Source code for planemo.commands.cmd_autoupdate

"""Module describing the planemo ``autoupdate`` command."""
import json
from typing import Callable

import click
import yaml
from galaxy.tool_util.parser.xml import XmlToolSource

from planemo import (
    autoupdate,
    options,
)
from planemo.cli import command_function
from planemo.config import planemo_option
from planemo.engine import (
    engine_context,
    is_galaxy_engine,
)
from planemo.engine.test import test_runnables
from planemo.exit_codes import (
    EXIT_CODE_GENERIC_FAILURE,
    EXIT_CODE_OK,
)
from planemo.io import (
    coalesce_return_codes,
    error,
    info,
)
from planemo.runnable import (
    for_paths,
    RunnableType,
)
from planemo.tools import (
    is_tool_load_error,
    yield_tool_sources_on_paths,
)


[docs]def dry_run_option() -> Callable: """Perform a dry run autoupdate without modifying the XML files""" return planemo_option( "--dry-run", is_flag=True, help="Perform a dry run autoupdate without modifying the XML files." )
[docs]def test_option() -> Callable: """Test updated XML files""" return planemo_option("--test", is_flag=True, help="Test updated XML files.")
[docs]def skiplist_option() -> Callable: """List of XML files to skip""" return planemo_option( "--skiplist", default=None, help="Skiplist file, containing a list of tools or workflows for which autoupdate should be skipped.", )
[docs]def skip_requirements_option() -> Callable: """List of requirements to skip""" return planemo_option( "--skip_requirements", default="python,r-base,perl", help="Comma-separated list of requirements which should be not be updated. Default is python,r-base,perl.", )
@click.command("autoupdate") # noqa C901 @options.optional_tools_arg(multiple=True) @dry_run_option() @options.recursive_option() @test_option() @skiplist_option() @skip_requirements_option() @options.test_options() @options.galaxy_target_options() @options.galaxy_config_options() @options.report_level_option() @options.report_xunit() @options.fail_level_option() @options.galaxy_url_option() @options.galaxy_user_key_option() @command_function def cli(ctx, paths, **kwds): # noqa C901 """Auto-update tool requirements by checking against Conda and updating if newer versions are available.""" assert_tools = kwds.get("assert_tools", True) recursive = kwds.get("recursive", False) exit_codes = [] modified_files = set() tools_to_skip = [line.rstrip() for line in open(kwds["skiplist"])] if kwds["skiplist"] else [] runnables = for_paths(paths) if any(r.type in {RunnableType.galaxy_tool, RunnableType.directory} for r in runnables): # update Galaxy tools for (tool_path, tool_xml) in yield_tool_sources_on_paths(ctx, paths, recursive): if tool_path.split("/")[-1] in tools_to_skip: info("Skipping tool %s" % tool_path) continue info("Auto-updating tool %s" % tool_path) try: updated = autoupdate.autoupdate_tool(ctx, tool_path, modified_files=modified_files, **kwds) if updated: modified_files.update(updated) except Exception as e: error(f"{tool_path} could not be updated - the following error was raised: {e.__str__()}") if handle_tool_load_error(tool_path, tool_xml): exit_codes.append(EXIT_CODE_GENERIC_FAILURE) continue else: exit_codes.append(EXIT_CODE_OK) workflows = [ r for r in runnables if r.type == RunnableType.galaxy_workflow and r.path.split("/")[-1] not in tools_to_skip ] modified_workflows = [] for workflow in workflows: tools_to_update = autoupdate.get_tools_to_update(ctx, workflow, tools_to_skip) if tools_to_update: modified_workflows.append(workflow) info("The following tools are outdated:") for tool, versions in tools_to_update.items(): info(f"{tool}: {versions['current']} -> {versions['updated']}") else: info("No newer tool versions were found, so the workflow was not updated.") if modified_workflows and not kwds.get("dry_run"): assert is_galaxy_engine(**kwds) if kwds.get("engine") != "external_galaxy": kwds["install_most_recent_revision"] = True kwds["install_resolver_dependencies"] = False kwds["install_repository_dependencies"] = False kwds["shed_install"] = True with engine_context(ctx, **kwds) as galaxy_engine: with galaxy_engine.ensure_runnables_served(modified_workflows) as config: for workflow in modified_workflows: if config.updated_repos.get(workflow.path) or kwds.get("engine") == "external_galaxy": info("Auto-updating workflow %s" % workflow.path) updated_workflow = autoupdate.autoupdate_wf(ctx, config, workflow) if workflow.path.endswith(".ga"): with open(workflow.path) as f: original_workflow = json.load(f) edited_workflow = autoupdate.fix_workflow_ga(original_workflow, updated_workflow) with open(workflow.path, "w") as f: json.dump(edited_workflow, f, indent=4) else: with open(workflow.path) as f: original_workflow = yaml.load(f, Loader=yaml.SafeLoader) edited_workflow = autoupdate.fix_workflow_gxformat2(original_workflow, updated_workflow) with open(workflow.path, "w") as f: yaml.dump(edited_workflow, f) if original_workflow.get("release"): info( f"The workflow release number has been updated from " f"{original_workflow.get('release')} to {edited_workflow.get('release')}." ) if kwds["test"]: if not modified_files and not modified_workflows: info("No tools or workflows were updated, so no tests were run.") else: modified_paths = [ path for path, tool_xml in yield_tool_sources_on_paths(ctx, paths, recursive) if path in modified_files ] info(f"Running tests for the following auto-updated tools: {', '.join(modified_paths)}") runnables = for_paths(modified_paths + modified_workflows) kwds["engine"] = "galaxy" return_value = test_runnables(ctx, runnables, original_paths=paths, **kwds) exit_codes.append(return_value) return coalesce_return_codes(exit_codes, assert_at_least_one=assert_tools)
[docs]def handle_tool_load_error(tool_path: str, tool_xml: XmlToolSource) -> bool: """Return True if tool_xml is tool load error (invalid XML), and print a helpful error message. """ is_error = False if is_tool_load_error(tool_xml): info("Could not update %s due to malformed xml." % tool_path) is_error = True return is_error