diff env/lib/python3.9/site-packages/galaxy/tool_util/deps/views.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/views.py	Mon Mar 22 18:12:50 2021 +0000
@@ -0,0 +1,414 @@
+from galaxy import exceptions
+from galaxy.util import asbool, listify
+from .dependencies import ToolInfo
+from .resolvers import (
+    ContainerDependency,
+    NullDependency,
+)
+
+
+class DependencyResolversView:
+    """ Provide a RESTfulish/JSONy interface to a galaxy.tool_util.deps.DependencyResolver
+    object. This can be adapted by the Galaxy web framework or other web apps.
+    """
+
+    def __init__(self, app):
+        self._app = app
+
+    def index(self):
+        return [r.to_dict() for r in self._dependency_resolvers]
+
+    def show(self, index):
+        return self._dependency_resolver(index).to_dict()
+
+    def reload(self):
+        self.toolbox.reload_dependency_manager()
+
+    def manager_requirements(self):
+        requirements = []
+        for index, resolver in enumerate(self._dependency_resolvers):
+            if not hasattr(resolver, "list_dependencies"):
+                continue
+            for requirement in resolver.list_dependencies():
+                requirements.append({"index": index, "requirement": requirement.to_dict()})
+        return requirements
+
+    def resolver_requirements(self, index):
+        requirements = []
+        resolver = self._dependency_resolver(index)
+        if not hasattr(resolver, "list_dependencies"):
+            raise exceptions.NotImplemented()
+        for requirement in resolver.list_dependencies():
+            requirements.append(requirement.to_dict())
+        return requirements
+
+    def manager_dependency(self, **kwds):
+        return self._dependency(**kwds)
+
+    def resolver_dependency(self, index, **kwds):
+        return self._dependency(**kwds)
+
+    def show_dependencies(self, tool_requirements_d, installed_tool_dependencies=None, **kwd):
+        """
+        Resolves dependencies to build a requirements status in the admin panel/API
+        """
+        to_deps_kwds = {
+            'install': False,
+            'return_null': True,
+            'installed_tool_dependencies': installed_tool_dependencies
+        }
+        to_deps_kwds.update(kwd)
+        dependencies_per_tool = {tool: self._dependency_manager.requirements_to_dependencies(requirements,
+                                                                                             **to_deps_kwds)
+                                 for tool, requirements in tool_requirements_d.items()}
+        return dependencies_per_tool
+
+    def uninstall_dependencies(self, index=None, resolver_type=None, container_type=None, **payload):
+        """Attempt to uninstall requirements. Returns 0 if successfull, else None."""
+        requirements = payload.get('requirements')
+        if not requirements:
+            return None
+        if index:
+            resolver = self._dependency_resolvers[index]
+            if resolver.can_uninstall_dependencies:
+                return resolver.uninstall(requirements)
+        elif resolver_type:
+            for resolver in self._dependency_resolvers:
+                if resolver.resolver_type == resolver_type and resolver.can_uninstall_dependencies:
+                    return resolver.uninstall(requirements)
+        elif container_type:
+            for resolver in self._dependency_resolvers:
+                if getattr(resolver, "container_type", None) == container_type and resolver.can_uninstall_dependencies:
+                    return resolver.uninstall(requirements)
+        else:
+            for index in self.uninstallable_resolvers:
+                return_code = self._dependency_resolvers[index].uninstall(requirements)
+                if return_code == 0:
+                    return return_code
+        return None
+
+    @property
+    def unused_dependency_paths(self):
+        """List dependencies that are not currently installed."""
+        unused_dependencies = []
+        toolbox_requirements_status = self.toolbox_requirements_status
+        for resolver in self._dependency_resolvers:
+            if hasattr(resolver, 'unused_dependency_paths'):
+                unused_dependencies.extend(resolver.unused_dependency_paths(toolbox_requirements_status))
+        return set(unused_dependencies)
+
+    def remove_unused_dependency_paths(self, envs):
+        """
+        Remove dependencies that are not currently used.
+
+        Returns a list of all environments that have been successfully removed.
+        """
+        envs_to_remove = set(envs)
+        toolbox_requirements_status = self.toolbox_requirements_status
+        removed_environments = set()
+        for resolver in self._dependency_resolvers:
+            if hasattr(resolver, 'unused_dependency_paths') and hasattr(resolver, 'uninstall_environments'):
+                unused_dependencies = resolver.unused_dependency_paths(toolbox_requirements_status)
+                can_remove = envs_to_remove & set(unused_dependencies)
+                exit_code = resolver.uninstall_environments(can_remove)
+                if exit_code == 0:
+                    removed_environments = removed_environments.union(can_remove)
+                    envs_to_remove = envs_to_remove.difference(can_remove)
+        return list(removed_environments)
+
+    def install_dependencies(self, requirements, **kwds):
+        kwds['install'] = True
+        return self._dependency_manager._requirements_to_dependencies_dict(requirements, **kwds)
+
+    def install_dependency(self, index=None, **payload):
+        """
+        Installs dependency using highest priority resolver that supports dependency installation
+        (Currently only the conda resolver supports this). If index is given, attempt
+        installation directly using the corresponding resolver.
+        Returns True on success, False on failure.
+        payload is dictionary that must container name, version and type,
+        e.g. {'name': 'numpy', version='1.9.1', type='package'}
+        """
+        if index:
+            return self._install_dependency(index, **payload)
+        else:
+            for index in self.installable_resolvers:
+                success = self._install_dependency(index, **payload)
+                if success:
+                    return success
+            return False
+
+    def _install_dependency(self, index, **payload):
+        """
+        Resolver install dependency should return True when installation succeeds,
+        False if not successful
+        """
+        resolver = self._dependency_resolver(index)
+        if resolver.read_only:
+            raise exceptions.RequestParameterInvalidException("Attempted to install on a read_only dependency resolver.")
+        if resolver.disabled:
+            raise exceptions.RequestParameterInvalidException("Attempted to install on a disabled dependency resolver.")
+
+        name, version, type, extra_kwds = self._parse_dependency_info(payload)
+        return resolver.install_dependency(
+            name=name,
+            version=version,
+            type=type,
+            **extra_kwds
+        )
+
+    def _dependency(self, index=None, **kwds):
+        if index is not None:
+            index = int(index)
+
+        name, version, type, extra_kwds = self._parse_dependency_info(kwds)
+        resolve_kwds = dict(
+            job_directory=None,
+            index=index,
+            **extra_kwds
+        )
+        dependency = self._dependency_manager.find_dep(
+            name, version=version, type=type, **resolve_kwds
+        )
+        return dependency.to_dict()
+
+    def _parse_dependency_info(self, kwds):
+        extra_kwds = kwds.copy()
+        name = extra_kwds.pop("name", None)
+        if name is None:
+            raise exceptions.RequestParameterMissingException("Missing 'name' parameter required for resolution.")
+        version = extra_kwds.pop("version", None)
+        type = extra_kwds.pop("type", "package")
+        return name, version, type, extra_kwds
+
+    def _dependency_resolver(self, index):
+        index = int(index)
+        return self._dependency_resolvers[index]
+
+    @property
+    def _dependency_manager(self):
+        return self._app.toolbox.dependency_manager
+
+    @property
+    def _dependency_resolvers(self):
+        dependency_manager = self._dependency_manager
+        dependency_resolvers = dependency_manager.dependency_resolvers
+        return dependency_resolvers
+
+    @property
+    def installable_resolvers(self):
+        """
+        List index for all active resolvers that have the 'install_dependency' attribute.
+        """
+        return [index for index, resolver in enumerate(self._dependency_resolvers) if not resolver.read_only and not resolver.disabled]
+
+    @property
+    def uninstallable_resolvers(self):
+        """
+        List index for all active resolvers that can uninstall dependencies that have been installed through this resolver.
+        """
+        return [index for index, resolver in enumerate(self._dependency_resolvers) if resolver.can_uninstall_dependencies and not resolver.disabled]
+
+    @property
+    def tool_ids_by_requirements(self):
+        """Dictionary with requirements as keys, and tool_ids as values."""
+        tool_ids_by_requirements = {}
+        if not self._app.toolbox.tools_by_id:
+            return {}
+        for tid, tool in self._app.toolbox.tools_by_id.items():
+            if tool.tool_requirements not in tool_ids_by_requirements:
+                tool_ids_by_requirements[tool.tool_requirements] = [tid]
+            else:
+                tool_ids_by_requirements[tool.tool_requirements].append(tid)
+        return tool_ids_by_requirements
+
+    @property
+    def toolbox_requirements_status(self):
+        return self.summarize_requirements()
+
+    def summarize_requirements(self, **kwds):
+        summary_kwds = {}
+        if 'index' in kwds:
+            summary_kwds['index'] = int(kwds['index'])
+        if 'include_containers' in kwds:
+            summary_kwds['include_containers'] = asbool(kwds['include_containers'])
+        if 'container_type' in kwds:
+            summary_kwds['container_type'] = kwds['container_type']
+        if 'resolver_type' in kwds:
+            summary_kwds['resolver_type'] = kwds['resolver_type']
+        if 'search' in kwds:
+            summary_kwds['search'] = asbool(kwds['search'])
+        if 'install' in kwds:
+            summary_kwds['install'] = asbool(kwds['install'])
+
+        tool_ids_by_requirements = self.tool_ids_by_requirements
+        statuses = {r: self.get_requirements_status(tool_requirements_d={tids[0]: r},
+                                                installed_tool_dependencies=self._app.toolbox.tools_by_id[tids[0]].installed_tool_dependencies, **summary_kwds)
+                for r, tids in tool_ids_by_requirements.items()}
+        if kwds.get("for_json", False):
+            # All public attributes of this class should be returning JSON - this is meant to mimic a restful API.
+            rval = []
+            for requirements, status in statuses.items():
+                item = {}
+                item["requirements"] = requirements.to_dict()
+                item["status"] = status
+                item["tool_ids"] = tool_ids_by_requirements[requirements]
+                rval.append(item)
+            statuses = rval
+        return statuses
+
+    def summarize_tools(self, **kwds):
+        summary_kwds = {}
+        if 'index' in kwds:
+            summary_kwds['index'] = int(kwds['index'])
+        if 'include_containers' in kwds:
+            summary_kwds['include_containers'] = asbool(kwds['include_containers'])
+        if 'container_type' in kwds:
+            summary_kwds['container_type'] = kwds['container_type']
+        if 'resolver_type' in kwds:
+            summary_kwds['resolver_type'] = kwds['resolver_type']
+        if 'search' in kwds:
+            summary_kwds['search'] = asbool(kwds['search'])
+        if 'install' in kwds:
+            summary_kwds['install'] = asbool(kwds['install'])
+
+        tool_ids = pop_tool_ids(kwds)
+
+        rval = []
+        for tid, tool in self._app.toolbox.tools_by_id.items():
+            if tool_ids and tid not in tool_ids:
+                continue
+
+            requirements = tool.tool_requirements
+            status = self.get_requirements_status(tool_requirements_d={tid: requirements},
+                                                  installed_tool_dependencies=tool.installed_tool_dependencies,
+                                                  tool_instance=tool, **summary_kwds)
+            item = {}
+            item["requirements"] = requirements.to_dict()
+            item["status"] = status
+            item["tool_ids"] = [tid]
+            rval.append(item)
+        return rval
+
+    def get_requirements_status(self, tool_requirements_d, installed_tool_dependencies=None, **kwd):
+        dependencies = self.show_dependencies(tool_requirements_d, installed_tool_dependencies, **kwd)
+        # dependencies is a dict keyed on tool_ids, value is a ToolRequirements object for that tool.
+        # We use the union of resolvable ToolRequirements to get resolved dependencies without duplicates.
+        requirements = [r.resolvable for r in tool_requirements_d.values()]
+        flat_tool_requirements = set().union(*requirements)
+        flat_dependencies = []
+        for requirements_odict in dependencies.values():
+            for requirement in requirements_odict:
+                if requirement in flat_tool_requirements:
+                    flat_dependencies.append(requirements_odict[requirement])
+                    flat_tool_requirements.remove(requirement)
+        return [d.to_dict() for d in flat_dependencies]
+
+    def clean(self, index=None, **kwds):
+        if index:
+            resolver = self._dependency_resolver(index)
+            if not hasattr(resolver, "clean"):
+                raise exceptions.NotImplemented()
+            else:
+                resolver.clean()
+                return "OK"
+        else:
+            [resolver.clean(**kwds) for resolver in self._dependency_resolvers if hasattr(resolver, 'clean')]
+            return "OK"
+
+
+class ContainerResolutionView:
+    """
+    """
+
+    def __init__(self, app):
+        self._app = app
+
+    def index(self):
+        return [r.to_dict() for r in self._container_resolvers]
+
+    def show(self, index):
+        return self._container_resolver(index).to_dict()
+
+    def resolve(self, **kwds):
+        find_best_kwds = {
+            'install': False,
+            'enabled_container_types': ['docker', 'singularity'],
+            'resolution_cache': kwds.get("resolution_cache"),
+            'session': kwds.get('session'),
+        }
+
+        if 'index' in kwds:
+            find_best_kwds['index'] = int(kwds['index'])
+        if 'container_type' in kwds:
+            find_best_kwds['enabled_container_types'] = [kwds['container_type']]
+        if 'resolver_type' in kwds:
+            find_best_kwds['resolver_type'] = kwds['resolver_type']
+        if 'install' in kwds:
+            find_best_kwds['install'] = asbool(kwds['install'])
+
+        tool_info_kwds = {}
+        tool_id = kwds["tool_id"]
+        tool = self._app.toolbox.tools_by_id[tool_id]
+
+        requirements = tool.tool_requirements
+        tool_info_kwds = dict(requirements=requirements)
+        requirements_only = asbool(kwds.get("requirements_only", False))
+        # If requirements_only, simply use the tool to load a requirement set from,
+        # mimics the default behavior of searching for containers through the dependency resolution
+        # component. Not useful for tool execution but perhaps when summarizing mulled containers for requirements.
+        if not requirements_only:
+            tool_info_kwds['container_descriptions'] = tool.containers
+            tool_info_kwds['requires_galaxy_python_environment'] = tool.requires_galaxy_python_environment
+            tool_info_kwds['tool_id'] = tool.id
+            tool_info_kwds['tool_version'] = tool.version
+
+        find_best_kwds["tool_info"] = ToolInfo(**tool_info_kwds)
+
+        # Consider implementing 'search' to match dependency resolution API.
+        resolved_container_description = self._app.container_finder.resolve(
+            **find_best_kwds
+        )
+        if resolved_container_description:
+            status = ContainerDependency(resolved_container_description.container_description, container_resolver=resolved_container_description.container_resolver).to_dict()
+        else:
+            status = NullDependency().to_dict()
+        return {
+            "tool_id": kwds["tool_id"],
+            "status": status,
+            "requirements": requirements.to_dict()
+        }
+
+    def resolve_toolbox(self, **kwds):
+        rval = []
+        resolve_kwds = kwds.copy()
+        tool_ids = pop_tool_ids(resolve_kwds)
+        resolve_kwds["resolution_cache"] = self._app.container_finder.resolution_cache()
+        if tool_ids is not None:
+            tool_ids = listify(tool_ids)
+        for tool_id, tool in self._app.toolbox.tools_by_id.items():
+            if tool_ids is not None and tool_id not in tool_ids:
+                continue
+
+            if tool.tool_action.produces_real_jobs:
+                rval.append(self.resolve(tool_id=tool_id, **resolve_kwds))
+        return rval
+
+    @property
+    def _container_resolvers(self):
+        return self._app.container_finder.container_resolvers
+
+    def _container_resolver(self, index):
+        index = int(index)
+        return self._container_resolvers[index]
+
+
+def pop_tool_ids(kwds):
+    tool_ids = None
+    if "tool_ids" in kwds:
+        tool_ids = listify(kwds.pop("tool_ids"))
+    if "tool_ids[]" in kwds:
+        tool_ids = listify(kwds.pop("tool_ids[]"))
+    if "tool_id" in kwds:
+        tool_ids = [kwds.pop("tool_id")]
+    return tool_ids