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Download Synapse Repository Services Free Java Code

Description

The Synapse Repository Services project is the home of the JSON REST web services for Synapse.

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Synapse Repository Services

Source Files

The download file Synapse-Repository-Services-master.zip has the following entries.


.gitignore/*w ww  .jav  a2 s . c  om*/
README.md
client/commandLineInterface/pom.xml
client/commandLineInterface/src/main/java/org/sagebionetworks/cli/CommandLineInterface.java
client/commandLineInterface/src/main/java/org/sagebionetworks/cli/UploadFile.java
client/commandLineInterface/src/main/resources/commons-logging.properties
client/commandLineInterface/src/main/resources/log4j.properties
client/commandLineInterface/src/main/scripts/synapse-cmd
client/commandLineInterface/src/main/scripts/synapse-upload-file
client/commandLineInterface/src/test/java/org/sagebionetworks/cli/UploadFileTest.java
client/commandLineInterface/synapse-cli-assembly.xml
client/pom.xml
client/synapseJavaClient/pom.xml
client/synapseJavaClient/src/main/java/org/sagebionetworks/client/AcceptAllCertificateHttpClientProvider.java
client/synapseJavaClient/src/main/java/org/sagebionetworks/client/DataUploader.java
client/synapseJavaClient/src/main/java/org/sagebionetworks/client/DataUploaderImpl.java
client/synapseJavaClient/src/main/java/org/sagebionetworks/client/DataUploaderMultipartImpl.java
client/synapseJavaClient/src/main/java/org/sagebionetworks/client/HttpClientProvider.java
client/synapseJavaClient/src/main/java/org/sagebionetworks/client/HttpClientProviderImpl.java
client/synapseJavaClient/src/main/java/org/sagebionetworks/client/ProgressListener.java
client/synapseJavaClient/src/main/java/org/sagebionetworks/client/SwingProgressListener.java
client/synapseJavaClient/src/main/java/org/sagebionetworks/client/Synapse.java
client/synapseJavaClient/src/main/java/org/sagebionetworks/client/SynapseAdministration.java
client/synapseJavaClient/src/main/java/org/sagebionetworks/client/TextProgressListener.java
client/synapseJavaClient/src/main/java/org/sagebionetworks/client/exceptions/SynapseBadRequestException.java
client/synapseJavaClient/src/main/java/org/sagebionetworks/client/exceptions/SynapseException.java
client/synapseJavaClient/src/main/java/org/sagebionetworks/client/exceptions/SynapseForbiddenException.java
client/synapseJavaClient/src/main/java/org/sagebionetworks/client/exceptions/SynapseNotFoundException.java
client/synapseJavaClient/src/main/java/org/sagebionetworks/client/exceptions/SynapseServiceException.java
client/synapseJavaClient/src/main/java/org/sagebionetworks/client/exceptions/SynapseTermsOfUseException.java
client/synapseJavaClient/src/main/java/org/sagebionetworks/client/exceptions/SynapseUnauthorizedException.java
client/synapseJavaClient/src/main/java/org/sagebionetworks/client/exceptions/SynapseUserException.java
client/synapseJavaClient/src/main/resources/org/sagebionetworks/client/synpaseClientExceptions.gwt.xml
client/synapseJavaClient/src/test/java/org/sagebionetworks/client/EntityCreator.java
client/synapseJavaClient/src/test/java/org/sagebionetworks/client/SynapseAdministrationTest.java
client/synapseJavaClient/src/test/java/org/sagebionetworks/client/SynapseTest.java
client/synapsePythonClient/main.py
client/synapsePythonClient/pom.xml
client/synapsePythonClient/progressbar/LICENSE
client/synapsePythonClient/progressbar/MANIFEST
client/synapsePythonClient/progressbar/MANIFEST.in
client/synapsePythonClient/progressbar/PKG-INFO
client/synapsePythonClient/progressbar/README
client/synapsePythonClient/progressbar/progressbar.py
client/synapsePythonClient/progressbar/setup.py
client/synapsePythonClient/setup.py
client/synapsePythonClient/synapse/__init__.py
client/synapsePythonClient/synapse/client.py
client/synapsePythonClient/synapse/integration_test.py
client/synapsePythonClient/synapse/tcgaMetadata.py
client/synapsePythonClient/synapse/utils.py
client/synapsePythonClient/synapsePythonClient-assembly.xml
configuration/awsIamPolicies/AdminGroupPolicy.txt
configuration/awsIamPolicies/BackupBucketGroup.policy
configuration/awsIamPolicies/bambooDataIamGroup.policy
configuration/awsIamPolicies/bambooSearchIndexUpdater.policy
configuration/awsIamPolicies/bambooServiceIamUser.policy
configuration/awsIamPolicies/devDataIamGroup.policy
configuration/awsIamPolicies/devSearchIndexUpdater.policy
configuration/awsIamPolicies/devServiceIamUser.policy
configuration/awsIamPolicies/devWorkflowIamUser.policy
configuration/awsIamPolicies/hudsonIamUser.policy
configuration/awsIamPolicies/nonProdWorkflow.policy
configuration/awsIamPolicies/prodDataIamGroup.policy
configuration/awsIamPolicies/prodSearchIndexUpdater.policy
configuration/awsIamPolicies/prodServiceIamUser.policy
configuration/awsIamPolicies/prodWorkflowIamUser.policy
configuration/awsIamPolicies/stagingDataIamGroup.policy
configuration/awsIamPolicies/stagingSearchIndexUpdater.policy
configuration/awsIamPolicies/stagingServiceIamUser.policy
configuration/awsIamPolicies/stagingWorkflowIamUser.policy
configuration/deployment/amazon/Copy of synapse.template
configuration/deployment/amazon/currentStack/apps.json
configuration/deployment/amazon/currentStack/environments.json
configuration/deployment/amazon/currentStack/options.json
configuration/deployment/amazon/currentStack/prod-reposervice.template
configuration/deployment/amazon/currentStack/settings.json
configuration/deployment/amazon/currentStack/test.json
configuration/deployment/amazon/currentStack/versions.json
configuration/deployment/amazon/samples/CloudFormer.template
configuration/deployment/amazon/samples/EC2InstanceWithSecurityGroupSample.template
configuration/deployment/amazon/samples/ElasticBeanstalkSample.template
configuration/deployment/amazon/samples/ElasticBeanstalkSampleWithRoute53.template
configuration/deployment/amazon/samples/Mutually_Referencing_EC2_Security_Groups.template
configuration/deployment/amazon/samples/RDS_Version.template
configuration/deployment/amazon/samples/S3_With_CloudFront_Distribution.template
configuration/deployment/amazon/samples/S3_bucket.template
configuration/deployment/amazon/samples/helloWorld.template
configuration/deployment/amazon/synapse.template
configuration/ebsDeltas/mysqld_safe
configuration/s3Policies/bamboodata.sagebase.org.https.policy
configuration/s3Policies/devdata.sagebase.org.https.policy
configuration/s3Policies/proddata.sagebase.org.https.policy
configuration/s3Policies/prodlogs.sagebase.org.https.policy
configuration/s3Policies/stagingdata.sagebase.org.https.policy
configuration/synapse-auth/etc/pam.d/rstudio
configuration/synapse-auth/lib/security/synapse_auth.py
integration-test/capture.txt
integration-test/mvn
integration-test/pom.xml
integration-test/src/main/java/org/sagebionetworks/PlaceHolder.java
integration-test/src/test/java/org/sagebionetworks/Helpers.java
integration-test/src/test/java/org/sagebionetworks/IT100BackupRestoration.java
integration-test/src/test/java/org/sagebionetworks/IT101Administration.java
integration-test/src/test/java/org/sagebionetworks/IT101LoadMigratedData.java
integration-test/src/test/java/org/sagebionetworks/IT300JSONPServices.java
integration-test/src/test/java/org/sagebionetworks/IT500SynapseJavaClient.java
integration-test/src/test/java/org/sagebionetworks/IT510SynapseJavaClientSearchTest.java
integration-test/src/test/java/org/sagebionetworks/IT550DocumentationGenerator.java
integration-test/src/test/java/org/sagebionetworks/IT940BCCSetup.java
integration-test/src/test/java/org/sagebionetworks/IT960TermsOfUse.java
integration-test/src/test/java/org/sagebionetworks/IT970UserProfileController.java
integration-test/src/test/java/org/sagebionetworks/IT980ResourceAccess.java
integration-test/src/test/java/org/sagebionetworks/IT990CrowdAuthentication.java
integration-test/src/test/java/org/sagebionetworks/ITCreationLoadTest.java
integration-test/src/test/java/org/sagebionetworks/ITMigrationQueryRunner.java
integration-test/src/test/java/org/sagebionetworks/ITPerCallProfileTest.java
integration-test/src/test/java/org/sagebionetworks/PERF1000RepoSvc.java
integration-test/src/test/java/org/sagebionetworks/utils/CookieSessionManager.java
integration-test/src/test/java/org/sagebionetworks/utils/PublicCookieManager.java
integration-test/src/test/resources/Backup-principals.zip
integration-test/src/test/resources/Backup-staging-A-66004-4066545524488105200.zip
integration-test/src/test/resources/images/IMAG0019.jpg
integration-test/src/test/resources/images/profile_pic.png
lib/communicationUtilities/pom.xml
lib/communicationUtilities/src/main/java/org/sagebionetworks/downloadtools/InternalInputStream.java
lib/communicationUtilities/src/main/java/org/sagebionetworks/downloadtools/TARDownloader.java
lib/communicationUtilities/src/main/java/org/sagebionetworks/utils/DefaultHttpClientSingleton.java
lib/communicationUtilities/src/main/java/org/sagebionetworks/utils/EmailUtils.java
lib/communicationUtilities/src/main/java/org/sagebionetworks/utils/ExternalProcessHelper.java
lib/communicationUtilities/src/main/java/org/sagebionetworks/utils/HttpClientHelper.java
lib/communicationUtilities/src/main/java/org/sagebionetworks/utils/HttpClientHelperException.java
lib/communicationUtilities/src/main/java/org/sagebionetworks/utils/MD5ChecksumHelper.java
lib/communicationUtilities/src/main/java/org/sagebionetworks/utils/SimpleObserver.java
lib/communicationUtilities/src/main/java/org/sagebionetworks/utils/WebCrawler.java
lib/communicationUtilities/src/main/resources/HttpClientHelperPublicCertsOnly.jks
lib/communicationUtilities/src/main/resources/email.properties
lib/communicationUtilities/src/test/java/org/sagebionetworks/utils/EmailUtilsTest.java
lib/communicationUtilities/src/test/java/org/sagebionetworks/utils/TARDownloaderTest.java
lib/communicationUtilities/src/test/java/org/sagebionetworks/utils/WebCrawlerITCase.java
lib/communicationUtilities/src/test/resources/test.tar
lib/id-generator/pom.xml
lib/id-generator/src/main/java/org/sagebionetworks/ids/ETagGenerator.java
lib/id-generator/src/main/java/org/sagebionetworks/ids/IdGenerator.java
lib/id-generator/src/main/java/org/sagebionetworks/ids/IdGeneratorImpl.java
lib/id-generator/src/main/java/org/sagebionetworks/ids/UuidETagGenerator.java
lib/id-generator/src/main/resources/domain-id-schema.sql
lib/id-generator/src/main/resources/id-generator.spb.xml
lib/id-generator/src/main/resources/log4j.properties
lib/id-generator/src/main/resources/logging.properties
lib/id-generator/src/test/java/org/sagebionetworks/ids/IdGeneratorConcurrencyTest.java
lib/id-generator/src/test/java/org/sagebionetworks/ids/IdGeneratorImplTest.java
lib/id-generator/src/test/java/org/sagebionetworks/ids/UuidETagGeneratorTest.java
lib/jdomodels/pom.xml
lib/jdomodels/src/main/java/org/sagebionetworks/repo/model/bootstrap/AccessBootstrapData.java
lib/jdomodels/src/main/java/org/sagebionetworks/repo/model/bootstrap/DatabasePreparation.java
lib/jdomodels/src/main/java/org/sagebionetworks/repo/model/bootstrap/EntityBootstrapData.java
lib/jdomodels/src/main/java/org/sagebionetworks/repo/model/bootstrap/EntityBootstrapper.java
lib/jdomodels/src/main/java/org/sagebionetworks/repo/model/bootstrap/EntityBootstrapperImpl.java
lib/jdomodels/src/main/java/org/sagebionetworks/repo/model/dbo/AutoIncrementDatabaseObject.java
lib/jdomodels/src/main/java/org/sagebionetworks/repo/model/dbo/DBOBasicDao.java
lib/jdomodels/src/main/java/org/sagebionetworks/repo/model/dbo/DBOBasicDaoImpl.java
lib/jdomodels/src/main/java/org/sagebionetworks/repo/model/dbo/DDLUtils.java
lib/jdomodels/src/main/java/org/sagebionetworks/repo/model/dbo/DDLUtilsImpl.java
lib/jdomodels/src/main/java/org/sagebionetworks/repo/model/dbo/DMLUtils.java
lib/jdomodels/src/main/java/org/sagebionetworks/repo/model/dbo/DatabaeMapping.java
lib/jdomodels/src/main/java/org/sagebionetworks/repo/model/dbo/DatabaseObject.java
lib/jdomodels/src/main/java/org/sagebionetworks/repo/model/dbo/FieldColumn.java
lib/jdomodels/src/main/java/org/sagebionetworks/repo/model/dbo/TableMapping.java
lib/jdomodels/src/main/java/org/sagebionetworks/repo/model/dbo/dao/AccessApprovalUtils.java
lib/jdomodels/src/main/java/org/sagebionetworks/repo/model/dbo/dao/AccessControlListUtils.java
lib/jdomodels/src/main/java/org/sagebionetworks/repo/model/dbo/dao/AccessRequirementUtils.java
lib/jdomodels/src/main/java/org/sagebionetworks/repo/model/dbo/dao/AnnotationUtils.java
lib/jdomodels/src/main/java/org/sagebionetworks/repo/model/dbo/dao/DBOAccessApprovalDAOImpl.java
lib/jdomodels/src/main/java/org/sagebionetworks/repo/model/dbo/dao/DBOAccessControlListDao.java
lib/jdomodels/src/main/java/org/sagebionetworks/repo/model/dbo/dao/DBOAccessControlListDaoImpl.java
lib/jdomodels/src/main/java/org/sagebionetworks/repo/model/dbo/dao/DBOAccessRequirementDAOImpl.java
lib/jdomodels/src/main/java/org/sagebionetworks/repo/model/dbo/dao/DBOAnnotationsDao.java
lib/jdomodels/src/main/java/org/sagebionetworks/repo/model/dbo/dao/DBOAnnotationsDaoImpl.java
lib/jdomodels/src/main/java/org/sagebionetworks/repo/model/dbo/dao/DBOChangeDAO.java
lib/jdomodels/src/main/java/org/sagebionetworks/repo/model/dbo/dao/DBOChangeDAOImpl.java
lib/jdomodels/src/main/java/org/sagebionetworks/repo/model/dbo/dao/DBOPreviewBlobDao.java
lib/jdomodels/src/main/java/org/sagebionetworks/repo/model/dbo/dao/DBOReferenceDao.java
lib/jdomodels/src/main/java/org/sagebionetworks/repo/model/dbo/dao/DBOReferenceDaoImpl.java
lib/jdomodels/src/main/java/org/sagebionetworks/repo/model/dbo/dao/DBOUserGroupDAOImpl.java
lib/jdomodels/src/main/java/org/sagebionetworks/repo/model/dbo/dao/DBOUserProfileDAOImpl.java
lib/jdomodels/src/main/java/org/sagebionetworks/repo/model/dbo/dao/NodeDAOImpl.java
lib/jdomodels/src/main/java/org/sagebionetworks/repo/model/dbo/dao/NodeUtils.java
lib/jdomodels/src/main/java/org/sagebionetworks/repo/model/dbo/dao/ReferenceUtil.java
lib/jdomodels/src/main/java/org/sagebionetworks/repo/model/dbo/dao/SchemaSerializationUtils.java
lib/jdomodels/src/main/java/org/sagebionetworks/repo/model/dbo/dao/StorageLocationDAOImpl.java
lib/jdomodels/src/main/java/org/sagebionetworks/repo/model/dbo/dao/StorageLocationUtils.java
lib/jdomodels/src/main/java/org/sagebionetworks/repo/model/dbo/dao/TagMessengerImpl.java
lib/jdomodels/src/main/java/org/sagebionetworks/repo/model/dbo/dao/UserGroupUtils.java
lib/jdomodels/src/main/java/org/sagebionetworks/repo/model/dbo/dao/UserProfileUtils.java
lib/jdomodels/src/main/java/org/sagebionetworks/repo/model/dbo/persistence/DBOAccessApproval.java
lib/jdomodels/src/main/java/org/sagebionetworks/repo/model/dbo/persistence/DBOAccessControlList.java
lib/jdomodels/src/main/java/org/sagebionetworks/repo/model/dbo/persistence/DBOAccessRequirement.java
lib/jdomodels/src/main/java/org/sagebionetworks/repo/model/dbo/persistence/DBOChange.java
lib/jdomodels/src/main/java/org/sagebionetworks/repo/model/dbo/persistence/DBODaemonStatus.java
lib/jdomodels/src/main/java/org/sagebionetworks/repo/model/dbo/persistence/DBODaemonTerminate.java
lib/jdomodels/src/main/java/org/sagebionetworks/repo/model/dbo/persistence/DBODateAnnotation.java
lib/jdomodels/src/main/java/org/sagebionetworks/repo/model/dbo/persistence/DBODoubleAnnotation.java
lib/jdomodels/src/main/java/org/sagebionetworks/repo/model/dbo/persistence/DBOLongAnnotation.java
lib/jdomodels/src/main/java/org/sagebionetworks/repo/model/dbo/persistence/DBONode.java
lib/jdomodels/src/main/java/org/sagebionetworks/repo/model/dbo/persistence/DBONodeAccessRequirement.java
lib/jdomodels/src/main/java/org/sagebionetworks/repo/model/dbo/persistence/DBONodeType.java
lib/jdomodels/src/main/java/org/sagebionetworks/repo/model/dbo/persistence/DBONodeTypeAlias.java
lib/jdomodels/src/main/java/org/sagebionetworks/repo/model/dbo/persistence/DBOReference.java
lib/jdomodels/src/main/java/org/sagebionetworks/repo/model/dbo/persistence/DBOResourceAccess.java
lib/jdomodels/src/main/java/org/sagebionetworks/repo/model/dbo/persistence/DBOResourceAccessType.java
lib/jdomodels/src/main/java/org/sagebionetworks/repo/model/dbo/persistence/DBORevision.java
lib/jdomodels/src/main/java/org/sagebionetworks/repo/model/dbo/persistence/DBOStackStatus.java
lib/jdomodels/src/main/java/org/sagebionetworks/repo/model/dbo/persistence/DBOStorageLocation.java
lib/jdomodels/src/main/java/org/sagebionetworks/repo/model/dbo/persistence/DBOStringAnnotation.java
lib/jdomodels/src/main/java/org/sagebionetworks/repo/model/dbo/persistence/DBOUserGroup.java
lib/jdomodels/src/main/java/org/sagebionetworks/repo/model/dbo/persistence/DBOUserProfile.java
lib/jdomodels/src/main/java/org/sagebionetworks/repo/model/jdo/AuthorizationSqlUtil.java
lib/jdomodels/src/main/java/org/sagebionetworks/repo/model/jdo/BackupRestoreStatusDAOImpl.java
lib/jdomodels/src/main/java/org/sagebionetworks/repo/model/jdo/BackupRestoreStatusUtil.java
lib/jdomodels/src/main/java/org/sagebionetworks/repo/model/jdo/BasicIdentifierFactory.java
lib/jdomodels/src/main/java/org/sagebionetworks/repo/model/jdo/ConnectionPoolLogger.java
lib/jdomodels/src/main/java/org/sagebionetworks/repo/model/jdo/EntityNameValidation.java
lib/jdomodels/src/main/java/org/sagebionetworks/repo/model/jdo/FieldTypeCache.java
lib/jdomodels/src/main/java/org/sagebionetworks/repo/model/jdo/JDOAccessControlListDAOImpl.java
lib/jdomodels/src/main/java/org/sagebionetworks/repo/model/jdo/JDOAnnotation.java
lib/jdomodels/src/main/java/org/sagebionetworks/repo/model/jdo/JDOBase.java
lib/jdomodels/src/main/java/org/sagebionetworks/repo/model/jdo/JDONodeInheritanceDAOImpl.java
lib/jdomodels/src/main/java/org/sagebionetworks/repo/model/jdo/JDORevisionUtils.java
lib/jdomodels/src/main/java/org/sagebionetworks/repo/model/jdo/JDOSecondaryPropertyUtils.java
lib/jdomodels/src/main/java/org/sagebionetworks/repo/model/jdo/KeyFactory.java
lib/jdomodels/src/main/java/org/sagebionetworks/repo/model/jdo/ObjectDescriptorUtils.java
lib/jdomodels/src/main/java/org/sagebionetworks/repo/model/jdo/StackStatusDaoImpl.java
lib/jdomodels/src/main/java/org/sagebionetworks/repo/model/jdo/UserGroupCache.java
lib/jdomodels/src/main/java/org/sagebionetworks/repo/model/jdo/UserGroupCacheImpl.java
lib/jdomodels/src/main/java/org/sagebionetworks/repo/model/jdo/UserGroupDAOInitializingBean.java
lib/jdomodels/src/main/java/org/sagebionetworks/repo/model/message/ChangeMessageUtils.java
lib/jdomodels/src/main/java/org/sagebionetworks/repo/model/message/TransactionSynchronizationProxy.java
lib/jdomodels/src/main/java/org/sagebionetworks/repo/model/message/TransactionSynchronizationProxyImpl.java
lib/jdomodels/src/main/java/org/sagebionetworks/repo/model/message/TransactionalMessengerImpl.java
lib/jdomodels/src/main/java/org/sagebionetworks/repo/model/query/jdo/JDONodeQueryDaoImpl.java
lib/jdomodels/src/main/java/org/sagebionetworks/repo/model/query/jdo/NodeAliasCache.java
lib/jdomodels/src/main/java/org/sagebionetworks/repo/model/query/jdo/NodeAliasCacheImpl.java
lib/jdomodels/src/main/java/org/sagebionetworks/repo/model/query/jdo/NodeField.java
lib/jdomodels/src/main/java/org/sagebionetworks/repo/model/query/jdo/QueryUtils.java
lib/jdomodels/src/main/java/org/sagebionetworks/repo/model/query/jdo/SizeLimitRowMapper.java
lib/jdomodels/src/main/java/org/sagebionetworks/repo/model/query/jdo/SqlConstants.java
lib/jdomodels/src/main/resources/bootstrap-entites-spb.xml
lib/jdomodels/src/main/resources/dao-beans.spb.xml
lib/jdomodels/src/main/resources/dbo-beans.spb.xml
lib/jdomodels/src/main/resources/log4j.properties
lib/jdomodels/src/main/resources/logging.properties
lib/jdomodels/src/main/resources/schema/ACL-ddl.sql
lib/jdomodels/src/main/resources/schema/AccessApproval-ddl.sql
lib/jdomodels/src/main/resources/schema/AccessRequirement-ddl.sql
lib/jdomodels/src/main/resources/schema/Changes-ddl.sql
lib/jdomodels/src/main/resources/schema/DaemonStatus-ddl.sql
lib/jdomodels/src/main/resources/schema/DaemonTerminate-ddl.sql
lib/jdomodels/src/main/resources/schema/DateAnnotation-ddl.sql
lib/jdomodels/src/main/resources/schema/DoubleAnnotation-ddl.sql
lib/jdomodels/src/main/resources/schema/LongAnnotation-ddl.sql
lib/jdomodels/src/main/resources/schema/Node-ddl.sql
lib/jdomodels/src/main/resources/schema/NodeAccessRequirement-ddl.sql
lib/jdomodels/src/main/resources/schema/NodeType-ddl.sql
lib/jdomodels/src/main/resources/schema/NodeTypeAlias-ddl.sql
lib/jdomodels/src/main/resources/schema/PreviewBlob-ddl.sql
lib/jdomodels/src/main/resources/schema/Reference-ddl.sql
lib/jdomodels/src/main/resources/schema/ResourceAccess-ddl.sql
lib/jdomodels/src/main/resources/schema/ResourceAccessType-ddl.sql
lib/jdomodels/src/main/resources/schema/Revision-ddl.sql
lib/jdomodels/src/main/resources/schema/StackStatus-ddl.sql
lib/jdomodels/src/main/resources/schema/StorageLocation-ddl.sql
lib/jdomodels/src/main/resources/schema/StringAnnotation-ddl.sql
lib/jdomodels/src/main/resources/schema/UserGroup-ddl.sql
lib/jdomodels/src/main/resources/schema/UserProfile-ddl.sql
lib/jdomodels/src/main/resources/transaction-spb.xml
lib/jdomodels/src/test/java/org/sagebionetworks/repo/model/bootstrap/BootstrapRootFolderTest.java
lib/jdomodels/src/test/java/org/sagebionetworks/repo/model/bootstrap/EntityBootstrapperAutowireTest.java
lib/jdomodels/src/test/java/org/sagebionetworks/repo/model/bootstrap/EntityBootstrapperUnitTest.java
lib/jdomodels/src/test/java/org/sagebionetworks/repo/model/dbo/DBOExample.java
lib/jdomodels/src/test/java/org/sagebionetworks/repo/model/dbo/DBOExampleTest.java
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lib/jdomodels/src/test/java/org/sagebionetworks/repo/model/dbo/dao/DBOChangeDAOImplTest.java
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lib/jdomodels/src/test/java/org/sagebionetworks/repo/model/dbo/dao/SchemaSerializationUtilsTest.java
lib/jdomodels/src/test/java/org/sagebionetworks/repo/model/dbo/dao/StorageLocationDAOImplTest.java
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lib/jdomodels/src/test/java/org/sagebionetworks/repo/model/dbo/dao/UserGroupUtilsTest.java
lib/jdomodels/src/test/java/org/sagebionetworks/repo/model/dbo/dao/UserProfileUtilsTest.java
lib/jdomodels/src/test/java/org/sagebionetworks/repo/model/dbo/persistence/DBOAccessApprovalTest.java
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lib/jdomodels/src/test/java/org/sagebionetworks/repo/model/dbo/persistence/DBONodeTest.java
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lib/jdomodels/src/test/java/org/sagebionetworks/repo/model/jdo/BackupRestoreStatusDAOImplTest.java
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lib/jdomodels/src/test/java/org/sagebionetworks/repo/model/jdo/EntityNameValidationTest.java
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lib/jdomodels/src/test/java/org/sagebionetworks/repo/model/jdo/NodeInheritanceDAOImplTest.java
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lib/jdomodels/src/test/java/org/sagebionetworks/repo/model/jdo/RandomAnnotationsUtil.java
lib/jdomodels/src/test/java/org/sagebionetworks/repo/model/jdo/StackStatusDaoImplTest.java
lib/jdomodels/src/test/java/org/sagebionetworks/repo/model/jdo/UserGroupCacheImplTest.java
lib/jdomodels/src/test/java/org/sagebionetworks/repo/model/jdo/UserInfoUtils.java
lib/jdomodels/src/test/java/org/sagebionetworks/repo/model/message/ChangeMessageUtilsTest.java
lib/jdomodels/src/test/java/org/sagebionetworks/repo/model/message/TransactionSynchronizationProxyStub.java
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lib/jdomodels/src/test/java/org/sagebionetworks/repo/model/query/jdo/JDONodeQueryAuthorizationTest.java
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lib/lib-auto-generated/src/main/resources/schema/org/sagebionetworks/repo/model/versionInfo/SynapseVersionInfo.json
lib/lib-auto-generated/src/test/java/org/sagebionetworks/JSONParseTest.java
lib/lib-auto-generated/src/test/java/org/sagebionetworks/JSONValidator.java
lib/lib-concepts/pom.xml
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lib/lib-concepts/src/main/java/org/sagebionetworks/repo/model/ontology/ConceptDAO.java
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lib/lib-concepts/src/main/resources/SYN.skos
lib/lib-concepts/src/main/resources/concept-dao-beans.spb.xml
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lib/lib-concepts/src/test/java/org/sagebionetworks/repo/model/ontology/ConceptComparatorTest.java
lib/lib-concepts/src/test/java/org/sagebionetworks/repo/model/ontology/ConceptJenaDAOImplTest.java
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lib/lib-concepts/src/test/resources/SYN.skos
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lib/lib-search/pom.xml
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lib/lib-search/src/main/java/org/sagebionetworks/search/SearchDao.java
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lib/lib-search/src/main/java/org/sagebionetworks/search/SearchSchemaLoader.java
lib/lib-search/src/main/resources/aws-spb.xml
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lib/lib-search/src/test/java/org/sagebionetworks/search/SearchDaoImplAutowireTest.java
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lib/lib-shared-models/src/main/java/org/sagebionetworks/repo/model/VariableContentPaginatedResults.java
lib/lib-shared-models/src/main/java/org/sagebionetworks/repo/model/search/AwesomeSearchFactory.java
lib/lib-shared-models/src/main/java/org/sagebionetworks/repo/model/util/ModelConstants.java
lib/lib-shared-models/src/main/resources/org/sagebionetworks/repo/SharedSynpaseDTOs.gwt.xml
lib/lib-shared-models/src/test/java/org/sagebionetworks/repo/model/AnnotationsTest.java
lib/lib-shared-models/src/test/java/org/sagebionetworks/repo/model/EntityBundleTest.java
lib/lib-shared-models/src/test/java/org/sagebionetworks/repo/model/GwtTestSuite.java
lib/lib-shared-models/src/test/java/org/sagebionetworks/repo/model/search/AwesomeSearchFactoryTest.java
lib/lib-worker/pom.xml
lib/lib-worker/src/main/java/org/sagebionetworks/asynchronous/workers/sqs/MessageQueue.java
lib/lib-worker/src/main/java/org/sagebionetworks/asynchronous/workers/sqs/MessageQueueImpl.java
lib/lib-worker/src/main/java/org/sagebionetworks/asynchronous/workers/sqs/MessageReceiver.java
lib/lib-worker/src/main/java/org/sagebionetworks/asynchronous/workers/sqs/MessageReceiverImpl.java
lib/lib-worker/src/main/java/org/sagebionetworks/asynchronous/workers/sqs/MessageUtils.java
lib/lib-worker/src/main/java/org/sagebionetworks/asynchronous/workers/sqs/MessageWorkerFactory.java
lib/lib-worker/src/main/java/org/sagebionetworks/asynchronous/workers/sqs/TopicAndQueueUtils.java
lib/lib-worker/src/main/java/org/sagebionetworks/asynchronous/workers/swf/Activity.java
lib/lib-worker/src/main/java/org/sagebionetworks/asynchronous/workers/swf/ActivityWorker.java
lib/lib-worker/src/main/java/org/sagebionetworks/asynchronous/workers/swf/Decider.java
lib/lib-worker/src/main/java/org/sagebionetworks/asynchronous/workers/swf/DecisionWorker.java
lib/lib-worker/src/main/java/org/sagebionetworks/asynchronous/workers/swf/SimpleWorkFlowRegister.java
lib/lib-worker/src/main/java/org/sagebionetworks/asynchronous/workers/swf/SimpleWorkFlowRegisterImpl.java
lib/lib-worker/src/main/java/org/sagebionetworks/asynchronous/workers/swf/SimpleWorkFlowWatcher.java
lib/lib-worker/src/main/java/org/sagebionetworks/asynchronous/workers/swf/SwfTaskUtils.java
lib/lib-worker/src/main/java/org/sagebionetworks/asynchronous/workers/swf/Task.java
lib/lib-worker/src/main/java/org/sagebionetworks/asynchronous/workers/swf/WorkFlow.java
lib/lib-worker/src/main/resources/aws-spb.xml
lib/lib-worker/src/main/resources/commons-logging.properties
lib/lib-worker/src/main/resources/log4j.properties
lib/lib-worker/src/test/java/org/sagebionetworks/asynchronous/workers/sqs/MessageReceiverImplTest.java
lib/lib-worker/src/test/java/org/sagebionetworks/asynchronous/workers/sqs/MessageUtilsTest.java
lib/lib-worker/src/test/java/org/sagebionetworks/asynchronous/workers/sqs/StubWorker.java
lib/lib-worker/src/test/java/org/sagebionetworks/asynchronous/workers/sqs/StubWorkerFactory.java
lib/lib-worker/src/test/java/org/sagebionetworks/asynchronous/workers/swf/SimpleWorkFlowWatcherTest.java
lib/lib-worker/src/test/java/org/sagebionetworks/asynchronous/workers/swf/SwfTaskUtilsTest.java
lib/logging/pom.xml
lib/logging/src/main/java/org/sagebionetworks/logging/SynapseEvent.java
lib/logging/src/main/java/org/sagebionetworks/logging/SynapseLoggingUtils.java
lib/logging/src/test/java/org/sagebionetworks/logging/LoggingUtilsTestHelper.java
lib/logging/src/test/java/org/sagebionetworks/logging/SynapseLoggingUtilsTest.java
lib/models/pom.xml
lib/models/src/main/java/org/sagebionetworks/repo/model/ACLInheritanceException.java
lib/models/src/main/java/org/sagebionetworks/repo/model/AccessApprovalDAO.java
lib/models/src/main/java/org/sagebionetworks/repo/model/AccessControlListDAO.java
lib/models/src/main/java/org/sagebionetworks/repo/model/AccessRequirementBackup.java
lib/models/src/main/java/org/sagebionetworks/repo/model/AccessRequirementDAO.java
lib/models/src/main/java/org/sagebionetworks/repo/model/AuthorizationConstants.java
lib/models/src/main/java/org/sagebionetworks/repo/model/BackupRestoreStatusDAO.java
lib/models/src/main/java/org/sagebionetworks/repo/model/BaseDAO.java
lib/models/src/main/java/org/sagebionetworks/repo/model/BooleanResult.java
lib/models/src/main/java/org/sagebionetworks/repo/model/ConflictingUpdateException.java
lib/models/src/main/java/org/sagebionetworks/repo/model/DaemonStatusUtil.java
lib/models/src/main/java/org/sagebionetworks/repo/model/DatastoreException.java
lib/models/src/main/java/org/sagebionetworks/repo/model/EntityType.java
lib/models/src/main/java/org/sagebionetworks/repo/model/EnvironmentDescriptorOld.java
lib/models/src/main/java/org/sagebionetworks/repo/model/ErrorResponse.java
lib/models/src/main/java/org/sagebionetworks/repo/model/InvalidModelException.java
lib/models/src/main/java/org/sagebionetworks/repo/model/MigratableDAO.java
lib/models/src/main/java/org/sagebionetworks/repo/model/NameConflictException.java
lib/models/src/main/java/org/sagebionetworks/repo/model/NamedAnnotations.java
lib/models/src/main/java/org/sagebionetworks/repo/model/Node.java
lib/models/src/main/java/org/sagebionetworks/repo/model/NodeBackup.java
lib/models/src/main/java/org/sagebionetworks/repo/model/NodeBackupDAO.java
lib/models/src/main/java/org/sagebionetworks/repo/model/NodeConstants.java
lib/models/src/main/java/org/sagebionetworks/repo/model/NodeDAO.java
lib/models/src/main/java/org/sagebionetworks/repo/model/NodeInheritanceDAO.java
lib/models/src/main/java/org/sagebionetworks/repo/model/NodeQueryDao.java
lib/models/src/main/java/org/sagebionetworks/repo/model/NodeQueryResults.java
lib/models/src/main/java/org/sagebionetworks/repo/model/NodeRevisionBackup.java
lib/models/src/main/java/org/sagebionetworks/repo/model/ObservableEntity.java
lib/models/src/main/java/org/sagebionetworks/repo/model/PrefixConst.java
lib/models/src/main/java/org/sagebionetworks/repo/model/PrincipalBackup.java
lib/models/src/main/java/org/sagebionetworks/repo/model/QueryResults.java
lib/models/src/main/java/org/sagebionetworks/repo/model/ReferenceDao.java
lib/models/src/main/java/org/sagebionetworks/repo/model/RestoreFile.java
lib/models/src/main/java/org/sagebionetworks/repo/model/SchemaCache.java
lib/models/src/main/java/org/sagebionetworks/repo/model/StackStatusDao.java
lib/models/src/main/java/org/sagebionetworks/repo/model/StorageLocationDAO.java
lib/models/src/main/java/org/sagebionetworks/repo/model/StorageLocations.java
lib/models/src/main/java/org/sagebionetworks/repo/model/TagMessenger.java
lib/models/src/main/java/org/sagebionetworks/repo/model/TaggableEntity.java
lib/models/src/main/java/org/sagebionetworks/repo/model/TransientField.java
lib/models/src/main/java/org/sagebionetworks/repo/model/UnauthorizedException.java
lib/models/src/main/java/org/sagebionetworks/repo/model/User.java
lib/models/src/main/java/org/sagebionetworks/repo/model/UserDAO.java
lib/models/src/main/java/org/sagebionetworks/repo/model/UserGroupDAO.java
lib/models/src/main/java/org/sagebionetworks/repo/model/UserInfo.java
lib/models/src/main/java/org/sagebionetworks/repo/model/UserProfileDAO.java
lib/models/src/main/java/org/sagebionetworks/repo/model/message/TransactionalMessenger.java
lib/models/src/main/java/org/sagebionetworks/repo/model/message/TransactionalMessengerObserver.java
lib/models/src/main/java/org/sagebionetworks/repo/model/query/BasicQuery.java
lib/models/src/main/java/org/sagebionetworks/repo/model/query/Comparator.java
lib/models/src/main/java/org/sagebionetworks/repo/model/query/CompoundId.java
lib/models/src/main/java/org/sagebionetworks/repo/model/query/Expression.java
lib/models/src/main/java/org/sagebionetworks/repo/model/query/FieldType.java
lib/models/src/main/java/org/sagebionetworks/repo/model/query/Operator.java
lib/models/src/main/java/org/sagebionetworks/repo/model/registry/EntityMigrationData.java
lib/models/src/main/java/org/sagebionetworks/repo/model/registry/MigrationDataLoader.java
lib/models/src/main/java/org/sagebionetworks/repo/model/registry/MigrationDataLoaderImpl.java
lib/models/src/main/java/org/sagebionetworks/repo/model/registry/MigrationSpecData.java
lib/models/src/main/java/org/sagebionetworks/repo/model/registry/MigrationSpecDataLoader.java
lib/models/src/main/java/org/sagebionetworks/repo/model/registry/MigrationSpecDataLoaderImpl.java
lib/models/src/main/java/org/sagebionetworks/repo/model/util/AccessControlListUtil.java
lib/models/src/main/java/org/sagebionetworks/repo/model/util/RandomAccessControlListUtil.java
lib/models/src/main/java/org/sagebionetworks/repo/model/util/RandomAnnotationsUtil.java
lib/models/src/main/java/org/sagebionetworks/repo/model/util/RandomNodeBackupUtil.java
lib/models/src/main/java/org/sagebionetworks/repo/model/util/RandomNodeRevisionUtil.java
lib/models/src/main/java/org/sagebionetworks/repo/model/util/RandomNodeUtil.java
lib/models/src/main/java/org/sagebionetworks/repo/model/util/RandomUtils.java
lib/models/src/main/java/org/sagebionetworks/repo/model/util/UserGroupUtil.java
lib/models/src/main/java/org/sagebionetworks/repo/web/ForbiddenException.java
lib/models/src/main/java/org/sagebionetworks/repo/web/NotFoundException.java
lib/models/src/test/java/org/sagebionetworks/repo/manager/SchemaCacheTest.java
lib/models/src/test/java/org/sagebionetworks/repo/model/AccessControlListInheritanceExceptionTest.java
lib/models/src/test/java/org/sagebionetworks/repo/model/AccessControlListTest.java
lib/models/src/test/java/org/sagebionetworks/repo/model/AllEntityTest.java
lib/models/src/test/java/org/sagebionetworks/repo/model/AnalysisTest.java
lib/models/src/test/java/org/sagebionetworks/repo/model/CodeTest.java
lib/models/src/test/java/org/sagebionetworks/repo/model/DatasetTest.java
lib/models/src/test/java/org/sagebionetworks/repo/model/EntityTypeTest.java
lib/models/src/test/java/org/sagebionetworks/repo/model/ExpressionDataTest.java
lib/models/src/test/java/org/sagebionetworks/repo/model/GenotypeDataTest.java
lib/models/src/test/java/org/sagebionetworks/repo/model/LayerTest.java
lib/models/src/test/java/org/sagebionetworks/repo/model/NamedAnnotationsTest.java
lib/models/src/test/java/org/sagebionetworks/repo/model/NodeTest.java
lib/models/src/test/java/org/sagebionetworks/repo/model/ObjectTypeTest.java
lib/models/src/test/java/org/sagebionetworks/repo/model/PaginatedResultsTest.java
lib/models/src/test/java/org/sagebionetworks/repo/model/PhenotypeDataTest.java
lib/models/src/test/java/org/sagebionetworks/repo/model/PreviewTest.java
lib/models/src/test/java/org/sagebionetworks/repo/model/ProjectTest.java
lib/models/src/test/java/org/sagebionetworks/repo/model/QueryResultsTest.java
lib/models/src/test/java/org/sagebionetworks/repo/model/RObjectTest.java
lib/models/src/test/java/org/sagebionetworks/repo/model/ResourceAccessTest.java
lib/models/src/test/java/org/sagebionetworks/repo/model/RuntimeExceptionTest.java
lib/models/src/test/java/org/sagebionetworks/repo/model/UserGroupTest.java
lib/models/src/test/java/org/sagebionetworks/repo/model/UserInfoTest.java
lib/models/src/test/java/org/sagebionetworks/repo/model/UserTest.java
lib/models/src/test/java/org/sagebionetworks/repo/model/registry/EntityMigrationTest.java
lib/models/src/test/java/org/sagebionetworks/repo/model/registry/MigrationDataLoaderImplTest.java
lib/models/src/test/java/org/sagebionetworks/repo/model/registry/MigrationSpecDataLoaderImplTest.java
lib/models/src/test/java/org/sagebionetworks/repo/model/registry/MigrationSpecTest.java
lib/pom.xml
lib/securityUtilities/pom.xml
lib/securityUtilities/src/main/java/org/sagebionetworks/securitytools/HMACUtils.java
lib/securityUtilities/src/test/java/org/sagebionetworks/securitytools/HMACUtilsTest.java
lib/stackConfiguration/pom.xml
lib/stackConfiguration/src/main/java/org/sagebionetworks/S3PropertyFileLoader.java
lib/stackConfiguration/src/main/java/org/sagebionetworks/SettingsLoader.java
lib/stackConfiguration/src/main/java/org/sagebionetworks/StackConfiguration.java
lib/stackConfiguration/src/main/java/org/sagebionetworks/StackConstants.java
lib/stackConfiguration/src/main/java/org/sagebionetworks/StackUtils.java
lib/stackConfiguration/src/main/java/org/sagebionetworks/StringEncrypter.java
lib/stackConfiguration/src/main/java/org/sagebionetworks/TemplatedConfiguration.java
lib/stackConfiguration/src/main/java/org/sagebionetworks/TemplatedConfigurationImpl.java
lib/stackConfiguration/src/main/resources/commons-logging.properties
lib/stackConfiguration/src/main/resources/log4j.properties
lib/stackConfiguration/src/main/resources/stack-configuration.spb.xml
lib/stackConfiguration/src/main/resources/stack.properties
lib/stackConfiguration/src/main/resources/template.properties
lib/stackConfiguration/src/test/java/org/sagebionetworks/ExpectedStackBeansTest.java
lib/stackConfiguration/src/test/java/org/sagebionetworks/S3PropertyFileLoaderTest.java
lib/stackConfiguration/src/test/java/org/sagebionetworks/SettingsLoaderTest.java
lib/stackConfiguration/src/test/java/org/sagebionetworks/StackConfigurationTest.java
lib/stackConfiguration/src/test/java/org/sagebionetworks/StackUtilsTest.java
lib/stackConfiguration/src/test/java/org/sagebionetworks/StringEncrypterTest.java
lib/stackConfiguration/src/test/resources/someBrandNewStack.properties
lib/stackConfiguration/src/test/resources/test-stack-config.spb.xml
pom.xml
pomSnapshotToGitHash.sh
pomSnapshotToLastGitTag.sh
pomVersioner.py
services/auth/pom.xml
services/auth/src/main/java/org/sagebionetworks/auth/AuthenticationController.java
services/auth/src/main/java/org/sagebionetworks/auth/BaseController.java
services/auth/src/main/java/org/sagebionetworks/auth/ErrorResponse.java
services/auth/src/main/java/org/sagebionetworks/auth/OpenIDInfo.java
services/auth/src/main/java/org/sagebionetworks/auth/ResourceAccessController.java
services/auth/src/main/java/org/sagebionetworks/auth/ResourceAccessManager.java
services/auth/src/main/java/org/sagebionetworks/auth/ResourceAccessToken.java
services/auth/src/main/java/org/sagebionetworks/auth/ResourceUserData.java
services/auth/src/main/java/org/sagebionetworks/auth/SampleConsumer.java
services/auth/src/main/java/org/sagebionetworks/auth/SecretKey.java
services/auth/src/main/resources/commons-logging.properties
services/auth/src/main/resources/log4j.properties
services/auth/src/main/resources/logging.properties
services/auth/src/main/webapp/META-INF/MANIFEST.MF
services/auth/src/main/webapp/WEB-INF/authentication-context.xml
services/auth/src/main/webapp/WEB-INF/authentication-servlet.xml
services/auth/src/main/webapp/WEB-INF/web.xml
services/auth/src/main/webapp/auth/v1/termsOfUse.html
services/auth/src/main/webapp/index.html
services/auth/src/test/java/org/sagebionetworks/auth/ResourceAccessManagerTest.java
services/auth/src/test/java/org/sagebionetworks/auth/SerializationTest.java
services/authutil/pom.xml
services/authutil/src/main/java/org/sagebionetworks/authutil/AuthenticationException.java
services/authutil/src/main/java/org/sagebionetworks/authutil/CrowdAuthUtil.java
services/authutil/src/main/java/org/sagebionetworks/authutil/CrowdAuthenticationFilter.java
services/authutil/src/main/java/org/sagebionetworks/authutil/CrowdUserDAO.java
services/authutil/src/main/java/org/sagebionetworks/authutil/ModParamHttpServletRequest.java
services/authutil/src/main/java/org/sagebionetworks/authutil/MyProvider.java
services/authutil/src/main/java/org/sagebionetworks/authutil/SendMail.java
services/authutil/src/main/java/org/sagebionetworks/authutil/Session.java
services/authutil/src/main/java/org/sagebionetworks/authutil/User.java
services/authutil/src/main/resources/authutil.properties
services/authutil/src/main/resources/resetpasswordEmail.txt
services/authutil/src/main/resources/setAPIpasswordEmail.txt
services/authutil/src/main/resources/setpasswordEmail.txt
services/authutil/src/test/java/org/sagebionetworks/authutil/CrowdAuthUtilTest.java
services/authutil/src/test/java/org/sagebionetworks/authutil/CrowdAuthenticationFilterTest.java
services/authutil/src/test/java/org/sagebionetworks/authutil/CrowdUserDAOTest.java
services/authutil/src/test/java/org/sagebionetworks/repo/model/CrowdUserDAOTest.java
services/dynamo/pom.xml
services/dynamo/src/main/java/org/sagebionetworks/dynamo/workers/sqs/DynamoQueueWorker.java
services/dynamo/src/main/java/org/sagebionetworks/dynamo/workers/sqs/DynamoQueueWorkerFactory.java
services/dynamo/src/main/resources/dynamo-spb.xml
services/dynamo/src/main/webapp/WEB-INF/dynamo-context.xml
services/dynamo/src/main/webapp/WEB-INF/web.xml
services/dynamo/src/test/java/org/sagebionetworks/dynamo/workers/sqs/DynamoQueueWorkerIntegrationTest.java
services/pom.xml
services/repository-managers/pom.xml
services/repository-managers/src/main/java/org/sagebionetworks/repo/manager/ACTUtils.java
services/repository-managers/src/main/java/org/sagebionetworks/repo/manager/AccessApprovalManager.java
services/repository-managers/src/main/java/org/sagebionetworks/repo/manager/AccessApprovalManagerImpl.java
services/repository-managers/src/main/java/org/sagebionetworks/repo/manager/AccessRequirementManager.java
services/repository-managers/src/main/java/org/sagebionetworks/repo/manager/AccessRequirementManagerImpl.java
services/repository-managers/src/main/java/org/sagebionetworks/repo/manager/AmazonS3Utility.java
services/repository-managers/src/main/java/org/sagebionetworks/repo/manager/AmazonS3UtilityImpl.java
services/repository-managers/src/main/java/org/sagebionetworks/repo/manager/AttachmentManager.java
services/repository-managers/src/main/java/org/sagebionetworks/repo/manager/AttachmentManagerImpl.java
services/repository-managers/src/main/java/org/sagebionetworks/repo/manager/AuthorizationManager.java
services/repository-managers/src/main/java/org/sagebionetworks/repo/manager/AuthorizationManagerImpl.java
services/repository-managers/src/main/java/org/sagebionetworks/repo/manager/EntityManager.java
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services/repository-managers/src/main/java/org/sagebionetworks/repo/manager/EntityToMapUtil.java
services/repository-managers/src/main/java/org/sagebionetworks/repo/manager/EntityWithAnnotations.java
services/repository-managers/src/main/java/org/sagebionetworks/repo/manager/NodeInheritanceManager.java
services/repository-managers/src/main/java/org/sagebionetworks/repo/manager/NodeInheritanceManagerImpl.java
services/repository-managers/src/main/java/org/sagebionetworks/repo/manager/NodeManager.java
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services/repository-managers/src/main/java/org/sagebionetworks/repo/manager/NodeTranslationUtils.java
services/repository-managers/src/main/java/org/sagebionetworks/repo/manager/PermissionsManager.java
services/repository-managers/src/main/java/org/sagebionetworks/repo/manager/PermissionsManagerImpl.java
services/repository-managers/src/main/java/org/sagebionetworks/repo/manager/PreviewWorker.java
services/repository-managers/src/main/java/org/sagebionetworks/repo/manager/S3TokenManager.java
services/repository-managers/src/main/java/org/sagebionetworks/repo/manager/S3TokenManagerImpl.java
services/repository-managers/src/main/java/org/sagebionetworks/repo/manager/SchemaManager.java
services/repository-managers/src/main/java/org/sagebionetworks/repo/manager/SchemaManagerImpl.java
services/repository-managers/src/main/java/org/sagebionetworks/repo/manager/SpecialUrlEncoding.java
services/repository-managers/src/main/java/org/sagebionetworks/repo/manager/StackStatusManager.java
services/repository-managers/src/main/java/org/sagebionetworks/repo/manager/StackStatusManagerImpl.java
services/repository-managers/src/main/java/org/sagebionetworks/repo/manager/StorageUsageManager.java
services/repository-managers/src/main/java/org/sagebionetworks/repo/manager/StorageUsageManagerImpl.java
services/repository-managers/src/main/java/org/sagebionetworks/repo/manager/TempMockAuthDao.java
services/repository-managers/src/main/java/org/sagebionetworks/repo/manager/TestUserDAO.java
services/repository-managers/src/main/java/org/sagebionetworks/repo/manager/UserManager.java
services/repository-managers/src/main/java/org/sagebionetworks/repo/manager/UserManagerImpl.java
services/repository-managers/src/main/java/org/sagebionetworks/repo/manager/UserProfileManager.java
services/repository-managers/src/main/java/org/sagebionetworks/repo/manager/UserProfileManagerImpl.java
services/repository-managers/src/main/java/org/sagebionetworks/repo/manager/UserProfileManagerUtils.java
services/repository-managers/src/main/java/org/sagebionetworks/repo/manager/backup/AccessRequirementBackupDriver.java
services/repository-managers/src/main/java/org/sagebionetworks/repo/manager/backup/GenericBackupDriver.java
services/repository-managers/src/main/java/org/sagebionetworks/repo/manager/backup/NodeBackupDestination.java
services/repository-managers/src/main/java/org/sagebionetworks/repo/manager/backup/NodeBackupDriverImpl.java
services/repository-managers/src/main/java/org/sagebionetworks/repo/manager/backup/NodeBackupManager.java
services/repository-managers/src/main/java/org/sagebionetworks/repo/manager/backup/NodeBackupManagerImpl.java
services/repository-managers/src/main/java/org/sagebionetworks/repo/manager/backup/NodeBackupSource.java
services/repository-managers/src/main/java/org/sagebionetworks/repo/manager/backup/NodeSerializer.java
services/repository-managers/src/main/java/org/sagebionetworks/repo/manager/backup/NodeSerializerImpl.java
services/repository-managers/src/main/java/org/sagebionetworks/repo/manager/backup/NodeSerializerUtil.java
services/repository-managers/src/main/java/org/sagebionetworks/repo/manager/backup/PrincipalBackupDriver.java
services/repository-managers/src/main/java/org/sagebionetworks/repo/manager/backup/Progress.java
services/repository-managers/src/main/java/org/sagebionetworks/repo/manager/backup/daemon/BackupDaemon.java
services/repository-managers/src/main/java/org/sagebionetworks/repo/manager/backup/daemon/BackupDaemonLauncher.java
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services/repository/src/test/java/org/sagebionetworks/repo/web/controller/AccessApprovalControllerAutowiredTest.java
services/repository/src/test/java/org/sagebionetworks/repo/web/controller/AccessRequirementControllerAutowiredTest.java
services/repository/src/test/java/org/sagebionetworks/repo/web/controller/ActivityLoggerTestHelper.java
services/repository/src/test/java/org/sagebionetworks/repo/web/controller/AdministrationControllerTest.java
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services/repository/src/test/java/org/sagebionetworks/repo/web/controller/DefaultControllerAutowiredTest.java
services/repository/src/test/java/org/sagebionetworks/repo/web/controller/DispatchServletSingleton.java
services/repository/src/test/java/org/sagebionetworks/repo/web/controller/EntityBundleControllerTest.java
services/repository/src/test/java/org/sagebionetworks/repo/web/controller/EntityControllerTest.java
services/repository/src/test/java/org/sagebionetworks/repo/web/controller/EntityObjectMapper.java
services/repository/src/test/java/org/sagebionetworks/repo/web/controller/EntityServletTestHelper.java
services/repository/src/test/java/org/sagebionetworks/repo/web/controller/HealthCheckControllerTest.java
services/repository/src/test/java/org/sagebionetworks/repo/web/controller/Helpers.java
services/repository/src/test/java/org/sagebionetworks/repo/web/controller/JSONEntityHttpMessageConverterTest.java
services/repository/src/test/java/org/sagebionetworks/repo/web/controller/JSONEntityHttpMessageStreamReadWrite.java
services/repository/src/test/java/org/sagebionetworks/repo/web/controller/JSONEntityUtilTest.java
services/repository/src/test/java/org/sagebionetworks/repo/web/controller/LayerAnnotationsControllerTest.java
services/repository/src/test/java/org/sagebionetworks/repo/web/controller/LayerControllerTest.java
services/repository/src/test/java/org/sagebionetworks/repo/web/controller/LocationableControllerTest.java
services/repository/src/test/java/org/sagebionetworks/repo/web/controller/MetadataProviderFactoryTest.java
services/repository/src/test/java/org/sagebionetworks/repo/web/controller/MockWebApplication.java
services/repository/src/test/java/org/sagebionetworks/repo/web/controller/MockWebApplicationContextLoader.java
services/repository/src/test/java/org/sagebionetworks/repo/web/controller/ObjectTypeFactory.java
services/repository/src/test/java/org/sagebionetworks/repo/web/controller/ObjectTypeSerializerTest.java
services/repository/src/test/java/org/sagebionetworks/repo/web/controller/PreviewControllerTest.java
services/repository/src/test/java/org/sagebionetworks/repo/web/controller/PrincipalsControllerAutowiredTest.java
services/repository/src/test/java/org/sagebionetworks/repo/web/controller/QueryControllerAutowireTest.java
services/repository/src/test/java/org/sagebionetworks/repo/web/controller/QueryControllerTest.java
services/repository/src/test/java/org/sagebionetworks/repo/web/controller/QueryControllerXMLTest.java
services/repository/src/test/java/org/sagebionetworks/repo/web/controller/QueryTranslatorTest.java
services/repository/src/test/java/org/sagebionetworks/repo/web/controller/S3TokenControllerTest.java
services/repository/src/test/java/org/sagebionetworks/repo/web/controller/SearchControllerTest.java
services/repository/src/test/java/org/sagebionetworks/repo/web/controller/ServletTestHelper.java
services/repository/src/test/java/org/sagebionetworks/repo/web/controller/ServletTestHelperException.java
services/repository/src/test/java/org/sagebionetworks/repo/web/controller/StepControllerTest.java
services/repository/src/test/java/org/sagebionetworks/repo/web/controller/StorageUsageControllerTest.java
services/repository/src/test/java/org/sagebionetworks/repo/web/controller/SynapseVersionInfoControllerTest.java
services/repository/src/test/java/org/sagebionetworks/repo/web/controller/UrlHelperTest.java
services/repository/src/test/java/org/sagebionetworks/repo/web/controller/UserProfileControllerTest.java
services/repository/src/test/java/org/sagebionetworks/repo/web/controller/metadata/AllTypesValidatorTest.java
services/repository/src/test/java/org/sagebionetworks/repo/web/controller/metadata/LayerMetadataProviderTest.java
services/repository/src/test/java/org/sagebionetworks/repo/web/controller/metadata/LocationableMetadataProviderTest.java
services/repository/src/test/java/org/sagebionetworks/repo/web/controller/metadata/PreviewMetadataProviderTest.java
services/repository/src/test/java/org/sagebionetworks/repo/web/controller/metadata/ProjectMetadataProviderTest.java
services/repository/src/test/java/org/sagebionetworks/repo/web/controller/metadata/StepMetadataProviderTest.java
services/repository/src/test/java/org/sagebionetworks/repo/web/service/EntityBundleServiceImplTest.java
services/repository/src/test/java/org/sagebionetworks/repo/web/service/SearchHelperTest.java
services/repository/src/test/java/org/sagebionetworks/repo/web/service/SearchServiceImplTest.java
services/repository/src/test/java/org/sagebionetworks/repo/web/service/SearchUtilTest.java
services/repository/src/test/java/org/sagebionetworks/repo/web/service/ServletTestHelper.java
services/repository/src/test/java/org/sagebionetworks/repo/web/service/StorageUsageServiceImplTest.java
services/repository/src/test/java/org/sagebionetworks/repo/web/service/UserProfileServiceScheduledTest.java
services/repository/src/test/java/org/sagebionetworks/repo/web/service/UserProfileServiceTest.java
services/repository/src/test/java/org/sagebionetworks/repo/web/util/UserProvider.java
services/repository/src/test/java/org/sagebionetworks/repo/web/util/UserProviderImpl.java
services/repository/src/test/java/org/sagebionetworks/sweeper/log4j/Compare.java
services/repository/src/test/java/org/sagebionetworks/sweeper/log4j/SweepActionTest.java
services/repository/src/test/java/org/sagebionetworks/sweeper/log4j/TimeBasedRollingToS3PolicyIntegrationTest.java
services/repository/src/test/java/org/sagebionetworks/sweeper/log4j/TimeBasedRollingToS3PolicyTest.java
services/repository/src/test/java/profiler/org/sagebionetworks/FrameTest.java
services/repository/src/test/java/profiler/org/sagebionetworks/cloudwatch/ConsumerTest.java
services/repository/src/test/java/profiler/org/sagebionetworks/cloudwatch/ControllerProfilerAutowiredTest.java
services/repository/src/test/java/profiler/org/sagebionetworks/cloudwatch/ControllerProfilerTest.java
services/repository/src/test/java/profiler/org/sagebionetworks/cloudwatch/ProfileDataTest.java
services/repository/src/test/java/profiler/org/sagebionetworks/cloudwatch/WatcherTest.java
services/repository/src/test/java/profiler/org/sagebionetworks/usagemetrics/ActivityLoggerAutowiredTest.java
services/repository/src/test/java/profiler/org/sagebionetworks/usagemetrics/ActivityLoggerTest.java
services/repository/src/test/resources/activityLoggerAutowired-spb.xml
services/repository/src/test/resources/controllerProfilerAutowired-spb.xml
services/repository/src/test/resources/images/notAnImage.txt
services/repository/src/test/resources/images/shortWide.gif
services/repository/src/test/resources/images/squarish.png
services/repository/src/test/resources/images/tallSkinny.jpg
services/repository/src/test/resources/org/sagebionetworks/sweeper/log4j/tbrts3-test.0.gz
services/repository/src/test/resources/org/sagebionetworks/sweeper/log4j/tbrts3-test.1.gz
services/repository/src/test/resources/org/sagebionetworks/sweeper/log4j/tbrts3-test.2.gz
services/repository/src/test/resources/org/sagebionetworks/sweeper/log4j/tbrts3-test.3
services/repository/src/test/resources/test-context.xml
services/search/pom.xml
services/search/src/main/java/org/sagebionetworks/search/controller/SearchController.java
services/search/src/main/java/org/sagebionetworks/search/workers/sqs/search/SearchQueueWorker.java
services/search/src/main/java/org/sagebionetworks/search/workers/sqs/search/SearchQueueWorkerFactory.java
services/search/src/main/resources/commons-logging.properties
services/search/src/main/resources/log4j.properties
services/search/src/main/resources/sqs-manager-spb.xml
services/search/src/main/webapp/WEB-INF/search-context.xml
services/search/src/main/webapp/WEB-INF/search-servlet.xml
services/search/src/main/webapp/WEB-INF/web.xml
services/search/src/main/webapp/index.html
services/search/src/test/java/org/sagebionetworks/search/workers/sqs/search/SearchQueueWorkerTest.java
services/search/src/test/java/org/sagebionetworks/search/workers/sqs/search/SearchWorkerIntegrationTest.java
services/search/src/test/resources/test-context.xml
tools/SynapseDeployer/.pydevproject
tools/SynapseDeployer/artifactoryClient.py
tools/SynapseDeployer/createSearchIndex.sh
tools/SynapseDeployer/exception.py
tools/SynapseDeployer/main.py
tools/SynapseDeployer/pom.xml
tools/SynapseDeployer/supervisord-init.d
tools/SynapseDeployer/synapseAwsEnvironment.py
tools/SynapseDeployer/synapseDeployer-assembly.xml
tools/bamboo/bin/customise-extras.sh
tools/bamboo/bin/mysqld_safe
tools/bamboo/bin/runR.sh
tools/bamboo/maven/dotm2/settings.xml
tools/bccSetup/pom.xml
tools/bccSetup/src/main/java/org/sagebionetworks/bccsetup/BccConfigHelper.java
tools/bccSetup/src/main/java/org/sagebionetworks/bccsetup/OAuthUtils.java
tools/bccSetup/src/main/java/org/sagebionetworks/bccsetup/SpreadsheetHelper.java
tools/bccSetup/src/main/resources/bccsetup.properties
tools/bccSetup/src/main/resources/bccsetupTemplate.properties
tools/datapacketTools/breakout_all_layers.sh
tools/datapacketTools/breakout_layers.sh
tools/datapacketTools/generate_md5sums.sh
tools/pom.xml
tools/tool-migration-utility/MigrateLocations.sh
tools/tool-migration-utility/MigrationUtilityUI.sh
tools/tool-migration-utility/pom.xml
tools/tool-migration-utility/run_migrator.sh
tools/tool-migration-utility/src/main/java/org/sagebionetworks/tool/migration/AllEntityDataWorker.java
tools/tool-migration-utility/src/main/java/org/sagebionetworks/tool/migration/ClientFactory.java
tools/tool-migration-utility/src/main/java/org/sagebionetworks/tool/migration/ClientFactoryImpl.java
tools/tool-migration-utility/src/main/java/org/sagebionetworks/tool/migration/Configuration.java
tools/tool-migration-utility/src/main/java/org/sagebionetworks/tool/migration/Constants.java
tools/tool-migration-utility/src/main/java/org/sagebionetworks/tool/migration/MigrationConfigurationImpl.java
tools/tool-migration-utility/src/main/java/org/sagebionetworks/tool/migration/Progress/AggregateProgress.java
tools/tool-migration-utility/src/main/java/org/sagebionetworks/tool/migration/Progress/BasicProgress.java
tools/tool-migration-utility/src/main/java/org/sagebionetworks/tool/migration/Progress/Progress.java
tools/tool-migration-utility/src/main/java/org/sagebionetworks/tool/migration/Progress/StatusData.java
tools/tool-migration-utility/src/main/java/org/sagebionetworks/tool/migration/RepositoryMigrationDriver.java
tools/tool-migration-utility/src/main/java/org/sagebionetworks/tool/migration/ResponseBundle.java
tools/tool-migration-utility/src/main/java/org/sagebionetworks/tool/migration/SynapseConnectionInfo.java
tools/tool-migration-utility/src/main/java/org/sagebionetworks/tool/migration/dao/EntityData.java
tools/tool-migration-utility/src/main/java/org/sagebionetworks/tool/migration/dao/EntityQueryResults.java
tools/tool-migration-utility/src/main/java/org/sagebionetworks/tool/migration/dao/MigrationQueryRunner.java
tools/tool-migration-utility/src/main/java/org/sagebionetworks/tool/migration/dao/QueryRunner.java
tools/tool-migration-utility/src/main/java/org/sagebionetworks/tool/migration/dao/QueryRunnerImpl.java
tools/tool-migration-utility/src/main/java/org/sagebionetworks/tool/migration/gui/MigrationConsoleUI.java
tools/tool-migration-utility/src/main/java/org/sagebionetworks/tool/migration/gui/PreviewUtil.java
tools/tool-migration-utility/src/main/java/org/sagebionetworks/tool/migration/gui/RepositoryType.java
tools/tool-migration-utility/src/main/java/org/sagebionetworks/tool/migration/gui/model/EntityCountModel.java
tools/tool-migration-utility/src/main/java/org/sagebionetworks/tool/migration/gui/presenter/MigrationControlPresenter.java
tools/tool-migration-utility/src/main/java/org/sagebionetworks/tool/migration/gui/presenter/StackStatusPresenter.java
tools/tool-migration-utility/src/main/java/org/sagebionetworks/tool/migration/gui/view/MigrationControlView.java
tools/tool-migration-utility/src/main/java/org/sagebionetworks/tool/migration/gui/view/StackStatusEditor.java
tools/tool-migration-utility/src/main/java/org/sagebionetworks/tool/migration/gui/view/StackStatusView.java
tools/tool-migration-utility/src/main/java/org/sagebionetworks/tool/migration/job/AWSInfo.java
tools/tool-migration-utility/src/main/java/org/sagebionetworks/tool/migration/job/AggregateResult.java
tools/tool-migration-utility/src/main/java/org/sagebionetworks/tool/migration/job/BuilderResponse.java
tools/tool-migration-utility/src/main/java/org/sagebionetworks/tool/migration/job/CreateJob.java
tools/tool-migration-utility/src/main/java/org/sagebionetworks/tool/migration/job/CreateUpdateWorker.java
tools/tool-migration-utility/src/main/java/org/sagebionetworks/tool/migration/job/CreationJobBuilder.java
tools/tool-migration-utility/src/main/java/org/sagebionetworks/tool/migration/job/DeleteJobBuilder.java
tools/tool-migration-utility/src/main/java/org/sagebionetworks/tool/migration/job/DeleteWorker.java
tools/tool-migration-utility/src/main/java/org/sagebionetworks/tool/migration/job/Job.java
tools/tool-migration-utility/src/main/java/org/sagebionetworks/tool/migration/job/JobQueueWorker.java
tools/tool-migration-utility/src/main/java/org/sagebionetworks/tool/migration/job/JobUtil.java
tools/tool-migration-utility/src/main/java/org/sagebionetworks/tool/migration/job/UpdateJobBuilder.java
tools/tool-migration-utility/src/main/java/org/sagebionetworks/tool/migration/job/WorkerResult.java
tools/tool-migration-utility/src/main/resources/commons-logging.properties
tools/tool-migration-utility/src/main/resources/configuation-template.properties
tools/tool-migration-utility/src/main/resources/icons/forward.png
tools/tool-migration-utility/src/main/resources/log4j.properties
tools/tool-migration-utility/src/main/resources/searchUpdater.properties
tools/tool-migration-utility/src/main/resources/searchUpdaterTemplate.properties
tools/tool-migration-utility/src/test/java/org/sagebionetworks/tool/migration/ConfigurationTest.java
tools/tool-migration-utility/src/test/java/org/sagebionetworks/tool/migration/MigrationDriverManualTest.java
tools/tool-migration-utility/src/test/java/org/sagebionetworks/tool/migration/MigrationDriverTest.java
tools/tool-migration-utility/src/test/java/org/sagebionetworks/tool/migration/QueryRunnerImplUnitTest.java
tools/tool-migration-utility/src/test/java/org/sagebionetworks/tool/migration/SanityCheck.java
tools/tool-migration-utility/src/test/java/org/sagebionetworks/tool/migration/dao/EntityDataTest.java
tools/tool-migration-utility/src/test/java/org/sagebionetworks/tool/migration/job/CreationJobBuilderTest.java
tools/tool-migration-utility/src/test/java/org/sagebionetworks/tool/migration/job/DeleteJobBuilderTest.java
tools/tool-migration-utility/src/test/java/org/sagebionetworks/tool/migration/job/UpdateJobBuilderTest.java
tools/tool-migration-utility/src/test/java/org/sagebionetworks/tool/migration/job/XestUtil.java
tools/tool-migration-utility/src/test/resources/configuation-test.properties
tools/usageMetrics/pom.xml
tools/usageMetrics/src/main/java/org/sagebionetworks/usagemetrics/AuthEvent.java
tools/usageMetrics/src/main/java/org/sagebionetworks/usagemetrics/CrowdLogParser.java
tools/usageMetrics/src/main/java/org/sagebionetworks/usagemetrics/ProjectActivityStats.java
tools/usageMetrics/src/main/java/org/sagebionetworks/usagemetrics/UsageMetricsUtils.java
tools/usageMetrics/src/test/java/org/sagebionetworks/usagemetrics/CrowdAuthParserTest.java
tools/usageMetrics/src/test/java/org/sagebionetworks/usagemetrics/ProjectActivityStatsTest.java
tools/wikiutil/generateProvenanceRESTAPIDocumentation.sh
tools/wikiutil/generateRESTAPIDocumentation.sh
tools/wikiutil/generateRepositoryServiceWiki.sh
tools/wikiutil/pom.xml
tools/wikiutil/src/main/java/org/sagebionetworks/client/DataUploaderRESTDocumentationGenerator.java
tools/wikiutil/src/main/java/org/sagebionetworks/client/EntityDocumentation.java
tools/wikiutil/src/main/java/org/sagebionetworks/client/ManualProvenanceDocumentation.java
tools/wikiutil/src/main/java/org/sagebionetworks/client/SynapseRESTDocumentationGenerator.java
tools/wikiutil/src/main/java/org/sagebionetworks/repo/CRUDWikiGenerator.java
tools/wikiutil/src/main/java/org/sagebionetworks/repo/ReadOnlyWikiGenerator.java
tools/wikiutil/src/main/java/org/sagebionetworks/repo/WikiGenerator.java
tools/wikiutil/src/main/resources/EntityDocumentationPrefix.html
tools/wikiutil/src/main/resources/EntityDocumentationSuffix.html
tools/wikiutil/src/main/resources/RepositoryWikiPrefix.txt
tools/wikiutil/src/main/resources/RepositoryWikiSuffix.txt
tools/wikiutil/src/main/resources/VersionStaticContent.txt
tools/wikiutil/src/main/resources/commons-logging.properties
tools/wikiutil/src/main/resources/log4j.properties
tools/wikiutil/src/test/java/org/sagebionetworks/repo/CRUDWikiGeneratorTest.java

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