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cBioPortal/iViz

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

      _.each(_.pluck(_vc.studies, 'patients'), function(_arr) {
        _selectedPatients = _selectedPatients.concat(_arr);
      });
Severity: Minor
Found in app/scripts/main.js and 1 other location - About 35 mins to fix
app/scripts/main.js on lines 820..822

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 46.

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

            selectedpatientUIDs: function(newVal, oldVal) {
              if (newVal.length !== oldVal.length) {
                this.selectedPatientsNum = newVal.length;
              }
            },
Severity: Minor
Found in app/scripts/vueCore.js and 1 other location - About 35 mins to fix
app/scripts/vueCore.js on lines 85..89

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 46.

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

              addAttr({
                attr_id: 'sequenced',
                display_name: 'With Mutation Data',
                priority: ismskimpact ? 0 : iViz.priorityManager.getDefaultPriority('sequenced'),
                description: 'If the sample has mutation data'
Severity: Minor
Found in app/scripts/model/dataProxy.js and 1 other location - About 35 mins to fix
app/scripts/model/dataProxy.js on lines 198..203

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 46.

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

            selectedsampleUIDs: function(newVal, oldVal) {
              if (newVal.length !== oldVal.length) {
                this.selectedSamplesNum = newVal.length;
              }
            },
Severity: Minor
Found in app/scripts/vueCore.js and 1 other location - About 35 mins to fix
app/scripts/vueCore.js on lines 90..94

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 46.

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

      _.each(_.pluck(_vc.studies, 'samples'), function(_arr) {
        _selectedSamples = _selectedSamples.concat(_arr);
      });
Severity: Minor
Found in app/scripts/main.js and 1 other location - About 35 mins to fix
app/scripts/main.js on lines 823..825

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 46.

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

Avoid too many return statements within this function.
Open

          return -1;
Severity: Major
Found in app/scripts/model/dataProxy.js - About 30 mins to fix

    Avoid too many return statements within this function.
    Open

            return '>' + formattedValue;
    Severity: Major
    Found in app/scripts/controller/util.js - About 30 mins to fix

      Avoid too many return statements within this function.
      Open

            return _returnValue;
      Severity: Major
      Found in app/scripts/controller/util.js - About 30 mins to fix

        Avoid too many return statements within this function.
        Open

                  return 1;
        Severity: Major
        Found in app/scripts/model/dataProxy.js - About 30 mins to fix

          Avoid too many return statements within this function.
          Open

                  return b.numOfDatum - a.numOfDatum;
          Severity: Major
          Found in app/scripts/model/dataProxy.js - About 30 mins to fix

            Similar blocks of code found in 4 locations. Consider refactoring.
            Open

                              _.each(geneSampleMap, function(item) {
                    item.sampleUids = item.sampleUids.concat(panelSamplesMap[isProfiledPanelId]);
                  });
            Severity: Major
            Found in app/scripts/model/dataProxy.js and 3 other locations - About 30 mins to fix
            app/scripts/main.js on lines 431..433
            app/scripts/main.js on lines 503..505
            app/scripts/views/components/dataTable/tableView.js on lines 143..145

            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 45.

            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

                            _.each(caseList.sequencedSampleIds, function(sampleId) {
                  _sequencedCaseUIDs.push(_studyToSampleToPatientMap[studyId].sample_to_uid[sampleId]);
                });
            Severity: Minor
            Found in app/scripts/model/dataProxy.js and 2 other locations - About 30 mins to fix
            app/scripts/model/dataProxy.js on lines 118..120
            app/scripts/model/dataProxy.js on lines 124..126

            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 45.

            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 4 locations. Consider refactoring.
            Open

                      _.each(selectedMap_, function(content) {
            content.case_uids = iViz.util.unique(content.case_ids);
          });
            Severity: Major
            Found in app/scripts/views/components/dataTable/tableView.js and 3 other locations - About 30 mins to fix
            app/scripts/main.js on lines 431..433
            app/scripts/main.js on lines 503..505
            app/scripts/model/dataProxy.js on lines 1452..1454

            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 45.

            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

                            _.each(caseList.allSampleIds, function(sampleId) {
                  _allCaseUIDs.push(_studyToSampleToPatientMap[studyId].sample_to_uid[sampleId]);
                });
            Severity: Minor
            Found in app/scripts/model/dataProxy.js and 2 other locations - About 30 mins to fix
            app/scripts/model/dataProxy.js on lines 118..120
            app/scripts/model/dataProxy.js on lines 121..123

            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 45.

            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

                            _.each(caseList.cnaSampleIds, function(sampleId) {
                  _cnaCaseUIDs.push(_studyToSampleToPatientMap[studyId].sample_to_uid[sampleId]);
                });
            Severity: Minor
            Found in app/scripts/model/dataProxy.js and 2 other locations - About 30 mins to fix
            app/scripts/model/dataProxy.js on lines 121..123
            app/scripts/model/dataProxy.js on lines 124..126

            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 45.

            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 (_hasMutationData) {
                    if (_sequencedCaseUIdsMap[_sampleUID] !== undefined) {
                      _sampleDatum.sequenced = 'YES';
                    }
                    _sampleDatum.mutated_genes = [];
            Severity: Minor
            Found in app/scripts/model/dataProxy.js and 1 other location - About 30 mins to fix
            app/scripts/model/dataProxy.js on lines 354..359

            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 45.

            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 4 locations. Consider refactoring.
            Open

                  _.each(_cnaMeta, function(content) {
        content.case_uids = iViz.util.unique(content.case_ids);
      });
            Severity: Major
            Found in app/scripts/main.js and 3 other locations - About 30 mins to fix
            app/scripts/main.js on lines 431..433
            app/scripts/model/dataProxy.js on lines 1452..1454
            app/scripts/views/components/dataTable/tableView.js on lines 143..145

            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 45.

            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 (_hasCnaSegmentData) {
                    if (_cnaCaseUIdsMap[_sampleUID] !== undefined) {
                      _sampleDatum.has_cna_data = 'YES';
                    }
                    _sampleDatum.cna_details = [];
            Severity: Minor
            Found in app/scripts/model/dataProxy.js and 1 other location - About 30 mins to fix
            app/scripts/model/dataProxy.js on lines 348..353

            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 45.

            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 4 locations. Consider refactoring.
            Open

                  _.each(_mutGeneMeta, function(content) {
        content.case_uids = iViz.util.unique(content.case_ids);
      });
            Severity: Major
            Found in app/scripts/main.js and 3 other locations - About 30 mins to fix
            app/scripts/main.js on lines 503..505
            app/scripts/model/dataProxy.js on lines 1452..1454
            app/scripts/views/components/dataTable/tableView.js on lines 143..145

            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 45.

            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 (this.data.meta[Math.ceil((this.data.meta.length * (1 / 2)))] < 0.001 &&
            Severity: Minor
            Found in app/scripts/views/components/barChart/barChartTemplate.js and 1 other location - About 30 mins to fix
            app/scripts/views/components/barChart/barChartTemplate.js on lines 185..185

            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 45.

            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

            Severity
            Category
            Status
            Source
            Language