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From sma...@apache.org
Subject [1/2] git commit: Updating Identifiers
Date Sun, 13 Jul 2014 13:59:44 GMT
Repository: airavata
Updated Branches:
  refs/heads/master b0618e404 -> 1a223e8c0


Updating Identifiers


Project: http://git-wip-us.apache.org/repos/asf/airavata/repo
Commit: http://git-wip-us.apache.org/repos/asf/airavata/commit/d83a8441
Tree: http://git-wip-us.apache.org/repos/asf/airavata/tree/d83a8441
Diff: http://git-wip-us.apache.org/repos/asf/airavata/diff/d83a8441

Branch: refs/heads/master
Commit: d83a84416e6785a00cfa558ffa7aad87192ab88b
Parents: 16d2d38
Author: Suresh Marru <smarru@apache.org>
Authored: Sun Jul 13 09:59:29 2014 -0400
Committer: Suresh Marru <smarru@apache.org>
Committed: Sun Jul 13 09:59:29 2014 -0400

----------------------------------------------------------------------
 .../resources/conf/app-catalog-identifiers.ini  | 26 ++++----
 .../tools/RegisterSampleApplications.java       | 70 ++++++++++----------
 2 files changed, 48 insertions(+), 48 deletions(-)
----------------------------------------------------------------------


http://git-wip-us.apache.org/repos/asf/airavata/blob/d83a8441/airavata-api/airavata-client-sdks/airavata-php-sdk/src/main/resources/conf/app-catalog-identifiers.ini
----------------------------------------------------------------------
diff --git a/airavata-api/airavata-client-sdks/airavata-php-sdk/src/main/resources/conf/app-catalog-identifiers.ini
b/airavata-api/airavata-client-sdks/airavata-php-sdk/src/main/resources/conf/app-catalog-identifiers.ini
index 3b3cb85..672a566 100644
--- a/airavata-api/airavata-client-sdks/airavata-php-sdk/src/main/resources/conf/app-catalog-identifiers.ini
+++ b/airavata-api/airavata-client-sdks/airavata-php-sdk/src/main/resources/conf/app-catalog-identifiers.ini
@@ -1,14 +1,14 @@
 #Apache Airavata Gateway to Airavata Deployment Identifiers
-#Sat Jul 12 18:13:37 EDT 2014
-espressoInterfaceId=ESPRESSO_a9c3acd6-4403-445b-b555-d4dbcc53afdb
-amberInterfaceId=Amber_26a8a2eb-a5a1-460f-a9c3-9bc5899433b3
-gromacsInterfaceId=GROMACS_c720c8f6-8b70-40be-b228-5f9ea72869f9
-trinityInterfaceId=Trinity_6068b270-157e-4ea0-9ec8-b2757b33a147
-stampedeResourceId=stampede.tacc.xsede.org_3da3cb46-851e-4124-a7bd-37449ca057a8
-bigredResourceId=bigred2.uits.iu.edu_fa40aa10-3703-48c6-a14c-c186d772cd58
-trestlesResourceId=trestles.sdsc.xsede.org_30fb9af6-7cd3-4373-87e4-9987e43cc904
-wrfInterfaceId=WRF_c3c67d74-5e60-4ec6-b50d-9a5d61843296
-autoDockInterfaceId=AutoDock_22c4cbbf-7785-4f96-85c6-8fe8404df6c8
-nwChemInterfaceId=NWChem_574c944e-b376-4e83-9871-96e4c9559a89
-lammpsInterfaceId=LAMMPS_752f3ea6-4ae5-4636-9dba-a6efeb1c4da9
-echoInterfaceId=Echo_c024a9c1-29b2-444d-b523-0729c6679ebb
+#Sun Jul 13 09:56:36 EDT 2014
+espressoInterfaceId=ESPRESSO_e13adcc6-5e6f-4660-a206-8ff0dada929f
+amberInterfaceId=Amber_7a99cdde-5cc1-423a-8ec9-47eddc809a9a
+gromacsInterfaceId=GROMACS_91ce8f05-c895-486e-8fc1-c1480d642754
+trinityInterfaceId=Trinity_9ae8f626-f263-44e1-8106-f18101337aa0
+stampedeResourceId=stampede.tacc.xsede.org_0a91c584-6814-48db-a7e2-723596a66d9f
+bigredResourceId=bigred2.uits.iu.edu_815a893b-d0a9-4798-a35f-27ea185a49fb
+trestlesResourceId=trestles.sdsc.xsede.org_b39751f9-1d02-4123-a797-41cfc2f050ad
+wrfInterfaceId=WRF_2957c31f-bd36-430a-8403-97f87f34958f
+autoDockInterfaceId=
+nwChemInterfaceId=NWChem_3aa63bba-d86d-4c4b-b3d6-588da6519752
+lammpsInterfaceId=LAMMPS_0646b241-2a94-4de7-8518-1fbfd01b1c83
+echoInterfaceId=Echo_c6e6aaac-7d9d-44fc-aba2-63b5100528e8

http://git-wip-us.apache.org/repos/asf/airavata/blob/d83a8441/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 ddc4848..781c216 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
@@ -86,10 +86,10 @@ public class RegisterSampleApplications {
     private static String echoModuleId;
     private static String amberModuleId;
     private static String autoDockModuleId;
-    private static String espressoModuleId;
+    private static String espressoModuleId = "ESPRESSO_54dc94da-5e2b-4add-b054-41ad88891fdc";
     private static String gromacsModuleId = "GROMACS_417271fd-7ac1-4f40-b2a5-ed0908a743eb";
     private static String lammpsModuleId;
-    private static String nwChemModuleId;
+    private static String nwChemModuleId = "NWChem_edbc318d-4c41-46a7-b216-32bad71eabdd";
     private static String trinityModuleId = "Trinity_8af45ca0-b628-4614-9087-c7b73f5f2fb6";
     private static String wrfModuleId;
 
@@ -245,7 +245,7 @@ public class RegisterSampleApplications {
         registerAmberInterface();
 
         //Registering AutoDock
-        registerAutoDockInterface();
+//        registerAutoDockInterface();
 
         //Registering Espresso
         registerEspressoInterface();
@@ -304,13 +304,13 @@ public class RegisterSampleApplications {
             appModules.add(amberModuleId);
 
             InputDataObjectType input1 = RegisterSampleApplicationsUtils.createAppInput("Heat_Restart_File",
null,
-                    DataType.URI, null, false, "Heating up the system equilibration stage",
null);
+                    DataType.URI, null, false, "Heating up the system equilibration stage
- 02_Heat.rst", null);
 
             InputDataObjectType input2 = RegisterSampleApplicationsUtils.createAppInput("Production_Control_File",
null,
-                    DataType.URI, null, false, "Constant pressure and temperature for production
stage", null);
+                    DataType.URI, null, false, "Constant pressure and temperature for production
stage - 03_Prod.in", null);
 
             InputDataObjectType input3 = RegisterSampleApplicationsUtils.createAppInput("Parameter_Topology_File",
null,
-                    DataType.URI, null, false, "Parameter and Topology coordinates", null);
+                    DataType.URI, null, false, "Parameter and Topology coordinates - prmtop",
null);
 
             List<InputDataObjectType> applicationInputs = new ArrayList<InputDataObjectType>();
             applicationInputs.add(input1);
@@ -383,20 +383,21 @@ public class RegisterSampleApplications {
             appModules.add(espressoModuleId);
 
             InputDataObjectType input1 = RegisterSampleApplicationsUtils.createAppInput("AI_Primitive_Cell",
null,
-                    DataType.URI, null, false, "AI_Metal_Input_File", null);
+                    DataType.URI, null, false, "AI_Metal_Input_File - Al.sample.in", null);
 
             InputDataObjectType input2 = RegisterSampleApplicationsUtils.createAppInput("AI_Pseudopotential_File",
null,
-                    DataType.URI, null, false, "Constant pressure and temperature for production
stage", null);
+                    DataType.URI, null, false, "Constant pressure and temperature for production
stage - Al.pz-vbc.UPF", null);
 
             List<InputDataObjectType> applicationInputs = new ArrayList<InputDataObjectType>();
             applicationInputs.add(input1);
             applicationInputs.add(input2);
 
-            OutputDataObjectType output1 = RegisterSampleApplicationsUtils.createAppOutput("Echoed_Output",
-                    "", DataType.STRING);
+            OutputDataObjectType output1 = RegisterSampleApplicationsUtils.createAppOutput("ESPRESSO_Execution_Log",null,DataType.URI);
+            OutputDataObjectType output2 = RegisterSampleApplicationsUtils.createAppOutput("ESPRESSO_WFC_Binary_file",null,DataType.URI);
 
             List<OutputDataObjectType> applicationOutputs = new ArrayList<OutputDataObjectType>();
             applicationOutputs.add(output1);
+            applicationOutputs.add(output2);
 
             espressoInterfaceId = airavataClient.registerApplicationInterface(
                     RegisterSampleApplicationsUtils.createApplicationInterfaceDescription(espressoName,
espressoDescription,
@@ -416,10 +417,10 @@ public class RegisterSampleApplications {
             appModules.add(gromacsModuleId);
 
             InputDataObjectType input1 = RegisterSampleApplicationsUtils.createAppInput("Portable_Input_Binary_File",
null,
-                    DataType.URI, null, false, "Coordinates velocities, molecular topology
and simulation parameters", null);
+                    DataType.URI, null, false, "Coordinates velocities, molecular topology
and simulation parameters - pdb1y6l-EM-vacuum.tpr", null);
 
             InputDataObjectType input2 = RegisterSampleApplicationsUtils.createAppInput("GROMOS_Coordinate_File",
null,
-                    DataType.URI, null, false, "Trajectory Coordinates Molecular Structure
in Gromos87 format", null);
+                    DataType.URI, null, false, "Trajectory Coordinates Molecular Structure
in Gromos87 format - pdb1y6l-EM-vacuum.gro", null);
 
             List<InputDataObjectType> applicationInputs = new ArrayList<InputDataObjectType>();
             applicationInputs.add(input1);
@@ -452,7 +453,7 @@ public class RegisterSampleApplications {
             appModules.add(lammpsModuleId);
 
             InputDataObjectType input1 = RegisterSampleApplicationsUtils.createAppInput("Friction_Simulation_Input",
null,
-                    DataType.URI, null, false, "Friction Simulation Input", null);
+                    DataType.URI, null, false, "Friction Simulation Input - in.friction",
null);
 
             List<InputDataObjectType> applicationInputs = new ArrayList<InputDataObjectType>();
             applicationInputs.add(input1);
@@ -480,13 +481,12 @@ public class RegisterSampleApplications {
             appModules.add(nwChemModuleId);
 
             InputDataObjectType input1 = RegisterSampleApplicationsUtils.createAppInput("Water_Molecule_Input",
null,
-                    DataType.URI, null, false, "Water Molecule Input File", null);
+                    DataType.URI, null, false, "Water Molecule Input File - water.nw", null);
 
             List<InputDataObjectType> applicationInputs = new ArrayList<InputDataObjectType>();
             applicationInputs.add(input1);
 
-            OutputDataObjectType output1 = RegisterSampleApplicationsUtils.createAppOutput("Echoed_Output",
-                    "", DataType.STRING);
+            OutputDataObjectType output1 = RegisterSampleApplicationsUtils.createAppOutput("NWChem_Execution_Log",null,DataType.URI);
 
             List<OutputDataObjectType> applicationOutputs = new ArrayList<OutputDataObjectType>();
             applicationOutputs.add(output1);
@@ -510,10 +510,10 @@ public class RegisterSampleApplications {
             appModules.add(trinityModuleId);
 
             InputDataObjectType input1 = RegisterSampleApplicationsUtils.createAppInput("RNA_Seq_Left_Input",
null,
-                    DataType.URI, null, false, "RNA-Seq Left Library", null);
+                    DataType.URI, null, false, "RNA-Seq Left Library - reads.left.fq", null);
 
             InputDataObjectType input2 = RegisterSampleApplicationsUtils.createAppInput("RNA_Seq_Right_Input",
null,
-                    DataType.URI, null, false, "RNA-Seq Right Library", null);
+                    DataType.URI, null, false, "RNA-Seq Right Library - reads.right.fq",
null);
 
             List<InputDataObjectType> applicationInputs = new ArrayList<InputDataObjectType>();
             applicationInputs.add(input1);
@@ -545,13 +545,13 @@ public class RegisterSampleApplications {
             appModules.add(wrfModuleId);
 
             InputDataObjectType input1 = RegisterSampleApplicationsUtils.createAppInput("Config_Namelist_File",
null,
-                    DataType.URI, null, false, "Namelist Configuration File", null);
+                    DataType.URI, null, false, "Namelist Configuration File - namelist.input",
null);
 
             InputDataObjectType input2 = RegisterSampleApplicationsUtils.createAppInput("WRF_Initial_Conditions",
null,
-                    DataType.URI, null, false, "Initial Conditions File", null);
+                    DataType.URI, null, false, "Initial Conditions File - wrfinput_d01",
null);
 
             InputDataObjectType input3 = RegisterSampleApplicationsUtils.createAppInput("WRF_Boundary_File",
null,
-                    DataType.URI, null, false, "Boundary Conditions File", null);
+                    DataType.URI, null, false, "Boundary Conditions File - wrfbdy_d01", null);
 
             List<InputDataObjectType> applicationInputs = new ArrayList<InputDataObjectType>();
             applicationInputs.add(input1);
@@ -697,24 +697,24 @@ public class RegisterSampleApplications {
 
             //Register AutoDock
             String autoDockDeployId = airavataClient.registerApplicationDeployment(
-                    RegisterSampleApplicationsUtils.createApplicationDeployment(nwChemModuleId,
bigredResourceId,
+                    RegisterSampleApplicationsUtils.createApplicationDeployment(autoDockModuleId,
bigredResourceId,
                             "/N/u/cgateway/BigRed2/production/app_wrappers/auto_dock_wrapper.sh",
ApplicationParallelismType.MPI,
                             autoDockDescription));
             System.out.println("AutoDock on bigredII deployment Id " + autoDockDeployId);
 
-            //Register GROMACS
-            String gromacsAppDeployId = airavataClient.registerApplicationDeployment(
-                    RegisterSampleApplicationsUtils.createApplicationDeployment(gromacsModuleId,
bigredResourceId,
-                            "/N/u/cgateway/BigRed2/production/app_wrappers/gromacs_wrapper.sh",
ApplicationParallelismType.MPI,
-                            gromacsDescription));
-            System.out.println("GROMACS on bigredII deployment Id " + gromacsAppDeployId);
-
-            //Register LAMMPS
-            String lammpsAppDeployId = airavataClient.registerApplicationDeployment(
-                    RegisterSampleApplicationsUtils.createApplicationDeployment(lammpsModuleId,
bigredResourceId,
-                            "/N/u/cgateway/BigRed2/production/app_wrappers/lammps_wrapper.sh",
ApplicationParallelismType.MPI,
-                            lammpsDescription));
-            System.out.println("LAMMPS on bigredII deployment Id " + lammpsAppDeployId);
+//            //Register GROMACS
+//            String gromacsAppDeployId = airavataClient.registerApplicationDeployment(
+//                    RegisterSampleApplicationsUtils.createApplicationDeployment(gromacsModuleId,
bigredResourceId,
+//                            "/N/u/cgateway/BigRed2/production/app_wrappers/gromacs_wrapper.sh",
ApplicationParallelismType.MPI,
+//                            gromacsDescription));
+//            System.out.println("GROMACS on bigredII deployment Id " + gromacsAppDeployId);
+//
+//            //Register LAMMPS
+//            String lammpsAppDeployId = airavataClient.registerApplicationDeployment(
+//                    RegisterSampleApplicationsUtils.createApplicationDeployment(lammpsModuleId,
bigredResourceId,
+//                            "/N/u/cgateway/BigRed2/production/app_wrappers/lammps_wrapper.sh",
ApplicationParallelismType.MPI,
+//                            lammpsDescription));
+//            System.out.println("LAMMPS on bigredII deployment Id " + lammpsAppDeployId);
 
         } catch (TException e) {
             e.printStackTrace();


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