Add --extra_tools option to serve.

jmchilton · jmchilton · commit 02a08a0f0eee · 2016-05-03T08:29:17.000-04:00
Once Galaxy will be able to "serve" workflows - this will be useful for specifying the location of extra tools.
diff --git a/planemo/galaxy/config.py b/planemo/galaxy/config.py
@@ -171,7 +171,8 @@ def config_join(*args):
         _ensure_directory(tool_dependency_dir)
 
         shed_tool_conf = kwds.get("shed_tool_conf") or config_join("shed_tools_conf.xml")
-        tool_definition = _tool_conf_entry_for(tool_paths)
+        all_tool_paths = list(tool_paths) + list(kwds.get("extra_tools", []))
+        tool_definition = _tool_conf_entry_for(all_tool_paths)
         empty_tool_conf = config_join("empty_tool_conf.xml")
 
         tool_conf = config_join("tool_conf.xml")
diff --git a/planemo/options.py b/planemo/options.py
@@ -38,6 +38,20 @@ def test_data_option():
     )
 
 
+def extra_tools_option():
+    return planemo_option(
+        "--extra_tools",
+        type=click.Path(exists=True,
+                        file_okay=True,
+                        dir_okay=True,
+                        resolve_path=True),
+        multiple=True,
+        help=("Extra tool sources to include in Galaxy's tool panel (file or "
+              "directory). These will not be linted/tested/etc... but they "
+              "will be available to workflows and for interactive use.")
+    )
+
+
 def tool_data_table_option():
     return planemo_option(
         "--tool_data_table",
@@ -766,6 +780,7 @@ def galaxy_serve_options():
     return _compose(
         galaxy_run_options(),
         galaxy_config_options(),
+        extra_tools_option(),
         daemon_option(),
         pid_file_option(),
     )
diff --git a/tests/test_cmd_serve.py b/tests/test_cmd_serve.py
@@ -11,6 +11,7 @@
     CliTestCase,
     skip_if_environ,
     TEST_REPOS_DIR,
+    PROJECT_TEMPLATES_DIR,
 )
 
 TEST_HISTORY_NAME = "Cool History 42"
@@ -37,6 +38,21 @@ def test_serve_daemon(self):
         assert len(user_gi.histories.get_histories(name=TEST_HISTORY_NAME)) == 0
         user_gi.histories.create_history(TEST_HISTORY_NAME)
 
+    @skip_if_environ("PLANEMO_SKIP_GALAXY_TESTS")
+    def test_serve_extra_tools(self):
+        port = network_util.get_free_port()
+        pid_file = os.path.join(self._home, "test.pid")
+        random_lines = os.path.join(PROJECT_TEMPLATES_DIR, "demo", "randomlines.xml")
+        extra_args = ["--daemon", "--pid_file", pid_file, "--extra_tools", random_lines]
+        serve = functools.partial(self._run, port, extra_args)
+        self._launch_thread_and_wait(serve, port)
+        admin_gi = api.gi(port)
+        user_api_key = api.user_api_key(admin_gi)
+        user_gi = api.gi(port, user_api_key)
+        assert len(user_gi.histories.get_histories(name=TEST_HISTORY_NAME)) == 0
+        user_gi.histories.create_history(TEST_HISTORY_NAME)
+        assert user_gi.tools.get_tools(tool_id="random_lines1")
+
     @skip_if_environ("PLANEMO_SKIP_GALAXY_TESTS")
     def test_serve_profile(self):
         port = network_util.get_free_port()
