Re: [galaxy-dev] AttributeError: type object 'InvalidJobException' has no attribute 'name'

8 Oct 2013


      In order to test that, I've just downloaded a new galaxy-central and
configured it to submit jobs in our SGE cluster. Same problem. The job
starts and finishes, but galaxy keeps informing it's still running.
I've also attached the job_conf.xml file.
Need help, please!
-Adhemar


galaxy.jobs.runners ERROR 2013-10-08 15:29:16,721 Unhandled exception
checking active jobs
Traceback (most recent call last):
  File
"/opt/bioinformatics/share/galaxy20131008/lib/galaxy/jobs/runners/__init__.py",
line 362, in monitor
    self.check_watched_items()
  File
"/opt/bioinformatics/share/galaxy20131008/lib/galaxy/jobs/runners/drmaa.py",
line 217, in check_watched_items
    log.warning( "(%s/%s) job check resulted in %s: %s", galaxy_id_tag,
external_job_id, e.__class__.name, e )
AttributeError: type object 'InvalidJobException' has no attribute 'name'


<?xml version="1.0"?>
<job_conf>
    <plugins workers="10">
        <!-- <plugin id="local" type="runner"
load="galaxy.jobs.runners.local:LocalJobRunner" workers="10"/> -->
        <plugin id="sge" type="runner"
load="galaxy.jobs.runners.drmaa:DRMAAJobRunner" workers="10"/>
    </plugins>
    <handlers default="handlers">
        <handler id="main"/>
        <handler id="handler0" tags="handlers"/>
        <handler id="handler1" tags="handlers"/>
        <handler id="handler2" tags="handlers"/>
        <handler id="handler3" tags="handlers"/>
        <handler id="handler4" tags="handlers"/>
        <handler id="handler5" tags="handlers"/>
        <handler id="handler6" tags="handlers"/>
        <handler id="handler7" tags="handlers"/>
        <handler id="handler8" tags="handlers"/>
        <handler id="handler9" tags="handlers"/>
    </handlers>
    <destinations default="sge_cluster">
        <!--
        <destination id="local" runner="local"/>
        -->
        <destination id="sge_cluster" runner="sge" tags="longjobs">
            <param id="nativeSpecification">-V -q galaxy.q</param>
        </destination>
    </destinations>
</job_conf>


2013/10/8 Adhemar <azneto@gmail.com>
...
Hi,
After the last update I'm getting the following error.
The job is submitted to SGE e executed, but galaxy doesn't get the result
and keeps showing the job is executing (yellow box).
Any clues?
Thanks,
Adhemar
galaxy.jobs.runners ERROR 2013-10-08 13:01:18,488 Unhandled exception
checking active jobs
Traceback (most recent call last):
  File
"/opt/bioinformatics/share/galaxy20130410/lib/galaxy/jobs/runners/__init__.py",
line 362, in monitor
    self.check_watched_items()
  File
"/opt/bioinformatics/share/galaxy20130410/lib/galaxy/jobs/runners/drmaa.py",
line 217, in check_watched_items
    log.warning( "(%s/%s) job check resulted in %s: %s", galaxy_id_tag,
external_job_id, e.__class__.name, e )
AttributeError: type object 'InvalidJobException' has no attribute 'name'