Re: [galaxy-dev] unit tests failures
Hi, Thanks a lot for your answer. I've manually changed lib/galaxy/objectstore/__init__.py while waiting for the fixed to be released. All the unit tests now pass. Anne. On 23 Jan 2012, at 18:51, Nate Coraor wrote: > On Jan 23, 2012, at 6:22 AM, Anne Pajon wrote: > >> Hello, >> >> I've installed recently galaxy on one of our test server with python2.7 and >> I am running out of ideas on how to solve the issue related to this unit >> test failure: galaxy.objectstore.DiskObjectStore. Here is the output when >> running sh run_unit_tests.sh. > > Hi Anne, > > This has been fixed in changeset 8a597b83448f. Unfortunately, this changeset > is not part of the current stable release. It will be in the next one, > however. > > https://bitbucket.org/galaxy/galaxy-central/changeset/8a597b83448f > > --nate > -- Anne Pajon, Ph.D. Cancer Research UK - Cambridge Research Institute Li Ka Shing Centre, Robinson Way, Cambridge CB2 0RE anne.pa...@cancer.org.uk | +44 (0)7958 511 353 NOTICE AND DISCLAIMER This e-mail (including any attachments) is intended for the above-named person(s). If you are not the intended recipient, notify the sender immediately, delete this email from your system and do not disclose or use for any purpose. We may monitor all incoming and outgoing emails in line with current legislation. We have taken steps to ensure that this email and attachments are free from any virus, but it remains your responsibility to ensure that viruses do not adversely affect you. Cancer Research UK Registered in England and Wales Company Registered Number: 4325234. Registered Charity Number: 1089464 and Scotland SC041666 Registered Office Address: Angel Building, 407 St John Street, London EC1V 4AD. ___ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
Re: [galaxy-dev] unit tests failures
On Jan 23, 2012, at 6:22 AM, Anne Pajon wrote: > Hello, > > I've installed recently galaxy on one of our test server with python2.7 and I > am running out of ideas on how to solve the issue related to this unit test > failure: galaxy.objectstore.DiskObjectStore. Here is the output when running > sh run_unit_tests.sh. Hi Anne, This has been fixed in changeset 8a597b83448f. Unfortunately, this changeset is not part of the current stable release. It will be in the next one, however. https://bitbucket.org/galaxy/galaxy-central/changeset/8a597b83448f --nate > > [webapp@uk-cri-lbio08 galaxy-dist]$ sh run_unit_tests.sh > Data (galaxy.datatypes.data) > Doctest: galaxy.datatypes.data.Data ... ok > sniff (galaxy.datatypes.images.Html) > Doctest: galaxy.datatypes.images.Html.sniff ... ok > sniff (galaxy.datatypes.interval.Bed) > Doctest: galaxy.datatypes.interval.Bed.sniff ... ok > sniff (galaxy.datatypes.interval.CustomTrack) > Doctest: galaxy.datatypes.interval.CustomTrack.sniff ... ok > sniff (galaxy.datatypes.interval.Gff) > Doctest: galaxy.datatypes.interval.Gff.sniff ... ok > sniff (galaxy.datatypes.interval.Gff3) > Doctest: galaxy.datatypes.interval.Gff3.sniff ... ok > sniff (galaxy.datatypes.interval.Gtf) > Doctest: galaxy.datatypes.interval.Gtf.sniff ... ok > sniff (galaxy.datatypes.interval.Interval) > Doctest: galaxy.datatypes.interval.Interval.sniff ... ok > sniff (galaxy.datatypes.interval.Wiggle) > Doctest: galaxy.datatypes.interval.Wiggle.sniff ... ok > sniff (galaxy.datatypes.qualityscore.QualityScore454) > Doctest: galaxy.datatypes.qualityscore.QualityScore454.sniff ... ok > sniff (galaxy.datatypes.qualityscore.QualityScoreSOLiD) > Doctest: galaxy.datatypes.qualityscore.QualityScoreSOLiD.sniff ... ok > sniff (galaxy.datatypes.sequence.Axt) > Doctest: galaxy.datatypes.sequence.Axt.sniff ... ok > sniff (galaxy.datatypes.sequence.Fasta) > Doctest: galaxy.datatypes.sequence.Fasta.sniff ... ok > sniff (galaxy.datatypes.sequence.Fastq) > Doctest: galaxy.datatypes.sequence.Fastq.sniff ... ok > sniff (galaxy.datatypes.sequence.Lav) > Doctest: galaxy.datatypes.sequence.Lav.sniff ... ok > sniff (galaxy.datatypes.sequence.Maf) > Doctest: galaxy.datatypes.sequence.Maf.sniff ... ok > get_split_commands_sequential (galaxy.datatypes.sequence.Sequence) > Doctest: galaxy.datatypes.sequence.Sequence.get_split_commands_sequential ... > ok > get_split_commands_with_toc (galaxy.datatypes.sequence.Sequence) > Doctest: galaxy.datatypes.sequence.Sequence.get_split_commands_with_toc ... ok > sniff (galaxy.datatypes.sequence.csFasta) > Doctest: galaxy.datatypes.sequence.csFasta.sniff ... ok > convert_newlines (galaxy.datatypes.sniff) > Doctest: galaxy.datatypes.sniff.convert_newlines ... ok > convert_newlines_sep2tabs (galaxy.datatypes.sniff) > Doctest: galaxy.datatypes.sniff.convert_newlines_sep2tabs ... ok > get_headers (galaxy.datatypes.sniff) > Doctest: galaxy.datatypes.sniff.get_headers ... ok > guess_ext (galaxy.datatypes.sniff) > Doctest: galaxy.datatypes.sniff.guess_ext ... ok > is_column_based (galaxy.datatypes.sniff) > Doctest: galaxy.datatypes.sniff.is_column_based ... ok > sep2tabs (galaxy.datatypes.sniff) > Doctest: galaxy.datatypes.sniff.sep2tabs ... ok > sniff (galaxy.datatypes.tabular.Pileup) > Doctest: galaxy.datatypes.tabular.Pileup.sniff ... ok > sniff (galaxy.datatypes.tabular.Sam) > Doctest: galaxy.datatypes.tabular.Sam.sniff ... ok > sniff (galaxy.datatypes.xml.BlastXml) > Doctest: galaxy.datatypes.xml.BlastXml.sniff ... ok > sniff (galaxy.datatypes.xml.GenericXml) > Doctest: galaxy.datatypes.xml.GenericXml.sniff ... ok > test_basic (galaxy.model.mapping_tests.MappingTests) ... ok > DiskObjectStore (galaxy.objectstore) > Doctest: galaxy.objectstore.DiskObjectStore ... FAIL > galaxy.tools.deps.tests.test > galaxy.tools.deps.tests.test ... ok > BooleanToolParameter (galaxy.tools.parameters.basic) > Doctest: galaxy.tools.parameters.basic.BooleanToolParameter ... ok > ColumnListParameter (galaxy.tools.parameters.basic) > Doctest: galaxy.tools.parameters.basic.ColumnListParameter ... ok > DrillDownSelectToolParameter (galaxy.tools.parameters.basic) > Doctest: galaxy.tools.parameters.basic.DrillDownSelectToolParameter ... ok > FileToolParameter (galaxy.tools.parameters.basic) > Doctest: galaxy.tools.parameters.basic.FileToolParameter ... ok > FloatToolParameter (galaxy.tools.parameters.basic) > Doctest: galaxy.tools.parameters.basic.FloatToolParameter ... ok > GenomeBuildParameter (galaxy.tools.parameters.basic) > Doctest: galaxy.tools.parameters.basic.GenomeBuildParameter ... ok > HiddenToolParameter (galaxy.tools.parameters.basic) > Doctest: galaxy.tools.parameters.basic.HiddenToolParameter ... ok > IntegerToolParameter (galaxy.tools.parameters.basic) > Doctest: galaxy.tools.parameters.basic.IntegerToolParameter ... ok > SelectToolParameter (galaxy.tools.parameters.basic) > Doctest: galaxy.tools.parameters.basic.SelectToolParameter ... ok > TextToolParameter (galaxy.tools.parameters.basic) >
