256 lines
10 KiB
Python
256 lines
10 KiB
Python
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"""
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This file contains definitions for a MEOW recipe based off of jupyter
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notebooks, along with an appropriate handler for said events.
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Author(s): David Marchant
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"""
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import os
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import nbformat
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import sys
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from typing import Any, Tuple, Dict
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from core.correctness.validation import check_type, valid_string, \
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valid_dict, valid_path, valid_dir_path, valid_event
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from core.correctness.vars import VALID_VARIABLE_NAME_CHARS, PYTHON_FUNC, \
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DEBUG_INFO, EVENT_TYPE_WATCHDOG, JOB_HASH, DEFAULT_JOB_QUEUE_DIR, \
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EVENT_PATH, JOB_TYPE_PAPERMILL, WATCHDOG_HASH, JOB_PARAMETERS, \
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JOB_ID, WATCHDOG_BASE, META_FILE, \
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PARAMS_FILE, JOB_STATUS, STATUS_QUEUED, EVENT_RULE, EVENT_TYPE, \
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EVENT_RULE, get_base_file
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from core.meow import BaseRecipe, BaseHandler
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from functionality.debug import setup_debugging, print_debug
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from functionality.file_io import make_dir, read_notebook, write_notebook, \
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write_yaml
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from functionality.meow import create_job, replace_keywords
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class JupyterNotebookRecipe(BaseRecipe):
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# A path to the jupyter notebook used to create this recipe
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source:str
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def __init__(self, name:str, recipe:Any, parameters:Dict[str,Any]={},
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requirements:Dict[str,Any]={}, source:str=""):
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"""JupyterNotebookRecipe Constructor. This is used to execute analysis
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code using the papermill module."""
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super().__init__(name, recipe, parameters, requirements)
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self._is_valid_source(source)
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self.source = source
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def _is_valid_source(self, source:str)->None:
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"""Validation check for 'source' variable from main constructor."""
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if source:
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valid_path(source, extension=".ipynb", min_length=0)
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def _is_valid_recipe(self, recipe:Dict[str,Any])->None:
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"""Validation check for 'recipe' variable from main constructor.
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Called within parent BaseRecipe constructor."""
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check_type(recipe, Dict, hint="JupyterNotebookRecipe.recipe")
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nbformat.validate(recipe)
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def _is_valid_parameters(self, parameters:Dict[str,Any])->None:
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"""Validation check for 'parameters' variable from main constructor.
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Called within parent BaseRecipe constructor."""
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valid_dict(parameters, str, Any, strict=False, min_length=0)
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for k in parameters.keys():
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valid_string(k, VALID_VARIABLE_NAME_CHARS)
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def _is_valid_requirements(self, requirements:Dict[str,Any])->None:
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"""Validation check for 'requirements' variable from main constructor.
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Called within parent BaseRecipe constructor."""
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valid_dict(requirements, str, Any, strict=False, min_length=0)
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for k in requirements.keys():
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valid_string(k, VALID_VARIABLE_NAME_CHARS)
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class PapermillHandler(BaseHandler):
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# Config option, above which debug messages are ignored
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debug_level:int
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# Where print messages are sent
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_print_target:Any
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def __init__(self, job_queue_dir:str=DEFAULT_JOB_QUEUE_DIR,
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print:Any=sys.stdout, logging:int=0)->None:
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"""PapermillHandler Constructor. This creats jobs to be executed using
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the papermill module. This does not run as a continuous thread to
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handle execution, but is invoked according to a factory pattern using
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the handle function. Note that if this handler is given to a MeowRunner
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object, the job_queue_dir will be overwridden."""
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super().__init__()
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self._is_valid_job_queue_dir(job_queue_dir)
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self.job_queue_dir = job_queue_dir
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self._print_target, self.debug_level = setup_debugging(print, logging)
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print_debug(self._print_target, self.debug_level,
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"Created new PapermillHandler instance", DEBUG_INFO)
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def handle(self, event:Dict[str,Any])->None:
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"""Function called to handle a given event."""
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print_debug(self._print_target, self.debug_level,
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f"Handling event {event[EVENT_PATH]}", DEBUG_INFO)
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rule = event[EVENT_RULE]
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# Assemble job parameters dict from pattern variables
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yaml_dict = {}
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for var, val in rule.pattern.parameters.items():
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yaml_dict[var] = val
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for var, val in rule.pattern.outputs.items():
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yaml_dict[var] = val
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yaml_dict[rule.pattern.triggering_file] = event[EVENT_PATH]
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# If no parameter sweeps, then one job will suffice
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if not rule.pattern.sweep:
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self.setup_job(event, yaml_dict)
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else:
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# If parameter sweeps, then many jobs created
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values_list = rule.pattern.expand_sweeps()
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for values in values_list:
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for value in values:
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yaml_dict[value[0]] = value[1]
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self.setup_job(event, yaml_dict)
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def valid_handle_criteria(self, event:Dict[str,Any])->Tuple[bool,str]:
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"""Function to determine given an event defintion, if this handler can
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process it or not. This handler accepts events from watchdog with
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jupyter notebook recipes."""
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try:
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valid_event(event)
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msg = ""
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if type(event[EVENT_RULE].recipe) != JupyterNotebookRecipe:
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msg = "Recipe is not a JupyterNotebookRecipe. "
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if event[EVENT_TYPE] != EVENT_TYPE_WATCHDOG:
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msg += f"Event type is not {EVENT_TYPE_WATCHDOG}."
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if msg:
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return False, msg
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else:
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return True, ""
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except Exception as e:
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return False, str(e)
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def _is_valid_job_queue_dir(self, job_queue_dir)->None:
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"""Validation check for 'job_queue_dir' variable from main
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constructor."""
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valid_dir_path(job_queue_dir, must_exist=False)
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if not os.path.exists(job_queue_dir):
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make_dir(job_queue_dir)
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def setup_job(self, event:Dict[str,Any], yaml_dict:Dict[str,Any])->None:
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"""Function to set up new job dict and send it to the runner to be
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executed."""
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meow_job = create_job(
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JOB_TYPE_PAPERMILL,
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event,
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extras={
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JOB_PARAMETERS:yaml_dict,
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JOB_HASH: event[WATCHDOG_HASH],
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PYTHON_FUNC:papermill_job_func,
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}
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)
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print_debug(self._print_target, self.debug_level,
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f"Creating job from event at {event[EVENT_PATH]} of type "
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f"{JOB_TYPE_PAPERMILL}.", DEBUG_INFO)
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# replace MEOW keyworks within variables dict
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yaml_dict = replace_keywords(
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meow_job[JOB_PARAMETERS],
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meow_job[JOB_ID],
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event[EVENT_PATH],
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event[WATCHDOG_BASE]
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)
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# Create a base job directory
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job_dir = os.path.join(self.job_queue_dir, meow_job[JOB_ID])
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make_dir(job_dir)
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# write a status file to the job directory
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meta_file = os.path.join(job_dir, META_FILE)
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write_yaml(meow_job, meta_file)
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# write an executable notebook to the job directory
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base_file = os.path.join(job_dir, get_base_file(JOB_TYPE_PAPERMILL))
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write_notebook(event[EVENT_RULE].recipe.recipe, base_file)
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# write a parameter file to the job directory
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param_file = os.path.join(job_dir, PARAMS_FILE)
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write_yaml(yaml_dict, param_file)
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meow_job[JOB_STATUS] = STATUS_QUEUED
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# update the status file with queued status
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write_yaml(meow_job, meta_file)
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# Send job directory, as actual definitons will be read from within it
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self.to_runner.send(job_dir)
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# Papermill job execution code, to be run within the conductor
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def papermill_job_func(job_dir):
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# Requires own imports as will be run in its own execution environment
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import os
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import papermill
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from datetime import datetime
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from core.correctness.vars import JOB_EVENT, JOB_ID, \
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EVENT_PATH, META_FILE, PARAMS_FILE, \
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JOB_STATUS, JOB_HASH, SHA256, STATUS_SKIPPED, JOB_END_TIME, \
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JOB_ERROR, STATUS_FAILED, get_job_file, \
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get_result_file
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from functionality.file_io import read_yaml, write_notebook, write_yaml
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from functionality.hashing import get_file_hash
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from functionality.parameterisation import parameterize_jupyter_notebook
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# Identify job files
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meta_file = os.path.join(job_dir, META_FILE)
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base_file = os.path.join(job_dir, get_base_file(JOB_TYPE_PAPERMILL))
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job_file = os.path.join(job_dir, get_job_file(JOB_TYPE_PAPERMILL))
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result_file = os.path.join(job_dir, get_result_file(JOB_TYPE_PAPERMILL))
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param_file = os.path.join(job_dir, PARAMS_FILE)
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# Get job defintions
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job = read_yaml(meta_file)
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yaml_dict = read_yaml(param_file)
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# Check the hash of the triggering file, if present. This addresses
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# potential race condition as file could have been modified since
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# triggering event
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if JOB_HASH in job:
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# get current hash
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triggerfile_hash = get_file_hash(job[JOB_EVENT][EVENT_PATH], SHA256)
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# If hash doesn't match, then abort the job. If its been modified, then
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# another job will have been scheduled anyway.
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if not triggerfile_hash \
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or triggerfile_hash != job[JOB_HASH]:
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job[JOB_STATUS] = STATUS_SKIPPED
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job[JOB_END_TIME] = datetime.now()
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msg = "Job was skipped as triggering file " + \
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f"'{job[JOB_EVENT][EVENT_PATH]}' has been modified since " + \
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"scheduling. Was expected to have hash " + \
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f"'{job[JOB_HASH]}' but has '{triggerfile_hash}'."
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job[JOB_ERROR] = msg
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write_yaml(job, meta_file)
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return
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# Create a parameterised version of the executable notebook
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try:
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base_notebook = read_notebook(base_file)
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# TODO read notebook from already written file rather than event
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job_notebook = parameterize_jupyter_notebook(
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base_notebook, yaml_dict
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)
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write_notebook(job_notebook, job_file)
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except Exception as e:
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job[JOB_STATUS] = STATUS_FAILED
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job[JOB_END_TIME] = datetime.now()
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msg = f"Job file {job[JOB_ID]} was not created successfully. {e}"
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job[JOB_ERROR] = msg
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write_yaml(job, meta_file)
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return
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# Execute the parameterised notebook
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try:
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papermill.execute_notebook(job_file, result_file, {})
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except Exception as e:
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job[JOB_STATUS] = STATUS_FAILED
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job[JOB_END_TIME] = datetime.now()
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msg = f"Result file {result_file} was not created successfully. {e}"
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job[JOB_ERROR] = msg
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write_yaml(job, meta_file)
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return
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