Premanand Achuthan
2015-01-26 17:20:18 UTC
HI
We recently upgraded our gbrowse version from 2.38 to 2.54, with fcgi
enabled.
We used to link out some of our tracks to external sites (eg: RefSeq) ie
when we mouse hover, we display the title with name: start..end and upon
clicking the same track, we link out to external site.
We noticed that this is not working for certain tracks after the upgrade.
In our configuration file, we have defined the feature type:source
definition as 'feature = processed_transcript:RefSeq ' and as we also
wanted to exclude certain feature types from our search results (ie don't
show in the search result if the type is processed_transcript), we have
added 'exclude types = processed_transcript' in our database definition
file.
Reading through the change logs, exclude types ([foo:database] exclude
types = type1 type2 type3) was introduced in version 2.29. In v2.44 the way
the Imagemap is generated was changed, 'time-consuming callbacks are only
executed when mouse hovers or clicks on the feature'.
Had a look at the modules/logs and on mouse hover/mouse click the search
routines are called correctly, fetches the results, and I guess at the end
it was filtering for the features that we have excluded (at
RegionSearch.pm's filter_features routine). So we are not getting any
result back and the links doesn't work. We can also restore to original
behaviour by setting the "inline imagemap" to true for the tracks that we
add 'exclude type' and the links on mouse hover/mouse clink works by doing
so.
So my hunch is that call backs failure on mouse hover/mouse click for
tracks that have "exclude type" defined in database_definition file is a
side effect of the new feature introduced in v2.44. I may be wrong as well.
Kindly excuse if so.
Wondering if anyone has had any similar issues and is it possible to have
the links working without adding the inline imagemap option (for excluded
types)?
Thanks
Prem
We recently upgraded our gbrowse version from 2.38 to 2.54, with fcgi
enabled.
We used to link out some of our tracks to external sites (eg: RefSeq) ie
when we mouse hover, we display the title with name: start..end and upon
clicking the same track, we link out to external site.
We noticed that this is not working for certain tracks after the upgrade.
In our configuration file, we have defined the feature type:source
definition as 'feature = processed_transcript:RefSeq ' and as we also
wanted to exclude certain feature types from our search results (ie don't
show in the search result if the type is processed_transcript), we have
added 'exclude types = processed_transcript' in our database definition
file.
Reading through the change logs, exclude types ([foo:database] exclude
types = type1 type2 type3) was introduced in version 2.29. In v2.44 the way
the Imagemap is generated was changed, 'time-consuming callbacks are only
executed when mouse hovers or clicks on the feature'.
Had a look at the modules/logs and on mouse hover/mouse click the search
routines are called correctly, fetches the results, and I guess at the end
it was filtering for the features that we have excluded (at
RegionSearch.pm's filter_features routine). So we are not getting any
result back and the links doesn't work. We can also restore to original
behaviour by setting the "inline imagemap" to true for the tracks that we
add 'exclude type' and the links on mouse hover/mouse clink works by doing
so.
So my hunch is that call backs failure on mouse hover/mouse click for
tracks that have "exclude type" defined in database_definition file is a
side effect of the new feature introduced in v2.44. I may be wrong as well.
Kindly excuse if so.
Wondering if anyone has had any similar issues and is it possible to have
the links working without adding the inline imagemap option (for excluded
types)?
Thanks
Prem