bioimageit_core.containers package

Submodules

bioimageit_core.containers.data_containers module

BioImageIT data containers.

Implements data containers defined in SciXTracer

Classes

Container Data RawData ProcessedData Dataset Experiment Run

class bioimageit_core.containers.data_containers.Container(md_uri='', uuid='')

Bases: object

Interface fo all BioImageIT containers

Containers are classes to store and interact with dedicated types of metadata

md_uri

URI of the metadata in the database or file system depending on backend

Type:: str

uuid

Unique identifier of the metadata

Type:: str

class bioimageit_core.containers.data_containers.Data

Bases: Container

Interface for data container

Data container aims at manipulating the metadata of a single data

name: Name of the data

author: Author of the data

date: Date when the data is created

format: Data format (txt, csv, tif, …)

uri: URI of the data as stored in the database

class bioimageit_core.containers.data_containers.Dataset

Bases: Container

Container for a dataset metadata

name: Name of the dataset

uris: List of the URIs of the data (metadata) in the URIs

size()

class bioimageit_core.containers.data_containers.DatasetInfo(name, url, uuid)

Bases: object

Contains the info of a dataset

name

Name of the dataset

Type:: str

url

URL of the metadata file

Type:: str

uuid

Unique ID of the dataset

Type:: str

class bioimageit_core.containers.data_containers.Experiment

Bases: Container

Container for an experiment .. attribute:: name

Name of the experiment

author: Username of the experiment author

date: Creation date of the experiment

raw_dataset: URI of the raw dataset

processed_datasets: URIs of the processed datasets

keys: List of vocabulary keys used in the experiment

set_key(key)

class bioimageit_core.containers.data_containers.ProcessedData

Bases: Data

Container for processed data

run: URI of the Run metadata file

inputs: Information about the inputs that generated this processed data. It is a list of ProcessedDataInputContainer

output: Information about how the output is referenced in the process that generates this processed data ex: {“name”: “o”, “label”: “Processed image”}

add_input(id_: str, data: Data)

add_input_(id_: str, uri: str, uuid: str, type_: str)

set_info(name='', author='', date='', format_='', url='')

set_output(id_: str, label: str)

class bioimageit_core.containers.data_containers.ProcessedDataInputContainer(name: str = '', uri: str = '', uuid: str = '', type_: str = 'raw')

Bases: object

Container for processed data origin input

name: Name of the input (the unique name in the process)

uri: The uri of the input metadata

class bioimageit_core.containers.data_containers.RawData

Bases: Data

Container for a Raw data

key_value_pairs

Dictionary containing the key-value pairs (key=value)

Type:: dict

metadata

Dictionary of extra metadata (ex: image acquisition settings)

Type:: dict

set_key_value_pair(key, value)

class bioimageit_core.containers.data_containers.Run

Bases: Container

Container for a run (processing or job execution)

process_name: Name of the process (ex: ndsafir)

process_uri: Unique URI of the process (ex: github url)

processed_dataset: URI of the processed dataset

parameters: List of parameters using the RunParameterContainer object

inputs: List of the run inputs using RunInputContainer object

add_input(name: str = '', dataset: str = '', query: str = '', origin_output_name: str = '')

add_parameter(name, value)

set_dataset(dataset)

set_process(name, uri)

class bioimageit_core.containers.data_containers.RunInputContainer(name: str = '', dataset: str = '', query: str = '', origin_output_name: str = '')

Bases: object

Container for a run input

name: Name of the input (ex -i)

dataset: Name of the dataset containing the inputs (ex ‘data’)

query: Query used to select images in the dataset (ex ‘name=image.tif’)

origin_output_name: Name of the output in the parent run if run on a processed dataset

class bioimageit_core.containers.data_containers.RunParameterContainer(name: str = '', value: str = '')

Bases: object

Container for a run parameter

name: Name of the parameter

value: Value of the parameter

bioimageit_core.containers.runners_containers module

class bioimageit_core.containers.runners_containers.Job

Bases: object

Container for a job information

A job information lists all the needed information to run a tool on an experiment

experiment

Container of the experiment to process

Type:: Experiment

tool

Tool to run

Type:: Tool

parameters

Set of parameters that setup the tool.

Type:: dict

inputs

Description of the job inputs in the database

Type:: JobInputs

output_dataset_name

Unique name of the output dataset

Type:: str

set_experiment(experiment)

set_input(name, dataset, query, origin_output_name='')

set_output_dataset_name(name)

set_param(key, value)

set_tool(tool)

class bioimageit_core.containers.runners_containers.JobInput(name: str = '', dataset: str = '', query: str = '', origin_output_name: str = '')

Bases: object

Container for a job input

A job input is all the information needed to select the input data files of a job in an experiment

name

Name of the input (ex -i)

Type:: str

dataset

Name of the dataset containing the inputs (ex ‘data’)

Type:: str

query

Query used to select images in the dataset (ex ‘name=image.tif’)

Type:: str

origin_output_name

Name of the output in the parent run if run on a processed dataset

Type:: str

class bioimageit_core.containers.runners_containers.JobInputs

Bases: object

Container for multiple inputs of a job

inputs

List of all the job inputs

Type:: list

add_input(name, dataset, query, origin_output_name='')

Add a job input

Parameters:

name (str) – Name of the input (ex -i)
dataset (str) – Name of the dataset containing the inputs (ex ‘data’)
query (str) – Query used to select images in the dataset (ex ‘name=image.tif’)
origin_output_name (str) – Name of the output in the parent run if run on a processed dataset

add_job_input(job_input)

Add a job input

Parameters:: job_input (JobInput) – input to be added

count(): get the number of input

bioimageit_core.containers.tools_containers module

BioIMageIT tool containers.

This module contains containers for Tool info and tool database

bioimageit_core.containers.tools_containers.PARAM_NUMBER()

bioimageit_core.containers.tools_containers.PARAM_STRING()

bioimageit_core.containers.tools_containers.PARAM_SELECT()

bioimageit_core.containers.tools_containers.PARAM_BOOLEAN()

bioimageit_core.containers.tools_containers.PARAM_FILE()

bioimageit_core.containers.tools_containers.IO_PARAM()

bioimageit_core.containers.tools_containers.IO_INPUT()

bioimageit_core.containers.tools_containers.IO_OUTPUT()

bioimageit_core.containers.tools_containers.Classes()

-------

bioimageit_core.containers.tools_containers.ToolsCategoryContainer()

bioimageit_core.containers.tools_containers.ToolIndexContainer()

bioimageit_core.containers.tools_containers.ToolContainer()

bioimageit_core.containers.tools_containers.ToolParameterContainer()

bioimageit_core.containers.tools_containers.ToolDatabaseContainer()

bioimageit_core.containers.tools_containers.CmdSelectContainer()

class bioimageit_core.containers.tools_containers.CmdSelectContainer

Bases: object

Container for a select parameter options

names

List of the options names

Type:: list

values

List of the options values

Type:: list

size(): Number of options

add(): Add an option

add(name: str, value: str)

Add an option

Parameters:

name – Name of the option
value – Value of the option

content_str()

size()

Calculate the number of options

Returns:: Number of options
Return type:: Int

class bioimageit_core.containers.tools_containers.Tool

Bases: object

Container for a tool parameter information

id

Id of the tool

Type:: str

name

Tool name

Type:: str

version

Tool version (ex 1.0.0)

Type:: str

description

Tool short description (used for the man page)

Type:: str

command

Command executed when tool is ran

Type:: str

inputs

Tool inputs stored in a list of ToolParameter

Type:: list

outputs

Tool outputs stored in a list of ToolParameter

Type:: list

tests

List of unit tests

Type:: list

help

Url to the help page

Type:: str

is_param(): Check if a parameter exists

inputs_size(): Returns the number of inputs

outputs_size(): Returns the number of outputs

display(): Display the tool information to console

container()

Get the first container in the requirements

Returns:: Description of the container requirement (origin, type, uri)
Return type:: dict

display(): Print the tool information to console.

fullname()

fullname of the tool

the full name is “{name}_v{version}”

inputs_size()

Calculate the number of inputs

Returns:: Number of inputs
Return type:: int

is_param(name: str) → bool

Check if a parameter exists

Parameters:: name – Name of the parameter to check
Returns:: True if the parameter exists, False otherwise
Return type:: bool

man(): Display the tool man page

outputs_size()

Calculate the number of outputs

Returns:: Number of outputs
Return type:: int

param_size()

Calculate the number of parameters

Returns:: Number of inputs
Return type:: int

class bioimageit_core.containers.tools_containers.ToolIndexContainer

Bases: object

Container for a tool main information

uri: URI of the XML file
id: str: Id of the tool
name: str: Tool name
version: str: Tool version (ex 1.0.0)
type: Tool type (‘sequential’, ‘merge’)
categories: List of the tool categories

serialize(direction: str = 'h', show_uri=False)

Serialize the tool main info

Parameters:

direction (str) – h for horizontal, and v for vertical
show_uri (bool) – True to show the tool URI

to_dict()

class bioimageit_core.containers.tools_containers.ToolParameterContainer

Bases: object

Container for a tool parameter information

name

Parameter name

Type:: str

description

Parameter description

Type:: str

value

Parameter value

Type:: str

type

Parameter type (format)

Type:: str

is_data

False if parameter is param and True if parameter is data

Type:: bool

io

IO type if parameter is IO (in IO_XXX names)

Type:: str

default_value

Parameter default value

Type:: str

select_info

Choices for a select parameter

Type:: BiCmdSelect

is_advanced

True if parameter is advanced

Type:: bool

display(): Display the tool parameter information to console

class bioimageit_core.containers.tools_containers.ToolTestParameterContainer

Bases: object

Container for a tool test information

type

Parameter type (param or output)

Type:: str

name

Name of the parameter

Type:: str

value

Value of the parameter

Type:: str

file

Reference file path for output

Type:: str

compare

Comparison method name

Type:: str

display(): Display the container content

class bioimageit_core.containers.tools_containers.ToolsCategoryContainer

Bases: object

Container for a category of tools

These are the metadata of a tools category for the tool-shed structure

id:: ID of the category. It must be a unique name
name:: Name of the category. It is the name printed to the user interfaces
thumbnail:: URI to an image that illustrate the category tools
parent:: ID of the parent category in the category tree. Set to ‘root’ for a top level category

Module contents

class bioimageit_core.containers.CmdSelectContainer

Bases: object

Container for a select parameter options

names

List of the options names

Type:: list

values

List of the options values

Type:: list

size(): Number of options

add(): Add an option

add(name: str, value: str)

Add an option

Parameters:

name – Name of the option
value – Value of the option

content_str()

size()

Calculate the number of options

Returns:: Number of options
Return type:: Int

class bioimageit_core.containers.Container(md_uri='', uuid='')

Bases: object

Interface fo all BioImageIT containers

Containers are classes to store and interact with dedicated types of metadata

md_uri

URI of the metadata in the database or file system depending on backend

Type:: str

uuid

Unique identifier of the metadata

Type:: str

class bioimageit_core.containers.Data

Bases: Container

Interface for data container

Data container aims at manipulating the metadata of a single data

name: Name of the data

author: Author of the data

date: Date when the data is created

format: Data format (txt, csv, tif, …)

uri: URI of the data as stored in the database

class bioimageit_core.containers.Dataset

Bases: Container

Container for a dataset metadata

name: Name of the dataset

uris: List of the URIs of the data (metadata) in the URIs

size()

class bioimageit_core.containers.DatasetInfo(name, url, uuid)

Bases: object

Contains the info of a dataset

name

Name of the dataset

Type:: str

url

URL of the metadata file

Type:: str

uuid

Unique ID of the dataset

Type:: str

class bioimageit_core.containers.Experiment

Bases: Container

Container for an experiment .. attribute:: name

Name of the experiment

author: Username of the experiment author

date: Creation date of the experiment

raw_dataset: URI of the raw dataset

processed_datasets: URIs of the processed datasets

keys: List of vocabulary keys used in the experiment

set_key(key)

class bioimageit_core.containers.Job

Bases: object

Container for a job information

A job information lists all the needed information to run a tool on an experiment

experiment

Container of the experiment to process

Type:: Experiment

tool

Tool to run

Type:: Tool

parameters

Set of parameters that setup the tool.

Type:: dict

inputs

Description of the job inputs in the database

Type:: JobInputs

output_dataset_name

Unique name of the output dataset

Type:: str

set_experiment(experiment)

set_input(name, dataset, query, origin_output_name='')

set_output_dataset_name(name)

set_param(key, value)

set_tool(tool)

class bioimageit_core.containers.JobInput(name: str = '', dataset: str = '', query: str = '', origin_output_name: str = '')

Bases: object

Container for a job input

A job input is all the information needed to select the input data files of a job in an experiment

name

Name of the input (ex -i)

Type:: str

dataset

Name of the dataset containing the inputs (ex ‘data’)

Type:: str

query

Query used to select images in the dataset (ex ‘name=image.tif’)

Type:: str

origin_output_name

Name of the output in the parent run if run on a processed dataset

Type:: str

class bioimageit_core.containers.ProcessedData

Bases: Data

Container for processed data

run: URI of the Run metadata file

inputs: Information about the inputs that generated this processed data. It is a list of ProcessedDataInputContainer

output: Information about how the output is referenced in the process that generates this processed data ex: {“name”: “o”, “label”: “Processed image”}

add_input(id_: str, data: Data)

add_input_(id_: str, uri: str, uuid: str, type_: str)

set_info(name='', author='', date='', format_='', url='')

set_output(id_: str, label: str)

class bioimageit_core.containers.ProcessedDataInputContainer(name: str = '', uri: str = '', uuid: str = '', type_: str = 'raw')

Bases: object

Container for processed data origin input

name: Name of the input (the unique name in the process)

uri: The uri of the input metadata

class bioimageit_core.containers.RawData

Bases: Data

Container for a Raw data

key_value_pairs

Dictionary containing the key-value pairs (key=value)

Type:: dict

metadata

Dictionary of extra metadata (ex: image acquisition settings)

Type:: dict

set_key_value_pair(key, value)

class bioimageit_core.containers.Run

Bases: Container

Container for a run (processing or job execution)

process_name: Name of the process (ex: ndsafir)

process_uri: Unique URI of the process (ex: github url)

processed_dataset: URI of the processed dataset

parameters: List of parameters using the RunParameterContainer object

inputs: List of the run inputs using RunInputContainer object

add_input(name: str = '', dataset: str = '', query: str = '', origin_output_name: str = '')

add_parameter(name, value)

set_dataset(dataset)

set_process(name, uri)

class bioimageit_core.containers.RunInputContainer(name: str = '', dataset: str = '', query: str = '', origin_output_name: str = '')

Bases: object

Container for a run input

name: Name of the input (ex -i)

dataset: Name of the dataset containing the inputs (ex ‘data’)

query: Query used to select images in the dataset (ex ‘name=image.tif’)

origin_output_name: Name of the output in the parent run if run on a processed dataset

class bioimageit_core.containers.RunParameterContainer(name: str = '', value: str = '')

Bases: object

Container for a run parameter

name: Name of the parameter

value: Value of the parameter

class bioimageit_core.containers.Tool

Bases: object

Container for a tool parameter information

id

Id of the tool

Type:: str

name

Tool name

Type:: str

version

Tool version (ex 1.0.0)

Type:: str

description

Tool short description (used for the man page)

Type:: str

command

Command executed when tool is ran

Type:: str

inputs

Tool inputs stored in a list of ToolParameter

Type:: list

outputs

Tool outputs stored in a list of ToolParameter

Type:: list

tests

List of unit tests

Type:: list

help

Url to the help page

Type:: str

is_param(): Check if a parameter exists

inputs_size(): Returns the number of inputs

outputs_size(): Returns the number of outputs

display(): Display the tool information to console

container()

Get the first container in the requirements

Returns:: Description of the container requirement (origin, type, uri)
Return type:: dict

display(): Print the tool information to console.

fullname()

fullname of the tool

the full name is “{name}_v{version}”

inputs_size()

Calculate the number of inputs

Returns:: Number of inputs
Return type:: int

is_param(name: str) → bool

Check if a parameter exists

Parameters:: name – Name of the parameter to check
Returns:: True if the parameter exists, False otherwise
Return type:: bool

man(): Display the tool man page

outputs_size()

Calculate the number of outputs

Returns:: Number of outputs
Return type:: int

param_size()

Calculate the number of parameters

Returns:: Number of inputs
Return type:: int

class bioimageit_core.containers.ToolIndexContainer

Bases: object

Container for a tool main information

uri: URI of the XML file
id: str: Id of the tool
name: str: Tool name
version: str: Tool version (ex 1.0.0)
type: Tool type (‘sequential’, ‘merge’)
categories: List of the tool categories

serialize(direction: str = 'h', show_uri=False)

Serialize the tool main info

Parameters:

direction (str) – h for horizontal, and v for vertical
show_uri (bool) – True to show the tool URI

to_dict()

class bioimageit_core.containers.ToolParameterContainer

Bases: object

Container for a tool parameter information

name

Parameter name

Type:: str

description

Parameter description

Type:: str

value

Parameter value

Type:: str

type

Parameter type (format)

Type:: str

is_data

False if parameter is param and True if parameter is data

Type:: bool

io

IO type if parameter is IO (in IO_XXX names)

Type:: str

default_value

Parameter default value

Type:: str

select_info

Choices for a select parameter

Type:: BiCmdSelect

is_advanced

True if parameter is advanced

Type:: bool

display(): Display the tool parameter information to console

class bioimageit_core.containers.ToolTestParameterContainer

Bases: object

Container for a tool test information

type

Parameter type (param or output)

Type:: str

name

Name of the parameter

Type:: str

value

Value of the parameter

Type:: str

file

Reference file path for output

Type:: str

compare

Comparison method name

Type:: str

display(): Display the container content

class bioimageit_core.containers.ToolsCategoryContainer

Bases: object

Container for a category of tools

These are the metadata of a tools category for the tool-shed structure

id:: ID of the category. It must be a unique name
name:: Name of the category. It is the name printed to the user interfaces
thumbnail:: URI to an image that illustrate the category tools
parent:: ID of the parent category in the category tree. Set to ‘root’ for a top level category