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Temporarily reverted library browsing.

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This commit is contained in:
Scott McManus
2012-11-02 15:38:54 -04:00
parent c41e8923b8
commit 7f07840a89
2 changed files with 673 additions and 58 deletions
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templates/library/common/browse_library.mako
+51 -58
View File
@@ -48,7 +48,6 @@
<%def name="javascripts()">
${parent.javascripts()}
${h.js("libs/json2")}
${h.js("libs/jquery/jstorage")}
${common_javascripts()}
${self.grid_javascripts()}
@@ -207,7 +206,7 @@
</script>
</%def>
<%def name="render_dataset( cntrller, ldda, library_dataset, can_modify, can_manage, selected, library, folder, pad, parent, row_counter, tracked_datasets, show_deleted=False, simple=False )">
<%def name="render_dataset( cntrller, ldda, library_dataset, selected, library, folder, pad, parent, row_counter, tracked_datasets, show_deleted=False, simple=False )">
<%
## The received ldda must always be a LibraryDatasetDatasetAssociation object. The object id passed to methods
## from the drop down menu should be the ldda id to prevent id collision ( which could happen when displaying
@@ -215,14 +214,22 @@
## library_dataset, so we display the attributes from the ldda.
from galaxy.webapps.galaxy.controllers.library_common import branch_deleted
is_admin = trans.user_is_admin() and cntrller == 'library_admin'
current_version = ( ldda == library_dataset.library_dataset_dataset_association )
if ldda == library_dataset.library_dataset_dataset_association:
current_version = True
if is_admin:
can_modify = can_manage = True
elif cntrller in [ 'library', 'requests' ]:
can_modify = trans.app.security_agent.can_modify_library_item( current_user_roles, library_dataset )
can_manage = trans.app.security_agent.can_manage_library_item( current_user_roles, library_dataset )
else:
can_modify = can_manage = False
else:
current_version = False
if current_version and ldda.state not in ( 'ok', 'error', 'empty', 'deleted', 'discarded' ):
tracked_datasets[ldda.id] = ldda.state
# SM: This causes a query to be emitted, but it quickly goes down a
# rabbit hole of many possible inheritable cases. It may not be
# possible to easily eliminate the extra query from this call.
info_association, inherited = ldda.get_info_association( restrict=True )
form_type = trans.model.FormDefinition.types.LIBRARY_INFO_TEMPLATE
%>
@@ -303,21 +310,9 @@
%endif
</%def>
<%def name="format_delta( tdelta )">
<%
from datetime import datetime
return "%d.%.6d" % ( tdelta.seconds, tdelta.microseconds )
%>
</%def>
<%def name="render_folder( cntrller, folder, folder_pad, created_ldda_ids, library, hidden_folder_ids, tracked_datasets, show_deleted=False, parent=None, row_counter=None, root_folder=False, simple=False )">
<%
from galaxy.webapps.galaxy.controllers.library_common import active_folders, active_folders_and_library_datasets, activatable_folders_and_library_datasets, map_library_datasets_to_lddas, branch_deleted, datasets_for_lddas
# SM: DELETEME
from datetime import datetime, timedelta
import logging
log = logging.getLogger( __name__ )
from galaxy.webapps.galaxy.controllers.library_common import active_folders, active_folders_and_library_datasets, activatable_folders_and_library_datasets, branch_deleted
is_admin = trans.user_is_admin() and cntrller == 'library_admin'
has_accessible_library_datasets = trans.app.security_agent.has_accessible_library_datasets( trans, folder, trans.user, current_user_roles, search_downward=False )
@@ -330,9 +325,6 @@
pad = folder_pad + 20
expander = h.url_for("/static/images/silk/resultset_next.png")
folder_img = h.url_for("/static/images/silk/folder.png")
# SM: If this is a comma-delimited list of LDDAs, then split them up
# into a list. For anything else, turn created_ldda_ids into a single
# item list.
if created_ldda_ids:
created_ldda_ids = util.listify( created_ldda_ids )
if str( folder.id ) in hidden_folder_ids:
@@ -434,39 +426,47 @@
%>
%endif
<%
# TODO: If show_deleted is set to True, then nothing is displayed. Why? This wasn't the case
# in the past.
if show_deleted:
sub_folders, library_datasets = activatable_folders_and_library_datasets( trans, folder )
else:
sub_folders, library_datasets = active_folders_and_library_datasets( trans, folder )
# Render all the subfolders:
# TODO: Check permissions first.
for sub_folder in sub_folders:
render_folder( cntrller, sub_folder, pad, created_ldda_ids, library, [], tracked_datasets, show_deleted=show_deleted, parent=my_row, row_counter=row_counter, root_folder=False )
# Map LibraryDatasets to LDDAs, then map LDDAs to Datasets.
# Then determine which Datasets are accessible and which are not.
# For every LibraryDataset, if there's an LDDA for it and it's
# accessible then display it.
if ( len( library_datasets ) > 0 ):
lib_dataset_ldda_map = map_library_datasets_to_lddas( trans, library_datasets )
dataset_list = datasets_for_lddas( trans, lib_dataset_ldda_map.values() )
#can_access_datasets = trans.app.security_agent.dataset_access_mapping( trans, current_user_roles, dataset_list )
can_access_datasets = trans.app.security_agent.dataset_permission_map_for_access( trans, current_user_roles, dataset_list )
can_modify_datasets = trans.app.security_agent.item_permission_map_for_modify( trans, current_user_roles, dataset_list )
can_manage_datasets = trans.app.security_agent.item_permission_map_for_manage( trans, current_user_roles, dataset_list )
for library_dataset in library_datasets:
ldda = lib_dataset_ldda_map[ library_dataset.id ]
if ldda:
# SMTODO: Fix awkard modify/manage permission checks.
can_access = is_admin or can_access_datasets[ ldda.dataset_id ]
can_modify = is_admin or ( cntrller in ['library', 'requests'] and can_modify_datasets[ ldda.dataset_id ])
can_manage = is_admin or ( cntrller in ['library', 'requests'] and can_manage_datasets[ ldda.dataset_id ])
selected = created_ldda_ids and str( ldda.id ) in created_ldda_ids
if can_access:
render_dataset( cntrller, ldda, library_dataset, can_modify, can_manage, selected, library, folder, pad, my_row, row_counter, tracked_datasets, show_deleted=show_deleted )
%>
%if is_admin:
%for sub_folder in sub_folders:
${render_folder( cntrller, sub_folder, pad, created_ldda_ids, library, [], tracked_datasets, show_deleted=show_deleted, parent=my_row, row_counter=row_counter, root_folder=False )}
%endfor
%for library_dataset in library_datasets:
<%
ldda = library_dataset.library_dataset_dataset_association
if ldda:
# There should always be an ldda, but some users running their own instances have reported that
# some of their LibraryDatasets have no associated lddas
selected = created_ldda_ids and str( ldda.id ) in created_ldda_ids
%>
%if ldda:
${render_dataset( cntrller, ldda, library_dataset, selected, library, folder, pad, my_row, row_counter, tracked_datasets, show_deleted=show_deleted )}
%endif
%endfor
%else:
%for sub_folder in sub_folders:
${render_folder( cntrller, sub_folder, pad, created_ldda_ids, library, hidden_folder_ids, tracked_datasets, show_deleted=show_deleted, parent=my_row, row_counter=row_counter, root_folder=False, simple=simple )}
%endfor
%for library_dataset in library_datasets:
<%
ldda = library_dataset.library_dataset_dataset_association
if ldda:
# There should always be an ldda, but some users running their own instances have reported that
# some of their LibraryDatasets have no associated lddas
can_access = trans.app.security_agent.can_access_dataset( current_user_roles, ldda.dataset )
selected = created_ldda_ids and str( ldda.id ) in created_ldda_ids
else:
can_access = False
%>
%if can_access:
${render_dataset( cntrller, ldda, library_dataset, selected, library, folder, pad, my_row, row_counter, tracked_datasets, show_deleted=show_deleted, simple=simple )}
%endif
%endfor
%endif
</%def>
<%def name="render_content(simple=False)">
@@ -474,8 +474,6 @@
from galaxy import util
from galaxy.webapps.galaxy.controllers.library_common import branch_deleted
from time import strftime
import logging
log = logging.getLogger( __name__ )
is_admin = trans.user_is_admin() and cntrller == 'library_admin'
@@ -491,8 +489,6 @@
info_association, inherited = library.get_info_association()
form_type = trans.model.FormDefinition.types.LIBRARY_INFO_TEMPLATE
# SM: These are mostly display-specific; ignore them for now.
# The has_accessible_folders determines if anything can be shown - use it.
self.has_accessible_datasets = trans.app.security_agent.has_accessible_library_datasets( trans, library.root_folder, trans.user, current_user_roles )
root_folder_has_accessible_library_datasets = trans.app.security_agent.has_accessible_library_datasets( trans, library.root_folder, trans.user, current_user_roles, search_downward=False )
has_accessible_folders = is_admin or trans.app.security_agent.has_accessible_folders( trans, library.root_folder, trans.user, current_user_roles )
@@ -585,16 +581,13 @@
</tr>
</thead>
<% row_counter = RowCounter() %>
## SM: Here is where we render the libraries based on admin/non-admin privileges:
%if cntrller in [ 'library', 'requests' ]:
${self.render_folder( 'library', library.root_folder, 0, created_ldda_ids, library, hidden_folder_ids, tracked_datasets, show_deleted=show_deleted, parent=None, row_counter=row_counter, root_folder=True, simple=simple )}
## SM: TODO: WTF?
%if not library.deleted and self.has_accessible_datasets and not simple:
${render_actions_on_multiple_items()}
%endif
%elif ( trans.user_is_admin() and cntrller in [ 'library_admin', 'requests_admin' ] ):
${self.render_folder( 'library_admin', library.root_folder, 0, created_ldda_ids, library, [], tracked_datasets, show_deleted=show_deleted, parent=None, row_counter=row_counter, root_folder=True )}
## SM: TODO: WTF?
%if not library.deleted and not show_deleted and self.has_accessible_datasets:
${render_actions_on_multiple_items()}
%endif
templates/library/common/browse_library_opt.mako
+622
View File
@@ -0,0 +1,622 @@
<%namespace file="/message.mako" import="render_msg" />
<%namespace file="/library/common/library_item_info.mako" import="render_library_item_info" />
<%namespace file="/library/common/common.mako" import="render_actions_on_multiple_items" />
<%namespace file="/library/common/common.mako" import="render_compression_types_help" />
<%namespace file="/library/common/common.mako" import="common_javascripts" />
<%!
def inherit(context):
if context.get('use_panels'):
return '/webapps/galaxy/base_panels.mako'
else:
return '/base.mako'
%>
<%inherit file="${inherit(context)}"/>
<%def name="init()">
<%
self.has_left_panel=False
self.has_right_panel=False
self.message_box_visible=False
self.active_view="user"
self.overlay_visible=False
self.has_accessible_datasets = False
%>
</%def>
##
## Override methods from base.mako and base_panels.mako
##
<%def name="center_panel()">
<div style="overflow: auto; height: 100%;">
<div class="page-container" style="padding: 10px;">
${render_content()}
</div>
</div>
</%def>
## Render the grid's basic elements. Each of these elements can be subclassed.
<%def name="body()">
${render_content()}
</%def>
<%def name="title()">Browse data library</%def>
<%def name="stylesheets()">
${parent.stylesheets()}
${h.css( "library" )}
</%def>
<%def name="javascripts()">
${parent.javascripts()}
${h.js("libs/json2")}
${h.js("libs/jquery/jstorage")}
${common_javascripts()}
${self.grid_javascripts()}
</%def>
<%def name="grid_javascripts()">
<script type="text/javascript">
var init_libraries = function() {
var storage_id = "library-expand-state-${trans.security.encode_id(library.id)}";
var restore_folder_state = function() {
var state = $.jStorage.get(storage_id);
if (state) {
for (var id in state) {
if (state[id] === true) {
var row = $("#" + id),
index = row.parent().children().index(row);
row.addClass("expanded").show();
row.siblings().filter("tr[parent='" + index + "']").show();
}
}
}
};
var save_folder_state = function() {
var state = {};
$("tr.folderRow").each( function() {
var folder = $(this);
state[folder.attr("id")] = folder.hasClass("expanded");
});
$.jStorage.set(storage_id, state);
};
$("#library-grid").each(function() {
var child_of_parent_cache = {};
// Recursively fill in children and descendents of each row
var process_row = function(q, parents) {
// Find my index
var parent = q.parent(),
this_level = child_of_parent_cache[parent] || (child_of_parent_cache[parent] = parent.children());
var index = this_level.index(q);
// Find my immediate children
var children = $(par_child_dict[index]);
// Recursively handle them
var descendents = children;
children.each( function() {
child_descendents = process_row( $(this), parents.add(q) );
descendents = descendents.add(child_descendents);
});
// Set up expand / hide link
var expand_fn = function() {
if ( q.hasClass("expanded") ) {
descendents.hide();
descendents.removeClass("expanded");
q.removeClass("expanded");
} else {
children.show();
q.addClass("expanded");
}
save_folder_state();
};
$("." + q.attr("id") + "-click").click(expand_fn);
// Check/uncheck boxes in subfolders.
q.children("td").children("input[type=checkbox]").click( function() {
if ( $(this).is(":checked") ) {
descendents.find("input[type=checkbox]").attr("checked", true);
} else {
descendents.find("input[type=checkbox]").attr("checked", false);
// If you uncheck a lower level checkbox, uncheck the boxes above it
// (since deselecting a child means the parent is not fully selected any more).
parents.children("td").children("input[type=checkbox]").attr("checked", false);
}
});
// return descendents for use by parent
return descendents;
}
// Initialize dict[parent_id] = rows_which_have_that_parent_id_as_parent_attr
var par_child_dict = {},
no_parent = [];
$(this).find("tbody tr").each( function() {
if ( $(this).attr("parent")) {
var parent = $(this).attr("parent");
if (par_child_dict[parent] !== undefined) {
par_child_dict[parent].push(this);
} else {
par_child_dict[parent] = [this];
}
} else {
no_parent.push(this);
}
});
$(no_parent).each( function() {
descendents = process_row( $(this), $([]) );
descendents.hide();
});
});
restore_folder_state();
};
$(function() {
init_libraries();
});
// Looks for changes in dataset state using an async request. Keeps
// calling itself (via setTimeout) until all datasets are in a terminal
// state.
var updater = function ( tracked_datasets ) {
// Check if there are any items left to track
var empty = true;
for ( i in tracked_datasets ) {
empty = false;
break;
}
if ( ! empty ) {
setTimeout( function() { updater_callback( tracked_datasets ) }, 3000 );
}
};
var updater_callback = function ( tracked_datasets ) {
// Build request data
var ids = []
var states = []
$.each( tracked_datasets, function ( id, state ) {
ids.push( id );
states.push( state );
});
// Make ajax call
$.ajax( {
type: "POST",
url: "${h.url_for( controller='library_common', action='library_item_updates' )}",
dataType: "json",
data: { ids: ids.join( "," ), states: states.join( "," ) },
success : function ( data ) {
$.each( data, function( id, val ) {
// Replace HTML
var cell = $("#libraryItem-" + id).find("#libraryItemInfo");
cell.html( val.html );
// If new state was terminal, stop tracking
if (( val.state == "ok") || ( val.state == "error") || ( val.state == "empty") || ( val.state == "deleted" ) || ( val.state == "discarded" )) {
delete tracked_datasets[ parseInt(id) ];
} else {
tracked_datasets[ parseInt(id) ] = val.state;
}
});
updater( tracked_datasets );
},
error: function() {
// Just retry, like the old method, should try to be smarter
updater( tracked_datasets );
}
});
};
</script>
</%def>
<%def name="render_dataset( cntrller, ldda, library_dataset, can_modify, can_manage, selected, library, folder, pad, parent, row_counter, tracked_datasets, show_deleted=False, simple=False )">
<%
## The received ldda must always be a LibraryDatasetDatasetAssociation object. The object id passed to methods
## from the drop down menu should be the ldda id to prevent id collision ( which could happen when displaying
## children, which are always lddas ). We also need to make sure we're displaying the latest version of this
## library_dataset, so we display the attributes from the ldda.
from galaxy.webapps.galaxy.controllers.library_common import branch_deleted
is_admin = trans.user_is_admin() and cntrller == 'library_admin'
current_version = ( ldda == library_dataset.library_dataset_dataset_association )
if current_version and ldda.state not in ( 'ok', 'error', 'empty', 'deleted', 'discarded' ):
tracked_datasets[ldda.id] = ldda.state
# SM: This causes a query to be emitted, but it quickly goes down a
# rabbit hole of many possible inheritable cases. It may not be
# possible to easily eliminate the extra query from this call.
info_association, inherited = ldda.get_info_association( restrict=True )
form_type = trans.model.FormDefinition.types.LIBRARY_INFO_TEMPLATE
%>
%if current_version and ( not ldda.library_dataset.deleted or show_deleted ):
<tr class="datasetRow"
%if parent is not None:
parent="${parent}"
%endif
id="libraryItem-${ldda.id}">
<td style="padding-left: ${pad+20}px;">
<input style="float: left;" type="checkbox" name="ldda_ids" id="${trans.security.encode_id( ldda.id )}" value="${trans.security.encode_id( ldda.id )}"
%if selected:
checked="checked"
%endif
/>
%if simple:
<label for="${trans.security.encode_id( ldda.id )}">${ util.unicodify( ldda.name )}</label>
%else:
<div style="float: left; margin-left: 1px;" class="menubutton split popup" id="dataset-${ldda.id}-popup">
<a class="view-info" href="${h.url_for( controller='library_common', action='ldda_info', cntrller=cntrller, library_id=trans.security.encode_id( library.id ), folder_id=trans.security.encode_id( folder.id ), id=trans.security.encode_id( ldda.id ), use_panels=use_panels, show_deleted=show_deleted )}">
%if ldda.library_dataset.deleted:
<div class="libraryItem-error">${util.unicodify( ldda.name )}</div>
%else:
${util.unicodify( ldda.name )}
%endif
</a>
</div>
%if not library.deleted:
<div popupmenu="dataset-${ldda.id}-popup">
%if not branch_deleted( folder ) and not ldda.library_dataset.deleted and can_modify:
<a class="action-button" href="${h.url_for( controller='library_common', action='ldda_edit_info', cntrller=cntrller, library_id=trans.security.encode_id( library.id ), folder_id=trans.security.encode_id( folder.id ), id=trans.security.encode_id( ldda.id ), use_panels=use_panels, show_deleted=show_deleted )}">Edit information</a>
<a class="action-button" href="${h.url_for( controller='library_common', action='move_library_item', cntrller=cntrller, item_type='ldda', item_id=trans.security.encode_id( ldda.id ), source_library_id=trans.security.encode_id( library.id ), use_panels=use_panels, show_deleted=show_deleted )}">Move this dataset</a>
%else:
<a class="action-button" href="${h.url_for( controller='library_common', action='ldda_info', cntrller=cntrller, library_id=trans.security.encode_id( library.id ), folder_id=trans.security.encode_id( folder.id ), id=trans.security.encode_id( ldda.id ), use_panels=use_panels, show_deleted=show_deleted )}">View information</a>
%endif
%if not branch_deleted( folder ) and not ldda.library_dataset.deleted and can_modify and not info_association:
<a class="action-button" href="${h.url_for( controller='library_common', action='add_template', cntrller=cntrller, item_type='ldda', form_type=form_type, library_id=trans.security.encode_id( library.id ), folder_id=trans.security.encode_id( folder.id ), ldda_id=trans.security.encode_id( ldda.id ), use_panels=use_panels, show_deleted=show_deleted )}">Use template</a>
%endif
%if not branch_deleted( folder ) and not ldda.library_dataset.deleted and can_modify and info_association:
<a class="action-button" href="${h.url_for( controller='library_common', action='edit_template', cntrller=cntrller, item_type='ldda', form_type=form_type, library_id=trans.security.encode_id( library.id ), folder_id=trans.security.encode_id( folder.id ), ldda_id=trans.security.encode_id( ldda.id ), use_panels=use_panels, show_deleted=show_deleted )}">Edit template</a>
<a class="action-button" href="${h.url_for( controller='library_common', action='delete_template', cntrller=cntrller, item_type='ldda', form_type=form_type, library_id=trans.security.encode_id( library.id ), folder_id=trans.security.encode_id( folder.id ), ldda_id=trans.security.encode_id( ldda.id ), use_panels=use_panels, show_deleted=show_deleted )}">Unuse template</a>
%endif
%if not branch_deleted( folder ) and not ldda.library_dataset.deleted and can_manage:
%if not trans.app.security_agent.dataset_is_public( ldda.dataset ):
<a class="action-button" href="${h.url_for( controller='library_common', action='make_library_item_public', cntrller=cntrller, library_id=trans.security.encode_id( library.id ), item_type='ldda', id=trans.security.encode_id( ldda.dataset.id ), use_panels=use_panels, show_deleted=show_deleted )}">Make public</a>
%endif
<a class="action-button" href="${h.url_for( controller='library_common', action='ldda_permissions', cntrller=cntrller, library_id=trans.security.encode_id( library.id ), folder_id=trans.security.encode_id( folder.id ), id=trans.security.encode_id( ldda.id ), use_panels=use_panels, show_deleted=show_deleted )}">Edit permissions</a>
%endif
%if not branch_deleted( folder ) and not ldda.library_dataset.deleted and can_modify:
<a class="action-button" href="${h.url_for( controller='library_common', action='upload_library_dataset', cntrller=cntrller, library_id=trans.security.encode_id( library.id ), folder_id=trans.security.encode_id( folder.id ), replace_id=trans.security.encode_id( library_dataset.id ), show_deleted=show_deleted )}">Upload a new version of this dataset</a>
%endif
%if not branch_deleted( folder ) and not ldda.library_dataset.deleted and ldda.has_data:
<a class="action-button" href="${h.url_for( controller='library_common', action='import_datasets_to_histories', cntrller=cntrller, library_id=trans.security.encode_id( library.id ), ldda_ids=trans.security.encode_id( ldda.id ), use_panels=use_panels, show_deleted=show_deleted )}">Import this dataset into selected histories</a>
<a class="action-button" href="${h.url_for( controller='library_common', action='download_dataset_from_folder', cntrller=cntrller, id=trans.security.encode_id( ldda.id ), library_id=trans.security.encode_id( library.id ), use_panels=use_panels )}">Download this dataset</a>
%endif
%if can_modify:
%if not library.deleted and not branch_deleted( folder ) and not ldda.library_dataset.deleted:
<a class="action-button" confirm="Click OK to delete dataset '${util.unicodify( ldda.name )}'." href="${h.url_for( controller='library_common', action='delete_library_item', cntrller=cntrller, library_id=trans.security.encode_id( library.id ), item_id=trans.security.encode_id( library_dataset.id ), item_type='library_dataset', show_deleted=show_deleted )}">Delete this dataset</a>
%elif not library.deleted and not branch_deleted( folder ) and not ldda.library_dataset.purged and ldda.library_dataset.deleted:
<a class="action-button" href="${h.url_for( controller='library_common', action='undelete_library_item', cntrller=cntrller, library_id=trans.security.encode_id( library.id ), item_id=trans.security.encode_id( library_dataset.id ), item_type='library_dataset', show_deleted=show_deleted )}">Undelete this dataset</a>
%endif
%endif
</div>
%endif
%endif
</td>
% if not simple:
<td id="libraryItemInfo">${render_library_item_info( ldda )}</td>
<td>${ldda.extension}</td>
% endif
<td>${ldda.create_time.strftime( "%Y-%m-%d" )}</td>
<td>${ldda.get_size( nice_size=True )}</td>
</tr>
<%
my_row = row_counter.count
row_counter.increment()
%>
%endif
</%def>
<%def name="format_delta( tdelta )">
<%
from datetime import datetime
return "%d.%.6d" % ( tdelta.seconds, tdelta.microseconds )
%>
</%def>
<%def name="render_folder( cntrller, folder, folder_pad, created_ldda_ids, library, hidden_folder_ids, tracked_datasets, show_deleted=False, parent=None, row_counter=None, root_folder=False, simple=False )">
<%
from galaxy.webapps.galaxy.controllers.library_common import active_folders, active_folders_and_library_datasets, activatable_folders_and_library_datasets, map_library_datasets_to_lddas, branch_deleted, datasets_for_lddas
# SM: DELETEME
from datetime import datetime, timedelta
import logging
log = logging.getLogger( __name__ )
is_admin = trans.user_is_admin() and cntrller == 'library_admin'
has_accessible_library_datasets = trans.app.security_agent.has_accessible_library_datasets( trans, folder, trans.user, current_user_roles, search_downward=False )
if root_folder:
pad = folder_pad
expander = h.url_for("/static/images/silk/resultset_bottom.png")
folder_img = h.url_for("/static/images/silk/folder_page.png")
else:
pad = folder_pad + 20
expander = h.url_for("/static/images/silk/resultset_next.png")
folder_img = h.url_for("/static/images/silk/folder.png")
# SM: If this is a comma-delimited list of LDDAs, then split them up
# into a list. For anything else, turn created_ldda_ids into a single
# item list.
if created_ldda_ids:
created_ldda_ids = util.listify( created_ldda_ids )
if str( folder.id ) in hidden_folder_ids:
return ""
my_row = None
if is_admin:
can_add = can_modify = can_manage = True
elif cntrller in [ 'library' ]:
can_access, folder_ids = trans.app.security_agent.check_folder_contents( trans.user, current_user_roles, folder )
if not can_access:
can_show, folder_ids = \
trans.app.security_agent.show_library_item( trans.user,
current_user_roles,
folder,
[ trans.app.security_agent.permitted_actions.LIBRARY_ADD,
trans.app.security_agent.permitted_actions.LIBRARY_MODIFY,
trans.app.security_agent.permitted_actions.LIBRARY_MANAGE ] )
if not can_show:
return ""
can_add = trans.app.security_agent.can_add_library_item( current_user_roles, folder )
can_modify = trans.app.security_agent.can_modify_library_item( current_user_roles, folder )
can_manage = trans.app.security_agent.can_manage_library_item( current_user_roles, folder )
else:
can_add = can_modify = can_manage = False
form_type = trans.model.FormDefinition.types.LIBRARY_INFO_TEMPLATE
info_association, inherited = folder.get_info_association( restrict=True )
%>
%if not root_folder and ( not folder.deleted or show_deleted ):
<% encoded_id = trans.security.encode_id( folder.id ) %>
<tr id="folder-${encoded_id}" class="folderRow libraryOrFolderRow"
%if parent is not None:
parent="${parent}"
style="display: none;"
%endif
>
<td style="padding-left: ${folder_pad}px;">
<input type="checkbox" class="folderCheckbox"/>
<span class="expandLink folder-${encoded_id}-click">
<div style="float: left; margin-left: 2px;" class="menubutton split popup" id="folder_img-${folder.id}-popup">
<a class="folder-${encoded_id}-click" href="javascript:void(0);">
<span class="rowIcon"></span>
%if folder.deleted:
<div class="libraryItem-error">${folder.name}</div>
%else:
${folder.name}
%endif
</a>
</div>
</span>
%if not library.deleted:
<div popupmenu="folder_img-${folder.id}-popup">
%if not branch_deleted( folder ) and can_add:
<a class="action-button" href="${h.url_for( controller='library_common', action='upload_library_dataset', cntrller=cntrller, library_id=trans.security.encode_id( library.id ), folder_id=trans.security.encode_id( folder.id ), use_panels=use_panels, show_deleted=show_deleted )}">Add datasets</a>
<a class="action-button" href="${h.url_for( controller='library_common', action='create_folder', cntrller=cntrller, parent_id=trans.security.encode_id( folder.id ), library_id=trans.security.encode_id( library.id ), use_panels=use_panels, show_deleted=show_deleted )}">Add sub-folder</a>
%endif
%if not branch_deleted( folder ):
%if has_accessible_library_datasets:
<a class="action-button" href="${h.url_for( controller='library_common', action='import_datasets_to_histories', cntrller=cntrller, library_id=trans.security.encode_id( library.id ), folder_id=trans.security.encode_id( folder.id ), use_panels=use_panels, show_deleted=show_deleted )}">Select datasets for import into selected histories</a>
%endif
%if can_modify:
<a class="action-button" href="${h.url_for( controller='library_common', action='folder_info', cntrller=cntrller, id=trans.security.encode_id( folder.id ), library_id=trans.security.encode_id( library.id ), use_panels=use_panels, show_deleted=show_deleted )}">Edit information</a>
<a class="action-button" href="${h.url_for( controller='library_common', action='move_library_item', cntrller=cntrller, item_type='folder', item_id=trans.security.encode_id( folder.id ), source_library_id=trans.security.encode_id( library.id ), use_panels=use_panels, show_deleted=show_deleted )}">Move this folder</a>
%else:
<a class="action-button" class="view-info" href="${h.url_for( controller='library_common', action='folder_info', cntrller=cntrller, id=trans.security.encode_id( folder.id ), library_id=trans.security.encode_id( library.id ), use_panels=use_panels, show_deleted=show_deleted )}">View information</a>
%endif
%endif
%if not branch_deleted( folder ) and can_modify and not info_association:
<a class="action-button" href="${h.url_for( controller='library_common', action='add_template', cntrller=cntrller, item_type='folder', form_type=form_type, library_id=trans.security.encode_id( library.id ), folder_id=trans.security.encode_id( folder.id ), use_panels=use_panels, show_deleted=show_deleted )}">Use template</a>
%endif
%if not branch_deleted( folder ) and can_modify and info_association:
<a class="action-button" href="${h.url_for( controller='library_common', action='edit_template', cntrller=cntrller, item_type='folder', form_type=form_type, library_id=trans.security.encode_id( library.id ), folder_id=trans.security.encode_id( folder.id ), use_panels=use_panels, show_deleted=show_deleted )}">Edit template</a>
<a class="action-button" href="${h.url_for( controller='library_common', action='delete_template', cntrller=cntrller, item_type='folder', form_type=form_type, library_id=trans.security.encode_id( library.id ), folder_id=trans.security.encode_id( folder.id ), use_panels=use_panels, show_deleted=show_deleted )}">Unuse template</a>
%endif
%if not branch_deleted( folder ) and can_manage:
%if not trans.app.security_agent.folder_is_public( folder ):
<a class="action-button" href="${h.url_for( controller='library_common', action='make_library_item_public', cntrller=cntrller, library_id=trans.security.encode_id( library.id ), item_type='folder', id=trans.security.encode_id( folder.id ), use_panels=use_panels, show_deleted=show_deleted )}">Make public</a>
%endif
<a class="action-button" href="${h.url_for( controller='library_common', action='folder_permissions', cntrller=cntrller, id=trans.security.encode_id( folder.id ), library_id=trans.security.encode_id( library.id ), use_panels=use_panels, show_deleted=show_deleted )}">Edit permissions</a>
%endif
%if can_modify:
%if not library.deleted and not folder.deleted:
<a class="action-button" confirm="Click OK to delete the folder '${folder.name}.'" href="${h.url_for( controller='library_common', action='delete_library_item', cntrller=cntrller, library_id=trans.security.encode_id( library.id ), item_id=trans.security.encode_id( folder.id ), item_type='folder', show_deleted=show_deleted )}">Delete this folder</a>
%elif not library.deleted and folder.deleted and not folder.purged:
<a class="action-button" href="${h.url_for( controller='library_common', action='undelete_library_item', cntrller=cntrller, library_id=trans.security.encode_id( library.id ), item_id=trans.security.encode_id( folder.id ), item_type='folder', show_deleted=show_deleted )}">Undelete this folder</a>
%endif
%endif
</div>
%endif
<td>
%if folder.description:
${folder.description}
%endif
<td colspan="3"></td>
</tr>
<%
my_row = row_counter.count
row_counter.increment()
%>
%endif
<%
# TODO: If show_deleted is set to True, then nothing is displayed. Why? This wasn't the case
# in the past.
if show_deleted:
sub_folders, library_datasets = activatable_folders_and_library_datasets( trans, folder )
else:
sub_folders, library_datasets = active_folders_and_library_datasets( trans, folder )
# Render all the subfolders:
# TODO: Check permissions first.
for sub_folder in sub_folders:
render_folder( cntrller, sub_folder, pad, created_ldda_ids, library, [], tracked_datasets, show_deleted=show_deleted, parent=my_row, row_counter=row_counter, root_folder=False )
# Map LibraryDatasets to LDDAs, then map LDDAs to Datasets.
# Then determine which Datasets are accessible and which are not.
# For every LibraryDataset, if there's an LDDA for it and it's
# accessible then display it.
if ( len( library_datasets ) > 0 ):
lib_dataset_ldda_map = map_library_datasets_to_lddas( trans, library_datasets )
dataset_list = datasets_for_lddas( trans, lib_dataset_ldda_map.values() )
#can_access_datasets = trans.app.security_agent.dataset_access_mapping( trans, current_user_roles, dataset_list )
can_access_datasets = trans.app.security_agent.dataset_permission_map_for_access( trans, current_user_roles, dataset_list )
can_modify_datasets = trans.app.security_agent.item_permission_map_for_modify( trans, current_user_roles, dataset_list )
can_manage_datasets = trans.app.security_agent.item_permission_map_for_manage( trans, current_user_roles, dataset_list )
for library_dataset in library_datasets:
ldda = lib_dataset_ldda_map[ library_dataset.id ]
if ldda:
# SMTODO: Fix awkard modify/manage permission checks.
can_access = is_admin or can_access_datasets[ ldda.dataset_id ]
can_modify = is_admin or ( cntrller in ['library', 'requests'] and can_modify_datasets[ ldda.dataset_id ])
can_manage = is_admin or ( cntrller in ['library', 'requests'] and can_manage_datasets[ ldda.dataset_id ])
selected = created_ldda_ids and str( ldda.id ) in created_ldda_ids
if can_access:
render_dataset( cntrller, ldda, library_dataset, can_modify, can_manage, selected, library, folder, pad, my_row, row_counter, tracked_datasets, show_deleted=show_deleted )
%>
</%def>
<%def name="render_content(simple=False)">
<%
from galaxy import util
from galaxy.webapps.galaxy.controllers.library_common import branch_deleted
from time import strftime
import logging
log = logging.getLogger( __name__ )
is_admin = trans.user_is_admin() and cntrller == 'library_admin'
if is_admin:
can_add = can_modify = can_manage = True
elif cntrller in [ 'library', 'requests' ]:
can_add = trans.app.security_agent.can_add_library_item( current_user_roles, library )
can_modify = trans.app.security_agent.can_modify_library_item( current_user_roles, library )
can_manage = trans.app.security_agent.can_manage_library_item( current_user_roles, library )
else:
can_add = can_modify = can_manage = False
info_association, inherited = library.get_info_association()
form_type = trans.model.FormDefinition.types.LIBRARY_INFO_TEMPLATE
# SM: These are mostly display-specific; ignore them for now.
# The has_accessible_folders determines if anything can be shown - use it.
self.has_accessible_datasets = trans.app.security_agent.has_accessible_library_datasets( trans, library.root_folder, trans.user, current_user_roles )
root_folder_has_accessible_library_datasets = trans.app.security_agent.has_accessible_library_datasets( trans, library.root_folder, trans.user, current_user_roles, search_downward=False )
has_accessible_folders = is_admin or trans.app.security_agent.has_accessible_folders( trans, library.root_folder, trans.user, current_user_roles )
tracked_datasets = {}
class RowCounter( object ):
def __init__( self ):
self.count = 0
def increment( self ):
self.count += 1
def __str__( self ):
return str( self.count )
%>
<h2>Data Library &ldquo;${library.name}&rdquo;</h2>
<ul class="manage-table-actions">
%if not library.deleted and ( is_admin or can_add ):
<li><a class="action-button" href="${h.url_for( controller='library_common', action='upload_library_dataset', cntrller=cntrller, library_id=trans.security.encode_id( library.id ), folder_id=trans.security.encode_id( library.root_folder.id ), use_panels=use_panels, show_deleted=show_deleted )}">Add datasets</a></li>
<li><a class="action-button" href="${h.url_for( controller='library_common', action='create_folder', cntrller=cntrller, parent_id=trans.security.encode_id( library.root_folder.id ), library_id=trans.security.encode_id( library.id ), use_panels=use_panels, show_deleted=show_deleted )}">Add folder</a></li>
%endif
%if ( ( not library.deleted ) and ( can_modify or can_manage ) ) or ( can_modify and not library.purged ) or ( library.purged ):
<li><a class="action-button" id="library-${library.id}-popup" class="menubutton">Library Actions</a></li>
<div popupmenu="library-${library.id}-popup">
%if not library.deleted:
%if can_modify:
<a class="action-button" href="${h.url_for( controller='library_common', action='library_info', cntrller=cntrller, id=trans.security.encode_id( library.id ), use_panels=use_panels, show_deleted=show_deleted )}">Edit information</a>
<a class="action-button" confirm="Click OK to delete the library named '${library.name}'." href="${h.url_for( controller='library_common', action='delete_library_item', cntrller=cntrller, library_id=trans.security.encode_id( library.id ), item_id=trans.security.encode_id( library.id ), item_type='library' )}">Delete this data library</a>
%if show_deleted:
<a class="action-button" href="${h.url_for( controller='library_common', action='browse_library', cntrller=cntrller, id=trans.security.encode_id( library.id ), use_panels=use_panels, show_deleted=False )}">Hide deleted items</a>
%else:
<a class="action-button" href="${h.url_for( controller='library_common', action='browse_library', cntrller=cntrller, id=trans.security.encode_id( library.id ), use_panels=use_panels, show_deleted=True )}">Show deleted items</a>
%endif
%endif
%if can_modify and not library.info_association:
<a class="action-button" href="${h.url_for( controller='library_common', action='add_template', cntrller=cntrller, item_type='library', form_type=form_type, library_id=trans.security.encode_id( library.id ), use_panels=use_panels, show_deleted=show_deleted )}">Use template</a>
%endif
%if can_modify and info_association:
<a class="action-button" href="${h.url_for( controller='library_common', action='edit_template', cntrller=cntrller, item_type='library', form_type=form_type, library_id=trans.security.encode_id( library.id ), use_panels=use_panels, show_deleted=show_deleted )}">Edit template</a>
<a class="action-button" href="${h.url_for( controller='library_common', action='delete_template', cntrller=cntrller, item_type='library', form_type=form_type, library_id=trans.security.encode_id( library.id ), use_panels=use_panels, show_deleted=show_deleted )}">Unuse template</a>
%endif
%if can_manage:
%if not trans.app.security_agent.library_is_public( library, contents=True ):
<a class="action-button" href="${h.url_for( controller='library_common', action='make_library_item_public', cntrller=cntrller, library_id=trans.security.encode_id( library.id ), item_type='library', id=trans.security.encode_id( library.id ), contents=True, use_panels=use_panels, show_deleted=show_deleted )}">Make public</a>
%endif
<a class="action-button" href="${h.url_for( controller='library_common', action='library_permissions', cntrller=cntrller, id=trans.security.encode_id( library.id ), use_panels=use_panels, show_deleted=show_deleted )}">Edit permissions</a>
%endif
%if root_folder_has_accessible_library_datasets:
<a class="action-button" href="${h.url_for( controller='library_common', action='import_datasets_to_histories', cntrller=cntrller, library_id=trans.security.encode_id( library.id ), folder_id=trans.security.encode_id( library.root_folder.id ), use_panels=use_panels, show_deleted=show_deleted )}">Select datasets for import into selected histories</a>
%endif
%elif can_modify and not library.purged:
<a class="action-button" href="${h.url_for( controller='library_common', action='undelete_library_item', cntrller=cntrller, library_id=trans.security.encode_id( library.id ), item_id=trans.security.encode_id( library.id ), item_type='library', use_panels=use_panels )}">Undelete this data library</a>
%elif library.purged:
<a class="action-button" href="${h.url_for( controller='library_common', action='browse_library', cntrller=cntrller, id=trans.security.encode_id( library.id ), use_panels=use_panels, show_deleted=show_deleted )}">This data library has been purged</a>
%endif
</div>
%endif
</ul>
%if message:
${render_msg( message, status )}
%endif
%if library.synopsis not in [ '', 'None', None ]:
<div class="libraryItemBody">
${library.synopsis}
</div>
%endif
%if self.has_accessible_datasets:
<form name="act_on_multiple_datasets" action="${h.url_for( controller='library_common', action='act_on_multiple_datasets', cntrller=cntrller, library_id=trans.security.encode_id( library.id ), use_panels=use_panels, show_deleted=show_deleted )}" onSubmit="javascript:return checkForm();" method="post">
%endif
%if has_accessible_folders:
<table cellspacing="0" cellpadding="0" border="0" width="100%" class="grid" id="library-grid">
<thead>
<tr class="libraryTitle">
<th>
%if self.has_accessible_datasets:
<input type="checkbox" id="checkAll" name=select_all_datasets_checkbox value="true" onclick='checkAllFields(1);'/><input type="hidden" name=select_all_datasets_checkbox value="true"/>
%endif
Name
</th>
% if not simple:
<th>Message</th>
<th>Data type</th>
% endif
<th>Date uploaded</th>
<th>File size</th>
</tr>
</thead>
<% row_counter = RowCounter() %>
## SM: Here is where we render the libraries based on admin/non-admin privileges:
%if cntrller in [ 'library', 'requests' ]:
${self.render_folder( 'library', library.root_folder, 0, created_ldda_ids, library, hidden_folder_ids, tracked_datasets, show_deleted=show_deleted, parent=None, row_counter=row_counter, root_folder=True, simple=simple )}
## SM: TODO: WTF?
%if not library.deleted and self.has_accessible_datasets and not simple:
${render_actions_on_multiple_items()}
%endif
%elif ( trans.user_is_admin() and cntrller in [ 'library_admin', 'requests_admin' ] ):
${self.render_folder( 'library_admin', library.root_folder, 0, created_ldda_ids, library, [], tracked_datasets, show_deleted=show_deleted, parent=None, row_counter=row_counter, root_folder=True )}
## SM: TODO: WTF?
%if not library.deleted and not show_deleted and self.has_accessible_datasets:
${render_actions_on_multiple_items()}
%endif
%endif
</table>
%endif
%if self.has_accessible_datasets:
</form>
%endif
%if tracked_datasets:
<script type="text/javascript">
// Updater
updater({${ ",".join( [ '"%s" : "%s"' % ( k, v ) for k, v in tracked_datasets.iteritems() ] ) }});
</script>
<!-- running: do not change this comment, used by TwillTestCase.library_wait -->
%endif
%if self.has_accessible_datasets and not simple:
${render_compression_types_help( comptypes )}
%endif
%if not has_accessible_folders:
The data library '${library.name}' does not contain any datasets that you can access.
%endif
</%def>