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https://gitlab.ub.uni-bielefeld.de/sfb1288inf/nopaque.git
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move blueprints in dedicated folder
This commit is contained in:
Patrick Jentsch
239
app/jobs/handle_jobs.py
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239
app/jobs/handle_jobs.py
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from app import db, docker_client, hashids, scheduler
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from app.models import (
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Job,
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JobResult,
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JobStatus,
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TesseractOCRPipelineModel,
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SpaCyNLPPipelineModel
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)
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from datetime import datetime
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from flask import current_app
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from werkzeug.utils import secure_filename
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import docker
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import json
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import os
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import shutil
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def job():
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with scheduler.app.app_context():
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_handle_jobs()
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def _handle_jobs():
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jobs = Job.query.all()
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for job in [x for x in jobs if x.status == JobStatus.SUBMITTED]:
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_create_job_service(job)
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for job in [x for x in jobs if x.status in [JobStatus.QUEUED, JobStatus.RUNNING]]:
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_checkout_job_service(job)
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for job in [x for x in jobs if x.status == JobStatus.CANCELING]:
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_remove_job_service(job)
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db.session.commit()
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def _create_job_service(job):
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''' # Docker service settings # '''
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''' ## Service specific settings ## '''
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if job.service == 'file-setup-pipeline':
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mem_mb = 512
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n_cores = 2
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executable = 'file-setup-pipeline'
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image = f'{current_app.config["NOPAQUE_DOCKER_IMAGE_PREFIX"]}file-setup-pipeline:v{job.service_version}'
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elif job.service == 'tesseract-ocr-pipeline':
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mem_mb = 1024
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n_cores = 4
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executable = 'tesseract-ocr-pipeline'
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image = f'{current_app.config["NOPAQUE_DOCKER_IMAGE_PREFIX"]}tesseract-ocr-pipeline:v{job.service_version}'
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elif job.service == 'transkribus-htr-pipeline':
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mem_mb = 1024
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n_cores = 4
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executable = 'transkribus-htr-pipeline'
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image = f'{current_app.config["NOPAQUE_DOCKER_IMAGE_PREFIX"]}transkribus-htr-pipeline:v{job.service_version}'
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elif job.service == 'spacy-nlp-pipeline':
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mem_mb = 1024
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n_cores = 1
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executable = 'spacy-nlp-pipeline'
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image = f'{current_app.config["NOPAQUE_DOCKER_IMAGE_PREFIX"]}spacy-nlp-pipeline:v{job.service_version}'
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''' ## Command ## '''
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command = f'{executable} -i /input -o /output'
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command += ' --log-dir /logs'
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command += f' --mem-mb {mem_mb}'
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command += f' --n-cores {n_cores}'
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if job.service == 'spacy-nlp-pipeline':
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model_id = hashids.decode(job.service_args['model'])
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model = SpaCyNLPPipelineModel.query.get(model_id)
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if model is None:
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job.status = JobStatus.FAILED
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return
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command += f' -m {model.pipeline_name}'
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if 'encoding_detection' in job.service_args and job.service_args['encoding_detection']:
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command += ' --check-encoding'
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elif job.service == 'tesseract-ocr-pipeline':
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command += f' -m {job.service_args["model"]}'
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if 'binarization' in job.service_args and job.service_args['binarization']:
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command += ' --binarize'
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if 'ocropus_nlbin_threshold' in job.service_args and job.service_args['ocropus_nlbin_threshold']:
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value = job.service_args['ocropus_nlbin_threshold']
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command += f' --ocropus-nlbin-threshold {value}'
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elif job.service == 'transkribus-htr-pipeline':
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transkribus_htr_pipeline_model_id = job.service_args['model']
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command += f' -m {transkribus_htr_pipeline_model_id}'
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readcoop_username = current_app.config.get('NOPAQUE_READCOOP_USERNAME')
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command += f' --readcoop-username "{readcoop_username}"'
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readcoop_password = current_app.config.get('NOPAQUE_READCOOP_PASSWORD')
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command += f' --readcoop-password "{readcoop_password}"'
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if 'binarization' in job.service_args and job.service_args['binarization']:
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command += ' --binarize'
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''' ## Constraints ## '''
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constraints = ['node.role==worker']
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''' ## Labels ## '''
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labels = {
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'origin': current_app.config['SERVER_NAME'],
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'type': 'job',
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'job_id': str(job.id)
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}
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''' ## Mounts ## '''
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mounts = []
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''' ### Input mount(s) ### '''
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input_mount_target_base = '/input'
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if job.service == 'file-setup-pipeline':
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input_mount_target_base += f'/{secure_filename(job.title)}'
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for job_input in job.inputs:
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input_mount_source = job_input.path
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input_mount_target = f'{input_mount_target_base}/{job_input.filename}'
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input_mount = f'{input_mount_source}:{input_mount_target}:ro'
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mounts.append(input_mount)
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if job.service == 'tesseract-ocr-pipeline':
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if isinstance(job.service_args['model'], str):
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model_id = hashids.decode(job.service_args['model'])
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elif isinstance(job.service_args['model'], int):
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model_id = job.service_args['model']
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else:
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job.status = JobStatus.FAILED
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return
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model = TesseractOCRPipelineModel.query.get(model_id)
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if model is None:
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job.status = JobStatus.FAILED
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return
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models_mount_source = model.path
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models_mount_target = f'/usr/local/share/tessdata/{model.id}.traineddata'
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models_mount = f'{models_mount_source}:{models_mount_target}:ro'
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mounts.append(models_mount)
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elif job.service == 'spacy-nlp-pipeline':
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model_id = hashids.decode(job.service_args['model'])
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model = SpaCyNLPPipelineModel.query.get(model_id)
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if model is None:
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job.status = JobStatus.FAILED
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return
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models_mount_source = model.path
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models_mount_target = f'/usr/local/share/spacy/models/{model.filename}'
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models_mount = f'{models_mount_source}:{models_mount_target}:ro'
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mounts.append(models_mount)
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''' ### Output mount ### '''
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output_mount_source = os.path.join(job.path, 'results')
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output_mount_target = '/output'
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output_mount = f'{output_mount_source}:{output_mount_target}:rw'
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# Make sure that their is no data in the output directory
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shutil.rmtree(output_mount_source, ignore_errors=True)
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os.makedirs(output_mount_source)
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mounts.append(output_mount)
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''' ### Pipeline data mount ### '''
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pyflow_data_mount_source = os.path.join(job.path, 'pipeline_data')
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pyflow_data_mount_target = '/logs/pyflow.data'
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pyflow_data_mount = f'{pyflow_data_mount_source}:{pyflow_data_mount_target}:rw'
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# Make sure that their is no data in the output directory
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shutil.rmtree(pyflow_data_mount_source, ignore_errors=True)
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os.makedirs(pyflow_data_mount_source)
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mounts.append(pyflow_data_mount)
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''' ## Name ## '''
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name = f'job_{job.id}'
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''' ## Resources ## '''
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resources = docker.types.Resources(
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cpu_reservation=n_cores * (10 ** 9),
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mem_reservation=mem_mb * (10 ** 6)
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)
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''' ## Restart policy ## '''
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restart_policy = docker.types.RestartPolicy()
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try:
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docker_client.services.create(
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image,
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command=command,
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constraints=constraints,
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labels=labels,
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mounts=mounts,
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name=name,
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resources=resources,
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restart_policy=restart_policy,
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user='0:0'
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)
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except docker.errors.DockerException as e:
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current_app.logger.error(f'Create service "{name}" failed: {e}')
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return
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job.status = JobStatus.QUEUED
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def _checkout_job_service(job):
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service_name = f'job_{job.id}'
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try:
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service = docker_client.services.get(service_name)
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except docker.errors.NotFound as e:
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current_app.logger.error(f'Get service "{service_name}" failed: {e}')
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job.status = JobStatus.FAILED
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return
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except docker.errors.DockerException as e:
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current_app.logger.error(f'Get service "{service_name}" failed: {e}')
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return
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service_tasks = service.tasks()
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if not service_tasks:
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return
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task_state = service_tasks[0].get('Status').get('State')
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if job.status == JobStatus.QUEUED and task_state != 'pending':
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job.status = JobStatus.RUNNING
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return
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elif job.status == JobStatus.RUNNING and task_state == 'complete':
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job.status = JobStatus.COMPLETED
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results_dir = os.path.join(job.path, 'results')
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with open(os.path.join(results_dir, 'outputs.json')) as f:
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outputs = json.load(f)
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for output in outputs:
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filename = os.path.basename(output['file'])
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job_result = JobResult(
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filename=filename,
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job=job,
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mimetype=output['mimetype']
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)
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if 'description' in output:
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job_result.description = output['description']
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db.session.add(job_result)
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db.session.flush(objects=[job_result])
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db.session.refresh(job_result)
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os.rename(
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os.path.join(results_dir, output['file']),
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job_result.path
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)
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elif job.status == JobStatus.RUNNING and task_state == 'failed':
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job.status = JobStatus.FAILED
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else:
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return
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job.end_date = datetime.utcnow()
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try:
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service.remove()
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except docker.errors.DockerException as e:
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current_app.logger.error(f'Remove service "{service_name}" failed: {e}')
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def _remove_job_service(job):
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service_name = f'job_{job.id}'
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try:
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service = docker_client.services.get(service_name)
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except docker.errors.NotFound:
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job.status = JobStatus.CANCELED
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return
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except docker.errors.DockerException as e:
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current_app.logger.error(f'Get service "{service_name}" failed: {e}')
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return
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try:
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service.update(mounts=None)
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except docker.errors.DockerException as e:
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current_app.logger.error(f'Update service "{service_name}" failed: {e}')
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return
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try:
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service.remove()
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except docker.errors.DockerException as e:
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current_app.logger.error(f'Remove "{service_name}" service failed: {e}')
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