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Showing 14,752 of 14,752 total issues

Method step has 92 lines of code (exceeds 25 allowed). Consider refactoring.
Open

    private PmmTimeSeries step(BufferedReader reader) throws IOException {
        // initialize next time series
        PmmTimeSeries next = new PmmTimeSeries();

        while (true) {
Severity: Major
Found in de.bund.bfr.knime.pmm.nodes/src/de/bund/bfr/knime/pmm/combaseio/lib/CombaseReader.java - About 3 hrs to fix

File PrimaryJoiner.java has 320 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: Minor
Found in de.bund.bfr.knime.pmm.nodes/src/de/bund/bfr/knime/pmm/modelanddatajoiner/PrimaryJoiner.java - About 3 hrs to fix

Method parse has 92 lines of code (exceeds 25 allowed). Consider refactoring.
Open

        private static TwoStepTertiaryModel parse(List<List<KnimeTuple>> tupleList, boolean isPMFX, int modelNum,
                String mdName, Metadata metadata, String notes) {

            final String modelExtension = isPMFX ? "pmf" : "sbml";
Severity: Major
Found in de.bund.bfr.knime.pmm.nodes/src/de/bund/bfr/knime/pmm/common/writer/WriterUtils.java - About 3 hrs to fix

Method createSbmlDocument has 92 lines of code (exceeds 25 allowed). Consider refactoring.
Open

  private static SBMLDocument createSbmlDocument(final FskMetaData template) {

    // Creates SBMLDocument for the primary model
    final SBMLDocument sbmlDocument = new SBMLDocument(TableReader.LEVEL, TableReader.VERSION);
Severity: Major
Found in de.bund.bfr.knime.fsklab.deprecatednodes/src-prerakip/de/bund/bfr/knime/pmm/fskx/writer/FskxWriterNodeModel.java - About 3 hrs to fix

Method performExecute has 92 lines of code (exceeds 25 allowed). Consider refactoring.
Open

  @Override
  protected PortObject[] performExecute(PortObject[] inObjects, ExecutionContext exec)
      throws Exception {

    MAPPER.enable(DeserializationFeature.ACCEPT_EMPTY_STRING_AS_NULL_OBJECT);
Severity: Major
Found in de.bund.bfr.knime.fsklab.deprecatednodes/src-1_7_2/de/bund/bfr/knime/fsklab/nodes/v1_7_2/joiner/JoinerNodeModel.java - About 3 hrs to fix

SettingsHelper has 30 methods (exceeds 20 allowed). Consider refactoring.
Open

public class SettingsHelper {

    private static final String CFGKEY_FILENAME = "FileName";
    private static final String CFGKEY_SHEETNAME = "SheetName";
    private static final String CFG_PRESERVE_IDS = "PreserveIds";
Severity: Minor
Found in de.bund.bfr.knime.pmm.nodes/src/de/bund/bfr/knime/pmm/xlstimeseriesreader/SettingsHelper.java - About 3 hrs to fix

ChartSelectionPanel has 30 methods (exceeds 20 allowed). Consider refactoring.
Open

public class ChartSelectionPanel extends JPanel implements ActionListener,
        CellEditorListener, ListSelectionListener {

    private static final String ID = "ID";
    private static final String SELECTED = "Selected";
Severity: Minor
Found in de.bund.bfr.knime.pmm.common/src/de/bund/bfr/knime/pmm/common/chart/ChartSelectionPanel.java - About 3 hrs to fix

KnimeTuple has 30 methods (exceeds 20 allowed). Consider refactoring.
Open

public class KnimeTuple implements DataRow {

    private KnimeSchema schema;
    private DataCell[] cell;
Severity: Minor
Found in de.bund.bfr.knime.pmm.common/src/de/bund/bfr/knime/pmm/common/generictablemodel/KnimeTuple.java - About 3 hrs to fix

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

    static {
      try {
        // ObjectMapper defaults to use a JsonFactory that automatically closes
        // the stream. When further entries are added to the archive the stream
        // is closed and fails. The AUTO_CLOSE_TARGET needs to be disabled.
Severity: Major
Found in de.bund.bfr.knime.fsklab.nodes/src/de/bund/bfr/knime/fsklab/v2_0/CombinedFskPortObject.java and 1 other location - About 3 hrs to fix
de.bund.bfr.knime.fsklab.deprecatednodes/src-1_9_0/de/bund/bfr/knime/fsklab/v1_9/CombinedFskPortObject.java on lines 241..274

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

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

    static {
      try {
        // ObjectMapper defaults to use a JsonFactory that automatically closes
        // the stream. When further entries are added to the archive the stream
        // is closed and fails. The AUTO_CLOSE_TARGET needs to be disabled.
Severity: Major
Found in de.bund.bfr.knime.fsklab.deprecatednodes/src-1_9_0/de/bund/bfr/knime/fsklab/v1_9/CombinedFskPortObject.java and 1 other location - About 3 hrs to fix
de.bund.bfr.knime.fsklab.nodes/src/de/bund/bfr/knime/fsklab/v2_0/CombinedFskPortObject.java on lines 237..270

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

            if (rs != null && rs.first()) {
                do  {
                    System.err.println(rs.getObject("Artikelnummer") + "\t" + rs.getObject("Bezeichnung") + "\t" + rs.getObject("ChargenNr") + "\t" +
                            rs.getObject("MHD_day") + "\t" + rs.getObject("MHD_month") + "\t" + rs.getObject("MHD_year") + "\t" +
                            rs.getObject("pd_day") + "\t" + rs.getObject("pd_month") + "\t" + rs.getObject("pd_year") + "\t" +
Severity: Major
Found in org.hsh.bfr.db/src/org/hsh/bfr/db/gui/actions/PlausibleAction.java and 1 other location - About 3 hrs to fix
org.hsh.bfr.db/src/org/hsh/bfr/db/gui/actions/PlausibleAction.java on lines 242..250

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

            if (rs != null && rs.first()) {
                do  {
                    System.err.println(rs.getInt("Station") + "\t" + rs.getObject("Artikelnummer") + "\t" + rs.getObject("Bezeichnung") + "\t" + rs.getObject("ChargenNr") + "\t" +
                            rs.getObject("MHD_day") + "\t" + rs.getObject("MHD_month") + "\t" + rs.getObject("MHD_year") + "\t" +
                            rs.getObject("pd_day") + "\t" + rs.getObject("pd_month") + "\t" + rs.getObject("pd_year") + "\t" +
Severity: Major
Found in org.hsh.bfr.db/src/org/hsh/bfr/db/gui/actions/PlausibleAction.java and 1 other location - About 3 hrs to fix
org.hsh.bfr.db/src/org/hsh/bfr/db/gui/actions/PlausibleAction.java on lines 271..280

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 3 locations. Consider refactoring.
Open

        if (this.options.showPaginationSwitch) {
            html.push(sprintf('<button class="btn' +
                    sprintf(' btn-%s', this.options.buttonsClass) +
                    sprintf(' btn-%s', this.options.iconSize) +
                    '" type="button" name="paginationSwitch" aria-label="pagination Switch" title="%s">',
Severity: Major
Found in de.bund.bfr.knime.pmm.nodes/js-lib/bootstrap-table/1_11_1/debug/js/bootstrap-table.js and 2 other locations - About 3 hrs to fix
de.bund.bfr.knime.pmm.nodes/js-lib/bootstrap-table/1_11_1/debug/js/bootstrap-table.js on lines 1075..1083
de.bund.bfr.knime.pmm.nodes/js-lib/bootstrap-table/1_11_1/debug/js/bootstrap-table.js on lines 1085..1093

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 108.

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 3 locations. Consider refactoring.
Open

        if (this.options.showRefresh) {
            html.push(sprintf('<button class="btn' +
                    sprintf(' btn-%s', this.options.buttonsClass) +
                    sprintf(' btn-%s', this.options.iconSize) +
                    '" type="button" name="refresh" aria-label="refresh" title="%s">',
Severity: Major
Found in de.bund.bfr.knime.pmm.nodes/js-lib/bootstrap-table/1_11_1/debug/js/bootstrap-table.js and 2 other locations - About 3 hrs to fix
de.bund.bfr.knime.pmm.nodes/js-lib/bootstrap-table/1_11_1/debug/js/bootstrap-table.js on lines 1065..1073
de.bund.bfr.knime.pmm.nodes/js-lib/bootstrap-table/1_11_1/debug/js/bootstrap-table.js on lines 1085..1093

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 108.

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 3 locations. Consider refactoring.
Open

        if (this.options.showToggle) {
            html.push(sprintf('<button class="btn' +
                    sprintf(' btn-%s', this.options.buttonsClass) +
                    sprintf(' btn-%s', this.options.iconSize) +
                    '" type="button" name="toggle" aria-label="toggle" title="%s">',
Severity: Major
Found in de.bund.bfr.knime.pmm.nodes/js-lib/bootstrap-table/1_11_1/debug/js/bootstrap-table.js and 2 other locations - About 3 hrs to fix
de.bund.bfr.knime.pmm.nodes/js-lib/bootstrap-table/1_11_1/debug/js/bootstrap-table.js on lines 1065..1073
de.bund.bfr.knime.pmm.nodes/js-lib/bootstrap-table/1_11_1/debug/js/bootstrap-table.js on lines 1075..1083

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 108.

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

Method loadSettings has 91 lines of code (exceeds 25 allowed). Consider refactoring.
Open

    public void loadSettings(NodeSettingsRO settings) {
        try {
            selectedIDs = XmlConverter.xmlToObject(
                    settings.getString(CFG_SELECTEDIDS),
                    new ArrayList<String>());
Severity: Major
Found in de.bund.bfr.knime.pmm.nodes/src/de/bund/bfr/knime/pmm/dataviewandselect/SettingsHelper.java - About 3 hrs to fix

Method deleteFMID has 91 lines of code (exceeds 25 allowed). Consider refactoring.
Open

    private int deleteFMID(Connection conn, int level, Object rowEstMID) {
        int numDBSuccesses = 0;
        Integer firstCLID = DBKernel.getMaxID("ChangeLog");
        if (firstCLID == null)
            firstCLID = 0;
Severity: Major
Found in de.bund.bfr.knime.pmm.nodes/src/de/bund/bfr/knime/pmm/dbdelete/DatabaseDeleteNodeModel.java - About 3 hrs to fix

Method plotFunctionSample has 91 lines of code (exceeds 25 allowed). Consider refactoring.
Open

    private void plotFunctionSample(XYPlot plot, Plotable plotable, String id,
            Color defaultColor, Shape defaultShape, double minX, double maxX,
            List<String> warnings) throws ConvertException {
        double[][] functionPoints = plotable.getFunctionPoints(paramX, paramY,
                unitX, unitY, transformX, transformY, minX, maxX,
Severity: Major
Found in de.bund.bfr.knime.pmm.common/src/de/bund/bfr/knime/pmm/common/chart/ChartCreator.java - About 3 hrs to fix

Function tokenBase has 91 lines of code (exceeds 25 allowed). Consider refactoring.
Open

  function tokenBase(stream, state) {
    var ch = stream.next(),
        mightBeFunction = false,
        isEQName = isEQNameAhead(stream);
Severity: Major
Found in de.bund.bfr.knime.js/js-lib/codemirror-5.49.2/mode/xquery/xquery.js - About 3 hrs to fix

File FittedParameterViewNodeDialog.java has 318 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: Minor
Found in de.bund.bfr.knime.pmm.nodes/src/de/bund/bfr/knime/pmm/fittedparameterview/FittedParameterViewNodeDialog.java - About 3 hrs to fix
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