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
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
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' )
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.from_json_string(
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
def check_for_updates( app, model, repository_id=None ):
message = ''
status = 'ok'
if repository_id is None:
success_count = 0
repository_names_not_updated = []
updated_count = 0
for repository in model.context.query( model.ToolShedRepository ) \
.filter( model.ToolShedRepository.table.c.deleted == false() ):
ok, updated = \
check_or_update_tool_shed_status_for_installed_repository( app, repository )
if ok:
success_count += 1
else:
repository_names_not_updated.append( '<b>%s</b>' % escape( str( repository.name ) ) )
if updated:
updated_count += 1
message = "Checked the status in the tool shed for %d repositories. " % success_count
message += "Updated the tool shed status for %d repositories. " % updated_count
if repository_names_not_updated:
message += "Unable to retrieve status from the tool shed for the following repositories:\n"
message += ", ".join( repository_names_not_updated )
else:
repository = suc.get_tool_shed_repository_by_id( app, repository_id )
ok, updated = \
check_or_update_tool_shed_status_for_installed_repository( app, repository )
if ok:
if updated:
message = "The tool shed status for repository <b>%s</b> has been updated." % escape( str( repository.name ) )
else:
message = "The status has not changed in the tool shed for repository <b>%s</b>." % escape( str( repository.name ) )
else:
message = "Unable to retrieve status from the tool shed for repository <b>%s</b>." % escape( str( repository.name ) )
status = 'error'
return message, status
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' )
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
def generate_workflow_image( trans, workflow_name, repository_metadata_id=None, repository_id=None ):
"""
Return an svg image representation of a workflow dictionary created when the workflow was exported. This method is called
from both Galaxy and the tool shed. When called from the tool shed, repository_metadata_id will have a value and repository_id
will be None. When called from Galaxy, repository_metadata_id will be None and repository_id will have a value.
"""
workflow_name = encoding_util.tool_shed_decode( workflow_name )
if trans.webapp.name == 'tool_shed':
# We're in the tool shed.
repository_metadata = metadata_util.get_repository_metadata_by_id( trans.app, repository_metadata_id )
repository_id = trans.security.encode_id( repository_metadata.repository_id )
changeset_revision = repository_metadata.changeset_revision
metadata = repository_metadata.metadata
else:
# We're in Galaxy.
repository = suc.get_tool_shed_repository_by_id( trans.app, repository_id )
changeset_revision = repository.changeset_revision
metadata = repository.metadata
# metadata[ 'workflows' ] is a list of tuples where each contained tuple is
# [ <relative path to the .ga file in the repository>, <exported workflow dict> ]
for workflow_tup in metadata[ 'workflows' ]:
workflow_dict = workflow_tup[1]
if workflow_dict[ 'name' ] == workflow_name:
break
if 'tools' in metadata:
tools_metadata = metadata[ 'tools' ]
else:
tools_metadata = []
workflow, missing_tool_tups = get_workflow_from_dict( trans=trans,
workflow_dict=workflow_dict,
tools_metadata=tools_metadata,
repository_id=repository_id,
changeset_revision=changeset_revision )
workflow_canvas = WorkflowCanvas()
canvas = workflow_canvas.canvas
# Store px width for boxes of each step.
for step in workflow.steps:
step.upgrade_messages = {}
module = module_factory.from_workflow_step( trans, repository_id, changeset_revision, tools_metadata, step )
tool_errors = module.type == 'tool' and not module.tool
module_data_inputs = get_workflow_data_inputs( step, module )
module_data_outputs = get_workflow_data_outputs( step, module, workflow.steps )
module_name = get_workflow_module_name( module, missing_tool_tups )
workflow_canvas.populate_data_for_step(
step,
module_name,
module_data_inputs,
module_data_outputs,
tool_errors=tool_errors
)
workflow_canvas.add_steps( highlight_errors=True )
workflow_canvas.finish( )
trans.response.set_content_type( "image/svg+xml" )
return canvas.tostring()
def generate_workflow_image( trans, workflow_name, repository_metadata_id=None, repository_id=None ):
"""
Return an svg image representation of a workflow dictionary created when the workflow was exported. This method is called
from both Galaxy and the tool shed. When called from the tool shed, repository_metadata_id will have a value and repository_id
will be None. When called from Galaxy, repository_metadata_id will be None and repository_id will have a value.
"""
workflow_name = encoding_util.tool_shed_decode( workflow_name )
if trans.webapp.name == 'tool_shed':
# We're in the tool shed.
repository_metadata = metadata_util.get_repository_metadata_by_id( trans.app, repository_metadata_id )
repository_id = trans.security.encode_id( repository_metadata.repository_id )
changeset_revision = repository_metadata.changeset_revision
metadata = repository_metadata.metadata
else:
# We're in Galaxy.
repository = suc.get_tool_shed_repository_by_id( trans.app, repository_id )
changeset_revision = repository.changeset_revision
metadata = repository.metadata
# metadata[ 'workflows' ] is a list of tuples where each contained tuple is
# [ <relative path to the .ga file in the repository>, <exported workflow dict> ]
for workflow_tup in metadata[ 'workflows' ]:
workflow_dict = workflow_tup[1]
if workflow_dict[ 'name' ] == workflow_name:
break
if 'tools' in metadata:
tools_metadata = metadata[ 'tools' ]
else:
tools_metadata = []
workflow, missing_tool_tups = get_workflow_from_dict( trans=trans,
workflow_dict=workflow_dict,
tools_metadata=tools_metadata,
repository_id=repository_id,
changeset_revision=changeset_revision )
workflow_canvas = WorkflowCanvas()
canvas = workflow_canvas.canvas
# Store px width for boxes of each step.
for step in workflow.steps:
step.upgrade_messages = {}
module = module_factory.from_workflow_step( trans, repository_id, changeset_revision, tools_metadata, step )
tool_errors = module.type == 'tool' and not module.tool
module_data_inputs = get_workflow_data_inputs( step, module )
module_data_outputs = get_workflow_data_outputs( step, module, workflow.steps )
module_name = get_workflow_module_name( module, missing_tool_tups )
workflow_canvas.populate_data_for_step(
step,
module_name,
module_data_inputs,
module_data_outputs,
tool_errors=tool_errors
)
workflow_canvas.add_steps( highlight_errors=True )
workflow_canvas.finish( )
trans.response.set_content_type( "image/svg+xml" )
return canvas.standalone_xml()
def display_tool_help_image_in_repository( self, trans, **kwd ):
repository_id = kwd.get( 'repository_id', None )
image_file = kwd.get( 'image_file', None )
if repository_id and image_file:
repository = suc.get_tool_shed_repository_by_id( trans, repository_id )
repo_files_dir = os.path.join( repository.repo_files_directory( trans.app ) )
default_path = os.path.abspath( os.path.join( repo_files_dir, 'static', 'images', image_file ) )
if os.path.exists( default_path ):
return open( default_path, 'r' )
else:
path_to_file = suc.get_absolute_path_to_file_in_repository( repo_files_dir, image_file )
if os.path.exists( path_to_file ):
return open( path_to_file, 'r' )
return None
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
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
def get_components_from_repository_dependency_for_installed_repository(
self, repository_dependency):
"""
Parse a repository dependency and return components necessary for proper display
in Galaxy on the Manage repository page.
"""
# Default prior_installation_required and only_if_compiling_contained_td to False.
prior_installation_required = 'False'
only_if_compiling_contained_td = 'False'
if len(repository_dependency) == 6:
# Metadata should have been reset on this installed repository, but it wasn't.
tool_shed_repository_id = repository_dependency[4]
installation_status = repository_dependency[5]
tool_shed, name, owner, changeset_revision = repository_dependency[
0:4]
repository_dependency = [
tool_shed, name, owner, changeset_revision,
prior_installation_required, only_if_compiling_contained_td
]
elif len(repository_dependency) == 7:
# We have a repository dependency tuple that includes a prior_installation_required value but not a only_if_compiling_contained_td value.
tool_shed_repository_id = repository_dependency[5]
installation_status = repository_dependency[6]
tool_shed, name, owner, changeset_revision, prior_installation_required = repository_dependency[
0:5]
repository_dependency = \
[ tool_shed, name, owner, changeset_revision, prior_installation_required, only_if_compiling_contained_td ]
elif len(repository_dependency) == 8:
# We have a repository dependency tuple that includes both a prior_installation_required value
# and a only_if_compiling_contained_td value.
tool_shed_repository_id = repository_dependency[6]
installation_status = repository_dependency[7]
repository_dependency = repository_dependency[0:6]
else:
tool_shed_repository_id = None
installation_status = 'unknown'
if tool_shed_repository_id:
tool_shed_repository = suc.get_tool_shed_repository_by_id(
self.app, self.app.security.encode_id(tool_shed_repository_id))
if tool_shed_repository:
if tool_shed_repository.missing_repository_dependencies:
installation_status = '%s, missing repository dependencies' % installation_status
elif tool_shed_repository.missing_tool_dependencies:
installation_status = '%s, missing tool dependencies' % installation_status
return tool_shed_repository_id, installation_status, repository_dependency
def display_tool_help_image_in_repository(self, trans, **kwd):
repository_id = kwd.get('repository_id', None)
image_file = kwd.get('image_file', None)
if repository_id and image_file:
repository = suc.get_tool_shed_repository_by_id(
trans, repository_id)
repo_files_dir = os.path.join(
repository.repo_files_directory(trans.app))
default_path = os.path.abspath(
os.path.join(repo_files_dir, 'static', 'images', image_file))
if os.path.exists(default_path):
return open(default_path, 'r')
else:
path_to_file = suc.get_absolute_path_to_file_in_repository(
repo_files_dir, image_file)
if os.path.exists(path_to_file):
return open(path_to_file, 'r')
return None
def status( self, trans, id, **kwd ):
"""
GET /api/tool_shed_repositories/{id}/status
Display a dictionary containing information about a specified repository's installation
status and a list of its dependencies and the status of each.
:param id: the repository's encoded id
"""
tool_shed_repository = suc.get_tool_shed_repository_by_id( self.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 ) )
tool_shed_repository_dict[ 'repository_dependencies' ] = self.__flatten_repository_dependency_list( trans, tool_shed_repository )
return tool_shed_repository_dict
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
try:
tool_shed_repository = suc.get_tool_shed_repository_by_id( trans, id )
tool_shed_repository_dict = tool_shed_repository.as_dict( value_mapper=default_tool_shed_repository_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
except Exception, e:
message = "Error in tool_shed_repositories API in index: " + str( e )
log.error( message, exc_info=True )
trans.response.status = 500
return message
def get_components_from_repository_dependency_for_installed_repository( self, repository_dependency ):
"""
Parse a repository dependency and return components necessary for proper display
in Galaxy on the Manage repository page.
"""
# Default prior_installation_required and only_if_compiling_contained_td to False.
prior_installation_required = 'False'
only_if_compiling_contained_td = 'False'
if len( repository_dependency ) == 6:
# Metadata should have been reset on this installed repository, but it wasn't.
tool_shed_repository_id = repository_dependency[ 4 ]
installation_status = repository_dependency[ 5 ]
tool_shed, name, owner, changeset_revision = repository_dependency[ 0:4 ]
repository_dependency = [ tool_shed, name, owner, changeset_revision, prior_installation_required, only_if_compiling_contained_td ]
elif len( repository_dependency ) == 7:
# We have a repository dependency tuple that includes a prior_installation_required value but not a only_if_compiling_contained_td value.
tool_shed_repository_id = repository_dependency[ 5 ]
installation_status = repository_dependency[ 6 ]
tool_shed, name, owner, changeset_revision, prior_installation_required = repository_dependency[ 0:5 ]
repository_dependency = \
[ tool_shed, name, owner, changeset_revision, prior_installation_required, only_if_compiling_contained_td ]
elif len( repository_dependency ) == 8:
# We have a repository dependency tuple that includes both a prior_installation_required value
# and a only_if_compiling_contained_td value.
tool_shed_repository_id = repository_dependency[ 6 ]
installation_status = repository_dependency[ 7 ]
repository_dependency = repository_dependency[ 0:6 ]
else:
tool_shed_repository_id = None
installation_status = 'unknown'
if tool_shed_repository_id:
tool_shed_repository = suc.get_tool_shed_repository_by_id( self.app,
self.app.security.encode_id( tool_shed_repository_id ) )
if tool_shed_repository:
if tool_shed_repository.missing_repository_dependencies:
installation_status = '%s, missing repository dependencies' % installation_status
elif tool_shed_repository.missing_tool_dependencies:
installation_status = '%s, missing tool dependencies' % installation_status
return tool_shed_repository_id, installation_status, repository_dependency
def check_for_updates(app, model, repository_id=None):
message = ''
status = 'ok'
if repository_id is None:
success_count = 0
repository_names_not_updated = []
updated_count = 0
for repository in model.context.query( model.ToolShedRepository ) \
.filter( model.ToolShedRepository.table.c.deleted == false() ):
ok, updated = \
check_or_update_tool_shed_status_for_installed_repository( app, repository )
if ok:
success_count += 1
else:
repository_names_not_updated.append(
'<b>%s</b>' % escape(str(repository.name)))
if updated:
updated_count += 1
message = "Checked the status in the tool shed for %d repositories. " % success_count
message += "Updated the tool shed status for %d repositories. " % updated_count
if repository_names_not_updated:
message += "Unable to retrieve status from the tool shed for the following repositories:\n"
message += ", ".join(repository_names_not_updated)
else:
repository = suc.get_tool_shed_repository_by_id(app, repository_id)
ok, updated = \
check_or_update_tool_shed_status_for_installed_repository( app, repository )
if ok:
if updated:
message = "The tool shed status for repository <b>%s</b> has been updated." % escape(
str(repository.name))
else:
message = "The status has not changed in the tool shed for repository <b>%s</b>." % escape(
str(repository.name))
else:
message = "Unable to retrieve status from the tool shed for repository <b>%s</b>." % escape(
str(repository.name))
status = 'error'
return message, status
def status(self, trans, id, **kwd):
"""
GET /api/tool_shed_repositories/{id}/status
Display a dictionary containing information about a specified repository's installation
status and a list of its dependencies and the status of each.
:param id: the repository's encoded id
"""
tool_shed_repository = suc.get_tool_shed_repository_by_id(self.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))
tool_shed_repository_dict[
'repository_dependencies'] = self.__flatten_repository_dependency_list(
trans, tool_shed_repository)
return tool_shed_repository_dict
def generate_workflow_image(trans,
workflow_name,
repository_metadata_id=None,
repository_id=None):
"""
Return an svg image representation of a workflow dictionary created when the workflow was exported. This method is called
from both Galaxy and the tool shed. When called from the tool shed, repository_metadata_id will have a value and repository_id
will be None. When called from Galaxy, repository_metadata_id will be None and repository_id will have a value.
"""
workflow_name = encoding_util.tool_shed_decode(workflow_name)
if trans.webapp.name == 'tool_shed':
# We're in the tool shed.
repository_metadata = metadata_util.get_repository_metadata_by_id(
trans, repository_metadata_id)
repository_id = trans.security.encode_id(
repository_metadata.repository_id)
changeset_revision = repository_metadata.changeset_revision
metadata = repository_metadata.metadata
else:
# We're in Galaxy.
repository = suc.get_tool_shed_repository_by_id(trans, repository_id)
changeset_revision = repository.changeset_revision
metadata = repository.metadata
# metadata[ 'workflows' ] is a list of tuples where each contained tuple is
# [ <relative path to the .ga file in the repository>, <exported workflow dict> ]
for workflow_tup in metadata['workflows']:
workflow_dict = workflow_tup[1]
if workflow_dict['name'] == workflow_name:
break
if 'tools' in metadata:
tools_metadata = metadata['tools']
else:
tools_metadata = []
workflow, missing_tool_tups = get_workflow_from_dict(
trans=trans,
workflow_dict=workflow_dict,
tools_metadata=tools_metadata,
repository_id=repository_id,
changeset_revision=changeset_revision)
data = []
canvas = svgfig.canvas(
style=
"stroke:black; fill:none; stroke-width:1px; stroke-linejoin:round; text-anchor:left"
)
text = svgfig.SVG("g")
connectors = svgfig.SVG("g")
boxes = svgfig.SVG("g")
svgfig.Text.defaults["font-size"] = "10px"
in_pos = {}
out_pos = {}
margin = 5
# Spacing between input/outputs.
line_px = 16
# Store px width for boxes of each step.
widths = {}
max_width, max_x, max_y = 0, 0, 0
for step in workflow.steps:
step.upgrade_messages = {}
module = module_factory.from_workflow_step(trans, repository_id,
changeset_revision,
tools_metadata, step)
tool_errors = module.type == 'tool' and not module.tool
module_data_inputs = get_workflow_data_inputs(step, module)
module_data_outputs = get_workflow_data_outputs(
step, module, workflow.steps)
step_dict = {
'id': step.order_index,
'data_inputs': module_data_inputs,
'data_outputs': module_data_outputs,
'position': step.position,
'tool_errors': tool_errors
}
input_conn_dict = {}
for conn in step.input_connections:
input_conn_dict[conn.input_name] = dict(
id=conn.output_step.order_index, output_name=conn.output_name)
step_dict['input_connections'] = input_conn_dict
data.append(step_dict)
x, y = step.position['left'], step.position['top']
count = 0
module_name = get_workflow_module_name(module, missing_tool_tups)
max_len = len(module_name) * 1.5
text.append(
svgfig.Text(x, y + 20, module_name, **{
"font-size": "14px"
}).SVG())
y += 45
for di in module_data_inputs:
cur_y = y + count * line_px
if step.order_index not in in_pos:
in_pos[step.order_index] = {}
in_pos[step.order_index][di['name']] = (x, cur_y)
text.append(svgfig.Text(x, cur_y, di['label']).SVG())
count += 1
max_len = max(max_len, len(di['label']))
if len(module.get_data_inputs()) > 0:
y += 15
for do in module_data_outputs:
cur_y = y + count * line_px
if step.order_index not in out_pos:
out_pos[step.order_index] = {}
out_pos[step.order_index][do['name']] = (x, cur_y)
text.append(svgfig.Text(x, cur_y, do['name']).SVG())
count += 1
max_len = max(max_len, len(do['name']))
widths[step.order_index] = max_len * 5.5
max_x = max(max_x, step.position['left'])
max_y = max(max_y, step.position['top'])
max_width = max(max_width, widths[step.order_index])
for step_dict in data:
tool_unavailable = step_dict['tool_errors']
width = widths[step_dict['id']]
x, y = step_dict['position']['left'], step_dict['position']['top']
# Only highlight missing tools if displaying in the tool shed.
if trans.webapp.name == 'tool_shed' and tool_unavailable:
fill = "#EBBCB2"
else:
fill = "#EBD9B2"
boxes.append(
svgfig.Rect(x - margin, y, x + width - margin, y + 30,
fill=fill).SVG())
box_height = (len(step_dict['data_inputs']) +
len(step_dict['data_outputs'])) * line_px + margin
# Draw separator line.
if len(step_dict['data_inputs']) > 0:
box_height += 15
sep_y = y + len(step_dict['data_inputs']) * line_px + 40
text.append(
svgfig.Line(x - margin, sep_y, x + width - margin,
sep_y).SVG())
# Define an input/output box.
boxes.append(
svgfig.Rect(x - margin,
y + 30,
x + width - margin,
y + 30 + box_height,
fill="#ffffff").SVG())
for conn, output_dict in step_dict['input_connections'].iteritems():
in_coords = in_pos[step_dict['id']][conn]
# out_pos_index will be a step number like 1, 2, 3...
out_pos_index = output_dict['id']
# out_pos_name will be a string like 'o', 'o2', etc.
out_pos_name = output_dict['output_name']
if out_pos_index in out_pos:
# out_conn_index_dict will be something like:
# 7: {'o': (824.5, 618)}
out_conn_index_dict = out_pos[out_pos_index]
if out_pos_name in out_conn_index_dict:
out_conn_pos = out_pos[out_pos_index][out_pos_name]
else:
# Take any key / value pair available in out_conn_index_dict.
# A problem will result if the dictionary is empty.
if out_conn_index_dict.keys():
key = out_conn_index_dict.keys()[0]
out_conn_pos = out_pos[out_pos_index][key]
adjusted = (out_conn_pos[0] + widths[output_dict['id']],
out_conn_pos[1])
text.append(
svgfig.SVG("circle",
cx=out_conn_pos[0] + widths[output_dict['id']] -
margin,
cy=out_conn_pos[1] - margin,
r=5,
fill="#ffffff"))
connectors.append(
svgfig.Line(adjusted[0],
adjusted[1] - margin,
in_coords[0] - 10,
in_coords[1],
arrow_end="true").SVG())
canvas.append(connectors)
canvas.append(boxes)
canvas.append(text)
width, height = (max_x + max_width + 50), max_y + 300
canvas['width'] = "%s px" % width
canvas['height'] = "%s px" % height
canvas['viewBox'] = "0 0 %s %s" % (width, height)
trans.response.set_content_type("image/svg+xml")
return canvas.standalone_xml()
def generate_workflow_image(trans, workflow_name, repository_metadata_id=None, repository_id=None):
"""
Return an svg image representation of a workflow dictionary created when the workflow was exported. This method is called
from both Galaxy and the tool shed. When called from the tool shed, repository_metadata_id will have a value and repository_id
will be None. When called from Galaxy, repository_metadata_id will be None and repository_id will have a value.
"""
workflow_name = encoding_util.tool_shed_decode(workflow_name)
if trans.webapp.name == "tool_shed":
# We're in the tool shed.
repository_metadata = metadata_util.get_repository_metadata_by_id(trans, repository_metadata_id)
repository_id = trans.security.encode_id(repository_metadata.repository_id)
changeset_revision = repository_metadata.changeset_revision
metadata = repository_metadata.metadata
else:
# We're in Galaxy.
repository = suc.get_tool_shed_repository_by_id(trans, repository_id)
changeset_revision = repository.changeset_revision
metadata = repository.metadata
# metadata[ 'workflows' ] is a list of tuples where each contained tuple is
# [ <relative path to the .ga file in the repository>, <exported workflow dict> ]
for workflow_tup in metadata["workflows"]:
workflow_dict = workflow_tup[1]
if workflow_dict["name"] == workflow_name:
break
if "tools" in metadata:
tools_metadata = metadata["tools"]
else:
tools_metadata = []
workflow, missing_tool_tups = get_workflow_from_dict(
trans=trans,
workflow_dict=workflow_dict,
tools_metadata=tools_metadata,
repository_id=repository_id,
changeset_revision=changeset_revision,
)
data = []
canvas = svgfig.canvas(style="stroke:black; fill:none; stroke-width:1px; stroke-linejoin:round; text-anchor:left")
text = svgfig.SVG("g")
connectors = svgfig.SVG("g")
boxes = svgfig.SVG("g")
svgfig.Text.defaults["font-size"] = "10px"
in_pos = {}
out_pos = {}
margin = 5
# Spacing between input/outputs.
line_px = 16
# Store px width for boxes of each step.
widths = {}
max_width, max_x, max_y = 0, 0, 0
for step in workflow.steps:
step.upgrade_messages = {}
module = module_factory.from_workflow_step(trans, repository_id, changeset_revision, tools_metadata, step)
tool_errors = module.type == "tool" and not module.tool
module_data_inputs = get_workflow_data_inputs(step, module)
module_data_outputs = get_workflow_data_outputs(step, module, workflow.steps)
step_dict = {
"id": step.order_index,
"data_inputs": module_data_inputs,
"data_outputs": module_data_outputs,
"position": step.position,
"tool_errors": tool_errors,
}
input_conn_dict = {}
for conn in step.input_connections:
input_conn_dict[conn.input_name] = dict(id=conn.output_step.order_index, output_name=conn.output_name)
step_dict["input_connections"] = input_conn_dict
data.append(step_dict)
x, y = step.position["left"], step.position["top"]
count = 0
module_name = get_workflow_module_name(module, missing_tool_tups)
max_len = len(module_name) * 1.5
text.append(svgfig.Text(x, y + 20, module_name, **{"font-size": "14px"}).SVG())
y += 45
for di in module_data_inputs:
cur_y = y + count * line_px
if step.order_index not in in_pos:
in_pos[step.order_index] = {}
in_pos[step.order_index][di["name"]] = (x, cur_y)
text.append(svgfig.Text(x, cur_y, di["label"]).SVG())
count += 1
max_len = max(max_len, len(di["label"]))
if len(module.get_data_inputs()) > 0:
y += 15
for do in module_data_outputs:
cur_y = y + count * line_px
if step.order_index not in out_pos:
out_pos[step.order_index] = {}
out_pos[step.order_index][do["name"]] = (x, cur_y)
text.append(svgfig.Text(x, cur_y, do["name"]).SVG())
count += 1
max_len = max(max_len, len(do["name"]))
widths[step.order_index] = max_len * 5.5
max_x = max(max_x, step.position["left"])
max_y = max(max_y, step.position["top"])
max_width = max(max_width, widths[step.order_index])
for step_dict in data:
tool_unavailable = step_dict["tool_errors"]
width = widths[step_dict["id"]]
x, y = step_dict["position"]["left"], step_dict["position"]["top"]
# Only highlight missing tools if displaying in the tool shed.
if trans.webapp.name == "tool_shed" and tool_unavailable:
fill = "#EBBCB2"
else:
fill = "#EBD9B2"
boxes.append(svgfig.Rect(x - margin, y, x + width - margin, y + 30, fill=fill).SVG())
box_height = (len(step_dict["data_inputs"]) + len(step_dict["data_outputs"])) * line_px + margin
# Draw separator line.
if len(step_dict["data_inputs"]) > 0:
box_height += 15
sep_y = y + len(step_dict["data_inputs"]) * line_px + 40
text.append(svgfig.Line(x - margin, sep_y, x + width - margin, sep_y).SVG())
# Define an input/output box.
boxes.append(svgfig.Rect(x - margin, y + 30, x + width - margin, y + 30 + box_height, fill="#ffffff").SVG())
for conn, output_dict in step_dict["input_connections"].iteritems():
in_coords = in_pos[step_dict["id"]][conn]
# out_pos_index will be a step number like 1, 2, 3...
out_pos_index = output_dict["id"]
# out_pos_name will be a string like 'o', 'o2', etc.
out_pos_name = output_dict["output_name"]
if out_pos_index in out_pos:
# out_conn_index_dict will be something like:
# 7: {'o': (824.5, 618)}
out_conn_index_dict = out_pos[out_pos_index]
if out_pos_name in out_conn_index_dict:
out_conn_pos = out_pos[out_pos_index][out_pos_name]
else:
# Take any key / value pair available in out_conn_index_dict.
# A problem will result if the dictionary is empty.
if out_conn_index_dict.keys():
key = out_conn_index_dict.keys()[0]
out_conn_pos = out_pos[out_pos_index][key]
adjusted = (out_conn_pos[0] + widths[output_dict["id"]], out_conn_pos[1])
text.append(
svgfig.SVG(
"circle",
cx=out_conn_pos[0] + widths[output_dict["id"]] - margin,
cy=out_conn_pos[1] - margin,
r=5,
fill="#ffffff",
)
)
connectors.append(
svgfig.Line(adjusted[0], adjusted[1] - margin, in_coords[0] - 10, in_coords[1], arrow_end="true").SVG()
)
canvas.append(connectors)
canvas.append(boxes)
canvas.append(text)
width, height = (max_x + max_width + 50), max_y + 300
canvas["width"] = "%s px" % width
canvas["height"] = "%s px" % height
canvas["viewBox"] = "0 0 %s %s" % (width, height)
trans.response.set_content_type("image/svg+xml")
return canvas.standalone_xml()
