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. 

[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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