SiLeBAT/FSK-Lab

File `NodeUtils.java` has 257 lines of code (exceeds 250 allowed). Consider refactoring.
package de.bund.bfr.knime.fsklab.nodes;
 
import java.io.File;
import java.io.IOException;
import java.net.URI;
import java.nio.charset.StandardCharsets;
import java.util.ArrayList;
import java.util.List;
import java.util.Map;
import java.util.UUID;
import org.apache.commons.io.FileUtils;
import org.apache.commons.lang3.StringUtils;
import org.knime.core.node.InvalidSettingsException;
import org.knime.core.node.workflow.FlowVariable;
import org.knime.core.node.workflow.NodeContext;
import com.fasterxml.jackson.core.JsonProcessingException;
import com.fasterxml.jackson.databind.JsonNode;
import com.sun.jna.Platform;
import de.bund.bfr.fskml.FSKML;
import de.bund.bfr.knime.fsklab.v2_0.FskSimulation;
import de.bund.bfr.knime.fsklab.v2_0.editor.FSKEditorJSNodeDialog.ModelType;
import de.bund.bfr.metadata.swagger.Assay;
import de.bund.bfr.metadata.swagger.ConsumptionModel;
import de.bund.bfr.metadata.swagger.Contact;
import de.bund.bfr.metadata.swagger.DataModel;
import de.bund.bfr.metadata.swagger.DataModelGeneralInformation;
import de.bund.bfr.metadata.swagger.DietaryAssessmentMethod;
import de.bund.bfr.metadata.swagger.DoseResponseModel;
import de.bund.bfr.metadata.swagger.DoseResponseModelGeneralInformation;
import de.bund.bfr.metadata.swagger.DoseResponseModelModelMath;
import de.bund.bfr.metadata.swagger.Exposure;
import de.bund.bfr.metadata.swagger.ExposureModel;
import de.bund.bfr.metadata.swagger.GenericModel;
import de.bund.bfr.metadata.swagger.GenericModelDataBackground;
import de.bund.bfr.metadata.swagger.GenericModelGeneralInformation;
import de.bund.bfr.metadata.swagger.GenericModelModelMath;
import de.bund.bfr.metadata.swagger.GenericModelScope;
import de.bund.bfr.metadata.swagger.Hazard;
import de.bund.bfr.metadata.swagger.HealthModel;
import de.bund.bfr.metadata.swagger.Laboratory;
import de.bund.bfr.metadata.swagger.Model;
import de.bund.bfr.metadata.swagger.ModelCategory;
import de.bund.bfr.metadata.swagger.ModelEquation;
import de.bund.bfr.metadata.swagger.OtherModel;
import de.bund.bfr.metadata.swagger.OtherModelGeneralInformation;
import de.bund.bfr.metadata.swagger.OtherModelModelMath;
import de.bund.bfr.metadata.swagger.Parameter;
import de.bund.bfr.metadata.swagger.Parameter.ClassificationEnum;
import metadata.SwaggerUtil;
import de.bund.bfr.metadata.swagger.PopulationGroup;
import de.bund.bfr.metadata.swagger.PredictiveModel;
import de.bund.bfr.metadata.swagger.PredictiveModelGeneralInformation;
import de.bund.bfr.metadata.swagger.PredictiveModelModelMath;
import de.bund.bfr.metadata.swagger.ProcessModel;
import de.bund.bfr.metadata.swagger.Product;
import de.bund.bfr.metadata.swagger.QraModel;
import de.bund.bfr.metadata.swagger.QualityMeasures;
import de.bund.bfr.metadata.swagger.Reference;
import de.bund.bfr.metadata.swagger.RiskModel;
import de.bund.bfr.metadata.swagger.Study;
import de.bund.bfr.metadata.swagger.StudySample;
import de.bund.bfr.metadata.swagger.ToxicologicalModel;
 
public class NodeUtils {
 
  public static final String DEFAULT_SIMULATION = "defaultSimulation";
 
  // used by Writer & Reader to identify Join-Relations in the SBML File
  public static final String METADATA_COMMAND_VALUE = "commandValue";
 
  /**
   * @return the libraries URI for the running platform.
   * @throws InvalidSettingsException if the running platform is not supported.
   */
Identical blocks of code found in 3 locations. Consider refactoring.
  public static URI getLibURI() throws InvalidSettingsException {
    if (Platform.isWindows()) {
      return FSKML.getURIS(1, 0, 12).get("zip");
    }
    if (Platform.isMac()) {
      return FSKML.getURIS(1, 0, 12).get("tgz");
    }
    if (Platform.isLinux()) {
      return FSKML.getURIS(1, 0, 12).get("tar_gz");
    }
    throw new InvalidSettingsException("Unsupported platform");
  }
 
Identical blocks of code found in 3 locations. Consider refactoring.
  public static FskSimulation createDefaultSimulation(List<Parameter> parameters) {
 
    final FskSimulation simulation = new FskSimulation(DEFAULT_SIMULATION);
 
    // The parameters to be inserted in order
    parameters.stream().filter(p -> p.getClassification() != ClassificationEnum.OUTPUT)
        .forEach(p -> simulation.getParameters().put(p.getId(), p.getValue()));
 
    return simulation;
  }
 
  /** Builds string with R parameters script out. */
Identical blocks of code found in 3 locations. Consider refactoring.
  public static String buildParameterScript(FskSimulation simulation) {
 
    final StringBuilder builder = new StringBuilder();
    for (final Map.Entry<String, String> entry : simulation.getParameters().entrySet()) {
      final String parameterName = entry.getKey();
      final String parameterValue = entry.getValue();
 
      builder.append(parameterName + " <- " + parameterValue + "\n");
    }
 
    return builder.toString();
  }
 
  /**
   * Read a configuration string from a file under a settings folder.
   *
   * @throws IOException
   */
Identical blocks of code found in 3 locations. Consider refactoring.
  public static String readConfigString(File settingsFolder, String filename) throws IOException {
    FlowVariable aFlowVariable = null;
    if (NodeContext.getContext().getNodeContainer().getFlowObjectStack() != null) {
      aFlowVariable = NodeContext.getContext().getNodeContainer().getFlowObjectStack()
          .getAvailableFlowVariables().get(filename);
    }
    if (aFlowVariable != null) {
      return aFlowVariable.getStringValue();
    } else {
      final File configFile = new File(settingsFolder, filename);
      return configFile.exists() ? FileUtils.readFileToString(configFile, StandardCharsets.UTF_8)
          : null;
    }
  }
 
  /**
   * Write a configuration string to a file under a settings folder
   *
   * @throws IOException
   */
Identical blocks of code found in 3 locations. Consider refactoring.
  public static void writeConfigString(String configString, File settingsFolder, String filename)
      throws IOException {
    if (configString != null) {
      final File configFile = new File(settingsFolder, filename);
      FileUtils.writeStringToFile(configFile, configString, StandardCharsets.UTF_8);
    }
  }
 
  /** Initialize and return an empty Generic model using the fluent API of the generated Swagger Models */
  public static Model initializeGenericModell() {
      return new GenericModel()
          .generalInformation(new GenericModelGeneralInformation()
Define a constant instead of duplicating this literal "Generic model" 4 times.
              .modelCategory(new ModelCategory().modelClass("Generic model"))
              .addAuthorItem(new Contact())
              .addCreatorItem(new Contact())
              .addReferenceItem(new Reference()))
          .dataBackground(new GenericModelDataBackground()
              .study(new Study())
              .addAssayItem(new Assay())
              .addDietaryAssessmentMethodItem(new DietaryAssessmentMethod())
              .addLaboratoryItem(new Laboratory())
              .addStudySampleItem(new StudySample()))
          .scope(new GenericModelScope()
              .addHazardItem(new Hazard())
              .addPopulationGroupItem(new PopulationGroup())
              .addProductItem(new Product())
              .addSpatialInformationItem(""))
          .modelMath(new GenericModelModelMath()
              .addEventItem("")
              .addExposureItem(new Exposure())
              .addModelEquationItem(new ModelEquation())
              .addParameterItem(new Parameter())
              .addQualityMeasuresItem(new QualityMeasures()))
Define a constant instead of duplicating this literal "genericModel" 5 times.
          .modelType("genericModel");
  }
 
  /**
   * Initialise and return a model for the passed type. The model is initialised
   * with an UUID and its model class.
   */
Method `initializeModel` has 85 lines of code (exceeds 25 allowed). Consider refactoring.
  public static Model initializeModel(ModelType modelType) {
    
    String modelId = UUID.randomUUID().toString();
 
    if (modelType == null)
      return new GenericModel()
          .generalInformation(new GenericModelGeneralInformation()
              .identifier(modelId)
              .modelCategory(new ModelCategory().modelClass("Generic model")))
          .modelType("genericModel");
 
    switch (modelType) {
      case genericModel:
        return new GenericModel().modelMath(new GenericModelModelMath())
            .generalInformation(new GenericModelGeneralInformation()
                .identifier(modelId)
                .modelCategory(new ModelCategory().modelClass("Generic model")))
            .modelType("genericModel");
      case dataModel:
        return new DataModel()
            .generalInformation(new DataModelGeneralInformation().identifier(modelId))
            .modelType("dataModel");
      case consumptionModel:
        return new ConsumptionModel().modelMath(new PredictiveModelModelMath())
            .generalInformation(new PredictiveModelGeneralInformation()
                .identifier(modelId)
                .modelCategory(new ModelCategory().modelClass("Consumption model")))
            .modelType("consumptionModel");
      case doseResponseModel:
        return new DoseResponseModel().modelMath(new DoseResponseModelModelMath())
            .generalInformation(new DoseResponseModelGeneralInformation()
                .identifier(modelId)
                .modelCategory(new ModelCategory().modelClass("Dose-response model")))
            .modelType("doseResponseModel");
      case exposureModel:
        return new ExposureModel().modelMath(new GenericModelModelMath())
            .generalInformation(new PredictiveModelGeneralInformation()
                .identifier(modelId)
                .modelCategory(new ModelCategory().modelClass("Exposure model")))
            .modelType("exposureModel");
      case healthModel:
        return new HealthModel().modelMath(new GenericModelModelMath())
            .generalInformation(new PredictiveModelGeneralInformation()
                .identifier(modelId)
                .modelCategory(new ModelCategory().modelClass("Health metrics model")))
            .modelType("healthModel");
      case otherModel:
        return new OtherModel().modelMath(new OtherModelModelMath())
            .generalInformation(new OtherModelGeneralInformation()
                .identifier(modelId)
                .modelCategory(new ModelCategory().modelClass("Other empirical models")))
            .modelType("otherModel");
      case predictiveModel:
        return new PredictiveModel().modelMath(new PredictiveModelModelMath())
            .generalInformation(new PredictiveModelGeneralInformation()
                .identifier(modelId)
                .modelCategory(new ModelCategory().modelClass("Predictive model")))
            .modelType("predictiveModel");
      case processModel:
        return new ProcessModel().modelMath(new PredictiveModelModelMath())
            .generalInformation(new PredictiveModelGeneralInformation()
                .identifier(modelId)
                .modelCategory(new ModelCategory().modelClass("Process model")))
            .modelType("processModel");
      case qraModel:
        return new QraModel().modelMath(new GenericModelModelMath())
            .generalInformation(new PredictiveModelGeneralInformation()
                .identifier(modelId)
                .modelCategory(new ModelCategory().modelClass("Quantitative risk assessment")))
            .modelType("qraModel");
      case riskModel:
        return new RiskModel().modelMath(new GenericModelModelMath())
            .generalInformation(new PredictiveModelGeneralInformation()
                .identifier(modelId)
                .modelCategory(new ModelCategory().modelClass("Risk characterization model")))
            .modelType("riskModel");
      case toxicologicalModel:
        return new ToxicologicalModel().modelMath(new GenericModelModelMath())
            .generalInformation(new PredictiveModelGeneralInformation()
                .identifier(modelId)
                .modelCategory(new ModelCategory().modelClass("Toxicological reference value")))
            .modelType("toxicologicalModel");
      default:
        return new GenericModel().modelMath(new GenericModelModelMath())
            .generalInformation(new GenericModelGeneralInformation()
                .identifier(modelId)
                .modelCategory(new ModelCategory().modelClass("Generic model")))
            .modelType("genericModel");
    }
  }
  
  /**
   * Initialise and return a reference List for the passed type and model. 
   */
Method `getReferenceList` has a Cognitive Complexity of 13 (exceeds 5 allowed). Consider refactoring.
Method `getReferenceList` has 29 lines of code (exceeds 25 allowed). Consider refactoring.
  public static List<Reference> getReferenceList(String modelType, Model metadata) {
    List<Reference> references = new ArrayList<>();
 
    if (modelType == null)
      references = ((GenericModel) metadata).getGeneralInformation().getReference();
    else if (modelType.equalsIgnoreCase("genericModel")) {
      references = ((GenericModel) metadata).getGeneralInformation().getReference();
    } else if (modelType.equalsIgnoreCase("dataModel")) {
      references = ((DataModel) metadata).getGeneralInformation().getReference();
    } else if (modelType.equalsIgnoreCase("consumptionModel")) {
      references = ((ConsumptionModel) metadata).getGeneralInformation().getReference();
    } else if (modelType.equalsIgnoreCase("doseResponseModel")) {
      references = ((DoseResponseModel) metadata).getGeneralInformation().getReference();
    } else if (modelType.equalsIgnoreCase("exposureModel")) {
      references = ((ExposureModel) metadata).getGeneralInformation().getReference();
    } else if (modelType.equalsIgnoreCase("healthModel")) {
      references = ((HealthModel) metadata).getGeneralInformation().getReference();
    } else if (modelType.equalsIgnoreCase("otherModel")) {
      references = ((OtherModel) metadata).getGeneralInformation().getReference();
    } else if (modelType.equalsIgnoreCase("predictiveModel")) {
      references = ((PredictiveModel) metadata).getGeneralInformation().getReference();
    } else if (modelType.equalsIgnoreCase("processModel")) {
      references = ((ProcessModel) metadata).getGeneralInformation().getReference();
    } else if (modelType.equalsIgnoreCase("qraModel")) {
      references = ((QraModel) metadata).getGeneralInformation().getReference();
    } else if (modelType.equalsIgnoreCase("riskModel")) {
      references = ((RiskModel) metadata).getGeneralInformation().getReference();
    } else if (modelType.equalsIgnoreCase("toxicologicalModel")) {
      references = ((ToxicologicalModel) metadata).getGeneralInformation().getReference();
    }
    return references;
  }
}