lib: fix dockerImage variable name
@@ -47,7 +47,7 @@ public class GeneDownloadManager extends DownloadManager {
private static final String GO_ANNOTATION_NAME = "EBI Gene Ontology Annotation";
private static final String DGIDB_NAME = "DGIdb";
private static final String GNOMAD_NAME = "gnomAD";
- private static String DOCKER_IMAGE;
+ private static String dockerImage;
private static final Map<String, String> GENE_UNIPROT_XREF_FILES;
@@ -65,7 +65,7 @@ public class GeneDownloadManager extends DownloadManager {
throws IOException, CellbaseException {
super(species, assembly, targetDirectory, configuration);
- DOCKER_IMAGE = "opencb/cellbase-builder:" + configuration.getApiVersion();
+ dockerImage = "opencb/cellbase-builder:" + configuration.getApiVersion();
}
public GeneDownloadManager(CellBaseConfiguration configuration, Path targetDirectory, SpeciesConfiguration speciesConfiguration,
@@ -74,8 +74,7 @@ public class GeneDownloadManager extends DownloadManager {
}
- @Override
- public List<DownloadFile> download() throws IOException, InterruptedException {
+ public List<DownloadFile> downloadEnsemblGene() throws IOException, InterruptedException {
logger.info("Downloading gene information ...");
Path geneFolder = downloadFolder.resolve("gene");
Files.createDirectories(geneFolder);
@@ -248,7 +247,7 @@ public class GeneDownloadManager extends DownloadManager {
String ensemblScriptParams = "/opt/cellbase/gene_extra_info.pl --verbose --outdir /ensembl-data";
try {
- DockerUtils.run(DOCKER_IMAGE, null, outputBinding, ensemblScriptParams, null);
+ DockerUtils.run(dockerImage, null, outputBinding, ensemblScriptParams, null);
} catch (IOException e) {
throw new IOException(e);
}
