Merge c7d0a56 into 07dc6e0

planemo/commands/cmd_test.py

@@ -79,7 +79,7 @@ def cli(ctx, paths, **kwds):
         kwds["engine"] = "galaxy" if not is_cwl else "cwltool"
 
     engine_type = kwds["engine"]
-    enable_test_engines = any([r.type not in [RunnableType.galaxy_tool, RunnableType.directory] for r in runnables])
+    enable_test_engines = any([r.type not in [RunnableType.galaxy_tool, RunnableType.galaxy_datamanager, RunnableType.directory] for r in runnables])
     enable_test_engines = enable_test_engines or engine_type != "galaxy"
     if enable_test_engines:
         ctx.vlog("Using test engine type %s" % engine_type)

planemo/engine/galaxy.py

@@ -25,7 +25,8 @@ class GalaxyEngine(BaseEngine):
         RunnableType.cwl_tool,
         RunnableType.cwl_workflow,
         RunnableType.galaxy_workflow,
-        RunnableType.galaxy_tool
+        RunnableType.galaxy_tool,
+        RunnableType.galaxy_datamanager,
     ]
 
     def _run(self, runnable, job_path):

planemo/galaxy/config.py

@@ -234,8 +234,7 @@ def simple_docker_volume(path):
 @contextlib.contextmanager
 def docker_galaxy_config(ctx, runnables, for_tests=False, **kwds):
     """Set up a ``GalaxyConfig`` for Docker container."""
-    tool_paths = [r.path for r in runnables if r.has_tools]
-    test_data_dir = _find_test_data(tool_paths, **kwds)
+    test_data_dir = _find_test_data(runnables, **kwds)
 
     with _config_directory(ctx, **kwds) as config_directory:
         def config_join(*args):
@@ -332,13 +331,13 @@ def config_join(*args):
 @contextlib.contextmanager
 def local_galaxy_config(ctx, runnables, for_tests=False, **kwds):
     """Set up a ``GalaxyConfig`` in an auto-cleaned context."""
-    tool_paths = [r.path for r in runnables if r.has_tools]
-    test_data_dir = _find_test_data(tool_paths, **kwds)
+    test_data_dir = _find_test_data(runnables, **kwds)
     tool_data_table = _find_tool_data_table(
-        tool_paths,
+        runnables,
         test_data_dir=test_data_dir,
         **kwds
     )
+    data_manager_config_paths = [r.data_manager_conf_path for r in runnables if r.data_manager_conf_path]
     galaxy_root = _find_galaxy_root(ctx, **kwds)
     install_galaxy = kwds.get("install_galaxy", False)
     if galaxy_root is not None:
@@ -454,6 +453,7 @@ def config_join(*args):
             watch_tools="auto",
             default_job_shell="/bin/bash",  # For conda dependency resolution
             tool_data_table_config_path=tool_data_table,
+            data_manager_config_file=",".join(data_manager_config_paths),
             integrated_tool_panel_config=("${temp_directory}/"
                                           "integrated_tool_panel_conf.xml"),
             # Use in-memory database for kombu to avoid database contention
@@ -523,7 +523,7 @@ def config_join(*args):
 
 
 def _all_tool_paths(runnables, **kwds):
-    tool_paths = [r.path for r in runnables if r.has_tools]
+    tool_paths = [r.path for r in runnables if r.has_tools and not r.data_manager_conf_path]
     all_tool_paths = list(tool_paths) + list(kwds.get("extra_tools", []))
     for runnable in runnables:
         if runnable.type.name == "galaxy_workflow":
@@ -1106,39 +1106,41 @@ def _find_galaxy_root(ctx, **kwds):
     return None
 
 
-def _find_test_data(tool_paths, **kwds):
-    path = "."
-    if len(tool_paths) > 0:
-        path = tool_paths[0]
+def _find_test_data(runnables, **kwds):
+    test_data_search_path = "."
+    runnables = [r for r in runnables if r.has_tools]
+    if len(runnables) > 0:
+        test_data_search_path = runnables[0].test_data_search_path
 
     # Find test data directory associated with path.
     test_data = kwds.get("test_data", None)
     if test_data:
         return os.path.abspath(test_data)
     else:
-        test_data = _search_tool_path_for(path, "test-data")
+        test_data = _search_tool_path_for(test_data_search_path, "test-data")
         if test_data:
             return test_data
     warn(NO_TEST_DATA_MESSAGE)
     return None
 
 
-def _find_tool_data_table(tool_paths, test_data_dir, **kwds):
-    path = "."
-    if len(tool_paths) > 0:
-        path = tool_paths[0]
+def _find_tool_data_table(runnables, test_data_dir, **kwds):
+    tool_data_search_path = "."
+    runnables = [r for r in runnables if r.has_tools]
+    if len(runnables) > 0:
+        tool_data_search_path = runnables[0].tool_data_search_path
 
     tool_data_table = kwds.get("tool_data_table", None)
     if tool_data_table:
         return os.path.abspath(tool_data_table)
     else:
         extra_paths = [test_data_dir] if test_data_dir else []
         return _search_tool_path_for(
-            path,
+            tool_data_search_path,
             "tool_data_table_conf.xml.test",
             extra_paths,
         ) or _search_tool_path_for(  # if all else fails just use sample
-            path,
+            tool_data_search_path,
             "tool_data_table_conf.xml.sample"
         )
 

planemo/runnable.py

@@ -13,6 +13,7 @@
 from galaxy.tools.loader_directory import (
     is_a_yaml_with_class,
     looks_like_a_cwl_artifact,
+    looks_like_a_data_manager_xml,
     looks_like_a_tool_cwl,
     looks_like_a_tool_xml,
 )
@@ -35,24 +36,57 @@
 
 
 RunnableType = aenum.Enum(
-    "RunnableType", 'galaxy_tool galaxy_workflow cwl_tool cwl_workflow directory'
+    "RunnableType", 'galaxy_tool galaxy_datamanager galaxy_workflow cwl_tool cwl_workflow directory'
 )
 
 
 @property
 def _runnable_type_has_tools(runnable_type):
-    return runnable_type.name in ["galaxy_tool", "cwl_tool", "directory"]
+    return runnable_type.name in ["galaxy_tool", "galaxy_datamanager", "cwl_tool", "directory"]
 
 
 @property
 def _runnable_type_is_single_artifact(runnable_type):
     return runnable_type.name not in ["directory"]
 
 
+@property
+def _runnable_type_test_data_in_parent_dir(runnable_type):
+    return runnable_type.name in ["galaxy_datamanager"]
+
+
 RunnableType.has_tools = _runnable_type_has_tools
 RunnableType.is_single_artifact = _runnable_type_is_single_artifact
+RunnableType.test_data_in_parent_dir = _runnable_type_test_data_in_parent_dir
+
+_Runnable = collections.namedtuple("Runnable", ["path", "type"])
+
+
+class Runnable(_Runnable):
+
+    @property
+    def test_data_search_path(self):
+        if self.type.name in ['galaxy_datamanager']:
+            return os.path.join(os.path.dirname(self.path), os.path.pardir)
+        else:
+            return self.path
 
-Runnable = collections.namedtuple("Runnable", ["path", "type"])
+    @property
+    def tool_data_search_path(self):
+        return self.test_data_search_path
+
+    @property
+    def data_manager_conf_path(self):
+        if self.type.name in ['galaxy_datamanager']:
+            return os.path.join(os.path.dirname(self.path), os.pardir, 'data_manager_conf.xml')
+
+    @property
+    def has_tools(self):
+        return _runnable_delegate_attribute('has_tools')
+
+    @property
+    def is_single_artifact(self):
+        return _runnable_delegate_attribute('is_single_artifact')
 
 
 def _runnable_delegate_attribute(attribute):
@@ -64,17 +98,15 @@ def getter(runnable):
     return getter
 
 
-Runnable.has_tools = _runnable_delegate_attribute('has_tools')
-Runnable.is_single_artifact = _runnable_delegate_attribute('is_single_artifact')
-
-
 def for_path(path):
     """Produce a class:`Runnable` for supplied path."""
     runnable_type = None
     if os.path.isdir(path):
         runnable_type = RunnableType.directory
     elif looks_like_a_tool_cwl(path):
         runnable_type = RunnableType.cwl_tool
+    elif looks_like_a_data_manager_xml:
+        runnable_type = RunnableType.galaxy_datamanager
     elif looks_like_a_tool_xml(path):
         runnable_type = RunnableType.galaxy_tool
     elif is_a_yaml_with_class(path, ["GalaxyWorkflow"]):