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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

Function link has 90 lines of code (exceeds 25 allowed). Consider refactoring.
Open

      link: function($scope) {
        $scope.queryStatus = 'Connecting to the server ...';
        $scope.activities = {};
        $scope.experiments = [];
        $scope.topMode = true;
Severity: Major
Found in interface/src/app/signature/signature.js - About 3 hrs to fix

    Function success has 90 lines of code (exceeds 25 allowed). Consider refactoring.
    Open

            function success(responseObject) {
          var edgeList = responseObject.objects;
          // Collect a list of distinct genes for query.
          var geneList = getQueriedGenes(edgeList);
          // Now retrieve the Gene objects using the geneList.
    Severity: Major
    Found in interface/src/app/gene/network/network.js - About 3 hrs to fix

      Function link has 88 lines of code (exceeds 25 allowed). Consider refactoring.
      Open

            link: function($scope) {
        $scope.queryStatus = 'Connecting to the server ...';

        $scope.topMode = true;
        $scope.topNum = 3;
      Severity: Major
      Found in interface/src/app/signature/signature.js - About 3 hrs to fix

        Function success has 74 lines of code (exceeds 25 allowed). Consider refactoring.
        Open

                    function success(responseObject) {
              setGenes(responseObject);
              if (genes.length === 0) {
                self.statusMessage =
                  'Gene(s) not found, please check the gene ID.';
        Severity: Major
        Found in interface/src/app/gene/network/network.js - About 2 hrs to fix

          Function getVolcanoPlotData has 68 lines of code (exceeds 25 allowed). Consider refactoring.
          Open

              getVolcanoPlotData: function() {
      // use sample lists for base-group and comp-group to produce output for
      // the volcano plot of the form:
      //   signature - diff - logsig,
      // where:
          Severity: Major
          Found in interface/src/app/analyze/analysis/sampleBin.js - About 2 hrs to fix

            Function check_and_import has a Cognitive Complexity of 19 (exceeds 5 allowed). Consider refactoring.
            Open

            def check_and_import(file_handle, ml_model, participation_type):
    """Read valid data lines into the database.  An exception will be
    raised if any errors are detected in file_handle.
    """
    signatures_in_file = set()
            Severity: Minor
            Found in adage/analyze/management/commands/import_signature_gene_network.py - About 2 hrs 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

            Function rebuildHeatmapActivity has 64 lines of code (exceeds 25 allowed). Consider refactoring.
            Open

                  rebuildHeatmapActivity: function() {
        if (!this.mlmodel.id) {
          // ignore "rebuild" requests until a model is specified
          $log.info(
            'rebuildHeatmapActivity: skipping because mlmodel=', this.mlmodel
            Severity: Major
            Found in interface/src/app/heatmap.service.js - About 2 hrs to fix

              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

              Cyclomatic complexity is too high in function check_and_import. (9)
              Open

              def check_and_import(file_handle, ml_model, participation_type):
    """Read valid data lines into the database.  An exception will be
    raised if any errors are detected in file_handle.
    """
    signatures_in_file = set()
              Severity: Minor
              Found in adage/analyze/management/commands/import_signature_gene_network.py by radon

              Cyclomatic Complexity

              Cyclomatic Complexity corresponds to the number of decisions a block of code contains plus 1. This number (also called McCabe number) is equal to the number of linearly independent paths through the code. This number can be used as a guide when testing conditional logic in blocks.

              Radon analyzes the AST tree of a Python program to compute Cyclomatic Complexity. Statements have the following effects on Cyclomatic Complexity:

              Construct Effect on CC Reasoning
              if +1 An if statement is a single decision.
              elif +1 The elif statement adds another decision.
              else +0 The else statement does not cause a new decision. The decision is at the if.
              for +1 There is a decision at the start of the loop.
              while +1 There is a decision at the while statement.
              except +1 Each except branch adds a new conditional path of execution.
              finally +0 The finally block is unconditionally executed.
              with +1 The with statement roughly corresponds to a try/except block (see PEP 343 for details).
              assert +1 The assert statement internally roughly equals a conditional statement.
              Comprehension +1 A list/set/dict comprehension of generator expression is equivalent to a for loop.
              Boolean Operator +1 Every boolean operator (and, or) adds a decision point.

              Source: http://radon.readthedocs.org/en/latest/intro.html

              Cyclomatic complexity is too high in method get_annotations. (9)
              Open

                  @staticmethod
    def get_annotations(request=None, **kwargs):
        """
        Return a tab-delimited file containing all samples for every Experiment
        with Sample properties for each and all annotations (by default) or, if
              Severity: Minor
              Found in adage/analyze/api.py by radon

              Cyclomatic Complexity

              Cyclomatic Complexity corresponds to the number of decisions a block of code contains plus 1. This number (also called McCabe number) is equal to the number of linearly independent paths through the code. This number can be used as a guide when testing conditional logic in blocks.

              Radon analyzes the AST tree of a Python program to compute Cyclomatic Complexity. Statements have the following effects on Cyclomatic Complexity:

              Construct Effect on CC Reasoning
              if +1 An if statement is a single decision.
              elif +1 The elif statement adds another decision.
              else +0 The else statement does not cause a new decision. The decision is at the if.
              for +1 There is a decision at the start of the loop.
              while +1 There is a decision at the while statement.
              except +1 Each except branch adds a new conditional path of execution.
              finally +0 The finally block is unconditionally executed.
              with +1 The with statement roughly corresponds to a try/except block (see PEP 343 for details).
              assert +1 The assert statement internally roughly equals a conditional statement.
              Comprehension +1 A list/set/dict comprehension of generator expression is equivalent to a for loop.
              Boolean Operator +1 Every boolean operator (and, or) adds a decision point.

              Source: http://radon.readthedocs.org/en/latest/intro.html

              Cyclomatic complexity is too high in function import_data_line. (9)
              Open

              def import_data_line(line_num, tokens, samples, organism):
    """
    Function that imports numerical values in input tokens into the database.
    An exception will be raised if any of the following errors are detected:
      * The number of columns on this line is not equal to the number of
              Severity: Minor
              Found in adage/analyze/management/commands/import_gene_sample_expr.py by radon

              Cyclomatic Complexity

              Cyclomatic Complexity corresponds to the number of decisions a block of code contains plus 1. This number (also called McCabe number) is equal to the number of linearly independent paths through the code. This number can be used as a guide when testing conditional logic in blocks.

              Radon analyzes the AST tree of a Python program to compute Cyclomatic Complexity. Statements have the following effects on Cyclomatic Complexity:

              Construct Effect on CC Reasoning
              if +1 An if statement is a single decision.
              elif +1 The elif statement adds another decision.
              else +0 The else statement does not cause a new decision. The decision is at the if.
              for +1 There is a decision at the start of the loop.
              while +1 There is a decision at the while statement.
              except +1 Each except branch adds a new conditional path of execution.
              finally +0 The finally block is unconditionally executed.
              with +1 The with statement roughly corresponds to a try/except block (see PEP 343 for details).
              assert +1 The assert statement internally roughly equals a conditional statement.
              Comprehension +1 A list/set/dict comprehension of generator expression is equivalent to a for loop.
              Boolean Operator +1 Every boolean operator (and, or) adds a decision point.

              Source: http://radon.readthedocs.org/en/latest/intro.html

              Function controller has 56 lines of code (exceeds 25 allowed). Consider refactoring.
              Open

                  function(Experiment, Sample, $log) {
      var ctrl = this;

      ctrl.$onInit = function() {
        ctrl.experiment = {
              Severity: Major
              Found in interface/src/app/experiment/experimentDetail.component.js - About 2 hrs to fix

                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

                Severity
                Category
                Status
                Source
                Language