Merge pull request #1303 from mvdbeek/restore_testing_against_directory

Restore running tool tests against directory

planemo/engine/galaxy.py

@@ -35,6 +35,7 @@ class GalaxyEngine(BaseEngine, metaclass=abc.ABCMeta):
         RunnableType.galaxy_workflow,
         RunnableType.galaxy_tool,
         RunnableType.galaxy_datamanager,
+        RunnableType.directory,
     ]
 
     def _run(self, runnables, job_paths):

planemo/runnable.py

@@ -49,6 +49,7 @@
     check_output,
     for_collections,
 )
+from planemo.tools import yield_tool_sources_on_paths
 
 TEST_SUFFIXES = ["-tests", "_tests", "-test", "_test"]
 TEST_EXTENSIONS = [".yml", ".yaml", ".json"]
@@ -211,6 +212,16 @@ def workflow_dir_runnables(path: str, return_all: bool = False) -> Optional[Unio
     return None
 
 
+def tool_dir_runnables(path: str, temp_path: Optional[str]) -> Optional[List[Runnable]]:
+    tool_sources = [p for p in yield_tool_sources_on_paths(ctx=None, paths=[path])]
+    if tool_sources:
+        if temp_path:
+            path = _copy_runnable_tree(path, RunnableType.directory, temp_path)
+        tool_sources = [p for p in yield_tool_sources_on_paths(ctx=None, paths=[path])]
+        return [for_path(p) for (p, _) in tool_sources]
+    return None
+
+
 @overload
 def for_path(path: str, temp_path: Optional[str] = None, return_all: Literal[False] = False) -> Runnable:
     ...
@@ -225,7 +236,7 @@ def for_path(path: str, temp_path: Optional[str] = None, return_all: bool = Fals
     """Produce a class:`Runnable` for supplied path."""
     runnable_type = None
     if os.path.isdir(path):
-        runnable = workflow_dir_runnables(path, return_all=return_all)
+        runnable = workflow_dir_runnables(path, return_all=return_all) or tool_dir_runnables(path, temp_path)
         if runnable:
             return runnable
         runnable_type = RunnableType.directory

planemo/tools.py

@@ -7,6 +7,7 @@
     Iterable,
     Iterator,
     List,
+    Optional,
     Tuple,
     TYPE_CHECKING,
     Union,
@@ -47,7 +48,7 @@ def uris_to_paths(ctx, uris):
 
 
 def yield_tool_sources_on_paths(
-    ctx: "PlanemoCliContext",
+    ctx: Optional["PlanemoCliContext"],
     paths: Iterable[str],
     recursive: bool = False,
     yield_load_errors: bool = True,
@@ -62,7 +63,7 @@ def yield_tool_sources_on_paths(
 
 
 def yield_tool_sources(
-    ctx: "PlanemoCliContext", path: str, recursive: bool = False, yield_load_errors: bool = True
+    ctx: Optional["PlanemoCliContext"], path: str, recursive: bool = False, yield_load_errors: bool = True
 ) -> Iterator[Tuple[str, Union[ToolSource, object]]]:
     """Walk single path and yield ToolSource objects discovered."""
     tools = load_tool_sources_from_path(
@@ -100,13 +101,13 @@ def _load_exception_handler(path, exc_info):
     traceback.print_exception(*exc_info, limit=1, file=sys.stderr)
 
 
-def _is_tool_source(ctx: "PlanemoCliContext", tool_path: str, tool_source: "ToolSource") -> bool:
+def _is_tool_source(ctx: Optional["PlanemoCliContext"], tool_path: str, tool_source: "ToolSource") -> bool:
     if os.path.basename(tool_path) in SHED_FILES:
         return False
     root = getattr(tool_source, "root", None)
     if root is not None:
         if root.tag != "tool":
-            if ctx.verbose:
+            if ctx and ctx.verbose:
                 info(SKIP_XML_MESSAGE % tool_path)
             return False
     return True

tests/data/tools/ok_test_assert_command.xml

@@ -1,7 +1,7 @@
 <tool id="copy" name="Copy Dataset" version="1.0">
     <description>copies a dataset</description>
     <command>
-        cp $input $output
+        cp '$input1' '$output'
     </command>
     <inputs>
         <param name="input1" type="data" format="txt" label="Concatenate Dataset"/>

tests/test_cmd_test.py

@@ -1,7 +1,11 @@
 """Module contains :class:`CmdTestTestCase` - integration tests for the ``test`` command."""
 import json
 import os
-from tempfile import NamedTemporaryFile
+import shutil
+from tempfile import (
+    NamedTemporaryFile,
+    TemporaryDirectory,
+)
 
 from .test_utils import (
     assert_exists,
@@ -30,6 +34,15 @@ def test_startup_timeout(self):
             )
             self._check_exit_code(test_command, exit_code=1)
 
+    @skip_if_environ("PLANEMO_SKIP_GALAXY_TESTS")
+    def test_tool_in_directory(self):
+        """Test with (single) tool in directory."""
+        with self._isolate(), TemporaryDirectory() as tempdir:
+            test_artifact = os.path.join(TEST_DATA_DIR, "tools", "ok_test_assert_command.xml")
+            shutil.copy(test_artifact, tempdir)
+            test_command = self._test_command(tempdir, "--no_dependency_resolution")
+            self._check_exit_code(test_command, exit_code=0)
+
     @skip_if_environ("PLANEMO_SKIP_GALAXY_TESTS")
     def test_data_manager(self):
         """Test testing a data manager test."""