def get_tool_dependencies(app, tool_shed_url, repository_name,
repository_owner, changeset_revision):
tool_dependencies = []
tool_shed_accessible = True
params = dict(name=repository_name,
owner=repository_owner,
changeset_revision=changeset_revision)
pathspec = ['repository', 'get_tool_dependencies']
try:
text = util.url_get(
tool_shed_url,
auth=app.tool_shed_registry.url_auth(tool_shed_url),
pathspec=pathspec,
params=params)
tool_shed_accessible = True
except Exception as e:
tool_shed_accessible = False
log.warning(
"The URL\n%s\nraised the exception:\n%s\n",
util.build_url(tool_shed_url, pathspec=pathspec, params=params), e)
if tool_shed_accessible:
if text:
tool_dependencies_dict = encoding_util.tool_shed_decode(text)
for requirements_dict in tool_dependencies_dict.values():
tool_dependency_name = requirements_dict['name']
tool_dependency_version = requirements_dict['version']
tool_dependency_type = requirements_dict['type']
tool_dependencies.append(
(tool_dependency_name, tool_dependency_version,
tool_dependency_type))
return tool_shed_accessible, tool_dependencies
def get_repository_dependencies(app, tool_shed_url, repository_name,
repository_owner, changeset_revision):
repository_dependencies_dict = {}
tool_shed_accessible = True
params = dict(name=repository_name,
owner=repository_owner,
changeset_revision=changeset_revision)
pathspec = ['repository', 'get_repository_dependencies']
try:
raw_text = util.url_get(
tool_shed_url,
auth=app.tool_shed_registry.url_auth(tool_shed_url),
pathspec=pathspec,
params=params)
tool_shed_accessible = True
except Exception as e:
tool_shed_accessible = False
log.warning(
"The URL\n%s\nraised the exception:\n%s\n",
util.build_url(tool_shed_url, pathspec=pathspec, params=params), e)
if tool_shed_accessible:
if len(raw_text) > 2:
encoded_text = json.loads(util.unicodify(raw_text))
repository_dependencies_dict = encoding_util.tool_shed_decode(
encoded_text)
return tool_shed_accessible, repository_dependencies_dict
def get_repository_dependencies_for_installed_tool_shed_repository(
self, app, repository):
"""
Send a request to the appropriate tool shed to retrieve the dictionary of repository dependencies defined
for the received repository which is installed into Galaxy. This method is called only from Galaxy.
"""
tool_shed_url = common_util.get_tool_shed_url_from_tool_shed_registry(
app, str(repository.tool_shed))
params = dict(name=str(repository.name),
owner=str(repository.owner),
changeset_revision=str(repository.changeset_revision))
pathspec = ['repository', 'get_repository_dependencies']
try:
raw_text = url_get(
tool_shed_url,
password_mgr=app.tool_shed_registry.url_auth(tool_shed_url),
pathspec=pathspec,
params=params)
except Exception:
log.exception(
"Error while trying to get URL: %s",
build_url(tool_shed_url, pathspec=pathspec, params=params))
return ''
if len(raw_text) > 2:
encoded_text = json.loads(raw_text)
text = encoding_util.tool_shed_decode(encoded_text)
else:
text = ''
return text
def get_tool_shed_status_for_installed_repository(app, repository):
"""
Send a request to the tool shed to retrieve information about newer installable repository revisions,
current revision updates, whether the repository revision is the latest downloadable revision, and
whether the repository has been deprecated in the tool shed. The received repository is a ToolShedRepository
object from Galaxy.
"""
tool_shed_url = common_util.get_tool_shed_url_from_tool_shed_registry(app, str(repository.tool_shed))
params = dict(name=repository.name, owner=repository.owner, changeset_revision=repository.changeset_revision)
pathspec = ['repository', 'status_for_installed_repository']
try:
encoded_tool_shed_status_dict = util.url_get(tool_shed_url, password_mgr=app.tool_shed_registry.url_auth(tool_shed_url), pathspec=pathspec, params=params)
tool_shed_status_dict = encoding_util.tool_shed_decode(encoded_tool_shed_status_dict)
return tool_shed_status_dict
except HTTPError as e:
# This should handle backward compatility to the Galaxy 12/20/12 release. We used to only handle updates for an installed revision
# using a boolean value.
log.debug("Error attempting to get tool shed status for installed repository %s: %s\nAttempting older 'check_for_updates' method.\n" %
(str(repository.name), str(e)))
pathspec = ['repository', 'check_for_updates']
params['from_update_manager'] = True
try:
# The value of text will be 'true' or 'false', depending upon whether there is an update available for the installed revision.
text = util.url_get(tool_shed_url, password_mgr=app.tool_shed_registry.url_auth(tool_shed_url), pathspec=pathspec, params=params)
return dict(revision_update=text)
except Exception:
# The required tool shed may be unavailable, so default the revision_update value to 'false'.
return dict(revision_update='false')
except Exception:
log.exception("Error attempting to get tool shed status for installed repository %s", str(repository.name))
return {}
def get_update_to_changeset_revision_and_ctx_rev(self, repository):
"""Return the changeset revision hash to which the repository can be updated."""
changeset_revision_dict = {}
tool_shed_url = get_tool_shed_url_from_tool_shed_registry(
self.app, str(repository.tool_shed))
params = dict(name=str(repository.name),
owner=str(repository.owner),
changeset_revision=str(
repository.installed_changeset_revision))
pathspec = ['repository', 'get_changeset_revision_and_ctx_rev']
try:
encoded_update_dict = util.url_get(
tool_shed_url,
password_mgr=self.app.tool_shed_registry.url_auth(
tool_shed_url),
pathspec=pathspec,
params=params)
if encoded_update_dict:
update_dict = tool_shed_decode(encoded_update_dict)
includes_data_managers = update_dict.get(
'includes_data_managers', False)
includes_datatypes = update_dict.get('includes_datatypes',
False)
includes_tools = update_dict.get('includes_tools', False)
includes_tools_for_display_in_tool_panel = update_dict.get(
'includes_tools_for_display_in_tool_panel', False)
includes_tool_dependencies = update_dict.get(
'includes_tool_dependencies', False)
includes_workflows = update_dict.get('includes_workflows',
False)
has_repository_dependencies = update_dict.get(
'has_repository_dependencies', False)
has_repository_dependencies_only_if_compiling_contained_td = update_dict.get(
'has_repository_dependencies_only_if_compiling_contained_td',
False)
changeset_revision = update_dict.get('changeset_revision',
None)
ctx_rev = update_dict.get('ctx_rev', None)
changeset_revision_dict[
'includes_data_managers'] = includes_data_managers
changeset_revision_dict['includes_datatypes'] = includes_datatypes
changeset_revision_dict['includes_tools'] = includes_tools
changeset_revision_dict[
'includes_tools_for_display_in_tool_panel'] = includes_tools_for_display_in_tool_panel
changeset_revision_dict[
'includes_tool_dependencies'] = includes_tool_dependencies
changeset_revision_dict['includes_workflows'] = includes_workflows
changeset_revision_dict[
'has_repository_dependencies'] = has_repository_dependencies
changeset_revision_dict[
'has_repository_dependencies_only_if_compiling_contained_td'] = has_repository_dependencies_only_if_compiling_contained_td
changeset_revision_dict['changeset_revision'] = changeset_revision
changeset_revision_dict['ctx_rev'] = ctx_rev
except Exception as e:
log.debug(
"Error getting change set revision for update from the tool shed for repository '%s': %s"
% (repository.name, str(e)))
changeset_revision_dict['includes_data_managers'] = False
changeset_revision_dict['includes_datatypes'] = False
changeset_revision_dict['includes_tools'] = False
changeset_revision_dict[
'includes_tools_for_display_in_tool_panel'] = False
changeset_revision_dict['includes_tool_dependencies'] = False
changeset_revision_dict['includes_workflows'] = False
changeset_revision_dict['has_repository_dependencies'] = False
changeset_revision_dict[
'has_repository_dependencies_only_if_compiling_contained_td'] = False
changeset_revision_dict['changeset_revision'] = None
changeset_revision_dict['ctx_rev'] = None
return changeset_revision_dict
def get_required_repo_info_dicts(self, tool_shed_url, repo_info_dicts):
"""
Inspect the list of repo_info_dicts for repository dependencies and append a repo_info_dict for each of
them to the list. All repository_dependency entries in each of the received repo_info_dicts includes
all required repositories, so only one pass through this method is required to retrieve all repository
dependencies.
"""
all_required_repo_info_dict = {}
all_repo_info_dicts = []
if repo_info_dicts:
# We'll send tuples of ( tool_shed, repository_name, repository_owner, changeset_revision ) to the tool
# shed to discover repository ids.
required_repository_tups = []
for repo_info_dict in repo_info_dicts:
if repo_info_dict not in all_repo_info_dicts:
all_repo_info_dicts.append(repo_info_dict)
for repository_name, repo_info_tup in repo_info_dict.items():
description, \
repository_clone_url, \
changeset_revision, \
ctx_rev, \
repository_owner, \
repository_dependencies, \
tool_dependencies = \
repository_util.get_repo_info_tuple_contents(repo_info_tup)
if repository_dependencies:
for key, val in repository_dependencies.items():
if key in ['root_key', 'description']:
continue
repository_components_tuple = get_components_from_key(
key)
components_list = repository_util.extract_components_from_tuple(
repository_components_tuple)
# Skip listing a repository dependency if it is required only to compile a tool dependency
# defined for the dependent repository since in this case, the repository dependency is really
# a dependency of the dependent repository's contained tool dependency, and only if that
# tool dependency requires compilation.
# For backward compatibility to the 12/20/12 Galaxy release.
only_if_compiling_contained_td = 'False'
if len(components_list) == 4:
only_if_compiling_contained_td = 'False'
elif len(components_list) == 5:
only_if_compiling_contained_td = 'False'
if not asbool(only_if_compiling_contained_td):
if components_list not in required_repository_tups:
required_repository_tups.append(
components_list)
for components_list in val:
try:
only_if_compiling_contained_td = components_list[
5]
except IndexError:
only_if_compiling_contained_td = 'False'
# Skip listing a repository dependency if it is required only to compile a tool dependency
# defined for the dependent repository (see above comment).
if not asbool(only_if_compiling_contained_td):
if components_list not in required_repository_tups:
required_repository_tups.append(
components_list)
else:
# We have a single repository with no dependencies.
components_list = [
tool_shed_url, repository_name, repository_owner,
changeset_revision
]
required_repository_tups.append(components_list)
if required_repository_tups:
# The value of required_repository_tups is a list of tuples, so we need to encode it.
encoded_required_repository_tups = []
for required_repository_tup in required_repository_tups:
# Convert every item in required_repository_tup to a string.
required_repository_tup = [
str(item) for item in required_repository_tup
]
encoded_required_repository_tups.append(
encoding_util.encoding_sep.join(
required_repository_tup))
encoded_required_repository_str = encoding_util.encoding_sep2.join(
encoded_required_repository_tups)
encoded_required_repository_str = encoding_util.tool_shed_encode(
encoded_required_repository_str)
if repository_util.is_tool_shed_client(self.app):
# Handle secure / insecure Tool Shed URL protocol changes and port changes.
tool_shed_url = common_util.get_tool_shed_url_from_tool_shed_registry(
self.app, tool_shed_url)
pathspec = ['repository', 'get_required_repo_info_dict']
url = build_url(tool_shed_url, pathspec=pathspec)
# Fix for handling 307 redirect not being handled nicely by urlopen() when the Request() has data provided
try:
url = _urlopen(url).geturl()
except HTTPError as e:
if e.code == 502:
pass
else:
raise
payload = urlencode(
dict(encoded_str=encoded_required_repository_str))
response = _urlopen(url, payload).read()
if response:
try:
required_repo_info_dict = json.loads(
unicodify(response))
except Exception as e:
log.exception(e)
return all_repo_info_dicts
required_repo_info_dicts = []
for k, v in required_repo_info_dict.items():
if k == 'repo_info_dicts':
encoded_dict_strings = required_repo_info_dict[
'repo_info_dicts']
for encoded_dict_str in encoded_dict_strings:
decoded_dict = encoding_util.tool_shed_decode(
encoded_dict_str)
required_repo_info_dicts.append(
decoded_dict)
else:
if k not in all_required_repo_info_dict:
all_required_repo_info_dict[k] = v
else:
if v and not all_required_repo_info_dict[k]:
all_required_repo_info_dict[k] = v
if required_repo_info_dicts:
for required_repo_info_dict in required_repo_info_dicts:
# Each required_repo_info_dict has a single entry, and all_repo_info_dicts is a list
# of dictionaries, each of which has a single entry. We'll check keys here rather than
# the entire dictionary because a dictionary entry in all_repo_info_dicts will include
# lists of discovered repository dependencies, but these lists will be empty in the
# required_repo_info_dict since dependency discovery has not yet been performed for these
# dictionaries.
required_repo_info_dict_key = next(
iter(required_repo_info_dict))
all_repo_info_dicts_keys = [
next(iter(d))
for d in all_repo_info_dicts
]
if required_repo_info_dict_key not in all_repo_info_dicts_keys:
all_repo_info_dicts.append(
required_repo_info_dict)
else:
# required_repo_info_dict_key corresponds to the repo name.
# A single install transaction might require the installation of 2 or more repos
# with the same repo name but different owners or versions.
# Therefore, if required_repo_info_dict_key is already in all_repo_info_dicts,
# check that the tool id is already present. If it is not, we are dealing with the same repo name,
# but a different owner/changeset revision or version and we add the repo to the list of repos to be installed.
tool_id = required_repo_info_dict[
required_repo_info_dict_key][1]
is_present = False
for repo_info_dict in all_repo_info_dicts:
for k, v in repo_info_dict.items():
if required_repo_info_dict_key == k:
if tool_id == v[1]:
is_present = True
break
if not is_present:
all_repo_info_dicts.append(
required_repo_info_dict)
all_required_repo_info_dict[
'all_repo_info_dicts'] = all_repo_info_dicts
return all_required_repo_info_dict
