Index

A

AbstractCache (class in caosadvancedtools.cache) AbstractCFood (class in caosadvancedtools.cfood) AbstractFileCFood (class in caosadvancedtools.cfood) access() (caosadvancedtools.cfood.FileGuide method) add() (caosadvancedtools.datamodel_problems.DataModelProblems static method) (caosadvancedtools.structure_mapping.EntityMapping method) add_files() (in module caosadvancedtools.cfood) add_header() (in module caosadvancedtools.pandoc_header_tools) add_value_list() (in module caosadvancedtools.scifolder.utils) all_groups_equal() (caosadvancedtools.cfood.CMeal class method) Analysis (caosadvancedtools.scifolder.withreadme.DataModel attribute) AnalysisCFood (class in caosadvancedtools.scifolder.analysis_cfood) append() (caosadvancedtools.models.data_model.DataModel method)

apply_list_of_updates() (in module caosadvancedtools.crawler) array_schema_from_model_schema() (in module caosadvancedtools.table_json_conversion.xlsx_utils) assert_equal_jsons() (in module caosadvancedtools.tools.test) assure_has_description() (in module caosadvancedtools.cfood) assure_has_parent() (in module caosadvancedtools.cfood) assure_has_property() (in module caosadvancedtools.cfood) assure_name_format() (in module caosadvancedtools.table_importer) assure_name_is() (in module caosadvancedtools.cfood) assure_object_is_in_list() (in module caosadvancedtools.cfood) assure_parents_are() (in module caosadvancedtools.cfood) assure_property_is() (in module caosadvancedtools.cfood) assure_special_is() (in module caosadvancedtools.cfood) attach() (caosadvancedtools.cfood.AbstractCFood method)

B

BaseTableExporter (class in caosadvancedtools.table_export)

belongs_to_meal() (caosadvancedtools.cfood.CMeal method) binaries (caosadvancedtools.scifolder.withreadme.DataModel attribute)

C

Cache (class in caosadvancedtools.cache) call_script() (in module caosadvancedtools.serverside.generic_analysis) caosadvancedtools module caosadvancedtools.cache module caosadvancedtools.cfood module caosadvancedtools.cfoods module caosadvancedtools.cfoods.h5 module caosadvancedtools.crawler module caosadvancedtools.datainconsistency module caosadvancedtools.datamodel_problems module caosadvancedtools.example_cfood module caosadvancedtools.export_related module caosadvancedtools.guard module caosadvancedtools.import_from_xml module caosadvancedtools.json_schema_exporter module caosadvancedtools.loadFiles module caosadvancedtools.models module caosadvancedtools.models.data_model module caosadvancedtools.models.parser module caosadvancedtools.pandoc_header_tools module caosadvancedtools.read_md_header module caosadvancedtools.scifolder module caosadvancedtools.scifolder.analysis_cfood module caosadvancedtools.scifolder.experiment_cfood module caosadvancedtools.scifolder.generic_pattern module caosadvancedtools.scifolder.publication_cfood module caosadvancedtools.scifolder.result_table_cfood module caosadvancedtools.scifolder.simulation_cfood module caosadvancedtools.scifolder.software_cfood module caosadvancedtools.scifolder.utils module caosadvancedtools.scifolder.withreadme module caosadvancedtools.serverside module caosadvancedtools.serverside.generic_analysis module caosadvancedtools.serverside.helper module caosadvancedtools.serverside.logging module caosadvancedtools.serverside.utils module caosadvancedtools.structure_mapping module caosadvancedtools.suppressKnown module caosadvancedtools.table_converter module caosadvancedtools.table_export module caosadvancedtools.table_importer module caosadvancedtools.table_json_conversion module

caosadvancedtools.table_json_conversion.convert module caosadvancedtools.table_json_conversion.export_import_xlsx module caosadvancedtools.table_json_conversion.fill_xlsx module caosadvancedtools.table_json_conversion.table_generator module caosadvancedtools.table_json_conversion.xlsx_utils module caosadvancedtools.tools module caosadvancedtools.tools.strip_null_from_list module caosadvancedtools.tools.test module caosadvancedtools.utils module caosadvancedtools.webui_formatter module check_cache() (caosadvancedtools.cache.AbstractCache method) check_columns() (caosadvancedtools.table_importer.TableImporter method) check_dataframe() (caosadvancedtools.table_importer.TableImporter method) check_datatype() (caosadvancedtools.table_importer.TableImporter method) check_existing() (caosadvancedtools.cache.IdentifiableCache method) check_matches() (caosadvancedtools.crawler.Crawler method) check_missing() (caosadvancedtools.table_importer.TableImporter method) check_reference_field() (in module caosadvancedtools.table_importer) check_referenced_script() (in module caosadvancedtools.serverside.generic_analysis) check_unique() (caosadvancedtools.table_importer.TableImporter method) check_win_path() (in module caosadvancedtools.utils) clean_header() (in module caosadvancedtools.pandoc_header_tools) cleanXML() (in module caosadvancedtools.cache) CMeal (class in caosadvancedtools.cfood) COL_TYPE (caosadvancedtools.table_json_conversion.xlsx_utils.RowType attribute) collect_cfoods() (caosadvancedtools.crawler.Crawler method) collect_entities() (caosadvancedtools.models.data_model.DataModel method) collect_existing_structure() (in module caosadvancedtools.structure_mapping) collect_information() (caosadvancedtools.cfood.AbstractCFood method) (caosadvancedtools.cfoods.h5.H5CFood method) (caosadvancedtools.scifolder.analysis_cfood.AnalysisCFood method) (caosadvancedtools.scifolder.experiment_cfood.ExperimentCFood method) (caosadvancedtools.scifolder.publication_cfood.PublicationCFood method) (caosadvancedtools.scifolder.simulation_cfood.SimulationCFood method) (caosadvancedtools.scifolder.software_cfood.SoftwareCFood method) (caosadvancedtools.table_export.BaseTableExporter method) ColumnType (class in caosadvancedtools.table_json_conversion.xlsx_utils) combine_ignore_files() (in module caosadvancedtools.loadFiles) compare_workbooks() (in module caosadvancedtools.tools.test) compile_file_list() (in module caosadvancedtools.loadFiles) configure_server_side_logging() (in module caosadvancedtools.serverside.logging) construct_mapping() (caosadvancedtools.models.parser.SafeLineLoader method) convert_path() (caosadvancedtools.scifolder.withreadme.WithREADME method) convert_size() (in module caosadvancedtools.loadFiles) convert_win_paths() (caosadvancedtools.scifolder.withreadme.WithREADME method) copy() (caosadvancedtools.table_json_conversion.fill_xlsx.TemplateFiller.Context method) crawl() (caosadvancedtools.crawler.Crawler method) crawled_file (caosadvancedtools.cfood.AbstractFileCFood property) Crawler (class in caosadvancedtools.crawler) create_cache() (caosadvancedtools.cache.AbstractCache method) (caosadvancedtools.cache.IdentifiableCache method) (caosadvancedtools.cache.UpdateCache method) (caosadvancedtools.suppressKnown.SuppressKnown method) create_dummy_file() (in module caosadvancedtools.import_from_xml) create_entity_link() (in module caosadvancedtools.utils) create_files_list() (in module caosadvancedtools.scifolder.utils) create_identifiable_experiment() (caosadvancedtools.scifolder.experiment_cfood.ExperimentCFood static method) create_identifiables() (caosadvancedtools.cfood.AbstractCFood method) (caosadvancedtools.cfood.RowCFood method) (caosadvancedtools.cfoods.h5.H5CFood method) (caosadvancedtools.example_cfood.ExampleCFood method) (caosadvancedtools.scifolder.analysis_cfood.AnalysisCFood method) (caosadvancedtools.scifolder.experiment_cfood.ExperimentCFood method) (caosadvancedtools.scifolder.publication_cfood.PublicationCFood method) (caosadvancedtools.scifolder.result_table_cfood.ResultTableCFood method) (caosadvancedtools.scifolder.simulation_cfood.SimulationCFood method) (caosadvancedtools.scifolder.software_cfood.SoftwareCFood method) create_query_for_identifiable() (caosadvancedtools.crawler.Crawler static method) create_re_for_file_list() (in module caosadvancedtools.loadFiles) create_structure() (caosadvancedtools.cfoods.h5.H5CFood class method) CSVImporter (class in caosadvancedtools.table_importer)

D

DataInconsistencyError DataModel (class in caosadvancedtools.models.data_model) (class in caosadvancedtools.scifolder.withreadme) DataModelError DataModelProblems (class in caosadvancedtools.datamodel_problems) date (caosadvancedtools.scifolder.withreadme.DataModel attribute)

date_converter() (in module caosadvancedtools.table_importer) datetime_converter() (in module caosadvancedtools.table_importer) deep_record_from_json() (in module caosadvancedtools.table_json_conversion.convert) defineParser() (in module caosadvancedtools.export_related) (in module caosadvancedtools.import_from_xml) description (caosadvancedtools.scifolder.withreadme.DataModel attribute)

E

EmptySchemaException entities_without() (caosadvancedtools.models.data_model.DataModel static method) EntityMapping (class in caosadvancedtools.structure_mapping) equals_with_casting() (in module caosadvancedtools.tools.test) escape_xml_representation() (in module caosadvancedtools.serverside.utils) evaluate_exception() (caosadvancedtools.datamodel_problems.DataModelProblems static method) ExampleCFood (class in caosadvancedtools.example_cfood)

existing_instances (caosadvancedtools.cfood.CMeal attribute) Experiment (caosadvancedtools.scifolder.withreadme.DataModel attribute) ExperimentCFood (class in caosadvancedtools.scifolder.experiment_cfood) export() (in module caosadvancedtools.export_related) export_container_to_xlsx() (in module caosadvancedtools.table_json_conversion.export_import_xlsx) export_related_to() (in module caosadvancedtools.export_related) extend() (caosadvancedtools.models.data_model.DataModel method)

F

FileCrawler (class in caosadvancedtools.crawler) FileGuide (class in caosadvancedtools.cfood) fill_data() (caosadvancedtools.table_json_conversion.fill_xlsx.TemplateFiller method) fill_from_data() (caosadvancedtools.table_json_conversion.fill_xlsx.TemplateFiller.Context method) fill_template() (in module caosadvancedtools.table_json_conversion.fill_xlsx) filter() (caosadvancedtools.suppressKnown.SuppressKnown method) find_existing() (caosadvancedtools.crawler.Crawler static method) find_or_insert_identifiables() (caosadvancedtools.crawler.Crawler static method)

find_records_that_reference_ids() (in module caosadvancedtools.utils) find_referenced_files() (caosadvancedtools.scifolder.withreadme.WithREADME method) folder_to_type() (in module caosadvancedtools.scifolder.publication_cfood) FOREIGN (caosadvancedtools.table_json_conversion.xlsx_utils.ColumnType attribute) ForeignError format() (caosadvancedtools.webui_formatter.WebUI_Formatter method) from_table() (in module caosadvancedtools.table_converter) from_tsv() (in module caosadvancedtools.table_converter)

G

generate() (caosadvancedtools.table_json_conversion.table_generator.TableTemplateGenerator method) (caosadvancedtools.table_json_conversion.table_generator.XLSXTemplateGenerator method) generate_property_name() (in module caosadvancedtools.table_converter) get() (caosadvancedtools.cache.UpdateCache method) get_argument_parser() (in module caosadvancedtools.serverside.helper) get_cache_schema_version() (caosadvancedtools.cache.AbstractCache method) (caosadvancedtools.cache.IdentifiableCache method) (caosadvancedtools.cache.UpdateCache method) get_cache_version() (caosadvancedtools.cache.AbstractCache method) get_column_type_row_index() (in module caosadvancedtools.table_json_conversion.xlsx_utils) get_data() (in module caosadvancedtools.serverside.helper) get_data_columns() (in module caosadvancedtools.table_json_conversion.xlsx_utils) get_deep() (caosadvancedtools.models.data_model.DataModel method) get_default_file_name() (caosadvancedtools.cache.AbstractCache method) (caosadvancedtools.cache.IdentifiableCache method) (caosadvancedtools.cache.UpdateCache method) get_defining_paths() (in module caosadvancedtools.table_json_conversion.xlsx_utils) get_description() (in module caosadvancedtools.scifolder.withreadme) get_entity() (in module caosadvancedtools.cfood) get_entity_for_path() (in module caosadvancedtools.cfood) get_entity_ids_from_include_file() (in module caosadvancedtools.scifolder.utils) get_error_str() (caosadvancedtools.table_json_conversion.convert.XLSXConverter method) get_errors() (caosadvancedtools.table_json_conversion.convert.XLSXConverter method) get_existing_entities() (caosadvancedtools.models.data_model.DataModel static method) get_file_via_download() (in module caosadvancedtools.serverside.helper) get_files_referenced_by_field() (in module caosadvancedtools.scifolder.utils) get_foreign_key_columns() (in module caosadvancedtools.table_json_conversion.xlsx_utils) get_glob() (in module caosadvancedtools.scifolder.withreadme) get_header() (in module caosadvancedtools.pandoc_header_tools) (in module caosadvancedtools.read_md_header) get_ids_for_entities_with_names() (in module caosadvancedtools.cfood)

get_ids_of_related_entities() (in module caosadvancedtools.export_related) get_inserts() (caosadvancedtools.cache.UpdateCache method) get_path_position() (in module caosadvancedtools.table_json_conversion.xlsx_utils) get_path_rows() (in module caosadvancedtools.table_json_conversion.xlsx_utils) get_pretty_xml() (in module caosadvancedtools.cache) get_previous_version() (caosadvancedtools.cache.UpdateCache static method) get_property() (in module caosadvancedtools.cfood) get_re() (caosadvancedtools.cfood.AbstractFileCFood class method) (caosadvancedtools.cfood.CMeal static method) (caosadvancedtools.cfoods.h5.H5CFood static method) (caosadvancedtools.example_cfood.ExampleCFood class method) (caosadvancedtools.scifolder.analysis_cfood.AnalysisCFood static method) (caosadvancedtools.scifolder.experiment_cfood.ExperimentCFood static method) (caosadvancedtools.scifolder.publication_cfood.PublicationCFood static method) (caosadvancedtools.scifolder.result_table_cfood.ResultTableCFood static method) (caosadvancedtools.scifolder.simulation_cfood.SimulationCFood static method) (caosadvancedtools.scifolder.software_cfood.SoftwareCFood static method) get_record() (in module caosadvancedtools.cfood) get_recordtype() (in module caosadvancedtools.cfood) get_referenced_files() (in module caosadvancedtools.utils) get_row_type_column_index() (in module caosadvancedtools.table_json_conversion.xlsx_utils) get_rt() (in module caosadvancedtools.scifolder.withreadme) get_shared_filename() (in module caosadvancedtools.serverside.helper) get_subschema() (in module caosadvancedtools.table_json_conversion.xlsx_utils) get_timestamp() (in module caosadvancedtools.serverside.helper) get_unique_savename() (caosadvancedtools.serverside.helper.NameCollector method) get_updates() (caosadvancedtools.cache.UpdateCache method) get_value() (in module caosadvancedtools.crawler) get_worksheet_for_path() (in module caosadvancedtools.table_json_conversion.xlsx_utils) get_xls_header() (in module caosadvancedtools.scifolder.utils) Guard (class in caosadvancedtools.guard)

H

h5_attr_to_property() (in module caosadvancedtools.cfoods.h5) H5CFood (class in caosadvancedtools.cfoods.h5) h5file (caosadvancedtools.cfoods.h5.H5CFood attribute) has_suitable_cfood() (caosadvancedtools.cfood.CMeal class method)

hash() (caosadvancedtools.suppressKnown.SuppressKnown method) hash_entity() (caosadvancedtools.cache.IdentifiableCache static method) header (caosadvancedtools.scifolder.withreadme.WithREADME property) HeaderField (class in caosadvancedtools.scifolder.withreadme)

I

IdentifiableCache (class in caosadvancedtools.cache) identifier (caosadvancedtools.scifolder.withreadme.DataModel attribute) IGNORE (caosadvancedtools.table_json_conversion.xlsx_utils.ColumnType attribute) (caosadvancedtools.table_json_conversion.xlsx_utils.RowType attribute) import_xml() (in module caosadvancedtools.import_from_xml) incomplete_date_converter() (in module caosadvancedtools.table_importer) init_data_model() (in module caosadvancedtools.serverside.helper) insert() (caosadvancedtools.cache.IdentifiableCache method) (caosadvancedtools.cache.UpdateCache method)

insert_id_based_on_name() (in module caosadvancedtools.cfood) insert_list() (caosadvancedtools.cache.IdentifiableCache method) insert_missing_structure() (caosadvancedtools.cfoods.h5.H5CFood method) invert_ids() (in module caosadvancedtools.export_related) is_exploded_sheet() (in module caosadvancedtools.table_json_conversion.xlsx_utils) is_filename_allowed() (in module caosadvancedtools.scifolder.utils) is_recursively_none() (in module caosadvancedtools.table_json_conversion.xlsx_utils) iteritems() (caosadvancedtools.crawler.Crawler method) (caosadvancedtools.crawler.FileCrawler method) (caosadvancedtools.crawler.TableCrawler method)

J

JsonSchemaDefinitionError

JsonSchemaExporter (class in caosadvancedtools.json_schema_exporter) JsonSchemaParser (class in caosadvancedtools.models.parser)

K

kw_present() (in module caosadvancedtools.pandoc_header_tools)

L

LIST (caosadvancedtools.table_json_conversion.xlsx_utils.ColumnType attribute) loadpath() (in module caosadvancedtools.loadFiles)

looking_for() (caosadvancedtools.cfood.AbstractCFood method) (caosadvancedtools.cfood.AbstractFileCFood method)

M

main() (in module caosadvancedtools.export_related) (in module caosadvancedtools.import_from_xml) (in module caosadvancedtools.loadFiles) (in module caosadvancedtools.models.parser) (in module caosadvancedtools.serverside.generic_analysis) (in module caosadvancedtools.table_converter) (in module caosadvancedtools.tools.strip_null_from_list) make_array() (in module caosadvancedtools.json_schema_exporter) match_item() (caosadvancedtools.cfood.AbstractCFood class method) (caosadvancedtools.cfood.AbstractFileCFood class method) matching_groups (caosadvancedtools.cfood.CMeal attribute) merge_schemas() (in module caosadvancedtools.json_schema_exporter) MetadataFileMissing missing (caosadvancedtools.datamodel_problems.DataModelProblems attribute) module caosadvancedtools caosadvancedtools.cache caosadvancedtools.cfood caosadvancedtools.cfoods caosadvancedtools.cfoods.h5 caosadvancedtools.crawler caosadvancedtools.datainconsistency caosadvancedtools.datamodel_problems caosadvancedtools.example_cfood caosadvancedtools.export_related caosadvancedtools.guard caosadvancedtools.import_from_xml caosadvancedtools.json_schema_exporter caosadvancedtools.loadFiles caosadvancedtools.models caosadvancedtools.models.data_model caosadvancedtools.models.parser caosadvancedtools.pandoc_header_tools caosadvancedtools.read_md_header caosadvancedtools.scifolder caosadvancedtools.scifolder.analysis_cfood caosadvancedtools.scifolder.experiment_cfood caosadvancedtools.scifolder.generic_pattern caosadvancedtools.scifolder.publication_cfood caosadvancedtools.scifolder.result_table_cfood caosadvancedtools.scifolder.simulation_cfood caosadvancedtools.scifolder.software_cfood caosadvancedtools.scifolder.utils caosadvancedtools.scifolder.withreadme caosadvancedtools.serverside caosadvancedtools.serverside.generic_analysis caosadvancedtools.serverside.helper caosadvancedtools.serverside.logging caosadvancedtools.serverside.utils caosadvancedtools.structure_mapping caosadvancedtools.suppressKnown caosadvancedtools.table_converter caosadvancedtools.table_export caosadvancedtools.table_importer caosadvancedtools.table_json_conversion caosadvancedtools.table_json_conversion.convert caosadvancedtools.table_json_conversion.export_import_xlsx caosadvancedtools.table_json_conversion.fill_xlsx caosadvancedtools.table_json_conversion.table_generator caosadvancedtools.table_json_conversion.xlsx_utils caosadvancedtools.tools caosadvancedtools.tools.strip_null_from_list caosadvancedtools.tools.test caosadvancedtools.utils caosadvancedtools.webui_formatter

MULTIPLE_CHOICE (caosadvancedtools.table_json_conversion.xlsx_utils.ColumnType attribute)

N

name_beautifier() (caosadvancedtools.scifolder.analysis_cfood.AnalysisCFood static method) (caosadvancedtools.scifolder.experiment_cfood.ExperimentCFood static method) (caosadvancedtools.scifolder.result_table_cfood.ResultTableCFood static method) NameCollector (class in caosadvancedtools.serverside.helper)

next_level() (caosadvancedtools.table_json_conversion.fill_xlsx.TemplateFiller.Context method) next_row_index() (in module caosadvancedtools.table_json_conversion.xlsx_utils) normalize_sheet_titles() (caosadvancedtools.table_json_conversion.table_generator.XLSXTemplateGenerator static method) NoValidHeader

P

p2s() (in module caosadvancedtools.table_json_conversion.xlsx_utils) parse_arguments() (in module caosadvancedtools.serverside.helper) parse_model_from_json_schema() (caosadvancedtools.models.parser.JsonSchemaParser method) (in module caosadvancedtools.models.parser) parse_model_from_string() (caosadvancedtools.models.parser.Parser method) (in module caosadvancedtools.models.parser) parse_model_from_yaml() (caosadvancedtools.models.parser.Parser method) (in module caosadvancedtools.models.parser) parse_multiple_choice() (in module caosadvancedtools.table_json_conversion.xlsx_utils) parse_responsibles() (in module caosadvancedtools.scifolder.utils) ParseErrorsInHeader PARSER (caosadvancedtools.table_json_conversion.convert.XLSXConverter attribute) Parser (class in caosadvancedtools.models.parser) PATH (caosadvancedtools.table_json_conversion.xlsx_utils.RowType attribute)

prepare_csv_export() (caosadvancedtools.table_export.BaseTableExporter method) print_bootstrap() (in module caosadvancedtools.serverside.helper) print_error() (in module caosadvancedtools.serverside.helper) print_info() (in module caosadvancedtools.serverside.helper) print_success() (in module caosadvancedtools.serverside.helper) print_warning() (in module caosadvancedtools.serverside.helper) ProhibitedException Project (caosadvancedtools.scifolder.withreadme.DataModel attribute) property_name_re (caosadvancedtools.scifolder.result_table_cfood.ResultTableCFood attribute) prune_none_objects() (in module caosadvancedtools.table_json_conversion.xlsx_utils) Publication (caosadvancedtools.scifolder.withreadme.DataModel attribute) PublicationCFood (class in caosadvancedtools.scifolder.publication_cfood) purge_from_json() (in module caosadvancedtools.tools.test) put_in_container() (in module caosadvancedtools.cache)

Q

query_files() (caosadvancedtools.crawler.FileCrawler static method)

R

re_from_extensions() (caosadvancedtools.cfood.AbstractFileCFood static method) read_field_as_list() (in module caosadvancedtools.utils) read_file() (caosadvancedtools.table_importer.CSVImporter method) (caosadvancedtools.table_importer.TableImporter method) (caosadvancedtools.table_importer.TSVImporter method) (caosadvancedtools.table_importer.XLSImporter method) read_or_dict() (in module caosadvancedtools.table_json_conversion.xlsx_utils) read_xls() (caosadvancedtools.table_importer.XLSImporter method) records_from_json() (in module caosadvancedtools.table_json_conversion.convert) recordtype_is_child_of() (in module caosadvancedtools.serverside.helper) recordtype_to_json_schema() (caosadvancedtools.json_schema_exporter.JsonSchemaExporter method) (in module caosadvancedtools.json_schema_exporter) recursively_collect_related() (in module caosadvancedtools.export_related) reference_files_from_header() (caosadvancedtools.scifolder.withreadme.WithREADME method)

reference_included_records() (caosadvancedtools.scifolder.withreadme.WithREADME method) reference_records_corresponding_to_files() (in module caosadvancedtools.scifolder.utils) remove_property() (caosadvancedtools.cfood.AbstractCFood static method) replace_path_prefix() (in module caosadvancedtools.utils) reset() (caosadvancedtools.suppressKnown.SuppressKnown method) responsible (caosadvancedtools.scifolder.withreadme.DataModel attribute) results (caosadvancedtools.scifolder.withreadme.DataModel attribute) ResultTableCFood (class in caosadvancedtools.scifolder.result_table_cfood) return_field_or_property() (in module caosadvancedtools.utils) revisionOf (caosadvancedtools.scifolder.withreadme.DataModel attribute) RowCFood (class in caosadvancedtools.cfood) RowType (class in caosadvancedtools.table_json_conversion.xlsx_utils) run() (in module caosadvancedtools.serverside.generic_analysis) run_sql_commands() (caosadvancedtools.cache.AbstractCache method)

S

safe_insert() (caosadvancedtools.guard.Guard method) safe_update() (caosadvancedtools.guard.Guard method) SafeLineLoader (class in caosadvancedtools.models.parser) save_form() (caosadvancedtools.crawler.Crawler static method) save_header() (in module caosadvancedtools.pandoc_header_tools) SCALAR (caosadvancedtools.table_json_conversion.xlsx_utils.ColumnType attribute) scripts (caosadvancedtools.scifolder.withreadme.DataModel attribute) send_mail() (caosadvancedtools.crawler.Crawler static method) (in module caosadvancedtools.serverside.helper) separated() (in module caosadvancedtools.crawler) set_level() (caosadvancedtools.guard.Guard method) set_log_level() (in module caosadvancedtools.utils) set_parents() (caosadvancedtools.cfood.AbstractCFood static method)

set_property() (caosadvancedtools.cfood.AbstractCFood static method) show_record() (in module caosadvancedtools.serverside.utils) Simulation (caosadvancedtools.scifolder.withreadme.DataModel attribute) SimulationCFood (class in caosadvancedtools.scifolder.simulation_cfood) SoftwareCFood (class in caosadvancedtools.scifolder.software_cfood) sourcecode (caosadvancedtools.scifolder.withreadme.DataModel attribute) sources (caosadvancedtools.scifolder.withreadme.DataModel attribute) special_treatment() (caosadvancedtools.cfoods.h5.H5CFood method) string_in_list() (in module caosadvancedtools.table_importer) string_to_person() (in module caosadvancedtools.utils) strip() (in module caosadvancedtools.tools.strip_null_from_list) SuppressKnown (class in caosadvancedtools.suppressKnown) sync_data_model() (caosadvancedtools.models.data_model.DataModel method) sync_ids_by_name() (caosadvancedtools.models.data_model.DataModel method)

T

table_re (caosadvancedtools.scifolder.result_table_cfood.ResultTableCFood attribute) TableCrawler (class in caosadvancedtools.crawler) TableExportError TableImporter (class in caosadvancedtools.table_importer) TableTemplateGenerator (class in caosadvancedtools.table_json_conversion.table_generator) tag_msg() (caosadvancedtools.suppressKnown.SuppressKnown method) TemplateFiller (class in caosadvancedtools.table_json_conversion.fill_xlsx)

TemplateFiller.Context (class in caosadvancedtools.table_json_conversion.fill_xlsx) to_dict() (caosadvancedtools.table_json_conversion.convert.XLSXConverter method) (in module caosadvancedtools.table_json_conversion.convert) to_table() (in module caosadvancedtools.table_converter) to_tsv() (in module caosadvancedtools.table_converter) TSVImporter (class in caosadvancedtools.table_importer) TwiceDefinedException

U

update_authorized_changes() (caosadvancedtools.crawler.Crawler static method) update_identifiables() (caosadvancedtools.cfood.AbstractCFood method) (caosadvancedtools.cfood.RowCFood method) (caosadvancedtools.cfoods.h5.H5CFood method) (caosadvancedtools.example_cfood.ExampleCFood method) (caosadvancedtools.scifolder.analysis_cfood.AnalysisCFood method) (caosadvancedtools.scifolder.experiment_cfood.ExperimentCFood method) (caosadvancedtools.scifolder.publication_cfood.PublicationCFood method) (caosadvancedtools.scifolder.result_table_cfood.ResultTableCFood method) (caosadvancedtools.scifolder.simulation_cfood.SimulationCFood method) (caosadvancedtools.scifolder.software_cfood.SoftwareCFood method)

update_ids_from_cache() (caosadvancedtools.cache.IdentifiableCache method) update_matched_entity() (in module caosadvancedtools.structure_mapping) update_structure() (in module caosadvancedtools.structure_mapping) UpdateCache (class in caosadvancedtools.cache)

V

validate_cache() (caosadvancedtools.cache.IdentifiableCache method)

W

was_tagged() (caosadvancedtools.suppressKnown.SuppressKnown method) WebUI_Formatter (class in caosadvancedtools.webui_formatter) win_path_converter() (in module caosadvancedtools.table_importer) win_path_list_converter() (in module caosadvancedtools.table_importer) win_paths (caosadvancedtools.scifolder.analysis_cfood.AnalysisCFood attribute) (caosadvancedtools.scifolder.experiment_cfood.ExperimentCFood attribute) (caosadvancedtools.scifolder.publication_cfood.PublicationCFood attribute) (caosadvancedtools.scifolder.result_table_cfood.ResultTableCFood attribute) (caosadvancedtools.scifolder.simulation_cfood.SimulationCFood attribute) (caosadvancedtools.scifolder.software_cfood.SoftwareCFood attribute)

WithREADME (class in caosadvancedtools.scifolder.withreadme) workbook (caosadvancedtools.table_json_conversion.fill_xlsx.TemplateFiller property) wrap_bootstrap_alert() (in module caosadvancedtools.serverside.helper)

X

XLSImporter (class in caosadvancedtools.table_importer)

XLSXConverter (class in caosadvancedtools.table_json_conversion.convert) XLSXTemplateGenerator (class in caosadvancedtools.table_json_conversion.table_generator)

Y

YamlDefinitionError

yes_no_converter() (in module caosadvancedtools.table_importer)