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Posted to commits@airavata.apache.org by ra...@apache.org on 2015/03/11 04:28:47 UTC
[2/2] airavata git commit: Fixed AIRAVATA-1597
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);