Fix cerberus logic

oicr-gsi · Oct 4, 2024 · faa948a · faa948a
1 parent a96f391
commit faa948a
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Showing 2 changed files with 8 additions and 18 deletions.
diff --git a/...erus/src/main/java/ca/on/oicr/gsi/shesmu/cerberus/SampleCerberusFileProvenanceRecord.java b/...erus/src/main/java/ca/on/oicr/gsi/shesmu/cerberus/SampleCerberusFileProvenanceRecord.java
@@ -4,12 +4,8 @@
 import ca.on.oicr.gsi.shesmu.gsicommon.IUSUtils;
 import ca.on.oicr.gsi.shesmu.plugin.Tuple;
 import ca.on.oicr.ws.dto.SampleProvenanceDto;
-import java.util.Collections;
-import java.util.Optional;
-import java.util.Set;
-import java.util.TreeSet;
+import java.util.*;
 import java.util.regex.Pattern;
-import java.util.stream.Collectors;
 
 public class SampleCerberusFileProvenanceRecord
     extends BaseCerberusFileProvenanceRecord<SampleProvenanceDto> {
@@ -28,10 +24,9 @@ public Optional<String> barcode_kit() {
 
   @Override
   public Set<String> batches() {
-    return limsAttr("batchIds")
-        .<Set<String>>map(
-            s -> COMMA.splitAsStream(s).collect(Collectors.toCollection(TreeSet::new)))
-        .orElse(Set.of());
+    List<String> potentialBatchIds = provenanceRecord.lims().getBatchIds();
+    if (potentialBatchIds == null || potentialBatchIds.isEmpty()) return new HashSet<>();
+    return new HashSet<>(potentialBatchIds);
   }
 
   @Override

diff --git a/...c/main/java/ca/on/oicr/gsi/shesmu/cerberus/SampleCerberusFileProvenanceSkippedRecord.java b/...c/main/java/ca/on/oicr/gsi/shesmu/cerberus/SampleCerberusFileProvenanceSkippedRecord.java
@@ -4,12 +4,8 @@
 import ca.on.oicr.gsi.shesmu.gsicommon.IUSUtils;
 import ca.on.oicr.gsi.shesmu.plugin.Tuple;
 import ca.on.oicr.ws.dto.SampleProvenanceDto;
-import java.util.Collections;
-import java.util.Optional;
-import java.util.Set;
-import java.util.TreeSet;
+import java.util.*;
 import java.util.regex.Pattern;
-import java.util.stream.Collectors;
 
 public class SampleCerberusFileProvenanceSkippedRecord
     extends BaseCerberusFileProvenanceSkippedRecord<SampleProvenanceDto> {
@@ -28,10 +24,9 @@ public Optional<String> barcode_kit() {
 
   @Override
   public Set<String> batches() {
-    return limsAttr("batchIds")
-        .<Set<String>>map(
-            s -> COMMA.splitAsStream(s).collect(Collectors.toCollection(TreeSet::new)))
-        .orElse(Set.of());
+    List<String> potentialBatchIds = provenanceRecord.lims().getBatchIds();
+    if (potentialBatchIds == null || potentialBatchIds.isEmpty()) return new HashSet<>();
+    return new HashSet<>(potentialBatchIds);
   }
 
   @Override