Use resolver.find_dep to determine dependency status

lib/galaxy/tools/deps/__init__.py

@@ -58,7 +58,7 @@ class NullDependencyManager( object ):
         return []
 
     def find_dep( self, name, version=None, type='package', **kwds ):
-        return INDETERMINATE_DEPENDENCY
+        return INDETERMINATE_DEPENDENCY(name=name, version=version)
 
 
 class DependencyManager( object ):
@@ -115,10 +115,10 @@ class DependencyManager( object ):
                 continue
             dependency = resolver.resolve( name, version, type, **kwds )
             if require_exact and not dependency.exact:
-                dependency = INDETERMINATE_DEPENDENCY
-            if dependency != INDETERMINATE_DEPENDENCY:
+                dependency = INDETERMINATE_DEPENDENCY(version=version, name=name)
+            if not isinstance(dependency, INDETERMINATE_DEPENDENCY):
                 return dependency
-        return INDETERMINATE_DEPENDENCY
+        return INDETERMINATE_DEPENDENCY(version=version, name=name)
 
     def __build_dependency_resolvers( self, conf_file ):
         if not conf_file:

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

@@ -72,7 +72,7 @@ class InstallableDependencyResolver:
 
 
 class Dependency(Dictifiable, object):
-    dict_collection_visible_keys = ['dependency_type', 'exact']
+    dict_collection_visible_keys = ['dependency_type', 'exact', 'name', 'version']
     __metaclass__ = ABCMeta
 
     @abstractmethod
@@ -92,8 +92,12 @@ class NullDependency( Dependency ):
     dependency_type = None
     exact = True
 
+    def __init__(self, version, name):
+        self.version = version
+        self.name = name
+
     def shell_commands( self, requirement ):
         return None
 
 
-INDETERMINATE_DEPENDENCY = NullDependency()
+INDETERMINATE_DEPENDENCY = NullDependency

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

@@ -31,10 +31,9 @@ class HomebrewToolShedDependencyResolver(
 
     def resolve(self, name, version, type, **kwds):
         if type != "package":
-            return INDETERMINATE_DEPENDENCY
-
+            return INDETERMINATE_DEPENDENCY(version=version, name=name)
         if version is None:
-            return INDETERMINATE_DEPENDENCY
+            return INDETERMINATE_DEPENDENCY(version=version, name=name)
 
         return self._find_tool_dependencies(name, version, type, **kwds)
 
@@ -49,7 +48,7 @@ class HomebrewToolShedDependencyResolver(
             if os.path.exists(tool_depenedencies_path):
                 return self._resolve_from_tool_dependencies_path(name, version, tool_depenedencies_path)
 
-        return INDETERMINATE_DEPENDENCY
+        return INDETERMINATE_DEPENDENCY(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
@@ -66,11 +65,11 @@ class HomebrewToolShedDependencyResolver(
             raw_dependencies = RawDependencies(tool_dependencies_path)
         except Exception:
             log.debug("Failed to parse dependencies in file %s" % tool_dependencies_path)
-            return INDETERMINATE_DEPENDENCY
+            return INDETERMINATE_DEPENDENCY(version=version, name=name)
 
         raw_dependency = raw_dependencies.find(name, version)
         if not raw_dependency:
-            return INDETERMINATE_DEPENDENCY
+            return INDETERMINATE_DEPENDENCY(version=version, name=name)
 
         recipe_name = build_recipe_name(
             package_name=name,

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

@@ -106,15 +106,10 @@ class CondaDependencyResolver(DependencyResolver, ListableDependencyResolver, In
         # 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):
-            return INDETERMINATE_DEPENDENCY
+            return INDETERMINATE_DEPENDENCY(version=version, name=name)
 
         if type != "package":
-            return INDETERMINATE_DEPENDENCY
-
-        job_directory = kwds.get("job_directory", None)
-        if job_directory is None:
-            log.warning("Conda dependency resolver not sent job directory.")
-            return INDETERMINATE_DEPENDENCY
+            return INDETERMINATE_DEPENDENCY(version=version, name=name)
 
         exact = not self.versionless or version is None
         if self.versionless:
@@ -124,11 +119,26 @@ class CondaDependencyResolver(DependencyResolver, ListableDependencyResolver, In
         is_installed = is_conda_target_installed(
             conda_target, conda_context=self.conda_context, verbose_install_check=self.verbose_install_check
         )
+
+        job_directory = kwds.get("job_directory", None)
+        if job_directory is None:  # Job directory is None when resolve() called by find_dep()
+            if is_installed:
+                return CondaDependency(
+                    False,
+                    os.path.join(self.conda_context.envs_path, conda_target.install_environment),
+                    exact,
+                    name=name,
+                    version=version
+                )
+            else:
+                log.warning("Conda dependency resolver not sent job directory.")
+                return INDETERMINATE_DEPENDENCY(version=version, name=name)
+
         if not is_installed and self.auto_install:
             is_installed = self.install_dependency(name, version, type)
 
         if not is_installed:
-            return INDETERMINATE_DEPENDENCY
+            return INDETERMINATE_DEPENDENCY(version=version, name=name)
 
         # Have installed conda_target and job_directory to send it too.
         # If dependency is for metadata generation, store environment in conda-metadata-env

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

@@ -39,7 +39,7 @@ class BaseGalaxyPackageDependencyResolver(DependencyResolver, UsesToolDependency
     def _find_dep_versioned( self, name, version, type='package', **kwds ):
         base_path = self.base_path
         path = join( base_path, name, version )
-        return self._galaxy_package_dep(path, version, True)
+        return self._galaxy_package_dep(path, version, name, True)
 
     def _find_dep_default( self, name, type='package', exact=True, **kwds ):
         base_path = self.base_path
@@ -49,15 +49,15 @@ class BaseGalaxyPackageDependencyResolver(DependencyResolver, UsesToolDependency
             real_version = basename( real_path )
             return self._galaxy_package_dep(real_path, real_version, exact)
         else:
-            return INDETERMINATE_DEPENDENCY
+            return INDETERMINATE_DEPENDENCY(version=None, name=name)
 
-    def _galaxy_package_dep( self, path, version, exact ):
+    def _galaxy_package_dep( self, path, version, name, exact ):
         script = join( path, 'env.sh' )
         if exists( script ):
             return GalaxyPackageDependency(script, path, version, exact)
         elif exists( join( path, 'bin' ) ):
             return GalaxyPackageDependency(None, path, version, exact)
-        return INDETERMINATE_DEPENDENCY
+        return INDETERMINATE_DEPENDENCY(version=version, name=name)
 
 
 class GalaxyPackageDependencyResolver(BaseGalaxyPackageDependencyResolver, ListableDependencyResolver):

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

@@ -41,7 +41,7 @@ class HomebrewDependencyResolver(DependencyResolver, UsesHomebrewMixin):
 
     def resolve(self, name, version, type, **kwds):
         if type != "package":
-            return INDETERMINATE_DEPENDENCY
+            return INDETERMINATE_DEPENDENCY(version=version, name=name)
 
         if version is None or self.versionless:
             return self._find_dep_default(name, version)

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

@@ -52,14 +52,14 @@ class ModuleDependencyResolver(DependencyResolver):
 
     def resolve( self, name, version, type, **kwds ):
         if type != "package":
-            return INDETERMINATE_DEPENDENCY
+            return INDETERMINATE_DEPENDENCY(version=version, name=name)
 
         if self.__has_module(name, version):
             return ModuleDependency(self, name, version, exact=True)
         elif self.versionless and self.__has_module(name, None):
             return ModuleDependency(self, name, None, exact=False)
 
-        return INDETERMINATE_DEPENDENCY
+        return INDETERMINATE_DEPENDENCY(version=version, name=name)
 
     def __has_module(self, name, version):
         return self.module_checker.has_module(name, version)

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

@@ -15,7 +15,7 @@ class UsesHomebrewMixin:
     def _find_dep_versioned(self, name, version):
         recipe_path = recipe_cellar_path(self.cellar_root, name, version)
         if not os.path.exists(recipe_path) or not os.path.isdir(recipe_path):
-            return INDETERMINATE_DEPENDENCY
+            return INDETERMINATE_DEPENDENCY(version=version, name=name)
 
         commands = build_env_statements(self.cellar_root, recipe_path, relaxed=True)
         return HomebrewDependency(commands)
@@ -23,7 +23,7 @@ class UsesHomebrewMixin:
     def _find_dep_default(self, name, version):
         installed_versions = self._installed_versions(name)
         if not installed_versions:
-            return INDETERMINATE_DEPENDENCY
+            return INDETERMINATE_DEPENDENCY(version=version, name=name)
 
         # Just grab newest installed version - may make sense some day to find
         # the linked version instead.

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

@@ -21,7 +21,7 @@ class ToolShedPackageDependencyResolver(BaseGalaxyPackageDependencyResolver, Use
             path = self._get_package_installed_dependency_path( installed_tool_dependency, name, version )
             return self._galaxy_package_dep(path, version, True)
         else:
-            return INDETERMINATE_DEPENDENCY
+            return INDETERMINATE_DEPENDENCY(version=version, name=name)
 
     def _find_dep_default( self, name, type='package', **kwds ):
         if type == 'set_environment' and kwds.get('installed_tool_dependencies', None):
@@ -33,7 +33,7 @@ class ToolShedPackageDependencyResolver(BaseGalaxyPackageDependencyResolver, Use
                 if has_script_dep:
                     # Environment settings do not use versions.
                     return GalaxyPackageDependency(dependency.script, dependency.path, None, True)
-        return INDETERMINATE_DEPENDENCY
+        return INDETERMINATE_DEPENDENCY(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
@@ -59,7 +59,7 @@ class ToolShedPackageDependencyResolver(BaseGalaxyPackageDependencyResolver, Use
         if exists( path ):
             script = join( path, 'env.sh' )
             return GalaxyPackageDependency(script, path, None, True)
-        return INDETERMINATE_DEPENDENCY
+        return INDETERMINATE_DEPENDENCY(version=None, name=name)
 
 
 __all__ = ['ToolShedPackageDependencyResolver']

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

@@ -48,7 +48,7 @@ class UnlinkedToolShedPackageDependencyResolver(BaseGalaxyPackageDependencyResol
             possibles = self._find_possible_depenencies(name, version, type)
             if len(possibles) == 0:
                 log.debug("Unable to find dependency,'%s' '%s' '%s'", name, version, type)
-                return INDETERMINATE_DEPENDENCY
+                return INDETERMINATE_DEPENDENCY(version=version, name=name)
             elif len(possibles) == 1:
                 # Only one candidate found so ignore any preference rules
                 return possibles[0].dependency
@@ -57,7 +57,7 @@ class UnlinkedToolShedPackageDependencyResolver(BaseGalaxyPackageDependencyResol
                 return self._select_preferred_dependency(possibles).dependency
         except:
             log.exception("Unexpected error hunting for dependency '%s' '%s''%s'", name, version, type)
-            return INDETERMINATE_DEPENDENCY
+            return INDETERMINATE_DEPENDENCY(version=version, name=name)
 
     # Finds all possible dependency to use
     # Should be extended as required

lib/galaxy/tools/deps/views.py

@@ -126,26 +126,4 @@ class DependencyResolversView(object):
         return [index for index, resolver in enumerate(self._dependency_resolvers) if hasattr(resolver, "install_dependency") and not resolver.disabled ]
 
     def get_requirements_status(self, requested_requirements):
-        result = []
-        for req in requested_requirements:
-            installed_requirement = self.requirement_installed(req)
-            if not installed_requirement:
-                req['status'] = "not installed"
-                req['exact'] = "NA"
-                req['resolver_type'] = None
-                result.append(req)
-            else:
-                result.append(installed_requirement)
-        return result
-
-    def requirement_installed(self, requirement):
-        installed_requirements = self.manager_requirements()
-        for ireq in installed_requirements:
-            if requirement['name'] == ireq['requirement']['name']:
-                requirement['resolver_type'] = self._dependency_resolvers[ireq['index']].resolver_type
-                versionless = self._dependency_resolvers[ireq['index']].versionless
-                if (requirement['version'] == ireq['requirement']['version'] and requirement['version'] and not versionless) or (versionless and not ireq['requirement']['version']):
-                    requirement['status'] = "installed"
-                    requirement['exact'] = not versionless
-                    return requirement
-        return None
+        return [self.manager_dependency(**req) for req in requested_requirements]

lib/galaxy/webapps/galaxy/api/tool_dependencies.py

@@ -95,7 +95,8 @@ class ToolDependenciesAPIController( BaseAPIController ):
         :returns:   a dictified description of the dependency, with attribute
                     ``dependency_type: null`` if no match was found.
         """
-        return self._view.install_dependency(id, **kwds)
+        self._view.install_dependency(id, **kwds)
+        return self._view.manager_dependency(**kwds)
 
     @expose_api
     @require_admin

templates/webapps/tool_shed/repository/common.mako

@@ -1044,9 +1044,9 @@
                         <tr>
                             <td>${dependency['name'] | h}</td>
                             <td>${dependency['version'] | h}</td>
-                            <td>${dependency['resolver_type'] | h}</td>
+                            <td>${dependency['dependency_type'] | h}</td>
                             <td>${dependency['exact'] | h}</td>
-                        %if dependency['status'] == 'not installed':
+                        %if dependency['dependency_type'] == None:
                             <td>
                                <img src="${h.url_for('/static')}/images/icon_error_sml.gif" title='Dependency not resolved'/>
                             </td>