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Showing 376 of 791 total issues

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

    def __init__(self,
Severity: Major
Found in datanator/data_source/protein_half_lives/victoria_parse_yeast_global_proteome_turnover.py - About 50 mins to fix

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

        def __init__(self,
    Severity: Major
    Found in datanator/data_source/protein_half_lives/victoria_parse_column_k0_mouse_brain.py - About 50 mins to fix

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

          def __init__(self,
      Severity: Major
      Found in datanator/data_source/protein_half_lives/victoria_parse_proteome_half_lives.py - About 50 mins to fix

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

            def is_equal(self, other,
        Severity: Major
        Found in datanator/util/molecule_util.py - About 50 mins to fix

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

              def __init__(self,
          Severity: Major
          Found in datanator/schema_2/transform.py - About 50 mins to fix

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

                def many_to_many(self, collection_str1='metabolites_meta',
            Severity: Major
            Found in datanator/util/calc_tanimoto.py - About 50 mins to fix

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

                  def __init__(self,
              Severity: Major
              Found in datanator/schema_2/transform_metabolite_concentrations.py - About 50 mins to fix

                Avoid deeply nested control flow statements.
                Open

                                    if locus_tag in list_locus_tags:
                        locus_tag = "{}_variation".format(locus_tag)
                    list_locus_tags.append(locus_tag)
                Severity: Major
                Found in datanator/data_source/process_rna_seq/core.py - About 45 mins to fix

                  Avoid deeply nested control flow statements.
                  Open

                                          if form.seq[i_monomer - 1] == monomers[seq[i_monomer - 1]]:
                            set_monomer = True
                            form.seq[i_monomer - 1] = monomer2
                            break
                    if not set_monomer:
                  Severity: Major
                  Found in datanator/data_source/protein_modification/pro.py - About 45 mins to fix

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

                        def __init__(self, MongoDB=None,
                    Severity: Minor
                    Found in datanator/data_source/metabolite_concentration/query_demo.py - About 45 mins to fix

                      Avoid deeply nested control flow statements.
                      Open

                                              if numpy.isinf(start_position):
                            protein['modified_errors'].append('Sequence does not contain residues {} for modification {}'.format(
                                ', '.join(origin), modification['monomer']))
                        else:
                            monomer2.start_position = start_position
                      Severity: Major
                      Found in datanator/data_source/protein_modification/pro.py - About 45 mins to fix

                        Avoid deeply nested control flow statements.
                        Open

                                                if i % 100 == 0 and self.verbose:
                            print("     Adding kinlaw_id {} into uniprot collection.".format(kinlaw_id))
                        self.collection.update_one({'uniprot_id': uniprot_id},
                        Severity: Major
                        Found in datanator/data_source/uniprot_nosql.py - About 45 mins to fix

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

                              def normalize_parameter_value(self, name, type, value, error, units, enzyme_molecular_weight):
                          Severity: Minor
                          Found in datanator/data_source/sabio_rk.py - About 45 mins to fix

                            Avoid deeply nested control flow statements.
                            Open

                                                    if monomer is None:
                            unsupported_codes.add(code)
                            monomer = bpforms.Monomer(id=code)
                        else:
                            monomer_codes[code] = monomer
                            Severity: Major
                            Found in datanator/data_source/modomics.py - About 45 mins to fix

                              Avoid deeply nested control flow statements.
                              Open

                                                  if characteristic.category.lower() in SYNONYMS_PRIORITY_LIST[i]:
                        try:
                            strain = "{}".format(characteristic.value)
                        except UnicodeEncodeError:
                            pass
                              Severity: Major
                              Found in datanator/data_source/array_express_tools/ensembl_tools.py - About 45 mins to fix

                                Avoid deeply nested control flow statements.
                                Open

                                                        if max_num_proteins is not None and len(proteins) >= max_num_proteins:
                            break
                        protein = {}
                                Severity: Major
                                Found in datanator/data_source/protein_modification/pro.py - About 45 mins to fix

                                  Avoid deeply nested control flow statements.
                                  Open

                                                          if not set_monomer:
                            protein['modified_errors'].append('Unable to set monomeric form')

        # crosslinks
        if protein['processing']:
                                  Severity: Major
                                  Found in datanator/data_source/protein_modification/pro.py - About 45 mins to fix

                                    Avoid deeply nested control flow statements.
                                    Open

                                                        if org_name.startswith(format_org_name(try_org)):
                        kegg_org_symbol = thing.split('  ')[0]
                        url = get_ref_seq_url(kegg_org_symbol)
                        spec_name = org_name.replace("-","_").replace(" ", "_")
                        full_strain_specificity ==True
                                    Severity: Major
                                    Found in datanator/data_source/array_express_tools/ensembl_tools.py - About 45 mins to fix

                                      Avoid deeply nested control flow statements.
                                      Open

                                                              if monomer is None:
                            unsupported_codes.add(code)
                            monomer = bpforms.Monomer(id=code)
                        else:
                            monomer_codes[code] = monomer
                                      Severity: Major
                                      Found in datanator/data_source/modomics.py - About 45 mins to fix

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

                                            def __init__(self,
                                        Severity: Minor
                                        Found in datanator/data_source/rna_localization/victoria_parse_LncAtlas.py - About 45 mins to fix
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