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

                    if (MathUtilities.isValid(min)) {
                        try {
                            constraints.add(new Constraint(parse(name + ">=" + min), 2, 4));
                        } catch (ParseException e) {
                            e.printStackTrace();
Severity: Minor
Found in de.bund.bfr.knime.pmm.nodes/src/de/bund/bfr/knime/pmm/sbmlwriter/SBMLWriterNodeModel.java and 1 other location - About 40 mins to fix
de.bund.bfr.knime.pmm.nodes/src/de/bund/bfr/knime/pmm/sbmlwriter/SBMLWriterNodeModel.java on lines 335..341

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 48.

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 rmsFieldFocusLost(FocusEvent e) {
        ParametricModel pm = table.getPM();
        if (pm != null) {
            try {
                pm.setRms(rmsField.getValue());
Severity: Minor
Found in de.bund.bfr.knime.pmm.nodes/src/de/bund/bfr/knime/pmm/manualmodelconf/ui/MMC_M.java and 1 other location - About 40 mins to fix
de.bund.bfr.knime.pmm.nodes/src/de/bund/bfr/knime/pmm/manualmodelconf/ui/MMC_M.java on lines 914..923

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 48.

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

                new String[]{"Bezeichnung",
                "Quantitativ","Identifizierung","Typisierung",
                "Methoden",
                "Matrix","MatrixDetail",
                "Agens","AgensDetail",
Severity: Minor
Found in org.hsh.bfr.db/src/org/hsh/bfr/db/MyDBTablesNew.java and 1 other location - About 40 mins to fix
org.hsh.bfr.db/src/org/hsh/bfr/db/MyDBTablesNew.java on lines 814..821

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 48.

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 (defAgent != null) {
            //c.getConfig("MdReaderUi").addInt(MdReaderUi.PARAM_AGENTID, defAgent);
            mdReaderUi.setAgensID(defAgent);
            mdReaderUi.setAgentString(""+DBKernel.getValue(db.getConnection(), "Agenzien", "ID", defAgent+"", "Agensname"));
        }
Severity: Minor
Found in de.bund.bfr.knime.pmm.nodes/src/de/bund/bfr/knime/pmm/estimatedmodelreader/EmReaderUi.java and 1 other location - About 40 mins to fix
de.bund.bfr.knime.pmm.nodes/src/de/bund/bfr/knime/pmm/estimatedmodelreader/EmReaderUi.java on lines 614..618

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 48.

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 (dialog.isApproved()) {
                    for (int i = 0; i < table.getModel().getRowCount(); i++) {
                        table.getModel().setValueAt(dialog.getScore(), i, index);
                    }
                }
Severity: Minor
Found in de.bund.bfr.knime.pmm.nodes/src/de/bund/bfr/knime/pmm/microbialdataedit/MicrobialDataEditNodeDialog.java and 1 other location - About 40 mins to fix
de.bund.bfr.knime.pmm.nodes/src/de/bund/bfr/knime/pmm/microbialdataedit/MicrobialDataEditNodeDialog.java on lines 563..567

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 48.

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 (StringUtils.isNotEmpty(viewValue.modelScriptTree)) {
      File configFile = new File(settingsFolder, "sourceTree.json");
      try {
        FileUtils.writeStringToFile(configFile, viewValue.modelScriptTree, StandardCharsets.UTF_8);
      } catch (IOException e) {
Severity: Minor
Found in de.bund.bfr.knime.fsklab.deprecatednodes/src-1_9_0/de/bund/bfr/knime/fsklab/v1_9/joiner/JoinerNodeModel.java and 1 other location - About 40 mins to fix
de.bund.bfr.knime.fsklab.deprecatednodes/src-1_9_0/de/bund/bfr/knime/fsklab/v1_9/joiner/JoinerNodeModel.java on lines 501..508

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 48.

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

  void setMatrixDataFromCompartment(final Compartment compartment) {
    PMFCompartment pmfCompartment = SBMLFactory.createPMFCompartment(compartment);

    if (compartment.isSetName())
      template.setMatrixName(compartment.getName());
Severity: Minor
Found in de.bund.bfr.knime.pmm.nodes/src/de/bund/bfr/knime/pmm/FSMRUtils.java and 1 other location - About 40 mins to fix
de.bund.bfr.knime.pmm.nodes/src/de/bund/bfr/knime/pmm/FSMRUtils.java on lines 295..302

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 48.

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 (StringUtils.isNotEmpty(viewValue.modelMetaData)) {
      File configFile = new File(settingsFolder, "modelMetaData.json");
      try {
        FileUtils.writeStringToFile(configFile, viewValue.modelMetaData, StandardCharsets.UTF_8);
      } catch (IOException e) {
Severity: Minor
Found in de.bund.bfr.knime.fsklab.deprecatednodes/src-1_9_0/de/bund/bfr/knime/fsklab/v1_9/joiner/JoinerNodeModel.java and 1 other location - About 40 mins to fix
de.bund.bfr.knime.fsklab.deprecatednodes/src-1_9_0/de/bund/bfr/knime/fsklab/v1_9/joiner/JoinerNodeModel.java on lines 528..535

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 48.

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 (set.getReferences().containsKey(id)) {
                PmmXmlDoc refXml = new PmmXmlDoc();

                refXml.getElementSet().addAll(set.getReferences().get(id));
                tuple.setValue(TimeSeriesSchema.ATT_LITMD, refXml);
Severity: Minor
Found in de.bund.bfr.knime.pmm.nodes/src/de/bund/bfr/knime/pmm/microbialdataedit/MicrobialDataEditNodeModel.java and 1 other location - About 40 mins to fix
de.bund.bfr.knime.pmm.nodes/src/de/bund/bfr/knime/pmm/microbialdataedit/MicrobialDataEditNodeModel.java on lines 170..176

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 48.

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 join has 5 arguments (exceeds 4 allowed). Consider refactoring.
Open

    private JsonNode join(JsonNode metadataA, Map<String, Object> originalClassA, JsonNode metadataB,
            Map<String, Object> originalClassB, Map<String, Object> targetClass) {
Severity: Minor
Found in de.bund.bfr.knime.fsklab.metadata.model/src/metadata/ConversionUtils.java - About 35 mins to fix

Method doLhm has 5 arguments (exceeds 4 allowed). Consider refactoring.
Open

    private void doLhm(SingleNodeContainer p2Container, LinkedHashMap<Integer, Double> lhm, LinkedHashMap<Integer, Matrix> lhmm, int fromPort, int toKey) throws SQLException {
Severity: Minor
Found in de.bund.bfr.knime.foodprocess/src/de/bund/bfr/knime/foodprocess/ui/CreateWorkflow.java - About 35 mins to fix

Method combineDateProperties has 5 arguments (exceeds 4 allowed). Consider refactoring.
Open

    private static JsonNode combineDateProperties(String key, Map<String, Object> propA, JsonNode metadataA,
            Map<String, Object> propB, JsonNode metadataB) {
Severity: Minor
Found in de.bund.bfr.knime.fsklab.metadata.model/src/metadata/ConversionUtils.java - About 35 mins to fix

Method calculateWeightedMean has 5 arguments (exceeds 4 allowed). Consider refactoring.
Open

    private static Double calculateWeightedMean(Double sum, final Double newVal, final Double partVol, final Double totalVol,
            final String defaultValue) {
Severity: Minor
Found in de.bund.bfr.knime.foodprocess/src/de/bund/bfr/knime/foodprocess/FoodProcessNodeModel.java - About 35 mins to fix

Method combineStringProperties has 5 arguments (exceeds 4 allowed). Consider refactoring.
Open

    private static String combineStringProperties(String key, Map<String, Object> propA, JsonNode metadataA,
            Map<String, Object> propB, JsonNode metadataB) {
Severity: Minor
Found in de.bund.bfr.knime.fsklab.metadata.model/src/metadata/ConversionUtils.java - About 35 mins to fix

Method getListCellRendererComponent has 5 arguments (exceeds 4 allowed). Consider refactoring.
Open

                public Component getListCellRendererComponent(JList<?> list, Object value, int index, boolean isSelected, boolean cellHasFocus) {
Severity: Minor
Found in de.bund.bfr.knime.foodprocess/src/de/bund/bfr/knime/foodprocess/FoodProcessNodeDialog.java - About 35 mins to fix

Method setSetting has 5 arguments (exceeds 4 allowed). Consider refactoring.
Open

    public void setSetting(LinkedList<Double> volumeDef, LinkedList<String> volumeUnitDef, 
            LinkedList<Integer> iarr, LinkedList<String> narr, boolean forMatrices) {
Severity: Minor
Found in de.bund.bfr.knime.foodprocess/src/de/bund/bfr/knime/foodprocess/addons/AddonNodeModel.java - About 35 mins to fix

Method getTableCellEditorComponent has 5 arguments (exceeds 4 allowed). Consider refactoring.
Open

        public Component getTableCellEditorComponent(JTable table, Object value, boolean isSelected, int row,
                int column) {
Severity: Minor
Found in de.bund.bfr.knime.pmm.nodes/src/de/bund/bfr/knime/pmm/microbialdataedit/MicrobialDataEditNodeDialog.java - About 35 mins to fix

Method getTableCellEditorComponent has 5 arguments (exceeds 4 allowed). Consider refactoring.
Open

        public Component getTableCellEditorComponent(JTable table, Object value, boolean isSelected, int row,
                int column) {
Severity: Minor
Found in de.bund.bfr.knime.pmm.nodes/src/de/bund/bfr/knime/pmm/microbialdataedit/MicrobialDataEditNodeDialog.java - About 35 mins to fix

Method getTableCellEditorComponent has 5 arguments (exceeds 4 allowed). Consider refactoring.
Open

        public Component getTableCellEditorComponent(JTable table, Object value, boolean isSelected, int row,
                int column) {
Severity: Minor
Found in de.bund.bfr.knime.pmm.nodes/src/de/bund/bfr/knime/pmm/microbialdataedit/MicrobialDataEditNodeDialog.java - About 35 mins to fix

Method doBuf has 5 arguments (exceeds 4 allowed). Consider refactoring.
Open

    private void doBuf(KnimeTuple tupleM1, PmmTimeSeries tstuple, List<KnimeTuple> rowSec, BufferedDataContainer buf, KnimeSchema ks) {
Severity: Minor
Found in de.bund.bfr.knime.pmm.nodes/src/de/bund/bfr/knime/pmm/manualmodelconf/ManualModelConfNodeModel.java - About 35 mins to fix
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