def validate(evaluation, canCancel, dry_run=False):
if type(evaluation) != Evaluation:
evaluation = syn.getEvaluation(evaluation)
print "\n\nValidating", evaluation.id, evaluation.name
print "-" * 60
sys.stdout.flush()
for submission, status in syn.getSubmissionBundles(evaluation, status='RECEIVED'):
## refetch the submission so that we get the file path
## to be later replaced by a "downloadFiles" flag on getSubmissionBundles
submission = syn.getSubmission(submission)
ex1 = None #Must define ex1 in case there is no error
print "validating", submission.id, submission.name
try:
is_valid, validation_message = conf.validate_submission(evaluation, submission)
except Exception as ex1:
is_valid = False
print "Exception during validation:", type(ex1), ex1, ex1.message
traceback.print_exc()
validation_message = str(ex1)
status.status = "VALIDATED" if is_valid else "INVALID"
if canCancel:
status.canCancel = True
if not is_valid:
failure_reason = {"FAILURE_REASON":validation_message}
else:
failure_reason = {"FAILURE_REASON":''}
add_annotations = synapseclient.annotations.to_submission_status_annotations(failure_reason,is_private=True)
status = update_single_submission_status(status, add_annotations)
if not dry_run:
status = syn.store(status)
## send message AFTER storing status to ensure we don't get repeat messages
profile = syn.getUserProfile(submission.userId)
if is_valid:
messages.validation_passed(
userIds=[submission.userId],
username=get_user_name(profile),
queue_name=evaluation.name,
submission_id=submission.id,
submission_name=submission.name)
else:
if isinstance(ex1, AssertionError):
sendTo = [submission.userId]
username = get_user_name(profile)
else:
sendTo = conf.ADMIN_USER_IDS
username = "******"
messages.validation_failed(
userIds= sendTo,
username=username,
queue_name=evaluation.name,
submission_id=submission.id,
submission_name=submission.name,
message=validation_message)
def validate(evaluation, token, dry_run=False):
if type(evaluation) != Evaluation:
evaluation = syn.getEvaluation(evaluation)
print "\n\nValidating", evaluation.id, evaluation.name
print "-" * 60
sys.stdout.flush()
for submission, status in syn.getSubmissionBundles(evaluation, status='RECEIVED'):
## refetch the submission so that we get the file path
## to be later replaced by a "downloadFiles" flag on getSubmissionBundles
sub = json.loads(submission['entityBundleJSON'])
if len(sub['fileHandles']) == 0:
submission = syn.getSubmission(submission)
else:
if sub['fileHandles'][0].get('externalURL') is None:
submission = syn.getSubmission(submission)
else:
submission = syn.getSubmission(submission,downloadFile=False)
print "validating", submission.id, submission.name
try:
is_valid, validation_message = conf.validate_submission(evaluation, submission, token)
except Exception as ex1:
is_valid = False
print "Exception during validation:", type(ex1), ex1, ex1.message
traceback.print_exc()
validation_message = str(ex1)
status.status = "VALIDATED" if is_valid else "INVALID"
if not dry_run:
status = syn.store(status)
## send message AFTER storing status to ensure we don't get repeat messages
profile = syn.getUserProfile(submission.userId)
if is_valid:
messages.validation_passed(
userIds=[submission.userId],
username=get_user_name(profile),
queue_name=evaluation.name,
submission_id=submission.id,
submission_name=submission.name)
else:
messages.validation_failed(
userIds=[submission.userId],
username=get_user_name(profile),
queue_name=evaluation.name,
submission_id=submission.id,
submission_name=submission.name,
message=validation_message)
def validate(evaluation, token, dry_run=False):
if type(evaluation) != Evaluation:
evaluation = syn.getEvaluation(evaluation)
print "\n\nValidating", evaluation.id, evaluation.name
print "-" * 60
sys.stdout.flush()
for submission, status in syn.getSubmissionBundles(evaluation,
status='RECEIVED'):
## refetch the submission so that we get the file path
## to be later replaced by a "downloadFiles" flag on getSubmissionBundles
sub = json.loads(submission['entityBundleJSON'])
if len(sub['fileHandles']) == 0:
submission = syn.getSubmission(submission)
else:
if sub['fileHandles'][0].get('externalURL') is None:
submission = syn.getSubmission(submission)
else:
submission = syn.getSubmission(submission, downloadFile=False)
print "validating", submission.id, submission.name
try:
is_valid, validation_message = conf.validate_submission(
evaluation, submission, token)
except Exception as ex1:
is_valid = False
print "Exception during validation:", type(ex1), ex1, ex1.message
traceback.print_exc()
validation_message = str(ex1)
status.status = "VALIDATED" if is_valid else "INVALID"
if not dry_run:
status = syn.store(status)
## send message AFTER storing status to ensure we don't get repeat messages
profile = syn.getUserProfile(submission.userId)
if is_valid:
messages.validation_passed(userIds=[submission.userId],
username=get_user_name(profile),
queue_name=evaluation.name,
submission_id=submission.id,
submission_name=submission.name)
else:
messages.validation_failed(userIds=[submission.userId],
username=get_user_name(profile),
queue_name=evaluation.name,
submission_id=submission.id,
submission_name=submission.name,
message=validation_message)
def validate(evaluation, dry_run=False):
if type(evaluation) != Evaluation:
evaluation = syn.getEvaluation(evaluation)
print "\n\nValidating", evaluation.id, evaluation.name
print "-" * 60
sys.stdout.flush()
for submission, status in syn.getSubmissionBundles(evaluation, status='RECEIVED'):
## refetch the submission so that we get the file path
## to be later replaced by a "downloadFiles" flag on getSubmissionBundles
submission = syn.getSubmission(submission)
print "validating", submission.id, submission.name
try:
is_valid, validation_message = conf.validate_submission(evaluation, submission)
except Exception as ex1:
is_valid = False
validation_message = str(ex1)
status.status = "VALIDATED" if is_valid else "INVALID"
if not dry_run:
status = syn.store(status)
## send message AFTER storing status to ensure we don't get repeat messages
profile = syn.getUserProfile(submission.userId)
if is_valid:
messages.validation_passed(
userIds=[submission.userId],
username=get_user_name(profile),
queue_name=evaluation.name,
submission_id=submission.id,
submission_name=submission.name)
else:
messages.validation_failed(
userIds=[submission.userId],
username=get_user_name(profile),
queue_name=evaluation.name,
submission_id=submission.id,
submission_name=submission.name,
message=validation_message)
def validate(evaluation, dry_run=False):
if type(evaluation) != Evaluation:
evaluation = syn.getEvaluation(evaluation)
print "\n\nValidating", evaluation.id, evaluation.name
print "-" * 60
sys.stdout.flush()
for submission, status in syn.getSubmissionBundles(evaluation,
status='RECEIVED'):
## refetch the submission so that we get the file path
## to be later replaced by a "downloadFiles" flag on getSubmissionBundles
submission = syn.getSubmission(submission)
print "validating", submission.id, submission.name
try:
is_valid, validation_message = conf.validate_submission(
evaluation, submission)
except Exception as ex1:
is_valid = False
validation_message = str(ex1)
status.status = "VALIDATED" if is_valid else "INVALID"
if not dry_run:
status = syn.store(status)
## send message AFTER storing status to ensure we don't get repeat messages
profile = syn.getUserProfile(submission.userId)
if is_valid:
messages.validation_passed(userIds=[submission.userId],
username=get_user_name(profile),
queue_name=evaluation.name,
submission_id=submission.id,
submission_name=submission.name)
else:
messages.validation_failed(userIds=[submission.userId],
username=get_user_name(profile),
queue_name=evaluation.name,
submission_id=submission.id,
submission_name=submission.name,
message=validation_message)
def validate(evaluation, canCancel, dry_run=False):
if type(evaluation) != Evaluation:
evaluation = syn.getEvaluation(evaluation)
print "\n\nValidating", evaluation.id, evaluation.name
print "-" * 60
sys.stdout.flush()
team_mapping_table = syn.tableQuery('select * from syn8220615')
team_mapping = team_mapping_table.asDataFrame()
#metadataPath = syn.get("syn8371011").path
#metadata = pd.read_csv(metadataPath)
#patientIds = set(metadata.patientId)
#HLA = metadata[['patientId','classIHLAalleles']][~metadata['classIHLAalleles'].isnull()]
metadataTable = syn.tableQuery('SELECT * FROM syn8292741')
metadata = metadataTable.asDataFrame()
HLA = metadata[['patientId','classIHLAalleles']][~metadata['classIHLAalleles'].isnull()]
HLA.drop_duplicates("classIHLAalleles",inplace=True)
patientIds = set(metadata['patientId'][~metadata['patientId'].isnull()].apply(int))
for submission, status in syn.getSubmissionBundles(evaluation, status='RECEIVED'):
## refetch the submission so that we get the file path
## to be later replaced by a "downloadFiles" flag on getSubmissionBundles
submission = syn.getSubmission(submission,downloadFile=False)
ex1 = None #Must define ex1 in case there is no error
print "validating", submission.id, submission.name
addAnnots = {}
try:
is_valid, validation_message, addAnnots = conf.validate_teamname(syn, evaluation, submission, team_mapping)
add_annotations = synapseclient.annotations.to_submission_status_annotations(addAnnots,is_private=True)
status = update_single_submission_status(status, add_annotations)
is_valid, validation_message, patientAnnot = conf.validate_submission(syn, evaluation, submission, patientIds, HLA)
addAnnots.update(patientAnnot)
except Exception as ex1:
is_valid = False
print "Exception during validation:", type(ex1), ex1, ex1.message
traceback.print_exc()
validation_message = str(ex1)
status.status = "VALIDATED" if is_valid else "INVALID"
if canCancel:
status.canCancel = True
if not is_valid:
#UPDATE ROUND NUMBER
addAnnots.update({"FAILURE_REASON":validation_message[0:1000], "round":'2'})
else:
#UPDATE ROUND NUMBER
addAnnots.update({"FAILURE_REASON":'',
"submissionName":submission.entity.name, "round":'2'})
uniqueId = randomString()
addAnnots.update({"uniqueId":uniqueId})
add_annotations = synapseclient.annotations.to_submission_status_annotations(addAnnots,is_private=False)
status = update_single_submission_status(status, add_annotations)
if not dry_run:
status = syn.store(status)
## send message AFTER storing status to ensure we don't get repeat messages
profile = syn.getUserProfile(submission.userId)
if is_valid:
messages.validation_passed(
userIds=[submission.userId],
username=get_user_name(profile),
queue_name=evaluation.name,
submission_id=uniqueId,
submission_name=submission.name)
else:
if isinstance(ex1, AssertionError):
sendTo = [submission.userId]
username = get_user_name(profile)
else:
sendTo = conf.ADMIN_USER_IDS
username = "******"
messages.validation_failed(
userIds= sendTo,
username=username,
queue_name=evaluation.name,
submission_id=uniqueId,
submission_name=submission.name,
message=validation_message)
def validate(evaluation, public=False, admin=None, dry_run=False):
if type(evaluation) != Evaluation:
evaluation = syn.getEvaluation(evaluation)
print("\n\nValidating", evaluation.id, evaluation.name)
print("-" * 60)
sys.stdout.flush()
if admin is not None:
try:
admin = syn.getUserProfile(admin)['userName']
except Exception as ex1:
admin = syn.getTeam(admin)['name']
for submission, status in syn.getSubmissionBundles(evaluation, status='RECEIVED'):
ex1 = None #Must define ex1 in case there is no error
print("validating", submission.id, submission.name)
try:
is_valid, validation_message = conf.validate_submission(syn, evaluation, submission, public=public, admin=admin)
except Exception as ex1:
is_valid = False
print("Exception during validation:", type(ex1), ex1, str(ex1))
traceback.print_exc()
validation_error = ex1
validation_message = str(ex1)
addannotations = {}
#Add team name
if 'teamId' in submission:
team = syn.restGET('/team/{id}'.format(id=submission.teamId))
if 'name' in team:
addannotations['team'] = team['name']
else:
addannotations['team'] = submission.teamId
elif 'userId' in submission:
profile = syn.getUserProfile(submission.userId)
addannotations['team'] = get_user_name(profile)
else:
addannotations['team'] = '?'
status.status = "VALIDATED" if is_valid else "INVALID"
if not is_valid:
addannotations["FAILURE_REASON"] = validation_message
else:
addannotations["FAILURE_REASON"] = ''
add_annotations = synapseclient.annotations.to_submission_status_annotations(addannotations,is_private=True)
status = update_single_submission_status(status, add_annotations)
if not dry_run:
status = syn.store(status)
## send message AFTER storing status to ensure we don't get repeat messages
profile = syn.getUserProfile(submission.userId)
if is_valid:
messages.validation_passed(
userIds=[submission.userId],
username=get_user_name(profile),
queue_name=evaluation.name,
submission_id=submission.id,
submission_name=submission.name)
else:
if isinstance(validation_error, AssertionError):
sendTo = [submission.userId]
username = get_user_name(profile)
else:
sendTo = conf.ADMIN_USER_IDS
username = "******"
messages.validation_failed(
userIds= sendTo,
username=username,
queue_name=evaluation.name,
submission_id=submission.id,
submission_name=submission.name,
message=validation_message)
