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ngi_pipeline/engines/sarek/database.py

Summary

Maintainability
D
1 day
Test Coverage

File database.py has 301 lines of code (exceeds 250 allowed). Consider refactoring.
Open

import contextlib

from ngi_pipeline.database.classes import CharonError, CharonSession
from ngi_pipeline.engines.sarek.process import ProcessRunning, ProcessExitStatusSuccessful, \
    ProcessExitStatusFailed, ProcessExitStatusUnknown, ProcessConnector, SlurmConnector
Severity: Minor
Found in ngi_pipeline/engines/sarek/database.py - About 3 hrs to fix

    Function set_sample_attribute has a Cognitive Complexity of 15 (exceeds 5 allowed). Consider refactoring.
    Open

        def set_sample_attribute(
            self, projectid, sampleid, sample_update_kwargs, seqrun_update_kwargs=None, recurse=False,
            restrict_to_libpreps=None, restrict_to_seqruns=None):
        """
        Update a sample according to the `sample_update_kwargs` dict. If recurse is True, the affected seqruns will be
    Severity: Minor
    Found in ngi_pipeline/engines/sarek/database.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 record_process_sample has 8 arguments (exceeds 4 allowed). Consider refactoring.
    Open

        def record_process_sample(
    Severity: Major
    Found in ngi_pipeline/engines/sarek/database.py - About 1 hr to fix

      Function set_sample_attribute has 7 arguments (exceeds 4 allowed). Consider refactoring.
      Open

          def set_sample_attribute(
      Severity: Major
      Found in ngi_pipeline/engines/sarek/database.py - About 50 mins to fix

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

            def analysis_status_from_process_status(self, process_status):
        """
        Translate a ProcessStatus to the corresponding status string used for the analysis status in Charon

        :param process_status: the process status class to translate
        Severity: Major
        Found in ngi_pipeline/engines/sarek/database.py and 1 other location - About 2 hrs to fix
        ngi_pipeline/engines/sarek/database.py on lines 240..254

        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 51.

        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 alignment_status_from_analysis_status(self, analysis_status):
        """
        Translate a sample analysis status used in Charon to the corresponding alignment status string used for
        seqruns in Charon
        Severity: Major
        Found in ngi_pipeline/engines/sarek/database.py and 1 other location - About 2 hrs to fix
        ngi_pipeline/engines/sarek/database.py on lines 225..238

        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 51.

        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

                try:
            return self.charon_session.sample_get(projectid, sampleid)["analysis_status"]
        except (KeyError, CharonError) as e:
            analysis_status_exception = SampleAnalysisStatusNotFoundError(projectid, sampleid, reason=e)
            self.log.error(analysis_status_exception)
        Severity: Major
        Found in ngi_pipeline/engines/sarek/database.py and 2 other locations - About 55 mins to fix
        ngi_pipeline/engines/sarek/database.py on lines 199..205
        ngi_pipeline/engines/sarek/database.py on lines 217..223

        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

                try:
            return [x for x in self.charon_session.sample_get_libpreps(projectid, sampleid)["libpreps"] 
                    if restrict_to is None or x["libprepid"] in restrict_to]
        except (KeyError, CharonError) as e:
            sample_libpreps_exception = SampleLookupError(projectid, sampleid, reason=e)
        Severity: Major
        Found in ngi_pipeline/engines/sarek/database.py and 2 other locations - About 55 mins to fix
        ngi_pipeline/engines/sarek/database.py on lines 66..71
        ngi_pipeline/engines/sarek/database.py on lines 217..223

        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

                try:
            return [x for x in self.charon_session.libprep_get_seqruns(projectid, sampleid, libprepid)["seqruns"] 
                    if restrict_to is None or x["seqrunid"] in restrict_to]
        except (KeyError, CharonError) as e:
            libprep_seqruns_exception = SampleLookupError(projectid, sampleid, reason=e)
        Severity: Major
        Found in ngi_pipeline/engines/sarek/database.py and 2 other locations - About 55 mins to fix
        ngi_pipeline/engines/sarek/database.py on lines 66..71
        ngi_pipeline/engines/sarek/database.py on lines 199..205

        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

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