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Merge branch 'release-3.x.x' into TASK-6981
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59 changes: 59 additions & 0 deletions
59
.../storage/core/variant/annotation/annotators/extensions/VariantAnnotatorExtensionTask.java
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| Original file line number | Diff line number | Diff line change |
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| @@ -0,0 +1,59 @@ | ||
| package org.opencb.opencga.storage.core.variant.annotation.annotators.extensions; | ||
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| import org.opencb.biodata.models.variant.avro.VariantAnnotation; | ||
| import org.opencb.commons.datastore.core.ObjectMap; | ||
| import org.opencb.commons.run.Task; | ||
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| import java.net.URI; | ||
| import java.util.List; | ||
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| public interface VariantAnnotatorExtensionTask extends Task<VariantAnnotation, VariantAnnotation> { | ||
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| /** | ||
| * Set up the annotator extension. | ||
| * This method will be called before any other method. It might generate extra files or data needed for the annotation. | ||
| * | ||
| * @param output Output directory where the annotator extension should write the files | ||
| * @return List of URIs of generated files (if any) | ||
| * @throws Exception if the annotator extension set up fails | ||
| */ | ||
| List<URI> setup(URI output) throws Exception; | ||
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| /** | ||
| * Check if the annotator extension is available for the given options. | ||
| * @throws IllegalArgumentException if the annotator extension is not available | ||
| */ | ||
| void checkAvailable() throws IllegalArgumentException; | ||
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| /** | ||
| * Check if the annotator extension is available for the given options. Do not throw any exception if the extension is not available. | ||
| * @return true if the annotator extension is available | ||
| */ | ||
| default boolean isAvailable() { | ||
| try { | ||
| checkAvailable(); | ||
| return true; | ||
| } catch (IllegalArgumentException e) { | ||
| return false; | ||
| } | ||
| } | ||
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| @Override | ||
| default void pre() throws Exception { | ||
| Task.super.pre(); | ||
| checkAvailable(); | ||
| } | ||
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| /** | ||
| * Get the options for the annotator extension. | ||
| * @return Options for the annotator extension | ||
| */ | ||
| ObjectMap getOptions(); | ||
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| /** | ||
| * Get the metadata for the annotator extension. | ||
| * @return Metadata for the annotator extension | ||
| */ | ||
| ObjectMap getMetadata(); | ||
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| } |
54 changes: 54 additions & 0 deletions
54
...rage/core/variant/annotation/annotators/extensions/VariantAnnotatorExtensionsFactory.java
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,54 @@ | ||
| package org.opencb.opencga.storage.core.variant.annotation.annotators.extensions; | ||
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| import org.opencb.commons.datastore.core.ObjectMap; | ||
| import org.opencb.opencga.storage.core.variant.VariantStorageOptions; | ||
| import org.opencb.opencga.storage.core.variant.annotation.annotators.extensions.cosmic.CosmicVariantAnnotatorExtensionTask; | ||
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| import java.lang.reflect.InvocationTargetException; | ||
| import java.util.LinkedList; | ||
| import java.util.List; | ||
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| public class VariantAnnotatorExtensionsFactory { | ||
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| public List<VariantAnnotatorExtensionTask> getVariantAnnotatorExtensions(ObjectMap options) { | ||
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| List<VariantAnnotatorExtensionTask> tasks = new LinkedList<>(); | ||
| for (String extensionId : options.getAsStringList(VariantStorageOptions.ANNOTATOR_EXTENSION_LIST.key())) { | ||
| VariantAnnotatorExtensionTask task = null; | ||
| switch (extensionId) { | ||
| case CosmicVariantAnnotatorExtensionTask.ID: | ||
| task = new CosmicVariantAnnotatorExtensionTask(options); | ||
| break; | ||
| default: | ||
| String extensionClass = options.getString(VariantStorageOptions.ANNOTATOR_EXTENSION_PREFIX.key() + extensionId); | ||
| if (extensionClass != null) { | ||
| task = getVariantAnnotatorExtension(extensionClass, options); | ||
| } else { | ||
| throw new IllegalArgumentException("Unknown annotator extension '" + extensionId + "'"); | ||
| } | ||
| } | ||
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| if (task == null) { | ||
| throw new IllegalArgumentException("Unable to create annotator extension '" + extensionId + "'"); | ||
| } | ||
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| tasks.add(task); | ||
| } | ||
| return tasks; | ||
| } | ||
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| private VariantAnnotatorExtensionTask getVariantAnnotatorExtension(String className, ObjectMap options) { | ||
| try { | ||
| Class<?> clazz = Class.forName(className); | ||
| return (VariantAnnotatorExtensionTask) clazz.getConstructor(ObjectMap.class).newInstance(options); | ||
| } catch (ClassNotFoundException | ||
| | NoSuchMethodException | ||
| | InstantiationException | ||
| | IllegalAccessException | ||
| | InvocationTargetException e) { | ||
| throw new IllegalArgumentException("Unable to create VariantAnnotatorExtensionTask from class " + className, e); | ||
| } | ||
| } | ||
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| } |
86 changes: 86 additions & 0 deletions
86
...age/core/variant/annotation/annotators/extensions/cosmic/CosmicExtensionTaskCallback.java
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,86 @@ | ||
| package org.opencb.opencga.storage.core.variant.annotation.annotators.extensions.cosmic; | ||
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| import com.fasterxml.jackson.core.JsonProcessingException; | ||
| import com.fasterxml.jackson.databind.ObjectMapper; | ||
| import org.apache.commons.collections4.CollectionUtils; | ||
| import org.apache.commons.lang3.StringUtils; | ||
| import org.opencb.biodata.formats.variant.cosmic.CosmicParserCallback; | ||
| import org.opencb.biodata.models.sequence.SequenceLocation; | ||
| import org.opencb.biodata.models.variant.Variant; | ||
| import org.opencb.biodata.models.variant.avro.EvidenceEntry; | ||
| import org.opencb.biodata.models.variant.exceptions.NonStandardCompliantSampleField; | ||
| import org.opencb.biodata.tools.variant.VariantNormalizer; | ||
| import org.opencb.opencga.core.common.JacksonUtils; | ||
| import org.rocksdb.RocksDB; | ||
| import org.rocksdb.RocksDBException; | ||
| import org.slf4j.Logger; | ||
| import org.slf4j.LoggerFactory; | ||
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| import java.util.Collections; | ||
| import java.util.List; | ||
| import java.util.stream.Collectors; | ||
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| public class CosmicExtensionTaskCallback implements CosmicParserCallback { | ||
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| private RocksDB rdb; | ||
| private VariantNormalizer variantNormalizer; | ||
| private ObjectMapper defaultObjectMapper; | ||
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| private static Logger logger = LoggerFactory.getLogger(CosmicExtensionTaskCallback.class); | ||
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| private static final String VARIANT_STRING_PATTERN = "([ACGTN]*)|(<CNV[0-9]+>)|(<DUP>)|(<DEL>)|(<INS>)|(<INV>)"; | ||
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| public CosmicExtensionTaskCallback(RocksDB rdb) { | ||
| this.rdb = rdb; | ||
| this.variantNormalizer = new VariantNormalizer(new VariantNormalizer.VariantNormalizerConfig() | ||
| .setReuseVariants(true) | ||
| .setNormalizeAlleles(true) | ||
| .setDecomposeMNVs(false)); | ||
| this.defaultObjectMapper = JacksonUtils.getDefaultObjectMapper(); | ||
| } | ||
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| @Override | ||
| public boolean processEvidenceEntries(SequenceLocation sequenceLocation, List<EvidenceEntry> evidenceEntries) { | ||
| // Add evidence entries in the RocksDB | ||
| // More than one variant being returned from the normalisation process would mean it's and MNV which has been decomposed | ||
| List<String> normalisedVariantStringList; | ||
| try { | ||
| normalisedVariantStringList = getNormalisedVariantString(sequenceLocation.getChromosome(), | ||
| sequenceLocation.getStart(), sequenceLocation.getReference(), sequenceLocation.getAlternate()); | ||
| if (CollectionUtils.isNotEmpty(normalisedVariantStringList)) { | ||
| for (String normalisedVariantString : normalisedVariantStringList) { | ||
| rdb.put(normalisedVariantString.getBytes(), defaultObjectMapper.writeValueAsBytes(evidenceEntries)); | ||
| } | ||
| return true; | ||
| } | ||
| return false; | ||
| } catch (NonStandardCompliantSampleField | RocksDBException | JsonProcessingException e) { | ||
| logger.warn(StringUtils.join(e.getStackTrace(), "\n")); | ||
| return false; | ||
| } | ||
| } | ||
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| protected List<String> getNormalisedVariantString(String chromosome, int start, String reference, String alternate) | ||
| throws NonStandardCompliantSampleField { | ||
| Variant variant = new Variant(chromosome, start, reference, alternate); | ||
| return getNormalisedVariantString(variant); | ||
| } | ||
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| protected List<String> getNormalisedVariantString(Variant variant) throws NonStandardCompliantSampleField { | ||
| // Checks no weird characters are part of the reference & alternate alleles | ||
| if (isValid(variant)) { | ||
| List<Variant> normalizedVariantList = variantNormalizer.normalize(Collections.singletonList(variant), true); | ||
| return normalizedVariantList.stream().map(Variant::toString).collect(Collectors.toList()); | ||
| } else { | ||
| logger.warn("Variant {} is not valid: skipping it!", variant); | ||
| } | ||
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| return Collections.emptyList(); | ||
| } | ||
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| protected boolean isValid(Variant variant) { | ||
| return (variant.getReference().matches(VARIANT_STRING_PATTERN) | ||
| && (variant.getAlternate().matches(VARIANT_STRING_PATTERN) | ||
| && !variant.getAlternate().equals(variant.getReference()))); | ||
| } | ||
| } |
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