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core/src/test/java/org/mskcc/cbio/portal/scripts/TestImportStructralVariantData.java
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core/src/test/java/org/mskcc/cbio/portal/scripts/TestImportStructuralVariantData.java
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| /* | ||
| * Copyright (c) 2018 The Hyve B.V. | ||
| * This code is licensed under the GNU Affero General Public License (AGPL), | ||
| * version 3, or (at your option) any later version. | ||
| */ | ||
|
|
||
| /* | ||
| * This file is part of cBioPortal. | ||
| * | ||
| * cBioPortal is free software: you can redistribute it and/or modify | ||
| * it under the terms of the GNU Affero General Public License as | ||
| * published by the Free Software Foundation, either version 3 of the | ||
| * License. | ||
| * | ||
| * This program is distributed in the hope that it will be useful, | ||
| * but WITHOUT ANY WARRANTY; without even the implied warranty of | ||
| * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the | ||
| * GNU Affero General Public License for more details. | ||
| * | ||
| * You should have received a copy of the GNU Affero General Public License | ||
| * along with this program. If not, see <http://www.gnu.org/licenses/>. | ||
| */ | ||
|
|
||
| /* | ||
| * @author Sander Tan | ||
| */ | ||
|
|
||
| package org.mskcc.cbio.portal.scripts; | ||
|
|
||
| import org.junit.Before; | ||
| import org.junit.Test; | ||
| import org.junit.runner.RunWith; | ||
| import org.mskcc.cbio.portal.dao.*; | ||
| import org.mskcc.cbio.portal.model.*; | ||
| import org.mskcc.cbio.portal.util.*; | ||
| import org.springframework.test.context.ContextConfiguration; | ||
| import org.springframework.test.context.junit4.SpringJUnit4ClassRunner; | ||
| import org.springframework.test.context.transaction.TransactionConfiguration; | ||
| import org.springframework.transaction.annotation.Transactional; | ||
| import static org.junit.Assert.*; | ||
| import java.io.*; | ||
| import java.sql.*; | ||
|
|
||
| /** | ||
| * Test class to test functionality of ImportStructralVariantData | ||
| */ | ||
| @SuppressWarnings("deprecation") | ||
| @RunWith(SpringJUnit4ClassRunner.class) | ||
| @ContextConfiguration(locations = { "classpath:/applicationContext-dao.xml" }) | ||
| @TransactionConfiguration(transactionManager = "transactionManager", defaultRollback = true) | ||
| @Transactional | ||
| public class TestImportStructuralVariantData{ | ||
| int studyId; | ||
| int geneticProfileId; | ||
|
|
||
| /** | ||
| * Extracts StructuralVariant record from ResultSet. | ||
| * @param rs | ||
| * @return StructuralVariant record | ||
| * @throws SQLException | ||
| * @throws DaoException | ||
| */ | ||
| private StructuralVariant extractStructuralVariant(ResultSet rs) throws SQLException, DaoException { | ||
| StructuralVariant structuralVariant = new StructuralVariant(); | ||
| structuralVariant.setGeneticProfileId(rs.getInt("GENETIC_PROFILE_ID")); | ||
| structuralVariant.setSampleIdInternal(rs.getInt("SAMPLE_ID")); | ||
| structuralVariant.setSite1EntrezGeneId(rs.getLong("SITE1_ENTREZ_GENE_ID")); | ||
| structuralVariant.setSite1EnsemblTranscriptId(rs.getString("SITE1_ENSEMBL_TRANSCRIPT_ID")); | ||
| structuralVariant.setSite1Exon(rs.getInt("SITE1_EXON")); | ||
| structuralVariant.setSite1Chromosome(rs.getString("SITE1_CHROMOSOME")); | ||
| structuralVariant.setSite1Position(rs.getInt("SITE1_POSITION")); | ||
| structuralVariant.setSite1Description(rs.getString("SITE1_DESCRIPTION")); | ||
| structuralVariant.setSite2EntrezGeneId(rs.getLong("SITE2_ENTREZ_GENE_ID")); | ||
| structuralVariant.setSite2EnsemblTranscriptId(rs.getString("SITE2_ENSEMBL_TRANSCRIPT_ID")); | ||
| structuralVariant.setSite2Exon(rs.getInt("SITE2_EXON")); | ||
| structuralVariant.setSite2Chromosome(rs.getString("SITE2_CHROMOSOME")); | ||
| structuralVariant.setSite2Position(rs.getInt("SITE2_POSITION")); | ||
| structuralVariant.setSite2Description(rs.getString("SITE2_DESCRIPTION")); | ||
| structuralVariant.setSite2EffectOnFrame(rs.getString("SITE2_EFFECT_ON_FRAME")); | ||
| structuralVariant.setNcbiBuild(rs.getString("NCBI_BUILD")); | ||
| structuralVariant.setDnaSupport(rs.getString("DNA_SUPPORT")); | ||
| structuralVariant.setRnaSupport(rs.getString("RNA_SUPPORT")); | ||
| structuralVariant.setNormalReadCount(rs.getInt("NORMAL_READ_COUNT")); | ||
| structuralVariant.setTumorReadCount(rs.getInt("TUMOR_READ_COUNT")); | ||
| structuralVariant.setNormalVariantCount(rs.getInt("NORMAL_VARIANT_COUNT")); | ||
| structuralVariant.setTumorVariantCount(rs.getInt("TUMOR_VARIANT_COUNT")); | ||
| structuralVariant.setNormalPairedEndReadCount(rs.getInt("NORMAL_PAIRED_END_READ_COUNT")); | ||
| structuralVariant.setTumorPairedEndReadCount(rs.getInt("TUMOR_PAIRED_END_READ_COUNT")); | ||
| structuralVariant.setNormalSplitReadCount(rs.getInt("NORMAL_SPLIT_READ_COUNT")); | ||
| structuralVariant.setTumorSplitReadCount(rs.getInt("TUMOR_SPLIT_READ_COUNT")); | ||
| structuralVariant.setAnnotation(rs.getString("ANNOTATION")); | ||
| structuralVariant.setBreakpointType(rs.getString("BREAKPOINT_TYPE")); | ||
| structuralVariant.setCenter(rs.getString("CENTER")); | ||
| structuralVariant.setConnectionType(rs.getString("CONNECTION_TYPE")); | ||
| structuralVariant.setEventInfo(rs.getString("EVENT_INFO")); | ||
| structuralVariant.setVariantClass(rs.getString("CLASS")); | ||
| structuralVariant.setLength(rs.getInt("LENGTH")); | ||
| structuralVariant.setComments(rs.getString("COMMENTS")); | ||
| structuralVariant.setExternalAnnotation(rs.getString("EXTERNAL_ANNOTATION")); | ||
| structuralVariant.setDriverFilter(rs.getString("DRIVER_FILTER")); | ||
| structuralVariant.setDriverFilterAnn(rs.getString("DRIVER_FILTER_ANNOTATION")); | ||
| structuralVariant.setDriverTiersFilter(rs.getString("DRIVER_TIERS_FILTER")); | ||
| structuralVariant.setDriverTiersFilterAnn(rs.getString("DRIVER_TIERS_FILTER_ANNOTATION")); | ||
| return structuralVariant; | ||
| } | ||
|
|
||
| @Before | ||
| public void setUp() throws DaoException | ||
| { | ||
| studyId = DaoCancerStudy.getCancerStudyByStableId("study_tcga_pub").getInternalId(); | ||
| geneticProfileId = DaoGeneticProfile.getGeneticProfileByStableId("study_tcga_pub_structural_variants").getGeneticProfileId(); | ||
| } | ||
|
|
||
| @Test | ||
| public void testImportStructuralVariantData() throws DaoException, IOException { | ||
| ProgressMonitor.setConsoleMode(false); | ||
|
|
||
| // Load test structural variants | ||
| File file = new File("src/test/resources/data_structural_variants.txt"); | ||
| ImportStructuralVariantData importer = new ImportStructuralVariantData(file, geneticProfileId, null); | ||
| importer.importData(); | ||
| MySQLbulkLoader.flushAll(); | ||
|
|
||
| // Retrieve all imported structural variants | ||
| Connection con = null; | ||
| PreparedStatement pstmt = null; | ||
| ResultSet rs = null; | ||
| try { | ||
| con = JdbcUtil.getDbConnection(DaoGeneset.class); | ||
| pstmt = con.prepareStatement("SELECT * FROM structural_variant"); | ||
| rs = pstmt.executeQuery(); | ||
|
|
||
| // Test first structural variant entry | ||
| rs.next(); | ||
| StructuralVariant structuralVariant = extractStructuralVariant(rs); | ||
| assertEquals("KIAA1549-BRAF.K16B10.COSF509_2", structuralVariant.getSite2Description()); | ||
|
|
||
| // Test second structural variant entry | ||
| rs.next(); | ||
| structuralVariant = extractStructuralVariant(rs); | ||
| assertEquals("ENST00000318522", structuralVariant.getSite1EnsemblTranscriptId()); | ||
| } | ||
| catch (SQLException e) { | ||
| throw new DaoException(e); | ||
| } | ||
| finally { | ||
| JdbcUtil.closeAll(DaoGeneset.class, con, pstmt, rs); | ||
| } | ||
| } | ||
| } |
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