def repository_spec_from_find_results(find_results, requirement_spec):
'''Create a new RepositorySpec with updated info from fetch_results.
Evolves repository_spec to match fetch results.'''
# TODO: do we still need to check the fetched version against the spec version?
# We do, since the unspecific version is None, so fetched versions wont match
# so we need a new repository_spec for install.
# TODO: this is more or less a verify/validate step or state transition
content_data = find_results.get('content', {})
resolved_version = content_data.get('version')
log.debug(
'version_spec "%s" for %s was requested and was resolved to version "%s"',
requirement_spec.version_spec, requirement_spec.label,
resolved_version)
# In theory, a fetch can return a different namespace/name than the one request. This
# is for things like server side aliases.
resolved_name = content_data.get('fetched_name', requirement_spec.name)
resolved_namespace = content_data.get('content_namespace',
requirement_spec.namespace)
# Build a RepositorySpec based on RequirementSpec and the extra info resolved in find()
spec_data = attr.asdict(requirement_spec)
del spec_data['version_spec']
spec_data['version'] = resolved_version
spec_data['namespace'] = resolved_namespace
spec_data['name'] = resolved_name
repository_spec = RepositorySpec.from_dict(spec_data)
return repository_spec
def load(data_or_file_object, repository_spec=None):
log.debug('START of load of requirements %s', data_or_file_object.name)
requirements_data = yaml.safe_load(data_or_file_object)
# log.debug('requirements_data: %s', pprint.pformat(requirements_data))
requirements_list = []
for req_data_item in requirements_data:
# log.debug('req_data_item: %s', req_data_item)
# log.debug('type(req_data_item): %s', type(req_data_item))
req_spec_data = yaml_parse.yaml_parse(req_data_item)
# log.debug('req_spec_data: %s', req_spec_data)
# name_info = content_name.parse_content_name(data_name)
# log.debug('data_name (after): %s', data_name)
# log.debug('name_info: %s', name_info)
req_spec = RepositorySpec.from_dict(req_spec_data)
# log.debug('req_spec: %s', req_spec)
req = Requirement(repository_spec=repository_spec,
op=RequirementOps.EQ,
requirement_spec=req_spec)
# log.debug('req: %s', req)
requirements_list.append(req)
log.debug('FINISH of load of requirements: %s: %s',
data_or_file_object.name, requirements_list)
return requirements_list
def from_dependency_spec_strings(dependency_spec_strings, namespace_override=None, editable=False):
deps = []
for dep_spec_string in dependency_spec_strings:
dep_spec_data = spec_data_from_string(dep_spec_string)
log.debug('dep_spec_data: %s', dep_spec_data)
dep_spec = RepositorySpec.from_dict(dep_spec_data)
log.debug('dep_spec: %s', dep_spec)
# Add a requirement, but with the 'RUNTIME' scope
requirement = Requirement(repository_spec=None, op=RequirementOps.EQ,
scope=RequirementScopes.RUNTIME,
requirement_spec=dep_spec)
deps.append(requirement)
return deps
def from_requirement_spec_strings(requirement_spec_strings,
namespace_override=None,
editable=False,
repository_spec=None):
reqs = []
for requirement_spec_string in requirement_spec_strings:
req_spec_data = spec_data_from_string(
requirement_spec_string,
namespace_override=namespace_override,
editable=editable)
req_spec = RepositorySpec.from_dict(req_spec_data)
req = Requirement(repository_spec=repository_spec,
op=RequirementOps.EQ,
requirement_spec=req_spec)
reqs.append(req)
return reqs
def install_repository_specs_loop(
galaxy_context,
repository_spec_strings=None,
requirements_list=None,
editable=False,
namespace_override=None,
display_callback=None,
# TODO: error handling callback ?
ignore_errors=False,
no_deps=False,
force_overwrite=False):
requirements_list = requirements_list or []
for repository_spec_string in repository_spec_strings:
fetch_method = \
repository_spec.choose_repository_fetch_method(repository_spec_string,
editable=editable)
log.debug('fetch_method: %s', fetch_method)
if fetch_method == FetchMethods.LOCAL_FILE:
# Since only know this is a local file we vaguely recognize, we have to
# open it up to get any more details. We _could_ attempt to parse the file
# name, but that rarely ends well...
spec_data = collection_artifact.load_data_from_collection_artifact(
repository_spec_string)
spec_data['fetch_method'] = fetch_method
else:
spec_data = repository_spec.spec_data_from_string(
repository_spec_string,
namespace_override=namespace_override,
editable=editable)
spec_data['fetch_method'] = fetch_method
log.debug('spec_data: %s', spec_data)
req_spec = RepositorySpec.from_dict(spec_data)
req = Requirement(repository_spec=None,
op=RequirementOps.EQ,
requirement_spec=req_spec)
requirements_list.append(req)
log.debug('requirements_list: %s', requirements_list)
for req in requirements_list:
display_callback('Installing %s' % req.requirement_spec.label,
level='info')
while True:
if not requirements_list:
break
just_installed_repositories = \
install_repositories_matching_repository_specs(galaxy_context,
requirements_list,
editable=editable,
namespace_override=namespace_override,
display_callback=display_callback,
ignore_errors=ignore_errors,
no_deps=no_deps,
force_overwrite=force_overwrite)
# set the repository_specs to search for to whatever the install reported as being needed yet
# requirements_list = new_requirements_list
requirements_list = find_new_deps_from_installed(
galaxy_context, just_installed_repositories, no_deps=no_deps)
for req in requirements_list:
if req.repository_spec:
msg = 'Installing requirement %s (required by %s)' % (
req.requirement_spec.label, req.repository_spec.label)
else:
msg = 'Installing requirement %s' % req.requirement_spec.label
display_callback(msg, level='info')
# FIXME: what results to return?
return 0