diff env/lib/python3.7/site-packages/cwltool/software_requirements.py @ 0:26e78fe6e8c4 draft

"planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/env/lib/python3.7/site-packages/cwltool/software_requirements.py	Sat May 02 07:14:21 2020 -0400
@@ -0,0 +1,135 @@
+"""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.")