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Source code for tool_shed.util.repository_util
import configparser
import logging
import os
import re
from markupsafe import escape
from sqlalchemy import false
from sqlalchemy.sql import select
import tool_shed.dependencies.repository
from galaxy import util
from galaxy import web
from galaxy.tool_shed.util.repository_util import (
check_for_updates,
check_or_update_tool_shed_status_for_installed_repository,
create_or_update_tool_shed_repository,
extract_components_from_tuple,
generate_tool_shed_repository_install_dir,
get_absolute_path_to_file_in_repository,
get_ids_of_tool_shed_repositories_being_installed,
get_installed_repository,
get_installed_tool_shed_repository,
get_prior_import_or_install_required_dict,
get_repo_info_tuple_contents,
get_repository_admin_role_name,
get_repository_and_repository_dependencies_from_repo_info_dict,
get_repository_by_id,
get_repository_by_name,
get_repository_by_name_and_owner,
get_repository_dependency_types,
get_repository_for_dependency_relationship,
get_repository_ids_requiring_prior_import_or_install,
get_repository_in_tool_shed,
get_repository_owner,
get_repository_owner_from_clone_url,
get_repository_query,
get_role_by_id,
get_tool_shed_from_clone_url,
get_tool_shed_repository_by_id,
get_tool_shed_status_for_installed_repository,
is_tool_shed_client,
repository_was_previously_installed,
set_repository_attributes,
)
from galaxy.util.tool_shed import common_util
from tool_shed.util.hg_util import (
changeset2rev,
create_hgrc_file,
get_hgrc_path,
init_repository,
)
from tool_shed.util.metadata_util import (
get_next_downloadable_changeset_revision,
get_repository_metadata_by_changeset_revision,
)
log = logging.getLogger(__name__)
VALID_REPOSITORYNAME_RE = re.compile(r"^[a-z0-9\_]+$")
[docs]def create_repo_info_dict(app, repository_clone_url, changeset_revision, ctx_rev, repository_owner, repository_name=None,
repository=None, repository_metadata=None, tool_dependencies=None, repository_dependencies=None):
"""
Return a dictionary that includes all of the information needed to install a repository into a local
Galaxy instance. The dictionary will also contain the recursive list of repository dependencies defined
for the repository, as well as the defined tool dependencies.
This method is called from Galaxy under four scenarios:
1. During the tool shed repository installation process via the tool shed's get_repository_information()
method. In this case both the received repository and repository_metadata will be objects, but
tool_dependencies and repository_dependencies will be None.
2. When getting updates for an installed repository where the updates include newly defined repository
dependency definitions. This scenario is similar to 1. above. The tool shed's get_repository_information()
method is the caller, and both the received repository and repository_metadata will be objects, but
tool_dependencies and repository_dependencies will be None.
3. When a tool shed repository that was uninstalled from a Galaxy instance is being reinstalled with no
updates available. In this case, both repository and repository_metadata will be None, but tool_dependencies
and repository_dependencies will be objects previously retrieved from the tool shed if the repository includes
definitions for them.
4. When a tool shed repository that was uninstalled from a Galaxy instance is being reinstalled with updates
available. In this case, this method is reached via the tool shed's get_updated_repository_information()
method, and both repository and repository_metadata will be objects but tool_dependencies and
repository_dependencies will be None.
"""
repo_info_dict = {}
repository = get_repository_by_name_and_owner(app, repository_name, repository_owner)
if app.name == 'tool_shed':
# We're in the tool shed.
repository_metadata = get_repository_metadata_by_changeset_revision(app,
app.security.encode_id(repository.id),
changeset_revision)
if repository_metadata:
metadata = repository_metadata.metadata
if metadata:
tool_shed_url = web.url_for('/', qualified=True).rstrip('/')
rb = tool_shed.dependencies.repository.relation_builder.RelationBuilder(app, repository, repository_metadata, tool_shed_url)
# Get a dictionary of all repositories upon which the contents of the received repository depends.
repository_dependencies = rb.get_repository_dependencies_for_changeset_revision()
tool_dependencies = metadata.get('tool_dependencies', {})
if tool_dependencies:
new_tool_dependencies = {}
for dependency_key, requirements_dict in tool_dependencies.items():
if dependency_key in ['set_environment']:
new_set_environment_dict_list = []
for set_environment_dict in requirements_dict:
set_environment_dict['repository_name'] = repository_name
set_environment_dict['repository_owner'] = repository_owner
set_environment_dict['changeset_revision'] = changeset_revision
new_set_environment_dict_list.append(set_environment_dict)
new_tool_dependencies[dependency_key] = new_set_environment_dict_list
else:
requirements_dict['repository_name'] = repository_name
requirements_dict['repository_owner'] = repository_owner
requirements_dict['changeset_revision'] = changeset_revision
new_tool_dependencies[dependency_key] = requirements_dict
tool_dependencies = new_tool_dependencies
repo_info_dict[repository.name] = (repository.description,
repository_clone_url,
changeset_revision,
ctx_rev,
repository_owner,
repository_dependencies,
tool_dependencies)
return repo_info_dict
[docs]def create_repository_admin_role(app, repository):
"""
Create a new role with name-spaced name based on the repository name and its owner's public user
name. This will ensure that the tole name is unique.
"""
sa_session = app.model.session
name = get_repository_admin_role_name(str(repository.name), str(repository.user.username))
description = 'A user or group member with this role can administer this repository.'
role = app.model.Role(name=name, description=description, type=app.model.Role.types.SYSTEM)
sa_session.add(role)
sa_session.flush()
# Associate the role with the repository owner.
app.model.UserRoleAssociation(repository.user, role)
# Associate the role with the repository.
rra = app.model.RepositoryRoleAssociation(repository, role)
sa_session.add(rra)
sa_session.flush()
return role
[docs]def create_repository(app, name, type, description, long_description, user_id, category_ids=None, remote_repository_url=None, homepage_url=None):
"""Create a new ToolShed repository"""
category_ids = category_ids or []
sa_session = app.model.session
# Add the repository record to the database.
repository = app.model.Repository(name=name,
type=type,
remote_repository_url=remote_repository_url,
homepage_url=homepage_url,
description=description,
long_description=long_description,
user_id=user_id)
# Flush to get the id.
sa_session.add(repository)
sa_session.flush()
# Create an admin role for the repository.
create_repository_admin_role(app, repository)
# Determine the repository's repo_path on disk.
dir = os.path.join(app.config.file_path, *util.directory_hash_id(repository.id))
# Create directory if it does not exist.
if not os.path.exists(dir):
os.makedirs(dir)
# Define repo name inside hashed directory.
repository_path = os.path.join(dir, "repo_%d" % repository.id)
# Create local repository directory.
if not os.path.exists(repository_path):
os.makedirs(repository_path)
# Create the local repository.
init_repository(repo_path=repository_path)
# Add an entry in the hgweb.config file for the local repository.
lhs = f"repos/{repository.user.username}/{repository.name}"
app.hgweb_config_manager.add_entry(lhs, repository_path)
# Create a .hg/hgrc file for the local repository.
create_hgrc_file(app, repository)
flush_needed = False
if category_ids:
# Create category associations
for category_id in category_ids:
category = sa_session.query(app.model.Category) \
.get(app.security.decode_id(category_id))
rca = app.model.RepositoryCategoryAssociation(repository, category)
sa_session.add(rca)
flush_needed = True
if flush_needed:
sa_session.flush()
# Update the repository registry.
app.repository_registry.add_entry(repository)
message = f"Repository <b>{escape(str(repository.name))}</b> has been created."
return repository, message
[docs]def generate_sharable_link_for_repository_in_tool_shed(repository, changeset_revision=None):
"""Generate the URL for sharing a repository that is in the tool shed."""
base_url = web.url_for('/', qualified=True).rstrip('/')
sharable_url = f'{base_url}/view/{repository.user.username}/{repository.name}'
if changeset_revision:
sharable_url += f'/{changeset_revision}'
return sharable_url
[docs]def get_repo_info_dict(app, user, repository_id, changeset_revision):
repository = get_repository_in_tool_shed(app, repository_id)
repository_clone_url = common_util.generate_clone_url_for_repository_in_tool_shed(user, repository)
repository_metadata = get_repository_metadata_by_changeset_revision(app,
repository_id,
changeset_revision)
if not repository_metadata:
# The received changeset_revision is no longer installable, so get the next changeset_revision
# in the repository's changelog. This generally occurs only with repositories of type
# repository_suite_definition or tool_dependency_definition.
next_downloadable_changeset_revision = \
get_next_downloadable_changeset_revision(app, repository, changeset_revision)
if next_downloadable_changeset_revision and next_downloadable_changeset_revision != changeset_revision:
repository_metadata = get_repository_metadata_by_changeset_revision(app,
repository_id,
next_downloadable_changeset_revision)
if repository_metadata:
# For now, we'll always assume that we'll get repository_metadata, but if we discover our assumption
# is not valid we'll have to enhance the callers to handle repository_metadata values of None in the
# returned repo_info_dict.
metadata = repository_metadata.metadata
if 'tools' in metadata:
includes_tools = True
else:
includes_tools = False
includes_tools_for_display_in_tool_panel = repository_metadata.includes_tools_for_display_in_tool_panel
repository_dependencies_dict = metadata.get('repository_dependencies', {})
repository_dependencies = repository_dependencies_dict.get('repository_dependencies', [])
has_repository_dependencies, has_repository_dependencies_only_if_compiling_contained_td = \
get_repository_dependency_types(repository_dependencies)
if 'tool_dependencies' in metadata:
includes_tool_dependencies = True
else:
includes_tool_dependencies = False
else:
# Here's where we may have to handle enhancements to the callers. See above comment.
includes_tools = False
has_repository_dependencies = False
has_repository_dependencies_only_if_compiling_contained_td = False
includes_tool_dependencies = False
includes_tools_for_display_in_tool_panel = False
repo_path = repository.repo_path(app)
ctx_rev = str(changeset2rev(repo_path, changeset_revision))
repo_info_dict = create_repo_info_dict(app=app,
repository_clone_url=repository_clone_url,
changeset_revision=changeset_revision,
ctx_rev=ctx_rev,
repository_owner=repository.user.username,
repository_name=repository.name,
repository=repository,
repository_metadata=repository_metadata,
tool_dependencies=None,
repository_dependencies=None)
return repo_info_dict, includes_tools, includes_tool_dependencies, includes_tools_for_display_in_tool_panel, \
has_repository_dependencies, has_repository_dependencies_only_if_compiling_contained_td
[docs]def get_repositories_by_category(app, category_id, installable=False, sort_order='asc', sort_key='name', page=None, per_page=25):
sa_session = app.model.session
query = sa_session.query(app.model.Repository) \
.join(app.model.RepositoryCategoryAssociation, app.model.Repository.id == app.model.RepositoryCategoryAssociation.repository_id) \
.join(app.model.User, app.model.User.id == app.model.Repository.user_id) \
.filter(app.model.RepositoryCategoryAssociation.category_id == category_id)
if installable:
subquery = select([app.model.RepositoryMetadata.table.c.repository_id])
query = query.filter(app.model.Repository.id.in_(subquery))
if sort_key == 'owner':
query = query.order_by(app.model.User.username) if sort_order == 'asc' else query.order_by(app.model.User.username.desc())
else:
query = query.order_by(app.model.Repository.name) if sort_order == 'asc' else query.order_by(app.model.Repository.name.desc())
if page is not None:
page = int(page)
query = query.limit(per_page)
if page > 1:
query = query.offset((page - 1) * per_page)
resultset = query.all()
repositories = []
for repository in resultset:
default_value_mapper = {'id': app.security.encode_id, 'user_id': app.security.encode_id, 'repository_id': app.security.encode_id}
repository_dict = repository.to_dict(value_mapper=default_value_mapper)
repository_dict['metadata'] = {}
for changeset, changehash in repository.installable_revisions(app):
encoded_id = app.security.encode_id(repository.id)
metadata = get_repository_metadata_by_changeset_revision(app, encoded_id, changehash)
repository_dict['metadata'][f'{changeset}:{changehash}'] = metadata.to_dict(value_mapper=default_value_mapper)
if installable:
if len(repository.installable_revisions(app)):
repositories.append(repository_dict)
else:
repositories.append(repository_dict)
return repositories
[docs]def get_tool_shed_repository_status_label(app, tool_shed_repository=None, name=None, owner=None, changeset_revision=None, repository_clone_url=None):
"""Return a color-coded label for the status of the received tool-shed_repository installed into Galaxy."""
if tool_shed_repository is None:
if name is not None and owner is not None and repository_clone_url is not None:
tool_shed = get_tool_shed_from_clone_url(repository_clone_url)
tool_shed_repository = get_installed_repository(app,
tool_shed=tool_shed,
name=name,
owner=owner,
installed_changeset_revision=changeset_revision)
if tool_shed_repository:
status_label = tool_shed_repository.status
if tool_shed_repository.status in [app.install_model.ToolShedRepository.installation_status.CLONING,
app.install_model.ToolShedRepository.installation_status.SETTING_TOOL_VERSIONS,
app.install_model.ToolShedRepository.installation_status.INSTALLING_REPOSITORY_DEPENDENCIES,
app.install_model.ToolShedRepository.installation_status.INSTALLING_TOOL_DEPENDENCIES,
app.install_model.ToolShedRepository.installation_status.LOADING_PROPRIETARY_DATATYPES]:
bgcolor = app.install_model.ToolShedRepository.states.INSTALLING
elif tool_shed_repository.status in [app.install_model.ToolShedRepository.installation_status.NEW,
app.install_model.ToolShedRepository.installation_status.UNINSTALLED]:
bgcolor = app.install_model.ToolShedRepository.states.UNINSTALLED
elif tool_shed_repository.status in [app.install_model.ToolShedRepository.installation_status.ERROR]:
bgcolor = app.install_model.ToolShedRepository.states.ERROR
elif tool_shed_repository.status in [app.install_model.ToolShedRepository.installation_status.DEACTIVATED]:
bgcolor = app.install_model.ToolShedRepository.states.WARNING
elif tool_shed_repository.status in [app.install_model.ToolShedRepository.installation_status.INSTALLED]:
if tool_shed_repository.repository_dependencies_being_installed:
bgcolor = app.install_model.ToolShedRepository.states.WARNING
status_label = '{}, {}'.format(status_label,
app.install_model.ToolShedRepository.installation_status.INSTALLING_REPOSITORY_DEPENDENCIES)
elif tool_shed_repository.missing_repository_dependencies:
bgcolor = app.install_model.ToolShedRepository.states.WARNING
status_label = f'{status_label}, missing repository dependencies'
elif tool_shed_repository.tool_dependencies_being_installed:
bgcolor = app.install_model.ToolShedRepository.states.WARNING
status_label = '{}, {}'.format(status_label,
app.install_model.ToolShedRepository.installation_status.INSTALLING_TOOL_DEPENDENCIES)
elif tool_shed_repository.missing_tool_dependencies:
bgcolor = app.install_model.ToolShedRepository.states.WARNING
status_label = f'{status_label}, missing tool dependencies'
else:
bgcolor = app.install_model.ToolShedRepository.states.OK
else:
bgcolor = app.install_model.ToolShedRepository.states.ERROR
else:
bgcolor = app.install_model.ToolShedRepository.states.WARNING
status_label = 'unknown status'
return f'<div class="count-box state-color-{bgcolor}">{status_label}</div>'
[docs]def handle_role_associations(app, role, repository, **kwd):
sa_session = app.model.session
message = escape(kwd.get('message', ''))
status = kwd.get('status', 'done')
repository_owner = repository.user
if kwd.get('manage_role_associations_button', False):
in_users_list = util.listify(kwd.get('in_users', []))
in_users = [sa_session.query(app.model.User).get(x) for x in in_users_list]
# Make sure the repository owner is always associated with the repostory's admin role.
owner_associated = False
for user in in_users:
if user.id == repository_owner.id:
owner_associated = True
break
if not owner_associated:
in_users.append(repository_owner)
message += "The repository owner must always be associated with the repository's administrator role. "
status = 'error'
in_groups_list = util.listify(kwd.get('in_groups', []))
in_groups = [sa_session.query(app.model.Group).get(x) for x in in_groups_list]
in_repositories = [repository]
app.security_agent.set_entity_role_associations(roles=[role],
users=in_users,
groups=in_groups,
repositories=in_repositories)
sa_session.refresh(role)
message += "Role <b>%s</b> has been associated with %d users, %d groups and %d repositories. " % \
(escape(str(role.name)), len(in_users), len(in_groups), len(in_repositories))
in_users = []
out_users = []
in_groups = []
out_groups = []
for user in sa_session.query(app.model.User) \
.filter(app.model.User.table.c.deleted == false()) \
.order_by(app.model.User.table.c.email):
if user in [x.user for x in role.users]:
in_users.append((user.id, user.email))
else:
out_users.append((user.id, user.email))
for group in sa_session.query(app.model.Group) \
.filter(app.model.Group.table.c.deleted == false()) \
.order_by(app.model.Group.table.c.name):
if group in [x.group for x in role.groups]:
in_groups.append((group.id, group.name))
else:
out_groups.append((group.id, group.name))
associations_dict = dict(in_users=in_users,
out_users=out_users,
in_groups=in_groups,
out_groups=out_groups,
message=message,
status=status)
return associations_dict
[docs]def change_repository_name_in_hgrc_file(hgrc_file, new_name):
config = configparser.ConfigParser()
config.read(hgrc_file)
config.set('web', 'name', new_name)
with open(hgrc_file, 'w') as fh:
config.write(fh)
[docs]def update_repository(app, trans, id, **kwds):
"""Update an existing ToolShed repository"""
message = None
flush_needed = False
sa_session = app.model.session
repository = sa_session.query(app.model.Repository).get(app.security.decode_id(id))
if repository is None:
return None, "Unknown repository ID"
if not (trans.user_is_admin
or trans.app.security_agent.user_can_administer_repository(trans.user, repository)):
message = "You are not the owner of this repository, so you cannot administer it."
return None, message
# Allowlist properties that can be changed via this method
for key in ('type', 'description', 'long_description', 'remote_repository_url', 'homepage_url'):
# If that key is available, not None and different than what's in the model
if key in kwds and kwds[key] is not None and kwds[key] != getattr(repository, key):
setattr(repository, key, kwds[key])
flush_needed = True
if 'category_ids' in kwds and isinstance(kwds['category_ids'], list):
# Get existing category associations
category_associations = sa_session.query(app.model.RepositoryCategoryAssociation) \
.filter(app.model.RepositoryCategoryAssociation.table.c.repository_id == app.security.decode_id(id))
# Remove all of them
for rca in category_associations:
sa_session.delete(rca)
# Then (re)create category associations
for category_id in kwds['category_ids']:
category = sa_session.query(app.model.Category) \
.get(app.security.decode_id(category_id))
if category:
rca = app.model.RepositoryCategoryAssociation(repository, category)
sa_session.add(rca)
else:
pass
flush_needed = True
# However some properties are special, like 'name'
if 'name' in kwds and kwds['name'] is not None and repository.name != kwds['name']:
if repository.times_downloaded != 0:
message = "Repository names cannot be changed if the repository has been cloned."
else:
message = validate_repository_name(trans.app, kwds['name'], trans.user)
if message:
return None, message
repo_dir = repository.repo_path(app)
# Change the entry in the hgweb.config file for the repository.
old_lhs = f"repos/{repository.user.username}/{repository.name}"
new_lhs = f"repos/{repository.user.username}/{kwds['name']}"
trans.app.hgweb_config_manager.change_entry(old_lhs, new_lhs, repo_dir)
# Change the entry in the repository's hgrc file.
hgrc_file = get_hgrc_path(repo_dir)
change_repository_name_in_hgrc_file(hgrc_file, kwds['name'])
# Rename the repository's admin role to match the new repository name.
repository_admin_role = repository.admin_role
repository_admin_role.name = get_repository_admin_role_name(str(kwds['name']), str(repository.user.username))
trans.sa_session.add(repository_admin_role)
repository.name = kwds['name']
flush_needed = True
if flush_needed:
trans.sa_session.add(repository)
trans.sa_session.flush()
message = "The repository information has been updated."
else:
message = None
return repository, message
[docs]def validate_repository_name(app, name, user):
"""
Validate whether the given name qualifies as a new TS repo name.
Repository names must be unique for each user, must be at least two characters
in length and must contain only lower-case letters, numbers, and the '_' character.
"""
if name in ['None', None, '']:
return 'Enter the required repository name.'
if name in ['repos']:
return f"The term '{name}' is a reserved word in the Tool Shed, so it cannot be used as a repository name."
check_existing = get_repository_by_name_and_owner(app, name, user.username)
if check_existing is not None:
if check_existing.deleted:
return f'You own a deleted repository named <b>{escape(name)}</b>, please choose a different name.'
else:
return f"You already own a repository named <b>{escape(name)}</b>, please choose a different name."
if len(name) < 2:
return "Repository names must be at least 2 characters in length."
if len(name) > 80:
return "Repository names cannot be more than 80 characters in length."
if not(VALID_REPOSITORYNAME_RE.match(name)):
return "Repository names must contain only lower-case letters, numbers and underscore."
return ''
__all__ = (
'change_repository_name_in_hgrc_file',
'check_for_updates',
'check_or_update_tool_shed_status_for_installed_repository',
'create_or_update_tool_shed_repository',
'create_repo_info_dict',
'create_repository_admin_role',
'create_repository',
'extract_components_from_tuple',
'generate_sharable_link_for_repository_in_tool_shed',
'generate_tool_shed_repository_install_dir',
'get_absolute_path_to_file_in_repository',
'get_ids_of_tool_shed_repositories_being_installed',
'get_installed_repository',
'get_installed_tool_shed_repository',
'get_prior_import_or_install_required_dict',
'get_repo_info_dict',
'get_repo_info_tuple_contents',
'get_repositories_by_category',
'get_repository_admin_role_name',
'get_repository_and_repository_dependencies_from_repo_info_dict',
'get_repository_by_id',
'get_repository_by_name',
'get_repository_by_name_and_owner',
'get_repository_dependency_types',
'get_repository_for_dependency_relationship',
'get_repository_ids_requiring_prior_import_or_install',
'get_repository_in_tool_shed',
'get_repository_owner',
'get_repository_owner_from_clone_url',
'get_repository_query',
'get_role_by_id',
'get_tool_shed_from_clone_url',
'get_tool_shed_repository_by_id',
'get_tool_shed_repository_status_label',
'get_tool_shed_status_for_installed_repository',
'handle_role_associations',
'is_tool_shed_client',
'repository_was_previously_installed',
'set_repository_attributes',
'update_repository',
'validate_repository_name',
)