- galaxy-dev - lists.galaxyproject.org

[hg] galaxy 2401: Fixes for deleting library items on the admin ...
by Nate Coraor 05 May '09

05 May '09

details: http://www.bx.psu.edu/hg/galaxy/rev/2e2b80fcbd47 changeset: 2401:2e2b80fcbd47 user: Greg Von Kuster <greg(a)bx.psu.edu> date: Tue May 05 13:48:01 2009 -0400 description: Fixes for deleting library items on the admin side. - Purged library items will not be displayed - Deleted library items can only be viewed or undeleted - Differentiate between displaying deleted libraries and displaying deleted items within an undeleted library 8 file(s) affected in this change: lib/galaxy/web/controllers/admin.py lib/galaxy/web/controllers/library.py templates/admin/dataset_security/group_create.mako templates/admin/library/browse_libraries.mako templates/admin/library/browse_library.mako templates/admin/library/common.mako templates/admin/library/ldda_info.mako templates/library/ldda_info.mako diffs (551 lines): diff -r 8da91a231cdf -r 2e2b80fcbd47 lib/galaxy/web/controllers/admin.py --- a/lib/galaxy/web/controllers/admin.py Tue May 05 13:03:23 2009 -0400 +++ b/lib/galaxy/web/controllers/admin.py Tue May 05 13:48:01 2009 -0400 @@ -678,6 +678,7 @@ libraries=trans.app.model.Library.filter( trans.app.model.Library.table.c.deleted==False ) \ .order_by( trans.app.model.Library.name ).all(), deleted=False, + show_deleted=False, msg=msg, messagetype=messagetype ) @web.expose @@ -687,6 +688,8 @@ msg = util.restore_text( params.get( 'msg', '' ) ) messagetype = params.get( 'messagetype', 'done' ) id = params.get( 'id', None ) + deleted = util.string_as_bool( params.get( 'deleted', False ) ) + show_deleted = util.string_as_bool( params.get( 'show_deleted', False ) ) if not id: msg = "You must specify a library id." return trans.response.send_redirect( web.url_for( controller='admin', @@ -701,9 +704,9 @@ msg=util.sanitize_text( msg ), messagetype='error' ) ) created_ldda_ids = params.get( 'created_ldda_ids', '' ) - show_deleted = util.string_as_bool( params.get( 'show_deleted', False ) ) return trans.fill_template( '/admin/library/browse_library.mako', library=trans.app.model.Library.get( id ), + deleted=deleted, created_ldda_ids=created_ldda_ids, msg=msg, messagetype=messagetype, @@ -842,7 +845,7 @@ deleted=True, msg=msg, messagetype=messagetype, - show_deleted = True ) + show_deleted=True ) @web.expose @web.require_admin def undelete_library( self, trans, **kwd ): @@ -1088,7 +1091,9 @@ def library_dataset_dataset_association( self, trans, library_id, folder_id, id=None, **kwd ): params = util.Params( kwd ) msg = util.restore_text( params.get( 'msg', '' ) ) - messagetype = params.get( 'messagetype', 'done' ) + messagetype = params.get( 'messagetype', 'done' ) + deleted = util.string_as_bool( params.get( 'deleted', False ) ) + show_deleted = util.string_as_bool( params.get( 'show_deleted', False ) ) dbkey = params.get( 'dbkey', None ) if isinstance( dbkey, list ): last_used_build = dbkey[0] @@ -1250,6 +1255,8 @@ return trans.fill_template( '/admin/library/ldda_info.mako', ldda=ldda, library_id=library_id, + deleted=deleted, + show_deleted=show_deleted, msg=msg, messagetype=messagetype ) elif action == 'edit_info': @@ -1322,8 +1329,6 @@ msg=msg, messagetype=messagetype ) elif params.get( 'delete', False ): - # TODO: need to revamp the way we remove datasets from disk. - # The user selected the "Remove this dataset from the library" pop-up menu option ldda.deleted = True ldda.flush() msg = 'Dataset %s has been removed from this library' % ldda.name @@ -1955,69 +1960,56 @@ id=library_id, msg=util.sanitize_text( msg ), messagetype=messagetype ) ) - @web.expose @web.require_admin - def delete_library_item( self, trans, library_id = None, library_item_id = None, library_item_type = None ): - #this action will handle deleting all types of library items in library browsing mode - library_item_types = { 'library': trans.app.model.Library, 'folder': trans.app.model.LibraryFolder, 'dataset': trans.app.model.LibraryDataset, } + def delete_library_item( self, trans, library_id, library_item_id, library_item_type ): + # This action will handle deleting all types of library items. State is saved for libraries and + # folders ( i.e., if undeleted, the state of contents of the library or folder will remain, so previously + # deleted / purged contents will have the same state ). When a library or folder has been deleted for + # the amount of time defined in the cleanup_datasets.py script, the library or folder and all of its + # contents will be purged. The association between this method and the cleanup_datasets.py script + # enables clean maintenance of libraries and library dataset disk files. This is also why the following + # 3 objects, and not any of the associations ( the cleanup_datasets.py scipot handles everything else ). + library_item_types = { 'library': trans.app.model.Library, + 'folder': trans.app.model.LibraryFolder, + 'library_dataset': trans.app.model.LibraryDataset } if library_item_type not in library_item_types: - raise ValueError( 'Bad library_item_type specified: %s' % library_item_types ) - if library_item_id is None: - raise ValueError( 'library_item_id not specified' ) - library_item = library_item_types[ library_item_type ].get( int( library_item_id ) ) - library_item.deleted = True - library_item.flush() - #need to str because unicode isn't accepted... - msg = str( "%s '%s' has been marked deleted" % ( library_item_type, library_item.name ) ) - messagetype = str( "done" ) - if library_item_type == 'library' or library_id is None: - return self.browse_libraries( trans, msg = msg, messagetype = messagetype ) + msg = 'Bad library_item_type specified: %s' % str( library_item_type ) + messagetype = 'error' else: - return self.browse_library( trans, id = library_id , msg = msg, messagetype = messagetype ) - + library_item = library_item_types[ library_item_type ].get( int( library_item_id ) ) + library_item.deleted = True + library_item.flush() + msg = util.sanitize_text( "%s '%s' has been marked deleted" % ( library_item_type, library_item.name ) ) + messagetype = 'done' + if library_item_type == 'library': + return self.browse_libraries( trans, msg=msg, messagetype=messagetype ) + else: + return self.browse_library( trans, id=library_id , msg=msg, messagetype=messagetype ) @web.expose @web.require_admin - def undelete_library_item( self, trans, library_id = None, library_item_id = None, library_item_type = None ): - #this action will handle deleting all types of library items in library browsing mode - library_item_types = { 'library': trans.app.model.Library, 'folder': trans.app.model.LibraryFolder, 'dataset': trans.app.model.LibraryDataset, } + def undelete_library_item( self, trans, library_id, library_item_id, library_item_type ): + # This action will handle undeleting all types of library items + library_item_types = { 'library': trans.app.model.Library, + 'folder': trans.app.model.LibraryFolder, + 'library_dataset': trans.app.model.LibraryDataset } if library_item_type not in library_item_types: - raise ValueError( 'Bad library_item_type specified: %s' % library_item_types ) - if library_item_id is None: - raise ValueError( 'library_item_id not specified' ) - library_item = library_item_types[ library_item_type ].get( int( library_item_id ) ) - if library_item.purged: - raise ValueError( '%s %s cannot be undeleted' % ( library_item_type, library_item.name ) ) - library_item.deleted = False - library_item.flush() - msg = str( "%s '%s' has been undeleted" % ( library_item_type, library_item.name ) ) - messagetype = str( "done" ) - if library_item_type == 'library' or library_id is None: - return self.browse_libraries( trans, msg = msg, messagetype = messagetype ) + msg = 'Bad library_item_type specified: %s' % str( library_item_type ) + messagetype = 'error' else: - return self.browse_library( trans, id = library_id , msg = msg, messagetype = messagetype ) - - - - #(a)web.expose - #(a)web.require_admin - #def delete_dataset( self, trans, id=None, **kwd): - # if id: - # # id is a LibraryDatasetDatasetAssociation.id - # ldda = trans.app.model.LibraryDatasetDatasetAssociation.get( id ) - # ldda.deleted = True - # ldda.flush() - # msg = "Dataset %s was deleted from library folder %s" % ( ldda.name, ldda.folder.name ) - # trans.response.send_redirect( web.url_for( action='folder', - # id=str( ldda.folder.id ), - # msg=util.sanitize_text( msg ), - # messagetype='done' ) ) - # msg = "You did not specify a dataset to delete." - # return trans.response.send_redirect( web.url_for( action='folder', - # id=str( ldda.folder.id ), - # msg=util.sanitize_text( msg ), - # messagetype='error' ) ) - + library_item = library_item_types[ library_item_type ].get( int( library_item_id ) ) + if library_item.purged: + msg = '%s %s has been purged, so it cannot be undeleted' % ( library_item_type, library_item.name ) + messagetype = 'error' + else: + library_item.deleted = False + library_item.flush() + msg = util.sanitize_text( "%s '%s' has been marked undeleted" % ( library_item_type, library_item.name ) ) + messagetype = 'done' + if library_item_type == 'library': + return self.browse_libraries( trans, msg=msg, messagetype=messagetype ) + else: + return self.browse_library( trans, id=library_id , msg=msg, messagetype=messagetype ) @web.expose @web.require_admin def memdump( self, trans, ids = 'None', sorts = 'None', pages = 'None', new_id = None, new_sort = None, **kwd ): diff -r 8da91a231cdf -r 2e2b80fcbd47 lib/galaxy/web/controllers/library.py --- a/lib/galaxy/web/controllers/library.py Tue May 05 13:03:23 2009 -0400 +++ b/lib/galaxy/web/controllers/library.py Tue May 05 13:48:01 2009 -0400 @@ -587,8 +587,6 @@ msg=msg, messagetype=messagetype ) elif params.get( 'delete', False ): - # TODO: need to revamp the way we remove datasets from disk. - # The user selected the "Remove this dataset from the library" pop-up menu option if trans.app.security_agent.allow_action( trans.user, trans.app.security_agent.permitted_actions.LIBRARY_MODIFY, library_item=folder ): diff -r 8da91a231cdf -r 2e2b80fcbd47 templates/admin/dataset_security/group_create.mako --- a/templates/admin/dataset_security/group_create.mako Tue May 05 13:03:23 2009 -0400 +++ b/templates/admin/dataset_security/group_create.mako Tue May 05 13:48:01 2009 -0400 @@ -57,24 +57,24 @@ </div> <div class="form-row"> <div style="float: left; margin-right: 10px;"> - <label>Groups associated with new role</label> + <label>Roles associated with new group</label> ${render_select( "in_roles", in_roles )}<br/> <input type="submit" id="roles_remove_button" value=">>"/> </div> <div> - <label>Groups not associated with new role</label> + <label>Roles not associated with new group</label> ${render_select( "out_roles", out_roles )}<br/> <input type="submit" id="roles_add_button" value="<<"/> </div> </div> <div class="form-row"> <div style="float: left; margin-right: 10px;"> - <label>Users associated with new role</label> + <label>Users associated with new group</label> ${render_select( "in_users", in_users )}<br/> <input type="submit" id="users_remove_button" value=">>"/> </div> <div> - <label>Users not associated with new role</label> + <label>Users not associated with new group</label> ${render_select( "out_users", out_users )}<br/> <input type="submit" id="users_add_button" value="<<"/> </div> diff -r 8da91a231cdf -r 2e2b80fcbd47 templates/admin/library/browse_libraries.mako --- a/templates/admin/library/browse_libraries.mako Tue May 05 13:03:23 2009 -0400 +++ b/templates/admin/library/browse_libraries.mako Tue May 05 13:48:01 2009 -0400 @@ -42,7 +42,7 @@ <tbody> %for library in libraries: <tr class="libraryRow libraryOrFolderRow" id="libraryRow"> - <td><a href="${h.url_for( controller='admin', action='browse_library', id=library.id )}">${library.name}</a></td> + <td><a href="${h.url_for( controller='admin', action='browse_library', id=library.id, deleted=deleted, show_deleted=show_deleted )}">${library.name}</a></td> <td><i>${library.description}</i></td> </tr> %endfor diff -r 8da91a231cdf -r 2e2b80fcbd47 templates/admin/library/browse_library.mako --- a/templates/admin/library/browse_library.mako Tue May 05 13:03:23 2009 -0400 +++ b/templates/admin/library/browse_library.mako Tue May 05 13:48:01 2009 -0400 @@ -72,20 +72,20 @@ } </script> -<%def name="render_folder( parent, parent_pad, deleted, created_ldda_ids, library_id )"> +<%def name="render_folder( folder, folder_pad, deleted, show_deleted, created_ldda_ids, library_id )"> <% - root_folder = not parent.parent + root_folder = not folder.parent if root_folder: - pad = parent_pad + pad = folder_pad else: - pad = parent_pad + 20 - if parent_pad == 0: + pad = folder_pad + 20 + if folder_pad == 0: expander = "/static/images/silk/resultset_bottom.png" - folder = "/static/images/silk/folder_page.png" + folder_img = "/static/images/silk/folder_page.png" subfolder = False else: expander = "/static/images/silk/resultset_next.png" - folder = "/static/images/silk/folder.png" + folder_img = "/static/images/silk/folder.png" subfolder = True created_ldda_id_list = util.listify( created_ldda_ids ) if created_ldda_id_list: @@ -93,35 +93,37 @@ %> %if not root_folder: <li class="folderRow libraryOrFolderRow" style="padding-left: ${pad}px;"> - <div class="rowTitle libraryItemDeleted-${parent.deleted}"> - <img src="${h.url_for( expander )}" class="expanderIcon"/><img src="${h.url_for( folder )}" class="rowIcon"/> - ${parent.name} - %if parent.description: - <i>- ${parent.description}</i> - %endif - <a id="folder-${parent.id}-popup" class="popup-arrow" style="display: none;">▼</a> - </div> - %if not parent.deleted: + %if not folder.deleted or show_deleted: + <div class="rowTitle libraryItemDeleted-${deleted}"> + <img src="${h.url_for( expander )}" class="expanderIcon"/><img src="${h.url_for( folder_img )}" class="rowIcon"/> + ${folder.name} + %if folder.description: + <i>- ${folder.description}</i> + %endif + <a id="folder-${folder.id}-popup" class="popup-arrow" style="display: none;">▼</a> + </div> + %endif + %if not folder.deleted: <% library_item_ids = {} - library_item_ids[ 'folder' ] = parent.id + library_item_ids[ 'folder' ] = folder.id %> - <div popupmenu="folder-${parent.id}-popup"> - <a class="action-button" href="${h.url_for( controller='admin', action='library_dataset_dataset_association', library_id=library_id, folder_id=parent.id )}">Add datasets to this folder</a> - <a class="action-button" href="${h.url_for( controller='admin', action='folder', new=True, id=parent.id, library_id=library_id )}">Create a new sub-folder in this folder</a> - <a class="action-button" href="${h.url_for( controller='admin', action='folder', information=True, id=parent.id, library_id=library_id )}">Edit this folder's information</a> - %if parent.library_folder_info_template_associations: - <% template = parent.get_library_item_info_templates( template_list=[], restrict=True )[0] %> - <a class="action-button" href="${h.url_for( controller='admin', action='info_template', library_id=library.id, id=template.id, edit_template=True )}">Edit this folder's information template</a> + <div popupmenu="folder-${folder.id}-popup"> + <a class="action-button" href="${h.url_for( controller='admin', action='library_dataset_dataset_association', library_id=library_id, folder_id=folder.id )}">Add datasets to this folder</a> + <a class="action-button" href="${h.url_for( controller='admin', action='folder', new=True, id=folder.id, library_id=library_id )}">Create a new sub-folder in this folder</a> + <a class="action-button" href="${h.url_for( controller='admin', action='folder', information=True, id=folder.id, library_id=library_id )}">Edit this folder's information</a> + %if folder.library_folder_info_template_associations: + <% template = folder.get_library_item_info_templates( template_list=[], restrict=True )[0] %> + <a class="action-button" href="${h.url_for( controller='admin', action='info_template', library_id=library_id, id=template.id, edit_template=True )}">Edit this folder's information template</a> %else: - <a class="action-button" href="${h.url_for( controller='admin', action='info_template', library_id=library.id, folder_id=parent.id, new_template=True )}">Add an information template to this folder</a> + <a class="action-button" href="${h.url_for( controller='admin', action='info_template', library_id=library_id, folder_id=folder.id, new_template=True )}">Add an information template to this folder</a> %endif - <a class="action-button" href="${h.url_for( controller='admin', action='folder', permissions=True, id=parent.id, library_id=library_id )}">Edit this folder's permissions</a> - <a class="action-button" confirm="Click OK to delete the folder '${parent.name}'" href="${h.url_for( controller='admin', action='delete_library_item', library_id=library_id, library_item_id=parent.id, library_item_type='folder' )}">Remove this folder and its contents from the library</a> + <a class="action-button" href="${h.url_for( controller='admin', action='folder', permissions=True, id=folder.id, library_id=library_id )}">Edit this folder's permissions</a> + <a class="action-button" confirm="Click OK to delete the folder '${folder.name}.'" href="${h.url_for( controller='admin', action='delete_library_item', library_id=library_id, library_item_id=folder.id, library_item_type='folder' )}">Delete this folder and its contents</a> </div> - %else: - <div popupmenu="folder-${parent.id}-popup"> - <a class="action-button" href="${h.url_for( controller='admin', action='undelete_library_item', library_id=library_id, library_item_id=parent.id, library_item_type='folder' )}">Undelete this folder</a> + %elif not deleted and folder.deleted and not folder.purged: + <div popupmenu="folder-${folder.id}-popup"> + <a class="action-button" href="${h.url_for( controller='admin', action='undelete_library_item', library_id=library_id, library_item_id=folder.id, library_item_type='folder' )}">Undelete this folder</a> </div> %endif </li> @@ -131,31 +133,31 @@ %else: <ul> %endif - %if deleted: + %if show_deleted: <% - parent_folders = parent.activatable_folders - parent_datasets = parent.activatable_datasets + parent_folders = folder.activatable_folders + parent_datasets = folder.activatable_datasets %> %else: <% - parent_folders = parent.active_folders - parent_datasets = parent.active_datasets + parent_folders = folder.active_folders + parent_datasets = folder.active_datasets %> %endif %for folder in name_sorted( parent_folders ): - ${render_folder( folder, pad, deleted, created_ldda_ids, library.id )} + ${render_folder( folder, pad, deleted, show_deleted, created_ldda_ids, library_id )} %endfor %for library_dataset in name_sorted( parent_datasets ): <% selected = created_ldda_ids and library_dataset.library_dataset_dataset_association.id in created_ldda_ids %> - <li class="datasetRow" style="padding-left: ${pad + 18}px;">${render_dataset( library_dataset, selected, library )}</li> + <li class="datasetRow" style="padding-left: ${pad + 18}px;">${render_dataset( library_dataset, selected, library, deleted, show_deleted )}</li> %endfor </ul> </%def> <h2> - %if library.deleted: + %if deleted: Deleted %endif Library '${library.name}' @@ -183,7 +185,7 @@ <table cellspacing="0" cellpadding="0" border="0" width="100%" class="libraryTitle"> <th width="*"> <img src="${h.url_for( '/static/images/silk/resultset_bottom.png' )}" class="expanderIcon"/><img src="${h.url_for( '/static/images/silk/book_open.png' )}" class="rowIcon"/> - <span class="libraryItemDeleted-${library.deleted}"> + <span class="libraryItemDeleted-${deleted}"> ${library.name} %if library.description: <i>- ${library.description}</i> @@ -191,7 +193,7 @@ </span> <a id="library-${library.id}-popup" class="popup-arrow" style="display: none;">▼</a> <div popupmenu="library-${library.id}-popup"> - %if not library.deleted: + %if not deleted: <% library_item_ids = {} library_item_ids[ 'library' ] = library.id @@ -205,14 +207,14 @@ <a class="action-button" href="${h.url_for( controller='admin', action='info_template', library_id=library.id, new_template=True )}">Add an information template to this library</a> %endif <a class="action-button" href="${h.url_for( controller='admin', action='library', id=library.id, permissions=True )}">Edit this library's permissions</a> - <a class="action-button" confirm="Current state will not be saved, so undeleting the library will restore all of its contents. Click OK to delete the library named '${library.name}'?" href="${h.url_for( controller='admin', action='delete_library_item', library_item_type='library', library_item_id=library.id )}">Delete this library and its contents</a> + <a class="action-button" confirm="Click OK to delete the library named '${library.name}'." href="${h.url_for( controller='admin', action='delete_library_item', library_id=library.id, library_item_id=library.id, library_item_type='library' )}">Delete this library and its contents</a> %if show_deleted: <a class="action-button" href="${h.url_for( controller='admin', action='browse_library', id=library.id, show_deleted=False )}">Hide deleted library items</a> %else: <a class="action-button" href="${h.url_for( controller='admin', action='browse_library', id=library.id, show_deleted=True )}">Show deleted library items</a> %endif %elif not library.purged: - <a class="action-button" href="${h.url_for( controller='admin', action='undelete_library_item', library_item_type='library', library_item_id=library.id )}">Undelete this library</a> + <a class="action-button" href="${h.url_for( controller='admin', action='undelete_library_item', library_id=library.id, library_item_id=library.id, library_item_type='library' )}">Undelete this library</a> %endif </div> </th> @@ -223,16 +225,16 @@ </div> </li> <ul> - ${render_folder( library.root_folder, 0, library.deleted or show_deleted, created_ldda_ids, library.id )} + ${render_folder( library.root_folder, 0, deleted, show_deleted, created_ldda_ids, library.id )} </ul> <br/> </ul> - %if not library.deleted: + %if not deleted and not show_deleted: <p> <b>Perform action on selected datasets:</b> <select name="action" id="action_on_datasets_select"> <option value="edit">Edit selected datasets' permissions</option> - ##TODO: fix deleting library items<option value="delete">Remove selected datasets from this library</option> + <option value="delete">Delete selected datasets</option> </select> <input type="submit" class="primary-button" name="action_on_datasets_button" id="action_on_datasets_button" value="Go"/> </p> diff -r 8da91a231cdf -r 2e2b80fcbd47 templates/admin/library/common.mako --- a/templates/admin/library/common.mako Tue May 05 13:03:23 2009 -0400 +++ b/templates/admin/library/common.mako Tue May 05 13:48:01 2009 -0400 @@ -1,6 +1,6 @@ <% from time import strftime %> -<%def name="render_dataset( library_dataset, selected, library, show_deleted = False )"> +<%def name="render_dataset( library_dataset, selected, library, deleted, show_deleted )"> <% ## The received data must always be a LibraryDataset object, but the object id passed to methods from the drop down menu ## should be the underlying ldda id to prevent id collision ( which could happen when displaying children, which are always @@ -28,10 +28,10 @@ <input type="checkbox" name="ldda_ids" value="${ldda.id}"/> %endif <span class="libraryItemDeleted-${library_dataset.deleted}"> - <a href="${h.url_for( controller='admin', action='library_dataset_dataset_association', library_id=library.id, folder_id=library_dataset.folder.id, id=ldda.id, info=True )}"><b>${ldda.name[:50]}</b></a> + <a href="${h.url_for( controller='admin', action='library_dataset_dataset_association', library_id=library.id, folder_id=library_dataset.folder.id, id=ldda.id, info=True, deleted=deleted, show_deleted=show_deleted )}"><b>${ldda.name[:50]}</b></a> </span> <a id="dataset-${ldda.id}-popup" class="popup-arrow" style="display: none;">▼</a> - %if not library_dataset.deleted: + %if not library.deleted and not library_dataset.folder.deleted and not library_dataset.deleted: <% library_item_ids = {} library_item_ids[ 'ldda' ] = ldda.id @@ -47,12 +47,11 @@ %if ldda.has_data: <a class="action-button" href="${h.url_for( controller='admin', action='download_dataset_from_folder', id=ldda.id, library_id=library.id )}">Download this dataset</a> %endif - ##TODO: need to revamp the way we remove datasets from disk. - <a class="action-button" confirm="Click OK to remove dataset '${ldda.name}'?" href="${h.url_for( controller='admin', action='delete_library_item', library_id=library.id, library_item_id=library_dataset.id, library_item_type='dataset' )}">Remove this dataset from the library</a> + <a class="action-button" confirm="Click OK to delete dataset '${ldda.name}'." href="${h.url_for( controller='admin', action='delete_library_item', library_id=library.id, library_item_id=library_dataset.id, library_item_type='library_dataset' )}">Delete this dataset</a> </div> - %else: + %elif not library.deleted and not library_dataset.folder.deleted and library_dataset.deleted: <div popupmenu="dataset-${ldda.id}-popup"> - <a class="action-button" href="${h.url_for( controller='admin', action='undelete_library_item', library_id=library.id, library_item_id=library_dataset.id, library_item_type='dataset' )}">Undelete this dataset</a> + <a class="action-button" href="${h.url_for( controller='admin', action='undelete_library_item', library_id=library.id, library_item_id=library_dataset.id, library_item_type='library_dataset' )}">Undelete this dataset</a> </div> %endif </td> diff -r 8da91a231cdf -r 2e2b80fcbd47 templates/admin/library/ldda_info.mako --- a/templates/admin/library/ldda_info.mako Tue May 05 13:03:23 2009 -0400 +++ b/templates/admin/library/ldda_info.mako Tue May 05 13:48:01 2009 -0400 @@ -5,6 +5,7 @@ <% from galaxy import util %> <% + library = trans.app.model.Library.get( library_id ) if ldda == ldda.library_dataset.library_dataset_dataset_association: current_version = True else: @@ -20,7 +21,7 @@ <ul class="manage-table-actions"> <li> - <a class="action-button" href="${h.url_for( controller='admin', action='browse_library', id=library_id )}"><span>Browse this library</span></a> + <a class="action-button" href="${h.url_for( controller='admin', action='browse_library', id=library_id, deleted=library.deleted, show_deleted=show_deleted )}"><span>Browse this library</span></a> </li> </ul> @@ -38,21 +39,24 @@ <div class="toolForm"> <div class="toolFormTitle"> Information about ${ldda.name} - <a id="dataset-${ldda.id}-popup" class="popup-arrow" style="display: none;">▼</a> - <div popupmenu="dataset-${ldda.id}-popup"> - <a class="action-button" href="${h.url_for( controller='admin', action='library_dataset_dataset_association', library_id=library_id, folder_id=ldda.library_dataset.folder.id, id=ldda.id, edit_info=True )}">Edit this dataset's information</a> - ## We're disabling the ability to add templates at the LDDA and LibraryDataset level, but will leave this here for possible future use - ##<a class="action-button" href="${h.url_for( controller='admin', action='info_template', library_id=library_id, library_dataset_id=ldda.library_dataset.id, new_template=True )}">Add an information template to this dataset</a> - <a class="action-button" href="${h.url_for( controller='admin', action='library_dataset_dataset_association', library_id=library_id, folder_id=ldda.library_dataset.folder.id, id=ldda.id, permissions=True )}">Edit this dataset's permissions</a> - %if current_version: - <a class="action-button" href="${h.url_for( controller='admin', action='library_dataset_dataset_association', library_id=library_id, folder_id=ldda.library_dataset.folder.id, replace_id=ldda.library_dataset.id )}">Upload a new version of this dataset</a> - %endif - %if ldda.has_data: - <a class="action-button" href="${h.url_for( controller='admin', action='download_dataset_from_folder', id=ldda.id, library_id=library_id )}">Download this dataset</a> - %endif - ##TODO: need to revamp the way we remove datasets from disk. - ##<a class="action-button" confirm="Click OK to remove dataset '${ldda.name}'?" href="${h.url_for( controller='admin', action='library_dataset_dataset_association', library_id=library_id, folder_id=ldda.library_dataset.folder.id, id=ldda.id, delete=True )}">Remove this dataset from the library</a> - </div> + %if not library.deleted and not ldda.library_dataset.folder.deleted and not ldda.deleted: + <a id="dataset-${ldda.id}-popup" class="popup-arrow" style="display: none;">▼</a> + <div popupmenu="dataset-${ldda.id}-popup"> + <a class="action-button" href="${h.url_for( controller='admin', action='library_dataset_dataset_association', library_id=library_id, folder_id=ldda.library_dataset.folder.id, id=ldda.id, edit_info=True )}">Edit this dataset's information</a> + ## We're disabling the ability to add templates at the LDDA and LibraryDataset level, but will leave this here for possible future use + ##<a class="action-button" href="${h.url_for( controller='admin', action='info_template', library_id=library_id, library_dataset_id=ldda.library_dataset.id, new_template=True )}">Add an information template to this dataset</a> + <a class="action-button" href="${h.url_for( controller='admin', action='library_dataset_dataset_association', library_id=library_id, folder_id=ldda.library_dataset.folder.id, id=ldda.id, permissions=True )}">Edit this dataset's permissions</a> + %if current_version: + <a class="action-button" href="${h.url_for( controller='admin', action='library_dataset_dataset_association', library_id=library_id, folder_id=ldda.library_dataset.folder.id, replace_id=ldda.library_dataset.id )}">Upload a new version of this dataset</a> + %endif + %if ldda.has_data: + <a class="action-button" href="${h.url_for( controller='admin', action='download_dataset_from_folder', id=ldda.id, library_id=library_id )}">Download this dataset</a> + %endif + %if not library.deleted and not ldda.library_dataset.folder.deleted and not ldda.deleted: + <a class="action-button" confirm="Click OK to remove dataset '${ldda.name}'?" href="${h.url_for( controller='admin', action='library_dataset_dataset_association', library_id=library_id, folder_id=ldda.library_dataset.folder.id, id=ldda.id, delete=True )}">Delete this dataset</a> + %endif + </div> + %endif </div> <div class="toolFormBody"> <div class="form-row"> @@ -104,7 +108,10 @@ <div> There are ${len( ldda.visible_children )} secondary datasets. %for idx, child in enumerate( ldda.visible_children ): - ${ render_dataset( child, selected, library.deleted ) } + ## TODO: do we need to clarify if the child is deleted? + %if not child.purged: + ${ render_dataset( child, selected, library, False, False ) } + %endif %endfor </div> %endif diff -r 8da91a231cdf -r 2e2b80fcbd47 templates/library/ldda_info.mako --- a/templates/library/ldda_info.mako Tue May 05 13:03:23 2009 -0400 +++ b/templates/library/ldda_info.mako Tue May 05 13:48:01 2009 -0400 @@ -111,7 +111,10 @@ <div> There are ${len( ldda.visible_children )} secondary datasets. %for idx, child in enumerate( ldda.visible_children ): - ${ render_dataset( child, selected, library.deleted ) } + ## TODO: do we need to clarify if the child is deleted? + %if not child.purged: + ${ render_dataset( child, selected, library ) } + %endif %endfor </div> %endif

1 0

[hg] galaxy 2402: Fix bug reported by Gunnar Raetsch wherein a t...
by Nate Coraor 05 May '09

05 May '09

details: http://www.bx.psu.edu/hg/galaxy/rev/dd21a47f8035 changeset: 2402:dd21a47f8035 user: Nate Coraor <nate(a)bx.psu.edu> date: Tue May 05 17:06:11 2009 -0400 description: Fix bug reported by Gunnar Raetsch wherein a traceback is displayed if you view a file while it's uploading. 5 file(s) affected in this change: lib/galaxy/web/controllers/dataset.py lib/galaxy/web/controllers/root.py static/images/eye_icon_grey.png static/images/pencil_icon_grey.png templates/root/history_common.mako diffs (47 lines): diff -r 2e2b80fcbd47 -r dd21a47f8035 lib/galaxy/web/controllers/dataset.py --- a/lib/galaxy/web/controllers/dataset.py Tue May 05 13:48:01 2009 -0400 +++ b/lib/galaxy/web/controllers/dataset.py Tue May 05 17:06:11 2009 -0400 @@ -103,6 +103,8 @@ if not data: raise paste.httpexceptions.HTTPRequestRangeNotSatisfiable( "Invalid reference dataset id: %s." % str( dataset_id ) ) if trans.app.security_agent.allow_action( trans.user, data.permitted_actions.DATASET_ACCESS, dataset = data ): + if data.state == trans.model.Dataset.states.UPLOAD: + return trans.show_error_message( "Please wait until this dataset finishes uploading before attempting to view it." ) if filename is None or filename.lower() == "index": mime = trans.app.datatypes_registry.get_mimetype_by_extension( data.extension.lower() ) trans.response.set_content_type(mime) diff -r 2e2b80fcbd47 -r dd21a47f8035 lib/galaxy/web/controllers/root.py --- a/lib/galaxy/web/controllers/root.py Tue May 05 13:48:01 2009 -0400 +++ b/lib/galaxy/web/controllers/root.py Tue May 05 17:06:11 2009 -0400 @@ -219,6 +219,8 @@ if id is not None and data.history.user is not None and data.history.user != trans.user: return trans.show_error_message( "This instance of a dataset (%s) in a history does not belong to you." % ( data.id ) ) if trans.app.security_agent.allow_action( trans.user, data.permitted_actions.DATASET_ACCESS, dataset=data ): + if data.state == trans.model.Dataset.states.UPLOAD: + return trans.show_error_message( "Please wait until this dataset finishes uploading before attempting to edit its metadata." ) params = util.Params( kwd, safe=False ) if params.change: # The user clicked the Save button on the 'Change data type' form diff -r 2e2b80fcbd47 -r dd21a47f8035 static/images/eye_icon_grey.png Binary file static/images/eye_icon_grey.png has changed diff -r 2e2b80fcbd47 -r dd21a47f8035 static/images/pencil_icon_grey.png Binary file static/images/pencil_icon_grey.png has changed diff -r 2e2b80fcbd47 -r dd21a47f8035 templates/root/history_common.mako --- a/templates/root/history_common.mako Tue May 05 13:48:01 2009 -0400 +++ b/templates/root/history_common.mako Tue May 05 17:06:11 2009 -0400 @@ -33,8 +33,13 @@ %endif </div> <div style="float: right;"> - <a href="${h.url_for( controller='dataset', dataset_id=data.id, action='display', filename='index')}" target="galaxy_main"><img src="${h.url_for('/static/images/eye_icon.png')}" rollover="${h.url_for('/static/images/eye_icon_dark.png')}" width='16' height='16' alt='display data' title='display data' class='displayButton' border='0'></a> - <a href="${h.url_for( controller='root', action='edit', id=data.id )}" target="galaxy_main"><img src="${h.url_for('/static/images/pencil_icon.png')}" rollover="${h.url_for('/static/images/pencil_icon_dark.png')}" width='16' height='16' alt='edit attributes' title='edit attributes' class='editButton' border='0'></a> + %if data_state == "upload": + <img src="${h.url_for('/static/images/eye_icon_grey.png')}" width='16' height='16' alt='display data' title='display data' class='displayButton' border='0'> + <img src="${h.url_for('/static/images/pencil_icon_grey.png')}" width='16' height='16' alt='edit attributes' title='edit attributes' class='editButton' border='0'> + %else: + <a href="${h.url_for( controller='dataset', dataset_id=data.id, action='display', filename='index')}" target="galaxy_main"><img src="${h.url_for('/static/images/eye_icon.png')}" rollover="${h.url_for('/static/images/eye_icon_dark.png')}" width='16' height='16' alt='display data' title='display data' class='displayButton' border='0'></a> + <a href="${h.url_for( controller='root', action='edit', id=data.id )}" target="galaxy_main"><img src="${h.url_for('/static/images/pencil_icon.png')}" rollover="${h.url_for('/static/images/pencil_icon_dark.png')}" width='16' height='16' alt='edit attributes' title='edit attributes' class='editButton' border='0'></a> + %endif <a href="${h.url_for( action='delete', id=data.id, show_deleted_on_refresh=show_deleted_on_refresh )}" class="historyItemDelete" id="historyItemDeleter-${data.id}"><img src="${h.url_for('/static/images/delete_icon.png')}" rollover="${h.url_for('/static/images/delete_icon_dark.png')}" width='16' height='16' alt='delete' class='deleteButton' border='0'></a> </div> <span class="historyItemTitle"><b>${hid}: ${data.display_name()}</b></span>

1 0

[hg] galaxy 2399: Directly stream .tar.gz and .tar.bz2 library d...
by Nate Coraor 05 May '09

05 May '09

details: http://www.bx.psu.edu/hg/galaxy/rev/3abf689d6f6f changeset: 2399:3abf689d6f6f user: Nate Coraor <nate(a)bx.psu.edu> date: Tue May 05 12:03:40 2009 -0400 description: Directly stream .tar.gz and .tar.bz2 library downloads. .zip is still created on-disk first since Python's zipfile can't write to file-like objects like tarfile can. For response body generators (e.g. this feature) to work properly, you must set use_interactive and debug to False in universe_wsgi.ini. 3 file(s) affected in this change: lib/galaxy/util/streamball.py lib/galaxy/web/controllers/library.py templates/library/browse_library.mako diffs (277 lines): diff -r 6c76023580e3 -r 3abf689d6f6f lib/galaxy/util/streamball.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/lib/galaxy/util/streamball.py Tue May 05 12:03:40 2009 -0400 @@ -0,0 +1,50 @@ +""" +A simple wrapper for writing tarballs as a stream. The work is performed in a +thread and data is written to a Queue instead of a file. +""" + +import logging, tarfile + +from Queue import Queue, Empty, Full +from threading import Thread + +log = logging.getLogger( __name__ ) + +class QueueArchive( object ): + queue_size = 32 + def __init__( self ): + self.queue = Queue( QueueArchive.queue_size ) + self.get = self.queue.get + self.empty = self.queue.empty + def write( self, data ): + self.queue.put( data, block=True, timeout=300 ) + def tell( self ): + return 0 + +class StreamBall( object ): + def __init__( self, mode, members={} ): + self.mode = mode + self.members = members + self.tarfileobj = QueueArchive() + def add( self, file, relpath ): + self.members[file] = relpath + def stream( self ): + t = Thread( target=self.thread_write ) + t.start() + while t.isAlive(): + try: + yield self.tarfileobj.get( block=False ) + except Empty: + pass + t.join() + # exhaust the queue + while not self.tarfileobj.empty(): + yield self.tarfileobj.get() + def thread_write( self ): + tf = tarfile.open( mode=self.mode, fileobj=self.tarfileobj ) + try: + for file, rel in self.members.items(): + tf.add( file, arcname=rel ) + tf.close() + except Full: + log.warning( 'Queue full for longer than 300 seconds, timing out' ) diff -r 6c76023580e3 -r 3abf689d6f6f lib/galaxy/web/controllers/library.py --- a/lib/galaxy/web/controllers/library.py Tue May 05 08:29:23 2009 -0400 +++ b/lib/galaxy/web/controllers/library.py Tue May 05 12:03:40 2009 -0400 @@ -2,6 +2,7 @@ from galaxy.model.orm import * from galaxy.datatypes import sniff from galaxy import util +from galaxy.util.streamball import StreamBall import logging, tempfile, zipfile, tarfile, os, sys if sys.version_info[:2] < ( 2, 6 ): @@ -10,6 +11,40 @@ zipfile.LargeZipFile = zipfile.error log = logging.getLogger( __name__ ) + +# Test for available compression types +tmpd = tempfile.mkdtemp() +comptypes = [] +for comptype in ( 'gz', 'bz2' ): + tmpf = os.path.join( tmpd, 'compression_test.tar.' + comptype ) + try: + archive = tarfile.open( tmpf, 'w:' + comptype ) + archive.close() + comptypes.append( comptype ) + except tarfile.CompressionError: + log.exception( "Compression error when testing %s compression. This option will be disabled for library downloads." % comptype ) + try: + os.unlink( tmpf ) + except OSError: + pass +ziptype = '32' +tmpf = os.path.join( tmpd, 'compression_test.zip' ) +try: + archive = zipfile.ZipFile( tmpf, 'w', zipfile.ZIP_DEFLATED, True ) + archive.close() + comptypes.append( 'zip' ) + ziptype = '64' +except RuntimeError: + log.exception( "Compression error when testing zip compression. This option will be disabled for library downloads." ) +except (TypeError, zipfile.LargeZipFile): + # ZIP64 is only in Python2.5+. Remove TypeError when 2.4 support is dropped + log.warning( 'Max zip file size is 2GB, ZIP64 not supported' ) + comptypes.append( 'zip' ) +try: + os.unlink( tmpf ) +except OSError: + pass +os.rmdir( tmpd ) class Library( BaseController ): @web.expose @@ -66,6 +101,7 @@ library=trans.app.model.Library.get( id ), created_ldda_ids=created_ldda_ids, default_action=params.get( 'default_action', None ), + comptypes=comptypes, msg=msg, messagetype=messagetype ) @web.expose @@ -195,49 +231,21 @@ msg=util.sanitize_text( msg ), messagetype=messagetype ) ) else: - # Can't use mkstemp - the file must not exist first try: - tmpd = tempfile.mkdtemp() - tmpf = os.path.join( tmpd, 'library_download.' + params.do_action ) if params.do_action == 'zip': - try: + # Can't use mkstemp - the file must not exist first + tmpd = tempfile.mkdtemp() + tmpf = os.path.join( tmpd, 'library_download.' + params.do_action ) + if ziptype == '64': archive = zipfile.ZipFile( tmpf, 'w', zipfile.ZIP_DEFLATED, True ) - except RuntimeError: - log.exception( "Compression error when opening zipfile for library download" ) - msg = "ZIP compression is not available in this Python, please notify an administrator" - return trans.response.send_redirect( web.url_for( controller='library', - action='browse_library', - id=library_id, - msg=util.sanitize_text( msg ), - messagetype='error' ) ) - except (TypeError, zipfile.LargeZipFile): - # ZIP64 is only in Python2.5+. Remove TypeError when 2.4 support is dropped - log.warning( 'Max zip file size is 2GB, ZIP64 not supported' ) + else: archive = zipfile.ZipFile( tmpf, 'w', zipfile.ZIP_DEFLATED ) archive.add = lambda x, y: archive.write( x, y.encode('CP437') ) elif params.do_action == 'tgz': - try: - archive = tarfile.open( tmpf, 'w:gz' ) - except tarfile.CompressionError: - log.exception( "Compression error when opening tarfile for library download" ) - msg = "gzip compression is not available in this Python, please notify an administrator" - return trans.response.send_redirect( web.url_for( controller='library', - action='browse_library', - id=library_id, - msg=util.sanitize_text( msg ), - messagetype='error' ) ) + archive = util.streamball.StreamBall( 'w|gz' ) elif params.do_action == 'tbz': - try: - archive = tarfile.open( tmpf, 'w:bz2' ) - except tarfile.CompressionError: - log.exception( "Compression error when opening tarfile for library download" ) - msg = "bzip2 compression is not available in this Python, please notify an administrator" - return trans.response.send_redirect( web.url_for( controller='library', - action='browse_library', - id=library_id, - msg=util.sanitize_text( msg ), - messagetype='error' ) ) - except (OSError, zipfile.BadZipFile, tarfile.ReadError): + archive = util.streamball.StreamBall( 'w|bz2' ) + except (OSError, zipfile.BadZipFile): log.exception( "Unable to create archive for download" ) msg = "Unable to create archive for download, please report this error" return trans.response.send_redirect( web.url_for( controller='library', @@ -255,9 +263,11 @@ path = "" parent_folder = ldda.library_dataset.folder while parent_folder is not None: - path = os.path.join( parent_folder.name, path ) + # Exclude the now-hidden "root folder" if parent_folder.parent is None: path = os.path.join( parent_folder.library_root[0].name, path ) + break + path = os.path.join( parent_folder.name, path ) parent_folder = parent_folder.parent path += ldda.name while path in seen: @@ -273,22 +283,28 @@ id=library_id, msg=util.sanitize_text( msg ), messagetype='error' ) ) - archive.close() - tmpfh = open( tmpf ) - # clean up now - try: - os.unlink( tmpf ) - os.rmdir( tmpd ) - except OSError: - log.exception( "Unable to remove temporary library download archive and directory" ) - msg = "Unable to create archive for download, please report this error" - return trans.response.send_redirect( web.url_for( controller='library', - action='browse_library', - id=library_id, - msg=util.sanitize_text( msg ), - messagetype='error' ) ) - trans.response.headers[ "Content-Disposition" ] = "attachment; filename=GalaxyLibraryFiles.%s" % params.do_action - return tmpfh + if params.do_action == 'zip': + archive.close() + tmpfh = open( tmpf ) + # clean up now + try: + os.unlink( tmpf ) + os.rmdir( tmpd ) + except OSError: + log.exception( "Unable to remove temporary library download archive and directory" ) + msg = "Unable to create archive for download, please report this error" + return trans.response.send_redirect( web.url_for( controller='library', + action='browse_library', + id=library_id, + msg=util.sanitize_text( msg ), + messagetype='error' ) ) + trans.response.set_content_type( "application/x-zip-compressed" ) + trans.response.headers[ "Content-Disposition" ] = "attachment; filename=GalaxyLibraryFiles.%s" % params.do_action + return tmpfh + else: + trans.response.set_content_type( "application/x-tar" ) + trans.response.headers[ "Content-Disposition" ] = "attachment; filename=GalaxyLibraryFiles.%s" % params.do_action + return archive.stream() @web.expose def download_dataset_from_folder(self, trans, id, library_id=None, **kwd): """Catches the dataset id and displays file contents as directed""" diff -r 6c76023580e3 -r 3abf689d6f6f templates/library/browse_library.mako --- a/templates/library/browse_library.mako Tue May 05 08:29:23 2009 -0400 +++ b/templates/library/browse_library.mako Tue May 05 12:03:40 2009 -0400 @@ -268,13 +268,38 @@ # This condition should not contain an else clause because the user is not authorized # to manage dataset permissions unless the default action is 'manage_permissions' %endif - %if default_action == 'download': - <option value="zip" selected>Download selected datasets as a .zip file</option> - %else: + %if 'bz2' in comptypes: + <option value="tbz" + %if default_action == 'download': + selected + %endif> + >Download selected datasets as a .tar.bz2 file</option> + %endif + %if 'gz' in comptypes: + <option value="tgz">Download selected datasets as a .tar.gz file</option> + %endif + %if 'zip' in comptypes: <option value="zip">Download selected datasets as a .zip file</option> %endif - <option value="tgz">Download selected datasets as a .tar.gz file</option> - <option value="tbz">Download selected datasets as a .tar.bz2 file</option> </select> <input type="submit" class="primary-button" name="action_on_datasets_button" id="action_on_datasets_button" value="Go"/> </form> + +%if len( comptypes ) > 1: + <div> + <p class="infomark"> + TIP: Multiple compression options are available for downloading library datasets: + </p> + <ul style="padding-left: 1em; list-style-type: disc;"> + %if 'bz2' in comptypes: + <li>bzip2: Compression takes the most time but is better for slower network connections (that transfer slower than the rate of compression) since the resulting file size is smallest.</li> + %endif + %if 'gz' in comptypes: + <li>gzip: Compression is faster and yields a larger file, making it more suitable for fast network connections.</li> + %endif + %if 'zip' in comptypes: + <li>ZIP: Not recommended but is provided as an option for those on Windows without WinZip (since WinZip can read .bz2 and .gz files).</li> + %endif + </ul> + </div> +%endif

1 0

[hg] galaxy 2400: Fix history deletion method in Galaxy check sc...
by Nate Coraor 05 May '09

05 May '09

details: http://www.bx.psu.edu/hg/galaxy/rev/8da91a231cdf changeset: 2400:8da91a231cdf user: Nate Coraor <nate(a)bx.psu.edu> date: Tue May 05 13:03:23 2009 -0400 description: Fix history deletion method in Galaxy check script 1 file(s) affected in this change: scripts/check_galaxy.py diffs (38 lines): diff -r 3abf689d6f6f -r 8da91a231cdf scripts/check_galaxy.py --- a/scripts/check_galaxy.py Tue May 05 12:03:40 2009 -0400 +++ b/scripts/check_galaxy.py Tue May 05 13:03:23 2009 -0400 @@ -141,15 +141,8 @@ print "Remaining datasets ids:", " ".join( p.dids ) raise Exception, "History still contains datasets after attempting to delete them" if new_history: - self.get("/root/history_options") - p = hidParser() - p.feed(tc.browser.get_html()) - if p.hid is None: - print "Unable to determine hid to delete old history" - sys.exit(1) - else: - self.get("/root/history_delete?id=%s" % p.hid) - tc.save_cookies(self.cookie_jar) + self.get("/history/delete_current") + tc.save_cookies(self.cookie_jar) def check_redir(self, url): try: @@ -334,16 +327,6 @@ self.dids.append( i[1].rsplit("historyItemContainer-", 1)[1] ) dprint("got a dataset id: %s" % self.dids[-1]) -class hidParser(htmllib.HTMLParser): - def __init__(self): - htmllib.HTMLParser.__init__(self, formatter.NullFormatter()) - self.hid = None - def start_a(self, attrs): - for i in attrs: - if i[0] == "href" and i[1].startswith("/root/history_delete"): - self.hid = i[1].rsplit("=", 1)[1] - dprint("got a history id: %s" % self.hid) - class loggedinParser(htmllib.HTMLParser): def __init__(self): htmllib.HTMLParser.__init__(self, formatter.NullFormatter())

1 0

[hg] galaxy 2398: Exclude controllers from unit tests to elimina...
by Nate Coraor 05 May '09

05 May '09

details: http://www.bx.psu.edu/hg/galaxy/rev/6c76023580e3 changeset: 2398:6c76023580e3 user: Greg Von Kuster <greg(a)bx.psu.edu> date: Tue May 05 08:29:23 2009 -0400 description: Exclude controllers from unit tests to eliminate the broken genetrack test. 1 file(s) affected in this change: run_unit_tests.sh diffs (12 lines): diff -r 8edceee8c818 -r 6c76023580e3 run_unit_tests.sh --- a/run_unit_tests.sh Mon May 04 12:20:26 2009 -0400 +++ b/run_unit_tests.sh Tue May 05 08:29:23 2009 -0400 @@ -1,5 +1,7 @@ #!/bin/sh + +## Excluding controllers due to the problematic genetrack dependency python -ES ./scripts/nosetests.py -v -w lib \ --with-nosehtml --html-report-file run_unit_tests.html \ - --with-doctest --exclude=functional --exclude="^get" + --with-doctest --exclude=functional --exclude="^get" --exclude=controllers

1 0

[hg] galaxy 2397: Fix closing label tags in 2 ldda_info_templates.
by Nate Coraor 05 May '09

05 May '09

details: http://www.bx.psu.edu/hg/galaxy/rev/8edceee8c818 changeset: 2397:8edceee8c818 user: Greg Von Kuster <greg(a)bx.psu.edu> date: Mon May 04 12:20:26 2009 -0400 description: Fix closing label tags in 2 ldda_info_templates. 2 file(s) affected in this change: templates/admin/library/ldda_info.mako templates/library/ldda_info.mako diffs (90 lines): diff -r 6de7eb773877 -r 8edceee8c818 templates/admin/library/ldda_info.mako --- a/templates/admin/library/ldda_info.mako Mon May 04 12:06:11 2009 -0400 +++ b/templates/admin/library/ldda_info.mako Mon May 04 12:20:26 2009 -0400 @@ -63,28 +63,28 @@ <div style="clear: both"></div> </div> <div class="form-row"> - <label>Uploaded by:</lable> + <label>Uploaded by:</label> <div style="float: left; width: 250px; margin-right: 10px;"> ${uploaded_by} </div> <div style="clear: both"></div> </div> <div class="form-row"> - <label>Date uploaded:</lable> + <label>Date uploaded:</label> <div style="float: left; width: 250px; margin-right: 10px;"> ${ldda.create_time.strftime( "%Y-%m-%d" )} </div> <div style="clear: both"></div> </div> <div class="form-row"> - <label>Build:</lable> + <label>Build:</label> <div style="float: left; width: 250px; margin-right: 10px;"> ${ldda.dbkey} </div> <div style="clear: both"></div> </div> <div class="form-row"> - <label>Miscellaneous information:</lable> + <label>Miscellaneous information:</label> <div style="float: left; width: 250px; margin-right: 10px;"> ${ldda.info} </div> @@ -96,7 +96,7 @@ <div class="form-row"> <div id="info${ldda.id}" class="historyItemBody"> %if ldda.peek != "no peek": - <label>Peek:</lable> + <label>Peek:</label> <div><pre id="peek${ldda.id}" class="peek">${ldda.display_peek()}</pre></div> %endif ## Recurse for child datasets diff -r 6de7eb773877 -r 8edceee8c818 templates/library/ldda_info.mako --- a/templates/library/ldda_info.mako Mon May 04 12:06:11 2009 -0400 +++ b/templates/library/ldda_info.mako Mon May 04 12:20:26 2009 -0400 @@ -70,28 +70,28 @@ <div style="clear: both"></div> </div> <div class="form-row"> - <label>Uploaded by:</lable> + <label>Uploaded by:</label> <div style="float: left; width: 250px; margin-right: 10px;"> ${uploaded_by} </div> <div style="clear: both"></div> </div> <div class="form-row"> - <label>Date uploaded:</lable> + <label>Date uploaded:</label> <div style="float: left; width: 250px; margin-right: 10px;"> ${ldda.create_time.strftime( "%Y-%m-%d" )} </div> <div style="clear: both"></div> </div> <div class="form-row"> - <label>Build:</lable> + <label>Build:</label> <div style="float: left; width: 250px; margin-right: 10px;"> ${ldda.dbkey} </div> <div style="clear: both"></div> </div> <div class="form-row"> - <label>Miscellaneous information:</lable> + <label>Miscellaneous information:</label> <div style="float: left; width: 250px; margin-right: 10px;"> ${ldda.info} </div> @@ -103,7 +103,7 @@ <div class="form-row"> <div id="info${ldda.id}" class="historyItemBody"> %if ldda.peek != "no peek": - <label>Peek:</lable> + <label>Peek:</label> <div><pre id="peek${ldda.id}" class="peek">${ldda.display_peek()}</pre></div> %endif ## Recurse for child datasets

1 0

[hg] galaxy 2396: Fix import history links, now using encode_id ...
by Nate Coraor 05 May '09

05 May '09

details: http://www.bx.psu.edu/hg/galaxy/rev/6de7eb773877 changeset: 2396:6de7eb773877 user: James Taylor <james(a)jamestaylor.org> date: Mon May 04 12:06:11 2009 -0400 description: Fix import history links, now using encode_id as well 2 file(s) affected in this change: lib/galaxy/web/controllers/history.py templates/history/share.mako diffs (73 lines): diff -r df824c53f2f3 -r 6de7eb773877 lib/galaxy/web/controllers/history.py --- a/lib/galaxy/web/controllers/history.py Fri May 01 17:19:17 2009 -0400 +++ b/lib/galaxy/web/controllers/history.py Mon May 04 12:06:11 2009 -0400 @@ -213,6 +213,57 @@ ## These have been moved from 'root' but not cleaned up @web.expose + def imp( self, trans, id=None, confirm=False, **kwd ): + msg = "" + user = trans.get_user() + user_history = trans.get_history() + if not id: + return trans.show_error_message( "You must specify a history you want to import.") + id = trans.security.decode_id( id ) + import_history = trans.app.model.History.get( id ) + if not import_history: + return trans.show_error_message( "The specified history does not exist.") + if user: + if import_history.user_id == user.id: + return trans.show_error_message( "You cannot import your own history.") + new_history = import_history.copy( target_user=trans.user ) + new_history.name = "imported: "+new_history.name + new_history.user_id = user.id + galaxy_session = trans.get_galaxy_session() + try: + association = trans.app.model.GalaxySessionToHistoryAssociation.filter_by( session_id=galaxy_session.id, history_id=new_history.id ).first() + except: + association = None + new_history.add_galaxy_session( galaxy_session, association=association ) + new_history.flush() + if not user_history.datasets: + trans.set_history( new_history ) + trans.log_event( "History imported, id: %s, name: '%s': " % (str(new_history.id) , new_history.name ) ) + return trans.show_ok_message( """ + History "%s" has been imported. Click <a href="%s">here</a> + to begin.""" % ( new_history.name, web.url_for( '/' ) ) ) + elif not user_history.datasets or confirm: + new_history = import_history.copy() + new_history.name = "imported: "+new_history.name + new_history.user_id = None + galaxy_session = trans.get_galaxy_session() + try: + association = trans.app.model.GalaxySessionToHistoryAssociation.filter_by( session_id=galaxy_session.id, history_id=new_history.id ).first() + except: + association = None + new_history.add_galaxy_session( galaxy_session, association=association ) + new_history.flush() + trans.set_history( new_history ) + trans.log_event( "History imported, id: %s, name: '%s': " % (str(new_history.id) , new_history.name ) ) + return trans.show_ok_message( """ + History "%s" has been imported. Click <a href="%s">here</a> + to begin.""" % ( new_history.name, web.url_for( '/' ) ) ) + return trans.show_warn_message( """ + Warning! If you import this history, you will lose your current + history. Click <a href="%s">here</a> to confirm. + """ % web.url_for( id=id, confirm=True ) ) + + @web.expose @web.require_login( "share histories with other users" ) def share( self, trans, id=None, email="", **kwd ): send_to_err = "" diff -r df824c53f2f3 -r 6de7eb773877 templates/history/share.mako --- a/templates/history/share.mako Fri May 01 17:19:17 2009 -0400 +++ b/templates/history/share.mako Mon May 04 12:06:11 2009 -0400 @@ -18,7 +18,7 @@ ${len(history.datasets)} %endif </td> - <td align="center"><a href="${h.url_for( action='history_import', id=history.id )}">${_('copy link to share')}</a></td> + <td align="center"><a href="${h.url_for( controller='history', action='imp', id=trans.security.encode_id(history.id) )}">${_('copy link to share')}</a></td> </tr> %endfor <tr><td>${_('Email of User to share with:')}</td><td><input type="text" name="email" value="${email}" size="40"></td></tr>

1 0

[hg] galaxy 2395: Simplifying the grid helper a bit. Fix a bug w...
by Nate Coraor 05 May '09

05 May '09

details: http://www.bx.psu.edu/hg/galaxy/rev/df824c53f2f3 changeset: 2395:df824c53f2f3 user: James Taylor <james(a)jamestaylor.org> date: Fri May 01 17:19:17 2009 -0400 description: Simplifying the grid helper a bit. Fix a bug where sort/filter were not retained when performing actions on multiple items 4 file(s) affected in this change: lib/galaxy/web/controllers/history.py lib/galaxy/web/framework/helpers/__init__.py lib/galaxy/web/framework/helpers/grids.py templates/grid.mako diffs (279 lines): diff -r 80e00a9cdeb0 -r df824c53f2f3 lib/galaxy/web/controllers/history.py --- a/lib/galaxy/web/controllers/history.py Fri May 01 12:24:24 2009 -0400 +++ b/lib/galaxy/web/controllers/history.py Fri May 01 17:19:17 2009 -0400 @@ -1,5 +1,5 @@ from galaxy.web.base.controller import * -from galaxy.web.framework.helpers.grids import * +from galaxy.web.framework.helpers import time_ago, iff, grids import webhelpers from datetime import datetime from cgi import escape @@ -9,42 +9,33 @@ # States for passing messages SUCCESS, INFO, WARNING, ERROR = "done", "info", "warning", "error" -def time_ago( x ): - return webhelpers.date.distance_of_time_in_words( x, datetime.utcnow() ) - -def iff( a, b, c ): - if a: - return b - else: - return c - -class HistoryListGrid( Grid ): +class HistoryListGrid( grids.Grid ): title = "Stored histories" model_class = model.History default_sort_key = "-create_time" columns = [ - GridColumn( "Name", key="name", + grids.GridColumn( "Name", key="name", link=( lambda item: iff( item.deleted, None, dict( operation="switch", id=item.id ) ) ), attach_popup=True ), - GridColumn( "Datasets (by state)", method='_build_datasets_by_state', ncells=4 ), - GridColumn( "Status", method='_build_status' ), - GridColumn( "Age", key="create_time", format=time_ago ), - GridColumn( "Last update", key="update_time", format=time_ago ), + grids.GridColumn( "Datasets (by state)", method='_build_datasets_by_state', ncells=4 ), + grids.GridColumn( "Status", method='_build_status' ), + grids.GridColumn( "Age", key="create_time", format=time_ago ), + grids.GridColumn( "Last update", key="update_time", format=time_ago ), # Valid for filtering but invisible - GridColumn( "Deleted", key="deleted", visible=False ) + grids.GridColumn( "Deleted", key="deleted", visible=False ) ] operations = [ - GridOperation( "Switch", allow_multiple=False, condition=( lambda item: not item.deleted ) ), - GridOperation( "Share", condition=( lambda item: not item.deleted ) ), - GridOperation( "Rename", condition=( lambda item: not item.deleted ) ), - GridOperation( "Delete", condition=( lambda item: not item.deleted ) ), - GridOperation( "Undelete", condition=( lambda item: item.deleted ) ) + grids.GridOperation( "Switch", allow_multiple=False, condition=( lambda item: not item.deleted ) ), + grids.GridOperation( "Share", condition=( lambda item: not item.deleted ) ), + grids.GridOperation( "Rename", condition=( lambda item: not item.deleted ) ), + grids.GridOperation( "Delete", condition=( lambda item: not item.deleted ) ), + grids.GridOperation( "Undelete", condition=( lambda item: item.deleted ) ) ] standard_filters = [ - GridColumnFilter( "Active", args=dict( deleted=False ) ), - GridColumnFilter( "Deleted", args=dict( deleted=True ) ), - GridColumnFilter( "All", args=dict( deleted='All' ) ) + grids.GridColumnFilter( "Active", args=dict( deleted=False ) ), + grids.GridColumnFilter( "Deleted", args=dict( deleted=True ) ), + grids.GridColumnFilter( "All", args=dict( deleted='All' ) ) ] default_filter = dict( deleted=False ) @@ -53,41 +44,7 @@ def apply_default_filter( self, trans, query ): return query.filter_by( user=trans.user, purged=False ) - - def handle_operation( self, trans, operation, history_ids ): - # Display no message by default - status, message = None, None - refresh_history = False - # Load the histories and ensure they all belong to the current user - histories = [] - for hid in history_ids: - history = model.History.get( hid ) - if history: - # Ensure history is owned by current user - if history.user_id != None and trans.user: - assert trans.user.id == history.user_id, "History does not belong to current user" - histories.append( history ) - else: - log.warn( "Invalid history id '%r' passed to list", hid ) - operation = operation.lower() - if operation == "switch": - status, message = self._list_switch( trans, histories ) - # Current history changed, refresh history frame - trans.template_context['refresh_frames'] = ['history'] - elif operation == "share": - ## Caught above for now - pass - elif operation == "rename": - ## Caught above for now - pass - elif operation == "delete": - status, message = self._list_delete( trans, histories ) - elif operation == "undelete": - status, message = self._list_undelete( trans, histories ) - trans.sa_session.flush() - # Render the list view - return status, message - + def _build_datasets_by_state( self, trans, history ): rval = [] for state in ( 'ok', 'running', 'queued', 'error' ): @@ -102,6 +59,64 @@ if history.deleted: return "deleted" return "" + +class HistoryController( BaseController ): + + @web.expose + def index( self, trans ): + return "" + + @web.expose + def list_as_xml( self, trans ): + """ + XML history list for functional tests + """ + return trans.fill_template( "/history/list_as_xml.mako" ) + + list_grid = HistoryListGrid() + + @web.expose + @web.require_login( "work with multiple histories" ) + def list( self, trans, **kwargs ): + """ + List all available histories + """ + status = message = None + if 'operation' in kwargs: + operation = kwargs['operation'].lower() + if operation == "share": + return self.share( trans, **kwargs ) + elif operation == "rename": + return self.rename( trans, **kwargs ) + # Display no message by default + status, message = None, None + refresh_history = False + # Load the histories and ensure they all belong to the current user + history_ids = kwargs.get( 'id', [] ) + if type( history_ids ) is not list: + history_ids = [ history_ids ] + histories = [] + for hid in history_ids: + history = model.History.get( hid ) + if history: + # Ensure history is owned by current user + if history.user_id != None and trans.user: + assert trans.user.id == history.user_id, "History does not belong to current user" + histories.append( history ) + else: + log.warn( "Invalid history id '%r' passed to list", hid ) + if histories: + if operation == "switch": + status, message = self._list_switch( trans, histories ) + # Current history changed, refresh history frame + trans.template_context['refresh_frames'] = ['history'] + elif operation == "delete": + status, message = self._list_delete( trans, histories ) + elif operation == "undelete": + status, message = self._list_undelete( trans, histories ) + trans.sa_session.flush() + # Render the list view + return self.list_grid( trans, status=status, message=message, **kwargs ) def _list_delete( self, trans, histories ): """Delete histories""" @@ -164,37 +179,6 @@ trans.log_event( "History switched to id: %s, name: '%s'" % (str(new_history.id), new_history.name ) ) # No message return None, None - -class HistoryController( BaseController ): - - @web.expose - def index( self, trans ): - return "" - - @web.expose - def list_as_xml( self, trans ): - """ - XML history list for functional tests - """ - return trans.fill_template( "/history/list_as_xml.mako" ) - - _list_grid = HistoryListGrid() - - @web.expose - @web.require_login( "work with multiple histories" ) - def list( self, trans, *args, **kwargs ): - """ - List all available histories - """ - # TODO: these two operations need to be updates still - operation = kwargs.get( 'operation', None ) - if operation: - operation = operation.lower() - if operation == "share": - return self.share( trans, **kwargs ) - elif operation == "rename": - return self.rename( trans, **kwargs ) - return self._list_grid( trans, *args, **kwargs ) @web.expose def delete_current( self, trans ): diff -r 80e00a9cdeb0 -r df824c53f2f3 lib/galaxy/web/framework/helpers/__init__.py --- a/lib/galaxy/web/framework/helpers/__init__.py Fri May 01 12:24:24 2009 -0400 +++ b/lib/galaxy/web/framework/helpers/__init__.py Fri May 01 17:19:17 2009 -0400 @@ -0,0 +1,12 @@ +from webhelpers import * + +from datetime import datetime + +def time_ago( x ): + return date.distance_of_time_in_words( x, datetime.utcnow() ) + +def iff( a, b, c ): + if a: + return b + else: + return c \ No newline at end of file diff -r 80e00a9cdeb0 -r df824c53f2f3 lib/galaxy/web/framework/helpers/grids.py --- a/lib/galaxy/web/framework/helpers/grids.py Fri May 01 12:24:24 2009 -0400 +++ b/lib/galaxy/web/framework/helpers/grids.py Fri May 01 17:19:17 2009 -0400 @@ -16,18 +16,13 @@ standard_filters = [] default_filter = None default_sort_key = None + pass_through_operations = {} def __init__( self ): pass def __call__( self, trans, **kwargs ): - # Session + status = kwargs.get( 'status', None ) + message = kwargs.get( 'message', None ) session = trans.sa_session - # Process any actions - status = message = None - ids = self.get_ids( **kwargs ) - operation = kwargs.get( 'operation', None ) - if operation: - operation = operation.lower() - status, message = self.handle_operation( trans, operation, ids ) # Build initial query query = self.build_initial_query( session ) query = self.apply_default_filter( trans, query ) @@ -83,7 +78,7 @@ encoded_sort_key=encoded_sort_key, sort_order=sort_order, current_item=current_item, - ids = ids, + ids = kwargs.get( 'id', [] ), url = url, message_type = status, message = message ) diff -r 80e00a9cdeb0 -r df824c53f2f3 templates/grid.mako --- a/templates/grid.mako Fri May 01 12:24:24 2009 -0400 +++ b/templates/grid.mako Fri May 01 17:19:17 2009 -0400 @@ -85,9 +85,7 @@ %endfor </div> -<form name="history_actions" action="${h.url_for()}" method="post" > - - <input type="hidden" name="sort" value="${sort_key}"> +<form name="history_actions" action="${url()}" method="post" > <table class="grid"> <thead>

1 0

[hg] galaxy 2393: Updating packed script for workflow editor
by Greg Von Kuster 01 May '09

01 May '09

details: http://www.bx.psu.edu/hg/galaxy/rev/a9d5f8e80bcd changeset: 2393:a9d5f8e80bcd user: James Taylor <james(a)jamestaylor.org> date: Fri May 01 12:24:07 2009 -0400 description: Updating packed script for workflow editor 1 file(s) affected in this change: static/scripts/packed/galaxy.workflow_editor.canvas.js diffs (8 lines): diff -r 84ecf82a2ce7 -r a9d5f8e80bcd static/scripts/packed/galaxy.workflow_editor.canvas.js --- a/static/scripts/packed/galaxy.workflow_editor.canvas.js Fri May 01 11:09:04 2009 -0400 +++ b/static/scripts/packed/galaxy.workflow_editor.canvas.js Fri May 01 12:24:07 2009 -0400 @@ -1,1 +1,1 @@ -function Terminal(a){this.element=a;this.connectors=[]}Terminal.prototype={connect:function(a){this.connectors.push(a);if(this.node){this.node.changed()}},disconnect:function(a){this.connectors.splice($.inArray(a,this.connectors),1);if(this.node){this.node.changed()}},redraw:function(){$.each(this.connectors,function(a,b){b.redraw()})},destroy:function(){$.each(this.connectors.slice(),function(a,b){b.destroy()})}};function OutputTerminal(a,b){Terminal.call(this,a);this.datatype=b}OutputTerminal.prototype=new Terminal;function InputTerminal(a,b){Terminal.call(this,a);this.datatypes=b}InputTerminal.prototype=new Terminal;$.extend(InputTerminal.prototype,{can_accept:function(a){if(this.connectors.length<1){for(t in this.datatypes){if(a.datatype=="input"){return true}if(issubtype(a.datatype,this.datatypes[t])){return true}}}return false}});function Connector(b,a){this.canvas=null;this.dragging=false;this.inner_color="#FFFFFF";this.outer_color="#D8B365";if(b&&a){this.connect(b,a) }}$.extend(Connector.prototype,{connect:function(b,a){this.handle1=b;this.handle1.connect(this);this.handle2=a;this.handle2.connect(this)},destroy:function(){if(this.handle1){this.handle1.disconnect(this)}if(this.handle2){this.handle2.disconnect(this)}$(this.canvas).remove()},redraw:function(){var d=$("#canvas-container");if(!this.canvas){this.canvas=document.createElement("canvas");if(window.G_vmlCanvasManager){G_vmlCanvasManager.initElement(this.canvas)}d.append($(this.canvas));if(this.dragging){this.canvas.style.zIndex="300"}}var m=function(c){return $(c).offset().left-d.offset().left};var h=function(c){return $(c).offset().top-d.offset().top};var g=m(this.handle1.element)+5;var f=h(this.handle1.element)+5;var o=m(this.handle2.element)+5;var l=h(this.handle2.element)+5;var e=100;var j=Math.min(g,o);var a=Math.max(g,o);var i=Math.min(f,l);var s=Math.max(f,l);var b=Math.min(Math.max(Math.abs(s-i)/2,100),300);var n=j-e;var r=i-e;var p=a-j+2*e;var k=s-i+2*e;this.canvas.style. left=n+"px";this.canvas.style.top=r+"px";this.canvas.setAttribute("width",p);this.canvas.setAttribute("height",k);g-=n;f-=r;o-=n;l-=r;var q=this.canvas.getContext("2d");q.lineCap="round";q.strokeStyle=this.outer_color;q.lineWidth=7;q.beginPath();q.moveTo(g,f);q.bezierCurveTo(g+b,f,o-b,l,o,l);q.stroke();q.strokeStyle=this.inner_color;q.lineWidth=5;q.beginPath();q.moveTo(g,f);q.bezierCurveTo(g+b,f,o-b,l,o,l);q.stroke()}});function Node(a){this.element=a;this.input_terminals={};this.output_terminals={};this.tool_errors={}}$.extend(Node.prototype,{enable_input_terminal:function(d,a,b){var c=this;$(d).each(function(){var e=this.terminal=new InputTerminal(this,b);e.node=c;e.name=a;$(this).bind("dropstart",function(f){f.dragProxy.terminal.connectors[0].inner_color="#BBFFBB"}).bind("dropend",function(f){f.dragProxy.terminal.connectors[0].inner_color="#FFFFFF"}).bind("drop",function(f){new Connector(f.dragTarget.terminal,f.dropTarget.terminal).redraw()}).bind("hover",function(){if(e. connectors.length>0){var f=$("<div class='callout'></div>").css({display:"none"}).appendTo("body").append($("<div class='buttons'></div>").append($("<img src='../images/delete_icon.png' />").click(function(){$.each(e.connectors,function(h,g){g.destroy()});f.remove()}))).bind("mouseleave",function(){$(this).remove()});f.css({top:$(this).offset().top-2,left:$(this).offset().left-f.width(),"padding-right":$(this).width()}).show()}});c.input_terminals[a]=e})},enable_output_terminal:function(d,a,b){var c=this;$(d).each(function(){var f=this;var e=this.terminal=new OutputTerminal(this,b);e.node=c;e.name=a;$(this).bind("dragstart",function(i){var g=$('<div class="drag-terminal" style="position: absolute;"></div>').appendTo("#canvas-container").get(0);g.terminal=new OutputTerminal(g);var j=new Connector();j.dragging=true;j.connect(this.terminal,g.terminal);$.dropManage({filter:function(h){return this.terminal.can_accept(e)}}).addClass("input-terminal-active");return g}).bind("drag", function(h){var g=function(){var j=$(h.dragProxy).offsetParent().offset(),i=h.offsetX-j.left,k=h.offsetY-j.top;$(h.dragProxy).css({left:i,top:k});h.dragProxy.terminal.redraw()};g();$("#canvas-container").get(0).scroll_panel.test(h,g)}).bind("dragend",function(g){g.dragProxy.terminal.connectors[0].destroy();$(g.dragProxy).remove();$.dropManage().removeClass("input-terminal-active")});c.output_terminals[a]=e})},redraw:function(){$.each(this.input_terminals,function(a,b){b.redraw()});$.each(this.output_terminals,function(a,b){b.redraw()})},destroy:function(){$.each(this.input_terminals,function(a,b){b.destroy()});$.each(this.output_terminals,function(a,b){b.destroy()});workflow.remove_node(this);$(this.element).remove()},make_active:function(){$(this.element).addClass("toolForm-active")},make_inactive:function(){var a=this.element.get(0);(function(b){b.removeChild(a);b.appendChild(a)})(a.parentNode);$(a).removeClass("toolForm-active")},init_field_data:function(e){var d=this.ele ment;if(e.type){this.type=e.type}this.form_html=e.form_html;this.tool_state=e.tool_state;this.tool_errors=e.tool_errors;if(this.tool_errors){d.addClass("tool-node-error")}else{d.removeClass("tool-node-error")}var c=this;var a=d.find(".toolFormBody");a.find("div").remove();var g=$("<div class='inputs'></div>").appendTo(a);$.each(e.data_inputs,function(h,b){var f=$("<div class='terminal input-terminal'></div>");c.enable_input_terminal(f,b.name,b.extensions);g.append($("<div class='form-row dataRow input-data-row' name='"+b.name+"'>"+b.label+"</div>").prepend(f))});if((e.data_inputs.length>0)&&(e.data_outputs.length>0)){a.append($("<div class='rule'></div>"))}$.each(e.data_outputs,function(j,b){var h=$("<div class='terminal output-terminal'></div>");c.enable_output_terminal(h,b.name,b.extension);var f=b.name;if(b.extension!="input"){f=f+" ("+b.extension+")"}a.append($("<div class='form-row dataRow'>"+f+"</div>").append(h))});workflow.node_changed(this)},update_field_data:functi on(e){var c=$(this.element),d=this;this.tool_state=e.tool_state;this.form_html=e.form_html;this.tool_errors=e.tool_errors;if(this.tool_errors){c.addClass("tool-node-error")}else{c.removeClass("tool-node-error")}var f=c.find("div.inputs");var b=$("<div class='inputs'></div>");var a=f.find("div.input-data-row");$.each(e.data_inputs,function(j,g){var h=$("<div class='terminal input-terminal'></div>");d.enable_input_terminal(h,g.name,g.extensions);f.find("div[name="+g.name+"]").each(function(){$(this).find(".input-terminal").each(function(){var i=this.terminal.connectors[0];if(i){h[0].terminal.connectors[0]=i;i.handle2=h[0].terminal}});$(this).remove()});b.append($("<div class='form-row dataRow input-data-row' name='"+g.name+"'>"+g.label+"</div>").prepend(h))});f.replaceWith(b);f.find("div.input-data-row > .terminal").each(function(){this.terminal.destroy()});this.changed();this.redraw()},error:function(d){var a=$(this.element).find(".toolFormBody");a.find("div").remove();var c= "<div style='color: red; text-style: italic;'>"+d+"</div>";this.form_html=c;a.html(c);workflow.node_changed(this)},changed:function(){workflow.node_changed(this)}});function Workflow(){this.id_counter=0;this.nodes={};this.name=null;this.has_changes=false}$.extend(Workflow.prototype,{add_node:function(a){a.id=this.id_counter;a.element.attr("id","wf-node-step-"+a.id);this.id_counter++;this.nodes[a.id]=a;this.has_changes=true;a.workflow=this},remove_node:function(a){if(this.active_node==a){this.clear_active_node()}delete this.nodes[a.id];this.has_changes=true},remove_all:function(){wf=this;$.each(this.nodes,function(b,a){a.destroy();wf.remove_node(a)})},to_simple:function(){var a={};$.each(this.nodes,function(b,d){var e={};$.each(d.input_terminals,function(f,g){e[g.name]=null;$.each(g.connectors,function(h,j){e[g.name]={id:j.handle1.node.id,output_name:j.handle1.name}})});var c={id:d.id,type:d.type,tool_id:d.tool_id,tool_state:d.tool_state,tool_errors:d.tool_errors,input_connec tions:e,position:$(d.element).position()};a[d.id]=c});return{steps:a}},from_simple:function(a){wf=this;var b=0;wf.name=a.name;$.each(a.steps,function(e,d){var c=prebuild_node("tool",d.name,d.tool_id);c.init_field_data(d);if(d.position){c.element.css({top:d.position.top,left:d.position.left})}c.id=d.id;wf.nodes[c.id]=c;b=Math.max(b,parseInt(e))});wf.id_counter=b+1;$.each(a.steps,function(e,d){var c=wf.nodes[e];$.each(d.input_connections,function(g,f){if(f){var h=wf.nodes[f.id];var i=new Connector();i.connect(h.output_terminals[f.output_name],c.input_terminals[g]);i.redraw()}})})},clear_active_node:function(){if(this.active_node){this.active_node.make_inactive();this.active_node=null}parent.show_form_for_tool("<div>No node selected</div>")},activate_node:function(a){if(this.active_node!=a){this.clear_active_node();parent.show_form_for_tool(a.form_html,a);a.make_active();this.active_node=a}},node_changed:function(a){this.has_changes=true;if(this.active_node==a){parent.show_form _for_tool(a.form_html,a)}}});function prebuild_node(j,h,m){var g=$("<div class='toolForm toolFormInCanvas'></div>");var d=new Node(g);d.type=j;if(j=="tool"){d.tool_id=m}var l=$("<div class='toolFormTitle unselectable'>"+h+"</div>");g.append(l);g.css("left",$(window).scrollLeft()+20);g.css("top",$(window).scrollTop()+20);var k=$("<div class='toolFormBody'></div>");var e="<div><img height='16' align='middle' src='../images/loading_small_white_bg.gif'/> loading tool info...</div>";k.append(e);d.form_html=e;g.append(k);var i=$("<div class='buttons' style='float: right;'></div>");i.append($("<img src='../images/delete_icon.png' />").click(function(b){d.destroy()}).hover(function(){$(this).attr("src","../images/delete_icon_dark.png")},function(){$(this).attr("src","../images/delete_icon.png")}));g.appendTo("#canvas-container");var c=$("#canvas-container").position();g.css({left:(-c.left)+10,top:(-c.top)+10});var a=g.width();i.prependTo(l);a+=(i.width()+10);g.css("width",a);$(g).bi nd("dragstart",function(){workflow.activate_node(d)}).bind("dragend",function(){workflow.node_changed(this)}).bind("dragclickonly",function(){workflow.activate_node(d)}).bind("drag",function(n){var f=$(this).offsetParent().offset(),b=n.offsetX-f.left,o=n.offsetY-f.top;$(this).css({left:b,top:o});$(this).find(".terminal").each(function(){this.terminal.redraw()})});return d}var ext_to_type=null;var type_to_type=null;function issubtype(b,a){b=ext_to_type[b];a=ext_to_type[a];return(a in type_to_type[b])}function populate_datatype_info(a){ext_to_type=a.ext_to_class_name;type_to_type=a.class_to_classes}function ScrollPanel(a){this.panel=a}$.extend(ScrollPanel.prototype,{test:function(f,c){clearTimeout(this.timeout);var a=f.pageX,g=f.pageY;b=$(this.panel),panel_pos=b.position(),panel_w=b.width(),panel_h=b.height();viewport=b.parent();viewport_w=viewport.width(),viewport_h=viewport.height(),viewport_offset=viewport.offset(),min_x=viewport_offset.left,min_y=viewport_offset.top,max_x= min_x+viewport.width(),max_y=min_y+viewport.height(),p_min_x=-(panel_w-viewport_w),p_min_y=-(panel_h-viewport_h),p_max_x=0,p_max_y=0,moved=false,close_dist=5,nudge=23;if(a-close_dist<min_x){if(panel_pos.left<p_max_x){var d=Math.min(nudge,p_max_x-panel_pos.left);b.css("left",panel_pos.left+d);moved=true}}else{if(a+close_dist>max_x){if(panel_pos.left>p_min_x){var d=Math.min(nudge,panel_pos.left-p_min_x);b.css("left",panel_pos.left-d);moved=true}}else{if(g-close_dist<min_y){if(panel_pos.top<p_max_y){var d=Math.min(nudge,p_max_y-panel_pos.top);b.css("top",panel_pos.top+d);moved=true}}else{if(g+close_dist>max_y){if(panel_pos.top>p_min_y){var d=Math.min(nudge,panel_pos.top-p_min_x);b.css("top",(panel_pos.top-d)+"px");moved=true}}}}}if(moved){c();var b=this;this.timeout=setTimeout(function(){b.test(f,c)},50)}},drag:function(g,h){clearTimeout(this.timeout);var c=g.dragProxy,a=this.panel,b=a.position(),i=a.width(),d=a.height();viewport=a.parent();viewport_w=viewport.width(),viewport_ h=viewport.height(),element_w=c.width(),element_h=c.height(),moved=false,close_dist=5,nudge=23,p_min_x=-(i-viewport_w),p_min_y=-(d-viewport_h),p_max_x=0,p_max_y=0,min_vis_x=-b.left,max_vis_x=min_vis_x+viewport_w,min_vis_y=-b.top,max_vis_y=min_vis_y+viewport_h,mouse_x=h.position.left+instance.offset.click.left;mouse_y=h.position.top+instance.offset.click.top;if((b.left<p_max_x)&&(mouse_x-close_dist<min_vis_x)){var j=Math.min(nudge,p_max_x-b.left);a.css("left",b.left+j);moved=true;instance.offset.parent.left+=j;h.position.left-=j}if((!moved)&&(b.left>p_min_x)&&(mouse_x+close_dist>max_vis_x)){var j=Math.min(nudge,b.left-p_min_x);a.css("left",b.left-j);moved=true;instance.offset.parent.left-=j;h.position.left+=j}if((!moved)&&(b.top<p_max_y)&&(mouse_y-close_dist<min_vis_y)){var j=Math.min(nudge,p_max_y-b.top);a.css("top",b.top+j);var f=a.position().top-b.top;instance.offset.parent.top+=f;h.position.top-=f;moved=true}if((!moved)&&(b.top>p_min_y)&&(mouse_y+close_dist>max_vis_y)){va r j=Math.min(nudge,b.top-p_min_x);a.css("top",(b.top-j)+"px");var f=b.top-a.position().top;instance.offset.parent.top-=f;h.position.top+=f;moved=true}h.position.left=Math.max(h.position.left,0);h.position.top=Math.max(h.position.top,0);h.position.left=Math.min(h.position.left,i-element_w);h.position.top=Math.min(h.position.top,d-element_h);if(moved){$.ui.ddmanager.prepareOffsets(instance,g)}if(moved){this.timeout=setTimeout(function(){instance.mouseMove(g)},50)}},stop:function(c,b){var a=$(this).data("draggable");clearTimeout(a.timeout)}}); \ No newline at end of file +function Terminal(a){this.element=a;this.connectors=[]}Terminal.prototype={connect:function(a){this.connectors.push(a);if(this.node){this.node.changed()}},disconnect:function(a){this.connectors.splice($.inArray(a,this.connectors),1);if(this.node){this.node.changed()}},redraw:function(){$.each(this.connectors,function(a,b){b.redraw()})},destroy:function(){$.each(this.connectors.slice(),function(a,b){b.destroy()})}};function OutputTerminal(a,b){Terminal.call(this,a);this.datatype=b}OutputTerminal.prototype=new Terminal;function InputTerminal(a,b){Terminal.call(this,a);this.datatypes=b}InputTerminal.prototype=new Terminal;$.extend(InputTerminal.prototype,{can_accept:function(a){if(this.connectors.length<1){for(t in this.datatypes){if(a.datatype=="input"){return true}if(issubtype(a.datatype,this.datatypes[t])){return true}}}return false}});function Connector(b,a){this.canvas=null;this.dragging=false;this.inner_color="#FFFFFF";this.outer_color="#D8B365";if(b&&a){this.connect(b,a) }}$.extend(Connector.prototype,{connect:function(b,a){this.handle1=b;this.handle1.connect(this);this.handle2=a;this.handle2.connect(this)},destroy:function(){if(this.handle1){this.handle1.disconnect(this)}if(this.handle2){this.handle2.disconnect(this)}$(this.canvas).remove()},redraw:function(){var d=$("#canvas-container");if(!this.canvas){this.canvas=document.createElement("canvas");if(window.G_vmlCanvasManager){G_vmlCanvasManager.initElement(this.canvas)}d.append($(this.canvas));if(this.dragging){this.canvas.style.zIndex="300"}}var o=function(c){return $(c).offset().left-d.offset().left};var j=function(c){return $(c).offset().top-d.offset().top};var i=o(this.handle1.element)+5;var g=j(this.handle1.element)+5;var q=o(this.handle2.element)+5;var n=j(this.handle2.element)+5;var f=100;var l=Math.min(i,q);var a=Math.max(i,q);var k=Math.min(g,n);var v=Math.max(g,n);var b=Math.min(Math.max(Math.abs(v-k)/2,100),300);var p=l-f;var u=k-f;var r=a-l+2*f;var m=v-k+2*f;this.canvas.style. left=p+"px";this.canvas.style.top=u+"px";this.canvas.setAttribute("width",r);this.canvas.setAttribute("height",m);i-=p;g-=u;q-=p;n-=u;var s=this.canvas.getContext("2d");s.lineCap="round";s.strokeStyle=this.outer_color;s.lineWidth=7;s.beginPath();s.moveTo(i,g);s.bezierCurveTo(i+b,g,q-b,n,q,n);s.stroke();s.strokeStyle=this.inner_color;s.lineWidth=5;s.beginPath();s.moveTo(i,g);s.bezierCurveTo(i+b,g,q-b,n,q,n);s.stroke()}});function Node(a){this.element=a;this.input_terminals={};this.output_terminals={};this.tool_errors={}}$.extend(Node.prototype,{enable_input_terminal:function(d,a,b){var c=this;$(d).each(function(){var f=this.terminal=new InputTerminal(this,b);f.node=c;f.name=a;$(this).bind("dropstart",function(g){g.dragProxy.terminal.connectors[0].inner_color="#BBFFBB"}).bind("dropend",function(g){g.dragProxy.terminal.connectors[0].inner_color="#FFFFFF"}).bind("drop",function(g){new Connector(g.dragTarget.terminal,g.dropTarget.terminal).redraw()}).bind("hover",function(){if(f. connectors.length>0){var g=$("<div class='callout'></div>").css({display:"none"}).appendTo("body").append($("<div class='buttons'></div>").append($("<img src='../images/delete_icon.png' />").click(function(){$.each(f.connectors,function(j,i){i.destroy()});g.remove()}))).bind("mouseleave",function(){$(this).remove()});g.css({top:$(this).offset().top-2,left:$(this).offset().left-g.width(),"padding-right":$(this).width()}).show()}});c.input_terminals[a]=f})},enable_output_terminal:function(d,a,b){var c=this;$(d).each(function(){var g=this;var f=this.terminal=new OutputTerminal(this,b);f.node=c;f.name=a;$(this).bind("dragstart",function(j){var i=$('<div class="drag-terminal" style="position: absolute;"></div>').appendTo("#canvas-container").get(0);i.terminal=new OutputTerminal(i);var k=new Connector();k.dragging=true;k.connect(this.terminal,i.terminal);$.dropManage({filter:function(l){return this.terminal.can_accept(f)}}).addClass("input-terminal-active");return i}).bind("drag", function(j){var i=function(){var l=$(j.dragProxy).offsetParent().offset(),k=j.offsetX-l.left,m=j.offsetY-l.top;$(j.dragProxy).css({left:k,top:m});j.dragProxy.terminal.redraw();canvas_manager.update_viewport_overlay()};i();$("#canvas-container").get(0).scroll_panel.test(j,i)}).bind("dragend",function(i){i.dragProxy.terminal.connectors[0].destroy();$(i.dragProxy).remove();$.dropManage().removeClass("input-terminal-active");$("#canvas-container").get(0).scroll_panel.stop()});c.output_terminals[a]=f})},redraw:function(){$.each(this.input_terminals,function(a,b){b.redraw()});$.each(this.output_terminals,function(a,b){b.redraw()})},destroy:function(){$.each(this.input_terminals,function(a,b){b.destroy()});$.each(this.output_terminals,function(a,b){b.destroy()});workflow.remove_node(this);$(this.element).remove()},make_active:function(){$(this.element).addClass("toolForm-active")},make_inactive:function(){var a=this.element.get(0);(function(b){b.removeChild(a);b.appendChild(a)})(a. parentNode);$(a).removeClass("toolForm-active")},init_field_data:function(g){var d=this.element;if(g.type){this.type=g.type}this.name=g.name;this.form_html=g.form_html;this.tool_state=g.tool_state;this.tool_errors=g.tool_errors;if(this.tool_errors){d.addClass("tool-node-error")}else{d.removeClass("tool-node-error")}var c=this;var a=d.find(".toolFormBody");a.find("div").remove();var i=$("<div class='inputs'></div>").appendTo(a);$.each(g.data_inputs,function(j,b){var f=$("<div class='terminal input-terminal'></div>");c.enable_input_terminal(f,b.name,b.extensions);i.append($("<div class='form-row dataRow input-data-row' name='"+b.name+"'>"+b.label+"</div>").prepend(f))});if((g.data_inputs.length>0)&&(g.data_outputs.length>0)){a.append($("<div class='rule'></div>"))}$.each(g.data_outputs,function(k,b){var j=$("<div class='terminal output-terminal'></div>");c.enable_output_terminal(j,b.name,b.extension);var f=b.name;if(b.extension!="input"){f=f+" ("+b.extension+")"}a.append($("<d iv class='form-row dataRow'>"+f+"</div>").append(j))});workflow.node_changed(this)},update_field_data:function(f){var c=$(this.element),d=this;this.tool_state=f.tool_state;this.form_html=f.form_html;this.tool_errors=f.tool_errors;if(this.tool_errors){c.addClass("tool-node-error")}else{c.removeClass("tool-node-error")}var g=c.find("div.inputs");var b=$("<div class='inputs'></div>");var a=g.find("div.input-data-row");$.each(f.data_inputs,function(l,j){var k=$("<div class='terminal input-terminal'></div>");d.enable_input_terminal(k,j.name,j.extensions);g.find("div[name="+j.name+"]").each(function(){$(this).find(".input-terminal").each(function(){var i=this.terminal.connectors[0];if(i){k[0].terminal.connectors[0]=i;i.handle2=k[0].terminal}});$(this).remove()});b.append($("<div class='form-row dataRow input-data-row' name='"+j.name+"'>"+j.label+"</div>").prepend(k))});g.replaceWith(b);g.find("div.input-data-row > .terminal").each(function(){this.terminal.destroy()});this.changed( );this.redraw()},error:function(d){var a=$(this.element).find(".toolFormBody");a.find("div").remove();var c="<div style='color: red; text-style: italic;'>"+d+"</div>";this.form_html=c;a.html(c);workflow.node_changed(this)},changed:function(){workflow.node_changed(this)}});function Workflow(a){this.canvas_container=a;this.id_counter=0;this.nodes={};this.name=null;this.has_changes=false}$.extend(Workflow.prototype,{add_node:function(a){a.id=this.id_counter;a.element.attr("id","wf-node-step-"+a.id);this.id_counter++;this.nodes[a.id]=a;this.has_changes=true;a.workflow=this},remove_node:function(a){if(this.active_node==a){this.clear_active_node()}delete this.nodes[a.id];this.has_changes=true},remove_all:function(){wf=this;$.each(this.nodes,function(b,a){a.destroy();wf.remove_node(a)})},to_simple:function(){var a={};$.each(this.nodes,function(b,d){var f={};$.each(d.input_terminals,function(g,i){f[i.name]=null;$.each(i.connectors,function(j,k){f[i.name]={id:k.handle1.node.id,output _name:k.handle1.name}})});var c={id:d.id,type:d.type,tool_id:d.tool_id,tool_state:d.tool_state,tool_errors:d.tool_errors,input_connections:f,position:$(d.element).position()};a[d.id]=c});return{steps:a}},from_simple:function(a){wf=this;var b=0;wf.name=a.name;$.each(a.steps,function(f,d){var c=prebuild_node("tool",d.name,d.tool_id);c.init_field_data(d);if(d.position){c.element.css({top:d.position.top,left:d.position.left})}c.id=d.id;wf.nodes[c.id]=c;b=Math.max(b,parseInt(f))});wf.id_counter=b+1;$.each(a.steps,function(f,d){var c=wf.nodes[f];$.each(d.input_connections,function(i,g){if(g){var j=wf.nodes[g.id];var l=new Connector();l.connect(j.output_terminals[g.output_name],c.input_terminals[i]);l.redraw()}})})},clear_active_node:function(){if(this.active_node){this.active_node.make_inactive();this.active_node=null}parent.show_form_for_tool("<div>No node selected</div>")},activate_node:function(a){if(this.active_node!=a){this.clear_active_node();parent.show_form_for_tool(a.form _html,a);a.make_active();this.active_node=a}},node_changed:function(a){this.has_changes=true;if(this.active_node==a){parent.show_form_for_tool(a.form_html,a)}},layout:function(){var a={};var b={};$.each(this.nodes,function(i,g){if(a[i]===undefined){a[i]=0}if(b[i]===undefined){b[i]=[]}});$.each(this.nodes,function(i,g){$.each(g.input_terminals,function(k,l){$.each(l.connectors,function(m,n){var j=n.handle1.node;a[g.id]+=1;b[j.id].push(g.id)})})});node_ids_by_level=[];while(true){level_parents=[];$.each(a,function(i,g){if(g==0){level_parents.push(i)}});if(level_parents.length==0){break}node_ids_by_level.push(level_parents);$.each(level_parents,function(i,g){delete a[g];$.each(b[g],function(k,j){a[j]-=1})})}if(a.length){return}var d=this.nodes;var c=80;v_pad=30;var f=c;$.each(node_ids_by_level,function(g,j){j.sort(function(m,i){return $(d[m].element).position().top-$(d[i].element).position().top});var k=0;var l=v_pad;$.each(j,function(i,o){var n=d[o];var m=$(n.element);$(m).css ({top:l,left:f});k=Math.max(k,$(m).width());l+=$(m).height()+v_pad});f+=k+c});$.each(d,function(g,i){i.redraw()})},bounds_for_all_nodes:function(){var d=Infinity,b=-Infinity,c=Infinity,a=-Infinity,f;$.each(this.nodes,function(i,g){e=$(g.element);f=e.position();d=Math.min(d,f.left);b=Math.max(b,f.left+e.width());c=Math.min(c,f.top);a=Math.max(a,f.top+e.width())});return{xmin:d,xmax:b,ymin:c,ymax:a}},fit_canvas_to_nodes:function(){var a=this.bounds_for_all_nodes();var f=this.canvas_container.position();var j=this.canvas_container.parent();var d=fix_delta(a.xmin,100);var i=fix_delta(a.ymin,100);d=Math.max(d,f.left);i=Math.max(i,f.top);var c=f.left-d;var g=f.top-i;var b=round_up(a.xmax+100,100)+d;var k=round_up(a.ymax+100,100)+i;b=Math.max(b,-c+j.width());k=Math.max(k,-g+j.height());this.canvas_container.css({left:c,top:g,width:b,height:k,});this.canvas_container.children().each(function(){var l=$(this).position();$(this).css("left",l.left+d);$(this).css("top",l.top+i)})}});func tion fix_delta(a,b){if(a<b||a>3*b){new_pos=(Math.ceil(((a%b))/b)+1)*b;return(-(a-new_pos))}return 0}function round_up(a,b){return Math.ceil(a/b)*b}function prebuild_node(m,k,s){var j=$("<div class='toolForm toolFormInCanvas'></div>");var g=new Node(j);g.type=m;if(m=="tool"){g.tool_id=s}var q=$("<div class='toolFormTitle unselectable'>"+k+"</div>");j.append(q);j.css("left",$(window).scrollLeft()+20);j.css("top",$(window).scrollTop()+20);var n=$("<div class='toolFormBody'></div>");var i="<div><img height='16' align='middle' src='../images/loading_small_white_bg.gif'/> loading tool info...</div>";n.append(i);g.form_html=i;j.append(n);var l=$("<div class='buttons' style='float: right;'></div>");l.append($("<img src='../images/delete_icon.png' />").click(function(b){g.destroy()}).hover(function(){$(this).attr("src","../images/delete_icon_dark.png")},function(){$(this).attr("src","../images/delete_icon.png")}));j.appendTo("#canvas-container");var d=$("#canvas-container").position( );var c=$("#canvas-container").parent();var a=j.width();var r=j.height();j.css({left:(-d.left)+(c.width()/2)-(a/2),top:(-d.top)+(c.height()/2)-(r/2)});l.prependTo(q);a+=(l.width()+10);j.css("width",a);$(j).bind("dragstart",function(){workflow.activate_node(g)}).bind("dragend",function(){workflow.node_changed(this);workflow.fit_canvas_to_nodes();canvas_manager.draw_overview()}).bind("dragclickonly",function(){workflow.activate_node(g)}).bind("drag",function(o){var f=$(this).offsetParent().offset(),b=o.offsetX-f.left,p=o.offsetY-f.top;$(this).css({left:b,top:p});$(this).find(".terminal").each(function(){this.terminal.redraw()})});return g}var ext_to_type=null;var type_to_type=null;function issubtype(b,a){b=ext_to_type[b];a=ext_to_type[a];return(type_to_type[b])&&(a in type_to_type[b])}function populate_datatype_info(a){ext_to_type=a.ext_to_class_name;type_to_type=a.class_to_classes}function ScrollPanel(a){this.panel=a}$.extend(ScrollPanel.prototype,{test:function(f,c){clearTim eout(this.timeout);var a=f.pageX,g=f.pageY;b=$(this.panel),panel_pos=b.position(),panel_w=b.width(),panel_h=b.height();viewport=b.parent();viewport_w=viewport.width(),viewport_h=viewport.height(),viewport_offset=viewport.offset(),min_x=viewport_offset.left,min_y=viewport_offset.top,max_x=min_x+viewport.width(),max_y=min_y+viewport.height(),p_min_x=-(panel_w-(viewport_w/2)),p_min_y=-(panel_h-(viewport_h/2)),p_max_x=(viewport_w/2),p_max_y=(viewport_h/2),moved=false,close_dist=5,nudge=23;if(a-close_dist<min_x){if(panel_pos.left<p_max_x){var d=Math.min(nudge,p_max_x-panel_pos.left);b.css("left",panel_pos.left+d);moved=true}}else{if(a+close_dist>max_x){if(panel_pos.left>p_min_x){var d=Math.min(nudge,panel_pos.left-p_min_x);b.css("left",panel_pos.left-d);moved=true}}else{if(g-close_dist<min_y){if(panel_pos.top<p_max_y){var d=Math.min(nudge,p_max_y-panel_pos.top);b.css("top",panel_pos.top+d);moved=true}}else{if(g+close_dist>max_y){if(panel_pos.top>p_min_y){var d=Math.min(nudge,pane l_pos.top-p_min_x);b.css("top",(panel_pos.top-d)+"px");moved=true}}}}}if(moved){c();var b=this;this.timeout=setTimeout(function(){b.test(f,c)},50)}},stop:function(b,a){clearTimeout(this.timeout)}});function CanvasManager(b,a){this.cv=b;this.cc=this.cv.find("#canvas-container");this.oc=a.find("#overview-canvas");this.ov=a.find("#overview-viewport");this.init_drag()}$.extend(CanvasManager.prototype,{init_drag:function(){var b=this;var a=function(f,g){f=Math.min(f,b.cv.width()/2);f=Math.max(f,-b.cc.width()+b.cv.width()/2);g=Math.min(g,b.cv.height()/2);g=Math.max(g,-b.cc.height()+b.cv.height()/2);b.cc.css({left:f,top:g});b.update_viewport_overlay()};this.cc.each(function(){this.scroll_panel=new ScrollPanel(this)});var d,c;this.cv.bind("dragstart",function(g){var i=$(this).offset();var f=b.cc.position();c=f.top-i.top;d=f.left-i.left}).bind("drag",function(f){a(f.offsetX+d,f.offsetY+c)}).bind("dragend",function(){workflow.fit_canvas_to_nodes();b.draw_overview()});this.ov.bind("dra g",function(l){var k=b.cc.width();var g=b.cc.height();var f=b.oc.width();var i=b.oc.height();var j=$(this).offsetParent().offset();var n=l.offsetX-j.left;var m=l.offsetY-j.top;a(-(n/f*k),-(m/i*g))}).bind("dragend",function(){workflow.fit_canvas_to_nodes();b.draw_overview()});$("#overview-border").bind("drag",function(g){var j=$(this).offsetParent();var i=j.offset();var f=Math.max(j.width()-(g.offsetX-i.left),j.height()-(g.offsetY-i.top));$(this).css({width:f,height:f});b.draw_overview()})},update_viewport_overlay:function(){var b=this.cc;var f=this.cv;var a=this.oc;var c=this.ov;var d=b.width();var k=b.height();var j=a.width();var g=a.height();var i=b.position();c.css({left:-(i.left/d*j),top:-(i.top/k*g),width:(f.width()/d*j)-2,height:(f.height()/k*g)-2})},draw_overview:function(){var k=$("#overview-canvas");var n=k.parent().parent().width();var j=k.get(0).getContext("2d");var d=$("#canvas-container").width();var m=$("#canvas-container").height();var g,a,l,f;var i=this.cv.wi dth();var b=this.cv.height();if(d<i&&m<b){l=d/i*n;f=(n-l)/2;g=m/b*n;a=(n-g)/2}else{if(d<m){a=0;g=n;l=Math.ceil(g*d/m);f=(n-l)/2}else{l=n;f=0;g=Math.ceil(l*m/d);a=(n-g)/2}}k.parent().css({left:f,top:a,width:l,height:g});k.attr("width",l);k.attr("height",g);j.fillStyle="#D2C099";j.strokeStyle="#D8B365";j.lineWidth=1;$.each(workflow.nodes,function(p,c){var o=$(c.element);position=o.position(),x=position.left/d*l,y=position.top/m*g,w=o.width()/d*l,h=o.height()/m*g;j.fillRect(x,y,w,h);j.strokeRect(x,y,w,h)});this.update_viewport_overlay()}}); \ No newline at end of file

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[hg] galaxy 2394: Tweaking styles for quickies
by Greg Von Kuster 01 May '09

01 May '09

details: http://www.bx.psu.edu/hg/galaxy/rev/80e00a9cdeb0 changeset: 2394:80e00a9cdeb0 user: James Taylor <james(a)jamestaylor.org> date: Fri May 01 12:24:24 2009 -0400 description: Tweaking styles for quickies 1 file(s) affected in this change: static/welcome.html diffs (108 lines): diff -r a9d5f8e80bcd -r 80e00a9cdeb0 static/welcome.html --- a/static/welcome.html Fri May 01 12:24:07 2009 -0400 +++ b/static/welcome.html Fri May 01 12:24:24 2009 -0400 @@ -8,39 +8,22 @@ <style type="text/css"> .quickie { text-align: center; - min-height: 100px; background: black; + margin: 10px; } .current-quickie { width: 100%; background: black; } - .quickie .head { - font-size: 200%; - color: white; - padding: 20px 20px; - } - .quickie .sub { - font-size: 150%; - color: orange; - padding: 20px 20px; - } .previous { width: 100%; overflow: auto; + border: solid #ccc 1px; } .previous .quickie { + padding-top: 10px; + min-height: 90px; min-width: 150px; - } - .previous .quickie .head { - font-size: 120%; - padding: 10px 10px; - text-decoration: none; - } - .previous .quickie .sub { - font-size: 100%; - padding: 10px 10px; - text-decoration: none; } #screencasts { max-width: 50em; @@ -64,7 +47,6 @@ <div id="screencasts"> <h2>Introducing Galactic Quickies</h2> -<hr> <p> Galactic quickies are <i>super-short</i> screencasts that are <i>always</i> under 5 minutes. We thought it may be a good way to spread the word about Galaxy's functionality while keeping the "annoyance factor" to the minimum. The quickies will be updated weekly. </p> @@ -84,35 +66,32 @@ </div> <h3>Previous Quickies</h3> -<hr> -<div class="previous"> +<div class="previous" id="previous"> <table border="0" cellpadding="0" cellspacing="0" width="100%"> <tr> - <td width="50%" style="border-right: solid white 10px; border-bottom: solid white 10px"> + <td> <a href="javascript:parent.show_in_overlay({url:'http://screencast.g2.bx.psu.edu/galaxy/quickie1_TabSeq/flow.html',width:640,height:500,scroll:'no'})"> <div class="quickie"> <img src="images/qk/quickie1_small.png" border="0"> </div> </a> </td> - <td width="50%" style="border-left: solid white 10px; border-bottom: solid white 10px"> + <td> <a href="javascript:parent.show_in_overlay({url:'http://screencast.g2.bx.psu.edu/galaxy/quickie2_Grouping/flow.html',width:640,height:500,scroll:'no'})"> <div class="quickie"> <img src="images/qk/quickie2_small.png" border="0"> </div> </a> </td> - </tr> - <tr> - <td width="50%" style="border-right: solid white 10px; border-top: solid white 10px" > + <td> <a href="javascript:parent.show_in_overlay({url:'http://screencast.g2.bx.psu.edu/galaxy/quickie3_Intervals/flow.html',width:640,height:500,scroll:'no'})"> <div class="quickie"> <img src="images/qk/quickie3_small.png" border="0"> </div> </a> </td> - <td width="50%" style="border-left: solid white 10px; border-top: solid white 10px" > + <td> <a href="javascript:parent.show_in_overlay({url:'http://screencast.g2.bx.psu.edu/galaxy/quickie4_whatsNew/flow.html',width:640,height:500,scroll:'no'})"> <div class="quickie"> <img src="images/qk/quickie4_small.png" border="0"> @@ -123,6 +102,11 @@ </table> </div> +<script type="text/javascript"> + // Scroll to last quickie in box + document.getElementById("previous").scrollLeft = 100000000; +</script> + <br/> <br/> <br/>

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