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Source code for galaxy.util.tool_shed.common_util

import errno
import json
import logging
import os
from collections import OrderedDict
from urllib.parse import urljoin

from routes import url_for

from galaxy import util
from galaxy.util.tool_shed import encoding_util, xml_util

log = logging.getLogger(__name__)

REPOSITORY_OWNER = 'devteam'
# not valid for installed Galaxy, fix
MIGRATE_DIR = os.path.abspath(os.path.join(
    os.path.dirname(__file__), os.pardir, os.pardir, os.pardir, 'galaxy', 'tool_shed', 'galaxy_install', 'migrate'))
TOOL_MIGRATION_SCRIPTS_DIR = os.path.join(MIGRATE_DIR, 'scripts')
TOOL_MIGRATION_VERSIONS_DIR = os.path.join(MIGRATE_DIR, 'versions')


[docs]def accumulate_tool_dependencies(tool_shed_accessible, tool_dependencies, all_tool_dependencies): if tool_shed_accessible: if tool_dependencies: for tool_dependency in tool_dependencies: if tool_dependency not in all_tool_dependencies: all_tool_dependencies.append(tool_dependency) return all_tool_dependencies
[docs]def check_for_missing_tools(app, tool_panel_configs, latest_tool_migration_script_number): # Get the 000x_tools.xml file associated with the current migrate_tools version number. tools_xml_file_path = os.path.abspath(os.path.join(os.path.dirname(__file__), os.pardir, 'galaxy_install', 'migrate', 'scripts', '%04d_tools.xml' % latest_tool_migration_script_number)) # Parse the XML and load the file attributes for later checking against the proprietary tool_panel_config. migrated_tool_configs_dict = OrderedDict() tree, error_message = xml_util.parse_xml(tools_xml_file_path) if tree is None: return False, OrderedDict() root = tree.getroot() tool_shed = root.get('name') tool_shed_url = get_tool_shed_url_from_tool_shed_registry(app, tool_shed) # The default behavior is that the tool shed is down. tool_shed_accessible = False missing_tool_configs_dict = OrderedDict() if tool_shed_url: for elem in root: if elem.tag == 'repository': repository_dependencies = [] all_tool_dependencies = [] repository_name = elem.get('name') changeset_revision = elem.get('changeset_revision') tool_shed_accessible, repository_dependencies_dict = get_repository_dependencies(app, tool_shed_url, repository_name, REPOSITORY_OWNER, changeset_revision) if tool_shed_accessible: # Accumulate all tool dependencies defined for repository dependencies for display to the user. for rd_key, rd_tups in repository_dependencies_dict.items(): if rd_key in ['root_key', 'description']: continue for rd_tup in rd_tups: tool_shed, name, owner, changeset_revision, prior_installation_required, only_if_compiling_contained_td = \ parse_repository_dependency_tuple(rd_tup) tool_shed_accessible, tool_dependencies = get_tool_dependencies(app, tool_shed_url, name, owner, changeset_revision) all_tool_dependencies = accumulate_tool_dependencies(tool_shed_accessible, tool_dependencies, all_tool_dependencies) tool_shed_accessible, tool_dependencies = get_tool_dependencies(app, tool_shed_url, repository_name, REPOSITORY_OWNER, changeset_revision) all_tool_dependencies = accumulate_tool_dependencies(tool_shed_accessible, tool_dependencies, all_tool_dependencies) for tool_elem in elem.findall('tool'): tool_config_file_name = tool_elem.get('file') if tool_config_file_name: # We currently do nothing with repository dependencies except install them (we do not display repositories that will be # installed to the user). However, we'll store them in the following dictionary in case we choose to display them in the # future. dependencies_dict = dict(tool_dependencies=all_tool_dependencies, repository_dependencies=repository_dependencies) migrated_tool_configs_dict[tool_config_file_name] = dependencies_dict else: break if tool_shed_accessible: # Parse the proprietary tool_panel_configs (the default is tool_conf.xml) and generate the list of missing tool config file names. for tool_panel_config in tool_panel_configs: tree, error_message = xml_util.parse_xml(tool_panel_config) if tree: root = tree.getroot() for elem in root: if elem.tag == 'tool': missing_tool_configs_dict = check_tool_tag_set(elem, migrated_tool_configs_dict, missing_tool_configs_dict) elif elem.tag == 'section': for section_elem in elem: if section_elem.tag == 'tool': missing_tool_configs_dict = check_tool_tag_set(section_elem, migrated_tool_configs_dict, missing_tool_configs_dict) else: exception_msg = f'\n\nThe entry for the main Galaxy tool shed at {tool_shed} is missing from the {app.config.tool_sheds_config} file. ' exception_msg += 'The entry for this tool shed must always be available in this file, so re-add it before attempting to start your Galaxy server.\n' raise Exception(exception_msg) return tool_shed_accessible, missing_tool_configs_dict
[docs]def check_tool_tag_set(elem, migrated_tool_configs_dict, missing_tool_configs_dict): file_path = elem.get('file', None) if file_path: name = os.path.basename(file_path) for migrated_tool_config in migrated_tool_configs_dict.keys(): if migrated_tool_config in [file_path, name]: missing_tool_configs_dict[name] = migrated_tool_configs_dict[migrated_tool_config] return missing_tool_configs_dict
[docs]def generate_clone_url_for_installed_repository(app, repository): """Generate the URL for cloning a repository that has been installed into a Galaxy instance.""" tool_shed_url = get_tool_shed_url_from_tool_shed_registry(app, str(repository.tool_shed)) return util.build_url(tool_shed_url, pathspec=['repos', str(repository.owner), str(repository.name)])
[docs]def generate_clone_url_for_repository_in_tool_shed(user, repository): """Generate the URL for cloning a repository that is in the tool shed.""" base_url = url_for('/', qualified=True).rstrip('/') if user: protocol, base = base_url.split('://') username = '%s@' % user.username return f'{protocol}://{username}{base}/repos/{repository.user.username}/{repository.name}' else: return f'{base_url}/repos/{repository.user.username}/{repository.name}'
[docs]def generate_clone_url_from_repo_info_tup(app, repo_info_tup): """Generate the URL for cloning a repository given a tuple of toolshed, name, owner, changeset_revision.""" # Example tuple: ['http://localhost:9009', 'blast_datatypes', 'test', '461a4216e8ab', False] toolshed, name, owner, changeset_revision, prior_installation_required, only_if_compiling_contained_td = \ parse_repository_dependency_tuple(repo_info_tup) tool_shed_url = get_tool_shed_url_from_tool_shed_registry(app, toolshed) # Don't include the changeset_revision in clone urls. return util.build_url(tool_shed_url, pathspec=['repos', owner, name])
[docs]def get_non_shed_tool_panel_configs(app): """Get the non-shed related tool panel configs - there can be more than one, and the default is tool_conf.xml.""" config_filenames = [] for config_filename in app.config.tool_configs: # Any config file that includes a tool_path attribute in the root tag set like the following is shed-related. # <toolbox tool_path="database/shed_tools"> try: tree, error_message = xml_util.parse_xml(config_filename) except OSError as exc: if (config_filename == app.config.shed_tool_conf and not app.config.shed_tool_conf_set and exc.errno == errno.ENOENT): continue raise if tree is None: continue root = tree.getroot() tool_path = root.get('tool_path', None) if tool_path is None: config_filenames.append(config_filename) return config_filenames
[docs]def get_repository_dependencies(app, tool_shed_url, repository_name, repository_owner, changeset_revision): repository_dependencies_dict = {} tool_shed_accessible = True params = dict(name=repository_name, owner=repository_owner, changeset_revision=changeset_revision) pathspec = ['repository', 'get_repository_dependencies'] try: raw_text = util.url_get(tool_shed_url, auth=app.tool_shed_registry.url_auth(tool_shed_url), pathspec=pathspec, params=params) tool_shed_accessible = True except Exception as e: tool_shed_accessible = False log.warning("The URL\n%s\nraised the exception:\n%s\n", util.build_url(tool_shed_url, pathspec=pathspec, params=params), e) if tool_shed_accessible: if len(raw_text) > 2: encoded_text = json.loads(util.unicodify(raw_text)) repository_dependencies_dict = encoding_util.tool_shed_decode(encoded_text) return tool_shed_accessible, repository_dependencies_dict
[docs]def get_protocol_from_tool_shed_url(tool_shed_url): """Return the protocol from the received tool_shed_url if it exists.""" try: if tool_shed_url.find('://') > 0: return tool_shed_url.split('://')[0].lower() except Exception: # We receive a lot of calls here where the tool_shed_url is None. The container_util uses # that value when creating a header row. If the tool_shed_url is not None, we have a problem. if tool_shed_url is not None: log.exception("Handled exception getting the protocol from Tool Shed URL %s", str(tool_shed_url)) # Default to HTTP protocol. return 'http'
[docs]def get_tool_dependencies(app, tool_shed_url, repository_name, repository_owner, changeset_revision): tool_dependencies = [] tool_shed_accessible = True params = dict(name=repository_name, owner=repository_owner, changeset_revision=changeset_revision) pathspec = ['repository', 'get_tool_dependencies'] try: text = util.url_get(tool_shed_url, auth=app.tool_shed_registry.url_auth(tool_shed_url), pathspec=pathspec, params=params) tool_shed_accessible = True except Exception as e: tool_shed_accessible = False log.warning("The URL\n%s\nraised the exception:\n%s\n", util.build_url(tool_shed_url, pathspec=pathspec, params=params), e) if tool_shed_accessible: if text: tool_dependencies_dict = encoding_util.tool_shed_decode(text) for requirements_dict in tool_dependencies_dict.values(): tool_dependency_name = requirements_dict['name'] tool_dependency_version = requirements_dict['version'] tool_dependency_type = requirements_dict['type'] tool_dependencies.append((tool_dependency_name, tool_dependency_version, tool_dependency_type)) return tool_shed_accessible, tool_dependencies
[docs]def get_tool_shed_repository_ids(as_string=False, **kwd): tsrid = kwd.get('tool_shed_repository_id', None) tsridslist = util.listify(kwd.get('tool_shed_repository_ids', None)) if not tsridslist: tsridslist = util.listify(kwd.get('id', None)) if tsridslist is not None: if tsrid is not None and tsrid not in tsridslist: tsridslist.append(tsrid) if as_string: return ','.join(tsridslist) return tsridslist else: tsridslist = util.listify(kwd.get('ordered_tsr_ids', None)) if tsridslist is not None: if as_string: return ','.join(tsridslist) return tsridslist if as_string: return '' return []
[docs]def get_tool_shed_url_from_tool_shed_registry(app, tool_shed): """ The value of tool_shed is something like: toolshed.g2.bx.psu.edu. We need the URL to this tool shed, which is something like: http://toolshed.g2.bx.psu.edu/ """ cleaned_tool_shed = remove_protocol_from_tool_shed_url(tool_shed) for shed_url in app.tool_shed_registry.tool_sheds.values(): if shed_url.find(cleaned_tool_shed) >= 0: if shed_url.endswith('/'): shed_url = shed_url.rstrip('/') return shed_url # The tool shed from which the repository was originally installed must no longer be configured in tool_sheds_conf.xml. return None
[docs]def get_tool_shed_repository_url(app, tool_shed, owner, name): tool_shed_url = get_tool_shed_url_from_tool_shed_registry(app, tool_shed) if tool_shed_url: # Append a slash to the tool shed URL, because urlparse.urljoin will eliminate # the last part of a URL if it does not end with a forward slash. tool_shed_url = '%s/' % tool_shed_url return urljoin(tool_shed_url, f'view/{owner}/{name}') return tool_shed_url
[docs]def get_user_by_username(app, username): """Get a user from the database by username.""" sa_session = app.model.context.current try: user = sa_session.query(app.model.User) \ .filter(app.model.User.table.c.username == username) \ .one() return user except Exception: return None
[docs]def handle_galaxy_url(trans, **kwd): galaxy_url = kwd.get('galaxy_url', None) if galaxy_url: trans.set_cookie(galaxy_url, name='toolshedgalaxyurl') else: galaxy_url = trans.get_cookie(name='toolshedgalaxyurl') return galaxy_url
[docs]def handle_tool_shed_url_protocol(app, shed_url): """Handle secure and insecure HTTP protocol since they may change over time.""" try: if app.name == 'galaxy': url = remove_protocol_from_tool_shed_url(shed_url) tool_shed_url = get_tool_shed_url_from_tool_shed_registry(app, url) else: tool_shed_url = str(url_for('/', qualified=True)).rstrip('/') return tool_shed_url except Exception: # We receive a lot of calls here where the tool_shed_url is None. The container_util uses # that value when creating a header row. If the tool_shed_url is not None, we have a problem. if shed_url is not None: log.exception("Handled exception removing protocol from URL %s", str(shed_url)) return shed_url
[docs]def parse_repository_dependency_tuple(repository_dependency_tuple, contains_error=False): # Default both prior_installation_required and only_if_compiling_contained_td to False in cases where metadata should be reset on the # repository containing the repository_dependency definition. prior_installation_required = 'False' only_if_compiling_contained_td = 'False' if contains_error: if len(repository_dependency_tuple) == 5: tool_shed, name, owner, changeset_revision, error = repository_dependency_tuple elif len(repository_dependency_tuple) == 6: tool_shed, name, owner, changeset_revision, prior_installation_required, error = repository_dependency_tuple elif len(repository_dependency_tuple) == 7: tool_shed, name, owner, changeset_revision, prior_installation_required, only_if_compiling_contained_td, error = \ repository_dependency_tuple return tool_shed, name, owner, changeset_revision, prior_installation_required, only_if_compiling_contained_td, error else: if len(repository_dependency_tuple) == 4: tool_shed, name, owner, changeset_revision = repository_dependency_tuple elif len(repository_dependency_tuple) == 5: tool_shed, name, owner, changeset_revision, prior_installation_required = repository_dependency_tuple elif len(repository_dependency_tuple) == 6: tool_shed, name, owner, changeset_revision, prior_installation_required, only_if_compiling_contained_td = repository_dependency_tuple return tool_shed, name, owner, changeset_revision, prior_installation_required, only_if_compiling_contained_td
[docs]def remove_port_from_tool_shed_url(tool_shed_url): """Return a partial Tool Shed URL, eliminating the port if it exists.""" try: if tool_shed_url.find(':') > 0: # Eliminate the port, if any, since it will result in an invalid directory name. new_tool_shed_url = tool_shed_url.split(':')[0] else: new_tool_shed_url = tool_shed_url return new_tool_shed_url.rstrip('/') except Exception: # We receive a lot of calls here where the tool_shed_url is None. The container_util uses # that value when creating a header row. If the tool_shed_url is not None, we have a problem. if tool_shed_url is not None: log.exception("Handled exception removing the port from Tool Shed URL %s", str(tool_shed_url)) return tool_shed_url
[docs]def remove_protocol_and_port_from_tool_shed_url(tool_shed_url): """Return a partial Tool Shed URL, eliminating the protocol and/or port if either exists.""" tool_shed = remove_protocol_from_tool_shed_url(tool_shed_url) tool_shed = remove_port_from_tool_shed_url(tool_shed) return tool_shed
[docs]def remove_protocol_and_user_from_clone_url(repository_clone_url): """Return a URL that can be used to clone a repository, eliminating the protocol and user if either exists.""" if repository_clone_url.find('@') > 0: # We have an url that includes an authenticated user, something like: # http://test@bx.psu.edu:9009/repos/some_username/column items = repository_clone_url.split('@') tmp_url = items[1] elif repository_clone_url.find('//') > 0: # We have an url that includes only a protocol, something like: # http://bx.psu.edu:9009/repos/some_username/column items = repository_clone_url.split('//') tmp_url = items[1] else: tmp_url = repository_clone_url return tmp_url.rstrip('/')
[docs]def remove_protocol_from_tool_shed_url(tool_shed_url): """Return a partial Tool Shed URL, eliminating the protocol if it exists.""" return util.remove_protocol_from_url(tool_shed_url)