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Source code for galaxy.workflow.modules

"""
Modules used in building workflows
"""
import logging
from json import loads
from xml.etree.ElementTree import (
    Element,
    XML
)

from galaxy import (
    exceptions,
    model,
    web
)
from galaxy.dataset_collections import matching
from galaxy.exceptions import ToolMissingException
from galaxy.jobs.actions.post import ActionBox
from galaxy.model import PostJobAction
from galaxy.tools import (
    DefaultToolState,
    ToolInputsNotReadyException
)
from galaxy.tools.execute import execute
from galaxy.tools.parameters import (
    check_param,
    params_to_incoming,
    visit_input_values
)
from galaxy.tools.parameters.basic import (
    BooleanToolParameter,
    DataCollectionToolParameter,
    DataToolParameter,
    parameter_types,
    RuntimeValue,
    SelectToolParameter,
    TextToolParameter,
    workflow_building_modes
)
from galaxy.tools.parameters.wrapped import make_dict_copy
from galaxy.util.bunch import Bunch
from galaxy.util.json import safe_loads
from galaxy.util.odict import odict
from tool_shed.util import common_util

log = logging.getLogger(__name__)

# Key into Tool state to describe invocation-specific runtime properties.
RUNTIME_STEP_META_STATE_KEY = "__STEP_META_STATE__"
# Key into step runtime state dict describing invocation-specific post job
# actions (i.e. PJA specified at runtime on top of the workflow-wide defined
# ones.
RUNTIME_POST_JOB_ACTIONS_KEY = "__POST_JOB_ACTIONS__"
NO_REPLACEMENT = object()


[docs]class WorkflowModule(object):
[docs] def __init__(self, trans, content_id=None, **kwds): self.trans = trans self.content_id = content_id self.state = DefaultToolState()
# ---- Creating modules from various representations ---------------------
[docs] @classmethod def from_dict(Class, trans, d, **kwds): module = Class(trans, **kwds) module.recover_state(d.get("tool_state")) module.label = d.get("label") return module
[docs] @classmethod def from_workflow_step(Class, trans, step, **kwds): module = Class(trans, **kwds) module.recover_state(step.tool_inputs) module.label = step.label return module
# ---- Saving in various forms ------------------------------------------
[docs] def save_to_step(self, step): step.type = self.type step.tool_inputs = self.get_state()
# ---- General attributes -----------------------------------------------
[docs] def get_type(self): return self.type
[docs] def get_name(self): return self.name
[docs] def get_version(self): return None
[docs] def get_content_id(self): """ If this component has an identifier external to the step (such as a tool or another workflow) return the identifier for that content. """ return None
[docs] def get_tooltip(self, static_path=''): return None
# ---- Configuration time -----------------------------------------------
[docs] def get_state(self, nested=True): """ Return a serializable representation of the persistable state of the step. """ inputs = self.get_inputs() if inputs: return self.state.encode(Bunch(inputs=inputs), self.trans.app, nested=nested) else: return self.state.inputs
[docs] def recover_state(self, state, **kwds): """ Recover state `dict` from simple dictionary describing configuration state (potentially from persisted step state). Sub-classes should supply a `default_state` method which contains the initial state `dict` with key, value pairs for all available attributes. """ self.state = DefaultToolState() inputs = self.get_inputs() if inputs: self.state.decode(state, Bunch(inputs=inputs), self.trans.app) else: self.state.inputs = safe_loads(state) or {}
[docs] def get_errors(self): """ This returns a step related error message as string or None """ return None
[docs] def get_inputs(self): """ This returns inputs displayed in the workflow editor """ return {}
[docs] def get_data_inputs(self): """ Get configure time data input descriptions. """ return []
[docs] def get_data_outputs(self): return []
[docs] def get_post_job_actions(self, incoming): return []
[docs] def check_and_update_state(self): """ If the state is not in sync with the current implementation of the module, try to update. Returns a list of messages to be displayed """ pass
[docs] def add_dummy_datasets(self, connections=None, steps=None): """ Replace connected inputs with placeholder/dummy values. """ pass
[docs] def get_config_form(self): """ Serializes input parameters of a module into input dictionaries. """ return { 'title' : self.name, 'inputs': [param.to_dict(self.trans) for param in self.get_inputs().values()] }
# ---- Run time ---------------------------------------------------------
[docs] def get_runtime_state(self): raise TypeError("Abstract method")
[docs] def get_runtime_inputs(self, **kwds): """ Used internally by modules and when displaying inputs in workflow editor and run workflow templates. """ return {}
[docs] def compute_runtime_state(self, trans, step_updates=None): """ Determine the runtime state (potentially different from self.state which describes configuration state). This (again unlike self.state) is currently always a `DefaultToolState` object. If `step_updates` is `None`, this is likely for rendering the run form for instance and no runtime properties are available and state must be solely determined by the default runtime state described by the step. If `step_updates` are available they describe the runtime properties supplied by the workflow runner. """ state = self.get_runtime_state() step_errors = {} if step_updates: def update_value(input, context, prefixed_name, **kwargs): if prefixed_name in step_updates: value, error = check_param(trans, input, step_updates.get(prefixed_name), context) if error is not None: step_errors[prefixed_name] = error return value return NO_REPLACEMENT visit_input_values(self.get_runtime_inputs(), state.inputs, update_value, no_replacement_value=NO_REPLACEMENT) return state, step_errors
[docs] def encode_runtime_state(self, runtime_state): """ Takes the computed runtime state and serializes it during run request creation. """ return runtime_state.encode(Bunch(inputs=self.get_runtime_inputs()), self.trans.app)
[docs] def decode_runtime_state(self, runtime_state): """ Takes the serialized runtime state and decodes it when running the workflow. """ state = DefaultToolState() state.decode(runtime_state, Bunch(inputs=self.get_runtime_inputs()), self.trans.app) return state
[docs] def execute(self, trans, progress, invocation, step): """ Execute the given workflow step in the given workflow invocation. Use the supplied workflow progress object to track outputs, find inputs, etc... """ raise TypeError("Abstract method")
[docs] def do_invocation_step_action(self, step, action): """ Update or set the workflow invocation state action - generic extension point meant to allows users to interact with interactive workflow modules. The action object returned from this method will be attached to the WorkflowInvocationStep and be available the next time the workflow scheduler visits the workflow. """ raise exceptions.RequestParameterInvalidException("Attempting to perform invocation step action on module that does not support actions.")
[docs] def recover_mapping(self, step, step_invocations, progress): """ Re-populate progress object with information about connections from previously executed steps recorded via step_invocations. """ raise TypeError("Abstract method")
[docs]class SubWorkflowModule(WorkflowModule): # Two step improvements to build runtime inputs for subworkflow modules # - First pass verify nested workflow doesn't have an RuntimeInputs # - Second pass actually turn RuntimeInputs into inputs if possible. type = "subworkflow" name = "Subworkflow"
[docs] @classmethod def from_dict(Class, trans, d, **kwds): module = super(SubWorkflowModule, Class).from_dict(trans, d, **kwds) if "subworkflow" in d: module.subworkflow = d["subworkflow"] elif "content_id" in d: from galaxy.managers.workflows import WorkflowsManager module.subworkflow = WorkflowsManager(trans.app).get_owned_workflow(trans, d["content_id"]) else: raise Exception("Step associated subworkflow could not be found.") return module
[docs] @classmethod def from_workflow_step(Class, trans, step, **kwds): module = super(SubWorkflowModule, Class).from_workflow_step(trans, step, **kwds) module.subworkflow = step.subworkflow return module
[docs] def save_to_step(self, step): step.type = self.type step.subworkflow = self.subworkflow
[docs] def get_name(self): if hasattr(self.subworkflow, 'name'): return self.subworkflow.name return self.name
[docs] def get_data_inputs(self): """ Get configure time data input descriptions. """ # Filter subworkflow steps and get inputs step_to_input_type = { "data_input": "dataset", "data_collection_input": "dataset_collection", } inputs = [] if hasattr(self.subworkflow, 'input_steps'): for step in self.subworkflow.input_steps: name = step.label if not name: step_module = module_factory.from_workflow_step(self.trans, step) name = "%s:%s" % (step.order_index, step_module.get_name()) step_type = step.type assert step_type in step_to_input_type input = dict( input_subworkflow_step_id=step.order_index, name=name, label=name, multiple=False, extensions=["data"], input_type=step_to_input_type[step_type], ) inputs.append(input) return inputs
[docs] def get_data_outputs(self): outputs = [] if hasattr(self.subworkflow, 'workflow_outputs'): for workflow_output in self.subworkflow.workflow_outputs: if workflow_output.workflow_step.type in {'data_input', 'data_collection_input'}: # It is just confusing to display the input data as output data in subworkflows continue output_step = workflow_output.workflow_step label = workflow_output.label target_output_name = workflow_output.output_name if not label: label = "%s:%s" % (output_step.order_index, target_output_name) output_module = module_factory.from_workflow_step(self.trans, output_step) data_outputs = output_module.get_data_outputs() target_output = {} for data_output in data_outputs: if data_output["name"] == target_output_name: target_output = data_output output = dict( name=label, label=label, extensions=target_output.get('extensions', ['input']), ) if target_output.get("collection"): output["collection"] = True output["collection_type"] = target_output["collection_type"] # TODO: collection_type_source should be set here to be more precise/correct - # but it can't be passed through as is since it would reference something # the editor can't see. Since we fix input collection types to workflows # the more correct thing to do would be to walk the subworkflow and # determine the effective collection type if collection_type_source # is set. outputs.append(output) return outputs
[docs] def get_content_id(self): return self.trans.security.encode_id(self.subworkflow.id)
[docs] def execute(self, trans, progress, invocation, step): """ Execute the given workflow step in the given workflow invocation. Use the supplied workflow progress object to track outputs, find inputs, etc... """ subworkflow_invoker = progress.subworkflow_invoker(trans, step) subworkflow_invoker.invoke() subworkflow = subworkflow_invoker.workflow subworkflow_progress = subworkflow_invoker.progress outputs = {} for workflow_output in subworkflow.workflow_outputs: workflow_output_label = workflow_output.label or "%s:%s" % (step.order_index, workflow_output.output_name) replacement = subworkflow_progress.get_replacement_workflow_output(workflow_output) outputs[workflow_output_label] = replacement progress.set_step_outputs(step, outputs) return None
[docs] def get_runtime_state(self): state = DefaultToolState() state.inputs = dict() return state
[docs]class InputModule(WorkflowModule):
[docs] def get_runtime_state(self): state = DefaultToolState() state.inputs = dict(input=None) return state
[docs] def get_data_inputs(self): return []
[docs] def execute(self, trans, progress, invocation, step): job, step_outputs = None, dict(output=step.state.inputs['input']) # Web controller may set copy_inputs_to_history, API controller always sets # inputs. if invocation.copy_inputs_to_history: for input_dataset_hda in list(step_outputs.values()): content_type = input_dataset_hda.history_content_type if content_type == "dataset": new_hda = input_dataset_hda.copy(copy_children=True) invocation.history.add_dataset(new_hda) step_outputs['input_ds_copy'] = new_hda elif content_type == "dataset_collection": new_hdca = input_dataset_hda.copy() invocation.history.add_dataset_collection(new_hdca) step_outputs['input_ds_copy'] = new_hdca else: raise Exception("Unknown history content encountered") # If coming from UI - we haven't registered invocation inputs yet, # so do that now so dependent steps can be recalculated. In the future # everything should come in from the API and this can be eliminated. if not invocation.has_input_for_step(step.id): content = next(iter(step_outputs.values())) if content: invocation.add_input(content, step.id) progress.set_outputs_for_input(step, step_outputs) return job
[docs] def recover_mapping(self, step, step_invocations, progress): progress.set_outputs_for_input(step)
[docs]class InputDataModule(InputModule): type = "data_input" name = "Input dataset"
[docs] def get_data_outputs(self): return [dict(name='output', extensions=['input'])]
[docs] def get_filter_set(self, connections=None): filter_set = [] if connections: for oc in connections: for ic in oc.input_step.module.get_data_inputs(): if 'extensions' in ic and ic['extensions'] != 'input' and ic['name'] == oc.input_name: filter_set += ic['extensions'] if not filter_set: filter_set = ['data'] return ', '.join(filter_set)
[docs] def get_runtime_inputs(self, connections=None): return dict(input=DataToolParameter(None, Element("param", name="input", label=self.label, multiple=False, type="data", format=self.get_filter_set(connections)), self.trans))
[docs]class InputDataCollectionModule(InputModule): type = "data_collection_input" name = "Input dataset collection" default_collection_type = "list" collection_type = default_collection_type
[docs] def get_inputs(self): collection_type = self.state.inputs.get("collection_type", self.default_collection_type) input_collection_type = TextToolParameter(None, XML( ''' <param name="collection_type" label="Collection type" type="text" value="%s"> <option value="list">List of Datasets</option> <option value="paired">Dataset Pair</option> <option value="list:paired">List of Dataset Pairs</option> </param> ''' % collection_type)) return dict(collection_type=input_collection_type)
[docs] def get_runtime_inputs(self, **kwds): collection_type = self.state.inputs.get("collection_type", self.default_collection_type) input_element = Element("param", name="input", label=self.label, type="data_collection", collection_type=collection_type) return dict(input=DataCollectionToolParameter(None, input_element, self.trans))
[docs] def get_data_outputs(self): return [ dict( name='output', extensions=['input_collection'], collection=True, collection_type=self.state.inputs.get('collection_type', self.default_collection_type) ) ]
[docs]class InputParameterModule(WorkflowModule): type = "parameter_input" name = "Input parameter" default_parameter_type = "text" default_optional = False parameter_type = default_parameter_type optional = default_optional
[docs] def get_inputs(self): # TODO: Use an external xml or yaml file to load the parameter definition parameter_type = self.state.inputs.get("parameter_type", self.default_parameter_type) optional = self.state.inputs.get("optional", self.default_optional) input_parameter_type = SelectToolParameter(None, XML( ''' <param name="parameter_type" label="Parameter type" type="select" value="%s"> <option value="text">Text</option> <option value="integer">Integer</option> <option value="float">Float</option> <option value="boolean">Boolean (True or False)</option> <option value="color">Color</option> </param> ''' % parameter_type)) return odict([("parameter_type", input_parameter_type), ("optional", BooleanToolParameter(None, Element("param", name="optional", label="Optional", type="boolean", value=optional)))])
[docs] def get_runtime_inputs(self, **kwds): parameter_type = self.state.inputs.get("parameter_type", self.default_parameter_type) optional = self.state.inputs.get("optional", self.default_optional) if parameter_type not in ["text", "boolean", "integer", "float", "color"]: raise ValueError("Invalid parameter type for workflow parameters encountered.") parameter_class = parameter_types[parameter_type] parameter_kwds = {} if parameter_type in ["integer", "float"]: parameter_kwds["value"] = str(0) # TODO: Use a dict-based description from YAML tool source element = Element("param", name="input", label=self.label, type=parameter_type, optional=str(optional), **parameter_kwds) input = parameter_class(None, element) return dict(input=input)
[docs] def get_runtime_state(self): state = DefaultToolState() state.inputs = dict(input=None) return state
[docs] def get_data_inputs(self): return []
[docs] def execute(self, trans, progress, invocation, step): job, step_outputs = None, dict(output=step.state.inputs['input']) progress.set_outputs_for_input(step, step_outputs) return job
[docs]class PauseModule(WorkflowModule): """ Initially this module will unconditionally pause a workflow - will aim to allow conditional pausing later on. """ type = "pause" name = "Pause for dataset review"
[docs] def get_data_inputs(self): input = dict( name="input", label="Dataset for Review", multiple=False, extensions='input', input_type="dataset", ) return [input]
[docs] def get_data_outputs(self): return [dict(name="output", label="Reviewed Dataset", extensions=['input'])]
[docs] def get_runtime_state(self): state = DefaultToolState() state.inputs = dict() return state
[docs] def execute(self, trans, progress, invocation, step): progress.mark_step_outputs_delayed(step, why="executing pause step") return None
[docs] def recover_mapping(self, step, step_invocations, progress): if step_invocations: step_invocation = step_invocations[0] action = step_invocation.action if action: connection = step.input_connections_by_name["input"][0] replacement = progress.replacement_for_connection(connection) progress.set_step_outputs(step, {'output': replacement}) return elif action is False: raise CancelWorkflowEvaluation() delayed_why = "workflow paused at this step waiting for review" raise DelayedWorkflowEvaluation(why=delayed_why)
[docs] def do_invocation_step_action(self, step, action): """ Update or set the workflow invocation state action - generic extension point meant to allows users to interact with interactive workflow modules. The action object returned from this method will be attached to the WorkflowInvocationStep and be available the next time the workflow scheduler visits the workflow. """ return bool(action)
[docs]class ToolModule(WorkflowModule): type = "tool" name = "Tool"
[docs] def __init__(self, trans, tool_id, tool_version=None, exact_tools=False, **kwds): super(ToolModule, self).__init__(trans, content_id=tool_id, **kwds) self.tool_id = tool_id self.tool_version = tool_version self.tool = trans.app.toolbox.get_tool(tool_id, tool_version=tool_version, exact=exact_tools) if self.tool and tool_version and exact_tools and str(self.tool.version) != str(tool_version): log.info("Exact tool specified during workflow module creation for [%s] but couldn't find correct version [%s]." % (tool_id, tool_version)) self.tool = None self.post_job_actions = {} self.runtime_post_job_actions = {} self.workflow_outputs = [] self.version_changes = []
# ---- Creating modules from various representations ---------------------
[docs] @classmethod def from_dict(Class, trans, d, exact_tools=False, **kwds): tool_id = d.get('content_id') or d.get('tool_id') if tool_id is None: raise exceptions.RequestParameterInvalidException("No tool id could be located for step [%s]." % d) tool_version = d.get('tool_version') if tool_version: tool_version = str(tool_version) module = super(ToolModule, Class).from_dict(trans, d, tool_id=tool_id, tool_version=tool_version, exact_tools=exact_tools) module.post_job_actions = d.get('post_job_actions', {}) module.workflow_outputs = d.get('workflow_outputs', []) if module.tool: message = "" if tool_id != module.tool_id: message += "The tool (id '%s') specified in this step is not available. Using the tool with id %s instead." % (tool_id, module.tool_id) if d.get('tool_version', 'Unspecified') != module.get_version(): message += "%s: using version '%s' instead of version '%s' specified in this workflow." % (tool_id, module.get_version(), d.get('tool_version', 'Unspecified')) if message: log.debug(message) module.version_changes.append(message) return module
[docs] @classmethod def from_workflow_step(Class, trans, step, **kwds): tool_id = trans.app.toolbox.get_tool_id(step.tool_id) or step.tool_id tool_version = step.tool_version module = super(ToolModule, Class).from_workflow_step(trans, step, tool_id=tool_id, tool_version=tool_version) module.workflow_outputs = step.workflow_outputs module.post_job_actions = {} for pja in step.post_job_actions: module.post_job_actions[pja.action_type] = pja if module.tool: message = "" if step.tool_id != module.tool_id: # This means the exact version of the tool is not installed. We inform the user. old_tool_shed = step.tool_id.split("/repos/")[0] if old_tool_shed not in tool_id: # Only display the following warning if the tool comes from a different tool shed old_tool_shed_url = common_util.get_tool_shed_url_from_tool_shed_registry(trans.app, old_tool_shed) if not old_tool_shed_url: # a tool from a different tool_shed has been found, but the original tool shed has been deactivated old_tool_shed_url = "http://" + old_tool_shed # let's just assume it's either http, or a http is forwarded to https. old_url = old_tool_shed_url + "/view/%s/%s/" % (module.tool.repository_owner, module.tool.repository_name) new_url = module.tool.sharable_url + '/%s/' % module.tool.changeset_revision new_tool_shed_url = new_url.split("/view")[0] message += "The tool \'%s\', version %s by the owner %s installed from <a href=\"%s\" target=\"_blank\">%s</a> is not available. " % (module.tool.name, tool_version, module.tool.repository_owner, old_url, old_tool_shed_url) message += "A derivation of this tool installed from <a href=\"%s\" target=\"_blank\">%s</a> will be used instead. " % (new_url, new_tool_shed_url) if step.tool_version and (step.tool_version != module.tool.version): message += "<span title=\"tool id '%s'\">Using version '%s' instead of version '%s' specified in this workflow. " % (tool_id, module.tool.version, step.tool_version) if message: log.debug(message) module.version_changes.append(message) else: log.warning("The tool '%s' is missing. Cannot build workflow module." % tool_id) return module
# ---- Saving in various forms ------------------------------------------
[docs] def save_to_step(self, step): super(ToolModule, self).save_to_step(step) step.tool_id = self.tool_id step.tool_version = self.get_version() for k, v in self.post_job_actions.items(): pja = self.__to_pja(k, v, step) self.trans.sa_session.add(pja)
# ---- General attributes ------------------------------------------------
[docs] def get_name(self): return self.tool.name if self.tool else self.tool_id
[docs] def get_content_id(self): return self.tool_id
[docs] def get_version(self): return self.tool.version if self.tool else self.tool_version
[docs] def get_tooltip(self, static_path=''): if self.tool and self.tool.help: return self.tool.help.render(host_url=web.url_for('/'), static_path=static_path)
# ---- Configuration time -----------------------------------------------
[docs] def get_errors(self): return None if self.tool else "Tool is not installed."
[docs] def get_inputs(self): return self.tool.inputs if self.tool else {}
[docs] def get_data_inputs(self): data_inputs = [] if self.tool: def callback(input, prefixed_name, prefixed_label, **kwargs): if not hasattr(input, 'hidden') or not input.hidden: if isinstance(input, DataToolParameter): data_inputs.append(dict( name=prefixed_name, label=prefixed_label, multiple=input.multiple, extensions=input.extensions, input_type="dataset", )) elif isinstance(input, DataCollectionToolParameter): data_inputs.append(dict( name=prefixed_name, label=prefixed_label, multiple=input.multiple, input_type="dataset_collection", collection_types=input.collection_types, extensions=input.extensions, )) visit_input_values(self.tool.inputs, self.state.inputs, callback) return data_inputs
[docs] def get_data_outputs(self): data_outputs = [] if self.tool: for name, tool_output in self.tool.outputs.items(): extra_kwds = {} if tool_output.collection: extra_kwds["collection"] = True extra_kwds["collection_type"] = tool_output.structure.collection_type extra_kwds["collection_type_source"] = tool_output.structure.collection_type_source formats = ['input'] # TODO: fix elif tool_output.format_source is not None: formats = ['input'] # default to special name "input" which remove restrictions on connections else: formats = [tool_output.format] for change_elem in tool_output.change_format: for when_elem in change_elem.findall('when'): format = when_elem.get('format', None) if format and format not in formats: formats.append(format) data_outputs.append( dict( name=name, extensions=formats, **extra_kwds ) ) return data_outputs
[docs] 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)
[docs] def check_and_update_state(self): if self.tool: return self.tool.check_and_update_param_values(self.state.inputs, self.trans, workflow_building_mode=True)
[docs] def add_dummy_datasets(self, connections=None, steps=None): if self.tool: if connections: # Store connections by input name input_connections_by_name = dict((conn.input_name, conn) for conn in connections) else: input_connections_by_name = {} # Any input needs to have value RuntimeValue or obtain the value from connected steps def callback(input, prefixed_name, context, **kwargs): if isinstance(input, DataToolParameter) or isinstance(input, DataCollectionToolParameter): if connections is not None and steps is not None and self.trans.workflow_building_mode is workflow_building_modes.USE_HISTORY: if prefixed_name in input_connections_by_name: connection = input_connections_by_name[prefixed_name] output_step = next(output_step for output_step in steps if connection.output_step_id == output_step.id) if output_step.type.startswith('data'): output_inputs = output_step.module.get_runtime_inputs(connections=connections) output_value = output_inputs['input'].get_initial_value(self.trans, context) if isinstance(input, DataToolParameter) and isinstance(output_value, self.trans.app.model.HistoryDatasetCollectionAssociation): return output_value.to_hda_representative() return output_value return RuntimeValue() else: return input.get_initial_value(self.trans, context) elif connections is None or prefixed_name in input_connections_by_name: return RuntimeValue() visit_input_values(self.tool.inputs, self.state.inputs, callback) else: raise ToolMissingException("Tool %s missing. Cannot add dummy datasets." % self.tool_id)
[docs] def get_post_job_actions(self, incoming): return ActionBox.handle_incoming(incoming)
# ---- Run time ---------------------------------------------------------
[docs] def get_runtime_state(self): state = DefaultToolState() state.inputs = self.state.inputs return state
[docs] def get_runtime_inputs(self, **kwds): return self.get_inputs()
[docs] def compute_runtime_state(self, trans, step_updates=None): # Warning: This method destructively modifies existing step state. if self.tool: step_errors = {} state = self.state self.runtime_post_job_actions = {} if step_updates: state, step_errors = super(ToolModule, self).compute_runtime_state(trans, step_updates) self.runtime_post_job_actions = step_updates.get(RUNTIME_POST_JOB_ACTIONS_KEY, {}) step_metadata_runtime_state = self.__step_meta_runtime_state() if step_metadata_runtime_state: state.inputs[RUNTIME_STEP_META_STATE_KEY] = step_metadata_runtime_state return state, step_errors else: raise ToolMissingException("Tool %s missing. Cannot compute runtime state." % self.tool_id)
[docs] def decode_runtime_state(self, runtime_state): """ Take runtime state from persisted invocation and convert it into a DefaultToolState object for use during workflow invocation. """ if self.tool: state = super(ToolModule, self).decode_runtime_state(runtime_state) if RUNTIME_STEP_META_STATE_KEY in runtime_state: self.__restore_step_meta_runtime_state(loads(runtime_state[RUNTIME_STEP_META_STATE_KEY])) return state else: raise ToolMissingException("Tool %s missing. Cannot recover runtime state." % self.tool_id)
[docs] def execute(self, trans, progress, invocation, step): tool = trans.app.toolbox.get_tool(step.tool_id, tool_version=step.tool_version) tool_state = step.state # Not strictly needed - but keep Tool state clean by stripping runtime # metadata parameters from it. if RUNTIME_STEP_META_STATE_KEY in tool_state.inputs: del tool_state.inputs[RUNTIME_STEP_META_STATE_KEY] collections_to_match = self._find_collections_to_match(tool, progress, step) # Have implicit collections... if collections_to_match.has_collections(): collection_info = self.trans.app.dataset_collections_service.match_collections(collections_to_match) else: collection_info = None param_combinations = [] if collection_info: iteration_elements_iter = collection_info.slice_collections() else: iteration_elements_iter = [None] for iteration_elements in iteration_elements_iter: execution_state = tool_state.copy() # TODO: Move next step into copy() execution_state.inputs = make_dict_copy(execution_state.inputs) expected_replacement_keys = set(step.input_connections_by_name.keys()) found_replacement_keys = set() # Connect up def callback(input, prefixed_name, **kwargs): replacement = NO_REPLACEMENT if isinstance(input, DataToolParameter) or isinstance(input, DataCollectionToolParameter): if iteration_elements and prefixed_name in iteration_elements: if isinstance(input, DataToolParameter): # Pull out dataset instance from element. replacement = iteration_elements[prefixed_name].dataset_instance if hasattr(iteration_elements[prefixed_name], u'element_identifier') and iteration_elements[prefixed_name].element_identifier: replacement.element_identifier = iteration_elements[prefixed_name].element_identifier else: # If collection - just use element model object. replacement = iteration_elements[prefixed_name] else: replacement = progress.replacement_for_tool_input(step, input, prefixed_name) else: replacement = progress.replacement_for_tool_input(step, input, prefixed_name) if replacement is not NO_REPLACEMENT: found_replacement_keys.add(prefixed_name) return replacement try: # Replace DummyDatasets with historydatasetassociations visit_input_values(tool.inputs, execution_state.inputs, callback, no_replacement_value=NO_REPLACEMENT) except KeyError as k: message_template = "Error due to input mapping of '%s' in '%s'. A common cause of this is conditional outputs that cannot be determined until runtime, please review your workflow." message = message_template % (tool.name, k.message) raise exceptions.MessageException(message) unmatched_input_connections = expected_replacement_keys - found_replacement_keys if unmatched_input_connections: log.warn("Failed to use input connections for inputs [%s]" % unmatched_input_connections) param_combinations.append(execution_state.inputs) try: execution_tracker = execute( trans=self.trans, tool=tool, param_combinations=param_combinations, history=invocation.history, collection_info=collection_info, workflow_invocation_uuid=invocation.uuid.hex ) except ToolInputsNotReadyException: delayed_why = "tool [%s] inputs are not ready, this special tool requires inputs to be ready" % tool.id raise DelayedWorkflowEvaluation(why=delayed_why) if collection_info: step_outputs = dict(execution_tracker.implicit_collections) else: step_outputs = dict(execution_tracker.output_datasets) step_outputs.update(execution_tracker.output_collections) progress.set_step_outputs(step, step_outputs) jobs = execution_tracker.successful_jobs for job in jobs: self._handle_post_job_actions(step, job, invocation.replacement_dict) if execution_tracker.execution_errors: failed_count = len(execution_tracker.execution_errors) success_count = len(execution_tracker.successful_jobs) all_count = failed_count + success_count message = "Failed to create %d out of %s job(s) for workflow step." % (failed_count, all_count) raise Exception(message) return jobs
[docs] def recover_mapping(self, step, step_invocations, progress): # Grab a job representing this invocation - for normal workflows # there will be just one job but if this step was mapped over there # may be many. job_0 = step_invocations[0].job outputs = {} for job_output in job_0.output_datasets: replacement_name = job_output.name replacement_value = job_output.dataset # If was a mapping step, grab the output mapped collection for # replacement instead. if replacement_value.hidden_beneath_collection_instance: replacement_value = replacement_value.hidden_beneath_collection_instance outputs[replacement_name] = replacement_value for job_output_collection in job_0.output_dataset_collection_instances: replacement_name = job_output_collection.name replacement_value = job_output_collection.dataset_collection_instance outputs[replacement_name] = replacement_value progress.set_step_outputs(step, outputs)
def _find_collections_to_match(self, tool, progress, step): collections_to_match = matching.CollectionsToMatch() def callback(input, prefixed_name, **kwargs): is_data_param = isinstance(input, DataToolParameter) if is_data_param and not input.multiple: data = progress.replacement_for_tool_input(step, input, prefixed_name) if isinstance(data, model.HistoryDatasetCollectionAssociation): collections_to_match.add(prefixed_name, data) is_data_collection_param = isinstance(input, DataCollectionToolParameter) if is_data_collection_param and not input.multiple: data = progress.replacement_for_tool_input(step, input, prefixed_name) history_query = input._history_query(self.trans) subcollection_type_description = history_query.can_map_over(data) if subcollection_type_description: collections_to_match.add(prefixed_name, data, subcollection_type=subcollection_type_description.collection_type) visit_input_values(tool.inputs, step.state.inputs, callback) return collections_to_match def _handle_post_job_actions(self, step, job, replacement_dict): # Create new PJA associations with the created job, to be run on completion. # PJA Parameter Replacement (only applies to immediate actions-- rename specifically, for now) # Pass along replacement dict with the execution of the PJA so we don't have to modify the object. # Combine workflow and runtime post job actions into the effective post # job actions for this execution. flush_required = False effective_post_job_actions = step.post_job_actions[:] for key, value in self.runtime_post_job_actions.items(): effective_post_job_actions.append(self.__to_pja(key, value, None)) for pja in effective_post_job_actions: if pja.action_type in ActionBox.immediate_actions: ActionBox.execute(self.trans.app, self.trans.sa_session, pja, job, replacement_dict) else: pjaa = model.PostJobActionAssociation(pja, job_id=job.id) self.trans.sa_session.add(pjaa) flush_required = True if flush_required: self.trans.sa_session.flush() def __restore_step_meta_runtime_state(self, step_runtime_state): if RUNTIME_POST_JOB_ACTIONS_KEY in step_runtime_state: self.runtime_post_job_actions = step_runtime_state[RUNTIME_POST_JOB_ACTIONS_KEY] def __step_meta_runtime_state(self): """ Build a dictionary a of meta-step runtime state (state about how the workflow step - not the tool state) to be serialized with the Tool state. """ return {RUNTIME_POST_JOB_ACTIONS_KEY: self.runtime_post_job_actions} def __to_pja(self, key, value, step): if 'output_name' in value: output_name = value['output_name'] else: output_name = None if 'action_arguments' in value: action_arguments = value['action_arguments'] else: action_arguments = None return PostJobAction(value['action_type'], step, output_name, action_arguments)
[docs]class WorkflowModuleFactory(object):
[docs] def __init__(self, module_types): self.module_types = module_types
[docs] def from_dict(self, trans, d, **kwargs): """ Return module initialized from the data in dictionary `d`. """ type = d['type'] assert type in self.module_types, "Unexpected workflow step type [%s] not found in [%s]" % (type, self.module_types.keys()) return self.module_types[type].from_dict(trans, d, **kwargs)
[docs] def from_workflow_step(self, trans, step): """ Return module initializd from the WorkflowStep object `step`. """ type = step.type return self.module_types[type].from_workflow_step(trans, step)
[docs]def is_tool_module_type(module_type): return not module_type or module_type == "tool"
module_types = dict( data_input=InputDataModule, data_collection_input=InputDataCollectionModule, parameter_input=InputParameterModule, pause=PauseModule, tool=ToolModule, subworkflow=SubWorkflowModule, ) module_factory = WorkflowModuleFactory(module_types)
[docs]def load_module_sections(trans): """ Get abstract description of the workflow modules this Galaxy instance is configured with. """ module_sections = {} module_sections['inputs'] = { "name": "inputs", "title": "Inputs", "modules": [ { "name": "data_input", "title": "Input Dataset", "description": "Input dataset" }, { "name": "data_collection_input", "title": "Input Dataset Collection", "description": "Input dataset collection" }, ], } if trans.app.config.enable_beta_workflow_modules: module_sections['experimental'] = { "name": "experimental", "title": "Experimental", "modules": [ { "name": "pause", "title": "Pause Workflow for Dataset Review", "description": "Pause for Review" }, { "name": "parameter_input", "title": "Parameter Input", "description": "Simple inputs used for workflow logic" }, ], } return module_sections
[docs]class DelayedWorkflowEvaluation(Exception):
[docs] def __init__(self, why=None): self.why = why
[docs]class CancelWorkflowEvaluation(Exception): pass
[docs]class WorkflowModuleInjector(object): """ Injects workflow step objects from the ORM with appropriate module and module generated/influenced state. """
[docs] def __init__(self, trans, allow_tool_state_corrections=False): self.trans = trans self.allow_tool_state_corrections = allow_tool_state_corrections
[docs] def inject(self, step, step_args=None, steps=None): """ Pre-condition: `step` is an ORM object coming from the database, if supplied `step_args` is the representation of the inputs for that step supplied via web form. Post-condition: The supplied `step` has new non-persistent attributes useful during workflow invocation. These include 'upgrade_messages', 'state', 'input_connections_by_name', and 'module'. If step_args is provided from a web form this is applied to generate 'state' else it is just obtained from the database. """ step_errors = None step.upgrade_messages = {} # Make connection information available on each step by input name. step.setup_input_connections_by_name() # Populate module. module = step.module = module_factory.from_workflow_step(self.trans, step) # Any connected input needs to have value DummyDataset (these # are not persisted so we need to do it every time) module.add_dummy_datasets(connections=step.input_connections, steps=steps) state, step_errors = module.compute_runtime_state(self.trans, step_args) step.state = state # Fix any missing parameters step.upgrade_messages = module.check_and_update_state() # Populate subworkflow components if step.type == "subworkflow": subworkflow = step.subworkflow populate_module_and_state(self.trans, subworkflow, param_map={}) return step_errors
[docs]def populate_module_and_state(trans, workflow, param_map, allow_tool_state_corrections=False, module_injector=None): """ Used by API but not web controller, walks through a workflow's steps and populates transient module and state attributes on each. """ if module_injector is None: module_injector = WorkflowModuleInjector(trans, allow_tool_state_corrections) for step in workflow.steps: step_args = param_map.get(step.id, {}) step_errors = module_injector.inject(step, step_args=step_args) if step_errors: raise exceptions.MessageException(step_errors, err_data={step.order_index: step_errors}) if step.upgrade_messages: if allow_tool_state_corrections: log.debug('Workflow step "%i" had upgrade messages: %s', step.id, step.upgrade_messages) else: raise exceptions.MessageException(step.upgrade_messages, err_data={step.order_index: step.upgrade_messages})