Mercurial > repos > guerler > springsuite

annotate planemo/lib/python3.7/site-packages/galaxy/tool_util/deps/dependencies.py @ 0:d30785e31577 draft

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"planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
author guerler
date Fri, 31 Jul 2020 00:18:57 -0400
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1 from galaxy.tool_util.deps.requirements import ToolRequirements
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2 from galaxy.util import bunch
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3 from .mulled.mulled_build import DEFAULT_CHANNELS
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4
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5
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6 class AppInfo(object):
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7
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8 def __init__(
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9 self,
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10 galaxy_root_dir=None,
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11 default_file_path=None,
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12 tool_data_path=None,
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13 shed_tool_data_path=None,
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14 outputs_to_working_directory=False,
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15 container_image_cache_path=None,
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16 library_import_dir=None,
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17 enable_mulled_containers=False,
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18 containers_resolvers_config_file=None,
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19 involucro_path=None,
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20 involucro_auto_init=True,
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21 mulled_channels=DEFAULT_CHANNELS,
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22 ):
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23 self.galaxy_root_dir = galaxy_root_dir
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24 self.default_file_path = default_file_path
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25 self.tool_data_path = tool_data_path
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26 self.shed_tool_data_path = shed_tool_data_path
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27 # TODO: Vary default value for docker_volumes based on this...
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28 self.outputs_to_working_directory = outputs_to_working_directory
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29 self.container_image_cache_path = container_image_cache_path
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30 self.library_import_dir = library_import_dir
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31 self.enable_mulled_containers = enable_mulled_containers
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32 self.containers_resolvers_config_file = containers_resolvers_config_file
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33 self.involucro_path = involucro_path
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34 self.involucro_auto_init = involucro_auto_init
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35 self.mulled_channels = mulled_channels
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36
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37
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38 class ToolInfo(object):
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39 # TODO: Introduce tool XML syntax to annotate the optional environment
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40 # variables they can consume (e.g. JVM options, license keys, etc..)
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41 # and add these to env_path_through
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42
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43 def __init__(self, container_descriptions=None, requirements=None, requires_galaxy_python_environment=False, env_pass_through=["GALAXY_SLOTS"], guest_ports=None, tool_id=None, tool_version=None, profile=-1):
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44 if container_descriptions is None:
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45 container_descriptions = []
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46 if requirements is None:
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47 requirements = []
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48 self.container_descriptions = container_descriptions
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49 self.requirements = requirements
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50 self.requires_galaxy_python_environment = requires_galaxy_python_environment
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51 self.env_pass_through = env_pass_through
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52 self.guest_ports = guest_ports
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53 self.tool_id = tool_id
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54 self.tool_version = tool_version
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55 self.profile = profile
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56
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57
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58 class JobInfo(object):
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59
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60 def __init__(
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61 self, working_directory, tool_directory, job_directory, tmp_directory, home_directory, job_directory_type,
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62 ):
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63 self.working_directory = working_directory
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64 # Tool files may be remote staged - so this is unintuitively a property
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65 # of the job not of the tool.
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66 self.tool_directory = tool_directory
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67 self.job_directory = job_directory
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68 self.tmp_directory = tmp_directory
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69 self.home_directory = home_directory
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70 self.job_directory_type = job_directory_type # "galaxy" or "pulsar"
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71
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72
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73 class DependenciesDescription(object):
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74 """ Capture (in a readily serializable way) context related a tool
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75 dependencies - both the tool's listed requirements and the tool shed
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76 related context required to resolve dependencies via the
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77 ToolShedPackageDependencyResolver.
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78
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79 This is meant to enable remote resolution of dependencies, by the Pulsar or
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80 other potential remote execution mechanisms.
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81 """
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82
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83 def __init__(self, requirements=[], installed_tool_dependencies=[]):
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84 self.requirements = requirements
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85 # tool shed installed tool dependencies...
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86 self.installed_tool_dependencies = installed_tool_dependencies
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87
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88 def to_dict(self):
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89 return dict(
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90 requirements=[r.to_dict() for r in self.requirements],
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91 installed_tool_dependencies=[DependenciesDescription._toolshed_install_dependency_to_dict(d) for d in self.installed_tool_dependencies]
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92 )
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93
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94 @staticmethod
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95 def from_dict(as_dict):
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96 if as_dict is None:
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97 return None
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98
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99 requirements_dicts = as_dict.get('requirements', [])
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100 requirements = ToolRequirements.from_list(requirements_dicts)
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101 installed_tool_dependencies_dicts = as_dict.get('installed_tool_dependencies', [])
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102 installed_tool_dependencies = list(map(DependenciesDescription._toolshed_install_dependency_from_dict, installed_tool_dependencies_dicts))
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103 return DependenciesDescription(
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104 requirements=requirements,
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105 installed_tool_dependencies=installed_tool_dependencies
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106 )
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107
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108 @staticmethod
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109 def _toolshed_install_dependency_from_dict(as_dict):
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110 # Rather than requiring full models in Pulsar, just use simple objects
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111 # containing only properties and associations used to resolve
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112 # dependencies for tool execution.
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113 repository_object = bunch.Bunch(
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114 name=as_dict['repository_name'],
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115 owner=as_dict['repository_owner'],
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116 installed_changeset_revision=as_dict['repository_installed_changeset'],
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117 )
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118 dependency_object = bunch.Bunch(
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119 name=as_dict['dependency_name'],
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120 version=as_dict['dependency_version'],
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121 type=as_dict['dependency_type'],
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122 tool_shed_repository=repository_object,
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123 )
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124 return dependency_object
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125
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126 @staticmethod
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127 def _toolshed_install_dependency_to_dict(tool_dependency):
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128 tool_shed_repository = tool_dependency.tool_shed_repository
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129 return dict(
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130 dependency_name=tool_dependency.name,
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131 dependency_version=tool_dependency.version,
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132 dependency_type=tool_dependency.type,
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133 repository_name=tool_shed_repository.name,
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134 repository_owner=tool_shed_repository.owner,
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135 repository_installed_changeset=tool_shed_repository.installed_changeset_revision,
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136 )