Mercurial > repos > shellac > sam_consensus_v3
annotate env/lib/python3.9/site-packages/galaxy/tool_util/deps/dependencies.py @ 0:4f3585e2f14b draft default tip
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author | shellac |
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date | Mon, 22 Mar 2021 18:12:50 +0000 |
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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: |
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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: |
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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=None, guest_ports=None, tool_id=None, tool_version=None, profile=-1): |
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44 if env_pass_through is None: |
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45 env_pass_through = ["GALAXY_SLOTS"] |
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46 if container_descriptions is None: |
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47 container_descriptions = [] |
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48 if requirements is None: |
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49 requirements = [] |
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50 self.container_descriptions = container_descriptions |
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51 self.requirements = requirements |
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52 self.requires_galaxy_python_environment = requires_galaxy_python_environment |
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53 self.env_pass_through = env_pass_through |
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54 self.guest_ports = guest_ports |
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55 self.tool_id = tool_id |
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56 self.tool_version = tool_version |
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57 self.profile = profile |
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58 |
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59 |
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60 class JobInfo: |
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61 |
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62 def __init__( |
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63 self, working_directory, tool_directory, job_directory, tmp_directory, home_directory, job_directory_type, |
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64 ): |
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65 self.working_directory = working_directory |
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66 # Tool files may be remote staged - so this is unintuitively a property |
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67 # of the job not of the tool. |
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68 self.tool_directory = tool_directory |
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69 self.job_directory = job_directory |
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70 self.tmp_directory = tmp_directory |
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71 self.home_directory = home_directory |
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72 self.job_directory_type = job_directory_type # "galaxy" or "pulsar" |
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73 |
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74 |
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75 class DependenciesDescription: |
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76 """ Capture (in a readily serializable way) context related a tool |
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77 dependencies - both the tool's listed requirements and the tool shed |
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78 related context required to resolve dependencies via the |
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79 ToolShedPackageDependencyResolver. |
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80 |
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81 This is meant to enable remote resolution of dependencies, by the Pulsar or |
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82 other potential remote execution mechanisms. |
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83 """ |
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84 |
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85 def __init__(self, requirements=None, installed_tool_dependencies=None): |
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86 requirements = requirements or ToolRequirements() |
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87 if installed_tool_dependencies is None: |
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88 installed_tool_dependencies = [] |
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89 self.requirements = requirements |
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90 # tool shed installed tool dependencies... |
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91 self.installed_tool_dependencies = installed_tool_dependencies |
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92 |
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93 def to_dict(self): |
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94 return dict( |
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95 requirements=[r.to_dict() for r in self.requirements], |
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96 installed_tool_dependencies=[DependenciesDescription._toolshed_install_dependency_to_dict(d) for d in self.installed_tool_dependencies] |
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97 ) |
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98 |
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99 @staticmethod |
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100 def from_dict(as_dict): |
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101 if as_dict is None: |
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102 return None |
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103 |
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104 requirements_dicts = as_dict.get('requirements', []) |
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105 requirements = ToolRequirements.from_list(requirements_dicts) |
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106 installed_tool_dependencies_dicts = as_dict.get('installed_tool_dependencies', []) |
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107 installed_tool_dependencies = list(map(DependenciesDescription._toolshed_install_dependency_from_dict, installed_tool_dependencies_dicts)) |
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108 return DependenciesDescription( |
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109 requirements=requirements, |
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110 installed_tool_dependencies=installed_tool_dependencies |
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111 ) |
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112 |
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113 @staticmethod |
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114 def _toolshed_install_dependency_from_dict(as_dict): |
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115 # Rather than requiring full models in Pulsar, just use simple objects |
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116 # containing only properties and associations used to resolve |
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117 # dependencies for tool execution. |
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118 repository_object = bunch.Bunch( |
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119 name=as_dict['repository_name'], |
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120 owner=as_dict['repository_owner'], |
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121 installed_changeset_revision=as_dict['repository_installed_changeset'], |
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122 ) |
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123 dependency_object = bunch.Bunch( |
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124 name=as_dict['dependency_name'], |
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125 version=as_dict['dependency_version'], |
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126 type=as_dict['dependency_type'], |
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127 tool_shed_repository=repository_object, |
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128 ) |
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129 return dependency_object |
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130 |
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131 @staticmethod |
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132 def _toolshed_install_dependency_to_dict(tool_dependency): |
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133 tool_shed_repository = tool_dependency.tool_shed_repository |
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134 return dict( |
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135 dependency_name=tool_dependency.name, |
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136 dependency_version=tool_dependency.version, |
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137 dependency_type=tool_dependency.type, |
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138 repository_name=tool_shed_repository.name, |
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139 repository_owner=tool_shed_repository.owner, |
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140 repository_installed_changeset=tool_shed_repository.installed_changeset_revision, |
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141 ) |