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renalreg/radar

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radar/models/patients.py

Summary

Maintainability
F
6 days
Test Coverage

Patient has 75 functions (exceeds 20 allowed). Consider refactoring.
Open

class Patient(db.Model, MetaModelMixin):
    __tablename__ = "patients"

    id = Column(Integer, Sequence("patients_seq"), primary_key=True)
    comments = Column(String)
Severity: Major
Found in radar/models/patients.py - About 1 day to fix

    File patients.py has 482 lines of code (exceeds 250 allowed). Consider refactoring.
    Open

    from datetime import datetime
from enum import Enum

from sqlalchemy import (
    Boolean,
    Severity: Minor
    Found in radar/models/patients.py - About 7 hrs to fix

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

          def consent_status(self):
        """Return what consent status patient is in."""
        if self.year_of_death:
            return CONSENT_STATUS.OK
      Severity: Minor
      Found in radar/models/patients.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

      Consider simplifying this complex logical expression.
      Open

                  if (
                (group is not None and group_patient.group == group)
                or (group is None and group_patient.group.type == GROUP_TYPE.SYSTEM)
            ) and (from_date is None or group_patient.from_date < from_date):
                from_date = group_patient.from_date
      Severity: Major
      Found in radar/models/patients.py - About 40 mins to fix

        Function _recruited_group_patient has a Cognitive Complexity of 7 (exceeds 5 allowed). Consider refactoring.
        Open

            def _recruited_group_patient(self, group=None):
        from_date = None
        recruited_group_patient = None

        for group_patient in self.group_patients:
        Severity: Minor
        Found in radar/models/patients.py - About 35 mins 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

        Avoid too many return statements within this function.
        Open

                    return CONSENT_STATUS.EXPIRED
        Severity: Major
        Found in radar/models/patients.py - About 30 mins to fix

          Avoid too many return statements within this function.
          Open

                      return CONSENT_STATUS.EXPIRED
          Severity: Major
          Found in radar/models/patients.py - About 30 mins to fix

            Avoid too many return statements within this function.
            Open

                        return CONSENT_STATUS.EXPIRED
            Severity: Major
            Found in radar/models/patients.py - About 30 mins to fix

              Avoid too many return statements within this function.
              Open

                          return CONSENT_STATUS.SOON
              Severity: Major
              Found in radar/models/patients.py - About 30 mins to fix

                Avoid too many return statements within this function.
                Open

                        return CONSENT_STATUS.OK
                Severity: Major
                Found in radar/models/patients.py - About 30 mins to fix

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

                      @property
    def first_names(self):
        values = [x.first_name for x in self.patient_demographics]
        values += [x.first_name for x in self.patient_aliases]
        values = clean(values)
                  Severity: Major
                  Found in radar/models/patients.py and 1 other location - About 2 hrs to fix
                  radar/models/patients.py on lines 470..475

                  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 56.

                  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

                      @property
    def last_names(self):
        values = [x.last_name for x in self.patient_demographics]
        values += [x.last_name for x in self.patient_aliases]
        values = clean(values)
                  Severity: Major
                  Found in radar/models/patients.py and 1 other location - About 2 hrs to fix
                  radar/models/patients.py on lines 463..468

                  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 56.

                  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

                      @property
    def available_ethnicity(self):
        ethnicities = [demog.ethnicity for demog in self.patient_demographics]
        first_available = next((ethn for ethn in ethnicities if ethn is not None), None)
        return first_available
                  Severity: Major
                  Found in radar/models/patients.py and 1 other location - About 2 hrs to fix
                  radar/models/patients.py on lines 280..286

                  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 54.

                  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

                      @property
    def available_gender(self):
        genders = [demog.gender for demog in self.patient_demographics]
        first_available = next(
            (gender for gender in genders if gender is not None), None
                  Severity: Major
                  Found in radar/models/patients.py and 1 other location - About 2 hrs to fix
                  radar/models/patients.py on lines 274..278

                  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 54.

                  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 2 locations. Consider refactoring.
                  Open

                          if group is not None:
            q = q.where(Group.id == group.id)
        else:
            q = q.where(Group.type == GROUP_TYPE.SYSTEM)
                  Severity: Major
                  Found in radar/models/patients.py and 1 other location - About 2 hrs to fix
                  radar/models/patients.py on lines 123..126

                  Duplicated Code

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

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

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

                  Tuning

                  This issue has a mass of 53.

                  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 2 locations. Consider refactoring.
                  Open

                          if group is not None:
            q = q.where(Group.id == group.id)
        else:
            q = q.where(Group.type == GROUP_TYPE.SYSTEM)
                  Severity: Major
                  Found in radar/models/patients.py and 1 other location - About 2 hrs to fix
                  radar/models/patients.py on lines 146..149

                  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 53.

                  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 recruited_group(self, group=None):
        group_patient = self._recruited_group_patient(group)

        if group_patient is None:
            group = None
                  Severity: Major
                  Found in radar/models/patients.py and 1 other location - About 1 hr to fix
                  radar/models/patients.py on lines 167..175

                  Duplicated Code

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

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

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

                  Tuning

                  This issue has a mass of 46.

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

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

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

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

                  Refactorings

                  Further Reading

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

                      def recruited_user(self, group=None):
        group_patient = self._recruited_group_patient(group)

        if group_patient is None:
            user = None
                  Severity: Major
                  Found in radar/models/patients.py and 1 other location - About 1 hr to fix
                  radar/models/patients.py on lines 177..185

                  Duplicated Code

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

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

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

                  Tuning

                  This issue has a mass of 46.

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

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

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

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

                  Refactorings

                  Further Reading

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

                      @property
    def year_of_death(self):
        date_of_death = self.date_of_death

        if date_of_death is None:
                  Severity: Major
                  Found in radar/models/patients.py and 3 other locations - About 1 hr to fix
                  radar/models/patient_demographics.py on lines 41..50
                  radar/models/patient_demographics.py on lines 52..61
                  radar/models/patients.py on lines 326..335

                  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 4 locations. Consider refactoring.
                  Open

                      @property
    def year_of_birth(self):
        date_of_birth = self.date_of_birth

        if date_of_birth is None:
                  Severity: Major
                  Found in radar/models/patients.py and 3 other locations - About 1 hr to fix
                  radar/models/patient_demographics.py on lines 41..50
                  radar/models/patient_demographics.py on lines 52..61
                  radar/models/patients.py on lines 345..354

                  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

                      @property
    def dates_of_birth(self):
        values = [x.date_of_birth for x in self.patient_demographics]
        values = clean(values)
        return values
                  Severity: Minor
                  Found in radar/models/patients.py and 1 other location - About 55 mins to fix
                  radar/models/patients.py on lines 483..487

                  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 37.

                  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

                      @property
    def genders(self):
        values = [x.gender for x in self.patient_demographics]
        values = clean(values)
        return values
                  Severity: Minor
                  Found in radar/models/patients.py and 1 other location - About 55 mins to fix
                  radar/models/patients.py on lines 477..481

                  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 37.

                  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

                      @property
    def hospitals(self):
        """Return groups of type GROUP_TYPE.HOSPITAL that patient belongs to."""
        return [group for group in self.groups if group.type == GROUP_TYPE.HOSPITAL]
                  Severity: Major
                  Found in radar/models/patients.py and 2 other locations - About 50 mins to fix
                  radar/models/patients.py on lines 79..82
                  radar/models/patients.py on lines 84..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 36.

                  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

                      @property
    def cohorts(self):
        """Return cohorts that patient belongs to."""
        return [group for group in self.groups if group.type == GROUP_TYPE.COHORT]
                  Severity: Major
                  Found in radar/models/patients.py and 2 other locations - About 50 mins to fix
                  radar/models/patients.py on lines 84..87
                  radar/models/patients.py on lines 89..92

                  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 36.

                  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

                      @property
    def systems(self):
        """Return groups of type GROUP_TYPE.SYSTEM that patient belongs to."""
        return [group for group in self.groups if group.type == GROUP_TYPE.SYSTEM]
                  Severity: Major
                  Found in radar/models/patients.py and 2 other locations - About 50 mins to fix
                  radar/models/patients.py on lines 79..82
                  radar/models/patients.py on lines 89..92

                  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 36.

                  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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