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galaxy.tool_util package

Subpackages

Submodules

galaxy.tool_util.fetcher module

class galaxy.tool_util.fetcher.ToolLocationFetcher[source]

Bases: object

__init__()[source]

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

to_tool_path(path_or_uri_like, **kwds)[source]

galaxy.tool_util.lint module

This modules contains the functions that drive the tool linting framework.

galaxy.tool_util.lint.lint_tool_source(tool_source, level='all', fail_level='warn', extra_modules=[], skip_types=[], name=None)[source]
galaxy.tool_util.lint.lint_xml(tool_xml, level='all', fail_level='warn', extra_modules=[], skip_types=[], name=None)[source]
galaxy.tool_util.lint.lint_tool_source_with(lint_context, tool_source, extra_modules=[])[source]
galaxy.tool_util.lint.lint_xml_with(lint_context, tool_xml, extra_modules=[])[source]
class galaxy.tool_util.lint.LintContext(level, skip_types=[], object_name=None)[source]

Bases: object

__init__(level, skip_types=[], object_name=None)[source]

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

lint(name, lint_func, lint_target)[source]
valid(message, *args)[source]
info(message, *args)[source]
error(message, *args)[source]
warn(message, *args)[source]
failed(fail_level)[source]

galaxy.tool_util.loader module

galaxy.tool_util.loader.load_tool(path)
galaxy.tool_util.loader.load_tool_with_refereces(path)

Load XML documentation from file system and preprocesses XML macros.

Return the XML representation of the expanded tree and paths to referenced files that were imported (macros).

galaxy.tool_util.loader.raw_tool_xml_tree(path)

Load raw (no macro expansion) tree representation of XML represented at the specified path.

galaxy.tool_util.loader.imported_macro_paths(root)[source]
galaxy.tool_util.loader.template_macro_params(root)[source]

Look for template macros and populate param_dict (for cheetah) with these.

galaxy.tool_util.loader_directory module

Utilities for loading and reasoning about unparsed tools in directories.

galaxy.tool_util.loader_directory.find_possible_tools_from_path(path, recursive=False, enable_beta_formats=False)[source]

Walk a directory and find potential tool files.

galaxy.tool_util.loader_directory.load_tool_sources_from_path(path, load_exception_handler=<function load_exception_handler>, recursive=False, register_load_errors=False)[source]

Walk a directory and ToolSource objects.

galaxy.tool_util.loader_directory.load_tool_elements_from_path(path, load_exception_handler=<function load_exception_handler>, recursive=False, register_load_errors=False)[source]

Walk a directory and load tool XML elements.

galaxy.tool_util.loader_directory.is_tool_load_error(obj)[source]

Predicate to determine if object loaded for tool is a tool error.

galaxy.tool_util.loader_directory.looks_like_a_tool_xml(path)[source]

Quick check to see if a file looks like it may be a Galaxy XML tool file.

galaxy.tool_util.loader_directory.is_a_yaml_with_class(path, classes)[source]

Determine if a file is a valid YAML with a supplied class entry.

galaxy.tool_util.loader_directory.looks_like_a_tool_yaml(path)[source]

Quick check to see if a file looks like it may be a Galaxy YAML tool file.

galaxy.tool_util.loader_directory.looks_like_a_cwl_artifact(path, classes=None)[source]

Quick check to see if a file looks like it may be a CWL artifact.

galaxy.tool_util.loader_directory.looks_like_a_tool_cwl(path)[source]

Quick check to see if a file looks like it may be a CWL tool.

galaxy.tool_util.output_checker module

galaxy.tool_util.output_checker.check_output_regex(job_id_tag, regex, stream, stream_name, job_messages, max_error_level)[source]

check a single regex against a stream

regex the regex to check stream the stream to search in job_messages a list where the descriptions of the detected regexes can be appended max_error_level the maximum error level that has been detected so far returns the max of the error_level of the regex and the given max_error_level

galaxy.tool_util.output_checker.check_output(stdio_regexes, stdio_exit_codes, stdout, stderr, tool_exit_code, job_id_tag)[source]

Check the output of a tool - given the stdout, stderr, and the tool’s exit code, return DETECTED_JOB_STATE.OK if the tool exited succesfully or error type otherwise. No exceptions should be thrown. If this code encounters an exception, it returns OK so that the workflow can continue; otherwise, a bug in this code could halt workflow progress.

Note that, if the tool did not define any exit code handling or any stdio/stderr handling, then it reverts back to previous behavior: if stderr contains anything, then False is returned.

galaxy.tool_util.provided_metadata module

galaxy.tool_util.provided_metadata.parse_tool_provided_metadata(meta_file, provided_metadata_style=None, job_wrapper=None)[source]

Return a ToolProvidedMetadata object for specified file path.

If meta_file is absent, return a NullToolProvidedMetadata. If provided_metadata_style is None attempt to guess tool provided metadata type.

class galaxy.tool_util.provided_metadata.BaseToolProvidedMetadata[source]

Bases: object

get_new_datasets(output_name)[source]

Find new datasets for dataset discovery for specified output.

Return a list of such datasets.

Called only in the context of discovering datasets when discover_via=”tool_provided_metadata” is defined in the tool.

has_failed_outputs()[source]

Determine if generation of any of the outputs failed.

If True, this method should also log information about at least the first such failed output.

get_new_dataset_meta_by_basename(output_name, basename)[source]

For a discovered dataset, get the corresponding metadata entry.

The discovery may have been from explicit listing in this file (returned from get_new_datasets) or via file regex, either way the basename of the file is used to index the fetching of the metadata entry.

get_unnamed_outputs()[source]

Return unnamed outputs dataset introduced for upload 2.0.

Needs more formal specification but see output_collect for how destinations, types, elements, etc… are consumed.

get_dataset_meta(output_name, dataset_id)[source]

Return primary dataset metadata for specified output.

rewrite()[source]

Write metadata back to the file system.

If metadata has not changed via outputs specified as mutable, the implementation class may opt to not re-write the file.

get_new_datasets_for_metadata_collection()[source]

Return all datasets tracked that are not explicit primary outputs.

class galaxy.tool_util.provided_metadata.NullToolProvidedMetadata[source]

Bases: galaxy.tool_util.provided_metadata.BaseToolProvidedMetadata

class galaxy.tool_util.provided_metadata.LegacyToolProvidedMetadata(meta_file, job_wrapper=None)[source]

Bases: galaxy.tool_util.provided_metadata.BaseToolProvidedMetadata

__init__(meta_file, job_wrapper=None)[source]

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

get_dataset_meta(output_name, dataset_id)[source]

Return primary dataset metadata for specified output.

get_new_dataset_meta_by_basename(output_name, basename)[source]

For a discovered dataset, get the corresponding metadata entry.

The discovery may have been from explicit listing in this file (returned from get_new_datasets) or via file regex, either way the basename of the file is used to index the fetching of the metadata entry.

get_new_datasets(output_name)[source]

Find new datasets for dataset discovery for specified output.

Return a list of such datasets.

Called only in the context of discovering datasets when discover_via=”tool_provided_metadata” is defined in the tool.

has_failed_outputs()[source]

Determine if generation of any of the outputs failed.

If True, this method should also log information about at least the first such failed output.

get_unnamed_outputs()[source]

Return unnamed outputs dataset introduced for upload 2.0.

Needs more formal specification but see output_collect for how destinations, types, elements, etc… are consumed.

rewrite()[source]

Write metadata back to the file system.

If metadata has not changed via outputs specified as mutable, the implementation class may opt to not re-write the file.

get_new_datasets_for_metadata_collection()[source]

Return all datasets tracked that are not explicit primary outputs.

class galaxy.tool_util.provided_metadata.ToolProvidedMetadata(meta_file)[source]

Bases: galaxy.tool_util.provided_metadata.BaseToolProvidedMetadata

__init__(meta_file)[source]

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

get_dataset_meta(output_name, dataset_id)[source]

Return primary dataset metadata for specified output.

get_new_dataset_meta_by_basename(output_name, basename)[source]

For a discovered dataset, get the corresponding metadata entry.

The discovery may have been from explicit listing in this file (returned from get_new_datasets) or via file regex, either way the basename of the file is used to index the fetching of the metadata entry.

get_new_datasets(output_name)[source]

Find new datasets for dataset discovery for specified output.

Return a list of such datasets.

Called only in the context of discovering datasets when discover_via=”tool_provided_metadata” is defined in the tool.

has_failed_outputs()[source]

Determine if generation of any of the outputs failed.

If True, this method should also log information about at least the first such failed output.

get_unnamed_outputs()[source]

Return unnamed outputs dataset introduced for upload 2.0.

Needs more formal specification but see output_collect for how destinations, types, elements, etc… are consumed.

rewrite()[source]

Write metadata back to the file system.

If metadata has not changed via outputs specified as mutable, the implementation class may opt to not re-write the file.