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storage: Add variant-walker tool #TASK-6722
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opencga-analysis/src/main/java/org/opencb/opencga/analysis/variant/VariantWalkerTool.java
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| /* | ||
| * 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. | ||
| */ | ||
|
|
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| package org.opencb.opencga.analysis.variant; | ||
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| import org.apache.solr.common.StringUtils; | ||
| import org.opencb.commons.datastore.core.Query; | ||
| import org.opencb.commons.datastore.core.QueryOptions; | ||
| import org.opencb.opencga.analysis.tools.OpenCgaTool; | ||
| import org.opencb.opencga.catalog.io.IOManager; | ||
| import org.opencb.opencga.core.common.UriUtils; | ||
| import org.opencb.opencga.core.models.common.Enums; | ||
| import org.opencb.opencga.core.models.variant.VariantWalkerParams; | ||
| import org.opencb.opencga.core.tools.annotations.Tool; | ||
| import org.opencb.opencga.core.tools.annotations.ToolParams; | ||
| import org.opencb.opencga.storage.core.variant.adaptors.VariantQueryParam; | ||
| import org.opencb.opencga.storage.core.variant.io.VariantWriterFactory; | ||
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|
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| import java.net.URI; | ||
| import java.nio.file.Path; | ||
| import java.util.ArrayList; | ||
| import java.util.Arrays; | ||
| import java.util.List; | ||
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| @Tool(id = VariantWalkerTool.ID, description = VariantWalkerTool.DESCRIPTION, | ||
| scope = Tool.Scope.PROJECT, resource = Enums.Resource.VARIANT) | ||
| public class VariantWalkerTool extends OpenCgaTool { | ||
| public static final String ID = "variant-walk"; | ||
| public static final String DESCRIPTION = "Filter and walk variants from the variant storage to produce a file"; | ||
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| @ToolParams | ||
| protected VariantWalkerParams toolParams = new VariantWalkerParams(); | ||
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| private VariantWriterFactory.VariantOutputFormat format; | ||
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| @Override | ||
| protected void check() throws Exception { | ||
| super.check(); | ||
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| if (StringUtils.isEmpty(toolParams.getFileFormat())) { | ||
| toolParams.setFileFormat(VariantWriterFactory.VariantOutputFormat.VCF.toString()); | ||
| } | ||
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| format = VariantWriterFactory.toOutputFormat(toolParams.getOutputFileName(), toolParams.getOutputFileName()); | ||
| } | ||
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| @Override | ||
| protected List<String> getSteps() { | ||
| return Arrays.asList(ID, "move-files"); | ||
| } | ||
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| @Override | ||
| protected void run() throws Exception { | ||
| List<URI> uris = new ArrayList<>(2); | ||
| step(ID, () -> { | ||
| // Use scratch directory to store intermediate files. Move files to final directory at the end | ||
| // The scratch directory is expected to be faster than the final directory | ||
| // This also avoids moving files to final directory if the tool fails | ||
| Path outDir = getScratchDir(); | ||
| String outputFile = StringUtils.isEmpty(toolParams.getOutputFileName()) | ||
| ? outDir.toString() | ||
| : outDir.resolve(toolParams.getOutputFileName()).toString(); | ||
| Query query = toolParams.toQuery(); | ||
| QueryOptions queryOptions = new QueryOptions(params); | ||
| for (VariantQueryParam param : VariantQueryParam.values()) { | ||
| queryOptions.remove(param.key()); | ||
| } | ||
| uris.addAll(variantStorageManager.walkData(outputFile, | ||
| format, query, queryOptions, toolParams.getDockerImage(), toolParams.getCommandLine(), token)); | ||
| }); | ||
| step("move-files", () -> { | ||
| // Move files to final directory | ||
| IOManager ioManager = catalogManager.getIoManagerFactory().get(uris.get(0)); | ||
| for (URI uri : uris) { | ||
| String fileName = UriUtils.fileName(uri); | ||
| logger.info("Moving file -- " + fileName); | ||
| ioManager.move(uri, getOutDir().resolve(fileName).toUri()); | ||
| } | ||
| }); | ||
| } | ||
| } |
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