File io.py has 2243 lines of code (exceeds 250 allowed). Consider refactoring.

Open

""" Reading/writing schema objects to/from files

* Comma separated values (.csv)
* XLSX (.xlsx)
* JavaScript Object Notation (.json)

Function run has a Cognitive Complexity of 147 (exceeds 5 allowed). Consider refactoring.

Open

    def run(self, path, schema_name=None, models=None,
            allow_multiple_sheets_per_model=False,
            ignore_missing_models=False, ignore_extra_models=False,
            ignore_sheet_order=False,
            include_all_attributes=True, ignore_missing_attributes=False, ignore_extra_attributes=False,

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Function read_model has a Cognitive Complexity of 109 (exceeds 5 allowed). Consider refactoring.

Open

    def read_model(self, reader, sheet_name, schema_name, model, include_all_attributes=True,
                   ignore_missing_attributes=False, ignore_extra_attributes=False,
                   ignore_attribute_order=False, ignore_empty_rows=True,
                   validate=True):
        """ Instantiate a list of objects from data in a table in a file

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Function write_model has a Cognitive Complexity of 94 (exceeds 5 allowed). Consider refactoring.

Open

    def write_model(self, writer, model, objects, schema_name, date, doc_metadata, doc_metadata_model, model_metadata, sheet_models,
                    include_all_attributes=True, encoded=None, write_empty_models=True, write_empty_cols=True,
                    extra_entries=0, protected=True):
        """ Write a list of model objects to a file

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Function link_model has a Cognitive Complexity of 61 (exceeds 5 allowed). Consider refactoring.

Open

    def link_model(self, model, attributes, data, objects, objects_by_primary_attribute, decoded=None):
        """ Construct object graph

        Args:
            model (:obj:`Model`): an :obj:`obj_tables.core.Model`

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Function read_sheet has a Cognitive Complexity of 40 (exceeds 5 allowed). Consider refactoring.

Open

    def read_sheet(self, model, reader, sheet_name, num_row_heading_columns=0, num_column_heading_rows=0,
                   ignore_empty_rows=False, ignore_empty_cols=False):
        """ Read worksheet or file into a two-dimensional list

        Args:

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Function run has a Cognitive Complexity of 38 (exceeds 5 allowed). Consider refactoring.

Open

    def run(self, path, objects, schema_name=None, doc_metadata=None, model_metadata=None,
            models=None, get_related=True, include_all_attributes=True,
            validate=True, title=None, description=None, keywords=None, version=None, language=None, creator=None,
            write_toc=False, write_schema=False, write_empty_models=True, write_empty_cols=True,
            extra_entries=0, group_objects_by_model=True,

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Function run has a Cognitive Complexity of 34 (exceeds 5 allowed). Consider refactoring.

Open

    def run(self, path, objects, schema_name=None, doc_metadata=None, model_metadata=None,
            models=None, get_related=True, include_all_attributes=True, validate=True,
            title=None, description=None, keywords=None, version=None, language=None, creator=None,
            write_toc=True, write_schema=False, write_empty_models=True, write_empty_cols=True,
            extra_entries=0, group_objects_by_model=True, data_repo_metadata=False, schema_package=None,

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Function run has a Cognitive Complexity of 22 (exceeds 5 allowed). Consider refactoring.

Open

    def run(self, path, schema_name=None, models=None,
            allow_multiple_sheets_per_model=False,
            ignore_missing_models=False, ignore_extra_models=False,
            ignore_sheet_order=False,
            include_all_attributes=True, ignore_missing_attributes=False, ignore_extra_attributes=False,

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Function run has 24 arguments (exceeds 4 allowed). Consider refactoring.

Open

    def run(self, path, objects, schema_name=None, doc_metadata=None, model_metadata=None, models=None,

Function run has 24 arguments (exceeds 4 allowed). Consider refactoring.

Open

    def run(self, path, objects, schema_name=None, doc_metadata=None, model_metadata=None,

Function run has 24 arguments (exceeds 4 allowed). Consider refactoring.

Open

    def run(self, path, objects, schema_name=None, doc_metadata=None, model_metadata=None,

Function run has 24 arguments (exceeds 4 allowed). Consider refactoring.

Open

    def run(self, path, objects, schema_name=None, doc_metadata=None, model_metadata=None,

Function run has 24 arguments (exceeds 4 allowed). Consider refactoring.

Open

    def run(self, path, objects, schema_name=None, doc_metadata=None, model_metadata=None,

Function read_worksheet_metadata has a Cognitive Complexity of 20 (exceeds 5 allowed). Consider refactoring.

Open

    def read_worksheet_metadata(cls, sheet_name, rows):
        """ Read worksheet metadata

        Args:
            sheet_name (:obj:`str`): sheet name

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Function write_sheet has a Cognitive Complexity of 18 (exceeds 5 allowed). Consider refactoring.

Open

    def write_sheet(self, writer, model, data, headings, metadata_headings, validation,
                    extra_entries=0, merge_ranges=None, protected=True):
        """ Write data to sheet

        Args:

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Function write_schema has a Cognitive Complexity of 17 (exceeds 5 allowed). Consider refactoring.

Open

    def write_schema(self, writer, models, name, date, doc_metadata, protected=True):
        """ Write a worksheet with a schema

        Args:
            writer (:obj:`wc_utils.workbook.io.Writer`): io writer

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Function run has a Cognitive Complexity of 17 (exceeds 5 allowed). Consider refactoring.

Open

    def run(self, path, objects, schema_name=None, doc_metadata=None, model_metadata=None,
            models=None, get_related=True, include_all_attributes=True, validate=True,
            title=None, description=None, keywords=None, version=None, language=None, creator=None,
            write_toc=True, write_schema=False, write_empty_models=True, write_empty_cols=True,
            extra_entries=0, group_objects_by_model=True, data_repo_metadata=False, schema_package=None,

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Function get_ordered_attributes has a Cognitive Complexity of 17 (exceeds 5 allowed). Consider refactoring.

Open

def get_ordered_attributes(cls, include_all_attributes=True):
    """ Get the attributes for a class in the order that they should be printed

    Args:
        cls (:obj:`type`): Model type (subclass of :obj:`Model`)

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Consider simplifying this complex logical expression.

Open

            if not row or all(cell in ['', None] for cell in row):
                rows.remove(row)
            elif row and isinstance(row[0], str) and \
                    row[0].startswith('%/') and row[0].endswith('/%') and \
                    not any(row[1:]):

Function create_template has 16 arguments (exceeds 4 allowed). Consider refactoring.

Open

def create_template(path, schema_name, models, title=None, description=None, keywords=None,

Function write_model has 15 arguments (exceeds 4 allowed). Consider refactoring.

Open

    def write_model(self, writer, model, objects, schema_name, date, doc_metadata, doc_metadata_model, model_metadata, sheet_models,

Function run has 14 arguments (exceeds 4 allowed). Consider refactoring.

Open

    def run(self, path, schema_name=None, models=None,

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

Open

def get_fields(cls, schema_name, date, doc_metadata, doc_metadata_model, model_metadata, include_all_attributes=True, sheet_models=None):
    """ Get the attributes, headings, and validation for a worksheet

    Args:
        cls (:obj:`type`): Model type (subclass of :obj:`Model`)

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Function run has 14 arguments (exceeds 4 allowed). Consider refactoring.

Open

    def run(self, path, schema_name=None, models=None,

Function run has 14 arguments (exceeds 4 allowed). Consider refactoring.

Open

    def run(self, path, schema_name=None, models=None,

Function convert has 14 arguments (exceeds 4 allowed). Consider refactoring.

Open

def convert(source, destination, schema_name=None, models=None,

Function run has 14 arguments (exceeds 4 allowed). Consider refactoring.

Open

    def run(self, path, schema_name=None, models=None,

Function run has 14 arguments (exceeds 4 allowed). Consider refactoring.

Open

    def run(self, path, schema_name=None, models=None,

Function write_sheet has a Cognitive Complexity of 13 (exceeds 5 allowed). Consider refactoring.

Open

    def write_sheet(self, writer, model, data, headings, metadata_headings, validation,
                    extra_entries=0, merge_ranges=None, protected=False):
        """ Write data to sheet

        Args:

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Function run has a Cognitive Complexity of 13 (exceeds 5 allowed). Consider refactoring.

Open

    def run(self, path, schema_name=None, models=None,
            allow_multiple_sheets_per_model=False,
            ignore_missing_models=False, ignore_extra_models=False,
            ignore_sheet_order=False,
            include_all_attributes=True, ignore_missing_attributes=False, ignore_extra_attributes=False,

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Function run has 39 lines of code (exceeds 25 allowed). Consider refactoring.

Open

    def run(self, path, schema_name=None, models=None,
            allow_multiple_sheets_per_model=False,
            ignore_missing_models=False, ignore_extra_models=False,
            ignore_sheet_order=False,
            include_all_attributes=True, ignore_missing_attributes=False, ignore_extra_attributes=False,

Function get_fields has 38 lines of code (exceeds 25 allowed). Consider refactoring.

Open

def get_fields(cls, schema_name, date, doc_metadata, doc_metadata_model, model_metadata, include_all_attributes=True, sheet_models=None):
    """ Get the attributes, headings, and validation for a worksheet

    Args:
        cls (:obj:`type`): Model type (subclass of :obj:`Model`)

Function make_metadata_objects has a Cognitive Complexity of 12 (exceeds 5 allowed). Consider refactoring.

Open

    def make_metadata_objects(self, data_repo_metadata, path, schema_package):
        """ Make models that store Git repository metadata

        Metadata models can only be created from suitable Git repos.
        Failures to obtain metadata are reported as warnings that do not interfeer with writing

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Function read_model has 10 arguments (exceeds 4 allowed). Consider refactoring.

Open

    def read_model(self, reader, sheet_name, schema_name, model, include_all_attributes=True,

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

Open

    def write_toc(self, writer, models, schema_name, date, doc_metadata, grouped_objects, write_schema=False, protected=True):
        """ Write a worksheet with a table of contents

        Args:
            writer (:obj:`wc_utils.workbook.io.Writer`): io writer

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Function write_sheet has 9 arguments (exceeds 4 allowed). Consider refactoring.

Open

    def write_sheet(self, writer, model, data, headings, metadata_headings, validation,

Function write_sheet has 9 arguments (exceeds 4 allowed). Consider refactoring.

Open

    def write_sheet(self, writer, model, data, headings, metadata_headings, validation,

Function run has 26 lines of code (exceeds 25 allowed). Consider refactoring.

Open

    def run(self, path, objects, schema_name=None, doc_metadata=None, model_metadata=None,
            models=None, get_related=True, include_all_attributes=True, validate=True,
            title=None, description=None, keywords=None, version=None, language=None, creator=None,
            write_toc=True, write_schema=False, write_empty_models=True, write_empty_cols=True,
            extra_entries=0, group_objects_by_model=True, data_repo_metadata=False, schema_package=None,

Function write_toc has 8 arguments (exceeds 4 allowed). Consider refactoring.

Open

    def write_toc(self, writer, models, schema_name, date, doc_metadata, grouped_objects, write_schema=False, protected=True):

Function get_fields has 8 arguments (exceeds 4 allowed). Consider refactoring.

Open

def get_fields(cls, schema_name, date, doc_metadata, doc_metadata_model, model_metadata, include_all_attributes=True, sheet_models=None):

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

Open

    def read_sheet(self, model, reader, sheet_name, num_row_heading_columns=0, num_column_heading_rows=0,

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

Open

    def run(self, objects, schema_name=None, models=None, get_related=True,

Avoid deeply nested control flow statements.

Open

                        if same_val:
                            for sub_attr in attr.related_class.Meta.attributes.values():
                                sub_val = getattr(val, sub_attr.name)
                                if isinstance(sub_val, list):
                                    setattr(val, sub_attr.name, [])

Function get_model_sheet_name has a Cognitive Complexity of 8 (exceeds 5 allowed). Consider refactoring.

Open

    def get_model_sheet_name(cls, sheet_names, model):
        """ Get the name of the worksheet/file which corresponds to a model

        Args:
            sheet_names (:obj:`list` of :obj:`str`): names of the sheets in the workbook/files

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Avoid deeply nested control flow statements.

Open

                        if merged_model_metadata[model][key] != val:
                            errors.append('Attribute "{}" for model "{}" is not consistent'.format(
                                key, model.__name__, ))
                    else:

Avoid deeply nested control flow statements.

Open

                            if deserialize_error:
                                deserialize_error.set_location_and_value(utils.source_report(obj, sub_attr.name),
                                                                         attr_value)
                                obj_errors.append(deserialize_error)
                            if validation_error:

Avoid deeply nested control flow statements.

Open

                        if attr.related_class not in objects_by_primary_attribute:
                            objects_by_primary_attribute[attr.related_class] = {}
                        serialized_val = val.serialize()

Avoid deeply nested control flow statements.

Open

                            if validation_error:
                                validation_error.set_location_and_value(utils.source_report(obj, sub_attr.name),
                                                                        attr_value)
                                obj_errors.append(validation_error)
                        setattr(obj, sub_attr.name, value)

Avoid deeply nested control flow statements.

Open

                        if is_col_empty:
                            row.pop(i_col)

Avoid deeply nested control flow statements.

Open

                        if not sub_obj:
                            sub_obj = group_attr.related_class()
                            setattr(obj, group_attr.name, sub_obj)
                        setattr(sub_obj, sub_attr.name, value)

Avoid deeply nested control flow statements.

Open

                        for sub_attr in sub_attrs:
                            if val:
                                sub_val = getattr(val, sub_attr.name)
                                if isinstance(sub_attr, RelatedAttribute):
                                    obj_data.append(sub_attr.serialize(sub_val, encoded=encoded))

Avoid deeply nested control flow statements.

Open

                        if not line.startswith('!!!'):
                            out_file.write(line)
                if i_path < len(all_tmp_paths) - 1:

Function write_schema has 6 arguments (exceeds 4 allowed). Consider refactoring.

Open

    def write_schema(self, writer, models, name, date, doc_metadata, protected=True):

Function link_model has 6 arguments (exceeds 4 allowed). Consider refactoring.

Open

    def link_model(self, model, attributes, data, objects, objects_by_primary_attribute, decoded=None):

Avoid too many return statements within this function.

Open

        return (sub_attrs, data, errors, objects)

Function parse_worksheet_heading_metadata has a Cognitive Complexity of 6 (exceeds 5 allowed). Consider refactoring.

Open

    def parse_worksheet_heading_metadata(cls, heading, sheet_name=None):
        """ Parse key-value pairs of metadata from heading

        Args:
            heading (:obj:`str`): heading with key-value pairs of metadata

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