- galaxy-commits - lists.galaxyproject.org

[hg] galaxy 3744: Fix bug that mucked up fetch for chrom lengths...
by Nate Coraor 10 May '10

10 May '10

details: http://www.bx.psu.edu/hg/galaxy/rev/5f59c890ee8d changeset: 3744:5f59c890ee8d user: jeremy goecks <jeremy.goecks(a)emory.edu> date: Tue May 04 22:27:05 2010 -0400 description: Fix bug that mucked up fetch for chrom lengths in new track browsers. diffstat: lib/galaxy/web/controllers/tracks.py | 32 ++++++++++++++++++++------------ templates/tracks/browser.mako | 7 ++++++- 2 files changed, 26 insertions(+), 13 deletions(-) diffs (76 lines): diff -r b5c76e1a28ea -r 5f59c890ee8d lib/galaxy/web/controllers/tracks.py --- a/lib/galaxy/web/controllers/tracks.py Tue May 04 21:57:26 2010 -0400 +++ b/lib/galaxy/web/controllers/tracks.py Tue May 04 22:27:05 2010 -0400 @@ -158,9 +158,9 @@ return trans.fill_template( 'tracks/browser.mako', config=config ) @web.json - def chroms(self, trans, vis_id=None ): + def chroms(self, trans, vis_id=None, dbkey=None ): """ - Returns a naturally sorted list of chroms/contigs for the given dbkey + Returns a naturally sorted list of chroms/contigs for either a given visualization or a given dbkey. """ def check_int(s): if s.isdigit(): @@ -171,25 +171,33 @@ def split_by_number(s): return [ check_int(c) for c in re.split('([0-9]+)', s) ] - # Get visualization and config. - visualization = self.get_visualization( trans, vis_id, check_ownership=False, check_accessible=True ) - visualization.config = self.get_visualization_config( trans, visualization ) - if visualization is None: - raise web.httpexceptions.HTTPNotFound() + # Must specify either vis_id or dbkey. + if not vis_id and not dbkey: + return trans.show_error_message("No visualization id or dbkey specified.") + + # Need to get user and dbkey in order to get chroms data. + if vis_id: + # Use user, dbkey from viz. + visualization = self.get_visualization( trans, vis_id, check_ownership=False, check_accessible=True ) + visualization.config = self.get_visualization_config( trans, visualization ) + vis_user = visualization.user + vis_dbkey = visualization.config['dbkey'] + else: + # No vis_id, so visualization is new. User is current user, dbkey must be given. + vis_user = trans.user + vis_dbkey = dbkey # Get chroms data. - chroms = self._chroms( trans, visualization ) + chroms = self._chroms( trans, vis_user, vis_dbkey ) to_sort = [{ 'chrom': chrom, 'len': length } for chrom, length in chroms.iteritems()] to_sort.sort(lambda a,b: cmp( split_by_number(a['chrom']), split_by_number(b['chrom']) )) return to_sort - def _chroms( self, trans, visualization ): + def _chroms( self, trans, user, dbkey ): """ - Called by the browser to get a list of valid chromosomes and lengths + Helper method that returns chrom lengths for a given user and dbkey. """ # If there is any dataset in the history of extension `len`, this will use it - user = visualization.user - dbkey = visualization.config['dbkey'] if 'dbkeys' in user.preferences: user_keys = from_json_string( user.preferences['dbkeys'] ) if dbkey in user_keys: diff -r b5c76e1a28ea -r 5f59c890ee8d templates/tracks/browser.mako --- a/templates/tracks/browser.mako Tue May 04 21:57:26 2010 -0400 +++ b/templates/tracks/browser.mako Tue May 04 22:27:05 2010 -0400 @@ -272,7 +272,12 @@ $.ajax({ url: "${h.url_for( action='chroms' )}", - data: { vis_id: view.vis_id }, + ## If vis is new, it doesn't have an id, so send the dbkey instead. + %if config.get('vis_id'): + data: { vis_id: view.vis_id }, + %else: + data: { dbkey: view.dbkey }, + %endif dataType: "json", success: function ( data ) { view.chrom_data = data;

1 0

[hg] galaxy 3742: trackster: fix BAM data error; display tweaks
by Nate Coraor 10 May '10

10 May '10

details: http://www.bx.psu.edu/hg/galaxy/rev/49c11691bc2e changeset: 3742:49c11691bc2e user: Kanwei Li <kanwei(a)gmail.com> date: Tue May 04 15:43:34 2010 -0400 description: trackster: fix BAM data error; display tweaks diffstat: lib/galaxy/datatypes/converters/bed_to_summary_tree_converter.py | 2 +- lib/galaxy/visualization/tracks/data/bam.py | 11 +++++++++- lib/galaxy/visualization/tracks/data/summary_tree.py | 4 +- static/scripts/trackster.js | 5 ++- 4 files changed, 16 insertions(+), 6 deletions(-) diffs (84 lines): diff -r c7607fba91b9 -r 49c11691bc2e lib/galaxy/datatypes/converters/bed_to_summary_tree_converter.py --- a/lib/galaxy/datatypes/converters/bed_to_summary_tree_converter.py Tue May 04 14:21:21 2010 -0400 +++ b/lib/galaxy/datatypes/converters/bed_to_summary_tree_converter.py Tue May 04 15:43:34 2010 -0400 @@ -15,7 +15,7 @@ reader = BedReader( open( input_fname ) ) - st = SummaryTree(block_size=100, levels=4, draw_cutoff=100, detail_cutoff=20) + st = SummaryTree(block_size=25, levels=6, draw_cutoff=150, detail_cutoff=30) for chrom, chrom_start, chrom_end, name, score in reader: st.insert_range(chrom, chrom_start, chrom_end) diff -r c7607fba91b9 -r 49c11691bc2e lib/galaxy/visualization/tracks/data/bam.py --- a/lib/galaxy/visualization/tracks/data/bam.py Tue May 04 14:21:21 2010 -0400 +++ b/lib/galaxy/visualization/tracks/data/bam.py Tue May 04 15:43:34 2010 -0400 @@ -10,6 +10,8 @@ import logging log = logging.getLogger(__name__) +MAX_VALS = 50 # only display first MAX_VALS datapoints + class BamDataProvider( object ): """ Provides access to intervals from a sorted indexed BAM file. @@ -26,18 +28,25 @@ start, end = int(start), int(end) # Attempt to open the BAM file with index bamfile = csamtools.Samfile( filename=self.original_dataset.file_name, mode='rb', index_filename=self.index.file_name ) + message = None try: data = bamfile.fetch(start=start, end=end, reference=chrom) except ValueError, e: # Some BAM files do not prefix chromosome names with chr, try without if chrom.startswith( 'chr' ): - data = bamfile.fetch( start=start, end=end, reference=chrom[3:] ) + try: + data = bamfile.fetch( start=start, end=end, reference=chrom[3:] ) + except: + return None else: return None # Encode reads as list of dictionaries results = [] paired_pending = {} for read in data: + if len(results) > MAX_VALS: + message = "Only the first %s pairs are being displayed." % MAX_VALS + break qname = read.qname if read.is_proper_pair: if qname in paired_pending: # one in dict is always first diff -r c7607fba91b9 -r 49c11691bc2e lib/galaxy/visualization/tracks/data/summary_tree.py --- a/lib/galaxy/visualization/tracks/data/summary_tree.py Tue May 04 14:21:21 2010 -0400 +++ b/lib/galaxy/visualization/tracks/data/summary_tree.py Tue May 04 15:43:34 2010 -0400 @@ -32,12 +32,12 @@ level = int(max( level, 0 )) if level <= 0: return None - + stats = st.chrom_stats[chrom] results = st.query(chrom, int(start), int(end), level) if results == "detail": return None - elif results == "draw": + elif results == "draw" or level <= 1: return "no_detail" else: return results, stats[level]["max"], stats[level]["avg"], stats[level]["delta"] diff -r c7607fba91b9 -r 49c11691bc2e static/scripts/trackster.js --- a/static/scripts/trackster.js Tue May 04 14:21:21 2010 -0400 +++ b/static/scripts/trackster.js Tue May 04 15:43:34 2010 -0400 @@ -439,8 +439,9 @@ return; } - var data = this.data_cache.get(key); - if (data === null) { return; } + var result = this.data_cache.get(key); + if (result === null) { return; } + console.log(result); canvas.css( { position: "absolute",

1 0

[hg] galaxy 3743: Removing debugging msg.
by Nate Coraor 10 May '10

10 May '10

details: http://www.bx.psu.edu/hg/galaxy/rev/b5c76e1a28ea changeset: 3743:b5c76e1a28ea user: jeremy goecks <jeremy.goecks(a)emory.edu> date: Tue May 04 21:57:26 2010 -0400 description: Removing debugging msg. diffstat: tools/ngs_rna/cuffcompare_wrapper.py | 1 - 1 files changed, 0 insertions(+), 1 deletions(-) diffs (11 lines): diff -r 49c11691bc2e -r b5c76e1a28ea tools/ngs_rna/cuffcompare_wrapper.py --- a/tools/ngs_rna/cuffcompare_wrapper.py Tue May 04 15:43:34 2010 -0400 +++ b/tools/ngs_rna/cuffcompare_wrapper.py Tue May 04 21:57:26 2010 -0400 @@ -52,7 +52,6 @@ input2_file_name = tmp_output_dir + "/input2" os.symlink( options.input2, input2_file_name ) cmd += " %s" % input2_file_name - print cmd # Run command. try:

1 0

[hg] galaxy 3741: Fix the recentrly introduced grid filter / sea...
by Nate Coraor 10 May '10

10 May '10

details: http://www.bx.psu.edu/hg/galaxy/rev/c7607fba91b9 changeset: 3741:c7607fba91b9 user: Greg Von Kuster <greg(a)bx.psu.edu> date: Tue May 04 14:21:21 2010 -0400 description: Fix the recentrly introduced grid filter / search bug. Revert the recently introduced grid filter_params hack for generating links since we now use a different approach to rendering links. Convert a few more 'message_type' params to be 'status' instead. Many fixes for the community space app. diffstat: lib/galaxy/tools/__init__.py | 4 +- lib/galaxy/web/framework/__init__.py | 2 +- lib/galaxy/web/framework/helpers/grids.py | 17 +- lib/galaxy/webapps/community/controllers/admin.py | 154 +++++++++++++------- lib/galaxy/webapps/community/controllers/common.py | 90 ++++++++--- lib/galaxy/webapps/community/controllers/tool.py | 157 +++++++++++--------- lib/galaxy/webapps/community/controllers/upload.py | 33 ++-- lib/galaxy/webapps/community/model/__init__.py | 4 +- templates/dataset/display_application/display.mako | 4 +- templates/display_common.mako | 4 +- templates/grid_base.mako | 16 +- templates/grid_base_async.mako | 2 +- templates/message.mako | 12 +- templates/page/select_items_grid_async.mako | 2 +- templates/webapps/community/admin/center.mako | 39 ++++- templates/webapps/community/tool/edit_tool.mako | 19 +- templates/webapps/community/tool/view_tool.mako | 25 ++- 17 files changed, 354 insertions(+), 230 deletions(-) diffs (1213 lines): diff -r 68fc85a43bb8 -r c7607fba91b9 lib/galaxy/tools/__init__.py --- a/lib/galaxy/tools/__init__.py Tue May 04 14:19:44 2010 -0400 +++ b/lib/galaxy/tools/__init__.py Tue May 04 14:21:21 2010 -0400 @@ -837,7 +837,7 @@ assert isinstance( out_data, odict ) return 'tool_executed.mako', dict( out_data=out_data ) except: - return 'message.mako', dict( message_type='error', message='odict not returned from tool execution', refresh_frames=[] ) + return 'message.mako', dict( status='error', message='odict not returned from tool execution', refresh_frames=[] ) # Otherwise move on to the next page else: state.page += 1 @@ -890,7 +890,7 @@ self.sa_session.add( data ) self.sa_session.flush() # It's unlikely the user will ever see this. - return 'message.mako', dict( message_type='error', message='Your upload was interrupted. If this was uninentional, please retry it.', refresh_frames=[], cont=None ) + return 'message.mako', dict( status='error', message='Your upload was interrupted. If this was uninentional, please retry it.', refresh_frames=[], cont=None ) def update_state( self, trans, inputs, state, incoming, prefix="", context=None, update_only=False, old_errors={}, item_callback=None ): diff -r 68fc85a43bb8 -r c7607fba91b9 lib/galaxy/web/framework/__init__.py --- a/lib/galaxy/web/framework/__init__.py Tue May 04 14:19:44 2010 -0400 +++ b/lib/galaxy/web/framework/__init__.py Tue May 04 14:21:21 2010 -0400 @@ -591,7 +591,7 @@ `refresh_frames`: names of frames in the interface that should be refreshed when the message is displayed """ - return self.fill_template( "message.mako", message_type=type, message=message, refresh_frames=refresh_frames, cont=cont, use_panels=use_panels, active_view=active_view ) + return self.fill_template( "message.mako", status=type, message=message, refresh_frames=refresh_frames, cont=cont, use_panels=use_panels, active_view=active_view ) def show_error_message( self, message, refresh_frames=[], use_panels=False, active_view="" ): """ Convenience method for displaying an error message. See `show_message`. diff -r 68fc85a43bb8 -r c7607fba91b9 lib/galaxy/web/framework/helpers/grids.py --- a/lib/galaxy/web/framework/helpers/grids.py Tue May 04 14:19:44 2010 -0400 +++ b/lib/galaxy/web/framework/helpers/grids.py Tue May 04 14:21:21 2010 -0400 @@ -134,13 +134,16 @@ column_filter = unicode(column_filter) extra_url_args[ "f-" + column.key ] = column_filter.encode("utf-8") # Process sort arguments. - sort_key = sort_order = None + sort_key = None + sort_order = None if 'sort' in kwargs: sort_key = kwargs['sort'] elif base_sort_key: sort_key = base_sort_key encoded_sort_key = sort_key if sort_key: + # TODO: what if the model object of the grid column being sorted is not + # the same object as self.model_class? if sort_key.startswith( "-" ): sort_key = sort_key[1:] sort_order = 'desc' @@ -230,10 +233,10 @@ current_item=current_item, ids = kwargs.get( 'id', [] ), url = url, - message_type = status, + status = status, message = message, use_panels=use_panels, - webapp=self.webapp, + webapp=webapp, # Pass back kwargs so that grid template can set and use args without # grid explicitly having to pass them. kwargs=kwargs ) @@ -290,9 +293,7 @@ if self.format: value = self.format( value ) return value - def get_link( self, trans, grid, item, filter_params ): - # FIXME: filter_params is only here so we can do grid filtering from - # column links. remove once a better way is created. + def get_link( self, trans, grid, item ): if self.link and self.link( item ): return self.link( item ) return None @@ -449,7 +450,7 @@ class PublicURLColumn( TextColumn ): """ Column displays item's public URL based on username and slug. """ - def get_link( self, trans, grid, item, filter_params ): + def get_link( self, trans, grid, item ): if item.user.username and item.slug: return dict( action='display_by_username_and_slug', username=item.user.username, slug=item.slug ) elif not item.user.username: @@ -485,7 +486,7 @@ if item.published: sharing_statuses.append( "Published" ) return ", ".join( sharing_statuses ) - def get_link( self, trans, grid, item, filter_params ): + def get_link( self, trans, grid, item ): if not item.deleted and ( item.users_shared_with or item.importable or item.published ): return dict( operation="share or publish", id=item.id ) return None diff -r 68fc85a43bb8 -r c7607fba91b9 lib/galaxy/webapps/community/controllers/admin.py --- a/lib/galaxy/webapps/community/controllers/admin.py Tue May 04 14:19:44 2010 -0400 +++ b/lib/galaxy/webapps/community/controllers/admin.py Tue May 04 14:21:21 2010 -0400 @@ -47,7 +47,7 @@ return "" class ToolsColumn( grids.TextColumn ): def get_value( self, trans, grid, user ): - return '<a href="browse_tools_by_user?operation=browse&id=%s">%s</a>' % ( trans.security.encode_id( user.id ), str( len( user.tools ) ) ) + return '<a href="browse_tools_by_user?operation=browse&id=%s&webapp=community">%s</a>' % ( trans.security.encode_id( user.id ), str( len( user.tools ) ) ) # Grid definition webapp = "community" @@ -77,7 +77,10 @@ attach_popup=False, filterable="advanced" ), # Columns that are valid for filtering but are not visible. - grids.DeletedColumn( "Deleted", key="deleted", visible=False, filterable="advanced" ) + grids.DeletedColumn( "Deleted", + key="deleted", + visible=False, + filterable="advanced" ) ] columns.append( grids.MulticolFilterColumn( "Search", cols_to_filter=[ columns[0], columns[1] ], @@ -168,7 +171,10 @@ UsersColumn( "Users", attach_popup=False ), StatusColumn( "Status", attach_popup=False ), # Columns that are valid for filtering but are not visible. - grids.DeletedColumn( "Deleted", key="deleted", visible=False, filterable="advanced" ) + grids.DeletedColumn( "Deleted", + key="deleted", + visible=False, + filterable="advanced" ) ] columns.append( grids.MulticolFilterColumn( "Search", cols_to_filter=[ columns[0], columns[1], columns[2] ], @@ -238,16 +244,20 @@ default_sort_key = "name" columns = [ NameColumn( "Name", - key="name", + #key="name", link=( lambda item: dict( operation="Manage users and roles", id=item.id, webapp="community" ) ), model_class=model.Group, - attach_popup=True, - filterable="advanced" ), + attach_popup=True + #filterable="advanced" + ), UsersColumn( "Users", attach_popup=False ), RolesColumn( "Roles", attach_popup=False ), StatusColumn( "Status", attach_popup=False ), # Columns that are valid for filtering but are not visible. - grids.DeletedColumn( "Deleted", key="deleted", visible=False, filterable="advanced" ) + grids.DeletedColumn( "Deleted", + key="deleted", + visible=False, + filterable="advanced" ) ] columns.append( grids.MulticolFilterColumn( "Search", cols_to_filter=[ columns[0], columns[1], columns[2] ], @@ -309,14 +319,18 @@ attach_popup=False, filterable="advanced" ), DescriptionColumn( "Description", + key="description", model_class=model.Category, attach_popup=False, filterable="advanced" ), # Columns that are valid for filtering but are not visible. - grids.DeletedColumn( "Deleted", key="deleted", visible=False, filterable="advanced" ) + grids.DeletedColumn( "Deleted", + key="deleted", + visible=False, + filterable="advanced" ) ] columns.append( grids.MulticolFilterColumn( "Search", - cols_to_filter=[ columns[0], columns[1], columns[2] ], + cols_to_filter=[ columns[0], columns[1] ], key="free-text-search", visible=False, filterable="standard" ) ) @@ -370,24 +384,34 @@ default_sort_key = "name" columns = [ NameColumn( "Name", - key="name", + # TODO: we cannot currently sort by columns since the grid may be filtered by tool ids + # and it is not clear if / how that will work. We need to be able to send to the grid helper + # the list of ids on which to filter when sorting on the column. + #key="name", + model_class=model.Category, link=( lambda item: dict( operation="Browse Category", id=item.id, webapp="community" ) ), - model_class=model.Category, - attach_popup=True, - filterable="advanced" ), + attach_popup=False + #filterable="advanced" + ), DescriptionColumn( "Description", + #key="description", model_class=model.Category, - attach_popup=False, - filterable="advanced" ), + attach_popup=False + #filterable="advanced" + ), ToolsColumn( "Tools", - model_class=model.Category, + model_class=model.Tool, attach_popup=False, filterable="advanced" ), # Columns that are valid for filtering but are not visible. - grids.DeletedColumn( "Deleted", key="deleted", visible=False, filterable="advanced" ) + grids.DeletedColumn( "Deleted", + key="deleted", + visible=False, + filterable="advanced" ) ] columns.append( grids.MulticolFilterColumn( "Search", - cols_to_filter=[ columns[0], columns[1], columns[2] ], + #cols_to_filter=[ columns[0], columns[1] ], + cols_to_filter=[], key="free-text-search", visible=False, filterable="standard" ) ) @@ -399,10 +423,17 @@ num_rows_per_page = 50 preserve_state = False use_paging = True - def get_current_item( self, trans ): - return None def build_initial_query( self, session ): return session.query( self.model_class ) + def apply_default_filter( self, trans, query, **kwd ): + ids = kwd.get( 'ids', False ) + if ids: + if str( ids ).lower() == 'none': + # No tools for display + return query.filter( model.Tool.id == None ) + ids = util.listify( ids ) + query = query.filter( or_( *map( lambda id: self.model_class.id == id, ids ) ) ) + return query class ToolListGrid( grids.Grid ): class NameColumn( grids.TextColumn ): @@ -419,7 +450,7 @@ if tool.categories: rval = '' for tca in tool.categories: - rval += '<a href="browse_category?id=%s">%s</a><br/>\n' % ( trans.security.encode_id( tca.category.id ), tca.category.name ) + rval += '<a href="browse_category?id=%s&webapp=community">%s</a><br/>\n' % ( trans.security.encode_id( tca.category.id ), tca.category.name ) return rval return 'not set' class StateColumn( grids.GridColumn ): @@ -450,7 +481,7 @@ return accepted_filters class UserColumn( grids.TextColumn ): def get_value( self, trans, grid, tool ): - return '<a href="browse_tools_by_user?operation=browse&id=%s">%s</a>' % ( trans.security.encode_id( tool.user.id ), tool.user.username ) + return '<a href="browse_tools_by_user?operation=browse&id=%s&webapp=community">%s</a>' % ( trans.security.encode_id( tool.user.id ), tool.user.username ) # Grid definition title = "Tools" model_class = model.Tool @@ -458,19 +489,25 @@ default_sort_key = "name" columns = [ NameColumn( "Name", - key="name", + # TODO: we cannot currently sort by columns since the grid may be filtered by tool ids + # and it is not clear if / how that will work. We need to be able to send to the grid helper + # the list of ids on which to filter when sorting on the column. + #key="name", + link=( lambda item: dict( operation="View Tool", id=item.id, cntrller="admin", webapp="community" ) ), model_class=model.Tool, - link=( lambda item: dict( operation="View Tool", id=item.id, cntrller='admin', webapp="community" ) ), - attach_popup=True, - filterable="advanced" ), + attach_popup=True + #filterable="advanced" + ), VersionColumn( "Version", model_class=model.Tool, attach_popup=False, filterable="advanced" ), DescriptionColumn( "Description", - model_class=model.Tool, - attach_popup=False, - filterable="advanced" ), + #key="description", + model_class=model.Tool, + attach_popup=False + #filterable="advanced" + ), CategoryColumn( "Category", model_class=model.Category, attach_popup=False, @@ -479,15 +516,19 @@ model_class=model.Event, attach_popup=False ), UserColumn( "Uploaded By", - key="username", model_class=model.User, attach_popup=False, filterable="advanced" ), # Columns that are valid for filtering but are not visible. - grids.DeletedColumn( "Deleted", model_class=model.Tool, key="deleted", visible=False, filterable="advanced" ) + grids.DeletedColumn( "Deleted", + model_class=model.Tool, + key="deleted", + visible=False, + filterable="advanced" ) ] columns.append( grids.MulticolFilterColumn( "Search", - cols_to_filter=[ columns[0], columns[1] ], + #cols_to_filter=[ columns[0], columns[2], columns[5] ], + cols_to_filter=[], key="free-text-search", visible=False, filterable="standard" ) ) @@ -499,7 +540,7 @@ ] standard_filters = [ grids.GridColumnFilter( "Deleted", args=dict( deleted=True ) ), - grids.GridColumnFilter( "All", args=dict( deleted='All' ) ) + grids.GridColumnFilter( "All", args=dict( deleted='All' ) ), ] default_filter = dict( name="All", deleted="False" ) num_rows_per_page = 50 @@ -508,15 +549,14 @@ def build_initial_query( self, session ): return session.query( self.model_class ) def apply_default_filter( self, trans, query, **kwd ): - tool_id = kwd.get( 'tool_id', False ) - if tool_id: - if str( tool_id ).lower() in [ '', 'none' ]: - # Return an empty query since the current user cannot view any - # tools (possibly due to state not being approved, etc). + ids = kwd.get( 'ids', False ) + if ids: + if str( ids ).lower() == 'none': + # No tools for display return query.filter( model.Tool.id == None ) - tool_id = util.listify( tool_id ) - query = query.filter( or_( *map( lambda id: self.model_class.id == id, tool_id ) ) ) - return query.filter( self.model_class.deleted==False ) + ids = util.listify( ids ) + query = query.filter( or_( *map( lambda id: self.model_class.id == id, ids ) ) ) + return query class AdminController( BaseController, Admin ): @@ -616,12 +656,12 @@ status='error' ) ) event = get_event( trans, id ) state = event.state - tool_id = get_tools_by_state( trans, state ) - if not tool_id: - tool_id = 'None' + ids = get_tools_by_state( trans, state ) + if not ids: + ids = 'none' return trans.response.send_redirect( web.url_for( controller='admin', action='browse_tools', - tool_id=tool_id ) ) + ids=ids ) ) @web.expose @web.require_admin def browse_category( self, trans, **kwd ): @@ -681,7 +721,10 @@ # If we're approving a tool, all previous versions must be set to archived for version in get_versions( trans, tool ): if version != tool and version.is_approved(): - self.set_tool_state( trans, trans.app.model.Tool.states.ARCHIVED, id=trans.app.security.encode_id( version.id ), redirect='False' ) + self.set_tool_state( trans, + trans.app.model.Tool.states.ARCHIVED, + id=trans.security.encode_id( version.id ), + redirect='False' ) event = trans.model.Event( state ) # Flush so we an get an id trans.sa_session.add( event ) @@ -842,33 +885,34 @@ ## ---- Utility methods ------------------------------------------------------- def get_tools_by_state( trans, state ): - tool_id = [] + # TODO: write this as a query using eagerload - will be much faster. + ids = [] if state == trans.model.Tool.states.NEW: for tool in get_tools( trans ): if tool.is_new(): - tool_id.append( tool.id ) + ids.append( tool.id ) elif state == trans.model.Tool.states.ERROR: for tool in get_tools( trans ): if tool.is_error(): - tool_id.append( tool.id ) + ids.append( tool.id ) elif state == trans.model.Tool.states.DELETED: for tool in get_tools( trans ): if tool.is_deleted(): - tool_id.append( tool.id ) + ids.append( tool.id ) elif state == trans.model.Tool.states.WAITING: for tool in get_tools( trans ): if tool.is_waiting(): - tool_id.append( tool.id ) + ids.append( tool.id ) elif state == trans.model.Tool.states.APPROVED: for tool in get_tools( trans ): if tool.is_approved(): - tool_id.append( tool.id ) + ids.append( tool.id ) elif state == trans.model.Tool.states.REJECTED: for tool in get_tools( trans ): if tool.is_rejected(): - tool_id.append( tool.id ) + ids.append( tool.id ) elif state == trans.model.Tool.states.ARCHIVED: for tool in get_tools( trans ): if tool.is_archived(): - tool_id.append( tool.id ) - return tool_id + ids.append( tool.id ) + return ids diff -r 68fc85a43bb8 -r c7607fba91b9 lib/galaxy/webapps/community/controllers/common.py --- a/lib/galaxy/webapps/community/controllers/common.py Tue May 04 14:19:44 2010 -0400 +++ b/lib/galaxy/webapps/community/controllers/common.py Tue May 04 14:21:21 2010 -0400 @@ -91,6 +91,35 @@ message=message, status=status ) @web.expose + def delete_tool( self, trans, cntrller, **kwd ): + params = util.Params( kwd ) + message = util.restore_text( params.get( 'message', '' ) ) + status = params.get( 'status', 'done' ) + id = params.get( 'id', None ) + if not id: + message='Select a tool to delete' + status='error' + else: + tool = get_tool( trans, id ) + # Create a new event + event = trans.model.Event( state=trans.model.Tool.states.DELETED ) + # Flush so we can get an event id + trans.sa_session.add( event ) + trans.sa_session.flush() + # Associate the tool with the event + tea = trans.model.ToolEventAssociation( tool=tool, event=event ) + # Delete the tool, keeping state for categories, events and versions + tool.deleted = True + trans.sa_session.add_all( ( tool, tea ) ) + trans.sa_session.flush() + # TODO: What if the tool has versions, should they all be deleted? + message = "Tool '%s' has been marked deleted" + status = 'done' + return trans.response.send_redirect( web.url_for( controller=cntrller, + action='browse_tools', + message=message, + status=status ) ) + @web.expose def upload_new_tool_version( self, trans, cntrller, **kwd ): params = util.Params( kwd ) message = util.restore_text( params.get( 'message', '' ) ) @@ -122,15 +151,15 @@ # If request came from the tool controller, then we need to filter by the state of the # tool in addition to the category. if cntrller == 'tool': - tool_id = get_approved_tools( trans, category=category ) + ids = get_approved_tools( trans, category=category ) else: # If request came from the admin controller, we don't filter on tool state. - tool_id = [ tca.tool.id for tca in category.tools ] - if not tool_id: - tool_id = 'None' + ids = [ tca.tool.id for tca in category.tools ] + if not ids: + ids = 'none' return trans.response.send_redirect( web.url_for( controller=cntrller, action='browse_tools', - tool_id=tool_id ) ) + ids=ids ) ) @web.expose def browse_tools_by_user( self, trans, cntrller, **kwd ): params = util.Params( kwd ) @@ -146,15 +175,21 @@ # If request came from the tool controller, then we need to filter by the state of the # tool if the user is not viewing his own tools if cntrller == 'tool': - tool_id = get_approved_tools( trans, user=user ) + ids = get_tools_uploaded_by( trans, user ) else: - # If request came from the admin controller, we don't filter on tool state. - tool_id = [ tool.id for tool in user.tools ] - if not tool_id: - tool_id = 'None' + # If request came from the admin controller we don't filter on tool state. + ids = [ tool.id for tool in user.tools ] + if not ids: + ids = 'none' + if cntrller == 'tool' and user != trans.user: + # If the user is browsing someone else's tools, then we do not want to + # use the BrowseToolsByUser list grid since it includes a status column. + return trans.response.send_redirect( web.url_for( controller=cntrller, + action='browse_tools', + ids=ids ) ) return trans.response.send_redirect( web.url_for( controller=cntrller, action='browse_tools_by_user', - tool_id=tool_id ) ) + ids=ids ) ) ## ---- Utility methods ------------------------------------------------------- @@ -202,30 +237,33 @@ return trans.sa_session.query( trans.model.Tool ).get( trans.app.security.decode_id( id ) ) def get_tools( trans ): return trans.sa_session.query( trans.model.Tool ).order_by( trans.model.Tool.name ) -def get_approved_tools( trans, category=None, user=None ): - tool_id = [] +def get_approved_tools( trans, category=None ): + # TODO: write this as a query using eagerload - will be much faster. + ids = [] if category: # Return only the approved tools in the category for tca in category.tools: tool = tca.tool if tool.is_approved(): - tool_id.append( tool.id ) - elif user: - if trans.user == user: - # If the current user is browsing his own tools, then don't filter on state - tool_id = [ tool.id for tool in user.tools ] - else: - # The current user is viewing all tools uploaded by another user, so show only - # approved tools - for tool in user.active_tools: - if tool.is_approved(): - tool_id.append( tool.id ) + ids.append( tool.id ) else: # Return all approved tools for tool in get_tools( trans ): if tool.is_approved(): - tool_id.append( tool.id ) - return tool_id + ids.append( tool.id ) + return ids +def get_tools_uploaded_by( trans, user ): + # TODO: write this as a query using eagerload - will be much faster. + ids = [] + if trans.user == user: + # If the current user is browsing his own tools, then don't filter on state + ids = [ tool.id for tool in user.tools ] + else: + # The current user is viewing tools uploaded by another user, so show only approved tools + for tool in user.active_tools: + if tool.is_approved(): + ids.append( tool.id ) + return ids def get_event( trans, id ): return trans.sa_session.query( trans.model.Event ).get( trans.security.decode_id( id ) ) def get_user( trans, id ): diff -r 68fc85a43bb8 -r c7607fba91b9 lib/galaxy/webapps/community/controllers/tool.py --- a/lib/galaxy/webapps/community/controllers/tool.py Tue May 04 14:19:44 2010 -0400 +++ b/lib/galaxy/webapps/community/controllers/tool.py Tue May 04 14:21:21 2010 -0400 @@ -26,12 +26,12 @@ if tool.categories: rval = '' for tca in tool.categories: - rval += '<a href="browse_category?id=%s">%s</a><br/>\n' % ( trans.security.encode_id( tca.category.id ), tca.category.name ) + rval += '<a href="browse_category?id=%s&webapp=community">%s</a><br/>\n' % ( trans.security.encode_id( tca.category.id ), tca.category.name ) return rval return 'not set' class UserColumn( grids.TextColumn ): def get_value( self, trans, grid, tool ): - return '<a href="browse_tools_by_user?operation=browse&id=%s">%s</a>' % ( trans.security.encode_id( tool.user.id ), tool.user.username ) + return '<a href="browse_tools_by_user?operation=browse&id=%s&webapp=community">%s</a>' % ( trans.security.encode_id( tool.user.id ), tool.user.username ) # Grid definition title = "Tools" model_class = model.Tool @@ -39,33 +39,44 @@ default_sort_key = "name" columns = [ NameColumn( "Name", - key="name", + # TODO: we cannot currently sort by columns since the grid may be filtered by tool ids + # and it is not clear if / how that will work. We need to be able to send to the grid helper + # the list of ids on which to filter when sorting on the column. + #key="name", model_class=model.Tool, link=( lambda item: dict( operation="View Tool", id=item.id, cntrller='tool', webapp="community" ) ), - attach_popup=True, - filterable="advanced" ), + attach_popup=True + #filterable="advanced" + ), VersionColumn( "Version", model_class=model.Tool, attach_popup=False, filterable="advanced" ), DescriptionColumn( "Description", - model_class=model.Tool, - attach_popup=False, - filterable="advanced" ), + #key="description", + model_class=model.Tool, + attach_popup=False + #filterable="advanced" + ), CategoryColumn( "Categories", model_class=model.Category, attach_popup=False, filterable="advanced" ), UserColumn( "Uploaded By", - key="username", + #key="username", model_class=model.User, - attach_popup=False, - filterable="advanced" ), + attach_popup=False + #filterable="advanced" + ), # Columns that are valid for filtering but are not visible. - grids.DeletedColumn( "Deleted", key="deleted", visible=False, filterable="advanced" ) + grids.DeletedColumn( "Deleted", + key="deleted", + visible=False, + filterable="advanced" ) ] columns.append( grids.MulticolFilterColumn( "Search", - cols_to_filter=[ columns[0], columns[1] ], + #cols_to_filter=[ columns[0], columns[2], columns[4] ], + cols_to_filter=[], key="free-text-search", visible=False, filterable="standard" ) ) @@ -86,21 +97,15 @@ def build_initial_query( self, session ): return session.query( self.model_class ) def apply_default_filter( self, trans, query, **kwd ): - def filter_query( query, tool_id ): - if str( tool_id ).lower() in [ '', 'none' ]: - # Return an empty query since the current user cannot view any - # tools (possibly due to state not being approved, etc). - return query.filter( model.Tool.id == None ) - tool_id = util.listify( tool_id ) - query = query.filter( or_( *map( lambda id: self.model_class.id == id, tool_id ) ) ) - return query.filter( self.model_class.deleted==False ) - tool_id = kwd.get( 'tool_id', False ) - if not tool_id: + ids = kwd.get( 'ids', False ) + if not ids: # Display only approved tools - tool_id = get_approved_tools( trans ) - if not tool_id: - tool_id = 'None' - return filter_query( query, tool_id ) + ids = get_approved_tools( trans ) + if not ids or str( ids ).lower() == 'none': + return query.filter( trans.model.Tool.id == None ) + ids = util.listify( ids ) + query = query.filter( or_( *map( lambda id: self.model_class.id == id, ids ) ) ) + return query class ToolsByUserListGrid( grids.Grid ): class NameColumn( grids.TextColumn ): @@ -117,7 +122,7 @@ if tool.categories: rval = '' for tca in tool.categories: - rval += '<a href="browse_category?id=%s">%s</a><br/>\n' % ( trans.security.encode_id( tca.category.id ), tca.category.name ) + rval += '<a href="browse_category?id=%s&webapp=community">%s</a><br/>\n' % ( trans.security.encode_id( tca.category.id ), tca.category.name ) return rval return 'not set' class StateColumn( grids.GridColumn ): @@ -148,7 +153,7 @@ return accepted_filters class UserColumn( grids.TextColumn ): def get_value( self, trans, grid, tool ): - return '<a href="browse_tools_by_user?operation=browse&id=%s">%s</a>' % ( trans.security.encode_id( tool.user.id ), tool.user.username ) + return '<a href="browse_tools_by_user?operation=browse&id=%s&webapp=community">%s</a>' % ( trans.security.encode_id( tool.user.id ), tool.user.username ) # Grid definition title = "Tools By User" model_class = model.Tool @@ -156,19 +161,24 @@ default_sort_key = "name" columns = [ NameColumn( "Name", - key="name", + # TODO: we cannot currently sort by columns since the grid may be filtered by tool ids + # and it is not clear if / how that will work. We need to be able to send to the grid helper + # the list of ids on which to filter when sorting on the column. + #key="name", model_class=model.Tool, link=( lambda item: dict( operation="View Tool", id=item.id, cntrller='tool', webapp="community" ) ), - attach_popup=True, - filterable="advanced" ), + attach_popup=True + #filterable="advanced" + ), VersionColumn( "Version", model_class=model.Tool, - attach_popup=False, - filterable="advanced" ), + attach_popup=False ), DescriptionColumn( "Description", - model_class=model.Tool, - attach_popup=False, - filterable="advanced" ), + #key="description", + model_class=model.Tool, + attach_popup=False + #filterable="advanced" + ), CategoryColumn( "Categories", model_class=model.Category, attach_popup=False, @@ -177,15 +187,20 @@ model_class=model.Event, attach_popup=False ), UserColumn( "Uploaded By", - key="username", + #key="username", model_class=model.User, - attach_popup=False, - filterable="advanced" ), + attach_popup=False + #filterable="advanced" + ), # Columns that are valid for filtering but are not visible. - grids.DeletedColumn( "Deleted", key="deleted", visible=False, filterable="advanced" ) + grids.DeletedColumn( "Deleted", + key="deleted", + visible=False, + filterable="advanced" ) ] columns.append( grids.MulticolFilterColumn( "Search", - cols_to_filter=[ columns[0], columns[1] ], + #cols_to_filter=[ columns[0], columns[2], columns[5] ], + cols_to_filter=[], key="free-text-search", visible=False, filterable="standard" ) ) @@ -199,30 +214,24 @@ grids.GridColumnFilter( "Deleted", args=dict( deleted=True ) ), grids.GridColumnFilter( "All", args=dict( deleted='All' ) ) ] - default_filter = dict( name="All", deleted="False", username="All" ) + default_filter = dict( name="All", deleted="False" ) num_rows_per_page = 50 preserve_state = False use_paging = True def build_initial_query( self, session ): return session.query( self.model_class ) def apply_default_filter( self, trans, query, **kwd ): - def filter_query( query, tool_id ): - if str( tool_id ).lower() in [ '', 'none' ]: - # Return an empty query since the current user cannot view any - # tools (possibly due to state not being approved, etc). - return query.filter( model.Tool.id == None ) - tool_id = util.listify( tool_id ) - query = query.filter( or_( *map( lambda id: self.model_class.id == id, tool_id ) ) ) - return query.filter( self.model_class.deleted==False ) - tool_id = kwd.get( 'tool_id', False ) - if not tool_id: + ids = kwd.get( 'ids', False ) + if not ids: # Display only approved tools - tool_id = get_approved_tools( trans ) - if not tool_id: - tool_id = 'None' - return filter_query( query, tool_id ) + ids = get_approved_tools( trans ) + if not ids or str( ids ).lower() == 'none': + return query.filter( trans.model.Tool.id == None ) + ids = util.listify( ids ) + query = query.filter( or_( *map( lambda id: self.model_class.id == id, ids ) ) ) + return query -class CategoryListGrid( grids.Grid ): +class ToolsByCategoryListGrid( grids.Grid ): class NameColumn( grids.TextColumn ): def get_value( self, trans, grid, category ): return category.name @@ -242,28 +251,36 @@ # Grid definition webapp = "community" - title = "Tool Categories" + title = "Tools by Category" model_class = model.Category template='/webapps/community/category/grid.mako' default_sort_key = "name" columns = [ NameColumn( "Name", - key="name", + # TODO: we cannot currently sort by columns since the grid may be filtered by tool ids + # and it is not clear if / how that will work. We need to be able to send to the grid helper + # the list of ids on which to filter when sorting on the column. + #key="name", model_class=model.Category, link=( lambda item: dict( operation="Browse Category", id=item.id, webapp="community" ) ), - attach_popup=False, - filterable="advanced" ), + attach_popup=False + #filterable="advanced" + ), DescriptionColumn( "Description", - key="description", - model_class=model.Category, - attach_popup=False, - filterable="advanced" ), + #key="description", + model_class=model.Category, + attach_popup=False + #filterable="advanced" + ), ToolsColumn( "Tools", model_class=model.Tool, attach_popup=False, filterable="advanced" ), # Columns that are valid for filtering but are not visible. - grids.DeletedColumn( "Deleted", key="deleted", visible=False, filterable="advanced" ) + grids.DeletedColumn( "Deleted", + key="deleted", + visible=False, + filterable="advanced" ) ] columns.append( grids.MulticolFilterColumn( "Search", cols_to_filter=[ columns[0], columns[1] ], @@ -280,14 +297,12 @@ use_paging = True def build_initial_query( self, session ): return session.query( self.model_class ) - def apply_default_filter( self, trans, query, **kwd ): - return query.filter( self.model_class.deleted==False ) class ToolController( BaseController ): tool_list_grid = ToolListGrid() tools_by_user_list_grid = ToolsByUserListGrid() - category_list_grid = CategoryListGrid() + tools_by_category_list_grid = ToolsByCategoryListGrid() @web.expose def index( self, trans, **kwd ): @@ -312,7 +327,7 @@ cntrller='tool', **kwd ) ) # Render the list view - return self.category_list_grid( trans, **kwd ) + return self.tools_by_category_list_grid( trans, **kwd ) @web.expose def browse_category( self, trans, **kwd ): return trans.response.send_redirect( web.url_for( controller='common', diff -r 68fc85a43bb8 -r c7607fba91b9 lib/galaxy/webapps/community/controllers/upload.py --- a/lib/galaxy/webapps/community/controllers/upload.py Tue May 04 14:19:44 2010 -0400 +++ b/lib/galaxy/webapps/community/controllers/upload.py Tue May 04 14:21:21 2010 -0400 @@ -60,28 +60,26 @@ obj = datatype.create_model_object( meta ) trans.sa_session.add( obj ) if isinstance( obj, trans.app.model.Tool ): - existing = trans.sa_session.query( trans.app.model.Tool ).filter_by( tool_id = meta.id ).all() + existing = trans.sa_session.query( trans.app.model.Tool ).filter_by( tool_id = meta.id ).first() if existing and replace_id is None: raise UploadError( 'A tool with the same ID already exists. If you are trying to update this tool to a new version, please use the upload form on the "Edit Tool" page. Otherwise, please choose a new ID.' ) elif existing: - replace_version = trans.sa_session.query( trans.app.model.Tool ).get( int( trans.app.security.decode_id( replace_id ) ) ) + replace_version = trans.sa_session.query( trans.app.model.Tool ).get( trans.security.decode_id( replace_id ) ) if replace_version.newer_version: # If the user has picked an old version, switch to the newest version replace_version = get_versions( trans, replace_version )[0] - if trans.user != replace_version.user: - raise UploadError( 'You are not the owner of this tool and may not upload new versions of it.' ) if replace_version.tool_id != meta.id: - raise UploadError( 'The new tool id (%s) does not match the old tool id (%s). Please check the tool XML file' % ( meta.id, replace_version.tool_id ) ) + raise UploadError( 'The new tool id (%s) does not match the old tool id (%s). Check the tool XML file' % ( meta.id, replace_version.tool_id ) ) for old_version in get_versions( trans, replace_version ): if old_version.version == meta.version: - raise UploadError( 'The new version (%s) matches an old version. Please check your version in the tool XML file' % meta.version ) + raise UploadError( 'The new version (%s) matches an old version. Check your version in the tool XML file' % meta.version ) if old_version.is_new(): - raise UploadError( 'There is an existing version of this tool which is unsubmitted. Please either <a href="%s">submit or delete it</a> before uploading a new version.' % url_for( controller='common', - action='view_tool', - cntrller='tool', - id=trans.app.security.encode_id( old_version.id ) ) ) + raise UploadError( 'There is an existing version of this tool which has not yet been submitted for approval, so either <a href="%s">submit or delete it</a> before uploading a new version.' % url_for( controller='common', + action='view_tool', + cntrller='tool', + id=trans.security.encode_id( old_version.id ) ) ) if old_version.is_waiting(): - raise UploadError( 'There is an existing version of this tool which is waiting for administrative approval. Please contact an administrator for help.' ) + raise UploadError( 'There is an existing version of this tool which is waiting for administrative approval, so contact an administrator for help.' ) # Defer setting the id since the newer version id doesn't exist until the new Tool object is flushed if category_ids: for category_id in category_ids: @@ -91,12 +89,15 @@ trans.sa_session.add( tca ) # Initialize the tool event event = trans.app.model.Event( state=trans.app.model.Tool.states.NEW ) + # Flush to get an event id + trans.sa_session.add( event ) + trans.sa_session.flush() tea = trans.app.model.ToolEventAssociation( obj, event ) - trans.sa_session.add_all( ( event, tea ) ) - trans.sa_session.flush() + trans.sa_session.add( tea ) if replace_version and replace_id: replace_version.newer_version_id = obj.id - trans.sa_session.flush() + trans.sa_session.add( replace_version ) + trans.sa_session.flush() try: os.link( uploaded_file.name, obj.file_name ) except OSError: @@ -117,10 +118,10 @@ old_version = None for old_version in get_versions( trans, replace_version ): if old_version.is_new(): - message = 'There is an existing version of this tool which is unsubmitted. Please either submit or delete it before uploading a new version.' + message = 'There is an existing version of this tool which has not been submitted for approval, so either submit or delete it before uploading a new version.' break if old_version.is_waiting(): - message = 'There is an existing version of this tool which is waiting for administrative approval. Please contact an administrator for help.' + message = 'There is an existing version of this tool which is waiting for administrative approval, so contact an administrator for help.' break else: old_version = None diff -r 68fc85a43bb8 -r c7607fba91b9 lib/galaxy/webapps/community/model/__init__.py --- a/lib/galaxy/webapps/community/model/__init__.py Tue May 04 14:19:44 2010 -0400 +++ b/lib/galaxy/webapps/community/model/__init__.py Tue May 04 14:21:21 2010 -0400 @@ -94,7 +94,8 @@ APPROVED = 'approved', REJECTED = 'rejected', ARCHIVED = 'archived' ) - def __init__( self, guid=None, tool_id=None, name=None, description=None, user_description=None, category=None, version=None, user_id=None, external_filename=None ): + def __init__( self, guid=None, tool_id=None, name=None, description=None, user_description=None, + category=None, version=None, user_id=None, external_filename=None ): self.guid = guid self.tool_id = tool_id self.name = name or "Unnamed tool" @@ -103,6 +104,7 @@ self.version = version or "1.0.0" self.user_id = user_id self.external_filename = external_filename + self.deleted = False self.__extension = None def get_file_name( self ): if not self.external_filename: diff -r 68fc85a43bb8 -r c7607fba91b9 templates/dataset/display_application/display.mako --- a/templates/dataset/display_application/display.mako Tue May 04 14:19:44 2010 -0400 +++ b/templates/dataset/display_application/display.mako Tue May 04 14:21:21 2010 -0400 @@ -1,8 +1,8 @@ <%inherit file="/base.mako"/> <%namespace file="/message.mako" import="render_msg" /> <%def name="title()">Display Application: ${display_link.link.display_application.name} ${display_link.link.name}</%def> -%for message, message_type in msg: - ${render_msg( message, message_type )} +%for message, status in msg: + ${render_msg( message, status )} %endfor %if refresh: <%def name="metas()"><meta http-equiv="refresh" content="10" /></%def> diff -r 68fc85a43bb8 -r c7607fba91b9 templates/display_common.mako --- a/templates/display_common.mako Tue May 04 14:19:44 2010 -0400 +++ b/templates/display_common.mako Tue May 04 14:21:21 2010 -0400 @@ -129,10 +129,10 @@ </%def> ## Render message. -<%def name="render_message( message, message_type )"> +<%def name="render_message( message, status )"> %if message: <p> - <div class="${message_type}message transient-message">${util.restore_text( message )}</div> + <div class="${status}message transient-message">${util.restore_text( message )}</div> <div style="clear: both"></div> </p> %endif diff -r 68fc85a43bb8 -r c7607fba91b9 templates/grid_base.mako --- a/templates/grid_base.mako Tue May 04 14:19:44 2010 -0400 +++ b/templates/grid_base.mako Tue May 04 14:21:21 2010 -0400 @@ -508,12 +508,10 @@ webapp = href_parms[index].split('=')[1]; } } - // Do operation. do_operation(webapp, operation, id); return false; } - } // Navigate window to the URL defined by url_args. This method should be used to short-circuit grid AJAXing. @@ -678,7 +676,7 @@ <tr> <td width="75%">${self.render_grid_header( grid )}</td> <td></td> - <td width="25%" id="grid-message" valign="top">${render_message( message, message_type )}</td> + <td width="25%" id="grid-message" valign="top">${render_message( message, status )}</td> </tr> </table> @@ -774,10 +772,6 @@ ## Render grid table body contents. <%def name="render_grid_table_body_contents(grid, show_item_checkboxes=False)"> - ## Include the webapp value in the form - <td style="width: 1.5em;"> - <input type="hidden" name="webapp" value="${webapp}" /> - </td> <% num_rows_rendered = 0 %> %if query.count() == 0: ## No results. @@ -801,12 +795,8 @@ %for column in grid.columns: %if column.visible: <% - # Get filter params for generating filter links - filter_params = {} - for k, v in cur_filter_dict.items(): - filter_params['f-' + k] = v # Link - link = column.get_link( trans, grid, item, filter_params ) + link = column.get_link( trans, grid, item ) if link: href = url( **link ) else: @@ -831,6 +821,7 @@ cls = "menubutton" if column.attach_popup and href: cls = "menubutton split" + %> %if href: <td><div id="${id}" class="${cls}" style="float: left;"><a class="label" href="${href}">${v}</a></div></td> @@ -915,3 +906,4 @@ </tr> %endif </%def> + diff -r 68fc85a43bb8 -r c7607fba91b9 templates/grid_base_async.mako --- a/templates/grid_base_async.mako Tue May 04 14:19:44 2010 -0400 +++ b/templates/grid_base_async.mako Tue May 04 14:21:21 2010 -0400 @@ -13,4 +13,4 @@ ***** ${num_pages} ***** -${render_message( message, message_type )} \ No newline at end of file +${render_message( message, status )} \ No newline at end of file diff -r 68fc85a43bb8 -r c7607fba91b9 templates/message.mako --- a/templates/message.mako Tue May 04 14:19:44 2010 -0400 +++ b/templates/message.mako Tue May 04 14:21:21 2010 -0400 @@ -66,21 +66,21 @@ ## <%def name="center_panel()"> - ${render_large_message( message, message_type )} + ${render_large_message( message, status )} </%def> <%def name="body()"> - ${render_large_message( message, message_type )} + ${render_large_message( message, status )} </%def> ## Render large message. -<%def name="render_large_message( message, message_type )"> - <div class="${message_type}messagelarge" style="margin: 1em">${_(message)}</div> +<%def name="render_large_message( message, status )"> + <div class="${status}messagelarge" style="margin: 1em">${_(message)}</div> </%def> ## Render a message -<%def name="render_msg( msg, messagetype='done' )"> - <div class="${messagetype}message">${_(msg)}</div> +<%def name="render_msg( msg, status='done' )"> + <div class="${status}message">${_(msg)}</div> <br/> </%def> diff -r 68fc85a43bb8 -r c7607fba91b9 templates/page/select_items_grid_async.mako --- a/templates/page/select_items_grid_async.mako Tue May 04 14:19:44 2010 -0400 +++ b/templates/page/select_items_grid_async.mako Tue May 04 14:21:21 2010 -0400 @@ -6,4 +6,4 @@ ***** ${num_pages} ***** -${render_message( message, message_type )} \ No newline at end of file +${render_message( message, status )} \ No newline at end of file diff -r 68fc85a43bb8 -r c7607fba91b9 templates/webapps/community/admin/center.mako --- a/templates/webapps/community/admin/center.mako Tue May 04 14:19:44 2010 -0400 +++ b/templates/webapps/community/admin/center.mako Tue May 04 14:21:21 2010 -0400 @@ -6,7 +6,36 @@ <p>The menu on the left provides the following features</p> <ul> - <li><strong>Security</strong> - see the <strong>Data Security and Data Libraries</strong> section below for details + <li> + <strong>Tools</strong> + <p/> + <ul> + <li> + <strong>Tools awaiting approval</strong> + </li> + <p/> + <li> + <strong>Browse by category</strong> + </li> + <p/> + <li> + <strong>Browse all tools</strong> + </li> + <p/> + </ul> + </li> + <li> + <strong>Categories</strong> + <p/> + <ul> + <li> + <strong>Manage categories</strong> + </li> + <p/> + </ul> + </li> + <li> + <strong>Security</strong> <p/> <ul> <li> @@ -29,13 +58,5 @@ </ul> </li> <p/> - <li><strong>Tools</strong> - <p/> - <ul> - <li> - <strong>Manage tools</strong> - coming soon... - </li> - </ul> - </li> </ul> <br/> diff -r 68fc85a43bb8 -r c7607fba91b9 templates/webapps/community/tool/edit_tool.mako --- a/templates/webapps/community/tool/edit_tool.mako Tue May 04 14:19:44 2010 -0400 +++ b/templates/webapps/community/tool/edit_tool.mako Tue May 04 14:21:21 2010 -0400 @@ -51,16 +51,21 @@ ${render_msg( message, status )} %endif -%if cntrller == 'admin' or ( tool.is_new() and trans.user == tool.user ): +%if cntrller == 'admin' or trans.user == tool.user: <form id="edit_tool" name="edit_tool" action="${h.url_for( controller='common', action='edit_tool' )}" method="post"> <div class="toolForm"> <div class="toolFormTitle">${tool.name} - <a id="tool-${tool.id}-popup" class="popup-arrow" style="display: none;">▼</a> - <div popupmenu="tool-${tool.id}-popup"> - <a class="action-button" href="${h.url_for( controller='common', action='view_tool', id=trans.app.security.encode_id( tool.id ), cntrller=cntrller )}">View information</a> - <a class="action-button" href="${h.url_for( controller='common', action='upload_new_tool_version', id=trans.app.security.encode_id( tool.id ), cntrller=cntrller )}">Upload a new version</a> - <a class="action-button" href="${h.url_for( controller='tool', action='download_tool', id=trans.app.security.encode_id( tool.id ) )}">Download tool</a> - </div> + %if not tool.deleted: + <a id="tool-${tool.id}-popup" class="popup-arrow" style="display: none;">▼</a> + <div popupmenu="tool-${tool.id}-popup"> + <a class="action-button" href="${h.url_for( controller='common', action='view_tool', id=trans.app.security.encode_id( tool.id ), cntrller=cntrller )}">View information</a> + <a class="action-button" href="${h.url_for( controller='tool', action='download_tool', id=trans.app.security.encode_id( tool.id ) )}">Download tool</a> + <a class="action-button" href="${h.url_for( controller='common', action='delete_tool', id=trans.app.security.encode_id( tool.id ), cntrller=cntrller )}">Delete tool</a> + %if not tool.is_new() and not tool.is_waiting(): + <a class="action-button" href="${h.url_for( controller='common', action='upload_new_tool_version', id=trans.app.security.encode_id( tool.id ), cntrller=cntrller )}">Upload a new version</a> + %endif + </div> + %endif </div> <div class="toolFormBody"> <input type="hidden" name="id" value="${trans.app.security.encode_id( tool.id )}"/> diff -r 68fc85a43bb8 -r c7607fba91b9 templates/webapps/community/tool/view_tool.mako --- a/templates/webapps/community/tool/view_tool.mako Tue May 04 14:19:44 2010 -0400 +++ b/templates/webapps/community/tool/view_tool.mako Tue May 04 14:21:21 2010 -0400 @@ -85,16 +85,21 @@ <div class="toolForm"> <div class="toolFormTitle">${tool.name} - <a id="tool-${tool.id}-popup" class="popup-arrow" style="display: none;">▼</a> - <div popupmenu="tool-${tool.id}-popup"> - %if cntrller=='admin' or can_edit: - <a class="action-button" href="${h.url_for( controller='common', action='edit_tool', id=trans.app.security.encode_id( tool.id ), cntrller=cntrller )}">Edit information</a> - %endif - %if cntrller=='admin' or can_upload_new_version: - <a class="action-button" href="${h.url_for( controller='common', action='upload_new_tool_version', id=trans.app.security.encode_id( tool.id ), cntrller=cntrller )}">Upload a new version</a> - %endif - <a class="action-button" href="${h.url_for( controller='tool', action='download_tool', id=trans.app.security.encode_id( tool.id ) )}">Download tool</a> - </div> + %if not tool.deleted: + <a id="tool-${tool.id}-popup" class="popup-arrow" style="display: none;">▼</a> + <div popupmenu="tool-${tool.id}-popup"> + %if cntrller=='admin' or can_edit: + <a class="action-button" href="${h.url_for( controller='common', action='edit_tool', id=trans.app.security.encode_id( tool.id ), cntrller=cntrller )}">Edit information</a> + %endif + <a class="action-button" href="${h.url_for( controller='tool', action='download_tool', id=trans.app.security.encode_id( tool.id ) )}">Download tool</a> + %if cntrller=='admin' or trans.user==tool.user: + <a class="action-button" href="${h.url_for( controller='common', action='delete_tool', id=trans.app.security.encode_id( tool.id ), cntrller=cntrller )}">Delete tool</a> + %endif + %if cntrller=='admin' or can_upload_new_version: + <a class="action-button" href="${h.url_for( controller='common', action='upload_new_tool_version', id=trans.app.security.encode_id( tool.id ), cntrller=cntrller )}">Upload a new version</a> + %endif + </div> + %endif </div> <div class="toolFormBody"> <div class="form-row">

1 0

[hg] galaxy 3740: Secure=True by default for workflows.
by Nate Coraor 10 May '10

10 May '10

details: http://www.bx.psu.edu/hg/galaxy/rev/68fc85a43bb8 changeset: 3740:68fc85a43bb8 user: Dannon Baker <dannon.baker(a)emory.edu> date: Tue May 04 14:19:44 2010 -0400 description: Secure=True by default for workflows. diffstat: lib/galaxy/workflow/modules.py | 6 +++--- 1 files changed, 3 insertions(+), 3 deletions(-) diffs (26 lines): diff -r 9057a05dc7d3 -r 68fc85a43bb8 lib/galaxy/workflow/modules.py --- a/lib/galaxy/workflow/modules.py Tue May 04 13:45:57 2010 -0400 +++ b/lib/galaxy/workflow/modules.py Tue May 04 14:19:44 2010 -0400 @@ -96,7 +96,7 @@ module.state = dict( name="Input Dataset" ) return module @classmethod - def from_dict( Class, trans, d, secure=False ): + def from_dict( Class, trans, d, secure=True ): module = Class( trans ) state = from_json_string( d["tool_state"] ) module.state = dict( name=state.get( "name", "Input Dataset" ) ) @@ -172,11 +172,11 @@ module.state = module.tool.new_state( trans, all_pages=True ) return module @classmethod - def from_dict( Class, trans, d, secure=False ): + def from_dict( Class, trans, d, secure=True ): tool_id = d['tool_id'] module = Class( trans, tool_id ) module.state = DefaultToolState() - module.state.decode( d["tool_state"], module.tool, module.trans.app, secure=False ) + module.state.decode( d["tool_state"], module.tool, module.trans.app, secure=secure ) module.errors = d.get( "tool_errors", None ) return module

1 0

[hg] galaxy 3739: Update types for cuffcompare output files.
by Nate Coraor 10 May '10

10 May '10

details: http://www.bx.psu.edu/hg/galaxy/rev/9057a05dc7d3 changeset: 3739:9057a05dc7d3 user: jeremy goecks <jeremy.goecks(a)emory.edu> date: Tue May 04 13:45:57 2010 -0400 description: Update types for cuffcompare output files. diffstat: tools/ngs_rna/cuffcompare_wrapper.xml | 12 ++++++------ 1 files changed, 6 insertions(+), 6 deletions(-) diffs (31 lines): diff -r a3f32c37d423 -r 9057a05dc7d3 tools/ngs_rna/cuffcompare_wrapper.xml --- a/tools/ngs_rna/cuffcompare_wrapper.xml Tue May 04 12:50:48 2010 -0400 +++ b/tools/ngs_rna/cuffcompare_wrapper.xml Tue May 04 13:45:57 2010 -0400 @@ -50,21 +50,21 @@ </inputs> <outputs> - <data format="tmap" name="input1_tmap" label="${tool.name} on ${on_string}: data ${input1.hid} tmap file"/> - <data format="refmap" name="input1_refmap" label="${tool.name} on ${on_string}: data ${input1.hid} refmap file"/> - <data format="tmap" name="input2_tmap" label="${tool.name} on ${on_string}: data ${second_gtf.input2.hid} tmap file"> + <data format="tabular" name="input1_tmap" label="${tool.name} on ${on_string}: data ${input1.hid} tmap file"/> + <data format="tabular" name="input1_refmap" label="${tool.name} on ${on_string}: data ${input1.hid} refmap file"/> + <data format="tabular" name="input2_tmap" label="${tool.name} on ${on_string}: data ${second_gtf.input2.hid} tmap file"> <filter>second_gtf['use_second_gtf'] == "Yes"</filter> </data> - <data format="refmap" name="input2_refmap" label="${tool.name} on ${on_string}: data ${second_gtf.input2.hid} refmap file"> + <data format="tabular" name="input2_refmap" label="${tool.name} on ${on_string}: data ${second_gtf.input2.hid} refmap file"> <filter>second_gtf['use_second_gtf'] == "Yes"</filter> </data> <data format="gtf" name="transcripts_combined" label="${tool.name} on ${on_string}: combined transcripts"> <filter>second_gtf['use_second_gtf'] == "Yes"</filter> </data> - <data format="tracking" name="transcripts_tracking" label="${tool.name} on ${on_string}: transcript tracking"> + <data format="tabular" name="transcripts_tracking" label="${tool.name} on ${on_string}: transcript tracking"> <filter>second_gtf['use_second_gtf'] == "Yes"</filter> </data> - <data format="gtf" name="transcripts_accuracy" label="${tool.name} on ${on_string}: transcript accuracy"/> + <data format="txt" name="transcripts_accuracy" label="${tool.name} on ${on_string}: transcript accuracy"/> </outputs> <tests>

1 0

[hg] galaxy 3738: trackster: add filled line display
by Nate Coraor 10 May '10

10 May '10

details: http://www.bx.psu.edu/hg/galaxy/rev/a3f32c37d423 changeset: 3738:a3f32c37d423 user: Kanwei Li <kanwei(a)gmail.com> date: Tue May 04 12:50:48 2010 -0400 description: trackster: add filled line display diffstat: static/scripts/trackster.js | 48 ++++++++++++++++++++++++++++++--------------- 1 files changed, 32 insertions(+), 16 deletions(-) diffs (128 lines): diff -r 3b81af3f51ab -r a3f32c37d423 static/scripts/trackster.js --- a/static/scripts/trackster.js Tue May 04 10:18:42 2010 -0400 +++ b/static/scripts/trackster.js Tue May 04 12:50:48 2010 -0400 @@ -352,7 +352,6 @@ TiledTrack.call( this ); this.height_px = 100; - this.container_div.addClass( "line-track" ); this.dataset_id = dataset_id; this.data_cache = new Cache(CACHED_DATA); this.tile_cache = new Cache(CACHED_TILES_LINE); @@ -369,6 +368,8 @@ track.vertical_range = undefined; this.init_each({ stats: true, chrom: track.view.chrom, low: null, high: null, dataset_id: track.dataset_id }, function(result) { + + track.container_div.addClass( "line-track" ); data = result.data; if ( isNaN(parseFloat(track.prefs.min_value)) || isNaN(parseFloat(track.prefs.max_value)) ) { track.prefs.min_value = data.min; @@ -387,10 +388,10 @@ var min_label = $("<div></div>").addClass('yaxislabel').attr("id", 'linetrack_' + track_id + '_minval').text(track.prefs.min_value); var max_label = $("<div></div>").addClass('yaxislabel').attr("id", 'linetrack_' + track_id + '_maxval').text(track.prefs.max_value); - max_label.css({ position: "relative", top: "25px" }); + max_label.css({ position: "relative", top: "25px", left: "10px" }); max_label.prependTo(track.container_div); - min_label.css({ position: "relative", top: track.height_px + 55 + "px" }); + min_label.css({ position: "relative", top: track.height_px + 55 + "px", left: "10px" }); min_label.prependTo(track.container_div); }); }, @@ -455,7 +456,8 @@ max_value = this.prefs.max_value, vertical_range = this.vertical_range, total_frequency = this.total_frequency, - height_px = this.height_px; + height_px = this.height_px, + mode = this.prefs.mode; ctx.beginPath(); @@ -466,16 +468,17 @@ var delta_x_px = 10; } + var x_scaled, y; + for ( var i = 0; i < data.length; i++ ) { - var x = data[i][0] - tile_low; - var y = data[i][1]; + x_scaled = (data[i][0] - tile_low) * w_scale; + y = data[i][1]; - if ( this.prefs.mode == "Intensity" ) { + if ( mode == "Intensity" ) { // DRAW INTENSITY if (y === null) { continue; } - x = x * w_scale; if (y <= min_value) { y = min_value; } else if (y >= max_value) { @@ -483,16 +486,17 @@ } y = 255 - Math.floor( (y - min_value) / vertical_range * 255 ); ctx.fillStyle = "rgb(" +y+ "," +y+ "," +y+ ")"; - ctx.fillRect(x, 0, delta_x_px, this.height_px); + ctx.fillRect(x_scaled, 0, delta_x_px, this.height_px); } else { // Missing data causes us to stop drawing if (y === null) { + if (in_path && mode === "Filled") { + ctx.lineTo(x_scaled, height_px); + } in_path = false; continue; } else { - // Translate - x = x * w_scale; // console.log(y, this.min_value, this.vertical_range, (y - this.min_value) / this.vertical_range * this.height_px); if (y <= min_value) { y = min_value; @@ -501,16 +505,28 @@ } y = Math.round( height_px - (y - min_value) / vertical_range * height_px ); // console.log(canvas.get(0).height, canvas.get(0).width); - if ( in_path ) { - ctx.lineTo( x, y ); + if (in_path) { + ctx.lineTo(x_scaled, y); } else { - ctx.moveTo( x, y ); in_path = true; + if (mode === "Filled") { + ctx.moveTo(x_scaled, height_px); + ctx.lineTo(x_scaled, y); + } else { + ctx.moveTo(x_scaled, y); + } } } } } - ctx.stroke(); + if (mode === "Filled") { + if (in_path) { + ctx.lineTo(x_scaled, height_px); + } + ctx.fill(); + } else { + ctx.stroke(); + } parent_element.append( canvas ); return canvas; }, gen_options: function(track_id) { @@ -527,7 +543,7 @@ max_input = $('<input></input>').attr("id", maxval).val(max_val), mode_label = $('<label></label>').attr("for", mode).text("Display mode:"), mode_val = (this.prefs.mode === undefined ? "Line" : this.prefs.mode), - mode_input = $('<select id="' +mode+ '"><option value="Line" id="mode_Line">Line</option><option value="Intensity" id="mode_Intensity">Intensity</option></select>'); + mode_input = $('<select id="' +mode+ '"><option value="Line" id="mode_Line">Line</option><option value="Filled" id="mode_Filled">Filled</option><option value="Intensity" id="mode_Intensity">Intensity</option></select>'); mode_input.children("#mode_"+mode_val).attr('selected', 'selected');

1 0

[hg] galaxy 3736: Very basic support for exporting and importing...
by Nate Coraor 10 May '10

10 May '10

details: http://www.bx.psu.edu/hg/galaxy/rev/eec050533545 changeset: 3736:eec050533545 user: James Taylor <james(a)jamestaylor.org> date: Mon May 03 17:35:54 2010 -0400 description: Very basic support for exporting and importing workflows among instances diffstat: lib/galaxy/tools/__init__.py | 24 +++-- lib/galaxy/web/__init__.py | 2 +- lib/galaxy/web/controllers/workflow.py | 153 ++++++++++++++++++++++++++++++++- lib/galaxy/web/framework/__init__.py | 9 + lib/galaxy/workflow/modules.py | 14 +- templates/form.mako | 6 +- 6 files changed, 187 insertions(+), 21 deletions(-) diffs (327 lines): diff -r c75c0f9b0bf7 -r eec050533545 lib/galaxy/tools/__init__.py --- a/lib/galaxy/tools/__init__.py Mon May 03 16:32:35 2010 -0400 +++ b/lib/galaxy/tools/__init__.py Mon May 03 17:35:54 2010 -0400 @@ -203,7 +203,7 @@ def __init__( self ): self.page = 0 self.inputs = None - def encode( self, tool, app ): + def encode( self, tool, app, secure=True ): """ Convert the data to a string """ @@ -213,18 +213,22 @@ value["__page__"] = self.page value = simplejson.dumps( value ) # Make it secure - a = hmac_new( app.config.tool_secret, value ) - b = binascii.hexlify( value ) - return "%s:%s" % ( a, b ) - def decode( self, value, tool, app ): + if secure: + a = hmac_new( app.config.tool_secret, value ) + b = binascii.hexlify( value ) + return "%s:%s" % ( a, b ) + else: + return value + def decode( self, value, tool, app, secure=True ): """ Restore the state from a string """ - # Extract and verify hash - a, b = value.split( ":" ) - value = binascii.unhexlify( b ) - test = hmac_new( app.config.tool_secret, value ) - assert a == test + if secure: + # Extract and verify hash + a, b = value.split( ":" ) + value = binascii.unhexlify( b ) + test = hmac_new( app.config.tool_secret, value ) + assert a == test # Restore from string values = json_fix( simplejson.loads( value ) ) self.page = values.pop( "__page__" ) diff -r c75c0f9b0bf7 -r eec050533545 lib/galaxy/web/__init__.py --- a/lib/galaxy/web/__init__.py Mon May 03 16:32:35 2010 -0400 +++ b/lib/galaxy/web/__init__.py Mon May 03 17:35:54 2010 -0400 @@ -2,6 +2,6 @@ The Galaxy web application. """ -from framework import expose, json, require_login, require_admin, url_for, error, form, FormBuilder +from framework import expose, json, json_pretty, require_login, require_admin, url_for, error, form, FormBuilder from framework.base import httpexceptions diff -r c75c0f9b0bf7 -r eec050533545 lib/galaxy/web/controllers/workflow.py --- a/lib/galaxy/web/controllers/workflow.py Mon May 03 16:32:35 2010 -0400 +++ b/lib/galaxy/web/controllers/workflow.py Mon May 03 17:35:54 2010 -0400 @@ -18,6 +18,8 @@ from galaxy.model.mapping import desc from galaxy.model.orm import * +import urllib2 + class StoredWorkflowListGrid( grids.Grid ): class StepsColumn( grids.GridColumn ): def get_value(self, trans, grid, workflow): @@ -621,7 +623,6 @@ step_dict['position'] = step.position # Add to return value data['steps'][step.order_index] = step_dict - print data['upgrade_messages'] return data @web.json @@ -660,7 +661,6 @@ workflow.has_errors = True # Stick this in the step temporarily step.temp_input_connections = step_dict['input_connections'] - # Save step annotation. annotation = step_dict[ 'annotation' ] if annotation: @@ -698,6 +698,155 @@ rval['name'] = workflow.name return rval + @web.json_pretty + def export_workflow( self, trans, id ): + """ + Get the latest Workflow for the StoredWorkflow identified by `id` and + encode it as a json string that can be imported back into Galaxy + + This has slightly different information than the above. In particular, + it does not attempt to decode forms and build UIs, it just stores + the raw state. + """ + user = trans.get_user() + id = trans.security.decode_id( id ) + trans.workflow_building_mode = True + # Load encoded workflow from database + stored = trans.sa_session.query( model.StoredWorkflow ).get( id ) + self.security_check( trans.get_user(), stored, False, True ) + workflow = stored.latest_workflow + # Pack workflow data into a dictionary and return + data = {} + data['name'] = workflow.name + data['steps'] = {} + # For each step, rebuild the form and encode the state + for step in workflow.steps: + # Load from database representation + module = module_factory.from_workflow_step( trans, step ) + # Get user annotation. + step_annotation = self.get_item_annotation_obj( trans, trans.user, step ) + annotation_str = "" + if step_annotation: + annotation_str = step_annotation.annotation + # Pack attributes into plain dictionary + step_dict = { + 'id': step.order_index, + 'type': module.type, + 'tool_id': module.get_tool_id(), + 'name': module.get_name(), + 'tool_state': module.get_state( secure=False ), + 'tool_errors': module.get_errors(), + ## 'data_inputs': module.get_data_inputs(), + ## 'data_outputs': module.get_data_outputs(), + 'annotation' : annotation_str + } + # Connections + input_connections = step.input_connections + if step.type is None or step.type == 'tool': + # Determine full (prefixed) names of valid input datasets + data_input_names = {} + def callback( input, value, prefixed_name, prefixed_label ): + if isinstance( input, DataToolParameter ): + data_input_names[ prefixed_name ] = True + visit_input_values( module.tool.inputs, module.state.inputs, callback ) + # Filter + # FIXME: this removes connection without displaying a message currently! + input_connections = [ conn for conn in input_connections if conn.input_name in data_input_names ] + # Encode input connections as dictionary + input_conn_dict = {} + for conn in input_connections: + input_conn_dict[ conn.input_name ] = \ + dict( id=conn.output_step.order_index, output_name=conn.output_name ) + step_dict['input_connections'] = input_conn_dict + # Position + step_dict['position'] = step.position + # Add to return value + data['steps'][step.order_index] = step_dict + return data + + @web.expose + def import_workflow( self, trans, workflow_text=None, url=None ): + if workflow_text is None and url is None: + return form( url_for(), "Import Workflow", submit_text="Import" ) \ + .add_text( "url", "URL to load workflow from", "" ) \ + .add_input( "textarea", "Encoded workflow (as generated by export workflow)", "workflow_text", "" ) + if url: + # Load workflow from external URL + # NOTE: blocks the web thread. + try: + workflow_data = urllib2.urlopen( url ).read() + except Exception, e: + return trans.show_error_message( "Failed to open URL %s<br><br>Message: %s" % ( url, str( e ) ) ) + else: + workflow_data = workflow_text + # Convert incoming workflow data from json + try: + data = simplejson.loads( workflow_data ) + except Exception, e: + return trans.show_error_message( "Data at '%s' does not appear to be a Galaxy workflow<br><br>Message: %s" % ( url, str( e ) ) ) + # Put parameters in workflow mode + trans.workflow_building_mode = True + # Create new workflow from incoming data + workflow = model.Workflow() + # Just keep the last name (user can rename later) + workflow.name = data['name'] + # Assume no errors until we find a step that has some + workflow.has_errors = False + # Create each step + steps = [] + # The editor will provide ids for each step that we don't need to save, + # but do need to use to make connections + steps_by_external_id = {} + # First pass to build step objects and populate basic values + for key, step_dict in data['steps'].iteritems(): + # Create the model class for the step + step = model.WorkflowStep() + steps.append( step ) + steps_by_external_id[ step_dict['id' ] ] = step + # FIXME: Position should be handled inside module + step.position = step_dict['position'] + module = module_factory.from_dict( trans, step_dict, secure=False ) + module.save_to_step( step ) + if step.tool_errors: + workflow.has_errors = True + # Stick this in the step temporarily + step.temp_input_connections = step_dict['input_connections'] + # Save step annotation. + annotation = step_dict[ 'annotation' ] + if annotation: + annotation = sanitize_html( annotation, 'utf-8', 'text/html' ) + self.add_item_annotation( trans, step, annotation ) + # Second pass to deal with connections between steps + for step in steps: + # Input connections + for input_name, conn_dict in step.temp_input_connections.iteritems(): + if conn_dict: + conn = model.WorkflowStepConnection() + conn.input_step = step + conn.input_name = input_name + conn.output_name = conn_dict['output_name'] + conn.output_step = steps_by_external_id[ conn_dict['id'] ] + del step.temp_input_connections + # Order the steps if possible + attach_ordered_steps( workflow, steps ) + # Connect up + stored = model.StoredWorkflow() + stored.name = workflow.name + workflow.stored_workflow = stored + stored.latest_workflow = workflow + stored.user = trans.user + # Persist + trans.sa_session.add( stored ) + trans.sa_session.flush() + # Return something informative + errors = [] + if workflow.has_errors: + return trans.show_warn_message( "Imported, but some steps in this workflow have validation errors" ) + if workflow.has_cycles: + return trans.show_warn_message( "Imported, but this workflow contains cycles" ) + else: + return trans.show_message( "Workflow '%s' imported" % workflow.name ) + @web.json def get_datatypes( self, trans ): ext_to_class_name = dict() diff -r c75c0f9b0bf7 -r eec050533545 lib/galaxy/web/framework/__init__.py --- a/lib/galaxy/web/framework/__init__.py Mon May 03 16:32:35 2010 -0400 +++ b/lib/galaxy/web/framework/__init__.py Mon May 03 17:35:54 2010 -0400 @@ -66,6 +66,15 @@ decorator.exposed = True return decorator +def json_pretty( func ): + def decorator( self, trans, *args, **kwargs ): + trans.response.set_content_type( "text/javascript" ) + return simplejson.dumps( func( self, trans, *args, **kwargs ), indent=4, sort_keys=True ) + if not hasattr(func, '_orig'): + decorator._orig = func + decorator.exposed = True + return decorator + def require_login( verb="perform this action", use_panels=False, webapp='galaxy' ): def argcatcher( func ): def decorator( self, trans, *args, **kwargs ): diff -r c75c0f9b0bf7 -r eec050533545 lib/galaxy/workflow/modules.py --- a/lib/galaxy/workflow/modules.py Mon May 03 16:32:35 2010 -0400 +++ b/lib/galaxy/workflow/modules.py Mon May 03 17:35:54 2010 -0400 @@ -96,7 +96,7 @@ module.state = dict( name="Input Dataset" ) return module @classmethod - def from_dict( Class, trans, d ): + def from_dict( Class, trans, d, secure=False ): module = Class( trans ) state = from_json_string( d["tool_state"] ) module.state = dict( name=state.get( "name", "Input Dataset" ) ) @@ -172,11 +172,11 @@ module.state = module.tool.new_state( trans, all_pages=True ) return module @classmethod - def from_dict( Class, trans, d ): + def from_dict( Class, trans, d, secure=False ): tool_id = d['tool_id'] module = Class( trans, tool_id ) module.state = DefaultToolState() - module.state.decode( d["tool_state"], module.tool, module.trans.app ) + module.state.decode( d["tool_state"], module.tool, module.trans.app, secure=False ) module.errors = d.get( "tool_errors", None ) return module @@ -199,8 +199,8 @@ return self.tool.name def get_tool_id( self ): return self.tool_id - def get_state( self ): - return self.state.encode( self.tool, self.trans.app ) + def get_state( self, secure=True ): + return self.state.encode( self.tool, self.trans.app, secure=secure ) def get_errors( self ): return self.errors def get_tooltip( self ): @@ -278,13 +278,13 @@ """ assert type in self.module_types return self.module_types[type].new( trans, tool_id ) - def from_dict( self, trans, d ): + def from_dict( self, trans, d, **kwargs ): """ Return module initialized from the data in dictionary `d`. """ type = d['type'] assert type in self.module_types - return self.module_types[type].from_dict( trans, d ) + return self.module_types[type].from_dict( trans, d, **kwargs ) def from_workflow_step( self, trans, step ): """ Return module initializd from the WorkflowStep object `step`. diff -r c75c0f9b0bf7 -r eec050533545 templates/form.mako --- a/templates/form.mako Mon May 03 16:32:35 2010 -0400 +++ b/templates/form.mako Mon May 03 17:35:54 2010 -0400 @@ -60,7 +60,11 @@ </label> %endif <div class="form-row-input"> - <input type="${input.type}" name="${input.name}" value="${input.value}" size="40"> + %if input.type == 'textarea': + <textarea name="${input.name}" cols="40">${input.value}</textarea> + %else: + <input type="${input.type}" name="${input.name}" value="${input.value}" size="40"> + %endif </div> %if input.error: <div class="form-row-error-message">${input.error}</div>

1 0

[hg] galaxy 3737: Add a tip to the upload tool about using url p...
by Nate Coraor 10 May '10

10 May '10

details: http://www.bx.psu.edu/hg/galaxy/rev/3b81af3f51ab changeset: 3737:3b81af3f51ab user: Nate Coraor <nate(a)bx.psu.edu> date: Tue May 04 10:18:42 2010 -0400 description: Add a tip to the upload tool about using url paste for big files diffstat: tools/data_source/upload.xml | 2 +- 1 files changed, 1 insertions(+), 1 deletions(-) diffs (12 lines): diff -r eec050533545 -r 3b81af3f51ab tools/data_source/upload.xml --- a/tools/data_source/upload.xml Mon May 03 17:35:54 2010 -0400 +++ b/tools/data_source/upload.xml Tue May 04 10:18:42 2010 -0400 @@ -25,7 +25,7 @@ </param> <param name="async_datasets" type="hidden" value="None"/> <upload_dataset name="files" title="Specify Files for Dataset" file_type_name="file_type" metadata_ref="files_metadata"> - <param name="file_data" type="file" size="30" label="File" ajax-upload="true"> + <param name="file_data" type="file" size="30" label="File" ajax-upload="true" help="TIP: For NGS and other large files (>~2GB), uploading via HTTP/FTP URL (below) is the most reliable method."> <validator type="expression" message="You will need to reselect the file you specified (%s)." substitute_value_in_message="True">not ( ( isinstance( value, unicode ) or isinstance( value, str ) ) and value != "" )</validator>  </param> <param name="url_paste" type="text" area="true" size="5x35" label="URL/Text" help="Here you may specify a list of URLs (one per line) or paste the contents of a file."/>

1 0

[hg] galaxy 3734: Community: add help for tool-related operations
by Nate Coraor 10 May '10

10 May '10

details: http://www.bx.psu.edu/hg/galaxy/rev/5ebac527fa31 changeset: 3734:5ebac527fa31 user: Nate Coraor <nate(a)bx.psu.edu> date: Mon May 03 15:33:34 2010 -0400 description: Community: add help for tool-related operations diffstat: lib/galaxy/webapps/community/controllers/tool.py | 6 + lib/galaxy/webapps/community/security/__init__.py | 2 +- templates/webapps/community/base_panels.mako | 1 + templates/webapps/community/tool/help.mako | 125 ++++++++++++++++++++++ templates/webapps/community/tool/view_tool.mako | 8 +- templates/webapps/community/upload/upload.mako | 8 +- 6 files changed, 139 insertions(+), 11 deletions(-) diffs (205 lines): diff -r 8bdbd5fc8721 -r 5ebac527fa31 lib/galaxy/webapps/community/controllers/tool.py --- a/lib/galaxy/webapps/community/controllers/tool.py Mon May 03 14:03:01 2010 -0400 +++ b/lib/galaxy/webapps/community/controllers/tool.py Mon May 03 15:33:34 2010 -0400 @@ -402,3 +402,9 @@ tool_file = tarfile.open( tool.file_name ).extractfile( tool_file_name ) trans.response.set_content_type( 'text/plain' ) return tool_file + @web.expose + def help( self, trans, **kwd ): + params = util.Params( kwd ) + message = util.restore_text( params.get( 'message', '' ) ) + status = params.get( 'status', 'done' ) + return trans.fill_template( '/webapps/community/tool/help.mako', message=message, status=status, **kwd ) diff -r 8bdbd5fc8721 -r 5ebac527fa31 lib/galaxy/webapps/community/security/__init__.py --- a/lib/galaxy/webapps/community/security/__init__.py Mon May 03 14:03:01 2010 -0400 +++ b/lib/galaxy/webapps/community/security/__init__.py Mon May 03 15:33:34 2010 -0400 @@ -170,7 +170,7 @@ def can_upload_new_version( self, user, item, versions ): state_ok = True for version in versions: - if version.is_new() or version.is_approved(): + if version.is_new() or version.is_waiting(): state_ok = False return user and user==item.user and state_ok diff -r 8bdbd5fc8721 -r 5ebac527fa31 templates/webapps/community/base_panels.mako --- a/templates/webapps/community/base_panels.mako Mon May 03 14:03:01 2010 -0400 +++ b/templates/webapps/community/base_panels.mako Mon May 03 15:33:34 2010 -0400 @@ -33,6 +33,7 @@ <a>Help</a> <div class="submenu"> <ul> + <li><a target="galaxy_main" href="${h.url_for( controller='tool', action='help' )}">How to upload, download and install tools</a></li> <li><a href="${app.config.get( "bugs_email", "mailto:galaxy-bugs@bx.psu.edu" )}">Email comments, bug reports, or suggestions</a></li> <li><a target="_blank" href="${app.config.get( "wiki_url", "http://bitbucket.org/galaxy/galaxy-central/wiki" )}">Galaxy Wiki</a></li> <li><a target="_blank" href="${app.config.get( "screencasts_url", "http://galaxycast.org" )}">Video tutorials (screencasts)</a></li> diff -r 8bdbd5fc8721 -r 5ebac527fa31 templates/webapps/community/tool/help.mako --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/templates/webapps/community/tool/help.mako Mon May 03 15:33:34 2010 -0400 @@ -0,0 +1,125 @@ +<%namespace file="/message.mako" import="render_msg" /> + +<%! + def inherit(context): + if context.get('use_panels'): + return '/webapps/community/base_panels.mako' + else: + return '/base.mako' +%> +<%inherit file="${inherit(context)}"/> + +<%def name="title()">Tool Help</%def> + +<h2>Tool Help</h2> + +%if message: + ${render_msg( message, status )} +%endif + +<h3>Uploading Tools</h3> + +<p><strong>Tool File Format</strong></p> +<p> + + A tool file is a tar-format (bzipped or gzipped tar are valid) archive + containing all the files necessary to load the tool in Galaxy. At the very + least, it must contain a + <a href="http://bitbucket.org/galaxy/galaxy-central/wiki/ToolConfigSyntax" target="_blank">Tool XML File</a>, + and will probably also include a tool script. If any steps are necessary + to install your tool beyond the basic instructions below, please include a + README file which details these steps. If the tool (or parts of it) are + written in C, the source code can be included (or put links to the source + in the README). Please do not include precompiled binaries without source, + since Galaxy is run on a wide variety of platforms. Also, if you are only + wrapping or providing a Galaxy config for a tool that is not your own, + please be sure the license allows for redistribution before including any + part of that tool in the tar archive! +</p> +<p> + There are no requirements about the directory structure inside the tar + archive, but for ease of use, it's generally a good idea to put everything + inside of a subdirectory, instead of directly at the top level. +</p> + +<p><strong>Tool File Example</strong></p> +<p> + To package up the LASTZ tool's config file, Galaxy wrapper, and the C source: + <pre> + user@host:~% tar jcvf ~/Desktop/galaxy_lastz_tool.tar.bz2 lastz + lastz/ + lastz/README + lastz/lastz_wrapper.py + lastz/lastz_wrapper.xml + lastz/lastz-distrib-1.02.00/ + lastz/lastz-distrib-1.02.00/src/ + lastz/lastz-distrib-1.02.00/src/Makefile + lastz/lastz-distrib-1.02.00/src/version.mak + lastz/lastz-distrib-1.02.00/src/lastz.c + lastz/lastz-distrib-1.02.00/src/lastz.h + ... + </pre> + <code>~/Desktop/galaxy_lastz_tool.tar.bz2</code> is now ready to be uploaded. +</p> + +<p><strong>Editing Information, Categories, and Submitting For Approval</strong></p> + +<p> + Simply uploading a tool to the Community will not allow other users to find + and download your tool. It will need to be approved by an administrator + before it appears in the tool list. +</p> +<p> + After the tool has successfully uploaded, you will be redirected to the + Edit Tool page. Please provide a detailed description of what the tool + does - this will be used by administrators to understand the tool before + approving it for display on the site. Once approved, this information will + be displayed to users who view your tool. In addition, the site + administrators will have configured a number of categories with which you + can associate your tool to make it easily findable by users looking to + solve specific problems. Please associate as many categories as are + relevant to your tool. You may change the description and associated + categories as often as you'd like until you click the "<strong>Submit for + approval</strong>" button. Once submitted, the tool will be approved or + rejected by an administrator. Once approved, it will be visible to + everyone. At that point, the description and associated categories can + only be changed by an administrator. +</p> +<p> + Once the tool has been approved or rejected, you may upload a new version + by browsing to the tool's "View Tool" page, clicking the context menu to + the right of the tool's name, and selecting "Upload a new version." +</p> + +<hr/> + +<h3>Downloading and Installing Tools</h3> + +<p> + A tool's download link will send you the tool tar archive. Once + downloaded, unpack the tool on your local Galaxy instance's server: + <pre> + user@host:~% tar xvf galaxy_tool.tar + ... + user@host:~% tar zxvf galaxy_tool.tar.gz + ... + user@host:~% tar jxvf galaxy_tool.tar.bz2 + ... + </pre> + If the tar archive includes a README file, consult it for installation + instructions. If not, follow these basic steps: + <ol> + <li>Create a directory under <code>galaxy_dist/tools/</code> to house downloaded tool(s).</li> + <li>In the new directory, place the XML and any script file(s) which were contained in the tar archive.</li> + <li>If the tool includes binaries, you'll need to copy them to a directory on your <code>$PATH</code>. If the tool depends on C binaries but does not come with them (only source), you'll need to compile the source first.</li> + <li>Add the tool to <code>galaxy_dist/tool_conf.xml</code>.</li> + <li>Restart the Galaxy server process.</li> + </ol> +</p> + +<p> + We plan to implement a more direct method to install tools via the Galaxy + administrator user interface instead of placing files on the filesystem and + managing the <code>tool_conf.xml</code> file by hand. In the meantime, + this is the process. +</p> diff -r 8bdbd5fc8721 -r 5ebac527fa31 templates/webapps/community/tool/view_tool.mako --- a/templates/webapps/community/tool/view_tool.mako Mon May 03 14:03:01 2010 -0400 +++ b/templates/webapps/community/tool/view_tool.mako Mon May 03 15:33:34 2010 -0400 @@ -125,9 +125,11 @@ <div class="form-row"> <label>Categories:</label> %if categories: - %for category in categories: - ${category.name} - %endfor + <ul> + %for category in categories: + <li>${category.name}</li> + %endfor + </ul> %else: none set %endif diff -r 8bdbd5fc8721 -r 5ebac527fa31 templates/webapps/community/upload/upload.mako --- a/templates/webapps/community/upload/upload.mako Mon May 03 14:03:01 2010 -0400 +++ b/templates/webapps/community/upload/upload.mako Mon May 03 15:33:34 2010 -0400 @@ -39,7 +39,7 @@ </select> </div> <div class="toolParamHelp" style="clear: both;"> - Need help creating a tool file? See help below. + Need help creating a tool file? See the <a href="${h.url_for( controller='tool', action='help' )}">Tool Help</a> page. </div> <div style="clear: both"></div> </div> @@ -77,9 +77,3 @@ </form> </div> </div> -<div class="toolHelp"> - <div class="toolHelpBody"> - <p><strong>Creating tool files</strong></p> - <p>Help coming...</p> - </div> -</div>

1 0