diff env/lib/python3.7/site-packages/cwltool/software_requirements.py @ 5:9b1c78e6ba9c draft default tip

"planemo upload commit 6c0a8142489327ece472c84e558c47da711a9142"

--- a/env/lib/python3.7/site-packages/cwltool/software_requirements.py	Thu May 14 16:47:39 2020 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,135 +0,0 @@
-"""This module handles resolution of SoftwareRequirement hints.
-
-This is accomplished mainly by adapting cwltool internals to galaxy-lib's
-concept of "dependencies". Despite the name, galaxy-lib is a light weight
-library that can be used to map SoftwareRequirements in all sorts of ways -
-Homebrew, Conda, custom scripts, environment modules. We'd be happy to find
-ways to adapt new packages managers and such as well.
-"""
-from __future__ import absolute_import
-
-import argparse  # pylint: disable=unused-import
-import os
-import string
-from typing import Dict, List, MutableSequence, Optional
-
-from typing_extensions import Text  # pylint: disable=unused-import
-# move to a regular typing import when Python 3.3-3.6 is no longer supported
-
-from .builder import Builder, HasReqsHints
-try:
-    from galaxy.tool_util.deps.requirements import ToolRequirement, ToolRequirements
-    from galaxy.tool_util import deps
-except ImportError:
-    ToolRequirement = None  # type: ignore
-    ToolRequirements = None  # type: ignore
-    deps = None  # type: ignore
-
-
-SOFTWARE_REQUIREMENTS_ENABLED = deps is not None
-
-COMMAND_WITH_DEPENDENCIES_TEMPLATE = string.Template("""#!/bin/bash
-$handle_dependencies
-python "run_job.py" "job.json"
-""")
-
-
-class DependenciesConfiguration(object):
-
-    def __init__(self, args):
-        # type: (argparse.Namespace) -> None
-        """Initialize."""
-        conf_file = getattr(args, "beta_dependency_resolvers_configuration", None)
-        tool_dependency_dir = getattr(args, "beta_dependencies_directory", None)
-        conda_dependencies = getattr(args, "beta_conda_dependencies", None)
-        if conf_file is not None and os.path.exists(conf_file):
-            self.use_tool_dependencies = True
-            if tool_dependency_dir is None:
-                tool_dependency_dir = os.path.abspath(os.path.dirname(conf_file))
-            self.tool_dependency_dir = tool_dependency_dir
-            self.dependency_resolvers_config_file = os.path.abspath(conf_file)
-        elif conda_dependencies is not None:
-            if tool_dependency_dir is None:
-                tool_dependency_dir = os.path.abspath("./cwltool_deps")
-            self.tool_dependency_dir = tool_dependency_dir
-            self.use_tool_dependencies = True
-            self.dependency_resolvers_config_file = None
-        else:
-            self.use_tool_dependencies = False
-
-    def build_job_script(self, builder, command):
-        # type: (Builder, List[str]) -> Text
-        ensure_galaxy_lib_available()
-        resolution_config_dict = {
-            'use': self.use_tool_dependencies,
-            'default_base_path': self.tool_dependency_dir,
-        }
-        app_config = {
-            'conda_auto_install': True,
-            'conda_auto_init': True,
-        }
-        tool_dependency_manager = deps.build_dependency_manager(
-            app_config_dict=app_config,
-            resolution_config_dict=resolution_config_dict,
-            conf_file=self.dependency_resolvers_config_file,
-        )  # type: deps.DependencyManager
-        dependencies = get_dependencies(builder)
-        handle_dependencies = ""  # str
-        if dependencies:
-            handle_dependencies = "\n".join(
-                tool_dependency_manager.dependency_shell_commands(
-                    dependencies, job_directory=builder.tmpdir))
-
-        template_kwds = dict(handle_dependencies=handle_dependencies)  # type: Dict[str, str]
-        job_script = COMMAND_WITH_DEPENDENCIES_TEMPLATE.substitute(template_kwds)
-        return job_script
-
-
-def get_dependencies(builder):  # type: (HasReqsHints) -> ToolRequirements
-    (software_requirement, _) = builder.get_requirement("SoftwareRequirement")
-    dependencies = []  # type: List[ToolRequirement]
-    if software_requirement and software_requirement.get("packages"):
-        packages = software_requirement.get("packages")
-        for package in packages:
-            version = package.get("version", None)
-            if isinstance(version, MutableSequence):
-                if version:
-                    version = version[0]
-                else:
-                    version = None
-            specs = [{"uri": s} for s in package.get("specs", [])]
-            dependencies.append(ToolRequirement.from_dict(dict(
-                name=package["package"].split("#")[-1],
-                version=version,
-                type="package",
-                specs=specs,
-            )))
-
-    return ToolRequirements.from_list(dependencies)
-
-
-def get_container_from_software_requirements(use_biocontainers, builder):
-    # type: (bool, HasReqsHints) -> Optional[Text]
-    if use_biocontainers:
-        ensure_galaxy_lib_available()
-        from galaxy.tool_util.deps.dependencies import AppInfo, ToolInfo
-        from galaxy.tool_util.deps.containers import ContainerRegistry, DOCKER_CONTAINER_TYPE
-        app_info = AppInfo(
-            involucro_auto_init=True,
-            enable_mulled_containers=True,
-            container_image_cache_path=".",
-        )  # type: AppInfo
-        container_registry = ContainerRegistry(app_info)  # type: ContainerRegistry
-        requirements = get_dependencies(builder)
-        tool_info = ToolInfo(requirements=requirements)  # type: ToolInfo
-        container_description = container_registry.find_best_container_description([DOCKER_CONTAINER_TYPE], tool_info)
-        if container_description:
-            return container_description.identifier
-
-    return None
-
-
-def ensure_galaxy_lib_available():
-    # type: () -> None
-    if not SOFTWARE_REQUIREMENTS_ENABLED:
-        raise Exception("Optional Python library galaxy-lib not available, it is required for this configuration.")