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

    config.db.analyses.update_one({'_id': analysis['_id']}, {'$set': {'inputs': inputs, 'files': outputs}})
Severity: Minor
Found in bin/database.py and 1 other location - About 40 mins to fix
bin/oneoffs/timezone_shift.py on lines 40..40

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 34.

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 3 locations. Consider refactoring.
Open

        if result and result.get(self.list_name):
            return result.get(self.list_name)[0]
Severity: Major
Found in api/dao/liststorage.py and 2 other locations - About 40 mins to fix
api/dao/liststorage.py on lines 115..116
api/dao/liststorage.py on lines 280..281

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 34.

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 3 locations. Consider refactoring.
Open

        if result and result.get(self.list_name):
            return result.get(self.list_name)[0]
Severity: Major
Found in api/dao/liststorage.py and 2 other locations - About 40 mins to fix
api/dao/liststorage.py on lines 179..180
api/dao/liststorage.py on lines 280..281

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 34.

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 3 locations. Consider refactoring.
Open

        if result and result.get(self.list_name):
            return result.get(self.list_name)[0]
Severity: Major
Found in api/dao/liststorage.py and 2 other locations - About 40 mins to fix
api/dao/liststorage.py on lines 115..116
api/dao/liststorage.py on lines 179..180

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 34.

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

                config.db.users.update_one({'_id': uid, 'avatar': {'$exists': False}}, {'$set':{'avatar': gravatar, 'modified': timestamp}})
Severity: Major
Found in api/auth/authproviders.py and 3 other locations - About 40 mins to fix
api/auth/authproviders.py on lines 63..63
api/auth/authproviders.py on lines 190..190
api/auth/authproviders.py on lines 192..192

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 34.

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

                acquisitions = config.db.acquisitions.find({'session': {'$in': session_ids}, 'deleted': {'$exists': False}}, {'_id': 1})
Severity: Minor
Found in api/download.py and 1 other location - About 40 mins to fix
api/handlers/reporthandler.py on lines 878..878

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 34.

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

                config.db.users.update_one({'_id': uid, 'avatars.gravatar': {'$ne': gravatar}},{'$set':{'avatars.gravatar': gravatar,'modified': timestamp}})
Severity: Major
Found in api/auth/authproviders.py and 3 other locations - About 40 mins to fix
api/auth/authproviders.py on lines 65..65
api/auth/authproviders.py on lines 190..190
api/auth/authproviders.py on lines 192..192

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 34.

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

        config.db.users.update_one({'_id': uid, 'avatars.provider': {'$ne': provider_avatar}}, {'$set':{'avatars.provider': provider_avatar, 'modified': timestamp}})
Severity: Major
Found in api/auth/authproviders.py and 3 other locations - About 40 mins to fix
api/auth/authproviders.py on lines 63..63
api/auth/authproviders.py on lines 65..65
api/auth/authproviders.py on lines 192..192

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 34.

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

                    try:
                        auth_provider = AuthProvider.factory(auth_type)
                    except NotImplementedError as e:
                        self.abort(401, str(e))
Severity: Minor
Found in api/web/base.py and 1 other location - About 40 mins to fix
api/web/base.py on lines 210..213

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 34.

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

        try:
            auth_provider = AuthProvider.factory(auth_type)
        except NotImplementedError as e:
            self.abort(400, str(e))
Severity: Minor
Found in api/web/base.py and 1 other location - About 40 mins to fix
api/web/base.py on lines 163..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 34.

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 self.is_true('info'):
                    try:
                        info = FileListHandler.build_zip_info(filepath)
                    except zipfile.BadZipfile:
                        self.abort(400, 'not a zip file')
Severity: Minor
Found in api/handlers/refererhandler.py and 1 other location - About 40 mins to fix
api/handlers/listhandler.py on lines 417..422

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 34.

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

        elif self.is_true('info'):
            try:
                info = self.build_zip_info(filepath)
            except zipfile.BadZipfile:
                self.abort(400, 'not a zip file')
Severity: Minor
Found in api/handlers/listhandler.py and 1 other location - About 40 mins to fix
api/handlers/refererhandler.py on lines 377..382

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 34.

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 f has 5 arguments (exceeds 4 allowed). Consider refactoring.
Open

        def f(method, _id=None, query=None, payload=None, projection=None):
Severity: Minor
Found in api/auth/groupauth.py - About 35 mins to fix

    Function eval_match has 5 arguments (exceeds 4 allowed). Consider refactoring.
    Open

    def eval_match(match_type, match_param, file_, container, regex=False):
    Severity: Minor
    Found in api/jobs/rules.py - About 35 mins to fix

      Function f has 5 arguments (exceeds 4 allowed). Consider refactoring.
      Open

              def f(method, _id, query_params = None, payload = None, exclude_params=None):
      Severity: Minor
      Found in api/auth/listauth.py - About 35 mins to fix

        Function f has 5 arguments (exceeds 4 allowed). Consider refactoring.
        Open

                def f(method, _id, query_params=None, payload=None, exclude_params=None):
        Severity: Minor
        Found in api/auth/listauth.py - About 35 mins to fix

          Function f has 5 arguments (exceeds 4 allowed). Consider refactoring.
          Open

                  def f(method, _id=None, query=None, payload=None, projection=None):
          Severity: Minor
          Found in api/auth/userauth.py - About 35 mins to fix

            Function f has 5 arguments (exceeds 4 allowed). Consider refactoring.
            Open

                    def f(method, query=None, user=None, public=False, projection=None):
            Severity: Minor
            Found in api/auth/containerauth.py - About 35 mins to fix

              Function f has 5 arguments (exceeds 4 allowed). Consider refactoring.
              Open

                      def f(method, _id, query_params = None, payload = None, exclude_params=None):
              Severity: Minor
              Found in api/auth/listauth.py - About 35 mins to fix

                Function f has 5 arguments (exceeds 4 allowed). Consider refactoring.
                Open

                        def f(method, _id, query_params = None, payload = None, exclude_params=None):
                Severity: Minor
                Found in api/auth/listauth.py - About 35 mins to fix
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