1 new commit in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/changeset/8a8a37bbdc2f/ changeset: 8a8a37bbdc2f user: inithello date: 2012-08-29 16:16:11 summary: Made download status page more informative, fixed intermittent indexing error. affected #: 2 files
diff -r 30c7f58f116d9e11a209ed8a5d193ec2d91de280 -r 8a8a37bbdc2fc233446966793b6545d553aa50d8 lib/galaxy/tools/genome_index/index_genome.py --- a/lib/galaxy/tools/genome_index/index_genome.py +++ b/lib/galaxy/tools/genome_index/index_genome.py @@ -54,6 +54,7 @@ self._log( self.locations ) self._log( 'Indexer %s completed successfully.' % indexer ) self._flush_files() + exit(0)
def _check_link( self ): self._log( 'Checking symlink to %s' % self.fafile )
diff -r 30c7f58f116d9e11a209ed8a5d193ec2d91de280 -r 8a8a37bbdc2fc233446966793b6545d553aa50d8 lib/galaxy/web/controllers/data_admin.py --- a/lib/galaxy/web/controllers/data_admin.py +++ b/lib/galaxy/web/controllers/data_admin.py @@ -148,7 +148,8 @@ dbkey = build[0] longname = build[1] break - assert dbkey is not '?', 'That build was not found' + if dbkey == '?': + return trans.fill_template( '/admin/data_admin/generic_error.mako', message='An invalid build was specified.' ) ftp = ftplib.FTP('hgdownload.cse.ucsc.edu') ftp.login('anonymous', trans.get_user().email) checker = [] @@ -189,7 +190,8 @@ dbkeys=trans.ucsc_builds ) elif source == 'Ensembl': dbkey = params.get( 'ensembl_dbkey', None ) - assert dbkey is not '?', 'That build was not found' + if dbkey == '?': + return trans.fill_template( '/admin/data_admin/generic_error.mako', message='An invalid build was specified.' ) for build in trans.ensembl_builds: if build[ 'dbkey' ] == dbkey: dbkey = build[ 'dbkey' ] @@ -199,7 +201,7 @@ break url = 'ftp://ftp.ensembl.org/pub/release-%s/fasta/%s/dna/%s.%s.%s.dna.toplevel.fa.gz' % ( release, pathname.lower(), pathname, dbkey, release ) else: - return trans.fill_template( '/admin/data_admin/generic_error.mako', message='Somehow an invalid data source was specified.' ) + return trans.fill_template( '/admin/data_admin/generic_error.mako', message='An invalid data source was specified.' ) if url is None: return trans.fill_template( '/admin/data_admin/generic_error.mako', message='Unable to generate a valid URL with the specified parameters.' ) params = dict( protocol='http', name=dbkey, datatype='fasta', url=url, user=trans.user.id ) @@ -248,7 +250,8 @@ sa = trans.app.model.context.current if jobtype == 'liftover': job = sa.query( model.TransferJob ).filter_by( id=jobid ).first() - joblabel = 'Download liftOver' + liftover = trans.app.job_manager.deferred_job_queue.plugins['LiftOverTransferPlugin'].get_job_status( jobid ) + joblabel = 'Download liftOver (%s to %s)' % ( liftover.params[ 'from_genome' ], liftover.params[ 'to_genome' ] ) elif jobtype == 'transfer': job = sa.query( model.TransferJob ).filter_by( id=jobid ).first() joblabel = 'Download Genome'
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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