bioimageit_core.plugins package

Submodules

bioimageit_core.plugins.data_factory module

bioimageit_core.plugins.data_local module

bioimageit_core.plugins.data_omero module

bioimageit_core.plugins.runner_allgo module

bioimageit_core.plugins.runner_conda module

bioimageit_core local process service.

This module implements the local service for process (Process class) execution.

Classes

ProcessServiceProvider

class bioimageit_core.plugins.runner_conda.CondaRunnerService

Bases: Observable

Service for local runner exec

To initialize the database, you need to set the xml_dirs from the configuration and then call initialize

exec(process: Tool, args, job_id: int)

Execute a process

Parameters:

• process – Metadata of the process

• args – list of arguments

• job_id (int) – unique ID of the job. 0 is main app, and positive is a subprocess

set_up(process: Tool, job_id: int)

setup the runner

Add here the code to initialize the runner

Parameters:

• process – Metadata of the process

• job_id (int) – unique ID of the job. 0 is main app, and positive is a subprocess

tear_down(process: Tool, job_id: int)

tear down the runner

Add here the code to down/clean the runner

Parameters:

• process – Metadata of the process

• job_id (int) – unique ID of the job. 0 is main app, and positive is a subprocess

class bioimageit_core.plugins.runner_conda.CondaRunnerServiceBuilder

Bases: object

Service builder for the runner service

bioimageit_core.plugins.runner_condadocker module

bioimageit_core local process service.

This module implements the local service for process (Process class) execution.

Classes

ProcessServiceProvider

class bioimageit_core.plugins.runner_condadocker.CondaDockerRunnerService

Bases: Observable

Service for runner that switch between conda and docker wrt the wrapper

To initialize the database, you need to set the xml_dirs from the configuration and then call initialize

static exec(process: Tool, args)

Execute a process

Parameters:

• process – Metadata of the process

• args – list of arguments

static set_up(process: Tool)

setup the runner

Add here the code to initialize the runner

Parameters:

process – Metadata of the process

static tear_down(process: Tool)

tear down the runner

Add here the code to down/clean the runner

Parameters:

process – Metadata of the process

class bioimageit_core.plugins.runner_condadocker.CondaDockerRunnerServiceBuilder

Bases: object

Service builder for the runner service

bioimageit_core.plugins.runner_docker module

bioimageit_core docker process service.

This module implements a service to run process in using Docker.

Classes

ProcessServiceProvider

class bioimageit_core.plugins.runner_docker.DockerRunnerService

Bases: Observable

Service for docker runner exec

To initialize the database, you need to set the xml_dirs from the configuration and then call initialize

exec(process: Tool, args)

Execute a process

Parameters:

• process – Metadata of the process

• args – list of arguments

static modify_io_path(arg: str, data_value: str, working_dir: str, docker_data_dir: str)

static relative_path(file: str, reference_file: str)

convert file absolute path to a relative path wrt reference_file

Parameters:

• reference_file – Reference file

• file – File to get absolute path

Return type:

relative path of uri wrt md_uri

set_up(process: Tool)

setup the runner

Add here the code to initialize the runner

Parameters:

process – Metadata of the process

tear_down(process: Tool)

tear down the runner

Add here the code to down/clean the runner

Parameters:

process – Metadata of the process

class bioimageit_core.plugins.runner_docker.DockerRunnerServiceBuilder

Bases: object

Service builder for the runner service

bioimageit_core.plugins.runner_docker.extract_image_name(process: Tool)

bioimageit_core.plugins.runner_docker.get_docker_working_dir()

bioimageit_core.plugins.runner_local module

bioimageit_core local process service.

This module implements the local service for process (Process class) execution.

Classes

ProcessServiceProvider

class bioimageit_core.plugins.runner_local.LocalRunnerService

Bases: Observable

Service for local runner exec

To initialize the database, you need to set the xml_dirs from the configuration and then call initialize

exec(process: Tool, args)

Execute a process

Parameters:

• process – Metadata of the process

• args – list of arguments

set_up(process: Tool)

setup the runner

Add here the code to initialize the runner

Parameters:

tool – Metadata of the tool

tear_down(process: Tool)

tear down the runner

Add here the code to down/clean the runner

Parameters:

process – Metadata of the process

class bioimageit_core.plugins.runner_local.LocalRunnerServiceBuilder

Bases: object

Service builder for the runner service

bioimageit_core.plugins.runner_singularity module

bioimageit_core.plugins.runner_factory module

bioimageit_core.plugins.tools_factory module

bioimageit_core.plugins.tools_local module

Module contents