Bug fix for empty .shed.yml file and more testing.

Author: jmchilton

planemo/shed.py

@@ -133,11 +133,14 @@ def shed_init(ctx, path, **kwds):
 
 def shed_repo_config(path):
     shed_yaml_path = os.path.join(path, SHED_CONFIG_NAME)
+    config = {}
     if os.path.exists(shed_yaml_path):
         with open(shed_yaml_path, "r") as f:
-            return yaml.load(f)
-    else:
-        return {}
+            config = yaml.load(f)
+
+    if config is None:  # yaml may yield None
+        config = {}
+    return config
 
 
 def tool_shed_client(ctx=None, **kwds):

tests/data/repos/multi_repos_nested/cat1/.shed.yml

@@ -0,0 +1,3 @@
+name: cat1
+owner: iuc
+description: cat1 tool

tests/data/repos/multi_repos_nested/cat2/.shed.yml

@@ -0,0 +1,3 @@
+name: cat2
+owner: iuc
+description: cat2 tool

tests/test_shed_upload.py

@@ -4,6 +4,7 @@
 from os.path import exists, join
 import os
 import tarfile
+import shutil
 
 from .test_utils import CliShedTestCase
 
@@ -47,6 +48,16 @@ def test_cannont_recreate(self):
             self._check_exit_code(create_command)
             self._check_exit_code(create_command, exit_code=1)
 
+    def test_upload_recusrive(self):
+        with self._isolate_repo("multi_repos_nested") as f:
+            upload_command = [
+                "shed_upload", "-r", "--force_repository_creation"
+            ]
+            upload_command.extend(self._shed_args())
+            self._check_exit_code(upload_command)
+            self._verify_upload(f, ["cat1.xml", "macros.xml"], ["cat1"])
+            self._verify_upload(f, ["cat2.xml", "macros.xml"], ["cat2"])
+
     def test_upload_filters_invalid_suite(self):
         with self._isolate_repo("suite_1") as f:
             # No .shed.yml, make sure to test it can infer type
@@ -85,11 +96,16 @@ def test_upload_not_filters_unrestricted(self):
             assert exists(join(target, "README.rst"))
 
     def _verify_single_uploaded(self, f):
-        target = self._download_repo(f)
-        assert exists(join(target, "cat.xml"))
+        self._verify_upload(f, ["cat.xml"])
+
+    def _verify_upload(self, f, download_files=[], download_args=[]):
+        target = self._download_repo(f, download_args)
+        for download_file in download_files:
+            assert exists(join(target, download_file))
 
-    def _download_repo(self, f):
+    def _download_repo(self, f, download_args=[]):
         download_command = ["shed_download"]
+        download_command.extend(download_args)
         download_command.extend(self._shed_args(read_only=True))
         self._check_exit_code(download_command)
         download = join(f, "shed_download.tar.gz")
@@ -98,6 +114,8 @@ def _download_repo(self, f):
 
     def _untar(self, f, path):
         target = join(f, "download")
+        if exists(target):
+            shutil.rmtree(target)
         os.makedirs(target)
         tar = tarfile.open(path, "r:gz")
         tar.extractall(path=target)

tests/test_utils.py

@@ -1,6 +1,7 @@
 """ Provide abstractions over click testing of the
 app and unittest.
 """
+from __future__ import print_function
 import contextlib
 import os
 from tempfile import mkdtemp
@@ -91,6 +92,14 @@ def _shed_args(self, read_only=False):
             args.extend(["--shed_key", "ignored"])
         return args
 
+    def _print_shed_info(self):
+        tsi = shed.tool_shed_client(
+            None,
+            shed_target=self.mock_shed.url,
+            key="ignored",
+        )
+        print(tsi.repositories.get_repositories())
+
 
 @contextlib.contextmanager
 def mock_shed_client():