DynamicDisplayApplicationBuilder error after updating Galaxy to latest

Question: DynamicDisplayApplicationBuilder error after updating Galaxy to latest_2014.10.06

4.0 years ago by

United States

Lance Parsons • 110 wrote:

After updating my local instance of Galaxy to latest_2014.10.06 I get a number of similar errors relating to DisplayApplications.

It seems that others have run into this problem as well (see http://dev.list.galaxyproject.org/Assertion-errors-when-starting-Galaxy-td4665805.html), but as of yet I haven't figured out the cause (or a workaround or solution).

An example is below:

galaxy.datatypes.registry ERROR 2014-12-11 10:57:01,183 Error loading display application (./display_applications/igv/vcf.xml): Filename and id attributes required for dynamic_links
Traceback (most recent call last):
  File "/data/galaxy-dev/galaxy-dev/lib/galaxy/datatypes/registry.py", line 576, in load_display_applications
    display_app = DisplayApplication.from_file( config_path, self )
  File "/data/galaxy-dev/galaxy-dev/lib/galaxy/datatypes/display_applications/application.py", line 170, in from_file
    return cls.from_elem( parse_xml( filename ).getroot(), datatypes_registry )
  File "/data/galaxy-dev/galaxy-dev/lib/galaxy/datatypes/display_applications/application.py", line 183, in from_elem
    for link in DynamicDisplayApplicationBuilder( dynamic_links, rval, datatypes_registry.build_sites ):
  File "/data/galaxy-dev/galaxy-dev/lib/galaxy/datatypes/display_applications/application.py", line 91, in __init__
    assert filename is not None, 'Filename and id attributes required for dynamic_links'
AssertionError: Filename and id attributes required for dynamic_links

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modified 4.0 years ago by Nate Coraor ♦ 3.2k • written 4.0 years ago by Lance Parsons • 110

Hi Lance,

can you please paste the content of your ./display_application/igv/vcf.xml file?

Thanks,

Bjoern

ADD REPLY • link written 4.0 years ago by Bjoern Gruening ♦ 5.1k

4.0 years ago by

Nate Coraor ♦ 3.2k

United States

Nate Coraor ♦ 3.2k wrote:

Here's my reply cross-posted from galaxy-dev:

This is occurring because in the last release, some options from the Galaxy config file (ucsc_display_sites, gbrowse_display_sites) as well as the list of genome builds for other display applications (which was previously a path in the display application's XML file in galaxy-dist/display_applications/) have been moved to the datatypes config file.

If you are using a locally modified version of datatypes_conf.xml, please update yours from config/datatypes_conf.xml.sample to include the new <build_sites> section at the bottom of the file. If you do not have local modifications, you can simply delete datatypes_conf.xml and Galaxy will use the sample version automatically, meaning you will not need to update it by hand when changes are made upstream.

ADD COMMENT • link written 4.0 years ago by Nate Coraor ♦ 3.2k

Thanks Nate, deleting the existing file worked like a charm. So is galaxy now using the .sample files instead of copying them when no custom one exists?

ADD REPLY • link written 4.0 years ago by Lance Parsons • 110

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