Support managing gx-it-proxy via gravity

gravity/config_manager.py

@@ -16,6 +16,9 @@
     CELERY_DEFAULT_CONFIG,
     DEFAULT_INSTANCE_NAME,
     GUNICORN_DEFAULT_CONFIG,
+    GXIT_DEFAULT_IP,
+    GXIT_DEFAULT_PORT,
+    GXIT_DEFAULT_SESSIONS,
 )
 from gravity.io import debug, error, exception, info, warn
 from gravity.state import (
@@ -85,6 +88,7 @@ def get_config(self, conf, defaults=None):
             "app_server": "gunicorn",
             "gunicorn": GUNICORN_DEFAULT_CONFIG,
             "celery": CELERY_DEFAULT_CONFIG,
+            "gx_it_proxy": {},
             "handlers": {},
         }
         if defaults is not None:
@@ -109,6 +113,7 @@ def get_config(self, conf, defaults=None):
         config.attribs["gunicorn"] = gravity_config["gunicorn"]
         config.attribs["celery"] = gravity_config["celery"]
         config.attribs["handlers"] = gravity_config["handlers"]
+        config.attribs["gx_it_proxy"] = gravity_config["gx_it_proxy"]
         # Store gravity version, in case we need to convert old setting
         config.attribs['gravity_version'] = __version__
         webapp_service_names = []
@@ -129,7 +134,6 @@ def get_config(self, conf, defaults=None):
         config.services.append(service_for_service_type("celery")(config_type=config.config_type))
         config.services.append(service_for_service_type("celery-beat")(config_type=config.config_type))
         # If this is a Galaxy config, parse job_conf.xml for any *static* standalone handlers
-        # Marius: Don't think that's gonna work if job config file not defined!
         # TODO: use galaxy config parsing ?
         # TODO: if not, need yaml job config parsing
         job_conf_xml = app_config.get("job_config_file", DEFAULT_JOB_CONFIG_FILE)
@@ -149,6 +153,7 @@ def get_config(self, conf, defaults=None):
         # doesn't parse that part of the job config. See logic in lib/galaxy/web_stack/handlers.py _get_is_handler() to
         # see how this is determined.
         self.create_handler_services(gravity_config, config)
+        self.create_gxit_services(gravity_config, app_config, config)
         return config
 
     def create_handler_services(self, gravity_config, config):
@@ -158,6 +163,17 @@ def create_handler_services(self, gravity_config, config):
             config.services.append(
                 service_for_service_type("standalone")(config_type=config.config_type, service_name=service_name, server_pools=pools))
 
+    def create_gxit_services(self, gravity_config, app_config, config):
+        if app_config.get("interactivetools_enable") and gravity_config["gx_it_proxy"].get("enable"):
+            # TODO: resolve against data_dir, or bring in galaxy-config ?
+            # CWD in supervisor template is galaxy_root, so this should work for simple cases as is
+            gxit_config = gravity_config['gx_it_proxy']
+            gxit_config["sessions"] = app_config.get("interactivetools_map", GXIT_DEFAULT_SESSIONS)
+            gxit_config["ip"] = gxit_config.get("ip", GXIT_DEFAULT_IP)
+            gxit_config["port"] = gxit_config.get("port", GXIT_DEFAULT_PORT)
+            gxit_config["verbose"] = '--verbose' if gxit_config.get("verbose") else ''
+            config.services.append(service_for_service_type("gx-it-proxy")(config_type=config.config_type, gxit=gxit_config))
+
     @staticmethod
     def expand_handlers(gravity_config, config):
         handlers = gravity_config.get("handlers", {})

gravity/defaults.py

@@ -14,3 +14,6 @@
     "concurrency": 2,
     "extra_args": ""
 }
+GXIT_DEFAULT_IP = "localhost"
+GXIT_DEFAULT_PORT = 4002
+GXIT_DEFAULT_SESSIONS = "database/interactivetools_map.sqlite"

gravity/process_manager/supervisor_manager.py

@@ -116,6 +116,26 @@
 {process_name_opt}
 """
 
+
+SUPERVISORD_SERVICE_TEMPLATES["gx-it-proxy"] = """;
+; This file is maintained by Galaxy - CHANGES WILL BE OVERWRITTEN
+;
+
+[program:{program_name}]
+command         = {command}
+directory       = {galaxy_root}
+umask           = {galaxy_umask}
+autostart       = true
+autorestart     = true
+startsecs       = 10
+stopwaitsecs    = 10
+numprocs        = 1
+stdout_logfile  = {log_file}
+redirect_stderr = true
+{process_name_opt}
+"""
+
+
 SUPERVISORD_SERVICE_TEMPLATES["standalone"] = """;
 ; This file is maintained by Galaxy - CHANGES WILL BE OVERWRITTEN
 ;
@@ -237,6 +257,7 @@ def __update_service(self, config_file, config, attribs, service, instance_conf_
             "attach_to_pool_opt": attach_to_pool_opt,
             "gunicorn": attribs["gunicorn"],
             "celery": attribs["celery"],
+            "gx_it_proxy": attribs["gx_it_proxy"],
             "galaxy_umask": service.get("umask", "022"),
             "program_name": program_name,
             "process_name_opt": process_name_opt,

gravity/state.py

@@ -81,6 +81,13 @@ class GalaxyCeleryBeatService(Service):
     command_template = "{virtualenv_bin}celery --app galaxy.celery beat --loglevel {celery[loglevel]}"
 
 
+class GalaxyGxItProxyService(Service):
+    service_type = "gx-it-proxy"
+    service_name = "gx-it-proxy"
+    command_template = "{virtualenv_bin}npx gx-it-proxy --ip {gx_it_proxy[ip]} --port {gx_it_proxy[port]}" \
+                       " --sessions {gx_it_proxy[sessions]} {gx_it_proxy[verbose]}"
+
+
 class GalaxyStandaloneService(Service):
     service_type = "standalone"
     service_name = "standalone"
@@ -164,5 +171,6 @@ def service_for_service_type(service_type):
     "unicornherder": GalaxyUnicornHerderService,
     "celery": GalaxyCeleryService,
     "celery-beat": GalaxyCeleryBeatService,
+    "gx-it-proxy": GalaxyGxItProxyService,
     "standalone": GalaxyStandaloneService,
 }

tests/test_process_manager.py

@@ -46,6 +46,19 @@
         - job-handler.special
 """
 
+GXIT_CONFIG = """
+gravity:
+  gx_it_proxy:
+    enable: true
+    proxy_port: 4002
+galaxy:
+  interactivetools_enable: true
+  interactivetools_map: database/interactivetools_map.sqlite
+  galaxy_infrastructure_url: http://localhost:8080
+  interactivetools_upstream_proxy: false
+  interactivetools_proxy_host: localhost:4002
+"""
+
 
 def test_update(galaxy_yml, default_config_manager):
     default_config_manager.add([str(galaxy_yml)])
@@ -97,3 +110,14 @@ def test_static_handlers(default_config_manager, galaxy_yml, job_conf):
         handler1_config_path = instance_conf_dir / 'galaxy_standalone_handler1.conf'
         assert handler1_config_path.exists()
         assert 'galaxy.yml --server-name=handler1 --pid-file=' in handler1_config_path.open().read()
+
+
+def test_gxit_handler(default_config_manager, galaxy_yml):
+    galaxy_yml.write(GXIT_CONFIG)
+    default_config_manager.add([str(galaxy_yml)])
+    with process_manager.process_manager(state_dir=default_config_manager.state_dir) as pm:
+        pm.update()
+        instance_conf_dir = Path(default_config_manager.state_dir) / 'supervisor' / 'supervisord.conf.d' / '_default_.d'
+        gxit_config_path = instance_conf_dir / 'galaxy_gx-it-proxy_gx-it-proxy.conf'
+        assert gxit_config_path.exists()
+        assert 'npx gx-it-proxy --ip localhost --port 4002 --sessions database/interactivetools_map.sqlite' in gxit_config_path.read_text()