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Showing 376 of 791 total issues

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

    def __init__(self, cache_dirname, MongoDB, db, verbose=False,
Severity: Major
Found in datanator/data_source/pax_nosql.py - About 1 hr to fix

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

        def __init__(self, MongoDB, db, replicaSet=None,
    Severity: Major
    Found in datanator/data_source/corum_nosql.py - About 1 hr to fix

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

          def __init__(self, MongoDB=None, db=None, collection_str=None, username=None,
      Severity: Major
      Found in datanator/data_source/metabolite_concentration/doi_10_1038_nchembio_2077.py - About 1 hr to fix

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

            def __init__(self, MongoDB=None, db=None, collection_str=None, username=None,
        Severity: Major
        Found in datanator/data_source/rna_modification/rna_modification.py - About 1 hr to fix

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

              def __init__(self, cache_dirname=None, MongoDB=None, db=None,
          Severity: Major
          Found in datanator/data_source/intact_nosql.py - About 1 hr to fix

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

                def __init__(self, db = None, MongoDB = None, cache_directory=None,
            Severity: Major
            Found in datanator/data_source/sabio_rk_json_mongo.py - About 1 hr to fix

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

                  def __init__(self, server=None, db='datanator', collection_str='rna_halflife', username=None,
              Severity: Major
              Found in datanator/data_source/rna_halflife/back_fill_gene_name.py - About 1 hr to fix

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

                    def __init__(self, cache_dirname, MongoDB, db, replicaSet=None,
                Severity: Major
                Found in datanator/data_source/taxon_tree.py - About 1 hr to fix

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

                      def __init__(self, dataset, directory, max_entries,
                  Severity: Major
                  Found in datanator/data_source/protein_localization/justin_parse_subcellular_location.py - About 1 hr to fix

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

                        def __init__(self, MongoDB=None, db=None, username=None, password=None,
                    Severity: Major
                    Found in datanator/data_source/brenda/reaction.py - About 1 hr to fix

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

                          def data_from_mongo_sabiork(self, server, db, username, password, verbose=False,
                      Severity: Major
                      Found in datanator/elasticsearch_kl/batch_load.py - About 1 hr to fix

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

                            def data_from_mongo_metabolite(self, server, db, username, password, verbose=False,
                        Severity: Major
                        Found in datanator/elasticsearch_kl/batch_load.py - About 1 hr to fix

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

                              def data_from_mongo_kegg_orthology(self, server, db, username, password, verbose=False,
                          Severity: Major
                          Found in datanator/elasticsearch_kl/batch_load.py - About 1 hr to fix

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

                                def __init__(self, profile_name=None, credential_path=None,
                            Severity: Major
                            Found in datanator/elasticsearch_kl/batch_load.py - About 1 hr to fix

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

                                  def data_from_mongo(self, server, db, username, password, verbose=False,
                              Severity: Major
                              Found in datanator/elasticsearch_kl/batch_load.py - About 1 hr to fix

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

                                        def process_doc(doc, final, i, total = total, collection_str1 = collection_str1,
                                Severity: Major
                                Found in datanator/util/calc_tanimoto.py - About 1 hr to fix

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

                                      def data_from_mongo_protein(self, server, db, username, password, verbose=False,
                                  Severity: Major
                                  Found in datanator/elasticsearch_kl/batch_load.py - About 1 hr to fix

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

                                        def data_from_mongo_sabiork_rxn_entries(self, server, db, username, password, verbose=False,
                                    Severity: Major
                                    Found in datanator/elasticsearch_kl/batch_load.py - About 1 hr to fix

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

                                          def __init__(self, cache_dirname=None, MongoDB=None, replicaSet=None, db=None,
                                      Severity: Major
                                      Found in datanator/util/index_collection.py - About 1 hr to fix

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

                                            def data_from_mongo_metabolites_meta(self, server, db, username, password, verbose=False,
                                        Severity: Major
                                        Found in datanator/elasticsearch_kl/batch_load.py - About 1 hr to fix
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