Hello, Peter The blank panel should definitely be handled more gracefully in this situation - I'll work on that.
Have you noticed though, since your patch, any particular pattern to which metadata names are turning out to equal None (some obviously missing metadata field)? Is there a particular datatype? Have you seen the assertion fail? C On Wed, Jan 16, 2013 at 11:31 AM, Peter Cock <p.j.a.c...@googlemail.com>wrote: > Hello all, > > I've noticed on my test setup (tracking galaxy-central) a problem with > some histories not displaying. If I click on saved histories, I am show > a list. Some will load (slower than I recall), but others result in a blank > right hand pane - with the following error from run.sh > > galaxy.webapps.galaxy.api.history_contents ERROR 2013-01-16 > 15:24:22,726 Error in history API at listing contents: <type > 'exceptions.TypeError'>, cannot concatenate 'str' and 'NoneType' > objects > > The same error and blank pane happens if I click on the reload > history icon. A screenshot is attached. > > This error is coming from HistoryContentsController in file > lib/galaxy/webapps/galaxy/api/history_contents.py - specifically > in the call to get_hda_dict. I tried modifying this for loop so that > any individual transaction with an error is ignored (but a debug > message logged), and I could then load the rest of the problem > histories. > > The error from get_hda_dict is from the first line, which takes > the galaxy.model.HistoryDatasetAssociation object and asks: > > hda_dict = hda.get_api_value( view='element' ) > > That takes us to lib/galaxy/model/__init__.py and the root of > the problem: I am seeing entries where both name and val > are None, meaning this line fails with the TypeError above: > > rval['metadata_' + name] = val > > Clearly some of my histories now have some 'bad' data in them, > and currently Galaxy is failing to cope. Based on the ID numbers > this has been happening for a while, so not a recent regression. > > Here is a patch which seems to help. > > Peter > > $ hg diff lib/galaxy/model/__init__.py > diff -r 81c3b8a6a621 lib/galaxy/model/__init__.py > --- a/lib/galaxy/model/__init__.py Wed Jan 16 15:14:04 2013 +0000 > +++ b/lib/galaxy/model/__init__.py Wed Jan 16 16:26:28 2013 +0000 > @@ -1530,7 +1530,11 @@ > val = val.file_name > elif isinstance( val, list ): > val = ', '.join( [str(v) for v in val] ) > - rval['metadata_' + name] = val > + if name is None: > + log.debug("get_api_value(view=%r) : name %r, val %r" > % (view, name, val)) > + assert val is None, "get_api_value(view=%r) : name > %r, val %r" % (view, name, val) > + else: > + rval['metadata_' + name] = val > return rval > > class HistoryDatasetAssociationDisplayAtAuthorization( object ): > > ___________________________________________________________ > Please keep all replies on the list by using "reply all" > in your mail client. To manage your subscriptions to this > and other Galaxy lists, please use the interface at: > > http://lists.bx.psu.edu/ >
___________________________________________________________ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/