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Merge pull request #429 from tcezard/EVA3496_merge_split_only_job
EVA-3496 - Add new job for running only the MERGE and SPLIT
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50 changes: 50 additions & 0 deletions
50
.../clustering/configuration/batch/jobs/ResolveMergeThenSplitCandidatesJobConfiguration.java
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|---|---|---|
| @@ -0,0 +1,50 @@ | ||
| /* | ||
| * Copyright 2020 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. | ||
| */ | ||
| package uk.ac.ebi.eva.accession.clustering.configuration.batch.jobs; | ||
|
|
||
| import org.springframework.batch.core.Job; | ||
| import org.springframework.batch.core.Step; | ||
| import org.springframework.batch.core.configuration.annotation.EnableBatchProcessing; | ||
| import org.springframework.batch.core.configuration.annotation.JobBuilderFactory; | ||
| import org.springframework.batch.core.launch.support.RunIdIncrementer; | ||
| import org.springframework.beans.factory.annotation.Qualifier; | ||
| import org.springframework.context.annotation.Bean; | ||
| import org.springframework.context.annotation.Configuration; | ||
|
|
||
| import static uk.ac.ebi.eva.accession.clustering.configuration.BeanNames.CLEAR_RS_MERGE_AND_SPLIT_CANDIDATES_STEP; | ||
| import static uk.ac.ebi.eva.accession.clustering.configuration.BeanNames.RESOLVE_MERGE_THEN_SPLIT_CANDIDATE_JOB; | ||
| import static uk.ac.ebi.eva.accession.clustering.configuration.BeanNames.PROCESS_RS_MERGE_CANDIDATES_STEP; | ||
| import static uk.ac.ebi.eva.accession.clustering.configuration.BeanNames.PROCESS_RS_SPLIT_CANDIDATES_STEP; | ||
|
|
||
| @Configuration | ||
| @EnableBatchProcessing | ||
| public class ResolveMergeThenSplitCandidatesJobConfiguration { | ||
| // Should be run after split or merge candidates have been processed in the step @see PROCESS_REMAPPED_VARIANTS_WITH_RS_JOB | ||
| // This job should only be run in parallel across instances | ||
| @Bean(RESOLVE_MERGE_THEN_SPLIT_CANDIDATE_JOB) | ||
| public Job clusteringFromMongoJob( | ||
| @Qualifier(PROCESS_RS_MERGE_CANDIDATES_STEP) Step processRSMergeCandidatesStep, | ||
| @Qualifier(PROCESS_RS_SPLIT_CANDIDATES_STEP) Step processRSSplitCandidatesStep, | ||
| @Qualifier(CLEAR_RS_MERGE_AND_SPLIT_CANDIDATES_STEP) Step clearRSMergeAndSplitCandidatesStep, | ||
| JobBuilderFactory jobBuilderFactory) { | ||
| return jobBuilderFactory.get(RESOLVE_MERGE_THEN_SPLIT_CANDIDATE_JOB) | ||
| .incrementer(new RunIdIncrementer()) | ||
| .start(processRSMergeCandidatesStep) | ||
| .next(processRSSplitCandidatesStep) | ||
| .next(clearRSMergeAndSplitCandidatesStep) | ||
| .build(); | ||
| } | ||
| } |
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69 changes: 69 additions & 0 deletions
69
...n-clustering/src/test/resources/test-data/submittedVariantOperationEntityMongoReader.json
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|---|---|---|
| @@ -0,0 +1,69 @@ | ||
| { | ||
| "submittedVariantOperationEntity": [ | ||
| { | ||
| "_id" : "RSMC_GCA_000000001.1_HASH", | ||
| "eventType" : "RS_MERGE_CANDIDATES", | ||
| "accession" : NumberLong("2222222222"), | ||
| "reason" : "RS mismatch with 1111111111", | ||
| "inactiveObjects" : [ | ||
| { | ||
| "seq" : "GCA_000000001.1", | ||
| "tax" : 3000, | ||
| "study" : "PRJEB00001", | ||
| "contig" : "CM000001.2", | ||
| "start" : NumberLong(3000), | ||
| "ref" : "C", | ||
| "alt" : "T", | ||
| "rs" : NumberLong("2222222222"), | ||
| "evidence" : true, | ||
| "asmMatch" : true, | ||
| "allelesMatch" : true, | ||
| "validated" : false, | ||
| "hashedMessage" : "45BD2A41D4C295DF0A85A54D6CB72C2BBABB0C7D", | ||
| "accession" : NumberLong(1000000000), | ||
| "version" : 1, | ||
| "createdDate" : ISODate("2022-04-26T08:33:26.562Z") | ||
| }, | ||
| { | ||
| "seq" : "GCA_000000001.1", | ||
| "tax" : 3000, | ||
| "study" : "PRJEB00002", | ||
| "contig" : "CM000001.2", | ||
| "start" : NumberLong(3000), | ||
| "ref" : "C", | ||
| "alt" : "T", | ||
| "rs" : NumberLong("2222222222"), | ||
| "remappedFrom" : "GCA_000003205.6", | ||
| "remappedDate" : ISODate("2021-08-12T02:53:48.966Z"), | ||
| "remappingId" : "E076D09482EF2504D3168AABB13BC94172A92C27", | ||
| "hashedMessage" : "C2C9770AE529AFD445CC15458CBA2C71F7A82DB8", | ||
| "accession" : NumberLong(1000000001), | ||
| "version" : 1, | ||
| "createdDate" : ISODate("2014-11-10T14:58:00Z") | ||
| }, | ||
| { | ||
| "seq" : "GCA_000000001.1", | ||
| "tax" : 3000, | ||
| "study" : "PRJEB38336", | ||
| "contig" : "CM000001.2", | ||
| "start" : NumberLong(3000), | ||
| "ref" : "C", | ||
| "alt" : "T", | ||
| "rs" : NumberLong("1111111111"), | ||
| "evidence" : true, | ||
| "asmMatch" : true, | ||
| "allelesMatch" : true, | ||
| "validated" : false, | ||
| "remappedFrom" : "GCA_000000000.1", | ||
| "remappedDate" : ISODate("2021-08-11T22:03:44.689Z"), | ||
| "remappingId" : "778BEEA595920286BA9CC9ECF13442A69F9DA73B", | ||
| "hashedMessage" : "581F717670A07D8D032E234212E0D74599943D44", | ||
| "accession" : NumberLong(1000000002), | ||
| "version" : 1, | ||
| "createdDate" : ISODate("2020-11-26T22:56:39.129Z") | ||
| } | ||
| ], | ||
| "createdDate" : ISODate("2023-05-07T04:52:59.110Z") | ||
| } | ||
| ] | ||
| } |