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Function put has a Cognitive Complexity of 11 (exceeds 5 allowed). Consider refactoring.
Open

    def put(self, _id):
        """
        Update a job. Updates timestamp.
        Enforces a valid state machine transition, if any.
        Rejects any change to a job that is not currently in 'pending' or 'running' state.
Severity: Minor
Found in api/jobs/handlers.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 scan_for_orphans has a Cognitive Complexity of 11 (exceeds 5 allowed). Consider refactoring.
Open

    def scan_for_orphans():
        """
        Scan the queue for orphaned jobs, mark them as failed, and possibly retry them.
        Should be called periodically.
        """
Severity: Minor
Found in api/jobs/queue.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 default_sublist has a Cognitive Complexity of 11 (exceeds 5 allowed). Consider refactoring.
Open

def default_sublist(handler, container):
    """
    This is the default permissions checker generator.
    The resulting permissions checker modifies the exec_op method by checking the user permissions
    on the container before actually executing this method.
Severity: Minor
Found in api/auth/listauth.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 upgrade_to_41_closure has a Cognitive Complexity of 11 (exceeds 5 allowed). Consider refactoring.
Open

def upgrade_to_41_closure(cont, cont_name):

    files = cont.get('files', [])
    for f in files:
        if 'tags' not in f:
Severity: Minor
Found in bin/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 process_cursor has a Cognitive Complexity of 11 (exceeds 5 allowed). Consider refactoring.
Open

def process_cursor(cursor, closure, context = None):
    """
    Given an iterable (say, a mongo cursor) and a closure, call that closure in parallel over the iterable.
    Call order is undefined. Currently launches N python process workers, where N is the number of vcpu cores.
Severity: Minor
Found in bin/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 extract_file_fields has a Cognitive Complexity of 11 (exceeds 5 allowed). Consider refactoring.
Open

def extract_file_fields(form):
    """Returns a list of file fields in the form, handling multiple values""" 
    result = []
    for fieldname in form:
        field = form[fieldname]
Severity: Minor
Found in api/upload.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

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

        return {
            'access_token': response['access_token'],
            'expires': datetime.datetime.utcnow() + datetime.timedelta(seconds=response['expires_in'])
Severity: Major
Found in api/auth/authproviders.py and 1 other location - About 1 hr to fix
api/auth/authproviders.py on lines 157..159

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

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

        if self.use_object_id:
            try:
                _id = bson.objectid.ObjectId(_id)
            except bson.errors.InvalidId as e:
                raise APIStorageException(e.message)
Severity: Major
Found in api/dao/liststorage.py and 1 other location - About 1 hr to fix
api/dao/liststorage.py on lines 230..234

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

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

        if self.use_object_id:
            try:
                _id = bson.objectid.ObjectId(_id)
            except bson.errors.InvalidId as e:
                raise APIStorageException(e.message)
Severity: Major
Found in api/dao/liststorage.py and 1 other location - About 1 hr to fix
api/dao/liststorage.py on lines 57..61

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

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

            self.log_user_access(AccessType.download_file, cont_name=cont_name, cont_id=cont_id, filename=os.path.basename(arcpath), multifile=True, origin_override=ticket['origin']) # log download
Severity: Major
Found in api/download.py and 1 other location - About 1 hr to fix
api/download.py on lines 292..292

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

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

        return {
            'access_token': response['access_token'],
            'expires': datetime.datetime.utcnow() + datetime.timedelta(seconds=response['expires_in'])
Severity: Major
Found in api/auth/authproviders.py and 1 other location - About 1 hr to fix
api/auth/authproviders.py on lines 238..240

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 _bulk_preflight_archivestream has a Cognitive Complexity of 11 (exceeds 5 allowed). Consider refactoring.
Open

    def _bulk_preflight_archivestream(self, file_refs):
        data_path = config.get_item('persistent', 'data_path')
        arc_prefix =  self.get_param('prefix', 'scitran')
        file_cnt = 0
        total_size = 0
Severity: Minor
Found in api/download.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 _upsert_container has a Cognitive Complexity of 11 (exceeds 5 allowed). Consider refactoring.
Open

def _upsert_container(cont, cont_type, parent, parent_type, upload_type, timestamp):
    cont['modified'] = timestamp

    if cont.get('timestamp'):
        cont['timestamp'] = dateutil.parser.parse(cont['timestamp'])
Severity: Minor
Found in api/dao/hierarchy.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 create_mappings has a Cognitive Complexity of 11 (exceeds 5 allowed). Consider refactoring.
Open

def create_mappings():
    public_dict = dicom._dicom_dict.DicomDictionary
    field_mappings = {}
    for k,v in public_dict.iteritems():
        vr_type = v[0]
Severity: Minor
Found in bin/dicom_doctype.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

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

                self.log_user_access(AccessType.download_file, cont_name=cont_name, cont_id=cont_id, filename=os.path.basename(arcpath), multifile=True, origin_override=ticket['origin']) # log download
Severity: Major
Found in api/download.py and 1 other location - About 1 hr to fix
api/download.py on lines 302..302

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 users has a Cognitive Complexity of 11 (exceeds 5 allowed). Consider refactoring.
Open

def users(filepath, api_url, http_headers, insecure):
    """
    Upserts the users/groups/permissions defined in filepath parameter.

    Raises:
Severity: Minor
Found in bin/load_users_drone_secret.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

        if states is not None and len(states) > 0:
            query['state'] = {"$in": states}
Severity: Major
Found in api/jobs/queue.py and 1 other location - About 1 hr to fix
api/jobs/queue.py on lines 351..352

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 40.

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 tags is not None and len(tags) > 0:
            query['tags'] = {"$in": tags}
Severity: Major
Found in api/jobs/queue.py and 1 other location - About 1 hr to fix
api/jobs/queue.py on lines 348..349

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 40.

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 post has 29 lines of code (exceeds 25 allowed). Consider refactoring.
Open

    def post(self):
        """
        Create a batch job proposal, insert as 'pending' if there are matched containers
        """
Severity: Minor
Found in api/jobs/handlers.py - About 1 hr to fix

    Function __init__ has 29 lines of code (exceeds 25 allowed). Consider refactoring.
    Open

        def __init__(self, gear_id, inputs, destination=None, tags=None,
                 attempt=1, previous_job_id=None, created=None,
                 modified=None, state='pending', request=None,
                 id_=None, config_=None, origin=None,
                 saved_files=None, produced_metadata=None, batch=None,
    Severity: Minor
    Found in api/jobs/jobs.py - About 1 hr to fix
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