mirror of
https://github.com/galaxyproject/galaxy.git
synced 2026-09-24 16:30:27 +08:00
Apply patch from Brad Chapman that fixes an issue when downloading a zip archive of library datasets. Also include some miscellansous imporvements and code cleanup related to changes made in change set 4964:82107691d26e.
This commit is contained in:
Greg Von Kuster
@@ -1,7 +1,7 @@
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"""
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A simple wrapper for writing tarballs as a stream.
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"""
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import os
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import logging, tarfile
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log = logging.getLogger( __name__ )
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@@ -26,3 +26,19 @@ class StreamBall( object ):
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tf.add( file, arcname=rel )
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tf.close()
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return []
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class ZipBall(object):
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def __init__(self, tmpf, tmpd):
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self._tmpf = tmpf
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self._tmpd = tmpd
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def stream(self, environ, start_response):
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response_write = start_response( self.wsgi_status, self.wsgi_headeritems )
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tmpfh = open( self._tmpf )
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response_write(tmpfh.read())
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tmpfh.close()
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try:
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os.unlink( self._tmpf )
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os.rmdir( self._tmpd )
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except OSError:
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log.exception( "Unable to remove temporary library download archive and directory" )
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return []
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@@ -35,7 +35,7 @@ class LibraryListGrid( grids.Grid ):
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attach_popup=False,
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filterable="advanced" ),
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]
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columns.append( grids.MulticolFilterColumn( "search library dataset name, info, message, dbkey",
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columns.append( grids.MulticolFilterColumn( "search dataset name, info, message, dbkey",
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cols_to_filter=[ columns[0], columns[1] ],
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key="free-text-search",
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visible=False,
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@@ -50,7 +50,7 @@ class LibraryListGrid( grids.Grid ):
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# Columns that are valid for filtering but are not visible.
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grids.DeletedColumn( "Deleted", key="deleted", visible=False, filterable="advanced" )
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]
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columns.append( grids.MulticolFilterColumn( "search library dataset name, info, message, dbkey",
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columns.append( grids.MulticolFilterColumn( "search dataset name, info, message, dbkey",
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cols_to_filter=[ columns[0], columns[1] ],
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key="free-text-search",
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visible=False,
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@@ -1706,20 +1706,12 @@ class LibraryCommon( BaseController, UsesFormDefinitions ):
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fname = lname.replace( ' ', '_' ) + '_files'
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if action == 'zip':
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archive.close()
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tmpfh = open( tmpf )
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# clean up now
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try:
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os.unlink( tmpf )
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os.rmdir( tmpd )
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except OSError:
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error = True
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log.exception( "Unable to remove temporary library download archive and directory" )
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message = "Unable to create archive for download, please report this error"
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status = 'error'
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if not error:
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trans.response.set_content_type( "application/x-zip-compressed" )
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trans.response.headers[ "Content-Disposition" ] = "attachment; filename=%s.%s" % (fname,outext)
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return tmpfh
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trans.response.set_content_type( "application/x-zip-compressed" )
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trans.response.headers[ "Content-Disposition" ] = "attachment; filename=%s.%s" % (fname,outext)
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archive = util.streamball.ZipBall(tmpf, tmpd)
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archive.wsgi_status = trans.response.wsgi_status()
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archive.wsgi_headeritems = trans.response.wsgi_headeritems()
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return archive.stream
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elif action == 'ngxzip':
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trans.response.set_content_type( "application/zip" )
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trans.response.headers[ "Content-Disposition" ] = "attachment; filename=%s.%s" % (fname,outext)
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@@ -1831,11 +1823,11 @@ class LibraryCommon( BaseController, UsesFormDefinitions ):
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hist_names_str = ", ".join( [ target_history.name for target_history in target_histories ] )
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num_source = len( ldda_ids ) - invalid_datasets
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num_target = len( target_histories )
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message = "%i %s have been imported into %i %s: %s" % ( num_source,
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inflector.cond_plural( num_source, "dataset" ),
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num_target,
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inflector.cond_plural( num_target, "history" ),
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hist_names_str )
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message = "%i %s imported into %i %s: %s" % ( num_source,
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inflector.cond_plural( num_source, "dataset" ),
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num_target,
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inflector.cond_plural( num_target, "history" ),
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hist_names_str )
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trans.sa_session.refresh( current_history )
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current_user_roles = trans.get_current_user_roles()
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source_lddas = []
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@@ -2240,7 +2232,7 @@ def whoosh_search( trans, cntrller, search_term, **kwd ):
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# Perform search
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parser = MultifieldParser( [ 'name', 'info', 'dbkey', 'message' ], schema=schema )
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# Search term with wildcards may be slow...
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results = searcher.search( parser.parse( '*' + search_term + '*' ), minscore=0.1 )
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results = searcher.search( parser.parse( '*' + search_term + '*' ), minscore=0.5 )
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ldda_ids = [ result[ 'id' ] for result in results ]
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lddas = []
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for ldda_id in ldda_ids:
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@@ -63,7 +63,10 @@ def get_lddas( sa_session ):
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else:
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info = ''
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dbkey = ldda.metadata.dbkey
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message = ldda.message
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if ldda.message:
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message = ldda.message
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else:
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message = ''
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yield id, name, info, dbkey, message
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def get_sa_session_and_needed_config_settings( ini_file ):
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@@ -1,6 +1,7 @@
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<%namespace file="/message.mako" import="render_msg" />
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<%namespace file="/library/common/library_item_info.mako" import="render_library_item_info" />
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<%namespace file="/library/common/common.mako" import="render_actions_on_multiple_items" />
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<%namespace file="/library/common/common.mako" import="render_compression_types_help" />
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<%namespace file="/library/common/common.mako" import="common_javascripts" />
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<%!
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@@ -564,34 +565,6 @@
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</script>
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<!-- running: do not change this comment, used by TwillTestCase.library_wait -->
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%endif
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## Help about compression types
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<div class="libraryItemBody">
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<p class="infomark">
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TIP: You can download individual library files by selecting "Download this dataset" from the context menu (triangle) next to the dataset's name.
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</p>
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</div>
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%if len( comptypes ) > 1:
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<div class="libraryItemBody">
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<p class="infomark">
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TIP: Multiple compression options are available for downloading library datasets:
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</p>
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<ul style="padding-left: 1em; list-style-type: disc;">
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%if 'gz' in comptypes:
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<li>gzip: Recommended for fast network connections
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%if trans.app.config.upstream_gzip:
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NOTE: The file you receive will be an uncompressed .tar file - this is because the Galaxy server compresses it and your browser decompresses it on the fly.
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%endif
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</li>
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%endif
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%if 'bz2' in comptypes:
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<li>bzip2: Recommended for slower network connections (smaller size but takes longer to compress)</li>
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%endif
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%if 'zip' in comptypes:
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<li>zip: Not recommended but is provided as an option for those who cannot open the above formats</li>
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%endif
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</ul>
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</div>
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%endif
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${render_compression_types_help( comptypes )}
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</%def>
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@@ -43,6 +43,36 @@
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</script>
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</%def>
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<%def name="render_compression_types_help( comptypes )">
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<div class="libraryItemBody">
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<p class="infomark">
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TIP: You can download individual library datasets by selecting "Download this dataset" from the context menu (triangle) next to each dataset's name.
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</p>
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</div>
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%if len( comptypes ) > 1:
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<div class="libraryItemBody">
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<p class="infomark">
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TIP: Several compression options are available for downloading multiple library datasets simultaneously:
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</p>
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<ul style="padding-left: 1em; list-style-type: disc;">
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%if 'gz' in comptypes:
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<li>gzip: Recommended for fast network connections
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%if trans.app.config.upstream_gzip:
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NOTE: The file you receive will be an uncompressed .tar file - this is because the Galaxy server compresses it and your browser decompresses it on the fly.
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%endif
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</li>
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%endif
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%if 'bz2' in comptypes:
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<li>bzip2: Recommended for slower network connections (smaller size but takes longer to compress)</li>
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%endif
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%if 'zip' in comptypes:
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<li>zip: Not recommended but is provided as an option for those who cannot open the above formats</li>
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%endif
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</ul>
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</div>
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%endif
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</%def>
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<%def name="render_upload_form( cntrller, upload_option, action, library_id, folder_id, replace_dataset, file_formats, dbkeys, space_to_tab, link_data_only, widgets, roles_select_list, history, show_deleted )">
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<%
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import os, os.path
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@@ -58,8 +58,14 @@ ${h.js( "jquery", "galaxy.base" )}
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<select id="single-dest-select" name="target_history_ids">
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<option value=""></option>
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%for i, target_history in enumerate( target_histories ):
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<% encoded_id = trans.security.encode_id( target_history.id ) %>
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<option value="${encoded_id}">${i + 1}: ${h.truncate( target_history.name, 30 )}</option>
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<%
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encoded_id = trans.security.encode_id( target_history.id )
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if target_history == current_history:
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current_history_text = " (current history)"
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else:
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current_history_text = ""
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%>
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<option value="${encoded_id}">${i + 1}: ${h.truncate( target_history.name, 30 )}${current_history_text}</option>
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%endfor
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</select>
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<br/><br/>
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@@ -68,12 +74,15 @@ ${h.js( "jquery", "galaxy.base" )}
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<div id="multiple-destination" style="display: none;">
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%for i, target_history in enumerate( target_histories ):
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<%
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cur_history_text = ""
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encoded_id = trans.security.encode_id( target_history.id )
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if target_history == current_history:
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current_history_text = " (current history)"
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else:
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current_history_text = ""
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%>
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<div class="form-row">
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<input type="checkbox" name="target_history_ids" id="target_history_${encoded_id}" value="${encoded_id}"/>
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<label for="target_history_${encoded_id}" style="display: inline; font-weight:normal;">${i + 1}: ${target_history.name}${cur_history_text}</label>
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<label for="target_history_${encoded_id}" style="display: inline; font-weight:normal;">${i + 1}: ${target_history.name}${current_history_text}</label>
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</div>
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%endfor
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</div>
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@@ -1,6 +1,7 @@
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<%namespace file="/message.mako" import="render_msg" />
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<%namespace file="/library/common/browse_library.mako" import="render_dataset" />
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<%namespace file="/library/common/common.mako" import="render_actions_on_multiple_items" />
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<%namespace file="/library/common/common.mako" import="render_compression_types_help" />
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<%namespace file="/library/common/common.mako" import="common_javascripts" />
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<%!
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@@ -127,35 +128,7 @@
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${render_actions_on_multiple_items( actions_to_exclude=[ 'manage_permissions' ] )}
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</table>
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</form>
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## Help about compression types
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<div class="libraryItemBody">
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<p class="infomark">
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TIP: You can download individual library files by selecting "Download this dataset" from the context menu (triangle) next to the dataset's name.
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</p>
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</div>
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%if len( comptypes ) > 1:
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<div class="libraryItemBody">
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<p class="infomark">
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TIP: Multiple compression options are available for downloading library datasets:
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</p>
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<ul style="padding-left: 1em; list-style-type: disc;">
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%if 'gz' in comptypes:
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<li>gzip: Recommended for fast network connections
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%if trans.app.config.upstream_gzip:
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NOTE: The file you receive will be an uncompressed .tar file - this is because the Galaxy server compresses it and your browser decompresses it on the fly.
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%endif
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</li>
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%endif
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%if 'bz2' in comptypes:
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<li>bzip2: Recommended for slower network connections (smaller size but takes longer to compress)</li>
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%endif
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%if 'zip' in comptypes:
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<li>zip: Not recommended but is provided as an option for those who cannot open the above formats</li>
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%endif
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</ul>
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</div>
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%endif
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${render_compression_types_help( comptypes )}
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%elif status != 'error':
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<p>The string "${search_term}" was not found in any of the following information components for any library datasets that you can access.</p>
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${render_searched_components()}
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@@ -300,7 +300,7 @@ class TestLibrarySecurity( TwillTestCase ):
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library_id=self.security.encode_id( library1.id ),
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ldda_ids=self.security.encode_id( ldda2.id ),
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new_history_name='goodbye',
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strings_displayed=[ '1 dataset have been imported into 1 history' ] )
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strings_displayed=[ '1 dataset imported into 1 history' ] )
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self.logout()
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# regular_user2 should not be able to see ldda2
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self.login( email=regular_user2.email )
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