Hi all,

I've just updated my Mac development machine with the latest
galaxy-central, and run.sh tells me the database needs to be updated
from 73 to 75. Note this is running on SQLite. Running manage_db.sh
upgrade gives an ImportError: No module named migrate.versioning.shell

I just grabbed a fresh hg clone and it worked, but in case there is an
obvious bug lurking here, the full output is below (and I'll keep the
broken install on disk a bit longer in case there is anything else you
need to know).

Regards,

Peter

--


$ ./run.sh
python path is:
/Users/pjcock/repositories/galaxy-central/eggs/numpy-1.3.0-py2.5-macosx-10.3-fat-ucs2.egg,
/Users/pjcock/repositories/galaxy-central/eggs/pysam-0.4.1_kanwei_ae2bd50d9945-py2.5-macosx-10.3-fat-ucs2.egg,
/Users/pjcock/repositories/galaxy-central/eggs/Whoosh-0.3.18-py2.5.egg,
/Users/pjcock/repositories/galaxy-central/eggs/pycrypto-2.0.1-py2.5-macosx-10.3-fat-ucs2.egg,
/Users/pjcock/repositories/galaxy-central/eggs/python_lzo-1.08_2.03_static-py2.5-macosx-10.3-fat-ucs2.egg,
/Users/pjcock/repositories/galaxy-central/eggs/bx_python-0.7.0_14b6a6c95da6-py2.5-macosx-10.3-fat-ucs2.egg,
/Users/pjcock/repositories/galaxy-central/eggs/amqplib-0.6.1-py2.5.egg,
/Users/pjcock/repositories/galaxy-central/eggs/pexpect-2.4-py2.5.egg,
/Users/pjcock/repositories/galaxy-central/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.5.egg,
/Users/pjcock/repositories/galaxy-central/eggs/Babel-0.9.4-py2.5.egg,
/Users/pjcock/repositories/galaxy-central/eggs/Beaker-1.4-py2.5.egg,
/Users/pjcock/repositories/galaxy-central/eggs/Mako-0.2.5-py2.5.egg,
/Users/pjcock/repositories/galaxy-central/eggs/WebHelpers-0.2-py2.5.egg,
/Users/pjcock/repositories/galaxy-central/eggs/simplejson-2.1.1-py2.5-macosx-10.3-fat-ucs2.egg,
/Users/pjcock/repositories/galaxy-central/eggs/wchartype-0.1-py2.5.egg,
/Users/pjcock/repositories/galaxy-central/eggs/elementtree-1.2.6_20050316-py2.5.egg,
/Users/pjcock/repositories/galaxy-central/eggs/docutils-0.7-py2.5.egg,
/Users/pjcock/repositories/galaxy-central/eggs/WebOb-0.8.5-py2.5.egg,
/Users/pjcock/repositories/galaxy-central/eggs/Routes-1.12.3-py2.5.egg,
/Users/pjcock/repositories/galaxy-central/eggs/Cheetah-2.2.2-py2.5-macosx-10.3-fat-ucs2.egg,
/Users/pjcock/repositories/galaxy-central/eggs/PasteDeploy-1.3.3-py2.5.egg,
/Users/pjcock/repositories/galaxy-central/eggs/PasteScript-1.7.3-py2.5.egg,
/Users/pjcock/repositories/galaxy-central/eggs/Paste-1.6-py2.5.egg,
/Users/pjcock/repositories/galaxy-central/lib,
/Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/site-packages/setuptools-0.6c8-py2.5.egg,
/Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/site-packages/MySQL_python-1.2.2-py2.5-macosx-10.3-i386.egg,
/Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/site-packages/TurboGears-1.0.7-py2.5.egg,
/Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/site-packages/TurboKid-1.0.4-py2.5.egg,
/Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/site-packages/TurboJson-1.1.4-py2.5.egg,
/Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/site-packages/TurboCheetah-1.0-py2.5.egg,
/Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/site-packages/RuleDispatch-0.5a0.dev_r2306-py2.5-macosx-10.5-i386.egg,
/Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/site-packages/FormEncode-1.1-py2.5.egg,
/Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/site-packages/DecoratorTools-1.7-py2.5.egg,
/Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/site-packages/configobj-4.5.3-py2.5.egg,
/Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/site-packages/CherryPy-2.3.0-py2.5.egg,
/Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/site-packages/kid-0.9.6-py2.5.egg,
/Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/site-packages/PyProtocols-1.0a0dev_r2302-py2.5-macosx-10.3-i386.egg,
/Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/site-packages/Genshi-0.5.1-py2.5-macosx-10.3-i386.egg,
/Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/site-packages/pydot-1.0.2-py2.5.egg,
/Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/site-packages/logilab_common-0.48.0-py2.5.egg,
/Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/site-packages/logilab_astng-0.19.3-py2.5.egg,
/Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/site-packages/pylint-0.19.0-py2.5.egg,
/Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/site-packages/nose-0.11.3-py2.5.egg,
/Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/site-packages/buildbot_slave-0.8.2-py2.5.egg,
/Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/site-packages/matplotlib-1.0.1_r0-py2.6-macosx-10.3-fat.egg,
/usr/local/lib/wxPython-unicode-2.8.10.1/lib/python2.5/site-packages,
/usr/local/lib/wxPython-unicode-2.8.10.1/lib/python2.5/site-packages/wx-2.8-mac-unicode,
/Library/Frameworks/Python.framework/Versions/2.5/lib/python25.zip,
/Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5,
/Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/plat-darwin,
/Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/plat-mac,
/Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/plat-mac/lib-scriptpackages,
/Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/lib-tk,
/Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/lib-dynload,
/Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/site-packages/Numeric,
/Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/site-packages/PIL,
/usr/local/lib/wxPython-unicode-2.8.10.1/lib/python2.5,
/Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/site-packages
galaxy.datatypes.registry DEBUG 2011-02-21 15:19:10,494 Loading
datatypes from datatypes_conf.xml
galaxy.datatypes.registry DEBUG 2011-02-21 15:19:10,499 Loaded display
application 'ucsc_bam' for datatype 'bam', inherit=False
galaxy.datatypes.registry DEBUG 2011-02-21 15:19:10,504 Loaded display
application 'ensembl_bam' for datatype 'bam', inherit=False
galaxy.datatypes.registry DEBUG 2011-02-21 15:19:10,505 Loaded display
application 'genetrack_interval' for datatype 'bed', inherit=False
galaxy.datatypes.registry DEBUG 2011-02-21 15:19:10,509 Loaded display
application 'ucsc_bigbed' for datatype 'bigbed', inherit=False
galaxy.datatypes.registry DEBUG 2011-02-21 15:19:10,513 Loaded display
application 'ucsc_bigwig' for datatype 'bigwig', inherit=False
galaxy.datatypes.registry DEBUG 2011-02-21 15:19:10,526 Loaded display
application 'ensembl_gff' for datatype 'gff', inherit=True
galaxy.datatypes.registry DEBUG 2011-02-21 15:19:10,527 Loaded display
application 'genetrack_interval' for datatype 'interval', inherit=True
galaxy.datatypes.registry DEBUG 2011-02-21 15:19:10,537 Loaded display
application 'ensembl_interval' for datatype 'interval', inherit=True
galaxy.datatypes.registry DEBUG 2011-02-21 15:19:10,542 Loaded display
application 'gbrowse_interval_as_bed' for datatype 'interval',
inherit=True
galaxy.datatypes.registry DEBUG 2011-02-21 15:19:10,546 Loaded display
application 'ucsc_maf_customtrack' for datatype 'mafcustomtrack',
inherit=False
galaxy.datatypes.assembly DEBUG 2011-02-21 15:19:10,548 Velvet log
info  JJ __init__
galaxy.datatypes.registry DEBUG 2011-02-21 15:19:10,559 Loaded sniffer
for datatype: galaxy.datatypes.binary:Bam
galaxy.datatypes.registry DEBUG 2011-02-21 15:19:10,559 Loaded sniffer
for datatype: galaxy.datatypes.binary:Sff
galaxy.datatypes.registry DEBUG 2011-02-21 15:19:10,559 Loaded sniffer
for datatype: galaxy.datatypes.xml:BlastXml
galaxy.datatypes.registry DEBUG 2011-02-21 15:19:10,559 Loaded sniffer
for datatype: galaxy.datatypes.sequence:Maf
galaxy.datatypes.registry DEBUG 2011-02-21 15:19:10,559 Loaded sniffer
for datatype: galaxy.datatypes.sequence:Lav
galaxy.datatypes.registry DEBUG 2011-02-21 15:19:10,559 Loaded sniffer
for datatype: galaxy.datatypes.sequence:csFasta
galaxy.datatypes.registry DEBUG 2011-02-21 15:19:10,559 Loaded sniffer
for datatype: galaxy.datatypes.qualityscore:QualityScoreSOLiD
galaxy.datatypes.registry DEBUG 2011-02-21 15:19:10,560 Loaded sniffer
for datatype: galaxy.datatypes.qualityscore:QualityScore454
galaxy.datatypes.registry DEBUG 2011-02-21 15:19:10,560 Loaded sniffer
for datatype: galaxy.datatypes.sequence:Fasta
galaxy.datatypes.registry DEBUG 2011-02-21 15:19:10,560 Loaded sniffer
for datatype: galaxy.datatypes.sequence:Fastq
galaxy.datatypes.registry DEBUG 2011-02-21 15:19:10,560 Loaded sniffer
for datatype: galaxy.datatypes.interval:Wiggle
galaxy.datatypes.registry DEBUG 2011-02-21 15:19:10,561 Loaded sniffer
for datatype: galaxy.datatypes.images:Html
galaxy.datatypes.registry DEBUG 2011-02-21 15:19:10,561 Loaded sniffer
for datatype: galaxy.datatypes.images:Pdf
galaxy.datatypes.registry DEBUG 2011-02-21 15:19:10,561 Loaded sniffer
for datatype: galaxy.datatypes.sequence:Axt
galaxy.datatypes.registry DEBUG 2011-02-21 15:19:10,561 Loaded sniffer
for datatype: galaxy.datatypes.interval:Bed
galaxy.datatypes.registry DEBUG 2011-02-21 15:19:10,561 Loaded sniffer
for datatype: galaxy.datatypes.interval:CustomTrack
galaxy.datatypes.registry DEBUG 2011-02-21 15:19:10,562 Loaded sniffer
for datatype: galaxy.datatypes.interval:Gtf
galaxy.datatypes.registry DEBUG 2011-02-21 15:19:10,562 Loaded sniffer
for datatype: galaxy.datatypes.interval:Gff
galaxy.datatypes.registry DEBUG 2011-02-21 15:19:10,562 Loaded sniffer
for datatype: galaxy.datatypes.interval:Gff3
galaxy.datatypes.registry DEBUG 2011-02-21 15:19:10,562 Loaded sniffer
for datatype: galaxy.datatypes.tabular:Pileup
galaxy.datatypes.registry DEBUG 2011-02-21 15:19:10,562 Loaded sniffer
for datatype: galaxy.datatypes.interval:Interval
galaxy.datatypes.registry DEBUG 2011-02-21 15:19:10,563 Loaded sniffer
for datatype: galaxy.datatypes.tabular:Sam
galaxy.datatypes.registry DEBUG 2011-02-21 15:19:10,563 Loaded sniffer
for datatype: galaxy.datatypes.tabular:Vcf
galaxy.model.migrate.check DEBUG 2011-02-21 15:19:10,606 pysqlite>=2
egg successfully loaded for sqlite dialect
Traceback (most recent call last):
  File "/Users/pjcock/repositories/galaxy-central/lib/galaxy/web/buildapp.py",
line 82, in app_factory
    app = UniverseApplication( global_conf = global_conf, **kwargs )
  File "/Users/pjcock/repositories/galaxy-central/lib/galaxy/app.py",
line 32, in __init__
    create_or_verify_database( db_url, self.config.database_engine_options )
  File 
"/Users/pjcock/repositories/galaxy-central/lib/galaxy/model/migrate/check.py",
line 102, in create_or_verify_database
    % ( db_schema.version, migrate_repository.versions.latest ) )
Exception: Your database has version '73' but this code expects
version '75'.  Please backup your database and then migrate the schema
by running 'sh manage_db.sh upgrade'.

$ sh manage_db.sh upgrade
Traceback (most recent call last):
  File "./scripts/manage_db.py", line 12, in <module>
    from migrate.versioning.shell import main
ImportError: No module named migrate.versioning.shell


In case it is of use (it was asked for on what looked like a similar issue),

$ ls lib/galaxy/model/migrate/versions/
0001_initial_tables.py
0038_add_inheritable_column_to_library_template_assoc_tables.py
0001_initial_tables.pyc
0038_add_inheritable_column_to_library_template_assoc_tables.pyc
0002_metadata_file_table.py
0039_add_synopsis_column_to_library_table.py
0002_metadata_file_table.pyc
0039_add_synopsis_column_to_library_table.pyc
0003_security_and_libraries.py
0040_page_annotations.py
0003_security_and_libraries.pyc
0040_page_annotations.pyc
0004_indexes_and_defaults.py
0041_workflow_invocation.py
0004_indexes_and_defaults.pyc
0041_workflow_invocation.pyc
0005_cleanup_datasets_fix.py
0042_workflow_invocation_fix.py
0005_cleanup_datasets_fix.pyc
0042_workflow_invocation_fix.pyc
0006_change_qual_datatype.py
0043_visualization_sharing_tagging_annotating.py
0006_change_qual_datatype.pyc
0043_visualization_sharing_tagging_annotating.pyc
0007_sharing_histories.py
0044_add_notify_column_to_request_table.py
0007_sharing_histories.pyc
0044_add_notify_column_to_request_table.pyc
0008_galaxy_forms.py
0045_request_type_permissions_table.py
0008_galaxy_forms.pyc
0045_request_type_permissions_table.pyc
0009_request_table.py
0046_post_job_actions.py
0009_request_table.pyc
0046_post_job_actions.pyc
0010_hda_display_at_authz_table.py
0047_job_table_user_id_column.py
0010_hda_display_at_authz_table.pyc
0047_job_table_user_id_column.pyc
0011_v0010_mysql_index_fix.py
0048_dataset_instance_state_column.py
0011_v0010_mysql_index_fix.pyc
0048_dataset_instance_state_column.pyc
0012_user_address.py
0049_api_keys_table.py
0012_user_address.pyc
0049_api_keys_table.pyc
0013_change_lib_item_templates_to_forms.py
0050_drop_cloud_tables.py
0013_change_lib_item_templates_to_forms.pyc
0050_drop_cloud_tables.pyc
0014_pages.py
0051_imported_col_for_jobs_table.py
0014_pages.pyc
0051_imported_col_for_jobs_table.pyc
0015_tagging.py
0052_sample_dataset_table.py
0015_tagging.pyc
0052_sample_dataset_table.pyc
0016_v0015_mysql_index_fix.py
0053_item_ratings.py
0016_v0015_mysql_index_fix.pyc
0053_item_ratings.pyc
0017_library_item_indexes.py
0054_visualization_dbkey.py
0017_library_item_indexes.pyc
0054_visualization_dbkey.pyc
0018_ordered_tags_and_page_tags.py
0055_add_pja_assoc_for_jobs.py
0018_ordered_tags_and_page_tags.pyc
0055_add_pja_assoc_for_jobs.pyc
0019_request_library_folder.py
0056_workflow_outputs.py
0019_request_library_folder.pyc
0056_workflow_outputs.pyc
0020_library_upload_job.py
0057_request_notify.py
0020_library_upload_job.pyc
0057_request_notify.pyc
0021_user_prefs.py
0058_history_import_export.py
0021_user_prefs.pyc
0058_history_import_export.pyc
0022_visualization_tables.py
0059_sample_dataset_file_path.py
0022_visualization_tables.pyc
0059_sample_dataset_file_path.pyc
0023_page_published_and_deleted_columns.py
0060_history_archive_import.py
0023_page_published_and_deleted_columns.pyc
0060_history_archive_import.pyc
0024_page_slug_unique_constraint.py                              0061_tasks.py
0024_page_slug_unique_constraint.pyc                             0061_tasks.pyc
0025_user_info.py
0062_user_openid_table.py
0025_user_info.pyc
0062_user_openid_table.pyc
0026_cloud_tables.py
0063_sequencer_table.py
0026_cloud_tables.pyc
0063_sequencer_table.pyc
0027_request_events.py
0064_add_run_and_sample_run_association_tables.py
0027_request_events.pyc
0064_add_run_and_sample_run_association_tables.pyc
0028_external_metadata_file_override.py
0065_add_name_to_form_fields_and_values.py
0028_external_metadata_file_override.pyc
0065_add_name_to_form_fields_and_values.pyc
0029_user_actions.py
0066_deferred_job_and_transfer_job_tables.py
0029_user_actions.pyc
0066_deferred_job_and_transfer_job_tables.pyc
0030_history_slug_column.py
0067_populate_sequencer_table.py
0030_history_slug_column.pyc
0067_populate_sequencer_table.pyc
0031_community_and_workflow_tags.py
0068_rename_sequencer_to_external_services.py
0031_community_and_workflow_tags.pyc
0068_rename_sequencer_to_external_services.pyc
0032_stored_workflow_slug_column.py
0069_rename_sequencer_form_type.py
0032_stored_workflow_slug_column.pyc
0069_rename_sequencer_form_type.pyc
0033_published_cols_for_histories_and_workflows.py
0070_add_info_column_to_deferred_job_table.py
0033_published_cols_for_histories_and_workflows.pyc
0070_add_info_column_to_deferred_job_table.pyc
0034_page_user_share_association.py
0071_add_history_and_workflow_to_sample.py
0034_page_user_share_association.pyc
0071_add_history_and_workflow_to_sample.pyc
0035_item_annotations_and_workflow_step_tags.py
0072_add_pid_and_socket_columns_to_transfer_job_table.py
0035_item_annotations_and_workflow_step_tags.pyc
0072_add_pid_and_socket_columns_to_transfer_job_table.pyc
0036_add_deleted_column_to_library_template_assoc_tables.py
0073_add_ldda_to_implicit_conversion_table.py
0036_add_deleted_column_to_library_template_assoc_tables.pyc
0073_add_ldda_to_implicit_conversion_table.pyc
0037_samples_library.py
0074_add_purged_column_to_library_dataset_table.py
0037_samples_library.pyc
0075_add_subindex_column_to_run_table.py
peter-cocks-mac-pro:galaxy-central pjcock$
_______________________________________________
To manage your subscriptions to this and other Galaxy lists, please use the 
interface at:

  http://lists.bx.psu.edu/

Reply via email to