):
gene = GeneInfo.objects.get(id=1)
json = get_json_for_gene(gene)
fields = {
'chromGrch37', 'chromGrch38', 'codingRegionSizeGrch37', 'codingRegionSizeGrch38', 'endGrch37', 'endGrch38',
'gencodeGeneType', 'geneId', 'geneSymbol', 'startGrch37', 'startGrch38',
}
self.assertSetEqual(set(json.keys()), fields)
user = User.objects.filter().first()
json = get_json_for_gene(
gene, user=user, add_dbnsfp=True, add_omim=True, add_constraints=True, add_notes=True, add_expression=True,
add_primate_ai=True)
fields.update({
'constraints', 'diseaseDesc', 'expression', 'functionDesc', 'notes', 'omimPhenotypes', 'mimNumber', 'primateAi'
})
self.assertSetEqual(set(json.keys()), fields)
def get_gene(gene_id, user):
gene = GeneInfo.objects.get(gene_id=gene_id)
gene_json = get_json_for_gene(gene,
user=user,
add_dbnsfp=True,
add_omim=True,
add_constraints=True,
add_notes=True,
add_mgi=True)
return gene_json
