diff env/lib/python3.9/site-packages/galaxy/tool_util/deps/resolvers/brewed_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/brewed_tool_shed_packages.py	Mon Mar 22 18:12:50 2021 +0000
@@ -0,0 +1,153 @@
+"""
+This dependency resolver resolves tool shed dependencies (those defined
+tool_dependencies.xml) installed using Platform Homebrew and converted
+via shed2tap (e.g. https://github.com/jmchilton/homebrew-toolshed).
+"""
+import logging
+import os
+
+from galaxy.util import parse_xml
+from . import (
+    DependencyResolver,
+    NullDependency
+)
+from .resolver_mixins import (
+    UsesHomebrewMixin,
+    UsesInstalledRepositoriesMixin,
+    UsesToolDependencyDirMixin,
+)
+
+log = logging.getLogger(__name__)
+
+
+class HomebrewToolShedDependencyResolver(
+    DependencyResolver,
+    UsesHomebrewMixin,
+    UsesToolDependencyDirMixin,
+    UsesInstalledRepositoriesMixin,
+):
+    resolver_type = "tool_shed_tap"
+
+    def __init__(self, dependency_manager, **kwds):
+        self._init_homebrew(**kwds)
+        self._init_base_path(dependency_manager, **kwds)
+
+    def resolve(self, requirement, **kwds):
+        name, version, type = requirement.name, requirement.version, requirement.type
+        if type != "package":
+            return NullDependency(version=version, name=name)
+        if version is None:
+            return NullDependency(version=version, name=name)
+
+        return self._find_tool_dependencies(name, version, type, **kwds)
+
+    def _find_tool_dependencies(self, name, version, type, **kwds):
+        installed_tool_dependency = self._get_installed_dependency(name, type, version=version, **kwds)
+        if installed_tool_dependency:
+            return self._resolve_from_installed_tool_dependency(name, version, installed_tool_dependency)
+
+        if "tool_dir" in kwds:
+            tool_directory = os.path.abspath(kwds["tool_dir"])
+            tool_depenedencies_path = os.path.join(tool_directory, "tool_dependencies.xml")
+            if os.path.exists(tool_depenedencies_path):
+                return self._resolve_from_tool_dependencies_path(name, version, tool_depenedencies_path)
+
+        return NullDependency(version=version, name=name)
+
+    def _resolve_from_installed_tool_dependency(self, name, version, installed_tool_dependency):
+        tool_shed_repository = installed_tool_dependency.tool_shed_repository
+        recipe_name = build_recipe_name(
+            package_name=name,
+            package_version=version,
+            repository_owner=tool_shed_repository.owner,
+            repository_name=tool_shed_repository.name,
+        )
+        return self._find_dep_default(recipe_name, None)
+
+    def _resolve_from_tool_dependencies_path(self, name, version, tool_dependencies_path):
+        try:
+            raw_dependencies = RawDependencies(tool_dependencies_path)
+        except Exception:
+            log.debug("Failed to parse dependencies in file %s" % tool_dependencies_path)
+            return NullDependency(version=version, name=name)
+
+        raw_dependency = raw_dependencies.find(name, version)
+        if not raw_dependency:
+            return NullDependency(version=version, name=name)
+
+        recipe_name = build_recipe_name(
+            package_name=name,
+            package_version=version,
+            repository_owner=raw_dependency.repository_owner,
+            repository_name=raw_dependency.repository_name
+        )
+        dep = self._find_dep_default(recipe_name, None)
+        return dep
+
+
+class RawDependencies:
+
+    def __init__(self, dependencies_file):
+        self.root = parse_xml(dependencies_file).getroot()
+        dependencies = []
+        package_els = self.root.findall("package") or []
+        for package_el in package_els:
+            repository_el = package_el.find("repository")
+            if repository_el is None:
+                continue
+            dependency = RawDependency(self, package_el, repository_el)
+            dependencies.append(dependency)
+        self.dependencies = dependencies
+
+    def find(self, package_name, package_version):
+        target_dependency = None
+
+        for dependency in self.dependencies:
+            if dependency.package_name == package_name and dependency.package_version == package_version:
+                target_dependency = dependency
+                break
+        return target_dependency
+
+
+class RawDependency:
+
+    def __init__(self, dependencies, package_el, repository_el):
+        self.dependencies = dependencies
+        self.package_el = package_el
+        self.repository_el = repository_el
+
+    def __repr__(self):
+        temp = "Dependency[package_name=%s,version=%s,dependent_package=%s]"
+        return temp % (
+            self.package_el.attrib["name"],
+            self.package_el.attrib["version"],
+            self.repository_el.attrib["name"]
+        )
+
+    @property
+    def repository_owner(self):
+        return self.repository_el.attrib["owner"]
+
+    @property
+    def repository_name(self):
+        return self.repository_el.attrib["name"]
+
+    @property
+    def package_name(self):
+        return self.package_el.attrib["name"]
+
+    @property
+    def package_version(self):
+        return self.package_el.attrib["version"]
+
+
+def build_recipe_name(package_name, package_version, repository_owner, repository_name):
+    # TODO: Consider baking package_name and package_version into name? (would be more "correct")
+    owner = repository_owner.replace("-", "")
+    name = repository_name
+    name = name.replace("_", "").replace("-", "")
+    base = f"{owner}_{name}"
+    return base
+
+
+__all__ = ('HomebrewToolShedDependencyResolver', )