caosadvancedtools package

Subpackages

• caosadvancedtools.cfoods package
  • Submodules
    • caosadvancedtools.cfoods.h5 module
      • H5CFood
      • h5_attr_to_property()
  • Module contents
• caosadvancedtools.models package
  • Submodules
    • caosadvancedtools.models.data_model module
      • DataModel
    • caosadvancedtools.models.parser module
      • JsonSchemaDefinitionError
      • JsonSchemaParser
      • Parser
      • SafeLineLoader
      • TwiceDefinedException
      • YamlDefinitionError
      • main()
      • parse_model_from_json_schema()
      • parse_model_from_string()
      • parse_model_from_yaml()
  • Module contents
• caosadvancedtools.scifolder package
  • Submodules
    • caosadvancedtools.scifolder.analysis_cfood module
      • AnalysisCFood
    • caosadvancedtools.scifolder.experiment_cfood module
      • ExperimentCFood
    • caosadvancedtools.scifolder.generic_pattern module
    • caosadvancedtools.scifolder.publication_cfood module
      • PublicationCFood
      • folder_to_type()
    • caosadvancedtools.scifolder.result_table_cfood module
      • ResultTableCFood
    • caosadvancedtools.scifolder.simulation_cfood module
      • SimulationCFood
    • caosadvancedtools.scifolder.software_cfood module
      • SoftwareCFood
    • caosadvancedtools.scifolder.utils module
      • add_value_list()
      • create_files_list()
      • get_entity_ids_from_include_file()
      • get_files_referenced_by_field()
      • get_xls_header()
      • is_filename_allowed()
      • parse_responsibles()
      • reference_records_corresponding_to_files()
    • caosadvancedtools.scifolder.withreadme module
      • DataModel
      • HeaderField
      • WithREADME
      • get_description()
      • get_glob()
      • get_rt()
  • Module contents
• caosadvancedtools.serverside package
  • Submodules
    • caosadvancedtools.serverside.generic_analysis module
      • call_script()
      • check_referenced_script()
      • main()
      • run()
    • caosadvancedtools.serverside.helper module
      • DataModelError
      • NameCollector
      • get_argument_parser()
      • get_data()
      • get_file_via_download()
      • get_shared_filename()
      • get_timestamp()
      • init_data_model()
      • parse_arguments()
      • print_bootstrap()
      • print_error()
      • print_info()
      • print_success()
      • print_warning()
      • recordtype_is_child_of()
      • send_mail()
      • wrap_bootstrap_alert()
    • caosadvancedtools.serverside.logging module
      • configure_server_side_logging()
    • caosadvancedtools.serverside.sync module
    • caosadvancedtools.serverside.utils module
      • escape_xml_representation()
      • show_record()
  • Module contents
• caosadvancedtools.table_json_conversion package
  • Submodules
    • caosadvancedtools.table_json_conversion.convert module
      • ForeignError
      • XLSXConverter
      • deep_record_from_json()
      • records_from_json()
      • to_dict()
    • caosadvancedtools.table_json_conversion.export_import_xlsx module
      • export_container_to_xlsx()
    • caosadvancedtools.table_json_conversion.fill_xlsx module
      • TemplateFiller
      • fill_template()
    • caosadvancedtools.table_json_conversion.table_generator module
      • EmptySchemaException
      • TableTemplateGenerator
      • XLSXTemplateGenerator
    • caosadvancedtools.table_json_conversion.xlsx_utils module
      • ColumnType
      • RowType
      • array_schema_from_model_schema()
      • get_column_type_row_index()
      • get_data_columns()
      • get_defining_paths()
      • get_foreign_key_columns()
      • get_path_position()
      • get_path_rows()
      • get_row_type_column_index()
      • get_subschema()
      • get_worksheet_for_path()
      • is_exploded_sheet()
      • is_recursively_none()
      • next_row_index()
      • p2s()
      • parse_multiple_choice()
      • prune_none_objects()
      • read_or_dict()
  • Module contents
• caosadvancedtools.tools package
  • Submodules
    • caosadvancedtools.tools.strip_null_from_list module
      • main()
      • strip()
    • caosadvancedtools.tools.test module
      • assert_equal_jsons()
      • compare_workbooks()
      • equals_with_casting()
      • purge_from_json()
  • Module contents

Submodules

• caosadvancedtools.cache module
  • AbstractCache
    • AbstractCache.check_cache()
    • AbstractCache.create_cache()
    • AbstractCache.get_cache_schema_version()
    • AbstractCache.get_cache_version()
    • AbstractCache.get_default_file_name()
    • AbstractCache.run_sql_commands()
  • Cache
  • IdentifiableCache
    • IdentifiableCache.check_existing()
    • IdentifiableCache.create_cache()
    • IdentifiableCache.get_cache_schema_version()
    • IdentifiableCache.get_default_file_name()
    • IdentifiableCache.hash_entity()
    • IdentifiableCache.insert()
    • IdentifiableCache.insert_list()
    • IdentifiableCache.update_ids_from_cache()
    • IdentifiableCache.validate_cache()
  • UpdateCache
    • UpdateCache.create_cache()
    • UpdateCache.get()
    • UpdateCache.get_cache_schema_version()
    • UpdateCache.get_default_file_name()
    • UpdateCache.get_inserts()
    • UpdateCache.get_previous_version()
    • UpdateCache.get_updates()
    • UpdateCache.insert()
  • cleanXML()
  • get_pretty_xml()
  • put_in_container()
• caosadvancedtools.cfood module
  • AbstractCFood
    • AbstractCFood.attach()
    • AbstractCFood.collect_information()
    • AbstractCFood.create_identifiables()
    • AbstractCFood.looking_for()
    • AbstractCFood.match_item()
    • AbstractCFood.remove_property()
    • AbstractCFood.set_parents()
    • AbstractCFood.set_property()
    • AbstractCFood.update_identifiables()
  • AbstractFileCFood
    • AbstractFileCFood.crawled_file
    • AbstractFileCFood.get_re()
    • AbstractFileCFood.looking_for()
    • AbstractFileCFood.match_item()
    • AbstractFileCFood.re_from_extensions()
  • CMeal
    • CMeal.all_groups_equal()
    • CMeal.belongs_to_meal()
    • CMeal.existing_instances
    • CMeal.get_re()
    • CMeal.has_suitable_cfood()
    • CMeal.matching_groups
  • FileGuide
    • FileGuide.access()
  • RowCFood
    • RowCFood.create_identifiables()
    • RowCFood.update_identifiables()
  • add_files()
  • assure_has_description()
  • assure_has_parent()
  • assure_has_property()
  • assure_name_is()
  • assure_object_is_in_list()
  • assure_parents_are()
  • assure_property_is()
  • assure_special_is()
  • get_entity()
  • get_entity_for_path()
  • get_ids_for_entities_with_names()
  • get_property()
  • get_record()
  • get_recordtype()
  • insert_id_based_on_name()
• caosadvancedtools.collect_datamodel module
  • compare()
  • get_dm()
  • get_parser()
  • load_dm()
  • lower()
  • main()
  • store()
• caosadvancedtools.crawler module
  • Crawler
    • Crawler.check_matches()
    • Crawler.collect_cfoods()
    • Crawler.crawl()
    • Crawler.create_query_for_identifiable()
    • Crawler.find_existing()
    • Crawler.find_or_insert_identifiables()
    • Crawler.iteritems()
    • Crawler.save_form()
    • Crawler.send_mail()
    • Crawler.update_authorized_changes()
  • FileCrawler
    • FileCrawler.iteritems()
    • FileCrawler.query_files()
  • TableCrawler
    • TableCrawler.iteritems()
  • apply_list_of_updates()
  • get_value()
  • separated()
• caosadvancedtools.datainconsistency module
  • DataInconsistencyError
• caosadvancedtools.datamodel_problems module
  • DataModelProblems
    • DataModelProblems.add()
    • DataModelProblems.evaluate_exception()
    • DataModelProblems.missing
• caosadvancedtools.example_cfood module
  • ExampleCFood
    • ExampleCFood.create_identifiables()
    • ExampleCFood.get_re()
    • ExampleCFood.update_identifiables()
• caosadvancedtools.export_related module
  • defineParser()
  • export()
  • export_related_to()
  • get_ids_of_related_entities()
  • invert_ids()
  • main()
  • recursively_collect_related()
• caosadvancedtools.guard module
  • Guard
    • Guard.safe_insert()
    • Guard.safe_update()
    • Guard.set_level()
  • ProhibitedException
• caosadvancedtools.import_from_xml module
  • create_dummy_file()
  • defineParser()
  • import_xml()
  • main()
• caosadvancedtools.json_schema_exporter module
  • JsonSchemaExporter
    • JsonSchemaExporter.get_unused_additional_ui_schema_keys()
    • JsonSchemaExporter.recordtype_to_json_schema()
  • make_array()
  • merge_schemas()
  • recordtype_to_json_schema()
• caosadvancedtools.loadFiles module
  • combine_ignore_files()
  • compile_file_list()
  • convert_size()
  • create_re_for_file_list()
  • loadpath()
  • main()
• caosadvancedtools.pandoc_header_tools module
  • MetadataFileMissing
  • NoValidHeader
  • ParseErrorsInHeader
  • add_header()
  • clean_header()
  • get_header()
  • kw_present()
  • save_header()
• caosadvancedtools.read_md_header module
  • get_header()
• caosadvancedtools.structure_mapping module
  • EntityMapping
    • EntityMapping.add()
  • collect_existing_structure()
  • update_matched_entity()
  • update_structure()
• caosadvancedtools.suppressKnown module
  • SuppressKnown
    • SuppressKnown.create_cache()
    • SuppressKnown.filter()
    • SuppressKnown.hash()
    • SuppressKnown.reset()
    • SuppressKnown.tag_msg()
    • SuppressKnown.was_tagged()
• caosadvancedtools.table_converter module
  • from_table()
  • from_tsv()
  • generate_property_name()
  • main()
  • to_table()
  • to_tsv()
• caosadvancedtools.table_export module
  • BaseTableExporter
    • BaseTableExporter.collect_information()
    • BaseTableExporter.prepare_csv_export()
  • TableExportError
• caosadvancedtools.table_importer module
  • CSVImporter
    • CSVImporter.read_file()
  • TSVImporter
    • TSVImporter.read_file()
  • TableImporter
    • TableImporter.check_columns()
    • TableImporter.check_dataframe()
    • TableImporter.check_datatype()
    • TableImporter.check_missing()
    • TableImporter.check_unique()
    • TableImporter.read_file()
  • XLSImporter
    • XLSImporter.read_file()
    • XLSImporter.read_xls()
  • assure_name_format()
  • check_reference_field()
  • date_converter()
  • datetime_converter()
  • incomplete_date_converter()
  • string_in_list()
  • win_path_converter()
  • win_path_list_converter()
  • yes_no_converter()
• caosadvancedtools.utils module
  • check_win_path()
  • create_entity_link()
  • find_records_that_reference_ids()
  • get_referenced_files()
  • read_field_as_list()
  • replace_path_prefix()
  • return_field_or_property()
  • set_log_level()
  • string_to_person()
• caosadvancedtools.version module
• caosadvancedtools.webui_formatter module
  • WebUI_Formatter
    • WebUI_Formatter.format()

Module contents