Merge pull request #138 from overture-stack/score-137-view-command-bu…

…gfix

Score 137 view command bugfix

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

@@ -57,7 +57,9 @@
 import java.util.Optional;
 
 import static bio.overture.score.client.cli.Parameters.checkParameter;
+import static java.util.Objects.isNull;
 import static java.util.stream.Collectors.toList;
+import static org.springframework.util.StringUtils.isEmpty;
 
 @Slf4j
 @Component
@@ -158,8 +160,9 @@ public int execute() throws Exception {
 
     if (sequenceFile != null) {
         v = new Viewer(referenceFile);
+        val indexFileExists = !isNull(indexFile);
         val builder = configureBuilder(v.getBuilder(sequenceFile,indexFile));
-        build(builder);
+        build(builder, indexFileExists);
     } else if (objectId != null) {
       // Ad-hoc single - supercedes --manifest
       if (manifestResource != null) {
@@ -211,10 +214,17 @@ private Entity getEntity(String oid) {
 
   public SamFileBuilder configureBuilder(SamFileBuilder builder) {
     builder = builder.programName(PROGRAM_NAME)
-      .version(VersionUtils.getScmInfo().get("git.commit.id.describe")).programId(ICGC).commandLine(getCommandLine())
-      .containedOnly(containedOnly).useOriginalHeader(useOriginalHeader).outputFormat(outputFormat).queries(query)
-      .outputDir(outputDir).bedFile(bedFile).outputIndex(outputIndex).stdout(stdout);
-
+        .version(VersionUtils.getScmInfo().get("git.commit.id.describe"))
+        .programId(ICGC)
+        .commandLine(getCommandLine())
+        .containedOnly(containedOnly)
+        .useOriginalHeader(useOriginalHeader)
+        .outputFormat(outputFormat)
+        .outputDir(outputDir)
+        .outputIndex(outputIndex)
+        .stdout(stdout)
+        .queries(query)
+        .bedFile(bedFile);
     log.info("Constructed SamFileBuilder: " + builder.toString());
     return builder;
   }
@@ -224,18 +234,26 @@ int process(String oid) {
     val entity = getEntity(oid);
     val urls = getPresignedUrls(entity);
 
+    val indexExists = !isNull(urls.index);
     val inputStream = Viewer.openInputStream(urls.file);
-    val indexStream = Viewer.openIndexStream(urls.index);
+    val indexStream = indexExists ? Viewer.openIndexStream(urls.index) : null;
     val isCram = isCRAM(entity.getFileName());
     val viewer = new Viewer(referenceFile);
 
     val builder = configureBuilder(viewer.getBuilder(inputStream, indexStream, isCram));
-    return build(builder.entity(entity));
+    return build(builder.entity(entity), indexExists);
+  }
+
+  private boolean isQueryDefined(){
+    return !isEmpty(bedFile) || !isNull(query) && !query.isEmpty();
   }
 
   @SneakyThrows
-  int build(SamFileBuilder builder) {
-    if (headerOnly) {
+  int build(SamFileBuilder builder, boolean hasIndex) {
+    if (isQueryDefined() && !hasIndex){
+      log.warn("Supplied query or bedfile will not be used since no index is available");
+    }
+    if (headerOnly || !hasIndex) {
       builder.buildHeaderOnly();
     } else {
       switch (outputType) {
@@ -272,11 +290,9 @@ private Optional<Entity> fetchEntity(String oid) {
 
   public PresignedUrls getPresignedUrls(Entity entity) {
     val indexEntity = metadataService.getIndexEntity(entity);
-    checkParameter(indexEntity.isPresent(), "No index file associated with BAM/CRAM file with object id '%s'",
-      entity.getId());
-
     val bamFileUrl = downloadService.getUrl(entity.getId());
-    val indexFileUrl = downloadService.getUrl(indexEntity.get().getId());
+    val indexFileUrl = indexEntity.map(x -> downloadService.getUrl(x.getId())).orElse(null);
+
     return new PresignedUrls(bamFileUrl, indexFileUrl);
   }
 

score-client/src/main/java/bio/overture/score/client/slicing/SamFileBuilder.java

@@ -1,18 +1,18 @@
 /*
- * Copyright (c) 2016 The Ontario Institute for Cancer Research. All rights reserved.                             
- *                                                                                                               
+ * Copyright (c) 2016 The Ontario Institute for Cancer Research. All rights reserved.
+ *
  * This program and the accompanying materials are made available under the terms of the GNU Public License v3.0.
- * You should have received a copy of the GNU General Public License along with                                  
- * this program. If not, see <http://www.gnu.org/licenses/>.                                                     
- *                                                                                                               
- * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY                           
- * EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES                          
- * OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT                           
- * SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT,                                
- * INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED                          
- * TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;                               
- * OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER                              
- * IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN                         
+ * You should have received a copy of the GNU General Public License along with
+ * this program. If not, see <http://www.gnu.org/licenses/>.
+ *
+ * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY
+ * EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES
+ * OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT
+ * SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT,
+ * INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED
+ * TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+ * 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.
  */
 package bio.overture.score.client.slicing;
@@ -22,8 +22,18 @@
 import com.google.common.base.Throwables;
 import com.google.common.collect.Lists;
 import com.google.common.collect.Sets;
-import htsjdk.samtools.*;
+import htsjdk.samtools.QueryInterval;
+import htsjdk.samtools.SAMFileHeader;
 import htsjdk.samtools.SAMFileHeader.SortOrder;
+import htsjdk.samtools.SAMFileWriter;
+import htsjdk.samtools.SAMFileWriterFactory;
+import htsjdk.samtools.SAMProgramRecord;
+import htsjdk.samtools.SAMReadGroupRecord;
+import htsjdk.samtools.SAMRecord;
+import htsjdk.samtools.SamInputResource;
+import htsjdk.samtools.SamReader;
+import htsjdk.samtools.SamReaderFactory;
+import htsjdk.samtools.ValidationStringency;
 import htsjdk.samtools.cram.ref.ReferenceSource;
 import htsjdk.samtools.util.RuntimeIOException;
 import lombok.Cleanup;
@@ -305,7 +315,7 @@ private void createTrimmed(SamReader reader, Entity entity, List<String> queries
 
   /**
    * Temporarily changed to public
-   * 
+   *
    * @param reader
    * @param queries
    * @return
@@ -339,7 +349,7 @@ public QueryInterval[] normalizeQueries(SamReader reader, List<String> queries)
 
   /**
    * Temporarily changed to public
-   * 
+   *
    * Returns list of SAMRecord alignments that satisfy the specified list of queries. Refers to the <b>containedOnly</b>
    * member variable.
    * @param reader Instance of the SAM Reader open to source SAM/BAM file
@@ -523,7 +533,7 @@ String generateHeaderOnlyOutputFileName(@NonNull Entity entity) {
   /**
    * In case of a large number of queries, we truncate the output filename if it is longer than MAX_FILENAME_LENGTH
    * characters long.
-   * 
+   *
    * @param originalName - file name including all query slices
    * @return file name truncated at MAX_FILENAME_LENGTH but retaining extension. Includes '~' to indicate that it has
    * been truncated
@@ -550,10 +560,7 @@ private String encodeQuery(String query) {
     return query.replace(":", "_");
   }
 
-  @SneakyThrows
   public void buildHeaderOnly() {
-    @Cleanup
-    val reader = createSamReader();
     createHeaderOnly(reader, entity); // use original filename and no query
   }
 

score-client/src/main/java/bio/overture/score/client/upload/UploadStateStore.java

@@ -79,7 +79,7 @@ public static void create(@NonNull File uploadFile, @NonNull ObjectSpecification
   }
 
   protected static String getStateName() {
-    return "uploadid";
+    return "uploadId";
   }
 
   public static Optional<String> fetchUploadId(@NonNull File uploadFile, @NonNull String objectId) {

score-client/src/main/java/bio/overture/score/client/view/Viewer.java

@@ -9,29 +9,39 @@
 import htsjdk.samtools.ValidationStringency;
 import htsjdk.samtools.cram.ref.ReferenceSource;
 import htsjdk.samtools.seekablestream.SeekableStream;
+import lombok.NonNull;
 import lombok.SneakyThrows;
 import lombok.val;
 
 import java.io.File;
-import java.io.InputStream;
 import java.net.URL;
 
+import static java.util.Objects.isNull;
+
 public class Viewer {
   File referenceFile=null;
 
   public Viewer(File referenceFile) {
     this.referenceFile=referenceFile;
   }
 
-  public static SamInputResource getFileResource(File bamFile, File baiFile) {
-    if (baiFile != null) {
+  public static SamInputResource getFileResource(@NonNull File bamFile, File baiFile) {
+    if (isNull(baiFile)) {
+      return SamInputResource.of(bamFile);
+    } else {
       return SamInputResource.of(bamFile).index(baiFile);
+    }
+  }
+
+  public static SamInputResource getStreamResource(@NonNull SeekableStream inputStream, SeekableStream indexStream) {
+    if (isNull(indexStream)) {
+      return SamInputResource.of(inputStream);
     } else {
-      return SamInputResource.of(bamFile);
+      return SamInputResource.of(inputStream).index(indexStream);
     }
   }
 
-  public static InputStream openInputStream(URL url) {
+  public static SeekableStream openInputStream(URL url) {
     return new NullSourceSeekableHTTPStream(url);
   }
 
@@ -40,18 +50,23 @@ public static SeekableStream openIndexStream(URL url) {
   }
 
   @SneakyThrows
-  public SamFileBuilder getBuilder(File sequenceFile, File indexFile) {
+  public SamFileBuilder getBuilder(@NonNull File sequenceFile, File indexFile) {
     val entity = new Entity();
     entity.setFileName(sequenceFile.toString());
     val reference=new ReferenceSource(referenceFile);
     val resource = getFileResource(sequenceFile, indexFile);
-    val builder=new SamFileBuilder().samInput(resource).cramReferenceSource(reference);
+    val builder = new SamFileBuilder()
+        .entity(entity)
+        .samInput(resource)
+        .cramReferenceSource(reference);
+    val reader = builder.createSamReader();
+    builder.reader(reader);
     return builder;
   }
 
   @SneakyThrows
-  public SamFileBuilder getBuilder(InputStream inputStream, SeekableStream indexStream, boolean isCram) {
-    val resource = SamInputResource.of(inputStream).index(indexStream);
+  public SamFileBuilder getBuilder(@NonNull SeekableStream inputStream, SeekableStream indexStream, boolean isCram) {
+    val resource =  getStreamResource(inputStream, indexStream);
     val builder = new SamFileBuilder().samInput(resource);
 
     if (isCram) {