def f(session):
feature = get_first(Feature, session, name=name.upper())
if feature is not None and not feature.type == "chromosome":
return feature
feature = get_first(Feature, session, gene_name=name.upper())
if feature is not None:
return feature
feature = session.query(Feature).filter(Feature.alias_names.contains(name.upper())).first()
if feature is not None:
return feature
return None
def f(session):
from model_old_schema.reference import RefTemp
#Move ref to reftemp and test that move was successful.
result = move_ref_to_reftemp(pubmed_id, session)
self.assertTrue(result)
#Test that new ref is valid.
reftemp = get_first(RefTemp, pubmed_id=pubmed_id)
test_validity(self, reftemp, validate_reftemp, session=session, pubmed_id=pubmed_id)
def f(session):
ref = get_first(Reference, session, pubmed_id=pubmed_id)
if ref is None:
raise RefDoesNotExistException(pubmed_id)
reftemp = RefTemp.as_unique(session, pubmed_id=pubmed_id)
session.add(reftemp)
session.delete(ref)
return True
def f(session):
reftemp = get_first(RefTemp, session, pubmed_id=pubmed_id)
if reftemp is None:
raise RefDoesNotExistException(pubmed_id)
refbad = RefBad.as_unique(session, pubmed_id=pubmed_id)
session.add(refbad)
session.delete(reftemp)
return True
def f(session):
from model_old_schema.reference import Reference
ref = get_first(Reference, session, pubmed_id=pmid)
message = "RefCurations:<br>"
for curation in ref.curations:
message = message + str(curation) + ", "
message = message + "<br>LitGuides:<br>"
for lit_guide in ref.litGuides:
message = message + str(lit_guide) + ", "
return message
def f(session):
reftemp = get_first(RefTemp, session, pubmed_id=pubmed_id)
log_it('got_reftemp', 'SUCCESS')
if reftemp is None:
raise RefDoesNotExistException(pubmed_id)
ref = Reference(session, pubmed_id=pubmed_id)
log_it('created reference', 'SUCCESS')
session.add(ref)
session.delete(reftemp)
log_it('adjusted session', 'SUCCESS')
return True
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):
word_to_feature = {}
features = []
r = get_first(RefTemp, pubmed_id=pubmed_id, session=session)
a = str(r.abstract).lower().translate(string.maketrans("", ""), string.punctuation)
words = a.split()
for word in words:
if not word in word_to_feature and not is_number(word):
f = get_feature_by_name(word, session)
word_to_feature[word] = f
if f is not None and not f.type == "chromosome":
features.append(f)
return features
def f(session):
reference = get_first(Reference, session, pubmed_id=pubmed_id)
for task in tasks:
gene_names = task.gene_names
if gene_names is not None and len(gene_names) > 0:
#Convert gene_names to features using the name_to_feature table.
features = set()
for gene_name in task.gene_names:
features.add(name_to_feature[gene_name.upper()])
## Create RefCuration objects and add them to the Reference.
for feature in features:
if task.ref_curation_name is not None:
curation = RefCuration.as_unique(session, reference_id=reference.id, task=task.ref_curation_name, feature_id=feature.id)
curation.comment = task.comment
reference.curations.append(curation)
## Create a LitGuide object and attach features to it.
lit_guide = LitGuide.as_unique(session, topic=task.topic, reference_id=reference.id)
for feature in features:
if not feature.id in lit_guide.feature_ids:
lit_guide.features.append(feature)
reference.litGuides.append(lit_guide)
else: ## no gene name provided
## if no gene name provided and "Reviews" was checked,
## no need to add any association
if task.type != TaskType.REVIEWS:
curation = RefCuration.as_unique(session, task=task.ref_curation_name, reference_id=reference.id, feature_id=None)
curation.comment = task.comment
reference.curations.append(curation)
## Create a LitGuide object.
if task.type == TaskType.HTP_PHENOTYPE_DATA or task.type == TaskType.OTHER_HTP_DATA or task.type == TaskType.REVIEWS:
lit_guide = LitGuide.as_unique(session, topic=task.topic, reference_id=reference.id)
reference.litGuides.append(lit_guide)
return True
def f(session):
from model_old_schema.reference import Reference
ref = get_first(Reference, session, pubmed_id=pmid)
curations = ref.curations
curation_summary = []
for curation in curations:
if curation.feature is None:
feature_name = '-'
elif curation.feature.gene_name is None:
feature_name = curation.feature.name
else:
feature_name = curation.feature.gene_name
if curation.comment is None:
comment = '-'
else:
comment = curation.comment
curation_summary.append({'task':curation.task, 'feature':feature_name, 'comment':comment})
litguides = ref.litGuides
litguide_summary = []
for litguide in litguides:
feature_names = []
for feature in litguide.features:
if feature.gene_name is None:
feature_names.append(feature.name)
else:
feature_names.append(feature.gene_name)
litguide_summary.append({'topic':litguide.topic, 'features': ', '.join(feature_names)})
ref_summary = {'curations':curation_summary, 'litguides':litguide_summary, 'message':"Reference for pmid = " + pmid + " has been added into the database and associated with the following data:",
'curationlink':'http://pastry.stanford.edu/cgi-bin/curation/litGuideCuration?user='******'&ref=' + pmid,
'sgdlink':'http://pastry.stanford.edu/cgi-bin/reference/reference.pl?dbid=' + ref.dbxref_id}
return json.dumps(ref_summary)
def f(session):
r = get_first(RefTemp, pubmed_id=pubmed_id, session=session)
a = str(r.abstract).lower().translate(string.maketrans("",""), string.punctuation)
words = [word.upper() for word in a.split()]
return validate_genes(words, session=session)
def test_get_ref(self, pubmed_id=1986222, ref_id=84):
from model_old_schema.reference import Reference
ref = get_first(Reference, id=ref_id)
self.model.execute(test_validity(self, ref, validate_ref, ref_id=ref_id))
def test_get_refbad(self, pubmed_id=16998476):
from model_old_schema.reference import RefBad
refbad = get_first(RefBad, pubmed_id=pubmed_id)
self.model.execute(test_validity(self, refbad, validate_refbad, pubmed_id=pubmed_id))
def test_get_reftemp(self, reftemp_id=81007, pubmed_id=23125886):
from model_old_schema.reference import RefTemp
reftemp = get_first(RefTemp, id=reftemp_id)
self.model.execute(test_validity(self, reftemp, validate_reftemp, reftemp_id=reftemp_id, pubmed_id=pubmed_id))
def test_get_feature(self, feature_id=1971, feature_name='yjl001W'):
from model_old_schema.feature import Feature
f = get_first(Feature, id=feature_id)
self.model.execute(test_validity(self, f, validate_feature, feature_id=feature_id, feature_name=feature_name))
