def get_required_repository_package_env_sh_path(self, package_name, package_version, required_repository):
"""Return path to env.sh file in required repository if the required repository has been installed."""
env_sh_file_dir = \
tool_dependency_util.get_tool_dependency_install_dir(app=self.app,
repository_name=required_repository.name,
repository_owner=required_repository.owner,
repository_changeset_revision=required_repository.installed_changeset_revision,
tool_dependency_type='package',
tool_dependency_name=package_name,
tool_dependency_version=package_version)
env_sh_file_path = os.path.join(env_sh_file_dir, 'env.sh')
return env_sh_file_path
def set_environment(self, elem, tool_shed_repository,
attr_tups_of_dependencies_for_install):
"""
Create a ToolDependency to set an environment variable. This is different from the process used to
set an environment variable that is associated with a package. An example entry in a tool_dependencies.xml
file is::
<set_environment version="1.0">
<environment_variable name="R_SCRIPT_PATH" action="set_to">$REPOSITORY_INSTALL_DIR</environment_variable>
</set_environment>
This method must also handle the sub-element tag::
<environment_variable name="R_SCRIPT_PATH" action="set_to">$REPOSITORY_INSTALL_DIR</environment_variable>
"""
# TODO: Add support for a repository dependency definition within this tool dependency type's tag set. This should look something like
# the following. See the implementation of support for this in the tool dependency package type's method above.
# This function is only called for set environment actions as defined below, not within an <install version="1.0"> tool
# dependency type. Here is an example of the tag set this function does handle:
# <action type="set_environment">
# <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR</environment_variable>
# </action>
# Here is an example of the tag set this function does not handle:
# <set_environment version="1.0">
# <repository toolshed="<tool shed>" name="<repository name>" owner="<repository owner>" changeset_revision="<changeset revision>" />
# </set_environment>
env_manager = EnvManager(self.app)
tool_dependencies = []
env_var_version = elem.get('version', '1.0')
tool_shed_repository_install_dir = os.path.abspath(
tool_shed_repository.repo_files_directory(self.app))
if elem.tag == 'environment_variable':
# <environment_variable name="R_SCRIPT_PATH" action="set_to">$REPOSITORY_INSTALL_DIR</environment_variable>
elems = [elem]
else:
# <set_environment version="1.0">
# <environment_variable name="R_SCRIPT_PATH" action="set_to">$REPOSITORY_INSTALL_DIR</environment_variable>
# </set_environment>
elems = [env_var_elem for env_var_elem in elem]
for env_var_elem in elems:
env_var_name = env_var_elem.get('name')
if not env_var_name:
raise Exception(
'The <environment_variable> tag must have a name attribute'
)
# The value of env_var_name must match the text value of at least 1 <requirement> tag in the
# tool config's <requirements> tag set whose "type" attribute is "set_environment" (e.g.,
# <requirement type="set_environment">R_SCRIPT_PATH</requirement>).
env_var_action = env_var_elem.get('action')
if not env_var_action:
raise Exception(
'The <environment_variable> tag must have an action attribute'
)
# Tool dependencies of type "set_environment" always have the version attribute set to None.
attr_tup = (env_var_name, None, 'set_environment')
if attr_tup in attr_tups_of_dependencies_for_install:
install_dir = \
tool_dependency_util.get_tool_dependency_install_dir(app=self.app,
repository_name=tool_shed_repository.name,
repository_owner=tool_shed_repository.owner,
repository_changeset_revision=tool_shed_repository.installed_changeset_revision,
tool_dependency_type='set_environment',
tool_dependency_name=env_var_name,
tool_dependency_version=None)
install_environment = InstallEnvironment(
app=self.app,
tool_shed_repository_install_dir=
tool_shed_repository_install_dir,
install_dir=install_dir)
env_var_dict = env_manager.create_env_var_dict(
elem=env_var_elem, install_environment=install_environment)
if not os.path.exists(install_dir):
os.makedirs(install_dir)
status = self.app.install_model.ToolDependency.installation_status.INSTALLING
tool_dependency = \
tool_dependency_util.create_or_update_tool_dependency(app=self.app,
tool_shed_repository=tool_shed_repository,
name=env_var_name,
version=None,
type='set_environment',
status=status,
set_status=True)
if env_var_version == '1.0':
# Create this tool dependency's env.sh file.
env_file_builder = EnvFileBuilder(install_dir)
return_code = env_file_builder.append_line(
make_executable=True, **env_var_dict)
if return_code:
error_message = 'Error creating env.sh file for tool dependency %s, return_code: %s' % \
(str(tool_dependency.name), str(return_code))
log.debug(error_message)
status = self.app.install_model.ToolDependency.installation_status.ERROR
tool_dependency = \
tool_dependency_util.set_tool_dependency_attributes(self.app,
tool_dependency=tool_dependency,
status=status,
error_message=error_message)
else:
if tool_dependency.status not in [
self.app.install_model.ToolDependency.
installation_status.ERROR,
self.app.install_model.ToolDependency.
installation_status.INSTALLED
]:
status = self.app.install_model.ToolDependency.installation_status.INSTALLED
tool_dependency = \
tool_dependency_util.set_tool_dependency_attributes(self.app,
tool_dependency=tool_dependency,
status=status)
log.debug(
'Environment variable %s set in %s for tool dependency %s.'
% (str(env_var_name), str(install_dir),
str(tool_dependency.name)))
else:
error_message = 'Only set_environment version 1.0 is currently supported (i.e., change your tag to be <set_environment version="1.0">).'
status = self.app.install_model.ToolDependency.installation_status.ERROR
tool_dependency = \
tool_dependency_util.set_tool_dependency_attributes(self.app,
tool_dependency=tool_dependency,
status=status,
error_message=error_message)
tool_dependencies.append(tool_dependency)
return tool_dependencies
def handle_complex_repository_dependency_for_package(
self,
elem,
package_name,
package_version,
tool_shed_repository,
from_tool_migration_manager=False):
"""
Inspect the repository defined by a complex repository dependency definition and take certain steps to
enable installation of the received package name and version to proceed. The received elem is the
<repository> tag set which defines the complex repository dependency. The received tool_shed_repository
is the installed tool shed repository for which the tool dependency defined by the received package_name
and package_version is being installed.
"""
handled_tool_dependencies = []
tool_shed_url = elem.attrib['toolshed']
required_repository_name = elem.attrib['name']
required_repository_owner = elem.attrib['owner']
default_required_repository_changeset_revision = elem.attrib[
'changeset_revision']
required_repository = get_repository_for_dependency_relationship(
self.app, tool_shed_url, required_repository_name,
required_repository_owner,
default_required_repository_changeset_revision)
tool_shed = remove_protocol_from_tool_shed_url(tool_shed_url)
tmp_filename = None
if required_repository:
required_repository_changeset_revision = required_repository.installed_changeset_revision
# Define the installation directory for the required tool dependency package in the required repository.
required_repository_package_install_dir = \
tool_dependency_util.get_tool_dependency_install_dir(app=self.app,
repository_name=required_repository_name,
repository_owner=required_repository_owner,
repository_changeset_revision=required_repository_changeset_revision,
tool_dependency_type='package',
tool_dependency_name=package_name,
tool_dependency_version=package_version)
# Define this dependent repository's tool dependency installation directory that will contain
# the env.sh file with a path to the required repository's installed tool dependency package.
dependent_install_dir = \
tool_dependency_util.get_tool_dependency_install_dir(app=self.app,
repository_name=tool_shed_repository.name,
repository_owner=tool_shed_repository.owner,
repository_changeset_revision=tool_shed_repository.installed_changeset_revision,
tool_dependency_type='package',
tool_dependency_name=package_name,
tool_dependency_version=package_version)
if os.path.exists(dependent_install_dir):
# The install manager handles tool migration stages and the sync_database_with_file_system()
# method handles two scenarios: (1) where a Galaxy file system environment related to installed
# Tool Shed repositories and tool dependencies has somehow gotten out of sync with the Galaxy
# database tables associated with these installed items, and (2) the Tool Shed's install and test
# framework which installs repositories in 2 stages, those of type tool_dependency_definition
# followed by those containing valid tools and tool functional test components. Neither of these
# scenarios apply when the install manager is running.
if from_tool_migration_manager:
can_install_tool_dependency = True
else:
# Notice that we'll throw away the following tool_dependency if it can be installed.
tool_dependency, can_install_tool_dependency = self.sync_database_with_file_system(
self.app,
tool_shed_repository,
package_name,
package_version,
dependent_install_dir,
tool_dependency_type='package')
if not can_install_tool_dependency:
log.debug(
"Tool dependency %s version %s cannot be installed (it was probably previously installed), "
"so appending it to the list of handled tool dependencies.",
str(tool_dependency.name),
str(tool_dependency.version))
handled_tool_dependencies.append(tool_dependency)
else:
can_install_tool_dependency = True
if can_install_tool_dependency:
# Set this dependent repository's tool dependency env.sh file with a path to the required repository's
# installed tool dependency package. We can get everything we need from the discovered installed
# required_repository.
if required_repository.is_deactivated_or_installed:
if not os.path.exists(
required_repository_package_install_dir):
log.error(
f'Missing required tool dependency directory {str(required_repository_package_install_dir)}'
)
repo_files_dir = required_repository.repo_files_directory(
self.app)
if not repo_files_dir:
message = "Unable to locate the repository directory for revision %s of installed repository %s owned by %s." % \
(str(required_repository.changeset_revision), str(required_repository.name), str(required_repository.owner))
raise Exception(message)
tool_dependencies_config = get_absolute_path_to_file_in_repository(
repo_files_dir, 'tool_dependencies.xml')
if tool_dependencies_config:
config_to_use = tool_dependencies_config
else:
message = "Unable to locate required tool_dependencies.xml file for revision %s of installed repository %s owned by %s." % \
(str(required_repository.changeset_revision), str(required_repository.name), str(required_repository.owner))
raise Exception(message)
else:
# Make a call to the tool shed to get the changeset revision to which the current value of required_repository_changeset_revision
# should be updated if it's not current.
text = get_updated_changeset_revisions_from_tool_shed(
app=self.app,
tool_shed_url=tool_shed,
name=required_repository_name,
owner=required_repository_owner,
changeset_revision=
required_repository_changeset_revision)
if text:
updated_changeset_revisions = listify(text)
# The list of changeset revisions is in reverse order, so the newest will be first.
required_repository_changeset_revision = updated_changeset_revisions[
0]
# Make a call to the tool shed to get the required repository's tool_dependencies.xml file.
tmp_filename = self.create_temporary_tool_dependencies_config(
tool_shed, required_repository_name,
required_repository_owner,
required_repository_changeset_revision)
config_to_use = tmp_filename
handled_tool_dependencies = \
self.create_tool_dependency_with_initialized_env_sh_file(dependent_install_dir=dependent_install_dir,
tool_shed_repository=tool_shed_repository,
required_repository=required_repository,
package_name=package_name,
package_version=package_version,
tool_dependencies_config=config_to_use)
self.remove_file(tmp_filename)
else:
message = "Unable to locate required tool shed repository named %s owned by %s with revision %s." % \
(str(required_repository_name), str(required_repository_owner), str(default_required_repository_changeset_revision))
raise Exception(message)
return handled_tool_dependencies
def process_tag_set(self,
tool_shed_repository,
tool_dependency,
package_elem,
package_name,
package_version,
from_tool_migration_manager=False,
tool_dependency_db_records=None):
# <install version="1.0">
# Get the installation directory for tool dependencies that will be installed for the received tool_shed_repository.
actions_elem_tuples = []
proceed_with_install = False
install_dir = \
tool_dependency_util.get_tool_dependency_install_dir(app=self.app,
repository_name=tool_shed_repository.name,
repository_owner=tool_shed_repository.owner,
repository_changeset_revision=tool_shed_repository.installed_changeset_revision,
tool_dependency_type='package',
tool_dependency_name=package_name,
tool_dependency_version=package_version)
if os.path.exists(install_dir):
# The tool_migration_manager handles tool migration stages and the sync_database_with_file_system()
# method handles two scenarios: (1) where a Galaxy file system environment related to installed
# Tool Shed repositories and tool dependencies has somehow gotten out of sync with the Galaxy
# database tables associated with these installed items, and (2) the Tool Shed's install and test
# framework which installs repositories in 2 stages, those of type tool_dependency_definition
# followed by those containing valid tools and tool functional test components. Neither of these
# scenarios apply when the install manager is running.
if from_tool_migration_manager:
proceed_with_install = True
else:
# Notice that we'll throw away the following tool_dependency if it can be installed.
tool_dependency, proceed_with_install = self.sync_database_with_file_system(
self.app,
tool_shed_repository,
package_name,
package_version,
install_dir,
tool_dependency_type='package')
if not proceed_with_install:
log.debug(
"Tool dependency %s version %s cannot be installed (it was probably previously installed), so returning it."
% (str(tool_dependency.name),
str(tool_dependency.version)))
return tool_dependency, proceed_with_install, actions_elem_tuples
else:
proceed_with_install = True
if proceed_with_install:
package_install_version = package_elem.get('version', '1.0')
status = self.app.install_model.ToolDependency.installation_status.INSTALLING
tool_dependency = \
tool_dependency_util.create_or_update_tool_dependency(app=self.app,
tool_shed_repository=tool_shed_repository,
name=package_name,
version=package_version,
type='package',
status=status,
set_status=True)
# Get the information about the current platform in case the tool dependency definition includes tag sets
# for installing compiled binaries.
platform_info_dict = tool_dependency_util.get_platform_info_dict()
if package_install_version == '1.0':
# Handle tool dependency installation using a fabric method included in the Galaxy framework.
actions_elem_tuples = tool_dependency_util.parse_package_elem(
package_elem,
platform_info_dict=platform_info_dict,
include_after_install_actions=True)
if not actions_elem_tuples:
proceed_with_install = False
error_message = f'Version {str(package_version)} of the {str(package_name)} package cannot be installed because '
error_message += 'the recipe for installing the package is missing either an <actions> tag set or an <actions_group> '
error_message += 'tag set.'
# Since there was an installation error, update the tool dependency status to Error.
# The remove_installation_path option must be left False here.
tool_dependency = tool_dependency_util.set_tool_dependency_attributes(
self.app,
tool_dependency=tool_dependency,
status=self.app.install_model.ToolDependency.
installation_status.ERROR,
error_message=error_message)
else:
raise NotImplementedError(
'Only install version 1.0 is currently supported (i.e., change your tag to be <install version="1.0">).'
)
return tool_dependency, proceed_with_install, actions_elem_tuples
