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.pajon(a)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. 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