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Source code for galaxy.tools.parameters.meta

import copy
import itertools
import logging
from collections import namedtuple

from galaxy import (
    exceptions,
    model,
    util
)
from galaxy.model.dataset_collections import matching, subcollections
from galaxy.util import permutations
from . import visit_input_values

log = logging.getLogger(__name__)

WorkflowParameterExpansion = namedtuple('WorkflowParameterExpansion', ['param_combinations', 'param_keys', 'input_combinations'])


[docs]class ParamKey:
[docs] def __init__(self, step_id, key): self.step_id = step_id self.key = key
[docs]class InputKey:
[docs] def __init__(self, input_id): self.input_id = input_id
[docs]def expand_workflow_inputs(param_inputs, inputs=None): """ Expands incoming encoded multiple payloads, into the set of all individual payload combinations >>> expansion = expand_workflow_inputs({'1': {'input': {'batch': True, 'product': True, 'values': [{'hid': '1'}, {'hid': '2'}] }}}) >>> print(["%s" % (p['1']['input']['hid']) for p in expansion.param_combinations]) ['1', '2'] >>> expansion = expand_workflow_inputs({'1': {'input': {'batch': True, 'values': [{'hid': '1'}, {'hid': '2'}] }}}) >>> print(["%s" % (p['1']['input']['hid']) for p in expansion.param_combinations]) ['1', '2'] >>> expansion = expand_workflow_inputs({'1': {'input': {'batch': True, 'values': [{'hid': '1'}, {'hid': '2'}] }}, '2': {'input': {'batch': True, 'values': [{'hid': '3'}, {'hid': '4'}] }}}) >>> print(["%s%s" % (p['1']['input']['hid'], p['2']['input']['hid']) for p in expansion.param_combinations]) ['13', '24'] >>> expansion = expand_workflow_inputs({'1': {'input': {'batch': True, 'product': True, 'values': [{'hid': '1'}, {'hid': '2'}] }}, '2': {'input': {'batch': True, 'values': [{'hid': '3'}, {'hid': '4'}, {'hid': '5'}] }}}) >>> print(["%s%s" % (p['1']['input']['hid'], p['2']['input']['hid']) for p in expansion.param_combinations]) ['13', '23', '14', '24', '15', '25'] >>> expansion = expand_workflow_inputs({'1': {'input': {'batch': True, 'product': True, 'values': [{'hid': '1'}, {'hid': '2'}] }}, '2': {'input': {'batch': True, 'product': True, 'values': [{'hid': '3'}, {'hid': '4'}, {'hid': '5'}] }}, '3': {'input': {'batch': True, 'product': True, 'values': [{'hid': '6'}, {'hid': '7'}, {'hid': '8'}] }}}) >>> print(["%s%s%s" % (p['1']['input']['hid'], p['2']['input']['hid'], p['3']['input']['hid']) for p in expansion.param_combinations]) ['136', '137', '138', '146', '147', '148', '156', '157', '158', '236', '237', '238', '246', '247', '248', '256', '257', '258'] >>> expansion = expand_workflow_inputs(None, inputs={'myinput': {'batch': True, 'product': True, 'values': [{'hid': '1'}, {'hid': '2'}] }}) >>> print(["%s" % (p['myinput']['hid']) for p in expansion.input_combinations]) ['1', '2'] """ param_inputs = param_inputs or {} inputs = inputs or {} linked_n = None linked = [] product = [] linked_keys = [] product_keys = [] def is_batch(value): return isinstance(value, dict) and 'batch' in value and value['batch'] is True and 'values' in value and isinstance(value['values'], list) for step_id, step in sorted(param_inputs.items()): for key, value in sorted(step.items()): if is_batch(value): nval = len(value['values']) if 'product' in value and value['product'] is True: product.append(value['values']) product_keys.append(ParamKey(step_id, key)) else: if linked_n is None: linked_n = nval elif linked_n != nval or nval == 0: raise exceptions.RequestParameterInvalidException('Failed to match linked batch selections. Please select equal number of data files.') linked.append(value['values']) linked_keys.append(ParamKey(step_id, key)) # Force it to a list to allow modification... input_items = list(inputs.items()) for input_id, value in input_items: if is_batch(value): nval = len(value['values']) if 'product' in value and value['product'] is True: product.append(value['values']) product_keys.append(InputKey(input_id)) else: if linked_n is None: linked_n = nval elif linked_n != nval or nval == 0: raise exceptions.RequestParameterInvalidException('Failed to match linked batch selections. Please select equal number of data files.') linked.append(value['values']) linked_keys.append(InputKey(input_id)) elif isinstance(value, dict) and 'batch' in value: # remove batch wrapper and render simplified input form rest of workflow # code expects inputs[input_id] = value['values'][0] param_combinations = [] input_combinations = [] params_keys = [] linked = linked or [[None]] product = product or [[None]] linked_keys = linked_keys or [None] product_keys = product_keys or [None] for linked_values, product_values in itertools.product(zip(*linked), itertools.product(*product)): new_params = copy.deepcopy(param_inputs) new_inputs = copy.deepcopy(inputs) new_keys = [] for input_key, value in list(zip(linked_keys, linked_values)) + list(zip(product_keys, product_values)): if input_key: if isinstance(input_key, ParamKey): step_id = input_key.step_id key = input_key.key assert step_id is not None new_params[step_id][key] = value if 'hid' in value: new_keys.append(str(value['hid'])) else: input_id = input_key.input_id assert input_id is not None new_inputs[input_id] = value if 'hid' in value: new_keys.append(str(value['hid'])) params_keys.append(new_keys) param_combinations.append(new_params) input_combinations.append(new_inputs) return WorkflowParameterExpansion(param_combinations, params_keys, input_combinations)
[docs]def process_key(incoming_key, incoming_value, d): key_parts = incoming_key.split('|') if len(key_parts) == 1: # Regular parameter if incoming_key in d and not incoming_value: # In case we get an empty repeat after we already filled in a repeat element return d[incoming_key] = incoming_value elif key_parts[0].rsplit('_', 1)[-1].isdigit(): # Repeat input_name, index = key_parts[0].rsplit('_', 1) index = int(index) d.setdefault(input_name, []) newlist = [{} for _ in range(index + 1)] d[input_name].extend(newlist[len(d[input_name]):]) subdict = d[input_name][index] process_key("|".join(key_parts[1:]), incoming_value=incoming_value, d=subdict) else: # Section / Conditional input_name = key_parts[0] subdict = {} d[input_name] = subdict process_key("|".join(key_parts[1:]), incoming_value=incoming_value, d=subdict)
[docs]def expand_meta_parameters(trans, tool, incoming): """ Take in a dictionary of raw incoming parameters and expand to a list of expanded incoming parameters (one set of parameters per tool execution). """ for key in list(incoming.keys()): if key.endswith("|__identifier__"): incoming.pop(key) # If we're going to multiply input dataset combinations # order matters, so the following reorders incoming # according to tool.inputs (which is ordered). incoming_copy = incoming.copy() nested_dict = {} for incoming_key, incoming_value in incoming_copy.items(): if not incoming_key.startswith('__'): process_key(incoming_key, incoming_value=incoming_value, d=nested_dict) reordered_incoming = {} def visitor(input, value, prefix, prefixed_name, prefixed_label, error, **kwargs): if prefixed_name in incoming_copy: reordered_incoming[prefixed_name] = incoming_copy[prefixed_name] del incoming_copy[prefixed_name] visit_input_values(inputs=tool.inputs, input_values=nested_dict, callback=visitor) reordered_incoming.update(incoming_copy) def classifier(input_key): value = incoming[input_key] if isinstance(value, dict) and 'values' in value: # Explicit meta wrapper for inputs... is_batch = value.get('batch', False) is_linked = value.get('linked', True) if is_batch and is_linked: classification = permutations.input_classification.MATCHED elif is_batch: classification = permutations.input_classification.MULTIPLIED else: classification = permutations.input_classification.SINGLE if __collection_multirun_parameter(value): collection_value = value['values'][0] values = __expand_collection_parameter(trans, input_key, collection_value, collections_to_match, linked=is_linked) else: values = value['values'] else: classification = permutations.input_classification.SINGLE values = value return classification, values collections_to_match = matching.CollectionsToMatch() # Stick an unexpanded version of multirun keys so they can be replaced, # by expand_mult_inputs. incoming_template = reordered_incoming expanded_incomings = permutations.expand_multi_inputs(incoming_template, classifier) if collections_to_match.has_collections(): collection_info = trans.app.dataset_collection_manager.match_collections(collections_to_match) else: collection_info = None return expanded_incomings, collection_info
def __expand_collection_parameter(trans, input_key, incoming_val, collections_to_match, linked=False): # If subcollectin multirun of data_collection param - value will # be "hdca_id|subcollection_type" else it will just be hdca_id if "|" in incoming_val: encoded_hdc_id, subcollection_type = incoming_val.split("|", 1) else: try: src = incoming_val["src"] if src != "hdca": raise exceptions.ToolMetaParameterException(f"Invalid dataset collection source type {src}") encoded_hdc_id = incoming_val["id"] subcollection_type = incoming_val.get('map_over_type', None) except TypeError: encoded_hdc_id = incoming_val subcollection_type = None hdc_id = trans.app.security.decode_id(encoded_hdc_id) hdc = trans.sa_session.query(model.HistoryDatasetCollectionAssociation).get(hdc_id) collections_to_match.add(input_key, hdc, subcollection_type=subcollection_type, linked=linked) if subcollection_type is not None: subcollection_elements = subcollections.split_dataset_collection_instance(hdc, subcollection_type) return subcollection_elements else: hdas = [] for element in hdc.collection.dataset_elements: hda = element.dataset_instance hda.element_identifier = element.element_identifier hdas.append(hda) return hdas def __collection_multirun_parameter(value): is_batch = value.get('batch', False) if not is_batch: return False batch_values = util.listify(value['values']) if len(batch_values) == 1: batch_over = batch_values[0] if isinstance(batch_over, dict) and ('src' in batch_over) and (batch_over['src'] in {'hdca', 'dce'}): return True return False