Update Gravity version to 1.0.0 pre-release

lib/galaxy/config/sample/galaxy.yml.sample

@@ -20,16 +20,55 @@
 # ``uwsgi:`` section will be ignored if Galaxy is started via Gravity commands (e.g ``./run.sh``, ``galaxy`` or ``galaxyctl``).
 gravity:
 
+  # Process manager to use.
+  # ``supervisor`` is the default process manager when Gravity is invoked as a non-root user.
+  # ``systemd`` is the default when Gravity is invoked as root.
+  # Valid options are: supervisor, systemd
+  # process_manager:
+
+  # What command to write to the process manager configs
+  # `gravity` (`galaxyctl exec <service-name>`) is the default
+  # `direct` (each service's actual command) is also supported.
+  # Valid options are: gravity, direct
+  # service_command_style: gravity
+
+  # Use the process manager's *service instance* functionality for services that can run multiple instances.
+  # Presently this includes services like gunicorn and Galaxy dynamic job handlers. Service instances are only supported if
+  # ``service_command_style`` is ``gravity``, and so this option is automatically set to ``false`` if
+  # ``service_command_style`` is set to ``direct``.
+  # use_service_instances: true
+
+  # umask under which services should be executed. Setting ``umask`` on an individual service overrides this value.
+  # umask: '022'
+
+  # Memory limit (in GB), processes exceeding the limit will be killed. Default is no limit. If set, this is default value
+  # for all services. Setting ``memory_limit`` on an individual service overrides this value. Ignored if ``process_manager``
+  # is ``supervisor``.
+  # memory_limit:
+
+  # Specify Galaxy config file (galaxy.yml), if the Gravity config is separate from the Galaxy config. Assumed to be the
+  # same file as the Gravity config if a ``galaxy`` key exists at the root level, otherwise, this option is required.
+  # galaxy_config_file:
+
   # Specify Galaxy's root directory.
   # Gravity will attempt to find the root directory, but you can set the directory explicitly with this option.
   # galaxy_root:
 
+  # User to run Galaxy as, required when using the systemd process manager as root.
+  # Ignored if ``process_manager`` is ``supervisor`` or user-mode (non-root) ``systemd``.
+  # galaxy_user:
+
+  # Group to run Galaxy as, optional when using the systemd process manager as root.
+  # Ignored if ``process_manager`` is ``supervisor`` or user-mode (non-root) ``systemd``.
+  # galaxy_group:
+
   # Set to a directory that should contain log files for the processes controlled by Gravity.
-  # If not specified defaults to ``<state_dir>/log``.
+  # If not specified defaults to ``<galaxy_data_dir>/gravity/log``.
   # log_dir:
 
   # Set to Galaxy's virtualenv directory.
-  # If not specified, Gravity assumes all processes are on PATH.
+  # If not specified, Gravity assumes all processes are on PATH. This option is required in most circumstances when using
+  # the ``systemd`` process manager.
   # virtualenv:
 
   # Select the application server.
@@ -43,7 +82,7 @@ gravity:
   # this is hidden from you when running a single instance.
   # instance_name: _default_
 
-  # Configuration for Gunicorn.
+  # Configuration for Gunicorn. Can be a list to run multiple gunicorns for rolling restarts.
   gunicorn:
 
     # Enable Galaxy gunicorn server.
@@ -70,6 +109,23 @@ gravity:
     # Consumes less memory when multiple processes are configured. Default is ``false`` if using unicornherder, else ``true``.
     # preload:
 
+    # umask under which service should be executed
+    # umask:
+
+    # Value of supervisor startsecs, systemd TimeoutStartSec
+    # start_timeout: 15
+
+    # Value of supervisor stopwaitsecs, systemd TimeoutStopSec
+    # stop_timeout: 65
+
+    # Amount of time to wait for a server to become alive when performing rolling restarts.
+    # restart_timeout: 300
+
+    # Memory limit (in GB). If the service exceeds the limit, it will be killed. Default is no limit or the value of the
+    # ``memory_limit`` setting at the top level of the Gravity configuration, if set. Ignored if ``process_manager`` is
+    # ``supervisor``.
+    # memory_limit:
+
     # Extra environment variables and their values to set when running the service. A dictionary where keys are the variable
     # names.
     # environment: {}
@@ -100,6 +156,20 @@ gravity:
     # Extra arguments to pass to Celery command line.
     # extra_args:
 
+    # umask under which service should be executed
+    # umask:
+
+    # Value of supervisor startsecs, systemd TimeoutStartSec
+    # start_timeout: 10
+
+    # Value of supervisor stopwaitsecs, systemd TimeoutStopSec
+    # stop_timeout: 10
+
+    # Memory limit (in GB). If the service exceeds the limit, it will be killed. Default is no limit or the value of the
+    # ``memory_limit`` setting at the top level of the Gravity configuration, if set. Ignored if ``process_manager`` is
+    # ``supervisor``.
+    # memory_limit:
+
     # Extra environment variables and their values to set when running the service. A dictionary where keys are the variable
     # names.
     # environment: {}
@@ -117,7 +187,8 @@ gravity:
     # port: 4002
 
     # Routes file to monitor.
-    # Should be set to the same path as ``interactivetools_map`` in the ``galaxy:`` section.
+    # Should be set to the same path as ``interactivetools_map`` in the ``galaxy:`` section. This is ignored if
+    # ``interactivetools_map is set``.
     # sessions: database/interactivetools_map.sqlite
 
     # Include verbose messages in gx-it-proxy
@@ -135,6 +206,20 @@ gravity:
     # This is an advanced option that is only needed when proxying to remote interactive tool container that cannot be reached through the local network.
     # reverse_proxy: false
 
+    # umask under which service should be executed
+    # umask:
+
+    # Value of supervisor startsecs, systemd TimeoutStartSec
+    # start_timeout: 10
+
+    # Value of supervisor stopwaitsecs, systemd TimeoutStopSec
+    # stop_timeout: 10
+
+    # Memory limit (in GB). If the service exceeds the limit, it will be killed. Default is no limit or the value of the
+    # ``memory_limit`` setting at the top level of the Gravity configuration, if set. Ignored if ``process_manager`` is
+    # ``supervisor``.
+    # memory_limit:
+
     # Extra environment variables and their values to set when running the service. A dictionary where keys are the variable
     # names.
     # environment: {}
@@ -161,20 +246,86 @@ gravity:
     # upload_dir:
 
     # Comma-separated string of enabled tusd hooks.
-    # 
+    #
     # Leave at the default value to require authorization at upload creation time.
     # This means Galaxy's web process does not need to be running after creating the initial
     # upload request.
-    # 
+    #
     # Set to empty string to disable all authorization. This means data can be uploaded (but not processed)
     # without the Galaxy web process being available.
-    # 
+    #
     # You can find a list of available hooks at https://github.com/tus/tusd/blob/master/docs/hooks.md#list-of-available-hooks.
     # hooks_enabled_events: pre-create
 
     # Extra arguments to pass to tusd command line.
     # extra_args:
 
+    # umask under which service should be executed
+    # umask:
+
+    # Value of supervisor startsecs, systemd TimeoutStartSec
+    # start_timeout: 10
+
+    # Value of supervisor stopwaitsecs, systemd TimeoutStopSec
+    # stop_timeout: 10
+
+    # Memory limit (in GB). If the service exceeds the limit, it will be killed. Default is no limit or the value of the
+    # ``memory_limit`` setting at the top level of the Gravity configuration, if set. Ignored if ``process_manager`` is
+    # ``supervisor``.
+    # memory_limit:
+
+    # Extra environment variables and their values to set when running the service. A dictionary where keys are the variable
+    # names.
+    # environment: {}
+
+  # Configuration for Galaxy Reports.
+  reports:
+
+    # Enable Galaxy Reports server.
+    # enable: false
+
+    # Path to reports.yml, relative to galaxy.yml if not absolute
+    # config_file: reports.yml
+
+    # The socket to bind. A string of the form: ``HOST``, ``HOST:PORT``, ``unix:PATH``, ``fd://FD``. An IP is a valid HOST.
+    # bind: localhost:9001
+
+    # Controls the number of Galaxy Reports application processes Gunicorn will spawn.
+    # It is not generally necessary to increase this for the low-traffic Reports server.
+    # workers: 1
+
+    # Gunicorn workers silent for more than this many seconds are killed and restarted.
+    # Value is a positive number or 0. Setting it to 0 has the effect of infinite timeouts by disabling timeouts for all workers entirely.
+    # timeout: 300
+
+    # URL prefix to serve from.
+    # The corresponding nginx configuration is (replace <url_prefix> and <bind> with the values from these options):
+    #
+    # location /<url_prefix>/ {
+    #     proxy_pass http://<bind>/;
+    # }
+    #
+    # If <bind> is a unix socket, you will need a ``:`` after the socket path but before the trailing slash like so:
+    #     proxy_pass http://unix:/run/reports.sock:/;
+    # url_prefix:
+
+    # Extra arguments to pass to Gunicorn command line.
+    # extra_args:
+
+    # umask under which service should be executed
+    # umask:
+
+    # Value of supervisor startsecs, systemd TimeoutStartSec
+    # start_timeout: 10
+
+    # Value of supervisor stopwaitsecs, systemd TimeoutStopSec
+    # stop_timeout: 10
+
+    # Memory limit (in GB). If the service exceeds the limit, it will be killed. Default is no limit or the value of the
+    # ``memory_limit`` setting at the top level of the Gravity configuration, if set. Ignored if ``process_manager`` is
+    # ``supervisor``.
+    # memory_limit:
+
     # Extra environment variables and their values to set when running the service. A dictionary where keys are the variable
     # names.
     # environment: {}

lib/galaxy/config/sample/job_conf.sample.yml

@@ -375,8 +375,15 @@ handling:
   # most of them). If unset, the default is any untagged handlers plus any handlers in the `job-handlers` (no tag) pool.
   #default: handler0
 
+  # Static handler configurations - Configuring these is generally not desirable, fully dynamic handlers are preferable
+  # unless you need to control plugin loading on a per-handler basis. See the scaling documentation linked above for
+  # instructions on configuring dynamic handlers.
+
   processes:
     handler0:
+      # Set environment variables that only apply to this handler
+      #environment:
+      #  FOO: foo
     handler1:
     sge_handler:
       # Restrict a handler to load specific runners, by default they will load all.

lib/galaxy/dependencies/pinned-requirements.txt

@@ -68,7 +68,7 @@ funcsigs==1.0.2 ; python_version >= "3.7" and python_version < "3.11"
 future==0.18.2 ; python_version >= "3.7" and python_version < "3.11"
 galaxy-sequence-utils==1.1.5 ; python_version >= "3.7" and python_version < "3.11"
 galaxy2cwl==0.1.4 ; python_version >= "3.7" and python_version < "3.11"
-gravity==0.13.5 ; python_version >= "3.7" and python_version < "3.11"
+gravity @ git+https://github.com/galaxyproject/gravity.git@release_1.x ; python_version >= "3.7" and python_version < "3.11"
 greenlet==2.0.1 ; python_version >= "3.7" and (platform_machine == "aarch64" or platform_machine == "ppc64le" or platform_machine == "x86_64" or platform_machine == "amd64" or platform_machine == "AMD64" or platform_machine == "win32" or platform_machine == "WIN32") and python_version < "3.11"
 gunicorn==20.1.0 ; python_version >= "3.7" and python_version < "3.11"
 gxformat2==0.16.0 ; python_version >= "3.7" and python_version < "3.11"

lib/galaxy_test/driver/driver_util.py

@@ -743,8 +743,10 @@ def launch_gravity(port, gxit_port=None, galaxy_config=None):
         galaxy_config["interactivetools_proxy_host"] = f"localhost:{gxit_port}"
     # Can't use in-memory celery broker, just fall back to sqlalchemy
     galaxy_config.update({"celery_conf": {"broker_url": None}})
+    state_dir = tempfile.mkdtemp(suffix="state")
     config = {
         "gravity": {
+            "log_dir": os.path.join(state_dir, "log"),
             "gunicorn": {"bind": f"localhost:{port}", "preload": "false"},
             "gx_it_proxy": {
                 "enable": galaxy_config.get("interactivetools_enable", False),
@@ -755,18 +757,16 @@ def launch_gravity(port, gxit_port=None, galaxy_config=None):
         },
         "galaxy": galaxy_config,
     }
-    state_dir = tempfile.mkdtemp(suffix="state")
     with tempfile.NamedTemporaryFile("w", dir=state_dir, delete=False, suffix=".galaxy.yml") as config_fh:
         json.dump(config, config_fh)
     with tempfile.NamedTemporaryFile(delete=True) as socket:
         supervisord_socket = socket.name
     gravity_env = os.environ.copy()
     gravity_env["SUPERVISORD_SOCKET"] = supervisord_socket
-    subprocess.check_output(["galaxyctl", "--state-dir", state_dir, "register", config_fh.name], env=gravity_env)
-    subprocess.check_output(["galaxyctl", "--state-dir", state_dir, "update"], env=gravity_env)
-    subprocess.check_output(["galaxyctl", "--state-dir", state_dir, "start"], env=gravity_env)
+    subprocess.check_output(["galaxyctl", "--config-file", config_fh.name, "update"], env=gravity_env)
+    subprocess.check_output(["galaxyctl", "--config-file", config_fh.name, "start"], env=gravity_env)
     return state_dir, lambda: subprocess.check_output(
-        ["galaxyctl", "--state-dir", state_dir, "shutdown"], env=gravity_env
+        ["galaxyctl", "--config-file", config_fh.name, "shutdown"], env=gravity_env
     )
 
 

scripts/common_startup.sh

@@ -163,7 +163,6 @@ if [ $SET_VENV -eq 1 ] && [ $CREATE_VENV -eq 1 ]; then
             fi
         fi
     fi
-    setup_gravity_state_dir
 fi
 
 # activate virtualenv or conda env, sets $GALAXY_VIRTUAL_ENV and $GALAXY_CONDA_ENV

scripts/common_startup_functions.sh

@@ -134,17 +134,6 @@ setup_python() {
     "$GALAXY_PYTHON" ./scripts/check_python.py || exit 1
 }
 
-setup_gravity_state_dir() {
-    # $GALAXY_VIRTUAL_ENV is expected to be set, and cwd must be galaxy root
-    if ! grep -q '^GRAVITY_STATE_DIR=' "${GALAXY_VIRTUAL_ENV}/bin/activate"; then
-        echo "Setting \$GRAVITY_STATE_DIR in ${GALAXY_VIRTUAL_ENV}/bin/activate"
-        echo '' >> "${GALAXY_VIRTUAL_ENV}/bin/activate"
-        echo '# Galaxy Gravity per-instance state directory configured by Galaxy common_startup.sh' >> "${GALAXY_VIRTUAL_ENV}/bin/activate"
-        echo "GRAVITY_STATE_DIR=\${GRAVITY_STATE_DIR:-'$(pwd)/database/gravity'}" >> "${GALAXY_VIRTUAL_ENV}/bin/activate"
-        echo 'export GRAVITY_STATE_DIR' >> "${GALAXY_VIRTUAL_ENV}/bin/activate"
-    fi
-}
-
 set_galaxy_config_file_var() {
     if [ -z "$GALAXY_CONFIG_FILE" ]; then
         GALAXY_CONFIG_FILE=$(PYTHONPATH=lib python -c "from __future__ import print_function; from galaxy.util.properties import find_config_file; print(find_config_file(['galaxy', 'universe_wsgi']) or '')")