details:
http://www.bx.psu.edu/hg/galaxy/rev/0b5d64cde142
changeset: 2475:0b5d64cde142
user: Greg Von Kuster <greg(a)bx.psu.edu>
date: Fri Jul 10 16:15:32 2009 -0400
description:
Fix for tool frame refresh when require_login config setting is true ( resolves ticket 100
), eliminate center instead of end of history item name in DataToolParameter if name is
> 30 chars ( resolves ticket # 64 ), and a log an error instead of raising an exception
in get_history() if None is returned ( better behavior ).
3 file(s) affected in this change:
lib/galaxy/tools/parameters/basic.py
lib/galaxy/web/controllers/user.py
lib/galaxy/web/framework/__init__.py
diffs (60 lines):
diff -r 615a0bcf870b -r 0b5d64cde142 lib/galaxy/tools/parameters/basic.py
--- a/lib/galaxy/tools/parameters/basic.py Fri Jul 10 15:24:01 2009 -0400
+++ b/lib/galaxy/tools/parameters/basic.py Fri Jul 10 16:15:32 2009 -0400
@@ -1115,6 +1115,10 @@
# CRUCIAL: the dataset_collector function needs to be local to
DataToolParameter.get_html_field()
def dataset_collector( hdas, parent_hid ):
for i, hda in enumerate( hdas ):
+ if len( hda.name ) > 30:
+ hda_name = '%s..%s' % ( hda.name[:17], hda.name[-11:] )
+ else:
+ hda_name = hda.name
if parent_hid is not None:
hid = "%s.%d" % ( parent_hid, i + 1 )
else:
@@ -1132,7 +1136,7 @@
continue
if isinstance( hda.datatype, self.formats):
selected = ( value and ( hda in value ) )
- field.add_option( "%s: %s" % ( hid, hda.name[:30] ),
hda.id, selected )
+ field.add_option( "%s: %s" % ( hid, hda_name ), hda.id,
selected )
else:
target_ext, converted_dataset = hda.find_conversion_destination(
self.formats, converter_safe = self.converter_safe( other_values, trans ) )
if target_ext:
@@ -1141,7 +1145,7 @@
if not trans.app.security_agent.allow_action( trans.user,
trans.app.security_agent.permitted_actions.DATASET_ACCESS, dataset=hda.dataset ):
continue
selected = ( value and ( hda in value ) )
- field.add_option( "%s: (as %s) %s" % ( hid,
target_ext, hda.name[:30] ), hda.id, selected )
+ field.add_option( "%s: (as %s) %s" % ( hid,
target_ext, hda_name ), hda.id, selected )
# Also collect children via association object
dataset_collector( hda.children, hid )
dataset_collector( history.active_datasets, None )
diff -r 615a0bcf870b -r 0b5d64cde142 lib/galaxy/web/controllers/user.py
--- a/lib/galaxy/web/controllers/user.py Fri Jul 10 15:24:01 2009 -0400
+++ b/lib/galaxy/web/controllers/user.py Fri Jul 10 16:15:32 2009 -0400
@@ -168,8 +168,8 @@
mail = os.popen("%s -t" % trans.app.config.sendmail_path,
'w')
mail.write("To: %s\nFrom: %s\nSubject: Join Mailing List\n\nJoin
Mailing list." % (trans.app.config.mailing_join_addr,email) )
if mail.close():
- return trans.show_warn_message( "Now logged in as " +
user.email+". However, subscribing to the mailing list has failed.",
refresh_frames=['masthead', 'history'] )
- return trans.show_ok_message( "Now logged in as " + user.email,
refresh_frames=['masthead', 'history'] )
+ return trans.show_warn_message( "Now logged in as " +
user.email+". However, subscribing to the mailing list has failed.",
refresh_frames=refresh_frames )
+ return trans.show_ok_message( "Now logged in as " + user.email,
refresh_frames=refresh_frames )
return trans.show_form(
web.FormBuilder( web.url_for(), "Create account",
submit_text="Create" )
.add_text( "email", "Email address", value=email,
error=email_error )
diff -r 615a0bcf870b -r 0b5d64cde142 lib/galaxy/web/framework/__init__.py
--- a/lib/galaxy/web/framework/__init__.py Fri Jul 10 15:24:01 2009 -0400
+++ b/lib/galaxy/web/framework/__init__.py Fri Jul 10 16:15:32 2009 -0400
@@ -456,7 +456,9 @@
if util.string_as_bool( create ):
history = self.new_history()
else:
- raise "get_history() returning None"
+ # Perhaps a bot is running a tool without having logged in to get a
history
+ log.debug( "Error: this request returned None from get_history():
%s" % self.request.browser_url )
+ return None
return history
def set_history( self, history ):
if history and not history.deleted: