Defect/download failure fix

score-client/src/main/conf/logback.xml

@@ -16,7 +16,7 @@ OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER
 IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN
 ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
 -->
-<configuration debug="false">
+<configuration debug="true">
 
   <property name="log.dir" value="${logging.path:-/tmp/score-client/logs}" />
   <property name="log.name" value="client" />
@@ -36,7 +36,7 @@ ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF S
     </encoder>
   </appender>
 
-  <root level="INFO">
+  <root level="DEBUG">
     <appender-ref ref="FILE" />
   </root>
 

score-client/src/main/java/bio/overture/score/client/command/DownloadCommand.java

@@ -34,6 +34,8 @@
 import lombok.SneakyThrows;
 import lombok.extern.slf4j.Slf4j;
 import lombok.val;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
 import org.springframework.beans.factory.annotation.Autowired;
 import org.springframework.stereotype.Component;
 
@@ -60,6 +62,8 @@ public enum OutputLayout {
     BUNDLE, FILENAME, ID
   }
 
+  private Logger session = LoggerFactory.getLogger("session");
+
   /**
    * Options
    */
@@ -148,7 +152,8 @@ private List<String> getIdsFromManifest(ManifestResource manifestResource) throw
     val manifest = manifestService.getDownloadManifest(manifestResource);
 
     validateManifest(manifest);
-
+    session.info("Download Command Class Parameters : manifest.getEntries() ::::"+manifest.getEntries());
+    terminal.println("Download Command Class Parameters : manifest.getEntries() ::::"+manifest.getEntries());
     val entries = manifest.getEntries();
     if (entries.isEmpty()) {
       throw new BadManifestException(format("Manifest '%s' is empty", manifestResource));
@@ -165,7 +170,10 @@ private List<String> getIdsFromAnalysis(String programId, String analysisId) {
   private int downloadObjects(List<String> objectIds) throws IOException {
     // Entities are defined in Meta service
     val entities = resolveEntities(objectIds);
-
+    terminal
+            .printLine()
+            .println("Downloading objects size ::::"+objectIds.size())
+            .printLine();
     if (!verifyLocalAvailableSpace(entities)) {
       return FAILURE_STATUS;
     }
@@ -178,6 +186,14 @@ private int downloadObjects(List<String> objectIds) throws IOException {
     if (layout != OutputLayout.ID) {
       entitySet = filterEntities(entities);
     }
+    terminal
+            .printLine()
+            .println("Filtered Entites ::::"+entitySet.size())
+            .printLine();
+    terminal
+            .printLine()
+            .println("Force value ::::"+force)
+            .printLine();
 
     // If --force is specified, delete all the old files first, so that we can resume later if the new downloads fail.
     if (force) {
@@ -200,7 +216,10 @@ private int downloadObjects(List<String> objectIds) throws IOException {
       val builder = DownloadRequest.builder();
       val request = builder.outputDir(outputDir).entity(entity).objectId(entity.getId()).offset(offset).length(length)
         .validate(validate).build();
-
+      terminal
+              .printLine()
+              .println("Request payload ::::"+request.toString())
+              .printLine();
       // only try to re-download a file that exists if --force was specified on the command line
       val target = getLayoutTarget(entity);
       if (target.exists()) {

score-client/src/main/java/bio/overture/score/client/command/UploadCommand.java

@@ -27,6 +27,8 @@
 import com.beust.jcommander.Parameters;
 import lombok.extern.slf4j.Slf4j;
 import lombok.val;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
 import org.springframework.beans.factory.annotation.Autowired;
 import org.springframework.context.annotation.Profile;
 import org.springframework.stereotype.Component;
@@ -43,6 +45,7 @@
 @Profile("!kf")
 public class UploadCommand extends RepositoryAccessCommand {
 
+  private Logger session = LoggerFactory.getLogger("session");
   /**
    * Options.
    */
@@ -90,6 +93,8 @@ public int execute() throws Exception {
         uploadFile(objectId, file, checksum);
       }
     } else {
+      session.info("Upload Command Class Parameters : file ::::"+file+"   objectId ::::::"+objectId+"     manifestResource   ::::::"+manifestResource+"   md5 ::::"+md5);
+      terminal.println("Upload Command Class Parameters : file ::::"+file+"   objectId ::::::"+objectId+"     manifestResource   ::::::"+manifestResource+"   md5 ::::"+md5);
       checkParameter(file != null, "--file must be specified if --object-id is specified");
       checkParameter(md5 != null, "--md5 must be specified if --object-id is specified");
       uploadFile(objectId, file, md5);

score-client/src/main/java/bio/overture/score/client/command/ViewCommand.java

@@ -305,7 +305,8 @@ private void validateParms() {
         terminal.println("When --stdout specified, output format forced to SAM.");
       }
     }
-
+    session.info("View Command Class parameters : objectId ::::"+objectId+"   sequenceFile ::::"+sequenceFile+"   manifestResource  ::::"+manifestResource);
+    terminal.println("View Command Class parameters : objectId ::::"+objectId+"   sequenceFile ::::"+sequenceFile+"   manifestResource  ::::"+manifestResource);
     checkParameter(objectId != null || sequenceFile != null || manifestResource != null,
       "One of --object-id, --input-file or --manifest must be specified. " +
               "For CRAM files, please additionally include --reference-file.");

score-client/src/main/java/bio/overture/score/client/download/DownloadService.java

@@ -155,6 +155,10 @@ private void resumeIfPossible(DownloadRequest request, boolean checksum)
     log.debug("Attempting to resume download for {}", request.toString());
     ObjectSpecification spec = null;
     try {
+      terminal
+              .printLine()
+              .println("Request payload in Download Service ::::"+request.toString())
+              .printLine();
       spec = downloadStateStore.getProgress(request.getOutputDir(), request.getObjectId());
     } catch (NotRetryableException e) {
       log.info("New download: {} because {}", request.getObjectId(), e.getMessage());