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Identical blocks of code found in 2 locations. Consider refactoring.
Open

        _createMenus() {
            return fskutil.createSubMenu("General information", [
                { "id": "generalInformation", "label": "General" },
                { "id": "author", "label": "Author" },
                { "id": "creator", "label": "Creator" },
Severity: Major
Found in de.bund.bfr.knime.js/js-lib/bfr/fskutil_1.0.0.js and 1 other location - About 1 day to fix
de.bund.bfr.knime.js/js-lib/bfr/fskutil_1.0.0.js on lines 1349..1366

Duplicated Code

Duplicated code can lead to software that is hard to understand and difficult to change. The Don't Repeat Yourself (DRY) principle states:

Every piece of knowledge must have a single, unambiguous, authoritative representation within a system.

When you violate DRY, bugs and maintenance problems are sure to follow. Duplicated code has a tendency to both continue to replicate and also to diverge (leaving bugs as two similar implementations differ in subtle ways).

Tuning

This issue has a mass of 231.

We set useful threshold defaults for the languages we support but you may want to adjust these settings based on your project guidelines.

The threshold configuration represents the minimum mass a code block must have to be analyzed for duplication. The lower the threshold, the more fine-grained the comparison.

If the engine is too easily reporting duplication, try raising the threshold. If you suspect that the engine isn't catching enough duplication, try lowering the threshold. The best setting tends to differ from language to language.

See codeclimate-duplication's documentation for more information about tuning the mass threshold in your .codeclimate.yml.

Refactorings

Further Reading

File SettingsHelper.java has 574 lines of code (exceeds 250 allowed). Consider refactoring.
Open

/*******************************************************************************
 * Copyright (c) 2015 Federal Institute for Risk Assessment (BfR), Germany
 *
 * This program is free software: you can redistribute it and/or modify
 * it under the terms of the GNU General Public License as published by
Severity: Major
Found in de.bund.bfr.knime.pmm.nodes/src/de/bund/bfr/knime/pmm/xlsmodelreader/SettingsHelper.java - About 1 day to fix

Similar blocks of code found in 2 locations. Consider refactoring.
Open

    function save_organism(modelNumber) {
        var organism_id = parseInt($('#ddlOrganism').val());
        var organism_name = '';
        var organism_detail = '';
        var organism_dbuuid = '';
Severity: Major
Found in de.bund.bfr.knime.pmm.nodes/js-src/de/bund/bfr/knime/pmm/editor/editor.js and 1 other location - About 1 day to fix
de.bund.bfr.knime.pmm.nodes/js-src/de/bund/bfr/knime/pmm/editor/editor.js on lines 402..426

Duplicated Code

Duplicated code can lead to software that is hard to understand and difficult to change. The Don't Repeat Yourself (DRY) principle states:

Every piece of knowledge must have a single, unambiguous, authoritative representation within a system.

When you violate DRY, bugs and maintenance problems are sure to follow. Duplicated code has a tendency to both continue to replicate and also to diverge (leaving bugs as two similar implementations differ in subtle ways).

Tuning

This issue has a mass of 230.

We set useful threshold defaults for the languages we support but you may want to adjust these settings based on your project guidelines.

The threshold configuration represents the minimum mass a code block must have to be analyzed for duplication. The lower the threshold, the more fine-grained the comparison.

If the engine is too easily reporting duplication, try raising the threshold. If you suspect that the engine isn't catching enough duplication, try lowering the threshold. The best setting tends to differ from language to language.

See codeclimate-duplication's documentation for more information about tuning the mass threshold in your .codeclimate.yml.

Refactorings

Further Reading

Similar blocks of code found in 2 locations. Consider refactoring.
Open

    function save_matrix(modelNumber) {

        var matrix_id = parseInt($('#ddlMatrix').val());
        var matrix_name = '';
        var matrix_detail = '';
Severity: Major
Found in de.bund.bfr.knime.pmm.nodes/js-src/de/bund/bfr/knime/pmm/editor/editor.js and 1 other location - About 1 day to fix
de.bund.bfr.knime.pmm.nodes/js-src/de/bund/bfr/knime/pmm/editor/editor.js on lines 344..367

Duplicated Code

Duplicated code can lead to software that is hard to understand and difficult to change. The Don't Repeat Yourself (DRY) principle states:

Every piece of knowledge must have a single, unambiguous, authoritative representation within a system.

When you violate DRY, bugs and maintenance problems are sure to follow. Duplicated code has a tendency to both continue to replicate and also to diverge (leaving bugs as two similar implementations differ in subtle ways).

Tuning

This issue has a mass of 230.

We set useful threshold defaults for the languages we support but you may want to adjust these settings based on your project guidelines.

The threshold configuration represents the minimum mass a code block must have to be analyzed for duplication. The lower the threshold, the more fine-grained the comparison.

If the engine is too easily reporting duplication, try raising the threshold. If you suspect that the engine isn't catching enough duplication, try lowering the threshold. The best setting tends to differ from language to language.

See codeclimate-duplication's documentation for more information about tuning the mass threshold in your .codeclimate.yml.

Refactorings

Further Reading

Similar blocks of code found in 2 locations. Consider refactoring.
Open

  Utils._convertData = function (data) {
    for (var originalKey in data) {
      var keys = originalKey.split('-');

      var dataLevel = data;
Severity: Major
Found in de.bund.bfr.knime.pmm.nodes/js-lib/select2/4_0_3/debug/js/select2.js and 1 other location - About 1 day to fix
de.bund.bfr.knime.js/src/js/lib/select2.full.js on lines 678..710

Duplicated Code

Duplicated code can lead to software that is hard to understand and difficult to change. The Don't Repeat Yourself (DRY) principle states:

Every piece of knowledge must have a single, unambiguous, authoritative representation within a system.

When you violate DRY, bugs and maintenance problems are sure to follow. Duplicated code has a tendency to both continue to replicate and also to diverge (leaving bugs as two similar implementations differ in subtle ways).

Tuning

This issue has a mass of 229.

We set useful threshold defaults for the languages we support but you may want to adjust these settings based on your project guidelines.

The threshold configuration represents the minimum mass a code block must have to be analyzed for duplication. The lower the threshold, the more fine-grained the comparison.

If the engine is too easily reporting duplication, try raising the threshold. If you suspect that the engine isn't catching enough duplication, try lowering the threshold. The best setting tends to differ from language to language.

See codeclimate-duplication's documentation for more information about tuning the mass threshold in your .codeclimate.yml.

Refactorings

Further Reading

Similar blocks of code found in 2 locations. Consider refactoring.
Open

  Utils._convertData = function (data) {
    for (var originalKey in data) {
      var keys = originalKey.split('-');

      var dataLevel = data;
Severity: Major
Found in de.bund.bfr.knime.js/src/js/lib/select2.full.js and 1 other location - About 1 day to fix
de.bund.bfr.knime.pmm.nodes/js-lib/select2/4_0_3/debug/js/select2.js on lines 674..706

Duplicated Code

Duplicated code can lead to software that is hard to understand and difficult to change. The Don't Repeat Yourself (DRY) principle states:

Every piece of knowledge must have a single, unambiguous, authoritative representation within a system.

When you violate DRY, bugs and maintenance problems are sure to follow. Duplicated code has a tendency to both continue to replicate and also to diverge (leaving bugs as two similar implementations differ in subtle ways).

Tuning

This issue has a mass of 229.

We set useful threshold defaults for the languages we support but you may want to adjust these settings based on your project guidelines.

The threshold configuration represents the minimum mass a code block must have to be analyzed for duplication. The lower the threshold, the more fine-grained the comparison.

If the engine is too easily reporting duplication, try raising the threshold. If you suspect that the engine isn't catching enough duplication, try lowering the threshold. The best setting tends to differ from language to language.

See codeclimate-duplication's documentation for more information about tuning the mass threshold in your .codeclimate.yml.

Refactorings

Further Reading

Function 2 has 242 lines of code (exceeds 25 allowed). Consider refactoring.
Open

},{"./src/equations":2,"./src/expressions":3,"./src/fractions":4,"./src/parser":7}],2:[function(require,module,exports){
var Expression = require('./expressions').Expression;
var Variable = require('./expressions').Variable;
var Term = require('./expressions').Term;
var Fraction = require('./fractions');
Severity: Major
Found in de.bund.bfr.knime.pmm.nodes/js-src/de/bund/bfr/knime/pmm/js/modelplotter/algebra-0.2.6.min.js - About 1 day to fix

Similar blocks of code found in 2 locations. Consider refactoring.
Open

    private void updateMatrixPanel() {
        List<String> items = new ArrayList<>();

        items.add(SettingsHelper.DO_NOT_USE);
        items.add(SettingsHelper.OTHER_PARAMETER);
Severity: Major
Found in de.bund.bfr.knime.pmm.nodes/src/de/bund/bfr/knime/pmm/xlsmodelreader/XLSModelReaderNodeDialog.java and 1 other location - About 1 day to fix
de.bund.bfr.knime.pmm.nodes/src/de/bund/bfr/knime/pmm/xlsmodelreader/XLSModelReaderNodeDialog.java on lines 1018..1101

Duplicated Code

Duplicated code can lead to software that is hard to understand and difficult to change. The Don't Repeat Yourself (DRY) principle states:

Every piece of knowledge must have a single, unambiguous, authoritative representation within a system.

When you violate DRY, bugs and maintenance problems are sure to follow. Duplicated code has a tendency to both continue to replicate and also to diverge (leaving bugs as two similar implementations differ in subtle ways).

Tuning

This issue has a mass of 589.

We set useful threshold defaults for the languages we support but you may want to adjust these settings based on your project guidelines.

The threshold configuration represents the minimum mass a code block must have to be analyzed for duplication. The lower the threshold, the more fine-grained the comparison.

If the engine is too easily reporting duplication, try raising the threshold. If you suspect that the engine isn't catching enough duplication, try lowering the threshold. The best setting tends to differ from language to language.

See codeclimate-duplication's documentation for more information about tuning the mass threshold in your .codeclimate.yml.

Refactorings

Further Reading

Similar blocks of code found in 2 locations. Consider refactoring.
Open

    private void updateAgentPanel() {
        List<String> items = new ArrayList<>();

        items.add(SettingsHelper.DO_NOT_USE);
        items.add(SettingsHelper.OTHER_PARAMETER);
Severity: Major
Found in de.bund.bfr.knime.pmm.nodes/src/de/bund/bfr/knime/pmm/xlsmodelreader/XLSModelReaderNodeDialog.java and 1 other location - About 1 day to fix
de.bund.bfr.knime.pmm.nodes/src/de/bund/bfr/knime/pmm/xlsmodelreader/XLSModelReaderNodeDialog.java on lines 1103..1186

Duplicated Code

Duplicated code can lead to software that is hard to understand and difficult to change. The Don't Repeat Yourself (DRY) principle states:

Every piece of knowledge must have a single, unambiguous, authoritative representation within a system.

When you violate DRY, bugs and maintenance problems are sure to follow. Duplicated code has a tendency to both continue to replicate and also to diverge (leaving bugs as two similar implementations differ in subtle ways).

Tuning

This issue has a mass of 589.

We set useful threshold defaults for the languages we support but you may want to adjust these settings based on your project guidelines.

The threshold configuration represents the minimum mass a code block must have to be analyzed for duplication. The lower the threshold, the more fine-grained the comparison.

If the engine is too easily reporting duplication, try raising the threshold. If you suspect that the engine isn't catching enough duplication, try lowering the threshold. The best setting tends to differ from language to language.

See codeclimate-duplication's documentation for more information about tuning the mass threshold in your .codeclimate.yml.

Refactorings

Further Reading

File FSMRTemplateImpl.java has 567 lines of code (exceeds 250 allowed). Consider refactoring.
Open

/*******************************************************************************
 * Copyright (c) 2015 Federal Institute for Risk Assessment (BfR), Germany
 * <p>
 * This program is free software: you can redistribute it and/or modify it under the terms of the
 * GNU General Public License as published by the Free Software Foundation, either version 3 of the
Severity: Major
Found in de.bund.bfr.knime.pmm.nodes/src/de/bund/bfr/openfsmr/FSMRTemplateImpl.java - About 1 day to fix

File bootstrap-touchspin.js has 566 lines of code (exceeds 250 allowed). Consider refactoring.
Open

/*
 *  Bootstrap TouchSpin - v4.2.5
 *  A mobile and touch friendly input spinner component for Bootstrap 3 & 4.
 *  http://www.virtuosoft.eu/code/bootstrap-touchspin/
 *
Severity: Major
Found in de.bund.bfr.knime.js/src/js/lib/bootstrap-touchspin.js - About 1 day to fix

Method getTimeSeriesTuples has 239 lines of code (exceeds 25 allowed). Consider refactoring.
Open

    public Map<String, KnimeTuple> getTimeSeriesTuples(File file, String sheet, Map<String, Object> columnMappings,
            String timeUnit, String concentrationUnit, String agentColumnName, Map<String, AgentXml> agentMappings,
            String matrixColumnName, Map<String, MatrixXml> matrixMappings, boolean preserveIds, List<Integer> usedIds)
                    throws Exception {
        Workbook wb = getWorkbook(file);
Severity: Major
Found in de.bund.bfr.knime.pmm.common/src/de/bund/bfr/knime/pmm/common/XLSReader.java - About 1 day to fix

Similar blocks of code found in 2 locations. Consider refactoring.
Open

  private static class PrimaryModelWDataReader implements Reader {

    public BufferedDataContainer[] read(File file, boolean isPMFX, ExecutionContext exec)
        throws Exception {
      // Creates table spec and container
Severity: Major
Found in de.bund.bfr.knime.pmm.nodes/src/de/bund/bfr/knime/pmm/common/reader/ReaderUtils.java and 1 other location - About 1 day to fix
de.bund.bfr.knime.pmm.nodes/src/de/bund/bfr/knime/pmm/common/reader/ReaderUtils.java on lines 392..462

Duplicated Code

Duplicated code can lead to software that is hard to understand and difficult to change. The Don't Repeat Yourself (DRY) principle states:

Every piece of knowledge must have a single, unambiguous, authoritative representation within a system.

When you violate DRY, bugs and maintenance problems are sure to follow. Duplicated code has a tendency to both continue to replicate and also to diverge (leaving bugs as two similar implementations differ in subtle ways).

Tuning

This issue has a mass of 582.

We set useful threshold defaults for the languages we support but you may want to adjust these settings based on your project guidelines.

The threshold configuration represents the minimum mass a code block must have to be analyzed for duplication. The lower the threshold, the more fine-grained the comparison.

If the engine is too easily reporting duplication, try raising the threshold. If you suspect that the engine isn't catching enough duplication, try lowering the threshold. The best setting tends to differ from language to language.

See codeclimate-duplication's documentation for more information about tuning the mass threshold in your .codeclimate.yml.

Refactorings

Further Reading

Similar blocks of code found in 2 locations. Consider refactoring.
Open

  private static class PrimaryModelWODataReader implements Reader {

    public BufferedDataContainer[] read(File file, boolean isPMFX, ExecutionContext exec)
        throws Exception {
      // Creates table spec and container
Severity: Major
Found in de.bund.bfr.knime.pmm.nodes/src/de/bund/bfr/knime/pmm/common/reader/ReaderUtils.java and 1 other location - About 1 day to fix
de.bund.bfr.knime.pmm.nodes/src/de/bund/bfr/knime/pmm/common/reader/ReaderUtils.java on lines 321..390

Duplicated Code

Duplicated code can lead to software that is hard to understand and difficult to change. The Don't Repeat Yourself (DRY) principle states:

Every piece of knowledge must have a single, unambiguous, authoritative representation within a system.

When you violate DRY, bugs and maintenance problems are sure to follow. Duplicated code has a tendency to both continue to replicate and also to diverge (leaving bugs as two similar implementations differ in subtle ways).

Tuning

This issue has a mass of 582.

We set useful threshold defaults for the languages we support but you may want to adjust these settings based on your project guidelines.

The threshold configuration represents the minimum mass a code block must have to be analyzed for duplication. The lower the threshold, the more fine-grained the comparison.

If the engine is too easily reporting duplication, try raising the threshold. If you suspect that the engine isn't catching enough duplication, try lowering the threshold. The best setting tends to differ from language to language.

See codeclimate-duplication's documentation for more information about tuning the mass threshold in your .codeclimate.yml.

Refactorings

Further Reading

File PlausibilityChecker.java has 563 lines of code (exceeds 250 allowed). Consider refactoring.
Open

/*******************************************************************************
 * Copyright (c) 2015 Federal Institute for Risk Assessment (BfR), Germany
 *
 * This program is free software: you can redistribute it and/or modify
 * it under the terms of the GNU General Public License as published by
Severity: Major
Found in org.hsh.bfr.db/src/org/hsh/bfr/db/PlausibilityChecker.java - About 1 day to fix

PredictiveModelGeneralInformation has 65 methods (exceeds 20 allowed). Consider refactoring.
Open

@javax.annotation.Generated(value = "io.swagger.codegen.languages.JavaClientCodegen", date = "2019-07-02T16:22:48.194+02:00")
public class PredictiveModelGeneralInformation {
  @SerializedName("name")
  private String name = null;
Severity: Major
Found in de.bund.bfr.knime.fsklab.metadata.model/gen/de/bund/bfr/metadata/swagger/PredictiveModelGeneralInformation.java - About 1 day to fix

DoseResponseModelGeneralInformation has 65 methods (exceeds 20 allowed). Consider refactoring.
Open

@javax.annotation.Generated(value = "io.swagger.codegen.languages.JavaClientCodegen", date = "2019-07-02T16:22:48.194+02:00")
public class DoseResponseModelGeneralInformation {
  @SerializedName("modelName")
  private String modelName = null;
Severity: Major
Found in de.bund.bfr.knime.fsklab.metadata.model/gen/de/bund/bfr/metadata/swagger/DoseResponseModelGeneralInformation.java - About 1 day to fix

OtherModelGeneralInformation has 65 methods (exceeds 20 allowed). Consider refactoring.
Open

@javax.annotation.Generated(value = "io.swagger.codegen.languages.JavaClientCodegen", date = "2019-07-02T16:22:48.194+02:00")
public class OtherModelGeneralInformation {
  @SerializedName("name")
  private String name = null;
Severity: Major
Found in de.bund.bfr.knime.fsklab.metadata.model/gen/de/bund/bfr/metadata/swagger/OtherModelGeneralInformation.java - About 1 day to fix

GenericModelGeneralInformation has 65 methods (exceeds 20 allowed). Consider refactoring.
Open

@javax.annotation.Generated(value = "io.swagger.codegen.languages.JavaClientCodegen", date = "2019-07-02T16:22:48.194+02:00")
public class GenericModelGeneralInformation {
  @SerializedName("name")
  private String name = null;
Severity: Major
Found in de.bund.bfr.knime.fsklab.metadata.model/gen/de/bund/bfr/metadata/swagger/GenericModelGeneralInformation.java - About 1 day to fix

MyDBPanel has 65 methods (exceeds 20 allowed). Consider refactoring.
Open

public class MyDBPanel extends JPanel {
    
    /**
     * 
     */
Severity: Major
Found in org.hsh.bfr.db/src/org/hsh/bfr/db/gui/dbtable/MyDBPanel.java - About 1 day to fix
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