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File agreement.py has 755 lines of code (exceeds 250 allowed). Consider refactoring.
Open

import os
import glob
import ntpath
import logging
Severity: Major
Found in src/bratutils/agreement.py - About 1 day to fix

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

            for ctag in ctags:
            if ctag.is_partial_to(tag):
                par = 0
                if tag.comp_status != MucTable.CORRECT:
                    tag.comp_status = MucTable.PARTIAL
    Severity: Major
    Found in src/bratutils/agreement.py and 1 other location - About 5 hrs to fix
    src/bratutils/agreement.py on lines 712..721

    Duplicated Code

    Duplicated code can lead to software that is hard to understand and difficult to change. The Don't Repeat Yourself (DRY) principle states:

    Every piece of knowledge must have a single, unambiguous, authoritative representation within a system.

    When you violate DRY, bugs and maintenance problems are sure to follow. Duplicated code has a tendency to both continue to replicate and also to diverge (leaving bugs as two similar implementations differ in subtle ways).

    Tuning

    This issue has a mass of 96.

    We set useful threshold defaults for the languages we support but you may want to adjust these settings based on your project guidelines.

    The threshold configuration represents the minimum mass a code block must have to be analyzed for duplication. The lower the threshold, the more fine-grained the comparison.

    If the engine is too easily reporting duplication, try raising the threshold. If you suspect that the engine isn't catching enough duplication, try lowering the threshold. The best setting tends to differ from language to language.

    See codeclimate-duplication's documentation for more information about tuning the mass threshold in your .codeclimate.yml.

    Refactorings

    Further Reading

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

                if tag.is_partial_to(ctag):
                par = 0
                if tag.comp_status != MucTable.CORRECT:
                    tag.comp_status = MucTable.PARTIAL
                    par = 1
    Severity: Major
    Found in src/bratutils/agreement.py and 1 other location - About 5 hrs to fix
    src/bratutils/agreement.py on lines 696..706

    Duplicated Code

    Duplicated code can lead to software that is hard to understand and difficult to change. The Don't Repeat Yourself (DRY) principle states:

    Every piece of knowledge must have a single, unambiguous, authoritative representation within a system.

    When you violate DRY, bugs and maintenance problems are sure to follow. Duplicated code has a tendency to both continue to replicate and also to diverge (leaving bugs as two similar implementations differ in subtle ways).

    Tuning

    This issue has a mass of 96.

    We set useful threshold defaults for the languages we support but you may want to adjust these settings based on your project guidelines.

    The threshold configuration represents the minimum mass a code block must have to be analyzed for duplication. The lower the threshold, the more fine-grained the comparison.

    If the engine is too easily reporting duplication, try raising the threshold. If you suspect that the engine isn't catching enough duplication, try lowering the threshold. The best setting tends to differ from language to language.

    See codeclimate-duplication's documentation for more information about tuning the mass threshold in your .codeclimate.yml.

    Refactorings

    Further Reading

    File bratdata.py has 322 lines of code (exceeds 250 allowed). Consider refactoring.
    Open

    __author__ = 'Aleksandar Savkov'

"""This module holds data structure classes and relevant methods for parsing
and manipulating brat annotation files.0
"""
    Severity: Minor
    Found in src/bratutils/bratdata.py - About 3 hrs to fix

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

          def get_coinciding_anns(self, parallel_anns):
        """Returns a list of annotations from a parallel annotation that
        conincide with the current annotation.

        :param parallel_anns: parallel annotation
      Severity: Major
      Found in src/bratutils/agreement.py and 1 other location - About 2 hrs to fix
      src/bratutils/agreement.py on lines 441..453

      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 59.

      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

          def get_contained_anns(self, parallel_anns):
        """Returns a list of parallel annotations contained in this annotation.

        :param parallel_anns: list of parallel annotations
        :return: list of contained annotations
      Severity: Major
      Found in src/bratutils/agreement.py and 1 other location - About 2 hrs to fix
      src/bratutils/agreement.py on lines 426..439

      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 59.

      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

      Annotation has 23 functions (exceeds 20 allowed). Consider refactoring.
      Open

      class Annotation:
    """Annotation data structure encoding the tag and position of an
    annotation, along with information about its comparison status.
    """
      Severity: Minor
      Found in src/bratutils/agreement.py - About 2 hrs to fix

        Function merge_brat_dox_dir has a Cognitive Complexity of 14 (exceeds 5 allowed). Consider refactoring.
        Open

        def merge_brat_dox_dir(dp_a, dp_b, dp_res):
    """Merges the annotation files across all subdirectories of `dp_a` and
    `dp_b`, deploying the results in `dp_res`.

    :param dp_a: directory path A
        Severity: Minor
        Found in src/bratutils/utils.py - About 1 hr 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 __init__ has a Cognitive Complexity of 13 (exceeds 5 allowed). Consider refactoring.
        Open

            def __init__(self, fp=None, ann_list=None):
        """Constructs a `Document` object from an annotation file using `fp` or
        using a collection of Annotation objects in `ann_list`.

        :param fp: annotation document file path
        Severity: Minor
        Found in src/bratutils/agreement.py - About 1 hr 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

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

                return "{0}\t{1} {2}\t{3}\n{4}".format(str(self.id), self.tag,
                                               ";".join([" ".join(b)
                                                         for b
                                                         in self.boundaries]),
                                               self.content, comment_str)
        Severity: Major
        Found in src/bratutils/bratdata.py and 1 other location - About 1 hr to fix
        src/bratutils/bratdata.py on lines 157..162

        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

                return "{0}\t{1} {2}\t{3}{4}".format(str(self.id),
                                             self.tag,
                                             ";".join([" ".join(b)
                                                       for b
                                                       in self.boundaries]),
        Severity: Major
        Found in src/bratutils/bratdata.py and 1 other location - About 1 hr to fix
        src/bratutils/bratdata.py on lines 149..153

        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 5 locations. Consider refactoring.
        Open

            @property
    def missing(self):
        """List of lists of missing annoations from this document collection.
        Severity: Major
        Found in src/bratutils/agreement.py and 4 other locations - About 1 hr to fix
        src/bratutils/agreement.py on lines 829..839
        src/bratutils/agreement.py on lines 841..851
        src/bratutils/agreement.py on lines 853..863
        src/bratutils/agreement.py on lines 865..875

        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 42.

        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 5 locations. Consider refactoring.
        Open

            @property
    def partial(self):
        """List of lists of partial annoations from this document collection.
        Severity: Major
        Found in src/bratutils/agreement.py and 4 other locations - About 1 hr to fix
        src/bratutils/agreement.py on lines 829..839
        src/bratutils/agreement.py on lines 841..851
        src/bratutils/agreement.py on lines 865..875
        src/bratutils/agreement.py on lines 877..887

        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 42.

        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 5 locations. Consider refactoring.
        Open

            @property
    def incorrect(self):
        """List of lists of incorrect annoations from this document collection.
        Severity: Major
        Found in src/bratutils/agreement.py and 4 other locations - About 1 hr to fix
        src/bratutils/agreement.py on lines 829..839
        src/bratutils/agreement.py on lines 853..863
        src/bratutils/agreement.py on lines 865..875
        src/bratutils/agreement.py on lines 877..887

        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 42.

        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 5 locations. Consider refactoring.
        Open

            @property
    def spurious(self):
        """List of lists of spurious annoations from this document collection.
        Severity: Major
        Found in src/bratutils/agreement.py and 4 other locations - About 1 hr to fix
        src/bratutils/agreement.py on lines 829..839
        src/bratutils/agreement.py on lines 841..851
        src/bratutils/agreement.py on lines 853..863
        src/bratutils/agreement.py on lines 877..887

        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 42.

        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 5 locations. Consider refactoring.
        Open

            @property
    def correct(self):
        """List of lists of correct annoations from this document collection.
        Severity: Major
        Found in src/bratutils/agreement.py and 4 other locations - About 1 hr to fix
        src/bratutils/agreement.py on lines 841..851
        src/bratutils/agreement.py on lines 853..863
        src/bratutils/agreement.py on lines 865..875
        src/bratutils/agreement.py on lines 877..887

        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 42.

        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

            def __repr__(self):
        atts = [self.tag_name, str(self.start_idx), str(self.end_idx),
                self.text]
        return " ".join(atts)
        Severity: Major
        Found in src/bratutils/agreement.py and 1 other location - About 1 hr to fix
        src/bratutils/agreement.py on lines 553..556

        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 41.

        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

            def __str__(self):
        atts = [self.tag_name, str(self.start_idx), str(self.end_idx),
                self.text]
        return " ".join(atts)
        Severity: Major
        Found in src/bratutils/agreement.py and 1 other location - About 1 hr to fix
        src/bratutils/agreement.py on lines 558..561

        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 41.

        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 _filter_borders has a Cognitive Complexity of 10 (exceeds 5 allowed). Consider refactoring.
        Open

            def _filter_borders(self, document):
        new_tags = []
        for tag in document.postag_list:
            for condition in self.conditions:
                in_range = tag.in_range(condition)
        Severity: Minor
        Found in src/bratutils/agreement.py - About 1 hr 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 validate_indices has a Cognitive Complexity of 10 (exceeds 5 allowed). Consider refactoring.
        Open

            def validate_indices(self):
        """Validates the annotation indices in this document.


        :return: True if indices are correct
        Severity: Minor
        Found in src/bratutils/bratdata.py - About 1 hr 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

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