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#!/usr/bin/env python3 |
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# -*- coding: utf-8 -*- |
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""" |
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Created on Thu Oct 25 11:27:52 2018 |
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@author: Paolo Cozzi <[email protected]> |
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""" |
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from celery import group |
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from celery.utils.log import get_task_logger |
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from common.tasks import BaseTask, NotifyAdminTaskMixin, exclusive_task |
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from image.celery import app as celery_app |
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from image_app.models import ( |
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DictCountry, DictBreed, DictSpecie, DictUberon, DictDevelStage, |
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DictPhysioStage) |
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from .helpers import ( |
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annotate_country, annotate_breed, annotate_specie, annotate_organismpart, |
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annotate_develstage, annotate_physiostage) |
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# Get an instance of a logger |
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logger = get_task_logger(__name__) |
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class AnnotateTaskMixin(NotifyAdminTaskMixin): |
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name = None |
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descripttion = None |
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model = None |
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annotate_func = None |
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def run(self): |
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"""This function is called when delay is called""" |
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logger.debug("Starting %s" % self.name.lower()) |
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# get all countries without a term |
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for term in self.model.objects.filter(term__isnull=True): |
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self.annotate_func(term) |
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logger.debug("%s completed" % self.name.lower()) |
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return "success" |
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class AnnotateCountries(AnnotateTaskMixin, BaseTask): |
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name = "Annotate Countries" |
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description = """Annotate countries with ontologies using Zooma tools""" |
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model = DictCountry |
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annotate_func = staticmethod(annotate_country) |
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@exclusive_task( |
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task_name="Annotate Countries", lock_id="AnnotateCountries") |
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def run(self): |
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return super().run() |
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class AnnotateBreeds(AnnotateTaskMixin, BaseTask): |
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name = "Annotate Breeds" |
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description = """Annotate breeds with ontologies using Zooma tools""" |
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model = DictBreed |
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annotate_func = staticmethod(annotate_breed) |
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@exclusive_task(task_name="Annotate Breeds", lock_id="AnnotateBreeds") |
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def run(self): |
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return super().run() |
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class AnnotateSpecies(AnnotateTaskMixin, BaseTask): |
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name = "Annotate Species" |
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description = """Annotate species with ontologies using Zooma tools""" |
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model = DictSpecie |
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annotate_func = staticmethod(annotate_specie) |
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@exclusive_task(task_name="Annotate Species", lock_id="AnnotateSpecies") |
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def run(self): |
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return super().run() |
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class AnnotateOrganismPart(AnnotateTaskMixin, BaseTask): |
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name = "Annotate OrganismPart" |
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description = "Annotate organism parts with ontologies using Zooma tools" |
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model = DictUberon |
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annotate_func = staticmethod(annotate_organismpart) |
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lock_id = "AnnotateOrganismPart" |
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@exclusive_task(task_name="Annotate Uberon", lock_id="AnnotateUberon") |
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def run(self): |
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return super().run() |
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class AnnotateDevelStage(AnnotateTaskMixin, BaseTask): |
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name = "Annotate DevelStage" |
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description = ( |
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"Annotate developmental stages with ontologies using Zooma tools") |
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model = DictDevelStage |
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annotate_func = staticmethod(annotate_develstage) |
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@exclusive_task( |
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task_name="Annotate DevelStage", |
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lock_id="AnnotateDevelStage") |
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def run(self): |
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return super().run() |
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class AnnotatePhysioStage(AnnotateTaskMixin, BaseTask): |
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name = "Annotate PhysioStage" |
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description = ( |
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"Annotate physiological stages with ontologies using Zooma tools") |
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model = DictPhysioStage |
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annotate_func = staticmethod(annotate_physiostage) |
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@exclusive_task( |
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task_name="Annotate PhysioStage", |
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lock_id="AnnotatePhysioStage") |
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def run(self): |
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return super().run() |
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class AnnotateAll(BaseTask): |
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name = "Annotate All" |
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description = """Annotate all dict tables using Zooma""" |
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@exclusive_task(task_name="Annotate All", lock_id="AnnotateAll") |
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def run(self): |
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""" |
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This function is called when delay is called. It will acquire a lock |
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in redis, so those tasks are mutually exclusive |
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Returns: |
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str: success if everything is ok. Different messages if task is |
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already running or exception is caught""" |
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# debugging instance |
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self.debug_task() |
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tasks = [ |
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AnnotateCountries(), AnnotateBreeds(), AnnotateSpecies(), |
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AnnotateOrganismPart(), AnnotateDevelStage(), |
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AnnotatePhysioStage() |
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] |
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# instantiate the group |
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annotate_task = group([task.s() for task in tasks]) |
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logger.debug("Starting task %s" % (annotate_task)) |
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# start the group task - shortcut for apply_asyinc |
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result = annotate_task.delay() |
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logger.debug(result) |
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# forget about called tasks and exit |
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return "success" |
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# --- task registering |
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# register explicitly tasks |
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# https://github.com/celery/celery/issues/3744#issuecomment-271366923 |
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celery_app.tasks.register(AnnotateCountries) |
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celery_app.tasks.register(AnnotateBreeds) |
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celery_app.tasks.register(AnnotateSpecies) |
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celery_app.tasks.register(AnnotateOrganismPart) |
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celery_app.tasks.register(AnnotateDevelStage) |
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celery_app.tasks.register(AnnotatePhysioStage) |
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celery_app.tasks.register(AnnotateAll) |
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cnr-ibba /
IMAGE-InjectTool
