app: update the CellBase loader for variation data according to the l…

…atest changes, #TASK-6142, #TASK-5564
opencb · Aug 1, 2024 · 38400c1 · 38400c1
1 parent d693f57
commit 38400c1
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Showing 2 changed files with 8 additions and 24 deletions.
diff --git a/...se-app/src/main/java/org/opencb/cellbase/app/cli/admin/executors/LoadCommandExecutor.java b/...se-app/src/main/java/org/opencb/cellbase/app/cli/admin/executors/LoadCommandExecutor.java
@@ -48,6 +48,7 @@
 import static org.opencb.cellbase.lib.builders.RefSeqGeneBuilder.REFSEQ_GENE_OUTPUT_FILENAME;
 import static org.opencb.cellbase.lib.builders.RegulatoryFeatureBuilder.*;
 import static org.opencb.cellbase.lib.builders.RepeatsBuilder.REPEATS_OUTPUT_FILENAME;
+import static org.opencb.cellbase.lib.builders.VariationBuilder.VARIATION_CHR_PREFIX;
 import static org.opencb.cellbase.lib.download.GenomeDownloadManager.GENOME_INFO_FILENAME;
 
 /**
@@ -139,8 +140,7 @@ public void execute() throws CellBaseException {
                             break;
                         }
                         case EtlCommons.VARIATION_DATA: {
-                            // Load data, create index and update release
-                            loadVariationData();
+                            loadVariation();
                             break;
                         }
                         case EtlCommons.VARIATION_FUNCTIONAL_SCORE_DATA: {
@@ -303,31 +303,15 @@ private void checkParameters() throws CellBaseException {
         dataRelease = getDataReleaseForLoading(dataReleaseManager).getRelease();
     }
 
-    private void loadVariationData() throws NoSuchMethodException, InterruptedException, ExecutionException,
+    private void loadVariation() throws NoSuchMethodException, InterruptedException, ExecutionException,
             InstantiationException, IllegalAccessException, InvocationTargetException, ClassNotFoundException,
             IOException, LoaderException, CellBaseException {
-        // First load data
-        // Common loading process from CellBase variation data models
         if (field == null) {
-            DirectoryStream<Path> stream = Files.newDirectoryStream(input,
-                    entry -> entry.getFileName().toString().startsWith("variation_chr"));
-
-            for (Path entry : stream) {
-                logger.info("Loading file '{}'", entry);
-                loadRunner.load(input.resolve(entry.getFileName()), "variation", dataRelease);
-            }
-
-            // Create index
-            createIndex("variation");
-
-            // Update release (collection and sources)
-            List<Path> sources = new ArrayList<>(Arrays.asList(
-                    input.resolve("ensemblVariationVersion.json")
-            ));
-            dataReleaseManager.update(dataRelease, "variation", sources);
-
-            // Custom update required e.g. population freqs loading
+            // First load data
+            // Common loading process from CellBase variation data models
+            loadData(input.resolve(VARIATION_DATA), VARIATION_DATA, VARIATION_CHR_PREFIX);
         } else {
+            // Custom update required e.g. population freqs loading
             logger.info("Loading file '{}'", input);
             loadRunner.load(input, "variation", dataRelease, field, innerFields);
         }

diff --git a/cellbase-lib/src/main/java/org/opencb/cellbase/lib/builders/VariationBuilder.java b/cellbase-lib/src/main/java/org/opencb/cellbase/lib/builders/VariationBuilder.java
@@ -36,7 +36,7 @@
 import static org.opencb.cellbase.lib.EtlCommons.HOMO_SAPIENS;
 
 /**
- * Created by jtarraga on 01/08/24
+ * Created by jtarraga on 01/08/24.
  */
 public class VariationBuilder extends AbstractBuilder {