Build a job runner ================== A walk through the steps of building a runner for Galaxy ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In this tutorial, we will look at how to build a runner in a block by block fashion (like building blocks), so we will divide the runner into components based on their function. We assume you are familiar with setting up and managing a local installation of Galaxy. To learn more about the basics, please refer to: https://galaxyproject.org/admin/get-galaxy/ To explore existing runners, please refer to: https://github.com/galaxyproject/galaxy/blob/dev/lib/galaxy/jobs/runners What is required to make a runner for Galaxy? ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ `galaxy.jobs.runners.\_\_init\_\_.py `__ contains the base runner implementation. To create a new runner, the base runner class (in most cases, ``AsynchronousJobRunner``) must be inherited and only certain methods need to be overridden with your logic. These are the methods that need to be implemented: 1. ``queue_job(job_wrapper)`` 2. ``check_watched_item(job_state)`` 3. ``stop_job(job)`` 4. ``recover(job, job_wrapper)`` In addition, you will almost certainly override the ``__init__(app, nworkers, **kwargs)`` method in order to add custom logic to initialize your runner. In doing so, make sure to call the parent class constructor: .. code-block:: python super().__init__(app, nworkers, **kwargs) Keep in mind that when you override a method, you should not reimplement any of the logic that is present in the base class: the above call to ``super()`` ensures that all that such logic is handled automatically. The big picture --------------- The above methods are invoked at various stages of job execution in Galaxy. These methods will act as a mediator between the Galaxy framework and the external execution platform. To learn when and how these methods are invoked, we will look at the implementation of the parent class and process lifecycle of a runner. Implementation of parent class (``galaxy.jobs.runners.__init__.py``) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Class Inheritance structure --------------------------- .. image:: inherit.png The big picture --------------- .. image:: runner_diag.png The whole process is divided into different stages for ease of understanding. Runner Methods in detail ~~~~~~~~~~~~~~~~~~~~~~~~ 1. ``__init__`` method - STAGE 1 -------------------------------- Input params: 1. ``app`` 2. ``nworkers`` (Number of threads specified in ``job_conf.xml``) 3. ``**kwargs`` (Variable length argument) Output params: NA The input params are read from ``job_conf.xml`` and passed to the runner by the Galaxy framework. Configuration of where to run jobs and external runner configuration is performed in the ``job_conf.xml`` file. More information about ``job_conf.xml`` is available `here `__. Have a look at the sample ``job_conf.xml``: .. code-block:: xml gosc HELLOWORLD 1 2 The data in ``job_conf.xml`` is manipulated through the following steps: **Step 1:** Define structure of data under plugins tag (in ``job_conf.xml``) as a dictionary. .. code-block:: python runner_param_specs = dict(user=dict(map=str), key=dict(map=str)) **Step 2:** Update the dictionary structure in kwargs. .. code-block:: python kwargs.update({'runner_param_specs': runner_param_specs}) **Step 3:** Now call the parent constructor to assign the values. .. code-block:: python super().__init__(app, nworkers, **kwargs) **Step 4:** The assigned values can be accessed in a runner in the following way. .. code-block:: python print(self.runner_params["user"]) print(self.runner_params["key"]) The output will be: :: gosc HELLOWORLD **Step 5:** Invoke the external API with the values obtained by the above method for initialization. Finally, the worker threads and monitor threads are invoked for galaxy to listen for incoming tool submissions. .. code-block:: python self._init_monitor_thread() self._init_worker_threads() 2. ``queue_job`` method - STAGE 2 --------------------------------- Input params: ``job_wrapper`` (Object of type `galaxy.jobs.JobWrapper `__) Output params: None ``galaxy.jobs.JobWrapper`` is a wrapper around 'model.Job' with convenience methods for running processes and state management. Functioning of ``queue_job`` method ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ The logic in the ``queue_job`` method follows these steps: **Step 1.** ``prepare_job()`` method is invoked to do some sanity checks that all runners' ``queue_job()`` methods are likely to want to do and also to build the runner command line for that job. Initial state and configuration of the job are set and all data is associated with **job\_wrapper**. **Step 2.** Submit job to the external runner and return the job id. Accessing jobs data (tool submitted in Galaxy webframework) is purely from ``job_wrapper``. eg: ``job_wrapper.get_state()`` -> gives state of a job (queued/running/failed/success/...) Let us look at how to access the external runner's configuration present under the destination tag of ``job_conf.xml`` in the above example. .. code-block:: python job_destination = job_wrapper.job_destination docker_cpu = int(job_destination.params["docker_cpu"]) docker_ram = int(job_destination.params["docker_memory"]) A special case. User Story: a docker based external runner is present. A default docker image for execution is set in ``job_conf.xml``. A tool can also specify the docker image for its execution. Specification in the tool is given more priority than the default specification. For this functionality we can use the following statement: .. code-block:: python docker_image = self._find_container(job_wrapper).container_id Note: This pre-written method is only for getting the external image/container/os. **Step 3.** After successful submission of a job to the external runner, submit the job to the Galaxy framework. To do that, make an object of type AsynchronousJobState and put it in the ``monitor_queue``. .. code-block:: python ajs = AsynchronousJobState(files_dir=job_wrapper.working_directory, job_wrapper=job_wrapper, job_id=job_id, job_destination=job_destination) self.monitor_queue.put(ajs) 3. ``check_watched_item`` method - STAGE 3 ------------------------------------------ Input params: ``job_state`` (Object of type `galaxy.jobs.runners.AsynchronousJobState `__) Output params: ``AsynchronousJobState`` object Without going into much detail, assume there is a queue to track the status of every job: .. image:: queue.png :align: center The galaxy framework updates the status of a job by iterating through the queue. During the iteration, it calls the ``check_watched_item`` method with the job. Your responsibility will be to get the status of execution of the job from the external runner and return the updated status of the job, and also to copy the output files for the completed jobs. Updated result after an iteration (after invocation of ``check_watched_item`` 6 times): .. image:: queue_b.png :align: center Note: Iterating through the queue is already taken care of by the framework. To inform Galaxy about the status of the job: - Get the job status from the external runner using ``job_id``. - Check if the job is queued/running/completed, etc. A general structure is provided below. - Call ``self.mark_as_finished(job_state)`` if the job has been successfully executed. - Call ``self.mark_as_failed(job_state)`` if the job has failed during execution. - To change the state of a job, change ``job_state.running`` and call ``job_state.job_wrapper.change_state()`` .. code-block:: python def check_watched_item(self, job_state): job_status = get_task_from_external_runner(job_state.job_id) if job_status == "over_with_success": job_state.running = False job_state.job_wrapper.change_state(model.Job.states.OK) create_log_files() self.mark_as_finished(job_state) return None elif job_status == "running": job_state.running = True job_state.job_wrapper.change_state(model.Job.states.RUNNING) return job_state elif job_status == "pending": return job_state elif job_status == "over_with_error": job_state.running = False job_state.job_wrapper.change_state(model.Job.states.ERROR) create_log_files() self.mark_as_failed(job_state) return None Note: - ``get_task_from_external_runner`` and ``create_log_files`` are user-defined methods. - The method should return ``job_state`` if the job should remain in the job runner's list of watched jobs (i.e. if it is running or pending). If it no longer needs to be watched (e.g. it has terminated either successfully or with an error) it should return None. ``create_log_files()`` is nothing but copying the files (``error_file``, ``output_file``, ``exit_code_file``) from the external runner's directory to the working directory of Galaxy. The source of the files is the output directory of your external runner. The destination of the files will be: - output file -> ``job_state.output_file`` - error file -> ``job_state.error_file`` - exit code file -> ``job_state.exit_code_file`` 4. ``stop_job`` method - STAGE 4 -------------------------------- Input params: job (Object of type `galaxy.model.Job `__) Output params: None Functionality: Attempts to delete a dispatched Job executing in an external runner. When a user requests that the execution of a job in the Galaxy framework be stopped, a call is made to the external runner to stop the job execution. The ``job_id`` of the job to be deleted is accessed by .. code-block:: python job.id 5. ``recover`` method - STAGE 5 ------------------------------- Input params: - ``job`` (Object of type `galaxy.model.Job `__). - ``job_wrapper`` (Object of type `galaxy.jobs.JobWrapper `__). Output params: None Functionality: Recovers any jobs stuck in a queued/running state when Galaxy starts. This method is invoked by Galaxy at the time of startup. Jobs in Running and Queued state in Galaxy are put in the ``monitor_queue`` by creating an ``AsynchronousJobState`` object. The following is a generic code snippet for the ``recover`` method. .. code-block:: python ajs = AsynchronousJobState(files_dir=job_wrapper.working_directory, job_wrapper=job_wrapper) asj.job_id = job.get_job_runner_external_id() ajs.job_destination = job_wrapper.job_destination job_wrapper.command_line = job.command_line ajs.job_wrapper = job_wrapper if job.state == model.Job.states.RUNNING: ajs.old_state = 'R' ajs.running = True self.monitor_queue.put(ajs) elif job.state == model.Job.states.QUEUED: ajs.old_state = 'Q' ajs.running = False self.monitor_queue.put(ajs)