# HG changeset patch
# User Catherine Wise <catherine.wise@csiro.au>
# Date 1389564644 -39600
# Node ID 8cf18ca6f13f41ae2c81f67548b9990d3c2e93b1
# Parent  b94a8f55b1da750bb10403f4d239a188ae2b23ad
ugh.

diff -r b94a8f55b1da -r 8cf18ca6f13f TrustStoreGalaxyImport.py
--- a/TrustStoreGalaxyImport.py	Mon Jan 13 08:51:17 2014 +1100
+++ b/TrustStoreGalaxyImport.py	Mon Jan 13 09:10:44 2014 +1100
@@ -62,24 +62,23 @@
                         print "File is compressed (gzip) but not valid."
                         sys.exit(4)
                     elif is_gzipped and is_valid:
-                        if link_data_only == 'copy_files':
-                            # We need to uncompress the temp_name file, but BAM files must remain compressed in the BGZF format
-                            CHUNK_SIZE = 2**20 # 1Mb
-                            fd, uncompressed = tempfile.mkstemp(prefix='data_id_%s_upload_gunzip_' % dataset.dataset_id, dir=os.path.dirname(outputFile), text=False )
-                            gzipped_file = gzip.GzipFile(download, 'rb')
-                            while 1:
-                                try:
-                                    chunk = gzipped_file.read(CHUNK_SIZE)
-                                except IOError:
-                                    os.close(fd)
-                                    os.remove(uncompressed)
-                                    print 'Problem decompressing gzipped data', dataset, json_file
-                                    sys.exit(4)
-                                if not chunk:
-                                    break
-                                os.write(fd, chunk)
-                            os.close(fd)
-                            gzipped_file.close()
+                        # We need to uncompress the temp_name file, but BAM files must remain compressed in the BGZF format
+                        CHUNK_SIZE = 2**20 # 1Mb
+                        fd, uncompressed = tempfile.mkstemp(prefix='data_id_%s_upload_gunzip_' % dataset.dataset_id, dir=os.path.dirname(outputFile), text=False )
+                        gzipped_file = gzip.GzipFile(download, 'rb')
+                        while 1:
+                            try:
+                                chunk = gzipped_file.read(CHUNK_SIZE)
+                            except IOError:
+                                os.close(fd)
+                                os.remove(uncompressed)
+                                print 'Problem decompressing gzipped data', dataset, json_file
+                                sys.exit(4)
+                            if not chunk:
+                                break
+                            os.write(fd, chunk)
+                        os.close(fd)
+                        gzipped_file.close()
 
                         shutil.copy(uncompressed, outputFile)
                     else: