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Merge pull request #325 from EBI-Metagenomics/feature/metagenomics_ex…
…change Feature/metagenomics exchange
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@@ -41,4 +41,4 @@ dumps | |
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/config/*.yml | ||
/config/*.yaml | ||
!/config/*local* | ||
!/config/*local* |
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196 changes: 196 additions & 0 deletions
196
emgapi/management/commands/populate_metagenomics_exchange.py
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#!/usr/bin/env python | ||
# -*- coding: utf-8 -*- | ||
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# Copyright 2017-2024 EMBL - European Bioinformatics Institute | ||
# | ||
# Licensed under the Apache License, Version 2.0 (the "License"); | ||
# you may not use this file except in compliance with the License. | ||
# You may obtain a copy of the License at | ||
# http://www.apache.org/licenses/LICENSE-2.0 | ||
# | ||
# Unless required by applicable law or agreed to in writing, software | ||
# distributed under the License is distributed on an "AS IS" BASIS, | ||
# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. | ||
# See the License for the specific language governing permissions and | ||
# limitations under the License. | ||
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import logging | ||
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from django.conf import settings | ||
from django.core.management import BaseCommand | ||
from django.utils import timezone | ||
from django.core.paginator import Paginator | ||
from datetime import timedelta | ||
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from emgapi.models import AnalysisJob | ||
from emgapi.metagenomics_exchange import MetagenomicsExchangeAPI | ||
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logger = logging.getLogger(__name__) | ||
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RETRY_COUNT = 5 | ||
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class Command(BaseCommand): | ||
help = "Check and populate metagenomics exchange (ME)." | ||
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def add_arguments(self, parser): | ||
super(Command, self).add_arguments(parser) | ||
parser.add_argument( | ||
"-s", | ||
"--study", | ||
required=False, | ||
type=str, | ||
help="Study accession list (rather than all)", | ||
nargs="+", | ||
) | ||
parser.add_argument( | ||
"-p", | ||
"--pipeline", | ||
help="Pipeline version (rather than all). Not applicable to Genomes.", | ||
action="store", | ||
dest="pipeline", | ||
choices=[1.0, 2.0, 3.0, 4.0, 4.1, 5.0], | ||
required=False, | ||
type=float, | ||
) | ||
parser.add_argument( | ||
"--dry-run", | ||
action="store_true", | ||
required=False, | ||
help="Dry mode, no population of ME", | ||
) | ||
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def handle(self, *args, **options): | ||
self.study_accession = options.get("study") | ||
self.dry_run = options.get("dry_run") | ||
self.pipeline_version = options.get("pipeline") | ||
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self.mgx_api = MetagenomicsExchangeAPI(base_url=settings.METAGENOMICS_EXCHANGE_API) | ||
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# never indexed or updated after indexed | ||
analyses_to_index_and_update = AnalysisJob.objects_for_mgx_indexing.to_add() | ||
# suppressed only | ||
analyses_to_delete = AnalysisJob.objects_for_mgx_indexing.to_delete() | ||
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if self.study_accession: | ||
analyses_to_index_and_update = analyses_to_index_and_update.filter( | ||
study__secondary_accession__in=self.study_accession | ||
) | ||
analyses_to_delete = analyses_to_delete.filter( | ||
study__secondary_accession__in=self.study_accession | ||
) | ||
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if self.pipeline_version: | ||
analyses_to_index_and_update = analyses_to_index_and_update.filter( | ||
pipeline__release_version=self.pipeline_version | ||
) | ||
analyses_to_delete = analyses_to_delete.filter( | ||
pipeline__release_version=self.pipeline_version | ||
) | ||
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self.process_to_index_and_update_records(analyses_to_index_and_update) | ||
self.process_to_delete_records(analyses_to_delete) | ||
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logging.info("Done") | ||
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def process_to_index_and_update_records(self, analyses_to_index_and_update): | ||
logging.info(f"Indexing {len(analyses_to_index_and_update)} new analyses") | ||
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for page in Paginator(analyses_to_index_and_update, settings.METAGENOMICS_EXCHANGE_PAGINATOR_NUMBER): | ||
jobs_to_update = [] | ||
for ajob in page: | ||
metadata = self.mgx_api.generate_metadata( | ||
mgya=ajob.accession, | ||
run_accession=ajob.run, | ||
status="public" if not ajob.is_private else "private", | ||
) | ||
registry_id, metadata_match = self.mgx_api.check_analysis( | ||
source_id=ajob.accession, sequence_id=ajob.run, metadata=metadata | ||
) | ||
# The job is not registered | ||
if not registry_id: | ||
logging.info(f"Add new {ajob}") | ||
if self.dry_run: | ||
logging.info(f"Dry-mode run: no addition to real ME for {ajob}") | ||
continue | ||
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response = self.mgx_api.add_analysis( | ||
mgya=ajob.accession, | ||
run_accession=ajob.run, | ||
public=not ajob.is_private, | ||
) | ||
if response.ok: | ||
logging.info(f"Successfully added {ajob}") | ||
registry_id, metadata_match = self.mgx_api.check_analysis( | ||
source_id=ajob.accession, sequence_id=ajob.run) | ||
ajob.mgx_accession = registry_id | ||
ajob.last_mgx_indexed = timezone.now() + timedelta(minutes=1) | ||
jobs_to_update.append(ajob) | ||
else: | ||
logging.error(f"Error adding {ajob}: {response.message}") | ||
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# else we have to check if the metadata matches, if not we need to update it | ||
else: | ||
if not metadata_match: | ||
logging.info(f"Patch existing {ajob}") | ||
if self.dry_run: | ||
logging.info( | ||
f"Dry-mode run: no patch to real ME for {ajob}" | ||
) | ||
continue | ||
if self.mgx_api.patch_analysis( | ||
registry_id=registry_id, data=metadata | ||
): | ||
logging.info(f"Analysis {ajob} updated successfully") | ||
# Just to be safe, update the MGX accession | ||
ajob.mgx_accession = registry_id | ||
ajob.last_mgx_indexed = timezone.now() + timedelta(minutes=1) | ||
jobs_to_update.append(ajob) | ||
else: | ||
logging.error(f"Analysis {ajob} update failed") | ||
else: | ||
logging.debug(f"No edit for {ajob}, metadata is correct") | ||
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AnalysisJob.objects.bulk_update( | ||
jobs_to_update, ["last_mgx_indexed", "mgx_accession"], batch_size=settings.METAGENOMICS_EXCHANGE_PAGINATOR_NUMBER | ||
) | ||
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def process_to_delete_records(self, analyses_to_delete): | ||
""" | ||
This function removes suppressed records from ME. | ||
""" | ||
logging.info(f"Processing {len(analyses_to_delete)} analyses to remove") | ||
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for page in Paginator(analyses_to_delete, settings.METAGENOMICS_EXCHANGE_PAGINATOR_NUMBER): | ||
jobs_to_update = [] | ||
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for ajob in page: | ||
metadata = self.mgx_api.generate_metadata( | ||
mgya=ajob.accession, | ||
run_accession=ajob.run, | ||
status="public" if not ajob.is_private else "private", | ||
) | ||
registry_id, _ = self.mgx_api.check_analysis( | ||
source_id=ajob.accession, sequence_id=ajob.run, metadata=metadata | ||
) | ||
if registry_id: | ||
logging.info(f"Deleting {ajob}") | ||
if self.dry_run: | ||
logging.info(f"Dry-mode run: no delete from real ME for {ajob}") | ||
continue | ||
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if self.mgx_api.delete_analysis(registry_id): | ||
logging.info(f"{ajob} successfully deleted") | ||
ajob.last_mgx_indexed = timezone.now() | ||
jobs_to_update.append(ajob) | ||
else: | ||
logging.info(f"{ajob} failed on delete") | ||
else: | ||
logging.info( | ||
f"{ajob} doesn't exist in the registry, nothing to delete" | ||
) | ||
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# BULK UPDATE # | ||
AnalysisJob.objects.bulk_update( | ||
jobs_to_update, ["last_mgx_indexed"], batch_size=settings.METAGENOMICS_EXCHANGE_PAGINATOR_NUMBER | ||
) |
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