def __api_import_new_workflow(self, trans, payload, **kwd):
data = payload['workflow']
raw_workflow_description = self.__normalize_workflow(trans, data)
data = raw_workflow_description.as_dict
import_tools = util.string_as_bool(payload.get("import_tools", False))
if import_tools and not trans.user_is_admin:
raise exceptions.AdminRequiredException()
from_dict_kwds = self.__import_or_update_kwds(payload)
publish = util.string_as_bool(payload.get("publish", False))
# If 'publish' set, default to importable.
importable = util.string_as_bool(payload.get("importable", publish))
if publish and not importable:
raise exceptions.RequestParameterInvalidException("Published workflow must be importable.")
from_dict_kwds["publish"] = publish
workflow, missing_tool_tups = self._workflow_from_dict(trans, raw_workflow_description, **from_dict_kwds)
if importable:
self._make_item_accessible(trans.sa_session, workflow)
trans.sa_session.flush()
# galaxy workflow newly created id
workflow_id = workflow.id
# api encoded, id
encoded_id = trans.security.encode_id(workflow_id)
item = workflow.to_dict(value_mapper={'id': trans.security.encode_id})
item['annotations'] = [x.annotation for x in workflow.annotations]
item['url'] = url_for('workflow', id=encoded_id)
item['owner'] = workflow.user.username
item['number_of_steps'] = len(workflow.latest_workflow.steps)
if import_tools:
tools = {}
for key in data['steps']:
item = data['steps'][key]
if item is not None:
if 'tool_shed_repository' in item:
tool_shed_repository = item['tool_shed_repository']
if 'owner' in tool_shed_repository and 'changeset_revision' in tool_shed_repository and 'name' in tool_shed_repository and 'tool_shed' in tool_shed_repository:
toolstr = tool_shed_repository['owner'] \
+ tool_shed_repository['changeset_revision'] \
+ tool_shed_repository['name'] \
+ tool_shed_repository['tool_shed']
tools[toolstr] = tool_shed_repository
irm = InstallRepositoryManager(self.app)
for k in tools:
item = tools[k]
tool_shed_url = 'https://' + item['tool_shed'] + '/'
name = item['name']
owner = item['owner']
changeset_revision = item['changeset_revision']
irm.install(tool_shed_url,
name,
owner,
changeset_revision,
payload)
return item
def __api_import_new_workflow(self, trans, payload, **kwd):
data = payload['workflow']
raw_workflow_description = self.__normalize_workflow(trans, data)
data = raw_workflow_description.as_dict
import_tools = util.string_as_bool(payload.get("import_tools", False))
if import_tools and not trans.user_is_admin:
raise exceptions.AdminRequiredException()
from_dict_kwds = self.__import_or_update_kwds(payload)
publish = util.string_as_bool(payload.get("publish", False))
# If 'publish' set, default to importable.
importable = util.string_as_bool(payload.get("importable", publish))
if publish and not importable:
raise exceptions.RequestParameterInvalidException("Published workflow must be importable.")
from_dict_kwds["publish"] = publish
workflow, missing_tool_tups = self._workflow_from_dict(trans, raw_workflow_description, **from_dict_kwds)
if importable:
self._make_item_accessible(trans.sa_session, workflow)
trans.sa_session.flush()
# galaxy workflow newly created id
workflow_id = workflow.id
# api encoded, id
encoded_id = trans.security.encode_id(workflow_id)
item = workflow.to_dict(value_mapper={'id': trans.security.encode_id})
item['url'] = url_for('workflow', id=encoded_id)
item['owner'] = workflow.user.username
item['number_of_steps'] = len(workflow.latest_workflow.steps)
if import_tools:
tools = {}
for key in data['steps']:
item = data['steps'][key]
if item is not None:
if 'tool_shed_repository' in item:
tool_shed_repository = item['tool_shed_repository']
if 'owner' in tool_shed_repository and 'changeset_revision' in tool_shed_repository and 'name' in tool_shed_repository and 'tool_shed' in tool_shed_repository:
toolstr = tool_shed_repository['owner'] \
+ tool_shed_repository['changeset_revision'] \
+ tool_shed_repository['name'] \
+ tool_shed_repository['tool_shed']
tools[toolstr] = tool_shed_repository
irm = InstallRepositoryManager(self.app)
for k in tools:
item = tools[k]
tool_shed_url = 'https://' + item['tool_shed'] + '/'
name = item['name']
owner = item['owner']
changeset_revision = item['changeset_revision']
irm.install(tool_shed_url,
name,
owner,
changeset_revision,
payload)
return item
def install_repository_revision(self, trans, payload, **kwd):
"""
POST /api/tool_shed_repositories/install_repository_revision
Install a specified repository revision from a specified tool shed into Galaxy.
:param key: the current Galaxy admin user's API key
The following parameters are included in the payload.
:param tool_shed_url (required): the base URL of the Tool Shed from which to install the Repository
:param name (required): the name of the Repository
:param owner (required): the owner of the Repository
:param changeset_revision (required): the changeset_revision of the RepositoryMetadata object associated with the Repository
:param new_tool_panel_section_label (optional): label of a new section to be added to the Galaxy tool panel in which to load
tools contained in the Repository. Either this parameter must be an empty string or
the tool_panel_section_id parameter must be an empty string or both must be an empty
string (both cannot be used simultaneously).
:param tool_panel_section_id (optional): id of the Galaxy tool panel section in which to load tools contained in the Repository.
If this parameter is an empty string and the above new_tool_panel_section_label parameter is an
empty string, tools will be loaded outside of any sections in the tool panel. Either this
parameter must be an empty string or the tool_panel_section_id parameter must be an empty string
of both must be an empty string (both cannot be used simultaneously).
:param install_repository_dependencies (optional): Set to True if you want to install repository dependencies defined for the specified
repository being installed. The default setting is False.
:param install_tool_dependencies (optional): Set to True if you want to install tool dependencies defined for the specified repository being
installed. The default setting is False.
:param shed_tool_conf (optional): The shed-related tool panel configuration file configured in the "tool_config_file" setting in the Galaxy config file
(e.g., galaxy.ini). At least one shed-related tool panel config file is required to be configured. Setting
this parameter to a specific file enables you to choose where the specified repository will be installed because
the tool_path attribute of the <toolbox> from the specified file is used as the installation location
(e.g., <toolbox tool_path="database/shed_tools">). If this parameter is not set, a shed-related tool panel
configuration file will be selected automatically.
"""
# Get the information about the repository to be installed from the payload.
tool_shed_url, name, owner, changeset_revision = self.__parse_repository_from_payload(
payload, include_changeset=True)
self.__ensure_can_install_repos(trans)
irm = InstallRepositoryManager(self.app)
installed_tool_shed_repositories = irm.install(tool_shed_url, name,
owner,
changeset_revision,
payload)
def to_dict(tool_shed_repository):
tool_shed_repository_dict = tool_shed_repository.as_dict(
value_mapper=self.__get_value_mapper(trans,
tool_shed_repository))
tool_shed_repository_dict['url'] = web.url_for(
controller='tool_shed_repositories',
action='show',
id=trans.security.encode_id(tool_shed_repository.id))
return tool_shed_repository_dict
if installed_tool_shed_repositories:
return list(map(to_dict, installed_tool_shed_repositories))
message = "No repositories were installed, possibly because the selected repository has already been installed."
return dict(status="ok", message=message)
def install_repository_revision( self, trans, payload, **kwd ):
"""
POST /api/tool_shed_repositories/install_repository_revision
Install a specified repository revision from a specified tool shed into Galaxy.
:param key: the current Galaxy admin user's API key
The following parameters are included in the payload.
:param tool_shed_url (required): the base URL of the Tool Shed from which to install the Repository
:param name (required): the name of the Repository
:param owner (required): the owner of the Repository
:param changeset_revision (required): the changeset_revision of the RepositoryMetadata object associated with the Repository
:param new_tool_panel_section_label (optional): label of a new section to be added to the Galaxy tool panel in which to load
tools contained in the Repository. Either this parameter must be an empty string or
the tool_panel_section_id parameter must be an empty string or both must be an empty
string (both cannot be used simultaneously).
:param tool_panel_section_id (optional): id of the Galaxy tool panel section in which to load tools contained in the Repository.
If this parameter is an empty string and the above new_tool_panel_section_label parameter is an
empty string, tools will be loaded outside of any sections in the tool panel. Either this
parameter must be an empty string or the tool_panel_section_id parameter must be an empty string
of both must be an empty string (both cannot be used simultaneously).
:param install_repository_dependencies (optional): Set to True if you want to install repository dependencies defined for the specified
repository being installed. The default setting is False.
:param install_tool_dependencies (optional): Set to True if you want to install tool dependencies defined for the specified repository being
installed. The default setting is False.
:param shed_tool_conf (optional): The shed-related tool panel configuration file configured in the "tool_config_file" setting in the Galaxy config file
(e.g., galaxy.ini). At least one shed-related tool panel config file is required to be configured. Setting
this parameter to a specific file enables you to choose where the specified repository will be installed because
the tool_path attribute of the <toolbox> from the specified file is used as the installation location
(e.g., <toolbox tool_path="../shed_tools">). If this parameter is not set, a shed-related tool panel configuration
file will be selected automatically.
"""
# Get the information about the repository to be installed from the payload.
tool_shed_url, name, owner, changeset_revision = self.__parse_repository_from_payload( payload, include_changeset=True )
self.__ensure_can_install_repos( trans )
irm = InstallRepositoryManager( self.app )
installed_tool_shed_repositories = irm.install( tool_shed_url,
name,
owner,
changeset_revision,
payload )
def to_dict( tool_shed_repository ):
tool_shed_repository_dict = tool_shed_repository.as_dict( value_mapper=self.__get_value_mapper( trans, tool_shed_repository ) )
tool_shed_repository_dict[ 'url' ] = web.url_for( controller='tool_shed_repositories',
action='show',
id=trans.security.encode_id( tool_shed_repository.id ) )
return tool_shed_repository_dict
if installed_tool_shed_repositories:
return map( to_dict, installed_tool_shed_repositories )
message = "No repositories were installed, possibly because the selected repository has already been installed."
return dict( status="ok", message=message )
def install(self, trans, **kwd):
"""
POST /api/tool_shed_repositories/install
Initiate the installation of a repository.
:param install_tool_dependencies: True to install tool dependencies.
:param install_repository_dependencies: True to install repository dependencies.
:param tool_panel_section_id: The unique identifier for an existing tool panel section
:param new_tool_panel_section_label: Create a new tool panel section with this label
:param shed_tool_conf: The shed tool config file to use for this installation
:param tool_shed_url: The URL for the toolshed whence this repository is being installed
:param changeset: The changeset to update to after cloning the repository
"""
params = dict()
irm = InstallRepositoryManager(self.app)
changeset = kwd.get('changeset', None)
tool_shed_url = kwd.get('tool_shed_url', None)
params['name'] = kwd.get('name', None)
params['owner'] = kwd.get('owner', None)
params['tool_panel_section_id'] = kwd.get('tool_panel_section_id',
None)
params['new_tool_panel_section_label'] = kwd.get(
'new_tool_panel_section', None)
params['tool_panel_section_mapping'] = json.loads(
kwd.get('tool_panel_section', '{}'))
params['install_tool_dependencies'] = util.asbool(
kwd.get('install_tool_dependencies', False))
params['install_repository_dependencies'] = util.asbool(
kwd.get('install_repository_dependencies', False))
params['shed_tool_conf'] = kwd.get('shed_tool_conf', None)
params['tool_path'] = suc.get_tool_path_by_shed_tool_conf_filename(
self.app, params['shed_tool_conf'])
try:
tool_shed_repositories = irm.install(tool_shed_url, params['name'],
params['owner'], changeset,
params)
if tool_shed_repositories is None:
message = "No repositories were installed, possibly because the selected repository has already been installed."
return dict(status="ok", message=message)
tsr_ids_for_monitoring = [
trans.security.encode_id(tsr.id)
for tsr in tool_shed_repositories
]
url = web.url_for(
controller='admin_toolshed',
action='monitor_repository_installation',
tool_shed_repository_ids=','.join(tsr_ids_for_monitoring))
return url
except RepositoriesInstalledException as e:
log.exception(e)
return dict(message=e.message, status='error')
def install( self, trans, **kwd ):
"""
POST /api/tool_shed_repositories/install
Initiate the installation of a repository.
:param install_resolver_dependencies: True to install resolvable dependencies.
:param install_tool_dependencies: True to install tool dependencies.
:param install_repository_dependencies: True to install repository dependencies.
:param tool_panel_section_id: The unique identifier for an existing tool panel section
:param new_tool_panel_section_label: Create a new tool panel section with this label
:param shed_tool_conf: The shed tool config file to use for this installation
:param tool_shed_url: The URL for the toolshed whence this repository is being installed
:param changeset: The changeset to update to after cloning the repository
"""
params = dict()
irm = InstallRepositoryManager( self.app )
changeset = kwd.get( 'changeset', None )
tool_shed_url = kwd.get( 'tool_shed_url', None )
params[ 'name' ] = kwd.get( 'name', None )
params[ 'owner' ] = kwd.get( 'owner', None )
params[ 'tool_panel_section_id' ] = kwd.get( 'tool_panel_section_id', None )
params[ 'new_tool_panel_section_label' ] = kwd.get( 'new_tool_panel_section', None )
params[ 'tool_panel_section_mapping' ] = json.loads( kwd.get( 'tool_panel_section', '{}' ) )
params[ 'install_resolver_dependencies' ] = util.asbool( kwd.get( 'install_resolver_dependencies', False ) )
params[ 'install_tool_dependencies' ] = util.asbool( kwd.get( 'install_tool_dependencies', False ) )
params[ 'install_repository_dependencies' ] = util.asbool( kwd.get( 'install_repository_dependencies', False ) )
params[ 'shed_tool_conf' ] = kwd.get( 'shed_tool_conf', None )
params[ 'tool_path' ] = suc.get_tool_path_by_shed_tool_conf_filename( self.app, params[ 'shed_tool_conf' ] )
try:
tool_shed_repositories = irm.install(
tool_shed_url,
params[ 'name' ],
params[ 'owner' ],
changeset,
params
)
if tool_shed_repositories is None:
message = "No repositories were installed, possibly because the selected repository has already been installed."
return dict( status="ok", message=message )
tsr_ids_for_monitoring = [ trans.security.encode_id( tsr.id ) for tsr in tool_shed_repositories ]
url = web.url_for( controller='admin_toolshed', action='monitor_repository_installation', tool_shed_repository_ids=','.join( tsr_ids_for_monitoring ) )
return url
except RepositoriesInstalledException as e:
log.exception( e )
return dict( message=e.message,
status='error' )
def __api_import_new_workflow(self, trans, payload, **kwd):
data = payload['workflow']
import_tools = util.string_as_bool(payload.get("import_tools", False))
if import_tools and not trans.user_is_admin():
raise exceptions.AdminRequiredException()
publish = util.string_as_bool(payload.get("publish", False))
# If 'publish' set, default to importable.
importable = util.string_as_bool(payload.get("importable", publish))
# Galaxy will try to upgrade tool versions that don't match exactly during import,
# this prevents that.
exact_tools = util.string_as_bool(payload.get("exact_tools", False))
if publish and not importable:
raise exceptions.RequestParameterInvalidException("Published workflow must be importable.")
from_dict_kwds = dict(
source="API",
publish=publish,
exact_tools=exact_tools,
)
workflow, missing_tool_tups = self._workflow_from_dict(trans, data, **from_dict_kwds)
if importable:
self._make_item_accessible(trans.sa_session, workflow)
trans.sa_session.flush()
# galaxy workflow newly created id
workflow_id = workflow.id
# api encoded, id
encoded_id = trans.security.encode_id(workflow_id)
# return list
rval = []
item = workflow.to_dict(value_mapper={'id': trans.security.encode_id})
item['url'] = url_for('workflow', id=encoded_id)
item['owner'] = workflow.user.username
item['number_of_steps'] = len(workflow.latest_workflow.steps)
rval.append(item)
#
if import_tools:
tools = {}
for key in data['steps']:
item = data['steps'][key]
if item is not None:
if 'tool_shed_repository' in item:
tool_shed_repository = item['tool_shed_repository']
if 'owner' in tool_shed_repository and 'changeset_revision' in tool_shed_repository and 'name' in tool_shed_repository and 'tool_shed' in tool_shed_repository:
toolstr = tool_shed_repository['owner'] \
+ tool_shed_repository['changeset_revision'] \
+ tool_shed_repository['name'] \
+ tool_shed_repository['tool_shed']
tools[toolstr] = tool_shed_repository
irm = InstallRepositoryManager(self.app)
for k in tools:
item = tools[k]
tool_shed_url = 'https://' + item['tool_shed'] + '/'
name = item['name']
owner = item['owner']
changeset_revision = item['changeset_revision']
irm.install(tool_shed_url,
name,
owner,
changeset_revision,
payload)
return item
def __api_import_new_workflow(self, trans, payload, **kwd):
data = payload['workflow']
import_tools = util.string_as_bool(payload.get("import_tools", False))
if import_tools and not trans.user_is_admin():
raise exceptions.AdminRequiredException()
publish = util.string_as_bool(payload.get("publish", False))
# If 'publish' set, default to importable.
importable = util.string_as_bool(payload.get("importable", publish))
# Galaxy will try to upgrade tool versions that don't match exactly during import,
# this prevents that.
exact_tools = util.string_as_bool(payload.get("exact_tools", False))
if publish and not importable:
raise exceptions.RequestParameterInvalidException(
"Published workflow must be importable.")
from_dict_kwds = dict(
source="API",
publish=publish,
exact_tools=exact_tools,
)
workflow, missing_tool_tups = self._workflow_from_dict(
trans, data, **from_dict_kwds)
if importable:
self._make_item_accessible(trans.sa_session, workflow)
trans.sa_session.flush()
# galaxy workflow newly created id
workflow_id = workflow.id
# api encoded, id
encoded_id = trans.security.encode_id(workflow_id)
# return list
rval = []
item = workflow.to_dict(value_mapper={'id': trans.security.encode_id})
item['url'] = url_for('workflow', id=encoded_id)
item['owner'] = workflow.user.username
item['number_of_steps'] = len(workflow.latest_workflow.steps)
rval.append(item)
#
if import_tools:
tools = {}
for key in data['steps']:
item = data['steps'][key]
if item is not None:
if 'tool_shed_repository' in item:
tool_shed_repository = item['tool_shed_repository']
if 'owner' in tool_shed_repository and 'changeset_revision' in tool_shed_repository and 'name' in tool_shed_repository and 'tool_shed' in tool_shed_repository:
toolstr = tool_shed_repository['owner'] \
+ tool_shed_repository['changeset_revision'] \
+ tool_shed_repository['name'] \
+ tool_shed_repository['tool_shed']
tools[toolstr] = tool_shed_repository
irm = InstallRepositoryManager(self.app)
for k in tools:
item = tools[k]
tool_shed_url = 'https://' + item['tool_shed'] + '/'
name = item['name']
owner = item['owner']
changeset_revision = item['changeset_revision']
irm.install(tool_shed_url, name, owner, changeset_revision,
payload)
return item
