Index

A

add() (bioimageit_core.containers.CmdSelectContainer method), [1] (bioimageit_core.containers.tools_containers.CmdSelectContainer method), [1] add_input() (bioimageit_core.containers.data_containers.ProcessedData method) (bioimageit_core.containers.data_containers.Run method) (bioimageit_core.containers.ProcessedData method) (bioimageit_core.containers.Run method) (bioimageit_core.containers.runners_containers.JobInputs method) add_input_() (bioimageit_core.containers.data_containers.ProcessedData method) (bioimageit_core.containers.ProcessedData method)

add_job_input() (bioimageit_core.containers.runners_containers.JobInputs method) add_observer() (bioimageit_core.core.observer.Observable method) add_parameter() (bioimageit_core.containers.data_containers.Run method) (bioimageit_core.containers.Run method) author (bioimageit_core.containers.Data attribute) (bioimageit_core.containers.data_containers.Data attribute) (bioimageit_core.containers.data_containers.Experiment attribute) (bioimageit_core.containers.Experiment attribute)

B

bioimageit_core.containers module bioimageit_core.containers.data_containers module bioimageit_core.containers.runners_containers module bioimageit_core.containers.tools_containers module bioimageit_core.core module bioimageit_core.core.config module bioimageit_core.core.exceptions module bioimageit_core.core.factory module bioimageit_core.core.log_observer module

bioimageit_core.core.observer module bioimageit_core.core.serialize module bioimageit_core.core.utils module bioimageit_core.plugins module bioimageit_core.plugins.runner_conda module bioimageit_core.plugins.runner_condadocker module bioimageit_core.plugins.runner_docker module bioimageit_core.plugins.runner_local module

C

Classes() (in module bioimageit_core.containers.tools_containers) CmdSelectContainer (class in bioimageit_core.containers) (class in bioimageit_core.containers.tools_containers) CmdSelectContainer() (in module bioimageit_core.containers.tools_containers) COL_B (bioimageit_core.core.observer.Observer attribute) COL_G (bioimageit_core.core.observer.Observer attribute) COL_O (bioimageit_core.core.observer.Observer attribute) COL_P (bioimageit_core.core.observer.Observer attribute) COL_R (bioimageit_core.core.observer.Observer attribute) COL_W (bioimageit_core.core.observer.Observer attribute) command (bioimageit_core.containers.Tool attribute) (bioimageit_core.containers.tools_containers.Tool attribute) compare (bioimageit_core.containers.tools_containers.ToolTestParameterContainer attribute) (bioimageit_core.containers.ToolTestParameterContainer attribute) CondaDockerRunnerService (class in bioimageit_core.plugins.runner_condadocker)

CondaDockerRunnerServiceBuilder (class in bioimageit_core.plugins.runner_condadocker) CondaRunnerService (class in bioimageit_core.plugins.runner_conda) CondaRunnerServiceBuilder (class in bioimageit_core.plugins.runner_conda) config (bioimageit_core.core.config.Config attribute) Config (class in bioimageit_core.core.config) ConfigAccess (class in bioimageit_core.core.config) ConfigError ConfigKeyNotFoundError Container (class in bioimageit_core.containers) (class in bioimageit_core.containers.data_containers) container() (bioimageit_core.containers.Tool method) (bioimageit_core.containers.tools_containers.Tool method) content_str() (bioimageit_core.containers.CmdSelectContainer method) (bioimageit_core.containers.tools_containers.CmdSelectContainer method) count() (bioimageit_core.containers.runners_containers.JobInputs method) create() (bioimageit_core.core.factory.ObjectFactory method)

D

Data (class in bioimageit_core.containers) (class in bioimageit_core.containers.data_containers) DataQueryError DataServiceError dataset (bioimageit_core.containers.data_containers.RunInputContainer attribute) (bioimageit_core.containers.JobInput attribute) (bioimageit_core.containers.RunInputContainer attribute) (bioimageit_core.containers.runners_containers.JobInput attribute) Dataset (class in bioimageit_core.containers) (class in bioimageit_core.containers.data_containers) DatasetInfo (class in bioimageit_core.containers) (class in bioimageit_core.containers.data_containers) date (bioimageit_core.containers.Data attribute) (bioimageit_core.containers.data_containers.Data attribute) (bioimageit_core.containers.data_containers.Experiment attribute) (bioimageit_core.containers.Experiment attribute)

default_value (bioimageit_core.containers.ToolParameterContainer attribute) (bioimageit_core.containers.tools_containers.ToolParameterContainer attribute) description (bioimageit_core.containers.Tool attribute) (bioimageit_core.containers.ToolParameterContainer attribute) (bioimageit_core.containers.tools_containers.Tool attribute) (bioimageit_core.containers.tools_containers.ToolParameterContainer attribute) display() (bioimageit_core.containers.Tool method), [1] (bioimageit_core.containers.ToolParameterContainer method) (bioimageit_core.containers.tools_containers.Tool method), [1] (bioimageit_core.containers.tools_containers.ToolParameterContainer method) (bioimageit_core.containers.tools_containers.ToolTestParameterContainer method) (bioimageit_core.containers.ToolTestParameterContainer method) DockerRunnerService (class in bioimageit_core.plugins.runner_docker) DockerRunnerServiceBuilder (class in bioimageit_core.plugins.runner_docker)

E

exec() (bioimageit_core.plugins.runner_conda.CondaRunnerService method) (bioimageit_core.plugins.runner_condadocker.CondaDockerRunnerService static method) (bioimageit_core.plugins.runner_docker.DockerRunnerService method) (bioimageit_core.plugins.runner_local.LocalRunnerService method) experiment (bioimageit_core.containers.Job attribute) (bioimageit_core.containers.runners_containers.Job attribute)

Experiment (class in bioimageit_core.containers) (class in bioimageit_core.containers.data_containers) extract_filename() (in module bioimageit_core.core.utils) extract_image_name() (in module bioimageit_core.plugins.runner_docker)

F

file (bioimageit_core.containers.tools_containers.ToolTestParameterContainer attribute) (bioimageit_core.containers.ToolTestParameterContainer attribute) file() (bioimageit_core.core.config.ConfigAccess static method) format (bioimageit_core.containers.Data attribute) (bioimageit_core.containers.data_containers.Data attribute)

format_date() (in module bioimageit_core.core.utils) fullname() (bioimageit_core.containers.Tool method) (bioimageit_core.containers.tools_containers.Tool method)

G

generate_uuid() (in module bioimageit_core.core.utils)

get() (bioimageit_core.core.config.Config method) get_docker_working_dir() (in module bioimageit_core.plugins.runner_docker)

H

help (bioimageit_core.containers.Tool attribute) (bioimageit_core.containers.tools_containers.Tool attribute)

I

id (bioimageit_core.containers.Tool attribute) (bioimageit_core.containers.tools_containers.Tool attribute) inputs (bioimageit_core.containers.data_containers.ProcessedData attribute) (bioimageit_core.containers.data_containers.Run attribute) (bioimageit_core.containers.Job attribute) (bioimageit_core.containers.ProcessedData attribute) (bioimageit_core.containers.Run attribute) (bioimageit_core.containers.runners_containers.Job attribute) (bioimageit_core.containers.runners_containers.JobInputs attribute) (bioimageit_core.containers.Tool attribute) (bioimageit_core.containers.tools_containers.Tool attribute) inputs_size() (bioimageit_core.containers.Tool method), [1] (bioimageit_core.containers.tools_containers.Tool method), [1]

instance() (bioimageit_core.core.config.ConfigAccess static method) io (bioimageit_core.containers.ToolParameterContainer attribute) (bioimageit_core.containers.tools_containers.ToolParameterContainer attribute) IO_INPUT() (in module bioimageit_core.containers.tools_containers) IO_OUTPUT() (in module bioimageit_core.containers.tools_containers) IO_PARAM() (in module bioimageit_core.containers.tools_containers) is_advanced (bioimageit_core.containers.ToolParameterContainer attribute) (bioimageit_core.containers.tools_containers.ToolParameterContainer attribute) is_data (bioimageit_core.containers.ToolParameterContainer attribute) (bioimageit_core.containers.tools_containers.ToolParameterContainer attribute) is_key() (bioimageit_core.core.config.Config method) is_param() (bioimageit_core.containers.Tool method), [1] (bioimageit_core.containers.tools_containers.Tool method), [1]

J

Job (class in bioimageit_core.containers) (class in bioimageit_core.containers.runners_containers)

JobInput (class in bioimageit_core.containers) (class in bioimageit_core.containers.runners_containers) JobInputs (class in bioimageit_core.containers.runners_containers)

K

key_value_pairs (bioimageit_core.containers.data_containers.RawData attribute) (bioimageit_core.containers.RawData attribute)

keys (bioimageit_core.containers.data_containers.Experiment attribute) (bioimageit_core.containers.Experiment attribute)

L

load() (bioimageit_core.core.config.Config method) LocalRunnerService (class in bioimageit_core.plugins.runner_local)

LocalRunnerServiceBuilder (class in bioimageit_core.plugins.runner_local) LogObserver (class in bioimageit_core.core.log_observer)

M

man() (bioimageit_core.containers.Tool method) (bioimageit_core.containers.tools_containers.Tool method) md_uri (bioimageit_core.containers.Container attribute) (bioimageit_core.containers.data_containers.Container attribute) metadata (bioimageit_core.containers.data_containers.RawData attribute) (bioimageit_core.containers.RawData attribute) modify_io_path() (bioimageit_core.plugins.runner_docker.DockerRunnerService static method) module bioimageit_core.containers bioimageit_core.containers.data_containers bioimageit_core.containers.runners_containers bioimageit_core.containers.tools_containers bioimageit_core.core bioimageit_core.core.config bioimageit_core.core.exceptions bioimageit_core.core.factory bioimageit_core.core.log_observer bioimageit_core.core.observer bioimageit_core.core.serialize bioimageit_core.core.utils bioimageit_core.plugins bioimageit_core.plugins.runner_conda bioimageit_core.plugins.runner_condadocker bioimageit_core.plugins.runner_docker bioimageit_core.plugins.runner_local

N

name (bioimageit_core.containers.Data attribute) (bioimageit_core.containers.data_containers.Data attribute) (bioimageit_core.containers.data_containers.Dataset attribute) (bioimageit_core.containers.data_containers.DatasetInfo attribute) (bioimageit_core.containers.data_containers.ProcessedDataInputContainer attribute) (bioimageit_core.containers.data_containers.RunInputContainer attribute) (bioimageit_core.containers.data_containers.RunParameterContainer attribute) (bioimageit_core.containers.Dataset attribute) (bioimageit_core.containers.DatasetInfo attribute) (bioimageit_core.containers.JobInput attribute) (bioimageit_core.containers.ProcessedDataInputContainer attribute) (bioimageit_core.containers.RunInputContainer attribute) (bioimageit_core.containers.runners_containers.JobInput attribute) (bioimageit_core.containers.RunParameterContainer attribute) (bioimageit_core.containers.Tool attribute) (bioimageit_core.containers.ToolParameterContainer attribute) (bioimageit_core.containers.tools_containers.Tool attribute) (bioimageit_core.containers.tools_containers.ToolParameterContainer attribute) (bioimageit_core.containers.tools_containers.ToolTestParameterContainer attribute) (bioimageit_core.containers.ToolTestParameterContainer attribute)

names (bioimageit_core.containers.CmdSelectContainer attribute) (bioimageit_core.containers.tools_containers.CmdSelectContainer attribute) new_job() (bioimageit_core.core.log_observer.LogObserver method) (bioimageit_core.core.observer.Observable method) (bioimageit_core.core.observer.Observer method) notify() (bioimageit_core.core.log_observer.LogObserver method) (bioimageit_core.core.observer.Observable method) (bioimageit_core.core.observer.Observer method) notify_error() (bioimageit_core.core.log_observer.LogObserver method) (bioimageit_core.core.observer.Observable method) (bioimageit_core.core.observer.Observer method) notify_progress() (bioimageit_core.core.log_observer.LogObserver method) (bioimageit_core.core.observer.Observable method) (bioimageit_core.core.observer.Observer method) notify_warning() (bioimageit_core.core.log_observer.LogObserver method) (bioimageit_core.core.observer.Observable method) (bioimageit_core.core.observer.Observer method)

O

ObjectFactory (class in bioimageit_core.core.factory) Observable (class in bioimageit_core.core.observer) Observer (class in bioimageit_core.core.observer) observers_count() (bioimageit_core.core.observer.Observable method) origin_output_name (bioimageit_core.containers.data_containers.RunInputContainer attribute) (bioimageit_core.containers.JobInput attribute) (bioimageit_core.containers.RunInputContainer attribute) (bioimageit_core.containers.runners_containers.JobInput attribute)

output (bioimageit_core.containers.data_containers.ProcessedData attribute) (bioimageit_core.containers.ProcessedData attribute) output_dataset_name (bioimageit_core.containers.Job attribute) (bioimageit_core.containers.runners_containers.Job attribute) outputs (bioimageit_core.containers.Tool attribute) (bioimageit_core.containers.tools_containers.Tool attribute) outputs_size() (bioimageit_core.containers.Tool method), [1] (bioimageit_core.containers.tools_containers.Tool method), [1]

P

PARAM_BOOLEAN() (in module bioimageit_core.containers.tools_containers) PARAM_FILE() (in module bioimageit_core.containers.tools_containers) PARAM_NUMBER() (in module bioimageit_core.containers.tools_containers) PARAM_SELECT() (in module bioimageit_core.containers.tools_containers) param_size() (bioimageit_core.containers.Tool method) (bioimageit_core.containers.tools_containers.Tool method) PARAM_STRING() (in module bioimageit_core.containers.tools_containers) parameters (bioimageit_core.containers.data_containers.Run attribute) (bioimageit_core.containers.Job attribute) (bioimageit_core.containers.Run attribute) (bioimageit_core.containers.runners_containers.Job attribute)

process_name (bioimageit_core.containers.data_containers.Run attribute) (bioimageit_core.containers.Run attribute) process_uri (bioimageit_core.containers.data_containers.Run attribute) (bioimageit_core.containers.Run attribute) processed_dataset (bioimageit_core.containers.data_containers.Run attribute) (bioimageit_core.containers.Run attribute) processed_datasets (bioimageit_core.containers.data_containers.Experiment attribute) (bioimageit_core.containers.Experiment attribute) ProcessedData (class in bioimageit_core.containers) (class in bioimageit_core.containers.data_containers) ProcessedDataInputContainer (class in bioimageit_core.containers) (class in bioimageit_core.containers.data_containers)

Q

query (bioimageit_core.containers.data_containers.RunInputContainer attribute) (bioimageit_core.containers.JobInput attribute) (bioimageit_core.containers.RunInputContainer attribute) (bioimageit_core.containers.runners_containers.JobInput attribute)

R

raw_dataset (bioimageit_core.containers.data_containers.Experiment attribute) (bioimageit_core.containers.Experiment attribute) RawData (class in bioimageit_core.containers) (class in bioimageit_core.containers.data_containers) register_builder() (bioimageit_core.core.factory.ObjectFactory method) relative_path() (bioimageit_core.plugins.runner_docker.DockerRunnerService static method) remove_observers() (bioimageit_core.core.observer.Observable method) run (bioimageit_core.containers.data_containers.ProcessedData attribute) (bioimageit_core.containers.ProcessedData attribute)

Run (class in bioimageit_core.containers) (class in bioimageit_core.containers.data_containers) RunInputContainer (class in bioimageit_core.containers) (class in bioimageit_core.containers.data_containers) RunnerExecError RunParameterContainer (class in bioimageit_core.containers) (class in bioimageit_core.containers.data_containers)

S

save() (bioimageit_core.core.config.Config method) select_info (bioimageit_core.containers.ToolParameterContainer attribute) (bioimageit_core.containers.tools_containers.ToolParameterContainer attribute) serialize() (bioimageit_core.containers.ToolIndexContainer method) (bioimageit_core.containers.tools_containers.ToolIndexContainer method) serialize_data() (in module bioimageit_core.core.serialize), [1] serialize_dataset() (in module bioimageit_core.core.serialize), [1] serialize_experiment() (in module bioimageit_core.core.serialize), [1] serialize_processed_data() (in module bioimageit_core.core.serialize), [1] serialize_raw_data() (in module bioimageit_core.core.serialize), [1] serialize_run() (in module bioimageit_core.core.serialize), [1] set() (bioimageit_core.core.config.Config method) set_dataset() (bioimageit_core.containers.data_containers.Run method) (bioimageit_core.containers.Run method) set_experiment() (bioimageit_core.containers.Job method) (bioimageit_core.containers.runners_containers.Job method) set_info() (bioimageit_core.containers.data_containers.ProcessedData method) (bioimageit_core.containers.ProcessedData method) set_input() (bioimageit_core.containers.Job method) (bioimageit_core.containers.runners_containers.Job method) set_key() (bioimageit_core.containers.data_containers.Experiment method) (bioimageit_core.containers.Experiment method)

set_key_value_pair() (bioimageit_core.containers.data_containers.RawData method) (bioimageit_core.containers.RawData method) set_output() (bioimageit_core.containers.data_containers.ProcessedData method) (bioimageit_core.containers.ProcessedData method) set_output_dataset_name() (bioimageit_core.containers.Job method) (bioimageit_core.containers.runners_containers.Job method) set_param() (bioimageit_core.containers.Job method) (bioimageit_core.containers.runners_containers.Job method) set_process() (bioimageit_core.containers.data_containers.Run method) (bioimageit_core.containers.Run method) set_tool() (bioimageit_core.containers.Job method) (bioimageit_core.containers.runners_containers.Job method) set_up() (bioimageit_core.plugins.runner_conda.CondaRunnerService method) (bioimageit_core.plugins.runner_condadocker.CondaDockerRunnerService static method) (bioimageit_core.plugins.runner_docker.DockerRunnerService method) (bioimageit_core.plugins.runner_local.LocalRunnerService method) size() (bioimageit_core.containers.CmdSelectContainer method), [1] (bioimageit_core.containers.data_containers.Dataset method) (bioimageit_core.containers.Dataset method) (bioimageit_core.containers.tools_containers.CmdSelectContainer method), [1]

T

tear_down() (bioimageit_core.plugins.runner_conda.CondaRunnerService method) (bioimageit_core.plugins.runner_condadocker.CondaDockerRunnerService static method) (bioimageit_core.plugins.runner_docker.DockerRunnerService method) (bioimageit_core.plugins.runner_local.LocalRunnerService method) tests (bioimageit_core.containers.Tool attribute) (bioimageit_core.containers.tools_containers.Tool attribute) to_dict() (bioimageit_core.containers.ToolIndexContainer method) (bioimageit_core.containers.tools_containers.ToolIndexContainer method) tool (bioimageit_core.containers.Job attribute) (bioimageit_core.containers.runners_containers.Job attribute) Tool (class in bioimageit_core.containers) (class in bioimageit_core.containers.tools_containers) ToolContainer() (in module bioimageit_core.containers.tools_containers) ToolDatabaseContainer() (in module bioimageit_core.containers.tools_containers) ToolIndexContainer (class in bioimageit_core.containers) (class in bioimageit_core.containers.tools_containers)

ToolIndexContainer() (in module bioimageit_core.containers.tools_containers) ToolNotFoundError ToolParameterContainer (class in bioimageit_core.containers) (class in bioimageit_core.containers.tools_containers) ToolParameterContainer() (in module bioimageit_core.containers.tools_containers) ToolsCategoryContainer (class in bioimageit_core.containers) (class in bioimageit_core.containers.tools_containers) ToolsCategoryContainer() (in module bioimageit_core.containers.tools_containers) ToolsServiceError ToolTestParameterContainer (class in bioimageit_core.containers) (class in bioimageit_core.containers.tools_containers) type (bioimageit_core.containers.ToolParameterContainer attribute) (bioimageit_core.containers.tools_containers.ToolParameterContainer attribute) (bioimageit_core.containers.tools_containers.ToolTestParameterContainer attribute) (bioimageit_core.containers.ToolTestParameterContainer attribute)

U

uri (bioimageit_core.containers.Data attribute) (bioimageit_core.containers.data_containers.Data attribute) (bioimageit_core.containers.data_containers.ProcessedDataInputContainer attribute) (bioimageit_core.containers.ProcessedDataInputContainer attribute) uris (bioimageit_core.containers.data_containers.Dataset attribute) (bioimageit_core.containers.Dataset attribute)

url (bioimageit_core.containers.data_containers.DatasetInfo attribute) (bioimageit_core.containers.DatasetInfo attribute) uuid (bioimageit_core.containers.Container attribute) (bioimageit_core.containers.data_containers.Container attribute) (bioimageit_core.containers.data_containers.DatasetInfo attribute) (bioimageit_core.containers.DatasetInfo attribute)

V

value (bioimageit_core.containers.data_containers.RunParameterContainer attribute) (bioimageit_core.containers.RunParameterContainer attribute) (bioimageit_core.containers.ToolParameterContainer attribute) (bioimageit_core.containers.tools_containers.ToolParameterContainer attribute) (bioimageit_core.containers.tools_containers.ToolTestParameterContainer attribute) (bioimageit_core.containers.ToolTestParameterContainer attribute)

values (bioimageit_core.containers.CmdSelectContainer attribute) (bioimageit_core.containers.tools_containers.CmdSelectContainer attribute) version (bioimageit_core.containers.Tool attribute) (bioimageit_core.containers.tools_containers.Tool attribute)