Repository: airavata Updated Branches: refs/heads/master 97b384b06 -> 5413e6718
fixed simple experiment run [AIRAVATA-1473] Project: http://git-wip-us.apache.org/repos/asf/airavata/repo Commit: http://git-wip-us.apache.org/repos/asf/airavata/commit/febd0c40 Tree: http://git-wip-us.apache.org/repos/asf/airavata/tree/febd0c40 Diff: http://git-wip-us.apache.org/repos/asf/airavata/diff/febd0c40 Branch: refs/heads/master Commit: febd0c40d6445d364d42fb13884075906e44507a Parents: 47e8214 Author: msmemon <[email protected]> Authored: Tue Nov 11 16:12:48 2014 +0100 Committer: msmemon <[email protected]> Committed: Tue Nov 11 16:12:48 2014 +0100 ---------------------------------------------------------------------- .../client/samples/CreateLaunchExperiment.java | 22 ++++-- .../tools/RegisterSampleApplications.java | 9 ++- .../server/src/main/assembly/bin-assembly.xml | 25 ++++--- .../gfac/bes/provider/impl/BESProvider.java | 16 ++--- .../bes/security/UNICORESecurityContext.java | 6 +- .../gfac/bes/utils/DataTransferrer.java | 53 +++++++++++++- .../airavata/gfac/bes/utils/JSDLUtils.java | 6 +- .../gfac/bes/utils/UASDataStagingProcessor.java | 73 +++++++++++--------- .../registry/jpa/impl/ExperimentRegistry.java | 7 +- 9 files changed, 148 insertions(+), 69 deletions(-) ---------------------------------------------------------------------- http://git-wip-us.apache.org/repos/asf/airavata/blob/febd0c40/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 2845bc6..e0b47bb 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 @@ -42,6 +42,8 @@ import org.slf4j.LoggerFactory; import java.util.ArrayList; import java.util.List; import java.util.Map; +import java.util.Random; +import java.util.UUID; public class CreateLaunchExperiment { @@ -53,7 +55,7 @@ public class CreateLaunchExperiment { private static final String DEFAULT_GATEWAY = "default.registry.gateway"; private static Airavata.Client airavataClient; - private static String echoAppId = "Echo_6281480a-9887-4a0f-8311-59bbaf738e54"; + private static String echoAppId = "Echo_70892623-ef16-4efb-a9f0-b12a2861e27a"; private static String wrfAppId = "WRF_5f097c9c-7066-49ec-aed7-4e39607b3adc"; private static String amberAppId = "Amber_89906be6-5678-49a6-9d04-a0604fbdef2e"; @@ -179,7 +181,7 @@ public class CreateLaunchExperiment { userConfigurationData.setAiravataAutoSchedule(false); userConfigurationData.setOverrideManualScheduledParams(false); userConfigurationData.setComputationalResourceScheduling(scheduling); - simpleExperiment.setUserConfigurationData(userConfigurationData); + return client.createExperiment(simpleExperiment); } } @@ -203,18 +205,24 @@ public class CreateLaunchExperiment { public static String createEchoExperimentForFSD(Airavata.Client client) throws TException { try { + // these are template variables and do not need to have values, as it is a data model. List<DataObjectType> exInputs = new ArrayList<DataObjectType>(); DataObjectType input = new DataObjectType(); input.setKey("Input_to_Echo"); input.setType(DataType.STRING); input.setValue("Echoed_Output=Hello World"); exInputs.add(input); + DataObjectType i2 = new DataObjectType(); + i2.setKey("Input_to_Echo1"); + i2.setType(DataType.URI); + i2.setValue("http://shrib.com/22QmrrX4";); + exInputs.add(i2); List<DataObjectType> exOut = new ArrayList<DataObjectType>(); DataObjectType output = new DataObjectType(); - output.setKey("echo_output"); + output.setKey("Echoed_Output"); output.setType(DataType.STRING); - output.setValue(""); + output.setValue("22QmrrX4"); exOut.add(output); @@ -235,7 +243,13 @@ public class CreateLaunchExperiment { userConfigurationData.setAiravataAutoSchedule(false); userConfigurationData.setOverrideManualScheduledParams(false); userConfigurationData.setComputationalResourceScheduling(scheduling); + + // set output directory + AdvancedOutputDataHandling dataHandling = new AdvancedOutputDataHandling(); + dataHandling.setOutputDataDir("/tmp/airavata/output/"+UUID.randomUUID().toString()+"/"); + userConfigurationData.setAdvanceOutputDataHandling(dataHandling); simpleExperiment.setUserConfigurationData(userConfigurationData); + return client.createExperiment(simpleExperiment); } } http://git-wip-us.apache.org/repos/asf/airavata/blob/febd0c40/airavata-api/airavata-client-sdks/java-client-samples/src/main/java/org/apache/airavata/client/tools/RegisterSampleApplications.java ---------------------------------------------------------------------- diff --git a/airavata-api/airavata-client-sdks/java-client-samples/src/main/java/org/apache/airavata/client/tools/RegisterSampleApplications.java b/airavata-api/airavata-client-sdks/java-client-samples/src/main/java/org/apache/airavata/client/tools/RegisterSampleApplications.java index bd4023b..1e4b591 100644 --- a/airavata-api/airavata-client-sdks/java-client-samples/src/main/java/org/apache/airavata/client/tools/RegisterSampleApplications.java +++ b/airavata-api/airavata-client-sdks/java-client-samples/src/main/java/org/apache/airavata/client/tools/RegisterSampleApplications.java @@ -531,12 +531,17 @@ public class RegisterSampleApplications { InputDataObjectType input1 = RegisterSampleApplicationsUtils.createAppInput("Input_to_Echo", "Hello World", DataType.STRING, null, false, "A test string to Echo", null); + + InputDataObjectType input2 = RegisterSampleApplicationsUtils.createAppInput("Input_to_Echo1", "http://shrib.com/22QmrrX4";, + DataType.URI, null, false, "A test uri to Echo", null); + List<InputDataObjectType> applicationInputs = new ArrayList<InputDataObjectType>(); applicationInputs.add(input1); + applicationInputs.add(input2); OutputDataObjectType output1 = RegisterSampleApplicationsUtils.createAppOutput("Echoed_Output", - "", DataType.STRING); + "22QmrrX4", DataType.STRING); List<OutputDataObjectType> applicationOutputs = new ArrayList<OutputDataObjectType>(); applicationOutputs.add(output1); @@ -1036,7 +1041,7 @@ public class RegisterSampleApplications { //Register Echo String echoAppDeployId = airavataClient.registerApplicationDeployment( RegisterSampleApplicationsUtils.createApplicationDeployment(echoModuleId, fsdResourceId, - "/bin/date", ApplicationParallelismType.SERIAL, echoDescription)); + "/bin/echo", ApplicationParallelismType.SERIAL, echoDescription)); System.out.println("Echo on FSD deployment Id " + echoAppDeployId); } catch (TException e) { http://git-wip-us.apache.org/repos/asf/airavata/blob/febd0c40/modules/distribution/server/src/main/assembly/bin-assembly.xml ---------------------------------------------------------------------- diff --git a/modules/distribution/server/src/main/assembly/bin-assembly.xml b/modules/distribution/server/src/main/assembly/bin-assembly.xml index 32cb5e7..6ab1d13 100644 --- a/modules/distribution/server/src/main/assembly/bin-assembly.xml +++ b/modules/distribution/server/src/main/assembly/bin-assembly.xml @@ -17,13 +17,13 @@ <!ELEMENT formats (format)*> <!ELEMENT format (#PCDATA)> <!ELEMENT fileSets (fileSet)*> - <!ELEMENT fileSet (directory|outputDirectory|includes)*> + <!ELEMENT fileSet (directory|outputDirectory|fileMode|includes)*> <!ELEMENT directory (#PCDATA)> <!ELEMENT outputDirectory (#PCDATA)> <!ELEMENT includes (include)*> <!ELEMENT include (#PCDATA)> <!ELEMENT dependencySets (dependencySet)*> - <!ELEMENT dependencySet (outputDirectory|includes)*> + <!ELEMENT dependencySet (outputDirectory|outputFileNameMapping|includes)*> ]> <assembly> <id>bin</id> @@ -159,8 +159,7 @@ <dependencySets> <dependencySet> <outputDirectory>lib</outputDirectory> - <outputFileNameMapping>${artifact.artifactId}.${artifact.extension} - </outputFileNameMapping> + <outputFileNameMapping>${artifact.artifactId}.${artifact.extension}</outputFileNameMapping> <includes> <include>org.apache.derby:derby:jar</include> <include>org.apache.derby:derbytools:jar</include> @@ -280,16 +279,17 @@ <include>pl.edu.icm.saml:samly2</include> <include>org.apache.ws.security:wss4j</include> <include>org.json:json</include> - <include>org.apache.cxf:cxf-rt-databinding-xmlbeans</include> - <include>org.apache.cxf:cxf-api</include> + <!-- CXF deps start --> <include>org.codehaus.woodstox:woodstox-core-asl</include> <include>org.codehaus.woodstox:stax2-api</include> + <include>org.apache.cxf:cxf-rt-databinding-xmlbeans</include> + <include>org.apache.cxf:cxf-api</include> <include>org.apache.ws.xmlschema:xmlschema-core</include> + <include>org.apache.cxf:cxf-api</include> + <include>org.apache.cxf:cxf-rt-databinding-xmlbeans</include> <include>org.apache.cxf:cxf-rt-core</include> - <include>com.sun.xml.bind:jaxb-impl</include> <include>org.apache.cxf:cxf-rt-frontend-jaxws</include> - <include>xml-resolver:xml-resolver</include> - <include>asm:asm</include> + <include>org.apache.cxf:cxf-rt-frontend-simple</include> <include>org.apache.cxf:cxf-rt-bindings-soap</include> <include>org.apache.cxf:cxf-rt-databinding-jaxb</include> <include>org.apache.cxf:cxf-rt-bindings-xml</include> @@ -298,8 +298,13 @@ <include>org.apache.cxf:cxf-rt-ws-policy</include> <include>org.apache.cxf:cxf-rt-transports-http</include> <include>org.apache.cxf:cxf-rt-features-clustering</include> - <include>org.apache.neethi:neethi</include> <include>org.apache.cxf:cxf-rt-frontend-jaxws</include> + <include>org.apache.cxf:cxf-bundle</include> + <!-- // CXF deps end --> + <include>com.sun.xml.bind:jaxb-impl</include> + <include>org.apache.neethi:neethi:3.0.2</include> + <include>xml-resolver:xml-resolver</include> + <include>asm:asm</include> <include>xml-resolver:xml-resolver</include> <include>org.eclipse.jetty:jetty-servlet</include> <include>org.eclipse.jetty:jetty-security</include> http://git-wip-us.apache.org/repos/asf/airavata/blob/febd0c40/modules/gfac/gfac-bes/src/main/java/org/apache/airavata/gfac/bes/provider/impl/BESProvider.java ---------------------------------------------------------------------- diff --git a/modules/gfac/gfac-bes/src/main/java/org/apache/airavata/gfac/bes/provider/impl/BESProvider.java b/modules/gfac/gfac-bes/src/main/java/org/apache/airavata/gfac/bes/provider/impl/BESProvider.java index 7ed038a..044ffa2 100644 --- a/modules/gfac/gfac-bes/src/main/java/org/apache/airavata/gfac/bes/provider/impl/BESProvider.java +++ b/modules/gfac/gfac-bes/src/main/java/org/apache/airavata/gfac/bes/provider/impl/BESProvider.java @@ -187,17 +187,17 @@ public class BESProvider extends AbstractProvider implements GFacProvider, .toString(); } log.info("JobID: " + jobId); - jobDetails.setJobID(activityEpr.toString()); - jobDetails.setJobDescription(activityEpr.toString()); + jobDetails.setJobID(jobId); + jobDetails.setJobDescription(jobId); jobExecutionContext.setJobDetails(jobDetails); try { log.info(formatStatusMessage(activityEpr.getAddress() .getStringValue(), factory.getActivityStatus(activityEpr) .toString())); - + jobExecutionContext.getNotifier().publish(new UnicoreJobIDEvent(jobId)); - GFacUtils.saveJobStatus(jobExecutionContext, details,JobState.SUBMITTED); +// GFacUtils.saveJobStatus(jobExecutionContext, details,JobState.SUBMITTED); factory.getActivityStatus(activityEpr); log.info(formatStatusMessage(activityEpr.getAddress() @@ -215,8 +215,8 @@ public class BESProvider extends AbstractProvider implements GFacProvider, JobState applicationJobStatus = getApplicationJobStatus(activityStatus); String jobStatusMessage = "Status of job " + jobId + "is " + applicationJobStatus; - GFacUtils.updateJobStatus(jobExecutionContext, jobDetails, - applicationJobStatus); + //TODO: properly use GFacUtils.. +// GFacUtils.updateJobStatus(jobExecutionContext, jobDetails, applicationJobStatus); jobExecutionContext.getNotifier().publish( new StatusChangeEvent(jobStatusMessage)); @@ -272,8 +272,8 @@ public class BESProvider extends AbstractProvider implements GFacProvider, + applicationJobStatus; jobExecutionContext.getNotifier().publish( new StatusChangeEvent(jobStatusMessage)); - GFacUtils.updateJobStatus(jobExecutionContext, jobDetails, - applicationJobStatus); + //TODO: properly use GFacUtils.. +// GFacUtils.updateJobStatus(jobExecutionContext, jobDetails, applicationJobStatus); throw new GFacProviderException( jobExecutionContext.getExperimentID() + "Job Canceled"); } http://git-wip-us.apache.org/repos/asf/airavata/blob/febd0c40/modules/gfac/gfac-bes/src/main/java/org/apache/airavata/gfac/bes/security/UNICORESecurityContext.java ---------------------------------------------------------------------- diff --git a/modules/gfac/gfac-bes/src/main/java/org/apache/airavata/gfac/bes/security/UNICORESecurityContext.java b/modules/gfac/gfac-bes/src/main/java/org/apache/airavata/gfac/bes/security/UNICORESecurityContext.java index 7285c2c..d5e2b9f 100644 --- a/modules/gfac/gfac-bes/src/main/java/org/apache/airavata/gfac/bes/security/UNICORESecurityContext.java +++ b/modules/gfac/gfac-bes/src/main/java/org/apache/airavata/gfac/bes/security/UNICORESecurityContext.java @@ -44,7 +44,7 @@ public class UNICORESecurityContext extends X509SecurityContext { try{ X509Credential cred = getX509Credentials(); secProperties = new DefaultClientConfiguration(dcValidator, cred); -// setExtraSettings(); + setExtraSettings(); } catch (Exception e) { throw new GFacException(e.getMessage(), e); @@ -103,8 +103,8 @@ public class UNICORESecurityContext extends X509SecurityContext { p = new Properties(); } - p.setProperty("http.connection.timeout", "300000"); - p.setProperty("http.socket.timeout", "300000"); + p.setProperty("http.connection.timeout", "5000"); + p.setProperty("http.socket.timeout", "5000"); secProperties.setExtraSettings(p); http://git-wip-us.apache.org/repos/asf/airavata/blob/febd0c40/modules/gfac/gfac-bes/src/main/java/org/apache/airavata/gfac/bes/utils/DataTransferrer.java ---------------------------------------------------------------------- diff --git a/modules/gfac/gfac-bes/src/main/java/org/apache/airavata/gfac/bes/utils/DataTransferrer.java b/modules/gfac/gfac-bes/src/main/java/org/apache/airavata/gfac/bes/utils/DataTransferrer.java index f811f97..79fbae4 100644 --- a/modules/gfac/gfac-bes/src/main/java/org/apache/airavata/gfac/bes/utils/DataTransferrer.java +++ b/modules/gfac/gfac-bes/src/main/java/org/apache/airavata/gfac/bes/utils/DataTransferrer.java @@ -26,7 +26,9 @@ import java.io.File; import java.io.FileNotFoundException; import java.io.FileReader; import java.io.IOException; +import java.util.ArrayList; import java.util.HashMap; +import java.util.List; import java.util.Map; import org.apache.airavata.commons.gfac.type.ActualParameter; @@ -39,6 +41,7 @@ import org.apache.airavata.schemas.gfac.ApplicationDeploymentDescriptionType; import org.apache.airavata.schemas.gfac.HpcApplicationDeploymentType; import org.apache.airavata.schemas.gfac.StringArrayType; import org.apache.airavata.schemas.gfac.StringParameterType; +import org.apache.airavata.schemas.gfac.URIArrayType; import org.apache.airavata.schemas.gfac.URIParameterType; import org.slf4j.Logger; import org.slf4j.LoggerFactory; @@ -119,7 +122,8 @@ public class DataTransferrer { String localFileName = null; //TODO: why analysis.tar? it wont scale to other gateways.. if(stringPrm == null || stringPrm.isEmpty()){ - localFileName = "analysis-results.tar"; + continue; +// localFileName = "analysis-results.tar"; }else{ localFileName = stringPrm.substring(stringPrm.lastIndexOf("/")+1); } @@ -199,16 +203,59 @@ public class DataTransferrer { throw new GFacProviderException(e.getLocalizedMessage(),e); } String stderrLocation = downloadLocation+File.separator+stderrFileName; - FileDownloader f2 = new FileDownloader(stderrFileName,stderrLocation, Mode.overwrite); +// FileDownloader f2 = new FileDownloader(stderrFileName,stderrLocation, Mode.overwrite); try { - f2.perform(storageClient); + f1.setFrom(stderrFileName); + f1.setTo(stderrLocation); + f1.perform(storageClient); String stderror = readFile(stderrLocation); appDesc.setStandardError(stderror); } catch (Exception e) { throw new GFacProviderException(e.getLocalizedMessage(),e); } + + if(UASDataStagingProcessor.isUnicoreEndpoint(jobContext)) { + String scriptExitCodeFName = "UNICORE_SCRIPT_EXIT_CODE"; + f1.setFrom(scriptExitCodeFName); + f1.setTo(downloadLocation+File.separator+scriptExitCodeFName); + + } + } + + public List<String> extractOutStringParams(JobExecutionContext context) { + + Map<String, Object> outputParams = context.getOutMessageContext() + .getParameters(); + + List<String> outPrmsList = new ArrayList<String>(); + + for (String paramKey : outputParams.keySet()) { + + ActualParameter outParam = (ActualParameter) outputParams + .get(paramKey); + + String paramDataType = outParam.getType().getType().toString(); + + if ("String".equals(paramDataType)) { + String strPrm = ((StringParameterType) outParam.getType()) + .getValue(); + outPrmsList.add(strPrm); + } + + else if (("StringArray").equals(paramDataType)) { + String[] uriArray = ((URIArrayType) outParam.getType()) + .getValueArray(); + for (String u : uriArray) { + outPrmsList.add(u); + } + + } + } + + return outPrmsList; } + private String readFile(String localFile) throws IOException { BufferedReader instream = new BufferedReader(new FileReader(localFile)); StringBuffer buff = new StringBuffer(); http://git-wip-us.apache.org/repos/asf/airavata/blob/febd0c40/modules/gfac/gfac-bes/src/main/java/org/apache/airavata/gfac/bes/utils/JSDLUtils.java ---------------------------------------------------------------------- diff --git a/modules/gfac/gfac-bes/src/main/java/org/apache/airavata/gfac/bes/utils/JSDLUtils.java b/modules/gfac/gfac-bes/src/main/java/org/apache/airavata/gfac/bes/utils/JSDLUtils.java index d2474f0..e7dc672 100644 --- a/modules/gfac/gfac-bes/src/main/java/org/apache/airavata/gfac/bes/utils/JSDLUtils.java +++ b/modules/gfac/gfac-bes/src/main/java/org/apache/airavata/gfac/bes/utils/JSDLUtils.java @@ -122,10 +122,12 @@ public class JSDLUtils SourceTargetType target = newDS.addNewTarget(); try { - uri = (uri == null) ? null : URIUtils.encodeAll(uri); + if (uri != null) { + URIUtils.encodeAll(uri); + target.setURI(uri); + } } catch (URIException e) { } - target.setURI(uri); newDS.setFileName(file); if (fileSystem != null && !fileSystem.equals("Work")) { //$NON-NLS-1$ newDS.setFilesystemName(fileSystem); http://git-wip-us.apache.org/repos/asf/airavata/blob/febd0c40/modules/gfac/gfac-bes/src/main/java/org/apache/airavata/gfac/bes/utils/UASDataStagingProcessor.java ---------------------------------------------------------------------- diff --git a/modules/gfac/gfac-bes/src/main/java/org/apache/airavata/gfac/bes/utils/UASDataStagingProcessor.java b/modules/gfac/gfac-bes/src/main/java/org/apache/airavata/gfac/bes/utils/UASDataStagingProcessor.java index 6ab7ed0..76624cc 100644 --- a/modules/gfac/gfac-bes/src/main/java/org/apache/airavata/gfac/bes/utils/UASDataStagingProcessor.java +++ b/modules/gfac/gfac-bes/src/main/java/org/apache/airavata/gfac/bes/utils/UASDataStagingProcessor.java @@ -22,6 +22,8 @@ package org.apache.airavata.gfac.bes.utils; import java.io.File; +import java.util.HashMap; +import java.util.List; import java.util.Map; import org.apache.airavata.commons.gfac.type.ActualParameter; @@ -48,17 +50,19 @@ public class UASDataStagingProcessor { if (context.getInMessageContext().getParameters().size() > 0) { buildDataStagingFromInputContext(context, value, smsUrl, appDepType); } - MessageContext outMessage = new MessageContext(); - ActualParameter a1 = new ActualParameter(); - a1.getType().changeType(StringParameterType.type); - ((StringParameterType)a1.getType()).setValue("analysis-results.tar"); - outMessage.addParameter("o1", a1); - context.setOutMessageContext(outMessage); - +// MessageContext outMessage = new MessageContext(); +// ActualParameter a1 = new ActualParameter(); +// a1.getType().changeType(StringParameterType.type); +// ((StringParameterType)a1.getType()).setValue("analysis-results.tar"); +// outMessage.addParameter("o1", a1); +// context.setOutMessageContext(outMessage); + + // now download for string typed outputs are to be done if (context.getOutMessageContext().getParameters().size() > 0) { buildFromOutputContext(context, value, smsUrl, appDepType); } - createStdOutURIs(value, appDepType, smsUrl, isUnicoreEndpoint(context)); + //TODO need a review for us3 gateway.. +// createStdOutURIs(value, appDepType, smsUrl, isUnicoreEndpoint(context)); } private static void createInURISMSElement(JobDefinitionType value, @@ -85,7 +89,16 @@ public class UASDataStagingProcessor { HpcApplicationDeploymentType appDepType, String smsUrl, boolean isUnicore) throws Exception { + // no need to use smsUrl for output location, because output location is activity's working directory + if(isUnicore) { + String scriptExitCodeFName = "UNICORE_SCRIPT_EXIT_CODE"; + String scriptExitCode = smsUrl+"#/output/"+scriptExitCodeFName; + JSDLUtils.addDataStagingTargetElement(value, null, + scriptExitCodeFName, null); + } + + if(!isUnicore) { String stdout = ApplicationProcessor.getApplicationStdOut(value, appDepType); String stderr = ApplicationProcessor.getApplicationStdErr(value, appDepType); @@ -93,20 +106,16 @@ public class UASDataStagingProcessor { String stdoutFileName = (stdout == null || stdout.equals("")) ? "stdout" : stdout; String stdoutURI = smsUrl+"#/output/"+stdoutFileName; + JSDLUtils.addDataStagingTargetElement(value, null, stdoutFileName, - stdoutURI); + null); String stderrFileName = (stdout == null || stderr.equals("")) ? "stderr" : stderr; String stderrURI = smsUrl+"#/output/"+stderrFileName; - JSDLUtils.addDataStagingTargetElement(value, null, stderrFileName, - stderrURI); - if(isUnicore) { - String scriptExitCodeFName = "UNICORE_SCRIPT_EXIT_CODE"; - String scriptExitCode = smsUrl+"#/output/"+scriptExitCodeFName; - JSDLUtils.addDataStagingTargetElement(value, null, - scriptExitCodeFName, scriptExitCode.toString()); + JSDLUtils.addDataStagingTargetElement(value, null, stderrFileName, + null); } } @@ -119,7 +128,7 @@ public class UASDataStagingProcessor { String finalSMSPath = smsUrl + "#/output/"+prmValue; - JSDLUtils.addDataStagingTargetElement(value, null, prmValue, finalSMSPath); + JSDLUtils.addDataStagingTargetElement(value, null, prmValue, null); } @@ -159,22 +168,19 @@ public class UASDataStagingProcessor { } } - else if ("String".equals(paramDataType) || "StringArray".equals(paramDataType)) { - return value; - } - else if ("String".equals(paramDataType)) { - String stringPrm = ((StringParameterType) outParam - .getType()).getValue(); - createOutStringElements(value, appDepType, smsUrl, stringPrm); - } - - else if ("StringArray".equals(paramDataType)) { - String[] valueArray = ((StringArrayType) outParam.getType()) - .getValueArray(); - for (String v : valueArray) { - createOutStringElements(value, appDepType, smsUrl, v); - } - } +// else if ("String".equals(paramDataType)) { +// String stringPrm = ((StringParameterType) outParam +// .getType()).getValue(); +// createOutStringElements(value, appDepType, smsUrl, stringPrm); +// } +// +// else if ("StringArray".equals(paramDataType)) { +// String[] valueArray = ((StringArrayType) outParam.getType()) +// .getValueArray(); +// for (String v : valueArray) { +// createOutStringElements(value, appDepType, smsUrl, v); +// } +// } } return value; @@ -212,7 +218,6 @@ public class UASDataStagingProcessor { ApplicationProcessor.addApplicationArgument(value, appDepType, stringPrm); } } - } public static boolean isUnicoreEndpoint(JobExecutionContext context) { http://git-wip-us.apache.org/repos/asf/airavata/blob/febd0c40/modules/registry/airavata-jpa-registry/src/main/java/org/apache/airavata/persistance/registry/jpa/impl/ExperimentRegistry.java ---------------------------------------------------------------------- diff --git a/modules/registry/airavata-jpa-registry/src/main/java/org/apache/airavata/persistance/registry/jpa/impl/ExperimentRegistry.java b/modules/registry/airavata-jpa-registry/src/main/java/org/apache/airavata/persistance/registry/jpa/impl/ExperimentRegistry.java index 03ca6fc..8e9ae58 100644 --- a/modules/registry/airavata-jpa-registry/src/main/java/org/apache/airavata/persistance/registry/jpa/impl/ExperimentRegistry.java +++ b/modules/registry/airavata-jpa-registry/src/main/java/org/apache/airavata/persistance/registry/jpa/impl/ExperimentRegistry.java @@ -93,9 +93,10 @@ public class ExperimentRegistry { List<DataObjectType> experimentOutputs = experiment.getExperimentOutputs(); if (experimentOutputs != null && !experimentOutputs.isEmpty()){ - for (DataObjectType output : experimentOutputs){ - output.setValue(""); - } + //TODO: short change. +// for (DataObjectType output : experimentOutputs){ +// output.setValue(""); +// } addExpOutputs(experimentOutputs, experimentID); }
