def __init__( self, app, latest_migration_script_number, tool_shed_install_config, migrated_tools_config, install_dependencies ):
"""
Check tool settings in tool_shed_install_config and install all repositories that are not already installed. The tool
panel configuration file is the received migrated_tools_config, which is the reserved file named migrated_tools_conf.xml.
"""
self.app = app
self.toolbox = self.app.toolbox
self.migrated_tools_config = migrated_tools_config
# If install_dependencies is True but tool_dependency_dir is not set, do not attempt to install but print informative error message.
if install_dependencies and app.config.tool_dependency_dir is None:
message = 'You are attempting to install tool dependencies but do not have a value for "tool_dependency_dir" set in your universe_wsgi.ini '
message += 'file. Set this location value to the path where you want tool dependencies installed and rerun the migration script.'
raise Exception( message )
# Get the local non-shed related tool panel configs (there can be more than one, and the default name is tool_conf.xml).
self.proprietary_tool_confs = self.non_shed_tool_panel_configs
self.proprietary_tool_panel_elems = self.get_proprietary_tool_panel_elems( latest_migration_script_number )
# Set the location where the repositories will be installed by retrieving the tool_path setting from migrated_tools_config.
tree = util.parse_xml( migrated_tools_config )
root = tree.getroot()
self.tool_path = root.get( 'tool_path' )
print "Repositories will be installed into configured tool_path location ", str( self.tool_path )
# Parse tool_shed_install_config to check each of the tools.
self.tool_shed_install_config = tool_shed_install_config
tree = util.parse_xml( tool_shed_install_config )
root = tree.getroot()
self.tool_shed = suc.clean_tool_shed_url( root.get( 'name' ) )
self.repository_owner = common_util.REPOSITORY_OWNER
index, self.shed_config_dict = suc.get_shed_tool_conf_dict( app, self.migrated_tools_config )
# Since tool migration scripts can be executed any number of times, we need to make sure the appropriate tools are defined in
# tool_conf.xml. If no tools associated with the migration stage are defined, no repositories will be installed on disk.
# The default behavior is that the tool shed is down.
tool_shed_accessible = False
tool_panel_configs = common_util.get_non_shed_tool_panel_configs( app )
if tool_panel_configs:
# The missing_tool_configs_dict contents are something like:
# {'emboss_antigenic.xml': [('emboss', '5.0.0', 'package', '\nreadme blah blah blah\n')]}
tool_shed_accessible, missing_tool_configs_dict = common_util.check_for_missing_tools( app, tool_panel_configs, latest_migration_script_number )
else:
# It doesn't matter if the tool shed is accessible since there are no migrated tools defined in the local Galaxy instance, but
# we have to set the value of tool_shed_accessible to True so that the value of migrate_tools.version can be correctly set in
# the database.
tool_shed_accessible = True
missing_tool_configs_dict = odict()
if tool_shed_accessible:
if len( self.proprietary_tool_confs ) == 1:
plural = ''
file_names = self.proprietary_tool_confs[ 0 ]
else:
plural = 's'
file_names = ', '.join( self.proprietary_tool_confs )
if missing_tool_configs_dict:
for repository_elem in root:
self.install_repository( repository_elem, install_dependencies )
else:
message = "\nNo tools associated with migration stage %s are defined in your " % str( latest_migration_script_number )
message += "file%s named %s,\nso no repositories will be installed on disk.\n" % ( plural, file_names )
print message
else:
message = "\nThe main Galaxy tool shed is not currently available, so skipped migration stage %s.\n" % str( latest_migration_script_number )
message += "Try again later.\n"
print message
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.
dialect = (url.split(":", 1))[0]
try:
egg = dialect_to_egg[dialect]
try:
pkg_resources.require(egg)
log.debug("%s egg successfully loaded for %s dialect" % (egg, dialect))
except:
# If the module is in the path elsewhere (i.e. non-egg), it'll still load.
log.warning("%s egg not found, but an attempt will be made to use %s anyway" % (egg, dialect))
except KeyError:
# Let this go, it could possibly work with db's we don't support
log.error("database_connection contains an unknown SQLAlchemy database dialect: %s" % dialect)
# Create engine and metadata
engine = create_engine(url, **engine_options)
meta = MetaData(bind=engine)
# The migrate_tools table was created in database version script 0092_add_migrate_tools_table.py.
version_table = Table("migrate_tools", meta, autoload=True)
# Verify that the code and the database are in sync.
db_schema = schema.ControlledSchema(engine, migrate_repository)
latest_tool_migration_script_number = migrate_repository.versions.latest
if latest_tool_migration_script_number != db_schema.version:
# The default behavior is that the tool shed is down.
tool_shed_accessible = False
if app.new_installation:
# New installations will not be missing tools, so we don't need to worry about them.
missing_tool_configs_dict = odict()
else:
tool_panel_configs = common_util.get_non_shed_tool_panel_configs(app)
if tool_panel_configs:
# The missing_tool_configs_dict contents are something like:
# {'emboss_antigenic.xml': [('emboss', '5.0.0', 'package', '\nreadme blah blah blah\n')]}
tool_shed_accessible, missing_tool_configs_dict = common_util.check_for_missing_tools(
app, tool_panel_configs, latest_tool_migration_script_number
)
else:
# It doesn't matter if the tool shed is accessible since there are no migrated tools defined in the local Galaxy instance, but
# we have to set the value of tool_shed_accessible to True so that the value of migrate_tools.version can be correctly set in
# the database.
tool_shed_accessible = True
missing_tool_configs_dict = odict()
have_tool_dependencies = False
for k, v in missing_tool_configs_dict.items():
if v:
have_tool_dependencies = True
break
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()), ".")
if not app.config.running_functional_tests:
if tool_shed_accessible:
# 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_dict:
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 and their dependencies can be\n"
msg += "automatically installed 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"
if have_tool_dependencies:
msg += "The following tool dependencies can also optionally be installed (see the option flag in the command below). If you\n"
msg += "choose to install them (recommended), they will be installed within the location specified by the 'tool_dependency_dir'\n"
msg += "setting in your main Galaxy configuration file (e.g., uninverse_wsgi.ini).\n"
processed_tool_dependencies = []
for missing_tool_config, tool_dependencies in missing_tool_configs_dict.items():
for tool_dependencies_tup in tool_dependencies:
if tool_dependencies_tup not in processed_tool_dependencies:
msg += "------------------------------------\n"
msg += "Tool Dependency\n"
msg += "------------------------------------\n"
msg += "Name: %s, Version: %s, Type: %s\n" % (
tool_dependencies_tup[0],
tool_dependencies_tup[1],
tool_dependencies_tup[2],
)
if tool_dependencies_tup[3]:
msg += "Requirements and installation information:\n"
msg += "%s\n" % tool_dependencies_tup[3]
else:
msg += "\n"
msg += "------------------------------------\n"
processed_tool_dependencies.append(tool_dependencies_tup)
msg += "\n"
msg += "%s" % output.replace("done", "")
msg += "vvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvv\n"
msg += "sh ./scripts/migrate_tools/%04d_tools.sh\n" % latest_tool_migration_script_number
msg += "^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n\n"
if have_tool_dependencies:
msg += "The tool dependencies listed above will be installed along with the repositories if you add the 'install_dependencies'\n"
msg += "option to the above command like this:\n\n"
msg += "vvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvv\n"
msg += (
"sh ./scripts/migrate_tools/%04d_tools.sh install_dependencies\n"
% latest_tool_migration_script_number
)
msg += "^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n\n"
msg += (
"Tool dependencies can be installed after the repositories have been installed as well.\n\n"
)
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 missing_tool_config, tool_dependencies in missing_tool_configs_dict.items():
msg += "%s\n" % missing_tool_config
msg += "<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<\n"
raise Exception(msg)
else:
log.debug(
"The main Galaxy tool shed is not currently available, so skipped tool migration %s until next server startup"
% db_schema.version
)
else:
log.info("At migrate_tools version %d" % db_schema.version)
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.
dialect = (url.split(':', 1))[0]
try:
egg = dialect_to_egg[dialect]
try:
pkg_resources.require(egg)
log.debug("%s egg successfully loaded for %s dialect" %
(egg, dialect))
except:
# If the module is in the path elsewhere (i.e. non-egg), it'll still load.
log.warning(
"%s egg not found, but an attempt will be made to use %s anyway"
% (egg, dialect))
except KeyError:
# Let this go, it could possibly work with db's we don't support
log.error(
"database_connection contains an unknown SQLAlchemy database dialect: %s"
% dialect)
# Create engine and metadata
engine = create_engine(url, **engine_options)
meta = MetaData(bind=engine)
# The migrate_tools table was created in database version script 0092_add_migrate_tools_table.py.
version_table = Table("migrate_tools", meta, autoload=True)
# Verify that the code and the database are in sync.
db_schema = schema.ControlledSchema(engine, migrate_repository)
latest_tool_migration_script_number = migrate_repository.versions.latest
if latest_tool_migration_script_number != db_schema.version:
# The default behavior is that the tool shed is down.
tool_shed_accessible = False
if app.new_installation:
# New installations will not be missing tools, so we don't need to worry about them.
missing_tool_configs_dict = odict()
else:
tool_panel_configs = common_util.get_non_shed_tool_panel_configs(
app)
if tool_panel_configs:
# The missing_tool_configs_dict contents are something like:
# {'emboss_antigenic.xml': [('emboss', '5.0.0', 'package', '\nreadme blah blah blah\n')]}
tool_shed_accessible, missing_tool_configs_dict = common_util.check_for_missing_tools(
app, tool_panel_configs,
latest_tool_migration_script_number)
else:
# It doesn't matter if the tool shed is accessible since there are no migrated tools defined in the local Galaxy instance, but
# we have to set the value of tool_shed_accessible to True so that the value of migrate_tools.version can be correctly set in
# the database.
tool_shed_accessible = True
missing_tool_configs_dict = odict()
have_tool_dependencies = False
for k, v in missing_tool_configs_dict.items():
if v:
have_tool_dependencies = True
break
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()), '.')
if not app.config.running_functional_tests:
if tool_shed_accessible:
# 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_dict:
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 and their dependencies can be\n"
msg += "automatically installed 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"
if have_tool_dependencies:
msg += "The following tool dependencies can also optionally be installed (see the option flag in the command below). If you\n"
msg += "choose to install them (recommended), they will be installed within the location specified by the 'tool_dependency_dir'\n"
msg += "setting in your main Galaxy configuration file (e.g., uninverse_wsgi.ini).\n"
processed_tool_dependencies = []
for missing_tool_config, tool_dependencies in missing_tool_configs_dict.items(
):
for tool_dependencies_tup in tool_dependencies:
if tool_dependencies_tup not in processed_tool_dependencies:
msg += "------------------------------------\n"
msg += "Tool Dependency\n"
msg += "------------------------------------\n"
msg += "Name: %s, Version: %s, Type: %s\n" % (
tool_dependencies_tup[0],
tool_dependencies_tup[1],
tool_dependencies_tup[2])
if tool_dependencies_tup[3]:
msg += "Requirements and installation information:\n"
msg += "%s\n" % tool_dependencies_tup[3]
else:
msg += "\n"
msg += "------------------------------------\n"
processed_tool_dependencies.append(
tool_dependencies_tup)
msg += "\n"
msg += "%s" % output.replace('done', '')
msg += "vvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvv\n"
msg += "sh ./scripts/migrate_tools/%04d_tools.sh\n" % latest_tool_migration_script_number
msg += "^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n\n"
if have_tool_dependencies:
msg += "The tool dependencies listed above will be installed along with the repositories if you add the 'install_dependencies'\n"
msg += "option to the above command like this:\n\n"
msg += "vvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvv\n"
msg += "sh ./scripts/migrate_tools/%04d_tools.sh install_dependencies\n" % latest_tool_migration_script_number
msg += "^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n\n"
msg += "Tool dependencies can be installed after the repositories have been installed as well.\n\n"
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 missing_tool_config, tool_dependencies in missing_tool_configs_dict.items(
):
msg += "%s\n" % missing_tool_config
msg += "<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<\n"
raise Exception(msg)
else:
log.debug(
"The main Galaxy tool shed is not currently available, so skipped tool migration %s until next server startup"
% db_schema.version)
else:
log.info("At migrate_tools version %d" % db_schema.version)
def __init__(self, app, latest_migration_script_number,
tool_shed_install_config, migrated_tools_config,
install_dependencies):
"""
Check tool settings in tool_shed_install_config and install all repositories that are not already installed. The tool
panel configuration file is the received migrated_tools_config, which is the reserved file named migrated_tools_conf.xml.
"""
self.app = app
self.toolbox = self.app.toolbox
self.migrated_tools_config = migrated_tools_config
# If install_dependencies is True but tool_dependency_dir is not set, do not attempt to install but print informative error message.
if install_dependencies and app.config.tool_dependency_dir is None:
message = 'You are attempting to install tool dependencies but do not have a value for "tool_dependency_dir" set in your universe_wsgi.ini '
message += 'file. Set this location value to the path where you want tool dependencies installed and rerun the migration script.'
raise Exception(message)
# Get the local non-shed related tool panel configs (there can be more than one, and the default name is tool_conf.xml).
self.proprietary_tool_confs = self.non_shed_tool_panel_configs
self.proprietary_tool_panel_elems = self.get_proprietary_tool_panel_elems(
latest_migration_script_number)
# Set the location where the repositories will be installed by retrieving the tool_path setting from migrated_tools_config.
tree = util.parse_xml(migrated_tools_config)
root = tree.getroot()
self.tool_path = root.get('tool_path')
print "Repositories will be installed into configured tool_path location ", str(
self.tool_path)
# Parse tool_shed_install_config to check each of the tools.
self.tool_shed_install_config = tool_shed_install_config
tree = util.parse_xml(tool_shed_install_config)
root = tree.getroot()
self.tool_shed = suc.clean_tool_shed_url(root.get('name'))
self.repository_owner = common_util.REPOSITORY_OWNER
index, self.shed_config_dict = suc.get_shed_tool_conf_dict(
app, self.migrated_tools_config)
# Since tool migration scripts can be executed any number of times, we need to make sure the appropriate tools are defined in
# tool_conf.xml. If no tools associated with the migration stage are defined, no repositories will be installed on disk.
# The default behavior is that the tool shed is down.
tool_shed_accessible = False
tool_panel_configs = common_util.get_non_shed_tool_panel_configs(app)
if tool_panel_configs:
# The missing_tool_configs_dict contents are something like:
# {'emboss_antigenic.xml': [('emboss', '5.0.0', 'package', '\nreadme blah blah blah\n')]}
tool_shed_accessible, missing_tool_configs_dict = common_util.check_for_missing_tools(
app, tool_panel_configs, latest_migration_script_number)
else:
# It doesn't matter if the tool shed is accessible since there are no migrated tools defined in the local Galaxy instance, but
# we have to set the value of tool_shed_accessible to True so that the value of migrate_tools.version can be correctly set in
# the database.
tool_shed_accessible = True
missing_tool_configs_dict = odict()
if tool_shed_accessible:
if len(self.proprietary_tool_confs) == 1:
plural = ''
file_names = self.proprietary_tool_confs[0]
else:
plural = 's'
file_names = ', '.join(self.proprietary_tool_confs)
if missing_tool_configs_dict:
for repository_elem in root:
self.install_repository(repository_elem,
install_dependencies)
else:
message = "\nNo tools associated with migration stage %s are defined in your " % str(
latest_migration_script_number)
message += "file%s named %s,\nso no repositories will be installed on disk.\n" % (
plural, file_names)
print message
else:
message = "\nThe main Galaxy tool shed is not currently available, so skipped migration stage %s.\n" % str(
latest_migration_script_number)
message += "Try again later.\n"
print message