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