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@cancer.org.uk | +44 (0)7958 511 353
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