Index

A

access_dict_by_index() (datanator_query_python.util.file_util.FileUtil method) aggregate_all_occurences() (datanator_query_python.aggregate.pipelines.Pipeline method) aggregate_common_canon_ancestors() (datanator_query_python.aggregate.pipelines.Pipeline method) aggregate_field_count() (datanator_query_python.aggregate.pipelines.Pipeline method) aggregate_kegg_orthology() (datanator_query_python.aggregate.pipelines.Pipeline method) aggregate_taxon_distance() (datanator_query_python.aggregate.pipelines.Pipeline method) aggregate_total_array_length() (datanator_query_python.aggregate.pipelines.Pipeline method)

App (class in datanator_query_python.__main__) App.Meta (class in datanator_query_python.__main__) arguments (datanator_query_python.__main__.BaseController.Meta attribute) (datanator_query_python.__main__.DefineSchema.Meta attribute) AtlasConfig (class in datanator_query_python.config.config) AUTHDB (datanator_query_python.config.config.AtlasConfig attribute) (datanator_query_python.config.config.Config attribute)

B

base26_dublet_for_bits_28_to_36() (in module datanator_query_python.util.base26) base26_dublet_for_bits_56_to_64() (in module datanator_query_python.util.base26) base26_triplet_1() (in module datanator_query_python.util.base26) base26_triplet_2() (in module datanator_query_python.util.base26) base26_triplet_3() (in module datanator_query_python.util.base26)

base26_triplet_4() (in module datanator_query_python.util.base26) base_controller (datanator_query_python.__main__.App.Meta attribute) BaseController (class in datanator_query_python.__main__) BaseController.Meta (class in datanator_query_python.__main__) bool_query() (datanator_query_python.query.full_text_search.FTX method) build_taxon_object() (datanator_query_python.util.mongo_util.MongoUtil method)

C

ChemUtil (class in datanator_query_python.util.chem_util) complex_lookup() (datanator_query_python.aggregate.lookups.Lookups method)

con_db() (datanator_query_python.util.mongo_util.MongoUtil method) Config (class in datanator_query_python.config.config) conn_protein() (datanator_query_python.config.query_schema_2_manager.QM method)

D

datanator_query_python (module) datanator_query_python.__main__ (module) datanator_query_python._version (module) datanator_query_python.aggregate (module) datanator_query_python.aggregate.lookups (module) datanator_query_python.aggregate.pipelines (module) datanator_query_python.aggregate.tabu (module) datanator_query_python.config (module) datanator_query_python.config.config (module) datanator_query_python.config.query_manager (module) datanator_query_python.config.query_schema_2_manager (module) datanator_query_python.query (module) datanator_query_python.query.full_text_search (module) datanator_query_python.query.query_corum (module) datanator_query_python.query.query_intact_complex (module) datanator_query_python.query.query_kegg_organism_code (module) datanator_query_python.query.query_kegg_orthology (module) datanator_query_python.query.query_metabolite_concentrations (module) datanator_query_python.query.query_metabolites (module) datanator_query_python.query.query_metabolites_meta (module) datanator_query_python.query.query_pax (module) datanator_query_python.query.query_protein (module) datanator_query_python.query.query_rna_halflife (module) datanator_query_python.query.query_sabio_compound (module) datanator_query_python.query.query_sabio_reaction_entries (module) datanator_query_python.query.query_sabiork (module)

datanator_query_python.query.query_sabiork_old (module) datanator_query_python.query.query_taxon_tree (module) datanator_query_python.query.query_uniprot (module) datanator_query_python.query.query_uniprot_org (module) datanator_query_python.query.query_xmdb (module) datanator_query_python.query_schema_2 (module) datanator_query_python.query_schema_2.ftx_search (module) datanator_query_python.query_schema_2.query_entity (module) datanator_query_python.query_schema_2.query_observation (module) datanator_query_python.query_schema_2.query_uniprot_v2 (module) datanator_query_python.util (module) datanator_query_python.util.base26 (module) datanator_query_python.util.chem_util (module) datanator_query_python.util.file_util (module) datanator_query_python.util.mapper_reducer (module) datanator_query_python.util.mongo_util (module) datanator_query_python.util.motor_util (module) datanator_query_python.util.parse_heroku_logs (module) DatanatorAdmin (class in datanator_query_python.config.config) DatanatorTest (class in datanator_query_python.config.config) default() (datanator_query_python.util.file_util.JSONEncoder method) define_schema() (datanator_query_python.util.mongo_util.MongoUtil method) DefineSchema (class in datanator_query_python.__main__) DefineSchema.Meta (class in datanator_query_python.__main__) description (datanator_query_python.__main__.BaseController.Meta attribute) (datanator_query_python.__main__.DefineSchema.Meta attribute)

E

each_under_category() (datanator_query_python.query.query_taxon_tree.QueryTaxonTree method) exists_key_value_pair() (datanator_query_python.util.file_util.FileUtil method)

extract_values() (datanator_query_python.util.file_util.FileUtil method) eymdb_manager() (datanator_query_python.config.query_manager.Manager method)

F

FileUtil (class in datanator_query_python.util.file_util) find_reaction_participants() (datanator_query_python.query.query_sabiork.QuerySabio method) flatten_collection() (datanator_query_python.util.mongo_util.MongoUtil method) flatten_json() (datanator_query_python.util.file_util.FileUtil method) FTX (class in datanator_query_python.query.full_text_search) (class in datanator_query_python.query_schema_2.ftx_search)

FTX_AWS_PROFILE (datanator_query_python.config.config.FtxConfig attribute) ftx_manager() (datanator_query_python.config.query_manager.FtxManager method) FtxConfig (class in datanator_query_python.config.config) FtxManager (class in datanator_query_python.config.query_manager)

G

get_abundance_by_id() (datanator_query_python.query.query_protein.QueryProtein method) get_abundance_by_ko() (datanator_query_python.query.query_protein.QueryProtein method) get_abundance_by_taxon() (datanator_query_python.query.query_protein.QueryProtein method) get_abundance_from_uniprot() (datanator_query_python.query.query_pax.QueryPax method) get_abundance_with_same_ko() (datanator_query_python.query.query_protein.QueryProtein method) get_all_concentrations() (datanator_query_python.query.query_xmdb.QueryXmdb method) get_all_kegg() (datanator_query_python.query.query_protein.QueryProtein method) get_all_ortho() (datanator_query_python.query.query_protein.QueryProtein method) get_all_species() (datanator_query_python.query.query_pax.QueryPax method) (datanator_query_python.query.query_taxon_tree.QueryTaxonTree method) get_anc_by_id() (datanator_query_python.query.query_taxon_tree.QueryTaxonTree method) get_anc_by_name() (datanator_query_python.query.query_taxon_tree.QueryTaxonTree method) get_canon_common_ancestor() (datanator_query_python.query.query_taxon_tree.QueryTaxonTree method) get_canon_common_ancestor_fast() (datanator_query_python.query.query_taxon_tree.QueryTaxonTree method) get_canon_rank_distance() (datanator_query_python.query.query_taxon_tree.QueryTaxonTree method) get_canon_rank_distance_by_name() (datanator_query_python.query.query_taxon_tree.QueryTaxonTree method) get_common() (datanator_query_python.util.file_util.FileUtil method) get_common_ancestor() (datanator_query_python.query.query_taxon_tree.QueryTaxonTree method) get_complex_with_ncbi() (datanator_query_python.query.query_intact_complex.QueryIntactComplex method) get_complexes_with_ncbi() (datanator_query_python.query.query_corum.QueryCorum method) get_complexes_with_uniprot() (datanator_query_python.query.query_corum.QueryCorum method) get_conc_by_taxon() (datanator_query_python.query.query_metabolite_concentrations.QueryMetaboliteConcentrations method) get_conc_count() (datanator_query_python.query.query_metabolite_concentrations.QueryMetaboliteConcentrations method) get_conc_from_inchi() (datanator_query_python.query.query_metabolites.QueryMetabolites method) get_concentration_count() (datanator_query_python.query.query_metabolites.QueryMetabolites method) get_def_by_kegg_id() (datanator_query_python.query.query_kegg_orthology.QueryKO method) get_doc_by_ko() (datanator_query_python.query.query_rna_halflife.QueryRNA method) get_doc_by_locus() (datanator_query_python.query.query_uniprot.QueryUniprot method) get_doc_by_name() (datanator_query_python.query.query_metabolites_meta.QueryMetabolitesMeta method) get_doc_by_names() (datanator_query_python.query.query_rna_halflife.QueryRNA method) get_doc_by_oln() (datanator_query_python.query.query_rna_halflife.QueryRNA method) get_doc_by_orthodb() (datanator_query_python.query.query_rna_halflife.QueryRNA method) get_duplicates() (datanator_query_python.util.mongo_util.MongoUtil method) get_entity_datatype() (datanator_query_python.query_schema_2.query_observation.QueryObs method) get_equivalent_kegg_with_anchor_obsolete() (datanator_query_python.query.query_protein.QueryProtein method) get_equivalent_protein() (datanator_query_python.query.query_protein.QueryProtein method) get_equivalent_protein_with_anchor() (datanator_query_python.query.query_protein.QueryProtein method) get_equivalent_species() (datanator_query_python.query.query_taxon_tree.QueryTaxonTree method) get_eymeta() (datanator_query_python.query.query_metabolites_meta.QueryMetabolitesMeta method) get_file_by_name() (datanator_query_python.query.query_pax.QueryPax method) get_file_by_ncbi_id() (datanator_query_python.query.query_pax.QueryPax method) get_file_by_organ() (datanator_query_python.query.query_pax.QueryPax method) get_file_by_publication() (datanator_query_python.query.query_pax.QueryPax method) get_file_by_quality() (datanator_query_python.query.query_pax.QueryPax method) get_gene_protein_name_by_embl() (datanator_query_python.query.query_uniprot.QueryUniprot method) get_gene_protein_name_by_oln() (datanator_query_python.query.query_uniprot.QueryUniprot method) get_genes_ko_count() (datanator_query_python.query.full_text_search.FTX method) get_genes_orthodb_count() (datanator_query_python.query.full_text_search.FTX method) get_id_by_name() (datanator_query_python.query.query_protein.QueryProtein method) (datanator_query_python.query.query_sabio_compound.QuerySabioCompound method) get_id_by_org_gene() (datanator_query_python.query.query_uniprot.QueryUniprot method) get_ids_by_name() (datanator_query_python.query.query_taxon_tree.QueryTaxonTree method) get_ids_by_participant_inchikey() (datanator_query_python.query.query_sabio_reaction_entries.QuerySabioRxn method) get_ids_from_hash() (datanator_query_python.query.query_metabolites_meta.QueryMetabolitesMeta method) get_ids_from_hashes() (datanator_query_python.query.query_metabolites_meta.QueryMetabolitesMeta method) get_inchikey_by_name() (datanator_query_python.query.query_sabio_compound.QuerySabioCompound method) get_index_in_page() (datanator_query_python.query.full_text_search.FTX method) get_index_ko_count() (datanator_query_python.query.full_text_search.FTX method) get_info_by_entrez_id() (datanator_query_python.query.query_uniprot.QueryUniprot method) get_info_by_entryid() (datanator_query_python.query.query_sabiork_old.QuerySabioOld method) get_info_by_ko() (datanator_query_python.query.query_protein.QueryProtein method) get_info_by_ko_abundance() (datanator_query_python.query.query_protein.QueryProtein method)

get_info_by_orthodb() (datanator_query_python.query.query_protein.QueryProtein method) get_info_by_taxonid() (datanator_query_python.query.query_protein.QueryProtein method) get_info_by_taxonid_abundance() (datanator_query_python.query.query_protein.QueryProtein method) get_info_by_text() (datanator_query_python.query.query_protein.QueryProtein method) get_info_by_text_abundances() (datanator_query_python.query.query_protein.QueryProtein method) get_kegg_ortholog() (datanator_query_python.query.query_uniprot_org.QueryUniprotOrg method) get_kegg_orthology() (datanator_query_python.query.query_protein.QueryProtein method) get_kinlaw_by_entryid() (datanator_query_python.query.query_sabiork_old.QuerySabioOld method) get_kinlaw_by_environment() (datanator_query_python.query.query_sabiork.QuerySabio method) (datanator_query_python.query.query_sabiork_old.QuerySabioOld method) get_kinlaw_by_id() (datanator_query_python.query.query_protein.QueryProtein method) get_kinlaw_by_name() (datanator_query_python.query.query_protein.QueryProtein method) get_kinlaw_by_rxn() (datanator_query_python.query.query_sabiork_old.QuerySabioOld method) get_kinlaw_by_rxn_name() (datanator_query_python.query.query_sabiork_old.QuerySabioOld method) get_kinlaw_by_rxn_ortho() (datanator_query_python.query.query_sabiork_old.QuerySabioOld method) get_kinlawid_by_inchi() (datanator_query_python.query.query_sabiork.QuerySabio method) get_kinlawid_by_name() (datanator_query_python.query.query_sabiork.QuerySabio method) get_kinlawid_by_rxn() (datanator_query_python.query.query_sabiork.QuerySabio method) (datanator_query_python.query.query_sabiork_old.QuerySabioOld method) get_ko_by_name() (datanator_query_python.query.query_kegg_orthology.QueryKO method) get_loci_by_id_org() (datanator_query_python.query.query_kegg_orthology.QueryKO method) get_meta_by_id() (datanator_query_python.query.query_protein.QueryProtein method) get_meta_by_kegg_id() (datanator_query_python.query.query_kegg_orthology.QueryKO method) get_meta_by_kegg_ids() (datanator_query_python.query.query_kegg_orthology.QueryKO method) get_meta_by_name_name() (datanator_query_python.query.query_protein.QueryProtein method) get_meta_by_name_taxon() (datanator_query_python.query.query_protein.QueryProtein method) get_meta_by_ortho_ids() (datanator_query_python.query.query_kegg_orthology.QueryKO method) get_meta_from_inchis() (datanator_query_python.query.query_metabolites.QueryMetabolites method) get_metabolite_hashed_inchi() (datanator_query_python.query.query_metabolites_meta.QueryMetabolitesMeta method) get_metabolite_inchi() (datanator_query_python.query.query_metabolites_meta.QueryMetabolitesMeta method) get_metabolite_name_by_hash() (datanator_query_python.query.query_metabolites_meta.QueryMetabolitesMeta method) get_metabolite_synonyms() (datanator_query_python.query.query_metabolites_meta.QueryMetabolitesMeta method) get_metabolites_meta() (datanator_query_python.query.query_metabolites_meta.QueryMetabolitesMeta method) get_name_by_id() (datanator_query_python.query.query_taxon_tree.QueryTaxonTree method) get_name_by_inchikey() (datanator_query_python.query.query_xmdb.QueryXmdb method) get_names_by_gene_name() (datanator_query_python.query.query_uniprot.QueryUniprot method) get_ncbi_by_org_code() (datanator_query_python.query.query_kegg_organism_code.QueryKOC method) get_num_source() (datanator_query_python.query.full_text_search.FTX method) get_org_code_by_ncbi() (datanator_query_python.query.query_kegg_organism_code.QueryKOC method) get_ortho_by_id() (datanator_query_python.query.query_protein.QueryProtein method) get_protein_name() (datanator_query_python.query.query_uniprot_org.QueryUniprotOrg method) get_protein_name_by_gn() (datanator_query_python.query.query_uniprot.QueryUniprot method) get_proximity_abundance_taxon() (datanator_query_python.query.query_protein.QueryProtein method) get_rank() (datanator_query_python.query.query_taxon_tree.QueryTaxonTree method) get_reaction_by_subunit() (datanator_query_python.query.query_sabiork_old.QuerySabioOld method) get_reaction_doc() (datanator_query_python.query.query_sabiork.QuerySabio method) (datanator_query_python.query.query_sabiork_old.QuerySabioOld method) get_rxn_oi() (datanator_query_python.query.full_text_search.FTX method) get_rxn_with_prm() (datanator_query_python.query.query_sabiork_old.QuerySabioOld method) get_schema() (datanator_query_python.util.mongo_util.MongoUtil method) get_sha256() (datanator_query_python.util.chem_util.ChemUtil method) get_similar_concentrations() (datanator_query_python.query.query_metabolite_concentrations.QueryMetaboliteConcentrations method) get_single_index_count() (datanator_query_python.query.full_text_search.FTX method) get_standard_ids_by_id() (datanator_query_python.query.query_xmdb.QueryXmdb method) get_subunit_by_id() (datanator_query_python.query.query_sabiork.QuerySabio method) get_uniprot_by_ko() (datanator_query_python.query.query_protein.QueryProtein method) get_uniprot_id() (datanator_query_python.query.query_uniprot_org.QueryUniprotOrg method) get_unique_entries() (datanator_query_python.query.query_sabiork_old.QuerySabioOld method) get_unique_metabolites() (datanator_query_python.query.query_metabolites_meta.QueryMetabolitesMeta method) get_unique_organism() (datanator_query_python.query.query_protein.QueryProtein method) get_unique_organisms() (datanator_query_python.query.query_sabiork_old.QuerySabioOld method) get_unique_protein() (datanator_query_python.query.query_protein.QueryProtein method) get_val_from_dict_list() (datanator_query_python.util.file_util.FileUtil method)

H

H1_HESC_PASSWORD (datanator_query_python.config.config.H1hescConfig attribute) H1_HESC_USERNAME (datanator_query_python.config.config.H1hescConfig attribute)

H1hescConfig (class in datanator_query_python.config.config) handlers (datanator_query_python.__main__.App.Meta attribute) hash_inchi() (datanator_query_python.util.chem_util.ChemUtil method)

I

inchi_to_inchikey() (datanator_query_python.util.chem_util.ChemUtil method)

J

JSONEncoder (class in datanator_query_python.util.file_util)

K

kegg_manager() (datanator_query_python.config.query_manager.KeggManager method)

KeggManager (class in datanator_query_python.config.query_manager)

L

label (datanator_query_python.__main__.App.Meta attribute) (datanator_query_python.__main__.BaseController.Meta attribute) (datanator_query_python.__main__.DefineSchema.Meta attribute)

list_all_collections() (datanator_query_python.util.mongo_util.MongoUtil method) Lookups (class in datanator_query_python.aggregate.lookups)

M

main() (in module datanator_query_python.__main__) (in module datanator_query_python.aggregate.tabu) make_dict() (datanator_query_python.util.file_util.FileUtil method) Manager (class in datanator_query_python.config.query_manager) MaRe (class in datanator_query_python.util.mapper_reducer)

merge_dict() (datanator_query_python.util.file_util.FileUtil method) metabolite_concentration_manager() (datanator_query_python.config.query_manager.Manager method) metabolites_meta_manager() (in module datanator_query_python.config.query_manager) MongoUtil (class in datanator_query_python.util.mongo_util) MotorUtil (class in datanator_query_python.util.motor_util)

P

parse_regex() (datanator_query_python.util.parse_heroku_logs.ParseLogs method) parse_router() (datanator_query_python.util.parse_heroku_logs.ParseLogs method) ParseLogs (class in datanator_query_python.util.parse_heroku_logs) PASSWORD (datanator_query_python.config.config.AtlasConfig attribute) (datanator_query_python.config.config.Config attribute) (datanator_query_python.config.config.DatanatorAdmin attribute) (datanator_query_python.config.config.DatanatorTest attribute) (datanator_query_python.config.config.SchemaMigration attribute) (datanator_query_python.config.config.TestConfig attribute)

Pipeline (class in datanator_query_python.aggregate.pipelines) PORT (datanator_query_python.config.config.AtlasConfig attribute) (datanator_query_python.config.config.Config attribute) PRODUCTION (datanator_query_python.config.config.AtlasConfig attribute) (datanator_query_python.config.config.Config attribute) (datanator_query_python.config.config.ProductionConfig attribute) ProductionConfig (class in datanator_query_python.config.config) protein_manager() (datanator_query_python.config.query_manager.Manager method)

Q

QM (class in datanator_query_python.config.query_schema_2_manager) query_entity() (datanator_query_python.query_schema_2.query_entity.QueryEn method) QueryCorum (class in datanator_query_python.query.query_corum) QueryEn (class in datanator_query_python.query_schema_2.query_entity) QueryIntactComplex (class in datanator_query_python.query.query_intact_complex) QueryKO (class in datanator_query_python.query.query_kegg_orthology) QueryKOC (class in datanator_query_python.query.query_kegg_organism_code) QueryMetaboliteConcentrations (class in datanator_query_python.query.query_metabolite_concentrations) QueryMetabolites (class in datanator_query_python.query.query_metabolites) QueryMetabolitesMeta (class in datanator_query_python.query.query_metabolites_meta) QueryObs (class in datanator_query_python.query_schema_2.query_observation)

QueryPax (class in datanator_query_python.query.query_pax) QueryProtein (class in datanator_query_python.query.query_protein) QueryRNA (class in datanator_query_python.query.query_rna_halflife) QuerySabio (class in datanator_query_python.query.query_sabiork) QuerySabioCompound (class in datanator_query_python.query.query_sabio_compound) QuerySabioOld (class in datanator_query_python.query.query_sabiork_old) QuerySabioRxn (class in datanator_query_python.query.query_sabio_reaction_entries) QueryTaxonTree (class in datanator_query_python.query.query_taxon_tree) QueryUniprot (class in datanator_query_python.query.query_uniprot) (class in datanator_query_python.query_schema_2.query_uniprot_v2) QueryUniprotOrg (class in datanator_query_python.query.query_uniprot_org) QueryXmdb (class in datanator_query_python.query.query_xmdb)

R

READ_PREFERENCE (datanator_query_python.config.config.AtlasConfig attribute) (datanator_query_python.config.config.Config attribute) (datanator_query_python.config.config.TestConfig attribute) replace_dict_key() (datanator_query_python.util.file_util.FileUtil method) REPLSET (datanator_query_python.config.config.AtlasConfig attribute) (datanator_query_python.config.config.Config attribute)

REST_FTX_AWS_PROFILE (datanator_query_python.config.config.FtxConfig attribute) rna_manager() (datanator_query_python.config.query_manager.RnaManager method) RnaManager (class in datanator_query_python.config.query_manager) rxn_manager() (datanator_query_python.config.query_manager.RxnManager method) RxnManager (class in datanator_query_python.config.query_manager)

S

SchemaMigration (class in datanator_query_python.config.config) search_dict_index() (datanator_query_python.util.file_util.FileUtil method) search_dict_list() (datanator_query_python.util.file_util.FileUtil method) search_taxon() (datanator_query_python.query_schema_2.ftx_search.FTX method) SERVER (datanator_query_python.config.config.AtlasConfig attribute) (datanator_query_python.config.config.Config attribute)

SESSION_KEY (datanator_query_python.config.config.Config attribute) simple_lookup() (datanator_query_python.aggregate.lookups.Lookups method) simple_query_string() (datanator_query_python.query.full_text_search.FTX method) simplify_inchi() (datanator_query_python.util.chem_util.ChemUtil method) snippet() (datanator_query_python.util.mapper_reducer.MaRe method) stacked_on (datanator_query_python.__main__.DefineSchema.Meta attribute) stacked_type (datanator_query_python.__main__.DefineSchema.Meta attribute)

T

Tabu (class in datanator_query_python.aggregate.tabu) taxon_dist() (datanator_query_python.aggregate.tabu.Tabu method) TaxonManager (class in datanator_query_python.config.query_manager)

TEST_FTX_PROFILE_NAME (datanator_query_python.config.config.FtxConfig attribute) TestConfig (class in datanator_query_python.config.config) txn_manager() (datanator_query_python.config.query_manager.TaxonManager method)

U

under_category() (datanator_query_python.query.query_taxon_tree.QueryTaxonTree method) uniprot_manager() (in module datanator_query_python.config.query_manager) uniprot_taxon_dist() (datanator_query_python.aggregate.tabu.Tabu method) unpack_list() (datanator_query_python.util.file_util.FileUtil method) update_entity() (datanator_query_python.util.mongo_util.MongoUtil method) update_observation() (datanator_query_python.util.mongo_util.MongoUtil method) UserAccountConfig (class in datanator_query_python.config.config) USERDAEMON (datanator_query_python.config.config.UserAccountConfig attribute)

USERDAEMON_AUTHDB (datanator_query_python.config.config.UserAccountConfig attribute) USERDAEMON_PASSWORD (datanator_query_python.config.config.UserAccountConfig attribute) USERNAME (datanator_query_python.config.config.AtlasConfig attribute) (datanator_query_python.config.config.Config attribute) (datanator_query_python.config.config.DatanatorAdmin attribute) (datanator_query_python.config.config.DatanatorTest attribute) (datanator_query_python.config.config.SchemaMigration attribute) (datanator_query_python.config.config.TestConfig attribute)