Implement read-only conda resolver.

doc/source/admin/dependency_resolvers.rst

@@ -236,3 +236,7 @@ copy_dependencies
     linking them when creating per job environments. This should be considered somewhat
     deprecated because Conda will do this as needed for newer versions of Conda - such
     as the version targeted with Galaxy 17.01+.
+
+read_only
+    If ``True``, Galaxy will not attempt to install or uninstall requirement sets into
+    this environment.

lib/galaxy/tool_util/deps/container_resolvers/__init__.py

@@ -25,6 +25,7 @@ class ContainerResolver(Dictifiable, metaclass=ABCMeta):
     dict_collection_visible_keys = ['resolver_type', 'can_uninstall_dependencies', 'builds_on_resolution']
     can_uninstall_dependencies = False
     builds_on_resolution = False
+    read_only = True  # not used for containers, but set for when they are used like dependency resolvers
 
     def __init__(self, app_info=None, **kwds):
         """Default initializer for ``ContainerResolver`` subclasses."""

lib/galaxy/tool_util/deps/resolvers/__init__.py

@@ -19,7 +19,7 @@ class DependencyResolver(Dictifiable, metaclass=ABCMeta):
     """Abstract description of a technique for resolving container images for tool execution."""
 
     # Keys for dictification.
-    dict_collection_visible_keys = ['resolver_type', 'resolves_simple_dependencies', 'can_uninstall_dependencies']
+    dict_collection_visible_keys = ['resolver_type', 'resolves_simple_dependencies', 'can_uninstall_dependencies', 'read_only']
     # A "simple" dependency is one that does not depend on the the tool
     # resolving the dependency. Classic tool shed dependencies are non-simple
     # because the repository install context is used in dependency resolution
@@ -29,6 +29,7 @@ class DependencyResolver(Dictifiable, metaclass=ABCMeta):
     resolves_simple_dependencies = True
     can_uninstall_dependencies = False
     config_options: Dict[str, Any] = {}
+    read_only = True
 
     @abstractmethod
     def resolve(self, requirement, **kwds):
@@ -241,9 +242,16 @@ class InstallableDependencyResolver(metaclass=ABCMeta):
     """ Mix this into a ``DependencyResolver`` and implement to indicate
     the dependency resolver can attempt to install new dependencies.
     """
+    read_only = False
+
+    def install_dependency(self, name, version, type, **kwds):
+        if self.read_only:
+            return False
+        else:
+            return self._install_dependency(name, version, type, **kwds)
 
     @abstractmethod
-    def install_dependency(self, name, version, type, **kwds):
+    def _install_dependency(self, name, version, type, **kwds):
         """ Attempt to install this dependency if a recipe to do so
         has been registered in some way.
         """

lib/galaxy/tool_util/deps/resolvers/conda.py

@@ -80,7 +80,9 @@ class CondaDependencyResolver(DependencyResolver, MultipleDependencyResolver, Li
     _specification_pattern = re.compile(r"https\:\/\/anaconda.org\/\w+\/\w+")
 
     def __init__(self, dependency_manager, **kwds):
-        self.can_uninstall_dependencies = True
+        read_only = _string_as_bool(kwds.get('read_only', 'false'))
+        self.read_only = read_only
+        self.can_uninstall_dependencies = not read_only
         self._setup_mapping(dependency_manager, **kwds)
         self.versionless = _string_as_bool(kwds.get('versionless', 'false'))
         self.dependency_manager = dependency_manager
@@ -167,6 +169,9 @@ class CondaDependencyResolver(DependencyResolver, MultipleDependencyResolver, Li
         return final_return_code
 
     def install_all(self, conda_targets):
+        if self.read_only:
+            return False
+
         env = self.merged_environment_name(conda_targets)
         return_code = install_conda_targets(conda_targets, conda_context=self.conda_context, env_name=env)
         if return_code != 0:
@@ -335,8 +340,11 @@ class CondaDependencyResolver(DependencyResolver, MultipleDependencyResolver, Li
             version = install_target.version
             yield self._to_requirement(name, version)
 
-    def install_dependency(self, name, version, type, **kwds):
+    def _install_dependency(self, name, version, type, **kwds):
         "Returns True on (seemingly) successfull installation"
+        # should be checked before called
+        assert not self.read_only
+
         if type != "package":
             log.warning("Cannot install dependencies of type '%s'" % type)
             return False

test/unit/tool_util/test_conda_resolution.py

@@ -23,6 +23,12 @@ def test_conda_resolution():
             auto_install=True,
             use_path_exec=False,  # For the test ensure this is always a clean install
         )
+        resolver.read_only = True
+        req = ToolRequirement(name="samtools", version=None, type="package")
+        dependency = resolver.resolve(req, job_directory=job_dir)
+        assert dependency.shell_commands() is None
+
+        resolver.read_only = False
         req = ToolRequirement(name="samtools", version=None, type="package")
         dependency = resolver.resolve(req, job_directory=job_dir)
         assert dependency.shell_commands() is not None