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server: update variant annotator to return the dbSNP IDs in the field…
… annotation.xrefs, #TASK-5821, #TASK-5789
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105 changes: 105 additions & 0 deletions
105
.../src/main/java/org/opencb/cellbase/lib/variant/annotation/futures/FutureSnpAnnotator.java
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,105 @@ | ||
| /* | ||
| * Copyright 2015-2020 OpenCB | ||
| * | ||
| * 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 org.opencb.cellbase.lib.variant.annotation.futures; | ||
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| import org.apache.commons.collections4.CollectionUtils; | ||
| import org.apache.commons.lang3.StringUtils; | ||
| import org.opencb.biodata.models.core.Snp; | ||
| import org.opencb.biodata.models.variant.Variant; | ||
| import org.opencb.biodata.models.variant.avro.VariantAnnotation; | ||
| import org.opencb.biodata.models.variant.avro.Xref; | ||
| import org.opencb.cellbase.core.api.SnpQuery; | ||
| import org.opencb.cellbase.core.result.CellBaseDataResult; | ||
| import org.opencb.cellbase.lib.managers.VariantManager; | ||
| import org.slf4j.Logger; | ||
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| import java.util.ArrayList; | ||
| import java.util.List; | ||
| import java.util.concurrent.*; | ||
|
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| public class FutureSnpAnnotator implements Callable<List<CellBaseDataResult<Snp>>> { | ||
| private VariantManager variantManager; | ||
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| private List<Variant> variantList; | ||
| private int dataRelease; | ||
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| private Logger logger; | ||
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| public FutureSnpAnnotator(List<Variant> variantList, int dataRelease, VariantManager variantManager, Logger logger) { | ||
| this.variantManager = variantManager; | ||
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| this.variantList = variantList; | ||
| this.dataRelease = dataRelease; | ||
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| this.logger = logger; | ||
| } | ||
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| @Override | ||
| public List<CellBaseDataResult<Snp>> call() throws Exception { | ||
| long startTime = System.currentTimeMillis(); | ||
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| List<CellBaseDataResult<Snp>> cellBaseDataResultList = new ArrayList<>(variantList.size()); | ||
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| logger.debug("SNP queries..."); | ||
| // Want to return only one CellBaseDataResult object per Variant | ||
| List<String> includes = new ArrayList<>(); | ||
| includes.add("id"); | ||
| includes.add("source"); | ||
| String logMsg = StringUtils.join(includes, ","); | ||
| logger.info("SNP annotation/search includes: {}", logMsg); | ||
| for (Variant variant : variantList) { | ||
| SnpQuery query = new SnpQuery(); | ||
| query.setChromosome(variant.getChromosome()); | ||
| query.setPosition(variant.getStart()); | ||
| query.setReference(variant.getReference()); | ||
| query.setDataRelease(dataRelease); | ||
| query.setIncludes(includes); | ||
| cellBaseDataResultList.add(variantManager.searchSnp(query)); | ||
| } | ||
| logger.info("SNP queries performance in {} ms for {} variants", System.currentTimeMillis() - startTime, variantList.size()); | ||
| return cellBaseDataResultList; | ||
| } | ||
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| public void processResults(Future<List<CellBaseDataResult<Snp>>> snpFuture, List<VariantAnnotation> variantAnnotationList) | ||
| throws InterruptedException, ExecutionException { | ||
| List<CellBaseDataResult<Snp>> snpCellBaseDataResults; | ||
| try { | ||
| snpCellBaseDataResults = snpFuture.get(30, TimeUnit.SECONDS); | ||
| } catch (TimeoutException e) { | ||
| snpFuture.cancel(true); | ||
| throw new ExecutionException("Unable to finish SNP query on time", e); | ||
| } | ||
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| if (CollectionUtils.isNotEmpty(snpCellBaseDataResults)) { | ||
| for (int i = 0; i < variantAnnotationList.size(); i++) { | ||
| CellBaseDataResult<Snp> snpResult = snpCellBaseDataResults.get(i); | ||
| if (snpResult != null && CollectionUtils.isNotEmpty(snpResult.getResults())) { | ||
| List<Xref> xrefs = new ArrayList<>(); | ||
| for (Snp snp : snpResult.getResults()) { | ||
| xrefs.add(new Xref(snp.getId(), snp.getSource())); | ||
| } | ||
| if (CollectionUtils.isNotEmpty(xrefs)) { | ||
| if (variantAnnotationList.get(i).getXrefs() == null) { | ||
| variantAnnotationList.get(i).setXrefs(new ArrayList<>()); | ||
| } | ||
| variantAnnotationList.get(i).getXrefs().addAll(xrefs); | ||
| } | ||
| } | ||
| } | ||
| } | ||
| } | ||
| } |
109 changes: 109 additions & 0 deletions
109
...n/java/org/opencb/cellbase/lib/variant/annotation/futures/FutureSpliceScoreAnnotator.java
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,109 @@ | ||
| /* | ||
| * Copyright 2015-2020 OpenCB | ||
| * | ||
| * 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 org.opencb.cellbase.lib.variant.annotation.futures; | ||
|
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| import org.apache.commons.collections4.CollectionUtils; | ||
| import org.apache.commons.lang3.StringUtils; | ||
| import org.opencb.biodata.models.core.SpliceScore; | ||
| import org.opencb.biodata.models.core.SpliceScoreAlternate; | ||
| import org.opencb.biodata.models.variant.Variant; | ||
| import org.opencb.biodata.models.variant.avro.ConsequenceType; | ||
| import org.opencb.biodata.models.variant.avro.SpliceScores; | ||
| import org.opencb.biodata.models.variant.avro.VariantAnnotation; | ||
| import org.opencb.cellbase.core.result.CellBaseDataResult; | ||
| import org.opencb.cellbase.lib.managers.VariantManager; | ||
| import org.slf4j.Logger; | ||
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| import java.util.ArrayList; | ||
| import java.util.List; | ||
| import java.util.concurrent.*; | ||
|
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| public class FutureSpliceScoreAnnotator implements Callable<List<CellBaseDataResult<SpliceScore>>> { | ||
| private List<Variant> variantList; | ||
| private int dataRelease; | ||
| private String apiKey; | ||
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| private VariantManager variantManager; | ||
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| private Logger logger; | ||
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| public FutureSpliceScoreAnnotator(List<Variant> variantList, int dataRelease, String apiKey, VariantManager variantManager, | ||
| Logger logger) { | ||
| this.variantList = variantList; | ||
| this.dataRelease = dataRelease; | ||
| this.apiKey = apiKey; | ||
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| this.variantManager = variantManager; | ||
|
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| this.logger = logger; | ||
| } | ||
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| @Override | ||
| public List<CellBaseDataResult<SpliceScore>> call() throws Exception { | ||
| long startTime = System.currentTimeMillis(); | ||
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| List<CellBaseDataResult<SpliceScore>> cellBaseDataResultList = new ArrayList<>(variantList.size()); | ||
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| logger.debug("Query splice"); | ||
| // Want to return only one CellBaseDataResult object per Variant | ||
| for (Variant variant : variantList) { | ||
| cellBaseDataResultList.add(variantManager.getSpliceScoreVariant(variant, apiKey, dataRelease)); | ||
| } | ||
| logger.debug("Splice score query performance is {}ms for {} variants", System.currentTimeMillis() - startTime, | ||
| variantList.size()); | ||
| return cellBaseDataResultList; | ||
| } | ||
|
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| public void processResults(Future<List<CellBaseDataResult<SpliceScore>>> spliceFuture, List<VariantAnnotation> variantAnnotationList) | ||
| throws InterruptedException, ExecutionException { | ||
| List<CellBaseDataResult<SpliceScore>> spliceCellBaseDataResults; | ||
| try { | ||
| spliceCellBaseDataResults = spliceFuture.get(30, TimeUnit.SECONDS); | ||
| } catch (TimeoutException e) { | ||
| spliceFuture.cancel(true); | ||
| throw new ExecutionException("Unable to finish splice score query on time", e); | ||
| } | ||
|
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| if (CollectionUtils.isNotEmpty(spliceCellBaseDataResults)) { | ||
| for (int i = 0; i < variantAnnotationList.size(); i++) { | ||
| CellBaseDataResult<SpliceScore> spliceScoreResult = spliceCellBaseDataResults.get(i); | ||
| if (spliceScoreResult != null && CollectionUtils.isNotEmpty(spliceScoreResult.getResults())) { | ||
| for (SpliceScore spliceScore : spliceScoreResult.getResults()) { | ||
| for (ConsequenceType ct : variantAnnotationList.get(i).getConsequenceTypes()) { | ||
| for (SpliceScoreAlternate spliceScoreAlt : spliceScore.getAlternates()) { | ||
| String alt = StringUtils.isEmpty(variantAnnotationList.get(i).getAlternate()) | ||
| ? "-" | ||
| : variantAnnotationList.get(i).getAlternate(); | ||
| if (alt.equals(spliceScoreAlt.getAltAllele())) { | ||
| if (StringUtils.isEmpty(spliceScore.getTranscriptId()) | ||
| || StringUtils.isEmpty(ct.getTranscriptId()) | ||
| || spliceScore.getTranscriptId().equals(ct.getTranscriptId())) { | ||
| SpliceScores scores = new SpliceScores(spliceScore.getSource(), spliceScoreAlt.getScores()); | ||
| if (ct.getSpliceScores() == null) { | ||
| ct.setSpliceScores(new ArrayList<>()); | ||
| } | ||
| ct.getSpliceScores().add(scores); | ||
| } | ||
| } | ||
| } | ||
| } | ||
| } | ||
| } | ||
| } | ||
| } | ||
| } | ||
| } |