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comparison 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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-1:000000000000 0:d30785e31577
1 from galaxy.tool_util.deps.requirements import ToolRequirements
2 from galaxy.util import bunch
3 from .mulled.mulled_build import DEFAULT_CHANNELS
4
5
6 class AppInfo(object):
7
8 def __init__(
9 self,
10 galaxy_root_dir=None,
11 default_file_path=None,
12 tool_data_path=None,
13 shed_tool_data_path=None,
14 outputs_to_working_directory=False,
15 container_image_cache_path=None,
16 library_import_dir=None,
17 enable_mulled_containers=False,
18 containers_resolvers_config_file=None,
19 involucro_path=None,
20 involucro_auto_init=True,
21 mulled_channels=DEFAULT_CHANNELS,
22 ):
23 self.galaxy_root_dir = galaxy_root_dir
24 self.default_file_path = default_file_path
25 self.tool_data_path = tool_data_path
26 self.shed_tool_data_path = shed_tool_data_path
27 # TODO: Vary default value for docker_volumes based on this...
28 self.outputs_to_working_directory = outputs_to_working_directory
29 self.container_image_cache_path = container_image_cache_path
30 self.library_import_dir = library_import_dir
31 self.enable_mulled_containers = enable_mulled_containers
32 self.containers_resolvers_config_file = containers_resolvers_config_file
33 self.involucro_path = involucro_path
34 self.involucro_auto_init = involucro_auto_init
35 self.mulled_channels = mulled_channels
36
37
38 class ToolInfo(object):
39 # TODO: Introduce tool XML syntax to annotate the optional environment
40 # variables they can consume (e.g. JVM options, license keys, etc..)
41 # and add these to env_path_through
42
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):
44 if container_descriptions is None:
45 container_descriptions = []
46 if requirements is None:
47 requirements = []
48 self.container_descriptions = container_descriptions
49 self.requirements = requirements
50 self.requires_galaxy_python_environment = requires_galaxy_python_environment
51 self.env_pass_through = env_pass_through
52 self.guest_ports = guest_ports
53 self.tool_id = tool_id
54 self.tool_version = tool_version
55 self.profile = profile
56
57
58 class JobInfo(object):
59
60 def __init__(
61 self, working_directory, tool_directory, job_directory, tmp_directory, home_directory, job_directory_type,
62 ):
63 self.working_directory = working_directory
64 # Tool files may be remote staged - so this is unintuitively a property
65 # of the job not of the tool.
66 self.tool_directory = tool_directory
67 self.job_directory = job_directory
68 self.tmp_directory = tmp_directory
69 self.home_directory = home_directory
70 self.job_directory_type = job_directory_type # "galaxy" or "pulsar"
71
72
73 class DependenciesDescription(object):
74 """ Capture (in a readily serializable way) context related a tool
75 dependencies - both the tool's listed requirements and the tool shed
76 related context required to resolve dependencies via the
77 ToolShedPackageDependencyResolver.
78
79 This is meant to enable remote resolution of dependencies, by the Pulsar or
80 other potential remote execution mechanisms.
81 """
82
83 def __init__(self, requirements=[], installed_tool_dependencies=[]):
84 self.requirements = requirements
85 # tool shed installed tool dependencies...
86 self.installed_tool_dependencies = installed_tool_dependencies
87
88 def to_dict(self):
89 return dict(
90 requirements=[r.to_dict() for r in self.requirements],
91 installed_tool_dependencies=[DependenciesDescription._toolshed_install_dependency_to_dict(d) for d in self.installed_tool_dependencies]
92 )
93
94 @staticmethod
95 def from_dict(as_dict):
96 if as_dict is None:
97 return None
98
99 requirements_dicts = as_dict.get('requirements', [])
100 requirements = ToolRequirements.from_list(requirements_dicts)
101 installed_tool_dependencies_dicts = as_dict.get('installed_tool_dependencies', [])
102 installed_tool_dependencies = list(map(DependenciesDescription._toolshed_install_dependency_from_dict, installed_tool_dependencies_dicts))
103 return DependenciesDescription(
104 requirements=requirements,
105 installed_tool_dependencies=installed_tool_dependencies
106 )
107
108 @staticmethod
109 def _toolshed_install_dependency_from_dict(as_dict):
110 # Rather than requiring full models in Pulsar, just use simple objects
111 # containing only properties and associations used to resolve
112 # dependencies for tool execution.
113 repository_object = bunch.Bunch(
114 name=as_dict['repository_name'],
115 owner=as_dict['repository_owner'],
116 installed_changeset_revision=as_dict['repository_installed_changeset'],
117 )
118 dependency_object = bunch.Bunch(
119 name=as_dict['dependency_name'],
120 version=as_dict['dependency_version'],
121 type=as_dict['dependency_type'],
122 tool_shed_repository=repository_object,
123 )
124 return dependency_object
125
126 @staticmethod
127 def _toolshed_install_dependency_to_dict(tool_dependency):
128 tool_shed_repository = tool_dependency.tool_shed_repository
129 return dict(
130 dependency_name=tool_dependency.name,
131 dependency_version=tool_dependency.version,
132 dependency_type=tool_dependency.type,
133 repository_name=tool_shed_repository.name,
134 repository_owner=tool_shed_repository.owner,
135 repository_installed_changeset=tool_shed_repository.installed_changeset_revision,
136 )