Index

A

add() (askomics.libaskomics.RdfGraph.RdfGraph method) add_galaxy_account() (askomics.libaskomics.LocalAuth.LocalAuth method) admin_required() (in module askomics.api.auth) apikey (askomics.libaskomics.Galaxy.Galaxy attribute) app (askomics.libaskomics.Params.Params attribute) askomics (module) askomics.api (module) askomics.api.admin (module) askomics.api.auth (module) askomics.api.catch_url (module) askomics.api.datasets (module) askomics.api.file (module) askomics.api.galaxy (module) askomics.api.query (module) askomics.api.results (module) askomics.api.sparql (module) askomics.api.start (module) askomics.api.view (module) askomics.app (module) askomics.libaskomics (module) askomics.libaskomics.BedFile (module) askomics.libaskomics.CsvFile (module) askomics.libaskomics.Database (module) askomics.libaskomics.Dataset (module) askomics.libaskomics.DatasetsHandler (module)

askomics.libaskomics.File (module) askomics.libaskomics.FilesHandler (module) askomics.libaskomics.FilesUtils (module) askomics.libaskomics.Galaxy (module) askomics.libaskomics.GffFile (module) askomics.libaskomics.LocalAuth (module) askomics.libaskomics.Params (module) askomics.libaskomics.PrefixManager (module) askomics.libaskomics.RdfFile (module) askomics.libaskomics.RdfGraph (module) askomics.libaskomics.Result (module) askomics.libaskomics.ResultsHandler (module) askomics.libaskomics.SparqlQueryBuilder (module) askomics.libaskomics.SparqlQueryLauncher (module) askomics.libaskomics.Start (module) askomics.libaskomics.TriplestoreExplorer (module) askomics.libaskomics.Utils (module) askomics_namespace (askomics.libaskomics.File.File attribute) (askomics.libaskomics.PrefixManager.PrefixManager attribute) (askomics.libaskomics.RdfGraph.RdfGraph attribute) askomics_prefix (askomics.libaskomics.File.File attribute) (askomics.libaskomics.PrefixManager.PrefixManager attribute) (askomics.libaskomics.RdfGraph.RdfGraph attribute) authenticate_user() (askomics.libaskomics.LocalAuth.LocalAuth method) authenticate_user_with_apikey() (askomics.libaskomics.LocalAuth.LocalAuth method)

B

BedFile (class in askomics.libaskomics.BedFile) bind() (askomics.libaskomics.RdfGraph.RdfGraph method)

BLUEPRINTS (in module askomics.app) build_query_from_json() (askomics.libaskomics.SparqlQueryBuilder.SparqlQueryBuilder method)

C

cached_property (class in askomics.libaskomics.Utils) catch_all() (in module askomics.api.catch_url) category_values (askomics.libaskomics.CsvFile.CsvFile attribute) celery_id (askomics.libaskomics.Dataset.Dataset attribute) (askomics.libaskomics.Result.Result attribute) check_columns_types() (askomics.libaskomics.CsvFile.CsvFile method) check_galaxy_instance() (askomics.libaskomics.Galaxy.Galaxy method) check_inputs() (askomics.libaskomics.LocalAuth.LocalAuth method) check_presence() (askomics.libaskomics.TriplestoreExplorer.TriplestoreExplorer method) clean_link() (askomics.libaskomics.Result.Result method) clean_node() (askomics.libaskomics.Result.Result method) columns_type (askomics.libaskomics.CsvFile.CsvFile attribute) convert_type() (askomics.libaskomics.File.File method)

create_app() (in module askomics.app) create_celery() (in module askomics.app) create_data_directory() (askomics.libaskomics.Start.Start method) create_database() (askomics.libaskomics.Start.Start method) create_datasets_table() (askomics.libaskomics.Database.Database method) create_directory() (askomics.libaskomics.LocalAuth.LocalAuth method) create_endpoints_table() (askomics.libaskomics.Database.Database method) create_files_table() (askomics.libaskomics.Database.Database method) create_galaxy_table() (askomics.libaskomics.Database.Database method) create_integration_table() (askomics.libaskomics.Database.Database method) create_results_table() (askomics.libaskomics.Database.Database method) create_user_directories() (askomics.libaskomics.LocalAuth.LocalAuth method) create_user_table() (askomics.libaskomics.Database.Database method) CsvFile (class in askomics.libaskomics.CsvFile)

D

data_directory (askomics.libaskomics.Start.Start attribute) Database (class in askomics.libaskomics.Database) database_path (askomics.libaskomics.Database.Database attribute) (askomics.libaskomics.Start.Start attribute) Dataset (class in askomics.libaskomics.Dataset) datasets (askomics.libaskomics.DatasetsHandler.DatasetsHandler attribute) datasets_info (askomics.libaskomics.DatasetsHandler.DatasetsHandler attribute) DatasetsHandler (class in askomics.libaskomics.DatasetsHandler) dc (askomics.libaskomics.File.File attribute) default_graph (askomics.libaskomics.File.File attribute) delete_datasets() (askomics.libaskomics.DatasetsHandler.DatasetsHandler method) (in module askomics.api.datasets) delete_datasets_in_db() (askomics.libaskomics.DatasetsHandler.DatasetsHandler method) delete_db_entry() (askomics.libaskomics.Result.Result method)

delete_file_from_db() (askomics.libaskomics.FilesHandler.FilesHandler method) delete_file_from_filesystem() (askomics.libaskomics.Result.Result method) delete_file_from_fs() (askomics.libaskomics.FilesHandler.FilesHandler method) delete_files() (askomics.libaskomics.FilesHandler.FilesHandler method) (in module askomics.api.file) delete_from_db() (askomics.libaskomics.Dataset.Dataset method) delete_result() (askomics.libaskomics.Result.Result method) (in module askomics.api.results) delete_results() (askomics.libaskomics.ResultsHandler.ResultsHandler method) dialect (askomics.libaskomics.CsvFile.CsvFile attribute) download_datasets() (askomics.libaskomics.Galaxy.Galaxy method) download_result() (in module askomics.api.results) download_url() (askomics.libaskomics.FilesHandler.FilesHandler method) drop_dataset() (askomics.libaskomics.SparqlQueryLauncher.SparqlQueryLauncher method)

E

endpoint (askomics.libaskomics.SparqlQueryLauncher.SparqlQueryLauncher attribute)

execute_query() (askomics.libaskomics.SparqlQueryLauncher.SparqlQueryLauncher method) execute_sql_query() (askomics.libaskomics.Database.Database method)

F

faldo (askomics.libaskomics.File.File attribute) faldo_entity (askomics.libaskomics.File.File attribute) File (class in askomics.libaskomics.File) file_graph (askomics.libaskomics.File.File attribute) file_id (askomics.libaskomics.Dataset.Dataset attribute) file_name (askomics.libaskomics.Result.Result attribute) file_path (askomics.libaskomics.Result.Result attribute) files (askomics.libaskomics.FilesHandler.FilesHandler attribute)

FilesHandler (class in askomics.libaskomics.FilesHandler) FilesUtils (class in askomics.libaskomics.FilesUtils) force_columns_type() (askomics.libaskomics.CsvFile.CsvFile method) format_graph_state() (askomics.libaskomics.Result.Result method) format_query() (askomics.libaskomics.SparqlQueryBuilder.SparqlQueryBuilder method) format_sparql_variable() (askomics.libaskomics.SparqlQueryBuilder.SparqlQueryBuilder method) format_uri() (askomics.libaskomics.File.File method) func (askomics.libaskomics.CsvFile.CsvFile attribute) (askomics.libaskomics.Utils.cached_property attribute), [1]

G

Galaxy (class in askomics.libaskomics.Galaxy) generate_rdf_content() (askomics.libaskomics.BedFile.BedFile method) (askomics.libaskomics.CsvFile.CsvFile method) (askomics.libaskomics.GffFile.GffFile method) get_abstraction() (askomics.libaskomics.TriplestoreExplorer.TriplestoreExplorer method) (in module askomics.api.query) get_abstraction_attributes() (askomics.libaskomics.TriplestoreExplorer.TriplestoreExplorer method) get_abstraction_entities() (askomics.libaskomics.TriplestoreExplorer.TriplestoreExplorer method) get_abstraction_relations() (askomics.libaskomics.TriplestoreExplorer.TriplestoreExplorer method) get_all_users() (askomics.libaskomics.LocalAuth.LocalAuth method) get_attribute_index() (askomics.libaskomics.TriplestoreExplorer.TriplestoreExplorer method) get_checked_asked_graphs() (askomics.libaskomics.SparqlQueryBuilder.SparqlQueryBuilder method) get_dataset_content() (askomics.libaskomics.Galaxy.Galaxy method) (in module askomics.api.galaxy) get_datasets() (askomics.libaskomics.DatasetsHandler.DatasetsHandler method) (in module askomics.api.datasets) (in module askomics.api.galaxy) get_datasets_and_histories() (askomics.libaskomics.Galaxy.Galaxy method) get_default_query() (askomics.libaskomics.SparqlQueryBuilder.SparqlQueryBuilder method) get_default_query_with_prefix() (askomics.libaskomics.SparqlQueryBuilder.SparqlQueryBuilder method) get_dir_path() (askomics.libaskomics.Result.Result method) get_error() (askomics.libaskomics.Params.Params method) get_error_message() (askomics.libaskomics.Params.Params method) get_faldo_strand() (askomics.libaskomics.File.File method) get_file_name() (askomics.libaskomics.FilesHandler.FilesHandler method) (askomics.libaskomics.Result.Result method) get_file_path() (askomics.libaskomics.FilesHandler.FilesHandler method) get_file_preview() (askomics.libaskomics.Result.Result method) get_files() (in module askomics.api.file) get_files_info() (askomics.libaskomics.ResultsHandler.ResultsHandler method) get_files_infos() (askomics.libaskomics.FilesHandler.FilesHandler method) get_froms() (askomics.libaskomics.SparqlQueryBuilder.SparqlQueryBuilder method)

get_froms_from_graphs() (askomics.libaskomics.SparqlQueryBuilder.SparqlQueryBuilder method) get_graph_state() (askomics.libaskomics.Result.Result method) (in module askomics.api.results) get_metadata() (askomics.libaskomics.File.File method) get_number_of_users() (askomics.libaskomics.LocalAuth.LocalAuth method) get_prefix() (askomics.libaskomics.PrefixManager.PrefixManager method) get_preview() (askomics.libaskomics.BedFile.BedFile method) (askomics.libaskomics.CsvFile.CsvFile method) (askomics.libaskomics.GffFile.GffFile method) (askomics.libaskomics.RdfFile.RdfFile method) (in module askomics.api.file) (in module askomics.api.query) (in module askomics.api.results) get_public_queries() (askomics.libaskomics.ResultsHandler.ResultsHandler method) get_queries() (in module askomics.api.galaxy) get_random_string() (askomics.libaskomics.Utils.Utils static method) get_rdf_type() (askomics.libaskomics.File.File method) get_results() (in module askomics.api.results) get_size_occupied_by_user() (askomics.libaskomics.FilesUtils.FilesUtils method) get_sparql_query() (askomics.libaskomics.Result.Result method) (in module askomics.api.results) get_startpoints() (askomics.libaskomics.TriplestoreExplorer.TriplestoreExplorer method) get_triple() (askomics.libaskomics.RdfGraph.RdfGraph method) get_triples_from_graph() (askomics.libaskomics.SparqlQueryLauncher.SparqlQueryLauncher method) get_type() (askomics.libaskomics.FilesHandler.FilesHandler method) get_user() (askomics.libaskomics.LocalAuth.LocalAuth method) get_users() (in module askomics.api.admin) GffFile (class in askomics.libaskomics.GffFile) graph (askomics.libaskomics.RdfGraph.RdfGraph attribute) graph_name (askomics.libaskomics.Dataset.Dataset attribute) graph_state (askomics.libaskomics.Result.Result attribute) guess_column_type() (askomics.libaskomics.CsvFile.CsvFile method)

H

handle_datasets() (askomics.libaskomics.DatasetsHandler.DatasetsHandler method) handle_files() (askomics.libaskomics.FilesHandler.FilesHandler method) header (askomics.libaskomics.CsvFile.CsvFile attribute) hello() (in module askomics.api.start)

home() (in module askomics.api.view) host_url (askomics.libaskomics.File.File attribute) (askomics.libaskomics.FilesHandler.FilesHandler attribute) humansize_to_bytes() (askomics.libaskomics.Utils.Utils static method)

I

id (askomics.libaskomics.Dataset.Dataset attribute) (askomics.libaskomics.File.File attribute) (askomics.libaskomics.Result.Result attribute) init_database() (askomics.libaskomics.Database.Database method) insert_data() (askomics.libaskomics.SparqlQueryLauncher.SparqlQueryLauncher method) insert_ttl_string() (askomics.libaskomics.SparqlQueryLauncher.SparqlQueryLauncher method) integrate() (askomics.libaskomics.BedFile.BedFile method) (askomics.libaskomics.CsvFile.CsvFile method) (askomics.libaskomics.File.File method) (askomics.libaskomics.GffFile.GffFile method) (askomics.libaskomics.RdfFile.RdfFile method) (in module askomics.api.file)

intersect() (askomics.libaskomics.Utils.Utils static method) is_bnode() (askomics.libaskomics.SparqlQueryBuilder.SparqlQueryBuilder method) is_category() (askomics.libaskomics.CsvFile.CsvFile method) is_decimal() (askomics.libaskomics.CsvFile.CsvFile static method) is_email_in_db() (askomics.libaskomics.LocalAuth.LocalAuth method) is_username_in_db() (askomics.libaskomics.LocalAuth.LocalAuth method)

L

load_data() (askomics.libaskomics.SparqlQueryLauncher.SparqlQueryLauncher method) load_data_fuseki() (askomics.libaskomics.SparqlQueryLauncher.SparqlQueryLauncher method) load_data_virtuoso() (askomics.libaskomics.SparqlQueryLauncher.SparqlQueryLauncher method) load_graph() (askomics.libaskomics.File.File method) LocalAuth (class in askomics.libaskomics.LocalAuth)

log (askomics.libaskomics.Params.Params attribute) logged_user() (askomics.libaskomics.Params.Params method) login() (in module askomics.api.auth) login_api_key() (in module askomics.api.auth) login_required() (in module askomics.api.auth) logout() (in module askomics.api.auth)

M

max_chunk_size (askomics.libaskomics.File.File attribute)

merge() (askomics.libaskomics.RdfGraph.RdfGraph method) method (askomics.libaskomics.File.File attribute)

N

name (askomics.libaskomics.Dataset.Dataset attribute) (askomics.libaskomics.File.File attribute)

now (askomics.libaskomics.File.File attribute) ntriple (askomics.libaskomics.RdfGraph.RdfGraph attribute) ntriples (askomics.libaskomics.File.File attribute)

P

Params (class in askomics.libaskomics.Params) parse_results() (askomics.libaskomics.SparqlQueryLauncher.SparqlQueryLauncher method) parse_results_old() (askomics.libaskomics.SparqlQueryLauncher.SparqlQueryLauncher method) path (askomics.libaskomics.File.File attribute) persist_chunk() (askomics.libaskomics.FilesHandler.FilesHandler method) persist_user() (askomics.libaskomics.LocalAuth.LocalAuth method) prefix (askomics.libaskomics.PrefixManager.PrefixManager attribute) prefix() (in module askomics.api.sparql) prefix_query() (askomics.libaskomics.SparqlQueryBuilder.SparqlQueryBuilder method) PrefixManager (class in askomics.libaskomics.PrefixManager) preview (askomics.libaskomics.CsvFile.CsvFile attribute)

private_graphs (askomics.libaskomics.SparqlQueryBuilder.SparqlQueryBuilder attribute) process_query() (askomics.libaskomics.SparqlQueryLauncher.SparqlQueryLauncher method) prov (askomics.libaskomics.File.File attribute) public (askomics.libaskomics.BedFile.BedFile attribute) (askomics.libaskomics.CsvFile.CsvFile attribute) (askomics.libaskomics.Dataset.Dataset attribute) (askomics.libaskomics.File.File attribute) (askomics.libaskomics.GffFile.GffFile attribute) (askomics.libaskomics.RdfFile.RdfFile attribute) public_graphs (askomics.libaskomics.SparqlQueryBuilder.SparqlQueryBuilder attribute) publish_query() (askomics.libaskomics.Result.Result method) (in module askomics.api.results)

Q

query() (in module askomics.api.query) (in module askomics.api.sparql)

query_time (askomics.libaskomics.SparqlQueryLauncher.SparqlQueryLauncher attribute)

R

RdfFile (class in askomics.libaskomics.RdfFile) RdfGraph (class in askomics.libaskomics.RdfGraph) Result (class in askomics.libaskomics.Result)

result_path (askomics.libaskomics.Result.Result attribute) ResultsHandler (class in askomics.libaskomics.ResultsHandler) rollback() (askomics.libaskomics.File.File method) (askomics.libaskomics.Result.Result method)

S

save_in_db() (askomics.libaskomics.Dataset.Dataset method) (askomics.libaskomics.Result.Result method) save_query() (in module askomics.api.sparql) save_result() (in module askomics.api.query) save_result_in_file() (askomics.libaskomics.Result.Result method) send2galaxy() (askomics.libaskomics.Result.Result method) (in module askomics.api.results) send_query_to_galaxy() (askomics.libaskomics.Result.Result method) send_result_to_galaxy() (askomics.libaskomics.Result.Result method) serialize() (askomics.libaskomics.RdfGraph.RdfGraph method) serve_file() (in module askomics.api.file) session (askomics.libaskomics.Params.Params attribute) set_admin() (askomics.libaskomics.LocalAuth.LocalAuth method) (in module askomics.api.admin) set_blocked() (askomics.libaskomics.LocalAuth.LocalAuth method) (in module askomics.api.admin) set_celery_id() (askomics.libaskomics.Result.Result method) set_columns_type() (askomics.libaskomics.CsvFile.CsvFile method) set_description() (in module askomics.api.results) set_graphs() (askomics.libaskomics.SparqlQueryBuilder.SparqlQueryBuilder method) set_info_from_db() (askomics.libaskomics.Dataset.Dataset method) set_info_from_db_with_id() (askomics.libaskomics.Result.Result method) set_preview() (askomics.libaskomics.BedFile.BedFile method) (askomics.libaskomics.CsvFile.CsvFile method) (askomics.libaskomics.GffFile.GffFile method) (askomics.libaskomics.RdfFile.RdfFile method)

set_preview_and_header() (askomics.libaskomics.CsvFile.CsvFile method) set_public() (in module askomics.api.results) set_quota() (askomics.libaskomics.LocalAuth.LocalAuth method) (in module askomics.api.admin) set_rdf_abstraction() (askomics.libaskomics.CsvFile.CsvFile method) set_rdf_abstraction_domain_knowledge() (askomics.libaskomics.BedFile.BedFile method) (askomics.libaskomics.CsvFile.CsvFile method) (askomics.libaskomics.GffFile.GffFile method) set_rdf_domain_knowledge() (askomics.libaskomics.CsvFile.CsvFile method) set_triples_number() (askomics.libaskomics.File.File method) settings (askomics.libaskomics.Params.Params attribute) signup() (in module askomics.api.auth) size (askomics.libaskomics.File.File attribute) SparqlQueryBuilder (class in askomics.libaskomics.SparqlQueryBuilder) SparqlQueryLauncher (class in askomics.libaskomics.SparqlQueryLauncher) Start (class in askomics.libaskomics.Start) start() (askomics.libaskomics.Start.Start method) (in module askomics.api.start) store_file_info_in_db() (askomics.libaskomics.FilesHandler.FilesHandler method) str_to_bool() (askomics.libaskomics.Params.Params method)

T

timestamp (askomics.libaskomics.File.File attribute) toggle_public() (askomics.libaskomics.Dataset.Dataset method) (askomics.libaskomics.SparqlQueryBuilder.SparqlQueryBuilder method) toogle_public() (in module askomics.api.datasets)

transposed_preview (askomics.libaskomics.CsvFile.CsvFile attribute) triplestore (askomics.libaskomics.SparqlQueryLauncher.SparqlQueryLauncher attribute) TriplestoreExplorer (class in askomics.libaskomics.TriplestoreExplorer) ttl_dir (askomics.libaskomics.File.File attribute) type (askomics.libaskomics.File.File attribute)

U

union() (askomics.libaskomics.Utils.Utils static method) unique() (askomics.libaskomics.Utils.Utils static method) update_apikey() (askomics.libaskomics.LocalAuth.LocalAuth method) (in module askomics.api.auth) update_celery() (askomics.libaskomics.Dataset.Dataset method) (askomics.libaskomics.Result.Result method) update_db_status() (askomics.libaskomics.Result.Result method) update_description() (askomics.libaskomics.Result.Result method) update_galaxy() (in module askomics.api.auth) update_galaxy_account() (askomics.libaskomics.LocalAuth.LocalAuth method) update_in_db() (askomics.libaskomics.Dataset.Dataset method) update_password() (askomics.libaskomics.LocalAuth.LocalAuth method) (in module askomics.api.auth)

update_profile() (askomics.libaskomics.LocalAuth.LocalAuth method) (in module askomics.api.auth) update_public_status() (askomics.libaskomics.Result.Result method) update_results_table() (askomics.libaskomics.Database.Database method) update_status_in_db() (askomics.libaskomics.DatasetsHandler.DatasetsHandler method) update_users_table() (askomics.libaskomics.Database.Database method) upload() (in module askomics.api.file) upload_chunk() (in module askomics.api.file) upload_datasets() (in module askomics.api.galaxy) upload_path (askomics.libaskomics.FilesHandler.FilesHandler attribute) upload_url() (in module askomics.api.file) url (askomics.libaskomics.Galaxy.Galaxy attribute) user_graph (askomics.libaskomics.File.File attribute) Utils (class in askomics.libaskomics.Utils)

W

write_data_into_file() (askomics.libaskomics.FilesHandler.FilesHandler method)