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https://github.com/galaxyproject/galaxy.git
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Add the ability to delete a dataset from a library folder. Also completed several bug fixes in the Admin GUI components.
This commit is contained in:
Greg Von Kuster
@@ -81,11 +81,14 @@ class Admin( BaseController ):
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order_by = [ galaxy.model.Group.table.c.name ] )
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groups = []
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for row in q.execute():
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total_datasets = 0
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permitted_actions = []
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# This 2nd query retrieves the number of datasets and dataset permitted_actions associated with each group
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q2 = sa.select( ( ( galaxy.model.Group.table.c.id ).label( 'group_id' ),
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( galaxy.model.GroupDatasetAssociation.table.c.permitted_actions ).label( 'permitted_actions' ),
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sa.func.count( galaxy.model.Dataset.table.c.id ).label( 'total_datasets' ) ),
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whereclause = galaxy.model.Group.table.c.id == row.group_id,
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whereclause = sa.and_( galaxy.model.Group.table.c.id == row.group_id,
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galaxy.model.Dataset.table.c.deleted == False ),
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from_obj = [ sa.outerjoin( galaxy.model.Group.table,
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galaxy.model.GroupDatasetAssociation.table
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).outerjoin( galaxy.model.Dataset.table ) ],
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@@ -354,7 +357,8 @@ class Admin( BaseController ):
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q2 = sa.select( ( ( galaxy.model.Group.table.c.id ).label( 'group_id' ),
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( galaxy.model.GroupDatasetAssociation.table.c.permitted_actions ).label( 'permitted_actions' ),
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sa.func.count( galaxy.model.Dataset.table.c.id ).label( 'total_datasets' ) ),
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whereclause = galaxy.model.Group.table.c.id == row.group_id,
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whereclause = sa.and_( galaxy.model.Group.table.c.id == row.group_id,
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galaxy.model.Dataset.table.c.deleted == False ),
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from_obj = [ sa.outerjoin( galaxy.model.Group.table,
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galaxy.model.GroupDatasetAssociation.table
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).outerjoin( galaxy.model.Dataset.table ) ],
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@@ -462,7 +466,8 @@ class Admin( BaseController ):
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q2 = sa.select( ( ( galaxy.model.Group.table.c.id ).label( 'group_id' ),
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( galaxy.model.GroupDatasetAssociation.table.c.permitted_actions ).label( 'permitted_actions' ),
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sa.func.count( galaxy.model.Dataset.table.c.id ).label( 'total_datasets' ) ),
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whereclause = galaxy.model.Group.table.c.id == row.group_id,
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whereclause = sa.and_( galaxy.model.Group.table.c.id == row.group_id,
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galaxy.model.Dataset.table.c.deleted == False ),
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from_obj = [ sa.outerjoin( galaxy.model.Group.table,
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galaxy.model.GroupDatasetAssociation.table
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).outerjoin( galaxy.model.Dataset.table ) ],
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@@ -651,15 +656,23 @@ class Admin( BaseController ):
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last_dataset_created = None
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data_file = kwd['file_data']
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url_paste = kwd['url_paste']
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if data_file == '' and url_paste == '':
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msg = 'Select a file, enter an URL or enter Text.'
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trans.response.send_redirect( web.url_for( action='dataset', folder_id=folder_id, msg=msg ) )
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space_to_tab = False
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if 'space_to_tab' in kwd:
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if kwd['space_to_tab'] not in ["None", None]:
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space_to_tab = True
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if 'groups' not in kwd:
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msg = 'The dataset must be associated with at least 1 group.'
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trans.response.send_redirect( web.url_for( action='dataset', folder_id=folder_id, msg=msg ) )
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groups = kwd['groups']
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if groups and not isinstance( groups, list ):
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# mako sends singleton lists as a string
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groups = [ groups ]
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if groups is None:
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elif groups is None:
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groups = []
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else:
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groups = []
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temp_name = ""
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data_list = []
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@@ -844,6 +857,38 @@ class Admin( BaseController ):
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msg=msg )
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else:
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return trans.show_error_message( "Invalid dataset specified" )
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@web.expose
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def delete_dataset( self, trans, id=None, **kwd):
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if not self.user_is_admin( trans ):
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return trans.show_error_message( no_privilege_msg )
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if id:
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# id is a LibraryFolderDatasetAssociation.id
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library_folder_dataset_assoc = trans.app.model.LibraryFolderDatasetAssociation.get( id )
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folder = library_folder_dataset_assoc.folder
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library = folder.library_root[0]
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dataset = library_folder_dataset_assoc.dataset
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# TODO: assuming 1 to 1 mapping between Dataset -> LibraryFolders ( i.e., is can the same
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# dataset record be shared across LibraryFolders?
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# Confirm that things should be deleted as follows
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# Delete the LibraryFolderDatasetAssociation
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library_folder_dataset_assoc.deleted = True
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library_folder_dataset_assoc.flush()
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# Delete any GroupDatasetAssociations
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for group_dataset_assoc in dataset.groups:
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group_dataset_assoc.delete()
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group_dataset_assoc.flush()
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# Delete any HistoryDatasetAssociations
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for history_dataset_assoc in dataset.history_associations:
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history_dataset_assoc.delete()
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history_dataset_assoc.flush()
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# Delete the dataset
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dataset.deleted = True
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dataset.flush()
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trans.log_event( "Dataset id %s deleted from library folder id %s" % ( str( id ), str( folder.id ) ) )
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msg = 'The dataset was deleted from the folder'
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# Refresh the library for display
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library.refresh()
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return trans.fill_template( '/admin/library/library.mako', library=library, msg=msg )
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def renderable( self, trans, component, group_id ):
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render = False
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if isinstance( component, trans.app.model.LibraryFolder ):
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@@ -4,11 +4,12 @@
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<%
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if isinstance( component, trans.app.model.LibraryFolder ):
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return render_folder( component )
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elif isinstance( component, trans.app.model.LibraryFolderDatasetAssociation ):
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elif isinstance( component, trans.app.model.LibraryFolderDatasetAssociation ) and not component.deleted:
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return render_dataset( component )
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%>
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</%def>
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## Render the dataset `data` as history item, using `hid` as the displayed id
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## Render the dataset `data` as folder item, using `hid` as the displayed id
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<%def name="render_dataset( data )">
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<%
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if data.state in ['no state','',None]:
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@@ -20,7 +21,7 @@
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<div class="toolFormTitle">${data.display_name()}</div>
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<div class="toolFormBody">
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<div class="form-row">
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## Header row for history items (name, state, action buttons)
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## Header row for folder items (name, state, action buttons)
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<div style="overflow: hidden;" class="historyItemTitleBar">
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%if data_state != 'ok':
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<div><img src="${h.url_for( "/static/style/data_%s.png" % data_state )}" border="0" align="middle"></div>
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@@ -37,10 +38,19 @@
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title='edit attributes'
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class='editButton'
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border='0'></a>
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<a href="${h.url_for( controller='admin',
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action='delete_dataset',
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id=data.id )}"<img src="${h.url_for('/static/images/delete_icon.png')}"
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rollover="${h.url_for('/static/images/delete_icon_dark.png')}"
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width='16'
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height='16'
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alt='delete'
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class='deleteButton'
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border='0'></a>
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</div>
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##<span class="historyItemTitle"><b>${data.display_name()}</b></span>
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</div>
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## Body for history items, extra info and actions, data "peek"
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## Body for folder items, extra info and actions, data "peek"
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<div id="info${data.id}" class="historyItemBody">
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%if data_state == "queued":
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<div>Job is waiting to run</div>
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@@ -76,6 +86,7 @@
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</div>
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</div>
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</%def>
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## Render a folder
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<%def name="render_folder( this_folder )">
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<div class="toolForm">
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@@ -7,6 +7,9 @@
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<a href="${h.url_for( controller='admin', action='groups' )}">Groups</a> |
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<a href="${h.url_for( controller='admin', action='users' )}">Users</a>
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</div>
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%if msg:
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<p class="ok_bgr">${msg}</p>
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%endif
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<div class="toolFormTitle">Manage Library '${library.name}'</div>
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<div class="toolFormBody">
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<form name="end_library" action="${h.url_for( controller='admin', action='library' )}" method="post" >
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@@ -7,6 +7,9 @@
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<a href="${h.url_for( controller='admin', action='groups' )}">Groups</a> |
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<tr><td><a href="${h.url_for( controller='admin', action='users' )}">Users</a></td></tr>
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</div>
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%if msg:
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<p class="ok_bgr">${msg}</p></td></tr>
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%endif
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<div class="toolFormTitle">Create a new Library Dataset</div>
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<div class="toolFormBody">
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<form name="tool_form" action="${h.url_for( controller='admin', action='dataset' )}" enctype="multipart/form-data" method="post">
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