Repository: airavata Updated Branches: refs/heads/auroraMesosIntegration 21b1923da -> 58db74346
Merge pull request #1 from apache/develop Merge airvata develop with local develop Project: http://git-wip-us.apache.org/repos/asf/airavata/repo Commit: http://git-wip-us.apache.org/repos/asf/airavata/commit/7dd85164 Tree: http://git-wip-us.apache.org/repos/asf/airavata/tree/7dd85164 Diff: http://git-wip-us.apache.org/repos/asf/airavata/diff/7dd85164 Branch: refs/heads/auroraMesosIntegration Commit: 7dd85164103ea492351e25695b4c9b48a9840703 Parents: 59142dd 76c9eaf Author: Gourav Shenoy <[email protected]> Authored: Sun Oct 23 13:01:27 2016 -0400 Committer: GitHub <[email protected]> Committed: Sun Oct 23 13:01:27 2016 -0400 ---------------------------------------------------------------------- airavata-api/airavata-api-server/pom.xml | 17 +- .../server/handler/AiravataServerHandler.java | 1073 +- .../java/org/apache/airavata/api/Airavata.java | 74743 +++++++++++------ .../main/resources/lib/airavata/Airavata.cpp | 42654 ++++++---- .../src/main/resources/lib/airavata/Airavata.h | 2838 +- .../lib/airavata/Airavata_server.skeleton.cpp | 371 +- .../resources/lib/airavata/airavata_api_types.h | 1 + .../airavata/compute_resource_model_types.cpp | 28 +- .../lib/airavata/compute_resource_model_types.h | 13 +- .../resources/lib/airavata/job_model_types.cpp | 30 +- .../resources/lib/airavata/job_model_types.h | 12 +- .../lib/airavata/process_model_types.cpp | 60 +- .../lib/airavata/process_model_types.h | 22 +- .../resources/lib/airavata/task_model_types.cpp | 60 +- .../resources/lib/airavata/task_model_types.h | 18 +- .../user_resource_profile_model_constants.cpp | 34 + .../user_resource_profile_model_constants.h | 41 + .../user_resource_profile_model_types.cpp | 737 + .../user_resource_profile_model_types.h | 326 + .../resources/lib/Airavata/API/Airavata.php | 18554 ++-- .../Model/AppCatalog/ComputeResource/Types.php | 2 + .../lib/Airavata/Model/Process/Types.php | 44 +- .../resources/lib/Airavata/Model/Task/Types.php | 44 +- .../resources/lib/Airavata/Model/job/Types.php | 22 +- .../lib/apache/airavata/api/Airavata-remote | 105 + .../lib/apache/airavata/api/Airavata.py | 18108 ++-- .../resources/lib/apache/airavata/api/ttypes.py | 1 + .../model/appcatalog/computeresource/ttypes.py | 5 + .../lib/apache/airavata/model/job/ttypes.py | 22 +- .../lib/apache/airavata/model/process/ttypes.py | 42 +- .../lib/apache/airavata/model/task/ttypes.py | 46 +- .../computeresource/LOCALSubmission.java | 53 +- .../appcatalog/computeresource/MonitorMode.java | 5 +- .../credentialsummary/CredentialSummary.java | 826 + .../UserComputeResourcePreference.java | 1381 + .../UserResourceProfile.java | 1169 + .../UserStoragePreference.java | 728 + .../org/apache/airavata/model/job/JobModel.java | 103 +- .../airavata/model/process/ProcessModel.java | 179 +- .../apache/airavata/model/task/TaskModel.java | 178 +- dev-tools/ansible/README.md | 15 +- dev-tools/ansible/group_vars/all.yml | 5 +- dev-tools/ansible/hosts | 2 +- .../templates/airavata-server.properties.j2 | 13 + 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.../store/store/impl/db/CredentialsDAO.java | 15 +- .../store/store/impl/db/CredentialsDAOTest.java | 3 +- .../store/store/impl/db/SSHCredentialTest.java | 2 +- .../store/cpi/CredentialStoreService.java | 4086 +- .../store/datamodel/CertificateCredential.java | 27 +- .../store/datamodel/CommunityUser.java | 26 +- .../store/datamodel/PasswordCredential.java | 27 +- .../store/datamodel/SSHCredential.java | 142 +- .../store/datamodel/SSHCredentialSummary.java | 914 + .../exception/CredentialStoreException.java | 2 +- modules/distribution/pom.xml | 75 +- .../src/main/assembly/bin-assembly.xml | 24 +- .../gfac/bes/provider/impl/BESProvider.java | 5 +- .../impl/JSDLGeneratorTestWithMyProxyAuth.java | 2 +- modules/gfac/gfac-core/pom.xml | 33 +- .../apache/airavata/gfac/core/GFacUtils.java | 209 +- .../apache/airavata/gfac/core/GroovyMap.java | 99 + .../airavata/gfac/core/JobDescriptor.java | 489 - .../org/apache/airavata/gfac/core/Script.java | 79 + .../gfac/core/cluster/OutputParser.java | 8 - .../gfac/core/context/ProcessContext.java | 20 +- .../airavata/gfac/core/context/TaskContext.java | 2 +- .../gfac/core/x2012/x12/AfterAnyList.java | 185 - .../gfac/core/x2012/x12/AfterOKList.java | 185 - .../gfac/core/x2012/x12/ExportProperties.java | 202 - .../airavata/gfac/core/x2012/x12/InputList.java | 185 - .../core/x2012/x12/JobDescriptorDocument.java | 131 - .../gfac/core/x2012/x12/ModuleLoadCommands.java | 185 - .../airavata/gfac/core/x2012/x12/PbsParams.java | 1500 - .../gfac/core/x2012/x12/PostJobCommands.java | 185 - .../gfac/core/x2012/x12/PreJobCommands.java | 185 - .../core/x2012/x12/impl/AfterAnyListImpl.java | 254 - .../core/x2012/x12/impl/AfterOKListImpl.java | 254 - .../x2012/x12/impl/ExportPropertiesImpl.java | 252 - .../gfac/core/x2012/x12/impl/InputListImpl.java | 254 - .../x12/impl/JobDescriptorDocumentImpl.java | 96 - .../x2012/x12/impl/ModuleLoadCommandsImpl.java | 254 - .../gfac/core/x2012/x12/impl/PbsParamsImpl.java | 4381 - 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.../gfac/monitor/email/EmailBasedMonitor.java | 6 +- .../services/impl/BigRed2TestWithSSHAuth.java | 2 +- .../impl/GSISSHProviderTestWithMyProxyAuth.java | 2 +- .../impl/SSHProviderTestWithSSHAuth.java | 2 +- .../airavata/gfac/server/GfacServerHandler.java | 41 +- modules/group-manager/pom.xml | 58 - .../internal/dao/PermissionEntryDAO.java | 286 - .../dao/hib3/Hib3PermissionEntryDAO.java | 1123 - .../grouper/permissions/PermissionFinder.java | 770 - .../airavata/grouper/AiravataGrouperUtil.java | 35 - .../airavata/grouper/GroupManagerCPI.java | 35 - .../airavata/grouper/GroupManagerException.java | 36 - .../airavata/grouper/GroupManagerFactory.java | 42 - .../airavata/grouper/GroupManagerImpl.java | 118 - .../apache/airavata/grouper/SubjectType.java | 14 - .../apache/airavata/grouper/group/Group.java | 108 - .../airavata/grouper/group/GroupMembership.java | 88 - .../grouper/group/GroupMembershipType.java | 12 - .../airavata/grouper/group/GroupService.java | 39 - 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| 114 + .../catalog/model/UserStoragePreference.java | 105 + .../catalog/model/UserStoragePreferencePK.java | 64 + .../resources/AppCatAbstractResource.java | 26 +- .../ComputeHostPreferenceResource.java | 4 + .../resources/LocalSubmissionResource.java | 12 +- .../UserComputeHostPreferenceResource.java | 457 + .../resources/UserResourceProfileResource.java | 454 + .../UserStoragePreferenceResource.java | 378 + .../app/catalog/util/AppCatalogJPAUtils.java | 73 + .../catalog/util/AppCatalogResourceType.java | 3 + .../util/AppCatalogThriftConversion.java | 64 + .../experiment/catalog/ExpCatResourceUtils.java | 12 +- .../catalog/impl/ExperimentRegistry.java | 8 + .../src/main/resources/META-INF/persistence.xml | 3 + .../src/main/resources/appcatalog-derby.sql | 1 + .../src/main/resources/appcatalog-mysql.sql | 1 + .../src/main/resources/credstore-mysql.sql | 10 +- .../app/catalog/UserResourceProfileTest.java | 129 + .../airavata/registry/cpi/AppCatalog.java | 7 + 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+ .../db/entities/GroupMembershipEntity.java | 123 + .../registry/db/entities/GroupMembershipPK.java | 88 + .../db/entities/PermissionTypeEntity.java | 126 + .../registry/db/entities/PermissionTypePK.java | 76 + .../registry/db/entities/SharingEntity.java | 147 + .../sharing/registry/db/entities/SharingPK.java | 114 + .../registry/db/entities/UserEntity.java | 158 + .../registry/db/entities/UserGroupEntity.java | 162 + .../registry/db/entities/UserGroupPK.java | 75 + .../sharing/registry/db/entities/UserPK.java | 75 + .../db/repositories/AbstractRepository.java | 138 + .../db/repositories/DomainRepository.java | 34 + .../db/repositories/EntityRepository.java | 149 + .../db/repositories/EntityTypeRepository.java | 35 + .../repositories/GroupMembershipRepository.java | 79 + .../repositories/PermissionTypeRepository.java | 53 + .../db/repositories/SharingRepository.java | 81 + .../db/repositories/UserGroupRepository.java | 54 + .../db/repositories/UserRepository.java | 54 + 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