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Avoid too many return statements within this function.
Open

                return (None, None, None, None, None)
Severity: Major
Found in datanator/data_source/sabio_rk.py - About 30 mins to fix

    Avoid too many return statements within this function.
    Open

                        return ('k_cat', 25, value * float(f) if value else None, error * float(f) if error else None, 's^(-1)')
    Severity: Major
    Found in datanator/data_source/sabio_rk.py - About 30 mins to fix

      Avoid too many return statements within this function.
      Open

                      return ('k_cat', 25, value, error, 's^(-1)')
      Severity: Major
      Found in datanator/data_source/sabio_rk.py - About 30 mins to fix

        Avoid too many return statements within this function.
        Open

                    return False
        Severity: Major
        Found in datanator/util/molecule_util.py - About 30 mins to fix

          Avoid too many return statements within this function.
          Open

                  return True
          Severity: Major
          Found in datanator/util/molecule_util.py - About 30 mins to fix

            Avoid too many return statements within this function.
            Open

                        return None
            Severity: Major
            Found in datanator/util/chem_util.py - About 30 mins to fix

              Avoid too many return statements within this function.
              Open

                                  return None
              Severity: Major
              Found in datanator/util/chem_util.py - About 30 mins to fix

                Avoid too many return statements within this function.
                Open

                            return None
                Severity: Major
                Found in datanator/util/molecule_util.py - About 30 mins to fix

                  Avoid too many return statements within this function.
                  Open

                              return False
                  Severity: Major
                  Found in datanator/util/molecule_util.py - About 30 mins to fix

                    Avoid too many return statements within this function.
                    Open

                                return False
                    Severity: Major
                    Found in datanator/util/molecule_util.py - About 30 mins to fix

                      Avoid too many return statements within this function.
                      Open

                                  return None
                      Severity: Major
                      Found in datanator/util/chem_util.py - About 30 mins to fix

                        Avoid too many return statements within this function.
                        Open

                                return "%s-%s%s%s-%s" % (major, minor, flag, flagver, flagproto)
                        Severity: Major
                        Found in datanator/util/chem_util.py - About 30 mins to fix

                          Avoid too many return statements within this function.
                          Open

                                          return None
                          Severity: Major
                          Found in datanator/util/chem_util.py - About 30 mins to fix

                            Avoid too many return statements within this function.
                            Open

                                        return False
                            Severity: Major
                            Found in datanator/util/molecule_util.py - About 30 mins to fix

                              Avoid too many return statements within this function.
                              Open

                                          return None
                              Severity: Major
                              Found in datanator/util/chem_util.py - About 30 mins to fix

                                Identical blocks of code found in 3 locations. Consider refactoring.
                                Open

                                                    values_p.append({"type":"RNA_"+rna_data[i]+"_specific_NX","value":data["RNA "+rna_data[i].replace("_"," ")+" specific NX"][x],"description":x.replace("\\","")})
                                Severity: Minor
                                Found in datanator/data_source/protein_localization/victoria_insert_protein_atlas.py and 2 other locations - About 30 mins to fix
                                datanator/data_source/protein_localization/victoria_insert_protein_atlas.py on lines 114..114
                                datanator/data_source/protein_localization/victoria_insert_protein_atlas.py on lines 115..115

                                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 32.

                                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 data["RNA "+rna_data[i].replace("_"," ")+" specific NX"]!=None:
                                Severity: Minor
                                Found in datanator/data_source/protein_localization/victoria_insert_protein_atlas.py and 2 other locations - About 30 mins to fix
                                datanator/data_source/protein_localization/victoria_insert_protein_atlas.py on lines 116..116
                                datanator/data_source/protein_localization/victoria_insert_protein_atlas.py on lines 115..115

                                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 32.

                                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

                                                for x in data["RNA "+rna_data[i].replace("_"," ")+" specific NX"].keys():
                                Severity: Minor
                                Found in datanator/data_source/protein_localization/victoria_insert_protein_atlas.py and 2 other locations - About 30 mins to fix
                                datanator/data_source/protein_localization/victoria_insert_protein_atlas.py on lines 114..114
                                datanator/data_source/protein_localization/victoria_insert_protein_atlas.py on lines 116..116

                                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 32.

                                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.commit_intermediate_results and (i_compound % 100 == 99):
                self.session.commit()
                                Severity: Minor
                                Found in datanator/data_source/sabio_rk.py and 1 other location - About 30 mins to fix
                                datanator/data_source/sabio_rk.py on lines 1658..1659

                                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 32.

                                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 3 locations. Consider refactoring.
                                Open

                                        data['entrez_id'] = data['entrez_id'].astype(str).str.replace(';', '')
                                Severity: Minor
                                Found in datanator/data_source/uniprot_nosql.py and 2 other locations - About 30 mins to fix
                                datanator/data_source/uniprot_nosql.py on lines 88..88
                                datanator/data_source/uniprot_nosql.py on lines 95..95

                                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 32.

                                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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