Merge pull request #1298 from mvdbeek/extend_startup_time

Make startup timeout configurable

planemo/galaxy/serve.py

@@ -53,12 +53,12 @@ def _serve(ctx, runnables, **kwds):
             raise Exception(message)
         host = kwds.get("host", "127.0.0.1")
 
-        timeout = 500
+        startup_timeout = kwds.get("galaxy_startup_timeout", 900)
         galaxy_url = f"http://{host}:{port}"
-        galaxy_alive = sleep(galaxy_url, verbose=ctx.verbose, timeout=timeout)
+        galaxy_alive = sleep(galaxy_url, verbose=ctx.verbose, timeout=startup_timeout)
         if not galaxy_alive:
             raise Exception(
-                "Attempted to serve Galaxy at %s, but it failed to start in %d seconds." % (galaxy_url, timeout)
+                f"Attempted to serve Galaxy at {galaxy_url}, but it failed to start in {startup_timeout} seconds."
             )
         config.install_workflows()
         if kwds.get("pid_file"):

planemo/options.py

@@ -422,6 +422,15 @@ def mulled_containers_option():
     )
 
 
+def galaxy_startup_timeout_option():
+    return planemo_option(
+        "--galaxy_startup_timeout",
+        type=click.IntRange(1),
+        default=900,
+        help="Wait for galaxy to start before assuming Galaxy did not start.",
+    )
+
+
 def install_galaxy_option():
     return planemo_option(
         "--install_galaxy", is_flag=True, help="Download and configure a disposable copy of Galaxy from github."
@@ -1191,6 +1200,7 @@ def galaxy_target_options():
         galaxy_email_option(),
         galaxy_docker_options(),
         mulled_containers_option(),
+        galaxy_startup_timeout_option(),
         # Profile options...
         job_config_option(),
         tool_dependency_dir_option(),

tests/test_cmd_test.py

@@ -20,6 +20,16 @@
 class CmdTestTestCase(CliTestCase):
     """Integration tests for the ``test`` command."""
 
+    @skip_if_environ("PLANEMO_SKIP_GALAXY_TESTS")
+    def test_startup_timeout(self):
+        """Test --galaxy_startup_timeout."""
+        with self._isolate():
+            test_artifact = os.path.join(TEST_DATA_DIR, DATA_MANAGER_TEST_PATH)
+            test_command = self._test_command(
+                "--galaxy_startup_timeout", "1", test_artifact, "--no_dependency_resolution"
+            )
+            self._check_exit_code(test_command, exit_code=1)
+
     @skip_if_environ("PLANEMO_SKIP_GALAXY_TESTS")
     def test_data_manager(self):
         """Test testing a data manager test."""