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HumanCellAtlas/ingest-client

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fix_bundle_links.py

Summary

Maintainability
A
25 mins
Test Coverage

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

    def _is_supplementary_file_link(self, link):
        input_type = link.get('input_type')
        if input_type == 'file':
            inputs = link.get('inputs')
            for file_uuid in inputs:
Severity: Minor
Found in fix_bundle_links.py - About 25 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

Remove this commented out code.
Open

    # report = bundle_manifest_service.update_bundle_manifest_links(project_uuid)
Severity: Major
Found in fix_bundle_links.py by sonar-python

Programmers should not comment out code as it bloats programs and reduces readability.

Unused code should be deleted and can be retrieved from source control history if required.

See

  • MISRA C:2004, 2.4 - Sections of code should not be "commented out".
  • MISRA C++:2008, 2-7-2 - Sections of code shall not be "commented out" using C-style comments.
  • MISRA C++:2008, 2-7-3 - Sections of code should not be "commented out" using C++ comments.
  • MISRA C:2012, Dir. 4.4 - Sections of code should not be "commented out"

Line too long (85 > 79 characters)
Open

    report = bundle_manifest_service.find_bundles_with_links_correction(project_uuid)
Severity: Minor
Found in fix_bundle_links.py by pep8

Limit all lines to a maximum of 79 characters.

There are still many devices around that are limited to 80 character
lines; plus, limiting windows to 80 characters makes it possible to
have several windows side-by-side.  The default wrapping on such
devices looks ugly.  Therefore, please limit all lines to a maximum
of 79 characters. For flowing long blocks of text (docstrings or
comments), limiting the length to 72 characters is recommended.

Reports error E501.

Line too long (80 > 79 characters)
Open

        reports['summary']['error_count'] = len(list(reports['bundles'].keys()))
Severity: Minor
Found in fix_bundle_links.py by pep8

Limit all lines to a maximum of 79 characters.

There are still many devices around that are limited to 80 character
lines; plus, limiting windows to 80 characters makes it possible to
have several windows side-by-side.  The default wrapping on such
devices looks ugly.  Therefore, please limit all lines to a maximum
of 79 characters. For flowing long blocks of text (docstrings or
comments), limiting the length to 72 characters is recommended.

Reports error E501.

Line too long (84 > 79 characters)
Open

        if len(newer_links) == len(new_links) and len(self.links) == len(new_links):
Severity: Minor
Found in fix_bundle_links.py by pep8

Limit all lines to a maximum of 79 characters.

There are still many devices around that are limited to 80 character
lines; plus, limiting windows to 80 characters makes it possible to
have several windows side-by-side.  The default wrapping on such
devices looks ugly.  Therefore, please limit all lines to a maximum
of 79 characters. For flowing long blocks of text (docstrings or
comments), limiting the length to 72 characters is recommended.

Reports error E501.

Line too long (81 > 79 characters)
Open

    # report = bundle_manifest_service.update_bundle_manifest_links(project_uuid)
Severity: Minor
Found in fix_bundle_links.py by pep8

Limit all lines to a maximum of 79 characters.

There are still many devices around that are limited to 80 character
lines; plus, limiting windows to 80 characters makes it possible to
have several windows side-by-side.  The default wrapping on such
devices looks ugly.  Therefore, please limit all lines to a maximum
of 79 characters. For flowing long blocks of text (docstrings or
comments), limiting the length to 72 characters is recommended.

Reports error E501.

Line too long (104 > 79 characters)
Open

        return self.ingest_api.get_related_entities_count("bundleManifests", project, "bundleManifests")
Severity: Minor
Found in fix_bundle_links.py by pep8

Limit all lines to a maximum of 79 characters.

There are still many devices around that are limited to 80 character
lines; plus, limiting windows to 80 characters makes it possible to
have several windows side-by-side.  The default wrapping on such
devices looks ugly.  Therefore, please limit all lines to a maximum
of 79 characters. For flowing long blocks of text (docstrings or
comments), limiting the length to 72 characters is recommended.

Reports error E501.

Line too long (84 > 79 characters)
Open

            print(f'Processing {i + 1}/{count} , bundle {bundle_manifest.fqid} ...')
Severity: Minor
Found in fix_bundle_links.py by pep8

Limit all lines to a maximum of 79 characters.

There are still many devices around that are limited to 80 character
lines; plus, limiting windows to 80 characters makes it possible to
have several windows side-by-side.  The default wrapping on such
devices looks ugly.  Therefore, please limit all lines to a maximum
of 79 characters. For flowing long blocks of text (docstrings or
comments), limiting the length to 72 characters is recommended.

Reports error E501.

Line too long (84 > 79 characters)
Open

        self._files_map = {file['name']: file for file in self._object.get('files')}
Severity: Minor
Found in fix_bundle_links.py by pep8

Limit all lines to a maximum of 79 characters.

There are still many devices around that are limited to 80 character
lines; plus, limiting windows to 80 characters makes it possible to
have several windows side-by-side.  The default wrapping on such
devices looks ugly.  Therefore, please limit all lines to a maximum
of 79 characters. For flowing long blocks of text (docstrings or
comments), limiting the length to 72 characters is recommended.

Reports error E501.

Line too long (98 > 79 characters)
Open

        return self.ingest_api.get_related_entities("bundleManifests", project, "bundleManifests")
Severity: Minor
Found in fix_bundle_links.py by pep8

Limit all lines to a maximum of 79 characters.

There are still many devices around that are limited to 80 character
lines; plus, limiting windows to 80 characters makes it possible to
have several windows side-by-side.  The default wrapping on such
devices looks ugly.  Therefore, please limit all lines to a maximum
of 79 characters. For flowing long blocks of text (docstrings or
comments), limiting the length to 72 characters is recommended.

Reports error E501.

Line too long (84 > 79 characters)
Open

        links_file_json = self.dss_api.get_file(links_file_uuid, links_file_version)
Severity: Minor
Found in fix_bundle_links.py by pep8

Limit all lines to a maximum of 79 characters.

There are still many devices around that are limited to 80 character
lines; plus, limiting windows to 80 characters makes it possible to
have several windows side-by-side.  The default wrapping on such
devices looks ugly.  Therefore, please limit all lines to a maximum
of 79 characters. For flowing long blocks of text (docstrings or
comments), limiting the length to 72 characters is recommended.

Reports error E501.

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