Mercurial > repos > shellac > guppy_basecaller

annotate env/lib/python3.7/site-packages/cwltool/checker.py @ 3:758bc20232e8 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
"planemo upload commit 2a0fe2cc28b09e101d37293e53e82f61762262ec"
author shellac
date Thu, 14 May 2020 16:20:52 -0400
parents 26e78fe6e8c4
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
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0
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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 Any, Dict, List, MutableMapping, MutableSequence, Optional
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4
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5 import six
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6 from schema_salad import validate
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7 from schema_salad.sourceline import SourceLine, bullets, strip_dup_lineno
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8 from typing_extensions import Text # pylint: disable=unused-import
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9 # move to a regular typing import when Python 3.3-3.6 is no longer supported
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10
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11 from .errors import WorkflowException
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12 from .loghandler import _logger
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13 from .process import shortname
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14 from .utils import json_dumps
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15
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16
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17 def _get_type(tp):
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18 # type: (Any) -> Any
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19 if isinstance(tp, MutableMapping):
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20 if tp.get("type") not in ("array", "record", "enum"):
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21 return tp["type"]
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22 return tp
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23
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24 def check_types(srctype, sinktype, linkMerge, valueFrom):
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25 # type: (Any, Any, Optional[Text], Optional[Text]) -> Text
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26 """
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27 Check if the source and sink types are correct.
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28
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29 Acceptable types are "pass", "warning", or "exception".
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30 """
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31 if valueFrom is not None:
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32 return "pass"
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33 if linkMerge is None:
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34 if can_assign_src_to_sink(srctype, sinktype, strict=True):
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35 return "pass"
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36 if can_assign_src_to_sink(srctype, sinktype, strict=False):
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37 return "warning"
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38 return "exception"
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39 if linkMerge == "merge_nested":
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40 return check_types({"items": _get_type(srctype), "type": "array"},
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41 _get_type(sinktype), None, None)
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42 if linkMerge == "merge_flattened":
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43 return check_types(merge_flatten_type(_get_type(srctype)), _get_type(sinktype), None, None)
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44 raise WorkflowException(u"Unrecognized linkMerge enum '{}'".format(linkMerge))
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45
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46
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47 def merge_flatten_type(src):
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48 # type: (Any) -> Any
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49 """Return the merge flattened type of the source type."""
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50 if isinstance(src, MutableSequence):
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51 return [merge_flatten_type(t) for t in src]
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52 if isinstance(src, MutableMapping) and src.get("type") == "array":
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53 return src
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54 return {"items": src, "type": "array"}
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55
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56
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57 def can_assign_src_to_sink(src, sink, strict=False): # type: (Any, Any, bool) -> bool
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58 """
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59 Check for identical type specifications, ignoring extra keys like inputBinding.
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60
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61 src: admissible source types
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62 sink: admissible sink types
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63
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64 In non-strict comparison, at least one source type must match one sink type.
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65 In strict comparison, all source types must match at least one sink type.
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66 """
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67 if src == "Any" or sink == "Any":
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68 return True
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69 if isinstance(src, MutableMapping) and isinstance(sink, MutableMapping):
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70 if sink.get("not_connected") and strict:
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71 return False
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72 if src["type"] == "array" and sink["type"] == "array":
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73 return can_assign_src_to_sink(src["items"], sink["items"], strict)
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74 if src["type"] == "record" and sink["type"] == "record":
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75 return _compare_records(src, sink, strict)
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76 if src["type"] == "File" and sink["type"] == "File":
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77 for sinksf in sink.get("secondaryFiles", []):
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78 if not [1 for srcsf in src.get("secondaryFiles", []) if sinksf == srcsf]:
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79 if strict:
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80 return False
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81 return True
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82 return can_assign_src_to_sink(src["type"], sink["type"], strict)
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83 if isinstance(src, MutableSequence):
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84 if strict:
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85 for this_src in src:
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86 if not can_assign_src_to_sink(this_src, sink):
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87 return False
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88 return True
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89 for this_src in src:
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90 if can_assign_src_to_sink(this_src, sink):
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91 return True
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92 return False
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93 if isinstance(sink, MutableSequence):
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94 for this_sink in sink:
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95 if can_assign_src_to_sink(src, this_sink):
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96 return True
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97 return False
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98 return bool(src == sink)
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99
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100
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101 def _compare_records(src, sink, strict=False):
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102 # type: (MutableMapping[Text, Any], MutableMapping[Text, Any], bool) -> bool
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103 """
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104 Compare two records, ensuring they have compatible fields.
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105
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106 This handles normalizing record names, which will be relative to workflow
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107 step, so that they can be compared.
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108 """
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109 def _rec_fields(rec): # type: (MutableMapping[Text, Any]) -> MutableMapping[Text, Any]
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110 out = {}
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111 for field in rec["fields"]:
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112 name = shortname(field["name"])
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113 out[name] = field["type"]
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114 return out
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115
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116 srcfields = _rec_fields(src)
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117 sinkfields = _rec_fields(sink)
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118 for key in six.iterkeys(sinkfields):
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119 if (not can_assign_src_to_sink(
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120 srcfields.get(key, "null"), sinkfields.get(key, "null"), strict)
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121 and sinkfields.get(key) is not None):
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122 _logger.info("Record comparison failure for %s and %s\n"
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123 "Did not match fields for %s: %s and %s",
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124 src["name"], sink["name"], key, srcfields.get(key),
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125 sinkfields.get(key))
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126 return False
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127 return True
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128
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129 def missing_subset(fullset, subset): # type: (List[Any], List[Any]) -> List[Any]
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130 missing = []
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131 for i in subset:
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132 if i not in fullset:
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133 missing.append(i)
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134 return missing
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135
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136 def static_checker(workflow_inputs, workflow_outputs, step_inputs, step_outputs, param_to_step):
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137 # type: (List[Dict[Text, Any]], List[Dict[Text, Any]], List[Dict[Text, Any]], List[Dict[Text, Any]], Dict[Text, Dict[Text, Any]]) -> None
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138 """Check if all source and sink types of a workflow are compatible before run time."""
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139 # source parameters: workflow_inputs and step_outputs
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140 # sink parameters: step_inputs and workflow_outputs
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141
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142 # make a dictionary of source parameters, indexed by the "id" field
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143 src_parms = workflow_inputs + step_outputs
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144 src_dict = {}
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145 for parm in src_parms:
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146 src_dict[parm["id"]] = parm
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147
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148 step_inputs_val = check_all_types(src_dict, step_inputs, "source")
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149 workflow_outputs_val = check_all_types(src_dict, workflow_outputs, "outputSource")
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150
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151 warnings = step_inputs_val["warning"] + workflow_outputs_val["warning"]
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152 exceptions = step_inputs_val["exception"] + workflow_outputs_val["exception"]
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153
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154 warning_msgs = []
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155 exception_msgs = []
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156 for warning in warnings:
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157 src = warning.src
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158 sink = warning.sink
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159 linkMerge = warning.linkMerge
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160 sinksf = sorted([p["pattern"] for p in sink.get("secondaryFiles", []) if p.get("required", True)])
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161 srcsf = sorted([p["pattern"] for p in src.get("secondaryFiles", [])])
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162 # Every secondaryFile required by the sink, should be declared
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163 # by the source
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164 missing = missing_subset(srcsf, sinksf)
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165 if missing:
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166 msg1 = "Parameter '%s' requires secondaryFiles %s but" % (shortname(sink["id"]), missing)
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167 msg3 = SourceLine(src, "id").makeError(
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168 "source '%s' does not provide those secondaryFiles." % (shortname(src["id"])))
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169 msg4 = SourceLine(src.get("_tool_entry", src), "secondaryFiles").makeError("To resolve, add missing secondaryFiles patterns to definition of '%s' or" % (shortname(src["id"])))
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170 msg5 = SourceLine(sink.get("_tool_entry", sink), "secondaryFiles").makeError("mark missing secondaryFiles in definition of '%s' as optional." % shortname(sink["id"]))
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171 msg = SourceLine(sink).makeError("%s\n%s" % (msg1, bullets([msg3, msg4, msg5], " ")))
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172 elif sink.get("not_connected"):
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173 msg = SourceLine(sink, "type").makeError(
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174 "'%s' is not an input parameter of %s, expected %s"
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175 % (shortname(sink["id"]), param_to_step[sink["id"]]["run"],
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176 ", ".join(shortname(s["id"])
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177 for s in param_to_step[sink["id"]]["inputs"]
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178 if not s.get("not_connected"))))
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179 else:
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180 msg = SourceLine(src, "type").makeError(
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181 "Source '%s' of type %s may be incompatible"
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182 % (shortname(src["id"]), json_dumps(src["type"]))) + "\n" + \
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183 SourceLine(sink, "type").makeError(
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184 " with sink '%s' of type %s"
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185 % (shortname(sink["id"]), json_dumps(sink["type"])))
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186 if linkMerge is not None:
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187 msg += "\n" + SourceLine(sink).makeError(" source has linkMerge method %s" % linkMerge)
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188
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189 warning_msgs.append(msg)
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190 for exception in exceptions:
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191 src = exception.src
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192 sink = exception.sink
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193 linkMerge = exception.linkMerge
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194 msg = SourceLine(src, "type").makeError(
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195 "Source '%s' of type %s is incompatible"
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196 % (shortname(src["id"]), json_dumps(src["type"]))) + "\n" + \
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197 SourceLine(sink, "type").makeError(
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198 " with sink '%s' of type %s"
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199 % (shortname(sink["id"]), json_dumps(sink["type"])))
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200 if linkMerge is not None:
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201 msg += "\n" + SourceLine(sink).makeError(" source has linkMerge method %s" % linkMerge)
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202 exception_msgs.append(msg)
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203
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204 for sink in step_inputs:
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205 if ('null' != sink["type"] and 'null' not in sink["type"]
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206 and "source" not in sink and "default" not in sink and "valueFrom" not in sink):
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207 msg = SourceLine(sink).makeError(
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208 "Required parameter '%s' does not have source, default, or valueFrom expression"
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209 % shortname(sink["id"]))
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210 exception_msgs.append(msg)
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211
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212 all_warning_msg = strip_dup_lineno("\n".join(warning_msgs))
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213 all_exception_msg = strip_dup_lineno("\n".join(exception_msgs))
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214
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215 if warnings:
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216 _logger.warning("Workflow checker warning:\n%s", all_warning_msg)
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217 if exceptions:
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218 raise validate.ValidationException(all_exception_msg)
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219
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220
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221 SrcSink = namedtuple("SrcSink", ["src", "sink", "linkMerge"])
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222
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223 def check_all_types(src_dict, sinks, sourceField):
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224 # type: (Dict[Text, Any], List[Dict[Text, Any]], Text) -> Dict[Text, List[SrcSink]]
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225 """
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226 Given a list of sinks, check if their types match with the types of their sources.
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227
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228 sourceField is either "soure" or "outputSource"
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229 """
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230 validation = {"warning": [], "exception": []} # type: Dict[Text, List[SrcSink]]
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231 for sink in sinks:
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232 if sourceField in sink:
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233 valueFrom = sink.get("valueFrom")
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234 if isinstance(sink[sourceField], MutableSequence):
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235 srcs_of_sink = [src_dict[parm_id] for parm_id in sink[sourceField]]
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236 linkMerge = sink.get("linkMerge", ("merge_nested"
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237 if len(sink[sourceField]) > 1 else None))
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238 else:
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239 parm_id = sink[sourceField]
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240 srcs_of_sink = [src_dict[parm_id]]
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241 linkMerge = None
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242 for src in srcs_of_sink:
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243 check_result = check_types(src, sink, linkMerge, valueFrom)
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244 if check_result == "warning":
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
245 validation["warning"].append(SrcSink(src, sink, linkMerge))
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
246 elif check_result == "exception":
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
247 validation["exception"].append(SrcSink(src, sink, linkMerge))
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
248 return validation