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

    public GenericModelModelMath retrieveModelMath(Sheet sheet) {

        GenericModelModelMath math = new GenericModelModelMath();

        for (int rownum = MM_PARAMETER_ROW; rownum < sheet.getLastRowNum(); rownum++) {
Severity: Major
Found in de.bund.bfr.knime.fsklab.metadata.model/src/metadata/SwaggerExposureSheetImporter.java and 1 other location - About 1 hr to fix
de.bund.bfr.knime.fsklab.metadata.model/src/metadata/SwaggerDoseResponseSheetImporter.java on lines 333..357

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 102.

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

        for (int i = 0; i < reader.getAllTuples().size(); i++) {
            KnimeTuple tuple = reader.getAllTuples().get(i);
            String id = reader.getAllIds().get(i);

            if (idSet.contains(id)) {
Severity: Major
Found in de.bund.bfr.knime.pmm.nodes/src/de/bund/bfr/knime/pmm/primarymodelviewandselect/PrimaryModelViewAndSelectNodeModel.java and 1 other location - About 1 hr to fix
de.bund.bfr.knime.pmm.nodes/src/de/bund/bfr/knime/pmm/dataviewandselect/DataViewAndSelectNodeModel.java on lines 87..98

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 102.

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

                for (String param : miscParams) {
                    plotable.addValueList(param, miscs.get(param));

                    if (categories.get(param) == null
                            || categories.get(param).equals(
Severity: Major
Found in de.bund.bfr.knime.pmm.nodes/src/de/bund/bfr/knime/pmm/secondarymodelanddataview/TableReader.java and 1 other location - About 1 hr to fix
de.bund.bfr.knime.pmm.nodes/src/de/bund/bfr/knime/pmm/secondarypredictorview/TableReader.java on lines 398..410

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 102.

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

    public void loadFromNodeSettings(NodeSettingsRO settings) {
        name = SettingsHelper.getString("name", settings);
        origname = SettingsHelper.getString("origname", settings);
        min = SettingsHelper.getDouble("min", settings);
        max = SettingsHelper.getDouble("max", settings);
Severity: Major
Found in de.bund.bfr.knime.pmm.nodes/src/de/bund/bfr/knime/pmm/js/common/Dep.java and 1 other location - About 1 hr to fix
de.bund.bfr.knime.pmm.nodes/src/de/bund/bfr/knime/pmm/js/common/Indep.java on lines 94..102

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 102.

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

        } else {
            conditions = null;
            conditionMinValues = null;
            conditionMaxValues = null;
            conditionUnits = null;
Severity: Major
Found in de.bund.bfr.knime.pmm.nodes/src/de/bund/bfr/knime/pmm/secondarypredictorview/TableReader.java and 1 other location - About 1 hr to fix
de.bund.bfr.knime.pmm.nodes/src/de/bund/bfr/knime/pmm/secondarymodelanddataview/TableReader.java on lines 154..167

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 102.

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

    public void loadFromNodeSettings(NodeSettingsRO settings) {
        name = SettingsHelper.getString("name", settings);
        origname = SettingsHelper.getString("origname", settings);
        min = SettingsHelper.getDouble("min", settings);
        max = SettingsHelper.getDouble("max", settings);
Severity: Major
Found in de.bund.bfr.knime.pmm.nodes/src/de/bund/bfr/knime/pmm/js/common/Indep.java and 1 other location - About 1 hr to fix
de.bund.bfr.knime.pmm.nodes/src/de/bund/bfr/knime/pmm/js/common/Dep.java on lines 75..83

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 102.

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

        } else {
            conditions = null;
            conditionMinValues = null;
            conditionMaxValues = null;
            conditionUnits = null;
Severity: Major
Found in de.bund.bfr.knime.pmm.nodes/src/de/bund/bfr/knime/pmm/secondarymodelanddataview/TableReader.java and 1 other location - About 1 hr to fix
de.bund.bfr.knime.pmm.nodes/src/de/bund/bfr/knime/pmm/secondarypredictorview/TableReader.java on lines 152..165

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 102.

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

                for (String param : miscParams) {
                    plotable.addValueList(param, miscs.get(param));

                    if (categories.get(param) == null
                            || categories.get(param).equals(
Severity: Major
Found in de.bund.bfr.knime.pmm.nodes/src/de/bund/bfr/knime/pmm/secondarypredictorview/TableReader.java and 1 other location - About 1 hr to fix
de.bund.bfr.knime.pmm.nodes/src/de/bund/bfr/knime/pmm/secondarymodelanddataview/TableReader.java on lines 405..417

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 102.

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

package de.bund.bfr.knime.util;

import static org.junit.Assert.assertEquals;

import org.junit.Test;
Severity: Major
Found in de.bund.bfr.knime.foodprocess.tests/src/de/bund/bfr/knime/util/MatrixTest.java and 1 other location - About 1 hr to fix
de.bund.bfr.knime.foodprocess.tests/src/de/bund/bfr/knime/util/AgentTest.java on lines 1..30

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 102.

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

        else {
            iarr = new int[lage.size()];
            narr = new String[lage.size()];
            for (int i=0;i<lage.size();i++) {
                if (lage.get(i) != null) {
Severity: Major
Found in de.bund.bfr.knime.foodprocess/src/de/bund/bfr/knime/foodprocess/addons/AddonC.java and 1 other location - About 1 hr to fix
de.bund.bfr.knime.foodprocess/src/de/bund/bfr/knime/foodprocess/addons/AddonC.java on lines 181..190

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 102.

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 (forMatrices) {
            iarr = new int[lmat.size()];
            narr = new String[lmat.size()];
            for (int i=0;i<lmat.size();i++) {
                if (lmat.get(i) != null) {
Severity: Major
Found in de.bund.bfr.knime.foodprocess/src/de/bund/bfr/knime/foodprocess/addons/AddonC.java and 1 other location - About 1 hr to fix
de.bund.bfr.knime.foodprocess/src/de/bund/bfr/knime/foodprocess/addons/AddonC.java on lines 191..200

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 102.

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

package de.bund.bfr.knime.util;

import static org.junit.Assert.assertEquals;

import org.junit.Test;
Severity: Major
Found in de.bund.bfr.knime.foodprocess.tests/src/de/bund/bfr/knime/util/AgentTest.java and 1 other location - About 1 hr to fix
de.bund.bfr.knime.foodprocess.tests/src/de/bund/bfr/knime/util/MatrixTest.java on lines 1..30

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 102.

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 retrieveAssay has 38 lines of code (exceeds 25 allowed). Consider refactoring.
Open

    public Assay retrieveAssay(Row row) {
        // Check first mandatory properties
        if (row.getCell(L).getCellType() != Cell.CELL_TYPE_STRING) {
            throw new IllegalArgumentException("Missing assay name");
        }
Severity: Minor
Found in de.bund.bfr.knime.fsklab.metadata.model/src/metadata/SwaggerDataModelSheetImporter.java - About 1 hr to fix

Method retrieveAssay has 38 lines of code (exceeds 25 allowed). Consider refactoring.
Open

    public Assay retrieveAssay(Row row) {
        // Check first mandatory properties
        if (row.getCell(L).getCellType() != Cell.CELL_TYPE_STRING) {
            throw new IllegalArgumentException("Missing assay name");
        }
Severity: Minor
Found in de.bund.bfr.knime.fsklab.metadata.model/src/metadata/SwaggerConsumptionSheetImporter.java - About 1 hr to fix

Method retrieveAssay has 38 lines of code (exceeds 25 allowed). Consider refactoring.
Open

    public Assay retrieveAssay(Row row) {
        // Check first mandatory properties
        if (row.getCell(L).getCellType() != Cell.CELL_TYPE_STRING) {
            throw new IllegalArgumentException("Missing assay name");
        }
Severity: Minor
Found in de.bund.bfr.knime.fsklab.metadata.model/src/metadata/SwaggerOtherModelSheetImporter.java - About 1 hr to fix

Method retrieveAssay has 38 lines of code (exceeds 25 allowed). Consider refactoring.
Open

    public Assay retrieveAssay(Row row) {
        // Check first mandatory properties
        if (row.getCell(L).getCellType() != Cell.CELL_TYPE_STRING) {
            throw new IllegalArgumentException("Missing assay name");
        }
Severity: Minor
Found in de.bund.bfr.knime.fsklab.metadata.model/src/metadata/RAKIPSheetImporter.java - About 1 hr to fix

Method retrieveAssay has 38 lines of code (exceeds 25 allowed). Consider refactoring.
Open

    public Assay retrieveAssay(Row row) {
        // Check first mandatory properties
        if (row.getCell(L).getCellType() != Cell.CELL_TYPE_STRING) {
            throw new IllegalArgumentException("Missing assay name");
        }
Severity: Minor
Found in de.bund.bfr.knime.fsklab.metadata.model/src/metadata/SwaggerHealthModelSheetImporter.java - About 1 hr to fix

Method retrieveAssay has 38 lines of code (exceeds 25 allowed). Consider refactoring.
Open

    public Assay retrieveAssay(Row row) {
        // Check first mandatory properties
        if (row.getCell(L).getCellType() != Cell.CELL_TYPE_STRING) {
            throw new IllegalArgumentException("Missing assay name");
        }
Severity: Minor
Found in de.bund.bfr.knime.fsklab.metadata.model/src/metadata/SwaggerToxicologicalSheetImporter.java - About 1 hr to fix

Method retrieveAssay has 38 lines of code (exceeds 25 allowed). Consider refactoring.
Open

    public Assay retrieveAssay(Row row) {
        // Check first mandatory properties
        if (row.getCell(L).getCellType() != Cell.CELL_TYPE_STRING) {
            throw new IllegalArgumentException("Missing assay name");
        }
Severity: Minor
Found in de.bund.bfr.knime.fsklab.metadata.model/src/metadata/SwaggerRiskModelSheetImporter.java - About 1 hr to fix

Method retrieveAssay has 38 lines of code (exceeds 25 allowed). Consider refactoring.
Open

    public Assay retrieveAssay(Row row) {
        // Check first mandatory properties
        if (row.getCell(L).getCellType() != Cell.CELL_TYPE_STRING) {
            throw new IllegalArgumentException("Missing assay name");
        }
Severity: Minor
Found in de.bund.bfr.knime.fsklab.metadata.model/src/metadata/SwaggerPredictiveModelSheetImporter.java - About 1 hr to fix
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