def test_teams(syn, project, schedule_for_cleanup):
name = "My Uniquely Named Team " + str(uuid.uuid4())
team = syn.store(Team(name=name, description="A fake team for testing..."))
schedule_for_cleanup(team)
# not logged in, teams are public
anonymous_syn = Synapse()
found_team = anonymous_syn.getTeam(team.id)
assert team == found_team
p = syn.getUserProfile()
found = None
for m in anonymous_syn.getTeamMembers(team):
if m.member.ownerId == p.ownerId:
found = m
break
assert found is not None, "Couldn't find user {} in team".format(
p.userName)
# needs to be retried 'cause appending to the search index is asynchronous
tries = 8
sleep_time = 1
found_team = None
while tries > 0:
try:
found_team = anonymous_syn.getTeam(name)
break
except ValueError:
tries -= 1
if tries > 0:
time.sleep(sleep_time)
sleep_time *= 2
assert team == found_team
def test_teams(syn):
unique_name = "Team Gnarly Rad " + str(uuid.uuid4())
team = Team(name=unique_name,
description="A gnarly rad team",
canPublicJoin=True)
team = syn.store(team)
team2 = syn.getTeam(team.id)
assert team == team2
# Asynchronously populates index, so wait 'til it's there
retry = 0
backoff = 0.2
while retry < 10:
retry += 1
time.sleep(backoff)
backoff *= 2
found_teams = list(syn._findTeam(team.name))
if len(found_teams) > 0:
break
else:
print("Failed to create team. May not be a real error.")
syn.delete(team)
assert team == found_teams[0]
def find_objects(uuid):
"""Based on the given UUID (as a string), find demo artifacts"""
found_objects = {}
results = list(
syn.chunkedQuery('select id from project where project.name == "%s"' %
(CHALLENGE_PROJECT_NAME + " " + uuid)))
if results:
found_objects['challenge_project'] = syn.get(results[0]['project.id'])
results = list(
syn.chunkedQuery('select id from project where project.name == "%s"' %
(PARTICIPANT_PROJECT_NAME + " " + uuid)))
if results:
found_objects['participant_project'] = syn.get(
results[0]['project.id'])
response = syn.restGET("/teams?fragment=" +
urllib.quote(CHALLENGE_PROJECT_NAME + " " + uuid +
" Participants"))
if len(response['results']) > 0:
found_objects['participants_team'] = Team(**response['results'][0])
else:
warnings.warn("Couldn't find team: %s" %
(CHALLENGE_PROJECT_NAME + " " + uuid + " Participants"))
response = syn.restGET("/teams?fragment=" +
urllib.quote(CHALLENGE_PROJECT_NAME + " " + uuid +
" Administrators"))
if len(response['results']) > 0:
found_objects['admin_team'] = Team(**response['results'][0])
else:
warnings.warn(
"Couldn't find team: %s" %
(CHALLENGE_PROJECT_NAME + " " + uuid + " Administrators"))
response = syn.restGET("/teams?fragment=" +
urllib.quote("My team " + uuid))
if len(response['results']) > 0:
found_objects['my_team'] = Team(**response['results'][0])
else:
warnings.warn("Couldn't find team: %s" % ("My team " + uuid))
return found_objects
def create_team(self, **kwargs):
"""Creates a new Team and adds it to the trash queue."""
if 'name' not in kwargs:
kwargs['name'] = self.uniq_name(prefix=kwargs.get('prefix', ''))
kwargs.pop('prefix', None)
team = SynapseProxy.client().store(Team(**kwargs))
self.dispose_of(team)
return team
def setup(self):
self.eval_id = 111
self.team_id = 123
self.team = Team(name="test", id=self.team_id)
self.hash = 3
self.member_eligible = {
'isEligible': True,
'isRegistered': True,
'isQuotaFilled': False,
'principalId': 222,
'hasConflictingSubmission': False
}
self.member_not_registered = {
'isEligible': False,
'isRegistered': False,
'isQuotaFilled': False,
'principalId': 223,
'hasConflictingSubmission': False
}
self.member_quota_filled = {
'isEligible': False,
'isRegistered': True,
'isQuotaFilled': True,
'principalId': 224,
'hasConflictingSubmission': False
}
self.member_has_conflict = {
'isEligible': True,
'isRegistered': True,
'isQuotaFilled': False,
'principalId': 225,
'hasConflictingSubmission': True
}
self.eligibility = {
'teamId':
self.team_id,
'evaluationId':
self.eval_id,
'teamEligibility': {
'isEligible': True,
'isRegistered': True,
'isQuotaFilled': False
},
'membersEligibility': [
self.member_eligible, self.member_not_registered,
self.member_quota_filled, self.member_has_conflict
],
'eligibilityStateHash':
self.hash
}
self.patch_restGET = patch.object(syn,
"restGET",
return_value=self.eligibility)
self.mock_restGET = self.patch_restGET.start()
def test_dispose(syn_client, syn_test_helper, temp_file):
project = syn_client.store(Project(name=syn_test_helper.uniq_name()))
folder = syn_client.store(
Folder(name=syn_test_helper.uniq_name(prefix='Folder '),
parent=project))
file = syn_client.store(
File(name=syn_test_helper.uniq_name(prefix='File '),
path=temp_file,
parent=folder))
team = syn_client.store(
Team(name=syn_test_helper.uniq_name(prefix='Team ')))
wiki = syn_client.store(
Wiki(title=syn_test_helper.uniq_name(prefix='Wiki '), owner=project))
wikiChild = syn_client.store(
Wiki(title=syn_test_helper.uniq_name(prefix='Wiki Child '),
owner=project,
parentWikiId=wiki.id))
syn_objects = [project, folder, file, team, wiki, wikiChild]
for syn_obj in syn_objects:
syn_test_helper.dispose_of(syn_obj)
assert syn_obj in syn_test_helper._trash
syn_test_helper.dispose()
assert len(syn_test_helper._trash) == 0
for syn_obj in syn_objects:
with pytest.raises(
synapseclient.core.exceptions.SynapseHTTPError) as ex:
if isinstance(syn_obj, Wiki):
syn_client.getWiki(syn_obj)
elif isinstance(syn_obj, Team):
syn_client.getTeam(syn_obj.id)
else:
syn_client.get(syn_obj, downloadFile=False)
err_str = str(ex.value)
assert "Not Found" in err_str or "cannot be found" in err_str or "is in trash can" in err_str or "does not exist" in err_str
try:
os.remove(temp_file)
except:
pass
def get_or_create_team(self, **kwargs) -> Team:
"""Gets an existing team by name or creates a new one.
Args:
Same arguments as synapseclient.Team
Returns:
A synapseclient.Team
"""
team = Team(**kwargs)
team = self._find_by_obj_or_create(team)
self.logger.info('{} Team {} ({})'.format(self._update_str, team.name,
team.id))
return team
def create_team(self, **kwargs):
"""Creates a new Team and adds it to the trash queue."""
if 'name' not in kwargs:
kwargs['name'] = self.uniq_name(prefix=kwargs.get('prefix', ''))
kwargs.pop('prefix', None)
team = SynapseProxy.client().store(Team(**kwargs))
# Wait for the team to be available in Synapse.
tries = 0
while True:
tries += 1
try:
SynapseProxy.client().getTeam(team.name)
break
except ValueError:
if tries >= 10:
raise Exception('Timed out waiting for Team to be available in Synapse.')
else:
time.sleep(3)
self.dispose_of(team)
return team
def test():
ids = {}
# teams are really just permissions groups, and we need to create a group
# that has permissions to submit to the challenge
try:
participants_team = syn.getTeam("Participants Group")
print "Loaded team %s %s" % (participants_team.id,
participants_team.name)
except:
participants_team = syn.store(
Team(
name='Participants Group',
description='A team for people who have joined the challenge'))
print syn.setPermissions(project, participants_team.id,
['READ', 'DOWNLOAD'])
for evaluation in find_or_create_evaluations():
print syn.setPermissions(evaluation, participants_team.id, [
'CREATE', 'READ', 'UPDATE', 'PARTICIPATE', 'SUBMIT',
'READ_PRIVATE_SUBMISSION'
])
print "Created team %s %s" % (participants_team.id,
participants_team.name)
ids['participants_team'] = participants_team.id
## the challenge object associates the challenge project with the
## participants team
try:
challenge_object = syn.restGET(
"/entity/{ID}/challenge".format(ID=urllib.quote(project.id)))
print "Loaded challenge object: %s" % challenge_object['id']
except:
raise
challenge_json = {
'participantTeamId': participants_team.id,
'projectId': project.id
}
challenge_object = syn.restPOST("/challenge",
body=json.dumps(challenge_json))
print "Created challenge object: %s" % challenge_object['id']
ids['challenge_object'] = challenge_object['id']
# get a submission team
test_submissions_teams = syn.restGET(
'/challenge/{challengeId}/challengeTeam'.format(
challengeId=challenge_object['id']))
if test_submissions_teams['totalNumberOfResults'] == 0:
# create a team that will make submissions
test_submissions_team = syn.store(
Team(name="Test Submission Team",
description='A team to test the submissions machinery'))
# register team with challenge
request_body = {
'teamId': test_submissions_team['teamId'],
'challengeId': challenge_object['id']
}
test_submissions_team = syn.restPOST(
'/challenge/{challengeId}/challengeTeam'.format(
challengeId=challenge_object['id']), json.dumps(request_body))
elif test_submissions_teams['totalNumberOfResults'] >= 1:
test_submissions_team = test_submissions_teams['results'][0]
ids['test_submissions_team'] = test_submissions_team['id']
print "Restored a team to test submissions: %s" % (
test_submissions_team['id'], )
else:
print test_submissions_teams
assert False, "We only expect a single test submission user."
# Create the participant project
try:
participant_project = syn.get("syn6170604")
except:
raise
participant_project = syn.store(
Project(name="Test Submission Team Project"))
print "Created project %s %s" % (participant_project.id,
participant_project.name)
for evaluation in find_or_create_evaluations():
participant_file = syn.store(
File(synapseclient.utils.make_bogus_data_file(),
parent=participant_project))
syn.submit(
evaluation=evaluation,
entity=participant_file,
team="Participants Group",
)
for evaluation in find_or_create_evaluations():
if evaluation.name == 'Between Cell Type Regression':
score_submission = score_regression_submission
else:
score_submission = score_classification_submission
validate(evaluation)
score(evaluation, score_submission)
return
def set_up():
try:
uuid_suffix = " " + str(uuid.uuid4())
# Create the Challenge Project
challenge_project = syn.store(
Project(name=CHALLENGE_PROJECT_NAME + uuid_suffix))
print "Created project %s %s" % (challenge_project.id,
challenge_project.name)
evaluation = syn.store(
Evaluation(
name=challenge_project.name,
contentSource=challenge_project.id,
status="OPEN",
submissionInstructionsMessage=
"To submit to the XYZ Challenge, send a tab-delimited file as described here: https://...",
submissionReceiptMessage=
"Your submission has been received. For further information, consult the leader board at https://..."
),
quota=dict(
numberOfRounds=1,
roundDurationMillis=1000 * 60 * 60 * 48, ## 48 hours
submissionLimit=20,
firstRoundStart=datetime.now().strftime(
synapseclient.utils.ISO_FORMAT)))
print "Created Evaluation %s %s" % (evaluation.id, evaluation.name)
# Create teams for participants and administrators
participants_team = syn.store(
Team(
name=CHALLENGE_PROJECT_NAME + uuid_suffix + ' Participants',
description='A team for people who have joined the challenge'))
print "Created team %s %s" % (participants_team.id,
participants_team.name)
admin_team = syn.store(
Team(name=CHALLENGE_PROJECT_NAME + uuid_suffix + ' Administrators',
description='A team for challenge administrators'))
print "Created team %s %s" % (admin_team.id, admin_team.name)
# give the teams permissions on challenge artifacts
# see: http://rest.synapse.org/org/sagebionetworks/repo/model/ACCESS_TYPE.html
# see: http://rest.synapse.org/org/sagebionetworks/evaluation/model/UserEvaluationPermissions.html
syn.setPermissions(challenge_project, admin_team.id, [
'CREATE', 'READ', 'UPDATE', 'DELETE', 'CHANGE_PERMISSIONS',
'DOWNLOAD', 'UPLOAD'
])
syn.setPermissions(challenge_project, participants_team.id,
['READ', 'DOWNLOAD'])
syn.setPermissions(evaluation, admin_team.id, [
'CREATE', 'READ', 'UPDATE', 'DELETE', 'CHANGE_PERMISSIONS',
'DOWNLOAD', 'PARTICIPATE', 'SUBMIT', 'DELETE_SUBMISSION',
'UPDATE_SUBMISSION', 'READ_PRIVATE_SUBMISSION'
])
syn.setPermissions(evaluation, participants_team.id, [
'CREATE', 'READ', 'UPDATE', 'PARTICIPATE', 'SUBMIT',
'READ_PRIVATE_SUBMISSION'
])
## the challenge object associates the challenge project with the
## participants team
challenge_object = create_challenge_object(challenge_project,
participants_team)
# create a team that will make submissions
my_team = syn.store(
Team(name="My team" + uuid_suffix,
description='A team to make submissions'))
# register team with challenge
request_body = {
'teamId': my_team.id,
'challengeId': challenge_object.id
}
syn.restPOST(
'/challenge/{challengeId}/challengeTeam'.format(
challengeId=challenge_object.id), json.dumps(request_body))
# Create the participant project
participant_project = syn.store(
Project(name=PARTICIPANT_PROJECT_NAME + uuid_suffix))
print "Created project %s %s" % (participant_project.id,
participant_project.name)
participant_file = syn.store(
File(synapseclient.utils.make_bogus_data_file(),
parent=participant_project))
# Write challenge config file, which is just an ordinary python
# script that can be manually edited later.
current_user = syn.getUserProfile()
write_config(challenge_syn_id=challenge_project.id,
challenge_name=CHALLENGE_PROJECT_NAME,
admin_user_ids=[current_user.ownerId],
evaluation_queues=[evaluation])
return dict(challenge_project=challenge_project,
challenge_object=challenge_object,
evaluation=evaluation,
participant_project=participant_project,
participant_file=participant_file,
participants_team=participants_team,
admin_team=admin_team,
my_team=my_team,
uuid_suffix=uuid_suffix)
except Exception as ex:
tear_down(locals())
raise
def create_team(name, description):
return syn.store(
Team(name=name, description=description, canPublicJoin=True))
