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Function main has a Cognitive Complexity of 64 (exceeds 5 allowed). Consider refactoring.
Open

def main():

    # assign constraints from input
    kwargs, variables, admin, searchargs = assign_constraints()
    # define directory where requests for downloads are stored
Severity: Minor
Found in ARCCSSive/cli/compare_ESGF.py - About 1 day 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 compare_instances has a Cognitive Complexity of 48 (exceeds 5 allowed). Consider refactoring.
Open

def compare_instances(db,remote,local,const_keys,admin):
    ''' Compare remote and local search results they're both a list of dictionaries
        :argument db: sqlalchemy local db session 
        :argument remote: each dict has keys version, files (objs), filenames, tracking_ids, dataset_id 
        :argument local:  list of version objects
Severity: Minor
Found in ARCCSSive/CMIP5/compare_helpers.py - About 7 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 update_files has a Cognitive Complexity of 33 (exceeds 5 allowed). Consider refactoring.
Open

def update_files(local,remote):
    ''' return urls of files to update '''
    urls=[]
    dataset_info=[]
    # this return too many we need to do it variable by variable
Severity: Minor
Found in ARCCSSive/CMIP5/compare_helpers.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

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

            ds_string=",".join([ds['variable'],inst['mip'],inst['model'],inst['experiment'],
                               inst['ensemble'],inst['realm'],inst['version'],ds['dataset_id'],
                               "/g/data1/ua6/unofficial-ESG-replica/tmp/tree"+path,ctype])+"\n"
Severity: Major
Found in ARCCSSive/CMIP5/compare_helpers.py and 1 other location - About 4 hrs to fix
ARCCSSive/CMIP5/compare_helpers.py on lines 164..166

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 82.

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 kw_instance['realm']=='NA':
        fpaths=[p for p in os.listdir(vers_path) if p.split("_")[0]==var]
        realm=check_realm(vers_path+"/"+fpaths[0])
Severity: Major
Found in database_updates/upload_tmptree.py and 1 other location - About 4 hrs to fix
database_updates/update_db.py on lines 98..100

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 82.

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

                ds_string=",".join([ds['variable'],inst['mip'],inst['model'],inst['experiment'],
                               inst['ensemble'],inst['realm'],inst['version'],ds['dataset_id'],
                               "/g/data1/ua6/unofficial-ESG-replica/tmp/tree"+path,ctype])+"\n"
Severity: Major
Found in ARCCSSive/CMIP5/compare_helpers.py and 1 other location - About 4 hrs to fix
ARCCSSive/CMIP5/compare_helpers.py on lines 120..122

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 82.

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 kw_instance['realm']=='NA':
        fpaths=[p for p in os.listdir(vers_path) if p.split("_")[0]==var]
        realm=check_realm(vers_path+"/"+fpaths[0])
Severity: Major
Found in database_updates/update_db.py and 1 other location - About 4 hrs to fix
database_updates/upload_tmptree.py on lines 73..75

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 82.

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

def main():

    # Calling parse_input() function to build kwargs from external arguments passed by user 
    kwargs=assign_constraints()
    all_versions=kwargs.pop("all_versions")
Severity: Minor
Found in ARCCSSive/cli/search_replica.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 new_files has a Cognitive Complexity of 27 (exceeds 5 allowed). Consider refactoring.
Open

def new_files(remote):
    ''' return urls of new files to download '''
    urls=[]
    dataset_info=[]
    # this return too many we need to do it variable by variable
Severity: Minor
Found in ARCCSSive/CMIP5/compare_helpers.py - About 3 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 compare_files has a Cognitive Complexity of 26 (exceeds 5 allowed). Consider refactoring.
Open

def compare_files(db,rds,v,admin):
    ''' Compare files of remote and local version of a dataset
        :argument rds: dictionary of remote dataset object selected attributes  
        :argument v:  local version object   
        :return: result set, NB updating VerisonFiles object in databse if calculating checksums
Severity: Minor
Found in ARCCSSive/CMIP5/compare_helpers.py - About 3 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

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

def check_realm(fpath):
    ''' Check for realm in netcdf file '''
    # open netcdf file
    try:
        f = cdms2.open(fpath,'r')
Severity: Major
Found in database_updates/upload_tmptree.py and 3 other locations - About 3 hrs to fix
database_updates/update_db.py on lines 30..44
database_updates/update_db.py on lines 47..61
database_updates/upload_tmptree.py on lines 18..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 69.

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

def check_version(fpath):
    ''' Check for version and/or creation date in netcdf file '''
    # open netcdf file
    try:
        f = cdms2.open(fpath,'r')
Severity: Major
Found in database_updates/update_db.py and 3 other locations - About 3 hrs to fix
database_updates/update_db.py on lines 47..61
database_updates/upload_tmptree.py on lines 18..32
database_updates/upload_tmptree.py on lines 35..49

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 69.

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

def check_realm(fpath):
    ''' Check for realm in netcdf file '''
    # open netcdf file
    try:
        f = cdms2.open(fpath,'r')
Severity: Major
Found in database_updates/update_db.py and 3 other locations - About 3 hrs to fix
database_updates/update_db.py on lines 30..44
database_updates/upload_tmptree.py on lines 18..32
database_updates/upload_tmptree.py on lines 35..49

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 69.

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

def check_version(fpath):
    ''' Check for version and/or creation date in netcdf file '''
    # open netcdf file
    try:
        f = cdms2.open(fpath,'r')
Severity: Major
Found in database_updates/upload_tmptree.py and 3 other locations - About 3 hrs to fix
database_updates/update_db.py on lines 30..44
database_updates/update_db.py on lines 47..61
database_updates/upload_tmptree.py on lines 35..49

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 69.

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 (button.data('hidden') === 'false') {
            // hide the code output
            button.parent().find('.go, .gp, .gt').hide();
            button.next('pre').find('.gt').nextUntil('.gp, .go').css('visibility', 'hidden');
            button.css('text-decoration', 'line-through');
Severity: Major
Found in docs/_static/copybutton.js and 1 other location - About 3 hrs to fix
docs/_static/copybutton.js on lines 55..62

Duplicated Code

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

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

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

Tuning

This issue has a mass of 102.

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

        } else {
            // show the code output
            button.parent().find('.go, .gp, .gt').show();
            button.next('pre').find('.gt').nextUntil('.gp, .go').css('visibility', 'visible');
            button.css('text-decoration', 'none');
Severity: Major
Found in docs/_static/copybutton.js and 1 other location - About 3 hrs to fix
docs/_static/copybutton.js on lines 48..55

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 102.

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 compare_helpers.py has 304 lines of code (exceeds 250 allowed). Consider refactoring.
Open

#!/usr/bin/env python
# This check data available on ESGF and on raijin that matches constraints passed on by user and return a summary.
"""
Copyright 2016 ARC Centre of Excellence for Climate Systems Science
Severity: Minor
Found in ARCCSSive/CMIP5/compare_helpers.py - About 3 hrs to fix

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

        if admin:
        if os.environ['USER'] not in ['pxp581','tae599']:
            print(os.environ['USER'] + " is not an authorised admin")
            sys.exit()
    Severity: Major
    Found in ARCCSSive/cli/compare_ESGF.py and 1 other location - About 2 hrs to fix
    database_updates/add_warning.py on lines 77..80

    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 admin:
        if os.environ['USER'] not in ['pxp581','tae599']:
            print(os.environ['USER'] + " is not an authorised admin")
            sys.exit()
    Severity: Major
    Found in database_updates/add_warning.py and 1 other location - About 2 hrs to fix
    ARCCSSive/cli/compare_ESGF.py on lines 85..88

    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 4 locations. Consider refactoring.
    Open

        for k,v in list(searchargs.items()):
        if v is None or v==[]: searchargs.pop(k)
    Severity: Major
    Found in ARCCSSive/cli/compare_ESGF.py and 3 other locations - About 1 hr to fix
    ARCCSSive/cli/compare_ESGF.py on lines 92..93
    database_updates/add_warning.py on lines 84..85
    examples/find_matching_variables.py on lines 70..71

    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 47.

    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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