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Posted to commits@airavata.apache.org by ch...@apache.org on 2015/10/26 19:30:31 UTC
airavata git commit: fixing build errors
Repository: airavata
Updated Branches:
refs/heads/master 4db026e5e -> d96f35ac2
fixing build errors
Project: http://git-wip-us.apache.org/repos/asf/airavata/repo
Commit: http://git-wip-us.apache.org/repos/asf/airavata/commit/d96f35ac
Tree: http://git-wip-us.apache.org/repos/asf/airavata/tree/d96f35ac
Diff: http://git-wip-us.apache.org/repos/asf/airavata/diff/d96f35ac
Branch: refs/heads/master
Commit: d96f35ac23d9a8148fd9be949f34612fee2c89ed
Parents: 4db026e
Author: Chathuri Wimalasena <ch...@apache.org>
Authored: Mon Oct 26 14:30:20 2015 -0400
Committer: Chathuri Wimalasena <ch...@apache.org>
Committed: Mon Oct 26 14:30:20 2015 -0400
----------------------------------------------------------------------
.../client/samples/CreateLaunchExperiment.java | 15 ++++++++-------
.../resources/AppEnvironmentResource.java | 18 +++++++++++++++---
.../catalog/util/AppCatalogThriftConversion.java | 9 ++++++---
.../airavata/app/catalog/AppDeploymentTest.java | 19 ++++++++++---------
.../src/test/resources/appcatalog-derby.sql | 1 +
.../src/test/resources/expcatalog-derby.sql | 11 +++++++----
6 files changed, 47 insertions(+), 26 deletions(-)
----------------------------------------------------------------------
http://git-wip-us.apache.org/repos/asf/airavata/blob/d96f35ac/airavata-api/airavata-client-sdks/java-client-samples/src/main/java/org/apache/airavata/client/samples/CreateLaunchExperiment.java
----------------------------------------------------------------------
diff --git a/airavata-api/airavata-client-sdks/java-client-samples/src/main/java/org/apache/airavata/client/samples/CreateLaunchExperiment.java b/airavata-api/airavata-client-sdks/java-client-samples/src/main/java/org/apache/airavata/client/samples/CreateLaunchExperiment.java
index 212c191..dbd8789 100644
--- a/airavata-api/airavata-client-sdks/java-client-samples/src/main/java/org/apache/airavata/client/samples/CreateLaunchExperiment.java
+++ b/airavata-api/airavata-client-sdks/java-client-samples/src/main/java/org/apache/airavata/client/samples/CreateLaunchExperiment.java
@@ -37,6 +37,7 @@ import org.apache.airavata.model.experiment.UserConfigurationDataModel;
import org.apache.airavata.model.scheduling.ComputationalResourceSchedulingModel;
import org.apache.airavata.model.security.AuthzToken;
import org.apache.airavata.model.status.ExperimentState;
+import org.apache.airavata.model.status.JobStatus;
import org.apache.airavata.model.util.ExperimentModelUtil;
import org.apache.airavata.model.util.ProjectModelUtil;
import org.apache.airavata.model.workspace.Gateway;
@@ -53,7 +54,7 @@ import java.util.Map;
public class CreateLaunchExperiment {
//FIXME: Read from a config file
- public static final String THRIFT_SERVER_HOST = "gw119.iu.xsede.org";
+ public static final String THRIFT_SERVER_HOST = "gw56.iu.xsede.org";
public static final int THRIFT_SERVER_PORT = 8930;
// public static final String THRIFT_SERVER_HOST = "gw111.iu.xsede.org";
// public static final int THRIFT_SERVER_PORT = 9930;
@@ -92,12 +93,12 @@ public class CreateLaunchExperiment {
AuthzToken token = new AuthzToken("empty_token");
System.out.println("API version is " + airavataClient.getAPIVersion(token));
// registerApplications(); // run this only the first time
-// Map<String, JobStatus> jobStatuses = airavataClient.getJobStatuses(token, "SLM1-Echo-BR2_ae9573d1-cc1e-49e5-b59c-99ad10bd09ee");
-// for (String jobId : jobStatuses.keySet()){
-// JobStatus jobStatus = jobStatuses.get(jobId);
-// System.out.println(jobId);
-// System.out.println(jobStatus.getJobState().toString());
-// }
+ Map<String, JobStatus> jobStatuses = airavataClient.getJobStatuses(token, "Test1_Nek_a706cdc7-8abf-4db2-b7c7-13679c714e90");
+ for (String jobId : jobStatuses.keySet()){
+ JobStatus jobStatus = jobStatuses.get(jobId);
+ System.out.println(jobId);
+ System.out.println(jobStatus.getJobState().toString());
+ }
// createAndLaunchExp();
}
http://git-wip-us.apache.org/repos/asf/airavata/blob/d96f35ac/modules/registry/registry-core/src/main/java/org/apache/airavata/registry/core/app/catalog/resources/AppEnvironmentResource.java
----------------------------------------------------------------------
diff --git a/modules/registry/registry-core/src/main/java/org/apache/airavata/registry/core/app/catalog/resources/AppEnvironmentResource.java b/modules/registry/registry-core/src/main/java/org/apache/airavata/registry/core/app/catalog/resources/AppEnvironmentResource.java
index f94b5bf..46d16dc 100644
--- a/modules/registry/registry-core/src/main/java/org/apache/airavata/registry/core/app/catalog/resources/AppEnvironmentResource.java
+++ b/modules/registry/registry-core/src/main/java/org/apache/airavata/registry/core/app/catalog/resources/AppEnvironmentResource.java
@@ -36,12 +36,12 @@ import javax.persistence.EntityManager;
import javax.persistence.Query;
import java.util.*;
-public class AppEnvironmentResource extends AppCatAbstractResource {
+public class AppEnvironmentResource extends AppCatAbstractResource{
private final static Logger logger = LoggerFactory.getLogger(AppEnvironmentResource.class);
private String deploymentId;
private String name;
private String value;
- private Integer order;
+ private Integer order = 0;
private AppDeploymentResource appDeploymentResource;
public String getDeploymentId() {
@@ -178,7 +178,17 @@ public class AppEnvironmentResource extends AppCatAbstractResource {
appEnvironmentList.add(resource);
}
Collections.sort(appEnvironmentList,
- (o1, o2) -> ((AppEnvironmentResource) o1).getOrder() - ((AppEnvironmentResource) o2).getOrder());
+ (o1, o2) -> {
+ AppEnvironmentResource order1 = (AppEnvironmentResource) o1;
+ AppEnvironmentResource order2 = (AppEnvironmentResource) o2;
+ if (order1.getOrder() == null){
+ return (order2.getOrder() == null) ? 0 : -1;
+ }
+ if (order2.getOrder() == null) {
+ return 1;
+ }
+ return order1.getOrder().compareTo(order2.getOrder());
+ });
}
} else {
em.getTransaction().commit();
@@ -233,12 +243,14 @@ public class AppEnvironmentResource extends AppCatAbstractResource {
if (existigAppEnv != null){
existigAppEnv.setValue(value);
existigAppEnv.setApplicationDeployment(deployment);
+ existigAppEnv.setOrder(order);
em.merge(existigAppEnv);
}else {
AppEnvironment appEnvironment = new AppEnvironment();
appEnvironment.setDeploymentID(deploymentId);
appEnvironment.setName(name);
appEnvironment.setValue(value);
+ appEnvironment.setOrder(order);
appEnvironment.setApplicationDeployment(deployment);
em.persist(appEnvironment);
}
http://git-wip-us.apache.org/repos/asf/airavata/blob/d96f35ac/modules/registry/registry-core/src/main/java/org/apache/airavata/registry/core/app/catalog/util/AppCatalogThriftConversion.java
----------------------------------------------------------------------
diff --git a/modules/registry/registry-core/src/main/java/org/apache/airavata/registry/core/app/catalog/util/AppCatalogThriftConversion.java b/modules/registry/registry-core/src/main/java/org/apache/airavata/registry/core/app/catalog/util/AppCatalogThriftConversion.java
index 604cadb..a399fe2 100644
--- a/modules/registry/registry-core/src/main/java/org/apache/airavata/registry/core/app/catalog/util/AppCatalogThriftConversion.java
+++ b/modules/registry/registry-core/src/main/java/org/apache/airavata/registry/core/app/catalog/util/AppCatalogThriftConversion.java
@@ -706,9 +706,12 @@ public class AppCatalogThriftConversion {
envPaths.setValue(((LibraryApendPathResource) resource).getValue());
return envPaths;
}else if (resource instanceof AppEnvironmentResource){
- envPaths.setName(((AppEnvironmentResource) resource).getName());
- envPaths.setValue(((AppEnvironmentResource) resource).getValue());
- envPaths.setEnvPathOrder(((AppEnvironmentResource) resource).getOrder());
+ AppEnvironmentResource environmentResource = (AppEnvironmentResource) resource;
+ envPaths.setName(environmentResource.getName());
+ envPaths.setValue(environmentResource.getValue());
+ if (environmentResource.getOrder() != null){
+ envPaths.setEnvPathOrder(environmentResource.getOrder());
+ }
return envPaths;
}else {
return null;
http://git-wip-us.apache.org/repos/asf/airavata/blob/d96f35ac/modules/registry/registry-core/src/test/java/org/apache/airavata/app/catalog/AppDeploymentTest.java
----------------------------------------------------------------------
diff --git a/modules/registry/registry-core/src/test/java/org/apache/airavata/app/catalog/AppDeploymentTest.java b/modules/registry/registry-core/src/test/java/org/apache/airavata/app/catalog/AppDeploymentTest.java
index 5ccb61d..a6b8a01 100644
--- a/modules/registry/registry-core/src/test/java/org/apache/airavata/app/catalog/AppDeploymentTest.java
+++ b/modules/registry/registry-core/src/test/java/org/apache/airavata/app/catalog/AppDeploymentTest.java
@@ -90,22 +90,22 @@ public class AppDeploymentTest {
cmd1.setCommand("cmd1");
cmd1.setCommandOrder(1);
CommandObject cmd2 = new CommandObject();
- cmd1.setCommand("cmd1");
- cmd1.setCommandOrder(1);
+ cmd2.setCommand("cmd1");
+ cmd2.setCommandOrder(1);
description.addToModuleLoadCmds(cmd1);
description.addToModuleLoadCmds(cmd2);
List<SetEnvPaths> libPrepandPaths = new ArrayList<SetEnvPaths>();
- libPrepandPaths.add(createSetEnvPath("name1", "val1"));
- libPrepandPaths.add(createSetEnvPath("name2", "val2"));
+ libPrepandPaths.add(createSetEnvPath("name1", "val1", 1));
+ libPrepandPaths.add(createSetEnvPath("name2", "val2", 2));
description.setLibPrependPaths(libPrepandPaths);
List<SetEnvPaths> libApendPaths = new ArrayList<SetEnvPaths>();
- libApendPaths.add(createSetEnvPath("name3", "val3"));
- libApendPaths.add(createSetEnvPath("name4", "val4"));
+ libApendPaths.add(createSetEnvPath("name3", "val3", 1));
+ libApendPaths.add(createSetEnvPath("name4", "val4", 2));
description.setLibAppendPaths(libApendPaths);
List<SetEnvPaths> appEvns = new ArrayList<SetEnvPaths>();
- appEvns.add(createSetEnvPath("name5", "val5"));
- appEvns.add(createSetEnvPath("name6", "val6"));
+ appEvns.add(createSetEnvPath("name5", "val5", 1));
+ appEvns.add(createSetEnvPath("name6", "val6", 2));
description.setSetEnvironment(appEvns);
String appDepId = appDep.addApplicationDeployment(description, ServerSettings.getDefaultUserGateway());
@@ -142,10 +142,11 @@ public class AppDeploymentTest {
assertTrue("App interface saved successfully", app != null);
}
- public SetEnvPaths createSetEnvPath (String name, String val){
+ public SetEnvPaths createSetEnvPath (String name, String val, int order){
SetEnvPaths setEnvPaths = new SetEnvPaths();
setEnvPaths.setName(name);
setEnvPaths.setValue(val);
+ setEnvPaths.setEnvPathOrder(order);
return setEnvPaths;
}
http://git-wip-us.apache.org/repos/asf/airavata/blob/d96f35ac/modules/registry/registry-core/src/test/resources/appcatalog-derby.sql
----------------------------------------------------------------------
diff --git a/modules/registry/registry-core/src/test/resources/appcatalog-derby.sql b/modules/registry/registry-core/src/test/resources/appcatalog-derby.sql
index a572618..3d57f0e 100644
--- a/modules/registry/registry-core/src/test/resources/appcatalog-derby.sql
+++ b/modules/registry/registry-core/src/test/resources/appcatalog-derby.sql
@@ -318,6 +318,7 @@ CREATE TABLE GATEWAY_PROFILE
GATEWAY_ID VARCHAR(255),
CREATION_TIME TIMESTAMP DEFAULT CURRENT_TIMESTAMP,
UPDATE_TIME TIMESTAMP DEFAULT '0000-00-00 00:00:00',
+ CS_TOKEN VARCHAR (255),
PRIMARY KEY(GATEWAY_ID)
);
http://git-wip-us.apache.org/repos/asf/airavata/blob/d96f35ac/modules/registry/registry-core/src/test/resources/expcatalog-derby.sql
----------------------------------------------------------------------
diff --git a/modules/registry/registry-core/src/test/resources/expcatalog-derby.sql b/modules/registry/registry-core/src/test/resources/expcatalog-derby.sql
index 31aa701..215dd7e 100644
--- a/modules/registry/registry-core/src/test/resources/expcatalog-derby.sql
+++ b/modules/registry/registry-core/src/test/resources/expcatalog-derby.sql
@@ -157,6 +157,7 @@ CREATE TABLE USER_CONFIGURATION_DATA (
QUEUE_NAME varchar(255),
WALL_TIME_LIMIT INT,
TOTAL_PHYSICAL_MEMORY INT,
+ STATIC_WORKING_DIR varchar(255),
PRIMARY KEY (EXPERIMENT_ID),
FOREIGN KEY (EXPERIMENT_ID) REFERENCES EXPERIMENT(EXPERIMENT_ID) ON DELETE CASCADE
);
@@ -258,6 +259,7 @@ CREATE TABLE PROCESS_RESOURCE_SCHEDULE (
QUEUE_NAME varchar(255),
WALL_TIME_LIMIT INT,
TOTAL_PHYSICAL_MEMORY INT,
+ STATIC_WORKING_DIR varchar(255),
PRIMARY KEY (PROCESS_ID),
FOREIGN KEY (PROCESS_ID) REFERENCES PROCESS(PROCESS_ID) ON DELETE CASCADE
);
@@ -294,19 +296,20 @@ CREATE TABLE TASK_ERROR (
TRANSIENT_OR_PERSISTENT SMALLINT,
ROOT_CAUSE_ERROR_ID_LIST CLOB,
PRIMARY KEY (ERROR_ID, TASK_ID),
- FOREIGN KEY (TASK_ID) REFERENCES TASK(TASK_ID) ON DELETE CASCADE);
+ FOREIGN KEY (TASK_ID) REFERENCES TASK(TASK_ID) ON DELETE CASCADE
+);
CREATE TABLE JOB (
JOB_ID varchar(255),
TASK_ID varchar(255),
PROCESS_ID varchar(255),
- JOB_DESCRIPTION CLOB,
+ JOB_DESCRIPTION CLOB NOT NULL,
CREATION_TIME timestamp DEFAULT '0000-00-00 00:00:00',
COMPUTE_RESOURCE_CONSUMED varchar(255),
JOB_NAME varchar(255),
WORKING_DIR varchar(255),
- STDOUT CLOB,
- STDERR CLOB,
+ STD_OUT CLOB,
+ STD_ERR CLOB,
EXIT_CODE INT,
PRIMARY KEY (JOB_ID, PROCESS_ID),
FOREIGN KEY (PROCESS_ID) REFERENCES PROCESS(PROCESS_ID) ON DELETE CASCADE