Mercurial > repos > shellac > sam_consensus_v3
annotate env/lib/python3.9/site-packages/cwltool/checker.py @ 0:4f3585e2f14b draft default tip
"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
author | shellac |
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date | Mon, 22 Mar 2021 18:12:50 +0000 |
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1 """Static checking of CWL workflow connectivity.""" |
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2 from collections import namedtuple |
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3 from typing import ( |
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4 Any, |
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5 Dict, |
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6 List, |
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7 MutableMapping, |
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8 MutableSequence, |
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9 Optional, |
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10 Sized, |
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11 Union, |
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12 cast, |
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13 ) |
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14 |
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15 from schema_salad.exceptions import ValidationException |
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16 from schema_salad.sourceline import SourceLine, bullets, strip_dup_lineno |
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17 from schema_salad.utils import json_dumps |
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18 |
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19 from .errors import WorkflowException |
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20 from .loghandler import _logger |
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21 from .process import shortname |
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22 from .utils import CWLObjectType, CWLOutputAtomType, CWLOutputType, SinkType, aslist |
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23 |
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24 |
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25 def _get_type(tp): |
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26 # type: (Any) -> Any |
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27 if isinstance(tp, MutableMapping): |
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28 if tp.get("type") not in ("array", "record", "enum"): |
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29 return tp["type"] |
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30 return tp |
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31 |
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32 |
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33 def check_types( |
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34 srctype: SinkType, |
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35 sinktype: SinkType, |
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36 linkMerge: Optional[str], |
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37 valueFrom: Optional[str], |
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38 ) -> str: |
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39 """ |
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40 Check if the source and sink types are correct. |
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41 |
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42 Acceptable types are "pass", "warning", or "exception". |
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43 """ |
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44 if valueFrom is not None: |
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45 return "pass" |
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46 if linkMerge is None: |
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47 if can_assign_src_to_sink(srctype, sinktype, strict=True): |
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48 return "pass" |
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49 if can_assign_src_to_sink(srctype, sinktype, strict=False): |
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50 return "warning" |
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51 return "exception" |
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52 if linkMerge == "merge_nested": |
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53 return check_types( |
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54 {"items": _get_type(srctype), "type": "array"}, |
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55 _get_type(sinktype), |
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56 None, |
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57 None, |
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58 ) |
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59 if linkMerge == "merge_flattened": |
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60 return check_types( |
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61 merge_flatten_type(_get_type(srctype)), _get_type(sinktype), None, None |
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62 ) |
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63 raise WorkflowException(f"Unrecognized linkMerge enum '{linkMerge}'") |
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64 |
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65 |
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66 def merge_flatten_type(src: SinkType) -> CWLOutputType: |
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67 """Return the merge flattened type of the source type.""" |
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68 if isinstance(src, MutableSequence): |
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69 return [merge_flatten_type(cast(SinkType, t)) for t in src] |
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70 if isinstance(src, MutableMapping) and src.get("type") == "array": |
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71 return src |
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72 return {"items": src, "type": "array"} |
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73 |
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74 |
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75 def can_assign_src_to_sink( |
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76 src: SinkType, sink: Optional[SinkType], strict: bool = False |
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77 ) -> bool: |
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78 """ |
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79 Check for identical type specifications, ignoring extra keys like inputBinding. |
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80 |
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81 src: admissible source types |
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82 sink: admissible sink types |
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83 |
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84 In non-strict comparison, at least one source type must match one sink type. |
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85 In strict comparison, all source types must match at least one sink type. |
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86 """ |
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87 if src == "Any" or sink == "Any": |
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88 return True |
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89 if isinstance(src, MutableMapping) and isinstance(sink, MutableMapping): |
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90 if sink.get("not_connected") and strict: |
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91 return False |
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92 if src["type"] == "array" and sink["type"] == "array": |
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93 return can_assign_src_to_sink( |
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94 cast(MutableSequence[CWLOutputAtomType], src["items"]), |
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95 cast(MutableSequence[CWLOutputAtomType], sink["items"]), |
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96 strict, |
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97 ) |
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98 if src["type"] == "record" and sink["type"] == "record": |
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99 return _compare_records(src, sink, strict) |
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100 if src["type"] == "File" and sink["type"] == "File": |
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101 for sinksf in cast(List[CWLObjectType], sink.get("secondaryFiles", [])): |
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102 if not [ |
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103 1 |
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104 for srcsf in cast( |
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105 List[CWLObjectType], src.get("secondaryFiles", []) |
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106 ) |
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107 if sinksf == srcsf |
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108 ]: |
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109 if strict: |
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110 return False |
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111 return True |
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112 return can_assign_src_to_sink( |
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113 cast(SinkType, src["type"]), cast(Optional[SinkType], sink["type"]), strict |
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114 ) |
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115 if isinstance(src, MutableSequence): |
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116 if strict: |
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117 for this_src in src: |
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118 if not can_assign_src_to_sink(cast(SinkType, this_src), sink): |
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119 return False |
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120 return True |
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121 for this_src in src: |
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122 if can_assign_src_to_sink(cast(SinkType, this_src), sink): |
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123 return True |
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124 return False |
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125 if isinstance(sink, MutableSequence): |
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126 for this_sink in sink: |
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127 if can_assign_src_to_sink(src, cast(SinkType, this_sink)): |
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128 return True |
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129 return False |
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130 return bool(src == sink) |
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131 |
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132 |
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133 def _compare_records( |
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134 src: CWLObjectType, sink: CWLObjectType, strict: bool = False |
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135 ) -> bool: |
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136 """ |
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137 Compare two records, ensuring they have compatible fields. |
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138 |
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139 This handles normalizing record names, which will be relative to workflow |
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140 step, so that they can be compared. |
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141 """ |
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142 |
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143 def _rec_fields( |
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144 rec, |
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145 ): # type: (MutableMapping[str, Any]) -> MutableMapping[str, Any] |
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146 out = {} |
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147 for field in rec["fields"]: |
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148 name = shortname(field["name"]) |
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149 out[name] = field["type"] |
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150 return out |
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151 |
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152 srcfields = _rec_fields(src) |
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153 sinkfields = _rec_fields(sink) |
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154 for key in sinkfields.keys(): |
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155 if ( |
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156 not can_assign_src_to_sink( |
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157 srcfields.get(key, "null"), sinkfields.get(key, "null"), strict |
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158 ) |
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159 and sinkfields.get(key) is not None |
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160 ): |
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161 _logger.info( |
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162 "Record comparison failure for %s and %s\n" |
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163 "Did not match fields for %s: %s and %s", |
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164 src["name"], |
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165 sink["name"], |
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166 key, |
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167 srcfields.get(key), |
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168 sinkfields.get(key), |
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169 ) |
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170 return False |
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171 return True |
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172 |
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173 |
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174 def missing_subset(fullset: List[Any], subset: List[Any]) -> List[Any]: |
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175 missing = [] |
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176 for i in subset: |
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177 if i not in fullset: |
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178 missing.append(i) |
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179 return missing |
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180 |
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181 |
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182 def static_checker( |
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183 workflow_inputs: List[CWLObjectType], |
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184 workflow_outputs: MutableSequence[CWLObjectType], |
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185 step_inputs: MutableSequence[CWLObjectType], |
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186 step_outputs: List[CWLObjectType], |
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187 param_to_step: Dict[str, CWLObjectType], |
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188 ) -> None: |
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189 """Check if all source and sink types of a workflow are compatible before run time.""" |
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190 # source parameters: workflow_inputs and step_outputs |
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191 # sink parameters: step_inputs and workflow_outputs |
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192 |
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193 # make a dictionary of source parameters, indexed by the "id" field |
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194 src_parms = workflow_inputs + step_outputs |
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195 src_dict = {} # type: Dict[str, CWLObjectType] |
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196 for parm in src_parms: |
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197 src_dict[cast(str, parm["id"])] = parm |
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198 |
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199 step_inputs_val = check_all_types(src_dict, step_inputs, "source", param_to_step) |
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200 workflow_outputs_val = check_all_types( |
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201 src_dict, workflow_outputs, "outputSource", param_to_step |
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202 ) |
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203 |
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204 warnings = step_inputs_val["warning"] + workflow_outputs_val["warning"] |
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205 exceptions = step_inputs_val["exception"] + workflow_outputs_val["exception"] |
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206 |
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207 warning_msgs = [] |
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208 exception_msgs = [] |
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209 for warning in warnings: |
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210 src = warning.src |
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211 sink = warning.sink |
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212 linkMerge = warning.linkMerge |
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213 sinksf = sorted( |
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214 [ |
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215 p["pattern"] |
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216 for p in sink.get("secondaryFiles", []) |
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217 if p.get("required", True) |
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218 ] |
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219 ) |
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220 srcsf = sorted([p["pattern"] for p in src.get("secondaryFiles", [])]) |
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221 # Every secondaryFile required by the sink, should be declared |
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222 # by the source |
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223 missing = missing_subset(srcsf, sinksf) |
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224 if missing: |
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225 msg1 = "Parameter '{}' requires secondaryFiles {} but".format( |
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226 shortname(sink["id"]), |
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227 missing, |
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228 ) |
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229 msg3 = SourceLine(src, "id").makeError( |
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230 "source '%s' does not provide those secondaryFiles." |
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231 % (shortname(src["id"])) |
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232 ) |
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233 msg4 = SourceLine(src.get("_tool_entry", src), "secondaryFiles").makeError( |
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234 "To resolve, add missing secondaryFiles patterns to definition of '%s' or" |
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235 % (shortname(src["id"])) |
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236 ) |
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237 msg5 = SourceLine( |
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238 sink.get("_tool_entry", sink), "secondaryFiles" |
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239 ).makeError( |
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240 "mark missing secondaryFiles in definition of '%s' as optional." |
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241 % shortname(sink["id"]) |
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242 ) |
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243 msg = SourceLine(sink).makeError( |
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244 "{}\n{}".format(msg1, bullets([msg3, msg4, msg5], " ")) |
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245 ) |
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246 elif sink.get("not_connected"): |
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247 if not sink.get("used_by_step"): |
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248 msg = SourceLine(sink, "type").makeError( |
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249 "'%s' is not an input parameter of %s, expected %s" |
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250 % ( |
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251 shortname(sink["id"]), |
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252 param_to_step[sink["id"]]["run"], |
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253 ", ".join( |
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254 shortname(cast(str, s["id"])) |
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255 for s in cast( |
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256 List[Dict[str, Union[str, bool]]], |
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257 param_to_step[sink["id"]]["inputs"], |
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258 ) |
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259 if not s.get("not_connected") |
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260 ), |
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261 ) |
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262 ) |
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263 else: |
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264 msg = "" |
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265 else: |
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266 msg = ( |
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267 SourceLine(src, "type").makeError( |
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268 "Source '%s' of type %s may be incompatible" |
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269 % (shortname(src["id"]), json_dumps(src["type"])) |
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270 ) |
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271 + "\n" |
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272 + SourceLine(sink, "type").makeError( |
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273 " with sink '%s' of type %s" |
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274 % (shortname(sink["id"]), json_dumps(sink["type"])) |
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275 ) |
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276 ) |
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277 if linkMerge is not None: |
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278 msg += "\n" + SourceLine(sink).makeError( |
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279 " source has linkMerge method %s" % linkMerge |
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280 ) |
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281 |
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282 if warning.message is not None: |
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283 msg += "\n" + SourceLine(sink).makeError(" " + warning.message) |
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284 |
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285 if msg: |
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286 warning_msgs.append(msg) |
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287 |
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288 for exception in exceptions: |
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289 src = exception.src |
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290 sink = exception.sink |
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291 linkMerge = exception.linkMerge |
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292 extra_message = exception.message |
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293 msg = ( |
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294 SourceLine(src, "type").makeError( |
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295 "Source '%s' of type %s is incompatible" |
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296 % (shortname(src["id"]), json_dumps(src["type"])) |
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297 ) |
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298 + "\n" |
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299 + SourceLine(sink, "type").makeError( |
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300 " with sink '%s' of type %s" |
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301 % (shortname(sink["id"]), json_dumps(sink["type"])) |
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302 ) |
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303 ) |
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304 if extra_message is not None: |
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305 msg += "\n" + SourceLine(sink).makeError(" " + extra_message) |
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306 |
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307 if linkMerge is not None: |
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308 msg += "\n" + SourceLine(sink).makeError( |
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309 " source has linkMerge method %s" % linkMerge |
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310 ) |
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311 exception_msgs.append(msg) |
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312 |
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313 for sink in step_inputs: |
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314 if ( |
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315 "null" != sink["type"] |
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316 and "null" not in sink["type"] |
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317 and "source" not in sink |
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318 and "default" not in sink |
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319 and "valueFrom" not in sink |
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320 ): |
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321 msg = SourceLine(sink).makeError( |
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322 "Required parameter '%s' does not have source, default, or valueFrom expression" |
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323 % shortname(sink["id"]) |
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324 ) |
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325 exception_msgs.append(msg) |
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326 |
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327 all_warning_msg = strip_dup_lineno("\n".join(warning_msgs)) |
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328 all_exception_msg = strip_dup_lineno("\n" + "\n".join(exception_msgs)) |
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329 |
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330 if all_warning_msg: |
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331 _logger.warning("Workflow checker warning:\n%s", all_warning_msg) |
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332 if exceptions: |
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333 raise ValidationException(all_exception_msg) |
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334 |
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335 |
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336 SrcSink = namedtuple("SrcSink", ["src", "sink", "linkMerge", "message"]) |
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337 |
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338 |
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339 def check_all_types( |
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340 src_dict: Dict[str, CWLObjectType], |
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341 sinks: MutableSequence[CWLObjectType], |
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342 sourceField: str, |
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343 param_to_step: Dict[str, CWLObjectType], |
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344 ) -> Dict[str, List[SrcSink]]: |
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345 """ |
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346 Given a list of sinks, check if their types match with the types of their sources. |
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347 |
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348 sourceField is either "soure" or "outputSource" |
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349 """ |
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350 validation = {"warning": [], "exception": []} # type: Dict[str, List[SrcSink]] |
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351 for sink in sinks: |
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352 if sourceField in sink: |
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353 |
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354 valueFrom = cast(Optional[str], sink.get("valueFrom")) |
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355 pickValue = cast(Optional[str], sink.get("pickValue")) |
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356 |
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357 extra_message = None |
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358 if pickValue is not None: |
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359 extra_message = "pickValue is: %s" % pickValue |
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360 |
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361 if isinstance(sink[sourceField], MutableSequence): |
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362 linkMerge = cast( |
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363 Optional[str], |
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364 sink.get( |
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365 "linkMerge", |
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366 ( |
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367 "merge_nested" |
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368 if len(cast(Sized, sink[sourceField])) > 1 |
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369 else None |
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370 ), |
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371 ), |
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372 ) # type: Optional[str] |
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373 |
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374 if pickValue in ["first_non_null", "the_only_non_null"]: |
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375 linkMerge = None |
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376 |
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377 srcs_of_sink = [] # type: List[CWLObjectType] |
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378 for parm_id in cast(MutableSequence[str], sink[sourceField]): |
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379 srcs_of_sink += [src_dict[parm_id]] |
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380 if ( |
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381 is_conditional_step(param_to_step, parm_id) |
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382 and pickValue is None |
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383 ): |
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384 validation["warning"].append( |
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385 SrcSink( |
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386 src_dict[parm_id], |
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387 sink, |
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388 linkMerge, |
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389 message="Source is from conditional step, but pickValue is not used", |
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390 ) |
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391 ) |
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392 else: |
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393 parm_id = cast(str, sink[sourceField]) |
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394 srcs_of_sink = [src_dict[parm_id]] |
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395 linkMerge = None |
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396 |
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397 if pickValue is not None: |
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398 validation["warning"].append( |
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399 SrcSink( |
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400 src_dict[parm_id], |
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401 sink, |
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402 linkMerge, |
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403 message="pickValue is used but only a single input source is declared", |
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404 ) |
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405 ) |
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406 |
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407 if is_conditional_step(param_to_step, parm_id): |
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408 src_typ = aslist(srcs_of_sink[0]["type"]) |
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409 snk_typ = sink["type"] |
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410 |
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411 if "null" not in src_typ: |
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412 src_typ = ["null"] + cast(List[Any], src_typ) |
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413 |
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414 if "null" not in cast( |
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415 Union[List[str], CWLObjectType], snk_typ |
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416 ): # Given our type names this works even if not a list |
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417 validation["warning"].append( |
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418 SrcSink( |
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419 src_dict[parm_id], |
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420 sink, |
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421 linkMerge, |
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422 message="Source is from conditional step and may produce `null`", |
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423 ) |
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424 ) |
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425 |
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426 srcs_of_sink[0]["type"] = src_typ |
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427 |
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428 for src in srcs_of_sink: |
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429 check_result = check_types(src, sink, linkMerge, valueFrom) |
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430 if check_result == "warning": |
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431 validation["warning"].append( |
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432 SrcSink(src, sink, linkMerge, message=extra_message) |
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433 ) |
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434 elif check_result == "exception": |
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435 validation["exception"].append( |
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436 SrcSink(src, sink, linkMerge, message=extra_message) |
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437 ) |
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438 |
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439 return validation |
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440 |
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441 |
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442 def is_conditional_step(param_to_step: Dict[str, CWLObjectType], parm_id: str) -> bool: |
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443 source_step = param_to_step.get(parm_id) |
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444 if source_step is not None: |
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445 if source_step.get("when") is not None: |
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446 return True |
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447 return False |