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admin_toolshed.py
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admin_toolshed.py
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import json
import logging
import os
from six import string_types
from sqlalchemy import or_
import tool_shed.repository_types.util as rt_util
from galaxy import util, web
from galaxy.tools.deps import views
from galaxy.util import unicodify
from galaxy.web.form_builder import CheckboxField
from tool_shed.galaxy_install import (
dependency_display,
install_manager
)
from tool_shed.galaxy_install.grids import admin_toolshed_grids
from tool_shed.galaxy_install.installed_repository_manager import InstalledRepositoryManager
from tool_shed.galaxy_install.metadata.installed_repository_metadata_manager import InstalledRepositoryMetadataManager
from tool_shed.galaxy_install.repository_dependencies import repository_dependency_manager
from tool_shed.galaxy_install.tools import (
data_manager,
tool_panel_manager
)
from tool_shed.util import (
common_util,
encoding_util,
hg_util,
readme_util,
repository_util,
shed_util_common as suc,
tool_dependency_util,
tool_util,
workflow_util
)
from tool_shed.util.web_util import escape
from .admin import AdminGalaxy
log = logging.getLogger(__name__)
class AdminToolshed(AdminGalaxy):
installed_repository_grid = admin_toolshed_grids.InstalledRepositoryGrid()
@web.expose
@web.require_admin
def activate_repository(self, trans, **kwd):
"""Activate a repository that was deactivated but not uninstalled."""
repository_id = kwd['id']
repository = repository_util.get_installed_tool_shed_repository(trans.app, repository_id)
try:
trans.app.installed_repository_manager.activate_repository(repository)
message = 'The <b>%s</b> repository has been activated.' % escape(repository.name)
status = 'done'
except Exception as e:
error_message = "Error activating repository %s: %s" % (escape(repository.name), str(e))
log.exception(error_message)
message = '%s.<br/>You may be able to resolve this by uninstalling and then reinstalling the repository. Click <a href="%s">here</a> to uninstall the repository.' \
% (error_message, web.url_for(controller='admin_toolshed', action='deactivate_or_uninstall_repository', id=trans.security.encode_id(repository.id)))
status = 'error'
return trans.response.send_redirect(web.url_for(controller='admin_toolshed',
action='manage_repository',
id=repository_id,
message=message,
status=status))
@web.expose
@web.require_admin
def browse_repository(self, trans, **kwd):
message = escape(kwd.get('message', ''))
status = kwd.get('status', 'done')
repository = repository_util.get_installed_tool_shed_repository(trans.app, kwd['id'])
return trans.fill_template('/admin/tool_shed_repository/browse_repository.mako',
repository=repository,
message=message,
status=status)
@web.expose_api
@web.require_admin
def browse_repositories(self, trans, **kwd):
message = kwd.get('message', '')
status = kwd.get('status', '')
if 'operation' in kwd:
operation = kwd.pop('operation').lower()
if operation == "update tool shed status":
message, status = repository_util.check_for_updates(trans.app, trans.install_model, kwd.get('id'))
if message and status:
kwd['message'] = util.sanitize_text(message)
kwd['status'] = 'success' if status in ['ok', 'done', 'success'] else 'error'
kwd['dict_format'] = True
return self.installed_repository_grid(trans, **kwd)
@web.expose
@web.require_admin
def restore_repository(self, trans, **kwd):
repository_id = kwd['id']
repository = repository_util.get_installed_tool_shed_repository(trans.app, repository_id)
if repository.uninstalled:
# Since we're reinstalling the repository we need to find the latest changeset revision to which it can
# be updated so that we can reset the metadata if necessary. This will ensure that information about
# repository dependencies and tool dependencies will be current. Only allow selecting a different section
# in the tool panel if the repository was uninstalled and it contained tools that should be displayed in
# the tool panel.
changeset_revision_dict = trans.app.update_repository_manager.get_update_to_changeset_revision_and_ctx_rev(repository)
current_changeset_revision = changeset_revision_dict.get('changeset_revision', None)
current_ctx_rev = changeset_revision_dict.get('ctx_rev', None)
if current_changeset_revision and current_ctx_rev:
if current_ctx_rev == repository.ctx_rev:
# The uninstalled repository is current.
return trans.response.send_redirect(web.url_for(controller='admin_toolshed',
action='reselect_tool_panel_section',
**kwd))
else:
# The uninstalled repository has updates available in the tool shed.
updated_repo_info_dict = \
self.get_updated_repository_information(trans=trans,
repository_id=trans.security.encode_id(repository.id),
repository_name=repository.name,
repository_owner=repository.owner,
changeset_revision=current_changeset_revision)
json_repo_info_dict = json.dumps(updated_repo_info_dict)
encoded_repo_info_dict = encoding_util.tool_shed_encode(json_repo_info_dict)
kwd['latest_changeset_revision'] = current_changeset_revision
kwd['latest_ctx_rev'] = current_ctx_rev
kwd['updated_repo_info_dict'] = encoded_repo_info_dict
return trans.response.send_redirect(web.url_for(controller='admin_toolshed',
action='reselect_tool_panel_section',
**kwd))
else:
message = "Unable to get latest revision for repository <b>%s</b> from " % escape(str(repository.name))
message += "the Tool Shed, so repository re-installation is not possible at this time."
status = "error"
return trans.response.send_redirect(web.url_for(controller='admin_toolshed',
action='manage_repository',
id=repository_id,
message=message,
status=status))
else:
return trans.response.send_redirect(web.url_for(controller='admin_toolshed',
action='activate_repository',
**kwd))
@web.expose
@web.require_admin
def browse_tool_dependency(self, trans, **kwd):
message = escape(kwd.get('message', ''))
status = kwd.get('status', 'done')
tool_dependency_ids = tool_dependency_util.get_tool_dependency_ids(as_string=False, **kwd)
tool_dependency = tool_dependency_util.get_tool_dependency(trans.app, tool_dependency_ids[0])
if tool_dependency.in_error_state:
message = "This tool dependency is not installed correctly (see the <b>Tool dependency installation error</b> below). "
message += "Choose <b>Uninstall this tool dependency</b> from the <b>Repository Actions</b> menu, correct problems "
message += "if necessary, and try installing the dependency again."
status = "error"
repository = tool_dependency.tool_shed_repository
return trans.fill_template('/admin/tool_shed_repository/browse_tool_dependency.mako',
repository=repository,
tool_dependency=tool_dependency,
message=message,
status=status)
@web.expose
@web.require_admin
def browse_tool_shed(self, trans, **kwd):
tool_shed_url = kwd.get('tool_shed_url', '')
tool_shed_url = common_util.get_tool_shed_url_from_tool_shed_registry(trans.app, tool_shed_url)
params = dict(galaxy_url=web.url_for('/', qualified=True))
url = util.build_url(tool_shed_url, pathspec=['repository', 'browse_valid_categories'], params=params)
return trans.response.send_redirect(url)
@web.expose
@web.require_admin
def browse_toolsheds(self, trans, **kwd):
app = {
'jscript': "adminToolshedApp"
}
return trans.fill_template('galaxy.panels.mako',
config={
'title': 'Galaxy Tool Sheds',
'app': app,
'bundle': 'adminToolshed'})
@web.expose
@web.require_admin
def browse_tool_sheds(self, trans, **kwd):
message = escape(kwd.get('message', ''))
return trans.fill_template('/webapps/galaxy/admin/tool_sheds.mako',
message=message,
status='error')
@web.expose
@web.require_admin
def check_for_updates(self, trans, **kwd):
"""Send a request to the relevant tool shed to see if there are any updates."""
repository_id = kwd.get('id', None)
repository = repository_util.get_installed_tool_shed_repository(trans.app, repository_id)
tool_shed_url = common_util.get_tool_shed_url_from_tool_shed_registry(trans.app, str(repository.tool_shed))
params = dict(galaxy_url=web.url_for('/', qualified=True),
name=str(repository.name),
owner=str(repository.owner),
changeset_revision=str(repository.changeset_revision))
pathspec = ['repository', 'check_for_updates']
url = util.build_url(tool_shed_url, pathspec=pathspec, params=params)
return trans.response.send_redirect(url)
@web.expose
@web.require_admin
def deactivate_or_uninstall_repository(self, trans, **kwd):
"""
Handle all changes when a tool shed repository is being deactivated or uninstalled. Notice
that if the repository contents include a file named tool_data_table_conf.xml.sample, its
entries are not removed from the defined config.shed_tool_data_table_config. This is because
it becomes a bit complex to determine if other installed repositories include tools that
require the same entry. For now we'll never delete entries from config.shed_tool_data_table_config,
but we may choose to do so in the future if it becomes necessary.
"""
message = escape(kwd.get('message', ''))
statuses = [None, '' 'info', 'done', 'warning', 'error']
status = kwd.get('status', 'done')
if status in statuses:
status = statuses.index(status)
else:
status = 1
remove_from_disk = kwd.get('remove_from_disk', '')
remove_from_disk_checked = CheckboxField.is_checked(remove_from_disk)
tool_shed_repositories = repository_util.get_installed_tool_shed_repository(trans.app, kwd['id'])
if not isinstance(tool_shed_repositories, list):
tool_shed_repositories = [tool_shed_repositories]
irm = InstalledRepositoryManager(app=trans.app)
for tool_shed_repository in tool_shed_repositories:
if kwd.get('deactivate_or_uninstall_repository_button', False):
errors = irm.uninstall_repository(repository=tool_shed_repository, remove_from_disk=remove_from_disk_checked)
action = 'uninstalled' if remove_from_disk_checked else 'deactivated'
status = max(status, statuses.index('done'))
message += 'The repository named <b>%s</b> has been %s. ' % (escape(tool_shed_repository.name), action)
if remove_from_disk_checked:
if errors:
message += 'Attempting to uninstall tool dependencies resulted in errors: %s' % errors
status = max(status, statuses.index('error'))
status = statuses[status]
remove_from_disk_check_box = CheckboxField('remove_from_disk', checked=remove_from_disk_checked)
return trans.fill_template('/admin/tool_shed_repository/deactivate_or_uninstall_repository.mako',
repository=tool_shed_repositories,
remove_from_disk_check_box=remove_from_disk_check_box,
message=message,
status=status)
@web.expose
def display_image_in_repository(self, trans, **kwd):
"""
Open an image file that is contained in an installed tool shed repository or that is referenced by a URL for display. The
image can be defined in either a README.rst file contained in the repository or the help section of a Galaxy tool config that
is contained in the repository. The following image definitions are all supported. The former $PATH_TO_IMAGES is no longer
required, and is now ignored.
.. image:: https://raw.github.com/galaxy/some_image.png
.. image:: $PATH_TO_IMAGES/some_image.png
.. image:: /static/images/some_image.gif
.. image:: some_image.jpg
.. image:: /deep/some_image.png
"""
repository_id = kwd.get('repository_id', None)
relative_path_to_image_file = kwd.get('image_file', None)
if repository_id and relative_path_to_image_file:
repository = repository_util.get_tool_shed_repository_by_id(trans.app, repository_id)
if repository:
repo_files_dir = repository.repo_files_directory(trans.app)
# The following line sometimes returns None. TODO: Figure out why.
path_to_file = repository_util.get_absolute_path_to_file_in_repository(repo_files_dir, relative_path_to_image_file)
if path_to_file and os.path.exists(path_to_file):
file_name = os.path.basename(relative_path_to_image_file)
try:
extension = file_name.split('.')[-1]
except Exception:
extension = None
if extension:
mimetype = trans.app.datatypes_registry.get_mimetype_by_extension(extension)
if mimetype:
trans.response.set_content_type(mimetype)
return open(path_to_file, 'r')
return None
@web.expose
@web.require_admin
def find_tools_in_tool_shed(self, trans, **kwd):
tool_shed_url = kwd.get('tool_shed_url', '')
tool_shed_url = common_util.get_tool_shed_url_from_tool_shed_registry(trans.app, tool_shed_url)
params = dict(galaxy_url=web.url_for('/', qualified=True))
url = util.build_url(tool_shed_url, pathspec=['repository', 'find_tools'], params=params)
return trans.response.send_redirect(url)
@web.expose
@web.require_admin
def find_workflows_in_tool_shed(self, trans, **kwd):
tool_shed_url = kwd.get('tool_shed_url', '')
tool_shed_url = common_util.get_tool_shed_url_from_tool_shed_registry(trans.app, tool_shed_url)
params = dict(galaxy_url=web.url_for('/', qualified=True))
url = util.build_url(tool_shed_url, pathspec=['repository', 'find_workflows'], params=params)
return trans.response.send_redirect(url)
@web.expose
@web.require_admin
def generate_workflow_image(self, trans, workflow_name, repository_id=None):
"""Return an svg image representation of a workflow dictionary created when the workflow was exported."""
return workflow_util.generate_workflow_image(trans, workflow_name, repository_metadata_id=None, repository_id=repository_id)
@web.json
@web.require_admin
def get_file_contents(self, trans, file_path, repository_id):
# Avoid caching
trans.response.headers['Pragma'] = 'no-cache'
trans.response.headers['Expires'] = '0'
return suc.get_repository_file_contents(trans.app, file_path, repository_id, is_admin=True)
@web.expose
@web.require_admin
def get_tool_dependencies(self, trans, repository_id, repository_name, repository_owner, changeset_revision):
"""
Send a request to the appropriate tool shed to retrieve the dictionary of tool dependencies defined for
the received repository name, owner and changeset revision. The received repository_id is the encoded id
of the installed tool shed repository in Galaxy. We need it so that we can derive the tool shed from which
it was installed.
"""
repository = repository_util.get_installed_tool_shed_repository(trans.app, repository_id)
tool_shed_url = common_util.get_tool_shed_url_from_tool_shed_registry(trans.app, str(repository.tool_shed))
if tool_shed_url is None or repository_name is None or repository_owner is None or changeset_revision is None:
message = "Unable to retrieve tool dependencies from the Tool Shed because one or more of the following required "
message += "parameters is None: tool_shed_url: %s, repository_name: %s, repository_owner: %s, changeset_revision: %s " % \
(str(tool_shed_url), str(repository_name), str(repository_owner), str(changeset_revision))
raise Exception(message)
params = dict(name=repository_name, owner=repository_owner, changeset_revision=changeset_revision)
pathspec = ['repository', 'get_tool_dependencies']
raw_text = util.url_get(tool_shed_url, password_mgr=self.app.tool_shed_registry.url_auth(tool_shed_url), pathspec=pathspec, params=params)
if len(raw_text) > 2:
encoded_text = json.loads(raw_text)
text = encoding_util.tool_shed_decode(encoded_text)
else:
text = ''
return text
@web.expose
@web.require_admin
def get_updated_repository_information(self, trans, repository_id, repository_name, repository_owner, changeset_revision):
"""
Send a request to the appropriate tool shed to retrieve the dictionary of information required to reinstall
an updated revision of an uninstalled tool shed repository.
"""
repository = repository_util.get_installed_tool_shed_repository(trans.app, repository_id)
tool_shed_url = common_util.get_tool_shed_url_from_tool_shed_registry(trans.app, str(repository.tool_shed))
if tool_shed_url is None or repository_name is None or repository_owner is None or changeset_revision is None:
message = "Unable to retrieve updated repository information from the Tool Shed because one or more of the following "
message += "required parameters is None: tool_shed_url: %s, repository_name: %s, repository_owner: %s, changeset_revision: %s " % \
(str(tool_shed_url), str(repository_name), str(repository_owner), str(changeset_revision))
raise Exception(message)
params = dict(name=str(repository_name),
owner=str(repository_owner),
changeset_revision=changeset_revision)
pathspec = ['repository', 'get_updated_repository_information']
raw_text = util.url_get(tool_shed_url, password_mgr=self.app.tool_shed_registry.url_auth(tool_shed_url), pathspec=pathspec, params=params)
repo_information_dict = json.loads(raw_text)
return repo_information_dict
@web.expose
@web.require_admin
def import_workflow(self, trans, workflow_name, repository_id, **kwd):
"""Import a workflow contained in an installed tool shed repository into Galaxy."""
message = str(escape(kwd.get('message', '')))
status = kwd.get('status', 'done')
if workflow_name:
workflow_name = encoding_util.tool_shed_decode(workflow_name)
repository = repository_util.get_tool_shed_repository_by_id(trans.app, repository_id)
if repository:
workflow, status, message = workflow_util.import_workflow(trans, repository, workflow_name)
if workflow:
workflow_name = encoding_util.tool_shed_encode(str(workflow.name))
else:
message += 'Unable to locate a workflow named <b>%s</b> within the installed tool shed repository named <b>%s</b>' % \
(escape(str(workflow_name)), escape(str(repository.name)))
status = 'error'
else:
message = 'Invalid repository id <b>%s</b> received.' % str(repository_id)
status = 'error'
else:
message = 'The value of workflow_name is required, but was not received.'
status = 'error'
return trans.response.send_redirect(web.url_for(controller='admin_toolshed',
action='view_workflow',
workflow_name=workflow_name,
repository_id=repository_id,
message=message,
status=status))
@web.expose
@web.require_admin
def initiate_tool_dependency_installation(self, trans, tool_dependencies, **kwd):
"""
Install specified dependencies for repository tools. The received list of tool_dependencies
are the database records for those dependencies defined in the tool_dependencies.xml file
(contained in the repository) that should be installed. This allows for filtering out dependencies
that have not been checked for installation on the 'Manage tool dependencies' page for an installed
tool shed repository.
"""
# Get the tool_shed_repository from one of the tool_dependencies.
message = str(escape(kwd.get('message', '')))
status = kwd.get('status', 'done')
err_msg = ''
tool_shed_repository = tool_dependencies[0].tool_shed_repository
# Get the tool_dependencies.xml file from the repository.
tool_dependencies_config = hg_util.get_config_from_disk(rt_util.TOOL_DEPENDENCY_DEFINITION_FILENAME,
tool_shed_repository.repo_path(trans.app))
itdm = install_manager.InstallToolDependencyManager(trans.app)
installed_tool_dependencies = itdm.install_specified_tool_dependencies(tool_shed_repository=tool_shed_repository,
tool_dependencies_config=tool_dependencies_config,
tool_dependencies=tool_dependencies,
from_tool_migration_manager=False)
for installed_tool_dependency in installed_tool_dependencies:
if installed_tool_dependency.status == trans.app.install_model.ToolDependency.installation_status.ERROR:
text = unicodify(installed_tool_dependency.error_message)
if text is not None:
err_msg += ' %s' % text
if err_msg:
message += err_msg
status = 'error'
message += "Installed tool dependencies: %s" % ', '.join(td.name for td in installed_tool_dependencies)
td_ids = [trans.security.encode_id(td.id) for td in tool_shed_repository.tool_dependencies]
return trans.response.send_redirect(web.url_for(controller='admin_toolshed',
action='manage_tool_dependencies',
tool_dependency_ids=td_ids,
message=message,
status=status))
@web.expose
@web.require_admin
def install_latest_repository_revision(self, trans, **kwd):
"""Install the latest installable revision of a repository that has been previously installed."""
repository_id = kwd.get('id', None)
if repository_id is not None:
repository = repository_util.get_installed_tool_shed_repository(trans.app, repository_id)
if repository is not None:
tool_shed_url = common_util.get_tool_shed_url_from_tool_shed_registry(trans.app, str(repository.tool_shed))
name = str(repository.name)
owner = str(repository.owner)
params = dict(galaxy_url=web.url_for('/', qualified=True),
name=name,
owner=owner)
pathspec = ['repository', 'get_latest_downloadable_changeset_revision']
raw_text = util.url_get(tool_shed_url, password_mgr=self.app.tool_shed_registry.url_auth(tool_shed_url), pathspec=pathspec, params=params)
url = util.build_url(tool_shed_url, pathspec=pathspec, params=params)
latest_downloadable_revision = json.loads(raw_text)
if latest_downloadable_revision == hg_util.INITIAL_CHANGELOG_HASH:
return trans.show_error_message('Error retrieving the latest downloadable revision for this repository via the url <b>%s</b>.' % url)
else:
# Make sure the latest changeset_revision of the repository has not already been installed.
# Updates to installed repository revisions may have occurred, so make sure to locate the
# appropriate repository revision if one exists. We need to create a temporary repo_info_tuple
# with the following entries to handle this.
# ( description, clone_url, changeset_revision, ctx_rev, owner, repository_dependencies, tool_dependencies )
tmp_clone_url = util.build_url(tool_shed_url, pathspec=['repos', owner, name])
tmp_repo_info_tuple = (None, tmp_clone_url, latest_downloadable_revision, None, owner, None, None)
installed_repository, installed_changeset_revision = \
repository_util.repository_was_previously_installed(trans.app, tool_shed_url, name, tmp_repo_info_tuple, from_tip=False)
if installed_repository:
current_changeset_revision = str(installed_repository.changeset_revision)
message = 'Revision <b>%s</b> of repository <b>%s</b> owned by <b>%s</b> has already been installed.' % \
(latest_downloadable_revision, name, owner)
if current_changeset_revision != latest_downloadable_revision:
message += ' The current changeset revision is <b>%s</b>.' % current_changeset_revision
return trans.show_error_message(message)
else:
# Install the latest downloadable revision of the repository.
params = dict(name=name,
owner=owner,
changeset_revisions=str(latest_downloadable_revision),
galaxy_url=web.url_for('/', qualified=True))
pathspec = ['repository', 'install_repositories_by_revision']
url = util.build_url(tool_shed_url, pathspec=pathspec, params=params)
return trans.response.send_redirect(url)
else:
return trans.show_error_message('Cannot locate installed tool shed repository with encoded id <b>%s</b>.' % str(repository_id))
else:
return trans.show_error_message('The request parameters did not include the required encoded <b>id</b> of installed repository.')
@web.expose
@web.require_admin
def install_tool_dependencies_with_update(self, trans, **kwd):
"""
Updating an installed tool shed repository where new tool dependencies but no new repository
dependencies are included in the updated revision.
"""
updating_repository_id = kwd.get('updating_repository_id', None)
repository = repository_util.get_installed_tool_shed_repository(trans.app, updating_repository_id)
# All received dependencies need to be installed - confirmed by the caller.
encoded_tool_dependencies_dict = kwd.get('encoded_tool_dependencies_dict', None)
if encoded_tool_dependencies_dict is not None:
tool_dependencies_dict = encoding_util.tool_shed_decode(encoded_tool_dependencies_dict)
else:
tool_dependencies_dict = {}
encoded_relative_install_dir = kwd.get('encoded_relative_install_dir', None)
if encoded_relative_install_dir is not None:
relative_install_dir = encoding_util.tool_shed_decode(encoded_relative_install_dir)
else:
relative_install_dir = ''
updating_to_changeset_revision = kwd.get('updating_to_changeset_revision', None)
updating_to_ctx_rev = kwd.get('updating_to_ctx_rev', None)
encoded_updated_metadata = kwd.get('encoded_updated_metadata', None)
message = escape(kwd.get('message', ''))
status = kwd.get('status', 'done')
if 'install_tool_dependencies_with_update_button' in kwd:
# Now that the user has chosen whether to install tool dependencies or not, we can
# update the repository record with the changes in the updated revision.
if encoded_updated_metadata:
updated_metadata = encoding_util.tool_shed_decode(encoded_updated_metadata)
else:
updated_metadata = None
repository = trans.app.update_repository_manager.update_repository_record(repository=repository,
updated_metadata_dict=updated_metadata,
updated_changeset_revision=updating_to_changeset_revision,
updated_ctx_rev=updating_to_ctx_rev)
if tool_dependencies_dict:
tool_dependencies = tool_dependency_util.create_tool_dependency_objects(trans.app,
repository,
relative_install_dir,
set_status=False)
message = "The installed repository named '%s' has been updated to change set revision '%s'. " % \
(escape(str(repository.name)), updating_to_changeset_revision)
self.initiate_tool_dependency_installation(trans, tool_dependencies, message=message, status=status)
# Handle tool dependencies check box.
if trans.app.config.tool_dependency_dir is None:
if tool_dependencies_dict:
message = ("Tool dependencies defined in this repository can be automatically installed if you set "
"the value of your <b>tool_dependency_dir</b> setting in your Galaxy config file "
"(galaxy.ini) and restart your Galaxy server.")
status = "warning"
install_tool_dependencies_check_box_checked = False
else:
install_tool_dependencies_check_box_checked = True
install_tool_dependencies_check_box = CheckboxField('install_tool_dependencies',
checked=install_tool_dependencies_check_box_checked)
view = views.DependencyResolversView(self.app)
if view.installable_resolvers:
install_resolver_dependencies_check_box = CheckboxField('install_resolver_dependencies', checked=True)
else:
install_resolver_dependencies_check_box = None
return trans.fill_template('/admin/tool_shed_repository/install_tool_dependencies_with_update.mako',
repository=repository,
updating_repository_id=updating_repository_id,
updating_to_ctx_rev=updating_to_ctx_rev,
updating_to_changeset_revision=updating_to_changeset_revision,
encoded_updated_metadata=encoded_updated_metadata,
encoded_relative_install_dir=encoded_relative_install_dir,
encoded_tool_dependencies_dict=encoded_tool_dependencies_dict,
install_resolver_dependencies_check_box=install_resolver_dependencies_check_box,
install_tool_dependencies_check_box=install_tool_dependencies_check_box,
tool_dependencies_dict=tool_dependencies_dict,
message=message,
status=status)
@web.expose
@web.require_admin
def install_repositories(self, trans, **kwd):
reinstalling = util.string_as_bool(kwd.get('reinstalling', False))
encoded_kwd = kwd.get('encoded_kwd')
decoded_kwd = encoding_util.tool_shed_decode(encoded_kwd) if encoded_kwd else {}
install_resolver_dependencies = CheckboxField.is_checked(decoded_kwd.get('install_resolver_dependencies', ''))
install_tool_dependencies = CheckboxField.is_checked(decoded_kwd.get('install_tool_dependencies', ''))
decoded_kwd['install_resolver_dependencies'] = install_resolver_dependencies
decoded_kwd['install_tool_dependencies'] = install_tool_dependencies
tsr_ids = decoded_kwd.get('tool_shed_repository_ids')
if not tsr_ids:
return self.message_exception(trans, 'Repository ids missing.')
irm = install_manager.InstallRepositoryManager(trans.app)
try:
tool_shed_repositories = irm.install_repositories(
tsr_ids=tsr_ids,
decoded_kwd=decoded_kwd,
reinstalling=reinstalling,
)
tsr_ids_for_monitoring = [trans.security.encode_id(tsr.id) for tsr in tool_shed_repositories]
return json.dumps(tsr_ids_for_monitoring)
except install_manager.RepositoriesInstalledException as e:
return self.message_exception(trans, e.message)
@web.expose
@web.require_admin
def manage_repository(self, trans, **kwd):
message = escape(kwd.get('message', ''))
status = kwd.get('status', 'done')
repository_id = kwd.get('id', None)
if repository_id is None:
return trans.show_error_message('Missing required encoded repository id.')
operation = kwd.get('operation', None)
repository = repository_util.get_installed_tool_shed_repository(trans.app, repository_id)
if repository is None:
return trans.show_error_message('Invalid repository specified.')
tool_shed_url = common_util.get_tool_shed_url_from_tool_shed_registry(trans.app, str(repository.tool_shed))
name = str(repository.name)
owner = str(repository.owner)
installed_changeset_revision = str(repository.installed_changeset_revision)
if repository.status in [trans.install_model.ToolShedRepository.installation_status.CLONING]:
tool_shed_repository_ids = [repository_id]
return trans.response.send_redirect(web.url_for(controller='admin_toolshed',
action='monitor_repository_installation',
tool_shed_repository_ids=tool_shed_repository_ids))
if repository.can_install and operation == 'install':
# Send a request to the tool shed to install the repository.
params = dict(name=name,
owner=owner,
changeset_revisions=installed_changeset_revision,
galaxy_url=web.url_for('/', qualified=True))
pathspec = ['repository', 'install_repositories_by_revision']
url = util.build_url(tool_shed_url, pathspec=pathspec, params=params)
return trans.response.send_redirect(url)
description = kwd.get('description', repository.description)
shed_tool_conf, tool_path, relative_install_dir = suc.get_tool_panel_config_tool_path_install_dir(trans.app, repository)
if relative_install_dir:
repo_files_dir = os.path.abspath(os.path.join(tool_path, relative_install_dir, name))
else:
repo_files_dir = None
if repository.in_error_state:
message = "This repository is not installed correctly (see the <b>Repository installation error</b> below). Choose "
message += "<b>Reset to install</b> from the <b>Repository Actions</b> menu, correct problems if necessary and try "
message += "installing the repository again."
status = "error"
elif repository.can_install:
message = "This repository is not installed. You can install it by choosing <b>Install</b> from the <b>Repository Actions</b> menu."
status = "error"
elif kwd.get('edit_repository_button', False):
if description != repository.description:
repository.description = description
trans.install_model.context.add(repository)
trans.install_model.context.flush()
message = "The repository information has been updated."
dd = dependency_display.DependencyDisplayer(trans.app)
containers_dict = dd.populate_containers_dict_from_repository_metadata(tool_shed_url=tool_shed_url,
tool_path=tool_path,
repository=repository,
reinstalling=False,
required_repo_info_dicts=None)
view = views.DependencyResolversView(self.app)
tool_requirements_d = suc.get_requirements_from_repository(repository)
requirements_status = view.get_requirements_status(tool_requirements_d, repository.installed_tool_dependencies)
return trans.fill_template('/admin/tool_shed_repository/manage_repository.mako',
repository=repository,
description=description,
repo_files_dir=repo_files_dir,
containers_dict=containers_dict,
requirements_status=requirements_status,
message=message,
status=status)
@web.expose
@web.require_admin
def manage_repository_tool_dependencies(self, trans, **kwd):
message = escape(kwd.get('message', ''))
status = kwd.get('status', 'done')
tool_dependency_ids = tool_dependency_util.get_tool_dependency_ids(as_string=False, **kwd)
if tool_dependency_ids:
# We need a tool_shed_repository, so get it from one of the tool_dependencies.
tool_dependency = tool_dependency_util.get_tool_dependency(trans.app, tool_dependency_ids[0])
tool_shed_repository = tool_dependency.tool_shed_repository
else:
# The user must be on the manage_repository_tool_dependencies page and clicked the button to either install or uninstall a
# tool dependency, but they didn't check any of the available tool dependencies on which to perform the action.
repository_id = kwd.get('repository_id', None)
tool_shed_repository = repository_util.get_tool_shed_repository_by_id(trans.app, repository_id)
if 'operation' in kwd:
operation = kwd['operation'].lower()
if not tool_dependency_ids:
message = 'Select at least 1 tool dependency to %s.' % operation
kwd['message'] = message
kwd['status'] = 'error'
del kwd['operation']
return trans.response.send_redirect(web.url_for(controller='admin_toolshed',
action='manage_repository_tool_dependencies',
**kwd))
if operation == 'browse':
return trans.response.send_redirect(web.url_for(controller='admin_toolshed',
action='browse_tool_dependency',
**kwd))
elif operation == 'uninstall':
tool_dependencies_for_uninstallation = []
for tool_dependency_id in tool_dependency_ids:
tool_dependency = tool_dependency_util.get_tool_dependency(trans.app, tool_dependency_id)
if tool_dependency.status in [trans.install_model.ToolDependency.installation_status.INSTALLED,
trans.install_model.ToolDependency.installation_status.ERROR]:
tool_dependencies_for_uninstallation.append(tool_dependency)
if tool_dependencies_for_uninstallation:
return trans.response.send_redirect(web.url_for(controller='admin_toolshed',
action='uninstall_tool_dependencies',
**kwd))
else:
message = 'No selected tool dependencies can be uninstalled, you may need to use the <b>Repair repository</b> feature.'
status = 'error'
elif operation == "install":
if trans.app.config.tool_dependency_dir:
tool_dependencies_for_installation = []
for tool_dependency_id in tool_dependency_ids:
tool_dependency = tool_dependency_util.get_tool_dependency(trans.app, tool_dependency_id)
if tool_dependency.status in [trans.install_model.ToolDependency.installation_status.NEVER_INSTALLED,
trans.install_model.ToolDependency.installation_status.UNINSTALLED]:
tool_dependencies_for_installation.append(tool_dependency)
if tool_dependencies_for_installation:
self.initiate_tool_dependency_installation(trans,
tool_dependencies_for_installation,
message=message,
status=status)
else:
message = 'All selected tool dependencies are already installed.'
status = 'error'
else:
message = 'Set the value of your <b>tool_dependency_dir</b> setting in your Galaxy config file (galaxy.ini) '
message += ' and restart your Galaxy server to install tool dependencies.'
status = 'error'
installed_tool_dependencies_select_field = \
tool_dependency_util.build_tool_dependencies_select_field(trans.app,
tool_shed_repository=tool_shed_repository,
name='inst_td_ids',
uninstalled_only=False)
uninstalled_tool_dependencies_select_field = \
tool_dependency_util.build_tool_dependencies_select_field(trans.app,
tool_shed_repository=tool_shed_repository,
name='uninstalled_tool_dependency_ids',
uninstalled_only=True)
return trans.fill_template('/admin/tool_shed_repository/manage_repository_tool_dependencies.mako',
repository=tool_shed_repository,
installed_tool_dependencies_select_field=installed_tool_dependencies_select_field,
uninstalled_tool_dependencies_select_field=uninstalled_tool_dependencies_select_field,
message=message,
status=status)
@web.expose
@web.require_admin
def manage_tool_dependencies(self, trans, **kwd):
# This method is called when tool dependencies are being installed. See the related manage_repository_tool_dependencies
# method for managing the tool dependencies for a specified installed tool shed repository.
message = escape(kwd.get('message', ''))
status = kwd.get('status', 'done')
tool_dependency_ids = tool_dependency_util.get_tool_dependency_ids(as_string=False, **kwd)
repository_id = kwd.get('repository_id', None)
if 'operation' in kwd:
operation = kwd['operation'].lower()
if not tool_dependency_ids:
message = 'Select at least 1 tool dependency to %s.' % operation
kwd['message'] = message
kwd['status'] = 'error'
del kwd['operation']
return trans.response.send_redirect(web.url_for(controller='admin_toolshed',
action='manage_tool_dependencies',
**kwd))
if operation == 'browse':
return trans.response.send_redirect(web.url_for(controller='admin_toolshed',
action='browse_tool_dependency',
**kwd))
elif operation == "install":
if trans.app.config.tool_dependency_dir:
tool_dependencies_for_installation = []
for tool_dependency_id in tool_dependency_ids:
tool_dependency = tool_dependency_util.get_tool_dependency(trans.app, tool_dependency_id)
if tool_dependency.status in [trans.install_model.ToolDependency.installation_status.NEVER_INSTALLED,
trans.install_model.ToolDependency.installation_status.UNINSTALLED]:
tool_dependencies_for_installation.append(tool_dependency)
if tool_dependencies_for_installation:
self.initiate_tool_dependency_installation(trans,
tool_dependencies_for_installation,
message=message,
status=status)
else:
kwd['message'] = 'All selected tool dependencies are already installed.'
kwd['status'] = 'error'
else:
message = 'Set the value of your <b>tool_dependency_dir</b> setting in your Galaxy config file (galaxy.ini) '
message += ' and restart your Galaxy server to install tool dependencies.'
kwd['message'] = message
kwd['status'] = 'error'
return trans.response.send_redirect(web.url_for(controller='admin_toolshed',
action='manage_repository_tool_dependencies',
tool_dependency_ids=tool_dependency_ids,
repository_id=repository_id,
message=message,
status=status))
@web.expose
@web.require_admin
def monitor_repository_installation(self, trans, **kwd):
tsr_ids = common_util.get_tool_shed_repository_ids(**kwd)
if not tsr_ids:
tsr_ids = repository_util.get_ids_of_tool_shed_repositories_being_installed(trans.app, as_string=False)
tsr_ids = [trans.security.decode_id(tsr_id) for tsr_id in tsr_ids]
tool_shed_repositories = []
for tsr_id in tsr_ids:
tsr = trans.install_model.context.query(trans.install_model.ToolShedRepository).get(tsr_id)
tool_shed_repositories.append(tsr)
clause_list = []
for tsr_id in tsr_ids:
clause_list.append(trans.install_model.ToolShedRepository.table.c.id == tsr_id)
query = trans.install_model.context.current.query(trans.install_model.ToolShedRepository).filter(or_(*clause_list))
return trans.fill_template('admin/tool_shed_repository/monitor_repository_installation.mako',
tool_shed_repositories=tool_shed_repositories,
query=query,
message=escape(kwd.get('message', '')),
status=kwd.get('status'))
@web.json
@web.require_admin
def open_folder(self, trans, folder_path, repository_id):
# Avoid caching
trans.response.headers['Pragma'] = 'no-cache'
trans.response.headers['Expires'] = '0'
return suc.open_repository_files_folder(trans.app, folder_path, repository_id, is_admin=True)
@web.expose
@web.require_admin
def prepare_for_install(self, trans, **kwd):
if not suc.have_shed_tool_conf_for_install(trans.app):
message = 'The <b>tool_config_file</b> setting in <b>galaxy.ini</b> must include at least one '
message += 'shed tool configuration file name with a <b><toolbox></b> tag that includes a <b>tool_path</b> '
message += 'attribute value which is a directory relative to the Galaxy installation directory in order '
message += 'to automatically install tools from a Galaxy Tool Shed (e.g., the file name <b>shed_tool_conf.xml</b> '
message += 'whose <b><toolbox></b> tag is <b><toolbox tool_path="../shed_tools"></b>).<p/>See the '
message += '<a href="https://galaxyproject.org/installing-repositories-to-galaxy/" target="_blank">Installation '
message += 'of Galaxy Tool Shed repository tools into a local Galaxy instance</a> section of the Galaxy Tool '
message += 'Shed wiki for all of the details.'
return trans.show_error_message(message)
message = escape(kwd.get('message', ''))
status = kwd.get('status', 'done')
shed_tool_conf = kwd.get('shed_tool_conf', None)
tool_shed_url = kwd.get('tool_shed_url', '')
tool_shed_url = common_util.get_tool_shed_url_from_tool_shed_registry(trans.app, tool_shed_url)
# Handle repository dependencies, which do not include those that are required only for compiling a dependent
# repository's tool dependencies.
has_repository_dependencies = util.string_as_bool(kwd.get('has_repository_dependencies', False))
install_repository_dependencies = kwd.get('install_repository_dependencies', '')
# Every repository will be installed into the same tool panel section or all will be installed outside of any sections.
new_tool_panel_section_label = kwd.get('new_tool_panel_section_label', '')
tool_panel_section_id = kwd.get('tool_panel_section_id', '')
tool_panel_section_keys = []
# One or more repositories may include tools, but not necessarily all of them.
includes_tools = util.string_as_bool(kwd.get('includes_tools', False))
# Some tools should not be displayed in the tool panel (e.g., DataManager tools and datatype converters).
includes_tools_for_display_in_tool_panel = util.string_as_bool(kwd.get('includes_tools_for_display_in_tool_panel', False))
includes_tool_dependencies = util.string_as_bool(kwd.get('includes_tool_dependencies', False))
install_resolver_dependencies = kwd.get('install_resolver_dependencies', '')
install_tool_dependencies = kwd.get('install_tool_dependencies', '')
# In addition to installing new repositories, this method is called when updating an installed repository
# to a new changeset_revision where the update includes newly defined repository dependencies.
updating = util.asbool(kwd.get('updating', False))
updating_repository_id = kwd.get('updating_repository_id', None)
updating_to_changeset_revision = kwd.get('updating_to_changeset_revision', None)
updating_to_ctx_rev = kwd.get('updating_to_ctx_rev', None)
encoded_updated_metadata = kwd.get('encoded_updated_metadata', None)
encoded_repo_info_dicts = kwd.get('encoded_repo_info_dicts', '')
if encoded_repo_info_dicts:
encoded_repo_info_dicts = encoded_repo_info_dicts.split(encoding_util.encoding_sep)
if not encoded_repo_info_dicts:
# The request originated in the tool shed via a tool search or from this controller's
# update_to_changeset_revision() method.
repository_ids = kwd.get('repository_ids', None)
if updating:
# We have updated an installed repository where the updates included newly defined repository
# and possibly tool dependencies. We will have arrived here only if the updates include newly
# defined repository dependencies. We're preparing to allow the user to elect to install these
# dependencies. At this point, the repository has been updated to the latest changeset revision,
# but the received repository id is from the Galaxy side (the caller is this controller's
# update_to_changeset_revision() method. We need to get the id of the same repository from the
# Tool Shed side.
repository = repository_util.get_tool_shed_repository_by_id(trans.app, updating_repository_id)
# For backward compatibility to the 12/20/12 Galaxy release.
try:
params = dict(name=str(repository.name), owner=str(repository.owner))
pathspec = ['repository', 'get_repository_id']
repository_ids = util.url_get(tool_shed_url, password_mgr=self.app.tool_shed_registry.url_auth(tool_shed_url), pathspec=pathspec, params=params)
except Exception as e:
# The Tool Shed cannot handle the get_repository_id request, so the code must be older than the
# 04/2014 Galaxy release when it was introduced. It will be safest to error out and let the
# Tool Shed admin update the Tool Shed to a later release.
message = 'The updates available for the repository <b>%s</b> ' % escape(str(repository.name))
message += 'include newly defined repository or tool dependency definitions, and attempting '
message += 'to update the repository resulted in the following error. Contact the Tool Shed '
message += 'administrator if necessary.<br/>%s' % str(e)
return trans.show_error_message(message)
changeset_revisions = updating_to_changeset_revision
else:
changeset_revisions = kwd.get('changeset_revisions', None)
# Get the information necessary to install each repository.
params = dict(repository_ids=str(repository_ids), changeset_revisions=str(changeset_revisions))
pathspec = ['repository', 'get_repository_information']
raw_text = util.url_get(tool_shed_url, password_mgr=self.app.tool_shed_registry.url_auth(tool_shed_url), pathspec=pathspec, params=params)
repo_information_dict = json.loads(raw_text)
for encoded_repo_info_dict in repo_information_dict.get('repo_info_dicts', []):
decoded_repo_info_dict = encoding_util.tool_shed_decode(encoded_repo_info_dict)
if not includes_tools:
includes_tools = util.string_as_bool(decoded_repo_info_dict.get('includes_tools', False))
if not includes_tools_for_display_in_tool_panel:
includes_tools_for_display_in_tool_panel = \
util.string_as_bool(decoded_repo_info_dict.get('includes_tools_for_display_in_tool_panel', False))
if not has_repository_dependencies:
has_repository_dependencies = util.string_as_bool(repo_information_dict.get('has_repository_dependencies', False))
if not includes_tool_dependencies:
includes_tool_dependencies = util.string_as_bool(repo_information_dict.get('includes_tool_dependencies', False))
encoded_repo_info_dicts = util.listify(repo_information_dict.get('repo_info_dicts', []))
repo_info_dicts = [encoding_util.tool_shed_decode(encoded_repo_info_dict) for encoded_repo_info_dict in encoded_repo_info_dicts]
dd = dependency_display.DependencyDisplayer(trans.app)
install_repository_manager = install_manager.InstallRepositoryManager(trans.app)
if kwd.get('select_tool_panel_section_button', False):
if updating:
repository = repository_util.get_tool_shed_repository_by_id(trans.app, updating_repository_id)
decoded_updated_metadata = encoding_util.tool_shed_decode(encoded_updated_metadata)
# Now that the user has decided whether they will handle dependencies, we can update
# the repository to the latest revision.
repository = trans.app.update_repository_manager.update_repository_record(repository=repository,
updated_metadata_dict=decoded_updated_metadata,
updated_changeset_revision=updating_to_changeset_revision,
updated_ctx_rev=updating_to_ctx_rev)
install_repository_dependencies = CheckboxField.is_checked(install_repository_dependencies)
if includes_tool_dependencies:
install_tool_dependencies = CheckboxField.is_checked(install_tool_dependencies)
else:
install_tool_dependencies = False
install_resolver_dependencies = CheckboxField.is_checked(install_resolver_dependencies)
tool_path = suc.get_tool_path_by_shed_tool_conf_filename(trans.app, shed_tool_conf)
installation_dict = dict(install_repository_dependencies=install_repository_dependencies,
new_tool_panel_section_label=new_tool_panel_section_label,
no_changes_checked=False,
repo_info_dicts=repo_info_dicts,
tool_panel_section_id=tool_panel_section_id,
tool_path=tool_path,
tool_shed_url=tool_shed_url)
created_or_updated_tool_shed_repositories, tool_panel_section_keys, repo_info_dicts, filtered_repo_info_dicts = \
install_repository_manager.handle_tool_shed_repositories(installation_dict)
if created_or_updated_tool_shed_repositories:
installation_dict = dict(created_or_updated_tool_shed_repositories=created_or_updated_tool_shed_repositories,
filtered_repo_info_dicts=filtered_repo_info_dicts,
has_repository_dependencies=has_repository_dependencies,
includes_tool_dependencies=includes_tool_dependencies,
includes_tools=includes_tools,
includes_tools_for_display_in_tool_panel=includes_tools_for_display_in_tool_panel,
install_repository_dependencies=install_repository_dependencies,
install_resolver_dependencies=install_resolver_dependencies,
install_tool_dependencies=install_tool_dependencies,
message=message,
new_tool_panel_section_label=new_tool_panel_section_label,
shed_tool_conf=shed_tool_conf,
status=status,
tool_panel_section_id=tool_panel_section_id,
tool_panel_section_keys=tool_panel_section_keys,
tool_path=tool_path,
tool_shed_url=tool_shed_url)
encoded_kwd, query, tool_shed_repositories, encoded_repository_ids = \
install_repository_manager.initiate_repository_installation(installation_dict)
return trans.fill_template('admin/tool_shed_repository/monitor_repository_installation.mako',
encoded_kwd=encoded_kwd,
query=query,
tool_shed_repositories=tool_shed_repositories,
initiate_repository_installation_ids=encoded_repository_ids,
reinstalling=False)
else:
kwd['message'] = message if message else 'Repository has already been installed.'
kwd['status'] = status
return trans.response.send_redirect(web.url_for(controller='admin_toolshed',
action='monitor_repository_installation',
**kwd))
shed_tool_conf_select_field = tool_util.build_shed_tool_conf_select_field(trans.app)
tool_path = suc.get_tool_path_by_shed_tool_conf_filename(trans.app, shed_tool_conf)
tool_panel_section_select_field = tool_util.build_tool_panel_section_select_field(trans.app)
tool_requirements = suc.get_tool_shed_repo_requirements(app=trans.app,
tool_shed_url=tool_shed_url,
repo_info_dicts=repo_info_dicts)
view = views.DependencyResolversView(self.app)
requirements_status = view.get_requirements_status(tool_requirements)
if len(repo_info_dicts) == 1:
# If we're installing or updating a single repository, see if it contains a readme or
# dependencies that we can display.
repo_info_dict = repo_info_dicts[0]
dependencies_for_repository_dict = \
trans.app.installed_repository_manager.get_dependencies_for_repository(tool_shed_url,
repo_info_dict,
includes_tool_dependencies,
updating=updating)
if not has_repository_dependencies:
has_repository_dependencies = dependencies_for_repository_dict.get('has_repository_dependencies', False)
if not includes_tool_dependencies:
includes_tool_dependencies = dependencies_for_repository_dict.get('includes_tool_dependencies', False)
if not includes_tools:
includes_tools = dependencies_for_repository_dict.get('includes_tools', False)
if not includes_tools_for_display_in_tool_panel:
includes_tools_for_display_in_tool_panel = \
dependencies_for_repository_dict.get('includes_tools_for_display_in_tool_panel', False)
installed_repository_dependencies = dependencies_for_repository_dict.get('installed_repository_dependencies', None)
installed_tool_dependencies = dependencies_for_repository_dict.get('installed_tool_dependencies', None)
missing_repository_dependencies = dependencies_for_repository_dict.get('missing_repository_dependencies', None)
missing_tool_dependencies = dependencies_for_repository_dict.get('missing_tool_dependencies', None)
readme_files_dict = readme_util.get_readme_files_dict_for_display(trans.app, tool_shed_url, repo_info_dict)
# We're handling 1 of 3 scenarios here: (1) we're installing a tool shed repository for the first time, so we've
# retrieved the list of installed and missing repository dependencies from the database (2) we're handling the
# scenario where an error occurred during the installation process, so we have a tool_shed_repository record in
# the database with associated repository dependency records. Since we have the repository dependencies in both
# of the above 2 cases, we'll merge the list of missing repository dependencies into the list of installed
# repository dependencies since each displayed repository dependency will display a status, whether installed or
# missing. The 3rd scenario is where we're updating an installed repository and the updates include newly
# defined repository (and possibly tool) dependencies. In this case, merging will result in newly defined