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

import logging
import os
import subprocess
import sys

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=None):
    # 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_options = engine_options or {}
    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 = {}
        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 = {}
        have_tool_dependencies = False
        for v in missing_tool_configs_dict.values():
            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 += f"be removed from your file{plural} named {tool_panel_config_file_names}.\n\n"
                    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 in missing_tool_configs_dict.keys():
                            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 += f"removed from your file{plural} named {tool_panel_config_file_names}.\n\n"
                    for missing_tool_config in missing_tool_configs_dict.keys():
                        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(f'Installing tools from version {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