Sign upLogin

greenelab/adage-server

View on GitHub
Star

Showing 230 of 230 total issues

Function exports has 471 lines of code (exceeds 25 allowed). Consider refactoring.
Open

module.exports = function ( grunt ) {

  /**
   * Load required Grunt tasks. These are installed based on the versions listed
   * in `package.json` when you do `npm install` in this directory.
Severity: Major
Found in interface/Gruntfile.js - About 2 days to fix

    File tests.py has 945 lines of code (exceeds 250 allowed). Consider refactoring.
    Open

    # coding: utf-8 (see https://www.python.org/dev/peps/pep-0263/)

from __future__ import unicode_literals
from __future__ import print_function
import os
    Severity: Major
    Found in adage/analyze/tests.py - About 2 days to fix

      Function GeneNetworkController has a Cognitive Complexity of 103 (exceeds 5 allowed). Consider refactoring.
      Open

          function GeneNetworkController(
      $stateParams, Edge, Signature, Gene, ExpressionValue, $log, errGen,
      $httpParamSerializerJQLike, $scope, MlModelTracker, $timeout
    ) {
      var self = this;
      Severity: Minor
      Found in interface/src/app/gene/network/network.js - About 2 days 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 GeneNetworkController has 414 lines of code (exceeds 25 allowed). Consider refactoring.
      Open

          function GeneNetworkController(
      $stateParams, Edge, Signature, Gene, ExpressionValue, $log, errGen,
      $httpParamSerializerJQLike, $scope, MlModelTracker, $timeout
    ) {
      var self = this;
      Severity: Major
      Found in interface/src/app/gene/network/network.js - About 2 days to fix

        File network.js has 477 lines of code (exceeds 250 allowed). Consider refactoring.
        Open

        /**
 * "adage.gene.network" module.
 */

angular.module('adage.gene.network', [
        Severity: Minor
        Found in interface/src/app/gene/network/network.js - About 7 hrs to fix

          File Gruntfile.js has 473 lines of code (exceeds 250 allowed). Consider refactoring.
          Open

          module.exports = function ( grunt ) {

  /**
   * Load required Grunt tasks. These are installed based on the versions listed
   * in `package.json` when you do `npm install` in this directory.
          Severity: Minor
          Found in interface/Gruntfile.js - About 7 hrs to fix

            Function bootstrap_database has a Cognitive Complexity of 45 (exceeds 5 allowed). Consider refactoring.
            Open

            def bootstrap_database(annotation_fh, dir_name=None):
    """
    Import initial experiment, sample and annotation data to initialize the
    ADAGE database. Assumes we are starting with an empty database, so this
    will fail if any existing data are found that conflict with what is being
            Severity: Minor
            Found in adage/analyze/management/commands/import_data.py - About 6 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

            APIResourceTestCase has 45 functions (exceeds 20 allowed). Consider refactoring.
            Open

            class APIResourceTestCase(ResourceTestCaseMixin, TestCase):
    # API tests:
    # For most of our interfaces, we should be able to GET, but every other
    # REST API should fail: POST, PUT, PATCH, DELETE. There are a few
    # exceptions for which we allow POST but the behavior is the same as GET.
            Severity: Minor
            Found in adage/analyze/tests.py - About 6 hrs to fix

              Function EnrichedSignatureController has 149 lines of code (exceeds 25 allowed). Consider refactoring.
              Open

                function EnrichedSignatureController($stateParams, Signature, Participation,
    Gene, MlModelTracker, MathFuncts, pValueCutoff, pValueDigits, $scope, $q,
    $log, errGen) {
    var self = this;
    self.isValidModel = false;
              Severity: Major
              Found in interface/src/app/gene/enriched_signatures.js - About 5 hrs to fix

                File api.py has 414 lines of code (exceeds 250 allowed). Consider refactoring.
                Open

                from django.conf.urls import url
from django.core.exceptions import ObjectDoesNotExist
from django.db.models import Q
from django.http import HttpResponse
from organisms.api import OrganismResource
                Severity: Minor
                Found in adage/analyze/api.py - About 5 hrs to fix

                  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

                  Cyclomatic complexity is too high in function bootstrap_database. (26)
                  Open

                  

def bootstrap_database(annotation_fh, dir_name=None):
    """
    Import initial experiment, sample and annotation data to initialize the
                  Severity: Minor
                  Found in adage/analyze/management/commands/import_data.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

                  File signature.js has 375 lines of code (exceeds 250 allowed). Consider refactoring.
                  Open

                  /**
 * "adage.signature" module.
 */

angular.module('adage.signature', [
                  Severity: Minor
                  Found in interface/src/app/signature/signature.js - About 5 hrs to fix

                    Function check_and_import has a Cognitive Complexity of 31 (exceeds 5 allowed). Consider refactoring.
                    Open

                    def check_and_import(file_handle, ml_model):
    """Read valid data lines into the database.  An exception will be raised
    if any errors are detected in file_handle.
    """
    # If the database already includes record(s) of the same ml_model,
                    Severity: Minor
                    Found in adage/analyze/management/commands/import_gene_network.py - About 4 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 drawNetwork has 103 lines of code (exceeds 25 allowed). Consider refactoring.
                    Open

                          function drawNetwork() {
        // Calculate svg size.
        var minSvgSize = 600;  // Minimum size of svg.
        var maxSvgSize = 1280; // Maximum size of svg.
        var svgSize = genes.length * 10;
                    Severity: Major
                    Found in interface/src/app/gene/network/network.js - About 4 hrs to fix

                      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

                      Cyclomatic complexity is too high in function check_and_import. (18)
                      Open

                      def check_and_import(file_handle, ml_model):
    """Read valid data lines into the database.  An exception will be raised
    if any errors are detected in file_handle.
    """
    # If the database already includes record(s) of the same ml_model,
                      Severity: Minor
                      Found in adage/analyze/management/commands/import_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

                      Severity
                      Category
                      Status
                      Source
                      Language