Source code for galaxy.webapps.galaxy.api.tool_shed_repositories
import logging
from paste.httpexceptions import HTTPBadRequest, HTTPForbidden
from time import strftime
from galaxy import util
from galaxy import web
from galaxy import exceptions
from galaxy.web import _future_expose_api as expose_api
from galaxy.util import json
from galaxy.web.base.controller import BaseAPIController
from tool_shed.galaxy_install.install_manager import InstallRepositoryManager
from tool_shed.galaxy_install.metadata.installed_repository_metadata_manager import InstalledRepositoryMetadataManager
from tool_shed.galaxy_install.repair_repository_manager import RepairRepositoryManager
from tool_shed.util import common_util
from tool_shed.util import encoding_util
from tool_shed.util import hg_util
from tool_shed.util import metadata_util
from tool_shed.util import workflow_util
from tool_shed.util import tool_util
import tool_shed.util.shed_util_common as suc
log = logging.getLogger( __name__ )
[docs]def get_message_for_no_shed_tool_config():
# This Galaxy instance is not configured with a shed-related tool panel configuration file.
message = 'The tool_config_file setting in galaxy.ini must include at least one shed tool configuration file name with a <toolbox> '
message += 'tag that includes a tool_path attribute value which is a directory relative to the Galaxy installation directory in order to '
message += 'automatically install tools from a tool shed into Galaxy (e.g., the file name shed_tool_conf.xml whose <toolbox> tag is '
message += '<toolbox tool_path="../shed_tools">). For details, see the "Installation of Galaxy tool shed repository tools into a local '
message += 'Galaxy instance" section of the Galaxy tool shed wiki at http://wiki.galaxyproject.org/InstallingRepositoriesToGalaxy#'
message += 'Installing_Galaxy_tool_shed_repository_tools_into_a_local_Galaxy_instance.'
return message
[docs]class ToolShedRepositoriesController( BaseAPIController ):
"""RESTful controller for interactions with tool shed repositories."""
def __ensure_can_install_repos( self, trans ):
# Make sure this Galaxy instance is configured with a shed-related tool panel configuration file.
if not suc.have_shed_tool_conf_for_install( trans.app ):
message = get_message_for_no_shed_tool_config()
log.debug( message )
return dict( status='error', error=message )
# Make sure the current user's API key proves he is an admin user in this Galaxy instance.
if not trans.user_is_admin():
raise exceptions.AdminRequiredException( 'You are not authorized to request the latest installable revision for a repository in this Galaxy instance.' )
@expose_api
[docs] def exported_workflows( self, trans, id, **kwd ):
"""
GET /api/tool_shed_repositories/{encoded_tool_shed_repository_id}/exported_workflows
Display a list of dictionaries containing information about this tool shed repository's exported workflows.
:param id: the encoded id of the ToolShedRepository object
"""
# Example URL: http://localhost:8763/api/tool_shed_repositories/f2db41e1fa331b3e/exported_workflows
# Since exported workflows are dictionaries with very few attributes that differentiate them from each
# other, we'll build the list based on the following dictionary of those few attributes.
exported_workflows = []
repository = suc.get_tool_shed_repository_by_id( trans.app, id )
metadata = repository.metadata
if metadata:
exported_workflow_tups = metadata.get( 'workflows', [] )
else:
exported_workflow_tups = []
for index, exported_workflow_tup in enumerate( exported_workflow_tups ):
# The exported_workflow_tup looks like ( relative_path, exported_workflow_dict ), where the value of
# relative_path is the location on disk (relative to the root of the installed repository) where the
# exported_workflow_dict file (.ga file) is located.
exported_workflow_dict = exported_workflow_tup[ 1 ]
annotation = exported_workflow_dict.get( 'annotation', '' )
format_version = exported_workflow_dict.get( 'format-version', '' )
workflow_name = exported_workflow_dict.get( 'name', '' )
# Since we don't have an in-memory object with an id, we'll identify the exported workflow via its
# location (i.e., index) in the list.
display_dict = dict( index=index, annotation=annotation, format_version=format_version, workflow_name=workflow_name )
exported_workflows.append( display_dict )
return exported_workflows
@expose_api
[docs] def get_latest_installable_revision( self, trans, payload, **kwd ):
"""
POST /api/tool_shed_repositories/get_latest_installable_revision
Get the latest installable revision of a specified repository from a specified Tool Shed.
: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 retrieve the Repository revision.
:param name (required): the name of the Repository
:param owner (required): the owner of the Repository
"""
# Get the information about the repository to be installed from the payload.
tool_shed_url, name, owner = self.__parse_repository_from_payload( payload )
# Make sure the current user's API key proves he is an admin user in this Galaxy instance.
if not trans.user_is_admin():
raise exceptions.AdminRequiredException( 'You are not authorized to request the latest installable revision for a repository in this Galaxy instance.' )
params = '?name=%s&owner=%s' % ( name, owner )
url = common_util.url_join( tool_shed_url,
'api/repositories/get_ordered_installable_revisions%s' % params )
try:
raw_text = common_util.tool_shed_get( trans.app, tool_shed_url, url )
except Exception, e:
message = "Error attempting to retrieve the latest installable revision from tool shed %s for repository %s owned by %s: %s" % \
( str( tool_shed_url ), str( name ), str( owner ), str( e ) )
log.debug( message )
return dict( status='error', error=message )
if raw_text:
# If successful, the response from get_ordered_installable_revisions will be a list of
# changeset_revision hash strings.
changeset_revisions = json.loads( raw_text )
if len( changeset_revisions ) >= 1:
return changeset_revisions[ -1 ]
return hg_util.INITIAL_CHANGELOG_HASH
def __get_value_mapper( self, trans, tool_shed_repository ):
value_mapper={ 'id' : trans.security.encode_id( tool_shed_repository.id ),
'error_message' : tool_shed_repository.error_message or '' }
return value_mapper
@expose_api
[docs] def import_workflow( self, trans, payload, **kwd ):
"""
POST /api/tool_shed_repositories/import_workflow
Import the specified exported workflow contained in the specified installed tool shed repository into Galaxy.
:param key: the API key of the Galaxy user with which the imported workflow will be associated.
:param id: the encoded id of the ToolShedRepository object
The following parameters are included in the payload.
:param index: the index location of the workflow tuple in the list of exported workflows stored in the metadata for the specified repository
"""
api_key = kwd.get( 'key', None )
if api_key is None:
raise HTTPBadRequest( detail="Missing required parameter 'key' whose value is the API key for the Galaxy user importing the specified workflow." )
tool_shed_repository_id = kwd.get( 'id', '' )
if not tool_shed_repository_id:
raise HTTPBadRequest( detail="Missing required parameter 'id'." )
index = payload.get( 'index', None )
if index is None:
raise HTTPBadRequest( detail="Missing required parameter 'index'." )
repository = suc.get_tool_shed_repository_by_id( trans.app, tool_shed_repository_id )
exported_workflows = json.loads( self.exported_workflows( trans, tool_shed_repository_id ) )
# Since we don't have an in-memory object with an id, we'll identify the exported workflow via its location (i.e., index) in the list.
exported_workflow = exported_workflows[ int( index ) ]
workflow_name = exported_workflow[ 'workflow_name' ]
workflow, status, error_message = workflow_util.import_workflow( trans, repository, workflow_name )
if status == 'error':
log.debug( error_message )
return {}
return workflow.to_dict( view='element' )
@expose_api
[docs] def import_workflows( self, trans, **kwd ):
"""
POST /api/tool_shed_repositories/import_workflows
Import all of the exported workflows contained in the specified installed tool shed repository into Galaxy.
:param key: the API key of the Galaxy user with which the imported workflows will be associated.
:param id: the encoded id of the ToolShedRepository object
"""
api_key = kwd.get( 'key', None )
if api_key is None:
raise HTTPBadRequest( detail="Missing required parameter 'key' whose value is the API key for the Galaxy user importing the specified workflow." )
tool_shed_repository_id = kwd.get( 'id', '' )
if not tool_shed_repository_id:
raise HTTPBadRequest( detail="Missing required parameter 'id'." )
repository = suc.get_tool_shed_repository_by_id( trans.app, tool_shed_repository_id )
exported_workflows = json.loads( self.exported_workflows( trans, tool_shed_repository_id ) )
imported_workflow_dicts = []
for exported_workflow_dict in exported_workflows:
workflow_name = exported_workflow_dict[ 'workflow_name' ]
workflow, status, error_message = workflow_util.import_workflow( trans, repository, workflow_name )
if status == 'error':
log.debug( error_message )
else:
imported_workflow_dicts.append( workflow.to_dict( view='element' ) )
return imported_workflow_dicts
@expose_api
[docs] def index( self, trans, **kwd ):
"""
GET /api/tool_shed_repositories
Display a list of dictionaries containing information about installed tool shed repositories.
"""
# Example URL: http://localhost:8763/api/tool_shed_repositories
tool_shed_repository_dicts = []
for tool_shed_repository in trans.install_model.context.query( trans.app.install_model.ToolShedRepository ) \
.order_by( trans.app.install_model.ToolShedRepository.table.c.name ):
tool_shed_repository_dict = \
tool_shed_repository.to_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 ) )
tool_shed_repository_dicts.append( tool_shed_repository_dict )
return tool_shed_repository_dicts
@expose_api
[docs] 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 )
install_repository_manager = InstallRepositoryManager( trans.app )
installed_tool_shed_repositories = install_repository_manager.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
return map( to_dict, installed_tool_shed_repositories )
@expose_api
[docs] def install_repository_revisions( self, trans, payload, **kwd ):
"""
POST /api/tool_shed_repositories/install_repository_revisions
Install one or more specified repository revisions from one or more specified tool sheds into Galaxy. The received parameters
must be ordered lists so that positional values in tool_shed_urls, names, owners and changeset_revisions are associated.
It's questionable whether this method is needed as the above method for installing a single repository can probably cover all
desired scenarios. We'll keep this one around just in case...
:param key: the current Galaxy admin user's API key
The following parameters are included in the payload.
:param tool_shed_urls: the base URLs of the Tool Sheds from which to install a specified Repository
:param names: the names of the Repositories to be installed
:param owners: the owners of the Repositories to be installed
:param changeset_revisions: the changeset_revisions of each RepositoryMetadata object associated with each Repository to be installed
: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, as both cannot be used.
:param tool_panel_section_id: optional id of the Galaxy tool panel section in which to load tools contained in the Repository.
If not set, 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,
as both cannot be used.
: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.
"""
self.__ensure_can_install_repos( trans )
# Get the information about all of the repositories to be installed.
tool_shed_urls = util.listify( payload.get( 'tool_shed_urls', '' ) )
names = util.listify( payload.get( 'names', '' ) )
owners = util.listify( payload.get( 'owners', '' ) )
changeset_revisions = util.listify( payload.get( 'changeset_revisions', '' ) )
num_specified_repositories = len( tool_shed_urls )
if len( names ) != num_specified_repositories or \
len( owners ) != num_specified_repositories or \
len( changeset_revisions ) != num_specified_repositories:
message = 'Error in tool_shed_repositories API in install_repository_revisions: the received parameters must be ordered '
message += 'lists so that positional values in tool_shed_urls, names, owners and changeset_revisions are associated.'
log.debug( message )
return dict( status='error', error=message )
# Get the information about the Galaxy components (e.g., tool pane section, tool config file, etc) that will contain information
# about each of the repositories being installed.
# TODO: we may want to enhance this method to allow for each of the following to be associated with each repository instead of
# forcing all repositories to use the same settings.
install_repository_dependencies = payload.get( 'install_repository_dependencies', False )
install_tool_dependencies = payload.get( 'install_tool_dependencies', False )
new_tool_panel_section_label = payload.get( 'new_tool_panel_section_label', '' )
shed_tool_conf = payload.get( 'shed_tool_conf', None )
tool_panel_section_id = payload.get( 'tool_panel_section_id', '' )
all_installed_tool_shed_repositories = []
for index, tool_shed_url in enumerate( tool_shed_urls ):
current_payload = {}
current_payload[ 'tool_shed_url' ] = tool_shed_url
current_payload[ 'name' ] = names[ index ]
current_payload[ 'owner' ] = owners[ index ]
current_payload[ 'changeset_revision' ] = changeset_revisions[ index ]
current_payload[ 'new_tool_panel_section_label' ] = new_tool_panel_section_label
current_payload[ 'tool_panel_section_id' ] = tool_panel_section_id
current_payload[ 'install_repository_dependencies' ] = install_repository_dependencies
current_payload[ 'install_tool_dependencies' ] = install_tool_dependencies
current_payload[ 'shed_tool_conf' ] = shed_tool_conf
installed_tool_shed_repositories = self.install_repository_revision( trans, **current_payload )
if isinstance( installed_tool_shed_repositories, dict ):
# We encountered an error.
return installed_tool_shed_repositories
elif isinstance( installed_tool_shed_repositories, list ):
all_installed_tool_shed_repositories.extend( installed_tool_shed_repositories )
return all_installed_tool_shed_repositories
@expose_api
[docs] def repair_repository_revision( self, trans, payload, **kwd ):
"""
POST /api/tool_shed_repositories/repair_repository_revision
Repair a specified repository revision previously installed 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 the Repository was installed
: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
"""
# 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 )
tool_shed_repositories = []
tool_shed_repository = suc.get_tool_shed_repository_by_shed_name_owner_changeset_revision( trans.app,
tool_shed_url,
name,
owner,
changeset_revision )
rrm = RepairRepositoryManager( trans.app )
repair_dict = rrm.get_repair_dict( tool_shed_repository )
ordered_tsr_ids = repair_dict.get( 'ordered_tsr_ids', [] )
ordered_repo_info_dicts = repair_dict.get( 'ordered_repo_info_dicts', [] )
if ordered_tsr_ids and ordered_repo_info_dicts:
for index, tsr_id in enumerate( ordered_tsr_ids ):
repository = trans.install_model.context.query( trans.install_model.ToolShedRepository ).get( trans.security.decode_id( tsr_id ) )
repo_info_dict = ordered_repo_info_dicts[ index ]
# TODO: handle errors in repair_dict.
repair_dict = rrm.repair_tool_shed_repository( repository,
encoding_util.tool_shed_encode( repo_info_dict ) )
repository_dict = repository.to_dict( value_mapper=self.__get_value_mapper( trans, repository ) )
repository_dict[ 'url' ] = web.url_for( controller='tool_shed_repositories',
action='show',
id=trans.security.encode_id( repository.id ) )
if repair_dict:
errors = repair_dict.get( repository.name, [] )
repository_dict[ 'errors_attempting_repair' ] = ' '.join( errors )
tool_shed_repositories.append( repository_dict )
# Display the list of repaired repositories.
return tool_shed_repositories
def __parse_repository_from_payload( self, payload, include_changeset=False ):
# Get the information about the repository to be installed from the payload.
tool_shed_url = payload.get( 'tool_shed_url', '' )
if not tool_shed_url:
raise exceptions.RequestParameterMissingException( "Missing required parameter 'tool_shed_url'." )
name = payload.get( 'name', '' )
if not name:
raise exceptions.RequestParameterMissingException( "Missing required parameter 'name'." )
owner = payload.get( 'owner', '' )
if not owner:
raise exceptions.RequestParameterMissingException( "Missing required parameter 'owner'." )
if not include_changeset:
return tool_shed_url, name, owner
changeset_revision = payload.get( 'changeset_revision', '' )
if not changeset_revision:
raise HTTPBadRequest( detail="Missing required parameter 'changeset_revision'." )
return tool_shed_url, name, owner, changeset_revision
@expose_api
[docs] def reset_metadata_on_installed_repositories( self, trans, payload, **kwd ):
"""
PUT /api/tool_shed_repositories/reset_metadata_on_installed_repositories
Resets all metadata on all repositories installed into Galaxy in an "orderly fashion".
:param key: the API key of the Galaxy admin user.
"""
start_time = strftime( "%Y-%m-%d %H:%M:%S" )
results = dict( start_time=start_time,
successful_count=0,
unsuccessful_count=0,
repository_status=[] )
# Make sure the current user's API key proves he is an admin user in this Galaxy instance.
if not trans.user_is_admin():
raise HTTPForbidden( detail='You are not authorized to reset metadata on repositories installed into this Galaxy instance.' )
irmm = InstalledRepositoryMetadataManager( trans.app )
query = irmm.get_query_for_setting_metadata_on_repositories( order=False )
# Now reset metadata on all remaining repositories.
for repository in query:
try:
irmm.set_repository( repository )
irmm.reset_all_metadata_on_installed_repository()
irmm_invalid_file_tups = irmm.get_invalid_file_tups()
if irmm_invalid_file_tups:
message = tool_util.generate_message_for_invalid_tools( trans.app,
irmm_invalid_file_tups,
repository,
None,
as_html=False )
results[ 'unsuccessful_count' ] += 1
else:
message = "Successfully reset metadata on repository %s owned by %s" % \
( str( repository.name ), str( repository.owner ) )
results[ 'successful_count' ] += 1
except Exception, e:
message = "Error resetting metadata on repository %s owned by %s: %s" % \
( str( repository.name ), str( repository.owner ), str( e ) )
results[ 'unsuccessful_count' ] += 1
results[ 'repository_status' ].append( message )
stop_time = strftime( "%Y-%m-%d %H:%M:%S" )
results[ 'stop_time' ] = stop_time
return json.dumps( results, sort_keys=True, indent=4 )
@expose_api
[docs] def show( self, trans, id, **kwd ):
"""
GET /api/tool_shed_repositories/{encoded_tool_shed_repsository_id}
Display a dictionary containing information about a specified tool_shed_repository.
:param id: the encoded id of the ToolShedRepository object
"""
# Example URL: http://localhost:8763/api/tool_shed_repositories/df7a1f0c02a5b08e
tool_shed_repository = suc.get_tool_shed_repository_by_id( trans.app, id )
if tool_shed_repository is None:
log.debug( "Unable to locate tool_shed_repository record for id %s." % ( str( id ) ) )
return {}
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