Eliminate deprecated XML-based abstraction from planemo.tools.

Using ToolSource to parse out tool name and ID in shed operations nows.

planemo/shed/__init__.py

@@ -33,7 +33,7 @@
    temp_directory,
)
from planemo.shed2tap.base import BasePackage
from planemo.tools import load_tool_elements_from_path
from planemo.tools import yield_tool_sources

from .diff import diff_and_remove
from .interface import (
@@ -418,7 +418,7 @@ def _diff_in(ctx, working, realized_repository, **kwds):
    return exit


def shed_repo_config(path, name=None):
def shed_repo_config(ctx, path, name=None):
    shed_yaml_path = os.path.join(path, SHED_CONFIG_NAME)
    config = {}
    if os.path.exists(shed_yaml_path):
@@ -427,7 +427,7 @@ def shed_repo_config(path, name=None):

    if config is None:  # yaml may yield None
        config = {}
    _expand_raw_config(config, path, name=name)
    _expand_raw_config(ctx, config, path, name=name)
    return config


@@ -504,7 +504,7 @@ def find_repository_id(ctx, shed_context, path, **kwds):
    repo_config = kwds.get("config", None)
    if repo_config is None:
        name = kwds.get("name", None)
        repo_config = shed_repo_config(path, name=name)
        repo_config = shed_repo_config(ctx, path, name=name)
    name = repo_config["name"]
    find_kwds = kwds.copy()
    if "name" in find_kwds:
@@ -537,7 +537,7 @@ def _owner(ctx, repo_config, shed_context=None, **kwds):
    return owner


def _expand_raw_config(config, path, name=None):
def _expand_raw_config(ctx, config, path, name=None):
    name_input = name
    if "name" not in config:
        config["name"] = name
@@ -554,7 +554,7 @@ def _expand_raw_config(config, path, name=None):
    if auto_tool_repos and name_input:
        raise Exception(AUTO_NAME_CONFLICT_MESSAGE)
    if auto_tool_repos:
        repos = _build_auto_tool_repos(path, config, auto_tool_repos)
        repos = _build_auto_tool_repos(ctx, path, config, auto_tool_repos)
    if suite_config:
        if repos is None:
            repos = odict.odict()
@@ -571,15 +571,15 @@ def _expand_raw_config(config, path, name=None):
    config["repositories"] = repos


def _build_auto_tool_repos(path, config, auto_tool_repos):
def _build_auto_tool_repos(ctx, path, config, auto_tool_repos):
    default_include = config.get("include", ["**"])
    tool_els = list(load_tool_elements_from_path(path, recursive=True))
    paths = list(map(lambda pair: pair[0], tool_els))
    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_el):
        tool_id = tool_el.getroot().get("id").lower()
        tool_name = tool_el.getroot().get("name")
    def _build_repository(tool_path, tool_source):
        tool_id = tool_source.parse_id().lower()
        tool_name = tool_source.parse_name()
        template_vars = dict(
            tool_id=tool_id,
            tool_name=tool_name,
@@ -600,8 +600,8 @@ def _build_repository(tool_path, tool_el):
        return repo_dict

    repos = odict.odict()
    for tool_path, tool_el in tool_els:
        repository_config = _build_repository(tool_path, tool_el)
    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
@@ -744,7 +744,7 @@ def find_raw_repositories(ctx, paths, **kwds):
    """Return a list of "raw" repository objects for each repo on paths."""
    raw_repo_objects = []
    for path in paths:
        raw_repo_objects.extend(_find_raw_repositories(path, **kwds))
        raw_repo_objects.extend(_find_raw_repositories(ctx, path, **kwds))
    return raw_repo_objects


@@ -804,7 +804,7 @@ def _realize_effective_repositories(ctx, path, **kwds):
    code repository but are published to the tool shed as one repository per
    tool).
    """
    raw_repo_objects = _find_raw_repositories(path, **kwds)
    raw_repo_objects = _find_raw_repositories(ctx, path, **kwds)
    failed = False
    with temp_directory() as base_dir:
        for raw_repo_object in raw_repo_objects:
@@ -904,7 +904,7 @@ def _path_on_disk(ctx, path):
            yield git_repo


def _find_raw_repositories(path, **kwds):
def _find_raw_repositories(ctx, path, **kwds):
    name = kwds.get("name", None)
    recursive = kwds.get("recursive", False)

@@ -916,7 +916,7 @@ def _find_raw_repositories(path, **kwds):
    if len(shed_file_dirs) == 1:
        shed_file_dir = shed_file_dirs[0]
        try:
            config = shed_repo_config(shed_file_dir, name=name)
            config = shed_repo_config(ctx, shed_file_dir, name=name)
        except Exception as e:
            error_message = PARSING_PROBLEM % (shed_file_dir, e)
            exception = RuntimeError(error_message)
@@ -932,10 +932,10 @@ def _find_raw_repositories(path, **kwds):
    raw_dirs = shed_file_dirs or [path]
    kwds_copy = kwds.copy()
    kwds_copy["name"] = name
    return _build_raw_repo_objects(raw_dirs, **kwds_copy)
    return _build_raw_repo_objects(ctx, raw_dirs, **kwds_copy)


def _build_raw_repo_objects(raw_dirs, **kwds):
def _build_raw_repo_objects(ctx, raw_dirs, **kwds):
    """
    From specific directories with .shed.yml files or specified directly from
    the command-line build abstract description of directories that should be
@@ -949,7 +949,7 @@ def _build_raw_repo_objects(raw_dirs, **kwds):
    raw_repo_objects = []
    for raw_dir in raw_dirs:
        try:
            config = shed_repo_config(raw_dir, name=name)
            config = shed_repo_config(ctx, raw_dir, name=name)
        except Exception as e:
            error_message = PARSING_PROBLEM % (raw_dir, e)
            exception = RuntimeError(error_message)

planemo/tools.py

@@ -60,18 +60,6 @@ def load_tool_sources_from_path(path, recursive, register_load_errors=False):
    )


# TODO: replace usage of this with tool source so planemo
# defers XML details to galaxy-lib.
def load_tool_elements_from_path(path, recursive, register_load_errors=False):
    """Generator for tool XML elements on a path."""
    return loader_directory.load_tool_elements_from_path(
        path,
        _load_exception_handler,
        recursive=recursive,
        register_load_errors=register_load_errors,
    )


def _load_exception_handler(path, exc_info):
    error("Error loading tool with path %s" % path)
    traceback.print_exception(*exc_info, limit=1, file=sys.stderr)
@@ -90,7 +78,6 @@ def _is_tool_source(ctx, tool_path, tool_source):


__all__ = (
    "load_tool_elements_from_path",
    "is_tool_load_error",
    "load_tool_sources_from_path",
    "yield_tool_sources",

tests/test_shed_operations.py

@@ -63,7 +63,7 @@ def test_find_category_ids():
def test_create_simple():
    with mock_shed_context() as shed_context:
        path = os.path.join(TEST_REPOS_DIR, "single_tool")
        repo_config = shed.shed_repo_config(path)
        repo_config = shed.shed_repo_config(shed_context, path)
        create_response = shed.create_repository_for(
            None,
            shed_context.tsi,