plugins & tests

WDL/runtime/config.py

@@ -308,13 +308,24 @@ def _parse_list(v: str) -> List[Any]:
 
 DEFAULT_PLUGINS = {
     "file_download": [
+        importlib_metadata.EntryPoint(
+            group="miniwdl.plugin.file_download",
+            name="s3",
+            value="WDL.runtime.download:awscli_downloader",
+        ),
         importlib_metadata.EntryPoint(
             group="miniwdl.plugin.file_download",
             name="gs",
             value="WDL.runtime.download:gsutil_downloader",
+        ),
+    ],
+    "directory_download": [
+        importlib_metadata.EntryPoint(
+            group="miniwdl.plugin.directory_download",
+            name="s3",
+            value="WDL.runtime.download:awscli_directory_downloader",
         )
     ],
-    "directory_download": [],
     "task": [],
     "workflow": [],
     "container_backend": [
@@ -331,8 +342,8 @@ def load_all_plugins(cfg: Loader, group: str) -> Iterable[Tuple[bool, Any]]:
     assert group in DEFAULT_PLUGINS.keys(), group
     enable_patterns = cfg["plugins"].get_list("enable_patterns")
     disable_patterns = cfg["plugins"].get_list("disable_patterns")
-    for plugin in importlib_metadata.entry_points().get(
-        f"miniwdl.plugin.{group}", DEFAULT_PLUGINS[group]
+    for plugin in DEFAULT_PLUGINS[group] + list(
+        importlib_metadata.entry_points().get(f"miniwdl.plugin.{group}", [])
     ):
         enabled = next(
             (pat for pat in enable_patterns if fnmatchcase(plugin.value, pat)), False

WDL/runtime/download.py

@@ -38,9 +38,8 @@ def _load(cfg: config.Loader):
         "https": aria2c_downloader,
         "http": aria2c_downloader,
         "ftp": aria2c_downloader,
-        "s3": awscli_downloader,
     }
-    directory_downloaders = {"s3": awscli_directory_downloader}
+    directory_downloaders = {}
 
     # plugins
     for plugin_name, plugin_fn in config.load_plugins(cfg, "file_download"):

setup.cfg

@@ -22,8 +22,6 @@ packages =
 [entry_points]
 console_scripts =
     miniwdl = WDL.CLI:main
-miniwdl.plugin.file_download =
-    gs = WDL.runtime.download:gsutil_downloader
 
 [pbr]
 skip_authors = True

tests/test_7runner.py

@@ -188,6 +188,35 @@ def test_directory_output(self):
             """, {})
         assert outp["d_out"] is None
 
+    def test_output_input(self):
+        # test outputting files/subdirectories inside input Directory
+        wdl = R"""
+        version development
+        task t {
+            input {
+                Directory d
+            }
+            command {}
+            output {
+                Array[File] files = ["~{d}/alice.txt", "~{d}/sub/bob.txt"]
+                Array[Directory] dirs = ["~{d}/sub/dir"]
+            }
+        }
+        """
+        os.makedirs(os.path.join(self._dir, "d/sub/dir"))
+        with open(os.path.join(self._dir, "d/alice.txt"), mode="w") as outfile:
+            print("Alice", file=outfile)
+        with open(os.path.join(self._dir, "d/sub/bob.txt"), mode="w") as outfile:
+            print("Bob", file=outfile)
+        with open(os.path.join(self._dir, "d/sub/dir/carol.txt"), mode="w") as outfile:
+            print("Carol", file=outfile)
+        outp = self._run(wdl, {"d": os.path.join(self._dir, "d")})
+        assert len(outp["files"]) == 2
+        for fn in outp["files"]:
+            assert os.path.isfile(fn)
+        assert len(outp["dirs"]) == 1
+        assert os.path.isdir(outp["dirs"][0])
+
     def test_errors(self):
         self._run(R"""
             version development