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galaxy.job_execution package

Submodules

galaxy.job_execution.datasets module

Utility classes allowing Job interface to reason about datasets.

galaxy.job_execution.datasets.dataset_path_rewrites(dataset_paths)

class galaxy.job_execution.datasets.DatasetPath(dataset_id, real_path, false_path=None, false_extra_files_path=None, false_metadata_path=None, mutable=True, dataset_uuid=None, object_store_id=None)

Bases: object

__init__(dataset_id, real_path, false_path=None, false_extra_files_path=None, false_metadata_path=None, mutable=True, dataset_uuid=None, object_store_id=None)

x.__init__(…) initializes x; see help(type(x)) for signature

with_path_for_job(false_path, false_extra_files_path=None, false_metadata_path=None)

Clone the dataset path but with a new false_path.

class galaxy.job_execution.datasets.DatasetPathRewriter

Bases: object

Used by runner to rewrite paths.

rewrite_dataset_path(dataset, dataset_type)

Dataset type is ‘input’ or ‘output’. Return None to indicate not to rewrite this path.

class galaxy.job_execution.datasets.NullDatasetPathRewriter

Bases: object

Used by default for jobwrapper, do not rewrite anything.

rewrite_dataset_path(dataset, dataset_type)

Keep path the same.

class galaxy.job_execution.datasets.OutputsToWorkingDirectoryPathRewriter(working_directory, outputs_directory_name)

Bases: object

Rewrites all paths to place them in the specified working directory for normal jobs when Galaxy is configured with app.config.outputs_to_working_directory. Job runner base class is responsible for copying these out after job is complete.

__init__(working_directory, outputs_directory_name)

x.__init__(…) initializes x; see help(type(x)) for signature

rewrite_dataset_path(dataset, dataset_type)

Keep path the same.

class galaxy.job_execution.datasets.TaskPathRewriter(working_directory, job_dataset_path_rewriter)

Bases: object

Rewrites all paths to place them in the specified working directory for TaskWrapper. TaskWrapper is responsible for putting them there and pulling them out.

__init__(working_directory, job_dataset_path_rewriter)

x.__init__(…) initializes x; see help(type(x)) for signature

rewrite_dataset_path(dataset, dataset_type)

galaxy.job_execution.output_collect module

Code allowing tools to define extra files associated with an output datset.

class galaxy.job_execution.output_collect.PermissionProvider(inp_data, security_agent, job)

Bases: object

__init__(inp_data, security_agent, job)

x.__init__(…) initializes x; see help(type(x)) for signature

permissions

set_default_hda_permissions(primary_data)

copy_dataset_permissions(init_from, primary_data)

class galaxy.job_execution.output_collect.MetadataSourceProvider(inp_data)

Bases: object

__init__(inp_data)

x.__init__(…) initializes x; see help(type(x)) for signature

get_metadata_source(input_name)

galaxy.job_execution.output_collect.collect_dynamic_outputs(job_context, output_collections)

class galaxy.job_execution.output_collect.BaseJobContext

Bases: object

add_dataset_collection(collection)

find_files(output_name, collection, dataset_collectors)

class galaxy.job_execution.output_collect.JobContext(tool, tool_provided_metadata, job, job_working_directory, permission_provider, metadata_source_provider, input_dbkey, object_store)

Bases: galaxy.model.store.discover.ModelPersistenceContext, galaxy.job_execution.output_collect.BaseJobContext

__init__(tool, tool_provided_metadata, job, job_working_directory, permission_provider, metadata_source_provider, input_dbkey, object_store)

x.__init__(…) initializes x; see help(type(x)) for signature

work_context

user

tag_handler

persist_object(obj)

Add the target to the persistence layer.

flush()

If database bound, flush the persisted objects to ensure IDs.

get_library_folder(destination)

get_hdca(object_id)

create_library_folder(parent_folder, name, description)

Create a library folder ready from supplied attributes for supplied parent.

create_hdca(name, structure)

add_output_dataset_association(name, dataset)

If discovering outputs for a job, persist output dataset association.

add_library_dataset_to_folder(library_folder, ld)

Add library dataset to persisted library folder.

add_datasets_to_history(datasets, for_output_dataset=None)

Add datasets to the history this context points at.

output_collection_def(name)

output_def(name)

job_id()

class galaxy.job_execution.output_collect.SessionlessJobContext(metadata_params, tool_provided_metadata, object_store, export_store, import_store, working_directory)

Bases: galaxy.model.store.discover.SessionlessModelPersistenceContext, galaxy.job_execution.output_collect.BaseJobContext

__init__(metadata_params, tool_provided_metadata, object_store, export_store, import_store, working_directory)

x.__init__(…) initializes x; see help(type(x)) for signature

output_collection_def(name)

output_def(name)

job_id()

get_hdca(object_id)

add_dataset_collection(collection)

add_output_dataset_association(name, dataset_instance)

No-op, no job context to persist this association for.

galaxy.job_execution.output_collect.collect_primary_datasets(job_context, output, input_ext)

galaxy.job_execution.output_collect.discover_files(output_name, tool_provided_metadata, extra_file_collectors, job_working_directory, matchable)

galaxy.job_execution.output_collect.walk_over_file_collectors(extra_file_collectors, job_working_directory, matchable)

galaxy.job_execution.output_collect.walk_over_extra_files(target_dir, extra_file_collector, job_working_directory, matchable)

Walks through all files in a given directory, and returns all files that match the given collector’s match criteria. If the collector has the recurse flag enabled, will also recursively descend into child folders.

galaxy.job_execution.output_collect.dataset_collector(dataset_collection_description)

class galaxy.job_execution.output_collect.ToolMetadataDatasetCollector(dataset_collection_description)

Bases: object

__init__(dataset_collection_description)

x.__init__(…) initializes x; see help(type(x)) for signature

class galaxy.job_execution.output_collect.DatasetCollector(dataset_collection_description)

Bases: object

__init__(dataset_collection_description)

x.__init__(…) initializes x; see help(type(x)) for signature

match(dataset_instance, filename, path=None)

sort(matches)

galaxy.job_execution.output_collect.read_exit_code_from(exit_code_file, id_tag)

Read exit code reported for a Galaxy job.

galaxy.job_execution.output_collect.default_exit_code_file(files_dir, id_tag)

galaxy.job_execution.output_collect.collect_extra_files(object_store, dataset, job_working_directory)