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Source code for galaxy.workflow.modules

Modules used in building workflows
import json
import logging
import re
from collections import OrderedDict
from xml.etree.ElementTree import (

from galaxy import (
from galaxy.exceptions import ToolMissingException
from galaxy.jobs.actions.post import ActionBox
from galaxy.model import PostJobAction
from galaxy.model.dataset_collections import matching
from galaxy.tool_util.parser.output_objects import ToolExpressionOutput
from galaxy.tools import (
from galaxy.tools.actions import filter_output
from galaxy.tools.execute import execute, MappingParameters, PartialJobExecution
from galaxy.tools.parameters import (
from galaxy.tools.parameters.basic import (
from galaxy.tools.parameters.history_query import HistoryQuery
from galaxy.tools.parameters.wrapped import make_dict_copy
from galaxy.util import unicodify
from galaxy.util.bunch import Bunch
from galaxy.util.json import safe_loads
from galaxy.util.rules_dsl import RuleSet
from galaxy.util.template import fill_template
from tool_shed.util import common_util

log = logging.getLogger(__name__)

# Key into Tool state to describe invocation-specific runtime properties.
# 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.

[docs]class NoReplacement(object): def __str__(self): return "NO_REPLACEMENT singleton"
NO_REPLACEMENT = NoReplacement()
[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) input_connections = d.get("input_connections", {}) module.recover_state(d.get("tool_state"), input_connections=input_connections, **kwds) 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, **kwargs): """ 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_all_inputs(self, data_only=False, connectable_only=False): return []
[docs] def get_data_inputs(self): """ Get configure time data input descriptions. """ return self.get_all_inputs(data_only=True)
[docs] def get_all_outputs(self, data_only=False): return []
[docs] def get_data_outputs(self): return self.get_all_outputs(data_only=True)
[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, step=None): """ 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=None, 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` is not `None`, it will be used to search for default values defined in workflow input steps. 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 is not None: def update_value(input, context, prefixed_name, **kwargs): step_input = step.get_input(prefixed_name) if step_input is None: return NO_REPLACEMENT if step_input.default_value_set: return step_input.default_value return NO_REPLACEMENT visit_input_values(self.get_runtime_inputs(), state.inputs, update_value, no_replacement_value=NO_REPLACEMENT) 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, use_cached_job=False): """ Execute the given workflow invocation step. Use the supplied workflow progress object to track outputs, find inputs, etc.... Return a False if there is additional processing required to on subsequent workflow scheduling runs, None or True means the workflow step executed properly. """ 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, invocation_step, progress): """ Re-populate progress object with information about connections from previously executed steps recorded via invocation_steps. """ outputs = {} for output_dataset_assoc in invocation_step.output_datasets: outputs[output_dataset_assoc.output_name] = output_dataset_assoc.dataset for output_dataset_collection_assoc in invocation_step.output_dataset_collections: outputs[output_dataset_collection_assoc.output_name] = output_dataset_collection_assoc.dataset_collection progress.set_step_outputs(invocation_step, outputs, already_persisted=True)
[docs] def get_replacement_parameters(self, step): """Return a list of replacement parameters.""" return []
[docs] def compute_collection_info(self, progress, step, all_inputs): """Use get_all_inputs (if implemented) to determine collection mapping for execution. Hopefully this can be reused for Tool and Subworkflow modules. """ collections_to_match = self._find_collections_to_match( progress, step, all_inputs ) # 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 return collection_info
def _find_collections_to_match(self, progress, step, all_inputs): collections_to_match = matching.CollectionsToMatch() dataset_collection_type_descriptions = self.trans.app.dataset_collections_service.collection_type_descriptions for input_dict in all_inputs: name = input_dict["name"] data = progress.replacement_for_input(step, input_dict) can_map_over = hasattr(data, "collection") # and data.collection.allow_implicit_mapping if not can_map_over: continue is_data_param = input_dict["input_type"] == "dataset" if is_data_param: multiple = input_dict["multiple"] if multiple: # multiple="true" data input, acts like "list" collection_type. # just need to figure out subcollection_type_description history_query = HistoryQuery.from_collection_types( ['list'], dataset_collection_type_descriptions, ) subcollection_type_description = history_query.can_map_over(data) if subcollection_type_description: collections_to_match.add(name, data, subcollection_type=subcollection_type_description) else: collections_to_match.add(name, data) continue is_data_collection_param = input_dict["input_type"] == "dataset_collection" if is_data_collection_param: history_query = HistoryQuery.from_collection_types( input_dict.get("collection_types", None), dataset_collection_type_descriptions, ) subcollection_type_description = history_query.can_map_over(data) if subcollection_type_description: collections_to_match.add(name, data, subcollection_type=subcollection_type_description.collection_type) continue if data is not NO_REPLACEMENT: collections_to_match.add(name, data) continue return collections_to_match
[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_all_inputs(self, data_only=False, connectable_only=False): """ Get configure time data input descriptions. """ # Filter subworkflow steps and get inputs step_to_input_type = { "data_input": "dataset", "data_collection_input": "dataset_collection", "parameter_input": "parameter", } 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], ) if step.type == 'data_collection_input': input['collection_type'] = step.tool_inputs.get('collection_type') if step.tool_inputs else None if step_type == 'parameter_input': input['type'] = step.tool_inputs['parameter_type'] inputs.append(input) return inputs
[docs] def get_modules(self): return [module_factory.from_workflow_step(self.trans, step) for step in self.subworkflow.steps]
[docs] def get_errors(self, **kwargs): errors = (module.get_errors(include_tool_id=True) for module in self.get_modules()) errors = [e for e in errors if e] if any(errors): return errors return None
[docs] def get_all_outputs(self, data_only=False): outputs = [] if hasattr(self.subworkflow, 'workflow_outputs'): from galaxy.managers.workflows import WorkflowContentsManager workflow_contents_manager = WorkflowContentsManager(self.trans.app) subworkflow_dict = workflow_contents_manager._workflow_to_dict_editor(trans=self.trans, stored=self.subworkflow.stored_workflow, workflow=self.subworkflow, tooltip=False, is_subworkflow=True) for order_index in sorted(subworkflow_dict['steps']): step = subworkflow_dict['steps'][order_index] data_outputs = step['outputs'] for workflow_output in step['workflow_outputs']: label = workflow_output['label'] if not label: label = "%s:%s" % (order_index, workflow_output['output_name']) workflow_output_uuid = workflow_output.get('uuid') or object() for data_output in data_outputs: data_output_uuid = data_output.get('uuid') or object() if data_output['name'] == workflow_output['output_name'] or data_output_uuid == workflow_output_uuid: data_output['label'] = label data_output['name'] = label # That's the right data_output break else: # This can happen when importing workflows with missing tools. # We can't raise an exception here, as that would prevent loading # the workflow. log.error("Workflow output '%s' defined, but not listed among data outputs" % workflow_output['output_name']) continue outputs.append(data_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, use_cached_job=False): """ Execute the given workflow step in the given workflow invocation. Use the supplied workflow progress object to track outputs, find inputs, etc... """ step = invocation_step.workflow_step subworkflow_invoker = progress.subworkflow_invoker(trans, step, use_cached_job=use_cached_job) 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" % (workflow_output.workflow_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(invocation_step, outputs) return None
[docs] def get_runtime_state(self): state = DefaultToolState() state.inputs = dict() return state
[docs] def get_runtime_inputs(self, connections=None): inputs = {} for step in self.subworkflow.steps: if step.type == "tool": tool = step.module.tool tool_inputs = step.module.state def callback(input, prefixed_name, prefixed_label, value=None, **kwds): # All data parameters are represented as runtime values, skip them # here. if input.type in ['data', 'data_collection']: return if is_runtime_value(value): input_name = "%d|%s" % (step.order_index, prefixed_name) inputs[input_name] = InputProxy(input, input_name) visit_input_values(tool.inputs, tool_inputs.inputs, callback) return inputs
[docs] def get_replacement_parameters(self, step): """Return a list of replacement parameters.""" replacement_parameters = set() for subworkflow_step in self.subworkflow.steps: module = subworkflow_step.module for replacement_parameter in module.get_replacement_parameters(subworkflow_step): replacement_parameters.add(replacement_parameter) return list(replacement_parameters)
[docs]class InputProxy(object): """Provide InputParameter-interfaces over inputs but renamed for workflow context."""
[docs] def __init__(self, input, prefixed_name): self.input = input self.prefixed_name = prefixed_name
@property def name(self): return self.prefixed_name @property def label(self): return self.prefixed_name
[docs] def to_dict(self, *args, **kwds): as_dict = self.input.to_dict(*args, **kwds) as_dict["name"] = self.prefixed_name return as_dict
[docs]class InputModule(WorkflowModule):
[docs] def get_runtime_state(self): state = DefaultToolState() state.inputs = dict(input=None) return state
[docs] def get_all_inputs(self, data_only=False, connectable_only=False): return []
[docs] def execute(self, trans, progress, invocation_step, use_cached_job=False): invocation = invocation_step.workflow_invocation step = invocation_step.workflow_step step_outputs = 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() 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(invocation_step, step_outputs)
[docs] def recover_mapping(self, invocation_step, progress): progress.set_outputs_for_input(invocation_step, already_persisted=True)
[docs]class InputDataModule(InputModule): type = "data_input" name = "Input dataset"
[docs] def get_all_outputs(self, data_only=False): 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_all_outputs(self, data_only=False): 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"> <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> ''')) for i, option in enumerate(input_parameter_type.static_options): option = list(option) if option[1] == parameter_type: # item 0 is option description, item 1 is value, item 2 is "selected" option[2] = True input_parameter_type.static_options[i] = tuple(option) return OrderedDict([("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_all_outputs(self, data_only=False): if data_only: return [] return [dict( name='output', label=self.label, type=self.state.inputs.get('parameter_type', self.parameter_type), parameter=True, )]
[docs] def execute(self, trans, progress, invocation_step, use_cached_job=False): step = invocation_step.workflow_step step_outputs = dict(output=step.state.inputs['input']) progress.set_outputs_for_input(invocation_step, step_outputs)
[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_all_inputs(self, data_only=False, connectable_only=False): input = dict( name="input", label="Dataset for Review", multiple=False, extensions='input', input_type="dataset", ) return [input] if not data_only else []
[docs] def get_all_outputs(self, data_only=False): 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, use_cached_job=False): step = invocation_step.workflow_step progress.mark_step_outputs_delayed(step, why="executing pause step")
[docs] def recover_mapping(self, invocation_step, progress): if invocation_step: step = invocation_step.workflow_step action = invocation_step.action if action: connection = step.input_connections_by_name["input"][0] replacement = progress.replacement_for_connection(connection) progress.set_step_outputs(invocation_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=True, tool_uuid=None, **kwds): super(ToolModule, self).__init__(trans, content_id=tool_id, **kwds) self.tool_id = tool_id self.tool_version = tool_version self.tool_uuid = tool_uuid self.tool = trans.app.toolbox.get_tool(tool_id, tool_version=tool_version, exact=exact_tools, tool_uuid=tool_uuid) 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, **kwds): tool_id = d.get('content_id') or d.get('tool_id') tool_version = d.get('tool_version') if tool_version: tool_version = str(tool_version) tool_uuid = d.get('tool_uuid', None) if tool_id is None and tool_uuid is None: tool_representation = d.get("tool_representation") if tool_representation: create_request = { "representation": tool_representation, } if not trans.user_is_admin: raise exceptions.AdminRequiredException("Only admin users can create tools dynamically.") dynamic_tool = trans.app.dynamic_tool_manager.create_tool( create_request, allow_load=False ) tool_uuid = dynamic_tool.uuid if tool_id is None and tool_uuid is None: raise exceptions.RequestParameterInvalidException("No content id could be located for for step [%s]" % d) module = super(ToolModule, Class).from_dict(trans, d, tool_id=tool_id, tool_version=tool_version, tool_uuid=tool_uuid, **kwds) 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): if step.tool_id is not None: tool_id = trans.app.toolbox.get_tool_id(step.tool_id) or step.tool_id else: tool_id = None tool_version = step.tool_version tool_uuid = step.tool_uuid module = super(ToolModule, Class).from_workflow_step(trans, step, tool_id=tool_id, tool_version=tool_version, tool_uuid=tool_uuid, **kwds) 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 and 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 if self.tool: step.tool_version = self.get_version() else: step.tool_version = self.tool_version tool_uuid = getattr(self, "tool_uuid", None) if tool_uuid: step.dynamic_tool = self.trans.app.dynamic_tool_manager.get_tool_by_uuid(tool_uuid) 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, include_tool_id=False, **kwargs): if not self.tool: if include_tool_id: return "%s is not installed" % self.tool_id else: return "Tool is not installed"
[docs] def get_inputs(self): return self.tool.inputs if self.tool else {}
[docs] def get_all_inputs(self, data_only=False, connectable_only=False): if data_only and connectable_only: raise Exception("Must specify at most one of data_only and connectable_only as True.") inputs = [] if self.tool: def callback(input, prefixed_name, prefixed_label, value=None, **kwargs): visible = not hasattr(input, 'hidden') or not input.hidden input_type = input.type is_data = isinstance(input, DataToolParameter) or isinstance(input, DataCollectionToolParameter) is_connectable = is_runtime_value(value) and runtime_to_json(value)["__class__"] == "ConnectedValue" if data_only: skip = not visible or not is_data elif connectable_only: skip = not visible or not (is_data or is_connectable) elif isinstance(input, HiddenToolParameter): skip = False else: skip = not visible if not skip: if isinstance(input, DataToolParameter): inputs.append(dict( name=prefixed_name, label=prefixed_label, multiple=input.multiple, extensions=input.extensions, input_type="dataset", )) elif isinstance(input, DataCollectionToolParameter): inputs.append(dict( name=prefixed_name, label=prefixed_label, multiple=input.multiple, input_type="dataset_collection", collection_types=input.collection_types, extensions=input.extensions, )) else: inputs.append( dict( name=prefixed_name, label=prefixed_label, multiple=False, input_type="parameter", type=input_type, ) ) visit_input_values(self.tool.inputs, self.state.inputs, callback) return inputs
[docs] def get_all_outputs(self, data_only=False): data_outputs = [] if self.tool: for name, tool_output in self.tool.outputs.items(): if filter_output(tool_output, self.state.inputs): continue extra_kwds = {} if isinstance(tool_output, ToolExpressionOutput): extra_kwds['parameter'] = True if tool_output.collection: extra_kwds["collection"] = True collection_type = tool_output.structure.collection_type if not collection_type and tool_output.structure.collection_type_from_rules: rule_param = tool_output.structure.collection_type_from_rules if rule_param in self.state.inputs: rule_json_str = self.state.inputs[rule_param] if rule_json_str: # initialized to None... rules = rule_json_str if rules: rule_set = RuleSet(rules) collection_type = rule_set.collection_type extra_kwds["collection_type"] = 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) if tool_output.label: try: params = make_dict_copy(self.state.inputs) params['on_string'] = 'input dataset(s)' params['tool'] = self.tool extra_kwds['label'] = fill_template(tool_output.label, context=params, python_template_version=self.tool.python_template_version) except Exception: pass data_outputs.append( dict( name=name, extensions=formats, type=tool_output.output_type, **extra_kwds ) ) return data_outputs
[docs] def get_config_form(self, step=None): if self.tool: self.add_dummy_datasets(connections=step and step.input_connections) 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): input_type = input.type is_data = input_type in ['data', 'data_collection'] if is_data and 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 input_type == "data" and isinstance(output_value, self.trans.app.model.HistoryDatasetCollectionAssociation): return output_value.to_hda_representative() return output_value return ConnectedValue() else: return input.get_initial_value(self.trans, context) elif (is_data and connections is None) or prefixed_name in input_connections_by_name: return ConnectedValue() visit_input_values(self.tool.inputs, self.state.inputs, callback) else: raise ToolMissingException("Tool %s missing. Cannot add dummy datasets." % self.tool_id, tool_id=self.tool_id)
[docs] def get_post_job_actions(self, incoming): return ActionBox.handle_incoming(incoming)
# ---- Run time ---------------------------------------------------------
[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. """ super(ToolModule, self).recover_state(state, **kwds) if kwds.get("fill_defaults", False) and self.tool: self.compute_runtime_state(self.trans, step=None, step_updates=None) self.augment_tool_state_for_input_connections(**kwds) self.tool.check_and_update_param_values(self.state.inputs, self.trans, workflow_building_mode=True)
[docs] def augment_tool_state_for_input_connections(self, **kwds): """Update tool state to accommodate specified input connections. Top-level and conditional inputs will automatically get populated with connected data outputs at runtime, but if there are not enough repeat instances in the tool state - the runtime replacement code will never visit the input elements it needs to in order to connect the data parameters to the tool state. This code then populates the required repeat instances in the tool state in order for these instances to be visited and inputs properly connected at runtime. I believe this should be run before check_and_update_param_values in recover_state so non-data parameters are properly populated with default values. The need to populate defaults is why this is done here instead of at runtime - but this might also be needed at runtime at some point (for workflows installed before their corresponding tools?). See the test case test_inputs_to_steps for an example of a workflow test case that exercises this code. """ # Ensure any repeats defined only by input_connections are populated. input_connections = kwds.get("input_connections", {}) expected_replacement_keys = input_connections.keys() def augment(expected_replacement_key, inputs, inputs_state): if "|" not in expected_replacement_key: return prefix, rest = expected_replacement_key.split("|", 1) if "_" not in prefix: return repeat_name, index = prefix.rsplit("_", 1) if not index.isdigit(): return index = int(index) repeat = self.tool.inputs[repeat_name] if repeat.type != "repeat": return if repeat_name not in inputs_states: inputs_states[repeat_name] = [] repeat_values = inputs_states[repeat_name] repeat_instance_state = None while index >= len(repeat_values): repeat_instance_state = {"__index__": len(repeat_values)} repeat_values.append(repeat_instance_state) if repeat_instance_state: # TODO: untest branch - no test case for nested repeats yet... augment(rest, repeat.inputs, repeat_instance_state) for expected_replacement_key in expected_replacement_keys: inputs_states = self.state.inputs inputs = self.tool.inputs augment(expected_replacement_key, inputs, inputs_states)
[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=None, step_updates=None): # Warning: This method destructively modifies existing step state. if self.tool: step_errors = {} state = self.state self.runtime_post_job_actions = {} state, step_errors = super(ToolModule, self).compute_runtime_state(trans, step, step_updates) if 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, tool_id=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(json.loads(runtime_state[RUNTIME_STEP_META_STATE_KEY])) return state else: raise ToolMissingException("Tool %s missing. Cannot recover runtime state." % self.tool_id, tool_id=self.tool_id)
[docs] def execute(self, trans, progress, invocation_step, use_cached_job=False): invocation = invocation_step.workflow_invocation step = invocation_step.workflow_step tool = trans.app.toolbox.get_tool(step.tool_id, tool_version=step.tool_version, tool_uuid=step.tool_uuid) if not tool.is_workflow_compatible: message = "Specified tool [%s] in workflow is not workflow-compatible." % tool.id raise Exception(message) 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] all_inputs = self.get_all_inputs() all_inputs_by_name = {} for input_dict in all_inputs: all_inputs_by_name[input_dict["name"]] = input_dict collection_info = self.compute_collection_info(progress, step, all_inputs) param_combinations = [] if collection_info: iteration_elements_iter = collection_info.slice_collections() else: iteration_elements_iter = [None] resource_parameters = invocation.resource_parameters 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): input_dict = all_inputs_by_name[prefixed_name] replacement = NO_REPLACEMENT dataset_instance = None if iteration_elements and prefixed_name in iteration_elements: dataset_instance = getattr(iteration_elements[prefixed_name], 'dataset_instance', None) if isinstance(input, DataToolParameter) and dataset_instance: # Pull out dataset instance (=HDA) from element and set a temporary element_identifier attribute # See https://github.com/galaxyproject/galaxy/pull/1693 for context. replacement = 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_input(step, input_dict) if replacement is not NO_REPLACEMENT: if not isinstance(input, BaseDataToolParameter): # Probably a parameter that can be replaced dataset = dataset_instance or replacement if getattr(dataset, 'extension', None) == 'expression.json': with open(dataset.file_name, 'r') as f: replacement = json.load(f) 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.warning("Failed to use input connections for inputs [%s]" % unmatched_input_connections) param_combinations.append(execution_state.inputs) complete = False completed_jobs = {} for i, param in enumerate(param_combinations): if use_cached_job: completed_jobs[i] = tool.job_search.by_tool_input( trans=trans, tool_id=tool.id, tool_version=tool.version, param=param, param_dump=tool.params_to_strings(param, trans.app, nested=True), job_state=None, ) else: completed_jobs[i] = None try: mapping_params = MappingParameters(tool_state.inputs, param_combinations) max_num_jobs = progress.maximum_jobs_to_schedule_or_none validate_outputs = False for pja in step.post_job_actions: if pja.action_type == "ValidateOutputsAction": validate_outputs = True execution_tracker = execute( trans=self.trans, tool=tool, mapping_params=mapping_params, history=invocation.history, collection_info=collection_info, workflow_invocation_uuid=invocation.uuid.hex, invocation_step=invocation_step, max_num_jobs=max_num_jobs, validate_outputs=validate_outputs, job_callback=lambda job: self._handle_post_job_actions(step, job, invocation.replacement_dict), completed_jobs=completed_jobs, workflow_resource_parameters=resource_parameters ) complete = True except PartialJobExecution as pje: execution_tracker = pje.execution_tracker 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) progress.record_executed_job_count(len(execution_tracker.successful_jobs)) 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(invocation_step, step_outputs, already_persisted=not invocation_step.is_new) if collection_info: step_inputs = mapping_params.param_template step_inputs.update(collection_info.collections) self._handle_mapped_over_post_job_actions(step, step_inputs, step_outputs, invocation.replacement_dict) if execution_tracker.execution_errors: message = "Failed to create one or more job(s) for workflow step." raise Exception(message) return complete
def _effective_post_job_actions(self, step): 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)) return effective_post_job_actions def _handle_mapped_over_post_job_actions(self, step, step_inputs, step_outputs, replacement_dict): effective_post_job_actions = self._effective_post_job_actions(step) for pja in effective_post_job_actions: if pja.action_type in ActionBox.mapped_over_output_actions: ActionBox.execute_on_mapped_over(self.trans, self.trans.sa_session, pja, step_inputs, step_outputs, replacement_dict) 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 = self._effective_post_job_actions(step) for pja in effective_post_job_actions: if pja.action_type in ActionBox.immediate_actions or isinstance(self.tool, DatabaseOperationTool): 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] def get_replacement_parameters(self, step): """Return a list of replacement parameters.""" replacement_parameters = set() for pja in step.post_job_actions: for argument in pja.action_arguments.values(): for match in re.findall(r'\$\{(.+?)\}', unicodify(argument)): replacement_parameters.add(match) return list(replacement_parameters)
[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, **kwargs): """ Return module initializd from the WorkflowStep object `step`. """ type = step.type return self.module_types[type].from_workflow_step(trans, step, **kwargs)
[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" }, { "name": "parameter_input", "title": "Parameter Input", "description": "Simple inputs used for workflow logic" }, ], } 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" } ], } 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, **kwargs): """ 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, **kwargs) # 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) # Populate subworkflow components if step.type == "subworkflow": subworkflow_param_map = step_args or {} unjsonified_subworkflow_param_map = {} for key, value in subworkflow_param_map.items(): unjsonified_subworkflow_param_map[int(key)] = value subworkflow = step.subworkflow populate_module_and_state(self.trans, subworkflow, param_map=unjsonified_subworkflow_param_map) state, step_errors = module.compute_runtime_state(self.trans, step, step_args) step.state = state # Fix any missing parameters step.upgrade_messages = module.check_and_update_state() 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})