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

class Command(BaseCommand):
    help = ("Import activity data from an input  spreadsheet.")

    def add_arguments(self, parser):
        parser.add_argument('activity_file', type=file)
Severity: Major
Found in adage/analyze/management/commands/import_activity.py and 2 other locations - About 5 hrs to fix
adage/analyze/management/commands/import_gene_network.py on lines 44..59
adage/analyze/management/commands/import_gene_sample_expr.py on lines 42..57

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 109.

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

class Command(BaseCommand):
    help = ("Imports gene-gene network data into Edge table in the database.")

    def add_arguments(self, parser):
        parser.add_argument('gene_network_file', type=file)
Severity: Major
Found in adage/analyze/management/commands/import_gene_network.py and 2 other locations - About 5 hrs to fix
adage/analyze/management/commands/import_activity.py on lines 30..45
adage/analyze/management/commands/import_gene_sample_expr.py on lines 42..57

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 109.

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

class Command(BaseCommand):
    help = ("Import gene-sample expression values from an input file.")

    def add_arguments(self, parser):
        parser.add_argument('expression_filename', type=file)
Severity: Major
Found in adage/analyze/management/commands/import_gene_sample_expr.py and 2 other locations - About 5 hrs to fix
adage/analyze/management/commands/import_activity.py on lines 30..45
adage/analyze/management/commands/import_gene_network.py on lines 44..59

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 109.

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

      ctrl.itemTooltip = function() {
        if (!ctrl.item) {
          return 'initializing...';
        }
Severity: Major
Found in interface/src/app/sampleBin/addItem.component.js and 1 other location - About 4 hrs to fix
interface/src/app/sampleBin/addItemAnalyze.component.js on lines 21..38

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 121.

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

      ctrl.itemTooltip = function() {
        if (!ctrl.item) {
          return 'initializing...';
        }
Severity: Major
Found in interface/src/app/sampleBin/addItemAnalyze.component.js and 1 other location - About 4 hrs to fix
interface/src/app/sampleBin/addItem.component.js on lines 15..32

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 121.

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

    with transaction.atomic():
        samples = []
        for line_index, line in enumerate(file_handle):
            tokens = line.rstrip('\r\n').split('\t')
            if line_index == 0:
Severity: Major
Found in adage/analyze/management/commands/import_gene_sample_expr.py and 1 other location - About 3 hrs to fix
adage/analyze/management/commands/import_activity.py on lines 67..76

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 89.

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

    with transaction.atomic():
        signatures = []
        for line_index, line in enumerate(file_handle):
            tokens = line.rstrip('\r\n').split('\t')
            if line_index == 0:
Severity: Major
Found in adage/analyze/management/commands/import_activity.py and 1 other location - About 3 hrs to fix
adage/analyze/management/commands/import_gene_sample_expr.py on lines 79..87

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 89.

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

angular.module('adage.sampleDetail.view', [
  'ui.router',
  'adage.sampleDetail.component',
  'adage.sampleBin.addItem',
  'adage.sampleBin.addItemAnalyze',
Severity: Major
Found in interface/src/app/sample/sampleDetail.view.js and 3 other locations - About 2 hrs to fix
interface/src/app/experiment/experimentDetail.view.js on lines 4..48
interface/src/app/gene/enriched_signatures.js on lines 5..227
interface/src/app/signature/signature_search.js on lines 5..62

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 89.

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

angular.module('adage.gene.enrichedSignatures', [
  'adage.signature.resources',
  'adage.participation.resources',
  'adage.gene.resource',
  'adage.utils',
Severity: Major
Found in interface/src/app/gene/enriched_signatures.js and 3 other locations - About 2 hrs to fix
interface/src/app/experiment/experimentDetail.view.js on lines 4..48
interface/src/app/sample/sampleDetail.view.js on lines 4..39
interface/src/app/signature/signature_search.js on lines 5..62

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 89.

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

angular.module('adage.experimentDetail.view', [
  'ui.router',
  'adage.experimentDetail.component',
  'adage.sampleBin.addItem',
  'adage.sampleBin.addItemAnalyze',
Severity: Major
Found in interface/src/app/experiment/experimentDetail.view.js and 3 other locations - About 2 hrs to fix
interface/src/app/gene/enriched_signatures.js on lines 5..227
interface/src/app/sample/sampleDetail.view.js on lines 4..39
interface/src/app/signature/signature_search.js on lines 5..62

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 89.

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

angular.module('adage.signatureSearch', [
  'ui.router',
  'ui.bootstrap',
  'adage.mlmodel.components',
  'adage.signature.resources',
Severity: Major
Found in interface/src/app/signature/signature_search.js and 3 other locations - About 2 hrs to fix
interface/src/app/experiment/experimentDetail.view.js on lines 4..48
interface/src/app/gene/enriched_signatures.js on lines 5..227
interface/src/app/sample/sampleDetail.view.js on lines 4..39

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 89.

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

      {
        'annotations': {
          'additional_notes': '9.5 h biofilms',
          'biotic_int_lv_1': 'Human',
          'biotic_int_lv_2': 'Lung epithelial cells (CFBE41o- cells)',
Severity: Major
Found in interface/src/app/sample/sampleMocks.spec.js and 1 other location - About 2 hrs to fix
interface/src/app/sample/sampleMocks.spec.js on lines 4..24

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 88.

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

  sample1: {
    'annotations': {
      'additional_notes': '9.5 h biofilms',
      'biotic_int_lv_1': 'Human',
      'biotic_int_lv_2': 'Lung epithelial cells (CFBE41o- cells)',
Severity: Major
Found in interface/src/app/sample/sampleMocks.spec.js and 1 other location - About 2 hrs to fix
interface/src/app/sample/sampleMocks.spec.js on lines 71..91

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 88.

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

        for i in range(gene_counter):
            Gene.objects.create(entrezid=(i + 1),
                                systematic_name="sys_name #" + str(i + 1),
                                standard_name="std_name #" + str(i + 1),
Severity: Major
Found in adage/analyze/tests.py and 2 other locations - About 2 hrs to fix
adage/analyze/tests.py on lines 244..247
adage/analyze/tests.py on lines 972..975

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 70.

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

        for i in range(num_genes):
            Gene.objects.create(entrezid=(i + 1),
                                systematic_name="sys_name #" + str(i + 1),
                                standard_name="std_name #" + str(i + 1),
Severity: Major
Found in adage/analyze/tests.py and 2 other locations - About 2 hrs to fix
adage/analyze/tests.py on lines 175..178
adage/analyze/tests.py on lines 972..975

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 70.

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

        for i in range(num_genes):
            Gene.objects.create(entrezid=(i + 1),
                                systematic_name="sys_name #" + str(i + 1),
                                standard_name="std_name #" + str(i + 1),
Severity: Major
Found in adage/analyze/tests.py and 2 other locations - About 2 hrs to fix
adage/analyze/tests.py on lines 175..178
adage/analyze/tests.py on lines 244..247

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 70.

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

  afterEach(function() {
    $httpBackend.verifyNoOutstandingExpectation();
    $httpBackend.verifyNoOutstandingRequest();
    // very useful $log capture information from:
    // http://www.jvandemo.com/how-to-access-angular-log-debug-messages-from-within-karma/
Severity: Major
Found in interface/src/app/sample/sampleDetail.component.spec.js and 3 other locations - About 2 hrs to fix
interface/src/app/experiment/experimentDetail.component.spec.js on lines 51..59
interface/src/app/sample_annotation/annotation.spec.js on lines 13..21
interface/src/app/sample.service.spec.js on lines 13..21

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 82.

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

  afterEach(function() {
    $httpBackend.verifyNoOutstandingExpectation();
    $httpBackend.verifyNoOutstandingRequest();
    // very useful $log capture information from:
    // http://www.jvandemo.com/how-to-access-angular-log-debug-messages-from-within-karma/
Severity: Major
Found in interface/src/app/sample_annotation/annotation.spec.js and 3 other locations - About 2 hrs to fix
interface/src/app/experiment/experimentDetail.component.spec.js on lines 51..59
interface/src/app/sample/sampleDetail.component.spec.js on lines 13..21
interface/src/app/sample.service.spec.js on lines 13..21

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 82.

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

  afterEach(function() {
    $httpBackend.verifyNoOutstandingExpectation();
    $httpBackend.verifyNoOutstandingRequest();
    // very useful $log capture information from:
    // http://www.jvandemo.com/how-to-access-angular-log-debug-messages-from-within-karma/
Severity: Major
Found in interface/src/app/experiment/experimentDetail.component.spec.js and 3 other locations - About 2 hrs to fix
interface/src/app/sample/sampleDetail.component.spec.js on lines 13..21
interface/src/app/sample_annotation/annotation.spec.js on lines 13..21
interface/src/app/sample.service.spec.js on lines 13..21

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 82.

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

  afterEach(function() {
    $httpBackend.verifyNoOutstandingExpectation();
    $httpBackend.verifyNoOutstandingRequest();
    // very useful $log capture information from:
    // http://www.jvandemo.com/how-to-access-angular-log-debug-messages-from-within-karma/
Severity: Major
Found in interface/src/app/sample.service.spec.js and 3 other locations - About 2 hrs to fix
interface/src/app/experiment/experimentDetail.component.spec.js on lines 51..59
interface/src/app/sample/sampleDetail.component.spec.js on lines 13..21
interface/src/app/sample_annotation/annotation.spec.js on lines 13..21

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 82.

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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