Index

A

AcquisitionActivity (class in nexusLIMS.schemas.activity) add_annotation_markers() (in module nexusLIMS.extractors.thumbnail_generator)

add_file() (nexusLIMS.schemas.activity.AcquisitionActivity method) as_xml() (nexusLIMS.schemas.activity.AcquisitionActivity method) AuthenticationError

B

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) build_service() (in module nexusLIMS.harvester.google_calendar)

C

category_value (nexusLIMS.harvester.google_calendar.GCalendarEvent attribute)

cluster_filelist_mtimes() (in module nexusLIMS.schemas.activity) created_by (nexusLIMS.harvester.google_calendar.GCalendarEvent attribute)

D

delete_record() (in module nexusLIMS.cdcs) down_sample_image() (in module nexusLIMS.extractors.thumbnail_generator) dry_run_file_find() (in module nexusLIMS.builder.record_builder)

dry_run_get_calendar_event() (in module nexusLIMS.builder.record_builder) dump_calendars() (in module nexusLIMS.harvester.sharepoint_calendar) dump_record() (in module nexusLIMS.builder.record_builder)

E

end_time (nexusLIMS.harvester.google_calendar.GCalendarEvent attribute)

experiment_purpose (nexusLIMS.harvester.google_calendar.GCalendarEvent attribute)

F

fetch_dict() (in module nexusLIMS.harvester.google_calendar) fetch_xml() (in module nexusLIMS.harvester.sharepoint_calendar) find_dirs_by_mtime() (in module nexusLIMS.utils)

find_files_by_mtime() (in module nexusLIMS.utils) flatten_dict() (in module nexusLIMS.extractors) from_dict() (nexusLIMS.harvester.google_calendar.GCalendarEvent class method)

G

GCalendarEvent (class in nexusLIMS.harvester.google_calendar) get_auth() (in module nexusLIMS.harvester.sharepoint_calendar) get_config() (in module nexusLIMS) get_dm3_metadata() (in module nexusLIMS.extractors.digital_micrograph) get_emi_from_ser() (in module nexusLIMS.extractors.fei_emi) get_events() (in module nexusLIMS.harvester.sharepoint_calendar) get_files() (in module nexusLIMS.builder.record_builder) get_from_db() (in module nexusLIMS.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_instrument_db() (in module nexusLIMS.instruments) get_nested_dict_key() (in module nexusLIMS.utils) get_nested_dict_value() (in module nexusLIMS.utils) get_nested_dict_value_by_path() (in module nexusLIMS.utils) get_nist_div_and_group() (in module nexusLIMS.utils) get_pre_path() (in module nexusLIMS.extractors.digital_micrograph) get_quanta_metadata() (in module nexusLIMS.extractors.quanta_tif) get_ser_metadata() (in module nexusLIMS.extractors.fei_emi) get_sessions_to_build() (in module nexusLIMS.db.session_handler) get_template_id() (in module nexusLIMS.cdcs) get_workspace_id() (in module nexusLIMS.cdcs) gnu_find_files_by_mtime() (in module nexusLIMS.utils)

I

insert_record_generation_event() (nexusLIMS.db.session_handler.Session method) Instrument (class in nexusLIMS.instruments)

instrument (nexusLIMS.harvester.google_calendar.GCalendarEvent attribute) instrument_db (in module nexusLIMS.instruments) is_subpath() (in module nexusLIMS.utils)

L

local_datetime() (in module nexusLIMS.utils)

M

make_db_query() (in module nexusLIMS.db) map_keys() (in module nexusLIMS.extractors.fei_emi) module nexusLIMS nexusLIMS.builder nexusLIMS.builder.record_builder nexusLIMS.cdcs nexusLIMS.db nexusLIMS.db.session_handler nexusLIMS.extractors nexusLIMS.extractors.digital_micrograph nexusLIMS.extractors.fei_emi nexusLIMS.extractors.quanta_tif nexusLIMS.extractors.thumbnail_generator nexusLIMS.harvester nexusLIMS.harvester.google_calendar nexusLIMS.harvester.sharepoint_calendar nexusLIMS.instruments nexusLIMS.schemas nexusLIMS.schemas.activity nexusLIMS.utils

N

nexus_req() (in module nexusLIMS.utils) nexusLIMS module nexusLIMS.builder module nexusLIMS.builder.record_builder module nexusLIMS.cdcs module nexusLIMS.db module nexusLIMS.db.session_handler module nexusLIMS.extractors module nexusLIMS.extractors.digital_micrograph module nexusLIMS.extractors.fei_emi module

nexusLIMS.extractors.quanta_tif module nexusLIMS.extractors.thumbnail_generator module nexusLIMS.harvester module nexusLIMS.harvester.google_calendar module nexusLIMS.harvester.sharepoint_calendar module nexusLIMS.instruments module nexusLIMS.schemas module nexusLIMS.schemas.activity module nexusLIMS.utils module

P

parse_642_jeol() (in module nexusLIMS.extractors.digital_micrograph) parse_642_titan() (in module nexusLIMS.extractors.digital_micrograph) parse_643_titan() (in module nexusLIMS.extractors.digital_micrograph) parse_acquire_info() (in module nexusLIMS.extractors.fei_emi) parse_beam_info() (in module nexusLIMS.extractors.quanta_tif) parse_data_type() (in module nexusLIMS.extractors.fei_emi) parse_det_info() (in module nexusLIMS.extractors.quanta_tif) parse_dm3_eds_info() (in module nexusLIMS.extractors.digital_micrograph) parse_dm3_eels_info() (in module nexusLIMS.extractors.digital_micrograph) parse_dm3_microscope_info() (in module nexusLIMS.extractors.digital_micrograph)

parse_dm3_spectrum_image_info() (in module nexusLIMS.extractors.digital_micrograph) parse_experimental_conditions() (in module nexusLIMS.extractors.fei_emi) parse_experimental_description() (in module nexusLIMS.extractors.fei_emi) parse_metadata() (in module nexusLIMS.extractors) parse_nx_meta() (in module nexusLIMS.extractors.quanta_tif) parse_scan_info() (in module nexusLIMS.extractors.quanta_tif) parse_system_info() (in module nexusLIMS.extractors.quanta_tif) parse_xml() (in module nexusLIMS.utils) process_new_records() (in module nexusLIMS.builder.record_builder) process_tecnai_microscope_info() (in module nexusLIMS.extractors.digital_micrograph) project_id (nexusLIMS.harvester.google_calendar.GCalendarEvent attribute)

S

sample_details (nexusLIMS.harvester.google_calendar.GCalendarEvent attribute) Session (class in nexusLIMS.db.session_handler) SessionLog (class in nexusLIMS.db.session_handler) set_nested_dict_value() (in module nexusLIMS.utils) setup_loggers() (in module nexusLIMS.utils)

sig_to_thumbnail() (in module nexusLIMS.extractors.thumbnail_generator) split_fei_metadata_units() (in module nexusLIMS.extractors.fei_emi) start_time (nexusLIMS.harvester.google_calendar.GCalendarEvent attribute) store_setup_params() (nexusLIMS.schemas.activity.AcquisitionActivity method) store_unique_metadata() (nexusLIMS.schemas.activity.AcquisitionActivity method) store_unique_params() (nexusLIMS.schemas.activity.AcquisitionActivity method)

T

title (nexusLIMS.harvester.google_calendar.GCalendarEvent attribute)

try_getting_dict_value() (in module nexusLIMS.utils)

U

update_session_status() (nexusLIMS.db.session_handler.Session method) updated (nexusLIMS.harvester.google_calendar.GCalendarEvent attribute)

upload_record_content() (in module nexusLIMS.cdcs) upload_record_files() (in module nexusLIMS.cdcs) username (nexusLIMS.harvester.google_calendar.GCalendarEvent attribute)

V

validate_config() (in module nexusLIMS)

validate_record() (in module nexusLIMS.builder.record_builder)

X

XSLT_PATH (in module nexusLIMS.builder.record_builder)