[galaxy-dev] [hg] galaxy 3502: Keep the state of displaying / hiding deleted ...

11 Mar 2010

details:   http://www.bx.psu.edu/hg/galaxy/rev/34babf71a09f
changeset: 3502:34babf71a09f
user:      Greg Von Kuster <greg@bx.psu.edu>
date:      Tue Mar 09 16:28:04 2010 -0500
description:
Keep the state of displaying / hiding deleted library items whn uploading library datasets.

diffstat:

 lib/galaxy/web/controllers/library_common.py |   7 +++++++
 lib/galaxy/web/controllers/tool_runner.py    |   1 -
 templates/base_panels.mako                   |   5 +++--
 templates/library/common/browse_library.mako |   2 +-
 templates/library/common/common.mako         |   3 ++-
 templates/library/common/upload.mako         |  14 +++++++-------
 6 files changed, 20 insertions(+), 12 deletions(-)

diffs (161 lines):

diff -r e4592fc99acc -r 34babf71a09f lib/galaxy/web/controllers/library_common.py

--- a/lib/galaxy/web/controllers/library_common.py	Tue Mar 09 15:25:23 2010 -0500
+++ b/lib/galaxy/web/controllers/library_common.py	Tue Mar 09 16:28:04 2010 -0500
@@ -659,6 +659,7 @@
         msg = util.restore_text( params.get( 'msg', ''  ) )
         messagetype = params.get( 'messagetype', 'done' )
         deleted = util.string_as_bool( params.get( 'deleted', False ) )
+        show_deleted = util.string_as_bool( params.get( 'show_deleted', False ) )
         dbkey = params.get( 'dbkey', '?' )
         if isinstance( dbkey, list ):
             last_used_build = dbkey[0]
@@ -705,6 +706,7 @@
                                                                            folder_id=folder_id,
                                                                            replace_id=replace_id,
                                                                            upload_option=upload_option,
+                                                                           show_deleted=show_deleted,
                                                                            msg=util.sanitize_text( msg ),
                                                                            messagetype='error' ) )
 
@@ -758,6 +760,7 @@
                                                                            id=library_id,
                                                                            default_action=default_action,
                                                                            created_ldda_ids=created_ldda_ids,
+                                                                           show_deleted=show_deleted,
                                                                            msg=util.sanitize_text( msg ), 
                                                                            messagetype='done' ) )
                         
@@ -770,6 +773,7 @@
                                                                cntrller=cntrller,
                                                                id=library_id,
                                                                created_ldda_ids=created_ldda_ids,
+                                                               show_deleted=show_deleted,
                                                                msg=util.sanitize_text( msg ),
                                                                messagetype=messagetype ) )
         # See if we have any inherited templates, but do not inherit contents.
@@ -819,6 +823,7 @@
                                     roles=roles,
                                     history=history,
                                     widgets=widgets,
+                                    show_deleted=show_deleted,
                                     msg=msg,
                                     messagetype=messagetype )
     def upload_dataset( self, trans, cntrller, library_id, folder_id, replace_dataset=None, **kwd ):
@@ -834,6 +839,7 @@
                 dataset_upload_inputs.append( input )
         # Library-specific params
         params = util.Params( kwd ) # is this filetoolparam safe?
+        show_deleted = util.string_as_bool( params.get( 'show_deleted', False ) )
         library_bunch = upload_common.handle_library_params( trans, params, folder_id, replace_dataset )
         msg = util.restore_text( params.get( 'msg', ''  ) )
         messagetype = params.get( 'messagetype', 'done' )
@@ -883,6 +889,7 @@
                                                        folder_id=folder_id,
                                                        replace_id=replace_id,
                                                        upload_option=upload_option,
+                                                       show_deleted=show_deleted,
                                                        msg=util.sanitize_text( msg ),
                                                        messagetype='error' ) )
         json_file_path = upload_common.create_paramfile( trans, uploaded_datasets )
diff -r e4592fc99acc -r 34babf71a09f lib/galaxy/web/controllers/tool_runner.py
--- a/lib/galaxy/web/controllers/tool_runner.py	Tue Mar 09 15:25:23 2010 -0500
+++ b/lib/galaxy/web/controllers/tool_runner.py	Tue Mar 09 16:28:04 2010 -0500
@@ -155,7 +155,6 @@
             permissions, in_roles, error, msg = trans.app.security_agent.derive_roles_from_access( trans, library_id, cntrller, library=True, **vars )
             if error:
                 return [ 'error', msg ]
-        permissions = trans.app.security_agent.history_get_default_permissions( trans.history )
         def create_dataset( name ):
             ud = Bunch( name=name, file_type=None, dbkey=None )
             if nonfile_params.get( 'folder_id', False ):
diff -r e4592fc99acc -r 34babf71a09f templates/base_panels.mako
--- a/templates/base_panels.mako	Tue Mar 09 15:25:23 2010 -0500
+++ b/templates/base_panels.mako	Tue Mar 09 16:28:04 2010 -0500
@@ -131,10 +131,11 @@
                             $(this).ajaxSubmit( { iframe: true } );
                             if ( $(this).find("input[name='folder_id']").val() != undefined ) {
                                 var library_id = $(this).find("input[name='library_id']").val();
+                                var show_deleted = $(this).find("input[name='show_deleted']").val();
                                 if ( location.pathname.indexOf( 'admin' ) != -1 ) {
-                                    $("iframe#galaxy_main").attr("src","${h.url_for( controller='library_common', action='browse_library' )}?cntrller=library_admin&id=" + library_id + "&created_ldda_ids=" + async_datasets);
+                                    $("iframe#galaxy_main").attr("src","${h.url_for( controller='library_common', action='browse_library' )}?cntrller=library_admin&id=" + library_id + "&created_ldda_ids=" + async_datasets + "&show_deleted=" + show_deleted);
                                 } else {
-                                    $("iframe#galaxy_main").attr("src","${h.url_for( controller='library_common', action='browse_library' )}?cntrller=library&id=" + library_id + "&created_ldda_ids=" + async_datasets);
+                                    $("iframe#galaxy_main").attr("src","${h.url_for( controller='library_common', action='browse_library' )}?cntrller=library&id=" + library_id + "&created_ldda_ids=" + async_datasets + "&show_deleted=" + show_deleted);
                                 }
                             } else {
                                 $("iframe#galaxy_main").attr("src","${h.url_for(controller='tool_runner', action='upload_async_message')}");
diff -r e4592fc99acc -r 34babf71a09f templates/library/common/browse_library.mako
--- a/templates/library/common/browse_library.mako	Tue Mar 09 15:25:23 2010 -0500
+++ b/templates/library/common/browse_library.mako	Tue Mar 09 16:28:04 2010 -0500
@@ -404,7 +404,7 @@
 
    <ul class="manage-table-actions">
        %if not library.deleted and ( cntrller in [ 'library_admin', 'requests_admin' ] or can_add ):
-           <li><a class="action-button" href="${h.url_for( controller='library_common', action='upload_library_dataset', cntrller=cntrller, library_id=trans.security.encode_id( library.id ), folder_id=trans.security.encode_id( library.root_folder.id ) )}"><span>Add datasets</span></a></li>
+           <li><a class="action-button" href="${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 )}"><span>Add datasets</span></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
    </ul>
diff -r e4592fc99acc -r 34babf71a09f templates/library/common/common.mako
--- a/templates/library/common/common.mako	Tue Mar 09 15:25:23 2010 -0500
+++ b/templates/library/common/common.mako	Tue Mar 09 16:28:04 2010 -0500
@@ -87,7 +87,7 @@
     %endif
 </%def>
 
-<%def name="render_upload_form( cntrller, upload_option, action, library_id, folder_id, replace_dataset, file_formats, dbkeys, widgets, roles, history )">
+<%def name="render_upload_form( cntrller, upload_option, action, library_id, folder_id, replace_dataset, file_formats, dbkeys, widgets, roles, history, show_deleted )">
     <% import os, os.path %>
     %if upload_option in [ 'upload_file', 'upload_directory', 'upload_paths' ]:
         <div class="toolForm" id="upload_library_dataset">
@@ -106,6 +106,7 @@
                     <input type="hidden" name="library_id" value="${library_id}"/>
                     <input type="hidden" name="folder_id" value="${folder_id}"/>
                     <input type="hidden" name="upload_option" value="${upload_option}"/>
+                    <input type="hidden" name="show_deleted" value="${show_deleted}"/>
                     %if replace_dataset not in [ None, 'None' ]:
                         <input type="hidden" name="replace_id" value="${trans.security.encode_id( replace_dataset.id )}"/>
                         <div class="form-row">
diff -r e4592fc99acc -r 34babf71a09f templates/library/common/upload.mako
--- a/templates/library/common/upload.mako	Tue Mar 09 15:25:23 2010 -0500
+++ b/templates/library/common/upload.mako	Tue Mar 09 16:28:04 2010 -0500
@@ -26,26 +26,26 @@
     ## Don't allow multiple datasets to be uploaded when replacing a dataset with a new version
     <a id="upload-librarydataset--popup" class="popup-arrow" style="display: none;">▼</a>
     <div popupmenu="upload-librarydataset--popup">
-        <a class="action-button" href="${h.url_for( controller='library_common', action='upload_library_dataset', cntrller=cntrller,library_id=library_id, folder_id=folder_id, replace_id=replace_id, upload_option='upload_file' )}">Upload files</a>
+        <a class="action-button" href="${h.url_for( controller='library_common', action='upload_library_dataset', cntrller=cntrller,library_id=library_id, folder_id=folder_id, replace_id=replace_id, upload_option='upload_file', show_deleted=show_deleted )}">Upload files</a>
         %if cntrller == 'library_admin':
             %if trans.app.config.library_import_dir and os.path.exists( trans.app.config.library_import_dir ):
-                <a class="action-button" href="${h.url_for( controller='library_common', action='upload_library_dataset', cntrller=cntrller, library_id=library_id, folder_id=folder_id, replace_id=replace_id, upload_option='upload_directory' )}">Upload directory of files</a>
+                <a class="action-button" href="${h.url_for( controller='library_common', action='upload_library_dataset', cntrller=cntrller, library_id=library_id, folder_id=folder_id, replace_id=replace_id, upload_option='upload_directory', show_deleted=show_deleted )}">Upload directory of files</a>
             %endif
             %if trans.app.config.allow_library_path_paste:
-                <a class="action-button" href="${h.url_for( controller='library_common', action='upload_library_dataset', cntrller=cntrller, library_id=library_id, folder_id=folder_id, replace_id=replace_id, upload_option='upload_paths' )}">Upload files from filesystem paths</a>
+                <a class="action-button" href="${h.url_for( controller='library_common', action='upload_library_dataset', cntrller=cntrller, library_id=library_id, folder_id=folder_id, replace_id=replace_id, upload_option='upload_paths', show_deleted=show_deleted )}">Upload files from filesystem paths</a>
             %endif
         %elif cntrller == 'library':
             %if trans.app.config.user_library_import_dir and os.path.exists( os.path.join( trans.app.config.user_library_import_dir, trans.user.email ) ):
-                <a class="action-button" href="${h.url_for( controller='library_common', action='upload_library_dataset', cntrller=cntrller, library_id=library_id, folder_id=folder_id, replace_id=replace_id, upload_option='upload_directory' )}">Upload directory of files</a>
+                <a class="action-button" href="${h.url_for( controller='library_common', action='upload_library_dataset', cntrller=cntrller, library_id=library_id, folder_id=folder_id, replace_id=replace_id, upload_option='upload_directory', show_deleted=show_deleted )}">Upload directory of files</a>
             %endif
         %endif
-        <a class="action-button" href="${h.url_for( controller='library_common', action='upload_library_dataset', cntrller=cntrller, library_id=library_id, folder_id=folder_id, replace_id=replace_id, upload_option='import_from_history' )}">Import datasets from your current history</a>
+        <a class="action-button" href="${h.url_for( controller='library_common', action='upload_library_dataset', cntrller=cntrller, library_id=library_id, folder_id=folder_id, replace_id=replace_id, upload_option='import_from_history', show_deleted=show_deleted )}">Import datasets from your current history</a>
     </div>
 %endif
 <br/><br/>
 <ul class="manage-table-actions">
     <li>
-        <a class="action-button" href="${h.url_for( controller='library_common', action='browse_library', cntrller=cntrller, id=library_id )}"><span>Browse this data library</span></a>
+        <a class="action-button" href="${h.url_for( controller='library_common', action='browse_library', cntrller=cntrller, id=library_id, show_deleted=show_deleted )}"><span>Browse this data library</span></a>
     </li>
 </ul>
 
@@ -53,4 +53,4 @@
     ${render_msg( msg, messagetype )}
 %endif
 
-${render_upload_form( cntrller, upload_option, action, library_id, folder_id, replace_dataset, file_formats, dbkeys, widgets, roles, history )}
+${render_upload_form( cntrller, upload_option, action, library_id, folder_id, replace_dataset, file_formats, dbkeys, widgets, roles, history, show_deleted )}

    