bioimageit_core package

Subpackages

• bioimageit_core.api package
  • Submodules
  • bioimageit_core.api.request module
  • Module contents
• bioimageit_core.containers package
  • Submodules
  • bioimageit_core.containers.data_containers module
    • Classes
    • Container
      • Container.md_uri
      • Container.uuid
    • Data
      • Data.name
      • Data.author
      • Data.date
      • Data.format
      • Data.uri
    • Dataset
      • Dataset.name
      • Dataset.uris
      • Dataset.size()
    • DatasetInfo
      • DatasetInfo.name
      • DatasetInfo.url
      • DatasetInfo.uuid
    • Experiment
      • Experiment.author
      • Experiment.date
      • Experiment.raw_dataset
      • Experiment.processed_datasets
      • Experiment.keys
      • Experiment.set_key()
    • ProcessedData
      • ProcessedData.run
      • ProcessedData.inputs
      • ProcessedData.output
      • ProcessedData.add_input()
      • ProcessedData.add_input_()
      • ProcessedData.set_info()
      • ProcessedData.set_output()
    • ProcessedDataInputContainer
      • ProcessedDataInputContainer.name
      • ProcessedDataInputContainer.uri
    • RawData
      • RawData.key_value_pairs
      • RawData.metadata
      • RawData.set_key_value_pair()
    • Run
      • Run.process_name
      • Run.process_uri
      • Run.processed_dataset
      • Run.parameters
      • Run.inputs
      • Run.add_input()
      • Run.add_parameter()
      • Run.set_dataset()
      • Run.set_process()
    • RunInputContainer
      • RunInputContainer.name
      • RunInputContainer.dataset
      • RunInputContainer.query
      • RunInputContainer.origin_output_name
    • RunParameterContainer
      • RunParameterContainer.name
      • RunParameterContainer.value
  • bioimageit_core.containers.runners_containers module
    • Job
      • Job.experiment
      • Job.tool
      • Job.parameters
      • Job.inputs
      • Job.output_dataset_name
      • Job.set_experiment()
      • Job.set_input()
      • Job.set_output_dataset_name()
      • Job.set_param()
      • Job.set_tool()
    • JobInput
      • JobInput.name
      • JobInput.dataset
      • JobInput.query
      • JobInput.origin_output_name
    • JobInputs
      • JobInputs.inputs
      • JobInputs.add_input()
      • JobInputs.add_job_input()
      • JobInputs.count()
  • bioimageit_core.containers.tools_containers module
    • PARAM_NUMBER()
    • PARAM_STRING()
    • PARAM_SELECT()
    • PARAM_BOOLEAN()
    • PARAM_FILE()
    • IO_PARAM()
    • IO_INPUT()
    • IO_OUTPUT()
    • Classes()
    • ToolsCategoryContainer()
    • ToolIndexContainer()
    • ToolContainer()
    • ToolParameterContainer()
    • ToolDatabaseContainer()
    • CmdSelectContainer()
    • CmdSelectContainer
      • CmdSelectContainer.names
      • CmdSelectContainer.values
      • CmdSelectContainer.size()
      • CmdSelectContainer.add()
      • CmdSelectContainer.add()
      • CmdSelectContainer.content_str()
      • CmdSelectContainer.size()
    • Tool
      • Tool.id
      • Tool.name
      • Tool.version
      • Tool.description
      • Tool.command
      • Tool.inputs
      • Tool.outputs
      • Tool.tests
      • Tool.help
      • Tool.is_param()
      • Tool.inputs_size()
      • Tool.outputs_size()
      • Tool.display()
      • Tool.container()
      • Tool.display()
      • Tool.fullname()
      • Tool.inputs_size()
      • Tool.is_param()
      • Tool.man()
      • Tool.outputs_size()
      • Tool.param_size()
    • ToolIndexContainer
      • ToolIndexContainer.serialize()
      • ToolIndexContainer.to_dict()
    • ToolParameterContainer
      • ToolParameterContainer.name
      • ToolParameterContainer.description
      • ToolParameterContainer.value
      • ToolParameterContainer.type
      • ToolParameterContainer.is_data
      • ToolParameterContainer.io
      • ToolParameterContainer.default_value
      • ToolParameterContainer.select_info
      • ToolParameterContainer.is_advanced
      • ToolParameterContainer.display()
    • ToolTestParameterContainer
      • ToolTestParameterContainer.type
      • ToolTestParameterContainer.name
      • ToolTestParameterContainer.value
      • ToolTestParameterContainer.file
      • ToolTestParameterContainer.compare
      • ToolTestParameterContainer.display()
    • ToolsCategoryContainer
  • Module contents
    • CmdSelectContainer
      • CmdSelectContainer.names
      • CmdSelectContainer.values
      • CmdSelectContainer.size()
      • CmdSelectContainer.add()
      • CmdSelectContainer.add()
      • CmdSelectContainer.content_str()
      • CmdSelectContainer.size()
    • Container
      • Container.md_uri
      • Container.uuid
    • Data
      • Data.name
      • Data.author
      • Data.date
      • Data.format
      • Data.uri
    • Dataset
      • Dataset.name
      • Dataset.uris
      • Dataset.size()
    • DatasetInfo
      • DatasetInfo.name
      • DatasetInfo.url
      • DatasetInfo.uuid
    • Experiment
      • Experiment.author
      • Experiment.date
      • Experiment.raw_dataset
      • Experiment.processed_datasets
      • Experiment.keys
      • Experiment.set_key()
    • Job
      • Job.experiment
      • Job.tool
      • Job.parameters
      • Job.inputs
      • Job.output_dataset_name
      • Job.set_experiment()
      • Job.set_input()
      • Job.set_output_dataset_name()
      • Job.set_param()
      • Job.set_tool()
    • JobInput
      • JobInput.name
      • JobInput.dataset
      • JobInput.query
      • JobInput.origin_output_name
    • ProcessedData
      • ProcessedData.run
      • ProcessedData.inputs
      • ProcessedData.output
      • ProcessedData.add_input()
      • ProcessedData.add_input_()
      • ProcessedData.set_info()
      • ProcessedData.set_output()
    • ProcessedDataInputContainer
      • ProcessedDataInputContainer.name
      • ProcessedDataInputContainer.uri
    • RawData
      • RawData.key_value_pairs
      • RawData.metadata
      • RawData.set_key_value_pair()
    • Run
      • Run.process_name
      • Run.process_uri
      • Run.processed_dataset
      • Run.parameters
      • Run.inputs
      • Run.add_input()
      • Run.add_parameter()
      • Run.set_dataset()
      • Run.set_process()
    • RunInputContainer
      • RunInputContainer.name
      • RunInputContainer.dataset
      • RunInputContainer.query
      • RunInputContainer.origin_output_name
    • RunParameterContainer
      • RunParameterContainer.name
      • RunParameterContainer.value
    • Tool
      • Tool.id
      • Tool.name
      • Tool.version
      • Tool.description
      • Tool.command
      • Tool.inputs
      • Tool.outputs
      • Tool.tests
      • Tool.help
      • Tool.is_param()
      • Tool.inputs_size()
      • Tool.outputs_size()
      • Tool.display()
      • Tool.container()
      • Tool.display()
      • Tool.fullname()
      • Tool.inputs_size()
      • Tool.is_param()
      • Tool.man()
      • Tool.outputs_size()
      • Tool.param_size()
    • ToolIndexContainer
      • ToolIndexContainer.serialize()
      • ToolIndexContainer.to_dict()
    • ToolParameterContainer
      • ToolParameterContainer.name
      • ToolParameterContainer.description
      • ToolParameterContainer.value
      • ToolParameterContainer.type
      • ToolParameterContainer.is_data
      • ToolParameterContainer.io
      • ToolParameterContainer.default_value
      • ToolParameterContainer.select_info
      • ToolParameterContainer.is_advanced
      • ToolParameterContainer.display()
    • ToolTestParameterContainer
      • ToolTestParameterContainer.type
      • ToolTestParameterContainer.name
      • ToolTestParameterContainer.value
      • ToolTestParameterContainer.file
      • ToolTestParameterContainer.compare
      • ToolTestParameterContainer.display()
    • ToolsCategoryContainer
• bioimageit_core.core package
  • Submodules
  • bioimageit_core.core.config module
    • Classes
    • Config
      • Config.config
      • Config.get()
      • Config.is_key()
      • Config.load()
      • Config.save()
      • Config.set()
    • ConfigAccess
      • ConfigAccess.file()
      • ConfigAccess.instance()
    • ConfigKeyNotFoundError
  • bioimageit_core.core.exceptions module
    • ConfigError
    • DataQueryError
    • DataServiceError
    • RunnerExecError
    • ToolNotFoundError
    • ToolsServiceError
  • bioimageit_core.core.factory module
    • Classes
    • ObjectFactory
      • ObjectFactory.create()
      • ObjectFactory.register_builder()
  • bioimageit_core.core.observer module
    • Observable
      • Observable.add_observer()
      • Observable.new_job()
      • Observable.notify()
      • Observable.notify_error()
      • Observable.notify_progress()
      • Observable.notify_warning()
      • Observable.observers_count()
      • Observable.remove_observers()
    • Observer
      • Observer.COL_B
      • Observer.COL_G
      • Observer.COL_O
      • Observer.COL_P
      • Observer.COL_R
      • Observer.COL_W
      • Observer.new_job()
      • Observer.notify()
      • Observer.notify_error()
      • Observer.notify_progress()
      • Observer.notify_warning()
  • bioimageit_core.core.log_observer module
    • LogObserver
      • LogObserver.new_job()
      • LogObserver.notify()
      • LogObserver.notify_error()
      • LogObserver.notify_progress()
      • LogObserver.notify_warning()
  • bioimageit_core.core.query module
  • bioimageit_core.core.run module
  • bioimageit_core.core.serialize module
    • serialize_data()
    • serialize_raw_data()
    • serialize_processed_data()
    • serialize_dataset()
    • serialize_experiment()
    • serialize_run()
    • serialize_data()
    • serialize_dataset()
    • serialize_experiment()
    • serialize_processed_data()
    • serialize_raw_data()
    • serialize_run()
  • bioimageit_core.core.toolboxes module
  • bioimageit_core.core.utils module
    • extract_filename()
    • format_date()
    • generate_uuid()
  • Module contents
• 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
    • Classes
    • CondaRunnerService
      • CondaRunnerService.exec()
      • CondaRunnerService.set_up()
      • CondaRunnerService.tear_down()
    • CondaRunnerServiceBuilder
  • bioimageit_core.plugins.runner_condadocker module
    • Classes
    • CondaDockerRunnerService
      • CondaDockerRunnerService.exec()
      • CondaDockerRunnerService.set_up()
      • CondaDockerRunnerService.tear_down()
    • CondaDockerRunnerServiceBuilder
  • bioimageit_core.plugins.runner_docker module
    • Classes
    • DockerRunnerService
      • DockerRunnerService.exec()
      • DockerRunnerService.modify_io_path()
      • DockerRunnerService.relative_path()
      • DockerRunnerService.set_up()
      • DockerRunnerService.tear_down()
    • DockerRunnerServiceBuilder
    • extract_image_name()
    • get_docker_working_dir()
  • bioimageit_core.plugins.runner_local module
    • Classes
    • LocalRunnerService
      • LocalRunnerService.exec()
      • LocalRunnerService.set_up()
      • LocalRunnerService.tear_down()
    • LocalRunnerServiceBuilder
  • 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