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build: create the MiRTarBase parser for .xlsx files, #TASK-5576, #TAS…
…K-5564 - This parser skips possible errors in the .xlsx file - No need to use the script fix-gene-symbol.sh (so it is removed) - Update configuration files (by removing comments about the fix-gene-symbol.sh references) - Add JUnit test for the MiRTarBase parser On branch TASK-5564 Changes to be committed: deleted: cellbase-app/app/scripts/mirtarbase/fix-gene-symbol.sh modified: cellbase-core/src/main/resources/configuration.yml modified: cellbase-core/src/test/resources/configuration.yml modified: cellbase-lib/src/main/java/org/opencb/cellbase/lib/builders/EnsemblGeneBuilder.java modified: cellbase-lib/src/main/java/org/opencb/cellbase/lib/builders/GeneBuilderIndexer.java new file: cellbase-lib/src/main/java/org/opencb/cellbase/lib/builders/MiRTarBaseIndexer.java modified: cellbase-lib/src/main/java/org/opencb/cellbase/lib/builders/RefSeqGeneBuilder.java new file: cellbase-lib/src/test/java/org/opencb/cellbase/lib/builders/GeneBuilderIndexerTest.java modified: cellbase-lib/src/test/resources/configuration.test.yaml
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cellbase-lib/src/main/java/org/opencb/cellbase/lib/builders/MiRTarBaseIndexer.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.cellbase.lib.builders; | ||
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| import org.apache.commons.lang3.StringUtils; | ||
| import org.apache.poi.ss.usermodel.*; | ||
| import org.apache.poi.xssf.usermodel.XSSFWorkbook; | ||
| import org.opencb.biodata.models.core.MirnaTarget; | ||
| import org.opencb.biodata.models.core.TargetGene; | ||
| import org.opencb.commons.utils.FileUtils; | ||
| import org.slf4j.Logger; | ||
| import org.slf4j.LoggerFactory; | ||
|
|
||
| import java.io.FileInputStream; | ||
| import java.io.IOException; | ||
| import java.io.InputStream; | ||
| import java.math.BigDecimal; | ||
| import java.nio.file.Path; | ||
| import java.util.ArrayList; | ||
| import java.util.HashMap; | ||
| import java.util.List; | ||
| import java.util.Map; | ||
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| import static org.opencb.cellbase.lib.EtlCommons.MIRTARBASE_DATA; | ||
| import static org.opencb.cellbase.lib.builders.CellBaseBuilder.PARSING_DONE_LOG_MESSAGE; | ||
| import static org.opencb.cellbase.lib.builders.CellBaseBuilder.PARSING_LOG_MESSAGE; | ||
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| public class MiRTarBaseIndexer { | ||
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| protected Logger logger; | ||
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| public MiRTarBaseIndexer() { | ||
| logger = LoggerFactory.getLogger(this.getClass()); | ||
| } | ||
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| public Map<String, List<MirnaTarget>> index(Path miRTarBaseFile) throws IOException { | ||
| FileUtils.checkFile(miRTarBaseFile); | ||
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| logger.info(PARSING_LOG_MESSAGE, miRTarBaseFile); | ||
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| Map<String, List<MirnaTarget>> geneToMirna = new HashMap<>(); | ||
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| try (InputStream fis = new FileInputStream(miRTarBaseFile.toFile()); | ||
| Workbook workbook = new XSSFWorkbook(fis)) { | ||
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| // Get the first sheet | ||
| Sheet sheet = workbook.getSheetAt(0); | ||
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| String currentMiRTarBaseId = null; | ||
| String currentMiRNA = null; | ||
| String currentGene = null; | ||
| List<TargetGene> targetGenes = new ArrayList<>(); | ||
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| for (int rowNum = sheet.getFirstRowNum() + 1; rowNum <= sheet.getLastRowNum(); rowNum++) { | ||
| Row row = sheet.getRow(rowNum); | ||
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| // Sanity check | ||
| if (row.getPhysicalNumberOfCells() != 9) { | ||
| logger.warn("Error parsing line {}: invalid number of columns {} (expected 9 columns). Line {}.", | ||
| rowNum + 1, row.getPhysicalNumberOfCells()); | ||
| continue; | ||
| } | ||
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| if (row.getCell(0).getCellType() != CellType.STRING || row.getCell(0).getStringCellValue() == null | ||
| || row.getCell(1).getCellType() != CellType.STRING || row.getCell(1).getStringCellValue() == null | ||
| || row.getCell(3).getCellType() != CellType.STRING || row.getCell(3).getStringCellValue() == null) { | ||
| logger.warn("Error parsing line {}: mandatory fields(miRTarBase ID, miRNA, Target Gene) are empty or wrong cell type.", | ||
| rowNum + 1); | ||
| continue; | ||
| } | ||
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| // #0: miRTarBase ID | ||
| Cell cell = row.getCell(0); | ||
| String miRTarBaseId = cell.getStringCellValue(); | ||
| if (currentMiRTarBaseId == null) { | ||
| currentMiRTarBaseId = miRTarBaseId; | ||
| } | ||
|
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| // #1: miRNA | ||
| cell = row.getCell(1); | ||
| String miRNA = cell.getStringCellValue(); | ||
| if (currentMiRNA == null) { | ||
| currentMiRNA = miRNA; | ||
| } | ||
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| // #2: Species (miRNA) | ||
|
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| // #3: Target Gene | ||
| cell = row.getCell(3); | ||
| String geneName = cell.getStringCellValue(); | ||
| if (currentGene == null) { | ||
| currentGene = geneName; | ||
| } | ||
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| // #4: Target Gene (Entrez ID) | ||
| // #5: Species (Target Gene) | ||
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| if (!miRTarBaseId.equals(currentMiRTarBaseId) || !geneName.equals(currentGene)) { | ||
| // new entry, store current one | ||
| MirnaTarget miRnaTarget = new MirnaTarget(currentMiRTarBaseId, MIRTARBASE_DATA, currentMiRNA, targetGenes); | ||
| GeneBuilderIndexer.addValueToMapElement(geneToMirna, currentGene, miRnaTarget); | ||
| targetGenes = new ArrayList<>(); | ||
| currentGene = geneName; | ||
| currentMiRTarBaseId = miRTarBaseId; | ||
| currentMiRNA = miRNA; | ||
| } | ||
|
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| // #6: Experiments | ||
| cell = row.getCell(6); | ||
| String experiment = (cell.getCellType() == CellType.STRING ? cell.getStringCellValue() : null); | ||
|
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| // #7: Support Type | ||
| cell = row.getCell(7); | ||
| String supportType = (cell.getCellType() == CellType.STRING ? cell.getStringCellValue() : null); | ||
|
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| // #8: pubmed | ||
| cell = row.getCell(8); | ||
| String pubmed = new BigDecimal(cell.getNumericCellValue()).toString(); | ||
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| if (StringUtils.isNotEmpty(experiment) || StringUtils.isNotEmpty(supportType) || StringUtils.isNotEmpty(pubmed)) { | ||
| targetGenes.add(new TargetGene(experiment, supportType, pubmed)); | ||
| } | ||
| } | ||
|
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| // parse last entry | ||
| MirnaTarget miRnaTarget = new MirnaTarget(currentMiRTarBaseId, MIRTARBASE_DATA, currentMiRNA, targetGenes); | ||
| GeneBuilderIndexer.addValueToMapElement(geneToMirna, currentGene, miRnaTarget); | ||
|
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| } | ||
| logger.info(PARSING_DONE_LOG_MESSAGE, miRTarBaseFile); | ||
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| return geneToMirna; | ||
| } | ||
| } |
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