def test_getChildren(): # setup a hierarchy for folders # PROJECT # | \ # File Folder # | # File project_name = str(uuid.uuid1()) test_project = syn.store(Project(name=project_name)) folder = syn.store(Folder(name="firstFolder", parent=test_project)) syn.store( File(path="~/doesntMatter.txt", name="file inside folders", parent=folder, synapseStore=False)) project_file = syn.store( File(path="~/doesntMatterAgain.txt", name="file inside project", parent=test_project, synapseStore=False)) schedule_for_cleanup(test_project) expected_id_set = {project_file.id, folder.id} children_id_set = {x['id'] for x in syn.getChildren(test_project.id)} assert_equals(expected_id_set, children_id_set)
def test_is_synapse_annotation(): assert is_synapse_annotations({'id': 'syn123', 'etag': '0f2977b9-0261-4811-a89e-c13e37ce4604', 'annotations': {}}) # missing id assert not is_synapse_annotations({'etag': '0f2977b9-0261-4811-a89e-c13e37ce4604', 'annotations': {}}) # missing etag assert not is_synapse_annotations({'id': 'syn123', 'annotations': {}}) # missing annotations assert not is_synapse_annotations({'id': 'syn123', 'etag': '0f2977b9-0261-4811-a89e-c13e37ce4604'}) # has additional keys assert is_synapse_annotations( {'id': 'syn123', 'etag': '0f2977b9-0261-4811-a89e-c13e37ce4604', 'annotations': {}, 'foo': 'bar'}) # annotations only assert not is_synapse_annotations({'annotations': {}}) # annotations + other keys assert not is_synapse_annotations({'annotations': {}, 'bar': 'baz'}) # sanity check: Any Entity subclass has id etag and annotations, # but its annotations are not in the format Synapse expects assert not is_synapse_annotations( File( '~/asdf.txt', id='syn123', etag='0f2977b9-0261-4811-a89e-c13e37ce4604', parentId='syn135' ) )
def test_provenance(): # Create a File Entity fname = utils.make_bogus_data_file() schedule_for_cleanup(fname) data_entity = syn.store(File(fname, parent=project['id'])) # Create a File Entity of Code fd, path = tempfile.mkstemp(suffix=".py") os.write( fd, """ ## Chris's fabulous random data generator ############################################################ import random random.seed(12345) data = [random.gauss(mu=0.0, sigma=1.0) for i in range(100)] """) os.close(fd) schedule_for_cleanup(path) code_entity = syn.store(File(path, parent=project['id'])) # Create a new Activity asserting that the Code Entity was 'used' activity = Activity(name='random.gauss', description='Generate some random numbers') activity.used(code_entity, wasExecuted=True) activity.used( { 'name': 'Superhack', 'url': 'https://github.com/joe_coder/Superhack' }, wasExecuted=True) activity = syn.setProvenance(data_entity, activity) # Retrieve and verify the saved Provenance record retrieved_activity = syn.getProvenance(data_entity) assert retrieved_activity == activity # Test Activity update new_description = 'Generate random numbers like a gangsta' retrieved_activity['description'] = new_description updated_activity = syn.updateActivity(retrieved_activity) assert updated_activity['name'] == retrieved_activity['name'] assert updated_activity['description'] == new_description # Test delete syn.deleteProvenance(data_entity) assert_raises(SynapseHTTPError, syn.getProvenance, data_entity['id'])
def test_parent_id_required(): xkcd1 = File('http://xkcd.com/1343/', name='XKCD: Manuals', parent='syn1000001', synapseStore=False) assert xkcd1.parentId == 'syn1000001' xkcd2 = File('http://xkcd.com/1343/', name='XKCD: Manuals', parentId='syn1000002', synapseStore=False) assert xkcd2.parentId == 'syn1000002' assert_raises(SynapseMalformedEntityError, File, 'http://xkcd.com/1343/', name='XKCD: Manuals', synapseStore=False)
def test_File_update_file_handle__External_non_sftp(): external_file_handle = { 'concreteType': 'org.sagebionetworks.repo.model.file.ExternalFileHandle', 'externalURL': "https://some.website" } f = File(parent="idk") assert_true(f.synapseStore) f._update_file_handle(external_file_handle) assert_false(f.synapseStore)
def test_keys(): f = File('foo.xyz', parent='syn1234', foo='bar') iter_keys = [] for key in f: iter_keys.append(key) assert 'parentId' in iter_keys assert 'name' in iter_keys assert 'foo' in iter_keys assert 'concreteType' in iter_keys
def test_ExternalObjectStore_roundtrip(): endpoint = "https://s3.amazonaws.com" bucket = "test-client-auth-s3" profile_name = syn._get_client_authenticated_s3_profile(endpoint, bucket) if profile_name != 'client-auth-s3-test': raise SkipTest( "This test only works on travis because it requires AWS credentials to a specific S3 bucket" ) proj = syn.store( Project(name=str(uuid.uuid4()) + "ExternalObjStoreProject")) schedule_for_cleanup(proj) storage_location = syn.createStorageLocationSetting( "ExternalObjectStorage", endpointUrl=endpoint, bucket=bucket) syn.setStorageLocation(proj, storage_location['storageLocationId']) file_path = utils.make_bogus_data_file() file_entity = File(file_path, name="TestName", parent=proj) file_entity = syn.store(file_entity) syn.cache.purge(time.time()) assert_is_none(syn.cache.get(file_entity['dataFileHandleId'])) # verify key is in s3 import boto3 boto_session = boto3.session.Session(profile_name=profile_name) s3 = boto_session.resource('s3', endpoint_url=endpoint) try: s3_file = s3.Object(file_entity._file_handle.bucket, file_entity._file_handle.fileKey) s3_file.load() except botocore.exceptions.ClientError as e: if e.response['Error']['Code'] == "404": raise Exception("The file was not uploaded to S3") file_entity_downloaded = syn.get(file_entity['id']) file_handle = file_entity_downloaded['_file_handle'] # verify file_handle metadata assert_equals(endpoint, file_handle['endpointUrl']) assert_equals(bucket, file_handle['bucket']) assert_equals( utils.md5_for_file(file_path).hexdigest(), file_handle['contentMd5']) assert_equals(os.stat(file_path).st_size, file_handle['contentSize']) assert_equals('text/plain', file_handle['contentType']) assert_not_equal(utils.normalize_path(file_path), utils.normalize_path(file_entity_downloaded['path'])) assert_true(filecmp.cmp(file_path, file_entity_downloaded['path'])) # clean up s3_file.delete()
def test_entity_constructors(): project = Project(name=str(uuid.uuid4()), description='Testing 123') folder = Folder(name='Musicians', parent=project, genre='Jazz', datatype='personnel') personnel_file = File(fname, parentId=folder.id, group='Miles Davis Quintet', album='Stockholm 1960 Complete')
def test_entity_constructors(): project = Project('TestProject', id='syn1001', foo='bar') assert project.name == 'TestProject' assert project['foo'] == 'bar' folder = Folder('MyFolder', parent=project, foo='bat', id='syn1002') assert folder.name == 'MyFolder' assert folder.foo == 'bat' assert folder.parentId == 'syn1001' a_file = File('/path/to/fabulous_things.zzz', parent=folder, foo='biz') #assert a_file.name == 'fabulous_things.zzz' assert a_file.entityType == 'org.sagebionetworks.repo.model.FileEntity' assert a_file.path == '/path/to/fabulous_things.zzz' assert a_file.foo == 'biz' assert a_file.parentId == 'syn1002'
def test_entity_version(): # Make an Entity and make sure the version is one entity = File(parent=project['id']) entity['path'] = utils.make_bogus_data_file() schedule_for_cleanup(entity['path']) entity = syn.createEntity(entity) syn.setAnnotations(entity, {'fizzbuzz': 111222}) entity = syn.getEntity(entity) assert entity.versionNumber == 1 # Update the Entity and make sure the version is incremented entity.foo = 998877 entity['name'] = 'foobarbat' entity['description'] = 'This is a test entity...' entity = syn.updateEntity(entity, incrementVersion=True, versionLabel="Prada remix") assert entity.versionNumber == 2 # Get the older data and verify the random stuff is still there annotations = syn.getAnnotations(entity, version=1) assert annotations['fizzbuzz'][0] == 111222 returnEntity = syn.getEntity(entity, version=1) assert returnEntity.versionNumber == 1 assert returnEntity['fizzbuzz'][0] == 111222 assert 'foo' not in returnEntity # Try the newer Entity returnEntity = syn.getEntity(entity) assert returnEntity.versionNumber == 2 assert returnEntity['foo'][0] == 998877 assert returnEntity['name'] == 'foobarbat' assert returnEntity['description'] == 'This is a test entity...' assert returnEntity['versionLabel'] == 'Prada remix' # Try the older Entity again returnEntity = syn.downloadEntity(entity, version=1) assert returnEntity.versionNumber == 1 assert returnEntity['fizzbuzz'][0] == 111222 assert 'foo' not in returnEntity # Delete version 2 syn.delete(entity, version=2) returnEntity = syn.getEntity(entity) assert returnEntity.versionNumber == 1
def test_md5_query(): # Add the same Entity several times path = utils.make_bogus_data_file() schedule_for_cleanup(path) repeated = File(path, parent=project['id'], description='Same data over and over again') # Retrieve the data via MD5 num = 5 stored = [] for i in range(num): repeated.name = 'Repeated data %d.dat' % i stored.append(syn.store(repeated).id) # Although we expect num results, it is possible for the MD5 to be non-unique results = syn.md5Query(utils.md5_for_file(path).hexdigest()) assert str(sorted(stored)) == str(sorted([res['id'] for res in results])) assert len(results) == num
def test_external_s3_upload(): #skip if not on the synapse-test user if syn.username != 'synapse-test': raise SkipTest( "This test is configured to work on synapse's TravisCI. If you wish to run this locally, please create an external S3 bucket that your Synapse username can access (http://docs.synapse.org/articles/custom_storage_location.html) and modify the EXTERNAL_S3_BUCKET variable" ) #setup project_id, storage_location_id = _set_up_external_s3_project() # create a temporary file for upload temp_file_path = utils.make_bogus_data_file() expected_md5 = utils.md5_for_file(temp_file_path).hexdigest() schedule_for_cleanup(temp_file_path) #upload the file uploaded_syn_file = syn.store(File(path=temp_file_path, parent=project_id)) #get file_handle of the uploaded file file_handle = syn.restGET('/entity/%s/filehandles' % uploaded_syn_file.id)['list'][0] #Verify correct file handle type assert_equals(file_handle['concreteType'], 'org.sagebionetworks.repo.model.file.S3FileHandle') # Verify storage location id to make sure it's using external S3 assert_equals(storage_location_id, file_handle['storageLocationId']) #Verify md5 of upload assert_equals(expected_md5, file_handle['contentMd5']) # clear the cache and download the file syn.cache.purge(time.time()) downloaded_syn_file = syn.get(uploaded_syn_file.id) #verify the correct file was downloaded assert_equals(os.path.basename(downloaded_syn_file['path']), os.path.basename(temp_file_path)) assert_not_equal(os.path.normpath(temp_file_path), os.path.normpath(downloaded_syn_file['path'])) assert filecmp.cmp(temp_file_path, downloaded_syn_file['path'])
def test_entity_constructors(): project = Project('TestProject', id='syn1001', foo='bar') assert_equals(project.name, 'TestProject') assert_equals(project['foo'], 'bar') folder = Folder('MyFolder', parent=project, foo='bat', id='syn1002') assert_equals(folder.name, 'MyFolder') assert_equals(folder.foo, 'bat') assert_equals(folder.parentId, 'syn1001') a_file = File('/path/to/fabulous_things.zzz', parent=folder, foo='biz', contentType='application/cattywampus') assert_equals(a_file.concreteType, 'org.sagebionetworks.repo.model.FileEntity') assert_equals(a_file.path, '/path/to/fabulous_things.zzz') assert_equals(a_file.foo, 'biz') assert_equals(a_file.parentId, 'syn1002') assert_equals(a_file.contentType, 'application/cattywampus') assert_in('contentType', a_file._file_handle)
def test_entity_constructors(): project = Project('TestProject', id='syn1001', foo='bar') assert project.name == 'TestProject' assert project['foo'] == 'bar' folder = Folder('MyFolder', parent=project, foo='bat', id='syn1002') assert folder.name == 'MyFolder' assert folder.foo == 'bat' assert folder.parentId == 'syn1001' a_file = File('/path/to/fabulous_things.zzz', parent=folder, foo='biz', contentType='application/cattywampus') #assert a_file.name == 'fabulous_things.zzz' assert a_file.concreteType == 'org.sagebionetworks.repo.model.FileEntity' assert a_file.path == '/path/to/fabulous_things.zzz' assert a_file.foo == 'biz' assert a_file.parentId == 'syn1002' assert a_file.contentType == 'application/cattywampus' assert 'contentType' in a_file.__dict__
def test_is_container(): ## result from a Synapse entity annotation query ## Note: prefix may be capitalized or not, depending on the from clause of the query result = { 'entity.versionNumber': 1, 'entity.nodeType': 'project', 'entity.concreteType': ['org.sagebionetworks.repo.model.Project'], 'entity.createdOn': 1451512703905, 'entity.id': 'syn5570912', 'entity.name': 'blah' } assert is_container(result) result = { 'Entity.nodeType': 'project', 'Entity.id': 'syn5570912', 'Entity.name': 'blah' } assert is_container(result) result = { 'entity.concreteType': ['org.sagebionetworks.repo.model.Folder'], 'entity.id': 'syn5570914', 'entity.name': 'flapdoodle' } assert is_container(result) result = { 'File.concreteType': ['org.sagebionetworks.repo.model.FileEntity'], 'File.id': 'syn5570914', 'File.name': 'flapdoodle' } assert not is_container(result) assert is_container(Folder("Stuff", parentId="syn12345")) assert is_container(Project("My Project", parentId="syn12345")) assert not is_container(File("asdf.png", parentId="syn12345"))
def test_md5_query(): # Create a project then add the same entity several times and retrieve them via MD5 project = create_project() path = utils.make_bogus_data_file() schedule_for_cleanup(path) repeated = File(path, parent=project['id'], description='Same data over and over again') num = 5 for i in range(num): try: repeated.name = 'Repeated data %d.dat' % i syn.store(repeated) except Exception as ex: print ex print ex.response.text results = syn.md5Query(utils.md5_for_file(path).hexdigest()) print[res['id'] for res in results] ## Not sure how to make this assertion more accurate ## Although we expect num results, it is possible for the MD5 to be non-unique assert len(results) == num
def test_external_s3_upload(): # setup project_id, storage_location_id = _set_up_external_s3_project() # create a temporary file for upload temp_file_path = utils.make_bogus_data_file() expected_md5 = utils.md5_for_file(temp_file_path).hexdigest() schedule_for_cleanup(temp_file_path) # upload the file uploaded_syn_file = syn.store(File(path=temp_file_path, parent=project_id)) # get file_handle of the uploaded file file_handle = syn.restGET('/entity/%s/filehandles' % uploaded_syn_file.id)['list'][0] # Verify correct file handle type assert_equals(file_handle['concreteType'], 'org.sagebionetworks.repo.model.file.S3FileHandle') # Verify storage location id to make sure it's using external S3 assert_equals(storage_location_id, file_handle['storageLocationId']) # Verify md5 of upload assert_equals(expected_md5, file_handle['contentMd5']) # clear the cache and download the file syn.cache.purge(time.time()) downloaded_syn_file = syn.get(uploaded_syn_file.id) # verify the correct file was downloaded assert_equals(os.path.basename(downloaded_syn_file['path']), os.path.basename(temp_file_path)) assert_not_equal(os.path.normpath(temp_file_path), os.path.normpath(downloaded_syn_file['path'])) assert_true(filecmp.cmp(temp_file_path, downloaded_syn_file['path']))
def test_evaluations(): ## create a new project project = create_project() name = 'Test Evaluation %s' % (str(uuid.uuid4()), ) try: #Create evaluation ev = Evaluation(name=name, description='Evaluation for testing', contentSource=project['id'], status='CLOSED') ev = syn.store(ev) #Update evaluation ev['status'] = 'OPEN' ev = syn.store(ev, createOrUpdate=True) assert ev.status == 'OPEN' ## add the current user as a participant user = syn.getUserProfile() syn.addEvaluationParticipant(ev, user['ownerId']) ## test getSubmissions with no submissions (SYNR-453) submissions = syn.getSubmissions(ev) assert len(list(submissions)) == 0 ## increase this to fully test paging by getEvaluationSubmissions num_of_submissions = 3 ## create a bunch of entities and submit them for evaluation sys.stdout.write('\ncreating evaluation submissions') for i in range(num_of_submissions): try: (fd, filename) = tempfile.mkstemp() with os.fdopen(fd, 'w') as f: f.write(str(random.gauss(0, 1))) f.write('\n') f = File(filename, parentId=project.id, name='entry-%02d' % i, description='An entry for testing evaluation') entity = syn.store(f) syn.submit(ev, entity) finally: os.remove(filename) sys.stdout.write('.') sys.stdout.flush() ## score the submissions submissions = syn.getSubmissions(ev) sys.stdout.write('\nscoring submissions') for submission in submissions: status = syn.getSubmissionStatus(submission) status.score = random.random() status.status = 'SCORED' status.report = 'a fabulous effort!' syn.store(status) sys.stdout.write('.') sys.stdout.flush() sys.stdout.write('\n') finally: syn.delete(ev) ## make sure it's deleted try: ev = syn.getEvaluation(ev) except Exception as e: print e assert e.response.status_code == 404
def test_evaluations(): # Create an Evaluation name = 'Test Evaluation %s' % str(uuid.uuid4()) ev = Evaluation(name=name, description='Evaluation for testing', contentSource=project['id'], status='CLOSED') ev = syn.store(ev) try: # -- Get the Evaluation by name evalNamed = syn.getEvaluationByName(name) assert_equals(ev['contentSource'], evalNamed['contentSource']) assert_equals(ev['createdOn'], evalNamed['createdOn']) assert_equals(ev['description'], evalNamed['description']) assert_equals(ev['etag'], evalNamed['etag']) assert_equals(ev['id'], evalNamed['id']) assert_equals(ev['name'], evalNamed['name']) assert_equals(ev['ownerId'], evalNamed['ownerId']) assert_equals(ev['status'], evalNamed['status']) # -- Get the Evaluation by project evalProj = syn.getEvaluationByContentSource(project) evalProj = next(evalProj) assert_equals(ev['contentSource'], evalProj['contentSource']) assert_equals(ev['createdOn'], evalProj['createdOn']) assert_equals(ev['description'], evalProj['description']) assert_equals(ev['etag'], evalProj['etag']) assert_equals(ev['id'], evalProj['id']) assert_equals(ev['name'], evalProj['name']) assert_equals(ev['ownerId'], evalProj['ownerId']) assert_equals(ev['status'], evalProj['status']) # Update the Evaluation ev['status'] = 'OPEN' ev = syn.store(ev, createOrUpdate=True) assert_equals(ev.status, 'OPEN') # Add the current user as a participant myOwnerId = int(syn.getUserProfile()['ownerId']) syn._allowParticipation(ev, myOwnerId) # AUTHENTICATED_USERS = 273948 # PUBLIC = 273949 syn.setPermissions(ev, 273948, accessType=['READ']) syn.setPermissions(ev, 273949, accessType=['READ']) # test getPermissions permissions = syn.getPermissions(ev, 273949) assert_equals(['READ'], permissions) permissions = syn.getPermissions(ev, syn.getUserProfile()['ownerId']) for p in [ 'READ', 'CREATE', 'DELETE', 'UPDATE', 'CHANGE_PERMISSIONS', 'READ_PRIVATE_SUBMISSION' ]: assert_in(p, permissions) # Test getSubmissions with no Submissions (SYNR-453) submissions = syn.getSubmissions(ev) assert_equals(len(list(submissions)), 0) # Increase this to fully test paging by getEvaluationSubmissions # not to be less than 2 num_of_submissions = 2 # Create a bunch of Entities and submit them for scoring for i in range(num_of_submissions): with tempfile.NamedTemporaryFile(mode="w", delete=False) as f: filename = f.name f.write(str(random.gauss(0, 1)) + '\n') f = File(filename, parentId=project.id, name='entry-%02d' % i, description='An entry for testing evaluation') entity = syn.store(f) syn.submit(ev, entity, name='Submission %02d' % i, submitterAlias='My Team') # Score the submissions submissions = syn.getSubmissions(ev, limit=num_of_submissions - 1) for submission in submissions: assert_true(re.match('Submission \d+', submission['name'])) status = syn.getSubmissionStatus(submission) status.score = random.random() if submission['name'] == 'Submission 01': status.status = 'INVALID' status.report = 'Uh-oh, something went wrong!' else: status.status = 'SCORED' status.report = 'a fabulous effort!' syn.store(status) # Annotate the submissions bogosity = {} submissions = syn.getSubmissions(ev) b = 123 for submission, status in syn.getSubmissionBundles(ev): bogosity[submission.id] = b a = dict(foo='bar', bogosity=b) b += 123 status['annotations'] = to_submission_status_annotations(a) set_privacy(status['annotations'], key='bogosity', is_private=False) syn.store(status) # Test that the annotations stuck for submission, status in syn.getSubmissionBundles(ev): a = from_submission_status_annotations(status.annotations) assert_equals(a['foo'], 'bar') assert_equals(a['bogosity'], bogosity[submission.id]) for kvp in status.annotations['longAnnos']: if kvp['key'] == 'bogosity': assert_false(kvp['isPrivate']) # test query by submission annotations # These queries run against an eventually consistent index table which is # populated by an asynchronous worker. Thus, the queries may remain out # of sync for some unbounded, but assumed to be short time. attempts = 2 while attempts > 0: try: results = syn.restGET( "/evaluation/submission/query?query=SELECT+*+FROM+evaluation_%s" % ev.id) assert_equals(len(results['rows']), num_of_submissions + 1) results = syn.restGET( "/evaluation/submission/query?query=SELECT+*+FROM+evaluation_%s where bogosity > 200" % ev.id) assert_equals(len(results['rows']), num_of_submissions) except AssertionError as ex1: attempts -= 1 time.sleep(2) else: attempts = 0 # Test that we can retrieve submissions with a specific status invalid_submissions = list(syn.getSubmissions(ev, status='INVALID')) assert_equals(len(invalid_submissions), 1, len(invalid_submissions)) assert_equals(invalid_submissions[0]['name'], 'Submission 01') finally: # Clean up syn.delete(ev) if 'testSyn' in locals(): if 'other_project' in locals(): # Clean up, since the current user can't access this project # This also removes references to the submitted object :) testSyn.delete(other_project) if 'team' in locals(): # remove team testSyn.delete(team) # Just deleted it. Shouldn't be able to get it. assert_raises(SynapseHTTPError, syn.getEvaluation, ev)
def test_evaluations(): # Create an Evaluation name = 'Test Evaluation %s' % str(uuid.uuid4()) ev = Evaluation(name=name, description='Evaluation for testing', contentSource=project['id'], status='CLOSED') ev = syn.store(ev) try: # -- Get the Evaluation by name evalNamed = syn.getEvaluationByName(name) assert ev['contentSource'] == evalNamed['contentSource'] assert ev['createdOn'] == evalNamed['createdOn'] assert ev['description'] == evalNamed['description'] assert ev['etag'] == evalNamed['etag'] assert ev['id'] == evalNamed['id'] assert ev['name'] == evalNamed['name'] assert ev['ownerId'] == evalNamed['ownerId'] assert ev['status'] == evalNamed['status'] # -- Get the Evaluation by project evalProj = syn.getEvaluationByContentSource(project) evalProj = next(evalProj) assert ev['contentSource'] == evalProj['contentSource'] assert ev['createdOn'] == evalProj['createdOn'] assert ev['description'] == evalProj['description'] assert ev['etag'] == evalProj['etag'] assert ev['id'] == evalProj['id'] assert ev['name'] == evalProj['name'] assert ev['ownerId'] == evalProj['ownerId'] assert ev['status'] == evalProj['status'] # Update the Evaluation ev['status'] = 'OPEN' ev = syn.store(ev, createOrUpdate=True) assert ev.status == 'OPEN' # # Add the current user as a participant myOwnerId = int(syn.getUserProfile()['ownerId']) syn._allowParticipation(ev, myOwnerId) # AUTHENTICATED_USERS = 273948 # PUBLIC = 273949 syn.setPermissions(ev, 273948, accessType=['READ']) syn.setPermissions(ev, 273949, accessType=['READ']) # test getPermissions permissions = syn.getPermissions(ev, 273949) assert ['READ'] == permissions permissions = syn.getPermissions(ev, syn.getUserProfile()['ownerId']) assert [ p in permissions for p in [ 'READ', 'CREATE', 'DELETE', 'UPDATE', 'CHANGE_PERMISSIONS', 'READ_PRIVATE_SUBMISSION' ] ] # Test getSubmissions with no Submissions (SYNR-453) submissions = syn.getSubmissions(ev) assert len(list(submissions)) == 0 # -- Get a Submission attachment belonging to another user (SYNR-541) -- # See if the configuration contains test authentication if other_user['username']: print("Testing SYNR-541") # Login as the test user testSyn = client.Synapse(skip_checks=True) testSyn.login(email=other_user['username'], password=other_user['password']) testOwnerId = int(testSyn.getUserProfile()['ownerId']) # Make a project other_project = Project(name=str(uuid.uuid4())) other_project = testSyn.createEntity(other_project) # Give the test user permission to read and join the evaluation syn._allowParticipation(ev, testOwnerId) # Make a file to submit with tempfile.NamedTemporaryFile(mode="w", delete=False) as f: filename = f.name f.write(str(random.gauss(0, 1)) + '\n') f = File(filename, parentId=other_project.id, name='Submission 999', description="Haha! I'm inaccessible...") entity = testSyn.store(f) ## test submission by evaluation ID submission = testSyn.submit(ev.id, entity, submitterAlias="My Nickname") # Mess up the cached file so that syn._getWithEntityBundle must download again os.utime(filename, (0, 0)) # Grab the Submission as the original user fetched = syn.getSubmission(submission['id']) assert os.path.exists(fetched['filePath']) # make sure the fetched file is the same as the original (PLFM-2666) assert filecmp.cmp(filename, fetched['filePath']) else: print( 'Skipping test for SYNR-541: No [test-authentication] in %s' % client.CONFIG_FILE) # Increase this to fully test paging by getEvaluationSubmissions # not to be less than 2 num_of_submissions = 2 # Create a bunch of Entities and submit them for scoring print("Creating Submissions") for i in range(num_of_submissions): with tempfile.NamedTemporaryFile(mode="w", delete=False) as f: filename = f.name f.write(str(random.gauss(0, 1)) + '\n') f = File(filename, parentId=project.id, name='entry-%02d' % i, description='An entry for testing evaluation') entity = syn.store(f) syn.submit(ev, entity, name='Submission %02d' % i, submitterAlias='My Team') # Score the submissions submissions = syn.getSubmissions(ev, limit=num_of_submissions - 1) print("Scoring Submissions") for submission in submissions: assert re.match('Submission \d+', submission['name']) status = syn.getSubmissionStatus(submission) status.score = random.random() if submission['name'] == 'Submission 01': status.status = 'INVALID' status.report = 'Uh-oh, something went wrong!' else: status.status = 'SCORED' status.report = 'a fabulous effort!' syn.store(status) # Annotate the submissions print("Annotating Submissions") bogosity = {} submissions = syn.getSubmissions(ev) b = 123 for submission, status in syn.getSubmissionBundles(ev): bogosity[submission.id] = b a = dict(foo='bar', bogosity=b) b += 123 status['annotations'] = to_submission_status_annotations(a) set_privacy(status['annotations'], key='bogosity', is_private=False) syn.store(status) # Test that the annotations stuck for submission, status in syn.getSubmissionBundles(ev): a = from_submission_status_annotations(status.annotations) assert a['foo'] == 'bar' assert a['bogosity'] == bogosity[submission.id] for kvp in status.annotations['longAnnos']: if kvp['key'] == 'bogosity': assert kvp['isPrivate'] == False # test query by submission annotations # These queries run against an eventually consistent index table which is # populated by an asynchronous worker. Thus, the queries may remain out # of sync for some unbounded, but assumed to be short time. attempts = 2 while attempts > 0: try: print("Querying for submissions") results = syn.restGET( "/evaluation/submission/query?query=SELECT+*+FROM+evaluation_%s" % ev.id) print(results) assert len(results['rows']) == num_of_submissions + 1 results = syn.restGET( "/evaluation/submission/query?query=SELECT+*+FROM+evaluation_%s where bogosity > 200" % ev.id) print(results) assert len(results['rows']) == num_of_submissions except AssertionError as ex1: print("failed query: ", ex1) attempts -= 1 if attempts > 0: print("retrying...") time.sleep(2) else: attempts = 0 ## Test that we can retrieve submissions with a specific status invalid_submissions = list(syn.getSubmissions(ev, status='INVALID')) assert len(invalid_submissions) == 1, len(invalid_submissions) assert invalid_submissions[0]['name'] == 'Submission 01' finally: # Clean up syn.delete(ev) if 'testSyn' in locals(): if 'other_project' in locals(): # Clean up, since the current user can't access this project # This also removes references to the submitted object :) testSyn.delete(other_project) if 'team' in locals(): ## remove team testSyn.delete(team) ## Just deleted it. Shouldn't be able to get it. assert_raises(SynapseHTTPError, syn.getEvaluation, ev)
def test_concrete_type(): f1 = File('http://en.wikipedia.org/wiki/File:Nettlebed_cave.jpg', name='Nettlebed Cave', parent='syn1234567', synapseStore=False) assert f1.concreteType == 'org.sagebionetworks.repo.model.FileEntity'
def test_attrs(): f = File('foo.xyz', parent='syn1234', foo='bar') assert hasattr(f, 'parentId') assert hasattr(f, 'foo') assert hasattr(f, 'path')