[galaxy-commits] commit/galaxy-central: smcmanus: Temporarily reverted library browsing.

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/154cda53407f/ changeset: 154cda53407f user: smcmanus date: 2012-11-02 20:38:54 summary: Temporarily reverted library browsing. affected #: 2 files diff -r 59a35ec1e2e7ce608d2ae566c7c1e201760c53a1 -r 154cda53407f8360ab00b54ec563c1985157c9a5 templates/library/common/browse_library.mako --- a/templates/library/common/browse_library.mako +++ b/templates/library/common/browse_library.mako @@ -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 ]) + %> + %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 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 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: ${render_actions_on_multiple_items()} %endif diff -r 59a35ec1e2e7ce608d2ae566c7c1e201760c53a1 -r 154cda53407f8360ab00b54ec563c1985157c9a5 templates/library/common/browse_library_opt.mako --- /dev/null +++ b/templates/library/common/browse_library_opt.mako @@ -0,0 +1,622 @@ +<%namespace file="/message.mako" import="render_msg" /> +<%namespace file="/library/common/library_item_info.mako" import="render_library_item_info" /> +<%namespace file="/library/common/common.mako" import="render_actions_on_multiple_items" /> +<%namespace file="/library/common/common.mako" import="render_compression_types_help" /> +<%namespace file="/library/common/common.mako" import="common_javascripts" /> + +<%! + def inherit(context): + if context.get('use_panels'): + return '/webapps/galaxy/base_panels.mako' + else: + return '/base.mako' +%> +<%inherit file="${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 “${library.name}”</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> Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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