Enabling UUID in file upload

lib/galaxy/tools/actions/upload_common.py

@@ -243,6 +243,7 @@ def get_uploaded_datasets( trans, cntrller, params, precreated_datasets, dataset
         else:
             data.extension = uploaded_dataset.file_type
             data.dbkey = uploaded_dataset.dbkey
+            data.uuid = uploaded_dataset.uuid
             trans.sa_session.add( data )
             trans.sa_session.flush()
             if library_bunch:

lib/galaxy/tools/parameters/grouping.py

@@ -278,6 +278,7 @@ class UploadDataset( Group ):
             ftp_files = context['ftp_files']
             name = context.get( 'NAME', None )
             info = context.get( 'INFO', None )
+            uuid = context.get( 'uuid', None )
             warnings = []
             to_posix_lines = False
             if context.get( 'to_posix_lines', None ) not in [ "None", None, False ]:
@@ -316,12 +317,14 @@ class UploadDataset( Group ):
                         break
             file_bunch.to_posix_lines = to_posix_lines
             file_bunch.space_to_tab = space_to_tab
+            file_bunch.uuid = uuid
             return file_bunch, warnings
         def get_filenames( context ):
             rval = []
             data_file = context['file_data']
             url_paste = context['url_paste']
             ftp_files = context['ftp_files']
+            uuid = context.get( 'uuid', None )
             name = context.get( 'NAME', None )
             info = context.get( 'INFO', None )
             to_posix_lines = False
@@ -332,12 +335,14 @@ class UploadDataset( Group ):
                 space_to_tab = True
             warnings = []
             file_bunch = get_data_file_filename( data_file, override_name = name, override_info = info )
+            file_bunch.uuid = uuid
             if file_bunch.path:
                 file_bunch.to_posix_lines = to_posix_lines
                 file_bunch.space_to_tab = space_to_tab
                 rval.append( file_bunch )
             for file_bunch in get_url_paste_urls_or_filename( context, override_name = name, override_info = info ):
                 if file_bunch.path:
+                    file_bunch.uuid = uuid
                     file_bunch.to_posix_lines = to_posix_lines
                     file_bunch.space_to_tab = space_to_tab
                     rval.append( file_bunch )

tools/data_source/upload.xml

@@ -41,6 +41,7 @@
       <!-- Swap the following parameter for the select one that follows to
            enable the to_posix_lines option in the Web GUI. See Bitbucket
            Pull Request 171 for more information. -->
+      <param name="uuid" type="text" required="False" />
       <param name="to_posix_lines" type="hidden" value="Yes" />
       <!--
       <param name="to_posix_lines" type="select" display="checkboxes" multiple="True" label="Convert universal line endings to Posix line endings" help="Turn this option off if you upload a gzip, bz2 or zip archive which contains a binary file." value="Yes">