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_property_from_data_element() (in module caosadvancedtools.converter.labfolder_export) 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) ApiClient (class in caosadvancedtools.bloxberg.swagger_client.api_client) ApiException append() (caosadvancedtools.models.data_model.DataModel method)

apply_list_of_updates() (in module caosadvancedtools.crawler) 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) attribute_map (caosadvancedtools.bloxberg.swagger_client.models.batch.Batch attribute) (caosadvancedtools.bloxberg.swagger_client.models.controller_cert_tools_generate_pdf_json_certificate.ControllerCertToolsGeneratePdfJsonCertificate attribute) (caosadvancedtools.bloxberg.swagger_client.models.controller_cert_tools_generate_unsigned_certificate_json_certificate.ControllerCertToolsGenerateUnsignedCertificateJsonCertificate attribute) (caosadvancedtools.bloxberg.swagger_client.models.http_validation_error.HTTPValidationError attribute) (caosadvancedtools.bloxberg.swagger_client.models.validation_error.ValidationError attribute) auth_settings() (caosadvancedtools.bloxberg.swagger_client.configuration.Configuration method)

B

BaseTableExporter (class in caosadvancedtools.table_export) Batch (class in caosadvancedtools.bloxberg.swagger_client.models.batch)

belongs_to_meal() (caosadvancedtools.cfood.CMeal method) binaries (caosadvancedtools.scifolder.withreadme.DataModel attribute) Bloxberg (class in caosadvancedtools.bloxberg.bloxberg)

C

Cache (class in caosadvancedtools.cache) call_api() (caosadvancedtools.bloxberg.swagger_client.api_client.ApiClient method) call_script() (in module caosadvancedtools.serverside.generic_analysis) caosadvancedtools module caosadvancedtools.bloxberg module caosadvancedtools.bloxberg.bloxberg module caosadvancedtools.bloxberg.swagger_client module caosadvancedtools.bloxberg.swagger_client.api module caosadvancedtools.bloxberg.swagger_client.api.certificate_api module caosadvancedtools.bloxberg.swagger_client.api.pdf_api module caosadvancedtools.bloxberg.swagger_client.api_client module caosadvancedtools.bloxberg.swagger_client.configuration module caosadvancedtools.bloxberg.swagger_client.models module caosadvancedtools.bloxberg.swagger_client.models.batch module caosadvancedtools.bloxberg.swagger_client.models.controller_cert_tools_generate_pdf_json_certificate module caosadvancedtools.bloxberg.swagger_client.models.controller_cert_tools_generate_unsigned_certificate_json_certificate module caosadvancedtools.bloxberg.swagger_client.models.http_validation_error module caosadvancedtools.bloxberg.swagger_client.models.validation_error module caosadvancedtools.bloxberg.swagger_client.rest module caosadvancedtools.cache module caosadvancedtools.cfood module caosadvancedtools.cfoods module caosadvancedtools.cfoods.h5 module caosadvancedtools.converter module caosadvancedtools.converter.labfolder_export 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.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.structure_mapping module caosadvancedtools.suppressKnown module caosadvancedtools.table_converter module caosadvancedtools.table_export module caosadvancedtools.table_importer module caosadvancedtools.utils module caosadvancedtools.webui_formatter module CertificateApi (class in caosadvancedtools.bloxberg.swagger_client.api.certificate_api) certify() (caosadvancedtools.bloxberg.bloxberg.Bloxberg method) certify_entity() (in module caosadvancedtools.bloxberg.bloxberg) 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) 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) combine_ignore_files() (in module caosadvancedtools.loadFiles) compile_file_list() (in module caosadvancedtools.loadFiles) Configuration (class in caosadvancedtools.bloxberg.swagger_client.configuration) configure_server_side_logging() (in module caosadvancedtools.serverside.logging) construct_mapping() (caosadvancedtools.models.parser.SafeLineLoader method) context() (caosadvancedtools.bloxberg.swagger_client.models.controller_cert_tools_generate_pdf_json_certificate.ControllerCertToolsGeneratePdfJsonCertificate property) (caosadvancedtools.bloxberg.swagger_client.models.controller_cert_tools_generate_unsigned_certificate_json_certificate.ControllerCertToolsGenerateUnsignedCertificateJsonCertificate property) ControllerCertToolsGeneratePdfJsonCertificate (class in caosadvancedtools.bloxberg.swagger_client.models.controller_cert_tools_generate_pdf_json_certificate) ControllerCertToolsGenerateUnsignedCertificateJsonCertificate (class in caosadvancedtools.bloxberg.swagger_client.models.controller_cert_tools_generate_unsigned_certificate_json_certificate) convert_path() (caosadvancedtools.scifolder.withreadme.WithREADME method) convert_size() (in module caosadvancedtools.loadFiles) convert_win_paths() (caosadvancedtools.scifolder.withreadme.WithREADME method) crawl() (caosadvancedtools.crawler.Crawler method) crawled_file() (caosadvancedtools.cfood.AbstractFileCFood property) Crawler (class in caosadvancedtools.crawler) create_bloxberg_certificate_create_bloxberg_certificate_post() (caosadvancedtools.bloxberg.swagger_client.api.certificate_api.CertificateApi method) create_bloxberg_certificate_create_bloxberg_certificate_post_with_http_info() (caosadvancedtools.bloxberg.swagger_client.api.certificate_api.CertificateApi method) 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_entry() (in module caosadvancedtools.converter.labfolder_export) create_file() (in module caosadvancedtools.converter.labfolder_export) 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_project() (in module caosadvancedtools.converter.labfolder_export) 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) credential_subject() (caosadvancedtools.bloxberg.swagger_client.models.controller_cert_tools_generate_pdf_json_certificate.ControllerCertToolsGeneratePdfJsonCertificate property) (caosadvancedtools.bloxberg.swagger_client.models.controller_cert_tools_generate_unsigned_certificate_json_certificate.ControllerCertToolsGenerateUnsignedCertificateJsonCertificate property) crid() (caosadvancedtools.bloxberg.swagger_client.models.batch.Batch property) (caosadvancedtools.bloxberg.swagger_client.models.controller_cert_tools_generate_pdf_json_certificate.ControllerCertToolsGeneratePdfJsonCertificate property) (caosadvancedtools.bloxberg.swagger_client.models.controller_cert_tools_generate_unsigned_certificate_json_certificate.ControllerCertToolsGenerateUnsignedCertificateJsonCertificate property) crid_type() (caosadvancedtools.bloxberg.swagger_client.models.batch.Batch property) (caosadvancedtools.bloxberg.swagger_client.models.controller_cert_tools_generate_pdf_json_certificate.ControllerCertToolsGeneratePdfJsonCertificate property) (caosadvancedtools.bloxberg.swagger_client.models.controller_cert_tools_generate_unsigned_certificate_json_certificate.ControllerCertToolsGenerateUnsignedCertificateJsonCertificate property) 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) debug() (caosadvancedtools.bloxberg.swagger_client.configuration.Configuration property)

defineParser() (in module caosadvancedtools.export_related) (in module caosadvancedtools.import_from_xml) DELETE() (caosadvancedtools.bloxberg.swagger_client.rest.RESTClientObject method) demo_run() (in module caosadvancedtools.bloxberg.bloxberg) description (caosadvancedtools.scifolder.withreadme.DataModel attribute) deserialize() (caosadvancedtools.bloxberg.swagger_client.api_client.ApiClient method) detail() (caosadvancedtools.bloxberg.swagger_client.models.http_validation_error.HTTPValidationError property) display_html() (caosadvancedtools.bloxberg.swagger_client.models.controller_cert_tools_generate_pdf_json_certificate.ControllerCertToolsGeneratePdfJsonCertificate property) (caosadvancedtools.bloxberg.swagger_client.models.controller_cert_tools_generate_unsigned_certificate_json_certificate.ControllerCertToolsGenerateUnsignedCertificateJsonCertificate property)

E

enable_ipfs() (caosadvancedtools.bloxberg.swagger_client.models.batch.Batch property) ensure_data_model() (in module caosadvancedtools.bloxberg.bloxberg) entities_without() (caosadvancedtools.models.data_model.DataModel static method) EntityMapping (class in caosadvancedtools.structure_mapping) 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_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) 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) format() (caosadvancedtools.webui_formatter.WebUI_Formatter method) from_table() (in module caosadvancedtools.table_converter) from_tsv() (in module caosadvancedtools.table_converter)

G

generate_pdf_generate_pdf_post() (caosadvancedtools.bloxberg.swagger_client.api.pdf_api.PdfApi method) generate_pdf_generate_pdf_post_with_http_info() (caosadvancedtools.bloxberg.swagger_client.api.pdf_api.PdfApi method) generate_property_name() (in module caosadvancedtools.table_converter) GET() (caosadvancedtools.bloxberg.swagger_client.rest.RESTClientObject method) get() (caosadvancedtools.cache.UpdateCache method) get_api_key_with_prefix() (caosadvancedtools.bloxberg.swagger_client.configuration.Configuration method) get_argument_parser() (in module caosadvancedtools.serverside.helper) get_author_from_entry() (in module caosadvancedtools.converter.labfolder_export) get_basic_auth_token() (caosadvancedtools.bloxberg.swagger_client.configuration.Configuration method) get_cache_schema_version() (caosadvancedtools.cache.AbstractCache method) (caosadvancedtools.cache.IdentifiableCache method) (caosadvancedtools.cache.UpdateCache method) get_cache_version() (caosadvancedtools.cache.AbstractCache method) get_data() (in module caosadvancedtools.serverside.helper) get_default_file_name() (caosadvancedtools.cache.AbstractCache method) (caosadvancedtools.cache.IdentifiableCache method) (caosadvancedtools.cache.UpdateCache method) 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_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_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_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_rt() (in module caosadvancedtools.scifolder.withreadme) get_shared_filename() (in module caosadvancedtools.serverside.helper) 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_xls_header() (in module caosadvancedtools.scifolder.utils) getheader() (caosadvancedtools.bloxberg.swagger_client.rest.RESTResponse method) getheaders() (caosadvancedtools.bloxberg.swagger_client.rest.RESTResponse method) 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) HEAD() (caosadvancedtools.bloxberg.swagger_client.rest.RESTClientObject method) header() (caosadvancedtools.scifolder.withreadme.WithREADME property) HeaderField (class in caosadvancedtools.scifolder.withreadme) HTTPValidationError (class in caosadvancedtools.bloxberg.swagger_client.models.http_validation_error)

I

id() (caosadvancedtools.bloxberg.swagger_client.models.controller_cert_tools_generate_pdf_json_certificate.ControllerCertToolsGeneratePdfJsonCertificate property) (caosadvancedtools.bloxberg.swagger_client.models.controller_cert_tools_generate_unsigned_certificate_json_certificate.ControllerCertToolsGenerateUnsignedCertificateJsonCertificate property) IdentifiableCache (class in caosadvancedtools.cache) identifier (caosadvancedtools.scifolder.withreadme.DataModel attribute) import_data() (in module caosadvancedtools.converter.labfolder_export) 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_filename_allowed() (in module caosadvancedtools.scifolder.utils) issuance_date() (caosadvancedtools.bloxberg.swagger_client.models.controller_cert_tools_generate_pdf_json_certificate.ControllerCertToolsGeneratePdfJsonCertificate property) (caosadvancedtools.bloxberg.swagger_client.models.controller_cert_tools_generate_unsigned_certificate_json_certificate.ControllerCertToolsGenerateUnsignedCertificateJsonCertificate property) issuer() (caosadvancedtools.bloxberg.swagger_client.models.controller_cert_tools_generate_pdf_json_certificate.ControllerCertToolsGeneratePdfJsonCertificate property) (caosadvancedtools.bloxberg.swagger_client.models.controller_cert_tools_generate_unsigned_certificate_json_certificate.ControllerCertToolsGenerateUnsignedCertificateJsonCertificate property) iteritems() (caosadvancedtools.crawler.Crawler method) (caosadvancedtools.crawler.FileCrawler method) (caosadvancedtools.crawler.TableCrawler method)

J

json_from_certificate() (caosadvancedtools.bloxberg.bloxberg.Bloxberg static method)

JsonSchemaDefinitionError JsonSchemaParser (class in caosadvancedtools.models.parser)

K

kw_present() (in module caosadvancedtools.pandoc_header_tools)

L

loadpath() (in module caosadvancedtools.loadFiles) loc() (caosadvancedtools.bloxberg.swagger_client.models.validation_error.ValidationError property) logger_file() (caosadvancedtools.bloxberg.swagger_client.configuration.Configuration property)

logger_format() (caosadvancedtools.bloxberg.swagger_client.configuration.Configuration property) looking_for() (caosadvancedtools.cfood.AbstractCFood method) (caosadvancedtools.cfood.AbstractFileCFood method)

M

main() (in module caosadvancedtools.loadFiles) (in module caosadvancedtools.serverside.generic_analysis) match_item() (caosadvancedtools.cfood.AbstractCFood class method) (caosadvancedtools.cfood.AbstractFileCFood class method) matching_groups (caosadvancedtools.cfood.CMeal attribute) metadata_json() (caosadvancedtools.bloxberg.swagger_client.models.batch.Batch property) (caosadvancedtools.bloxberg.swagger_client.models.controller_cert_tools_generate_pdf_json_certificate.ControllerCertToolsGeneratePdfJsonCertificate property) (caosadvancedtools.bloxberg.swagger_client.models.controller_cert_tools_generate_unsigned_certificate_json_certificate.ControllerCertToolsGenerateUnsignedCertificateJsonCertificate property) MetadataFileMissing missing (caosadvancedtools.datamodel_problems.DataModelProblems attribute) module caosadvancedtools caosadvancedtools.bloxberg caosadvancedtools.bloxberg.bloxberg caosadvancedtools.bloxberg.swagger_client caosadvancedtools.bloxberg.swagger_client.api caosadvancedtools.bloxberg.swagger_client.api.certificate_api caosadvancedtools.bloxberg.swagger_client.api.pdf_api caosadvancedtools.bloxberg.swagger_client.api_client caosadvancedtools.bloxberg.swagger_client.configuration caosadvancedtools.bloxberg.swagger_client.models caosadvancedtools.bloxberg.swagger_client.models.batch caosadvancedtools.bloxberg.swagger_client.models.controller_cert_tools_generate_pdf_json_certificate caosadvancedtools.bloxberg.swagger_client.models.controller_cert_tools_generate_unsigned_certificate_json_certificate caosadvancedtools.bloxberg.swagger_client.models.http_validation_error caosadvancedtools.bloxberg.swagger_client.models.validation_error caosadvancedtools.bloxberg.swagger_client.rest caosadvancedtools.cache caosadvancedtools.cfood caosadvancedtools.cfoods caosadvancedtools.cfoods.h5 caosadvancedtools.converter caosadvancedtools.converter.labfolder_export caosadvancedtools.crawler caosadvancedtools.datainconsistency caosadvancedtools.datamodel_problems caosadvancedtools.example_cfood caosadvancedtools.export_related caosadvancedtools.guard caosadvancedtools.import_from_xml 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.structure_mapping caosadvancedtools.suppressKnown caosadvancedtools.table_converter caosadvancedtools.table_export caosadvancedtools.table_importer caosadvancedtools.utils caosadvancedtools.webui_formatter

msg() (caosadvancedtools.bloxberg.swagger_client.models.validation_error.ValidationError property)

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) NATIVE_TYPES_MAPPING (caosadvancedtools.bloxberg.swagger_client.api_client.ApiClient attribute) NoValidHeader

O

OPTIONS() (caosadvancedtools.bloxberg.swagger_client.rest.RESTClientObject method)

P

parameters_to_tuples() (caosadvancedtools.bloxberg.swagger_client.api_client.ApiClient method) 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_responsibles() (in module caosadvancedtools.scifolder.utils) ParseErrorsInHeader Parser (class in caosadvancedtools.models.parser) PATCH() (caosadvancedtools.bloxberg.swagger_client.rest.RESTClientObject method) PdfApi (class in caosadvancedtools.bloxberg.swagger_client.api.pdf_api) POST() (caosadvancedtools.bloxberg.swagger_client.rest.RESTClientObject method) prepare_csv_export() (caosadvancedtools.table_export.BaseTableExporter method) prepare_post_parameters() (caosadvancedtools.bloxberg.swagger_client.api_client.ApiClient method)

PRIMITIVE_TYPES (caosadvancedtools.bloxberg.swagger_client.api_client.ApiClient attribute) 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) proof() (caosadvancedtools.bloxberg.swagger_client.models.controller_cert_tools_generate_pdf_json_certificate.ControllerCertToolsGeneratePdfJsonCertificate property) (caosadvancedtools.bloxberg.swagger_client.models.controller_cert_tools_generate_unsigned_certificate_json_certificate.ControllerCertToolsGenerateUnsignedCertificateJsonCertificate property) property_name_re (caosadvancedtools.scifolder.result_table_cfood.ResultTableCFood attribute) public_key() (caosadvancedtools.bloxberg.swagger_client.models.batch.Batch property) Publication (caosadvancedtools.scifolder.withreadme.DataModel attribute) PublicationCFood (class in caosadvancedtools.scifolder.publication_cfood) PUT() (caosadvancedtools.bloxberg.swagger_client.rest.RESTClientObject method) 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_xls() (caosadvancedtools.table_importer.XLSImporter method) recordtype_is_child_of() (in module caosadvancedtools.serverside.helper) 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) request() (caosadvancedtools.bloxberg.swagger_client.api_client.ApiClient method) (caosadvancedtools.bloxberg.swagger_client.rest.RESTClientObject method) reset() (caosadvancedtools.suppressKnown.SuppressKnown method) responsible (caosadvancedtools.scifolder.withreadme.DataModel attribute) RESTClientObject (class in caosadvancedtools.bloxberg.swagger_client.rest) RESTResponse (class in caosadvancedtools.bloxberg.swagger_client.rest) 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) 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) sanitize_for_serialization() (caosadvancedtools.bloxberg.swagger_client.api_client.ApiClient method) save_form() (caosadvancedtools.crawler.Crawler static method) save_header() (in module caosadvancedtools.pandoc_header_tools) scripts (caosadvancedtools.scifolder.withreadme.DataModel attribute) select_header_accept() (caosadvancedtools.bloxberg.swagger_client.api_client.ApiClient method) select_header_content_type() (caosadvancedtools.bloxberg.swagger_client.api_client.ApiClient method) send_mail() (caosadvancedtools.crawler.Crawler static method) (in module caosadvancedtools.serverside.helper) separated() (in module caosadvancedtools.crawler) set_default() (caosadvancedtools.bloxberg.swagger_client.configuration.TypeWithDefault method) set_default_header() (caosadvancedtools.bloxberg.swagger_client.api_client.ApiClient method) 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) 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) SuppressKnown (class in caosadvancedtools.suppressKnown) swagger_types (caosadvancedtools.bloxberg.swagger_client.models.batch.Batch attribute) (caosadvancedtools.bloxberg.swagger_client.models.controller_cert_tools_generate_pdf_json_certificate.ControllerCertToolsGeneratePdfJsonCertificate attribute) (caosadvancedtools.bloxberg.swagger_client.models.controller_cert_tools_generate_unsigned_certificate_json_certificate.ControllerCertToolsGenerateUnsignedCertificateJsonCertificate attribute) (caosadvancedtools.bloxberg.swagger_client.models.http_validation_error.HTTPValidationError attribute) (caosadvancedtools.bloxberg.swagger_client.models.validation_error.ValidationError attribute) 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) tag_msg() (caosadvancedtools.suppressKnown.SuppressKnown method) to_debug_report() (caosadvancedtools.bloxberg.swagger_client.configuration.Configuration method) to_dict() (caosadvancedtools.bloxberg.swagger_client.models.batch.Batch method) (caosadvancedtools.bloxberg.swagger_client.models.controller_cert_tools_generate_pdf_json_certificate.ControllerCertToolsGeneratePdfJsonCertificate method) (caosadvancedtools.bloxberg.swagger_client.models.controller_cert_tools_generate_unsigned_certificate_json_certificate.ControllerCertToolsGenerateUnsignedCertificateJsonCertificate method) (caosadvancedtools.bloxberg.swagger_client.models.http_validation_error.HTTPValidationError method) (caosadvancedtools.bloxberg.swagger_client.models.validation_error.ValidationError method) to_str() (caosadvancedtools.bloxberg.swagger_client.models.batch.Batch method) (caosadvancedtools.bloxberg.swagger_client.models.controller_cert_tools_generate_pdf_json_certificate.ControllerCertToolsGeneratePdfJsonCertificate method) (caosadvancedtools.bloxberg.swagger_client.models.controller_cert_tools_generate_unsigned_certificate_json_certificate.ControllerCertToolsGenerateUnsignedCertificateJsonCertificate method) (caosadvancedtools.bloxberg.swagger_client.models.http_validation_error.HTTPValidationError method) (caosadvancedtools.bloxberg.swagger_client.models.validation_error.ValidationError method)

to_table() (in module caosadvancedtools.table_converter) to_tsv() (in module caosadvancedtools.table_converter) treat_project() (in module caosadvancedtools.converter.labfolder_export) TSVImporter (class in caosadvancedtools.table_importer) TwiceDefinedException type() (caosadvancedtools.bloxberg.swagger_client.models.controller_cert_tools_generate_pdf_json_certificate.ControllerCertToolsGeneratePdfJsonCertificate property) (caosadvancedtools.bloxberg.swagger_client.models.controller_cert_tools_generate_unsigned_certificate_json_certificate.ControllerCertToolsGenerateUnsignedCertificateJsonCertificate property) (caosadvancedtools.bloxberg.swagger_client.models.validation_error.ValidationError property) TypeWithDefault (class in caosadvancedtools.bloxberg.swagger_client.configuration)

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_params_for_auth() (caosadvancedtools.bloxberg.swagger_client.api_client.ApiClient method) update_structure() (in module caosadvancedtools.structure_mapping) UpdateCache (class in caosadvancedtools.cache) user_agent() (caosadvancedtools.bloxberg.swagger_client.api_client.ApiClient property)

V

val_or_none() (in module caosadvancedtools.converter.labfolder_export) validate_cache() (caosadvancedtools.cache.IdentifiableCache method)

ValidationError (class in caosadvancedtools.bloxberg.swagger_client.models.validation_error) verify() (caosadvancedtools.bloxberg.bloxberg.Bloxberg 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) wrap_bootstrap_alert() (in module caosadvancedtools.serverside.helper)

X

XLSImporter (class in caosadvancedtools.table_importer)

Y

YamlDefinitionError

yes_no_converter() (in module caosadvancedtools.table_importer)