Fix default behavior for planemo lint to use current directory.

jmchilton · jmchilton · commit 1e3668afacf2 · 2015-05-12T13:30:54.000-04:00
Add tests to verify the default behavior when explicit paths are not supplied. Broken with 343902d. Thanks to @nekrut for the bug report.
diff --git a/planemo/options.py b/planemo/options.py
@@ -1,5 +1,8 @@
 """ Click definitions for various shared options and arguments.
 """
+
+import os
+
 import click
 from galaxy.tools.deps import docker_util
 
@@ -142,6 +145,13 @@ def required_tool_arg():
     return click.argument('path', metavar="TOOL_PATH", type=arg_type)
 
 
+def _optional_tools_default(ctx, param, value):
+    if param.name == "paths" and len(value) == 0:
+        return [os.path.abspath(os.getcwd())]
+    else:
+        return value
+
+
 def optional_tools_arg(multiple=False):
     """ Decorate click method as optionally taking in the path to a tool
     or directory of tools. If no such argument is given the current working
@@ -159,9 +169,9 @@ def optional_tools_arg(multiple=False):
     return click.argument(
         name,
         metavar="TOOL_PATH",
-        default=".",
         type=arg_type,
         nargs=nargs,
+        callback=_optional_tools_default,
     )
 
 
diff --git a/tests/data/repos/single_tool/cat.xml b/tests/data/repos/single_tool/cat.xml
@@ -4,13 +4,13 @@
         cat $input1 #for $q in $queries# ${q.input2} #end for# > $out_file1
     </command>
     <inputs>
-        <param name="input1" type="data" label="Concatenate Dataset"/>
+        <param name="input1" type="data" label="Concatenate Dataset" format="data" />
         <repeat name="queries" title="Dataset">
-            <param name="input2" type="data" label="Select" />
+            <param name="input2" type="data" label="Select" format="data" />
         </repeat>
     </inputs>
     <outputs>
-        <data name="out_file1" format="input" metadata_source="input1"/>
+        <data name="out_file1" format_source="input1" metadata_source="input1"/>
     </outputs>
     <tests>
       <test>
@@ -19,5 +19,6 @@
       </test>
     </tests>
     <help>
+        Concatenate datasets.
     </help>
 </tool>
diff --git a/tests/test_lint.py b/tests/test_lint.py
@@ -22,6 +22,12 @@ def test_fail_tools(self):
             lint_cmd = ["lint", fail_tool]
             self._check_exit_code(lint_cmd, exit_code=1)
 
+    def test_lint_default(self):
+        with self._isolate_repo("single_tool"):
+            self._check_exit_code(["lint", "--skip", "citations"])
+        with self._isolate_repo("single_tool"):
+            self._check_exit_code(["lint"], exit_code=1)
+
     def test_lint_multiple(self):
         names = ["fail_citation.xml", "fail_order.xml"]
         paths = list(map(lambda p: os.path.join(TEST_TOOLS_DIR, p), names))
