Tweak pre-creating empty outputs to fix #8756.

lib/galaxy/tool_util/provided_metadata.py

@@ -54,7 +54,7 @@ class BaseToolProvidedMetadata(object):
     def has_failed_outputs(self):
         """Determine if generation of any of the outputs failed.
 
-        If True, this method should also log information about at the first such failed output.
+        If True, this method should also log information about at least the first such failed output.
         """
         return False
 

lib/galaxy/tools/evaluation.py

@@ -332,10 +332,12 @@ class ToolEvaluator(object):
             # Write outputs to the working directory (for security purposes)
             # if desired.
             param_dict[name] = DatasetFilenameWrapper(hda, compute_environment=self.compute_environment, io_type="output")
-            try:
-                open(str(param_dict[name]), 'w').close()
-            except EnvironmentError:
-                pass  # May well not exist - e.g. Pulsar.
+            output_path = str(param_dict[name])
+            # Conditionally create empty output:
+            # - may already exist (e.g. symlink output)
+            # - parent directory might not exist (e.g. Pulsar)
+            if not os.path.exists(output_path) and os.path.exists(os.path.dirname(output_path)):
+                open(output_path, 'w').close()
 
             # Provide access to a path to store additional files
             # TODO: move compute path logic into compute environment, move setting files_path

test/integration/test_upload_configuration_options.py

@@ -213,6 +213,18 @@ class AdminsCanPasteFilePathsTestCase(BaseUploadContentConfigurationTestCase):
         # Test regression where this was getting deleted in this mode.
         assert os.path.exists(path)
 
+    def test_admin_path_paste_libraries_link(self):
+        library = self.library_populator.new_private_library("pathpasteallowedlibraries")
+        path = "%s/1.txt" % TEST_DATA_DIRECTORY
+        assert os.path.exists(path)
+        payload, files = self.library_populator.create_dataset_request(library, upload_option="upload_paths", paths=path, link_data=True)
+        response = self.library_populator.raw_library_contents_create(library["id"], payload, files=files)
+        assert response.status_code == 200
+        assert os.path.exists(path)
+        self.library_populator.wait_on_library_dataset(library, response.json()[0])
+        # We should probably verify the linking, but this was enough for now to exhibit
+        # https://github.com/galaxyproject/galaxy/issues/8756
+
     def test_admin_fetch(self):
         path = os.path.join(TEST_DATA_DIRECTORY, "1.txt")
         elements = [{"src": "path", "path": path}]