def __to_incoming(self, state, **kwds):
new_incoming = {}
params_to_incoming(new_incoming, self.tool.inputs, state.inputs,
self.app)
new_incoming["tool_state"] = self.__state_to_string(state)
new_incoming.update(kwds)
return new_incoming
def __to_incoming( self, state, **kwds ):
new_incoming = {}
params_to_incoming( new_incoming, self.tool.inputs, state.inputs, self.app )
# Copy meta parameters over lost by params_to_incoming...
for key, value in state.inputs.iteritems():
if key.endswith( "|__multirun__" ):
new_incoming[ key ] = value
new_incoming[ "tool_state" ] = self.__state_to_string( state )
new_incoming.update( kwds )
return new_incoming
def __to_incoming(self, state, **kwds):
new_incoming = {}
params_to_incoming(new_incoming, self.tool.inputs, state.inputs,
self.app)
# Copy meta parameters over lost by params_to_incoming...
for key, value in state.inputs.iteritems():
if key.endswith("|__multirun__"):
new_incoming[key] = value
new_incoming["tool_state"] = self.__state_to_string(state)
new_incoming.update(kwds)
return new_incoming
def render_body(context, **pageargs):
context.caller_stack._push_frame()
try:
__M_locals = __M_dict_builtin(pageargs=pageargs)
h = context.get("h", UNDEFINED)
tool = context.get("tool", UNDEFINED)
module = context.get("module", UNDEFINED)
job = context.get("job", UNDEFINED)
trans = context.get("trans", UNDEFINED)
self = context.get("self", UNDEFINED)
__M_writer = context.writer()
# SOURCE LINE 1
## TEMPORARY: create tool dictionary in mako while both tool forms are in use.
## This avoids making two separate requests since the classic form requires the mako anyway.
from galaxy.tools.parameters import params_to_incoming
incoming = {}
params_to_incoming(incoming, tool.inputs, module.state.inputs, trans.app, to_html=False)
self.form_config = tool.to_json(trans, incoming, is_workflow=True)
self.form_config.update(
{
"id": tool.id,
"job_id": trans.security.encode_id(job.id) if job else None,
"history_id": trans.security.encode_id(trans.history.id),
"container": "#right-content",
}
)
__M_locals_builtin_stored = __M_locals_builtin()
__M_locals.update(
__M_dict_builtin(
[
(__M_key, __M_locals_builtin_stored[__M_key])
for __M_key in ["params_to_incoming", "incoming"]
if __M_key in __M_locals_builtin_stored
]
)
)
# SOURCE LINE 14
__M_writer(u"\n")
# SOURCE LINE 15
__M_writer(unicode(h.dumps(self.form_config)))
return ""
finally:
context.caller_stack._pop_frame()
def __to_incoming(self, state, **kwds):
new_incoming = {}
params_to_incoming(new_incoming, self.tool.inputs, state.inputs, self.app)
new_incoming["tool_state"] = self.__state_to_string(state)
new_incoming.update(kwds)
return new_incoming
def _workflow_to_dict_run(self, trans, stored):
"""
Builds workflow dictionary used by run workflow form
"""
workflow = stored.latest_workflow
if len(workflow.steps) == 0:
raise exceptions.MessageException(
'Workflow cannot be run because it does not have any steps.')
if attach_ordered_steps(workflow, workflow.steps):
raise exceptions.MessageException(
'Workflow cannot be run because it contains cycles.')
trans.workflow_building_mode = workflow_building_modes.USE_HISTORY
module_injector = WorkflowModuleInjector(trans)
has_upgrade_messages = False
step_version_changes = []
missing_tools = []
errors = {}
for step in workflow.steps:
try:
module_injector.inject(step,
steps=workflow.steps,
exact_tools=False)
except exceptions.ToolMissingException:
if step.tool_id not in missing_tools:
missing_tools.append(step.tool_id)
continue
if step.upgrade_messages:
has_upgrade_messages = True
if step.type == 'tool' or step.type is None:
if step.module.version_changes:
step_version_changes.extend(step.module.version_changes)
step_errors = step.module.get_errors()
if step_errors:
errors[step.id] = step_errors
if missing_tools:
workflow.annotation = self.get_item_annotation_str(
trans.sa_session, trans.user, workflow)
raise exceptions.MessageException('Following tools missing: %s' %
', '.join(missing_tools))
workflow.annotation = self.get_item_annotation_str(
trans.sa_session, trans.user, workflow)
step_order_indices = {}
for step in workflow.steps:
step_order_indices[step.id] = step.order_index
step_models = []
for i, step in enumerate(workflow.steps):
step_model = None
if step.type == 'tool':
incoming = {}
tool = trans.app.toolbox.get_tool(
step.tool_id, tool_version=step.tool_version)
params_to_incoming(incoming, tool.inputs, step.state.inputs,
trans.app)
step_model = tool.to_json(
trans,
incoming,
workflow_building_mode=workflow_building_modes.USE_HISTORY)
step_model['post_job_actions'] = [{
'short_str':
ActionBox.get_short_str(pja),
'action_type':
pja.action_type,
'output_name':
pja.output_name,
'action_arguments':
pja.action_arguments
} for pja in step.post_job_actions]
else:
inputs = step.module.get_runtime_inputs(
connections=step.output_connections)
step_model = {
'inputs':
[input.to_dict(trans) for input in inputs.values()]
}
step_model['step_type'] = step.type
step_model['step_label'] = step.label
step_model['step_name'] = step.module.get_name()
step_model['step_version'] = step.module.get_version()
step_model['step_index'] = step.order_index
step_model['output_connections'] = [{
'input_step_index':
step_order_indices.get(oc.input_step_id),
'output_step_index':
step_order_indices.get(oc.output_step_id),
'input_name':
oc.input_name,
'output_name':
oc.output_name
} for oc in step.output_connections]
if step.annotations:
step_model['annotation'] = step.annotations[0].annotation
if step.upgrade_messages:
step_model['messages'] = step.upgrade_messages
step_models.append(step_model)
return {
'id':
trans.app.security.encode_id(stored.id),
'history_id':
trans.app.security.encode_id(trans.history.id)
if trans.history else None,
'name':
stored.name,
'steps':
step_models,
'step_version_changes':
step_version_changes,
'has_upgrade_messages':
has_upgrade_messages,
'workflow_resource_parameters':
self._workflow_resource_parameters(trans, stored, workflow),
}
def rerun(self, trans, id=None, from_noframe=None, **kwd):
"""
Given a HistoryDatasetAssociation id, find the job and that created
the dataset, extract the parameters, and display the appropriate tool
form with parameters already filled in.
"""
if not id:
error("'id' parameter is required")
try:
id = int(id)
except:
# it's not an un-encoded id, try to parse as encoded
try:
id = trans.security.decode_id(id)
except:
error("Invalid value for 'id' parameter")
# Get the dataset object
data = trans.sa_session.query(
trans.app.model.HistoryDatasetAssociation).get(id)
#only allow rerunning if user is allowed access to the dataset.
if not (trans.user_is_admin()
or trans.app.security_agent.can_access_dataset(
trans.get_current_user_roles(), data.dataset)):
error("You are not allowed to access this dataset")
# Get the associated job, if any.
job = data.creating_job
if not job:
raise Exception(
"Failed to get job information for dataset hid %d" % data.hid)
# Get the tool object
tool_id = job.tool_id
tool_version = job.tool_version
try:
tool_version_select_field, tools, tool = self.__get_tool_components(
tool_id,
tool_version=tool_version,
get_loaded_tools_by_lineage=False,
set_selected=True)
if (tool.id == job.tool_id or tool.old_id
== job.tool_id) and tool.version == job.tool_version:
tool_id_version_message = ''
elif tool.id == job.tool_id:
if job.tool_version == None:
# For some reason jobs don't always keep track of the tool version.
tool_id_version_message = ''
else:
tool_id_version_message = 'This job was initially run with tool version "%s", which is not currently available. ' % job.tool_version
if len(tools) > 1:
tool_id_version_message += 'You can rerun the job with the selected tool or choose another derivation of the tool.'
else:
tool_id_version_message += 'You can rerun the job with this tool version, which is a derivation of the original tool.'
else:
if len(tools) > 1:
tool_id_version_message = 'This job was initially run with tool version "%s", which is not currently available. ' % job.tool_version
tool_id_version_message += 'You can rerun the job with the selected tool or choose another derivation of the tool.'
else:
tool_id_version_message = 'This job was initially run with tool id "%s", version "%s", which is not ' % (
job.tool_id, job.tool_version)
tool_id_version_message += 'currently available. You can rerun the job with this tool, which is a derivation of the original tool.'
assert tool is not None, 'Requested tool has not been loaded.'
except:
# This is expected so not an exception.
tool_id_version_message = ''
error(
"This dataset was created by an obsolete tool (%s). Can't re-run."
% tool_id)
# Can't rerun upload, external data sources, et cetera. Workflow compatible will proxy this for now
if not tool.is_workflow_compatible:
error("The '%s' tool does not currently support rerunning." %
tool.name)
# Get the job's parameters
try:
params_objects = job.get_param_values(trans.app,
ignore_errors=True)
except:
raise Exception("Failed to get parameters for dataset id %d " %
data.id)
upgrade_messages = tool.check_and_update_param_values(
params_objects, trans, update_values=False)
# Need to remap dataset parameters. Job parameters point to original
# dataset used; parameter should be the analygous dataset in the
# current history.
history = trans.get_history()
hda_source_dict = {} # Mapping from HDA in history to source HDAs.
for hda in history.datasets:
source_hda = hda.copied_from_history_dataset_association
while source_hda: #should this check library datasets as well?
#FIXME: could be multiple copies of a hda in a single history, this does a better job of matching on cloned histories,
#but is still less than perfect when eg individual datasets are copied between histories
if source_hda not in hda_source_dict or source_hda.hid == hda.hid:
hda_source_dict[source_hda] = hda
source_hda = source_hda.copied_from_history_dataset_association
# Unpack unvalidated values to strings, they'll be validated when the
# form is submitted (this happens when re-running a job that was
# initially run by a workflow)
#This needs to be done recursively through grouping parameters
def rerun_callback(input, value, prefixed_name, prefixed_label):
if isinstance(value, UnvalidatedValue):
return str(value)
if isinstance(input, DataToolParameter):
if isinstance(value, list):
values = []
for val in value:
if is_hashable(val):
if val in history.datasets:
values.append(val)
elif val in hda_source_dict:
values.append(hda_source_dict[val])
return values
if is_hashable(
value
) and value not in history.datasets and value in hda_source_dict:
return hda_source_dict[value]
visit_input_values(tool.inputs, params_objects, rerun_callback)
# Create a fake tool_state for the tool, with the parameters values
state = tool.new_state(trans)
state.inputs = params_objects
# If the job failed and has dependencies, allow dependency remap
if job.state == job.states.ERROR:
try:
if [
hda.dependent_jobs for hda in
[jtod.dataset for jtod in job.output_datasets]
if hda.dependent_jobs
]:
state.rerun_remap_job_id = trans.app.security.encode_id(
job.id)
except:
# Job has no outputs?
pass
#create an incoming object from the original job's dataset-modified param objects
incoming = {}
params_to_incoming(incoming, tool.inputs, params_objects, trans.app)
incoming["tool_state"] = galaxy.util.object_to_string(
state.encode(tool, trans.app))
template, vars = tool.handle_input(
trans, incoming,
old_errors=upgrade_messages) #update new state with old parameters
# Is the "add frame" stuff neccesary here?
add_frame = AddFrameData()
add_frame.debug = trans.debug
if from_noframe is not None:
add_frame.wiki_url = trans.app.config.wiki_url
add_frame.from_noframe = True
return trans.fill_template(
template,
history=history,
toolbox=self.get_toolbox(),
tool_version_select_field=tool_version_select_field,
tool=tool,
util=galaxy.util,
add_frame=add_frame,
tool_id_version_message=tool_id_version_message,
**vars)
def rerun( self, trans, id=None, from_noframe=None, **kwd ):
"""
Given a HistoryDatasetAssociation id, find the job and that created
the dataset, extract the parameters, and display the appropriate tool
form with parameters already filled in.
"""
if not id:
error( "'id' parameter is required" );
try:
id = int( id )
except:
# it's not an un-encoded id, try to parse as encoded
try:
id = trans.security.decode_id( id )
except:
error( "Invalid value for 'id' parameter" )
# Get the dataset object
data = trans.sa_session.query( trans.app.model.HistoryDatasetAssociation ).get( id )
#only allow rerunning if user is allowed access to the dataset.
if not ( trans.user_is_admin() or trans.app.security_agent.can_access_dataset( trans.get_current_user_roles(), data.dataset ) ):
error( "You are not allowed to access this dataset" )
# Get the associated job, if any.
job = data.creating_job
if not job:
raise Exception("Failed to get job information for dataset hid %d" % data.hid)
# Get the tool object
tool_id = job.tool_id
tool_version = job.tool_version
try:
tool_version_select_field, tools, tool = self.__get_tool_components( tool_id,
tool_version=tool_version,
get_loaded_tools_by_lineage=False,
set_selected=True )
if ( tool.id == job.tool_id or tool.old_id == job.tool_id ) and tool.version == job.tool_version:
tool_id_version_message = ''
elif tool.id == job.tool_id:
if job.tool_version == None:
# For some reason jobs don't always keep track of the tool version.
tool_id_version_message = ''
else:
tool_id_version_message = 'This job was initially run with tool version "%s", which is not currently available. ' % job.tool_version
if len( tools ) > 1:
tool_id_version_message += 'You can rerun the job with the selected tool or choose another derivation of the tool.'
else:
tool_id_version_message += 'You can rerun the job with this tool version, which is a derivation of the original tool.'
else:
if len( tools ) > 1:
tool_id_version_message = 'This job was initially run with tool version "%s", which is not currently available. ' % job.tool_version
tool_id_version_message += 'You can rerun the job with the selected tool or choose another derivation of the tool.'
else:
tool_id_version_message = 'This job was initially run with tool id "%s", version "%s", which is not ' % ( job.tool_id, job.tool_version )
tool_id_version_message += 'currently available. You can rerun the job with this tool, which is a derivation of the original tool.'
assert tool is not None, 'Requested tool has not been loaded.'
except:
# This is expected so not an exception.
tool_id_version_message = ''
error( "This dataset was created by an obsolete tool (%s). Can't re-run." % tool_id )
# Can't rerun upload, external data sources, et cetera. Workflow compatible will proxy this for now
if not tool.is_workflow_compatible:
error( "The '%s' tool does not currently support rerunning." % tool.name )
# Get the job's parameters
try:
params_objects = job.get_param_values( trans.app, ignore_errors = True )
except:
raise Exception( "Failed to get parameters for dataset id %d " % data.id )
upgrade_messages = tool.check_and_update_param_values( params_objects, trans, update_values=False )
# Need to remap dataset parameters. Job parameters point to original
# dataset used; parameter should be the analygous dataset in the
# current history.
history = trans.get_history()
hda_source_dict = {} # Mapping from HDA in history to source HDAs.
for hda in history.datasets:
source_hda = hda.copied_from_history_dataset_association
while source_hda:#should this check library datasets as well?
#FIXME: could be multiple copies of a hda in a single history, this does a better job of matching on cloned histories,
#but is still less than perfect when eg individual datasets are copied between histories
if source_hda not in hda_source_dict or source_hda.hid == hda.hid:
hda_source_dict[ source_hda ] = hda
source_hda = source_hda.copied_from_history_dataset_association
# Unpack unvalidated values to strings, they'll be validated when the
# form is submitted (this happens when re-running a job that was
# initially run by a workflow)
#This needs to be done recursively through grouping parameters
def rerun_callback( input, value, prefixed_name, prefixed_label ):
if isinstance( value, UnvalidatedValue ):
return str( value )
if isinstance( input, DataToolParameter ):
if isinstance(value,list):
values = []
for val in value:
if is_hashable( val ):
if val in history.datasets:
values.append( val )
elif val in hda_source_dict:
values.append( hda_source_dict[ val ])
return values
if is_hashable( value ) and value not in history.datasets and value in hda_source_dict:
return hda_source_dict[ value ]
visit_input_values( tool.inputs, params_objects, rerun_callback )
# Create a fake tool_state for the tool, with the parameters values
state = tool.new_state( trans )
state.inputs = params_objects
# If the job failed and has dependencies, allow dependency remap
if job.state == job.states.ERROR:
try:
if [ hda.dependent_jobs for hda in [ jtod.dataset for jtod in job.output_datasets ] if hda.dependent_jobs ]:
state.rerun_remap_job_id = trans.app.security.encode_id(job.id)
except:
# Job has no outputs?
pass
#create an incoming object from the original job's dataset-modified param objects
incoming = {}
params_to_incoming( incoming, tool.inputs, params_objects, trans.app )
incoming[ "tool_state" ] = galaxy.util.object_to_string( state.encode( tool, trans.app ) )
template, vars = tool.handle_input( trans, incoming, old_errors=upgrade_messages ) #update new state with old parameters
# Is the "add frame" stuff neccesary here?
add_frame = AddFrameData()
add_frame.debug = trans.debug
if from_noframe is not None:
add_frame.wiki_url = trans.app.config.wiki_url
add_frame.from_noframe = True
return trans.fill_template( template,
history=history,
toolbox=self.get_toolbox(),
tool_version_select_field=tool_version_select_field,
tool=tool,
util=galaxy.util,
add_frame=add_frame,
tool_id_version_message=tool_id_version_message,
**vars )
def get_config_form(self):
if self.tool:
self.add_dummy_datasets()
incoming = {}
params_to_incoming(incoming, self.tool.inputs, self.state.inputs, self.trans.app)
return self.tool.to_json(self.trans, incoming, workflow_building_mode=True)
class ToolRunner(BaseUIController):
# Hack to get biomart to work, ideally, we could pass tool_id to biomart and receive it back
@web.expose
def biomart(self, trans, tool_id='biomart', **kwd):
"""Catches the tool id and redirects as needed"""
return self.index(trans, tool_id=tool_id, **kwd)
# test to get hapmap to work, ideally, we could pass tool_id to hapmap biomart and receive it back
@web.expose
def hapmapmart(self, trans, tool_id='hapmapmart', **kwd):
"""Catches the tool id and redirects as needed"""
return self.index(trans, tool_id=tool_id, **kwd)
@web.expose
def default(self, trans, tool_id=None, **kwd):
"""Catches the tool id and redirects as needed"""
return self.index(trans, tool_id=tool_id, **kwd)
def __get_tool_components(self,
tool_id,
tool_version=None,
get_loaded_tools_by_lineage=False,
set_selected=False):
return self.get_toolbox().get_tool_components(
tool_id, tool_version, get_loaded_tools_by_lineage, set_selected)
@web.expose
def index(self, trans, tool_id=None, from_noframe=None, **kwd):
# No tool id passed, redirect to main page
if tool_id is None:
return trans.response.send_redirect(
url_for(controller="root", action="welcome"))
# When the tool form is initially loaded, the received kwd will not include a 'refresh'
# entry (which only is included when another option is selected in the tool_version_select_field),
# so the default selected option should be the most recent version of the tool. The following
# check will mae sure this occurs.
refreshed_on_change = kwd.get('refresh', False)
tool_version_select_field, tools, tool = self.__get_tool_components(
tool_id,
tool_version=None,
get_loaded_tools_by_lineage=False,
set_selected=refreshed_on_change)
# No tool matching the tool id, display an error (shouldn't happen)
if not tool or not tool.allow_user_access(trans.user):
log.error("index called with tool id '%s' but no such tool exists",
tool_id)
trans.log_event("Tool id '%s' does not exist" % tool_id)
trans.response.status = 404
return trans.show_error_message("Tool '%s' does not exist." %
(escape(tool_id)))
if tool.require_login and not trans.user:
message = "You must be logged in to use this tool."
status = "info"
redirect = url_for(controller='tool_runner',
action='index',
tool_id=tool_id,
**kwd)
return trans.response.send_redirect(
url_for(controller='user',
action='login',
cntrller='user',
message=message,
status=status,
redirect=redirect))
def _validated_params_for(kwd):
params = galaxy.util.Params(
kwd, sanitize=False
) # Sanitize parameters when substituting into command line via input wrappers
# do param translation here, used by datasource tools
if tool.input_translator:
tool.input_translator.translate(params)
return params
params = _validated_params_for(kwd)
# We may be visiting Galaxy for the first time ( e.g., sending data from UCSC ),
# so make sure to create a new history if we've never had one before.
history = tool.get_default_history_by_trans(trans, create=True)
try:
template, vars = tool.handle_input(trans, params.__dict__)
except KeyError:
# This error indicates (or at least can indicate) there was a
# problem with the stored tool_state - it is incompatible with
# this variant of the tool - possibly because the tool changed
# or because the tool version changed.
del kwd["tool_state"]
params = _validated_params_for(kwd)
template, vars = tool.handle_input(trans, params.__dict__)
if len(params) > 0:
trans.log_event("Tool params: %s" % (str(params)), tool_id=tool_id)
add_frame = AddFrameData()
add_frame.debug = trans.debug
if from_noframe is not None:
add_frame.wiki_url = trans.app.config.wiki_url
add_frame.from_noframe = True
return trans.fill_template(
template,
history=history,
toolbox=self.get_toolbox(),
tool_version_select_field=tool_version_select_field,
tool=tool,
util=galaxy.util,
add_frame=add_frame,
form_input_auto_focus=True,
**vars)
@web.expose
def rerun(self, trans, id=None, from_noframe=None, job_id=None, **kwd):
"""
Given a HistoryDatasetAssociation id, find the job and that created
the dataset, extract the parameters, and display the appropriate tool
form with parameters already filled in.
"""
if job_id:
try:
job_id = trans.security.decode_id(job_id)
job = trans.sa_session.query(trans.app.model.Job).get(job_id)
except:
error("Invalid value for 'job_id' parameter")
if not trans.user_is_admin():
for data_assoc in job.output_datasets:
# only allow rerunning if user is allowed access to the dataset.
if not trans.app.security_agent.can_access_dataset(
trans.get_current_user_roles(),
data_assoc.dataset.dataset):
error("You are not allowed to rerun this job")
param_error_text = "Failed to get parameters for job id %d " % job_id
else:
if not id:
error("'id' parameter is required")
try:
id = int(id)
except:
# it's not an un-encoded id, try to parse as encoded
try:
id = trans.security.decode_id(id)
except:
error("Invalid value for 'id' parameter")
# Get the dataset object
data = trans.sa_session.query(
trans.app.model.HistoryDatasetAssociation).get(id)
# only allow rerunning if user is allowed access to the dataset.
if not (trans.user_is_admin()
or trans.app.security_agent.can_access_dataset(
trans.get_current_user_roles(), data.dataset)):
error("You are not allowed to access this dataset")
# Get the associated job, if any.
job = data.creating_job
if not job:
raise Exception(
"Failed to get job information for dataset hid %d" %
data.hid)
param_error_text = "Failed to get parameters for dataset id %d " % data.id
# Get the tool object
tool_id = job.tool_id
tool_version = job.tool_version
try:
tool_version_select_field, tools, tool = self.__get_tool_components(
tool_id,
tool_version=tool_version,
get_loaded_tools_by_lineage=False,
set_selected=True)
if (tool.id == job.tool_id or tool.old_id
== job.tool_id) and tool.version == job.tool_version:
tool_id_version_message = ''
elif tool.id == job.tool_id:
if job.tool_version is None:
# For some reason jobs don't always keep track of the tool version.
tool_id_version_message = ''
else:
tool_id_version_message = 'This job was initially run with tool version "%s", which is not currently available. ' % job.tool_version
if len(tools) > 1:
tool_id_version_message += 'You can rerun the job with the selected tool or choose another derivation of the tool.'
else:
tool_id_version_message += 'You can rerun the job with this tool version, which is a derivation of the original tool.'
else:
if len(tools) > 1:
tool_id_version_message = 'This job was initially run with tool version "%s", which is not currently available. ' % job.tool_version
tool_id_version_message += 'You can rerun the job with the selected tool or choose another derivation of the tool.'
else:
tool_id_version_message = 'This job was initially run with tool id "%s", version "%s", which is not ' % (
job.tool_id, job.tool_version)
tool_id_version_message += 'currently available. You can rerun the job with this tool, which is a derivation of the original tool.'
assert tool is not None, 'Requested tool has not been loaded.'
except:
# This is expected so not an exception.
tool_id_version_message = ''
error(
"This dataset was created by an obsolete tool (%s). Can't re-run."
% tool_id)
if not tool.allow_user_access(trans.user):
error("The requested tool is unknown.")
# Can't rerun upload, external data sources, et cetera. Workflow compatible will proxy this for now
if not tool.is_workflow_compatible:
error("The '%s' tool does not currently support rerunning." %
tool.name)
# Get the job's parameters
try:
params_objects = job.get_param_values(trans.app,
ignore_errors=True)
except:
raise Exception(param_error_text)
upgrade_messages = tool.check_and_update_param_values(
params_objects, trans, update_values=False)
# Need to remap dataset parameters. Job parameters point to original
# dataset used; parameter should be the analygous dataset in the
# current history.
history = trans.get_history()
hda_source_dict = {} # Mapping from HDA in history to source HDAs.
for hda in history.datasets:
source_hda = hda.copied_from_history_dataset_association
while source_hda: # should this check library datasets as well?
# FIXME: could be multiple copies of a hda in a single history, this does a better job of matching on cloned histories,
# but is still less than perfect when eg individual datasets are copied between histories
if source_hda not in hda_source_dict or source_hda.hid == hda.hid:
hda_source_dict[source_hda] = hda
source_hda = source_hda.copied_from_history_dataset_association
# Ditto for dataset collections.
hdca_source_dict = {}
for hdca in history.dataset_collections:
source_hdca = hdca.copied_from_history_dataset_collection_association
while source_hdca:
if source_hdca not in hdca_source_dict or source_hdca.hid == hdca.hid:
hdca_source_dict[source_hdca] = hdca
source_hdca = source_hdca.copied_from_history_dataset_collection_association
# Unpack unvalidated values to strings, they'll be validated when the
# form is submitted (this happens when re-running a job that was
# initially run by a workflow)
# This needs to be done recursively through grouping parameters
def rerun_callback(input, value, prefixed_name, prefixed_label):
if isinstance(value, UnvalidatedValue):
try:
return input.to_html_value(value.value, trans.app)
except Exception, e:
# Need to determine when (if ever) the to_html_value call could fail.
log.debug(
"Failed to use input.to_html_value to determine value of unvalidated parameter, defaulting to string: %s"
% (e))
return str(value)
if isinstance(input, DataToolParameter):
if isinstance(value, list):
values = []
for val in value:
if is_hashable(val):
if val in history.datasets:
values.append(val)
elif val in hda_source_dict:
values.append(hda_source_dict[val])
return values
if is_hashable(
value
) and value not in history.datasets and value in hda_source_dict:
return hda_source_dict[value]
elif isinstance(input, DataCollectionToolParameter):
if is_hashable(
value
) and value not in history.dataset_collections and value in hdca_source_dict:
return hdca_source_dict[value]
visit_input_values(tool.inputs, params_objects, rerun_callback)
# Create a fake tool_state for the tool, with the parameters values
state = tool.new_state(trans)
state.inputs = params_objects
# If the job failed and has dependencies, allow dependency remap
if job.state == job.states.ERROR:
try:
if [
hda.dependent_jobs for hda in
[jtod.dataset for jtod in job.output_datasets]
if hda.dependent_jobs
]:
state.rerun_remap_job_id = trans.app.security.encode_id(
job.id)
except:
# Job has no outputs?
pass
# create an incoming object from the original job's dataset-modified param objects
incoming = {}
params_to_incoming(incoming, tool.inputs, params_objects, trans.app)
incoming["tool_state"] = galaxy.util.object_to_string(
state.encode(tool, trans.app))
template, vars = tool.handle_input(
trans, incoming, old_errors=upgrade_messages
) # update new state with old parameters
# Is the "add frame" stuff neccesary here?
add_frame = AddFrameData()
add_frame.debug = trans.debug
if from_noframe is not None:
add_frame.wiki_url = trans.app.config.wiki_url
add_frame.from_noframe = True
return trans.fill_template(
template,
history=history,
toolbox=self.get_toolbox(),
tool_version_select_field=tool_version_select_field,
tool=tool,
job=job,
util=galaxy.util,
add_frame=add_frame,
tool_id_version_message=tool_id_version_message,
**vars)
def _workflow_to_dict_run(self, trans, stored):
"""
Builds workflow dictionary used by run workflow form
"""
workflow = stored.latest_workflow
if len(workflow.steps) == 0:
raise exceptions.MessageException('Workflow cannot be run because it does not have any steps.')
if attach_ordered_steps(workflow, workflow.steps):
raise exceptions.MessageException('Workflow cannot be run because it contains cycles.')
trans.workflow_building_mode = workflow_building_modes.USE_HISTORY
module_injector = WorkflowModuleInjector(trans)
has_upgrade_messages = False
step_version_changes = []
missing_tools = []
errors = {}
for step in workflow.steps:
try:
module_injector.inject(step, steps=workflow.steps, exact_tools=False)
except exceptions.ToolMissingException:
if step.tool_id not in missing_tools:
missing_tools.append(step.tool_id)
continue
if step.upgrade_messages:
has_upgrade_messages = True
if step.type == 'tool' or step.type is None:
if step.module.version_changes:
step_version_changes.extend(step.module.version_changes)
step_errors = step.module.get_errors()
if step_errors:
errors[step.id] = step_errors
if missing_tools:
workflow.annotation = self.get_item_annotation_str(trans.sa_session, trans.user, workflow)
raise exceptions.MessageException('Following tools missing: %s' % missing_tools)
workflow.annotation = self.get_item_annotation_str(trans.sa_session, trans.user, workflow)
step_order_indices = {}
for step in workflow.steps:
step_order_indices[step.id] = step.order_index
step_models = []
for i, step in enumerate(workflow.steps):
step_model = None
if step.type == 'tool':
incoming = {}
tool = trans.app.toolbox.get_tool(step.tool_id, tool_version=step.tool_version)
params_to_incoming(incoming, tool.inputs, step.state.inputs, trans.app)
step_model = tool.to_json(trans, incoming, workflow_building_mode=workflow_building_modes.USE_HISTORY)
step_model['post_job_actions'] = [{
'short_str' : ActionBox.get_short_str(pja),
'action_type' : pja.action_type,
'output_name' : pja.output_name,
'action_arguments' : pja.action_arguments
} for pja in step.post_job_actions]
else:
inputs = step.module.get_runtime_inputs(connections=step.output_connections)
step_model = {
'inputs' : [input.to_dict(trans) for input in inputs.values()]
}
step_model['step_type'] = step.type
step_model['step_label'] = step.label
step_model['step_name'] = step.module.get_name()
step_model['step_version'] = step.module.get_version()
step_model['step_index'] = step.order_index
step_model['output_connections'] = [{
'input_step_index' : step_order_indices.get(oc.input_step_id),
'output_step_index' : step_order_indices.get(oc.output_step_id),
'input_name' : oc.input_name,
'output_name' : oc.output_name
} for oc in step.output_connections]
if step.annotations:
step_model['annotation'] = step.annotations[0].annotation
if step.upgrade_messages:
step_model['messages'] = step.upgrade_messages
step_models.append(step_model)
return {
'id': trans.app.security.encode_id(stored.id),
'history_id': trans.app.security.encode_id(trans.history.id) if trans.history else None,
'name': stored.name,
'steps': step_models,
'step_version_changes': step_version_changes,
'has_upgrade_messages': has_upgrade_messages,
'workflow_resource_parameters': self._workflow_resource_parameters(trans, stored, workflow),
}
job = data.creating_job
if not job:
trans.response.status = 500
return { 'error': 'Creating job not found.' }
except Exception, exception:
trans.response.status = 500
return { 'error': 'Failed to get job information.' }
# load job parameters into incoming
tool_message = ''
if job:
try:
job_params = job.get_param_values( trans.app, ignore_errors = True )
job_messages = tool.check_and_update_param_values( job_params, trans, update_values=False )
tool_message = self._compare_tool_version(trans, tool, job)
params_to_incoming( kwd, tool.inputs, job_params, trans.app )
except Exception, exception:
trans.response.status = 500
return { 'error': str( exception ) }
# create parameter object
params = galaxy.util.Params( kwd, sanitize = False )
# convert value to jsonifiable value
def convert(v):
# check if value is numeric
isnumber = False
try:
float(v)
isnumber = True
except Exception:
def get_config_form( self ):
if self.tool:
self.add_dummy_datasets()
incoming = {}
params_to_incoming( incoming, self.tool.inputs, self.state.inputs, self.trans.app )
return self.tool.to_json( self.trans, incoming, workflow_building_mode=True )
