galaxy/doc/source/dev/build_a_job_runner.rst

Build a job runner
==================

A walk through the steps of building a runner for Galaxy
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

In this tutorial, we will 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 <https://github.com/galaxyproject/galaxy/blob/dev/lib/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 methods that 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 stages of job execution in
Galaxy. These methods will act as a mediator between the Galaxy
framework and the external execution platform. To know 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``)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

-  .. 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 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 <https://galaxyproject.org/admin/config/jobs/>`__.

Have a look at the sample ``job_conf.xml``:

.. code-block:: xml

    <job_conf>
        <plugins>
            <plugin id="local" type="runner" load="galaxy.jobs.runners.local:LocalJobRunner" workers="4"/>
            <plugin id="godocker" type="runner" load="galaxy.jobs.runners.godocker:GodockerJobRunner">
                <param id="user">gosc</param>
                <param id="key">HELLOWORLD</param>
            </plugin>
        </plugins>
        <handlers>
            <handler id="main"/>
        </handlers>
        <destinations default="god">
            <destination id="local" runner="local"/>
            <destination id="god" runner="godocker">
                <param id="docker_cpu">1</param>
                <param id="docker_memory">2</param>
            </destination>
        </destinations>
    </job_conf>

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.

.. code-block:: python

    runner_param_specs = dict(user=dict(map=str), key=dict(map=str))

B: Update the dictionary structure in kwargs.

.. code-block:: python

    kwargs.update({'runner_param_specs': runner_param_specs})

C: Now call the parent constructor to assign the values.

.. code-block:: python

    super(GodockerJobRunner, self).__init__(app, nworkers, **kwargs)

D: The assigned values can be accessed in runner in the following way.

.. code-block:: python

    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.

.. code-block:: python

    self._init_monitor_thread()
    self._init_worker_threads()

2. ``queue_job`` method - STAGE 2
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Input params: ``job_wrapper`` (Object of
`galaxy.jobs.JobWrapper <https://github.com/galaxyproject/galaxy/blob/dev/lib/galaxy/jobs/__init__.py#L743>`__)

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.

.. 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 tool
is given more priority than the default specification. To achieve such a
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..

C. 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
`galaxy.jobs.runners.AsynchronousJobState <https://github.com/galaxyproject/galaxy/blob/dev/lib/galaxy/jobs/runners/__init__.py#L400>`__)

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 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 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()``

.. 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.

-  Return value is ``job_state`` for running, pending jobs and None for any remaining states of a job.

``create_log_files()`` are nothing but copying the files (``error_file``,
``output_file``, ``exit_code_file``) from the external runner's directory to
the 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 <https://github.com/galaxyproject/galaxy/blob/dev/lib/galaxy/model/__init__.py#L344>`__)

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 `galaxy.model.Job <https://github.com/galaxyproject/galaxy/blob/dev/lib/galaxy/model/__init__.py#L344>`__).

-  ``job_wrapper`` (Object of `galaxy.jobs.JobWrapper <https://github.com/galaxyproject/galaxy/blob/dev/lib/galaxy/jobs/__init__.py#L743>`__).


Output params: None

Functionality: Recovers any jobs stuck in a queued/running state when
Galaxy was 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 the ``recover`` method.

.. code-block:: python

    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)