def lint_repository_tools(ctx, realized_repository, lint_ctx, lint_args):
path = realized_repository.path
for (tool_path, tool_source) in yield_tool_sources(ctx,
path,
recursive=True):
original_path = tool_path.replace(path, realized_repository.real_path)
info("+Linting tool %s" % original_path)
if handle_tool_load_error(tool_path, tool_source):
return True
lint_tool_source_with(lint_ctx,
tool_source,
extra_modules=lint_args["extra_modules"])
def lint_repository_tools(ctx, realized_repository, lint_ctx, lint_args):
path = realized_repository.path
for (tool_path, tool_source) in yield_tool_sources(ctx, path,
recursive=True):
original_path = tool_path.replace(path, realized_repository.real_path)
info("+Linting tool %s" % original_path)
if handle_tool_load_error(tool_path, tool_source):
return True
lint_tool_source_with(
lint_ctx,
tool_source,
extra_modules=lint_args["extra_modules"]
)
def _build_auto_tool_repos(ctx, path, config, auto_tool_repos):
default_include = config.get("include", ["**"])
tool_source_pairs = list(yield_tool_sources(ctx, path, recursive=True))
paths = [_[0] for _ in tool_source_pairs]
excludes = _shed_config_excludes(config)
def _build_repository(tool_path, tool_source):
tool_id = tool_source.parse_id().lower()
tool_name = tool_source.parse_name()
description = tool_source.parse_description()
template_vars = dict(
tool_id=tool_id,
tool_name=tool_name,
description=description,
)
other_paths = paths[:]
other_paths.remove(tool_path)
tool_excludes = excludes + list(other_paths)
repo_dict = {
"include": default_include,
"exclude": tool_excludes,
}
for key in ["name", "description", "long_description"]:
template_key = "%s_template" % key
template = auto_tool_repos.get(template_key)
if template:
value = templates.render(template, **template_vars)
repo_dict[key] = value
return repo_dict
repos = odict.odict()
for tool_path, tool_source in tool_source_pairs:
repository_config = _build_repository(tool_path, tool_source)
repository_name = repository_config["name"]
repos[repository_name] = repository_config
return repos
def _build_auto_tool_repos(ctx, path, config, auto_tool_repos):
default_include = config.get("include", ["**"])
tool_source_pairs = list(yield_tool_sources(ctx, path, recursive=True))
paths = list(map(lambda pair: pair[0], tool_source_pairs))
excludes = _shed_config_excludes(config)
def _build_repository(tool_path, tool_source):
tool_id = tool_source.parse_id().lower()
tool_name = tool_source.parse_name()
description = tool_source.parse_description()
template_vars = dict(
tool_id=tool_id,
tool_name=tool_name,
description=description,
)
other_paths = paths[:]
other_paths.remove(tool_path)
tool_excludes = excludes + list(other_paths)
repo_dict = {
"include": default_include,
"exclude": tool_excludes,
}
for key in ["name", "description", "long_description"]:
template_key = "%s_template" % key
template = auto_tool_repos.get(template_key, None)
if template:
value = templates.render(template, **template_vars)
repo_dict[key] = value
return repo_dict
repos = odict.odict()
for tool_path, tool_source in tool_source_pairs:
repository_config = _build_repository(tool_path, tool_source)
repository_name = repository_config["name"]
repos[repository_name] = repository_config
return repos
def lint_repository(ctx, realized_repository, **kwds):
"""Lint a realized shed repository.
See :module:`planemo.shed` for details on constructing a realized
repository data structure.
"""
# TODO: this really needs to start working with realized path.
failed = False
path = realized_repository.real_path
info("Linting repository %s" % path)
lint_args, lint_ctx = setup_lint(ctx, **kwds)
lint_ctx.lint(
"lint_expansion",
lint_expansion,
realized_repository,
)
lint_ctx.lint(
"lint_expected_files",
lint_expected_files,
realized_repository,
)
lint_ctx.lint(
"lint_tool_dependencies_xsd",
lint_tool_dependencies_xsd,
path,
)
lint_ctx.lint(
"lint_tool_dependencies_sha256sum",
lint_tool_dependencies_sha256sum,
path,
)
lint_ctx.lint(
"lint_tool_dependencies_actions",
lint_tool_dependencies_actions,
path,
)
lint_ctx.lint(
"lint_repository_dependencies",
lint_repository_dependencies,
path,
)
lint_ctx.lint(
"lint_shed_yaml",
lint_shed_yaml,
realized_repository,
)
lint_ctx.lint(
"lint_readme",
lint_readme,
path,
)
if kwds["urls"]:
lint_ctx.lint(
"lint_urls",
lint_tool_dependencies_urls,
path,
)
if kwds["tools"]:
for (tool_path, tool_source) in yield_tool_sources(ctx, path,
recursive=True):
info("+Linting tool %s" % tool_path)
if handle_tool_load_error(tool_path, tool_source):
failed = True
continue
lint_tool_source_with(
lint_ctx,
tool_source,
extra_modules=lint_args["extra_modules"]
)
if kwds["ensure_metadata"]:
lint_ctx.lint(
"lint_shed_metadata",
lint_shed_metadata,
realized_repository,
)
return handle_lint_complete(lint_ctx, lint_args, failed=failed)
def lint_repository(ctx, realized_repository, **kwds):
"""Lint a realized shed repository.
See :module:`planemo.shed` for details on constructing a realized
repository data structure.
"""
# TODO: this really needs to start working with realized path.
failed = False
path = realized_repository.real_path
info("Linting repository %s" % path)
lint_args, lint_ctx = setup_lint(ctx, **kwds)
lint_ctx.lint(
"lint_expansion",
lint_expansion,
realized_repository,
)
lint_ctx.lint(
"lint_expected_files",
lint_expected_files,
realized_repository,
)
lint_ctx.lint(
"lint_tool_dependencies_xsd",
lint_tool_dependencies_xsd,
path,
)
lint_ctx.lint(
"lint_tool_dependencies_sha256sum",
lint_tool_dependencies_sha256sum,
path,
)
lint_ctx.lint(
"lint_tool_dependencies_actions",
lint_tool_dependencies_actions,
path,
)
lint_ctx.lint(
"lint_repository_dependencies",
lint_repository_dependencies,
path,
)
lint_ctx.lint(
"lint_shed_yaml",
lint_shed_yaml,
realized_repository,
)
lint_ctx.lint(
"lint_readme",
lint_readme,
path,
)
if kwds["urls"]:
lint_ctx.lint(
"lint_urls",
lint_tool_dependencies_urls,
path,
)
if kwds["tools"]:
for (tool_path, tool_source) in yield_tool_sources(ctx,
path,
recursive=True):
info("+Linting tool %s" % tool_path)
if handle_tool_load_error(tool_path, tool_source):
failed = True
continue
lint_tool_source_with(lint_ctx,
tool_source,
extra_modules=lint_args["extra_modules"])
if kwds["ensure_metadata"]:
lint_ctx.lint(
"lint_shed_metadata",
lint_shed_metadata,
realized_repository,
)
return handle_lint_complete(lint_ctx, lint_args, failed=failed)