Build a job runner ================== A walk through the steps of building a runner for Galaxy ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In this tutorial, we would build the runner in a block by block fashion (like the building blocks), so we would 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 `__ has the base runner implementation. To create a new runner, that base runner must be inherited and only certain methods need to be overridden with your logic. These are the following methods which need to be implemented: 1. \_\_init\_\_(app, nworkers, \*\*kwargs) 2. queue\_job(job\_wrapper) 3. check\_watched\_item(job\_state) 4. stop\_job(job) 5. recover(job, job\_wrapper) The big picture --------------- The above methods are invoked at various state of a job execution in Galaxy. These methods will act as a mediator between the Galaxy framework and the external executor framework. To know, when and how these methods are invoked, we will see about the implementation of parent class and process lifecycle of the runner. Implementation of parent class (galaxy.jobs.runners.\_\_init\_\_.py) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - .. rubric:: Class Inheritance structure :name: class-inheritance-structure .. image:: inherit.png - .. rubric:: The big picture! :name: the-big-picture-1 .. image:: runner_diag.png The whole process is divided into different stages for understanding purpose. Runner Methods in detail ~~~~~~~~~~~~~~~~~~~~~~~~ 1. \_\_init\_\_ method - STAGE 1 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Input params: 1. app 2. nworkers (Number of threads specified in job\_conf) 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: :: gosc HELLOWORLD 1 2 The following steps are followed to manipulate the data in job\_conf.xml A: Define structure of data under plugin tag (plugin tag in job\_conf.xml) as a dictionary. :: runner_param_specs = dict(user=dict(map=str), key=dict(map=str)) B: Update the dictionary structure in kwargs. :: kwargs['runner_param_specs'].update(runner_param_specs) C: Now call the parent constructor to assign the values. :: super(GodockerJobRunner, self).__init__(app, nworkers, **kwargs) D: The assigned values can be accessed in runner in the following way. :: print self.runner_params["user"] print self.runner_params["key"] The output will be: :: gosc HELLOWORLD E: 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. :: self._init_monitor_thread() self._init_worker_threads() 2. queue\_job method - STAGE 2 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Input params: job\_wrapper (Object of `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. A. 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 runner command line for that job. Initial state and configuration of the job are set and every data is associated with **job\_wrapper**. B. Submit job to the external runner and return the jobid. 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 a means of accessing external runner's configuration present under destination tag of job\_conf.xml in the above example. :: 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 tool is given more priority than the default specification. To achieve such a functionality. We can use the following statement: :: docker_image = self._find_container(job_wrapper).container_id Note: This pre-written method is only for getting the external image/container/os.. C. After successful submission of job in the external runner, submit the job to Galaxy framework. To do that,make an object of AsynchronousJobState and put it in monitor\_queue. :: 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 `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. eg: .. image:: queue.png :align: center The galaxy framework updates the status of a job by iterating through the queue. During the iteration, it calls 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 by the framework. To inform galaxy about the status of the job: - Get the job status from external runner using the 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 state of a job, change job\_state.running and job\_state.job\_wrapper.change\_state() :: 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_file() 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_file() self.mark_as_failed(job_state) return None Note: - Methods prefixed with ! are user-defined methods. - Return value is job\_state for running,pending jobs and None for rest of the states of jobs. create\_log\_files() are nothing but copying the files (error\_file, output\_file, exit\_code\_file) from external runner's directory to working directory of Galaxy. Source of the files are from the output directory of your external runner. 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 `galaxy.model.Job `__) Output params: None Functionality: Attempts to delete a dispatched executing Job in external runner. When an user requests to stop the execution of job in Galaxy framework, 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 :: job.id 5. recover method - STAGE 5 ~~~~~~~~~~~~~~~~~~~~~~~~~~~ Input params: - job (Object of `galaxy.model.Job `__). - job\_wrapper (Object of `galaxy.jobs.JobWrapper `__). Output params: None Functionality: Recovers jobs stuck in the queued/running state when Galaxy started. This method is invoked by Galaxy at the time of startup. Jobs in Running & Queued status in Galaxy are put in the monitor\_queue by creating an AsynchronousJobState object. The following is a generic code snippet for recover method. :: ajs = AsynchronousJobState(files_dir=job_wrapper.working_directory, job_wrapper=job_wrapper) ajs.job_id = str(job_wrapper.job_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)