Merge pull request #362 from overture-stack/score-client-quality-of-l…

…ife-changes Updates to address #229 - #346
overture-stack · Apr 27, 2023 · 9c09662 · 9c09662
2 parents e8a8f47 + 598b3ca
commit 9c09662
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Showing 4 changed files with 8 additions and 2 deletions.
diff --git a/score-client/src/main/bin/score-client b/score-client/src/main/bin/score-client
@@ -51,7 +51,6 @@ CLIENT_DIR="$(cd ${BASE_DIR} && pwd -P)"
 exec java -Xmx3G \
 	--add-opens=java.base/jdk.internal.ref=ALL-UNNAMED \
 	--add-opens=java.base/java.nio=ALL-UNNAMED \
-	--illegal-access=deny \
 	-Dlogging.path=${BASE_DIR}/logs \
 	-Dspring.config.additional-location=${CLIENT_DIR}/conf/ \
 	-Dlogging.config=${CLIENT_DIR}/conf/logback.xml \

diff --git a/score-client/src/main/java/bio/overture/score/client/ClientMain.java b/score-client/src/main/java/bio/overture/score/client/ClientMain.java
@@ -23,6 +23,7 @@
 import bio.overture.score.client.exception.BadManifestException;
 import bio.overture.score.client.metadata.EntityNotFoundException;
 import com.beust.jcommander.*;
+import htsjdk.samtools.util.Log;
 import lombok.Getter;
 import lombok.extern.slf4j.Slf4j;
 import lombok.val;
@@ -89,6 +90,8 @@ public class ClientMain implements CommandLineRunner {
 
   public static void main(String[] args) {
     try {
+      Log.setGlobalLogLevel(Log.LogLevel.ERROR);
+
       // Bootstrap
       val profiles = bootstrap(args);
 

diff --git a/score-client/src/main/java/bio/overture/score/client/command/ViewCommand.java b/score-client/src/main/java/bio/overture/score/client/command/ViewCommand.java
@@ -307,7 +307,8 @@ private void validateParms() {
     }
 
     checkParameter(objectId != null || sequenceFile != null || manifestResource != null,
-      "One of --object-id, --input-file or --manifest must be specified");
+      "One of --object-id, --input-file or --manifest must be specified. " +
+              "For CRAM files, please additionally include --reference-file.");
 
     if (objectId == null && sequenceFile == null) {
       checkParameter(manifestResource != null && outputDir != null,

diff --git a/score-client/src/main/java/bio/overture/score/client/view/Viewer.java b/score-client/src/main/java/bio/overture/score/client/view/Viewer.java
@@ -73,6 +73,9 @@ public SamFileBuilder getBuilder(@NonNull SeekableStream inputStream, SeekableSt
       // Since CRAM is a compressed form of BAM file that saves space by only recording
       // the differences between an individual BAM file and a standard reference file.
       // we need to have the reference file in order to decode the CRAM file.
+      if(referenceFile == null){
+        throw new RuntimeException("CRAM file type detected, an indexed (fai) reference file (fa, fasta) must be provided. Please specify via --reference-file.");
+      }
       val reference = new ReferenceSource(referenceFile);
       val primitiveReader = new CRAMFileReader(inputStream, indexStream,reference, ValidationStringency.DEFAULT_STRINGENCY);
       val reader = new SamReader.PrimitiveSamReaderToSamReaderAdapter(