Merge branch '5.8.3'

JBEI · Jan 14, 2021 · cb2a7a7 · cb2a7a7
2 parents 08beee6 + 2c309b1
commit cb2a7a7
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Showing 4 changed files with 11 additions and 12 deletions.
diff --git a/src/main/java/org/jbei/ice/lib/entry/EntriesAsCSV.java b/src/main/java/org/jbei/ice/lib/entry/EntriesAsCSV.java
@@ -232,7 +232,7 @@ private void writeZip(Set<Long> sequenceSet) {
             for (long entryId : sequenceSet) {
                 for (String format : formats) {
                     InputStreamWrapper wrapper = new PartSequence(userId, Long.toString(entryId))
-                            .toFile(SequenceFormat.fromString(format), true, false);
+                            .toFile(SequenceFormat.fromString(format), true);
                     putZipEntry(wrapper, zos);
                 }
             }
@@ -318,7 +318,7 @@ public ByteArrayOutputStream customize(EntrySelection selection, SequenceFormat
                 }
 
                 // get the sequence
-                InputStreamWrapper wrapper = new PartSequence(userId, Long.toString(entryId)).toFile(format, onePerFolder, false);
+                InputStreamWrapper wrapper = new PartSequence(userId, Long.toString(entryId)).toFile(format, onePerFolder);
                 if (wrapper == null) {
                     Logger.error("ERROR : no sequence " + entryId);
                     continue;

diff --git a/src/main/java/org/jbei/ice/lib/entry/sequence/PartSequence.java b/src/main/java/org/jbei/ice/lib/entry/sequence/PartSequence.java
@@ -518,21 +518,20 @@ private boolean checkSameFeature(SequenceFeature existingSequenceFeature, Sequen
     /**
      * Convert sequence to a byte array of the specified format with the intention of being written to a file
      *
-     * @param format                 specified format for sequence conversion
-     * @param useFileName            whether to use the original filename of the sequence if the original uploaded sequence is
-     *                               available
-     * @param useOriginalIfAvailable whether to use specified format if is it the same as the uploaded format
+     * @param format      specified format for sequence conversion
+     * @param useFileName whether to use the original filename of the sequence if the original uploaded sequence is
+     *                    available
      * @return wrapper around the outputstream for the converted format and name
      */
-    public InputStreamWrapper toFile(SequenceFormat format, boolean useFileName, boolean useOriginalIfAvailable) {
+    public InputStreamWrapper toFile(SequenceFormat format, boolean useFileName) {
         entryAuthorization.expectRead(userId, entry);
         Sequence sequence = sequenceDAO.getByEntry(entry);
         if (sequence == null)
             return null;
 
-        // if requested format is the same as the original format (if original exist) then get the original instead
-        if (useOriginalIfAvailable && sequenceDAO.hasOriginalSequence(entry.getId()))
-            format = SequenceFormat.ORIGINAL;
+        // default format of genbank
+        if (format == null)
+            format = SequenceFormat.GENBANK;
 
         return new SequenceAsString(format, entry.getId(), useFileName).get();
     }

diff --git a/src/main/java/org/jbei/ice/lib/entry/sequence/SequenceAsString.java b/src/main/java/org/jbei/ice/lib/entry/sequence/SequenceAsString.java
@@ -35,7 +35,7 @@ public SequenceAsString(SequenceFormat format, long partId, boolean useFileName)
         switch (format) {
             case ORIGINAL:
                 sequenceString = sequence.getSequenceUser();
-                if (!useFileName && !StringUtils.isEmpty(sequence.getFileName())) {
+                if (StringUtils.isEmpty(sequence.getFileName()) || !useFileName) {
                     name = entry.getPartNumber() + ".gb";
                 } else {
                     name = sequence.getFileName();

diff --git a/src/main/java/org/jbei/ice/services/rest/FileResource.java b/src/main/java/org/jbei/ice/services/rest/FileResource.java
@@ -210,7 +210,7 @@ public Response downloadSequence(
 
             return addHeaders(Response.ok(stream), wrapper.getName());
         } else {
-            InputStreamWrapper wrapper = new PartSequence(userId, partId).toFile(SequenceFormat.fromString(downloadType), true, true);
+            InputStreamWrapper wrapper = new PartSequence(userId, partId).toFile(SequenceFormat.fromString(downloadType), true);
             StreamingOutput stream = output -> IOUtils.copy(wrapper.getInputStream(), output);
             return addHeaders(Response.ok(stream), wrapper.getName());
         }