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 <[email protected]> Authored: Tue Mar 10 23:28:34 2015 -0400 Committer: raminder <[email protected]> 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);
