details:
http://www.bx.psu.edu/hg/galaxy/rev/34babf71a09f
changeset: 3502:34babf71a09f
user: Greg Von Kuster <greg(a)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 )}