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ALS-6330: Fix java config typo
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ramari16 committed Jun 26, 2024
1 parent cf79b80 commit d25c178
Showing 1 changed file with 6 additions and 1 deletion.
Original file line number Diff line number Diff line change
@@ -1,6 +1,8 @@
package edu.harvard.hms.dbmi.avillach.hpds.processing;

import edu.harvard.hms.dbmi.avillach.hpds.processing.genomic.GenomicProcessorRestClient;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import org.springframework.beans.factory.annotation.Value;
import org.springframework.boot.autoconfigure.condition.ConditionalOnMissingBean;
import org.springframework.boot.autoconfigure.condition.ConditionalOnProperty;
Expand All @@ -20,6 +22,8 @@ public class GenomicProcessorConfig {
@Value("${HPDS_GENOMIC_DATA_DIRECTORY:/opt/local/hpds/all/}")
private String hpdsGenomicDataDirectory;

private static Logger log = LoggerFactory.getLogger(GenomicProcessorConfig.class);


@Bean(name = "localGenomicProcessor")
@ConditionalOnProperty(prefix = "hpds.genomicProcessor", name = "impl", havingValue = "local")
Expand Down Expand Up @@ -61,7 +65,7 @@ public GenomicProcessor localPatientDistributedGenomicProcessor() {
return new GenomicProcessorPatientMergingParentImpl(studyGroupedGenomicProcessors);
}
@Bean(name = "localPatientOnlyDistributedGenomicProcessor")
@ConditionalOnProperty(prefix = "hpds.genomicProcessor", name = "impl", havingValue = "localPatientDistributed")
@ConditionalOnProperty(prefix = "hpds.genomicProcessor", name = "impl", havingValue = "localPatientOnlyDistributed")
public GenomicProcessor localPatientOnlyDistributedGenomicProcessor() {
// assumed for now that all first level directories contain a genomic dataset for a group of studies
File[] directories = new File(hpdsGenomicDataDirectory).listFiles(File::isDirectory);
Expand All @@ -72,6 +76,7 @@ public GenomicProcessor localPatientOnlyDistributedGenomicProcessor() {
List<GenomicProcessor> studyGroupedGenomicProcessors = new ArrayList<>();

for (File directory : directories) {
log.info("Loading partition: " + directory.getName());
studyGroupedGenomicProcessors.add(new GenomicProcessorNodeImpl(directory.getAbsolutePath()));
}

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