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de.bund.bfr.knime.pmm.nodes/src/de/bund/bfr/knime/pmm/predictorview/TableReader.java

Summary

Maintainability
D
3 days
Test Coverage

File TableReader.java has 665 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/predictorview/TableReader.java - About 1 day to fix

TableReader has 27 methods (exceeds 20 allowed). Consider refactoring.
Open

public class TableReader {

    private static final String IDENTIFIER = "Identifier";

    private List<String> ids;
Severity: Minor
Found in de.bund.bfr.knime.pmm.nodes/src/de/bund/bfr/knime/pmm/predictorview/TableReader.java - About 3 hrs to fix

Avoid deeply nested control flow statements.
Open

                        for (PmmXmlElementConvertable el : tuple.getPmmXml(
                                TimeSeriesSchema.ATT_MISC).getElementSet()) {
                            MiscXml element = (MiscXml) el;

                            if (miscParams.get(i).equals(element.name)) {
Severity: Major
Found in de.bund.bfr.knime.pmm.nodes/src/de/bund/bfr/knime/pmm/predictorview/TableReader.java - About 45 mins to fix

Avoid deeply nested control flow statements.
Open

                        if (lagParams.containsKey(oldID)) {
                            newLagParams.put(newID, lagParams.get(oldID));
                        }
Severity: Major
Found in de.bund.bfr.knime.pmm.nodes/src/de/bund/bfr/knime/pmm/predictorview/TableReader.java - About 45 mins to fix

Method getConcentrationRange has a Cognitive Complexity of 8 (exceeds 5 allowed). Consider refactoring.
Open

    private static Point2D getConcentrationRange(List<KnimeTuple> tuples) {
        double min = Double.POSITIVE_INFINITY;
        double max = Double.NEGATIVE_INFINITY;

        for (KnimeTuple tuple : tuples) {
Severity: Minor
Found in de.bund.bfr.knime.pmm.nodes/src/de/bund/bfr/knime/pmm/predictorview/TableReader.java - About 45 mins to fix

Cognitive Complexity

Cognitive Complexity is a measure of how difficult a unit of code is to intuitively understand. Unlike Cyclomatic Complexity, which determines how difficult your code will be to test, Cognitive Complexity tells you how difficult your code will be to read and comprehend.

A method's cognitive complexity is based on a few simple rules:

  • Code is not considered more complex when it uses shorthand that the language provides for collapsing multiple statements into one
  • Code is considered more complex for each "break in the linear flow of the code"
  • Code is considered more complex when "flow breaking structures are nested"

Further reading

Avoid deeply nested control flow statements.
Open

                        if (initParams.containsKey(oldID)) {
                            newInitParams.put(newID, initParams.get(oldID));
                        }
Severity: Major
Found in de.bund.bfr.knime.pmm.nodes/src/de/bund/bfr/knime/pmm/predictorview/TableReader.java - About 45 mins to fix

Avoid deeply nested control flow statements.
Open

                        if (miscParams.get(i).equals(element.name)) {
                            min = element.min;
                            max = element.max;
                            unit = element.unit;
                            break;
Severity: Major
Found in de.bund.bfr.knime.pmm.nodes/src/de/bund/bfr/knime/pmm/predictorview/TableReader.java - About 45 mins to fix

Avoid deeply nested control flow statements.
Open

                        if (unit != null) {
                            units.put(miscParams.get(i), unit);
                            categories.put(
                                    miscParams.get(i),
                                    Arrays.asList(Categories.getCategoryByUnit(
Severity: Major
Found in de.bund.bfr.knime.pmm.nodes/src/de/bund/bfr/knime/pmm/predictorview/TableReader.java - About 45 mins to fix

Refactor this method to reduce its Cognitive Complexity from 204 to the 15 allowed.
Open

    public TableReader(List<KnimeTuple> tuples, Map<String, String> initParams,
Severity: Critical
Found in de.bund.bfr.knime.pmm.nodes/src/de/bund/bfr/knime/pmm/predictorview/TableReader.java by sonar-java

Cognitive Complexity is a measure of how hard the control flow of a method is to understand. Methods with high Cognitive Complexity will be difficult to maintain.

See

Define a constant instead of duplicating this literal "Comment" 3 times.
Open

            stringColumns.put("Comment", new ArrayList<String>());
Severity: Critical
Found in de.bund.bfr.knime.pmm.nodes/src/de/bund/bfr/knime/pmm/predictorview/TableReader.java by sonar-java

Duplicated string literals make the process of refactoring error-prone, since you must be sure to update all occurrences.

On the other hand, constants can be referenced from many places, but only need to be updated in a single place.

Noncompliant Code Example

With the default threshold of 3:

public void run() {
  prepare("action1");                              // Noncompliant - "action1" is duplicated 3 times
  execute("action1");
  release("action1");
}

@SuppressWarning("all")                            // Compliant - annotations are excluded
private void method1() { /* ... */ }
@SuppressWarning("all")
private void method2() { /* ... */ }

public String method3(String a) {
  System.out.println("'" + a + "'");               // Compliant - literal "'" has less than 5 characters and is excluded
  return "";                                       // Compliant - literal "" has less than 5 characters and is excluded
}

Compliant Solution

private static final String ACTION_1 = "action1";  // Compliant

public void run() {
  prepare(ACTION_1);                               // Compliant
  execute(ACTION_1);
  release(ACTION_1);
}

Exceptions

To prevent generating some false-positives, literals having less than 5 characters are excluded.

Identical blocks of code found in 3 locations. Consider refactoring.
Open

            if (!plotable.isPlotable()) {
                stringColumns.get(ChartConstants.STATUS).add(
                        ChartConstants.FAILED);
            } else if (PmmUtilities.isOutOfRange(paramXml)) {
                stringColumns.get(ChartConstants.STATUS).add(
Severity: Major
Found in de.bund.bfr.knime.pmm.nodes/src/de/bund/bfr/knime/pmm/predictorview/TableReader.java and 2 other locations - About 1 hr to fix
de.bund.bfr.knime.pmm.nodes/src/de/bund/bfr/knime/pmm/modelselectiontertiary/TableReader.java on lines 474..485
de.bund.bfr.knime.pmm.nodes/src/de/bund/bfr/knime/pmm/primarymodelviewandselect/TableReader.java on lines 458..469

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 96.

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 4 locations. Consider refactoring.
Open

                if (tuple.getString(TimeSeriesSchema.ATT_COMBASEID) != null) {
                    dataName = tuple.getString(TimeSeriesSchema.ATT_COMBASEID);
                } else {
                    dataName = "" + tuple.getInt(TimeSeriesSchema.ATT_CONDID);
                }
Severity: Major
Found in de.bund.bfr.knime.pmm.nodes/src/de/bund/bfr/knime/pmm/predictorview/TableReader.java and 3 other locations - About 40 mins to fix
de.bund.bfr.knime.pmm.nodes/src/de/bund/bfr/knime/pmm/dataviewandselect/TableReader.java on lines 133..137
de.bund.bfr.knime.pmm.nodes/src/de/bund/bfr/knime/pmm/modelselectiontertiary/TableReader.java on lines 331..335
de.bund.bfr.knime.pmm.nodes/src/de/bund/bfr/knime/pmm/primarymodelviewandselect/TableReader.java on lines 321..325

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 50.

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 4 locations. Consider refactoring.
Open

            for (String param : miscParams) {
                conditions.add(param);
                conditionMinValues.add(new ArrayList<Double>());
                conditionMaxValues.add(new ArrayList<Double>());
                conditionUnits.add(new ArrayList<String>());
Severity: Major
Found in de.bund.bfr.knime.pmm.nodes/src/de/bund/bfr/knime/pmm/predictorview/TableReader.java and 3 other locations - About 40 mins to fix
de.bund.bfr.knime.pmm.nodes/src/de/bund/bfr/knime/pmm/fittedparameterview/TableReader.java on lines 93..99
de.bund.bfr.knime.pmm.nodes/src/de/bund/bfr/knime/pmm/secondarymodelanddataview/TableReader.java on lines 135..141
de.bund.bfr.knime.pmm.nodes/src/de/bund/bfr/knime/pmm/secondarypredictorview/TableReader.java on lines 133..139

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 50.

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 (element.max != null) {
                    varData.put(element.name + " Max", element.max
                            + " " + units.get(element.name));
                }
Severity: Minor
Found in de.bund.bfr.knime.pmm.nodes/src/de/bund/bfr/knime/pmm/predictorview/TableReader.java and 1 other location - About 35 mins to fix
de.bund.bfr.knime.pmm.nodes/src/de/bund/bfr/knime/pmm/predictorview/TableReader.java on lines 635..638

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 44.

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 (element.min != null) {
                    varData.put(element.name + " Min", element.min
                            + " " + units.get(element.name));
                }
Severity: Minor
Found in de.bund.bfr.knime.pmm.nodes/src/de/bund/bfr/knime/pmm/predictorview/TableReader.java and 1 other location - About 35 mins to fix
de.bund.bfr.knime.pmm.nodes/src/de/bund/bfr/knime/pmm/predictorview/TableReader.java on lines 640..643

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 44.

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 (PmmXmlElementConvertable el2 : paramXml
                            .getElementSet()) {
                        cov.put(((ParamXml) el2).name, element.correlations.get(((ParamXml) el2).origName));
                    }
Severity: Minor
Found in de.bund.bfr.knime.pmm.nodes/src/de/bund/bfr/knime/pmm/predictorview/TableReader.java and 1 other location - About 30 mins to fix
de.bund.bfr.knime.pmm.nodes/src/de/bund/bfr/knime/pmm/primarymodelviewandselect/TableReader.java on lines 261..263

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 40.

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

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