Index

Symbols

--app <app> flexiznam-add-password command line option --config_folder <config_folder> flexiznam-config command line option --conflicts <conflicts> flexiznam-yaml-to-flexilims command line option --flexilims_username <flexilims_username> flexiznam-add-mouse command line option --mcms_animal_name <mcms_animal_name> flexiznam-add-mouse command line option --mcms_username <mcms_username> flexiznam-add-mouse command line option --mouse_name <mouse_name> flexiznam-add-mouse command line option --no-overwrite flexiznam-process-yaml command line option --no-update flexiznam-config command line option --overwrite flexiznam-process-yaml command line option --password <password> flexiznam-add-password command line option --password_file <password_file> flexiznam-add-password command line option --project_id <project_id> flexiznam-add-mouse command line option --raw_data_folder <raw_data_folder> flexiznam-process-yaml command line option flexiznam-yaml-to-flexilims command line option --source_yaml <source_yaml> flexiznam-process-yaml command line option flexiznam-yaml-to-flexilims command line option

--target_yaml <target_yaml> flexiznam-process-yaml command line option --template <template> flexiznam-config command line option --update flexiznam-config command line option --username <username> flexiznam-add-password command line option -a flexiznam-add-password command line option -c flexiznam-yaml-to-flexilims command line option -m flexiznam-add-mouse command line option -p flexiznam-add-mouse command line option flexiznam-add-password command line option -r flexiznam-process-yaml command line option flexiznam-yaml-to-flexilims command line option -s flexiznam-process-yaml command line option flexiznam-yaml-to-flexilims command line option -t flexiznam-config command line option flexiznam-process-yaml command line option -u flexiznam-add-password command line option

A

add_dataset() (in module flexiznam.main) add_entity() (in module flexiznam.main) add_experimental_session() (in module flexiznam.main) add_mouse() (in module flexiznam.main)

add_password() (in module flexiznam.config.config_tools) add_recording() (in module flexiznam.main) add_sample() (in module flexiznam.main) associated_files() (flexiznam.schema.datasets.Dataset method)

C

CameraData (class in flexiznam.schema.camera_data) clean_dictionary_recursively() (in module flexiznam.utils) clean_yaml() (in module flexiznam.camp.sync_data) compare_series() (in module flexiznam.utils)

ConfigurationError create_config() (in module flexiznam.config.config_tools) create_dataset() (in module flexiznam.camp.sync_data) create_sample_datasets() (in module flexiznam.camp.sync_data)

D

Dataset (class in flexiznam.schema.datasets) DATASET_TYPE (flexiznam.schema.camera_data.CameraData attribute) dataset_type (flexiznam.schema.datasets.Dataset property) DATASET_TYPE (flexiznam.schema.harp_data.HarpData attribute) (flexiznam.schema.microscopy_data.MicroscopyData attribute) (flexiznam.schema.scanimage_data.ScanimageData attribute)

DatasetError download_mouse_info() (in module flexiznam.mcms.main)

F

find_xxerrorxx() (in module flexiznam.camp.sync_data) flexilims_report() (flexiznam.schema.datasets.Dataset method) flexilims_status() (flexiznam.schema.datasets.Dataset method) FlexilimsError flexiznam module flexiznam-add-mouse command line option --flexilims_username <flexilims_username> --mcms_animal_name <mcms_animal_name> --mcms_username <mcms_username> --mouse_name <mouse_name> --project_id <project_id> -m -p flexiznam-add-password command line option --app <app> --password <password> --password_file <password_file> --username <username> -a -p -u flexiznam-config command line option --config_folder <config_folder> --no-update --template <template> --update -t flexiznam-process-yaml command line option --no-overwrite --overwrite --raw_data_folder <raw_data_folder> --source_yaml <source_yaml> --target_yaml <target_yaml> -r -s -t flexiznam-yaml-to-flexilims command line option --conflicts <conflicts> --raw_data_folder <raw_data_folder> --source_yaml <source_yaml> -c -r -s

flexiznam.camp module flexiznam.camp.sync_data module flexiznam.config module flexiznam.config.config_tools module flexiznam.config.default_config module flexiznam.errors module flexiznam.main module flexiznam.mcms module flexiznam.mcms.main module flexiznam.schema module flexiznam.schema.camera_data module flexiznam.schema.datasets module flexiznam.schema.harp_data module flexiznam.schema.microscopy_data module flexiznam.schema.scanimage_data module flexiznam.utils module format() (flexiznam.schema.datasets.Dataset method) format_results() (in module flexiznam.main) from_flexilims() (flexiznam.schema.camera_data.CameraData method) (flexiznam.schema.datasets.Dataset static method) (flexiznam.schema.harp_data.HarpData class method) (flexiznam.schema.microscopy_data.MicroscopyData method) (flexiznam.schema.scanimage_data.ScanimageData method) from_folder() (flexiznam.schema.camera_data.CameraData static method) (flexiznam.schema.datasets.Dataset class method) (flexiznam.schema.harp_data.HarpData class method) (flexiznam.schema.microscopy_data.MicroscopyData static method) (flexiznam.schema.scanimage_data.ScanimageData static method) from_origin() (flexiznam.schema.datasets.Dataset static method)

G

generate_name() (in module flexiznam.main) get_children() (in module flexiznam.main) get_datasets() (in module flexiznam.main) get_datatype() (in module flexiznam.main) get_entities() (in module flexiznam.main) get_entity() (in module flexiznam.main)

get_experimental_sessions() (in module flexiznam.main) get_flexilims_entry() (flexiznam.schema.datasets.Dataset method) get_flexilims_session() (in module flexiznam.main) get_id() (in module flexiznam.main) get_mouse_df() (in module flexiznam.mcms.main) get_password() (in module flexiznam.config.config_tools) get_path() (in module flexiznam.main)

H

HarpData (class in flexiznam.schema.harp_data)

I

is_raw (flexiznam.schema.datasets.Dataset property) is_valid() (flexiznam.schema.camera_data.CameraData method) (flexiznam.schema.datasets.Dataset method) (flexiznam.schema.harp_data.HarpData method) (flexiznam.schema.microscopy_data.MicroscopyData method) (flexiznam.schema.scanimage_data.ScanimageData method)

L

load_param() (in module flexiznam.config.config_tools)

M

MicroscopyData (class in flexiznam.schema.microscopy_data) module flexiznam flexiznam.camp flexiznam.camp.sync_data flexiznam.config flexiznam.config.config_tools flexiznam.config.default_config flexiznam.errors flexiznam.main flexiznam.mcms flexiznam.mcms.main flexiznam.schema flexiznam.schema.camera_data flexiznam.schema.datasets flexiznam.schema.harp_data flexiznam.schema.microscopy_data flexiznam.schema.scanimage_data flexiznam.utils

N

name (flexiznam.schema.datasets.Dataset property)

NameNotUniqueError

P

parse_dataset_name() (flexiznam.schema.datasets.Dataset static method) parse_yaml() (in module flexiznam.camp.sync_data) path_full (flexiznam.schema.datasets.Dataset property)

path_root (flexiznam.schema.datasets.Dataset property) project (flexiznam.schema.datasets.Dataset property) project_id (flexiznam.schema.datasets.Dataset property)

R

read_dataset() (in module flexiznam.camp.sync_data) read_level() (in module flexiznam.camp.sync_data)

read_recording() (in module flexiznam.camp.sync_data) read_sample() (in module flexiznam.camp.sync_data)

S

ScanimageData (class in flexiznam.schema.scanimage_data)

SUBCLASSES (flexiznam.schema.datasets.Dataset attribute) SyncYmlError

T

tif_files (flexiznam.schema.scanimage_data.ScanimageData property)

trim_paths() (in module flexiznam.camp.sync_data)

U

update_config() (in module flexiznam.config.config_tools) update_entity() (in module flexiznam.main)

update_flexilims() (flexiznam.schema.datasets.Dataset method) upload_yaml() (in module flexiznam.camp.sync_data)

V

VALID_EXTENSIONS (flexiznam.schema.camera_data.CameraData attribute) (flexiznam.schema.microscopy_data.MicroscopyData attribute)

VIDEO_EXTENSIONS (flexiznam.schema.camera_data.CameraData attribute)

W

write_session_data_as_yaml() (in module flexiznam.camp.sync_data)