Merge pull request #1373 from nsoranzo/fix_test_run_gxtool_randomlines

Fix ``test_run_gxtool_randomlines`` test on Galaxy dev branch
galaxyproject · Jun 21, 2023 · c017ef6 · c017ef6
2 parents 2abf1a2 + 6b2e31d
commit c017ef6
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diff --git a/planemo/galaxy/config.py b/planemo/galaxy/config.py
@@ -103,6 +103,14 @@
 </job_metrics>
 """
 
+FILE_SOURCES_TEMPLATE = """
+- type: posix
+  root: '${test_data_dir}'
+  id: test_data_dir
+  label: Test data directory
+  doc: Test data directory for the runnables being tested
+"""
+
 TOOL_SHEDS_CONF = """<tool_sheds>
   <tool_shed name="Target Shed" url="${shed_target_url}" />
 </tool_sheds>
@@ -362,6 +370,7 @@ def config_join(*args):
         all_tool_paths = _all_tool_paths(runnables, galaxy_root=galaxy_root, extra_tools=kwds.get("extra_tools"))
         _handle_job_config_file(config_directory, server_name, test_data_dir, all_tool_paths, kwds)
         _handle_job_metrics(config_directory, kwds)
+        _handle_file_sources(config_directory, test_data_dir, kwds)
         _handle_refgenie_config(config_directory, galaxy_root, kwds)
         file_path = kwds.get("file_path") or config_join("files")
         _ensure_directory(file_path)
@@ -1384,6 +1393,13 @@ def _handle_job_metrics(config_directory, kwds):
     kwds["job_metrics_config_file"] = metrics_conf
 
 
+def _handle_file_sources(config_directory, test_data_dir, kwds):
+    file_sources_conf = os.path.join(config_directory, "file_sources_conf.yml")
+    file_sources_conf_contents = _sub(FILE_SOURCES_TEMPLATE, {"test_data_dir": test_data_dir})
+    write_file(file_sources_conf, file_sources_conf_contents)
+    kwds["file_sources_config_file"] = file_sources_conf
+
+
 def _handle_refgenie_config(config_directory, galaxy_root, kwds):
     refgenie_dir = os.path.join(config_directory, "refgenie")
     _ensure_directory(refgenie_dir)

diff --git a/tests/test_run.py b/tests/test_run.py
@@ -66,6 +66,8 @@ def test_run_gxtool_randomlines(self):
                 "--no_dependency_resolution",
                 "--galaxy_branch",
                 target_galaxy_branch(),
+                "--test_data",
+                TEST_DATA_DIR,
                 tool_path,
                 job_path,
             ]