diff env/lib/python3.9/site-packages/galaxy/tool_util/deps/resolvers/tool_shed_packages.py @ 0:4f3585e2f14b draft default tip

"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/env/lib/python3.9/site-packages/galaxy/tool_util/deps/resolvers/tool_shed_packages.py	Mon Mar 22 18:12:50 2021 +0000
@@ -0,0 +1,69 @@
+from os.path import abspath, exists, join
+
+from . import NullDependency
+from .galaxy_packages import (
+    BaseGalaxyPackageDependencyResolver,
+    ToolShedDependency
+)
+from .resolver_mixins import UsesInstalledRepositoriesMixin
+
+
+class ToolShedPackageDependencyResolver(BaseGalaxyPackageDependencyResolver, UsesInstalledRepositoriesMixin):
+    resolver_type = "tool_shed_packages"
+    # Resolution of these dependencies depends on more than just the requirement
+    # tag, it depends on the tool installation context - therefore these are
+    # non-simple.
+    dependency_type = ToolShedDependency
+    resolves_simple_dependencies = False
+
+    def __init__(self, dependency_manager, **kwds):
+        super().__init__(dependency_manager, **kwds)
+
+    def _find_dep_versioned(self, name, version, type='package', **kwds):
+        installed_tool_dependency = self._get_installed_dependency(name, type, version=version, **kwds)
+        if installed_tool_dependency:
+            path = self._get_package_installed_dependency_path(installed_tool_dependency, name, version)
+            return self._galaxy_package_dep(path, version, name, type, True)
+        else:
+            return NullDependency(version=version, name=name)
+
+    def _find_dep_default(self, name, type='package', **kwds):
+        if type == 'set_environment' and kwds.get('installed_tool_dependencies', None):
+            installed_tool_dependency = self._get_installed_dependency(name, type, version=None, **kwds)
+            if installed_tool_dependency:
+                dependency = self._get_set_environment_installed_dependency_script_path(installed_tool_dependency, name)
+                is_galaxy_dep = isinstance(dependency, ToolShedDependency)
+                has_script_dep = is_galaxy_dep and dependency.script and dependency.path
+                if has_script_dep:
+                    # Environment settings do not use versions.
+                    return ToolShedDependency(dependency.script, dependency.path, name, 'set_environment', None, True, dependency_resolver=self)
+        return NullDependency(version=None, name=name)
+
+    def _get_package_installed_dependency_path(self, installed_tool_dependency, name, version):
+        tool_shed_repository = installed_tool_dependency.tool_shed_repository
+        base_path = self.base_path
+        return join(
+            base_path,
+            name,
+            version,
+            tool_shed_repository.owner,
+            tool_shed_repository.name,
+            tool_shed_repository.installed_changeset_revision
+        )
+
+    def _get_set_environment_installed_dependency_script_path(self, installed_tool_dependency, name):
+        tool_shed_repository = installed_tool_dependency.tool_shed_repository
+        base_path = self.base_path
+        path = abspath(join(base_path,
+                            'environment_settings',
+                            name,
+                            tool_shed_repository.owner,
+                            tool_shed_repository.name,
+                            tool_shed_repository.installed_changeset_revision))
+        if exists(path):
+            script = join(path, 'env.sh')
+            return ToolShedDependency(script, path, name, 'set_environment', None, True, dependency_resolver=self)
+        return NullDependency(version=None, name=name)
+
+
+__all__ = ('ToolShedPackageDependencyResolver', )