caosadvancedtools

• caosadvancedtools package
  • Subpackages
    • caosadvancedtools.bloxberg package
      • Subpackages
      • Submodules
      • caosadvancedtools.bloxberg.bloxberg module
      • Module contents
    • caosadvancedtools.cfoods package
      • Submodules
      • caosadvancedtools.cfoods.h5 module
      • Module contents
    • caosadvancedtools.converter package
      • Submodules
      • caosadvancedtools.converter.labfolder_api module
      • caosadvancedtools.converter.labfolder_export module
      • Module contents
    • caosadvancedtools.models package
      • Submodules
      • caosadvancedtools.models.data_model module
      • caosadvancedtools.models.parser module
      • Module contents
    • caosadvancedtools.scifolder package
      • Submodules
      • 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
      • Module contents
    • caosadvancedtools.serverside package
      • Submodules
      • caosadvancedtools.serverside.generic_analysis module
      • caosadvancedtools.serverside.helper module
      • caosadvancedtools.serverside.logging module
      • caosadvancedtools.serverside.sync module
      • Module contents
    • caosadvancedtools.table_json_conversion package
      • Submodules
      • caosadvancedtools.table_json_conversion.convert module
      • caosadvancedtools.table_json_conversion.fill_xlsx module
      • caosadvancedtools.table_json_conversion.table_generator module
      • caosadvancedtools.table_json_conversion.xlsx_utils module
      • 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
  • 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()
    • 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()
  • caosadvancedtools.json_schema_exporter module
    • JsonSchemaExporter
      • 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()
    • 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.webui_formatter module
    • WebUI_Formatter
      • WebUI_Formatter.format()
  • Module contents