Package org.apache.airavata.commons.gfac.type

Examples of org.apache.airavata.commons.gfac.type.ActualParameter

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    public static Map<String, ActualParameter> fillOutputFromStdout(Map<String, Object> output, String stdout, String stderr) throws Exception {

        Map<String, ActualParameter> result = new HashMap<String, ActualParameter>();
        Set<String> keys = output.keySet();
        for (String paramName : keys) {
          ActualParameter actual = (ActualParameter) output.get(paramName);
            // if parameter value is not already set, we let it go
           
            if (actual == null) {
                continue;
            }
            if ("StdOut".equals(actual.getType().getType().toString())) {
                ((StdOutParameterType) actual.getType()).setValue(stdout);
                result.put(paramName, actual);
            } else if ("StdErr".equals(actual.getType().getType().toString())) {
                ((StdErrParameterType) actual.getType()).setValue(stderr);
                result.put(paramName, actual);
            } else {
              if ("URI".equals(actual.getType().getType().toString()) &&  !((URIParameterType) actual.getType()).getValue().isEmpty()){
                continue;
              }
                String parseStdout = parseStdout(stdout, paramName);
                if (parseStdout != null) {
                    MappingFactory.fromString(actual, parseStdout);
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          MessageContext inputNew = new MessageContext();
          try {
              MessageContext input = jobExecutionContext.getInMessageContext();
              Set<String> parameters = input.getParameters().keySet();
              for (String paramName : parameters) {
                  ActualParameter actualParameter = (ActualParameter) input.getParameters().get(paramName);
                  String paramValue = MappingFactory.toString(actualParameter);
                  //TODO: Review this with type
                  if ("URI".equals(actualParameter.getType().getType().toString())) {
                      ((URIParameterType) actualParameter.getType()).setValue(stageInputFiles(jobExecutionContext, paramValue));
                  } else if ("URIArray".equals(actualParameter.getType().getType().toString())) {
                      List<String> split = Arrays.asList(StringUtil.getElementsFromString(paramValue));
                      List<String> newFiles = new ArrayList<String>();
                      for (String paramValueEach : split) {
                          newFiles.add(stageInputFiles(jobExecutionContext, paramValueEach));
                      }
                      ((URIArrayType) actualParameter.getType()).setValueArray(newFiles.toArray(new String[newFiles.size()]));
                  }
                  inputNew.getParameters().put(paramName, actualParameter);
              }
          } catch (Exception e) {
              log.error(e.getMessage());
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                    Map<String, Object> output = jobExecutionContext.getOutMessageContext().getParameters();
                    Set<String> keys = output.keySet();
                    for (String paramName : keys) {
                        ActualParameter actualParameter = (ActualParameter) output.get(paramName);
                        if ("URIArray".equals(actualParameter.getType().getType().toString())) {
                            URI outputURI = GFacUtils.createGsiftpURI(endpoint, app.getOutputDataDirectory());
                            List<String> outputList = ftp.listDir(outputURI, gssCred);
                            String[] valueList = outputList.toArray(new String[outputList.size()]);
                            ((URIArrayType) actualParameter.getType()).setValueArray(valueList);
                            // why to instantiate new instance?
//                            stringMap = new HashMap<String, ActualParameter>();
                            stringMap.put(paramName, actualParameter);
                        }else if ("StringArray".equals(actualParameter.getType().getType().toString())) {
                            String[] valueList = OutputUtils.parseStdoutArray(stdout, paramName);
                            ((StringArrayType) actualParameter.getType()).setValueArray(valueList);
//                            stringMap = new HashMap<String, ActualParameter>();
                            stringMap.put(paramName, actualParameter);
                        } else if ("URI".equals(actualParameter.getType().getType().toString())) {
                            URI outputURI = GFacUtils.createGsiftpURI(endpoint, app.getOutputDataDirectory());
                              List<String> outputList = ftp.listDir(outputURI, gssCred);
              if (outputList.size() == 0 || outputList.get(0).isEmpty()) {
                stringMap = OutputUtils.fillOutputFromStdout(output, stdout, stderr);
              } else {
                String valueList = outputList.get(0);
                ((URIParameterType) actualParameter.getType()).setValue(valueList);
                stringMap = new HashMap<String, ActualParameter>();
                stringMap.put(paramName, actualParameter);
              }
                        }
                        else {
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        MessageContext outputNew = new MessageContext();
        MessageContext output = jobExecutionContext.getOutMessageContext();
        Map<String, Object> parameters = output.getParameters();
        for (String paramName : parameters.keySet()) {
            ActualParameter actualParameter = (ActualParameter) parameters
                    .get(paramName);

            GridFtp ftp = new GridFtp();
            GSSCredential gssCred = ((GSISecurityContext)jobExecutionContext.getSecurityContext(GSISecurityContext.GSI_SECURITY_CONTEXT)).getGssCredentials();
            try {
                if ("URI".equals(actualParameter.getType().getType().toString())) {
                    for (String endpoint : gridFTPEndpointArray) {
                        ((URIParameterType) actualParameter.getType()).setValue(doStaging(outputFileStagingPath,
                                MappingFactory.toString(actualParameter), ftp, gssCred, endpoint));
                    }
                } else if ("URIArray".equals(actualParameter.getType().getType().toString())) {
                    List<String> split = Arrays.asList(StringUtil.getElementsFromString(MappingFactory.toString(actualParameter)));
                    List<String> newFiles = new ArrayList<String>();
                    for (String endpoint : gridFTPEndpointArray) {
                        for (String paramValueEach : split) {
                            newFiles.add(doStaging(outputFileStagingPath, paramValueEach, ftp, gssCred, endpoint));
                        }
                        ((URIArrayType) actualParameter.getType()).setValueArray(newFiles.toArray(new String[newFiles.size()]));
                    }

                }
            } catch (URISyntaxException e) {
                log.error(e.getMessage());
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            // if parameter value is not already set, we let it go
            if (outMessage.getValue(parameterName) == null) {
                continue;
            }

            ActualParameter actual = outMessage.getValue(parameterName);

            if ("StdOut".equals(actual.getType().getType().toString())){
              ((StdOutParameterType)actual.getType()).setValue(stdout);
              result.put(parameterName, actual);
            }else if ("StdErr".equals(actual.getType().getType().toString())){
        ((StdErrParameterType)actual.getType()).setValue(stderr);
        result.put(parameterName, actual);
      }
            else{
              String parseStdout = parseStdout(stdout, parameterName);
              if(parseStdout != null){
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      /*
       * Input
       */
      ParameterContextImpl input = new ParameterContextImpl();
      ActualParameter echo_input = new ActualParameter();
      ((StringParameterType)echo_input.getType()).setValue("echo_output=hello");
      input.add("echo_input", echo_input);

      /*
       * Output
       */
      ParameterContextImpl output = new ParameterContextImpl();
      ActualParameter echo_output = new ActualParameter();
      output.add("echo_output", echo_output);

      // parameter
      ct.setInput(input);
      ct.setOutput(output);
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                    String stderr = ftp.readRemoteFile(stderrURI, gssCred, localStdErrFile);
                    Map<String,ActualParameter> stringMap = null;
                    MessageContext<Object> output = invocationContext.getOutput();
                    for (Iterator<String> iterator = output.getNames(); iterator.hasNext(); ) {
                        String paramName = iterator.next();
                        ActualParameter actualParameter = (ActualParameter) output.getValue(paramName);
            if ("URIArray".equals(actualParameter.getType().getType().toString())) {
              URI outputURI = GfacUtils.createGsiftpURI(endpoint,app.getOutputDataDirectory());
              List<String> outputList = ftp.listDir(outputURI,gssCred);
              String[] valueList = outputList.toArray(new String[outputList.size()]);
              ((URIArrayType) actualParameter.getType()).setValueArray(valueList);
              stringMap = new HashMap<String, ActualParameter>();
              stringMap.put(paramName, actualParameter);
              invocationContext.getExecutionContext().getNotifier().output(invocationContext, actualParameter.toString());
            }
                      else{
                      // This is to handle exception during the output parsing.
                        stringMap = OutputUtils.fillOutputFromStdout(invocationContext.<ActualParameter>getOutput(), stdout,stderr);
                        String paramValue = output.getStringValue(paramName);
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        try {
    MessageContext<Object> input = invocationContext.getInput();
        for (Iterator<String> iterator = input.getNames(); iterator.hasNext();) {
      String paramName = iterator.next();
      String paramValue = input.getStringValue(paramName);
      ActualParameter actualParameter = (ActualParameter) input
          .getValue(paramName);
      //TODO: Review this with type
      if ("URI".equals(actualParameter.getType().getType().toString())) {
                        ((URIParameterType) actualParameter.getType()).setValue(stageInputFiles(invocationContext, paramValue, actualParameter));
            }else if("URIArray".equals(actualParameter.getType().getType().toString())){
                List<String> split = Arrays.asList(paramValue.split(","));
                List<String> newFiles = new ArrayList<String>();
                    for (String paramValueEach : split) {
                        newFiles.add(stageInputFiles(invocationContext, paramValueEach, actualParameter));
                    }
                ((URIArrayType) actualParameter.getType()).setValueArray(newFiles.toArray(new String[newFiles.size()]));
            }
      inputNew.add(paramName, actualParameter);
    }
        }catch (Exception e){
//           invocationContext.getExecutionContext().getNotifier().executionFail(invocationContext,e,"Error during Input File staging");
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        MessageContext<ActualParameter> outputNew = new ParameterContextImpl();
        MessageContext<Object> input = invocationContext.getOutput();
        for (Iterator<String> iterator = input.getNames(); iterator.hasNext(); ) {
            String paramName = iterator.next();
            String paramValue = input.getStringValue(paramName);
            ActualParameter actualParameter = (ActualParameter) input
                    .getValue(paramName);
            //TODO: Review this with type
            GlobusHostType host = (GlobusHostType) invocationContext.getExecutionDescription().getHost().getType();
            GridFtp ftp = new GridFtp();
            gssContext = (GSISecurityContext) invocationContext.getSecurityContext(MYPROXY_SECURITY_CONTEXT);
            GSSCredential gssCred = null;
            try {
                gssCred = gssContext.getGssCredentails();
            } catch (SecurityException e) {
                e.printStackTrace();  //To change body of catch statement use File | Settings | File Templates.
            }
            try {
                if ("URI".equals(actualParameter.getType().getType().toString())) {
                    for (String endpoint : host.getGridFTPEndPointArray()) {
                        ((URIParameterType) actualParameter.getType()).setValue(doStaging(outputFileStagingPath,
                                paramValue, actualParameter, ftp, gssCred, endpoint));
                    }
                } else if ("URIArray".equals(actualParameter.getType().getType().toString())) {
                    List<String> split = Arrays.asList(paramValue.split(","));
                    List<String> newFiles = new ArrayList<String>();
                    for (String endpoint : host.getGridFTPEndPointArray()) {
                        for (String paramValueEach : split) {
                            newFiles.add(doStaging(outputFileStagingPath, paramValueEach, actualParameter, ftp, gssCred, endpoint));
                        }
                        ((URIArrayType) actualParameter.getType()).setValueArray(newFiles.toArray(new String[newFiles.size()]));
                    }

                }
            } catch (URISyntaxException e) {
                throw new ProviderException(e.getMessage(), e, invocationContext);
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        ParameterContextImpl outputParam = new ParameterContextImpl();


        // List<Parameter> outputs = serviceDescription.getOutputParameters();
        for (OutputParameterType parameter : serviceDescriptionType.getOutputParametersArray()) {
            ActualParameter actualParameter = new ActualParameter();
            if ("String".equals(parameter.getParameterType().getName())) {
                actualParameter.getType().changeType(StringParameterType.type);
            } else if ("Double".equals(parameter.getParameterType().getName())) {
                actualParameter.getType().changeType(DoubleParameterType.type);
            } else if ("Integer".equals(parameter.getParameterType().getName())) {
                actualParameter.getType().changeType(IntegerParameterType.type);
            } else if ("Float".equals(parameter.getParameterType().getName())) {
                actualParameter.getType().changeType(FloatParameterType.type);
            } else if ("Boolean".equals(parameter.getParameterType().getName())) {
                actualParameter.getType().changeType(BooleanParameterType.type);
            } else if ("File".equals(parameter.getParameterType().getName())) {
                actualParameter.getType().changeType(FileParameterType.type);
            } else if ("URI".equals(parameter.getParameterType().getName())) {
                actualParameter.getType().changeType(URIParameterType.type);
            } else if ("StringArray".equals(parameter.getParameterType().getName())) {
                actualParameter.getType().changeType(StringArrayType.type);
            } else if ("DoubleArray".equals(parameter.getParameterType().getName())) {
                actualParameter.getType().changeType(DoubleArrayType.type);
            } else if ("IntegerArray".equals(parameter.getParameterType().getName())) {
                actualParameter.getType().changeType(IntegerArrayType.type);
            } else if ("FloatArray".equals(parameter.getParameterType().getName())) {
                actualParameter.getType().changeType(FloatArrayType.type);
            } else if ("BooleanArray".equals(parameter.getParameterType().getName())) {
                actualParameter.getType().changeType(BooleanArrayType.type);
            } else if ("FileArray".equals(parameter.getParameterType().getName())) {
                actualParameter.getType().changeType(FileArrayType.type);
            } else if ("URIArray".equals(parameter.getParameterType().getName())) {
                actualParameter.getType().changeType(URIArrayType.type);
            } else if ("StdOut".equals(parameter.getParameterType().getName())) {
                actualParameter.getType().changeType(StdOutParameterType.type);
            } else if ("StdErr".equals(parameter.getParameterType().getName())) {
                actualParameter.getType().changeType(StdErrParameterType.type);
            }
            outputParam.add(parameter.getParameterName(), actualParameter);
        }

        invocationContext.setInput(inputParam);
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