def get_tool_dependencies( self, app, changeset_revision ):
repo = hg.repository( ui.ui(), self.repo_path( app ) )
changeset_revision = metadata_util.get_next_downloadable_changeset_revision( self, repo, changeset_revision )
for downloadable_revision in self.downloadable_revisions:
if downloadable_revision.changeset_revision == changeset_revision:
return downloadable_revision.metadata.get( 'tool_dependencies', {} )
return {}
def get_tool_dependencies(self, app, changeset_revision):
repo = hg.repository(ui.ui(), self.repo_path(app))
changeset_revision = metadata_util.get_next_downloadable_changeset_revision(self, repo, changeset_revision)
for downloadable_revision in self.downloadable_revisions:
if downloadable_revision.changeset_revision == changeset_revision:
return downloadable_revision.metadata.get('tool_dependencies', {})
return {}
def get_tool_dependencies(self, app, changeset_revision):
changeset_revision = metadata_util.get_next_downloadable_changeset_revision(
app, self, changeset_revision)
for downloadable_revision in self.downloadable_revisions:
if downloadable_revision.changeset_revision == changeset_revision:
return downloadable_revision.metadata.get(
'tool_dependencies', {})
return {}
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
def repository_dependencies(self, trans, id, **kwd):
"""
GET /api/repository_revisions/{encoded repository_metadata id}/repository_dependencies
Returns a list of dictionaries that each define a specific downloadable revision of a
repository in the Tool Shed. This method returns dictionaries with more information in
them than other methods in this controller. The information about repository_metdata is
enhanced to include information about the repository (e.g., name, owner, etc) associated
with the repository_metadata record.
:param id: the encoded id of the `RepositoryMetadata` object
"""
# Example URL: http://localhost:9009/api/repository_revisions/repository_dependencies/bb125606ff9ea620
repository_dependencies_dicts = []
repository_metadata = metadata_util.get_repository_metadata_by_id(trans.app, id)
if repository_metadata is None:
log.debug('Invalid repository_metadata id received: %s' % str(id))
return repository_dependencies_dicts
metadata = repository_metadata.metadata
if metadata is None:
log.debug('The repository_metadata record with id %s has no metadata.' % str(id))
return repository_dependencies_dicts
if 'repository_dependencies' in metadata:
rd_tups = metadata['repository_dependencies']['repository_dependencies']
for rd_tup in rd_tups:
tool_shed, name, owner, changeset_revision = rd_tup[0:4]
repository_dependency = repository_util.get_repository_by_name_and_owner(trans.app, name, owner)
if repository_dependency is None:
log.dbug('Cannot locate repository dependency %s owned by %s.' % (name, owner))
continue
repository_dependency_id = trans.security.encode_id(repository_dependency.id)
repository_dependency_repository_metadata = \
metadata_util.get_repository_metadata_by_changeset_revision(trans.app, repository_dependency_id, changeset_revision)
if repository_dependency_repository_metadata is None:
# The changeset_revision column in the repository_metadata table has been updated with a new
# value value, so find the changeset_revision to which we need to update.
repo = hg_util.get_repo_for_repository(trans.app,
repository=repository_dependency,
repo_path=None,
create=False)
new_changeset_revision = metadata_util.get_next_downloadable_changeset_revision(repository_dependency,
repo,
changeset_revision)
if new_changeset_revision != changeset_revision:
repository_dependency_repository_metadata = \
metadata_util.get_repository_metadata_by_changeset_revision(trans.app,
repository_dependency_id,
new_changeset_revision)
changeset_revision = new_changeset_revision
else:
decoded_repository_dependency_id = trans.security.decode_id(repository_dependency_id)
debug_msg = 'Cannot locate repository_metadata with id %d for repository dependency %s owned by %s ' % \
(decoded_repository_dependency_id, str(name), str(owner))
debug_msg += 'using either of these changeset_revisions: %s, %s.' % \
(str(changeset_revision), str(new_changeset_revision))
log.debug(debug_msg)
continue
repository_dependency_metadata_dict = \
repository_dependency_repository_metadata.to_dict(view='element',
value_mapper=self.__get_value_mapper(trans))
repository_dependency_dict = repository_dependency.to_dict(view='element',
value_mapper=self.__get_value_mapper(trans))
# We need to be careful with the entries in our repository_dependency_dict here since this Tool Shed API
# controller is working with repository_metadata records. The above to_dict() method returns a dictionary
# with an id entry for the repository record. However, all of the other methods in this controller have
# the id entry associated with a repository_metadata record id. To avoid confusion, we'll update the
# repository_dependency_metadata_dict with entries from the repository_dependency_dict without using the
# Python dictionary update() method because we do not want to overwrite existing entries.
for k, v in repository_dependency_dict.items():
if k not in repository_dependency_metadata_dict:
repository_dependency_metadata_dict[k] = v
repository_dependency_metadata_dict['url'] = web.url_for(controller='repositories',
action='show',
id=repository_dependency_id)
repository_dependencies_dicts.append(repository_dependency_metadata_dict)
return repository_dependencies_dicts
def repository_dependencies(self, trans, id, **kwd):
"""
GET /api/repository_revisions/{encoded repository_metadata id}/repository_dependencies
Returns a list of dictionaries that each define a specific downloadable revision of a
repository in the Tool Shed. This method returns dictionaries with more information in
them than other methods in this controller. The information about repository_metdata is
enhanced to include information about the repository (e.g., name, owner, etc) associated
with the repository_metadata record.
:param id: the encoded id of the `RepositoryMetadata` object
"""
# Example URL: http://localhost:9009/api/repository_revisions/repository_dependencies/bb125606ff9ea620
repository_dependencies_dicts = []
repository_metadata = metadata_util.get_repository_metadata_by_id(
trans.app, id)
if repository_metadata is None:
log.debug('Invalid repository_metadata id received: %s' % str(id))
return repository_dependencies_dicts
metadata = repository_metadata.metadata
if metadata is None:
log.debug(
'The repository_metadata record with id %s has no metadata.' %
str(id))
return repository_dependencies_dicts
if 'repository_dependencies' in metadata:
rd_tups = metadata['repository_dependencies'][
'repository_dependencies']
for rd_tup in rd_tups:
tool_shed, name, owner, changeset_revision = rd_tup[0:4]
repository_dependency = repository_util.get_repository_by_name_and_owner(
trans.app, name, owner)
if repository_dependency is None:
log.dbug(
'Cannot locate repository dependency %s owned by %s.' %
(name, owner))
continue
repository_dependency_id = trans.security.encode_id(
repository_dependency.id)
repository_dependency_repository_metadata = \
metadata_util.get_repository_metadata_by_changeset_revision(trans.app, repository_dependency_id, changeset_revision)
if repository_dependency_repository_metadata is None:
# The changeset_revision column in the repository_metadata table has been updated with a new
# value value, so find the changeset_revision to which we need to update.
new_changeset_revision = metadata_util.get_next_downloadable_changeset_revision(
trans.app, repository_dependency, changeset_revision)
if new_changeset_revision != changeset_revision:
repository_dependency_repository_metadata = \
metadata_util.get_repository_metadata_by_changeset_revision(trans.app,
repository_dependency_id,
new_changeset_revision)
changeset_revision = new_changeset_revision
else:
decoded_repository_dependency_id = trans.security.decode_id(
repository_dependency_id)
debug_msg = 'Cannot locate repository_metadata with id %d for repository dependency %s owned by %s ' % \
(decoded_repository_dependency_id, str(name), str(owner))
debug_msg += 'using either of these changeset_revisions: %s, %s.' % \
(str(changeset_revision), str(new_changeset_revision))
log.debug(debug_msg)
continue
repository_dependency_metadata_dict = \
repository_dependency_repository_metadata.to_dict(view='element',
value_mapper=self.__get_value_mapper(trans))
repository_dependency_dict = repository_dependency.to_dict(
view='element',
value_mapper=self.__get_value_mapper(trans))
# We need to be careful with the entries in our repository_dependency_dict here since this Tool Shed API
# controller is working with repository_metadata records. The above to_dict() method returns a dictionary
# with an id entry for the repository record. However, all of the other methods in this controller have
# the id entry associated with a repository_metadata record id. To avoid confusion, we'll update the
# repository_dependency_metadata_dict with entries from the repository_dependency_dict without using the
# Python dictionary update() method because we do not want to overwrite existing entries.
for k, v in repository_dependency_dict.items():
if k not in repository_dependency_metadata_dict:
repository_dependency_metadata_dict[k] = v
repository_dependency_metadata_dict['url'] = web.url_for(
controller='repositories',
action='show',
id=repository_dependency_id)
repository_dependencies_dicts.append(
repository_dependency_metadata_dict)
return repository_dependencies_dicts
def get_updated_changeset_revisions_for_repository_dependencies(self, key_rd_dicts):
updated_key_rd_dicts = []
for key_rd_dict in key_rd_dicts:
key = next(iter(key_rd_dict))
repository_dependency = key_rd_dict[key]
rd_toolshed, rd_name, rd_owner, rd_changeset_revision, \
rd_prior_installation_required, \
rd_only_if_compiling_contained_td = \
common_util.parse_repository_dependency_tuple(repository_dependency)
if suc.tool_shed_is_this_tool_shed(rd_toolshed):
repository = tool_shed.util.repository_util.get_repository_by_name_and_owner(self.app, rd_name, rd_owner)
if repository:
repository_id = self.app.security.encode_id(repository.id)
repository_metadata = \
metadata_util.get_repository_metadata_by_repository_id_changeset_revision(self.app,
repository_id,
rd_changeset_revision)
if repository_metadata:
# The repository changeset_revision is installable, so no updates are available.
new_key_rd_dict = {}
new_key_rd_dict[key] = repository_dependency
updated_key_rd_dicts.append(key_rd_dict)
else:
# The repository changeset_revision is no longer installable, so see if there's been an update.
changeset_revision = metadata_util.get_next_downloadable_changeset_revision(self.app, repository, rd_changeset_revision)
if changeset_revision != rd_changeset_revision:
repository_metadata = \
metadata_util.get_repository_metadata_by_repository_id_changeset_revision(self.app,
repository_id,
changeset_revision)
if repository_metadata:
new_key_rd_dict = {}
new_key_rd_dict[key] = \
[rd_toolshed,
rd_name,
rd_owner,
repository_metadata.changeset_revision,
rd_prior_installation_required,
rd_only_if_compiling_contained_td]
# We have the updated changeset revision.
updated_key_rd_dicts.append(new_key_rd_dict)
else:
repository_components_tuple = container_util.get_components_from_key(key)
components_list = tool_shed.util.repository_util.extract_components_from_tuple(repository_components_tuple)
toolshed, repository_name, repository_owner, repository_changeset_revision = components_list[0:4]
# For backward compatibility to the 12/20/12 Galaxy release.
if len(components_list) in (4, 5):
rd_only_if_compiling_contained_td = 'False'
message = "The revision %s defined for repository %s owned by %s is invalid, so repository " % \
(str(rd_changeset_revision), str(rd_name), str(rd_owner))
message += "dependencies defined for repository %s will be ignored." % str(repository_name)
log.debug(message)
else:
repository_components_tuple = container_util.get_components_from_key(key)
components_list = tool_shed.util.repository_util.extract_components_from_tuple(repository_components_tuple)
toolshed, repository_name, repository_owner, repository_changeset_revision = components_list[0:4]
message = "The revision %s defined for repository %s owned by %s is invalid, so repository " % \
(str(rd_changeset_revision), str(rd_name), str(rd_owner))
message += "dependencies defined for repository %s will be ignored." % str(repository_name)
log.debug(message)
return updated_key_rd_dicts
def get_updated_changeset_revisions_for_repository_dependencies( self, key_rd_dicts ):
updated_key_rd_dicts = []
for key_rd_dict in key_rd_dicts:
key = next(iter(key_rd_dict))
repository_dependency = key_rd_dict[ key ]
rd_toolshed, rd_name, rd_owner, rd_changeset_revision, \
rd_prior_installation_required, \
rd_only_if_compiling_contained_td = \
common_util.parse_repository_dependency_tuple( repository_dependency )
if suc.tool_shed_is_this_tool_shed( rd_toolshed ):
repository = tool_shed.util.repository_util.get_repository_by_name_and_owner( self.app, rd_name, rd_owner )
if repository:
repository_id = self.app.security.encode_id( repository.id )
repository_metadata = \
metadata_util.get_repository_metadata_by_repository_id_changeset_revision( self.app,
repository_id,
rd_changeset_revision )
if repository_metadata:
# The repository changeset_revision is installable, so no updates are available.
new_key_rd_dict = {}
new_key_rd_dict[ key ] = repository_dependency
updated_key_rd_dicts.append( key_rd_dict )
else:
# The repository changeset_revision is no longer installable, so see if there's been an update.
repo = hg_util.get_repo_for_repository( self.app, repository=repository, repo_path=None, create=False )
changeset_revision = metadata_util.get_next_downloadable_changeset_revision( repository, repo, rd_changeset_revision )
if changeset_revision != rd_changeset_revision:
repository_metadata = \
metadata_util.get_repository_metadata_by_repository_id_changeset_revision( self.app,
repository_id,
changeset_revision )
if repository_metadata:
new_key_rd_dict = {}
new_key_rd_dict[ key ] = \
[ rd_toolshed,
rd_name,
rd_owner,
repository_metadata.changeset_revision,
rd_prior_installation_required,
rd_only_if_compiling_contained_td ]
# We have the updated changeset revision.
updated_key_rd_dicts.append( new_key_rd_dict )
else:
repository_components_tuple = container_util.get_components_from_key( key )
components_list = tool_shed.util.repository_util.extract_components_from_tuple( repository_components_tuple )
toolshed, repository_name, repository_owner, repository_changeset_revision = components_list[ 0:4 ]
# For backward compatibility to the 12/20/12 Galaxy release.
if len( components_list ) in (4, 5):
rd_only_if_compiling_contained_td = 'False'
message = "The revision %s defined for repository %s owned by %s is invalid, so repository " % \
( str( rd_changeset_revision ), str( rd_name ), str( rd_owner ) )
message += "dependencies defined for repository %s will be ignored." % str( repository_name )
log.debug( message )
else:
repository_components_tuple = container_util.get_components_from_key( key )
components_list = tool_shed.util.repository_util.extract_components_from_tuple( repository_components_tuple )
toolshed, repository_name, repository_owner, repository_changeset_revision = components_list[ 0:4 ]
message = "The revision %s defined for repository %s owned by %s is invalid, so repository " % \
( str( rd_changeset_revision ), str( rd_name ), str( rd_owner ) )
message += "dependencies defined for repository %s will be ignored." % str( repository_name )
log.debug( message )
return updated_key_rd_dicts
def get_tool_dependencies(self, app, changeset_revision):
changeset_revision = metadata_util.get_next_downloadable_changeset_revision(app, self, changeset_revision)
for downloadable_revision in self.downloadable_revisions:
if downloadable_revision.changeset_revision == changeset_revision:
return downloadable_revision.metadata.get('tool_dependencies', {})
return {}
def get_repository_revision_install_info(self, trans, name, owner, changeset_revision, **kwd):
"""
GET /api/repositories/get_repository_revision_install_info
:param name: the name of the Repository
:param owner: the owner of the Repository
:param changeset_revision: the changeset_revision of the RepositoryMetadata object associated with the Repository
Returns a list of the following dictionaries::
- a dictionary defining the Repository. For example:
{
"deleted": false,
"deprecated": false,
"description": "add_column hello",
"id": "f9cad7b01a472135",
"long_description": "add_column hello",
"name": "add_column",
"owner": "test",
"private": false,
"times_downloaded": 6,
"url": "/api/repositories/f9cad7b01a472135",
"user_id": "f9cad7b01a472135"
}
- a dictionary defining the Repository revision (RepositoryMetadata). For example:
{
"changeset_revision": "3a08cc21466f",
"downloadable": true,
"has_repository_dependencies": false,
"has_repository_dependencies_only_if_compiling_contained_td": false,
"id": "f9cad7b01a472135",
"includes_datatypes": false,
"includes_tool_dependencies": false,
"includes_tools": true,
"includes_tools_for_display_in_tool_panel": true,
"includes_workflows": false,
"malicious": false,
"repository_id": "f9cad7b01a472135",
"url": "/api/repository_revisions/f9cad7b01a472135",
"valid_tools": [{u'add_to_tool_panel': True,
u'description': u'data on any column using simple expressions',
u'guid': u'localhost:9009/repos/enis/sample_repo_1/Filter1/2.2.0',
u'id': u'Filter1',
u'name': u'Filter',
u'requirements': [],
u'tests': [{u'inputs': [[u'input', u'1.bed'], [u'cond', u"c1=='chr22'"]],
u'name': u'Test-1',
u'outputs': [[u'out_file1', u'filter1_test1.bed']],
u'required_files': [u'1.bed', u'filter1_test1.bed']}],
u'tool_config': u'database/community_files/000/repo_1/filtering.xml',
u'tool_type': u'default',
u'version': u'2.2.0',
u'version_string_cmd': None}]
}
- a dictionary including the additional information required to install the repository. For example:
{
"add_column": [
"add_column hello",
"http://test@localhost:9009/repos/test/add_column",
"3a08cc21466f",
"1",
"test",
{},
{}
]
}
"""
# Example URL:
# http://<xyz>/api/repositories/get_repository_revision_install_info?name=<n>&owner=<o>&changeset_revision=<cr>
if name and owner and changeset_revision:
# Get the repository information.
repository = repository_util.get_repository_by_name_and_owner(self.app, name, owner)
if repository is None:
log.debug("Cannot locate repository %s owned by %s" % (str(name), str(owner)))
return {}, {}, {}
encoded_repository_id = trans.security.encode_id(repository.id)
repository_dict = repository.to_dict(view="element", value_mapper=self.__get_value_mapper(trans))
repository_dict["url"] = web.url_for(controller="repositories", action="show", id=encoded_repository_id)
# Get the repository_metadata information.
repository_metadata = metadata_util.get_repository_metadata_by_changeset_revision(
self.app, encoded_repository_id, changeset_revision
)
if repository_metadata is None:
# The changeset_revision column in the repository_metadata table has been updated with a new
# value value, so find the changeset_revision to which we need to update.
repo = hg_util.get_repo_for_repository(self.app, repository=repository, repo_path=None, create=False)
new_changeset_revision = metadata_util.get_next_downloadable_changeset_revision(
repository, repo, changeset_revision
)
repository_metadata = metadata_util.get_repository_metadata_by_changeset_revision(
self.app, encoded_repository_id, new_changeset_revision
)
changeset_revision = new_changeset_revision
if repository_metadata is not None:
encoded_repository_metadata_id = trans.security.encode_id(repository_metadata.id)
repository_metadata_dict = repository_metadata.to_dict(
view="collection", value_mapper=self.__get_value_mapper(trans)
)
repository_metadata_dict["url"] = web.url_for(
controller="repository_revisions", action="show", id=encoded_repository_metadata_id
)
if "tools" in repository_metadata.metadata:
repository_metadata_dict["valid_tools"] = repository_metadata.metadata["tools"]
# Get the repo_info_dict for installing the repository.
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 = repository_util.get_repo_info_dict(
self.app, trans.user, encoded_repository_id, changeset_revision
)
return repository_dict, repository_metadata_dict, repo_info_dict
else:
log.debug(
"Unable to locate repository_metadata record for repository id %s and changeset_revision %s"
% (str(repository.id), str(changeset_revision))
)
return repository_dict, {}, {}
else:
debug_msg = "Error in the Tool Shed repositories API in get_repository_revision_install_info: "
debug_msg += "Invalid name %s or owner %s or changeset_revision %s received." % (
str(name),
str(owner),
str(changeset_revision),
)
log.debug(debug_msg)
return {}, {}, {}
