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

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

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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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            jobAttr.setStdin(app.getStandardInput());
        } else {
            MessageContext<Object> input = context.getInput();
            for (Iterator<String> iterator = input.getNames(); iterator.hasNext(); ) {
                String paramName = iterator.next();
                ActualParameter actualParameter = (ActualParameter) input.getValue(paramName);
                if ("URIArray".equals(actualParameter.getType().getType().toString())) {
                    String[] values = ((URIArrayType) actualParameter.getType()).getValueArray();
                    for (String value : values) {
                        jobAttr.addArgument(value);
                    }
                } else {
                    String paramValue = input.getStringValue(paramName);
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            ct.setServiceName("SimpleMPIEcho");

            /* Input */
            ParameterContextImpl input = new ParameterContextImpl();
            ActualParameter echo_input = new ActualParameter();
            ((StringParameterType) echo_input.getType()).setValue("echo_mpi_output=hi");
            input.add("echo_mpi_input", echo_input);

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

            /* parameter */
            ct.setInput(input);
            ct.setOutput(output);
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            ct.setServiceName("MockPwscfMPIService");

            /* Input */
            ParameterContextImpl input = new ParameterContextImpl();
            ActualParameter echo_input = new ActualParameter();
            ((StringParameterType) echo_input.getType()).setValue("echo_mpi_output=hi");
            input.add("echo_mpi_input", echo_input);

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

            /* parameter */
            ct.setInput(input);
            ct.setOutput(output);
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            /*
            * Input
            */
            ParameterContextImpl input = new ParameterContextImpl();
            ActualParameter input_file = new ActualParameter();
//            URI InputFile =  URI.create("/gpfs1/u/ac/ccguser/alatop.inp");
            String InputFile =  "/gpfs1/u/ac/ccguser/alatop.inp";
            input_file.getType().changeType(URIParameterType.type);
            ((URIParameterType) input_file.getType()).setValue(InputFile);
            input.add("input_file", input_file);

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

            // parameter
            ct.setInput(input);
            ct.setOutput(output);
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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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        List<String> inputValues = new ArrayList<String>();
        MessageContext input = jobExecutionContext.getInMessageContext();
        Map<String, Object> inputs = input.getParameters();
        Set<String> keys = inputs.keySet();
        for (String paramName : keys) {
            ActualParameter actualParameter = (ActualParameter) inputs.get(paramName);
            if ("URIArray".equals(actualParameter.getType().getType().toString()) || "StringArray".equals(actualParameter.getType().getType().toString())
                    || "FileArray".equals(actualParameter.getType().getType().toString())) {
                String[] values = null;
                if (actualParameter.getType() instanceof URIArrayType) {
                    values = ((URIArrayType) actualParameter.getType()).getValueArray();
                } else if (actualParameter.getType() instanceof StringArrayType) {
                    values = ((StringArrayType) actualParameter.getType()).getValueArray();
                } else if (actualParameter.getType() instanceof FileArrayType) {
                    values = ((FileArrayType) actualParameter.getType()).getValueArray();
                }
                String value = StringUtil.createDelimiteredString(values, " ");
                inputValues.add(value);
            } else {
                String paramValue = MappingFactory.toString(actualParameter);
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            log.info("Invoking SCPInputHandler");

            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())) {
                    if (index < oldIndex) {
                        log.info("Input File: " + paramValue + " is already transfered, so we skip this operation !!!");
                        ((URIParameterType) actualParameter.getType()).setValue(oldFiles.get(index));
                        data.append(oldFiles.get(index++)).append(","); // we get already transfered file and increment the index
                    } else {
                        String s = stageInputFiles(jobExecutionContext, paramValue);
                        ((URIParameterType) actualParameter.getType()).setValue(s);
                        StringBuffer temp = new StringBuffer(data.append(s).append(",").toString());
                        GFacUtils.savePluginData(jobExecutionContext, temp.insert(0, ++index), this.getClass().getName());
                    }
                } 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) {
                        if (index < oldIndex) {
                            log.info("Input File: " + paramValue + " is already transfered, so we skip this operation !!!");
                            newFiles.add(oldFiles.get(index));
                            data.append(oldFiles.get(index++)).append(",");
                        } else {
                            String stageInputFiles = stageInputFiles(jobExecutionContext, paramValueEach);
                            status.setTransferState(TransferState.UPLOAD);
                            detail.setTransferStatus(status);
                            detail.setTransferDescription("Input Data Staged: " + stageInputFiles);
                            registry.add(ChildDataType.DATA_TRANSFER_DETAIL, detail, jobExecutionContext.getTaskData().getTaskID());
                            StringBuffer temp = new StringBuffer(data.append(stageInputFiles).append(",").toString());
                            GFacUtils.savePluginData(jobExecutionContext, temp.insert(0, ++index), this.getClass().getName());
                            newFiles.add(stageInputFiles);
                        }

                    }
                    ((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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                GFacUtils.savePluginData(jobExecutionContext, temp.insert(0, ++index), this.getClass().getName());
            }
            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())) {
                    if (index < oldIndex) {
                        log.info("Input File: " + paramValue + " is already transfered, so we skip this operation !!!");
                        ((URIParameterType) actualParameter.getType()).setValue(oldFiles.get(index));
                        data.append(oldFiles.get(index++)).append(","); // we get already transfered file and increment the index
                    } else {
                        String s = stageInputFiles(pbsCluster, paramValue, parentPath);
                        ((URIParameterType) actualParameter.getType()).setValue(s);
                        StringBuffer temp = new StringBuffer(data.append(s).append(",").toString());
                        GFacUtils.savePluginData(jobExecutionContext, temp.insert(0, ++index), this.getClass().getName());
                    }
                } 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) {
                        if (index < oldIndex) {
                            log.info("Input File: " + paramValue + " is already transfered, so we skip this operation !!!");
                            newFiles.add(oldFiles.get(index));
                            data.append(oldFiles.get(index++)).append(",");
                        } else {
                            String stageInputFiles = stageInputFiles(pbsCluster, paramValueEach, parentPath);
                            StringBuffer temp = new StringBuffer(data.append(stageInputFiles).append(",").toString());
                            GFacUtils.savePluginData(jobExecutionContext, temp.insert(0, ++index), this.getClass().getName());
                            newFiles.add(stageInputFiles);
                        }
                    }
                    ((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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            //todo this is a mess we have to fix this
            List<DataObjectType> outputArray = new ArrayList<DataObjectType>();
            Map<String, Object> output = jobExecutionContext.getOutMessageContext().getParameters();
            Set<String> keys = output.keySet();
            for (String paramName : keys) {
                ActualParameter actualParameter = (ActualParameter) output.get(paramName);
                if ("URI".equals(actualParameter.getType().getType().toString())) {

                    List<String> outputList = cluster.listDirectory(app.getOutputDataDirectory());
                    if (outputList.size() == 0 || outputList.get(0).isEmpty()) {
                        OutputUtils.fillOutputFromStdout(output, stdOutStr, stdErrStr, outputArray);
                        Set<String> strings = output.keySet();
                        outputArray.clear();
                        for (String key : strings) {
                            ActualParameter actualParameter1 = (ActualParameter) output.get(key);
                            if ("URI".equals(actualParameter1.getType().getType().toString())) {
                                String downloadFile = MappingFactory.toString(actualParameter1);
                                String localFile;
                                if (index < oldIndex) {
                                    localFile = oldFiles.get(index);
                                    data.append(oldFiles.get(index++)).append(",");
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