This document is for an in-development version of Galaxy. You can alternatively view this page in the latest release if it exists or view the top of the latest release's documentation.

Source code for galaxy.tool_shed.galaxy_install.migrate.check

import logging
import os
import subprocess
import sys
from collections import OrderedDict

from migrate.versioning import repository, schema
from sqlalchemy import create_engine, MetaData, Table

from galaxy.util import get_executable
from galaxy.util.tool_shed import common_util

log = logging.getLogger(__name__)

# Path relative to galaxy
migrate_repository_directory = os.path.abspath(os.path.dirname(__file__)).replace(os.getcwd() + os.path.sep, '', 1)
migrate_repository = repository.Repository(migrate_repository_directory)

[docs]def verify_tools(app, url, galaxy_config_file=None, 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. # 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. 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 = OrderedDict() 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 = OrderedDict() have_tool_dependencies = False for k, v in missing_tool_configs_dict.items(): if v: have_tool_dependencies = True break if not app.config.running_functional_tests: if tool_shed_accessible: # Automatically update the value of the migrate_tools.version database table column. manage_tools = os.path.abspath(os.path.join(os.path.dirname(__file__), 'scripts', 'manage_tools.py')) cmd = [get_executable(), manage_tools, 'upgrade', 'tools'] if galaxy_config_file: cmd[2:2] = ['-c', galaxy_config_file] proc = subprocess.Popen(args=cmd, 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{} named {}.\n\n".format(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="database/shed_tools">). The default location\n' msg += "setting is 'database/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 missing_tool_configs_dict[missing_tool_config]['tool_dependencies']: if tool_dependencies_tup not in processed_tool_dependencies: msg += "------------------------------------\n" msg += "Tool Dependency\n" msg += "------------------------------------\n" msg += "Name: {}, Version: {}, Type: {}\n".format(tool_dependencies_tup[0], tool_dependencies_tup[1], tool_dependencies_tup[2]) if len(tool_dependencies_tup) >= 4: 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 tools have been\n" msg += "removed from your file{} named {}.\n\n".format(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)
[docs]def migrate_to_current_version(engine, schema): # Changes to get to current version. changeset = schema.changeset(None) for ver, change in changeset: nextver = ver + changeset.step log.info('Installing tools from version {} -> {}... '.format(ver, nextver)) old_stdout = sys.stdout class FakeStdout: def __init__(self): self.buffer = [] def write(self, s): self.buffer.append(s) def flush(self): pass sys.stdout = FakeStdout() try: schema.runchange(ver, change, changeset.step) finally: for message in "".join(sys.stdout.buffer).split("\n"): log.info(message) sys.stdout = old_stdout