Mercurial > repos > shellac > guppy_basecaller

annotate env/lib/python3.7/site-packages/cwltool/workflow.py @ 2:6af9afd405e9 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
"planemo upload commit 0a63dd5f4d38a1f6944587f52a8cd79874177fc1"
author shellac
date Thu, 14 May 2020 14:56:58 -0400
parents 26e78fe6e8c4
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
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0
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1 from __future__ import absolute_import
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2
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3 import copy
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4 import datetime
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5 import functools
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6 import logging
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7 import random
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8 import tempfile
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9 from collections import namedtuple
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10 from typing import (Any, Callable, Dict, Generator, Iterable, List,
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11 Mapping, MutableMapping, MutableSequence,
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12 Optional, Sequence, Tuple, Union, cast)
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13 from uuid import UUID # pylint: disable=unused-import
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14
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15 import threading
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16 from ruamel.yaml.comments import CommentedMap
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17 from schema_salad import validate
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18 from schema_salad.sourceline import SourceLine, indent
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19 from six import string_types, iteritems
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20 from six.moves import range
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21 from future.utils import raise_from
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22 from typing_extensions import Text # pylint: disable=unused-import
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23 # move to a regular typing import when Python 3.3-3.6 is no longer supported
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24
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25 from . import command_line_tool, context, expression, procgenerator
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26 from .command_line_tool import CallbackJob, ExpressionTool
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27 from .job import JobBase
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28 from .builder import content_limit_respected_read
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29 from .checker import can_assign_src_to_sink, static_checker
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30 from .context import LoadingContext # pylint: disable=unused-import
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31 from .context import RuntimeContext, getdefault
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32 from .errors import WorkflowException
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33 from .load_tool import load_tool
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34 from .loghandler import _logger
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35 from .mutation import MutationManager # pylint: disable=unused-import
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36 from .pathmapper import adjustDirObjs, get_listing
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37 from .process import Process, get_overrides, shortname, uniquename
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38 from .provenance import ProvenanceProfile
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39 from .software_requirements import ( # pylint: disable=unused-import
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40 DependenciesConfiguration)
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41 from .stdfsaccess import StdFsAccess
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42 from .utils import DEFAULT_TMP_PREFIX, aslist, json_dumps
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43
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44 WorkflowStateItem = namedtuple('WorkflowStateItem', ['parameter', 'value', 'success'])
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45
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46
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47 def default_make_tool(toolpath_object, # type: MutableMapping[Text, Any]
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48 loadingContext # type: LoadingContext
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49 ): # type: (...) -> Process
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50 if not isinstance(toolpath_object, MutableMapping):
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51 raise WorkflowException(u"Not a dict: '%s'" % toolpath_object)
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52 if "class" in toolpath_object:
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53 if toolpath_object["class"] == "CommandLineTool":
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54 return command_line_tool.CommandLineTool(toolpath_object, loadingContext)
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55 if toolpath_object["class"] == "ExpressionTool":
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56 return command_line_tool.ExpressionTool(toolpath_object, loadingContext)
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57 if toolpath_object["class"] == "Workflow":
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58 return Workflow(toolpath_object, loadingContext)
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59 if toolpath_object["class"] == "ProcessGenerator":
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60 return procgenerator.ProcessGenerator(toolpath_object, loadingContext)
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61
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62 raise WorkflowException(
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63 u"Missing or invalid 'class' field in "
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64 "%s, expecting one of: CommandLineTool, ExpressionTool, Workflow" %
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65 toolpath_object["id"])
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66
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67
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68 context.default_make_tool = default_make_tool
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69
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70 def findfiles(wo, fn=None): # type: (Any, Optional[List[MutableMapping[Text, Any]]]) -> List[MutableMapping[Text, Any]]
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71 if fn is None:
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72 fn = []
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73 if isinstance(wo, MutableMapping):
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74 if wo.get("class") == "File":
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75 fn.append(wo)
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76 findfiles(wo.get("secondaryFiles", None), fn)
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77 else:
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78 for w in wo.values():
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79 findfiles(w, fn)
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80 elif isinstance(wo, MutableSequence):
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81 for w in wo:
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82 findfiles(w, fn)
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83 return fn
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84
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85
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86 def match_types(sinktype, # type: Union[List[Text], Text]
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87 src, # type: WorkflowStateItem
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88 iid, # type: Text
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89 inputobj, # type: Dict[Text, Any]
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90 linkMerge, # type: Text
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91 valueFrom # type: Optional[Text]
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92 ): # type: (...) -> bool
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93 if isinstance(sinktype, MutableSequence):
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94 # Sink is union type
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95 for st in sinktype:
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96 if match_types(st, src, iid, inputobj, linkMerge, valueFrom):
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97 return True
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98 elif isinstance(src.parameter["type"], MutableSequence):
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99 # Source is union type
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100 # Check that at least one source type is compatible with the sink.
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101 original_types = src.parameter["type"]
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102 for source_type in original_types:
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103 src.parameter["type"] = source_type
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104 match = match_types(
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105 sinktype, src, iid, inputobj, linkMerge, valueFrom)
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106 if match:
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107 src.parameter["type"] = original_types
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108 return True
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109 src.parameter["type"] = original_types
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110 return False
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111 elif linkMerge:
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112 if iid not in inputobj:
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113 inputobj[iid] = []
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114 if linkMerge == "merge_nested":
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115 inputobj[iid].append(src.value)
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116 elif linkMerge == "merge_flattened":
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117 if isinstance(src.value, MutableSequence):
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118 inputobj[iid].extend(src.value)
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119 else:
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120 inputobj[iid].append(src.value)
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121 else:
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122 raise WorkflowException(u"Unrecognized linkMerge enum '%s'" % linkMerge)
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123 return True
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124 elif valueFrom is not None \
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125 or can_assign_src_to_sink(src.parameter["type"], sinktype) \
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126 or sinktype == "Any":
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127 # simply assign the value from state to input
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128 inputobj[iid] = copy.deepcopy(src.value)
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129 return True
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130 return False
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131
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132
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133 def object_from_state(state, # type: Dict[Text, Optional[WorkflowStateItem]]
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134 parms, # type: List[Dict[Text, Any]]
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135 frag_only, # type: bool
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136 supportsMultipleInput, # type: bool
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137 sourceField, # type: Text
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138 incomplete=False # type: bool
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139 ): # type: (...) -> Optional[Dict[Text, Any]]
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140 inputobj = {} # type: Dict[Text, Any]
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141 for inp in parms:
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142 iid = inp["id"]
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143 if frag_only:
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144 iid = shortname(iid)
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145 if sourceField in inp:
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146 connections = aslist(inp[sourceField])
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147 if (len(connections) > 1 and
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148 not supportsMultipleInput):
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149 raise WorkflowException(
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150 "Workflow contains multiple inbound links to a single "
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151 "parameter but MultipleInputFeatureRequirement is not "
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152 "declared.")
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153 for src in connections:
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154 a_state = state.get(src, None)
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155 if a_state is not None and (a_state.success == "success" or incomplete):
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156 if not match_types(
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157 inp["type"], a_state, iid, inputobj,
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158 inp.get("linkMerge", ("merge_nested"
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159 if len(connections) > 1 else None)),
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160 valueFrom=inp.get("valueFrom")):
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161 raise WorkflowException(
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162 u"Type mismatch between source '%s' (%s) and "
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163 "sink '%s' (%s)" % (src,
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164 a_state.parameter["type"], inp["id"],
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165 inp["type"]))
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166 elif src not in state:
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167 raise WorkflowException(
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168 u"Connect source '%s' on parameter '%s' does not "
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169 "exist" % (src, inp["id"]))
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170 elif not incomplete:
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171 return None
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172
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173 if inputobj.get(iid) is None and "default" in inp:
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174 inputobj[iid] = inp["default"]
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175
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176 if iid not in inputobj and ("valueFrom" in inp or incomplete):
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177 inputobj[iid] = None
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178
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179 if iid not in inputobj:
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180 raise WorkflowException(u"Value for %s not specified" % (inp["id"]))
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181 return inputobj
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182
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183
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184 class WorkflowJobStep(object):
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185 def __init__(self, step):
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186 # type: (WorkflowStep) -> None
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187 """Initialize this WorkflowJobStep."""
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188 self.step = step
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189 self.tool = step.tool
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190 self.id = step.id
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191 self.submitted = False
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192 self.completed = False
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193 self.iterable = None # type: Optional[Generator[Union[ExpressionTool.ExpressionJob, JobBase, CallbackJob, None], None, None]]
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194 self.name = uniquename(u"step %s" % shortname(self.id))
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195 self.prov_obj = step.prov_obj
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196 self.parent_wf = step.parent_wf
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197
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198 def job(self,
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199 joborder, # type: Mapping[Text, Text]
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200 output_callback, # type: functools.partial[None]
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201 runtimeContext # type: RuntimeContext
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202 ):
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203 # type: (...) -> Generator[Union[ExpressionTool.ExpressionJob, JobBase, CallbackJob], None, None]
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204 runtimeContext = runtimeContext.copy()
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205 runtimeContext.part_of = self.name
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206 runtimeContext.name = shortname(self.id)
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207
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208 _logger.info(u"[%s] start", self.name)
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209
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210 for j in self.step.job(joborder, output_callback, runtimeContext):
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211 yield j
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212
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213 class WorkflowJob(object):
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214 def __init__(self, workflow, runtimeContext):
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215 # type: (Workflow, RuntimeContext) -> None
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216 """Initialize this WorkflowJob."""
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217 self.workflow = workflow
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218 self.prov_obj = None # type: Optional[ProvenanceProfile]
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219 self.parent_wf = None # type: Optional[ProvenanceProfile]
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220 self.tool = workflow.tool
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221 if runtimeContext.research_obj is not None:
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222 self.prov_obj = workflow.provenance_object
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223 self.parent_wf = workflow.parent_wf
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224 self.steps = [WorkflowJobStep(s) for s in workflow.steps]
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225 self.state = {} # type: Dict[Text, Optional[WorkflowStateItem]]
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226 self.processStatus = u""
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227 self.did_callback = False
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228 self.made_progress = None # type: Optional[bool]
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229
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230 if runtimeContext.outdir is not None:
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231 self.outdir = runtimeContext.outdir
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232 else:
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233 self.outdir = tempfile.mkdtemp(
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234 prefix=getdefault(runtimeContext.tmp_outdir_prefix, DEFAULT_TMP_PREFIX))
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235
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236 self.name = uniquename(u"workflow {}".format(
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237 getdefault(runtimeContext.name,
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238 shortname(self.workflow.tool.get("id", "embedded")))))
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239
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240 _logger.debug(
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241 u"[%s] initialized from %s", self.name,
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242 self.tool.get("id", "workflow embedded in %s" % runtimeContext.part_of))
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243
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244 def do_output_callback(self, final_output_callback):
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245 # type: (Callable[[Any, Any], Any]) -> None
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246
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247 supportsMultipleInput = bool(self.workflow.get_requirement("MultipleInputFeatureRequirement")[0])
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248
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249 wo = None # type: Optional[Dict[Text, Text]]
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250 try:
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251 wo = object_from_state(
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252 self.state, self.tool["outputs"], True, supportsMultipleInput,
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253 "outputSource", incomplete=True)
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254 except WorkflowException as err:
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255 _logger.error(
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256 u"[%s] Cannot collect workflow output: %s", self.name, Text(err))
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257 self.processStatus = "permanentFail"
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258 if self.prov_obj and self.parent_wf \
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259 and self.prov_obj.workflow_run_uri != self.parent_wf.workflow_run_uri:
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260 process_run_id = None
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261 self.prov_obj.generate_output_prov(wo or {}, process_run_id, self.name)
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262 self.prov_obj.document.wasEndedBy(
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263 self.prov_obj.workflow_run_uri, None, self.prov_obj.engine_uuid,
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264 datetime.datetime.now())
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265 prov_ids = self.prov_obj.finalize_prov_profile(self.name)
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266 # Tell parent to associate our provenance files with our wf run
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267 self.parent_wf.activity_has_provenance(self.prov_obj.workflow_run_uri, prov_ids)
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268
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269 _logger.info(u"[%s] completed %s", self.name, self.processStatus)
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270 if _logger.isEnabledFor(logging.DEBUG):
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271 _logger.debug(u"[%s] %s", self.name, json_dumps(wo, indent=4))
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272
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273 self.did_callback = True
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274
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275 final_output_callback(wo, self.processStatus)
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276
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277 def receive_output(self, step, outputparms, final_output_callback, jobout, processStatus):
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278 # type: (WorkflowJobStep, List[Dict[Text,Text]], Callable[[Any, Any], Any], Dict[Text,Text], Text) -> None
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279
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280 for i in outputparms:
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281 if "id" in i:
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282 if i["id"] in jobout:
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283 self.state[i["id"]] = WorkflowStateItem(i, jobout[i["id"]], processStatus)
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284 else:
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285 _logger.error(u"[%s] Output is missing expected field %s", step.name, i["id"])
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286 processStatus = "permanentFail"
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287 if _logger.isEnabledFor(logging.DEBUG):
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288 _logger.debug(u"[%s] produced output %s", step.name,
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289 json_dumps(jobout, indent=4))
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290
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291 if processStatus != "success":
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292 if self.processStatus != "permanentFail":
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293 self.processStatus = processStatus
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294
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295 _logger.warning(u"[%s] completed %s", step.name, processStatus)
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296 else:
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297 _logger.info(u"[%s] completed %s", step.name, processStatus)
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298
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299 step.completed = True
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300 # Release the iterable related to this step to
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301 # reclaim memory.
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302 step.iterable = None
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303 self.made_progress = True
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304
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305 completed = sum(1 for s in self.steps if s.completed)
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306 if completed == len(self.steps):
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307 self.do_output_callback(final_output_callback)
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308
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309 def try_make_job(self,
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310 step, # type: WorkflowJobStep
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311 final_output_callback, # type: Callable[[Any, Any], Any]
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312 runtimeContext # type: RuntimeContext
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313 ): # type: (...) -> Generator[Union[ExpressionTool.ExpressionJob, JobBase, CallbackJob, None], None, None]
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314
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315 inputparms = step.tool["inputs"]
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316 outputparms = step.tool["outputs"]
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317
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318 supportsMultipleInput = bool(self.workflow.get_requirement(
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319 "MultipleInputFeatureRequirement")[0])
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320
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321 try:
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322 inputobj = object_from_state(
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parents:
diff changeset
323 self.state, inputparms, False, supportsMultipleInput, "source")
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parents:
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324 if inputobj is None:
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parents:
diff changeset
325 _logger.debug(u"[%s] job step %s not ready", self.name, step.id)
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diff changeset
326 return
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327
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parents:
diff changeset
328 if step.submitted:
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diff changeset
329 return
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parents:
diff changeset
330 _logger.info(u"[%s] starting %s", self.name, step.name)
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parents:
diff changeset
331
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diff changeset
332 callback = functools.partial(self.receive_output, step, outputparms, final_output_callback)
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diff changeset
333
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334
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diff changeset
335 valueFrom = {
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diff changeset
336 i["id"]: i["valueFrom"] for i in step.tool["inputs"]
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parents:
diff changeset
337 if "valueFrom" in i}
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diff changeset
338
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diff changeset
339 loadContents = set(i["id"] for i in step.tool["inputs"]
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parents:
diff changeset
340 if i.get("loadContents"))
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diff changeset
341
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diff changeset
342 if len(valueFrom) > 0 and not bool(self.workflow.get_requirement("StepInputExpressionRequirement")[0]):
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parents:
diff changeset
343 raise WorkflowException(
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344 "Workflow step contains valueFrom but StepInputExpressionRequirement not in requirements")
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diff changeset
345
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346 vfinputs = {shortname(k): v for k, v in iteritems(inputobj)}
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347
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parents:
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348 def postScatterEval(io):
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parents:
diff changeset
349 # type: (MutableMapping[Text, Any]) -> Dict[Text, Any]
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parents:
diff changeset
350 shortio = {shortname(k): v for k, v in iteritems(io)}
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351
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352 fs_access = getdefault(runtimeContext.make_fs_access, StdFsAccess)("")
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parents:
diff changeset
353 for k, v in io.items():
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parents:
diff changeset
354 if k in loadContents and v.get("contents") is None:
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parents:
diff changeset
355 with fs_access.open(v["location"], "rb") as f:
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parents:
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356 v["contents"] = content_limit_respected_read(f)
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357
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358 def valueFromFunc(k, v): # type: (Any, Any) -> Any
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359 if k in valueFrom:
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diff changeset
360 adjustDirObjs(v, functools.partial(get_listing,
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diff changeset
361 fs_access, recursive=True))
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362 return expression.do_eval(
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363 valueFrom[k], shortio, self.workflow.requirements,
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364 None, None, {}, context=v,
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365 debug=runtimeContext.debug,
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366 js_console=runtimeContext.js_console,
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parents:
diff changeset
367 timeout=runtimeContext.eval_timeout)
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368 return v
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369
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370 return {k: valueFromFunc(k, v) for k, v in io.items()}
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371
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372 if "scatter" in step.tool:
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373 scatter = aslist(step.tool["scatter"])
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diff changeset
374 method = step.tool.get("scatterMethod")
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
375 if method is None and len(scatter) != 1:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
376 raise WorkflowException("Must specify scatterMethod when scattering over multiple inputs")
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
377 runtimeContext = runtimeContext.copy()
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
378 runtimeContext.postScatterEval = postScatterEval
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
379
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
380 emptyscatter = [shortname(s) for s in scatter if len(inputobj[s]) == 0]
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
381 if emptyscatter:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
382 _logger.warning(
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
383 "[job %s] Notice: scattering over empty input in "
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
384 "'%s'. All outputs will be empty.", step.name,
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
385 "', '".join(emptyscatter))
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
386
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
387 if method == "dotproduct" or method is None:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
388 jobs = dotproduct_scatter(
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
389 step, inputobj, scatter, callback, runtimeContext)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
390 elif method == "nested_crossproduct":
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
391 jobs = nested_crossproduct_scatter(
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
392 step, inputobj, scatter, callback, runtimeContext)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
393 elif method == "flat_crossproduct":
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
394 jobs = flat_crossproduct_scatter(
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
395 step, inputobj, scatter, callback, runtimeContext)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
396 else:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
397 if _logger.isEnabledFor(logging.DEBUG):
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
398 _logger.debug(u"[job %s] job input %s", step.name,
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
399 json_dumps(inputobj, indent=4))
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
400
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
401 inputobj = postScatterEval(inputobj)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
402
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
403 if _logger.isEnabledFor(logging.DEBUG):
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
404 _logger.debug(u"[job %s] evaluated job input to %s",
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
405 step.name, json_dumps(inputobj, indent=4))
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
406 jobs = step.job(inputobj, callback, runtimeContext)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
407
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
408 step.submitted = True
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
409
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
410 for j in jobs:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
411 yield j
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
412 except WorkflowException:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
413 raise
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
414 except Exception:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
415 _logger.exception("Unhandled exception")
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
416 self.processStatus = "permanentFail"
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
417 step.completed = True
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
418
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
419
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
420 def run(self,
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
421 runtimeContext, # type: RuntimeContext
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
422 tmpdir_lock=None # type: Optional[threading.Lock]
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
423 ): # type: (...) -> None
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
424 """Log the start of each workflow."""
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
425 _logger.info(u"[%s] start", self.name)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
426
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
427 def job(self,
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
428 joborder, # type: Mapping[Text, Any]
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
429 output_callback, # type: Callable[[Any, Any], Any]
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
430 runtimeContext # type: RuntimeContext
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
431 ): # type: (...) -> Generator[Union[ExpressionTool.ExpressionJob, JobBase, CallbackJob, None], None, None]
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
432 self.state = {}
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
433 self.processStatus = "success"
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
434
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
435 if _logger.isEnabledFor(logging.DEBUG):
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
436 _logger.debug(u"[%s] %s", self.name, json_dumps(joborder, indent=4))
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
437
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
438 runtimeContext = runtimeContext.copy()
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
439 runtimeContext.outdir = None
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
440
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
441 for index, inp in enumerate(self.tool["inputs"]):
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
442 with SourceLine(self.tool["inputs"], index, WorkflowException,
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
443 _logger.isEnabledFor(logging.DEBUG)):
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
444 inp_id = shortname(inp["id"])
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
445 if inp_id in joborder:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
446 self.state[inp["id"]] = WorkflowStateItem(
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
447 inp, joborder[inp_id], "success")
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
448 elif "default" in inp:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
449 self.state[inp["id"]] = WorkflowStateItem(
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
450 inp, inp["default"], "success")
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
451 else:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
452 raise WorkflowException(
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
453 u"Input '%s' not in input object and does not have a "
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
454 " default value." % (inp["id"]))
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
455
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
456 for step in self.steps:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
457 for out in step.tool["outputs"]:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
458 self.state[out["id"]] = None
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
459
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
460 completed = 0
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
461 while completed < len(self.steps):
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
462 self.made_progress = False
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
463
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
464 for step in self.steps:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
465 if getdefault(runtimeContext.on_error, "stop") == "stop" and self.processStatus != "success":
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
466 break
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
467
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
468 if not step.submitted:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
469 try:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
470 step.iterable = self.try_make_job(
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
471 step, output_callback, runtimeContext)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
472 except WorkflowException as exc:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
473 _logger.error(u"[%s] Cannot make job: %s", step.name, Text(exc))
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
474 _logger.debug("", exc_info=True)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
475 self.processStatus = "permanentFail"
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
476
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
477 if step.iterable is not None:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
478 try:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
479 for newjob in step.iterable:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
480 if getdefault(runtimeContext.on_error, "stop") == "stop" \
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
481 and self.processStatus != "success":
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
482 break
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
483 if newjob is not None:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
484 self.made_progress = True
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
485 yield newjob
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
486 else:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
487 break
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
488 except WorkflowException as exc:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
489 _logger.error(u"[%s] Cannot make job: %s", step.name, Text(exc))
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
490 _logger.debug("", exc_info=True)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
491 self.processStatus = "permanentFail"
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
492
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
493 completed = sum(1 for s in self.steps if s.completed)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
494
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
495 if not self.made_progress and completed < len(self.steps):
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
496 if self.processStatus != "success":
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
497 break
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
498 else:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
499 yield None
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
500
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
501 if not self.did_callback:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
502 self.do_output_callback(output_callback) # could have called earlier on line 336;
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503 #depends which one comes first. All steps are completed
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504 #or all outputs have been produced.
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505
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506 class Workflow(Process):
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507 def __init__(self,
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508 toolpath_object, # type: MutableMapping[Text, Any]
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509 loadingContext # type: LoadingContext
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510 ): # type: (...) -> None
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511 """Initializet this Workflow."""
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512 super(Workflow, self).__init__(
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513 toolpath_object, loadingContext)
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514 self.provenance_object = None # type: Optional[ProvenanceProfile]
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515 if loadingContext.research_obj is not None:
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516 run_uuid = None # type: Optional[UUID]
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517 is_master = not loadingContext.prov_obj # Not yet set
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518 if is_master:
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519 run_uuid = loadingContext.research_obj.ro_uuid
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520
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521 self.provenance_object = ProvenanceProfile(
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522 loadingContext.research_obj,
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523 full_name=loadingContext.cwl_full_name,
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524 host_provenance=loadingContext.host_provenance,
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525 user_provenance=loadingContext.user_provenance,
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526 orcid=loadingContext.orcid,
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527 run_uuid=run_uuid,
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528 fsaccess=loadingContext.research_obj.fsaccess) # inherit RO UUID for master wf run
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529 # TODO: Is Workflow(..) only called when we are the master workflow?
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530 self.parent_wf = self.provenance_object
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531
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532 # FIXME: Won't this overwrite prov_obj for nested workflows?
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533 loadingContext.prov_obj = self.provenance_object
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534 loadingContext = loadingContext.copy()
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535 loadingContext.requirements = self.requirements
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536 loadingContext.hints = self.hints
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537
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538 self.steps = [] # type: List[WorkflowStep]
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539 validation_errors = []
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540 for index, step in enumerate(self.tool.get("steps", [])):
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541 try:
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542 self.steps.append(self.make_workflow_step(step, index, loadingContext,
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543 loadingContext.prov_obj))
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544 except validate.ValidationException as vexc:
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545 if _logger.isEnabledFor(logging.DEBUG):
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546 _logger.exception("Validation failed at")
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547 validation_errors.append(vexc)
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548
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549 if validation_errors:
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550 raise validate.ValidationException("\n".join(str(v) for v in validation_errors))
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551
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552 random.shuffle(self.steps)
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553
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554 # statically validate data links instead of doing it at runtime.
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555 workflow_inputs = self.tool["inputs"]
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556 workflow_outputs = self.tool["outputs"]
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557
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558 step_inputs = [] # type: List[Any]
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559 step_outputs = [] # type: List[Any]
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560 param_to_step = {} # type: Dict[Text, Dict[Text, Any]]
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561 for step in self.steps:
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562 step_inputs.extend(step.tool["inputs"])
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563 step_outputs.extend(step.tool["outputs"])
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564 for s in step.tool["inputs"]:
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565 param_to_step[s["id"]] = step.tool
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566
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567 if getdefault(loadingContext.do_validate, True):
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568 static_checker(workflow_inputs, workflow_outputs, step_inputs, step_outputs, param_to_step)
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569
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570 def make_workflow_step(self,
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571 toolpath_object, # type: Dict[Text, Any]
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572 pos, # type: int
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573 loadingContext, # type: LoadingContext
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574 parentworkflowProv=None # type: Optional[ProvenanceProfile]
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575 ): # type: (...) -> WorkflowStep
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576 return WorkflowStep(toolpath_object, pos, loadingContext, parentworkflowProv)
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577
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578 def job(self,
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579 job_order, # type: Mapping[Text, Any]
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580 output_callbacks, # type: Callable[[Any, Any], Any]
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581 runtimeContext # type: RuntimeContext
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582 ): # type: (...) -> Generator[Union[WorkflowJob, ExpressionTool.ExpressionJob, JobBase, CallbackJob, None], None, None]
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parents:
diff changeset
583 builder = self._init_job(job_order, runtimeContext)
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584
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diff changeset
585 if runtimeContext.research_obj is not None:
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parents:
diff changeset
586 if runtimeContext.toplevel:
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diff changeset
587 # Record primary-job.json
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diff changeset
588 runtimeContext.research_obj.fsaccess = runtimeContext.make_fs_access('')
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parents:
diff changeset
589 runtimeContext.research_obj.create_job(builder.job, self.job)
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diff changeset
590
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diff changeset
591 job = WorkflowJob(self, runtimeContext)
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parents:
diff changeset
592 yield job
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593
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594 runtimeContext = runtimeContext.copy()
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diff changeset
595 runtimeContext.part_of = u"workflow %s" % job.name
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diff changeset
596 runtimeContext.toplevel = False
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diff changeset
597
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diff changeset
598 for wjob in job.job(builder.job, output_callbacks, runtimeContext):
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diff changeset
599 yield wjob
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600
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diff changeset
601 def visit(self, op): # type: (Callable[[MutableMapping[Text, Any]], Any]) -> None
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602 op(self.tool)
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603 for step in self.steps:
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diff changeset
604 step.visit(op)
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diff changeset
605
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606
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607
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608 class WorkflowStep(Process):
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609 def __init__(self,
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610 toolpath_object, # type: Dict[Text, Any]
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parents:
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611 pos, # type: int
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diff changeset
612 loadingContext, # type: LoadingContext
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613 parentworkflowProv=None # type: Optional[ProvenanceProfile]
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diff changeset
614 ): # type: (...) -> None
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diff changeset
615 """Initialize this WorkflowStep."""
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616 if "id" in toolpath_object:
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617 self.id = toolpath_object["id"]
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618 else:
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619 self.id = "#step" + Text(pos)
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620
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621 loadingContext = loadingContext.copy()
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622
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diff changeset
623 loadingContext.requirements = copy.deepcopy(getdefault(loadingContext.requirements, []))
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624 assert loadingContext.requirements is not None # nosec
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625 loadingContext.requirements.extend(toolpath_object.get("requirements", []))
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diff changeset
626 loadingContext.requirements.extend(get_overrides(getdefault(loadingContext.overrides_list, []),
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diff changeset
627 self.id).get("requirements", []))
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
628
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
629 hints = copy.deepcopy(getdefault(loadingContext.hints, []))
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
630 hints.extend(toolpath_object.get("hints", []))
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
631 loadingContext.hints = hints
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
632
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
633
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
634 try:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
635 if isinstance(toolpath_object["run"], MutableMapping):
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
636 self.embedded_tool = loadingContext.construct_tool_object(
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
637 toolpath_object["run"], loadingContext) # type: Process
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
638 else:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
639 loadingContext.metadata = {}
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
640 self.embedded_tool = load_tool(
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
641 toolpath_object["run"], loadingContext)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
642 except validate.ValidationException as vexc:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
643 if loadingContext.debug:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
644 _logger.exception("Validation exception")
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
645 raise_from(WorkflowException(
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
646 u"Tool definition %s failed validation:\n%s" %
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
647 (toolpath_object["run"], indent(str(vexc)))), vexc)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
648
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
649 validation_errors = []
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
650 self.tool = toolpath_object = copy.deepcopy(toolpath_object)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
651 bound = set()
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
652 for stepfield, toolfield in (("in", "inputs"), ("out", "outputs")):
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
653 toolpath_object[toolfield] = []
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
654 for index, step_entry in enumerate(toolpath_object[stepfield]):
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
655 if isinstance(step_entry, string_types):
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
656 param = CommentedMap() # type: CommentedMap
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
657 inputid = step_entry
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
658 else:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
659 param = CommentedMap(iteritems(step_entry))
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
660 inputid = step_entry["id"]
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
661
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
662 shortinputid = shortname(inputid)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
663 found = False
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
664 for tool_entry in self.embedded_tool.tool[toolfield]:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
665 frag = shortname(tool_entry["id"])
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
666 if frag == shortinputid:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
667 #if the case that the step has a default for a parameter,
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
668 #we do not want the default of the tool to override it
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
669 step_default = None
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
670 if "default" in param and "default" in tool_entry:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
671 step_default = param["default"]
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
672 param.update(tool_entry)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
673 param["_tool_entry"] = tool_entry
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
674 if step_default is not None:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
675 param["default"] = step_default
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
676 found = True
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
677 bound.add(frag)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
678 break
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
679 if not found:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
680 if stepfield == "in":
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
681 param["type"] = "Any"
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
682 param["not_connected"] = True
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
683 else:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
684 if isinstance(step_entry, Mapping):
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
685 step_entry_name = step_entry['id']
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
686 else:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
687 step_entry_name = step_entry
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
688 validation_errors.append(
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
689 SourceLine(self.tool["out"], index).makeError(
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
690 "Workflow step output '%s' does not correspond to"
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
691 % shortname(step_entry_name))
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
692 + "\n" + SourceLine(self.embedded_tool.tool, "outputs").makeError(
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
693 " tool output (expected '%s')" % (
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
694 "', '".join(
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
695 [shortname(tool_entry["id"]) for tool_entry in
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
696 self.embedded_tool.tool['outputs']]))))
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
697 param["id"] = inputid
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
698 param.lc.line = toolpath_object[stepfield].lc.data[index][0]
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
699 param.lc.col = toolpath_object[stepfield].lc.data[index][1]
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
700 param.lc.filename = toolpath_object[stepfield].lc.filename
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
701 toolpath_object[toolfield].append(param)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
702
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
703 missing_values = []
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
704 for _, tool_entry in enumerate(self.embedded_tool.tool["inputs"]):
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
705 if shortname(tool_entry["id"]) not in bound:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
706 if "null" not in tool_entry["type"] and "default" not in tool_entry:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
707 missing_values.append(shortname(tool_entry["id"]))
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
708
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
709 if missing_values:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
710 validation_errors.append(SourceLine(self.tool, "in").makeError(
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
711 "Step is missing required parameter%s '%s'" %
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
712 ("s" if len(missing_values) > 1 else "", "', '".join(missing_values))))
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
713
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
714 if validation_errors:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
715 raise validate.ValidationException("\n".join(validation_errors))
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
716
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
717 super(WorkflowStep, self).__init__(toolpath_object, loadingContext)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
718
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
719 if self.embedded_tool.tool["class"] == "Workflow":
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
720 (feature, _) = self.get_requirement("SubworkflowFeatureRequirement")
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
721 if not feature:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
722 raise WorkflowException(
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
723 "Workflow contains embedded workflow but "
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
724 "SubworkflowFeatureRequirement not in requirements")
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
725
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
726 if "scatter" in self.tool:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
727 (feature, _) = self.get_requirement("ScatterFeatureRequirement")
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
728 if not feature:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
729 raise WorkflowException(
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
730 "Workflow contains scatter but ScatterFeatureRequirement "
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
731 "not in requirements")
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
732
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
733 inputparms = copy.deepcopy(self.tool["inputs"])
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
734 outputparms = copy.deepcopy(self.tool["outputs"])
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
735 scatter = aslist(self.tool["scatter"])
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
736
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
737 method = self.tool.get("scatterMethod")
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
738 if method is None and len(scatter) != 1:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
739 raise validate.ValidationException(
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
740 "Must specify scatterMethod when scattering over multiple inputs")
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
741
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
742 inp_map = {i["id"]: i for i in inputparms}
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
743 for inp in scatter:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
744 if inp not in inp_map:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
745 raise validate.ValidationException(
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
746 SourceLine(self.tool, "scatter").makeError(
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
747 "Scatter parameter '%s' does not correspond to "
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
748 "an input parameter of this step, expecting '%s'"
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
749 % (shortname(inp), "', '".join(
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
750 shortname(k) for k in inp_map.keys()))))
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
751
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
752 inp_map[inp]["type"] = {"type": "array", "items": inp_map[inp]["type"]}
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
753
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
754 if self.tool.get("scatterMethod") == "nested_crossproduct":
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
755 nesting = len(scatter)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
756 else:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
757 nesting = 1
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
758
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
759 for _ in range(0, nesting):
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
760 for oparam in outputparms:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
761 oparam["type"] = {"type": "array", "items": oparam["type"]}
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
762 self.tool["inputs"] = inputparms
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
763 self.tool["outputs"] = outputparms
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
764 self.prov_obj = None # type: Optional[ProvenanceProfile]
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
765 if loadingContext.research_obj is not None:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
766 self.prov_obj = parentworkflowProv
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
767 if self.embedded_tool.tool["class"] == "Workflow":
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
768 self.parent_wf = self.embedded_tool.parent_wf
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
769 else:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
770 self.parent_wf = self.prov_obj
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
771
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
772 def receive_output(self, output_callback, jobout, processStatus):
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
773 # type: (Callable[...,Any], Dict[Text, Text], Text) -> None
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
774 output = {}
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
775 for i in self.tool["outputs"]:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
776 field = shortname(i["id"])
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
777 if field in jobout:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
778 output[i["id"]] = jobout[field]
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
779 else:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
780 processStatus = "permanentFail"
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
781 output_callback(output, processStatus)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
782
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
783 def job(self,
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
784 job_order, # type: Mapping[Text, Text]
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
785 output_callbacks, # type: Callable[[Any, Any], Any]
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
786 runtimeContext, # type: RuntimeContext
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
787 ): # type: (...) -> Generator[Union[ExpressionTool.ExpressionJob, JobBase, CallbackJob], None, None]
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
788 #initialize sub-workflow as a step in the parent profile
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
789
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
790 if self.embedded_tool.tool["class"] == "Workflow" \
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
791 and runtimeContext.research_obj and self.prov_obj \
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
792 and self.embedded_tool.provenance_object:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
793 self.embedded_tool.parent_wf = self.prov_obj
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
794 process_name = self.tool["id"].split("#")[1]
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
795 self.prov_obj.start_process(
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
796 process_name, datetime.datetime.now(),
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
797 self.embedded_tool.provenance_object.workflow_run_uri)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
798
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
799 step_input = {}
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
800 for inp in self.tool["inputs"]:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
801 field = shortname(inp["id"])
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
802 if not inp.get("not_connected"):
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
803 step_input[field] = job_order[inp["id"]]
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
804
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
805 try:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
806 for tool in self.embedded_tool.job(
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
807 step_input,
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
808 functools.partial(self.receive_output, output_callbacks),
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
809 runtimeContext):
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
810 yield tool
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
811 except WorkflowException:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
812 _logger.error(u"Exception on step '%s'", runtimeContext.name)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
813 raise
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
814 except Exception as exc:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
815 _logger.exception("Unexpected exception")
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
816 raise_from(WorkflowException(Text(exc)), exc)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
817
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
818 def visit(self, op): # type: (Callable[[MutableMapping[Text, Any]], Any]) -> None
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
819 self.embedded_tool.visit(op)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
820
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
821
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
822 class ReceiveScatterOutput(object):
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
823 def __init__(self,
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
824 output_callback, # type: Callable[..., Any]
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
825 dest, # type: Dict[Text, List[Optional[Text]]]
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
826 total # type: int
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
827 ): # type: (...) -> None
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
828 """Initialize."""
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
829 self.dest = dest
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
830 self.completed = 0
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
831 self.processStatus = u"success"
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
832 self.total = total
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
833 self.output_callback = output_callback
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
834 self.steps = [] # type: List[Optional[Generator[Union[ExpressionTool.ExpressionJob, JobBase, CallbackJob, None], None, None]]]
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
835
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
836 def receive_scatter_output(self, index, jobout, processStatus):
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
837 # type: (int, Dict[Text, Text], Text) -> None
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
838 for key, val in jobout.items():
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
839 self.dest[key][index] = val
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
840
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
841 # Release the iterable related to this step to
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
842 # reclaim memory.
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
843 if self.steps:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
844 self.steps[index] = None
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
845
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
846 if processStatus != "success":
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
847 if self.processStatus != "permanentFail":
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
848 self.processStatus = processStatus
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
849
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
850 self.completed += 1
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
851
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
852 if self.completed == self.total:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
853 self.output_callback(self.dest, self.processStatus)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
854
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
855 def setTotal(self, total, steps): # type: (int, List[Optional[Generator[Union[ExpressionTool.ExpressionJob, JobBase, CallbackJob, None], None, None]]]) -> None
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
856 self.total = total
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
857 self.steps = steps
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
858 if self.completed == self.total:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
859 self.output_callback(self.dest, self.processStatus)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
860
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
861
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
862 def parallel_steps(steps, rc, runtimeContext):
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
863 # type: (List[Optional[Generator[Union[ExpressionTool.ExpressionJob, JobBase, CallbackJob, None], None, None]]], ReceiveScatterOutput, RuntimeContext) -> Generator[Union[ExpressionTool.ExpressionJob, JobBase, CallbackJob, None], None, None]
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
864 while rc.completed < rc.total:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
865 made_progress = False
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
866 for index, step in enumerate(steps):
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
867 if getdefault(runtimeContext.on_error, "stop") == "stop" and rc.processStatus != "success":
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
868 break
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
869 if step is None:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
870 continue
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
871 try:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
872 for j in step:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
873 if getdefault(runtimeContext.on_error, "stop") == "stop" and rc.processStatus != "success":
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
874 break
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
875 if j is not None:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
876 made_progress = True
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
877 yield j
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
878 else:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
879 break
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
880 if made_progress:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
881 break
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
882 except WorkflowException as exc:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
883 _logger.error(u"Cannot make scatter job: %s", Text(exc))
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
884 _logger.debug("", exc_info=True)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
885 rc.receive_scatter_output(index, {}, "permanentFail")
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
886 if not made_progress and rc.completed < rc.total:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
887 yield None
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
888
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
889
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
890 def dotproduct_scatter(process, # type: WorkflowJobStep
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
891 joborder, # type: MutableMapping[Text, Any]
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
892 scatter_keys, # type: MutableSequence[Text]
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
893 output_callback, # type: Callable[..., Any]
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
894 runtimeContext # type: RuntimeContext
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
895 ): # type: (...) -> Generator[Union[ExpressionTool.ExpressionJob, JobBase, CallbackJob, None], None, None]
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
896 jobl = None # type: Optional[int]
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
897 for key in scatter_keys:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
898 if jobl is None:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
899 jobl = len(joborder[key])
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
900 elif jobl != len(joborder[key]):
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
901 raise WorkflowException(
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
902 "Length of input arrays must be equal when performing "
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
903 "dotproduct scatter.")
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
904 if jobl is None:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
905 raise Exception("Impossible codepath")
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
906
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
907 output = {} # type: Dict[Text,List[Optional[Text]]]
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
908 for i in process.tool["outputs"]:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
909 output[i["id"]] = [None] * jobl
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
910
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
911 rc = ReceiveScatterOutput(output_callback, output, jobl)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
912
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
913 steps = [] # type: List[Optional[Generator[Union[ExpressionTool.ExpressionJob, JobBase, CallbackJob, None], None, None]]]
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
914 for index in range(0, jobl):
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
915 sjobo = copy.copy(joborder)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
916 for key in scatter_keys:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
917 sjobo[key] = joborder[key][index]
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
918
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
919 if runtimeContext.postScatterEval is not None:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
920 sjobo = runtimeContext.postScatterEval(sjobo)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
921
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
922 steps.append(process.job(
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
923 sjobo, functools.partial(rc.receive_scatter_output, index),
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
924 runtimeContext))
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
925
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
926 rc.setTotal(jobl, steps)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
927 return parallel_steps(steps, rc, runtimeContext)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
928
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
929
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
930 def nested_crossproduct_scatter(process, # type: WorkflowJobStep
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
931 joborder, # type: MutableMapping[Text, Any]
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
932 scatter_keys, # type: MutableSequence[Text]
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
933 output_callback, # type: Callable[..., Any]
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
934 runtimeContext # type: RuntimeContext
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
935 ): # type: (...) -> Generator[Union[ExpressionTool.ExpressionJob, JobBase, CallbackJob, None], None, None]
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
936 scatter_key = scatter_keys[0]
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
937 jobl = len(joborder[scatter_key])
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
938 output = {} # type: Dict[Text, List[Optional[Text]]]
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
939 for i in process.tool["outputs"]:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
940 output[i["id"]] = [None] * jobl
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
941
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
942 rc = ReceiveScatterOutput(output_callback, output, jobl)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
943
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
944 steps = [] # type: List[Optional[Generator[Union[ExpressionTool.ExpressionJob, JobBase, CallbackJob, None], None, None]]]
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
945 for index in range(0, jobl):
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
946 sjob = copy.copy(joborder)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
947 sjob[scatter_key] = joborder[scatter_key][index]
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
948
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
949 if len(scatter_keys) == 1:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
950 if runtimeContext.postScatterEval is not None:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
951 sjob = runtimeContext.postScatterEval(sjob)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
952 steps.append(process.job(
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
953 sjob, functools.partial(rc.receive_scatter_output, index),
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
954 runtimeContext))
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
955 else:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
956 steps.append(nested_crossproduct_scatter(
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
957 process, sjob, scatter_keys[1:],
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
958 functools.partial(rc.receive_scatter_output, index),
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
959 runtimeContext))
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
960
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
961 rc.setTotal(jobl, steps)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
962 return parallel_steps(steps, rc, runtimeContext)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
963
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
964
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
965 def crossproduct_size(joborder, scatter_keys):
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
966 # type: (MutableMapping[Text, Any], MutableSequence[Text]) -> int
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
967 scatter_key = scatter_keys[0]
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
968 if len(scatter_keys) == 1:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
969 ssum = len(joborder[scatter_key])
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
970 else:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
971 ssum = 0
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
972 for _ in range(0, len(joborder[scatter_key])):
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
973 ssum += crossproduct_size(joborder, scatter_keys[1:])
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
974 return ssum
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
975
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
976 def flat_crossproduct_scatter(process, # type: WorkflowJobStep
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
977 joborder, # type: MutableMapping[Text, Any]
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
978 scatter_keys, # type: MutableSequence[Text]
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
979 output_callback, # type: Callable[..., Any]
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
980 runtimeContext # type: RuntimeContext
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
981 ): # type: (...) -> Generator[Union[ExpressionTool.ExpressionJob, JobBase, CallbackJob, None], None, None]
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
982 output = {} # type: Dict[Text, List[Optional[Text]]]
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
983 for i in process.tool["outputs"]:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
984 output[i["id"]] = [None] * crossproduct_size(joborder, scatter_keys)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
985 callback = ReceiveScatterOutput(output_callback, output, 0)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
986 (steps, total) = _flat_crossproduct_scatter(
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
987 process, joborder, scatter_keys, callback, 0, runtimeContext)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
988 callback.setTotal(total, steps)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
989 return parallel_steps(steps, callback, runtimeContext)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
990
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
991 def _flat_crossproduct_scatter(process, # type: WorkflowJobStep
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
992 joborder, # type: MutableMapping[Text, Any]
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
993 scatter_keys, # type: MutableSequence[Text]
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
994 callback, # type: ReceiveScatterOutput
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
995 startindex, # type: int
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
996 runtimeContext # type: RuntimeContext
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
997 ): # type: (...) -> Tuple[List[Optional[Generator[Union[ExpressionTool.ExpressionJob, JobBase, CallbackJob, None], None, None]]], int]
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
998 """Inner loop."""
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
999 scatter_key = scatter_keys[0]
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1000 jobl = len(joborder[scatter_key])
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1001 steps = [] # type: List[Optional[Generator[Union[ExpressionTool.ExpressionJob, JobBase, CallbackJob, None], None, None]]]
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1002 put = startindex
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shellac
parents:
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1003 for index in range(0, jobl):
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shellac
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1004 sjob = copy.copy(joborder)
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shellac
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1005 sjob[scatter_key] = joborder[scatter_key][index]
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shellac
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1006
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shellac
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1007 if len(scatter_keys) == 1:
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shellac
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1008 if runtimeContext.postScatterEval is not None:
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shellac
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1009 sjob = runtimeContext.postScatterEval(sjob)
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shellac
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1010 steps.append(process.job(
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shellac
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1011 sjob, functools.partial(callback.receive_scatter_output, put),
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shellac
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1012 runtimeContext))
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shellac
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1013 put += 1
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shellac
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1014 else:
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shellac
parents:
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1015 (add, _) = _flat_crossproduct_scatter(
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shellac
parents:
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1016 process, sjob, scatter_keys[1:], callback, put, runtimeContext)
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shellac
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1017 put += len(add)
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shellac
parents:
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1018 steps.extend(add)
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shellac
parents:
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1019
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shellac
parents:
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1020 return (steps, put)