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"
}
- 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 = suc.get_repository_by_name_and_owner( trans.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 = suc.get_repository_metadata_by_changeset_revision( trans.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( trans.app, repository=repository, repo_path=None, create=False )
new_changeset_revision = suc.get_next_downloadable_changeset_revision( repository, repo, changeset_revision )
repository_metadata = suc.get_repository_metadata_by_changeset_revision( trans.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 )
# 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( trans.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 {}, {}, {}
def show_tools(self, trans, id, changeset, **kwd):
repository_metadata = metadata_util.get_repository_metadata_by_changeset_revision(self.app, id, changeset)
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, id, changeset
)
return repository_metadata_dict
else:
log.debug(
"Unable to locate repository_metadata record for repository id %s and changeset_revision %s"
% (str(id), str(changeset))
)
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"
}
- 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 = suc.get_repository_by_name_and_owner(
trans.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 = suc.get_repository_metadata_by_changeset_revision(
trans.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(trans.app,
repository=repository,
repo_path=None,
create=False)
new_changeset_revision = suc.get_next_downloadable_changeset_revision(
repository, repo, changeset_revision)
repository_metadata = suc.get_repository_metadata_by_changeset_revision(
trans.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)
# 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( trans.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 {}, {}, {}
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 {}, {}, {}
