You are viewing a plain text version of this content. The canonical link for it is here.
Posted to commits@airavata.apache.org by sc...@apache.org on 2017/05/22 16:19:11 UTC
[01/12] airavata git commit: handling a corner case in email handling
from Airavata custom emails
Repository: airavata
Updated Branches:
refs/heads/develop 11f12dfc2 -> d71c2aa8f
handling a corner case in email handling from Airavata custom emails
Project: http://git-wip-us.apache.org/repos/asf/airavata/repo
Commit: http://git-wip-us.apache.org/repos/asf/airavata/commit/56fefc98
Tree: http://git-wip-us.apache.org/repos/asf/airavata/tree/56fefc98
Diff: http://git-wip-us.apache.org/repos/asf/airavata/diff/56fefc98
Branch: refs/heads/develop
Commit: 56fefc9845ab926f225edb7c787c1a676eefadb3
Parents: 7975778
Author: scnakandala <su...@gmail.com>
Authored: Mon Mar 6 13:05:45 2017 -0500
Committer: scnakandala <su...@gmail.com>
Committed: Mon Mar 6 13:05:45 2017 -0500
----------------------------------------------------------------------
.../airavata/gfac/monitor/email/EmailBasedMonitor.java | 11 +++++++++--
1 file changed, 9 insertions(+), 2 deletions(-)
----------------------------------------------------------------------
http://git-wip-us.apache.org/repos/asf/airavata/blob/56fefc98/modules/gfac/gfac-impl/src/main/java/org/apache/airavata/gfac/monitor/email/EmailBasedMonitor.java
----------------------------------------------------------------------
diff --git a/modules/gfac/gfac-impl/src/main/java/org/apache/airavata/gfac/monitor/email/EmailBasedMonitor.java b/modules/gfac/gfac-impl/src/main/java/org/apache/airavata/gfac/monitor/email/EmailBasedMonitor.java
index 02dfa00..92f0d78 100644
--- a/modules/gfac/gfac-impl/src/main/java/org/apache/airavata/gfac/monitor/email/EmailBasedMonitor.java
+++ b/modules/gfac/gfac-impl/src/main/java/org/apache/airavata/gfac/monitor/email/EmailBasedMonitor.java
@@ -279,6 +279,12 @@ public class EmailBasedMonitor implements JobMonitor, Runnable{
if (taskContext != null) {
process(jobStatusResult, taskContext);
processedMessages.add(message);
+
+ } else if (addressMap.get(message.getFrom()).equals(ResourceJobManagerType.AIRAVATA_CUSTOM)
+ && (new Date()).getTime() - message.getSentDate().getTime() > 1000 * 6 * 5) {
+ //marking old custom Airavata emails as read
+ processedMessages.add(message);
+ log.info("Marking old Airavata custom emails as read, message subject --> {}", message.getSubject());
} else {
// we can get JobExecutionContext null in multiple Gfac instances environment,
// where this job is not submitted by this Gfac instance hence we ignore this message.
@@ -357,14 +363,15 @@ public class EmailBasedMonitor implements JobMonitor, Runnable{
if (currentState != null && currentState == JobState.COMPLETE) {
jobMonitorMap.remove(jobStatusResult.getJobId());
runOutflowTasks = false;
- log.info("[EJM]: Job Complete email received , removed job from job monitoring. " + jobDetails);
+ log.info("[EJM]: Authoritative job Complete email received after early Airavata custom complete email," +
+ " removed job from job monitoring. " + jobDetails);
} else {
jobMonitorMap.remove(jobStatusResult.getJobId());
runOutflowTasks = true;
jobStatus.setJobState(JobState.COMPLETE);
jobStatus.setReason("Complete email received");
jobStatus.setTimeOfStateChange(AiravataUtils.getCurrentTimestamp().getTime());
- log.info("[EJM]: Job Complete email received , removed job from job monitoring. " + jobDetails);
+ log.info("[EJM]: Authoritative job Complete email received , removed job from job monitoring. " + jobDetails);
}
} else {
runOutflowTasks = true;
[04/12] airavata git commit: uncommenting actual username and password
Posted by sc...@apache.org.
uncommenting actual username and password
Project: http://git-wip-us.apache.org/repos/asf/airavata/repo
Commit: http://git-wip-us.apache.org/repos/asf/airavata/commit/fc07b995
Tree: http://git-wip-us.apache.org/repos/asf/airavata/tree/fc07b995
Diff: http://git-wip-us.apache.org/repos/asf/airavata/diff/fc07b995
Branch: refs/heads/develop
Commit: fc07b995cfdbeed9ad9726c4b8c8a8bae20807b0
Parents: 2c30522
Author: scnakandala <su...@gmail.com>
Authored: Mon Mar 6 14:22:56 2017 -0500
Committer: scnakandala <su...@gmail.com>
Committed: Mon Mar 6 14:22:56 2017 -0500
----------------------------------------------------------------------
sandbox/job-status-rest-server/app.py | 8 ++++----
1 file changed, 4 insertions(+), 4 deletions(-)
----------------------------------------------------------------------
http://git-wip-us.apache.org/repos/asf/airavata/blob/fc07b995/sandbox/job-status-rest-server/app.py
----------------------------------------------------------------------
diff --git a/sandbox/job-status-rest-server/app.py b/sandbox/job-status-rest-server/app.py
index e894650..dba8290 100644
--- a/sandbox/job-status-rest-server/app.py
+++ b/sandbox/job-status-rest-server/app.py
@@ -10,10 +10,10 @@ import sys
app = Flask(__name__)
-email_username = 'gw56jobs@scigap.org'
-email_password = 'XseDe2015'
+email_username = ''
+email_password = ''
status_string = "COMPLETED"
-from_address = 'gw56jobs@scigap.org'
+from_address = 'emailtrigger@scigap.org'
@app.route('/job_status', methods=['POST'])
@@ -42,7 +42,7 @@ def job_status():
if __name__ == '__main__':
app.config.update(
- DEBUG=True
+ DEBUG=False
)
app.run(
host="localhost",
[05/12] airavata git commit: adding logs to identify file transfer
issue
Posted by sc...@apache.org.
adding logs to identify file transfer issue
Project: http://git-wip-us.apache.org/repos/asf/airavata/repo
Commit: http://git-wip-us.apache.org/repos/asf/airavata/commit/7177cac6
Tree: http://git-wip-us.apache.org/repos/asf/airavata/tree/7177cac6
Diff: http://git-wip-us.apache.org/repos/asf/airavata/diff/7177cac6
Branch: refs/heads/develop
Commit: 7177cac6b247a525ee2a56bbe461e521134aba50
Parents: fc07b99
Author: Ajinkya Dhamnaskar <ad...@umail.iu.edu>
Authored: Tue Mar 7 15:14:23 2017 -0500
Committer: Ajinkya Dhamnaskar <ad...@umail.iu.edu>
Committed: Tue Mar 7 15:14:23 2017 -0500
----------------------------------------------------------------------
.../java/org/apache/airavata/gfac/impl/SSHUtils.java | 13 ++++++++++++-
1 file changed, 12 insertions(+), 1 deletion(-)
----------------------------------------------------------------------
http://git-wip-us.apache.org/repos/asf/airavata/blob/7177cac6/modules/gfac/gfac-impl/src/main/java/org/apache/airavata/gfac/impl/SSHUtils.java
----------------------------------------------------------------------
diff --git a/modules/gfac/gfac-impl/src/main/java/org/apache/airavata/gfac/impl/SSHUtils.java b/modules/gfac/gfac-impl/src/main/java/org/apache/airavata/gfac/impl/SSHUtils.java
index ace8e1b..60fc2d3 100644
--- a/modules/gfac/gfac-impl/src/main/java/org/apache/airavata/gfac/impl/SSHUtils.java
+++ b/modules/gfac/gfac-impl/src/main/java/org/apache/airavata/gfac/impl/SSHUtils.java
@@ -293,7 +293,6 @@ public class SSHUtils {
sin = sourceChannel.getInputStream();
sourceChannel.connect();
-
boolean ptimestamp = true;
// exec 'scp -t destinationFile'
String command = "scp " + (ptimestamp ? "-p" : "") + " -t " + destinationFile;
@@ -320,6 +319,8 @@ public class SSHUtils {
sout.write(buf, 0, 1);
sout.flush();
+ log.info("Initiating transfer from:" + sourceFile + " To: " + destinationFile + ", Ignore Empty file : " + ignoreEmptyFile);
+
while (true) {
int c = checkAck(sin);
if (c != 'C') {
@@ -347,6 +348,14 @@ public class SSHUtils {
break;
}
}
+
+ //FIXME: Remove me after fixing file transfer issue
+ if(fileSize == 0L){
+ log.warn("*****Zero byte file*****. Transferring from:" + sourceFile + " To: " + destinationFile + ", File Size : " + fileSize + ", Ignore Empty file : " + ignoreEmptyFile);
+ }else{
+ log.info("Transferring from:" + sourceFile + " To: " + destinationFile + ", File Size : " + fileSize + ", Ignore Empty file : " + ignoreEmptyFile);
+ }
+
if (fileSize == 0L && !ignoreEmptyFile){
String error = "Input file is empty...";
log.error(error);
@@ -505,12 +514,14 @@ public class SSHUtils {
sb.append((char) c);
}
while (c != '\n');
+ //FIXME: Redundant
if (b == 1) { // error
System.out.print(sb.toString());
}
if (b == 2) { // fatal error
System.out.print(sb.toString());
}
+ log.warn(sb.toString());
}
return b;
}
[03/12] airavata git commit: updating readme
Posted by sc...@apache.org.
updating readme
Project: http://git-wip-us.apache.org/repos/asf/airavata/repo
Commit: http://git-wip-us.apache.org/repos/asf/airavata/commit/2c305225
Tree: http://git-wip-us.apache.org/repos/asf/airavata/tree/2c305225
Diff: http://git-wip-us.apache.org/repos/asf/airavata/diff/2c305225
Branch: refs/heads/develop
Commit: 2c3052252f26f8548cae77e5f6c978b16cffbaf7
Parents: a749a7c
Author: scnakandala <su...@gmail.com>
Authored: Mon Mar 6 14:10:58 2017 -0500
Committer: scnakandala <su...@gmail.com>
Committed: Mon Mar 6 14:10:58 2017 -0500
----------------------------------------------------------------------
sandbox/job-status-rest-server/README.MD | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
----------------------------------------------------------------------
http://git-wip-us.apache.org/repos/asf/airavata/blob/2c305225/sandbox/job-status-rest-server/README.MD
----------------------------------------------------------------------
diff --git a/sandbox/job-status-rest-server/README.MD b/sandbox/job-status-rest-server/README.MD
index 104e10a..dac6b39 100644
--- a/sandbox/job-status-rest-server/README.MD
+++ b/sandbox/job-status-rest-server/README.MD
@@ -6,4 +6,4 @@ Requirement
* pip install flask-restful
Sample CURL Command
-curl -X POST -d "job_id=ABC&job_name=Test&status=0&emails[]=supun.nakandala@gmail.com,eabeysin@iu.edu" http://localhost:8089/job_status
\ No newline at end of file
+curl -X POST -d "job_id=ABC&job_name=Test&status=0&emails[]=supun.nakandala@gmail.com&emails[]=eabeysin@iu.edu" http://localhost:8089/job_status
\ No newline at end of file
[12/12] airavata git commit: merging airavata pull request 110:
Airavata build failures
Posted by sc...@apache.org.
merging airavata pull request 110: Airavata build failures
Project: http://git-wip-us.apache.org/repos/asf/airavata/repo
Commit: http://git-wip-us.apache.org/repos/asf/airavata/commit/d71c2aa8
Tree: http://git-wip-us.apache.org/repos/asf/airavata/tree/d71c2aa8
Diff: http://git-wip-us.apache.org/repos/asf/airavata/diff/d71c2aa8
Branch: refs/heads/develop
Commit: d71c2aa8f3091c385241419f8254486a968923d4
Parents: 11f12df 706e01d
Author: scnakandala <su...@gmail.com>
Authored: Mon May 22 12:17:50 2017 -0400
Committer: scnakandala <su...@gmail.com>
Committed: Mon May 22 12:17:50 2017 -0400
----------------------------------------------------------------------
airavata-api/airavata-api-server/pom.xml | 5 -----
modules/commons/pom.xml | 6 ------
modules/user-profile-migration/pom.xml | 2 +-
.../main/java/org/apache/airavata/MigrationManager.java | 8 +++++---
.../apache/airavata/UserProfileAiravataThriftClient.java | 11 ++++-------
5 files changed, 10 insertions(+), 22 deletions(-)
----------------------------------------------------------------------
[09/12] airavata git commit: Renaming user-profile-stubs to
profile-service-stubs
Posted by sc...@apache.org.
Renaming user-profile-stubs to profile-service-stubs
Project: http://git-wip-us.apache.org/repos/asf/airavata/repo
Commit: http://git-wip-us.apache.org/repos/asf/airavata/commit/78a3cafc
Tree: http://git-wip-us.apache.org/repos/asf/airavata/tree/78a3cafc
Diff: http://git-wip-us.apache.org/repos/asf/airavata/diff/78a3cafc
Branch: refs/heads/develop
Commit: 78a3cafce78a0810b9c282419f420426e5cb18ff
Parents: 1cfda99
Author: Ajinkya Dhamnaskar <ad...@umail.iu.edu>
Authored: Wed May 17 14:13:59 2017 -0400
Committer: Ajinkya Dhamnaskar <ad...@umail.iu.edu>
Committed: Wed May 17 14:13:59 2017 -0400
----------------------------------------------------------------------
modules/user-profile-migration/pom.xml | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
----------------------------------------------------------------------
http://git-wip-us.apache.org/repos/asf/airavata/blob/78a3cafc/modules/user-profile-migration/pom.xml
----------------------------------------------------------------------
diff --git a/modules/user-profile-migration/pom.xml b/modules/user-profile-migration/pom.xml
index c76610e..1baa85b 100755
--- a/modules/user-profile-migration/pom.xml
+++ b/modules/user-profile-migration/pom.xml
@@ -69,7 +69,7 @@
</dependency>
<dependency>
<groupId>org.apache.airavata</groupId>
- <artifactId>user-profile-stubs</artifactId>
+ <artifactId>profile-service-stubs</artifactId>
<version>${project.version}</version>
</dependency>
<dependency>
[06/12] airavata git commit: Merge remote-tracking branch
'upstream/develop' into develop
Posted by sc...@apache.org.
Merge remote-tracking branch 'upstream/develop' into develop
Project: http://git-wip-us.apache.org/repos/asf/airavata/repo
Commit: http://git-wip-us.apache.org/repos/asf/airavata/commit/9f57e1f3
Tree: http://git-wip-us.apache.org/repos/asf/airavata/tree/9f57e1f3
Diff: http://git-wip-us.apache.org/repos/asf/airavata/diff/9f57e1f3
Branch: refs/heads/develop
Commit: 9f57e1f3d03d14423d142ee64c0815b6721d2e4e
Parents: 7177cac e988672
Author: Ajinkya Dhamnaskar <ad...@umail.iu.edu>
Authored: Wed May 17 13:59:04 2017 -0400
Committer: Ajinkya Dhamnaskar <ad...@umail.iu.edu>
Committed: Wed May 17 13:59:04 2017 -0400
----------------------------------------------------------------------
README | 3 -
airavata-api/airavata-api-server/pom.xml | 51 +-
.../airavata/api/server/AiravataAPIServer.java | 12 +-
.../api/server/AiravataDerbyServer.java | 4 +-
.../server/handler/AiravataServerHandler.java | 193 +-
.../AiravataExperimentStatusUpdator.java | 6 +-
.../listener/ExperimentStatusChangedEvent.java | 19 +
.../security/AiravataSecurityManager.java | 43 -
.../DefaultAiravataSecurityManager.java | 273 -
.../api/server/security/IdentityContext.java | 44 -
.../airavata/api/server/security/Main.java | 179 -
.../server/security/SecurityManagerFactory.java | 60 -
.../server/security/authzcache/AuthzCache.java | 61 -
.../security/authzcache/AuthzCacheEntry.java | 63 -
.../security/authzcache/AuthzCacheIndex.java | 90 -
.../security/authzcache/AuthzCacheManager.java | 80 -
.../authzcache/AuthzCacheManagerFactory.java | 60 -
.../security/authzcache/AuthzCachedStatus.java | 34 -
.../authzcache/DefaultAuthzCacheManager.java | 106 -
.../security/interceptor/SecurityCheck.java | 36 -
.../interceptor/SecurityInterceptor.java | 83 -
.../security/interceptor/SecurityModule.java | 43 -
.../security/oauth/DefaultOAuthClient.java | 91 -
.../server/security/xacml/DefaultPAPClient.java | 125 -
.../server/security/xacml/DefaultXACMLPEP.java | 133 -
.../airavata/api/server/util/Constants.java | 4 +-
.../api/server/util/ThriftClientPool.java | 5 +-
airavata-api/airavata-api-stubs/pom.xml | 31 +-
.../java/org/apache/airavata/api/Airavata.java | 55575 ++++++++++-------
.../api/client/AiravataClientFactory.java | 4 +-
.../airavata-cpp-sdk/pom.xml | 27 +-
.../src/main/assembly/bin-assembly.xml | 29 +-
.../main/resources/lib/airavata/Airavata.cpp | 17236 ++---
.../src/main/resources/lib/airavata/Airavata.h | 1230 +-
.../lib/airavata/Airavata_server.skeleton.cpp | 30 +
.../resources/lib/airavata/airavata_api_types.h | 1 +
.../lib/airavata/airavata_data_models_types.h | 2 +
.../lib/airavata/airavata_errors_types.cpp | 205 +-
.../lib/airavata/airavata_errors_types.h | 44 +
.../application_deployment_model_types.cpp | 24 +-
.../application_deployment_model_types.h | 12 +-
.../airavata/compute_resource_model_types.cpp | 88 +
.../lib/airavata/compute_resource_model_types.h | 36 +-
.../lib/airavata/db_event_model_constants.cpp | 34 +
.../lib/airavata/db_event_model_constants.h | 41 +
.../lib/airavata/db_event_model_types.cpp | 627 +
.../lib/airavata/db_event_model_types.h | 318 +
.../lib/airavata/messaging_events_types.cpp | 8 +-
.../lib/airavata/messaging_events_types.h | 3 +-
.../airavata/replica_catalog_models_types.cpp | 726 +-
.../lib/airavata/replica_catalog_models_types.h | 274 +-
.../airavata/tenant_profile_model_constants.cpp | 34 +
.../airavata/tenant_profile_model_constants.h | 41 +
.../lib/airavata/tenant_profile_model_types.cpp | 541 +
.../lib/airavata/tenant_profile_model_types.h | 244 +
.../lib/airavata/user_profile_model_types.cpp | 239 +-
.../lib/airavata/user_profile_model_types.h | 59 +-
.../airavata-php-sdk/pom.xml | 27 +-
.../src/main/assembly/bin-assembly.xml | 29 +-
.../resources/lib/Airavata/API/Airavata.php | 11335 ++--
.../resources/lib/Airavata/API/Error/Types.php | 82 +
.../Model/AppCatalog/AppDeployment/Types.php | 25 +-
.../Model/AppCatalog/ComputeResource/Types.php | 94 +-
.../lib/Airavata/Model/Application/Io/Types.php | 6 +-
.../lib/Airavata/Model/Data/Replica/Types.php | 572 +-
.../lib/Airavata/Model/Dbevent/Types.php | 573 +
.../Airavata/Model/Messaging/Event/Types.php | 2 +
.../lib/Airavata/Model/Tenant/Types.php | 528 +
.../resources/lib/Airavata/Model/User/Types.php | 279 +-
.../src/main/resources/lib/Types.php | 13 +
.../airavata-python-sdk/pom.xml | 27 +-
.../src/main/assembly/bin-assembly.xml | 29 +-
.../lib/apache/airavata/api/Airavata-remote | 42 +
.../lib/apache/airavata/api/Airavata.py | 8090 ++-
.../lib/apache/airavata/api/error/ttypes.py | 76 +
.../resources/lib/apache/airavata/api/ttypes.py | 1 +
.../model/appcatalog/appdeployment/ttypes.py | 19 +-
.../model/appcatalog/computeresource/ttypes.py | 54 +-
.../airavata/model/data/replica/ttypes.py | 430 +-
.../apache/airavata/model/dbevent/__init__.py | 1 +
.../apache/airavata/model/dbevent/constants.py | 11 +
.../lib/apache/airavata/model/dbevent/ttypes.py | 494 +
.../airavata/model/messaging/event/ttypes.py | 3 +
.../apache/airavata/model/tenant/__init__.py | 1 +
.../apache/airavata/model/tenant/constants.py | 11 +
.../lib/apache/airavata/model/tenant/ttypes.py | 352 +
.../lib/apache/airavata/model/ttypes.py | 2 +
.../lib/apache/airavata/model/user/ttypes.py | 231 +-
.../java-client-samples/pom.xml | 26 +-
.../client/samples/CancelExperiments.java | 4 +-
.../client/samples/CreateLaunchBES.java | 3 +-
.../client/samples/CreateLaunchExperiment.java | 4 +-
.../samples/CreateLaunchExperimentUS3.java | 2 +-
.../client/samples/ReplicaCatalogSample.java | 5 +-
.../client/samples/SampleEchoExperiment.java | 4 +-
.../client/OAuthAppRegisteringClient.java | 3 +-
.../client/OAuthTokenRetrievalClient.java | 3 +-
.../client/secure/client/Properties.java | 3 +-
.../client/secure/client/SecureClient.java | 3 +-
.../tools/RegisterOGCEUS3Application.java | 6 +-
.../tools/RegisterSampleApplications.java | 5 +-
.../tools/RegisterSampleApplicationsUtils.java | 19 +
.../client/tools/RegisterUS3Application.java | 6 +-
airavata-api/airavata-client-sdks/pom.xml | 26 +-
airavata-api/airavata-data-models/pom.xml | 31 +-
.../ApplicationDeploymentDescription.java | 117 +-
.../application_deployment_modelConstants.java | 28 +-
.../application_interface_modelConstants.java | 28 +-
.../ComputeResourceDescription.java | 404 +-
.../computeresource/ResourceJobManagerType.java | 4 +
.../compute_resource_modelConstants.java | 28 +-
.../gatewayprofile/DataStoragePreference.java | 28 +-
.../application/io/InputDataObjectType.java | 63 +-
.../credential/store/SSHCredentialSummary.java | 28 +-
.../model/data/replica/DataProductModel.java | 84 +-
.../data/replica/DataReplicaLocationModel.java | 44 +-
.../apache/airavata/model/dbevent/CrudType.java | 68 +
.../airavata/model/dbevent/DBEventMessage.java | 622 +
.../model/dbevent/DBEventMessageContext.java | 387 +
.../model/dbevent/DBEventPublisher.java | 411 +
.../model/dbevent/DBEventPublisherContext.java | 641 +
.../model/dbevent/DBEventSubscriber.java | 406 +
.../airavata/model/dbevent/DBEventType.java | 62 +
.../airavata/model/dbevent/EntityType.java | 80 +
.../model/error/DuplicateEntryException.java | 413 +
.../model/messaging/event/MessageType.java | 5 +-
.../model/messaging/event/TaskSubmitEvent.java | 28 +-
.../messaging/event/TaskTerminateEvent.java | 28 +-
.../event/messaging_eventsConstants.java | 28 +-
.../apache/airavata/model/tenant/Tenant.java | 2322 +
.../model/tenant/TenantApprovalStatus.java | 77 +
.../airavata/model/user/NSFDemographics.java | 149 +-
.../apache/airavata/model/user/UserProfile.java | 882 +-
.../model/workflow_data_modelConstants.java | 28 +-
airavata-api/airavata-model-utils/pom.xml | 31 +-
.../airavata/model/util/AppDeploymentUtil.java | 4 +-
.../airavata/model/util/AppInterfaceUtil.java | 4 +-
.../model/util/ComputeResourceUtil.java | 4 +-
.../airavata/model/util/ExecutionType.java | 4 +-
.../model/util/ExperimentModelUtil.java | 4 +-
.../airavata/model/util/ProjectModelUtil.java | 2 +-
airavata-api/pom.xml | 26 +-
airavata-services/pom.xml | 70 +
.../iam-admin-services-core/pom.xml | 62 +
.../core/impl/TenantManagementKeycloakImpl.java | 351 +
.../interfaces/TenantManagementInterface.java | 101 +
.../services/core/tests/SetupNewGateway.java | 117 +
airavata-services/profile-service/pom.xml | 39 +
.../java-client-samples/pom.xml | 37 +
.../client/samples/TenantProfileSample.java | 61 +
.../client/samples/UserProfileSample.java | 124 +
.../client/util/ProfileServiceClientUtil.java | 47 +
.../resources/profile-client-sample.properties | 29 +
.../profile-service-client-sdks/pom.xml | 34 +
.../profile-service-commons/pom.xml | 117 +
.../repositories/AbstractRepository.java | 106 +
.../commons/tenant/entities/GatewayEntity.java | 254 +
.../user/entities/NSFDemographicsEntity.java | 108 +
.../user/entities/UserProfileEntity.java | 334 +
.../profile/commons/utils/Committer.java | 27 +
.../profile/commons/utils/JPAConstants.java | 34 +
.../service/profile/commons/utils/JPAUtils.java | 79 +
.../commons/utils/ObjectMapperSingleton.java | 39 +
.../profile/commons/utils/QueryConstants.java | 23 +
.../service/profile/commons/utils/Utils.java | 147 +
.../src/main/resources/META-INF/persistence.xml | 35 +
.../profile-service-server/pom.xml | 59 +
.../handlers/IamAdminServicesHandler.java | 131 +
.../handlers/TenantProfileServiceHandler.java | 194 +
.../handlers/UserProfileServiceHandler.java | 173 +
.../profile/server/ProfileServiceServer.java | 181 +
.../profile/utils/ProfileServiceUtils.java | 70 +
.../profile-service-stubs/pom.xml | 37 +
.../client/ProfileServiceClientFactory.java | 63 +
.../admin/services/cpi/IamAdminServices.java | 8240 +++
.../exception/IamAdminServicesException.java | 407 +
.../cpi/iam_admin_services_cpiConstants.java | 59 +
.../tenant/cpi/TenantProfileService.java | 8359 +++
.../TenantProfileServiceException.java | 407 +
.../tenant/cpi/profile_tenant_cpiConstants.java | 59 +
.../profile/user/cpi/UserProfileService.java | 7894 +++
.../exception/UserProfileServiceException.java | 407 +
.../user/cpi/profile_user_cpiConstants.java | 59 +
.../profile-service/profile-tenant-core/pom.xml | 40 +
.../repositories/TenantProfileRepository.java | 71 +
.../profile-service/profile-user-core/pom.xml | 85 +
.../UserProfileRegistryException.java | 28 +
.../repositories/UserProfileRepository.java | 91 +
.../src/main/resources/user_profile_catalog.sql | 84 +
.../repositories/WorkspaceRepositoryTest.java | 176 +
airavata-services/services-security/pom.xml | 92 +
.../security/AiravataSecurityManager.java | 43 +
.../DefaultAiravataSecurityManager.java | 273 +
.../service/security/IdentityContext.java | 44 +
.../security/KeyCloakSecurityManager.java | 289 +
.../apache/airavata/service/security/Main.java | 179 +
.../security/SecurityManagerFactory.java | 60 +
.../service/security/authzcache/AuthzCache.java | 61 +
.../security/authzcache/AuthzCacheEntry.java | 63 +
.../security/authzcache/AuthzCacheIndex.java | 90 +
.../security/authzcache/AuthzCacheManager.java | 80 +
.../authzcache/AuthzCacheManagerFactory.java | 60 +
.../security/authzcache/AuthzCachedStatus.java | 34 +
.../authzcache/DefaultAuthzCacheManager.java | 106 +
.../security/interceptor/SecurityCheck.java | 37 +
.../interceptor/SecurityInterceptor.java | 83 +
.../security/interceptor/SecurityModule.java | 43 +
.../security/oauth/DefaultOAuthClient.java | 91 +
.../security/xacml/DefaultPAPClient.java | 125 +
.../service/security/xacml/DefaultXACMLPEP.java | 133 +
dev-tools/ansible/.gitignore | 2 +
dev-tools/ansible/README.md | 10 +-
dev-tools/ansible/airavata-iam-setup.yml | 8 +
dev-tools/ansible/airavata.yml | 59 +
dev-tools/ansible/ansible.cfg | 2 +
dev-tools/ansible/dev_airavata_deploy.yml | 20 +
dev-tools/ansible/dev_pga_deploy.yml | 20 +
dev-tools/ansible/group_vars/.gitignore | 1 -
dev-tools/ansible/group_vars/all.yml | 91 -
dev-tools/ansible/group_vars/dev-airavata.yml | 2 -
dev-tools/ansible/group_vars/dev-pga.yml | 3 -
dev-tools/ansible/group_vars/local.yml.template | 4 -
dev-tools/ansible/hosts | 35 -
.../inventories/airavata-iam/group_vars/all.yml | 16 +
.../ansible/inventories/airavata-iam/hosts | 8 +
.../inventories/develop/group_vars/.gitignore | 1 +
.../inventories/develop/group_vars/all.yml | 123 +
.../develop/group_vars/dev-airavata.yml | 22 +
.../inventories/develop/group_vars/dev-pga.yml | 23 +
.../develop/group_vars/local.yml.template | 4 +
dev-tools/ansible/inventories/develop/hosts | 35 +
.../geogateway-dev/group_vars/pga/vars.yml | 53 +
.../geogateway-dev/group_vars/pga/vault.yml | 18 +
.../ansible/inventories/geogateway-dev/hosts | 2 +
.../dreg-production/files/pga-ssl-vhost.conf.j2 | 31 +
.../dreg-production/group_vars/pga/vars.yml | 67 +
.../dreg-production/group_vars/pga/vault.yml | 18 +
.../inventories/scigap/dreg-production/hosts | 21 +
.../scigap/production/files/airavata.jks | 76 +
.../scigap/production/files/airavata_sym.jks | 30 +
.../production/files/client_truststore.jks | 126 +
.../scigap/production/group_vars/all/vars.yml | 126 +
.../scigap/production/group_vars/all/vault.yml | 20 +
.../ansible/inventories/scigap/production/hosts | 20 +
.../production/pga_config/brandeis/vars.yml | 51 +
.../production/pga_config/brandeis/vault.yml | 18 +
.../production/pga_config/cinetvtech/vars.yml | 55 +
.../production/pga_config/cinetvtech/vault.yml | 18 +
.../cornell-dnasequence/pga-ssl-vhost.conf.j2 | 31 +
.../pga_config/cornell-dnasequence/vars.yml | 63 +
.../pga_config/cornell-dnasequence/vault.yml | 18 +
.../production/pga_config/georgiastate/vars.yml | 55 +
.../pga_config/georgiastate/vault.yml | 18 +
.../production/pga_config/iugateway/vars.yml | 55 +
.../production/pga_config/iugateway/vault.yml | 18 +
.../scigap/production/pga_config/lsu/vars.yml | 51 +
.../scigap/production/pga_config/lsu/vault.yml | 18 +
.../scigap/production/pga_config/nsg/vars.yml | 56 +
.../scigap/production/pga_config/nsg/vault.yml | 18 +
.../production/pga_config/oiitandy/vars.yml | 55 +
.../production/pga_config/oiitandy/vault.yml | 18 +
.../scigap/production/pga_config/oscer/vars.yml | 55 +
.../production/pga_config/oscer/vault.yml | 18 +
.../production/pga_config/phasta/vars.yml | 55 +
.../production/pga_config/phasta/vault.yml | 18 +
.../production/pga_config/scigap/vars.yml | 56 +
.../production/pga_config/scigap/vault.yml | 18 +
.../production/pga_config/seagrid/vars.yml | 56 +
.../production/pga_config/seagrid/vault.yml | 18 +
.../production/pga_config/simvascular/vars.yml | 55 +
.../production/pga_config/simvascular/vault.yml | 18 +
.../production/pga_config/southdakota/vars.yml | 55 +
.../production/pga_config/southdakota/vault.yml | 18 +
.../pga_config/southernillinois/vars.yml | 55 +
.../pga_config/southernillinois/vault.yml | 18 +
.../production/pga_config/testdrive/vars.yml | 56 +
.../production/pga_config/testdrive/vault.yml | 18 +
.../production/pga_config/ultrascan/vars.yml | 64 +
.../production/pga_config/ultrascan/vault.yml | 18 +
.../scigap/production/pga_config/utah/vars.yml | 55 +
.../scigap/production/pga_config/utah/vault.yml | 18 +
.../testing-0.17-scigap/group_vars/all/vars.yml | 111 +
.../group_vars/all/vault.yml | 7 +
.../testing-0.17-scigap/group_vars/pga/vars.yml | 52 +
.../group_vars/pga/vault.yml | 18 +
.../inventories/testing-0.17-scigap/hosts | 23 +
.../group_vars/all/vars.yml | 111 +
.../group_vars/all/vault.yml | 7 +
.../group_vars/pga/vars.yml | 51 +
.../group_vars/pga/vault.yml | 18 +
.../inventories/testing-0.17-testdrive/hosts | 23 +
.../inventories/testing-0.17/files/airavata.jks | 76 +
.../testing-0.17/files/airavata_sym.jks | 30 +
.../testing-0.17/files/client_truststore.jks | 271 +
.../testing-0.17/group_vars/all/vars.yml | 115 +
.../testing-0.17/group_vars/all/vault.yml | 13 +
.../testing-0.17/group_vars/pga/vars.yml | 54 +
.../testing-0.17/group_vars/pga/vault.yml | 18 +
.../ansible/inventories/testing-0.17/hosts | 23 +
dev-tools/ansible/local_airavata_deploy.yml | 20 +
dev-tools/ansible/pga-scigap-prod.yml | 41 +
dev-tools/ansible/pga-single-vhost.yml | 37 +
dev-tools/ansible/pga.yml | 28 +
.../ansible/roles/airavata_build/tasks/main.yml | 20 +
.../roles/airavata_deploy/defaults/main.yml | 20 +
.../roles/airavata_deploy/handlers/main.yml | 20 +
.../roles/airavata_deploy/tasks/main.yml | 20 +
.../ansible/roles/api-orch/defaults/main.yml | 27 +
.../ansible/roles/api-orch/handlers/main.yml | 20 +
dev-tools/ansible/roles/api-orch/tasks/main.yml | 42 +-
.../templates/airavata-server.properties.j2 | 54 +-
.../api-orch/templates/gfac-config.yaml.j2 | 6 +
.../roles/api-orch/templates/logback.xml.j2 | 55 +
.../ansible/roles/common/defaults/main.yml | 23 +
dev-tools/ansible/roles/common/tasks/main.yml | 32 +-
dev-tools/ansible/roles/common/vars/main.yml | 20 +
.../ansible/roles/database/defaults/main.yml | 21 +
.../database/files/MariaDB_yum_CentOS_7.repo | 7 +
.../ansible/roles/database/files/mysql-tmp.te | 9 +
.../ansible/roles/database/handlers/main.yml | 20 +
dev-tools/ansible/roles/database/tasks/main.yml | 81 +-
.../roles/database/tasks/secure_install.yml | 20 +
dev-tools/ansible/roles/database/vars/main.yml | 29 +-
.../ansible/roles/env_setup/tasks/main.yml | 30 +-
.../ansible/roles/env_setup/tasks/redhat.yml | 20 +
dev-tools/ansible/roles/gfac/defaults/main.yml | 21 +
dev-tools/ansible/roles/gfac/handlers/main.yml | 20 +
dev-tools/ansible/roles/gfac/tasks/main.yml | 34 +-
.../templates/airavata-server.properties.j2 | 21 +-
.../roles/gfac/templates/gfac-config.yaml.j2 | 8 +
.../ansible/roles/gfac/templates/logback.xml.j2 | 55 +
dev-tools/ansible/roles/java/tasks/main.yml | 26 +
dev-tools/ansible/roles/java/vars/main.yml | 20 +
dev-tools/ansible/roles/keycloak/README.md | 14 +
.../ansible/roles/keycloak/defaults/main.yml | 12 +
.../ansible/roles/keycloak/files/README.md | 36 +
dev-tools/ansible/roles/keycloak/tasks/main.yml | 180 +
.../templates/keycloak-hacluster-init.j2 | 49 +
.../templates/keycloak-standalone-init.j2 | 46 +
.../ansible/roles/keycloak/templates/module.j2 | 12 +
.../keycloak/templates/standalone-ha.xml.j2 | 533 +
.../roles/keycloak/templates/standalone.xml.j2 | 493 +
dev-tools/ansible/roles/pga/defaults/main.yml | 77 +
dev-tools/ansible/roles/pga/files/default.conf | 5 +
dev-tools/ansible/roles/pga/handlers/main.yml | 24 +-
.../roles/pga/tasks/install_deps_CentOS_7.yml | 54 +
.../roles/pga/tasks/install_deps_Ubuntu_14.yml | 68 +
.../roles/pga/tasks/install_deps_Ubuntu_16.yml | 81 +
dev-tools/ansible/roles/pga/tasks/main.yml | 175 +-
.../ansible/roles/pga/templates/httpd.conf.j2 | 353 -
.../roles/pga/templates/pga-ssl-vhost.conf.j2 | 29 +
.../roles/pga/templates/pga-vhost.conf.j2 | 14 +
.../roles/pga/templates/pga_config.php.j2 | 44 +-
dev-tools/ansible/roles/pga/vars/main.yml | 30 -
.../ansible/roles/pga_deploy/handlers/main.yml | 20 +
.../ansible/roles/pga_deploy/tasks/main.yml | 20 +
.../ansible/roles/rabbitmq/handlers/main.yml | 20 +
dev-tools/ansible/roles/rabbitmq/tasks/main.yml | 20 +
dev-tools/ansible/roles/rabbitmq/vars/main.yml | 20 +
dev-tools/ansible/roles/registry/tasks/main.yml | 20 +
.../templates/airavata-server.properties.j2 | 7 +
dev-tools/ansible/roles/wso2_is/tasks/main.yml | 20 +
dev-tools/ansible/roles/wso2_is/vars/main.yml | 20 +
.../ansible/roles/zookeeper/handlers/main.yml | 20 +
.../ansible/roles/zookeeper/tasks/main.yml | 20 +
dev-tools/ansible/roles/zookeeper/vars/main.yml | 20 +
dev-tools/ansible/site.yml | 20 +
modules/cloud/cloud-provisioning/pom.xml | 5 -
modules/cluster-monitoring/pom.xml | 25 +-
.../monitoring/ClusterStatusMonitorJob.java | 5 +-
.../ClusterStatusMonitorJobScheduler.java | 5 +-
modules/commons/pom.xml | 35 +-
.../airavata/common/utils/BuildConstant.java | 4 +-
.../airavata/common/context/RequestContext.java | 4 +-
.../common/context/WorkflowContext.java | 4 +-
.../AiravataConfigurationException.java | 4 +-
.../common/exception/AiravataException.java | 4 +-
.../exception/AiravataStartupException.java | 4 +-
.../exception/ApplicationSettingsException.java | 4 +-
.../airavata/common/logging/Exception.java | 3 +-
.../airavata/common/logging/LogEntry.java | 3 +-
.../airavata/common/logging/MDCConstants.java | 3 +-
.../apache/airavata/common/logging/MDCUtil.java | 19 +
.../airavata/common/logging/ServerId.java | 3 +-
.../common/logging/kafka/KafkaAppender.java | 3 +-
.../airavata/common/utils/AiravataJobState.java | 5 +-
.../airavata/common/utils/AiravataUtils.java | 4 +-
.../airavata/common/utils/AiravataZKUtils.java | 5 +-
.../common/utils/ApplicationSettings.java | 24 +-
.../airavata/common/utils/AwsMetadata.java | 3 +-
.../airavata/common/utils/BrowserLauncher.java | 4 +-
.../airavata/common/utils/ClientSettings.java | 4 +-
.../apache/airavata/common/utils/Constants.java | 4 +-
.../common/utils/DBEventManagerConstants.java | 99 +
.../airavata/common/utils/DBEventService.java | 42 +
.../apache/airavata/common/utils/DBUtil.java | 4 +-
.../common/utils/DatabaseTestCases.java | 4 +-
.../utils/DefaultKeyStorePasswordCallback.java | 4 +-
.../apache/airavata/common/utils/DerbyUtil.java | 4 +-
.../airavata/common/utils/ExecutionMode.java | 4 +-
.../apache/airavata/common/utils/IOUtil.java | 4 +-
.../apache/airavata/common/utils/IServer.java | 4 +-
.../apache/airavata/common/utils/JSONUtil.java | 4 +-
.../common/utils/KeyStorePasswordCallback.java | 19 +
.../common/utils/LocalEventPublisher.java | 5 +-
.../airavata/common/utils/NameValidator.java | 4 +-
.../org/apache/airavata/common/utils/Pair.java | 4 +-
.../airavata/common/utils/SecurityUtil.java | 4 +-
.../airavata/common/utils/ServerSettings.java | 26 +-
.../airavata/common/utils/ServiceUtils.java | 19 +
.../airavata/common/utils/StringUtil.java | 4 +-
.../apache/airavata/common/utils/SwingUtil.java | 4 +-
.../airavata/common/utils/ThriftUtils.java | 4 +-
.../apache/airavata/common/utils/Version.java | 4 +-
.../airavata/common/utils/WSConstants.java | 4 +-
.../apache/airavata/common/utils/WSDLUtil.java | 4 +-
.../airavata/common/utils/ZkConstants.java | 3 +-
.../listener/AbstractActivityListener.java | 4 +-
.../listener/AbstractStateChangeRequest.java | 4 +-
.../common/utils/listener/PublisherMessage.java | 4 +-
.../common/utils/ApplicationSettingsTest.java | 4 +-
.../airavata/common/utils/SecurityUtilTest.java | 4 +-
modules/configuration/client/pom.xml | 26 +-
modules/configuration/pom.xml | 26 +-
modules/configuration/server/pom.xml | 26 +-
.../src/main/resources/LSF_Groovy.template | 3 +
.../src/main/resources/UGE_Groovy.template | 3 +-
.../resources/airavata-default-xacml-policy.xml | 18 +-
.../main/resources/airavata-server.properties | 39 +-
.../src/main/resources/client_truststore.jks | Bin 2423 -> 5312 bytes
.../server/src/main/resources/log4j.properties | 48 -
.../server/src/main/resources/logback.xml | 70 +-
.../credential-store-service/pom.xml | 33 +-
.../credential/store/credential/AuditInfo.java | 4 +-
.../store/credential/CommunityUser.java | 4 +-
.../credential/store/credential/Credential.java | 4 +-
.../store/credential/CredentialOwnerType.java | 19 +
.../impl/certificate/CertificateAuditInfo.java | 6 +-
.../impl/certificate/CertificateCredential.java | 4 +-
.../impl/password/PasswordCredential.java | 4 +-
.../credential/impl/ssh/SSHCredential.java | 4 +-
.../impl/ssh/SSHCredentialGenerator.java | 4 +-
.../store/notifier/CredentialStoreNotifier.java | 19 +
.../store/notifier/NotificationMessage.java | 4 +-
.../store/notifier/NotifierBootstrap.java | 4 +-
.../notifier/impl/EmailNotificationMessage.java | 4 +-
.../store/notifier/impl/EmailNotifier.java | 4 +-
.../impl/EmailNotifierConfiguration.java | 4 +-
.../store/server/CredentialStoreServer.java | 3 +-
.../server/CredentialStoreServerHandler.java | 3 +-
.../store/servlet/CredentialBootstrapper.java | 4 +-
.../servlet/CredentialStoreCallbackServlet.java | 4 +-
.../servlet/CredentialStoreStartServlet.java | 4 +-
.../store/store/CredentialReader.java | 4 +-
.../store/store/CredentialReaderFactory.java | 4 +-
.../store/store/CredentialStoreException.java | 4 +-
.../store/store/CredentialWriter.java | 4 +-
.../store/impl/CertificateCredentialWriter.java | 4 +-
.../store/store/impl/CredentialReaderImpl.java | 4 +-
.../store/store/impl/SSHCredentialWriter.java | 4 +-
.../store/store/impl/db/CommunityUserDAO.java | 4 +-
.../store/store/impl/db/CredentialsDAO.java | 6 +-
.../store/store/impl/db/ParentDAO.java | 4 +-
.../store/store/impl/util/ConnectionPool.java | 5 +-
.../impl/util/CredentialStoreInitUtil.java | 5 +-
.../store/store/impl/util/DatabaseCreator.java | 5 +-
.../store/store/impl/util/JdbcStorage.java | 5 +-
.../store/util/ConfigurationReader.java | 4 +-
.../store/util/CredentialStoreConstants.java | 4 +-
.../credential/store/util/PrivateKeyStore.java | 4 +-
.../credential/store/util/TokenGenerator.java | 4 +-
.../airavata/credential/store/util/Utility.java | 4 +-
.../cpi/SSHSummaryTest/SSHSummaryTest.java | 19 +
.../store/notifier/impl/EmailNotifierTest.java | 4 +-
.../store/impl/db/CommunityUserDAOTest.java | 4 +-
.../store/store/impl/db/CredentialsDAOTest.java | 4 +-
.../store/store/impl/db/SSHCredentialTest.java | 4 +-
.../store/util/ConfigurationReaderTest.java | 4 +-
.../store/util/TokenGeneratorTest.java | 4 +-
.../credential-store-stubs/pom.xml | 31 +-
.../client/CredentialStoreClientFactory.java | 4 +-
.../credential/store/client/TestSSLClient.java | 3 +-
.../store/cpi/CredentialStoreService.java | 19 +
.../cpi/credential_store_cpiConstants.java | 19 +
.../exception/CredentialStoreException.java | 19 +
modules/credential-store/pom.xml | 26 +-
modules/db-event-manager/pom.xml | 41 +
.../db/event/manager/DBEventManagerRunner.java | 78 +
.../messaging/DBEventManagerException.java | 42 +
.../DBEventManagerMessagingFactory.java | 76 +
.../messaging/impl/DBEventMessageHandler.java | 112 +
.../db/event/manager/utils/Constants.java | 33 +
.../manager/utils/DbEventManagerZkUtils.java | 126 +
.../db-event-manager/src/test/java/Test.java | 25 +
modules/distribution/pom.xml | 64 +-
.../src/main/assembly/bin-assembly.xml | 32 +-
.../src/main/assembly/src-assembly.xml | 37 +-
.../main/resources/bin/airavata-server-start.sh | 17 +-
.../gfac-application-specific-handlers/pom.xml | 31 +-
.../gaussian/handler/GaussianHandler.java | 19 +
modules/gfac/gfac-bes/pom.xml | 29 +-
.../gfac/bes/handlers/AbstractSMSHandler.java | 19 +
.../gfac/bes/handlers/SMSByteIOInHandler.java | 19 +
.../gfac/bes/handlers/SMSByteIOOutHandler.java | 19 +
.../gfac/bes/handlers/SMSDirectoryHandler.java | 19 +
.../gfac/bes/provider/impl/BESProvider.java | 3 +-
.../bes/security/UNICORESecurityContext.java | 19 +
.../gfac/bes/security/X509SecurityContext.java | 5 +-
.../airavata/gfac/bes/utils/ActivityInfo.java | 19 +
.../gfac/bes/utils/ApplicationProcessor.java | 4 +-
.../airavata/gfac/bes/utils/BESConstants.java | 19 +
.../gfac/bes/utils/DataTransferrer.java | 4 +-
.../airavata/gfac/bes/utils/FileDownloader.java | 4 +-
.../gfac/bes/utils/FileTransferBase.java | 4 +-
.../airavata/gfac/bes/utils/FileUploader.java | 4 +-
.../airavata/gfac/bes/utils/JSDLGenerator.java | 3 +-
.../airavata/gfac/bes/utils/JSDLUtils.java | 4 +-
.../apache/airavata/gfac/bes/utils/Mode.java | 4 +-
.../airavata/gfac/bes/utils/MyProxyLogon.java | 19 +
.../airavata/gfac/bes/utils/OSRequirement.java | 4 +-
.../apache/airavata/gfac/bes/utils/OSType.java | 4 +-
.../gfac/bes/utils/ProcessorRequirement.java | 6 +-
.../airavata/gfac/bes/utils/RangeValueType.java | 4 +-
.../gfac/bes/utils/ResourceProcessor.java | 4 +-
.../airavata/gfac/bes/utils/SPMDProcessor.java | 4 +-
.../airavata/gfac/bes/utils/SPMDVariations.java | 4 +-
.../airavata/gfac/bes/utils/SecurityUtils.java | 19 +
.../airavata/gfac/bes/utils/StorageCreator.java | 4 +-
.../gfac/bes/utils/UASDataStagingProcessor.java | 4 +-
.../airavata/gfac/bes/utils/URIUtils.java | 4 +-
.../impl/JSDLGeneratorTestWithMyProxyAuth.java | 4 +-
modules/gfac/gfac-client/pom.xml | 31 +-
.../airavata/gfac/client/GFACInstance.java | 5 +-
.../airavata/gfac/client/GFacClientFactory.java | 5 +-
.../apache/airavata/gfac/cpi/GfacService.java | 21 +-
.../airavata/gfac/cpi/gfac_cpiConstants.java | 19 +
.../apache/airavata/gfac/core/GFacUtils.java | 8 +-
.../gfac/core/cluster/OutputParser.java | 2 +-
.../gfac/core/cluster/RemoteCluster.java | 12 +-
.../gfac/core/context/ProcessContext.java | 49 +-
modules/gfac/gfac-impl/pom.xml | 26 +-
.../java/com/jcraft/jsch/ExtendedSession.java | 4 +-
.../com/jcraft/jsch/GSISSHIdentityFile.java | 4 +-
.../jcraft/jsch/GSISSHIdentityRepository.java | 4 +-
.../java/com/jcraft/jsch/GSSContextX509.java | 4 +-
.../UserAuthGSSAPIWithMICGSSCredentials.java | 4 +-
.../apache/airavata/gfac/impl/AuroraUtils.java | 3 +-
.../airavata/gfac/impl/BESRemoteCluster.java | 28 +-
.../gfac/impl/DefaultHostScheduler.java | 3 +-
.../org/apache/airavata/gfac/impl/Factory.java | 3 +-
.../airavata/gfac/impl/GFacEngineImpl.java | 6 +-
.../apache/airavata/gfac/impl/GFacWorker.java | 4 +-
.../airavata/gfac/impl/HPCRemoteCluster.java | 32 +-
.../apache/airavata/gfac/impl/HTTPUtils.java | 19 +
.../airavata/gfac/impl/LocalCommandOutput.java | 3 +-
.../airavata/gfac/impl/LocalRemoteCluster.java | 21 +-
.../org/apache/airavata/gfac/impl/SSHUtils.java | 3 +-
.../airavata/gfac/impl/StandardOutReader.java | 5 +-
.../job/AiravataCustomCommandOutputParser.java | 6 +-
.../gfac/impl/job/ForkJobConfiguration.java | 6 +-
.../gfac/impl/job/ForkOutputParser.java | 6 +-
.../apache/airavata/gfac/impl/job/JobUtil.java | 3 +-
.../gfac/impl/job/LSFJobConfiguration.java | 5 +-
.../airavata/gfac/impl/job/LSFOutputParser.java | 11 +-
.../gfac/impl/job/PBSJobConfiguration.java | 5 +-
.../airavata/gfac/impl/job/PBSOutputParser.java | 5 +-
.../gfac/impl/job/SlurmJobConfiguration.java | 5 +-
.../gfac/impl/job/SlurmOutputParser.java | 5 +-
.../gfac/impl/job/UGEJobConfiguration.java | 5 +-
.../airavata/gfac/impl/job/UGEOutputParser.java | 5 +-
.../airavata/gfac/impl/task/ArchiveTask.java | 3 +-
.../gfac/impl/task/AuroraJobSubmissionTask.java | 3 +-
.../gfac/impl/task/BESJobSubmissionTask.java | 19 +
.../airavata/gfac/impl/task/DataStageTask.java | 3 +-
.../gfac/impl/task/DataStreamingTask.java | 6 +-
.../impl/task/DefaultJobSubmissionTask.java | 6 +-
.../gfac/impl/task/EnvironmentSetupTask.java | 3 +-
.../gfac/impl/task/ForkJobSubmissionTask.java | 6 +-
.../gfac/impl/task/LocalJobSubmissionTask.java | 6 +-
.../gfac/impl/task/SCPDataStageTask.java | 30 +-
.../airavata/gfac/impl/task/TaskUtils.java | 3 +-
.../gfac/impl/task/utils/StreamData.java | 6 +-
.../gfac/impl/task/utils/bes/ActivityInfo.java | 19 +
.../task/utils/bes/ApplicationProcessor.java | 4 +-
.../gfac/impl/task/utils/bes/BESConstants.java | 19 +
.../impl/task/utils/bes/DataTransferrer.java | 4 +-
.../impl/task/utils/bes/FileDownloader.java | 4 +-
.../impl/task/utils/bes/FileTransferBase.java | 4 +-
.../gfac/impl/task/utils/bes/FileUploader.java | 4 +-
.../gfac/impl/task/utils/bes/JSDLGenerator.java | 3 +-
.../gfac/impl/task/utils/bes/JSDLUtils.java | 4 +-
.../airavata/gfac/impl/task/utils/bes/Mode.java | 4 +-
.../gfac/impl/task/utils/bes/MyProxyLogon.java | 19 +
.../gfac/impl/task/utils/bes/OSType.java | 4 +-
.../task/utils/bes/ProcessorRequirement.java | 6 +-
.../impl/task/utils/bes/RangeValueType.java | 4 +-
.../impl/task/utils/bes/ResourceProcessor.java | 4 +-
.../task/utils/bes/ResourceRequirement.java | 4 +-
.../impl/task/utils/bes/SPMDVariations.java | 4 +-
.../gfac/impl/task/utils/bes/SecurityUtils.java | 19 +
.../impl/task/utils/bes/StorageCreator.java | 4 +-
.../task/utils/bes/UASDataStagingProcessor.java | 4 +-
.../task/utils/bes/UNICORESecurityContext.java | 19 +
.../gfac/impl/task/utils/bes/URIUtils.java | 4 +-
.../task/utils/bes/X509SecurityContext.java | 5 +-
.../impl/watcher/CancelRequestWatcherImpl.java | 3 +-
.../watcher/RedeliveryRequestWatcherImpl.java | 3 +-
.../handler/LocalDirectorySetupHandler.java | 19 +
.../gfac/local/handler/LocalInputHandler.java | 19 +
.../gfac/local/provider/impl/LocalProvider.java | 19 +
.../local/utils/InputStreamToFileWriter.java | 5 +-
.../airavata/gfac/local/utils/InputUtils.java | 5 +-
.../gfac/local/utils/LocalProviderUtil.java | 19 +
.../gfac/monitor/cloud/AuroraJobMonitor.java | 3 +-
.../gfac/monitor/email/EmailBasedMonitor.java | 5 +-
.../email/parser/AiravataCustomMailParser.java | 5 +-
.../monitor/email/parser/LSFEmailParser.java | 6 +-
.../monitor/email/parser/PBSEmailParser.java | 5 +-
.../monitor/email/parser/SLURMEmailParser.java | 5 +-
.../monitor/email/parser/UGEEmailParser.java | 5 +-
.../exception/AiravataMonitorException.java | 5 +-
.../gfac/ssh/context/SSHAuthWrapper.java | 5 +-
.../gfac/ssh/security/SSHSecurityContext.java | 3 +-
.../gfac/ssh/security/TokenizedSSHAuthInfo.java | 5 +-
.../services/impl/BigRed2TestWithSSHAuth.java | 19 +
.../gfac/services/impl/CredentialStoreTest.java | 19 +
.../impl/GSISSHProviderTestWithMyProxyAuth.java | 19 +
.../gfac/services/impl/LocalProviderTest.java | 19 +
.../impl/SSHProviderTestWithSSHAuth.java | 19 +
.../GSISecurityContextTestWithMyProxyAuth.java | 19 +
.../email/parser/PBSEmailParserTest.java | 19 +
.../gfac/ssh/config/ConfigReaderTest.java | 19 +
.../impl/DefaultSSHApiTestWithMyProxyAuth.java | 19 +
.../gfac/ssh/impl/VanilaTestWithSSHAuth.java | 19 +
.../apache/airavata/job/AMQPMonitorTest.java | 19 +
.../job/QstatMonitorTestWithMyProxyAuth.java | 19 +
modules/gfac/gfac-service/pom.xml | 31 +-
.../apache/airavata/gfac/server/GfacServer.java | 5 +-
.../airavata/gfac/server/GfacServerHandler.java | 5 +-
.../gfac/client/GfacClientFactoryTest.java | 6 +-
.../airavata/gfac/client/util/Initialize.java | 4 +-
modules/gfac/pom.xml | 26 +-
modules/integration-tests/pom.xml | 26 +-
.../org/apache/airavata/integration/Man.java | 4 +-
.../integration/AbstractIntegrationTest.java | 4 +-
.../apache/airavata/integration/BaseCaseIT.java | 4 +-
.../airavata/integration/DataRetrievalIT.java | 4 +-
.../airavata/integration/ForEachCaseIT.java | 4 +-
.../apache/airavata/integration/OsUtils.java | 4 +-
.../integration/PasswordCallbackImpl.java | 19 +
.../airavata/integration/SimpleEchoIT.java | 4 +-
.../SingleAppIntegrationTestBase.java | 3 +-
.../WorkflowIntegrationTestBase.java | 4 +-
.../integration/WorkflowSamplesCaseIT.java | 4 +-
.../integration/tools/DocumentCreatorNew.java | 5 +-
.../integration/tools/DocumentCreatorUtils.java | 4 +-
.../integration-tests/src/test/java/suite.xml | 30 +-
modules/messaging/client/pom.xml | 26 +-
.../messaging/client/RabbitMQListener.java | 4 +-
.../airavata/messaging/client/TestReader.java | 3 +-
modules/messaging/core/pom.xml | 32 +-
.../airavata/messaging/core/MessageContext.java | 4 +-
.../airavata/messaging/core/MessageHandler.java | 4 +-
.../messaging/core/MessagingConstants.java | 4 +-
.../messaging/core/MessagingFactory.java | 33 +-
.../airavata/messaging/core/Publisher.java | 14 +-
.../messaging/core/PublisherFactory.java | 19 +
.../messaging/core/RabbitMQProperties.java | 3 +-
.../airavata/messaging/core/Subscriber.java | 4 +-
.../airavata/messaging/core/TestClient.java | 4 +-
.../apache/airavata/messaging/core/Type.java | 3 +-
.../messaging/core/impl/ExperimentConsumer.java | 3 +-
.../messaging/core/impl/MessageConsumer.java | 94 +
.../messaging/core/impl/ProcessConsumer.java | 3 +-
.../impl/RabbitMQProcessLaunchConsumer.java | 19 +
.../impl/RabbitMQProcessLaunchPublisher.java | 19 +
.../messaging/core/impl/RabbitMQProducer.java | 19 +
.../messaging/core/impl/RabbitMQPublisher.java | 40 +-
.../core/impl/RabbitMQStatusPublisher.java | 19 +
.../core/impl/RabbitMQStatusSubscriber.java | 19 +
.../messaging/core/impl/RabbitMQSubscriber.java | 4 +-
.../messaging/core/impl/StatusConsumer.java | 3 +-
.../messaging/core/stats/CountWriterTask.java | 3 +-
.../messaging/core/stats/LatencyWriterTask.java | 3 +-
.../messaging/core/stats/StatCounter.java | 3 +-
modules/messaging/pom.xml | 26 +-
modules/monitoring/pom.xml | 31 +-
.../org/apache/airavata/monitoring/Main.java | 3 +-
.../airavata/monitoring/MessageExtract.java | 3 +-
.../org/apache/airavata/monitoring/Util.java | 3 +-
.../monitoring/consumer/StatusConsumer.java | 3 +-
.../monitoring/consumer/StatusReceiver.java | 3 +-
.../monitoring/mailbox/GmailSMTPMailBox.java | 3 +-
.../airavata/monitoring/mailbox/MailBox.java | 3 +-
.../airavata/monitoring/mailbox/MailConfig.java | 3 +-
.../producer/RabbitMQEmailPublisher.java | 3 +-
.../monitoring/simulator/FetchPublish.java | 3 +-
.../monitoring/simulator/Simulator.java | 3 +-
modules/orchestrator/NULL | 1 -
.../orchestrator/orchestrator-client/pom.xml | 31 +-
.../client/OrchestratorClientFactory.java | 4 +-
.../orchestrator/cpi/OrchestratorService.java | 22 +-
.../cpi/orchestrator_cpiConstants.java | 19 +
.../sample/OrchestratorClientSample.java | 6 +-
modules/orchestrator/orchestrator-core/pom.xml | 31 +-
.../core/OrchestratorConfiguration.java | 5 +-
.../core/context/OrchestratorContext.java | 5 +-
.../core/exception/OrchestratorException.java | 5 +-
.../core/impl/GFACPassiveJobSubmitter.java | 5 +-
.../orchestrator/core/job/JobSubmitter.java | 5 +-
.../core/utils/OrchestratorConstants.java | 5 +-
.../core/utils/OrchestratorUtils.java | 5 +-
.../core/validator/JobMetadataValidator.java | 5 +-
.../validator/impl/BatchQueueValidator.java | 5 +-
.../impl/ExperimentStatusValidator.java | 5 +-
.../airavata/orchestrator/cpi/Orchestrator.java | 5 +-
.../cpi/impl/AbstractOrchestrator.java | 5 +-
.../cpi/impl/SimpleOrchestratorImpl.java | 5 +-
.../orchestrator/core/BaseOrchestratorTest.java | 5 +-
.../orchestrator/core/NewOrchestratorTest.java | 5 +-
.../core/OrchestratorTestWithGRAM.java | 5 +-
.../core/OrchestratorTestWithMyProxyAuth.java | 5 +-
.../orchestrator/core/ValidatorTest.java | 19 +
.../orchestrator/core/util/Initialize.java | 4 +-
.../orchestrator/core/util/SecondValidator.java | 19 +
.../orchestrator/core/util/TestValidator.java | 19 +
.../orchestrator/orchestrator-service/pom.xml | 31 +-
.../orchestrator/server/OrchestratorServer.java | 11 +-
.../server/OrchestratorServerHandler.java | 4 +-
.../airavata/orchestrator/util/Constants.java | 4 +-
.../OrchestratorServerThreadPoolExecutor.java | 4 +-
.../orchestrator/util/OrchestratorUtils.java | 3 +-
.../client/OrchestratorClientFactoryTest.java | 6 +-
.../orchestrator/client/util/Initialize.java | 4 +-
modules/orchestrator/pom.xml | 26 +-
modules/registry-refactoring/pom.xml | 132 -
.../registry/core/RegistryException.java | 28 -
.../workspacecatalog/GatewayEntity.java | 221 -
.../workspacecatalog/NSFDemographicsEntity.java | 94 -
.../workspacecatalog/NotificationEntity.java | 110 -
.../workspacecatalog/ProjectEntity.java | 92 -
.../workspacecatalog/UserProfileEntity.java | 247 -
.../core/repositories/AbstractRepository.java | 98 -
.../workspacecatalog/GatewayRepository.java | 36 -
.../NotificationRepository.java | 35 -
.../workspacecatalog/ProjectRepository.java | 35 -
.../workspacecatalog/UserProfileRepository.java | 88 -
.../airavata/registry/core/utils/Committer.java | 27 -
.../registry/core/utils/JPAConstants.java | 32 -
.../airavata/registry/core/utils/JPAUtils.java | 83 -
.../core/utils/ObjectMapperSingleton.java | 39 -
.../registry/core/utils/QueryConstants.java | 22 -
.../airavata/registry/core/utils/Utils.java | 156 -
.../src/main/resources/META-INF/persistence.xml | 32 -
.../src/main/resources/workspace_catalog.sql | 125 -
.../repositories/WorkspaceRepositoryTest.java | 197 -
modules/registry/pom.xml | 26 +-
modules/registry/registry-core/pom.xml | 26 +-
.../core/app/catalog/impl/AppCatalogImpl.java | 4 +-
.../catalog/impl/ApplicationDeploymentImpl.java | 6 +-
.../catalog/impl/ApplicationInterfaceImpl.java | 4 +-
.../app/catalog/impl/ComputeResourceImpl.java | 4 +-
.../catalog/impl/GwyResourceProfileImpl.java | 4 +-
.../app/catalog/impl/StorageResourceImpl.java | 4 +-
.../catalog/impl/UsrResourceProfileImpl.java | 8 +-
.../core/app/catalog/model/AppEnvironment.java | 4 +-
.../app/catalog/model/AppEnvironment_PK.java | 4 +-
.../core/app/catalog/model/AppInput_PK.java | 4 +-
.../app/catalog/model/AppModuleMapping.java | 4 +-
.../app/catalog/model/AppModuleMapping_PK.java | 4 +-
.../core/app/catalog/model/AppOutput_PK.java | 4 +-
.../catalog/model/ApplicationDeployment.java | 14 +-
.../app/catalog/model/ApplicationIntInput.java | 4 +-
.../app/catalog/model/ApplicationIntOutput.java | 4 +-
.../app/catalog/model/ApplicationInterface.java | 4 +-
.../app/catalog/model/ApplicationModule.java | 4 +-
.../core/app/catalog/model/BatchQueue.java | 4 +-
.../core/app/catalog/model/BatchQueue_PK.java | 4 +-
.../app/catalog/model/CloudJobSubmission.java | 5 +-
.../core/app/catalog/model/ComputeResource.java | 48 +-
.../model/ComputeResourceFileSystem.java | 4 +-
.../model/ComputeResourceFileSystem_PK.java | 4 +-
.../model/ComputeResourcePreference.java | 4 +-
.../model/ComputeResourcePreferencePK.java | 4 +-
.../core/app/catalog/model/Configuration.java | 19 +
.../app/catalog/model/Configuration_PK.java | 4 +-
.../catalog/model/DataMovementInterface.java | 4 +-
.../catalog/model/DataMovementInterface_PK.java | 4 +-
.../app/catalog/model/DataStorageResource.java | 4 +-
.../core/app/catalog/model/GSISSHExport.java | 4 +-
.../core/app/catalog/model/GSISSHExportPK.java | 4 +-
.../app/catalog/model/GSISSHSubmission.java | 4 +-
.../core/app/catalog/model/GatewayProfile.java | 4 +-
.../app/catalog/model/GlobusGKEndPointPK.java | 4 +-
.../app/catalog/model/GlobusGKEndpoint.java | 4 +-
.../app/catalog/model/GlobusJobSubmission.java | 4 +-
.../app/catalog/model/GridftpDataMovement.java | 4 +-
.../core/app/catalog/model/GridftpEndpoint.java | 4 +-
.../app/catalog/model/GridftpEndpoint_PK.java | 4 +-
.../core/app/catalog/model/HostAlias.java | 4 +-
.../core/app/catalog/model/HostAliasPK.java | 4 +-
.../core/app/catalog/model/HostIPAddress.java | 4 +-
.../core/app/catalog/model/HostIPAddressPK.java | 4 +-
.../app/catalog/model/JobManagerCommand.java | 4 +-
.../app/catalog/model/JobManagerCommand_PK.java | 4 +-
.../catalog/model/JobSubmissionInterface.java | 4 +-
.../model/JobSubmissionInterface_PK.java | 4 +-
.../app/catalog/model/LibraryApendPath.java | 4 +-
.../app/catalog/model/LibraryApendPath_PK.java | 4 +-
.../app/catalog/model/LibraryPrepandPath.java | 4 +-
.../catalog/model/LibraryPrepandPath_PK.java | 4 +-
.../app/catalog/model/LocalDataMovement.java | 4 +-
.../core/app/catalog/model/LocalSubmission.java | 4 +-
.../core/app/catalog/model/ModuleLoadCmd.java | 4 +-
.../app/catalog/model/ModuleLoadCmd_PK.java | 4 +-
.../catalog/model/ParallelismPrefixCommand.java | 4 +-
.../model/ParallelismPrefixCommand_PK.java | 4 +-
.../core/app/catalog/model/PostJobCommand.java | 4 +-
.../app/catalog/model/PostJobCommandPK.java | 4 +-
.../core/app/catalog/model/PreJobCommand.java | 4 +-
.../core/app/catalog/model/PreJobCommandPK.java | 4 +-
.../app/catalog/model/ResourceJobManager.java | 4 +-
.../core/app/catalog/model/ScpDataMovement.java | 4 +-
.../app/catalog/model/SshJobSubmission.java | 4 +-
.../app/catalog/model/StorageInterface.java | 4 +-
.../app/catalog/model/StorageInterface_PK.java | 4 +-
.../app/catalog/model/StoragePreference.java | 4 +-
.../app/catalog/model/StoragePreferencePK.java | 4 +-
.../core/app/catalog/model/StorageResource.java | 4 +-
.../app/catalog/model/UnicoreDataMovement.java | 6 +-
.../app/catalog/model/UnicoreJobSubmission.java | 6 +-
.../model/UserComputeResourcePreference.java | 10 +-
.../model/UserComputeResourcePreferencePK.java | 28 +-
.../app/catalog/model/UserResourceProfile.java | 4 +-
.../catalog/model/UserResourceProfilePK.java | 4 +-
.../catalog/model/UserStoragePreference.java | 10 +-
.../catalog/model/UserStoragePreferencePK.java | 26 +-
.../resources/AppCatAbstractResource.java | 4 +-
.../catalog/resources/AppCatalogResource.java | 19 +
.../resources/AppDeploymentResource.java | 15 +-
.../resources/AppEnvironmentResource.java | 4 +-
.../catalog/resources/AppInterfaceResource.java | 4 +-
...ppModuleMappingAppCatalogResourceAppCat.java | 4 +-
.../catalog/resources/AppModuleResource.java | 4 +-
.../resources/ApplicationInputResource.java | 2 +-
.../resources/ApplicationOutputResource.java | 2 +-
.../catalog/resources/BatchQueueResource.java | 4 +-
.../resources/CloudSubmissionResource.java | 5 +-
.../ComputeHostPreferenceResource.java | 4 +-
.../ComputeResourceFileSystemResource.java | 4 +-
.../resources/ComputeResourceResource.java | 46 +-
.../DataMovementInterfaceResource.java | 4 +-
.../catalog/resources/GSISSHExportResource.java | 2 +-
.../resources/GSISSHSubmissionResource.java | 2 +-
.../resources/GatewayProfileResource.java | 2 +-
.../resources/GlobusGKEndpointResource.java | 2 +-
.../resources/GlobusJobSubmissionResource.java | 2 +-
.../resources/GridftpDataMovementResource.java | 2 +-
.../resources/GridftpEndpointResource.java | 2 +-
.../catalog/resources/HostAliasAppResource.java | 2 +-
.../resources/HostIPAddressResource.java | 2 +-
.../resources/JobManagerCommandResource.java | 4 +-
.../JobSubmissionInterfaceResource.java | 4 +-
.../resources/LibraryApendPathResource.java | 4 +-
.../resources/LibraryPrepandPathResource.java | 4 +-
.../resources/LocalDataMovementResource.java | 4 +-
.../resources/LocalSubmissionResource.java | 4 +-
.../resources/ModuleLoadCmdResource.java | 4 +-
.../ParallelismPrefixCommandResource.java | 4 +-
.../resources/PostJobCommandResource.java | 2 +-
.../resources/PreJobCommandResource.java | 2 +-
.../resources/ResourceJobManagerResource.java | 4 +-
.../resources/ScpDataMovementResource.java | 2 +-
.../resources/SshJobSubmissionResource.java | 2 +-
.../resources/StorageInterfaceResource.java | 4 +-
.../resources/StoragePreferenceResource.java | 4 +-
.../resources/StorageResourceResource.java | 4 +-
.../resources/UnicoreDataMovementResource.java | 6 +-
.../resources/UnicoreJobSubmissionResource.java | 6 +-
.../UserComputeHostPreferenceResource.java | 14 +-
.../resources/UserResourceProfileResource.java | 2 +-
.../UserStoragePreferenceResource.java | 18 +-
.../app/catalog/util/AppCatalogJPAUtils.java | 9 +-
.../catalog/util/AppCatalogQueryGenerator.java | 4 +-
.../catalog/util/AppCatalogResourceType.java | 4 +-
.../util/AppCatalogThriftConversion.java | 13 +-
.../core/app/catalog/util/AppCatalogUtils.java | 4 +-
.../experiment/catalog/ExpCatResourceUtils.java | 5 +-
.../catalog/ExperimentCatResource.java | 5 +-
.../core/experiment/catalog/JPAConstants.java | 4 +-
.../core/experiment/catalog/ResourceType.java | 5 +-
.../catalog/impl/ExperimentCatalogImpl.java | 4 +-
.../catalog/impl/ExperimentRegistry.java | 14 +-
.../catalog/impl/GatewayRegistry.java | 4 +-
.../catalog/impl/NotificationRegistry.java | 4 +-
.../catalog/impl/ProjectRegistry.java | 48 +-
.../catalog/impl/RegistryFactory.java | 4 +-
.../experiment/catalog/impl/UserRegistry.java | 4 +-
.../experiment/catalog/model/Experiment.java | 5 +-
.../catalog/model/ExperimentError.java | 5 +-
.../catalog/model/ExperimentErrorPK.java | 5 +-
.../catalog/model/ExperimentInput.java | 5 +-
.../catalog/model/ExperimentInputPK.java | 5 +-
.../catalog/model/ExperimentOutput.java | 5 +-
.../catalog/model/ExperimentOutputPK.java | 5 +-
.../catalog/model/ExperimentStatus.java | 5 +-
.../catalog/model/ExperimentStatusPK.java | 5 +-
.../catalog/model/ExperimentSummary.java | 5 +-
.../core/experiment/catalog/model/Gateway.java | 5 +-
.../experiment/catalog/model/GatewayWorker.java | 5 +-
.../catalog/model/GatewayWorkerPK.java | 5 +-
.../core/experiment/catalog/model/Job.java | 5 +-
.../core/experiment/catalog/model/JobPK.java | 5 +-
.../experiment/catalog/model/JobStatus.java | 5 +-
.../experiment/catalog/model/JobStatusPK.java | 5 +-
.../experiment/catalog/model/Notification.java | 5 +-
.../core/experiment/catalog/model/Process.java | 5 +-
.../experiment/catalog/model/ProcessError.java | 5 +-
.../catalog/model/ProcessErrorPK.java | 5 +-
.../experiment/catalog/model/ProcessInput.java | 5 +-
.../catalog/model/ProcessInputPK.java | 5 +-
.../experiment/catalog/model/ProcessOutput.java | 5 +-
.../catalog/model/ProcessOutputPK.java | 5 +-
.../catalog/model/ProcessResourceSchedule.java | 5 +-
.../experiment/catalog/model/ProcessStatus.java | 5 +-
.../catalog/model/ProcessStatusPK.java | 5 +-
.../core/experiment/catalog/model/Project.java | 5 +-
.../experiment/catalog/model/ProjectUser.java | 5 +-
.../experiment/catalog/model/ProjectUserPK.java | 5 +-
.../experiment/catalog/model/QueueStatus.java | 5 +-
.../experiment/catalog/model/QueueStatusPK.java | 5 +-
.../core/experiment/catalog/model/Task.java | 5 +-
.../experiment/catalog/model/TaskError.java | 5 +-
.../experiment/catalog/model/TaskErrorPK.java | 5 +-
.../experiment/catalog/model/TaskStatus.java | 5 +-
.../experiment/catalog/model/TaskStatusPK.java | 5 +-
.../catalog/model/UserConfigurationData.java | 5 +-
.../core/experiment/catalog/model/UserPK.java | 5 +-
.../core/experiment/catalog/model/Users.java | 5 +-
.../resources/AbstractExpCatResource.java | 3 +-
.../resources/ExperimentErrorResource.java | 4 +-
.../resources/ExperimentInputResource.java | 4 +-
.../resources/ExperimentOutputResource.java | 4 +-
.../catalog/resources/ExperimentResource.java | 4 +-
.../resources/ExperimentStatisticsResource.java | 5 +-
.../resources/ExperimentStatusResource.java | 4 +-
.../resources/ExperimentSummaryResource.java | 5 +-
.../catalog/resources/GatewayResource.java | 5 +-
.../catalog/resources/JobResource.java | 4 +-
.../catalog/resources/JobStatusResource.java | 4 +-
.../catalog/resources/NotificationResource.java | 5 +-
.../catalog/resources/ProcessErrorResource.java | 4 +-
.../catalog/resources/ProcessInputResource.java | 4 +-
.../resources/ProcessOutputResource.java | 4 +-
.../catalog/resources/ProcessResource.java | 4 +-
.../ProcessResourceScheduleResource.java | 4 +-
.../resources/ProcessStatusResource.java | 4 +-
.../catalog/resources/ProjectResource.java | 5 +-
.../catalog/resources/ProjectUserResource.java | 4 +-
.../catalog/resources/QueueStatusResource.java | 5 +-
.../catalog/resources/TaskErrorResource.java | 4 +-
.../catalog/resources/TaskResource.java | 4 +-
.../catalog/resources/TaskStatusResource.java | 4 +-
.../UserConfigurationDataResource.java | 4 +-
.../catalog/resources/UserResource.java | 5 +-
.../experiment/catalog/resources/Utils.java | 3 +-
.../catalog/resources/WorkerResource.java | 9 +-
.../catalog/utils/QueryGenerator.java | 4 +-
.../utils/ThriftDataModelConversion.java | 19 +
.../registry/core/impl/RegistryImpl.java | 6 +-
.../catalog/impl/ReplicaCatalogImpl.java | 48 +-
.../replica/catalog/model/Configuration.java | 19 +
.../replica/catalog/model/Configuration_PK.java | 4 +-
.../core/replica/catalog/model/DataProduct.java | 5 +-
.../catalog/model/DataProductMetaData.java | 5 +-
.../catalog/model/DataProductMetaData_PK.java | 5 +-
.../catalog/model/DataReplicaLocation.java | 5 +-
.../catalog/model/DataReplicaMetaData.java | 5 +-
.../catalog/model/DataReplicaMetaData_PK.java | 5 +-
.../catalog/utils/ReplicaCatalogConstants.java | 3 +-
.../catalog/utils/ReplicaCatalogJPAUtils.java | 4 +-
.../utils/ReplicaCatalogQueryGenerator.java | 4 +-
.../utils/ThriftDataModelConversion.java | 19 +
.../catalog/impl/WorkflowCatalogImpl.java | 4 +-
.../workflow/catalog/model/ComponentStatus.java | 4 +-
.../core/workflow/catalog/model/Edge.java | 4 +-
.../core/workflow/catalog/model/Edge_PK.java | 4 +-
.../core/workflow/catalog/model/Node.java | 4 +-
.../core/workflow/catalog/model/Node_PK.java | 4 +-
.../core/workflow/catalog/model/Port.java | 4 +-
.../core/workflow/catalog/model/Port_PK.java | 4 +-
.../core/workflow/catalog/model/Workflow.java | 4 +-
.../workflow/catalog/model/WorkflowInput.java | 4 +-
.../catalog/model/WorkflowInput_PK.java | 4 +-
.../workflow/catalog/model/WorkflowOutput.java | 4 +-
.../catalog/model/WorkflowOutput_PK.java | 4 +-
.../workflow/catalog/model/WorkflowStatus.java | 4 +-
.../catalog/model/WorkflowStatus_PK.java | 4 +-
.../resources/ComponentStatusResource.java | 2 +-
.../catalog/resources/EdgeResource.java | 2 +-
.../catalog/resources/NodeResource.java | 2 +-
.../catalog/resources/PortResource.java | 2 +-
.../resources/WorkflowCatAbstractResource.java | 4 +-
.../resources/WorkflowCatalogResource.java | 19 +
.../resources/WorkflowInputResource.java | 2 +-
.../resources/WorkflowOutputResource.java | 2 +-
.../catalog/resources/WorkflowResource.java | 4 +-
.../resources/WorkflowStatusResource.java | 2 +-
.../catalog/utils/WorkflowCatalogJPAUtils.java | 4 +-
.../utils/WorkflowCatalogQueryGenerator.java | 4 +-
.../utils/WorkflowCatalogResourceType.java | 4 +-
.../utils/WorkflowCatalogThriftConversion.java | 4 +-
.../catalog/utils/WorkflowCatalogUtils.java | 4 +-
.../src/main/resources/appcatalog-derby.sql | 5 +
.../src/main/resources/appcatalog-mysql.sql | 5 +
.../main/resources/workflowcatalog-mysql.sql | 3 +-
.../airavata/app/catalog/AppDeploymentTest.java | 4 +-
.../airavata/app/catalog/AppInterfaceTest.java | 4 +-
...puteAppCatalogExperimentCatResourceTest.java | 4 +-
.../app/catalog/GatewayProfileTest.java | 4 +-
.../catalog/StorageResourceAppCatalogTest.java | 4 +-
.../app/catalog/UserResourceProfileTest.java | 4 +-
.../airavata/app/catalog/util/Initialize.java | 4 +-
.../catalog/AbstractResourceTest.java | 4 +-
.../catalog/ExperimentInputResourceTest.java | 19 +
.../catalog/ExperimentOutputResourceTest.java | 19 +
.../catalog/ExperimentResourceTest.java | 19 +
.../experiment/catalog/GatewayResourceTest.java | 19 +
.../experiment/catalog/JobResourceTest.java | 2 +-
.../experiment/catalog/ProcessResourceTest.java | 2 +-
.../catalog/QueueStatusResourceTest.java | 19 +
.../experiment/catalog/TaskResourceTest.java | 2 +-
.../catalog/UserConfigurationDataTest.java | 4 +-
.../experiment/catalog/UserResourceTest.java | 19 +
.../experiment/catalog/util/Initialize.java | 4 +-
.../replica/catalog/ReplicaCatalogTest.java | 7 +-
.../replica/catalog/util/Initialize.java | 4 +-
modules/registry/registry-cpi/pom.xml | 26 +-
.../airavata/registry/cpi/AppCatalog.java | 2 +-
.../registry/cpi/AppCatalogException.java | 2 +-
.../registry/cpi/ApplicationDeployment.java | 2 +-
.../registry/cpi/ApplicationInterface.java | 2 +-
.../registry/cpi/CompositeIdentifier.java | 16 +-
.../airavata/registry/cpi/ComputeResource.java | 2 +-
.../registry/cpi/ExpCatChildDataType.java | 2 +-
.../registry/cpi/ExpCatParentDataType.java | 2 +-
.../registry/cpi/ExperimentCatalog.java | 2 +-
.../cpi/ExperimentCatalogException.java | 6 +-
.../cpi/ExperimentCatalogModelType.java | 2 +-
.../registry/cpi/GwyClientCredential.java | 2 +-
.../registry/cpi/GwyResourceProfile.java | 2 +-
.../apache/airavata/registry/cpi/Registry.java | 6 +-
.../registry/cpi/RegistryException.java | 4 +-
.../airavata/registry/cpi/ReplicaCatalog.java | 5 +-
.../registry/cpi/ReplicaCatalogException.java | 2 +-
.../airavata/registry/cpi/ResultOrderType.java | 19 +
.../airavata/registry/cpi/StorageResource.java | 8 +-
.../registry/cpi/UsrResourceProfile.java | 2 +-
.../airavata/registry/cpi/WorkflowCatalog.java | 6 +-
.../registry/cpi/WorkflowCatalogException.java | 2 +-
.../airavata/registry/cpi/utils/Constants.java | 4 +-
.../airavata/registry/cpi/utils/StatusType.java | 2 +-
modules/registry/registry-server/pom.xml | 28 +-
.../registry-api-service/pom.xml | 26 +
.../registry/api/service/RegistryAPIServer.java | 36 +-
.../service/handler/RegistryServerHandler.java | 57 +-
.../RegistryServiceDBEventHandler.java | 159 +
.../RegistryServiceDBEventMessagingFactory.java | 94 +
.../api/service/util/AppCatalogInitUtil.java | 19 +
.../api/service/util/ConnectionPool.java | 6 +-
.../registry/api/service/util/Constants.java | 14 +-
.../api/service/util/DatabaseCreator.java | 41 +-
.../service/util/ExperimentCatalogInitUtil.java | 19 +
.../registry/api/service/util/JdbcStorage.java | 5 +-
.../service/util/ReplicaCatalogInitUtil.java | 19 +
.../service/util/WorkflowCatalogInitUtil.java | 19 +
.../registry-server/registry-api-stubs/pom.xml | 21 +
.../airavata/registry/api/RegistryService.java | 8997 ++-
.../client/RegistryServiceClientFactory.java | 4 +-
.../api/exception/RegistryServiceException.java | 21 +-
.../registry/api/registry_apiConstants.java | 19 +
modules/registry/registry-tools/jpa-gen/pom.xml | 26 +-
.../computeresource/BatchQueueGenerator.java | 4 +-
.../ComputeResourceDescriptionGenerator.java | 4 +-
.../DataMovementInterfaceGenerator.java | 4 +-
.../computeresource/FileSystemsGenerator.java | 4 +-
.../GridFTPDataMovementGenerator.java | 4 +-
.../GridFTPEndpointsGenerator.java | 4 +-
.../JobManagerCommandGenerator.java | 4 +-
.../JobSubmissionInterfaceGenerator.java | 4 +-
.../LocalDataMovementGenerator.java | 4 +-
.../LocalSubmissionGenerator.java | 4 +-
.../computeresource/ModuleCMDGenerator.java | 4 +-
.../ResourceJobManagerGenerator.java | 4 +-
.../SCPDataMovementGenerator.java | 4 +-
.../SSHJobSubmissionGenerator.java | 4 +-
.../main/java/generators/AbstractGenerator.java | 19 +
.../main/java/generators/JPAClassGenerator.java | 19 +
.../generators/JPAResourceClassGenerator.java | 19 +
.../src/main/java/generators/SQLGenerator.java | 19 +
.../src/main/java/model/JPAClassField.java | 19 +
.../src/main/java/model/JPAClassModel.java | 19 +
.../src/main/java/model/JPAPKClassModel.java | 19 +
.../main/java/model/JPAResourceClassModel.java | 19 +
.../jpa-gen/src/main/java/model/SQLData.java | 19 +
.../jpa-gen/src/main/java/test/Test.java | 19 +
modules/registry/registry-tools/pom.xml | 26 +-
.../registry-tools/registry-tool/pom.xml | 26 +-
.../airavata/registry/tool/DBMigrator.java | 4 +-
.../DeltaScripts/appCatalog_schema_delta.sql | 84 +
.../credentialStore_schema_delta.sql | 37 +
.../DeltaScripts/expCatalog_schema_delta.sql | 54 +
.../replicaCatalog_schema_delta.sql | 32 +
.../DeltaScripts/workFlow_schema_delta.sql | 31 +
.../0.16-0.17/migration-notes.md | 10 +
modules/security/pom.xml | 30 +-
.../security/AbstractAuthenticator.java | 4 +-
.../security/AbstractDatabaseAuthenticator.java | 4 +-
.../security/AiravataSecurityException.java | 3 +-
.../security/AuthenticationException.java | 4 +-
.../apache/airavata/security/Authenticator.java | 4 +-
.../apache/airavata/security/Authoriser.java | 4 +-
.../org/apache/airavata/security/UserStore.java | 4 +-
.../airavata/security/UserStoreException.java | 4 +-
.../AbstractConfigurationReader.java | 4 +-
.../AuthenticatorConfigurationReader.java | 4 +-
.../userstore/AbstractJDBCUserStore.java | 4 +-
.../security/userstore/JDBCUserStore.java | 4 +-
.../security/userstore/LDAPUserStore.java | 4 +-
.../security/userstore/SessionDBUserStore.java | 4 +-
.../security/util/PasswordDigester.java | 4 +-
.../security/util/TrustStoreManager.java | 3 +-
.../AuthenticatorConfigurationReaderTest.java | 4 +-
.../configurations/TestDBAuthenticator1.java | 4 +-
.../configurations/TestDBAuthenticator2.java | 4 +-
.../configurations/TestDBAuthenticator3.java | 4 +-
.../security/configurations/TestUserStore.java | 36 +-
.../security/userstore/JDBCUserStoreTest.java | 36 +-
.../security/userstore/LDAPUserStoreTest.java | 36 +-
.../userstore/SessionDBUserStoreTest.java | 36 +-
modules/server/pom.xml | 30 +-
.../org/apache/airavata/server/ServerMain.java | 7 +-
modules/sharing-registry/pom.xml | 21 +
.../sharing-data-migrator/pom.xml | 21 +
.../migrator/airavata/AiravataDataMigrator.java | 35 +-
.../migrator/airavata/ConnectionFactory.java | 5 +-
.../sharing-registry-distribution/pom.xml | 21 +
.../src/main/assembly/bin-assembly.xml | 37 +-
.../sharing-registry-server/pom.xml | 32 +
.../registry/db/entities/DomainEntity.java | 5 +-
.../registry/db/entities/EntityEntity.java | 16 +-
.../sharing/registry/db/entities/EntityPK.java | 5 +-
.../registry/db/entities/EntityTypeEntity.java | 5 +-
.../registry/db/entities/EntityTypePK.java | 5 +-
.../db/entities/GroupMembershipEntity.java | 5 +-
.../registry/db/entities/GroupMembershipPK.java | 5 +-
.../db/entities/PermissionTypeEntity.java | 5 +-
.../registry/db/entities/PermissionTypePK.java | 5 +-
.../registry/db/entities/SharingEntity.java | 5 +-
.../sharing/registry/db/entities/SharingPK.java | 5 +-
.../registry/db/entities/UserEntity.java | 5 +-
.../registry/db/entities/UserGroupEntity.java | 5 +-
.../registry/db/entities/UserGroupPK.java | 5 +-
.../sharing/registry/db/entities/UserPK.java | 5 +-
.../db/repositories/AbstractRepository.java | 5 +-
.../db/repositories/DomainRepository.java | 5 +-
.../db/repositories/EntityRepository.java | 18 +-
.../db/repositories/EntityTypeRepository.java | 5 +-
.../repositories/GroupMembershipRepository.java | 5 +-
.../repositories/PermissionTypeRepository.java | 5 +-
.../db/repositories/SharingRepository.java | 16 +-
.../db/repositories/UserGroupRepository.java | 19 +-
.../db/repositories/UserRepository.java | 5 +-
.../sharing/registry/db/utils/Committer.java | 5 +-
.../registry/db/utils/ConnectionPool.java | 5 +-
.../sharing/registry/db/utils/DBConstants.java | 6 +-
.../registry/db/utils/DatabaseCreator.java | 5 +-
.../sharing/registry/db/utils/JPAUtils.java | 5 +-
.../sharing/registry/db/utils/JdbcStorage.java | 5 +-
.../db/utils/ObjectMapperSingleton.java | 5 +-
.../messaging/SharingServiceDBEventHandler.java | 243 +
.../SharingServiceDBEventMessagingFactory.java | 111 +
.../sharing/registry/server/ServerMain.java | 5 +-
.../registry/server/SharingRegistryServer.java | 25 +-
.../server/SharingRegistryServerHandler.java | 185 +-
.../sharing/registry/utils/Constants.java | 38 +
.../utils/ThriftDataModelConversion.java | 28 +
.../main/resources/sharing-registry-derby.sql | 3 +-
.../main/resources/sharing-registry-mysql.sql | 1 +
.../airavata/sharing/registry/CipresTest.java | 5 +-
.../SharingRegistryServerHandlerTest.java | 5 +-
.../registry/SharingRegistryServiceTest.java | 33 +-
.../sharing/registry/util/Initialize.java | 4 +-
.../sharing-registry-stubs/pom.xml | 26 +
.../SharingRegistryServiceClientFactory.java | 6 +-
.../sharing/registry/models/Domain.java | 19 +
.../sharing/registry/models/Entity.java | 167 +-
.../registry/models/EntitySearchField.java | 25 +-
.../sharing/registry/models/EntityType.java | 19 +
.../registry/models/GroupCardinality.java | 19 +
.../sharing/registry/models/GroupChildType.java | 19 +
.../registry/models/GroupMembership.java | 19 +
.../sharing/registry/models/GroupType.java | 19 +
.../sharing/registry/models/PermissionType.java | 19 +
.../registry/models/SearchCondition.java | 23 +-
.../sharing/registry/models/SearchCriteria.java | 19 +
.../sharing/registry/models/Sharing.java | 19 +
.../models/SharingRegistryException.java | 19 +
.../sharing/registry/models/SharingType.java | 19 +
.../airavata/sharing/registry/models/User.java | 19 +
.../sharing/registry/models/UserGroup.java | 19 +
.../models/sharing_modelsConstants.java | 19 +
.../service/cpi/SharingRegistryService.java | 19874 ++++--
.../sharing-service-docs/api-docs/index.html | 146 +
.../api-docs/sharing_cpi.html | 64 +-
.../api-docs/sharing_models.html | 55 +-
.../sharing-service-docs/api-docs/style.css | 22 +-
.../sharing-service-docs/index.html | 21 +
.../sharing-service-docs/style.css | 22 +-
.../thrift_models/sharing_cpi.thrift | 33 +-
.../thrift_models/sharing_models.thrift | 15 +-
.../thrift_models/thrift-gen.sh | 24 +-
.../test-suite/multi-tenanted-airavata/pom.xml | 26 +-
.../multitenantedairavata/AiravataClient.java | 6 +-
.../multitenantedairavata/AiravataIT.java | 6 +-
.../ApplicationRegister.java | 6 +-
.../ComputeResourceRegister.java | 6 +-
.../ExperimentExecution.java | 6 +-
.../FrameworkBootstrapping.java | 19 +
.../multitenantedairavata/FrameworkSetup.java | 6 +-
.../multitenantedairavata/GatewayRegister.java | 6 +-
.../StorageResourceRegister.java | 19 +
.../TestFrameworkProps.java | 6 +-
.../utils/ApplicationProperties.java | 19 +
.../utils/ComputeResourceProperties.java | 19 +
.../utils/FrameworkUtils.java | 6 +-
.../utils/PropertyFileType.java | 6 +-
.../utils/PropertyReader.java | 6 +-
.../utils/TestFrameworkConstants.java | 6 +-
.../main/resources/airavata-server.properties | 31 +-
modules/test-suite/pom.xml | 26 +-
modules/user-profile-migration/pom.xml | 33 +-
.../apache/airavata/ISLoginCredentialsDAO.java | 59 -
.../apache/airavata/IdentityServerClient.java | 118 -
.../airavata/KeycloakIdentityServerClient.java | 77 +
.../org/apache/airavata/MigrationManager.java | 46 +-
.../UserProfileAiravataThriftClient.java | 12 +-
.../org/apache/airavata/UserProfileDAO.java | 4 +-
.../airavata/Wso2ISLoginCredentialsDAO.java | 78 +
.../airavata/Wso2IdentityServerClient.java | 137 +
modules/user-profile/pom.xml | 29 -
.../user-profile/user-profile-service/pom.xml | 29 -
.../user/profile/server/UserProfileServer.java | 159 -
.../server/UserProfileServiceHandler.java | 139 -
modules/user-profile/user-profile-stubs/pom.xml | 63 -
.../userprofile/cpi/UserProfileService.java | 7504 ---
.../client/UserProfileServiceClientFactory.java | 43 -
.../exception/UserProfileServiceException.java | 407 -
.../cpi/user_profile_cpiConstants.java | 57 -
modules/workflow-model/pom.xml | 26 +-
modules/workflow-model/workflow-engine/pom.xml | 26 +-
.../catalog/WorkflowCatalogFactory.java | 4 +-
.../workflow/engine/WorkflowEngine.java | 4 +-
.../engine/WorkflowEngineException.java | 4 +-
.../workflow/engine/WorkflowEngineFactory.java | 4 +-
.../workflow/engine/WorkflowEngineImpl.java | 4 +-
.../airavata/workflow/engine/WorkflowUtils.java | 4 +-
.../engine/concurrent/PredicatedExecutable.java | 5 +-
.../engine/concurrent/PredicatedTaskRunner.java | 5 +-
.../engine/core/amazon/AmazonCredential.java | 4 +-
.../engine/core/amazon/EC2InstanceResult.java | 19 +
.../engine/core/generators/XmlBeansFiler.java | 4 +-
.../core/workflow/ParameterListModel.java | 4 +-
.../engine/datadriven/WorkflowHarvester.java | 4 +-
.../engine/file/XBayaPathConstants.java | 4 +-
.../engine/gfac/GFacRegistryClient.java | 4 +-
.../workflow/engine/gfac/SimpleWSClient.java | 4 +-
.../engine/globus/FileTransferConstants.java | 4 +-
.../globus/GridFTPFileTransferClient.java | 19 +
.../engine/graph/controller/NodeController.java | 19 +
.../engine/interpretor/DoWhileHandler.java | 3 +-
.../engine/interpretor/HeaderConstants.java | 4 +-
.../SSWorkflowInterpreterInteractorImpl.java | 4 +-
.../interpretor/SystemComponentInvoker.java | 4 +-
.../WorkFlowInterpreterException.java | 4 +-
.../interpretor/WorkflowExecutionMessage.java | 4 +-
.../engine/interpretor/WorkflowInterpreter.java | 4 +-
.../WorkflowInterpreterConfiguration.java | 4 +-
.../WorkflowInterpreterInteractor.java | 4 +-
.../interpretor/WorkflowInterpreterInvoker.java | 4 +-
.../WorkflowInterpreterSkeleton2.java | 19 +
.../engine/invoker/AsynchronousInvoker.java | 4 +-
.../workflow/engine/invoker/DynamicInvoker.java | 4 +-
.../workflow/engine/invoker/Invoker.java | 4 +-
.../invoker/MsgBoxWsaResponsesCorrelator.java | 19 +
.../workflow/engine/invoker/SimpleInvoker.java | 4 +-
.../engine/invoker/WorkflowInputUtil.java | 5 +-
.../workflow/engine/util/AmazonUtil.java | 4 +-
.../airavata/workflow/engine/util/Data.java | 4 +-
.../workflow/engine/util/GOConstants.java | 4 +-
.../workflow/engine/util/GlobusOnlineUtils.java | 19 +
.../workflow/engine/util/InterpreterUtil.java | 3 +-
.../engine/util/ProxyMonitorPublisher.java | 4 +-
.../workflow/engine/util/RegistryConstants.java | 4 +-
.../workflow/engine/util/TransferFile.java | 4 +-
.../workflow/engine/util/XBayaUtil.java | 4 +-
.../workflow/WorkflowEngineException.java | 4 +-
.../engine/workflow/proxy/ProxyWSDL.java | 4 +-
.../engine/workflow/proxy/WorkflowClient.java | 4 +-
.../engine/workflow/proxy/WorkflowContext.java | 4 +-
.../workflow/proxy/WorkflowProxyException.java | 4 +-
.../interpreter/ComplexForEachWorkflowTest.java | 19 +
.../xbaya/interpreter/ComplexMathService.java | 4 +-
.../interpreter/ComplexMathWorkflowTest.java | 19 +
.../interpreter/CrossProductWorkflowTest.java | 19 +
.../airavata/xbaya/interpreter/EchoService.java | 3 +-
.../xbaya/interpreter/ForEachWorkflowTest.java | 19 +
.../interpreter/LevenshteinDistanceService.java | 4 +-
.../airavata/xbaya/interpreter/Listener.java | 19 +
.../xbaya/interpreter/NotificationSender.java | 19 +
.../xbaya/interpreter/RegistryServiceTest.java | 19 +
.../interpreter/SimpleForEachWorkflowTest.java | 19 +
.../interpreter/SimpleMathWorkflowTest.java | 19 +
.../xbaya/interpreter/WorkflowTest.java | 19 +
.../xbaya/interpreter/WorkflowTrackingTest.java | 19 +
.../xbaya/interpreter/XBayaClientTest.java | 5 +-
.../interpreter/XBayaConsolidatedTestSuite.java | 19 +
.../xbaya/interpreter/utils/ConfigKeys.java | 5 +-
.../xbaya/interpreter/utils/TestUtilServer.java | 19 +
.../interpreter/utils/WorkflowTestUtils.java | 19 +
.../workflow-model-component/pom.xml | 26 +-
.../registry/JCRComponentReference.java | 4 +-
.../registry/JCRComponentRegistry.java | 4 +-
.../workflow-model/workflow-model-core/pom.xml | 26 +-
.../workflow/model/component/Component.java | 4 +-
.../model/component/ComponentControlPort.java | 4 +-
.../model/component/ComponentDataPort.java | 4 +-
.../model/component/ComponentEPRPort.java | 4 +-
.../model/component/ComponentException.java | 4 +-
.../component/ComponentOperationReference.java | 4 +-
.../workflow/model/component/ComponentPort.java | 4 +-
.../model/component/ComponentReference.java | 4 +-
.../model/component/ComponentRegistry.java | 4 +-
.../component/ComponentRegistryException.java | 4 +-
.../amazon/AmazonComponentRegistry.java | 4 +-
.../component/amazon/InstanceComponent.java | 4 +-
.../amazon/InstanceComponentDataPort.java | 4 +-
.../amazon/TerminateInstanceComponent.java | 4 +-
.../component/dynamic/DynamicComponent.java | 4 +-
.../component/dynamic/DynamicComponentPort.java | 4 +-
.../local/LocalComponentReference.java | 4 +-
.../component/local/LocalComponentRegistry.java | 4 +-
.../model/component/system/BlockComponent.java | 4 +-
.../component/system/ConstantComponent.java | 4 +-
.../system/DifferedInputComponent.java | 8 +-
.../component/system/DoWhileComponent.java | 4 +-
.../component/system/EndBlockComponent.java | 4 +-
.../component/system/EndDoWhileComponent.java | 4 +-
.../component/system/EndForEachComponent.java | 4 +-
.../model/component/system/EndifComponent.java | 4 +-
.../model/component/system/ExitComponent.java | 4 +-
.../component/system/ForEachComponent.java | 4 +-
.../model/component/system/IfComponent.java | 4 +-
.../model/component/system/InputComponent.java | 4 +-
.../model/component/system/MemoComponent.java | 4 +-
.../model/component/system/OutputComponent.java | 4 +-
.../component/system/ReceiveComponent.java | 4 +-
.../component/system/S3InputComponent.java | 4 +-
.../component/system/StreamSourceComponent.java | 4 +-
.../component/system/SubWorkflowComponent.java | 4 +-
.../model/component/system/SystemComponent.java | 4 +-
.../system/SystemComponentDataPort.java | 4 +-
.../system/SystemComponentReference.java | 4 +-
.../system/SystemComponentRegistry.java | 4 +-
.../component/url/URLComponentReference.java | 4 +-
.../component/url/URLComponentRegistry.java | 4 +-
.../component/web/WebComponentReference.java | 4 +-
.../component/web/WebComponentRegistry.java | 4 +-
.../model/component/ws/WSComponent.java | 4 +-
.../component/ws/WSComponentApplication.java | 4 +-
.../ws/WSComponentApplicationParameter.java | 4 +-
.../model/component/ws/WSComponentFactory.java | 4 +-
.../model/component/ws/WSComponentKey.java | 4 +-
.../model/component/ws/WSComponentPort.java | 4 +-
.../component/ws/WSComponentReference.java | 4 +-
.../model/component/ws/WSComponentRegistry.java | 4 +-
.../model/component/ws/WorkflowComponent.java | 4 +-
.../exceptions/LazyLoadedDataException.java | 4 +-
.../model/exceptions/UtilsException.java | 4 +-
.../model/exceptions/WorkflowException.java | 4 +-
.../exceptions/WorkflowRuntimeException.java | 4 +-
.../airavata/workflow/model/gpel/DSCUtil.java | 4 +-
.../workflow/model/gpel/script/BPELScript.java | 4 +-
.../model/gpel/script/BPELScriptType.java | 4 +-
.../model/gpel/script/WorkflowWSDL.java | 4 +-
.../workflow/model/graph/ControlEdge.java | 4 +-
.../workflow/model/graph/ControlPort.java | 4 +-
.../airavata/workflow/model/graph/DataEdge.java | 4 +-
.../airavata/workflow/model/graph/DataPort.java | 4 +-
.../airavata/workflow/model/graph/EPRPort.java | 4 +-
.../airavata/workflow/model/graph/Edge.java | 4 +-
.../model/graph/ForEachExecutableNode.java | 5 +-
.../airavata/workflow/model/graph/Graph.java | 4 +-
.../workflow/model/graph/GraphException.java | 4 +-
.../workflow/model/graph/GraphFactory.java | 4 +-
.../workflow/model/graph/GraphPiece.java | 4 +-
.../workflow/model/graph/GraphSchema.java | 4 +-
.../airavata/workflow/model/graph/Node.java | 4 +-
.../airavata/workflow/model/graph/Port.java | 4 +-
.../model/graph/amazon/InstanceDataPort.java | 4 +-
.../model/graph/amazon/InstanceNode.java | 4 +-
.../model/graph/amazon/ResourceNode.java | 4 +-
.../graph/amazon/TerminateInstanceNode.java | 4 +-
.../model/graph/dynamic/BasicTypeMapping.java | 4 +-
.../model/graph/dynamic/DynamicNode.java | 4 +-
.../model/graph/dynamic/DynamicPort.java | 4 +-
.../model/graph/dynamic/PortAddable.java | 4 +-
.../model/graph/dynamic/SchemaCompilerUtil.java | 4 +-
.../workflow/model/graph/impl/EdgeImpl.java | 4 +-
.../workflow/model/graph/impl/GraphImpl.java | 4 +-
.../workflow/model/graph/impl/NodeImpl.java | 4 +-
.../workflow/model/graph/impl/PortImpl.java | 4 +-
.../graph/subworkflow/SubWorkflowNode.java | 4 +-
.../workflow/model/graph/system/BlockNode.java | 4 +-
.../model/graph/system/ConstantNode.java | 4 +-
.../model/graph/system/DifferedInputNode.java | 7 +-
.../model/graph/system/DoWhileNode.java | 4 +-
.../model/graph/system/EndBlockNode.java | 4 +-
.../model/graph/system/EndDoWhileNode.java | 4 +-
.../model/graph/system/EndForEachNode.java | 4 +-
.../workflow/model/graph/system/EndifNode.java | 4 +-
.../workflow/model/graph/system/ExitNode.java | 4 +-
.../model/graph/system/ForEachNode.java | 4 +-
.../workflow/model/graph/system/IfNode.java | 4 +-
.../workflow/model/graph/system/InputNode.java | 4 +-
.../workflow/model/graph/system/MemoNode.java | 4 +-
.../workflow/model/graph/system/OutputNode.java | 4 +-
.../model/graph/system/ParameterNode.java | 4 +-
.../model/graph/system/ReceiveNode.java | 4 +-
.../model/graph/system/S3InputNode.java | 4 +-
.../model/graph/system/StreamSourceNode.java | 4 +-
.../model/graph/system/SystemDataPort.java | 4 +-
.../workflow/model/graph/system/SystemNode.java | 4 +-
.../workflow/model/graph/util/GraphUtil.java | 4 +-
.../workflow/model/graph/ws/WSGraph.java | 4 +-
.../workflow/model/graph/ws/WSGraphFactory.java | 4 +-
.../workflow/model/graph/ws/WSNode.java | 4 +-
.../workflow/model/graph/ws/WSPort.java | 4 +-
.../workflow/model/graph/ws/WorkflowNode.java | 4 +-
.../workflow/model/ode/ODEBPELTransformer.java | 19 +
.../airavata/workflow/model/ode/ODEClient.java | 19 +
.../model/ode/ODEDeploymentDescriptor.java | 19 +
.../workflow/model/ode/ODEWSDLTransformer.java | 19 +
.../workflow/model/ode/WSDLCleaner.java | 19 +
.../model/utils/ApplicationVersion.java | 4 +-
.../workflow/model/utils/FileConstants.java | 4 +-
.../workflow/model/utils/MessageConstants.java | 4 +-
.../workflow/model/utils/WorkflowConstants.java | 4 +-
.../model/wf/InvalidDataFormatException.java | 4 +-
.../workflow/model/wf/TridentTransformer.java | 4 +-
.../airavata/workflow/model/wf/Workflow.java | 4 +-
.../workflow/model/wf/WorkflowData.java | 4 +-
.../model/wf/WorkflowExecutionState.java | 4 +-
.../workflow/model/wf/WorkflowInput.java | 4 +-
.../workflow/model/xsd/GFacSimpleTypesXSD.java | 4 +-
.../model/xsd/LeadContextHeaderXSD.java | 4 +-
.../workflow/model/xsd/LeadCrosscutXSD.java | 4 +-
modules/workflow/pom.xml | 31 +-
modules/workflow/workflow-core/pom.xml | 31 +-
.../airavata/workflow/core/WorkflowBuilder.java | 4 +-
.../workflow/core/WorkflowEnactmentService.java | 4 +-
.../airavata/workflow/core/WorkflowFactory.java | 4 +-
.../airavata/workflow/core/WorkflowInfo.java | 3 +-
.../workflow/core/WorkflowInterpreter.java | 4 +-
.../apache/airavata/workflow/core/XMLUtil.java | 4 +-
.../airavata/workflow/core/XmlFormatter.java | 4 +-
.../workflow/core/dag/edge/DirectedEdge.java | 4 +-
.../airavata/workflow/core/dag/edge/Edge.java | 4 +-
.../core/dag/nodes/ApplicationNode.java | 4 +-
.../core/dag/nodes/ApplicationNodeImpl.java | 4 +-
.../workflow/core/dag/nodes/InputNode.java | 4 +-
.../workflow/core/dag/nodes/InputNodeImpl.java | 4 +-
.../workflow/core/dag/nodes/NodeType.java | 4 +-
.../workflow/core/dag/nodes/OutputNode.java | 4 +-
.../workflow/core/dag/nodes/OutputNodeImpl.java | 4 +-
.../workflow/core/dag/nodes/WorkflowNode.java | 4 +-
.../airavata/workflow/core/dag/port/InPort.java | 4 +-
.../workflow/core/dag/port/InputPortIml.java | 4 +-
.../workflow/core/dag/port/OutPort.java | 4 +-
.../workflow/core/dag/port/OutPortImpl.java | 4 +-
.../airavata/workflow/core/dag/port/Port.java | 4 +-
.../core/parser/JsonWorkflowParser.java | 4 +-
.../workflow/core/parser/ParserException.java | 3 +-
.../workflow/core/parser/WorkflowParser.java | 4 +-
.../airavata/workflow/core/XMLUtilTest.java | 5 +-
.../core/parser/JsonWorkflowParserTest.java | 4 +-
modules/xbaya-gui/pom.xml | 26 +-
.../apache/airavata/xbaya/ThriftClientData.java | 4 +-
.../airavata/xbaya/ThriftServiceType.java | 4 +-
.../java/org/apache/airavata/xbaya/XBaya.java | 4 +-
.../airavata/xbaya/XBayaConfiguration.java | 4 +-
.../apache/airavata/xbaya/XBayaConstants.java | 4 +-
.../org/apache/airavata/xbaya/XBayaEngine.java | 4 +-
.../org/apache/airavata/xbaya/XBayaVersion.java | 4 +-
.../component/registry/ComponentController.java | 4 +-
.../registry/ComponentRegistryLoader.java | 4 +-
.../xbaya/concurrent/PredicatedExecutable.java | 5 +-
.../xbaya/concurrent/PredicatedTaskRunner.java | 5 +-
.../xbaya/core/amazon/AmazonCredential.java | 4 +-
.../xbaya/core/amazon/EC2InstanceResult.java | 4 +-
.../xbaya/core/generators/BPELFiler.java | 4 +-
.../xbaya/core/generators/ImageFiler.java | 4 +-
.../xbaya/core/generators/JythonFiler.java | 4 +-
.../xbaya/core/generators/ODEScriptFiler.java | 4 +-
.../xbaya/core/generators/ScuflFiler.java | 4 +-
.../xbaya/core/generators/WorkflowFiler.java | 4 +-
.../xbaya/core/generators/XmlBeansFiler.java | 4 +-
.../core/ide/XBayaExecutionModeListener.java | 4 +-
.../xbaya/core/workflow/ParameterListModel.java | 4 +-
.../xbaya/datadriven/WorkflowHarvester.java | 4 +-
.../airavata/xbaya/file/XBayaPathConstants.java | 4 +-
.../airavata/xbaya/gfac/GFacRegistryClient.java | 4 +-
.../airavata/xbaya/gfac/SimpleWSClient.java | 4 +-
.../xbaya/globus/FileTransferConstants.java | 4 +-
.../xbaya/globus/GridFTPFileTransferClient.java | 19 +
.../xbaya/graph/controller/NodeController.java | 4 +-
.../xbaya/interpretor/ExperimentTemplate.java | 19 +
.../GUIWorkflowInterpreterInteractorImpl.java | 19 +
.../xbaya/interpretor/HeaderConstants.java | 4 +-
.../SSWorkflowInterpreterInteractorImpl.java | 19 +
.../StandaloneNotificationSender.java | 4 +-
.../WorkFlowInterpreterException.java | 4 +-
.../interpretor/WorkflowExecutionMessage.java | 4 +-
.../interpretor/WorkflowExecutionTemplate.java | 19 +
.../xbaya/interpretor/WorkflowInterpreter.java | 19 +
.../WorkflowInterpreterConfiguration.java | 19 +
.../WorkflowInterpreterInteractor.java | 19 +
.../interpretor/WorkflowInterpreterInvoker.java | 4 +-
.../WorkflowInterpretorEventListener.java | 19 +
...WorkflowInterpretorMessageReceiverInOut.java | 19 +
.../WorkflowInterpretorSkeleton.java | 19 +
.../xbaya/jython/lib/GFacServiceCreator.java | 4 +-
.../xbaya/jython/lib/NotificationSender.java | 19 +
.../xbaya/jython/lib/ServiceNotifiable.java | 4 +-
.../jython/lib/ServiceNotificationSender.java | 19 +
.../StandaloneServiceNotificationSender.java | 4 +-
.../xbaya/jython/lib/WorkflowNotifiable.java | 4 +-
.../xbaya/jython/runner/JythonClassLoader.java | 4 +-
.../jython/runner/JythonOneTimeRunner.java | 4 +-
.../jython/runner/JythonOneTimeRunnerImpl.java | 4 +-
.../xbaya/jython/runner/JythonRunner.java | 4 +-
.../xbaya/jython/script/JythonScript.java | 4 +-
.../xbaya/menues/tools/ToolsMenuItem.java | 4 +-
.../airavata/xbaya/messaging/EventData.java | 4 +-
.../xbaya/messaging/EventDataListener.java | 4 +-
.../xbaya/messaging/EventDataRepository.java | 4 +-
.../airavata/xbaya/messaging/Monitor.java | 4 +-
.../xbaya/messaging/MonitorException.java | 4 +-
.../xbaya/messaging/NotificationHandler.java | 4 +-
.../airavata/xbaya/messaging/event/Event.java | 4 +-
.../xbaya/messaging/event/EventListener.java | 4 +-
.../xbaya/messaging/event/EventProducer.java | 4 +-
.../xbaya/modifier/WorkflowModifier.java | 4 +-
.../xbaya/registry/PasswordCallbackImpl.java | 19 +
.../xbaya/scufl/script/ScuflScript.java | 19 +
.../xbaya/test/util/WorkflowCreator.java | 19 +
.../org/apache/airavata/xbaya/ui/XBayaGUI.java | 4 +-
.../ui/actions/AbstractBrowserActionItem.java | 4 +-
.../ui/actions/registry/browser/AddAction.java | 4 +-
.../actions/registry/browser/BrowserAction.java | 4 +-
.../ui/actions/registry/browser/CopyAction.java | 4 +-
.../actions/registry/browser/DeleteAction.java | 4 +-
.../ui/actions/registry/browser/EditAction.java | 4 +-
.../actions/registry/browser/ImportAction.java | 4 +-
.../actions/registry/browser/RefreshAction.java | 4 +-
.../ui/actions/registry/browser/ViewAction.java | 4 +-
.../airavata/xbaya/ui/dialogs/AboutWindow.java | 4 +-
.../airavata/xbaya/ui/dialogs/ErrorWindow.java | 4 +-
.../ui/dialogs/GlobusFileTransferWindow.java | 19 +
.../airavata/xbaya/ui/dialogs/TextWindow.java | 4 +-
.../airavata/xbaya/ui/dialogs/WaitDialog.java | 4 +-
.../airavata/xbaya/ui/dialogs/XBayaDialog.java | 4 +-
.../dialogs/amazon/AmazonEC2InvokerWindow.java | 4 +-
.../ui/dialogs/amazon/AmazonS3UtilsWindow.java | 4 +-
.../xbaya/ui/dialogs/amazon/BucketsLoader.java | 4 +-
.../dialogs/amazon/ChangeCredentialWindow.java | 4 +-
.../amazon/EC2InstancesManagementWindow.java | 4 +-
.../ui/dialogs/amazon/EC2LaunchWindow.java | 4 +-
.../ui/dialogs/amazon/InstancesLoader.java | 4 +-
.../xbaya/ui/dialogs/amazon/S3Downloader.java | 4 +-
.../xbaya/ui/dialogs/amazon/S3Uploader.java | 4 +-
.../ui/dialogs/component/URLRegistryWindow.java | 4 +-
.../ui/dialogs/component/WebResigtryWindow.java | 4 +-
.../amazon/InstanceConfigurationDialog.java | 4 +-
.../system/ConstantConfigurationDialog.java | 4 +-
.../DifferedInputConfigurationDialog.java | 4 +-
.../graph/system/DoWhileConfigrationDialog.java | 4 +-
.../system/EndBlockConfigurationDialog.java | 4 +-
.../system/EndDoWhileConfigurationDialog.java | 4 +-
.../system/EndForEachConfigurationDialog.java | 4 +-
.../graph/system/EndifConfigurationDialog.java | 4 +-
.../system/ForEachConfigurationDialog.java | 4 +-
.../graph/system/IfConfigurationDialog.java | 4 +-
.../graph/system/InputConfigurationDialog.java | 4 +-
.../graph/system/MemoConfigurationDialog.java | 4 +-
.../graph/system/OutputConfigurationDialog.java | 4 +-
.../system/ReceiveConfigurationDialog.java | 4 +-
.../ui/dialogs/graph/system/S3FileChooser.java | 4 +-
.../system/StreamSourceConfigurationDialog.java | 4 +-
.../graph/ws/ServiceInteractionWindow.java | 4 +-
.../xbaya/ui/dialogs/graph/ws/WSNodeWindow.java | 4 +-
.../monitor/MonitorConfigurationWindow.java | 4 +-
.../xbaya/ui/dialogs/monitor/MonitorWindow.java | 4 +-
.../dialogs/registry/NewRegistryUserDialog.java | 4 +-
.../ui/dialogs/registry/RegistryWindow.java | 4 +-
.../registry/browser/JCRBrowserDialog.java | 4 +-
.../workflow/ParameterPropertyWindow.java | 4 +-
.../dialogs/workflow/WorkflowImportWindow.java | 4 +-
.../workflow/WorkflowPropertyWindow.java | 4 +-
.../xbaya/ui/experiment/ExperimentMenu.java | 4 +-
.../ui/experiment/LaunchApplicationWindow.java | 4 +-
.../ui/experiment/RegistrySearchResult.java | 4 +-
.../RegistryWorkflowPublisherWindow.java | 4 +-
.../WorkflowInterpreterLaunchWindow.java | 4 +-
.../apache/airavata/xbaya/ui/graph/EdgeGUI.java | 4 +-
.../airavata/xbaya/ui/graph/GraphCanvas.java | 4 +-
.../xbaya/ui/graph/GraphCanvasEvent.java | 4 +-
.../xbaya/ui/graph/GraphCanvasListener.java | 4 +-
.../airavata/xbaya/ui/graph/GraphGUI.java | 4 +-
.../airavata/xbaya/ui/graph/GraphPieceGUI.java | 4 +-
.../apache/airavata/xbaya/ui/graph/NodeGUI.java | 4 +-
.../airavata/xbaya/ui/graph/Paintable.java | 4 +-
.../apache/airavata/xbaya/ui/graph/PortGUI.java | 4 +-
.../xbaya/ui/graph/amazon/InstanceNodeGUI.java | 4 +-
.../graph/amazon/TerminateInstanceNodeGUI.java | 4 +-
.../graph/subworkflow/SubWorkflowNodeGUI.java | 4 +-
.../xbaya/ui/graph/system/BlockNodeGUI.java | 4 +-
.../ui/graph/system/ConfigurableNodeGUI.java | 4 +-
.../xbaya/ui/graph/system/ConstantNodeGUI.java | 4 +-
.../ui/graph/system/DifferedInputHandler.java | 3 +-
.../ui/graph/system/DifferedInputNodeGUI.java | 3 +-
.../xbaya/ui/graph/system/DoWhileNodeGUI.java | 4 +-
.../xbaya/ui/graph/system/EndBlockNodeGUI.java | 4 +-
.../ui/graph/system/EndDoWhileNodeGUI.java | 4 +-
.../ui/graph/system/EndForEachNodeGUI.java | 4 +-
.../xbaya/ui/graph/system/EndifNodeGUI.java | 4 +-
.../xbaya/ui/graph/system/ExitNodeGUI.java | 4 +-
.../xbaya/ui/graph/system/ForEachNodeGUI.java | 4 +-
.../xbaya/ui/graph/system/IfNodeGUI.java | 4 +-
.../xbaya/ui/graph/system/InputNodeGUI.java | 4 +-
.../xbaya/ui/graph/system/MemoNodeGUI.java | 4 +-
.../xbaya/ui/graph/system/OutputNodeGUI.java | 4 +-
.../xbaya/ui/graph/system/ReceiveNodeGUI.java | 4 +-
.../xbaya/ui/graph/system/S3InputNodeGUI.java | 4 +-
.../ui/graph/system/StreamSourceNodeGUI.java | 4 +-
.../airavata/xbaya/ui/graph/ws/WSNodeGUI.java | 4 +-
.../xbaya/ui/graph/ws/WorkflowNodeGUI.java | 4 +-
.../xbaya/ui/menues/AmazonEC2MenuItem.java | 4 +-
.../xbaya/ui/menues/ApplicationMenuItem.java | 4 +-
.../airavata/xbaya/ui/menues/EditMenuItem.java | 4 +-
.../airavata/xbaya/ui/menues/MenuIcons.java | 4 +-
.../xbaya/ui/menues/RegistryMenuItem.java | 4 +-
.../airavata/xbaya/ui/menues/RunMenuItem.java | 4 +-
.../airavata/xbaya/ui/menues/ViewMenuItem.java | 4 +-
.../airavata/xbaya/ui/menues/XBayaMenu.java | 4 +-
.../airavata/xbaya/ui/menues/XBayaMenuItem.java | 4 +-
.../xbaya/ui/monitor/MonitorEventHandler.java | 4 +-
.../xbaya/ui/monitor/MonitorStarter.java | 4 +-
.../xbaya/ui/monitor/ResourcePaintable.java | 4 +-
.../airavata/xbaya/ui/utils/Cancelable.java | 4 +-
.../airavata/xbaya/ui/utils/DrawUtils.java | 4 +-
.../airavata/xbaya/ui/utils/ErrorMessages.java | 4 +-
.../xbaya/ui/views/ComponentViewer.java | 4 +-
.../xbaya/ui/views/JCRBrowserPanel.java | 19 +
.../airavata/xbaya/ui/views/MonitorPanel.java | 4 +-
.../xbaya/ui/views/ParameterPropertyPanel.java | 4 +-
.../airavata/xbaya/ui/views/PortViewer.java | 4 +-
.../airavata/xbaya/ui/widgets/GridPanel.java | 4 +-
.../airavata/xbaya/ui/widgets/ScrollPanel.java | 4 +-
.../xbaya/ui/widgets/TabLabelButton.java | 4 +-
.../xbaya/ui/widgets/TableRenderable.java | 4 +-
.../xbaya/ui/widgets/ToolbarButton.java | 4 +-
.../xbaya/ui/widgets/XBayaComboBox.java | 4 +-
.../xbaya/ui/widgets/XBayaComponent.java | 4 +-
.../airavata/xbaya/ui/widgets/XBayaLabel.java | 3 +-
.../xbaya/ui/widgets/XBayaLinkButton.java | 4 +-
.../airavata/xbaya/ui/widgets/XBayaList.java | 4 +-
.../xbaya/ui/widgets/XBayaTextArea.java | 4 +-
.../xbaya/ui/widgets/XBayaTextComponent.java | 4 +-
.../xbaya/ui/widgets/XBayaTextField.java | 4 +-
.../airavata/xbaya/ui/widgets/XBayaToolBar.java | 4 +-
.../xbaya/ui/widgets/XbayaEnhancedList.java | 4 +-
.../xbaya/ui/widgets/amazon/S3Tree.java | 4 +-
.../xbaya/ui/widgets/amazon/S3TreeModel.java | 4 +-
.../ui/widgets/component/ComponentSelector.java | 4 +-
.../component/ComponentSelectorEvent.java | 4 +-
.../component/ComponentSelectorListener.java | 4 +-
.../component/ComponentSourceTransferable.java | 4 +-
.../widgets/component/ComponentTreeModel.java | 4 +-
.../ui/widgets/component/ComponentTreeNode.java | 4 +-
.../apache/airavata/xbaya/util/AmazonUtil.java | 4 +-
.../org/apache/airavata/xbaya/util/Data.java | 4 +-
.../apache/airavata/xbaya/util/GOConstants.java | 4 +-
.../airavata/xbaya/util/GlobusOnlineUtils.java | 19 +
.../airavata/xbaya/util/RegistryConstants.java | 4 +-
.../airavata/xbaya/util/TransferFile.java | 4 +-
.../apache/airavata/xbaya/util/XBayaUtil.java | 4 +-
.../airavata/xbaya/workflow/WorkflowClient.java | 4 +-
.../xbaya/workflow/WorkflowEngineException.java | 4 +-
.../xbaya/workflow/proxy/ProxyWSDL.java | 4 +-
.../xbaya/workflow/proxy/WorkflowClient.java | 4 +-
.../xbaya/workflow/proxy/WorkflowContext.java | 4 +-
.../workflow/proxy/WorkflowProxyException.java | 4 +-
.../interpreter/ComplexForEachWorkflowTest.java | 19 +
.../xbaya/interpreter/ComplexMathService.java | 4 +-
.../interpreter/ComplexMathWorkflowTest.java | 19 +
.../interpreter/CrossProductWorkflowTest.java | 19 +
.../airavata/xbaya/interpreter/EchoService.java | 3 +-
.../xbaya/interpreter/ForEachWorkflowTest.java | 19 +
.../interpreter/LevenshteinDistanceService.java | 4 +-
.../airavata/xbaya/interpreter/Listener.java | 19 +
.../xbaya/interpreter/NotificationSender.java | 19 +
.../xbaya/interpreter/RegistryServiceTest.java | 19 +
.../interpreter/SimpleForEachWorkflowTest.java | 19 +
.../interpreter/SimpleMathWorkflowTest.java | 19 +
.../xbaya/interpreter/WorkflowTest.java | 19 +
.../xbaya/interpreter/WorkflowTrackingTest.java | 19 +
.../xbaya/interpreter/XBayaClientTest.java | 5 +-
.../interpreter/XBayaConsolidatedTestSuite.java | 19 +
.../xbaya/interpreter/utils/ConfigKeys.java | 5 +-
.../xbaya/interpreter/utils/TestUtilServer.java | 19 +
.../interpreter/utils/WorkflowTestUtils.java | 19 +
pom.xml | 102 +-
sandbox/amqpwstunnel/python/amqpwstunnel.py | 20 +
sandbox/amqpwstunnel/wstest.html | 21 +
sandbox/job-status-rest-server/api_test.py | 20 +
sandbox/job-status-rest-server/app.py | 20 +
.../example/logfile_checker/generate_logs.sh | 20 +
.../example/logfile_checker/log_consumer.py | 20 +
.../example/logfile_checker/log_streamer.py | 20 +
.../simstream/example/logfile_checker/test.txt | 20 +
.../example/mem_streamer/memory_consumption.py | 20 +
.../example/mem_streamer/memory_streamer.py | 20 +
.../application/alanine_dipeptide.py | 20 +
.../example/openmm_example/openmm_consumer.py | 20 +
.../openmm_example/openmm_log_consumer.py | 20 +
.../openmm_example/openmm_rmsd_consumer.py | 20 +
.../example/openmm_example/openmm_streamer.py | 20 +
.../simstream/example/openmm_example/test.txt | 20 +
sandbox/simstream/setup.py | 20 +
sandbox/simstream/simstream/__init__.py | 20 +
sandbox/simstream/simstream/datacollector.py | 20 +
sandbox/simstream/simstream/datareporter.py | 20 +
sandbox/simstream/simstream/eventhandler.py | 20 +
sandbox/simstream/simstream/eventmonitor.py | 20 +
.../simstream/simstream/pikaasyncconsumer.py | 20 +
sandbox/simstream/simstream/pikaproducer.py | 20 +
sandbox/simstream/simstream/simstream.py | 20 +
.../airavata-apis/airavata_api.thrift | 42 +-
.../airavata-apis/airavata_errors.thrift | 9 +
.../airavata-apis/db_event_model.thrift | 81 +
.../airavata-apis/messaging_events.thrift | 3 +-
.../component-cpis/generate-cpi-stubs.sh | 32 +-
.../component-cpis/registry-api.thrift | 20 +-
.../component-cpis/user-profile-cpi.thrift | 2 +-
.../data-models/airavata_data_models.thrift | 6 +-
.../application_deployment_model.thrift | 3 +-
.../replica_catalog_models.thrift | 31 +-
.../compute_resource_model.thrift | 6 +-
.../user_resource_profile_model.thrift | 2 +-
.../group_manager_model.thrift | 48 -
.../user-group-models/user_profile_model.thrift | 185 -
.../group_manager_model.thrift | 48 +
.../tenant_profile_model.thrift | 58 +
.../user_profile_model.thrift | 196 +
.../generate-thrift-stubs.sh | 42 +-
.../service-cpis/generate-service-cpi-stubs.sh | 181 +
.../iam-admin-services-cpi.thrift | 81 +
.../iam_admin_services_cpi_errors.thrift | 32 +
.../profile-service/profile-service-cpi.thrift | 34 +
.../profile-tenant/profile-tenant-cpi.thrift | 70 +
.../profile_tenant_cpi_errors.thrift | 32 +
.../profile-user/profile-user-cpi.thrift | 74 +
.../profile-user/profile_user_cpi_errors.thrift | 32 +
tools/gsissh-cli-tools/README.txt | 20 +
tools/gsissh-cli-tools/pom.xml | 29 +-
.../ssh/cli/SSHApiClientWithMyProxyAuth.java | 4 +-
tools/phoebus-integration/pom.xml | 26 +-
.../impl/PhoebusGridConfigurationHandler.java | 4 +-
.../airavata/core/gfac/utils/PhoebusUtils.java | 4 +-
tools/pom.xml | 26 +-
tools/rabbitmq-download-start.sh | 20 +
1792 files changed, 137341 insertions(+), 66743 deletions(-)
----------------------------------------------------------------------
[11/12] airavata git commit: Code clean up
Posted by sc...@apache.org.
Code clean up
Project: http://git-wip-us.apache.org/repos/asf/airavata/repo
Commit: http://git-wip-us.apache.org/repos/asf/airavata/commit/706e01d8
Tree: http://git-wip-us.apache.org/repos/asf/airavata/tree/706e01d8
Diff: http://git-wip-us.apache.org/repos/asf/airavata/diff/706e01d8
Branch: refs/heads/develop
Commit: 706e01d8d6039f2e8c98771dffbf092d44c6a8b7
Parents: 8462205
Author: Ajinkya Dhamnaskar <ad...@umail.iu.edu>
Authored: Wed May 17 14:55:52 2017 -0400
Committer: Ajinkya Dhamnaskar <ad...@umail.iu.edu>
Committed: Wed May 17 14:55:52 2017 -0400
----------------------------------------------------------------------
modules/commons/pom.xml | 1 -
1 file changed, 1 deletion(-)
----------------------------------------------------------------------
http://git-wip-us.apache.org/repos/asf/airavata/blob/706e01d8/modules/commons/pom.xml
----------------------------------------------------------------------
diff --git a/modules/commons/pom.xml b/modules/commons/pom.xml
index b00c9ee..e0ad64e 100644
--- a/modules/commons/pom.xml
+++ b/modules/commons/pom.xml
@@ -139,7 +139,6 @@
<version>${logback.version}</version>
</dependency>
</dependencies>
-
<properties>
<project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
<project.reporting.outputEncoding>UTF-8</project.reporting.outputEncoding>
[02/12] airavata git commit: fixing minor bug in the condition check
Posted by sc...@apache.org.
fixing minor bug in the condition check
Project: http://git-wip-us.apache.org/repos/asf/airavata/repo
Commit: http://git-wip-us.apache.org/repos/asf/airavata/commit/a749a7c8
Tree: http://git-wip-us.apache.org/repos/asf/airavata/tree/a749a7c8
Diff: http://git-wip-us.apache.org/repos/asf/airavata/diff/a749a7c8
Branch: refs/heads/develop
Commit: a749a7c8d5fd010deb138ea009ce2bbed2d965d7
Parents: 56fefc9
Author: scnakandala <su...@gmail.com>
Authored: Mon Mar 6 13:38:38 2017 -0500
Committer: scnakandala <su...@gmail.com>
Committed: Mon Mar 6 13:38:38 2017 -0500
----------------------------------------------------------------------
.../apache/airavata/gfac/monitor/email/EmailBasedMonitor.java | 4 ++--
1 file changed, 2 insertions(+), 2 deletions(-)
----------------------------------------------------------------------
http://git-wip-us.apache.org/repos/asf/airavata/blob/a749a7c8/modules/gfac/gfac-impl/src/main/java/org/apache/airavata/gfac/monitor/email/EmailBasedMonitor.java
----------------------------------------------------------------------
diff --git a/modules/gfac/gfac-impl/src/main/java/org/apache/airavata/gfac/monitor/email/EmailBasedMonitor.java b/modules/gfac/gfac-impl/src/main/java/org/apache/airavata/gfac/monitor/email/EmailBasedMonitor.java
index 92f0d78..9db1b84 100644
--- a/modules/gfac/gfac-impl/src/main/java/org/apache/airavata/gfac/monitor/email/EmailBasedMonitor.java
+++ b/modules/gfac/gfac-impl/src/main/java/org/apache/airavata/gfac/monitor/email/EmailBasedMonitor.java
@@ -280,8 +280,8 @@ public class EmailBasedMonitor implements JobMonitor, Runnable{
process(jobStatusResult, taskContext);
processedMessages.add(message);
- } else if (addressMap.get(message.getFrom()).equals(ResourceJobManagerType.AIRAVATA_CUSTOM)
- && (new Date()).getTime() - message.getSentDate().getTime() > 1000 * 6 * 5) {
+ } else if (!jobStatusResult.isAuthoritative()
+ && (new Date()).getTime() - message.getSentDate().getTime() > 1000 * 60 * 5) {
//marking old custom Airavata emails as read
processedMessages.add(message);
log.info("Marking old Airavata custom emails as read, message subject --> {}", message.getSubject());
[07/12] airavata git commit: Removing older reference to
usr-profile-stubs
Posted by sc...@apache.org.
Removing older reference to usr-profile-stubs
Project: http://git-wip-us.apache.org/repos/asf/airavata/repo
Commit: http://git-wip-us.apache.org/repos/asf/airavata/commit/aa68a44a
Tree: http://git-wip-us.apache.org/repos/asf/airavata/tree/aa68a44a
Diff: http://git-wip-us.apache.org/repos/asf/airavata/diff/aa68a44a
Branch: refs/heads/develop
Commit: aa68a44a5c7f25cb554ade1e8a79bba28c155511
Parents: 9f57e1f
Author: Ajinkya Dhamnaskar <ad...@umail.iu.edu>
Authored: Wed May 17 14:12:27 2017 -0400
Committer: Ajinkya Dhamnaskar <ad...@umail.iu.edu>
Committed: Wed May 17 14:12:27 2017 -0400
----------------------------------------------------------------------
airavata-api/airavata-api-server/pom.xml | 5 -----
1 file changed, 5 deletions(-)
----------------------------------------------------------------------
http://git-wip-us.apache.org/repos/asf/airavata/blob/aa68a44a/airavata-api/airavata-api-server/pom.xml
----------------------------------------------------------------------
diff --git a/airavata-api/airavata-api-server/pom.xml b/airavata-api/airavata-api-server/pom.xml
index 8cbb8fa..ada0b8f 100644
--- a/airavata-api/airavata-api-server/pom.xml
+++ b/airavata-api/airavata-api-server/pom.xml
@@ -165,11 +165,6 @@
</dependency>
<dependency>
<groupId>org.apache.airavata</groupId>
- <artifactId>user-profile-stubs</artifactId>
- <version>${project.version}</version>
- </dependency>
- <dependency>
- <groupId>org.apache.airavata</groupId>
<artifactId>profile-service-stubs</artifactId>
<version>${project.version}</version>
</dependency>
[10/12] airavata git commit: Changes related to profile-service-stubs
Posted by sc...@apache.org.
Changes related to profile-service-stubs
Project: http://git-wip-us.apache.org/repos/asf/airavata/repo
Commit: http://git-wip-us.apache.org/repos/asf/airavata/commit/84622059
Tree: http://git-wip-us.apache.org/repos/asf/airavata/tree/84622059
Diff: http://git-wip-us.apache.org/repos/asf/airavata/diff/84622059
Branch: refs/heads/develop
Commit: 846220595f111a9edd83076648e728be6e460fb4
Parents: 78a3caf
Author: Ajinkya Dhamnaskar <ad...@umail.iu.edu>
Authored: Wed May 17 14:14:23 2017 -0400
Committer: Ajinkya Dhamnaskar <ad...@umail.iu.edu>
Committed: Wed May 17 14:14:23 2017 -0400
----------------------------------------------------------------------
.../main/java/org/apache/airavata/MigrationManager.java | 8 +++++---
.../apache/airavata/UserProfileAiravataThriftClient.java | 11 ++++-------
2 files changed, 9 insertions(+), 10 deletions(-)
----------------------------------------------------------------------
http://git-wip-us.apache.org/repos/asf/airavata/blob/84622059/modules/user-profile-migration/src/main/java/org/apache/airavata/MigrationManager.java
----------------------------------------------------------------------
diff --git a/modules/user-profile-migration/src/main/java/org/apache/airavata/MigrationManager.java b/modules/user-profile-migration/src/main/java/org/apache/airavata/MigrationManager.java
index 1b4c649..ba52de4 100644
--- a/modules/user-profile-migration/src/main/java/org/apache/airavata/MigrationManager.java
+++ b/modules/user-profile-migration/src/main/java/org/apache/airavata/MigrationManager.java
@@ -20,8 +20,9 @@
package org.apache.airavata;
import org.apache.airavata.common.exception.ApplicationSettingsException;
+import org.apache.airavata.model.security.AuthzToken;
import org.apache.airavata.model.user.UserProfile;
-import org.apache.airavata.userprofile.cpi.UserProfileService;
+import org.apache.airavata.service.profile.user.cpi.UserProfileService;
import org.apache.thrift.TException;
import org.wso2.carbon.um.ws.api.stub.ClaimValue;
import org.wso2.carbon.um.ws.api.stub.RemoteUserStoreManagerServiceStub;
@@ -34,7 +35,7 @@ import java.util.List;
public class MigrationManager {
private ArrayList<Wso2ISLoginCredentialsDAO> adminCredentials = new ArrayList<Wso2ISLoginCredentialsDAO>();
-
+ private static AuthzToken authzToken = new AuthzToken("empy_token");
/*Add the credentials for all the tenants from which the profile should be migrated to Airavata DB*/
public void setISLoginCredentials(){
@@ -120,7 +121,8 @@ public class MigrationManager {
airavataUserProfile.setHomeOrganization(ISProfile.getOrganization());
airavataUserProfile.setPhones(ISProfile.getPhones());
airavataUserProfile.setCountry(ISProfile.getCountry());
- client.addUserProfile(airavataUserProfile);
+ //TODO: fix authtzToken, for now we are using empty token
+ client.addUserProfile(authzToken, airavataUserProfile);
}
return false;
}
http://git-wip-us.apache.org/repos/asf/airavata/blob/84622059/modules/user-profile-migration/src/main/java/org/apache/airavata/UserProfileAiravataThriftClient.java
----------------------------------------------------------------------
diff --git a/modules/user-profile-migration/src/main/java/org/apache/airavata/UserProfileAiravataThriftClient.java b/modules/user-profile-migration/src/main/java/org/apache/airavata/UserProfileAiravataThriftClient.java
index 71dff21..56f2235 100644
--- a/modules/user-profile-migration/src/main/java/org/apache/airavata/UserProfileAiravataThriftClient.java
+++ b/modules/user-profile-migration/src/main/java/org/apache/airavata/UserProfileAiravataThriftClient.java
@@ -21,14 +21,11 @@ package org.apache.airavata;
import org.apache.airavata.common.exception.ApplicationSettingsException;
import org.apache.airavata.common.utils.ServerSettings;
-import org.apache.airavata.userprofile.cpi.UserProfileService;
-import org.apache.airavata.userprofile.cpi.exception.UserProfileServiceException;
-import org.apache.airavata.userprofile.cpi.client.UserProfileServiceClientFactory;
+import org.apache.airavata.service.profile.client.ProfileServiceClientFactory;
+import org.apache.airavata.service.profile.user.cpi.UserProfileService;
+import org.apache.airavata.service.profile.user.cpi.exception.UserProfileServiceException;
import org.apache.thrift.TException;
-import java.util.ArrayList;
-import java.util.List;
-
public class UserProfileAiravataThriftClient {
public UserProfileService.Client getUserProfileServiceClient() throws TException, ApplicationSettingsException {
@@ -36,7 +33,7 @@ public class UserProfileAiravataThriftClient {
final int serverPort = Integer.parseInt(ServerSettings.getUserProfileServerPort());
final String serverHost = ServerSettings.getUserProfileServerHost();
try {
- return UserProfileServiceClientFactory.createUserProfileServiceClient(serverHost, serverPort);
+ return ProfileServiceClientFactory.createUserProfileServiceClient(serverHost, serverPort);
} catch (UserProfileServiceException e) {
throw new TException("Unable to create registry client...", e);
}
[08/12] airavata git commit: Removing airavata-commons refrence from
itself
Posted by sc...@apache.org.
Removing airavata-commons refrence from itself
Project: http://git-wip-us.apache.org/repos/asf/airavata/repo
Commit: http://git-wip-us.apache.org/repos/asf/airavata/commit/1cfda99e
Tree: http://git-wip-us.apache.org/repos/asf/airavata/tree/1cfda99e
Diff: http://git-wip-us.apache.org/repos/asf/airavata/diff/1cfda99e
Branch: refs/heads/develop
Commit: 1cfda99ec345694c0115bdbed9432f7b47778015
Parents: aa68a44
Author: Ajinkya Dhamnaskar <ad...@umail.iu.edu>
Authored: Wed May 17 14:13:17 2017 -0400
Committer: Ajinkya Dhamnaskar <ad...@umail.iu.edu>
Committed: Wed May 17 14:13:17 2017 -0400
----------------------------------------------------------------------
modules/commons/pom.xml | 5 -----
1 file changed, 5 deletions(-)
----------------------------------------------------------------------
http://git-wip-us.apache.org/repos/asf/airavata/blob/1cfda99e/modules/commons/pom.xml
----------------------------------------------------------------------
diff --git a/modules/commons/pom.xml b/modules/commons/pom.xml
index e4c1bab..b00c9ee 100644
--- a/modules/commons/pom.xml
+++ b/modules/commons/pom.xml
@@ -138,11 +138,6 @@
<artifactId>logback-classic</artifactId>
<version>${logback.version}</version>
</dependency>
- <dependency>
- <groupId>org.apache.airavata</groupId>
- <artifactId>airavata-commons</artifactId>
- <version>0.17-SNAPSHOT</version>
- </dependency>
</dependencies>
<properties>