def f(session):
log_it('validate_genes', 'BEGIN')
all_gene_names = set()
for task in tasks:
all_gene_names.update([gene_name.upper() for gene_name in task.gene_names])
genes = validate_genes(all_gene_names, session)
log_it('validate_genes', 'SUCCESS')
log_it('move_reftemp_to_ref', 'BEGIN')
#If some of the gene names are aliases or are just not gene names, throw an exception.
if len(genes['aliases']) > 0 or len(genes['not_genes']) > 0:
raise GeneNamesNotFountException(genes['alias_message'], genes['not_genes_message'])
#Move reftemp to ref table. Raise an exception if something goes wrong.
moved = move_reftemp_to_ref(pmid, session)
if not moved:
raise ReferenceNotMovedException(pmid)
log_it('move_reftemp_to_ref', 'SUCCESS')
log_it('associate', 'BEGIN')
#Associate reference with LitGuide and RefCuration objects. Raise an exception if something goes wrong.
associated = associate(pmid, genes['features'], tasks, session)
if not associated:
raise AssociateException(pmid)
return True
log_it('associate', 'SUCCESS')
def test_validate_genes(self):
gene_names = ['YAL002W', 'CEN1', 'SPO7', 'YAL016C-B', 'YAL009W']
feature_ids = [6102, 2899, 6347, 7398, 6347]
name_to_feature = self.model.execute(validate_genes(gene_names))
self.assertEqual(len(gene_names), len(name_to_feature))
for i in range(0, len(gene_names)):
self.assertEqual(name_to_feature[gene_names[i]].id, feature_ids[i])
def f(session):
pubmed_id = 23105524
gene_names = ['ACT1', 'CEN1', 'SPO7', 'YAL016C-B', 'YAL009W']
from model_old_schema.reference import Reference
move_reftemp_to_ref(pubmed_id, session=session)
name_to_feature = self.model.execute(validate_genes(gene_names))
tasks = [Task(TaskType.HIGH_PRIORITY, None, "Comment"),
Task(TaskType.DELAY, None, "Comment"),
Task(TaskType.HTP_PHENOTYPE_DATA, None, "Comment"),
Task(TaskType.OTHER_HTP_DATA, None, "Comment"),
Task(TaskType.CLASSICAL_PHENOTYPE_INFORMATION, ['ACT1'], "Comment"),
Task(TaskType.GO_INFORMATION, ['ACT1'], "Comment"),
Task(TaskType.HEADLINE_INFORMATION, ['YAL009W', 'YAL016C-B'], "Comment"),
Task(TaskType.ADDITIONAL_LITERATURE, None, "Comment"),
Task(TaskType.REVIEWS, None, "Comment")
]
result = associate(pubmed_id, name_to_feature, tasks, session=session)
self.assertTrue(result)
curations = get_first(Reference, session=session, pubmed_id=pubmed_id).curations
lit_guides = get_first(Reference, session=session, pubmed_id=pubmed_id).litGuides
self.assertEqual(len(curations), 9)
for curation in curations:
self.assertTrue(curation.comment is not None)
if curation.task == 'Gene Link':
self.assertTrue(False, 'The two Tasks with name Gene Link: ADD_TO_DATABASE and REVIEWS have no genes. They should not have curaitons.')
self.assertEqual(len(lit_guides), 6)
for lit_guide in lit_guides:
if curation.task == 'Reviews':
self.assertEqual(len(lit_guide.features), 0)
def f(session):
all_gene_names = set()
for task in tasks:
all_gene_names.update(task.gene_names)
name_to_feature = validate_genes(all_gene_names, session)
#If we don't get back as many features as we have gene names, find the bad ones and raise an exception.
if len(name_to_feature) < len(all_gene_names):
bad_gene_names = set(all_gene_names) - set(name_to_feature.keys())
raise GeneNamesNotFountException(bad_gene_names)
#Move reftemp to ref table. Raise an exception if something goes wrong.
moved = move_reftemp_to_ref(pmid, session)
if not moved:
raise ReferenceNotMovedException(pmid)
#Associate reference with LitGuide and RefCuration objects. Raise an exception if something goes wrong.
associated = associate(pmid, name_to_feature, tasks, session)
if not associated:
raise AssociateException(pmid)
return True
