Index

A

acceleration_voltage (nexusLIMS.schemas.metadata.DiffractionMetadata attribute) (nexusLIMS.schemas.metadata.ImageMetadata attribute) acquisition_device (nexusLIMS.schemas.metadata.DiffractionMetadata attribute) (nexusLIMS.schemas.metadata.ImageMetadata attribute) acquisition_time (nexusLIMS.schemas.metadata.SpectrumMetadata attribute) AcquisitionActivity (class in nexusLIMS.schemas.activity) action_add() (nexusLIMS.tui.apps.instruments.screens.InstrumentListScreen method) (nexusLIMS.tui.common.base_screens.BaseListScreen method) action_cancel() (nexusLIMS.tui.apps.config.screens.ConfigScreen method) (nexusLIMS.tui.common.base_screens.BaseFormScreen method) action_cancel_dialog() (nexusLIMS.tui.apps.config.screens.LabArchivesGetUidDialog method) action_cycle_sort() (nexusLIMS.tui.common.base_screens.BaseListScreen method) action_delete() (nexusLIMS.tui.apps.instruments.screens.InstrumentListScreen method) (nexusLIMS.tui.common.base_screens.BaseListScreen method) action_dismiss() (nexusLIMS.tui.common.base_app.HelpScreen method) action_dismiss_detail() (nexusLIMS.tui.apps.config.screens.FieldDetailScreen method) action_edit() (nexusLIMS.tui.common.base_screens.BaseListScreen method) action_focus_filter() (nexusLIMS.tui.common.base_screens.BaseListScreen method) action_help() (nexusLIMS.tui.apps.config.app.ConfiguratorApp method) (nexusLIMS.tui.common.base_app.BaseNexusApp method) (nexusLIMS.tui.common.base_screens.BaseFormScreen method) (nexusLIMS.tui.common.base_screens.BaseListScreen method) action_next_tab() (nexusLIMS.tui.apps.config.screens.ConfigScreen method) action_previous_tab() (nexusLIMS.tui.apps.config.screens.ConfigScreen method) action_quit() (nexusLIMS.tui.common.base_screens.BaseListScreen method)

action_refresh() (nexusLIMS.tui.common.base_screens.BaseListScreen method) action_save() (nexusLIMS.tui.apps.config.screens.ConfigScreen method) (nexusLIMS.tui.common.base_screens.BaseFormScreen method) action_show_field_detail() (nexusLIMS.tui.apps.config.screens.ConfigScreen method) action_toggle_theme() (nexusLIMS.tui.common.base_app.BaseNexusApp method) activities (nexusLIMS.builder.record_builder.RecordBuildResult attribute) (nexusLIMS.exporters.base.ExportContext attribute) add_all_usage_events_to_db() (in module nexusLIMS.harvesters.nemo.utils) add_annotation_markers() (in module nexusLIMS.extractors.plugins.preview_generators.hyperspy_preview) add_attachment() (nexusLIMS.utils.labarchives.LabArchivesClient method) add_entry() (nexusLIMS.utils.labarchives.LabArchivesClient method) add_file() (nexusLIMS.schemas.activity.AcquisitionActivity method) add_metadata_warnings() (in module nexusLIMS.extractors.plugins.profiles.fei_titan_stem_643) add_result() (nexusLIMS.exporters.base.ExportContext method) add_to_extensions() (in module nexusLIMS.extractors.utils) address (nexusLIMS.config.NemoHarvesterConfig attribute) all_extractors (nexusLIMS.extractors.registry.ExtractorRegistry property) api_url (nexusLIMS.db.models.Instrument attribute) Archived (nexusLIMS.utils.elabftw.State attribute) as_xml() (nexusLIMS.harvesters.reservation_event.ReservationEvent method) (nexusLIMS.schemas.activity.AcquisitionActivity method) attach_file() (nexusLIMS.utils.labarchives.LabArchivesClient method) AuthenticationError AUTO_FOCUS (nexusLIMS.tui.apps.instruments.screens.InstrumentAddScreen attribute) AutocompleteInput (class in nexusLIMS.tui.common.widgets) azimuthal_angle (nexusLIMS.schemas.metadata.SpectrumMetadata attribute)

B

BaseExtractor (class in nexusLIMS.extractors.base) BaseFormScreen (class in nexusLIMS.tui.common.base_screens) BaseListScreen (class in nexusLIMS.tui.common.base_screens) BaseNexusApp (class in nexusLIMS.tui.common.base_app) BasicFileInfoExtractor (class in nexusLIMS.extractors.plugins.basic_metadata) beam_current (nexusLIMS.schemas.metadata.ImageMetadata attribute) BINDINGS (nexusLIMS.tui.apps.config.screens.ConfigScreen attribute) (nexusLIMS.tui.apps.config.screens.FieldDetailScreen attribute) (nexusLIMS.tui.apps.config.screens.LabArchivesGetUidDialog attribute) (nexusLIMS.tui.common.base_app.BaseNexusApp attribute) (nexusLIMS.tui.common.base_app.HelpScreen attribute) (nexusLIMS.tui.common.base_screens.BaseFormScreen attribute) (nexusLIMS.tui.common.base_screens.BaseListScreen attribute)

blank_value_on_duplicate (nexusLIMS.exporters.destinations.elabftw.ExtraField attribute) branch_labels (in module nexusLIMS.db.migrations.versions.v1_4_3_initial_schema_baseline) (in module nexusLIMS.db.migrations.versions.v2_4_0a_add_upload_log_table) (in module nexusLIMS.db.migrations.versions.v2_4_0b_add_check_constraints) (in module nexusLIMS.db.migrations.versions.v2_5_0a_add_external_user_identifiers) (in module nexusLIMS.db.migrations.versions.v2_5_0b_remove_computer_fields) build_acq_activities() (in module nexusLIMS.builder.record_builder) build_new_session_records() (in module nexusLIMS.builder.record_builder) build_record() (in module nexusLIMS.builder.record_builder) BUILT_NOT_EXPORTED (nexusLIMS.db.enums.RecordStatus attribute)

C

cache_ok (nexusLIMS.db.models.TZDateTime attribute) calendar_url (nexusLIMS.db.models.Instrument attribute) camera_length (nexusLIMS.schemas.metadata.DiffractionMetadata attribute) CDCS (nexusLIMS.db.enums.ExternalSystem attribute) CDCSDataRecord (class in nexusLIMS.utils.cdcs) CDCSDestination (class in nexusLIMS.exporters.destinations.cdcs) channel_size (nexusLIMS.schemas.metadata.SpectrumMetadata attribute) check_log_for_errors() (in module nexusLIMS.cli.process_records) check_uniqueness() (in module nexusLIMS.tui.common.db_utils) CheckResult (class in nexusLIMS.builder.preflight) clear() (nexusLIMS.extractors.profiles.InstrumentProfileRegistry method) (nexusLIMS.extractors.registry.ExtractorRegistry method) clear_settings() (in module nexusLIMS.config) cluster_filelist_mtimes() (in module nexusLIMS.schemas.activity) collect_form_data() (nexusLIMS.tui.apps.instruments.screens.InstrumentAddScreen method) (nexusLIMS.tui.common.base_screens.BaseFormScreen method) COMPLETED (nexusLIMS.db.enums.RecordStatus attribute) compose() (nexusLIMS.tui.apps.config.screens.ConfigScreen method) (nexusLIMS.tui.apps.config.screens.FieldDetailScreen method) (nexusLIMS.tui.apps.config.screens.LabArchivesGetUidDialog method) (nexusLIMS.tui.apps.db_browser.NexusLIMSTableViewerPane method) (nexusLIMS.tui.apps.instruments.screens.WelcomeDialog method) (nexusLIMS.tui.common.base_app.HelpScreen method) (nexusLIMS.tui.common.base_screens.BaseFormScreen method) (nexusLIMS.tui.common.base_screens.BaseListScreen method) (nexusLIMS.tui.common.base_screens.ConfirmDialog method) (nexusLIMS.tui.common.widgets.FormField method)

config (in module nexusLIMS.db.migrations.env) ConfigScreen (class in nexusLIMS.tui.apps.config.screens) ConfiguratorApp (class in nexusLIMS.tui.apps.config.app) ConfirmDialog (class in nexusLIMS.tui.common.base_screens) console (in module nexusLIMS.cli.process_records) ContentType (class in nexusLIMS.utils.elabftw) convergence_angle (nexusLIMS.schemas.metadata.DiffractionMetadata attribute) create_backup() (in module nexusLIMS.db.migrations.utils) create_demo_database() (in module nexusLIMS.tui.demo_helpers) create_experiment() (nexusLIMS.utils.elabftw.ELabFTWClient method) create_preview() (in module nexusLIMS.extractors) create_res_event_from_usage_event() (in module nexusLIMS.harvesters.nemo) created_at (nexusLIMS.db.models.ExternalUserIdentifier attribute) created_by (nexusLIMS.harvesters.reservation_event.ReservationEvent attribute) created_by_full_name (nexusLIMS.harvesters.reservation_event.ReservationEvent attribute) creation_time (nexusLIMS.schemas.metadata.NexusMetadata attribute) CSS_PATH (nexusLIMS.tui.apps.config.app.ConfiguratorApp attribute) (nexusLIMS.tui.apps.config.screens.ConfigScreen attribute) (nexusLIMS.tui.apps.config.screens.FieldDetailScreen attribute) (nexusLIMS.tui.apps.config.screens.LabArchivesGetUidDialog attribute) (nexusLIMS.tui.apps.db_browser.NexusLIMSDBApp attribute) (nexusLIMS.tui.apps.instruments.screens.InstrumentAddScreen attribute) (nexusLIMS.tui.apps.instruments.screens.WelcomeDialog attribute) (nexusLIMS.tui.common.base_app.BaseNexusApp attribute) (nexusLIMS.tui.common.base_screens.BaseListScreen attribute) (nexusLIMS.tui.common.base_screens.ConfirmDialog attribute) current_system_tz() (in module nexusLIMS.utils.time) current_system_tz_name() (in module nexusLIMS.utils.time)

D

data_dimensions (nexusLIMS.schemas.metadata.NexusMetadata attribute) data_type (nexusLIMS.schemas.metadata.NexusMetadata attribute) dataset_type (nexusLIMS.schemas.metadata.DiffractionMetadata attribute) (nexusLIMS.schemas.metadata.ImageMetadata attribute) (nexusLIMS.schemas.metadata.NexusMetadata attribute) (nexusLIMS.schemas.metadata.SpectrumImageMetadata attribute) (nexusLIMS.schemas.metadata.SpectrumMetadata attribute) date (nexusLIMS.schemas.metadata.ExtractionDetails attribute) db_path (nexusLIMS.tui.apps.instruments.app.InstrumentManagerApp property) DEFAULT_CSS (nexusLIMS.tui.apps.db_browser.NexusLIMSDBApp attribute) (nexusLIMS.tui.apps.db_browser.NexusLIMSTableViewerPane attribute) delete_experiment() (nexusLIMS.utils.elabftw.ELabFTWClient method) delete_instrument() (nexusLIMS.tui.apps.instruments.screens.InstrumentListScreen method) delete_record() (in module nexusLIMS.utils.cdcs) Deleted (nexusLIMS.utils.elabftw.State attribute) depends_on (in module nexusLIMS.db.migrations.versions.v1_4_3_initial_schema_baseline) (in module nexusLIMS.db.migrations.versions.v2_4_0a_add_upload_log_table) (in module nexusLIMS.db.migrations.versions.v2_4_0b_add_check_constraints) (in module nexusLIMS.db.migrations.versions.v2_5_0a_add_external_user_identifiers) (in module nexusLIMS.db.migrations.versions.v2_5_0b_remove_computer_fields) description (nexusLIMS.exporters.destinations.elabftw.ExtraField attribute) deserialize_quantity() (in module nexusLIMS.schemas.units) destination_name (nexusLIMS.db.models.UploadLog attribute) (nexusLIMS.exporters.base.ExportResult attribute) detect_diffraction_from_filename() (in module nexusLIMS.extractors.plugins.profiles.jeol_jem_642) detect_diffraction_mode() (in module nexusLIMS.extractors.plugins.profiles.fei_titan_tem_642) detect_eftem_diffraction() (in module nexusLIMS.extractors.plugins.profiles.fei_titan_stem_643)

detector_energy_resolution (nexusLIMS.schemas.metadata.SpectrumMetadata attribute) detector_type (nexusLIMS.schemas.metadata.ImageMetadata attribute) DiffractionMetadata (class in nexusLIMS.schemas.metadata) discover_plugins() (nexusLIMS.exporters.registry.ExporterRegistry method) (nexusLIMS.extractors.registry.ExtractorRegistry method) display_main_text (nexusLIMS.exporters.destinations.elabftw.ELabFTWConfig attribute) display_name (nexusLIMS.db.models.Instrument attribute) division (nexusLIMS.harvesters.reservation_event.ReservationEvent attribute) DM3Extractor (class in nexusLIMS.extractors.plugins.digital_micrograph) down_revision (in module nexusLIMS.db.migrations.versions.v1_4_3_initial_schema_baseline) (in module nexusLIMS.db.migrations.versions.v2_4_0a_add_upload_log_table) (in module nexusLIMS.db.migrations.versions.v2_4_0b_add_check_constraints) (in module nexusLIMS.db.migrations.versions.v2_5_0a_add_external_user_identifiers) (in module nexusLIMS.db.migrations.versions.v2_5_0b_remove_computer_fields) down_sample_image() (in module nexusLIMS.extractors.plugins.preview_generators.image_preview) downgrade() (in module nexusLIMS.db.migrations.versions.v1_4_3_initial_schema_baseline) (in module nexusLIMS.db.migrations.versions.v2_4_0a_add_upload_log_table) (in module nexusLIMS.db.migrations.versions.v2_4_0b_add_check_constraints) (in module nexusLIMS.db.migrations.versions.v2_5_0a_add_external_user_identifiers) (in module nexusLIMS.db.migrations.versions.v2_5_0b_remove_computer_fields) download_record() (in module nexusLIMS.utils.cdcs) dry_run_file_find() (in module nexusLIMS.builder.record_builder) dt_from (nexusLIMS.exporters.base.ExportContext attribute) dt_to (nexusLIMS.exporters.base.ExportContext attribute) dump() (in module nexusLIMS.cli.config) dump_record() (in module nexusLIMS.builder.record_builder) dwell_time (nexusLIMS.schemas.metadata.ImageMetadata attribute)

E

edit() (in module nexusLIMS.cli.config) elabftw (nexusLIMS.exporters.destinations.elabftw.ExtraFieldsMetadata attribute) ELabFTWAuthenticationError ELabFTWClient (class in nexusLIMS.utils.elabftw) ELabFTWConfig (class in nexusLIMS.exporters.destinations.elabftw) ELabFTWDestination (class in nexusLIMS.exporters.destinations.elabftw) ELabFTWError ELabFTWNotFoundError elements (nexusLIMS.schemas.metadata.SpectrumMetadata attribute) elevation_angle (nexusLIMS.schemas.metadata.SpectrumMetadata attribute) EM_GLOSSARY_TO_XML_DISPLAY_NAMES (in module nexusLIMS.extractors.xml_serialization) email (nexusLIMS.db.models.ExternalUserIdentifier attribute) email_config() (nexusLIMS.config.Settings method) EmailConfig (class in nexusLIMS.config) EMG (in module nexusLIMS.schemas.em_glossary) emg_field() (in module nexusLIMS.schemas.metadata) EMG_OWL_PATH (in module nexusLIMS.schemas.em_glossary) EMG_VERSION (in module nexusLIMS.schemas.em_glossary) emission_current (nexusLIMS.schemas.metadata.ImageMetadata attribute) enabled (nexusLIMS.exporters.base.ExportDestination property) (nexusLIMS.exporters.destinations.cdcs.CDCSDestination property) (nexusLIMS.exporters.destinations.elabftw.ELabFTWDestination property) (nexusLIMS.exporters.destinations.labarchives.LabArchivesDestination property) END (nexusLIMS.db.enums.EventType attribute) end (nexusLIMS.schemas.activity.AcquisitionActivity attribute) end_time (nexusLIMS.harvesters.reservation_event.ReservationEvent attribute) env_path (nexusLIMS.tui.apps.config.app.ConfiguratorApp property) ERROR (nexusLIMS.db.enums.RecordStatus attribute) Error (nexusLIMS.utils.elabftw.State attribute) error_message (nexusLIMS.db.models.UploadLog attribute) (nexusLIMS.exporters.base.ExportResult attribute) (nexusLIMS.tui.common.widgets.FormField property) (nexusLIMS.tui.common.widgets.ValidatedInput property) ERROR_PATTERNS (in module nexusLIMS.cli.process_records) event_type (nexusLIMS.db.models.SessionLog attribute) EventType (class in nexusLIMS.db.enums) EXCLUDE_PATTERNS (in module nexusLIMS.cli.process_records) execute_strategy() (in module nexusLIMS.exporters.strategies) experiment_purpose (nexusLIMS.harvesters.reservation_event.ReservationEvent attribute)

experiment_title (nexusLIMS.harvesters.reservation_event.ReservationEvent attribute) export() (nexusLIMS.exporters.base.ExportDestination method) (nexusLIMS.exporters.destinations.cdcs.CDCSDestination method) (nexusLIMS.exporters.destinations.elabftw.ELabFTWDestination method) (nexusLIMS.exporters.destinations.labarchives.LabArchivesDestination method) export_records() (in module nexusLIMS.exporters) export_to_all() (nexusLIMS.exporters.registry.ExporterRegistry method) ExportContext (class in nexusLIMS.exporters.base) ExportDestination (class in nexusLIMS.exporters.base) ExporterRegistry (class in nexusLIMS.exporters.registry) ExportResult (class in nexusLIMS.exporters.base) ExportStrategy (in module nexusLIMS.exporters.registry) extension_fields (nexusLIMS.extractors.base.InstrumentProfile attribute) extensions (nexusLIMS.schemas.metadata.NexusMetadata attribute) external_id (nexusLIMS.db.models.ExternalUserIdentifier attribute) external_system (nexusLIMS.db.models.ExternalUserIdentifier attribute) ExternalSystem (class in nexusLIMS.db.enums) ExternalUserIdentifier (class in nexusLIMS.db.models) extra_fields (nexusLIMS.exporters.destinations.elabftw.ExtraFieldsMetadata attribute) extra_fields_groups (nexusLIMS.exporters.destinations.elabftw.ELabFTWConfig attribute) extract() (nexusLIMS.extractors.base.BaseExtractor method) (nexusLIMS.extractors.plugins.basic_metadata.BasicFileInfoExtractor method) (nexusLIMS.extractors.plugins.digital_micrograph.DM3Extractor method) (nexusLIMS.extractors.plugins.edax.MsaExtractor method) (nexusLIMS.extractors.plugins.edax.SpcExtractor method) (nexusLIMS.extractors.plugins.fei_emi.SerEmiExtractor method) (nexusLIMS.extractors.plugins.orion_HIM_tif.OrionTiffExtractor method) (nexusLIMS.extractors.plugins.quanta_tif.QuantaTiffExtractor method) (nexusLIMS.extractors.plugins.tescan_tif.TescanTiffExtractor method) (nexusLIMS.extractors.plugins.tofwerk_pfib.TofwerkPfibExtractor method) ExtractionContext (class in nexusLIMS.extractors.base) ExtractionDetails (class in nexusLIMS.schemas.metadata) extractor_names (nexusLIMS.extractors.registry.ExtractorRegistry property) extractor_warnings (nexusLIMS.schemas.metadata.ExtractionDetails attribute) ExtractorRegistry (class in nexusLIMS.extractors.registry) extractors (nexusLIMS.extractors.registry.ExtractorRegistry property) ExtraField (class in nexusLIMS.exporters.destinations.elabftw) ExtraFieldsGroup (class in nexusLIMS.exporters.destinations.elabftw) ExtraFieldsMetadata (class in nexusLIMS.exporters.destinations.elabftw)

F

factor (nexusLIMS.extractors.base.FieldDefinition attribute) FEI_TIFF_TAG (in module nexusLIMS.extractors.plugins.quanta_tif) fei_titan_stem_643_profile (in module nexusLIMS.extractors.plugins.profiles.fei_titan_stem_643) fei_titan_tem_642_profile (in module nexusLIMS.extractors.plugins.profiles.fei_titan_tem_642) fei_unit_to_pint() (in module nexusLIMS.extractors.plugins.fei_emi) FEI_XML_TIFF_TAG (in module nexusLIMS.extractors.plugins.quanta_tif) FIBICS_TIFF_TAG (in module nexusLIMS.extractors.plugins.orion_HIM_tif) FieldDefinition (class in nexusLIMS.extractors.base) FieldDetailScreen (class in nexusLIMS.tui.apps.config.screens)

file_path (nexusLIMS.extractors.base.ExtractionContext attribute) files (nexusLIMS.schemas.activity.AcquisitionActivity attribute) filestore_path (nexusLIMS.db.models.Instrument attribute) find_conflicting_instrument() (in module nexusLIMS.tui.common.db_utils) find_dirs_by_mtime() (in module nexusLIMS.utils.files) find_files_by_mtime() (in module nexusLIMS.utils.files) flatten_dict() (in module nexusLIMS.extractors) FormField (class in nexusLIMS.tui.common.widgets) FormField.Changed (class in nexusLIMS.tui.common.widgets)

G

generate() (nexusLIMS.extractors.base.PreviewGenerator method) (nexusLIMS.extractors.plugins.preview_generators.hyperspy_preview.HyperSpyPreviewGenerator method) (nexusLIMS.extractors.plugins.preview_generators.image_preview.ImagePreviewGenerator method) (nexusLIMS.extractors.plugins.preview_generators.text_preview.TextPreviewGenerator method) (nexusLIMS.extractors.plugins.preview_generators.tofwerk_pfib_preview.TofwerkPfibPreviewGenerator method) get_all_emg_terms() (in module nexusLIMS.schemas.em_glossary) get_all_external_ids() (in module nexusLIMS.db.models) get_all_mapped_fields() (in module nexusLIMS.schemas.em_glossary) get_all_profiles() (nexusLIMS.extractors.profiles.InstrumentProfileRegistry method) get_all_session_logs() (in module nexusLIMS.db.session_handler) get_app_name() (nexusLIMS.tui.apps.config.app.ConfiguratorApp method) (nexusLIMS.tui.apps.instruments.app.InstrumentManagerApp method) (nexusLIMS.tui.common.base_app.BaseNexusApp method) get_attachment_content() (nexusLIMS.utils.labarchives.LabArchivesClient method) get_basic_metadata() (in module nexusLIMS.extractors.plugins.basic_metadata) get_ca_bundle_content() (in module nexusLIMS.harvesters) get_ca_bundle_path() (in module nexusLIMS.harvesters) get_cdcs_url() (in module nexusLIMS.utils.cdcs) get_columns() (nexusLIMS.tui.apps.instruments.screens.InstrumentListScreen method) (nexusLIMS.tui.common.base_screens.BaseListScreen method) get_command() (nexusLIMS.cli.main.LazyGroup method) get_connector_by_base_url() (in module nexusLIMS.harvesters.nemo.utils) get_connector_for_session() (in module nexusLIMS.harvesters.nemo.utils) get_data() (nexusLIMS.tui.apps.instruments.screens.InstrumentListScreen method) (nexusLIMS.tui.common.base_screens.BaseListScreen method) get_description() (in module nexusLIMS.schemas.em_glossary) get_display_name() (in module nexusLIMS.schemas.em_glossary) get_dm3_metadata() (in module nexusLIMS.extractors.plugins.digital_micrograph) get_elabftw_client() (in module nexusLIMS.utils.elabftw) get_emg_definition() (in module nexusLIMS.schemas.em_glossary) get_emg_id() (in module nexusLIMS.extractors.xml_serialization) (in module nexusLIMS.schemas.em_glossary) get_emg_label() (in module nexusLIMS.schemas.em_glossary) get_emg_uri() (in module nexusLIMS.schemas.em_glossary) get_emi_from_ser() (in module nexusLIMS.extractors.plugins.fei_emi) get_enabled_destinations() (nexusLIMS.exporters.registry.ExporterRegistry method) get_engine() (in module nexusLIMS.db.engine) get_example_values() (in module nexusLIMS.tui.apps.instruments.validators) get_experiment() (nexusLIMS.utils.elabftw.ELabFTWClient method) get_external_id() (in module nexusLIMS.db.models) get_extractor() (nexusLIMS.extractors.registry.ExtractorRegistry method) get_extractors_for_extension() (nexusLIMS.extractors.registry.ExtractorRegistry method) get_fields_with_emg_ids() (in module nexusLIMS.schemas.em_glossary) get_files() (in module nexusLIMS.builder.record_builder) get_form_fields() (nexusLIMS.tui.apps.instruments.screens.InstrumentAddScreen method) (nexusLIMS.tui.common.base_screens.BaseFormScreen method) get_harvesters_enabled() (in module nexusLIMS.harvesters.nemo.utils)

get_instr_from_api_url() (in module nexusLIMS.instruments) get_instr_from_calendar_name() (in module nexusLIMS.instruments) get_instr_from_filepath() (in module nexusLIMS.instruments) get_keybindings() (nexusLIMS.tui.apps.config.app.ConfiguratorApp method) (nexusLIMS.tui.apps.instruments.app.InstrumentManagerApp method) (nexusLIMS.tui.common.base_app.BaseNexusApp method) get_known_tool_ids() (nexusLIMS.harvesters.nemo.connector.NemoConnector method) get_labarchives_client() (in module nexusLIMS.utils.labarchives) get_msa_metadata() (in module nexusLIMS.extractors.plugins.edax) get_nested_dict_value_by_path() (in module nexusLIMS.utils.dicts) get_nexuslims_username() (in module nexusLIMS.db.models) get_page_entries() (nexusLIMS.utils.labarchives.LabArchivesClient method) get_pre_path() (in module nexusLIMS.extractors.plugins.digital_micrograph) get_preview_generator() (nexusLIMS.extractors.registry.ExtractorRegistry method) get_profile() (nexusLIMS.extractors.profiles.InstrumentProfileRegistry method) get_profile_registry() (in module nexusLIMS.extractors.profiles) get_projects() (nexusLIMS.harvesters.nemo.connector.NemoConnector method) get_quanta_metadata() (in module nexusLIMS.extractors.plugins.quanta_tif) get_qudt_uri() (in module nexusLIMS.extractors.xml_serialization) (in module nexusLIMS.schemas.units) get_registry() (in module nexusLIMS.exporters.registry) (in module nexusLIMS.extractors.registry) get_reservation_event() (in module nexusLIMS.builder.record_builder) get_reservations() (nexusLIMS.harvesters.nemo.connector.NemoConnector method) get_result() (nexusLIMS.exporters.base.ExportContext method) get_schema_for_dataset_type() (in module nexusLIMS.extractors) get_ser_metadata() (in module nexusLIMS.extractors.plugins.fei_emi) get_session_from_usage_event() (nexusLIMS.harvesters.nemo.connector.NemoConnector method) get_session_log_count() (in module nexusLIMS.tui.common.db_utils) get_sessions_to_build() (in module nexusLIMS.db.session_handler) get_spc_metadata() (in module nexusLIMS.extractors.plugins.edax) get_supported_extensions() (nexusLIMS.extractors.registry.ExtractorRegistry method) get_template_id() (in module nexusLIMS.utils.cdcs) get_timespan_overlap() (in module nexusLIMS.utils.time) get_tools() (nexusLIMS.harvesters.nemo.connector.NemoConnector method) get_tree_level() (nexusLIMS.utils.labarchives.LabArchivesClient method) get_usage_events() (nexusLIMS.harvesters.nemo.connector.NemoConnector method) get_usage_events_as_sessions() (in module nexusLIMS.harvesters.nemo.utils) get_user_info() (nexusLIMS.utils.labarchives.LabArchivesClient method) get_user_info_by_uid() (nexusLIMS.utils.labarchives.LabArchivesClient method) get_users() (nexusLIMS.harvesters.nemo.connector.NemoConnector method) get_users_by_username() (nexusLIMS.harvesters.nemo.connector.NemoConnector method) get_workspace_id() (in module nexusLIMS.utils.cdcs) get_xml_field_name() (in module nexusLIMS.extractors.xml_serialization) gnu_find_files_by_mtime() (in module nexusLIMS.utils.files) group (nexusLIMS.harvesters.reservation_event.ReservationEvent attribute) group_id (nexusLIMS.exporters.destinations.elabftw.ExtraField attribute)

H

handle_config_error() (in module nexusLIMS.cli) harvester (nexusLIMS.db.models.Instrument attribute) has_delay_passed() (in module nexusLIMS.utils.time) has_emg_id() (in module nexusLIMS.schemas.em_glossary) has_successful_export() (nexusLIMS.exporters.base.ExportContext method)

has_valid_question_data() (in module nexusLIMS.harvesters.nemo.utils) HelpScreen (class in nexusLIMS.tui.common.base_app) horizontal_field_width (nexusLIMS.schemas.metadata.ImageMetadata attribute) HTML (nexusLIMS.utils.elabftw.ContentType attribute) HyperSpyPreviewGenerator (class in nexusLIMS.extractors.plugins.preview_generators.hyperspy_preview)

I

id (nexusLIMS.db.models.ExternalUserIdentifier attribute) (nexusLIMS.db.models.UploadLog attribute) (nexusLIMS.exporters.destinations.elabftw.ExtraFieldsGroup attribute) id_from_url() (in module nexusLIMS.harvesters.nemo.utils) id_session_log (nexusLIMS.db.models.SessionLog attribute) image_to_square_thumbnail() (in module nexusLIMS.extractors.plugins.preview_generators.image_preview) ImageMetadata (class in nexusLIMS.schemas.metadata) ImagePreviewGenerator (class in nexusLIMS.extractors.plugins.preview_generators.image_preview) impl (nexusLIMS.db.models.TZDateTime attribute) insert_folder() (nexusLIMS.utils.labarchives.LabArchivesClient method) insert_log() (nexusLIMS.db.models.SessionLog method) insert_page() (nexusLIMS.utils.labarchives.LabArchivesClient method) insert_record_generation_event() (nexusLIMS.db.session_handler.Session method) Instrument (class in nexusLIMS.db.models) instrument (nexusLIMS.db.models.SessionLog attribute) (nexusLIMS.extractors.base.ExtractionContext attribute) (nexusLIMS.harvesters.reservation_event.ReservationEvent attribute)

instrument_db (in module nexusLIMS.instruments) instrument_id (nexusLIMS.extractors.base.InstrumentProfile attribute) (nexusLIMS.schemas.metadata.NexusMetadata attribute) instrument_obj (nexusLIMS.db.models.SessionLog attribute) instrument_pid (nexusLIMS.db.models.Instrument attribute) (nexusLIMS.exporters.base.ExportContext attribute) InstrumentAddScreen (class in nexusLIMS.tui.apps.instruments.screens) InstrumentEditScreen (class in nexusLIMS.tui.apps.instruments.screens) InstrumentListScreen (class in nexusLIMS.tui.apps.instruments.screens) InstrumentManagerApp (class in nexusLIMS.tui.apps.instruments.app) InstrumentProfile (class in nexusLIMS.extractors.base) InstrumentProfileRegistry (class in nexusLIMS.extractors.profiles) internal_id (nexusLIMS.harvesters.reservation_event.ReservationEvent attribute) is_string (nexusLIMS.extractors.base.FieldDefinition attribute) is_subpath() (in module nexusLIMS.utils.paths) is_valid (nexusLIMS.tui.common.widgets.FormField property) (nexusLIMS.tui.common.widgets.ValidatedInput property)

J

jeol_jem_642_profile (in module nexusLIMS.extractors.plugins.profiles.jeol_jem_642)

join_instrument_filestore_path() (in module nexusLIMS.utils.paths)

L

LABARCHIVES_ELN (nexusLIMS.db.enums.ExternalSystem attribute) labarchives_get_uid() (in module nexusLIMS.cli.config) LABARCHIVES_SCHEDULER (nexusLIMS.db.enums.ExternalSystem attribute) LabArchivesAuthenticationError LabArchivesClient (class in nexusLIMS.utils.labarchives) LabArchivesDestination (class in nexusLIMS.exporters.destinations.labarchives) LabArchivesError LabArchivesGetUidDialog (class in nexusLIMS.tui.apps.config.screens) LabArchivesNotFoundError LabArchivesPermissionError LabArchivesRateLimitError last_updated (nexusLIMS.harvesters.reservation_event.ReservationEvent attribute) last_verified_at (nexusLIMS.db.models.ExternalUserIdentifier attribute)

LazyGroup (class in nexusLIMS.cli.main) list_commands() (nexusLIMS.cli.main.LazyGroup method) list_experiments() (nexusLIMS.utils.elabftw.ELabFTWClient method) live_time (nexusLIMS.schemas.metadata.SpectrumMetadata attribute) load() (in module nexusLIMS.cli.config) localize_datetime() (nexusLIMS.db.models.Instrument method) localize_datetime_str() (nexusLIMS.db.models.Instrument method) location (nexusLIMS.db.models.Instrument attribute) lock_file_path (nexusLIMS.config.Settings property) log_dir_path (nexusLIMS.config.Settings property) logger (in module nexusLIMS.cli.config) (in module nexusLIMS.cli.manage_instruments) (in module nexusLIMS.cli.process_records) (in module nexusLIMS.schemas.units)

M

magnification (nexusLIMS.schemas.metadata.ImageMetadata attribute) main() (in module nexusLIMS.cli.config) (in module nexusLIMS.cli.main) (in module nexusLIMS.cli.manage_instruments) (in module nexusLIMS.cli.migrate) (in module nexusLIMS.cli.process_records) map_keys_with_units() (in module nexusLIMS.extractors.plugins.fei_emi) MARKDOWN (nexusLIMS.utils.elabftw.ContentType attribute) message (nexusLIMS.builder.preflight.CheckResult attribute) meta (nexusLIMS.schemas.activity.AcquisitionActivity attribute) metadata (nexusLIMS.exporters.base.ExportContext attribute) (nexusLIMS.exporters.base.ExportResult attribute) metadata_json (nexusLIMS.db.models.UploadLog attribute) mode (nexusLIMS.schemas.activity.AcquisitionActivity attribute) model_config (nexusLIMS.config.Settings attribute) (nexusLIMS.exporters.destinations.elabftw.ExtraField attribute) (nexusLIMS.schemas.metadata.ExtractionDetails attribute) (nexusLIMS.schemas.metadata.NexusMetadata attribute) (nexusLIMS.schemas.metadata.StagePosition attribute) module nexusLIMS nexusLIMS.__main__ nexusLIMS.builder nexusLIMS.builder.preflight nexusLIMS.builder.record_builder nexusLIMS.cli nexusLIMS.cli.config nexusLIMS.cli.main nexusLIMS.cli.manage_instruments nexusLIMS.cli.migrate nexusLIMS.cli.process_records nexusLIMS.config nexusLIMS.db nexusLIMS.db.engine nexusLIMS.db.enums nexusLIMS.db.migrations nexusLIMS.db.migrations.env nexusLIMS.db.migrations.utils nexusLIMS.db.migrations.versions nexusLIMS.db.migrations.versions.v1_4_3_initial_schema_baseline nexusLIMS.db.migrations.versions.v2_4_0a_add_upload_log_table nexusLIMS.db.migrations.versions.v2_4_0b_add_check_constraints nexusLIMS.db.migrations.versions.v2_5_0a_add_external_user_identifiers nexusLIMS.db.migrations.versions.v2_5_0b_remove_computer_fields nexusLIMS.db.models nexusLIMS.db.session_handler nexusLIMS.exporters nexusLIMS.exporters.base nexusLIMS.exporters.destinations nexusLIMS.exporters.destinations.cdcs nexusLIMS.exporters.destinations.elabftw nexusLIMS.exporters.destinations.labarchives nexusLIMS.exporters.registry nexusLIMS.exporters.strategies nexusLIMS.extractors nexusLIMS.extractors.base nexusLIMS.extractors.plugins nexusLIMS.extractors.plugins.basic_metadata nexusLIMS.extractors.plugins.digital_micrograph nexusLIMS.extractors.plugins.edax nexusLIMS.extractors.plugins.fei_emi nexusLIMS.extractors.plugins.orion_HIM_tif nexusLIMS.extractors.plugins.preview_generators nexusLIMS.extractors.plugins.preview_generators.hyperspy_preview nexusLIMS.extractors.plugins.preview_generators.image_preview nexusLIMS.extractors.plugins.preview_generators.text_preview nexusLIMS.extractors.plugins.preview_generators.tofwerk_pfib_preview nexusLIMS.extractors.plugins.profiles nexusLIMS.extractors.plugins.profiles.fei_titan_stem_643 nexusLIMS.extractors.plugins.profiles.fei_titan_tem_642 nexusLIMS.extractors.plugins.profiles.jeol_jem_642 nexusLIMS.extractors.plugins.quanta_tif nexusLIMS.extractors.plugins.tescan_tif nexusLIMS.extractors.plugins.tofwerk_pfib nexusLIMS.extractors.profiles nexusLIMS.extractors.registry nexusLIMS.extractors.utils nexusLIMS.extractors.xml_serialization nexusLIMS.harvesters nexusLIMS.harvesters.nemo nexusLIMS.harvesters.nemo.connector nexusLIMS.harvesters.nemo.exceptions nexusLIMS.harvesters.nemo.utils nexusLIMS.harvesters.reservation_event nexusLIMS.instruments nexusLIMS.schemas nexusLIMS.schemas.activity nexusLIMS.schemas.em_glossary nexusLIMS.schemas.metadata nexusLIMS.schemas.pint_types nexusLIMS.schemas.units nexusLIMS.tui nexusLIMS.tui.apps nexusLIMS.tui.apps.config nexusLIMS.tui.apps.config.app nexusLIMS.tui.apps.config.screens nexusLIMS.tui.apps.config.validators nexusLIMS.tui.apps.db_browser nexusLIMS.tui.apps.instruments nexusLIMS.tui.apps.instruments.app nexusLIMS.tui.apps.instruments.screens nexusLIMS.tui.apps.instruments.validators nexusLIMS.tui.common nexusLIMS.tui.common.base_app nexusLIMS.tui.common.base_screens nexusLIMS.tui.common.db_utils nexusLIMS.tui.common.validators nexusLIMS.tui.common.widgets nexusLIMS.tui.demo_helpers nexusLIMS.utils nexusLIMS.utils.cdcs nexusLIMS.utils.dicts nexusLIMS.utils.elabftw nexusLIMS.utils.files nexusLIMS.utils.labarchives nexusLIMS.utils.logging nexusLIMS.utils.network nexusLIMS.utils.paths nexusLIMS.utils.time

module (nexusLIMS.schemas.metadata.ExtractionDetails attribute) MsaExtractor (class in nexusLIMS.extractors.plugins.edax)

N

name (nexusLIMS.builder.preflight.CheckResult attribute) (nexusLIMS.db.models.Instrument property) (nexusLIMS.exporters.base.ExportDestination attribute) (nexusLIMS.exporters.destinations.cdcs.CDCSDestination attribute) (nexusLIMS.exporters.destinations.elabftw.ELabFTWDestination attribute) (nexusLIMS.exporters.destinations.elabftw.ExtraFieldsGroup attribute) (nexusLIMS.exporters.destinations.labarchives.LabArchivesDestination attribute) (nexusLIMS.extractors.base.BaseExtractor attribute) (nexusLIMS.extractors.base.PreviewGenerator attribute) (nexusLIMS.extractors.plugins.basic_metadata.BasicFileInfoExtractor attribute) (nexusLIMS.extractors.plugins.digital_micrograph.DM3Extractor attribute) (nexusLIMS.extractors.plugins.edax.MsaExtractor attribute) (nexusLIMS.extractors.plugins.edax.SpcExtractor attribute) (nexusLIMS.extractors.plugins.fei_emi.SerEmiExtractor attribute) (nexusLIMS.extractors.plugins.orion_HIM_tif.OrionTiffExtractor attribute) (nexusLIMS.extractors.plugins.preview_generators.hyperspy_preview.HyperSpyPreviewGenerator attribute) (nexusLIMS.extractors.plugins.preview_generators.image_preview.ImagePreviewGenerator attribute) (nexusLIMS.extractors.plugins.preview_generators.text_preview.TextPreviewGenerator attribute) (nexusLIMS.extractors.plugins.preview_generators.tofwerk_pfib_preview.TofwerkPfibPreviewGenerator attribute) (nexusLIMS.extractors.plugins.quanta_tif.QuantaTiffExtractor attribute) (nexusLIMS.extractors.plugins.tescan_tif.TescanTiffExtractor attribute) (nexusLIMS.extractors.plugins.tofwerk_pfib.TofwerkPfibExtractor attribute) NEMO (nexusLIMS.db.enums.ExternalSystem attribute) nemo_harvesters() (nexusLIMS.config.Settings method) NemoConnector (class in nexusLIMS.harvesters.nemo.connector) NemoHarvesterConfig (class in nexusLIMS.config) nexus_req() (in module nexusLIMS.utils.network) nexusLIMS module nexusLIMS.__main__ module nexusLIMS.builder module nexusLIMS.builder.preflight module nexusLIMS.builder.record_builder module nexusLIMS.cli module nexusLIMS.cli.config module nexusLIMS.cli.main module nexusLIMS.cli.manage_instruments module nexusLIMS.cli.migrate module nexusLIMS.cli.process_records module nexusLIMS.config module nexusLIMS.db module nexusLIMS.db.engine module nexusLIMS.db.enums module nexusLIMS.db.migrations module nexusLIMS.db.migrations.env module nexusLIMS.db.migrations.utils module nexusLIMS.db.migrations.versions module nexusLIMS.db.migrations.versions.v1_4_3_initial_schema_baseline module nexusLIMS.db.migrations.versions.v2_4_0a_add_upload_log_table module nexusLIMS.db.migrations.versions.v2_4_0b_add_check_constraints module nexusLIMS.db.migrations.versions.v2_5_0a_add_external_user_identifiers module nexusLIMS.db.migrations.versions.v2_5_0b_remove_computer_fields module nexusLIMS.db.models module nexusLIMS.db.session_handler module nexusLIMS.exporters module nexusLIMS.exporters.base module nexusLIMS.exporters.destinations module nexusLIMS.exporters.destinations.cdcs module nexusLIMS.exporters.destinations.elabftw module nexusLIMS.exporters.destinations.labarchives module nexusLIMS.exporters.registry module nexusLIMS.exporters.strategies module nexusLIMS.extractors module nexusLIMS.extractors.base module nexusLIMS.extractors.plugins module nexusLIMS.extractors.plugins.basic_metadata module nexusLIMS.extractors.plugins.digital_micrograph module nexusLIMS.extractors.plugins.edax module nexusLIMS.extractors.plugins.fei_emi module nexusLIMS.extractors.plugins.orion_HIM_tif module nexusLIMS.extractors.plugins.preview_generators module nexusLIMS.extractors.plugins.preview_generators.hyperspy_preview module nexusLIMS.extractors.plugins.preview_generators.image_preview module nexusLIMS.extractors.plugins.preview_generators.text_preview module nexusLIMS.extractors.plugins.preview_generators.tofwerk_pfib_preview module nexusLIMS.extractors.plugins.profiles module nexusLIMS.extractors.plugins.profiles.fei_titan_stem_643 module nexusLIMS.extractors.plugins.profiles.fei_titan_tem_642 module nexusLIMS.extractors.plugins.profiles.jeol_jem_642 module nexusLIMS.extractors.plugins.quanta_tif module nexusLIMS.extractors.plugins.tescan_tif module

nexusLIMS.extractors.plugins.tofwerk_pfib module nexusLIMS.extractors.profiles module nexusLIMS.extractors.registry module nexusLIMS.extractors.utils module nexusLIMS.extractors.xml_serialization module nexusLIMS.harvesters module nexusLIMS.harvesters.nemo module nexusLIMS.harvesters.nemo.connector module nexusLIMS.harvesters.nemo.exceptions module nexusLIMS.harvesters.nemo.utils module nexusLIMS.harvesters.reservation_event module nexusLIMS.instruments module nexusLIMS.schemas module nexusLIMS.schemas.activity module nexusLIMS.schemas.em_glossary module nexusLIMS.schemas.metadata module nexusLIMS.schemas.pint_types module nexusLIMS.schemas.units module nexusLIMS.tui module nexusLIMS.tui.apps module nexusLIMS.tui.apps.config module nexusLIMS.tui.apps.config.app module nexusLIMS.tui.apps.config.screens module nexusLIMS.tui.apps.config.validators module nexusLIMS.tui.apps.db_browser module nexusLIMS.tui.apps.instruments module nexusLIMS.tui.apps.instruments.app module nexusLIMS.tui.apps.instruments.screens module nexusLIMS.tui.apps.instruments.validators module nexusLIMS.tui.common module nexusLIMS.tui.common.base_app module nexusLIMS.tui.common.base_screens module nexusLIMS.tui.common.db_utils module nexusLIMS.tui.common.validators module nexusLIMS.tui.common.widgets module nexusLIMS.tui.demo_helpers module nexusLIMS.utils module nexusLIMS.utils.cdcs module nexusLIMS.utils.dicts module nexusLIMS.utils.elabftw module nexusLIMS.utils.files module nexusLIMS.utils.labarchives module nexusLIMS.utils.logging module nexusLIMS.utils.network module nexusLIMS.utils.paths module nexusLIMS.utils.time module nexuslims_extraction (nexusLIMS.schemas.metadata.NexusMetadata attribute) nexuslims_instrument_data_path (nexusLIMS.config.Settings property) NEXUSLIMS_TO_EMG_MAPPINGS (in module nexusLIMS.schemas.em_glossary) nexuslims_username (nexusLIMS.db.models.ExternalUserIdentifier attribute) NexusLIMSDBApp (class in nexusLIMS.tui.apps.db_browser) NexusLIMSTableViewerPane (class in nexusLIMS.tui.apps.db_browser) NexusMetadata (class in nexusLIMS.schemas.metadata) NO_CONSENT (nexusLIMS.db.enums.RecordStatus attribute) NO_FILES_FOUND (nexusLIMS.db.enums.RecordStatus attribute) NO_RESERVATION (nexusLIMS.db.enums.RecordStatus attribute) NoDataConsentError NoMatchingReservationError Normal (nexusLIMS.utils.elabftw.State attribute) normalize_quantity() (in module nexusLIMS.schemas.units) notes (nexusLIMS.db.models.ExternalUserIdentifier attribute) NumpadInput (class in nexusLIMS.tui.common.widgets) NX_CDCS_TOKEN (nexusLIMS.config.Settings attribute) NX_CDCS_URL (nexusLIMS.config.Settings attribute) NX_CERT_BUNDLE (nexusLIMS.config.Settings attribute) NX_CERT_BUNDLE_FILE (nexusLIMS.config.Settings attribute) NX_CLUSTERING_SENSITIVITY (nexusLIMS.config.Settings attribute) NX_DATA_PATH (nexusLIMS.config.Settings attribute) NX_DB_PATH (nexusLIMS.config.Settings attribute) NX_DISABLE_SSL_VERIFY (nexusLIMS.config.Settings attribute) NX_ELABFTW_API_KEY (nexusLIMS.config.Settings attribute) NX_ELABFTW_EXPERIMENT_CATEGORY (nexusLIMS.config.Settings attribute) NX_ELABFTW_EXPERIMENT_STATUS (nexusLIMS.config.Settings attribute) NX_ELABFTW_URL (nexusLIMS.config.Settings attribute) NX_EXPORT_STRATEGY (nexusLIMS.config.Settings attribute) NX_FILE_DELAY_DAYS (nexusLIMS.config.Settings attribute) NX_FILE_STRATEGY (nexusLIMS.config.Settings attribute) NX_IGNORE_PATTERNS (nexusLIMS.config.Settings attribute) NX_INSTRUMENT_DATA_PATH (nexusLIMS.config.Settings attribute) NX_LABARCHIVES_ACCESS_KEY_ID (nexusLIMS.config.Settings attribute) NX_LABARCHIVES_ACCESS_PASSWORD (nexusLIMS.config.Settings attribute) NX_LABARCHIVES_NOTEBOOK_ID (nexusLIMS.config.Settings attribute) NX_LABARCHIVES_URL (nexusLIMS.config.Settings attribute) NX_LABARCHIVES_USER_ID (nexusLIMS.config.Settings attribute) NX_LOCAL_PROFILES_PATH (nexusLIMS.config.Settings attribute) NX_LOG_PATH (nexusLIMS.config.Settings attribute) NX_RECORDS_PATH (nexusLIMS.config.Settings attribute)

O

OBO (in module nexusLIMS.schemas.em_glossary) on_add_complete() (nexusLIMS.tui.apps.instruments.screens.InstrumentListScreen method) on_button_pressed() (nexusLIMS.tui.apps.config.screens.ConfigScreen method) (nexusLIMS.tui.apps.instruments.screens.WelcomeDialog method) on_cancel_button() (nexusLIMS.tui.common.base_screens.BaseFormScreen method) on_edit_complete() (nexusLIMS.tui.apps.instruments.screens.InstrumentListScreen method) on_filter_changed() (nexusLIMS.tui.common.base_screens.BaseListScreen method) on_header_selected() (nexusLIMS.tui.common.base_screens.BaseListScreen method) on_input_changed() (nexusLIMS.tui.common.widgets.FormField method) on_key() (nexusLIMS.tui.common.widgets.NumpadInput method) on_mount() (nexusLIMS.tui.apps.config.app.ConfiguratorApp method) (nexusLIMS.tui.apps.config.screens.ConfigScreen method) (nexusLIMS.tui.apps.db_browser.NexusLIMSTableViewerPane method) (nexusLIMS.tui.apps.instruments.app.InstrumentManagerApp method) (nexusLIMS.tui.apps.instruments.screens.InstrumentAddScreen method) (nexusLIMS.tui.apps.instruments.screens.InstrumentEditScreen method) (nexusLIMS.tui.apps.instruments.screens.InstrumentListScreen method) (nexusLIMS.tui.common.base_app.BaseNexusApp method) (nexusLIMS.tui.common.base_screens.BaseListScreen method)

on_no() (nexusLIMS.tui.common.base_screens.ConfirmDialog method) on_row_selected() (nexusLIMS.tui.apps.instruments.screens.InstrumentListScreen method) (nexusLIMS.tui.common.base_screens.BaseListScreen method) on_row_selected_event() (nexusLIMS.tui.common.base_screens.BaseListScreen method) on_save() (nexusLIMS.tui.apps.instruments.screens.InstrumentAddScreen method) (nexusLIMS.tui.apps.instruments.screens.InstrumentEditScreen method) (nexusLIMS.tui.common.base_screens.BaseFormScreen method) on_save_button() (nexusLIMS.tui.common.base_screens.BaseFormScreen method) on_unmount() (nexusLIMS.tui.common.base_app.BaseNexusApp method) on_welcome_complete() (nexusLIMS.tui.apps.instruments.screens.InstrumentListScreen method) on_yes() (nexusLIMS.tui.common.base_screens.ConfirmDialog method) OrionTiffExtractor (class in nexusLIMS.extractors.plugins.orion_HIM_tif) output_key (nexusLIMS.extractors.base.FieldDefinition attribute)

P

parse_acquire_info() (in module nexusLIMS.extractors.plugins.fei_emi) parse_basic_info() (in module nexusLIMS.extractors.plugins.fei_emi) parse_data_type() (in module nexusLIMS.extractors.plugins.fei_emi) parse_dm3_eds_info() (in module nexusLIMS.extractors.plugins.digital_micrograph) parse_dm3_eels_info() (in module nexusLIMS.extractors.plugins.digital_micrograph) parse_dm3_microscope_info() (in module nexusLIMS.extractors.plugins.digital_micrograph) parse_dm3_spectrum_image_info() (in module nexusLIMS.extractors.plugins.digital_micrograph) parse_experimental_conditions() (in module nexusLIMS.extractors.plugins.fei_emi) parse_experimental_description() (in module nexusLIMS.extractors.plugins.fei_emi) parse_metadata() (in module nexusLIMS.extractors) parse_quantity() (in module nexusLIMS.schemas.units) parse_tecnai_metadata() (in module nexusLIMS.extractors.plugins.profiles.fei_titan_tem_642) parsers (nexusLIMS.extractors.base.InstrumentProfile attribute) passed (nexusLIMS.builder.preflight.CheckResult attribute) Pending (nexusLIMS.utils.elabftw.State attribute) PintQuantity (in module nexusLIMS.schemas.pint_types) pixel_height (nexusLIMS.schemas.metadata.ImageMetadata attribute) pixel_time (nexusLIMS.schemas.metadata.SpectrumImageMetadata attribute) pixel_width (nexusLIMS.schemas.metadata.ImageMetadata attribute) PLACEHOLDER_PREVIEW (in module nexusLIMS.extractors) position (nexusLIMS.exporters.destinations.elabftw.ExtraField attribute) PREFERRED_UNITS (in module nexusLIMS.schemas.units) PreflightError prepare_metadata_for_xml() (in module nexusLIMS.extractors.xml_serialization) PreviewGenerator (class in nexusLIMS.extractors.base) previews (nexusLIMS.schemas.activity.AcquisitionActivity attribute) previous_results (nexusLIMS.exporters.base.ExportContext attribute) priority (nexusLIMS.exporters.base.ExportDestination attribute) (nexusLIMS.exporters.destinations.cdcs.CDCSDestination attribute) (nexusLIMS.exporters.destinations.elabftw.ELabFTWDestination attribute) (nexusLIMS.exporters.destinations.labarchives.LabArchivesDestination attribute) (nexusLIMS.extractors.base.BaseExtractor attribute) (nexusLIMS.extractors.base.PreviewGenerator attribute) (nexusLIMS.extractors.plugins.basic_metadata.BasicFileInfoExtractor attribute) (nexusLIMS.extractors.plugins.digital_micrograph.DM3Extractor attribute) (nexusLIMS.extractors.plugins.edax.MsaExtractor attribute) (nexusLIMS.extractors.plugins.edax.SpcExtractor attribute) (nexusLIMS.extractors.plugins.fei_emi.SerEmiExtractor attribute) (nexusLIMS.extractors.plugins.orion_HIM_tif.OrionTiffExtractor attribute) (nexusLIMS.extractors.plugins.preview_generators.hyperspy_preview.HyperSpyPreviewGenerator attribute) (nexusLIMS.extractors.plugins.preview_generators.image_preview.ImagePreviewGenerator attribute) (nexusLIMS.extractors.plugins.preview_generators.text_preview.TextPreviewGenerator attribute) (nexusLIMS.extractors.plugins.preview_generators.tofwerk_pfib_preview.TofwerkPfibPreviewGenerator attribute) (nexusLIMS.extractors.plugins.quanta_tif.QuantaTiffExtractor attribute) (nexusLIMS.extractors.plugins.tescan_tif.TescanTiffExtractor attribute) (nexusLIMS.extractors.plugins.tofwerk_pfib.TofwerkPfibExtractor attribute)

process_bind_param() (nexusLIMS.db.models.TZDateTime method) process_new_records() (in module nexusLIMS.builder.record_builder) process_res_question_samples() (in module nexusLIMS.harvesters.nemo.utils) process_result_value() (nexusLIMS.db.models.TZDateTime method) process_revision_directives() (in module nexusLIMS.db.migrations.env) process_tecnai_microscope_info() (in module nexusLIMS.extractors.plugins.digital_micrograph) Processing (nexusLIMS.utils.elabftw.State attribute) project_id (nexusLIMS.harvesters.reservation_event.ReservationEvent attribute) project_name (nexusLIMS.harvesters.reservation_event.ReservationEvent attribute) project_ref (nexusLIMS.harvesters.reservation_event.ReservationEvent attribute) projects (nexusLIMS.harvesters.nemo.connector.NemoConnector attribute) property_tag (nexusLIMS.db.models.Instrument attribute)

Q

QuantaTiffExtractor (class in nexusLIMS.extractors.plugins.quanta_tif) quantity_to_xml_parts() (in module nexusLIMS.schemas.units)

QUDT_UNIT (in module nexusLIMS.schemas.units) QUDT_UNIT_TTL_PATH (in module nexusLIMS.schemas.units) QUDT_VERSION (in module nexusLIMS.schemas.units)

R

read_labarchives_env() (in module nexusLIMS.config) recipients (nexusLIMS.config.EmailConfig attribute) RECORD_GENERATION (nexusLIMS.db.enums.EventType attribute) record_id (nexusLIMS.db.models.UploadLog attribute) (nexusLIMS.exporters.base.ExportResult attribute) record_status (nexusLIMS.db.models.SessionLog attribute) record_url (nexusLIMS.db.models.UploadLog attribute) (nexusLIMS.exporters.base.ExportResult attribute) RecordBuildResult (class in nexusLIMS.builder.record_builder) records_dir_path (nexusLIMS.config.Settings property) RecordStatus (class in nexusLIMS.db.enums) refresh_data() (nexusLIMS.tui.common.base_screens.BaseListScreen method) refresh_settings() (in module nexusLIMS.config) register() (nexusLIMS.extractors.profiles.InstrumentProfileRegistry method) register_all_profiles() (in module nexusLIMS.extractors.plugins.profiles) register_extractor() (nexusLIMS.extractors.registry.ExtractorRegistry method) register_preview_generator() (nexusLIMS.extractors.registry.ExtractorRegistry method)

remove_dict_nones() (in module nexusLIMS.utils.dicts) remove_dtb_element() (in module nexusLIMS.utils.dicts) replace_instrument_data_path() (in module nexusLIMS.utils.paths) required (nexusLIMS.exporters.destinations.elabftw.ExtraField attribute) res_event_from_session() (in module nexusLIMS.harvesters.nemo) reservation_event (nexusLIMS.builder.record_builder.RecordBuildResult attribute) (nexusLIMS.exporters.base.ExportContext attribute) reservation_type (nexusLIMS.harvesters.reservation_event.ReservationEvent attribute) ReservationEvent (class in nexusLIMS.harvesters.reservation_event) revision (in module nexusLIMS.db.migrations.versions.v1_4_3_initial_schema_baseline) (in module nexusLIMS.db.migrations.versions.v2_4_0a_add_upload_log_table) (in module nexusLIMS.db.migrations.versions.v2_4_0b_add_check_constraints) (in module nexusLIMS.db.migrations.versions.v2_5_0a_add_external_user_identifiers) (in module nexusLIMS.db.migrations.versions.v2_5_0b_remove_computer_fields) rotation (nexusLIMS.schemas.metadata.StagePosition attribute) run_migrations_offline() (in module nexusLIMS.db.migrations.env) run_migrations_online() (in module nexusLIMS.db.migrations.env) run_preflight_checks() (in module nexusLIMS.builder.preflight)

S

sample_details (nexusLIMS.harvesters.reservation_event.ReservationEvent attribute) sample_elements (nexusLIMS.harvesters.reservation_event.ReservationEvent attribute) sample_name (nexusLIMS.harvesters.reservation_event.ReservationEvent attribute) sample_pid (nexusLIMS.harvesters.reservation_event.ReservationEvent attribute) scan_mode (nexusLIMS.schemas.metadata.SpectrumImageMetadata attribute) scan_rotation (nexusLIMS.schemas.metadata.ImageMetadata attribute) search_records() (in module nexusLIMS.utils.cdcs) section (nexusLIMS.extractors.base.FieldDefinition attribute) send_error_notification() (in module nexusLIMS.cli.process_records) sender (nexusLIMS.config.EmailConfig attribute) SerEmiExtractor (class in nexusLIMS.extractors.plugins.fei_emi) serialize_quantity() (in module nexusLIMS.schemas.units) serialize_quantity_to_xml() (in module nexusLIMS.extractors.xml_serialization) Session (class in nexusLIMS.db.session_handler) session_identifier (nexusLIMS.db.models.SessionLog attribute) (nexusLIMS.db.models.UploadLog attribute) (nexusLIMS.exporters.base.ExportContext attribute) session_logs (nexusLIMS.db.models.Instrument attribute) SessionLog (class in nexusLIMS.db.models) set_nested_dict_value() (in module nexusLIMS.utils.dicts) set_suggestions() (nexusLIMS.tui.common.widgets.AutocompleteInput method) Settings (class in nexusLIMS.config) settings (in module nexusLIMS.config) setup_file_logging() (in module nexusLIMS.cli.process_records) setup_loggers() (in module nexusLIMS.utils.logging) setup_params (nexusLIMS.schemas.activity.AcquisitionActivity attribute) severity (nexusLIMS.builder.preflight.CheckResult attribute) show_error() (nexusLIMS.tui.common.base_app.BaseNexusApp method) show_success() (nexusLIMS.tui.common.base_app.BaseNexusApp method) show_warning() (nexusLIMS.tui.common.base_app.BaseNexusApp method) sig_to_thumbnail() (in module nexusLIMS.extractors.plugins.preview_generators.hyperspy_preview) signal_index (nexusLIMS.extractors.base.ExtractionContext attribute) sleep (in module nexusLIMS.utils.time) smtp_host (nexusLIMS.config.EmailConfig attribute) smtp_password (nexusLIMS.config.EmailConfig attribute) smtp_port (nexusLIMS.config.EmailConfig attribute) smtp_username (nexusLIMS.config.EmailConfig attribute) sort_dict() (in module nexusLIMS.utils.dicts) source_key (nexusLIMS.extractors.base.FieldDefinition attribute) SpcExtractor (class in nexusLIMS.extractors.plugins.edax) SPECTRUM_IMAGE_LOGO (in module nexusLIMS.extractors.plugins.preview_generators.hyperspy_preview) SpectrumImageMetadata (class in nexusLIMS.schemas.metadata) SpectrumMetadata (class in nexusLIMS.schemas.metadata) split_fei_metadata_units() (in module nexusLIMS.extractors.plugins.fei_emi) stage_position (nexusLIMS.schemas.metadata.ImageMetadata attribute) StagePosition (class in nexusLIMS.schemas.metadata)

START (nexusLIMS.db.enums.EventType attribute) start (nexusLIMS.schemas.activity.AcquisitionActivity attribute) start_time (nexusLIMS.harvesters.reservation_event.ReservationEvent attribute) starting_energy (nexusLIMS.schemas.metadata.SpectrumMetadata attribute) State (class in nexusLIMS.utils.elabftw) store_external_id() (in module nexusLIMS.db.models) store_setup_params() (nexusLIMS.schemas.activity.AcquisitionActivity method) store_unique_metadata() (nexusLIMS.schemas.activity.AcquisitionActivity method) store_unique_params() (nexusLIMS.schemas.activity.AcquisitionActivity method) strftime() (nexusLIMS.harvesters.nemo.connector.NemoConnector method) strftime_fmt (nexusLIMS.config.NemoHarvesterConfig attribute) strptime() (nexusLIMS.harvesters.nemo.connector.NemoConnector method) strptime_fmt (nexusLIMS.config.NemoHarvesterConfig attribute) success (nexusLIMS.db.models.UploadLog attribute) (nexusLIMS.exporters.base.ExportResult attribute) supported_extensions (nexusLIMS.extractors.base.BaseExtractor attribute) (nexusLIMS.extractors.base.PreviewGenerator attribute) (nexusLIMS.extractors.plugins.basic_metadata.BasicFileInfoExtractor attribute) (nexusLIMS.extractors.plugins.digital_micrograph.DM3Extractor attribute) (nexusLIMS.extractors.plugins.edax.MsaExtractor attribute) (nexusLIMS.extractors.plugins.edax.SpcExtractor attribute) (nexusLIMS.extractors.plugins.fei_emi.SerEmiExtractor attribute) (nexusLIMS.extractors.plugins.orion_HIM_tif.OrionTiffExtractor attribute) (nexusLIMS.extractors.plugins.preview_generators.hyperspy_preview.HyperSpyPreviewGenerator attribute) (nexusLIMS.extractors.plugins.preview_generators.image_preview.ImagePreviewGenerator attribute) (nexusLIMS.extractors.plugins.preview_generators.text_preview.TextPreviewGenerator attribute) (nexusLIMS.extractors.plugins.preview_generators.tofwerk_pfib_preview.TofwerkPfibPreviewGenerator attribute) (nexusLIMS.extractors.plugins.quanta_tif.QuantaTiffExtractor attribute) (nexusLIMS.extractors.plugins.tescan_tif.TescanTiffExtractor attribute) (nexusLIMS.extractors.plugins.tofwerk_pfib.TofwerkPfibExtractor attribute) supports() (nexusLIMS.extractors.base.BaseExtractor method) (nexusLIMS.extractors.base.PreviewGenerator method) (nexusLIMS.extractors.plugins.basic_metadata.BasicFileInfoExtractor method) (nexusLIMS.extractors.plugins.digital_micrograph.DM3Extractor method) (nexusLIMS.extractors.plugins.edax.MsaExtractor method) (nexusLIMS.extractors.plugins.edax.SpcExtractor method) (nexusLIMS.extractors.plugins.fei_emi.SerEmiExtractor method) (nexusLIMS.extractors.plugins.orion_HIM_tif.OrionTiffExtractor method) (nexusLIMS.extractors.plugins.preview_generators.hyperspy_preview.HyperSpyPreviewGenerator method) (nexusLIMS.extractors.plugins.preview_generators.image_preview.ImagePreviewGenerator method) (nexusLIMS.extractors.plugins.preview_generators.text_preview.TextPreviewGenerator method) (nexusLIMS.extractors.plugins.preview_generators.tofwerk_pfib_preview.TofwerkPfibPreviewGenerator method) (nexusLIMS.extractors.plugins.quanta_tif.QuantaTiffExtractor method) (nexusLIMS.extractors.plugins.tescan_tif.TescanTiffExtractor method) (nexusLIMS.extractors.plugins.tofwerk_pfib.TofwerkPfibExtractor method) suppress_zero (nexusLIMS.extractors.base.FieldDefinition attribute)

T

takeoff_angle (nexusLIMS.schemas.metadata.SpectrumMetadata attribute) target_metadata (in module nexusLIMS.db.migrations.env) target_unit (nexusLIMS.extractors.base.FieldDefinition attribute) TESCAN_TIFF_TAG (in module nexusLIMS.extractors.plugins.tescan_tif) TescanTiffExtractor (class in nexusLIMS.extractors.plugins.tescan_tif) TEST_MODE (in module nexusLIMS.config) text_to_thumbnail() (in module nexusLIMS.extractors.plugins.preview_generators.text_preview) TextPreviewGenerator (class in nexusLIMS.extractors.plugins.preview_generators.text_preview) tilt_alpha (nexusLIMS.schemas.metadata.StagePosition attribute) tilt_beta (nexusLIMS.schemas.metadata.StagePosition attribute) timestamp (nexusLIMS.db.models.SessionLog attribute) (nexusLIMS.db.models.UploadLog attribute) (nexusLIMS.exporters.base.ExportResult attribute)

timezone (nexusLIMS.db.models.Instrument property) timezone_str (nexusLIMS.db.models.Instrument attribute) TO_BE_BUILT (nexusLIMS.db.enums.RecordStatus attribute) to_dict() (nexusLIMS.db.models.Instrument method) to_json() (nexusLIMS.db.models.Instrument method) TofwerkPfibExtractor (class in nexusLIMS.extractors.plugins.tofwerk_pfib) TofwerkPfibPreviewGenerator (class in nexusLIMS.extractors.plugins.preview_generators.tofwerk_pfib_preview) token (nexusLIMS.config.NemoHarvesterConfig attribute) tools (nexusLIMS.harvesters.nemo.connector.NemoConnector attribute) transformations (nexusLIMS.extractors.base.InstrumentProfile attribute) try_getting_dict_value() (in module nexusLIMS.utils.dicts) type (nexusLIMS.exporters.destinations.elabftw.ExtraField attribute) tz (nexusLIMS.config.NemoHarvesterConfig attribute) TZDateTime (class in nexusLIMS.db.models)

U

unextracted_preview_map (in module nexusLIMS.extractors) unique_meta (nexusLIMS.schemas.activity.AcquisitionActivity attribute) unique_params (nexusLIMS.schemas.activity.AcquisitionActivity attribute) update_experiment() (nexusLIMS.utils.elabftw.ELabFTWClient method) update_session_status() (nexusLIMS.db.session_handler.Session method) update_ui() (nexusLIMS.tui.apps.db_browser.NexusLIMSDBApp method) upgrade() (in module nexusLIMS.db.migrations.versions.v1_4_3_initial_schema_baseline) (in module nexusLIMS.db.migrations.versions.v2_4_0a_add_upload_log_table) (in module nexusLIMS.db.migrations.versions.v2_4_0b_add_check_constraints) (in module nexusLIMS.db.migrations.versions.v2_5_0a_add_external_user_identifiers) (in module nexusLIMS.db.migrations.versions.v2_5_0b_remove_computer_fields) upload_file_to_experiment() (nexusLIMS.utils.elabftw.ELabFTWClient method)

upload_record_content() (in module nexusLIMS.utils.cdcs) upload_record_files() (in module nexusLIMS.utils.cdcs) UploadLog (class in nexusLIMS.db.models) ureg (in module nexusLIMS.schemas.units) url (nexusLIMS.harvesters.reservation_event.ReservationEvent attribute) use_tls (nexusLIMS.config.EmailConfig attribute) user (nexusLIMS.db.models.SessionLog attribute) (nexusLIMS.exporters.base.ExportContext attribute) user_full_name (nexusLIMS.harvesters.reservation_event.ReservationEvent attribute) username (nexusLIMS.harvesters.reservation_event.ReservationEvent attribute) users (nexusLIMS.harvesters.nemo.connector.NemoConnector attribute) users_by_username (nexusLIMS.harvesters.nemo.connector.NemoConnector attribute)

V

validate_api_url_unique() (in module nexusLIMS.tui.apps.instruments.validators) validate_config() (nexusLIMS.exporters.base.ExportDestination method) (nexusLIMS.exporters.destinations.cdcs.CDCSDestination method) (nexusLIMS.exporters.destinations.elabftw.ELabFTWDestination method) (nexusLIMS.exporters.destinations.labarchives.LabArchivesDestination method) validate_data_type_not_empty() (nexusLIMS.schemas.metadata.NexusMetadata class method) validate_float_nonneg() (in module nexusLIMS.tui.apps.config.validators) validate_float_positive() (in module nexusLIMS.tui.apps.config.validators) validate_form() (nexusLIMS.tui.apps.instruments.screens.InstrumentAddScreen method) (nexusLIMS.tui.apps.instruments.screens.InstrumentEditScreen method) (nexusLIMS.tui.common.base_screens.BaseFormScreen method) validate_harvester() (in module nexusLIMS.tui.apps.instruments.validators) validate_instrument_pid() (in module nexusLIMS.tui.apps.instruments.validators) validate_ip_address() (in module nexusLIMS.tui.common.validators) validate_iso_timestamp() (nexusLIMS.schemas.metadata.NexusMetadata class method) validate_location() (in module nexusLIMS.tui.apps.instruments.validators) validate_max_length() (in module nexusLIMS.tui.common.validators) validate_nemo_address() (in module nexusLIMS.tui.apps.config.validators) validate_nx_meta() (in module nexusLIMS.extractors)

validate_optional_iana_timezone() (in module nexusLIMS.tui.apps.config.validators) validate_optional_int() (in module nexusLIMS.tui.apps.config.validators) validate_optional_url() (in module nexusLIMS.tui.apps.config.validators) validate_path() (in module nexusLIMS.tui.common.validators) validate_property_tag() (in module nexusLIMS.tui.apps.instruments.validators) validate_record() (in module nexusLIMS.builder.record_builder) validate_required() (in module nexusLIMS.tui.common.validators) validate_smtp_port() (in module nexusLIMS.tui.apps.config.validators) validate_spectrum_image_fields() (nexusLIMS.schemas.metadata.SpectrumImageMetadata method) validate_timezone() (in module nexusLIMS.tui.common.validators) validate_trailing_slash() (nexusLIMS.config.NemoHarvesterConfig class method) validate_url() (in module nexusLIMS.tui.common.validators) validate_value() (nexusLIMS.tui.common.widgets.ValidatedInput method) ValidatedInput (class in nexusLIMS.tui.common.widgets) value (nexusLIMS.exporters.destinations.elabftw.ExtraField attribute) (nexusLIMS.tui.common.widgets.FormField property) verify_table_integrity() (in module nexusLIMS.db.migrations.utils) version (nexusLIMS.schemas.metadata.ExtractionDetails attribute) vertical_field_width (nexusLIMS.schemas.metadata.ImageMetadata attribute)

W

WAITING_FOR_END (nexusLIMS.db.enums.RecordStatus attribute) warnings (nexusLIMS.schemas.activity.AcquisitionActivity attribute) (nexusLIMS.schemas.metadata.NexusMetadata attribute)

was_successfully_exported() (in module nexusLIMS.exporters) WelcomeDialog (class in nexusLIMS.tui.apps.instruments.screens) working_distance (nexusLIMS.schemas.metadata.ImageMetadata attribute) write_usage_event_to_session_log() (nexusLIMS.harvesters.nemo.connector.NemoConnector method)

X

x (nexusLIMS.schemas.metadata.StagePosition attribute) xml_file_path (nexusLIMS.exporters.base.ExportContext attribute)

xml_text (nexusLIMS.builder.record_builder.RecordBuildResult attribute) XSD_PATH (in module nexusLIMS.builder.record_builder)

Y

y (nexusLIMS.schemas.metadata.StagePosition attribute)

Z

z (nexusLIMS.schemas.metadata.StagePosition attribute)

ZEISS_TIFF_TAG (in module nexusLIMS.extractors.plugins.orion_HIM_tif)