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)
> Doctest: galaxy.tools.parameters.basic.TextToolParameter ... ok
> ToolInputTranslator (galaxy.tools.parameters.input_translation)
> Doctest: galaxy.tools.parameters.input_translation.ToolInputTranslator ... ok
> ToolParameterSanitizer (galaxy.tools.parameters.sanitize)
> Doctest: galaxy.tools.parameters.sanitize.ToolParameterSanitizer ... ok
> ExpressionValidator (galaxy.tools.parameters.validation)
> Doctest: galaxy.tools.parameters.validation.ExpressionValidator ... ok
> InRangeValidator (galaxy.tools.parameters.validation)
> Doctest: galaxy.tools.parameters.validation.InRangeValidator ... ok
> LengthValidator (galaxy.tools.parameters.validation)
> Doctest: galaxy.tools.parameters.validation.LengthValidator ... ok
> RegexValidator (galaxy.tools.parameters.validation)
> Doctest: galaxy.tools.parameters.validation.RegexValidator ... ok
> Params (galaxy.util)
> Doctest: galaxy.util.Params ... ok
> file_iter (galaxy.util)
> Doctest: galaxy.util.file_iter ... ok
> nice_size (galaxy.util)
> Doctest: galaxy.util.nice_size ... ok
> unique_id (galaxy.util)
> Doctest: galaxy.util.unique_id ... ok
> CheckboxField (galaxy.web.form_builder)
> Doctest: galaxy.web.form_builder.CheckboxField ... ok
> DrillDownField (galaxy.web.form_builder)
> Doctest: galaxy.web.form_builder.DrillDownField ... ok
> FileField (galaxy.web.form_builder)
> Doctest: galaxy.web.form_builder.FileField ... ok
> HiddenField (galaxy.web.form_builder)
> Doctest: galaxy.web.form_builder.HiddenField ... ok
> PasswordField (galaxy.web.form_builder)
> Doctest: galaxy.web.form_builder.PasswordField ... ok
> SelectField (galaxy.web.form_builder)
> Doctest: galaxy.web.form_builder.SelectField ... ok
> TextArea (galaxy.web.form_builder)
> Doctest: galaxy.web.form_builder.TextArea ... ok
> TextField (galaxy.web.form_builder)
> Doctest: galaxy.web.form_builder.TextField ... ok
> 
> ======================================================================
> FAIL: DiskObjectStore (galaxy.objectstore)
> Doctest: galaxy.objectstore.DiskObjectStore
> ----------------------------------------------------------------------
> Traceback (most recent call last):
>  File "/opt/local/home/webapp/galaxy/python/lib/python2.7/doctest.py", line 
> 2166, in runTest
>    raise self.failureException(self.format_failure(new.getvalue()))
> AssertionError: Failed doctest test for galaxy.objectstore.DiskObjectStore
>  File 
> "/opt/local/home/webapp/galaxy/galaxy-dist/lib/galaxy/objectstore/__init__.py",
>  line 190, in DiskObjectStore
> 
> ----------------------------------------------------------------------
> File 
> "/opt/local/home/webapp/galaxy/galaxy-dist/lib/galaxy/objectstore/__init__.py",
>  line 198, in galaxy.objectstore.DiskObjectStore
> Failed example:
>    s = DiskObjectStore(Bunch(umask=077), file_path=file_path)
> Exception raised:
>    Traceback (most recent call last):
>      File "/opt/local/home/webapp/galaxy/python/lib/python2.7/doctest.py", 
> line 1254, in __run
>        compileflags, 1) in test.globs
>      File "<doctest galaxy.objectstore.DiskObjectStore[3]>", line 1, in 
> <module>
>        s = DiskObjectStore(Bunch(umask=077), file_path=file_path)
>      File 
> "/opt/local/home/webapp/galaxy/galaxy-dist/lib/galaxy/objectstore/__init__.py",
>  line 208, in __init__
>        self.extra_dirs['job_work'] = config.job_working_directory
>    AttributeError: 'Bunch' object has no attribute 'job_working_directory'
> ----------------------------------------------------------------------
> File 
> "/opt/local/home/webapp/galaxy/galaxy-dist/lib/galaxy/objectstore/__init__.py",
>  line 199, in galaxy.objectstore.DiskObjectStore
> Failed example:
>    s.create(1)
> Exception raised:
>    Traceback (most recent call last):
>      File "/opt/local/home/webapp/galaxy/python/lib/python2.7/doctest.py", 
> line 1254, in __run
>        compileflags, 1) in test.globs
>      File "<doctest galaxy.objectstore.DiskObjectStore[4]>", line 1, in 
> <module>
>        s.create(1)
>    NameError: name 's' is not defined
> ----------------------------------------------------------------------
> File 
> "/opt/local/home/webapp/galaxy/galaxy-dist/lib/galaxy/objectstore/__init__.py",
>  line 200, in galaxy.objectstore.DiskObjectStore
> Failed example:
>    s.exists(1)
> Exception raised:
>    Traceback (most recent call last):
>      File "/opt/local/home/webapp/galaxy/python/lib/python2.7/doctest.py", 
> line 1254, in __run
>        compileflags, 1) in test.globs
>      File "<doctest galaxy.objectstore.DiskObjectStore[5]>", line 1, in 
> <module>
>        s.exists(1)
>    NameError: name 's' is not defined
> ----------------------------------------------------------------------
> File 
> "/opt/local/home/webapp/galaxy/galaxy-dist/lib/galaxy/objectstore/__init__.py",
>  line 202, in galaxy.objectstore.DiskObjectStore
> Failed example:
>    assert s.get_filename(1) == file_path + '/000/dataset_1.dat'
> Exception raised:
>    Traceback (most recent call last):
>      File "/opt/local/home/webapp/galaxy/python/lib/python2.7/doctest.py", 
> line 1254, in __run
>        compileflags, 1) in test.globs
>      File "<doctest galaxy.objectstore.DiskObjectStore[6]>", line 1, in 
> <module>
>        assert s.get_filename(1) == file_path + '/000/dataset_1.dat'
>    NameError: name 's' is not defined
> 
> 
> ----------------------------------------------------------------------
> Ran 60 tests in 3.651s
> 
> FAILED (failures=1)
> 
> Thanks in advance for your help.
> Anne.
> 
> --
> 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
> 
> 
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