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Refactor CSVLoaderService into separate class
Split CSVLoaderService into its own file for better modularity and maintainability. Removed the duplicate implementation from CSVLoaderNewSearch.
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etl/src/main/java/edu/harvard/hms/dbmi/avillach/hpds/etl/phenotype/csv/CSVLoaderService.java
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,94 @@ | ||
| package edu.harvard.hms.dbmi.avillach.hpds.etl.phenotype.csv; | ||
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| import edu.harvard.hms.dbmi.avillach.hpds.crypto.Crypto; | ||
| import edu.harvard.hms.dbmi.avillach.hpds.data.phenotype.PhenoCube; | ||
| import edu.harvard.hms.dbmi.avillach.hpds.etl.LoadingStore; | ||
| import org.apache.commons.csv.CSVFormat; | ||
| import org.apache.commons.csv.CSVRecord; | ||
| import org.slf4j.Logger; | ||
| import org.slf4j.LoggerFactory; | ||
| import org.springframework.beans.factory.annotation.Value; | ||
| import org.springframework.stereotype.Service; | ||
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| import java.io.*; | ||
| import java.util.Date; | ||
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| @Service | ||
| public class CSVLoaderService { | ||
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| private static final Logger log = LoggerFactory.getLogger(CSVLoaderService.class); | ||
| private final LoadingStore store = new LoadingStore(); | ||
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| @Value("${etl.hpds.directory:/opt/local/hpds/}") | ||
| private String hpdsDirectory; | ||
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| @Value("${etl.rollup.enabled:true}") | ||
| private boolean rollupEnabled; | ||
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| public void runEtlProcess() throws IOException { | ||
| log.info("Starting ETL process... Rollup Enabled: {}", rollupEnabled); | ||
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| store.allObservationsStore = new RandomAccessFile(hpdsDirectory + "allObservationsStore.javabin", "rw"); | ||
| initialLoad(); | ||
| store.saveStore(hpdsDirectory); | ||
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| log.info("ETL process completed."); | ||
| } | ||
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| private void initialLoad() throws IOException { | ||
| Crypto.loadDefaultKey(); | ||
| Reader in = new FileReader(hpdsDirectory + "allConcepts.csv"); | ||
| Iterable<CSVRecord> records = CSVFormat.DEFAULT | ||
| .withFirstRecordAsHeader() | ||
| .withSkipHeaderRecord(true) | ||
| .parse(new BufferedReader(in, 256 * 1024)); | ||
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| final PhenoCube[] currentConcept = new PhenoCube[1]; | ||
| for (CSVRecord record : records) { | ||
| processRecord(currentConcept, record); | ||
| } | ||
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| } | ||
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| private void processRecord(final PhenoCube[] currentConcept, CSVRecord record) { | ||
| if (record.size() < 4) { | ||
| log.warn("Skipping record #{} due to missing fields.", record.getRecordNumber()); | ||
| return; | ||
| } | ||
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| String conceptPath = CSVParserUtil.parseConceptPath(record, rollupEnabled); | ||
| String numericValue = record.get(CSVParserUtil.NUMERIC_VALUE); | ||
| boolean isAlpha = (numericValue == null || numericValue.isEmpty()); | ||
| String value = isAlpha ? record.get(CSVParserUtil.TEXT_VALUE) : numericValue; | ||
| currentConcept[0] = getPhenoCube(currentConcept[0], conceptPath, isAlpha); | ||
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| if (value != null && !value.trim().isEmpty() && | ||
| ((isAlpha && currentConcept[0].vType == String.class) || (!isAlpha && currentConcept[0].vType == Double.class))) { | ||
| value = value.trim(); | ||
| currentConcept[0].setColumnWidth(isAlpha ? Math.max(currentConcept[0].getColumnWidth(), value.getBytes().length) : Double.BYTES); | ||
| int patientId = Integer.parseInt(record.get(CSVParserUtil.PATIENT_NUM)); | ||
| Date date = null; | ||
| if (record.size() > 4 && record.get(CSVParserUtil.DATETIME) != null && !record.get(CSVParserUtil.DATETIME).isEmpty()) { | ||
| date = new Date(Long.parseLong(record.get(CSVParserUtil.DATETIME))); | ||
| } | ||
| currentConcept[0].add(patientId, isAlpha ? value : Double.parseDouble(value), date); | ||
| store.allIds.add(patientId); | ||
| } | ||
| } | ||
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| private PhenoCube getPhenoCube(PhenoCube currentConcept, String conceptPath, boolean isAlpha) { | ||
| if (currentConcept == null || !currentConcept.name.equals(conceptPath)) { | ||
| currentConcept = store.store.getIfPresent(conceptPath); | ||
| if (currentConcept == null) { | ||
| log.info("Writing - " + conceptPath); | ||
| // safe to invalidate and write store? | ||
| store.store.invalidateAll(); // force onremoval to free up cache per concept | ||
| store.store.cleanUp(); | ||
| currentConcept = new PhenoCube(conceptPath, isAlpha ? String.class : Double.class); | ||
| store.store.put(conceptPath, currentConcept); | ||
| } | ||
| } | ||
| return currentConcept; | ||
| } | ||
| } |