1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/9e9f489c6488/ changeset: 9e9f489c6488 user: greg date: 2012-04-18 20:29:01 summary: Fix for functinal tests when GALAXY_TEST_DBURI is not set in os.environ. affected #: 1 file diff -r 66c3172dff142cef1bdcecc257db797adc6e4584 -r 9e9f489c6488e63a5d8b86ae64a81c9b4ddd306d lib/galaxy/tool_shed/migrate/check.py --- a/lib/galaxy/tool_shed/migrate/check.py +++ b/lib/galaxy/tool_shed/migrate/check.py @@ -21,6 +21,7 @@ def verify_tools( app, url, galaxy_config_file, engine_options={} ): # Check the value in the migrate_tools.version database table column to verify that the number is in # sync with the number of version scripts in ~/lib/galaxy/tools/migrate/versions. + running_functional_tests = galaxy_config_file.endswith( '.sample' ) dialect = ( url.split( ':', 1 ) )[0] try: egg = dialect_to_egg[ dialect ] @@ -54,51 +55,52 @@ config_arg = '' if os.path.abspath( os.path.join( os.getcwd(), 'universe_wsgi.ini' ) ) != galaxy_config_file: config_arg = ' -c %s' % galaxy_config_file.replace( os.path.abspath( os.getcwd() ), '.' ) - # Automatically update the value of the migrate_tools.version database table column. - cmd = 'sh manage_tools.sh%s upgrade' % config_arg - proc = subprocess.Popen( args=cmd, shell=True, stdout=subprocess.PIPE, stderr=subprocess.STDOUT ) - return_code = proc.wait() - output = proc.stdout.read( 32768 ) - if return_code != 0: - raise Exception( "Error attempting to update the value of migrate_tools.version: %s" % output ) - elif missing_tool_configs: - if len( tool_panel_configs ) == 1: - plural = '' - tool_panel_config_file_names = tool_panel_configs[ 0 ] - else: - plural = 's' - tool_panel_config_file_names = ', '.join( tool_panel_configs ) - msg = "\n>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>" - msg += "\n\nThe list of files at the end of this message refers to tools that are configured to load into the tool panel for\n" - msg += "this Galaxy instance, but have been removed from the Galaxy distribution. These tools can be automatically installed\n" - msg += "from the Galaxy tool shed at http://toolshed.g2.bx.psu.edu.\n\n" - msg += "To skip this process, attempt to start your Galaxy server again (e.g., sh run.sh or whatever you use). If you do this,\n" - msg += "be aware that these tools will no longer be available in your Galaxy tool panel, and entries for each of them should\n" - msg += "be removed from your file%s named %s.\n\n" % ( plural, tool_panel_config_file_names ) - msg += "CRITICAL NOTE IF YOU PLAN TO INSTALL\n" - msg += "The location in which the tool repositories will be installed is the value of the 'tool_path' attribute in the <tool>\n" - msg += 'tag of the file named ./migrated_tool_conf.xml (i.e., <toolbox tool_path="../shed_tools">). The default location\n' - msg += "setting is '../shed_tools', which may be problematic for some cluster environments, so make sure to change it before\n" - msg += "you execute the installation process if appropriate. The configured location must be outside of the Galaxy installation\n" - msg += "directory or it must be in a sub-directory protected by a properly configured .hgignore file if the directory is within\n" - msg += "the Galaxy installation directory hierarchy. This is because tool shed repositories will be installed using mercurial's\n" - msg += "clone feature, which creates .hg directories and associated mercurial repository files. Not having .hgignore properly\n" - msg += "configured could result in undesired behavior when modifying or updating your local Galaxy instance or the tool shed\n" - msg += "repositories if they are in directories that pose conflicts. See mercurial's .hgignore documentation at the following\n" - msg += "URL for details.\n\nhttp://mercurial.selenic.com/wiki/.hgignore\n\n" - msg += output - msg += "After the installation process finishes, you can start your Galaxy server. As part of this installation process,\n" - msg += "entries for each of the following tool config files will be added to the file named ./migrated_tool_conf.xml, so these\n" - msg += "tools will continue to be loaded into your tool panel. Because of this, existing entries for these files should be\n" - msg += "removed from your file%s named %s, but only after the installation process finishes.\n\n" % ( plural, tool_panel_config_file_names ) - for i, missing_tool_config in enumerate( missing_tool_configs ): - msg += "%s\n" % missing_tool_config - # Should we do the following? - #if i > 10: - # msg += "\n...and %d more tools...\n" % ( len( missing_tool_configs ) - ( i + 1 ) ) - # break - msg += "<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<\n" - raise Exception( msg ) + if not running_functional_tests: + # Automatically update the value of the migrate_tools.version database table column. + cmd = 'sh manage_tools.sh%s upgrade' % config_arg + proc = subprocess.Popen( args=cmd, shell=True, stdout=subprocess.PIPE, stderr=subprocess.STDOUT ) + return_code = proc.wait() + output = proc.stdout.read( 32768 ) + if return_code != 0: + raise Exception( "Error attempting to update the value of migrate_tools.version: %s" % output ) + elif missing_tool_configs: + if len( tool_panel_configs ) == 1: + plural = '' + tool_panel_config_file_names = tool_panel_configs[ 0 ] + else: + plural = 's' + tool_panel_config_file_names = ', '.join( tool_panel_configs ) + msg = "\n>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>" + msg += "\n\nThe list of files at the end of this message refers to tools that are configured to load into the tool panel for\n" + msg += "this Galaxy instance, but have been removed from the Galaxy distribution. These tools can be automatically installed\n" + msg += "from the Galaxy tool shed at http://toolshed.g2.bx.psu.edu.\n\n" + msg += "To skip this process, attempt to start your Galaxy server again (e.g., sh run.sh or whatever you use). If you do this,\n" + msg += "be aware that these tools will no longer be available in your Galaxy tool panel, and entries for each of them should\n" + msg += "be removed from your file%s named %s.\n\n" % ( plural, tool_panel_config_file_names ) + msg += "CRITICAL NOTE IF YOU PLAN TO INSTALL\n" + msg += "The location in which the tool repositories will be installed is the value of the 'tool_path' attribute in the <tool>\n" + msg += 'tag of the file named ./migrated_tool_conf.xml (i.e., <toolbox tool_path="../shed_tools">). The default location\n' + msg += "setting is '../shed_tools', which may be problematic for some cluster environments, so make sure to change it before\n" + msg += "you execute the installation process if appropriate. The configured location must be outside of the Galaxy installation\n" + msg += "directory or it must be in a sub-directory protected by a properly configured .hgignore file if the directory is within\n" + msg += "the Galaxy installation directory hierarchy. This is because tool shed repositories will be installed using mercurial's\n" + msg += "clone feature, which creates .hg directories and associated mercurial repository files. Not having .hgignore properly\n" + msg += "configured could result in undesired behavior when modifying or updating your local Galaxy instance or the tool shed\n" + msg += "repositories if they are in directories that pose conflicts. See mercurial's .hgignore documentation at the following\n" + msg += "URL for details.\n\nhttp://mercurial.selenic.com/wiki/.hgignore\n\n" + msg += output + msg += "After the installation process finishes, you can start your Galaxy server. As part of this installation process,\n" + msg += "entries for each of the following tool config files will be added to the file named ./migrated_tool_conf.xml, so these\n" + msg += "tools will continue to be loaded into your tool panel. Because of this, existing entries for these files should be\n" + msg += "removed from your file%s named %s, but only after the installation process finishes.\n\n" % ( plural, tool_panel_config_file_names ) + for i, missing_tool_config in enumerate( missing_tool_configs ): + msg += "%s\n" % missing_tool_config + # Should we do the following? + #if i > 10: + # msg += "\n...and %d more tools...\n" % ( len( missing_tool_configs ) - ( i + 1 ) ) + # break + msg += "<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<\n" + raise Exception( msg ) else: log.info( "At migrate_tools version %d" % db_schema.version ) Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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