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 ):
>
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