Change interface of depependency resolver's resolve for consistency.

If resolve_all takes in requirements, then so should resolve.

lib/galaxy/tools/deps/__init__.py

@@ -155,17 +155,7 @@ def _requirements_to_dependencies_dict(self, requirements, **kwds):
                     continue
 
                 if requirement.type in ['package', 'set_environment']:
-                    name = requirement.name
-                    version = requirement.version
-                    specs = requirement.specs
-
-                    if hasattr(resolver, "find_specification"):
-                        spec = resolver.find_specification(specs)
-                        if spec is not None:
-                            name = spec.short_name
-                            version = spec.version or version
-
-                    dependency = resolver.resolve( name, version, requirement.type, **kwds )
+                    dependency = resolver.resolve( requirement, **kwds )
                     if require_exact and not dependency.exact:
                         continue
 

lib/galaxy/tools/deps/requirements.py

@@ -1,3 +1,5 @@
+import copy
+
 from galaxy.util import asbool, xml_text
 
 DEFAULT_REQUIREMENT_TYPE = "package"
@@ -20,6 +22,9 @@ def to_dict( self ):
         specs = [s.to_dict() for s in self.specs]
         return dict(name=self.name, type=self.type, version=self.version, specs=specs)
 
+    def copy( self ):
+        return copy.deepcopy( self )
+
     @staticmethod
     def from_dict( dict ):
         version = dict.get( "version", None )

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

@@ -26,7 +26,7 @@ class DependencyResolver(Dictifiable, object):
     __metaclass__ = ABCMeta
 
     @abstractmethod
-    def resolve( self, name, version, type, **kwds ):
+    def resolve( self, requirement, **kwds ):
         """Given inputs describing dependency in the abstract yield a Dependency object.
 
         The Dependency object describes various attributes (script, bin,
@@ -92,6 +92,22 @@ def find_specification(self, specs):
                 return spec
         return None
 
+    def resolve_specs(self, requirement):
+        name = requirement.name
+        version = requirement.version
+        specs = requirement.specs
+
+        spec = self.find_specification(specs)
+        if spec is not None:
+            name = spec.short_name
+            version = spec.version or version
+
+            requirement = requirement.copy()
+            requirement.name = name
+            requirement.version = version
+
+        return requirement
+
 
 class InstallableDependencyResolver:
     """ Mix this into a ``DependencyResolver`` and implement to indicate

lib/galaxy/tools/deps/resolvers/brewed_tool_shed_packages.py

@@ -29,7 +29,8 @@ def __init__(self, dependency_manager, **kwds):
         self._init_homebrew(**kwds)
         self._init_base_path(dependency_manager, **kwds)
 
-    def resolve(self, name, version, type, **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:

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

@@ -146,6 +146,8 @@ def resolve_all(self, requirements, **kwds):
 
         conda_targets = []
         for requirement in requirements:
+            requirement = self.resolve_specs(requirement)
+
             version = requirement.version
             if self.versionless:
                 version = None
@@ -183,7 +185,10 @@ def merged_environment_name(self, conda_targets):
             assert len(conda_targets) == 1
             return conda_targets[0].install_environment
 
-    def resolve(self, name, version, type, **kwds):
+    def resolve(self, requirement, **kwds):
+        requirement = self.resolve_specs(requirement)
+        name, version, type = requirement.name, requirement.version, requirement.type
+
         # Check for conda just not being there, this way we can enable
         # conda by default and just do nothing in not configured.
         if not os.path.isdir(self.conda_context.conda_prefix):

lib/galaxy/tools/deps/resolvers/galaxy_packages.py

@@ -66,11 +66,13 @@ def __init__(self, dependency_manager, **kwds):
         self.versionless = str(kwds.get('versionless', "false")).lower() == "true"
         self._init_base_path( dependency_manager, **kwds )
 
-    def resolve( self, name, version, type, **kwds ):
+    def resolve(self, requirement, **kwds):
         """
         Attempt to find a dependency named `name` at version `version`. If version is None, return the "default" version as determined using a
         symbolic link (if found). Returns a triple of: env_script, base_path, real_version
         """
+        name, version, type = requirement.name, requirement.version, requirement.type
+
         if version is None or self.versionless:
             exact = not self.versionless or version is None
             return self._find_dep_default( name, type=type, exact=exact, **kwds )

lib/galaxy/tools/deps/resolvers/homebrew.py

@@ -39,7 +39,9 @@ def __init__(self, dependency_manager, **kwds):
 
         self._init_homebrew(**kwds)
 
-    def resolve(self, name, version, type, **kwds):
+    def resolve(self, requirement, **kwds):
+        name, version, type = requirement.name, requirement.version, requirement.type
+
         if type != "package":
             return NullDependency(version=version, name=name)
 

lib/galaxy/tools/deps/resolvers/modules.py

@@ -51,7 +51,9 @@ def __default_modulespath(self):
             module_path = DEFAULT_MODULE_PATH
         return module_path
 
-    def resolve( self, name, version, type, **kwds ):
+    def resolve(self, requirement, **kwds):
+        name, version, type = requirement.name, requirement.version, requirement.type
+
         if type != "package":
             return NullDependency(version=version, name=name)
 

test/unit/tools/test_tool_deps.py

@@ -14,6 +14,7 @@
 from subprocess import PIPE, Popen
 
 from galaxy.tools.deps import DependencyManager
+from galaxy.tools.deps.requirements import ToolRequirement
 from galaxy.tools.deps.resolvers import NullDependency
 from galaxy.tools.deps.resolvers.galaxy_packages import GalaxyPackageDependency
 from galaxy.tools.deps.resolvers.modules import ModuleDependency, ModuleDependencyResolver
@@ -141,15 +142,15 @@ def test_module_dependency_resolver():
 advisor/2013/update3    intel/12.0              mkl/10.2.7.041
 ''')
         resolver = ModuleDependencyResolver(None, modulecmd=module_script)
-        module = resolver.resolve( name="R", version=None, type="package" )
+        module = resolver.resolve( ToolRequirement( name="R", version=None, type="package" ) )
         assert module.module_name == "R"
         assert module.module_version is None
 
-        module = resolver.resolve( name="R", version="3.0.1", type="package" )
+        module = resolver.resolve( ToolRequirement( name="R", version="3.0.1", type="package" ) )
         assert module.module_name == "R"
         assert module.module_version == "3.0.1"
 
-        module = resolver.resolve( name="R", version="3.0.4", type="package" )
+        module = resolver.resolve( ToolRequirement( name="R", version="3.0.4", type="package" ) )
         assert isinstance(module, NullDependency)