Merge pull request #1647 from mvdbeek/fix-shed-lint-required-files-symlink

Fix false-positive RequiredFilesExist lint in shed_lint (#1646)

Author: jmchilton

planemo/shed/__init__.py

@@ -1139,7 +1139,7 @@ def realize_to(self, directory):
             if os.path.isdir(source_path):
                 os.makedirs(target_path)
             else:
-                os.symlink(source_path, target_path)
+                shutil.copy2(source_path, target_path)
 
     @staticmethod
     def realized_files_for(path, include_info):

tests/data/repos/single_tool_required_files/.shed.yml

@@ -0,0 +1,8 @@
+name: "single_tool_required_files"
+owner: "iuc"
+description: "a simple tool with a required helper file"
+type: "unrestricted"
+remote_repository_url: "https://github.com/galaxyproject/planemo/tree/master/tests/data/repos/single_tool_required_files"
+homepage_url: "http://planemo.readthedocs.org/en/latest/"
+categories:
+  - "Text Manipulation"

tests/data/repos/single_tool_required_files/cat.xml

@@ -0,0 +1,27 @@
+<tool id="cat_required" name="Concatenate with helper" version="1.0" profile="22.05">
+    <description>tail-to-head, depends on a helper script</description>
+    <required_files>
+        <include path="helper.py" />
+    </required_files>
+    <command>
+        python '$__tool_directory__/helper.py' &amp;&amp; cat $input1 > $out_file1
+    </command>
+    <inputs>
+        <param name="input1" type="data" label="Concatenate Dataset" format="data" />
+    </inputs>
+    <outputs>
+        <data name="out_file1" format_source="input1" metadata_source="input1"/>
+    </outputs>
+    <tests>
+      <test>
+        <param name="input1" value="1.bed"/>
+        <output name="out_file1" file="1.bed"/>
+      </test>
+    </tests>
+    <help>
+        Concatenate datasets via a helper script.
+    </help>
+    <citations>
+        <citation type="doi">10.1093/bioinformatics/bts573</citation>
+    </citations>
+</tool>

tests/data/repos/single_tool_required_files/helper.py

@@ -0,0 +1,4 @@
+"""Helper script declared as a required file for the test tool."""
+
+if __name__ == "__main__":
+    print("hello from helper")

tests/data/repos/single_tool_required_files/test-data/1.bed

@@ -0,0 +1,2 @@
+chr1	147962192	147962580	CCDS989.1_cds_0_0_chr1_147962193_r	0	-
+chr1	147984545	147984630	CCDS990.1_cds_0_0_chr1_147984546_f	0	+

tests/test_shed_lint.py

@@ -44,6 +44,13 @@ def test_tool_linting(self):
         with self._isolate_repo("bad_tool_no_citations"):
             self._check_exit_code(["shed_lint", "--tools"], exit_code=1)
 
+    def test_tool_linting_required_files(self):
+        # Regression test for https://github.com/galaxyproject/planemo/issues/1646:
+        # a sibling file declared in <required_files> must be found in the
+        # realized repository even though shed_lint copies files into a temp dir.
+        with self._isolate_repo("single_tool_required_files"):
+            self._check_exit_code(["shed_lint", "--tools", "--skip", "shed_remote_repository_url"])
+
     def test_invalid_nested(self):
         # Created a nested repository with one good and one
         # invalid repository and make sure it runs and produces