details: http://www.bx.psu.edu/hg/galaxy/rev/45033114f82d changeset: 1543:45033114f82d user: Dan Blankenberg dan@bx.psu.edu date: Thu Oct 02 16:37:32 2008 -0400 description: Add the ability to undelete deleted datasets from a history.

A new selection under History Options allows users to select a history view containing deleted (and undeletable) datasets.

Known Issues: 1. When adding a new dataset to a history (tool execution), the history is always refreshed to show only non-deleted datasets. 2. When doing an ajax delete of a dataset while viewing deleted datasets, the newly deleted dataset is still removed from the current view of the history (instead of appearing with the deleted message), a refresh will bring it back.

8 file(s) affected in this change:

lib/galaxy/model/__init__.py lib/galaxy/model/mapping.py lib/galaxy/util/__init__.py lib/galaxy/web/controllers/dataset.py lib/galaxy/web/controllers/root.py templates/history/options.mako templates/root/history.mako templates/root/history_common.mako

diffs (190 lines):

diff -r 20591fa0d05d -r 45033114f82d lib/galaxy/model/__init__.py --- a/lib/galaxy/model/__init__.py Thu Oct 02 15:51:17 2008 -0400 +++ b/lib/galaxy/model/__init__.py Thu Oct 02 16:37:32 2008 -0400 @@ -281,7 +281,15 @@ for child in self.children: child.mark_deleted()

- + def mark_undeleted( self, include_children=True ): + self.deleted = False + if include_children: + for child in self.children: + child.mark_undeleted() + def undeletable( self ): + if self.purged: + return False + return True

class History( object ): def __init__( self, id=None, name=None, user=None ): diff -r 20591fa0d05d -r 45033114f82d lib/galaxy/model/mapping.py --- a/lib/galaxy/model/mapping.py Thu Oct 02 15:51:17 2008 -0400 +++ b/lib/galaxy/model/mapping.py Thu Oct 02 16:37:32 2008 -0400 @@ -288,7 +288,9 @@ assign_mapper( context, History, History.table, properties=dict( galaxy_sessions=relation( GalaxySessionToHistoryAssociation ), datasets=relation( HistoryDatasetAssociation, backref="history", order_by=asc(HistoryDatasetAssociation.table.c.hid) ), - active_datasets=relation( HistoryDatasetAssociation, primaryjoin=( ( HistoryDatasetAssociation.table.c.history_id == History.table.c.id ) & ( not_( HistoryDatasetAssociation.table.c.deleted ) ) ), order_by=asc( HistoryDatasetAssociation.table.c.hid ), lazy=False, viewonly=True ) ) ) + active_datasets=relation( HistoryDatasetAssociation, primaryjoin=( ( HistoryDatasetAssociation.table.c.history_id == History.table.c.id ) & ( not_( HistoryDatasetAssociation.table.c.deleted ) ) ), order_by=asc( HistoryDatasetAssociation.table.c.hid ), lazy=False, viewonly=True ), + activatable_datasets=relation( HistoryDatasetAssociation, primaryjoin=( ( HistoryDatasetAssociation.table.c.history_id == History.table.c.id ) & ( not_( Dataset.table.c.purged ) ) ), order_by=asc( HistoryDatasetAssociation.table.c.hid ), lazy=False, viewonly=True ) + ) )

assign_mapper( context, User, User.table, properties=dict( histories=relation( History, backref="user", diff -r 20591fa0d05d -r 45033114f82d lib/galaxy/util/__init__.py --- a/lib/galaxy/util/__init__.py Thu Oct 02 15:51:17 2008 -0400 +++ b/lib/galaxy/util/__init__.py Thu Oct 02 16:37:32 2008 -0400 @@ -206,7 +206,7 @@ return ''

def string_as_bool( string ): - if string.lower() in ( 'true', 'yes', 'on' ): + if str( string ).lower() in ( 'true', 'yes', 'on' ): return True else: return False diff -r 20591fa0d05d -r 45033114f82d lib/galaxy/web/controllers/dataset.py --- a/lib/galaxy/web/controllers/dataset.py Thu Oct 02 15:51:17 2008 -0400 +++ b/lib/galaxy/web/controllers/dataset.py Thu Oct 02 16:37:32 2008 -0400 @@ -128,3 +128,19 @@ return open(file_path) except: raise paste.httpexceptions.HTTPNotFound( "File Not Found (%s)." % (filename) ) + + @web.expose + def undelete( self, trans, id ): + history = trans.get_history() + data = self.app.model.HistoryDatasetAssociation.get( id ) + if data and data.undeletable: + # Walk up parent datasets to find the containing history + topmost_parent = data + while topmost_parent.parent: + topmost_parent = topmost_parent.parent + assert topmost_parent in history.datasets, "Data does not belong to current history" + # Mark undeleted + data.mark_undeleted() + self.app.model.flush() + trans.log_event( "Dataset id %s has been undeleted" % str(id) ) + return trans.response.send_redirect( web.url_for( controller='root', action='history', show_deleted = True ) ) diff -r 20591fa0d05d -r 45033114f82d lib/galaxy/web/controllers/root.py --- a/lib/galaxy/web/controllers/root.py Thu Oct 02 15:51:17 2008 -0400 +++ b/lib/galaxy/web/controllers/root.py Thu Oct 02 16:37:32 2008 -0400 @@ -48,7 +48,7 @@ ## ---- Root history display ---------------------------------------------

@web.expose - def history( self, trans, as_xml=False ): + def history( self, trans, as_xml=False, show_deleted=False ): """ Display the current history, creating a new history if neccesary.

@@ -63,7 +63,7 @@ return trans.fill_template_mako( "root/history_as_xml.mako", history=history ) else: template = "root/history.mako" - return trans.fill_template( "root/history.mako", history=history ) + return trans.fill_template( "root/history.mako", history = history, show_deleted = util.string_as_bool( show_deleted ) )

@web.expose def dataset_state ( self, trans, id=None, stamp=None ): @@ -271,7 +271,7 @@ datatypes=ldatatypes, err=None )

@web.expose - def delete( self, trans, id = None, **kwd): + def delete( self, trans, id = None, show_deleted_on_refresh = False, **kwd): if id: if isinstance( id, list ): dataset_ids = id @@ -300,7 +300,7 @@ self.app.job_stop_queue.put( data.creating_job_associations[0].job ) except IndexError: pass # upload tool will cause this since it doesn't have a job - return self.history( trans ) + return self.history( trans, show_deleted = show_deleted_on_refresh )

@web.expose def delete_async( self, trans, id = None, **kwd): diff -r 20591fa0d05d -r 45033114f82d templates/history/options.mako --- a/templates/history/options.mako Thu Oct 02 15:51:17 2008 -0400 +++ b/templates/history/options.mako Thu Oct 02 16:37:32 2008 -0400 @@ -19,6 +19,7 @@ <li><a href="${h.url_for( controller='workflow', action='build_from_current_history' )}">Construct workflow</a> from the current history</li> <li><a href="${h.url_for( action='history_share' )}" target="galaxy_main">Share</a> current history</div> %endif + <li><a href="${h.url_for( action='history', show_deleted=True)}" target="galaxy_history">Show deleted</a> datasets in history</li> <li><a href="${h.url_for( action='history_delete', id=history.id )}" confirm="Are you sure you want to delete the current history?">Delete</a> current history</div> </ul>

diff -r 20591fa0d05d -r 45033114f82d templates/root/history.mako --- a/templates/root/history.mako Thu Oct 02 15:51:17 2008 -0400 +++ b/templates/root/history.mako Thu Oct 02 16:37:32 2008 -0400 @@ -209,7 +209,10 @@ <body class="historyPage">

<div id="top-links" class="historyLinks"> - <a href="${h.url_for('history')}">refresh</a> + <a href="${h.url_for('history', show_deleted=show_deleted)}">refresh</a> + %if show_deleted: + | <a href="${h.url_for('history', show_deleted=False)}">hide deleted</a> + %endif </div>

%if history.deleted: @@ -221,11 +224,19 @@

<%namespace file="history_common.mako" import="render_dataset" />

-%if len(history.active_datasets) < 1: +%if ( show_deleted and len( history.datasets ) < 1 ) or len( history.active_datasets ) < 1: <div class="infomessagesmall" id="emptyHistoryMessage"> %else: - ## Render all active (not deleted) datasets, ordered from newest to oldest - %for data in reversed( history.active_datasets ): + <% + if show_deleted: + #all datasets + datasets_to_show = history.activatable_datasets + else: + #active (not deleted) + datasets_to_show = history.active_datasets + %> + ## Render requested datasets, ordered from newest to oldest + %for data in reversed( datasets_to_show ): %if data.visible: <div class="historyItemContainer" id="historyItemContainer-${data.id}"> ${render_dataset( data, data.hid )} diff -r 20591fa0d05d -r 45033114f82d templates/root/history_common.mako --- a/templates/root/history_common.mako Thu Oct 02 15:51:17 2008 -0400 +++ b/templates/root/history_common.mako Thu Oct 02 16:37:32 2008 -0400 @@ -8,8 +8,12 @@ %> <div class="historyItemWrapper historyItem historyItem-${data_state}" id="historyItem-${data.id}">

+ %if data.deleted: + <div class="warningmessagesmall"> + <strong>This dataset has been deleted. Click <a href="${h.url_for( controller='dataset', action='undelete', id=data.id )}" target="galaxy_history">here</a> to undelete.</strong> + </div> + %endif ## Header row for history items (name, state, action buttons) - <div style="overflow: hidden;" class="historyItemTitleBar"> <div style="float: left; padding-right: 3px;"> <div style='display: none;' id="progress-${data.id}"> @@ -24,7 +28,7 @@ <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( 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> - <a href="${h.url_for( action='delete', id=data.id )}" class="historyItemDelete" id="historyItemDelter-${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> + <a href="${h.url_for( action='delete', id=data.id, show_deleted_on_refresh=show_deleted )}" class="historyItemDelete" id="historyItemDelter-${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> </div> @@ -100,4 +104,4 @@ </div> </div>

-</%def> \ No newline at end of file +</%def>