Changes from PR

hms-dbmi · Oct 10, 2024 · beab7a3 · beab7a3
1 parent f3f64c2
commit beab7a3
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Showing 6 changed files with 11 additions and 7 deletions.
diff --git a/data/src/main/java/edu/harvard/hms/dbmi/avillach/hpds/data/genotype/VariantStore.java b/data/src/main/java/edu/harvard/hms/dbmi/avillach/hpds/data/genotype/VariantStore.java
@@ -21,8 +21,6 @@ public class VariantStore implements Serializable {
 	private static Logger log = LoggerFactory.getLogger(VariantStore.class);
 	public static final int BUCKET_SIZE = 1000;
 
-	public static final String VARIANT_SPEC_INDEX_FILE = VARIANT_SPEC_INDEX_JAVABIN_FILENAME;
-
 	private BigInteger emptyBitmask;
 	private String[] patientIds;
 
@@ -157,7 +155,7 @@ public BigInteger emptyBitmask() {
 
 	@SuppressWarnings("unchecked")
 	public static String[] loadVariantIndexFromFile(String genomicDataDirectory) {
-		try (ObjectInputStream objectInputStream = new ObjectInputStream(new GZIPInputStream(new FileInputStream(genomicDataDirectory + "/" + VARIANT_SPEC_INDEX_FILE)));){
+		try (ObjectInputStream objectInputStream = new ObjectInputStream(new GZIPInputStream(new FileInputStream(genomicDataDirectory + "/" + VARIANT_SPEC_INDEX_JAVABIN_FILENAME)));){
 
 			List<String> variants = (List<String>) objectInputStream.readObject();
 			return variants.toArray(new String[0]);

diff --git a/...essing/src/main/java/edu/harvard/hms/dbmi/avillach/hpds/processing/AbstractProcessor.java b/...essing/src/main/java/edu/harvard/hms/dbmi/avillach/hpds/processing/AbstractProcessor.java
@@ -342,7 +342,6 @@ public PhenoCube<?> load(String key) throws Exception {
 										return ret;
 									}else {
 										log.warn("ColumnMeta not found for : [{}]", key);
-										log.info(Joiner.on(",").join(phenotypeMetaStore.getColumnNames()));
 										return null;
 									}
 								}

diff --git a/processing/src/main/java/edu/harvard/hms/dbmi/avillach/hpds/processing/GenomicProcessor.java b/processing/src/main/java/edu/harvard/hms/dbmi/avillach/hpds/processing/GenomicProcessor.java
@@ -29,6 +29,5 @@ public interface GenomicProcessor {
 
     List<InfoColumnMeta> getInfoColumnMeta();
 
-    // todo: make the map value a Set instead of array
     Map<String, Set<String>> getVariantMetadata(Collection<String> variantList);
 }
diff --git a/...essing/src/main/java/edu/harvard/hms/dbmi/avillach/hpds/processing/VariantIndexCache.java b/...essing/src/main/java/edu/harvard/hms/dbmi/avillach/hpds/processing/VariantIndexCache.java
@@ -79,7 +79,6 @@ public VariantIndex load(String infoColumn_valueKey) throws IOException {
                 boolean[] variantIndexArray = new boolean[variantIndex.length];
                 int x = 0;
                 for(Integer variantIndex : variantIndexIntArray) {
-                    // todo: shouldn't this be greater than or equal to 0? 0 is a valid index
                     if (variantIndex >= 0) {
                         variantIndexArray[variantIndex] = true;
                     }

diff --git a/processing/src/test/java/edu/harvard/hms/dbmi/avillach/hpds/processing/VariantUtilsTest.java b/processing/src/test/java/edu/harvard/hms/dbmi/avillach/hpds/processing/VariantUtilsTest.java
@@ -14,4 +14,14 @@ public void pathIsVariantSpec_oldFormat() {
     public void pathIsVariantSpec_newFormat() {
         assertTrue(VariantUtils.pathIsVariantSpec("chr21,5032061,A,G,LOC102723996,missense_variant"));
     }
+
+    @Test
+    public void pathIsVariantSpec_notMatching() {
+        assertFalse(VariantUtils.pathIsVariantSpec("chr21,5032061,A,Z,LOC102723996,missense_variant"));
+        assertFalse(VariantUtils.pathIsVariantSpec("chr21,5032061,Q,G,LOC102723996,missense_variant"));
+        assertFalse(VariantUtils.pathIsVariantSpec("chr21,5032061,A,G,LOC102723996"));
+        assertFalse(VariantUtils.pathIsVariantSpec("chr21,5032061,A,G,^&*,missense_variant"));
+        assertFalse(VariantUtils.pathIsVariantSpec("chr21,5032061,A,G,LOC102723996,&*("));
+        assertFalse(VariantUtils.pathIsVariantSpec("chr21,ABC,A,G,LOC102723996,missense_variant"));
+    }
 }
diff --git a/service/src/main/resources/application-bdc-auth.properties b/service/src/main/resources/application-bdc-auth.properties
@@ -1,7 +1,6 @@
 SMALL_JOB_LIMIT = 100
 SMALL_TASK_THREADS = 1
 LARGE_TASK_THREADS = 1
-VCF_EXCERPT_ENABLED=true
 
 hpds.genomicProcessor.impl=localPatientDistributed
 HPDS_GENOMIC_DATA_DIRECTORY=/opt/local/hpds/all/