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From shame...@apache.org
Subject [1/6] airavata git commit: Merge pull request #1 from apache/develop
Date Tue, 01 Nov 2016 16:12:24 GMT
Repository: airavata
Updated Branches:
  refs/heads/develop 325d1630c -> 6d51651ca


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/develop
Commit: 7dd85164103ea492351e25695b4c9b48a9840703
Parents: 59142dd 76c9eaf
Author: Gourav Shenoy <shenoy.200@gmail.com>
Authored: Sun Oct 23 13:01:27 2016 -0400
Committer: GitHub <noreply@github.com>
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 +
 .../templates/airavata-server.properties.j2     |    13 +
 .../roles/pga/templates/pga_config.php.j2       |     2 +-
 .../templates/airavata-server.properties.j2     |    13 +
 modules/cloud/ansible-playbooks/README.md       |    61 +-
 .../roles/openstack/tasks/main.yml              |    28 +
 .../roles/openstack/vars/main.yml               |    10 +
 .../openstack/vars/openstack-credentials.yml    |    10 +
 modules/cloud/ansible-playbooks/site.yml        |     5 +
 modules/commons/pom.xml                         |    22 +-
 .../airavata/common/utils/BuildConstant.java    |    26 +
 .../airavata/common/logging/Exception.java      |    66 +
 .../airavata/common/logging/LogEntry.java       |   132 +
 .../airavata/common/logging/MDCConstants.java   |    30 +
 .../apache/airavata/common/logging/MDCUtil.java |    32 +
 .../airavata/common/logging/ServerId.java       |    68 +
 .../common/logging/kafka/KafkaAppender.java     |   115 +
 .../airavata/common/utils/AiravataUtils.java    |     2 +-
 .../airavata/common/utils/AiravataZKUtils.java  |    13 +-
 .../common/utils/ApplicationSettings.java       |    34 +-
 .../airavata/common/utils/AwsMetadata.java      |   137 +
 .../airavata/common/utils/ServerSettings.java   |    34 +
 .../apache/airavata/common/utils/XMLUtil.java   |   586 -
 .../airavata/common/utils/XmlFormatter.java     |    82 -
 .../airavata/common/utils/XMLUtilTest.java      |    56 -
 .../src/main/resources/FORK_Groovy.template     |    13 +
 .../server/src/main/resources/ForkTemplate.xslt |    24 -
 .../server/src/main/resources/LSFTemplate.xslt  |    92 -
 .../src/main/resources/LSF_Groovy.template      |    27 +
 .../server/src/main/resources/PBSTemplate.xslt  |   107 -
 .../src/main/resources/PBS_Groovy.template      |    31 +
 .../src/main/resources/SLURMTemplate.xslt       |   102 -
 .../src/main/resources/SLURM_Groovy.template    |    28 +
 .../server/src/main/resources/UGETemplate.xslt  |    78 -
 .../src/main/resources/UGE_Groovy.template      |    28 +
 .../main/resources/airavata-server.properties   |    27 +-
 .../server/src/main/resources/gfac-config.yaml  |     4 +-
 .../server/src/main/resources/logback.xml       |    31 +
 .../credential/store/credential/Credential.java |    13 +
 .../server/CredentialStoreServerHandler.java    |    96 +-
 .../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 -
 .../x2012/x12/impl/PostJobCommandsImpl.java     |   254 -
 .../core/x2012/x12/impl/PreJobCommandsImpl.java |   254 -
 .../src/main/resources/PBSJobDescriptor.xsd     |   116 -
 .../src/main/resources/gsissh-schemas.xsdconfig |    14 -
 .../airavata/gfac/core/GFacUtilsTest.java       |    13 +
 .../org/apache/airavata/gfac/impl/Factory.java  |    11 +-
 .../airavata/gfac/impl/GFacEngineImpl.java      |    16 +-
 .../apache/airavata/gfac/impl/HTTPUtils.java    |     7 +
 .../airavata/gfac/impl/LocalRemoteCluster.java  |    42 +-
 .../gfac/impl/job/ForkOutputParser.java         |     5 -
 .../airavata/gfac/impl/job/LSFOutputParser.java |    10 +-
 .../airavata/gfac/impl/job/PBSOutputParser.java |    90 +-
 .../gfac/impl/job/SlurmOutputParser.java        |    61 +-
 .../airavata/gfac/impl/job/UGEOutputParser.java |    89 +-
 .../gfac/impl/task/BESJobSubmissionTask.java    |     5 +-
 .../impl/task/DefaultJobSubmissionTask.java     |     8 +-
 .../gfac/impl/task/ForkJobSubmissionTask.java   |     6 +-
 .../gfac/impl/task/LocalJobSubmissionTask.java  |   150 +-
 .../airavata/gfac/impl/task/TaskUtils.java      |     2 +-
 .../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 -
 .../grouper/group/GroupServiceImpl.java         |   412 -
 .../grouper/permission/PermissionAction.java    |    15 -
 .../permission/PermissionServiceImpl.java       |    86 -
 .../airavata/grouper/resource/Resource.java     |   145 -
 .../resource/ResourceNotFoundException.java     |    35 -
 .../grouper/resource/ResourceServiceImpl.java   |   343 -
 .../airavata/grouper/resource/ResourceType.java |    51 -
 .../airavata/grouper/role/RoleServiceImpl.java  |   112 -
 .../Owasp.CsrfGuard.overlay.properties          |    78 -
 .../main/resources/Owasp.CsrfGuard.properties   |   403 -
 .../group-manager/src/main/resources/README.txt |    21 -
 .../src/main/resources/ehcache.xml              |  1517 -
 .../resources/grouper-loader.base.properties    |   351 -
 .../main/resources/grouper-loader.properties    |    25 -
 .../src/main/resources/grouper.base.properties  |  1017 -
 .../resources/grouper.client.base.properties    |   552 -
 .../main/resources/grouper.client.properties    |   552 -
 .../resources/grouper.hibernate.base.properties |   120 -
 .../main/resources/grouper.hibernate.properties |    10 -
 .../src/main/resources/grouper.properties       |  1017 -
 .../src/main/resources/grouperUtf8.txt          |     1 -
 .../src/main/resources/log4j.properties         |   154 -
 .../src/main/resources/morphString.properties   |    21 -
 .../src/main/resources/server.properties        |    26 -
 .../src/main/resources/sources.xml              |   875 -
 .../src/main/resources/spy.properties           |    54 -
 .../group-manager/src/main/resources/sqltool.rc |     6 -
 .../src/main/resources/subject.base.properties  |    46 -
 .../src/main/resources/subject.properties       |    27 -
 .../cpi/impl/SimpleOrchestratorImpl.java        |    12 +-
 .../server/OrchestratorServerHandler.java       |    33 +-
 modules/registry/registry-core/pom.xml          |    27 -
 .../core/app/catalog/impl/AppCatalogImpl.java   |     5 +
 .../app/catalog/impl/ComputeResourceImpl.java   |     1 +
 .../catalog/impl/UsrResourceProfileImpl.java    |   369 +
 .../core/app/catalog/model/LocalSubmission.java |    11 +
 .../model/UserComputeResourcePreference.java    |   185 +
 .../model/UserComputeResourcePreferencePK.java  |    63 +
 .../app/catalog/model/UserResourceProfile.java  |   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 +
 .../registry/cpi/UsrResourceProfile.java        |    90 +
 .../service/handler/RegistryServerHandler.java  |   568 +-
 .../airavata/registry/api/RegistryService.java  | 21916 ++++-
 .../api/exception/RegistryServiceException.java |     2 +-
 .../org/apache/airavata/server/ServerMain.java  |    39 +-
 modules/sharing-registry/README.md              |     3 +
 modules/sharing-registry/pom.xml                |    31 +
 .../sharing-data-migrator/pom.xml               |    22 +
 .../migrator/airavata/AiravataDataMigrator.java |   162 +
 .../migrator/airavata/ConnectionFactory.java    |    59 +
 .../sharing-registry-distribution/pom.xml       |    91 +
 .../src/main/assembly/bin-assembly.xml          |    70 +
 .../src/main/resources/bin/setenv.sh            |    61 +
 .../src/main/resources/bin/sharing-registry.sh  |    90 +
 .../sharing-registry-server/pom.xml             |   112 +
 .../registry/db/entities/DomainEntity.java      |   113 +
 .../registry/db/entities/EntityEntity.java      |   202 +
 .../sharing/registry/db/entities/EntityPK.java  |    76 +
 .../registry/db/entities/EntityTypeEntity.java  |   126 +
 .../registry/db/entities/EntityTypePK.java      |    76 +
 .../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 +
 .../sharing/registry/db/utils/Committer.java    |    27 +
 .../registry/db/utils/ConnectionPool.java       |   382 +
 .../sharing/registry/db/utils/DBConstants.java  |   106 +
 .../registry/db/utils/DatabaseCreator.java      |   353 +
 .../sharing/registry/db/utils/JPAUtils.java     |   230 +
 .../sharing/registry/db/utils/JdbcStorage.java  |   175 +
 .../db/utils/ObjectMapperSingleton.java         |    39 +
 .../sharing/registry/server/ServerMain.java     |   102 +
 .../registry/server/SharingRegistryServer.java  |   147 +
 .../server/SharingRegistryServerHandler.java    |   947 +
 .../src/main/resources/META-INF/persistence.xml |    15 +
 .../main/resources/sharing-registry-derby.sql   |   138 +
 .../main/resources/sharing-registry-mysql.sql   |   138 +
 .../SharingRegistryServerHandlerTest.java       |   278 +
 .../registry/SharingRegistryServiceTest.java    |   314 +
 .../sharing/registry/util/Initialize.java       |   298 +
 .../sharing-registry-stubs/pom.xml              |    56 +
 .../sharing/registry/models/Domain.java         |   811 +
 .../sharing/registry/models/Entity.java         |  1583 +
 .../registry/models/EntitySearchField.java      |    70 +
 .../sharing/registry/models/EntityType.java     |   931 +
 .../registry/models/GroupCardinality.java       |    50 +
 .../sharing/registry/models/GroupChildType.java |    49 +
 .../registry/models/GroupMembership.java        |   941 +
 .../sharing/registry/models/GroupType.java      |    49 +
 .../sharing/registry/models/PermissionType.java |   931 +
 .../registry/models/SearchCondition.java        |    63 +
 .../sharing/registry/models/SearchCriteria.java |   649 +
 .../sharing/registry/models/Sharing.java        |  1155 +
 .../models/SharingRegistryException.java        |   395 +
 .../sharing/registry/models/SharingType.java    |    52 +
 .../airavata/sharing/registry/models/User.java  |  1266 +
 .../sharing/registry/models/UserGroup.java      |  1287 +
 .../models/sharing_modelsConstants.java         |    41 +
 .../service/cpi/SharingRegistryService.java     | 49079 +++++++++++
 .../sharing-service-docs/api-docs/index.html    |    79 +
 .../api-docs/sharing_cpi.html                   |   297 +
 .../api-docs/sharing_models.html                |   283 +
 .../sharing-service-docs/api-docs/style.css     |   184 +
 .../sharing-service-docs/index.html             |   362 +
 .../sharing-service-docs/sharing_overview.png   |   Bin 0 -> 49205 bytes
 .../sharing-service-docs/style.css              |   184 +
 .../thrift_models/sharing_cpi.thrift            |   211 +
 .../thrift_models/sharing_models.thrift         |   274 +
 .../thrift_models/thrift-gen.sh                 |    22 +
 .../utils/PropertyReader.java                   |     3 +-
 .../core/AbstractThriftDeserializer.java        |     3 +-
 .../engine/interpretor/WorkflowInterpreter.java |     1 -
 .../invoker/MsgBoxWsaResponsesCorrelator.java   |     2 +-
 .../component/ws/WSComponentApplication.java    |     1 -
 .../workflow/model/gpel/script/BPELScript.java  |     2 -
 .../model/gpel/script/WorkflowWSDL.java         |     1 -
 .../airavata/workflow/model/wf/Workflow.java    |     1 -
 modules/workflow/workflow-core/pom.xml          |    11 +-
 .../apache/airavata/workflow/core/XMLUtil.java  |   587 +
 .../airavata/workflow/core/XmlFormatter.java    |    82 +
 .../airavata/workflow/core/XMLUtilTest.java     |    56 +
 pom.xml                                         |    69 +-
 .../airavata-apis/airavata_api.thrift           |   426 +-
 .../component-cpis/credential-store-cpi.thrift  |     9 +-
 .../credential_store_data_models.thrift         |    62 -
 .../component-cpis/registry-api.thrift          |   316 +
 .../credential_store_data_models.thrift         |    72 +
 .../compute_resource_model.thrift               |     5 +-
 .../credential_summary.thrift                   |    32 +
 .../resource_catalog_models.thrift              |     4 +-
 .../user_resource_profile_model.thrift          |   105 +
 .../generate-thrift-stubs.sh                    |    24 +
 324 files changed, 209896 insertions(+), 79409 deletions(-)
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