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Source code for tool_shed.util.shed_util_common

import json
import logging
import os
import socket
import string

import sqlalchemy.orm.exc
from sqlalchemy import and_, false, true

import galaxy.tool_util.deps.requirements
from galaxy import util
from galaxy.tool_shed.util.shed_util_common import (
    can_eliminate_repository_dependency,
    can_eliminate_tool_dependency,
    clean_dependency_relationships,
    generate_tool_guid,
    get_ctx_rev,
    get_next_prior_import_or_install_required_dict_entry,
    get_tool_panel_config_tool_path_install_dir,
    get_user,
    have_shed_tool_conf_for_install,
    set_image_paths,
    tool_shed_is_this_tool_shed,
)
from galaxy.util import (
    checkers,
    unicodify,
)
from tool_shed.util import (
    basic_util,
    common_util,
    hg_util,
    repository_util
)

log = logging.getLogger(__name__)

MAX_CONTENT_SIZE = 1048576
DATATYPES_CONFIG_FILENAME = 'datatypes_conf.xml'
REPOSITORY_DATA_MANAGER_CONFIG_FILENAME = 'data_manager_conf.xml'

new_repo_email_alert_template = """
Sharable link:         ${sharable_link}
Repository name:       ${repository_name}
Revision:              ${revision}
Change description:
${description}

Uploaded by:           ${username}
Date content uploaded: ${display_date}

${content_alert_str}

-----------------------------------------------------------------------------
This change alert was sent from the Galaxy tool shed hosted on the server
"${host}"
-----------------------------------------------------------------------------
You received this alert because you registered to receive email when
new repositories were created in the Galaxy tool shed named "${host}".
-----------------------------------------------------------------------------
"""

email_alert_template = """
Sharable link:         ${sharable_link}
Repository name:       ${repository_name}
Revision:              ${revision}
Change description:
${description}

Changed by:     ${username}
Date of change: ${display_date}

${content_alert_str}

-----------------------------------------------------------------------------
This change alert was sent from the Galaxy tool shed hosted on the server
"${host}"
-----------------------------------------------------------------------------
You received this alert because you registered to receive email whenever
changes were made to the repository named "${repository_name}".
-----------------------------------------------------------------------------
"""

contact_owner_template = """
GALAXY TOOL SHED REPOSITORY MESSAGE
------------------------

The user '${username}' sent you the following message regarding your tool shed
repository named '${repository_name}'.  You can respond by sending a reply to
the user's email address: ${email}.
-----------------------------------------------------------------------------
${message}
-----------------------------------------------------------------------------
This message was sent from the Galaxy Tool Shed instance hosted on the server
'${host}'
"""


[docs]def count_repositories_in_category(app, category_id): sa_session = app.model.context.current return sa_session.query(app.model.RepositoryCategoryAssociation) \ .filter(app.model.RepositoryCategoryAssociation.table.c.category_id == app.security.decode_id(category_id)) \ .count()
[docs]def get_categories(app): """Get all categories from the database.""" sa_session = app.model.context.current return sa_session.query(app.model.Category) \ .filter(app.model.Category.table.c.deleted == false()) \ .order_by(app.model.Category.table.c.name) \ .all()
[docs]def get_category(app, id): """Get a category from the database.""" sa_session = app.model.context.current return sa_session.query(app.model.Category).get(app.security.decode_id(id))
[docs]def get_category_by_name(app, name): """Get a category from the database via name.""" sa_session = app.model.context.current try: return sa_session.query(app.model.Category).filter_by(name=name).one() except sqlalchemy.orm.exc.NoResultFound: return None
[docs]def get_tool_shed_repo_requirements(app, tool_shed_url, repositories=None, repo_info_dicts=None): """ Contact tool_shed_url for a list of requirements for a repository or a list of repositories. Returns a list of requirements, where each requirement is a dictionary with name and version as keys. """ if not repositories and not repo_info_dicts: raise Exception("Need to pass either repository or repo_info_dicts") if repositories: if not isinstance(repositories, list): repositories = [repositories] repository_params = [{'name': repository.name, 'owner': repository.owner, 'changeset_revision': repository.changeset_revision} for repository in repositories] else: if not isinstance(repo_info_dicts, list): repo_info_dicts = [repo_info_dicts] repository_params = [] for repo_info_dict in repo_info_dicts: for name, repo_info_tuple in repo_info_dict.items(): # repo_info_tuple is a list, but keep terminology owner = repo_info_tuple[4] changeset_revision = repo_info_tuple[2] repository_params.append({'name': name, 'owner': owner, 'changeset_revision': changeset_revision}) pathspec = ["api", "repositories", "get_repository_revision_install_info"] tools = [] for params in repository_params: response = util.url_get(tool_shed_url, auth=app.tool_shed_registry.url_auth(tool_shed_url), pathspec=pathspec, params=params ) json_response = json.loads(response) valid_tools = json_response[1].get('valid_tools', []) if valid_tools: tools.extend(valid_tools) return get_requirements_from_tools(tools)
[docs]def get_requirements_from_tools(tools): return {tool['id']: galaxy.tool_util.deps.requirements.ToolRequirements.from_list(tool['requirements']) for tool in tools}
[docs]def get_requirements_from_repository(repository): if not repository.includes_tools: return {} else: return get_requirements_from_tools(repository.metadata.get('tools', []))
[docs]def get_repository_categories(app, id): """Get categories of a repository on the tool shed side from the database via id""" sa_session = app.model.context.current return sa_session.query(app.model.RepositoryCategoryAssociation) \ .filter(app.model.RepositoryCategoryAssociation.table.c.repository_id == app.security.decode_id(id))
[docs]def get_repository_file_contents(app, file_path, repository_id, is_admin=False): """Return the display-safe contents of a repository file for display in a browser.""" safe_str = '' if not is_path_browsable(app, file_path, repository_id, is_admin): log.warning('Request tries to access a file outside of the repository location. File path: %s', file_path) return 'Invalid file path' # Symlink targets are checked by is_path_browsable if os.path.islink(file_path): safe_str = 'link to: ' + basic_util.to_html_string(os.readlink(file_path)) return safe_str elif checkers.is_gzip(file_path): return '<br/>gzip compressed file<br/>' elif checkers.is_bz2(file_path): return '<br/>bz2 compressed file<br/>' elif checkers.is_zip(file_path): return '<br/>zip compressed file<br/>' elif checkers.check_binary(file_path): return '<br/>Binary file<br/>' else: for i, line in enumerate(open(file_path)): safe_str = '{}{}'.format(safe_str, basic_util.to_html_string(line)) # Stop reading after string is larger than MAX_CONTENT_SIZE. if len(safe_str) > MAX_CONTENT_SIZE: large_str = \ '<br/>File contents truncated because file size is larger than maximum viewing size of %s<br/>' % \ util.nice_size(MAX_CONTENT_SIZE) safe_str = f'{safe_str}{large_str}' break if len(safe_str) > basic_util.MAX_DISPLAY_SIZE: # Eliminate the middle of the file to display a file no larger than basic_util.MAX_DISPLAY_SIZE. # This may not be ideal if the file is larger than MAX_CONTENT_SIZE. join_by_str = \ "<br/><br/>...some text eliminated here because file size is larger than maximum viewing size of %s...<br/><br/>" % \ util.nice_size(basic_util.MAX_DISPLAY_SIZE) safe_str = util.shrink_string_by_size(safe_str, basic_util.MAX_DISPLAY_SIZE, join_by=join_by_str, left_larger=True, beginning_on_size_error=True) return safe_str
def get_repository_files(folder_path): """Return the file hierarchy of a tool shed repository.""" contents = [] for item in os.listdir(folder_path): # Skip .hg directories if item.startswith('.hg'): continue contents.append(item) if contents: contents.sort() return contents def get_repository_from_refresh_on_change(app, **kwd): # The changeset_revision_select_field in several grids performs a refresh_on_change which sends in request parameters like # changeset_revison_1, changeset_revision_2, etc. One of the many select fields on the grid performed the refresh_on_change, # so we loop through all of the received values to see which value is not the repository tip. If we find it, we know the # refresh_on_change occurred and we have the necessary repository id and change set revision to pass on. repository_id = None v = None for k, v in kwd.items(): changeset_revision_str = 'changeset_revision_' if k.startswith(changeset_revision_str): repository_id = app.security.encode_id(int(k.lstrip(changeset_revision_str))) repository = repository_util.get_repository_in_tool_shed(app, repository_id) if repository.tip() != v: return v, repository # This should never be reached - raise an exception? return v, None
[docs]def get_repository_type_from_tool_shed(app, tool_shed_url, name, owner): """ Send a request to the tool shed to retrieve the type for a repository defined by the combination of a name and owner. """ tool_shed_url = common_util.get_tool_shed_url_from_tool_shed_registry(app, tool_shed_url) params = dict(name=name, owner=owner) pathspec = ['repository', 'get_repository_type'] repository_type = util.url_get(tool_shed_url, auth=app.tool_shed_registry.url_auth(tool_shed_url), pathspec=pathspec, params=params) return repository_type
[docs]def get_tool_dependency_definition_metadata_from_tool_shed(app, tool_shed_url, name, owner): """ Send a request to the tool shed to retrieve the current metadata for a repository of type tool_dependency_definition defined by the combination of a name and owner. """ tool_shed_url = common_util.get_tool_shed_url_from_tool_shed_registry(app, tool_shed_url) params = dict(name=name, owner=owner) pathspec = ['repository', 'get_tool_dependency_definition_metadata'] metadata = util.url_get(tool_shed_url, auth=app.tool_shed_registry.url_auth(tool_shed_url), pathspec=pathspec, params=params) return metadata
[docs]def get_tool_path_by_shed_tool_conf_filename(app, shed_tool_conf): """ Return the tool_path config setting for the received shed_tool_conf file by searching the tool box's in-memory list of shed_tool_confs for the dictionary whose config_filename key has a value matching the received shed_tool_conf. """ for shed_tool_conf_dict in app.toolbox.dynamic_confs(include_migrated_tool_conf=True): config_filename = shed_tool_conf_dict['config_filename'] if config_filename == shed_tool_conf: return shed_tool_conf_dict['tool_path'] else: file_name = basic_util.strip_path(config_filename) if file_name == shed_tool_conf: return shed_tool_conf_dict['tool_path'] return None
[docs]def handle_email_alerts(app, host, repository, content_alert_str='', new_repo_alert=False, admin_only=False): """ There are 2 complementary features that enable a tool shed user to receive email notification: 1. Within User Preferences, they can elect to receive email when the first (or first valid) change set is produced for a new repository. 2. When viewing or managing a repository, they can check the box labeled "Receive email alerts" which caused them to receive email alerts when updates to the repository occur. This same feature is available on a per-repository basis on the repository grid within the tool shed. There are currently 4 scenarios for sending email notification when a change is made to a repository: 1. An admin user elects to receive email when the first change set is produced for a new repository from User Preferences. The change set does not have to include any valid content. This allows for the capture of inappropriate content being uploaded to new repositories. 2. A regular user elects to receive email when the first valid change set is produced for a new repository from User Preferences. This differs from 1 above in that the user will not receive email until a change set tha tincludes valid content is produced. 3. An admin user checks the "Receive email alerts" check box on the manage repository page. Since the user is an admin user, the email will include information about both HTML and image content that was included in the change set. 4. A regular user checks the "Receive email alerts" check box on the manage repository page. Since the user is not an admin user, the email will not include any information about both HTML and image content that was included in the change set. """ sa_session = app.model.context.current repo = repository.hg_repo sharable_link = repository_util.generate_sharable_link_for_repository_in_tool_shed(repository, changeset_revision=None) smtp_server = app.config.smtp_server if smtp_server and (new_repo_alert or repository.email_alerts): # Send email alert to users that want them. if app.config.email_from is not None: email_from = app.config.email_from elif host.split(':')[0] in ['localhost', '127.0.0.1', '0.0.0.0']: email_from = 'galaxy-no-reply@' + socket.getfqdn() else: email_from = 'galaxy-no-reply@' + host.split(':')[0] ctx = repo[repo.changelog.tip()] username = unicodify(ctx.user()) try: username = username.split()[0] except Exception: pass # We'll use 2 template bodies because we only want to send content # alerts to tool shed admin users. if new_repo_alert: template = new_repo_email_alert_template else: template = email_alert_template display_date = hg_util.get_readable_ctx_date(ctx) description = unicodify(ctx.description()) revision = f'{ctx.rev()}:{ctx}' admin_body = string.Template(template).safe_substitute(host=host, sharable_link=sharable_link, repository_name=repository.name, revision=revision, display_date=display_date, description=description, username=username, content_alert_str=content_alert_str) body = string.Template(template).safe_substitute(host=host, sharable_link=sharable_link, repository_name=repository.name, revision=revision, display_date=display_date, description=description, username=username, content_alert_str='') admin_users = app.config.get("admin_users", "").split(",") frm = email_from if new_repo_alert: subject = "Galaxy tool shed alert for new repository named %s" % str(repository.name) subject = subject[:80] email_alerts = [] for user in sa_session.query(app.model.User) \ .filter(and_(app.model.User.table.c.deleted == false(), app.model.User.table.c.new_repo_alert == true())): if admin_only: if user.email in admin_users: email_alerts.append(user.email) else: email_alerts.append(user.email) else: subject = "Galaxy tool shed update alert for repository named %s" % str(repository.name) email_alerts = json.loads(repository.email_alerts) for email in email_alerts: to = email.strip() # Send it try: if to in admin_users: util.send_mail(frm, to, subject, admin_body, app.config) else: util.send_mail(frm, to, subject, body, app.config) except Exception: log.exception("An error occurred sending a tool shed repository update alert by email.")
[docs]def is_path_browsable(app, path, repository_id, is_admin=False): """ Detects whether the given path is browsable i.e. is within the allowed repository folders. Admins can additionaly browse folders with tool dependencies. """ if is_admin and is_path_within_dependency_dir(app, path): return True return is_path_within_repo(app, path, repository_id)
[docs]def is_path_within_dependency_dir(app, path): """ Detect whether the given path is within the tool_dependency_dir folder on the disk. (Specified by the config option). Use to filter malicious symlinks targeting outside paths. """ allowed = False resolved_path = os.path.realpath(path) tool_dependency_dir = app.config.get('tool_dependency_dir', None) if tool_dependency_dir: dependency_path = os.path.abspath(tool_dependency_dir) allowed = os.path.commonprefix([dependency_path, resolved_path]) == dependency_path return allowed
[docs]def is_path_within_repo(app, path, repository_id): """ Detect whether the given path is within the repository folder on the disk. Use to filter malicious symlinks targeting outside paths. """ repo_path = os.path.abspath(repository_util.get_repository_by_id(app, repository_id).repo_path(app)) resolved_path = os.path.realpath(path) return os.path.commonprefix([repo_path, resolved_path]) == repo_path
[docs]def open_repository_files_folder(app, folder_path, repository_id, is_admin=False): """ Return a list of dictionaries, each of which contains information for a file or directory contained within a directory in a repository file hierarchy. """ if not is_path_browsable(app, folder_path, repository_id, is_admin): log.warning('Request tries to access a folder outside of the allowed locations. Folder path: %s', folder_path) return [] try: files_list = get_repository_files(folder_path) except OSError as e: if str(e).find('No such file or directory') >= 0: # We have a repository with no contents. return [] folder_contents = [] for filename in files_list: is_folder = False full_path = os.path.join(folder_path, filename) is_link = os.path.islink(full_path) path_is_browsable = is_path_browsable(app, full_path, repository_id) if is_link and not path_is_browsable: log.warning('Valid folder contains a symlink outside of the repository location. Link found in: ' + str(full_path)) if filename: if os.path.isdir(full_path) and path_is_browsable: # Append a '/' character so that our jquery dynatree will function properly. filename = '%s/' % filename full_path = '%s/' % full_path is_folder = True node = {"title": filename, "isFolder": is_folder, "isLazy": is_folder, "tooltip": full_path, "key": full_path} folder_contents.append(node) return folder_contents
__all__ = ( 'can_eliminate_repository_dependency', 'can_eliminate_tool_dependency', 'clean_dependency_relationships', 'count_repositories_in_category', 'generate_tool_guid', 'get_categories', 'get_category', 'get_category_by_name', 'get_requirements_from_tools', 'get_requirements_from_repository', 'get_tool_shed_repo_requirements', 'get_ctx_rev', 'get_next_prior_import_or_install_required_dict_entry', 'get_repository_categories', 'get_repository_file_contents', 'get_repository_type_from_tool_shed', 'get_tool_dependency_definition_metadata_from_tool_shed', 'get_tool_panel_config_tool_path_install_dir', 'get_tool_path_by_shed_tool_conf_filename', 'get_user', 'handle_email_alerts', 'have_shed_tool_conf_for_install', 'is_path_browsable', 'is_path_within_dependency_dir', 'is_path_within_repo', 'open_repository_files_folder', 'set_image_paths', 'tool_shed_is_this_tool_shed', )