Mercurial > repos > shellac > guppy_basecaller

annotate env/lib/python3.7/site-packages/cwltool/software_requirements.py @ 3:758bc20232e8 draft

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"planemo upload commit 2a0fe2cc28b09e101d37293e53e82f61762262ec"
author shellac
date Thu, 14 May 2020 16:20:52 -0400
parents 26e78fe6e8c4
children
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1 """This module handles resolution of SoftwareRequirement hints.
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2
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3 This is accomplished mainly by adapting cwltool internals to galaxy-lib's
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4 concept of "dependencies". Despite the name, galaxy-lib is a light weight
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5 library that can be used to map SoftwareRequirements in all sorts of ways -
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6 Homebrew, Conda, custom scripts, environment modules. We'd be happy to find
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7 ways to adapt new packages managers and such as well.
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8 """
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9 from __future__ import absolute_import
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10
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11 import argparse # pylint: disable=unused-import
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12 import os
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13 import string
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14 from typing import Dict, List, MutableSequence, Optional
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15
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16 from typing_extensions import Text # pylint: disable=unused-import
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17 # move to a regular typing import when Python 3.3-3.6 is no longer supported
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18
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19 from .builder import Builder, HasReqsHints
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20 try:
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21 from galaxy.tool_util.deps.requirements import ToolRequirement, ToolRequirements
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22 from galaxy.tool_util import deps
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23 except ImportError:
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24 ToolRequirement = None # type: ignore
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25 ToolRequirements = None # type: ignore
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26 deps = None # type: ignore
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27
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28
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29 SOFTWARE_REQUIREMENTS_ENABLED = deps is not None
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30
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31 COMMAND_WITH_DEPENDENCIES_TEMPLATE = string.Template("""#!/bin/bash
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32 $handle_dependencies
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33 python "run_job.py" "job.json"
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34 """)
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35
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36
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37 class DependenciesConfiguration(object):
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38
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39 def __init__(self, args):
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40 # type: (argparse.Namespace) -> None
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41 """Initialize."""
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42 conf_file = getattr(args, "beta_dependency_resolvers_configuration", None)
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43 tool_dependency_dir = getattr(args, "beta_dependencies_directory", None)
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44 conda_dependencies = getattr(args, "beta_conda_dependencies", None)
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45 if conf_file is not None and os.path.exists(conf_file):
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46 self.use_tool_dependencies = True
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47 if tool_dependency_dir is None:
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48 tool_dependency_dir = os.path.abspath(os.path.dirname(conf_file))
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49 self.tool_dependency_dir = tool_dependency_dir
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50 self.dependency_resolvers_config_file = os.path.abspath(conf_file)
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51 elif conda_dependencies is not None:
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52 if tool_dependency_dir is None:
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53 tool_dependency_dir = os.path.abspath("./cwltool_deps")
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54 self.tool_dependency_dir = tool_dependency_dir
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55 self.use_tool_dependencies = True
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56 self.dependency_resolvers_config_file = None
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57 else:
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58 self.use_tool_dependencies = False
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59
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60 def build_job_script(self, builder, command):
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61 # type: (Builder, List[str]) -> Text
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62 ensure_galaxy_lib_available()
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63 resolution_config_dict = {
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64 'use': self.use_tool_dependencies,
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65 'default_base_path': self.tool_dependency_dir,
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66 }
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67 app_config = {
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68 'conda_auto_install': True,
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69 'conda_auto_init': True,
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70 }
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71 tool_dependency_manager = deps.build_dependency_manager(
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72 app_config_dict=app_config,
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73 resolution_config_dict=resolution_config_dict,
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74 conf_file=self.dependency_resolvers_config_file,
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75 ) # type: deps.DependencyManager
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76 dependencies = get_dependencies(builder)
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77 handle_dependencies = "" # str
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78 if dependencies:
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79 handle_dependencies = "\n".join(
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80 tool_dependency_manager.dependency_shell_commands(
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81 dependencies, job_directory=builder.tmpdir))
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82
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83 template_kwds = dict(handle_dependencies=handle_dependencies) # type: Dict[str, str]
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84 job_script = COMMAND_WITH_DEPENDENCIES_TEMPLATE.substitute(template_kwds)
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85 return job_script
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86
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87
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88 def get_dependencies(builder): # type: (HasReqsHints) -> ToolRequirements
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89 (software_requirement, _) = builder.get_requirement("SoftwareRequirement")
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90 dependencies = [] # type: List[ToolRequirement]
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91 if software_requirement and software_requirement.get("packages"):
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92 packages = software_requirement.get("packages")
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93 for package in packages:
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94 version = package.get("version", None)
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95 if isinstance(version, MutableSequence):
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96 if version:
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97 version = version[0]
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98 else:
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99 version = None
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100 specs = [{"uri": s} for s in package.get("specs", [])]
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101 dependencies.append(ToolRequirement.from_dict(dict(
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102 name=package["package"].split("#")[-1],
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103 version=version,
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104 type="package",
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105 specs=specs,
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106 )))
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107
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108 return ToolRequirements.from_list(dependencies)
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109
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110
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111 def get_container_from_software_requirements(use_biocontainers, builder):
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112 # type: (bool, HasReqsHints) -> Optional[Text]
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113 if use_biocontainers:
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114 ensure_galaxy_lib_available()
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115 from galaxy.tool_util.deps.dependencies import AppInfo, ToolInfo
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116 from galaxy.tool_util.deps.containers import ContainerRegistry, DOCKER_CONTAINER_TYPE
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117 app_info = AppInfo(
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118 involucro_auto_init=True,
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119 enable_mulled_containers=True,
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120 container_image_cache_path=".",
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121 ) # type: AppInfo
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122 container_registry = ContainerRegistry(app_info) # type: ContainerRegistry
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123 requirements = get_dependencies(builder)
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124 tool_info = ToolInfo(requirements=requirements) # type: ToolInfo
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125 container_description = container_registry.find_best_container_description([DOCKER_CONTAINER_TYPE], tool_info)
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126 if container_description:
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127 return container_description.identifier
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128
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129 return None
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130
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131
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132 def ensure_galaxy_lib_available():
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133 # type: () -> None
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134 if not SOFTWARE_REQUIREMENTS_ENABLED:
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135 raise Exception("Optional Python library galaxy-lib not available, it is required for this configuration.")