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Posted to commits@airavata.apache.org by ra...@apache.org on 2015/03/11 04:28:46 UTC
[1/2] airavata git commit: Fixed AIRAVATA-1596
Repository: airavata
Updated Branches:
refs/heads/master 4000b82c0 -> 10c5abfdb
Fixed AIRAVATA-1596
Project: http://git-wip-us.apache.org/repos/asf/airavata/repo
Commit: http://git-wip-us.apache.org/repos/asf/airavata/commit/b746118e
Tree: http://git-wip-us.apache.org/repos/asf/airavata/tree/b746118e
Diff: http://git-wip-us.apache.org/repos/asf/airavata/diff/b746118e
Branch: refs/heads/master
Commit: b746118e5cc06ac5698c9504f6a4b1c29bc802ca
Parents: 4000b82
Author: raminder <ra...@apache.org>
Authored: Tue Mar 10 23:28:07 2015 -0400
Committer: raminder <ra...@apache.org>
Committed: Tue Mar 10 23:28:07 2015 -0400
----------------------------------------------------------------------
.../tools/RegisterSampleApplications.java | 158 +++++++++++++++++--
1 file changed, 143 insertions(+), 15 deletions(-)
----------------------------------------------------------------------
http://git-wip-us.apache.org/repos/asf/airavata/blob/b746118e/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 55dbcf8..58dafbb 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
@@ -55,6 +55,8 @@ public class RegisterSampleApplications {
private static String trestlesResourceId = "trestles.sdsc.xsede.org_db29986e-5a27-4949-ae7f-04a6012d0d35";
private static String bigredResourceId = "bigred2.uits.iu.edu_3eae6e9d-a1a7-44ec-ac85-3796ef726ef1";
private static String lsfResourceId = "lsf_3eae6e9d-a1a7-44ec-ac85-3796ef726ef1";
+ private static String alamoResourceId;
+
private static String fsdResourceId;
// unicore service endpoint url
@@ -76,7 +78,8 @@ public class RegisterSampleApplications {
private static final String gaussianName = "Gaussian";
private static final String gamessName = "Gamess";
private static final String stressMemName = "StressMem";
-
+ private static final String ultrascanName = "Ultrascan";
+
//Appplication Descriptions
private static final String echoDescription = "A Simple Echo Application";
private static final String amberDescription = "Assisted Model Building with Energy Refinement MD Package";
@@ -92,8 +95,8 @@ public class RegisterSampleApplications {
private static final String monteXDescription = "Grid Chem Tinker Monte Application";
private static final String gaussianDescription = "Grid Chem Gaussian Application";
private static final String gamessDescription = "A Gamess Application";
-
-
+ private static final String ultrascanDescription = "Ultrascan Application";
+
//App Module Id's
private static String echoModuleId;
private static String amberModuleId;
@@ -124,6 +127,8 @@ public class RegisterSampleApplications {
private static String wrfInterfaceId;
private static String phastaInterfaceId;
private static String gamessInterfaceId;
+ private static String ultrascanModuleId;
+ private static String ultrascanInterfaceId;
public RegisterSampleApplications(Airavata.Client airavataClient) {
this.airavataClient = airavataClient;
@@ -209,6 +214,12 @@ public class RegisterSampleApplications {
fsdResourceId = registerUnicoreEndpoint("fsd-cloud15.zam.kfa-juelich.de", "interop host", JobSubmissionProtocol.UNICORE, SecurityProtocol.GSI);
System.out.println("FSd Resource Id: "+fsdResourceId);
+ //Register Alamo
+ alamoResourceId = registerComputeHost("alamo.uthscsa.edu", "Alamo Cluster",
+ ResourceJobManagerType.PBS, "push", "/usr/bin/", SecurityProtocol.SSH_KEYS, 22, "/usr/bin/mpiexec -np");
+ System.out.println("Alamo Cluster " + alamoResourceId);
+
+
} catch (TException e) {
e.printStackTrace();
}
@@ -335,6 +346,11 @@ public class RegisterSampleApplications {
RegisterSampleApplicationsUtils.createApplicationModule(
gamessName, "17May13", gamessDescription));
System.out.println("Gamess Module Id " + gamessModuleId);
+ //Register Ultrascan
+ ultrascanModuleId = airavataClient.registerApplicationModule(DEFAULT_GATEWAY,
+ RegisterSampleApplicationsUtils.createApplicationModule(
+ ultrascanName, "1.0", ultrascanDescription));
+ System.out.println("Ultrascan Module Id " + ultrascanModuleId);
} catch (TException e) {
e.printStackTrace();
@@ -360,6 +376,9 @@ public class RegisterSampleApplications {
registerFSDApps();
registerLSFApps();
+
+ //Registering Alamo Apps
+ registerAlamoApps();
}
@@ -404,6 +423,9 @@ public class RegisterSampleApplications {
registerTinkerMonteInterface();
registerGaussianInterface();
+
+ // Register Ultrascan
+ registerUltrascanInterface();
}
@@ -432,7 +454,10 @@ public class RegisterSampleApplications {
"", DataType.URI, false, true));
applicationOutputs.add(RegisterSampleApplicationsUtils.createAppOutput("f10_file",
"", DataType.URI, false, true));
-
+ applicationOutputs.add(RegisterSampleApplicationsUtils.createAppOutput("STDOUT",
+ "", DataType.STDOUT, false, true));
+ applicationOutputs.add(RegisterSampleApplicationsUtils.createAppOutput("STDERR",
+ "", DataType.STDERR, false, true));
gamessInterfaceId = airavataClient.registerApplicationInterface(DEFAULT_GATEWAY,
RegisterSampleApplicationsUtils.createApplicationInterfaceDescription("gamess", "gamess",
@@ -458,11 +483,14 @@ public class RegisterSampleApplications {
List<InputDataObjectType> applicationInputs = new ArrayList<InputDataObjectType>();
applicationInputs.add(input1);
- OutputDataObjectType output1 = RegisterSampleApplicationsUtils.createAppOutput("echo_output",
- "", DataType.STRING, false, false);
+ OutputDataObjectType output1 = RegisterSampleApplicationsUtils.createAppOutput("STDOUT",
+ "", DataType.STDOUT, false, false);
+ OutputDataObjectType output2 = RegisterSampleApplicationsUtils.createAppOutput("STDERR",
+ "", DataType.STDERR, false, false);
List<OutputDataObjectType> applicationOutputs = new ArrayList<OutputDataObjectType>();
applicationOutputs.add(output1);
+ applicationOutputs.add(output2);
echoLocalInterfaceId = airavataClient.registerApplicationInterface(DEFAULT_GATEWAY,
RegisterSampleApplicationsUtils.createApplicationInterfaceDescription(echoName, echoDescription,
@@ -531,11 +559,14 @@ public class RegisterSampleApplications {
List<InputDataObjectType> applicationInputs = new ArrayList<InputDataObjectType>();
applicationInputs.add(input1);
- OutputDataObjectType output1 = RegisterSampleApplicationsUtils.createAppOutput("Sample_Output",
- "", DataType.STRING, false, false);
+ OutputDataObjectType output1 = RegisterSampleApplicationsUtils.createAppOutput("STDOutput",
+ "", DataType.STDOUT, true, true);
+ OutputDataObjectType output2 = RegisterSampleApplicationsUtils.createAppOutput("STDErr",
+ "", DataType.STDERR, true, true);
List<OutputDataObjectType> applicationOutputs = new ArrayList<OutputDataObjectType>();
applicationOutputs.add(output1);
+ applicationOutputs.add(output2);
mpiInterfaceId = airavataClient.registerApplicationInterface(DEFAULT_GATEWAY,
@@ -609,17 +640,19 @@ public class RegisterSampleApplications {
InputDataObjectType input3 = RegisterSampleApplicationsUtils.createAppInput("Parameter_Topology_File", null,
DataType.URI, null, 3,true, true, false, "Parameter and Topology coordinates", null);
-
+
List<InputDataObjectType> applicationInputs = new ArrayList<InputDataObjectType>();
applicationInputs.add(input1);
applicationInputs.add(input2);
applicationInputs.add(input3);
- OutputDataObjectType output1 = RegisterSampleApplicationsUtils.createAppOutput("Echoed_Output",
- "", DataType.STRING, true, true);
+ OutputDataObjectType output1 = RegisterSampleApplicationsUtils.createAppOutput("STDOUT",null,DataType.STDOUT, true, true);
+ OutputDataObjectType output2 = RegisterSampleApplicationsUtils.createAppOutput("STDERR",null,DataType.STDERR, true, true);
+
List<OutputDataObjectType> applicationOutputs = new ArrayList<OutputDataObjectType>();
applicationOutputs.add(output1);
+ applicationOutputs.add(output2);
autoDockInterfaceId = airavataClient.registerApplicationInterface(DEFAULT_GATEWAY,
RegisterSampleApplicationsUtils.createApplicationInterfaceDescription(autoDockName, autoDockDescription,
@@ -723,9 +756,14 @@ public class RegisterSampleApplications {
applicationInputs.add(input1);
OutputDataObjectType output1 = RegisterSampleApplicationsUtils.createAppOutput("LAMMPS_Simulation_Log",null,DataType.URI, true, true);
-
+ OutputDataObjectType output2 = RegisterSampleApplicationsUtils.createAppOutput("STDOUT",null,DataType.STDOUT, true, true);
+ OutputDataObjectType output3 = RegisterSampleApplicationsUtils.createAppOutput("STDERR",null,DataType.STDERR, true, true);
+
+
List<OutputDataObjectType> applicationOutputs = new ArrayList<OutputDataObjectType>();
applicationOutputs.add(output1);
+ applicationOutputs.add(output2);
+ applicationOutputs.add(output3);
lammpsInterfaceId = airavataClient.registerApplicationInterface(DEFAULT_GATEWAY,
RegisterSampleApplicationsUtils.createApplicationInterfaceDescription(lammpsName, lammpsDescription,
@@ -752,9 +790,14 @@ public class RegisterSampleApplications {
OutputDataObjectType output1 = RegisterSampleApplicationsUtils.createAppOutput("NWChem_Execution_Log",
null, DataType.URI, true, false);
+ OutputDataObjectType output2 = RegisterSampleApplicationsUtils.createAppOutput("STDOUT",null,DataType.STDOUT, true, true);
+ OutputDataObjectType output3 = RegisterSampleApplicationsUtils.createAppOutput("STDERR",null,DataType.STDERR, true, true);
+
List<OutputDataObjectType> applicationOutputs = new ArrayList<OutputDataObjectType>();
applicationOutputs.add(output1);
+ applicationOutputs.add(output2);
+ applicationOutputs.add(output3);
nwChemInterfaceId = airavataClient.registerApplicationInterface(DEFAULT_GATEWAY,
RegisterSampleApplicationsUtils.createApplicationInterfaceDescription(nwChemName, nwChemDescription,
@@ -786,10 +829,14 @@ public class RegisterSampleApplications {
OutputDataObjectType output1 = RegisterSampleApplicationsUtils.createAppOutput("Trinity_Execution_Log",null,DataType.URI, true, true);
OutputDataObjectType output2 = RegisterSampleApplicationsUtils.createAppOutput("Trinity_FASTA_File",null,DataType.URI, true, true);
+ OutputDataObjectType output3 = RegisterSampleApplicationsUtils.createAppOutput("STDOUT",null,DataType.STDOUT, true, true);
+ OutputDataObjectType output4 = RegisterSampleApplicationsUtils.createAppOutput("STDERR",null,DataType.STDERR, true, true);
List<OutputDataObjectType> applicationOutputs = new ArrayList<OutputDataObjectType>();
applicationOutputs.add(output1);
applicationOutputs.add(output2);
+ applicationOutputs.add(output3);
+ applicationOutputs.add(output4);
trinityInterfaceId = airavataClient.registerApplicationInterface(DEFAULT_GATEWAY,
RegisterSampleApplicationsUtils.createApplicationInterfaceDescription(trinityName, trinityDescription,
@@ -828,11 +875,16 @@ public class RegisterSampleApplications {
OutputDataObjectType output2 = RegisterSampleApplicationsUtils.createAppOutput("WRF_Execution_Log",
"", DataType.URI, true, true);
+ OutputDataObjectType output3 = RegisterSampleApplicationsUtils.createAppOutput("STDOUT",null,DataType.STDOUT, true, true);
+ OutputDataObjectType output4 = RegisterSampleApplicationsUtils.createAppOutput("STDERR",null,DataType.STDERR, true, true);
+
List<OutputDataObjectType> applicationOutputs = new ArrayList<OutputDataObjectType>();
applicationOutputs.add(output1);
applicationOutputs.add(output2);
-
+ applicationOutputs.add(output3);
+ applicationOutputs.add(output4);
+
wrfInterfaceId = airavataClient.registerApplicationInterface(DEFAULT_GATEWAY,
RegisterSampleApplicationsUtils.createApplicationInterfaceDescription(wrfName, wrfDescription,
appModules, applicationInputs, applicationOutputs));
@@ -866,12 +918,18 @@ public class RegisterSampleApplications {
OutputDataObjectType output1 = RegisterSampleApplicationsUtils.createAppOutput("PHASTA_Execution_Log",null,DataType.URI, true, true);
OutputDataObjectType output2 = RegisterSampleApplicationsUtils.createAppOutput("PHASTA_Output_tar",null,DataType.URI, true, true);
+ OutputDataObjectType output3 = RegisterSampleApplicationsUtils.createAppOutput("STDOUT",null,DataType.STDOUT, true, true);
+ OutputDataObjectType output4 = RegisterSampleApplicationsUtils.createAppOutput("STDERR",null,DataType.STDERR, true, true);
+
List<OutputDataObjectType> applicationOutputs = new ArrayList<OutputDataObjectType>();
applicationOutputs.add(output1);
applicationOutputs.add(output2);
+ applicationOutputs.add(output3);
+ applicationOutputs.add(output4);
- amberInterfaceId = airavataClient.registerApplicationInterface(DEFAULT_GATEWAY,
+
+ phastaInterfaceId = airavataClient.registerApplicationInterface(DEFAULT_GATEWAY,
RegisterSampleApplicationsUtils.createApplicationInterfaceDescription(phastaName, phastaDescription,
appModules, applicationInputs, applicationOutputs));
System.out.println("phasta Application Interface Id " + phastaInterfaceId);
@@ -911,10 +969,15 @@ public class RegisterSampleApplications {
OutputDataObjectType output1 = RegisterSampleApplicationsUtils.createAppOutput("gaussian.out",
"", DataType.URI, true, true );
+ OutputDataObjectType output2 = RegisterSampleApplicationsUtils.createAppOutput("STDOUT",null,DataType.STDOUT, true, true);
+ OutputDataObjectType output3 = RegisterSampleApplicationsUtils.createAppOutput("STDERR",null,DataType.STDERR, true, true);
+
List<OutputDataObjectType> applicationOutputs = new ArrayList<OutputDataObjectType>();
applicationOutputs.add(output1);
-
+ applicationOutputs.add(output2);
+ applicationOutputs.add(output3);
+
String addApplicationInterfaceId = airavataClient.registerApplicationInterface(DEFAULT_GATEWAY,
RegisterSampleApplicationsUtils.createApplicationInterfaceDescription("Gaussian", "Gaussian application",
appModules, applicationInputs, applicationOutputs));
@@ -958,9 +1021,14 @@ public class RegisterSampleApplications {
OutputDataObjectType output1 = RegisterSampleApplicationsUtils.createAppOutput("Diskoutputfile_with_dir",
"", DataType.URI, false, false);
+ OutputDataObjectType output2 = RegisterSampleApplicationsUtils.createAppOutput("STDOUT",null,DataType.STDOUT, true, true);
+ OutputDataObjectType output3 = RegisterSampleApplicationsUtils.createAppOutput("STDERR",null,DataType.STDERR, true, true);
+
List<OutputDataObjectType> applicationOutputs = new ArrayList<OutputDataObjectType>();
applicationOutputs.add(output1);
+ applicationOutputs.add(output2);
+ applicationOutputs.add(output3);
String addApplicationInterfaceId = airavataClient.registerApplicationInterface(DEFAULT_GATEWAY,
RegisterSampleApplicationsUtils.createApplicationInterfaceDescription("Tinker_Monte", "Monte application",
@@ -1254,6 +1322,9 @@ public class RegisterSampleApplications {
ComputeResourcePreference fsdResourcePreferences = RegisterSampleApplicationsUtils.
createComputeResourcePreference(fsdResourceId, null, false, null, JobSubmissionProtocol.UNICORE, DataMovementProtocol.UNICORE_STORAGE_SERVICE,null);
+ ComputeResourcePreference alamoResourcePreferences = RegisterSampleApplicationsUtils.
+ createComputeResourcePreference(alamoResourceId, null, false, null, JobSubmissionProtocol.SSH, DataMovementProtocol.SCP,"/home/us3/work/uslims3_cauma3-03896");
+
GatewayResourceProfile gatewayResourceProfile = new GatewayResourceProfile();
gatewayResourceProfile.setGatewayID(DEFAULT_GATEWAY);
gatewayResourceProfile.addToComputeResourcePreferences(stampedeResourcePreferences);
@@ -1298,5 +1369,62 @@ public class RegisterSampleApplications {
e.printStackTrace();
}
}
+ public void registerAlamoApps() {
+ try {
+ System.out.println("#### Registering Application Deployments on Alamo #### \n");
+
+ //Register Ultrascan on Alamo
+ List<String> ultrascanMouldes = new ArrayList<String>();
+ ultrascanMouldes.add("module load intel/2015/64");
+ ultrascanMouldes.add("module load openmpi/intel/1.8.4");
+ ultrascanMouldes.add("module load qt4/4.8.6");
+ ultrascanMouldes.add("module load ultrascan3/3.3");
+
+ String ultrascanAppDeployId = airavataClient.registerApplicationDeployment(DEFAULT_GATEWAY,
+ RegisterSampleApplicationsUtils.createApplicationDeployment(ultrascanModuleId, alamoResourceId,
+ "/home/us3/bin/us_mpi_analysis", ApplicationParallelismType.OPENMP, ultrascanDescription, ultrascanMouldes , null, null));
+ System.out.println("Ultrascan on alamo deployment Id " + ultrascanAppDeployId);
+
+ } catch (TException e) {
+ e.printStackTrace();
+ }
+ }
+
+ private void registerUltrascanInterface() {
+ try {
+ System.out.println("#### Registering Ultrascan Application Interface ####");
+
+ List<String> appModules = new ArrayList<String>();
+ appModules.add(ultrascanModuleId);
+
+ InputDataObjectType input1 = RegisterSampleApplicationsUtils.createAppInput("input", null,
+ DataType.URI, null, 1, true, true, false, "input file", null);
+
+ List<InputDataObjectType> applicationInputs = new ArrayList<InputDataObjectType>();
+ applicationInputs.add(input1);
+
+ OutputDataObjectType output1 = RegisterSampleApplicationsUtils.createAppOutput("output/analysis-results.tar",
+ "", DataType.URI, true, true );
+
+ OutputDataObjectType output2 = RegisterSampleApplicationsUtils.createAppOutput("STDOUT",
+ "", DataType.STDOUT, true, true );
+
+ OutputDataObjectType output3 = RegisterSampleApplicationsUtils.createAppOutput("STDERR",
+ "", DataType.STDERR, true, true );
+
+ List<OutputDataObjectType> applicationOutputs = new ArrayList<OutputDataObjectType>();
+ applicationOutputs.add(output1);
+ applicationOutputs.add(output2);
+ applicationOutputs.add(output3);
+
+ String ultrascanInterfaceId = airavataClient.registerApplicationInterface(DEFAULT_GATEWAY,
+ RegisterSampleApplicationsUtils.createApplicationInterfaceDescription("Ultrascan", "Ultrascan application",
+ appModules, applicationInputs, applicationOutputs));
+ System.out.println("Ultrascan Application Interface Id " + ultrascanInterfaceId);
+
+ } catch (TException e) {
+ e.printStackTrace();
+ }
+ }
}
[2/2] airavata git commit: Fixed AIRAVATA-1597
Posted by ra...@apache.org.
Fixed AIRAVATA-1597
Project: http://git-wip-us.apache.org/repos/asf/airavata/repo
Commit: http://git-wip-us.apache.org/repos/asf/airavata/commit/10c5abfd
Tree: http://git-wip-us.apache.org/repos/asf/airavata/tree/10c5abfd
Diff: http://git-wip-us.apache.org/repos/asf/airavata/diff/10c5abfd
Branch: refs/heads/master
Commit: 10c5abfdb478c57ba77e0dacdc1b02bec5ff8ed6
Parents: b746118
Author: raminder <ra...@apache.org>
Authored: Tue Mar 10 23:28:34 2015 -0400
Committer: raminder <ra...@apache.org>
Committed: Tue Mar 10 23:28:34 2015 -0400
----------------------------------------------------------------------
.../client/samples/CreateLaunchExperiment.java | 569 +++++--------------
1 file changed, 146 insertions(+), 423 deletions(-)
----------------------------------------------------------------------
http://git-wip-us.apache.org/repos/asf/airavata/blob/10c5abfd/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 6110f53..bb914fa 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
@@ -293,36 +293,18 @@ public class CreateLaunchExperiment {
public static String createEchoExperimentForFSD(Airavata.Client client) throws TException {
try {
- List<InputDataObjectType> exInputs = new ArrayList<InputDataObjectType>();
- InputDataObjectType input = new InputDataObjectType();
- input.setName("Input_to_Echo");
- input.setType(DataType.STRING);
- input.setValue("Hello World");
-
-
- InputDataObjectType i2 = new InputDataObjectType();
- i2.setName("Input_to_Echo2");
- i2.setType(DataType.URI);
- i2.setValue("http://www.textfiles.com/100/ad.txt");
-
- InputDataObjectType i3 = new InputDataObjectType();
- i3.setName("Input_to_Echo3");
- i3.setType(DataType.URI);
- i3.setValue("file:///tmp/test.txt");
-
- exInputs.add(input);
- exInputs.add(i2);
- exInputs.add(i3);
+ List<InputDataObjectType> exInputs = client.getApplicationInputs(echoAppId);
+ for (InputDataObjectType inputDataObjectType : exInputs) {
+ if (inputDataObjectType.getName().equalsIgnoreCase("Input_to_Echo")) {
+ inputDataObjectType.setValue("Hello World");
+ }else if (inputDataObjectType.getName().equalsIgnoreCase("Input_to_Echo2")) {
+ inputDataObjectType.setValue("http://www.textfiles.com/100/ad.txt");
+ }else if (inputDataObjectType.getName().equalsIgnoreCase("Input_to_Echo3")) {
+ inputDataObjectType.setValue("file:///tmp/test.txt");
+ }
+ }
+ List<OutputDataObjectType> exOut = client.getApplicationOutputs(echoAppId);
- List<OutputDataObjectType> exOut = new ArrayList<OutputDataObjectType>();
-
- OutputDataObjectType output = new OutputDataObjectType();
- output.setName("Echoed_Output");
- output.setType(DataType.STRING);
- output.setValue("test.txt");
- exOut.add(output);
-
-
Experiment simpleExperiment =
ExperimentModelUtil.createSimpleExperiment("default", "admin", "echoExperiment", "SimpleEcho2", echoAppId, exInputs);
simpleExperiment.setExperimentOutputs(exOut);
@@ -369,24 +351,18 @@ public class CreateLaunchExperiment {
public static String createMPIExperimentForFSD(Airavata.Client client) throws TException {
try {
-
- List<InputDataObjectType> exInputs = new ArrayList<InputDataObjectType>();
- InputDataObjectType input = new InputDataObjectType();
- input.setName("Sample_Input");
- input.setType(DataType.STRING);
- input.setValue("");
- exInputs.add(input);
-
- List<OutputDataObjectType> exOut = new ArrayList<OutputDataObjectType>();
- OutputDataObjectType output = new OutputDataObjectType();
- output.setName("Sample_Output");
- output.setType(DataType.STRING);
- output.setValue("");
- exOut.add(output);
-
+ List<InputDataObjectType> exInputs = client.getApplicationInputs(mpiAppId);
+ for (InputDataObjectType inputDataObjectType : exInputs) {
+ if (inputDataObjectType.getName().equalsIgnoreCase("Sample_Input")) {
+ inputDataObjectType.setValue("");
+ }
+ }
+ List<OutputDataObjectType> exOut = client.getApplicationOutputs(mpiAppId);
+
+
Experiment simpleExperiment =
ExperimentModelUtil.createSimpleExperiment("default", "admin", "mpiExperiment", "HelloMPI", mpiAppId, null);
-// simpleExperiment.setExperimentOutputs(exOut);
+ simpleExperiment.setExperimentOutputs(exOut);
@@ -432,43 +408,10 @@ public class CreateLaunchExperiment {
public static String createExperimentWRFStampede(Airavata.Client client) throws TException {
try {
- List<InputDataObjectType> exInputs = new ArrayList<InputDataObjectType>();
- InputDataObjectType input = new InputDataObjectType();
- input.setName("Config_Namelist_File");
- input.setType(DataType.URI);
- input.setValue("/Users/shameera/Downloads/PHP-Gateway-Scripts/appScripts/WRF_FILES/namelist.input");
-
- InputDataObjectType input1 = new InputDataObjectType();
- input1.setName("WRF_Initial_Conditions");
- input1.setType(DataType.URI);
- input1.setValue("/Users/shameera/Downloads/PHP-Gateway-Scripts/appScripts/WRF_FILES/wrfinput_d01");
-
- InputDataObjectType input2 = new InputDataObjectType();
- input2.setName("WRF_Boundary_File");
- input2.setType(DataType.URI);
- input2.setValue("/Users/shameera/Downloads/PHP-Gateway-Scripts/appScripts/WRF_FILES/wrfbdy_d01");
-
- exInputs.add(input);
- exInputs.add(input1);
- exInputs.add(input2);
-
-
- List<OutputDataObjectType> exOut = new ArrayList<OutputDataObjectType>();
- OutputDataObjectType output = new OutputDataObjectType();
- output.setName("WRF_Output");
- output.setType(DataType.URI);
- output.setValue("");
-
- OutputDataObjectType output1 = new OutputDataObjectType();
- output1.setName("WRF_Execution_Log");
- output1.setType(DataType.URI);
- output1.setValue("");
-
-
- exOut.add(output);
- exOut.add(output1);
-
-
+ List<InputDataObjectType> exInputs = client.getApplicationInputs(wrfAppId);
+ setWRFInputs(exInputs);
+ List<OutputDataObjectType> exOut = client.getApplicationOutputs(wrfAppId);
+
Experiment simpleExperiment =
ExperimentModelUtil.createSimpleExperiment("default", "admin", "WRFExperiment", "Testing", wrfAppId, exInputs);
simpleExperiment.setExperimentOutputs(exOut);
@@ -505,57 +448,26 @@ public class CreateLaunchExperiment {
}
- public static String createExperimentGROMACSStampede(Airavata.Client client) throws TException {
- try {
- List<InputDataObjectType> exInputs = new ArrayList<InputDataObjectType>();
- InputDataObjectType input = new InputDataObjectType();
- input.setName("GROMOS_Coordinate_File");
- input.setType(DataType.URI);
- input.setValue("/Users/shameera/Downloads/PHP-Gateway-Scripts/appScripts/GROMMACS_FILES/pdb1y6l-EM-vacuum.gro");
-
- InputDataObjectType input1 = new InputDataObjectType();
- input1.setName("Portable_Input_Binary_File");
- input1.setType(DataType.URI);
- input1.setValue("/Users/shameera/Downloads/PHP-Gateway-Scripts/appScripts/GROMMACS_FILES/pdb1y6l-EM-vacuum.tpr");
-
- exInputs.add(input);
- exInputs.add(input1);
-
-
- List<OutputDataObjectType> exOut = new ArrayList<OutputDataObjectType>();
- OutputDataObjectType output = new OutputDataObjectType();
- output.setName("pdb1y6l-EM-vacuum.tpr.trr");
- output.setType(DataType.URI);
- output.setValue("");
-
- OutputDataObjectType output1 = new OutputDataObjectType();
- output1.setName("pdb1y6l-EM-vacuum.tpr.edr");
- output1.setType(DataType.URI);
- output1.setValue("");
-
- OutputDataObjectType output2 = new OutputDataObjectType();
- output2.setName("pdb1y6l-EM-vacuum.tpr.log");
- output2.setType(DataType.URI);
- output2.setValue("");
-
- OutputDataObjectType output3 = new OutputDataObjectType();
- output3.setName("pdb1y6l-EM-vacuum.gro");
- output3.setType(DataType.URI);
- output3.setValue("");
-
- OutputDataObjectType output4 = new OutputDataObjectType();
- output4.setName("GROMACS.oJobID");
- output4.setType(DataType.URI);
- output4.setValue("");
-
-
- exOut.add(output);
- exOut.add(output1);
- exOut.add(output2);
- exOut.add(output3);
- exOut.add(output4);
+ private static void setWRFInputs(List<InputDataObjectType> exInputs) {
+ for (InputDataObjectType inputDataObjectType : exInputs) {
+ if (inputDataObjectType.getName().equalsIgnoreCase("Config_Namelist_File")) {
+ inputDataObjectType.setValue("/Users/shameera/Downloads/PHP-Gateway-Scripts/appScripts/WRF_FILES/namelist.input");
+ }else if (inputDataObjectType.getName().equalsIgnoreCase("WRF_Initial_Conditions")) {
+ inputDataObjectType.setValue("/Users/shameera/Downloads/PHP-Gateway-Scripts/appScripts/WRF_FILES/wrfinput_d01");
+ }else if (inputDataObjectType.getName().equalsIgnoreCase("WRF_Boundary_File")) {
+ inputDataObjectType.setValue("/Users/shameera/Downloads/PHP-Gateway-Scripts/appScripts/WRF_FILES/wrfbdy_d01");
+ }
+ }
+ }
+ public static String createExperimentGROMACSStampede(Airavata.Client client) throws TException {
+ try {
+
+ List<InputDataObjectType> exInputs = client.getApplicationInputs(gromacsAppId);
+ setGROMACSInputs(exInputs);
+ List<OutputDataObjectType> exOut = client.getApplicationOutputs(gromacsAppId);
+
Experiment simpleExperiment =
ExperimentModelUtil.createSimpleExperiment("default", "admin", "GromacsExperiment", "Testing", gromacsAppId, exInputs);
simpleExperiment.setExperimentOutputs(exOut);
@@ -591,69 +503,21 @@ public class CreateLaunchExperiment {
return null;
}
+ private static void setGROMACSInputs(List<InputDataObjectType> exInputs) {
+ for (InputDataObjectType inputDataObjectType : exInputs) {
+ if (inputDataObjectType.getName().equalsIgnoreCase("GROMOS_Coordinate_File")) {
+ inputDataObjectType.setValue("/Users/shameera/Downloads/PHP-Gateway-Scripts/appScripts/GROMMACS_FILES/pdb1y6l-EM-vacuum.gro");
+ }else if (inputDataObjectType.getName().equalsIgnoreCase("Portable_Input_Binary_File")) {
+ inputDataObjectType.setValue("/Users/shameera/Downloads/PHP-Gateway-Scripts/appScripts/GROMMACS_FILES/pdb1y6l-EM-vacuum.tpr");
+ }
+ }
+ }
public static String createExperimentESPRESSOStampede(Airavata.Client client) throws TException {
try {
- List<InputDataObjectType> exInputs = new ArrayList<InputDataObjectType>();
- InputDataObjectType input = new InputDataObjectType();
- input.setName("AI_Pseudopotential_File");
- input.setType(DataType.URI);
- input.setValue("/Users/shameera/Downloads/PHP-Gateway-Scripts/appScripts/ESPRESSO_FILES/Al.sample.in");
-
- InputDataObjectType input1 = new InputDataObjectType();
- input1.setName("AI_Primitive_Cell");
- input1.setType(DataType.URI);
- input1.setValue("/Users/shameera/Downloads/PHP-Gateway-Scripts/appScripts/ESPRESSO_FILES/Al.pz-vbc.UPF");
-
- exInputs.add(input);
- exInputs.add(input1);
-
-
- List<OutputDataObjectType> exOut = new ArrayList<OutputDataObjectType>();
- OutputDataObjectType output = new OutputDataObjectType();
- output.setName("ESPRESSO_Execution_Log");
- output.setType(DataType.URI);
- output.setValue("");
-
- OutputDataObjectType output1 = new OutputDataObjectType();
- output1.setName("ESPRESSO_WFC_Binary_file");
- output1.setType(DataType.URI);
- output1.setValue("");
-
- OutputDataObjectType output2 = new OutputDataObjectType();
- output2.setName("Al_exc3.wfc1");
- output2.setType(DataType.URI);
- output2.setValue("");
-
- OutputDataObjectType output3 = new OutputDataObjectType();
- output3.setName("Al_exc3.wfc2");
- output3.setType(DataType.URI);
- output3.setValue("");
-
- OutputDataObjectType output4 = new OutputDataObjectType();
- output4.setName("Al_exc3.wfc3");
- output4.setType(DataType.URI);
- output4.setValue("");
-
- OutputDataObjectType output5 = new OutputDataObjectType();
- output5.setName("Al_exc3.wfc4");
- output5.setType(DataType.URI);
- output5.setValue("");
-
- OutputDataObjectType output6 = new OutputDataObjectType();
- output6.setName("ESPRESSO.oJobID");
- output6.setType(DataType.URI);
- output6.setValue("");
-
-
- exOut.add(output);
- exOut.add(output1);
- exOut.add(output2);
- exOut.add(output3);
- exOut.add(output4);
- exOut.add(output5);
- exOut.add(output6);
-
-
+ List<InputDataObjectType> exInputs = client.getApplicationInputs(espressoAppId);
+ setESPRESSOInputs(exInputs);
+ List<OutputDataObjectType> exOut = client.getApplicationOutputs(espressoAppId);
+
Experiment simpleExperiment =
ExperimentModelUtil.createSimpleExperiment("default", "admin", "EspressoExperiment", "Testing", espressoAppId, exInputs);
simpleExperiment.setExperimentOutputs(exOut);
@@ -688,45 +552,22 @@ public class CreateLaunchExperiment {
}
return null;
}
+ private static void setESPRESSOInputs(List<InputDataObjectType> exInputs) {
+ for (InputDataObjectType inputDataObjectType : exInputs) {
+ if (inputDataObjectType.getName().equalsIgnoreCase("AI_Pseudopotential_File")) {
+ inputDataObjectType.setValue("/Users/shameera/Downloads/PHP-Gateway-Scripts/appScripts/ESPRESSO_FILES/Al.sample.in");
+ }else if (inputDataObjectType.getName().equalsIgnoreCase("AI_Primitive_Cell")) {
+ inputDataObjectType.setValue("/Users/shameera/Downloads/PHP-Gateway-Scripts/appScripts/ESPRESSO_FILES/Al.pz-vbc.UPF");
+ }
+ }
+}
public static String createExperimentTRINITYStampede(Airavata.Client client) throws TException {
try {
- List<InputDataObjectType> exInputs = new ArrayList<InputDataObjectType>();
- InputDataObjectType input = new InputDataObjectType();
- input.setName("RNA_Seq_Left_Input");
- input.setType(DataType.URI);
- input.setValue("/Users/shameera/Downloads/PHP-Gateway-Scripts/appScripts/TRINITY_FILES/reads.left.fq");
-
- InputDataObjectType input1 = new InputDataObjectType();
- input1.setName("RNA_Seq_Right_Input");
- input1.setType(DataType.URI);
- input1.setValue("/Users/shameera/Downloads/PHP-Gateway-Scripts/appScripts/TRINITY_FILES/reads.right.fq");
-
- exInputs.add(input);
- exInputs.add(input1);
-
-
- List<OutputDataObjectType> exOut = new ArrayList<OutputDataObjectType>();
- OutputDataObjectType output = new OutputDataObjectType();
- output.setName("Trinity_Execution_Log");
- output.setType(DataType.URI);
- output.setValue("");
-
- OutputDataObjectType output1 = new OutputDataObjectType();
- output1.setName("Trinity_FASTA_File");
- output1.setType(DataType.URI);
- output1.setValue("");
-
- OutputDataObjectType output2 = new OutputDataObjectType();
- output2.setName("Trinity.oJobID");
- output2.setType(DataType.URI);
- output2.setValue("");
-
-
- exOut.add(output);
- exOut.add(output1);
- exOut.add(output2);
-
+ List<InputDataObjectType> exInputs = client.getApplicationInputs(trinityAppId);
+ setTRINITYInputs(exInputs);
+ List<OutputDataObjectType> exOut = client.getApplicationOutputs(trinityAppId);
+
Experiment simpleExperiment =
ExperimentModelUtil.createSimpleExperiment("default", "admin", "TrinityExperiment", "Testing", trinityAppId, exInputs);
simpleExperiment.setExperimentOutputs(exOut);
@@ -761,31 +602,21 @@ public class CreateLaunchExperiment {
}
return null;
}
-
+ private static void setTRINITYInputs(List<InputDataObjectType> exInputs) {
+ for (InputDataObjectType inputDataObjectType : exInputs) {
+ if (inputDataObjectType.getName().equalsIgnoreCase("RNA_Seq_Left_Input")) {
+ inputDataObjectType.setValue("/Users/shameera/Downloads/PHP-Gateway-Scripts/appScripts/TRINITY_FILES/reads.left.fq");
+ }else if (inputDataObjectType.getName().equalsIgnoreCase("RNA_Seq_Right_Input")) {
+ inputDataObjectType.setValue("/Users/shameera/Downloads/PHP-Gateway-Scripts/appScripts/TRINITY_FILES/reads.right.fq");
+ }
+ }
+ }
public static String createExperimentLAMMPSStampede(Airavata.Client client) throws TException {
try {
- List<InputDataObjectType> exInputs = new ArrayList<InputDataObjectType>();
- InputDataObjectType input = new InputDataObjectType();
- input.setName("Friction_Simulation_Input");
- input.setType(DataType.URI);
- input.setValue("/Users/shameera/Downloads/PHP-Gateway-Scripts/appScripts/LAMMPS_FILES/in.friction");
-
- exInputs.add(input);
-
- List<OutputDataObjectType> exOut = new ArrayList<OutputDataObjectType>();
- OutputDataObjectType output = new OutputDataObjectType();
- output.setName("LAMMPS_Simulation_Log");
- output.setType(DataType.URI);
- output.setValue("");
-
- OutputDataObjectType output1 = new OutputDataObjectType();
- output1.setName("LAMMPS.oJobID");
- output1.setType(DataType.URI);
- output1.setValue("");
-
- exOut.add(output);
- exOut.add(output1);
-
+ List<InputDataObjectType> exInputs = client.getApplicationInputs(lammpsAppId);
+ setLAMMPSInputs(exInputs);
+ List<OutputDataObjectType> exOut = client.getApplicationOutputs(lammpsAppId);
+
Experiment simpleExperiment =
ExperimentModelUtil.createSimpleExperiment("default", "admin", "LAMMPSExperiment", "Testing", lammpsAppId, exInputs);
simpleExperiment.setExperimentOutputs(exOut);
@@ -820,24 +651,18 @@ public class CreateLaunchExperiment {
}
return null;
}
-
+ private static void setLAMMPSInputs(List<InputDataObjectType> exInputs) {
+ for (InputDataObjectType inputDataObjectType : exInputs) {
+ if (inputDataObjectType.getName().equalsIgnoreCase("Friction_Simulation_Input")) {
+ inputDataObjectType.setValue("/Users/shameera/Downloads/PHP-Gateway-Scripts/appScripts/LAMMPS_FILES/in.friction");
+ }
+ }
+ }
public static String createExperimentNWCHEMStampede(Airavata.Client client) throws TException {
try {
- List<InputDataObjectType> exInputs = new ArrayList<InputDataObjectType>();
- InputDataObjectType input = new InputDataObjectType();
- input.setName("Water_Molecule_Input");
- input.setType(DataType.URI);
- input.setValue("/Users/shameera/Downloads/PHP-Gateway-Scripts/appScripts/NWCHEM_FILES/water.nw");
-
- exInputs.add(input);
-
- List<OutputDataObjectType> exOut = new ArrayList<OutputDataObjectType>();
- OutputDataObjectType output = new OutputDataObjectType();
- output.setName("NWChem_Execution_Log");
- output.setType(DataType.URI);
- output.setValue("");
-
- exOut.add(output);
+ List<InputDataObjectType> exInputs = client.getApplicationInputs(nwchemAppId);
+ setNWCHEMInputs(exInputs);
+ List<OutputDataObjectType> exOut = client.getApplicationOutputs(nwchemAppId);
Experiment simpleExperiment =
ExperimentModelUtil.createSimpleExperiment("default", "admin", "NWchemExperiment", "Testing", nwchemAppId, exInputs);
@@ -873,96 +698,18 @@ public class CreateLaunchExperiment {
}
return null;
}
+ private static void setNWCHEMInputs(List<InputDataObjectType> exInputs) {
+ for (InputDataObjectType inputDataObjectType : exInputs) {
+ if (inputDataObjectType.getName().equalsIgnoreCase("Water_Molecule_Input")) {
+ inputDataObjectType.setValue("/Users/shameera/Downloads/PHP-Gateway-Scripts/appScripts/NWCHEM_FILES/water.nw");
+ }
+ }
+ }
public static String createExperimentAUTODOCKStampede(Airavata.Client client) throws TException {
try {
- List<InputDataObjectType> exInputs = new ArrayList<InputDataObjectType>();
- InputDataObjectType input = new InputDataObjectType();
- input.setName("AD4_parameters.dat");
- input.setType(DataType.URI);
- input.setValue("/Users/shameera/Downloads/PHP-Gateway-Scripts/appScripts/AUTODOCK_FILES/AD4_parameters.dat");
-
- InputDataObjectType input1 = new InputDataObjectType();
- input1.setName("hsg1.A.map");
- input1.setType(DataType.URI);
- input1.setValue("/Users/shameera/Downloads/PHP-Gateway-Scripts/appScripts/AUTODOCK_FILES/hsg1.A.map");
-
- InputDataObjectType input2 = new InputDataObjectType();
- input2.setName("hsg1.C.map");
- input2.setType(DataType.URI);
- input2.setValue("/Users/shameera/Downloads/PHP-Gateway-Scripts/appScripts/AUTODOCK_FILES/hsg1.C.map");
-
- InputDataObjectType input3 = new InputDataObjectType();
- input3.setName("hsg1.d.map");
- input3.setType(DataType.URI);
- input3.setValue("/Users/shameera/Downloads/PHP-Gateway-Scripts/appScripts/AUTODOCK_FILES/hsg1.d.map");
-
- InputDataObjectType input4 = new InputDataObjectType();
- input4.setName("hsg1.e.map");
- input4.setType(DataType.URI);
- input4.setValue("/Users/shameera/Downloads/PHP-Gateway-Scripts/appScripts/AUTODOCK_FILES/hsg1.e.map");
-
- InputDataObjectType input5 = new InputDataObjectType();
- input5.setName("hsg1.HD.map");
- input5.setType(DataType.URI);
- input5.setValue("/Users/shameera/Downloads/PHP-Gateway-Scripts/appScripts/AUTODOCK_FILES/hsg1.HD.map");
-
- InputDataObjectType input6 = new InputDataObjectType();
- input6.setName("hsg1.maps.fld");
- input6.setType(DataType.URI);
- input6.setValue("/Users/shameera/Downloads/PHP-Gateway-Scripts/appScripts/AUTODOCK_FILES/hsg1.maps.fld");
-
- InputDataObjectType input7 = new InputDataObjectType();
- input7.setName("hsg1.NA.map");
- input7.setType(DataType.URI);
- input7.setValue("/Users/shameera/Downloads/PHP-Gateway-Scripts/appScripts/AUTODOCK_FILES/hsg1.NA.map");
-
- InputDataObjectType input8 = new InputDataObjectType();
- input8.setName("hsg1.N.map");
- input8.setType(DataType.URI);
- input8.setValue("/Users/shameera/Downloads/PHP-Gateway-Scripts/appScripts/AUTODOCK_FILES/hsg1.N.map");
-
- InputDataObjectType input9 = new InputDataObjectType();
- input9.setName("hsg1.OA.map");
- input9.setType(DataType.URI);
- input9.setValue("/Users/shameera/Downloads/PHP-Gateway-Scripts/appScripts/AUTODOCK_FILES/hsg1.OA.map");
-
- InputDataObjectType input10 = new InputDataObjectType();
- input10.setName("ind.dpf");
- input10.setType(DataType.URI);
- input10.setValue("/Users/shameera/Downloads/PHP-Gateway-Scripts/appScripts/AUTODOCK_FILES/ind.dpf");
-
- InputDataObjectType input11 = new InputDataObjectType();
- input11.setName("ind.pdbqt");
- input11.setType(DataType.URI);
- input11.setValue("/Users/shameera/Downloads/PHP-Gateway-Scripts/appScripts/AUTODOCK_FILES/ind.pdbqt");
-
-
- exInputs.add(input);
- exInputs.add(input1);
- exInputs.add(input2);
- exInputs.add(input3);
- exInputs.add(input4);
- exInputs.add(input5);
- exInputs.add(input6);
- exInputs.add(input7);
- exInputs.add(input8);
- exInputs.add(input9);
- exInputs.add(input10);
- exInputs.add(input11);
-
- List<OutputDataObjectType> exOut = new ArrayList<OutputDataObjectType>();
- OutputDataObjectType output = new OutputDataObjectType();
- output.setName("ind.dlg");
- output.setType(DataType.URI);
- output.setValue("");
-
- OutputDataObjectType output1 = new OutputDataObjectType();
- output1.setName("Autodock.oJobID");
- output1.setType(DataType.URI);
- output1.setValue("");
-
- exOut.add(output);
- exOut.add(output1);
+ List<InputDataObjectType> exInputs = client.getApplicationInputs(nwchemAppId);
+ setAUTODOCKInputs(exInputs);
+ List<OutputDataObjectType> exOut = client.getApplicationOutputs(nwchemAppId);
Experiment simpleExperiment =
ExperimentModelUtil.createSimpleExperiment("default", "admin", "AutoDockExperiment", "Testing", autodockAppId, exInputs);
@@ -998,47 +745,43 @@ public class CreateLaunchExperiment {
}
return null;
}
-
+ private static void setAUTODOCKInputs(List<InputDataObjectType> exInputs) {
+
+ for (InputDataObjectType inputDataObjectType : exInputs) {
+ if (inputDataObjectType.getName().equalsIgnoreCase("AD4_parameters.dat")) {
+ inputDataObjectType.setValue("/Users/shameera/Downloads/PHP-Gateway-Scripts/appScripts/AUTODOCK_FILES/AD4_parameters.dat");
+ } else if (inputDataObjectType.getName().equalsIgnoreCase("hsg1.A.map")) {
+ inputDataObjectType.setValue("/Users/shameera/Downloads/PHP-Gateway-Scripts/appScripts/AUTODOCK_FILES/hsg1.A.map");
+ } else if (inputDataObjectType.getName().equalsIgnoreCase("hsg1.C.map")) {
+ inputDataObjectType.setValue("/Users/shameera/Downloads/PHP-Gateway-Scripts/appScripts/AUTODOCK_FILES/hsg1.C.map");
+ } else if (inputDataObjectType.getName().equalsIgnoreCase("hsg1.d.map")) {
+ inputDataObjectType.setValue("/Users/shameera/Downloads/PHP-Gateway-Scripts/appScripts/AUTODOCK_FILES/hsg1.d.map");
+ } else if (inputDataObjectType.getName().equalsIgnoreCase("hsg1.e.map")) {
+ inputDataObjectType.setValue("/Users/shameera/Downloads/PHP-Gateway-Scripts/appScripts/AUTODOCK_FILES/hsg1.e.map");
+ } else if (inputDataObjectType.getName().equalsIgnoreCase("hsg1.HD.map")) {
+ inputDataObjectType.setValue("/Users/shameera/Downloads/PHP-Gateway-Scripts/appScripts/AUTODOCK_FILES/hsg1.HD.map");
+ } else if (inputDataObjectType.getName().equalsIgnoreCase("hsg1.maps.fld")) {
+ inputDataObjectType.setValue("/Users/shameera/Downloads/PHP-Gateway-Scripts/appScripts/AUTODOCK_FILES/hsg1.maps.fld");
+ } else if (inputDataObjectType.getName().equalsIgnoreCase("hsg1.NA.map")) {
+ inputDataObjectType.setValue("/Users/shameera/Downloads/PHP-Gateway-Scripts/appScripts/AUTODOCK_FILES/hsg1.NA.map");
+ } else if (inputDataObjectType.getName().equalsIgnoreCase("hsg1.N.map")) {
+ inputDataObjectType.setValue("/Users/shameera/Downloads/PHP-Gateway-Scripts/appScripts/AUTODOCK_FILES/hsg1.N.map");
+ } else if (inputDataObjectType.getName().equalsIgnoreCase("hsg1.OA.map")) {
+ inputDataObjectType.setValue("/Users/shameera/Downloads/PHP-Gateway-Scripts/appScripts/AUTODOCK_FILES/hsg1.OA.map");
+ } else if (inputDataObjectType.getName().equalsIgnoreCase("ind.dpf")) {
+ inputDataObjectType.setValue("/Users/shameera/Downloads/PHP-Gateway-Scripts/appScripts/AUTODOCK_FILES/ind.dpf");
+ } else if (inputDataObjectType.getName().equalsIgnoreCase("ind.pdbqt")) {
+ inputDataObjectType.setValue("/Users/shameera/Downloads/PHP-Gateway-Scripts/appScripts/AUTODOCK_FILES/ind.pdbqt");
+ }
+ }
+ }
public static String createExperimentWRFTrestles(Airavata.Client client) throws TException {
try {
- List<InputDataObjectType> exInputs = new ArrayList<InputDataObjectType>();
- InputDataObjectType input = new InputDataObjectType();
- input.setName("WRF_Namelist");
- input.setType(DataType.URI);
- input.setValue("/Users/shameera/Downloads/PHP-Gateway-Scripts/appScripts/WRF_FILES/namelist.input");
-
- InputDataObjectType input1 = new InputDataObjectType();
- input1.setName("WRF_Input_File");
- input1.setType(DataType.URI);
- input1.setValue("/Users/shameera/Downloads/PHP-Gateway-Scripts/appScripts/WRF_FILES/wrfinput_d01");
-
- InputDataObjectType input2 = new InputDataObjectType();
- input2.setName("WRF_Boundary_File");
- input2.setType(DataType.URI);
- input2.setValue("/Users/shameera/Downloads/PHP-Gateway-Scripts/appScripts/WRF_FILES/wrfbdy_d01");
-
- exInputs.add(input);
- exInputs.add(input1);
- exInputs.add(input2);
-
-
- List<OutputDataObjectType> exOut = new ArrayList<OutputDataObjectType>();
- OutputDataObjectType output = new OutputDataObjectType();
- output.setName("WRF_Output");
- output.setType(DataType.URI);
- output.setValue("");
-
- OutputDataObjectType output1 = new OutputDataObjectType();
- output1.setName("WRF_Execution_Log");
- output1.setType(DataType.URI);
- output1.setValue("");
-
-
- exOut.add(output);
- exOut.add(output1);
-
-
- Experiment simpleExperiment =
+ List<InputDataObjectType> exInputs = client.getApplicationInputs(wrfAppId);
+ setWRFInputs(exInputs);
+ List<OutputDataObjectType> exOut = client.getApplicationOutputs(wrfAppId);
+
+ Experiment simpleExperiment =
ExperimentModelUtil.createSimpleExperiment("default", "admin", "WRFExperiment", "Testing", wrfAppId, exInputs);
simpleExperiment.setExperimentOutputs(exOut);
@@ -1315,19 +1058,14 @@ public class CreateLaunchExperiment {
public static String createExperimentForBR2(Airavata.Client client) throws TException {
try {
- List<InputDataObjectType> exInputs = new ArrayList<InputDataObjectType>();
- InputDataObjectType input = new InputDataObjectType();
- input.setName("Input_to_Echo");
- input.setType(DataType.STRING);
- input.setValue("Echoed_Output=Hello World");
- exInputs.add(input);
+ List<InputDataObjectType> exInputs = client.getApplicationInputs(echoAppId);
+ for (InputDataObjectType inputDataObjectType : exInputs) {
+ if (inputDataObjectType.getName().equalsIgnoreCase("Input_to_Echo")) {
+ inputDataObjectType.setValue("Hello World");
+ }
+ }
+ List<OutputDataObjectType> exOut = client.getApplicationOutputs(echoAppId);
- List<OutputDataObjectType> exOut = new ArrayList<OutputDataObjectType>();
- OutputDataObjectType output = new OutputDataObjectType();
- output.setName("Echoed_Output");
- output.setType(DataType.STRING);
- output.setValue("");
- exOut.add(output);
Project project = ProjectModelUtil.createProject("default", "lahiru", "test project");
String projectId = client.createProject(DEFAULT_GATEWAY, project);
@@ -1374,24 +1112,9 @@ public class CreateLaunchExperiment {
for (InputDataObjectType inputDataObjectType : exInputs) {
inputDataObjectType.setValue("Hello World");
}
- /*List<InputDataObjectType> exInputs = new ArrayList<InputDataObjectType>();
- InputDataObjectType input = new InputDataObjectType();
- input.setName("Input_to_Echo");
- input.setType(DataType.STRING);
- input.setValue("Echoed_Output=Hello World");
- input.setRequiredToAddedToCommandLine(true);
- exInputs.add(input);*/
-
+
List<OutputDataObjectType> exOut = client.getApplicationOutputs(echoAppId);
- /*
- List<OutputDataObjectType> exOut = new ArrayList<OutputDataObjectType>();
- OutputDataObjectType output = new OutputDataObjectType();
- output.setName("output_file");
- output.setType(DataType.URI);
- output.setValue("");
-
- exOut.add(output);*/
-
+
Project project = ProjectModelUtil.createProject("default", "lg11w", "test project");
String projectId = client.createProject(DEFAULT_GATEWAY, project);