Mercurial > repos > shellac > sam_consensus_v3
annotate env/lib/python3.9/site-packages/galaxy/tool_util/deps/resolvers/tool_shed_packages.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 os.path import abspath, exists, join |
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2 |
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3 from . import NullDependency |
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4 from .galaxy_packages import ( |
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5 BaseGalaxyPackageDependencyResolver, |
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6 ToolShedDependency |
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7 ) |
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8 from .resolver_mixins import UsesInstalledRepositoriesMixin |
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9 |
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10 |
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11 class ToolShedPackageDependencyResolver(BaseGalaxyPackageDependencyResolver, UsesInstalledRepositoriesMixin): |
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12 resolver_type = "tool_shed_packages" |
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13 # Resolution of these dependencies depends on more than just the requirement |
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14 # tag, it depends on the tool installation context - therefore these are |
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15 # non-simple. |
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16 dependency_type = ToolShedDependency |
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17 resolves_simple_dependencies = False |
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18 |
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19 def __init__(self, dependency_manager, **kwds): |
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20 super().__init__(dependency_manager, **kwds) |
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21 |
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22 def _find_dep_versioned(self, name, version, type='package', **kwds): |
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23 installed_tool_dependency = self._get_installed_dependency(name, type, version=version, **kwds) |
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24 if installed_tool_dependency: |
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25 path = self._get_package_installed_dependency_path(installed_tool_dependency, name, version) |
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26 return self._galaxy_package_dep(path, version, name, type, True) |
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27 else: |
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28 return NullDependency(version=version, name=name) |
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29 |
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30 def _find_dep_default(self, name, type='package', **kwds): |
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31 if type == 'set_environment' and kwds.get('installed_tool_dependencies', None): |
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32 installed_tool_dependency = self._get_installed_dependency(name, type, version=None, **kwds) |
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33 if installed_tool_dependency: |
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34 dependency = self._get_set_environment_installed_dependency_script_path(installed_tool_dependency, name) |
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35 is_galaxy_dep = isinstance(dependency, ToolShedDependency) |
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36 has_script_dep = is_galaxy_dep and dependency.script and dependency.path |
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37 if has_script_dep: |
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38 # Environment settings do not use versions. |
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39 return ToolShedDependency(dependency.script, dependency.path, name, 'set_environment', None, True, dependency_resolver=self) |
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40 return NullDependency(version=None, name=name) |
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41 |
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42 def _get_package_installed_dependency_path(self, installed_tool_dependency, name, version): |
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43 tool_shed_repository = installed_tool_dependency.tool_shed_repository |
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44 base_path = self.base_path |
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45 return join( |
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46 base_path, |
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47 name, |
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48 version, |
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49 tool_shed_repository.owner, |
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50 tool_shed_repository.name, |
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51 tool_shed_repository.installed_changeset_revision |
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52 ) |
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53 |
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54 def _get_set_environment_installed_dependency_script_path(self, installed_tool_dependency, name): |
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55 tool_shed_repository = installed_tool_dependency.tool_shed_repository |
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56 base_path = self.base_path |
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57 path = abspath(join(base_path, |
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58 'environment_settings', |
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59 name, |
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60 tool_shed_repository.owner, |
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61 tool_shed_repository.name, |
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62 tool_shed_repository.installed_changeset_revision)) |
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63 if exists(path): |
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64 script = join(path, 'env.sh') |
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65 return ToolShedDependency(script, path, name, 'set_environment', None, True, dependency_resolver=self) |
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66 return NullDependency(version=None, name=name) |
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67 |
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68 |
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69 __all__ = ('ToolShedPackageDependencyResolver', ) |