Fix setting environment vars on handlers

README.rst

@@ -304,15 +304,13 @@ In ``gravity.yml`` on the job handler host::
 Galaxy Job Handlers
 -------------------
 
-Gravity has limited support for reading Galaxy's job configuration: it can read statically configured job handlers in
-the ``job_conf.xml`` file, but cannot read the newer YAML-format job configuration, or the job configuration inline from
-``galaxy.yml``. Improved support for reading Galaxy's job configuration is planned, but for the time being, Gravity will
-run standalone Galaxy job handler processes if you:
+Gravity has support for reading Galaxy's job configuration: it can read statically configured job handlers in the
+``job_conf.yml`` or ``job_conf.yml`` files, or the job configuration inline from the ``job_config`` option in
+``galaxy.yml``. However, unless you need to statically define handlers, it is simpler to configure Gravity to run
+`dynamically defined handlers`_ as detailed in the Galaxy scaling documentation.
 
-1. Set ``job_handler_count`` to a number greater than ``0``. **NOTE:** You must also explicitly set the `job handler
-   assignment method`_ to ``db-skip-locked`` or ``db-transaction-isolation`` to prevent the web process from also
-   handling jobs. This is the preferred method for specifying job handlers.
-2. Define static ``<handler id="..."/>`` handlers in the XML-format job configuration file.
+When using dynamically defined handlers, be sure to explicitly set the `job handler assignment method`_ to
+``db-skip-locked`` or ``db-transaction-isolation`` to prevent the web process from also handling jobs.
 
 Configuration Precedence
 ------------------------
@@ -466,5 +464,6 @@ A ``configstate.yaml`` file for a Galaxy service might look like::
 .. _FastAPI: https://fastapi.tiangolo.com/
 .. _unicornherder: https://github.com/alphagov/unicornherder
 .. _job handler assignment method: https://docs.galaxyproject.org/en/master/admin/scaling.html#job-handler-assignment-methods
+.. _dynamically defined handlers: https://docs.galaxyproject.org/en/latest/admin/scaling.html#dynamically-defined-handlers
 .. _Ansible: http://www.ansible.com/
 .. _Issue #6: https://github.com/galaxyproject/gravity/issues/6

gravity/config_manager.py

@@ -140,8 +140,12 @@ def get_config(self, conf, defaults=None):
                 if not exists(job_config):
                     job_config = None
         if config.config_type == "galaxy" and job_config:
-            for service_name in [x["service_name"] for x in ConfigManager.get_job_config(job_config) if x["service_name"] not in webapp_service_names]:
-                config.services.append(service_for_service_type("standalone")(config_type=config.config_type, service_name=service_name))
+            for handler_settings in [x for x in ConfigManager.get_job_config(job_config) if x["service_name"] not in webapp_service_names]:
+                config.services.append(service_for_service_type("standalone")(
+                    config_type=config.config_type,
+                    service_name=handler_settings["service_name"],
+                    environment=handler_settings.get("environment")
+                ))
 
         # Dynamic job handlers are configured using `job_handler_count` in galaxy.yml.
         #
@@ -157,8 +161,14 @@ def create_handler_services(self, gravity_config: Settings, config):
         expanded_handlers = self.expand_handlers(gravity_config, config)
         for service_name, handler_settings in expanded_handlers.items():
             pools = handler_settings.get('pools')
+            environment = handler_settings.get("environment")
             config.services.append(
-                service_for_service_type("standalone")(config_type=config.config_type, service_name=service_name, server_pools=pools))
+                service_for_service_type("standalone")(
+                    config_type=config.config_type,
+                    service_name=service_name,
+                    server_pools=pools,
+                    environment=environment
+                ))
 
     def create_gxit_services(self, gravity_config: Settings, app_config, config):
         if app_config.get("interactivetools_enable") and gravity_config.gx_it_proxy.enable:

gravity/state.py

@@ -147,6 +147,9 @@ class GalaxyStandaloneService(Service):
     command_template = "{virtualenv_bin}python ./lib/galaxy/main.py -c {galaxy_conf} --server-name={server_name}{attach_to_pool_opt}" \
                        " --pid-file={supervisor_state_dir}/{program_name}.pid"
 
+    def get_environment(self):
+        return self.get("environment") or {}
+
 
 class ConfigFile(AttributeDict):
     def __init__(self, *args, **kwargs):

tests/test_config_manager.py

@@ -42,12 +42,14 @@ def test_preload_default(galaxy_yml, default_config_manager):
 
 def test_register_non_default(galaxy_yml, default_config_manager):
     new_bind = 'localhost:8081'
+    environment = {'FOO': 'foo'}
     concurrency = 4
     galaxy_yml.write(json.dumps({
         'galaxy': None,
         'gravity': {
             'gunicorn': {
-                'bind': new_bind
+                'bind': new_bind,
+                'environment': environment
             },
             'celery': {
                 'concurrency': concurrency
@@ -58,6 +60,7 @@ def test_register_non_default(galaxy_yml, default_config_manager):
     state = default_config_manager.state['config_files'][str(galaxy_yml)]
     gunicorn_attributes = state['attribs']['gunicorn']
     assert gunicorn_attributes['bind'] == new_bind
+    assert gunicorn_attributes['environment'] == environment
     default_settings = Settings()
     assert gunicorn_attributes['workers'] == default_settings.gunicorn.workers
     celery_attributes = state['attribs']['celery']

tests/test_process_manager.py

@@ -21,6 +21,8 @@
   processes:
     handler0:
     handler1:
+      environment:
+        BAZ: baz
     sge_handler:
       # Restrict a handler to load specific runners, by default they will load all.
       plugins: ['sge']
@@ -58,10 +60,14 @@
       pools:
         - job-handlers
         - workflow-schedulers
+      environment:
+        FOO: foo
     handler1:
       processes: 1
       pools:
         - job-handlers.special
+      environment:
+        BAR: bar
     handler2:
       processes: 1
       pools:
@@ -123,9 +129,11 @@ def test_dynamic_handlers(default_config_manager, galaxy_yml, job_conf):
         handler0_config = handler_config_paths[0].open().read()
         assert " --server-name=handler0" in handler0_config
         assert " --attach-to-pool=job-handlers --attach-to-pool=workflow-schedulers" in handler0_config
+        assert " FOO=foo" in handler0_config
         handler1_config = handler_config_paths[1].open().read()
         assert " --server-name=handler1" in handler1_config
         assert " --attach-to-pool=job-handlers.special" in handler1_config
+        assert " BAR=bar" in handler1_config
         handler2_config = handler_config_paths[2].open().read()
         assert " --server-name=handler2" in handler2_config
         assert " --attach-to-pool=job-handlers --attach-to-pool=job-handlers.special" in handler2_config
@@ -166,7 +174,9 @@ def test_static_handlers_yaml(default_config_manager, galaxy_yml, job_conf):
         assert '.yml --server-name=handler0 --pid-file=' in handler0_config_path.open().read()
         handler1_config_path = instance_conf_dir / 'galaxy_standalone_handler1.conf'
         assert handler1_config_path.exists()
-        assert '.yml --server-name=handler1 --pid-file=' in handler1_config_path.open().read()
+        handler1_config = handler1_config_path.open().read()
+        assert '.yml --server-name=handler1 --pid-file=' in handler1_config
+        assert 'BAZ=baz' in handler1_config
         assert (instance_conf_dir / 'galaxy_standalone_sge_handler.conf').exists()
         assert (instance_conf_dir / 'galaxy_standalone_special_handler0.conf').exists()
         assert (instance_conf_dir / 'galaxy_standalone_special_handler1.conf').exists()