annotate env/lib/python3.9/site-packages/galaxy/util/rules_dsl.py @ 0:4f3585e2f14b draft default tip

"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
author shellac
date Mon, 22 Mar 2021 18:12:50 +0000
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1 import abc
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2 import itertools
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3 import re
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4 from typing import List, Type
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5
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6 import yaml
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7 from pkg_resources import resource_stream
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8
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9
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10 def get_rules_specification():
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11 return yaml.safe_load(resource_stream(__name__, 'rules_dsl_spec.yml'))
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12
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13
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14 def _ensure_rule_contains_keys(rule, keys):
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15 for key, instance_class in keys.items():
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16 if key not in rule:
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17 raise ValueError("Rule of type [{}] does not contain key [{}].".format(rule["type"], key))
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18 value = rule[key]
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19 if not isinstance(value, instance_class):
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20 raise ValueError("Rule of type [{}] does not contain correct value type for key [{}].".format(rule["type"], key))
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21
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22
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23 def _ensure_key_value_in(rule, key, values):
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24 value = rule[key]
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25 if value not in values:
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26 raise ValueError(f"Invalid value [{value}] for [{key}] encountered.")
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27
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28
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29 def _ensure_valid_pattern(expression):
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30 re.compile(expression)
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31
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32
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33 def apply_regex(regex, target, data, replacement=None, group_count=None):
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34 pattern = re.compile(regex)
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35
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36 def new_row(row):
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37 source = row[target]
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38 if replacement is None:
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39 match = pattern.search(source)
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40 if not match:
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41 raise Exception(f"Problem applying regular expression [{regex}] to [{source}].")
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42
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43 if group_count:
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44 if len(match.groups()) != group_count:
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45 raise Exception("Problem applying regular expression, wrong number of groups found.")
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46
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47 result = row + list(match.groups())
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48 else:
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49 result = row + [match.group(0)]
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50 else:
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51 result = row + [pattern.search(source).expand(replacement)]
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52
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53 return result
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54
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55 new_data = list(map(new_row, data))
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56 return new_data
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57
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58
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59 class BaseRuleDefinition(metaclass=abc.ABCMeta):
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60
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61 @abc.abstractproperty
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62 def rule_type(self):
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63 """Short string describing type of rule (plugin class) to use."""
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64
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65 @abc.abstractmethod
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66 def validate_rule(self, rule):
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67 """Validate dictified rule definition of this type."""
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68
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69 @abc.abstractmethod
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70 def apply(self, rule, data, sources):
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71 """Apply validated, dictified rule definition to supplied data."""
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72
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73
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74 class AddColumnMetadataRuleDefinition(BaseRuleDefinition):
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75 rule_type = "add_column_metadata"
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76
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77 def validate_rule(self, rule):
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78 _ensure_rule_contains_keys(rule, {"value": str})
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79
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80 def apply(self, rule, data, sources):
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81 rule_value = rule["value"]
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82 if rule_value.startswith("identifier"):
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83 identifier_index = int(rule_value[len("identifier"):])
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84
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85 new_rows = []
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86 for index, row in enumerate(data):
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87 new_rows.append(row + [sources[index]["identifiers"][identifier_index]])
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88
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89 elif rule_value == "tags":
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90
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91 def sorted_tags(index):
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92 tags = sorted(sources[index]["tags"])
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93 return [",".join(tags)]
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94
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95 new_rows = []
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96 for index, row in enumerate(data):
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97 new_rows.append(row + sorted_tags(index))
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98
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99 return new_rows, sources
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100
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101
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102 class AddColumnGroupTagValueRuleDefinition(BaseRuleDefinition):
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103 rule_type = "add_column_group_tag_value"
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104
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105 def validate_rule(self, rule):
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106 _ensure_rule_contains_keys(rule, {"value": str})
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107
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108 def apply(self, rule, data, sources):
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109 rule_value = rule["value"]
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110 tag_prefix = "group:%s:" % rule_value
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111
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112 new_rows = []
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113 for index, row in enumerate(data):
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114 group_tag_value = None
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115 source = sources[index]
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116 tags = source["tags"]
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117 for tag in sorted(tags):
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118 if tag.startswith(tag_prefix):
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119 group_tag_value = tag[len(tag_prefix):]
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120 break
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121
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122 if group_tag_value is None:
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123 group_tag_value = rule.get("default_value", "")
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124
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125 new_rows.append(row + [group_tag_value])
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126
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127 return new_rows, sources
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128
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129
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130 class AddColumnConcatenateRuleDefinition(BaseRuleDefinition):
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131 rule_type = "add_column_concatenate"
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132
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133 def validate_rule(self, rule):
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134 _ensure_rule_contains_keys(rule, {"target_column_0": int, "target_column_1": int})
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135
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136 def apply(self, rule, data, sources):
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137 column_0 = rule["target_column_0"]
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138 column_1 = rule["target_column_1"]
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139
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140 new_rows = []
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141 for row in data:
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142 new_rows.append(row + [row[column_0] + row[column_1]])
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143
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144 return new_rows, sources
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145
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146
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147 class AddColumnBasenameRuleDefinition(BaseRuleDefinition):
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148 rule_type = "add_column_basename"
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149
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150 def validate_rule(self, rule):
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151 _ensure_rule_contains_keys(rule, {"target_column": int})
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152
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153 def apply(self, rule, data, sources):
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154 column = rule["target_column"]
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155 re = r"[^/]*$"
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156 return apply_regex(re, column, data), sources
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157
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158
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159 class AddColumnRegexRuleDefinition(BaseRuleDefinition):
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160 rule_type = "add_column_regex"
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161
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162 def validate_rule(self, rule):
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163 _ensure_rule_contains_keys(rule, {"target_column": int, "expression": str})
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164 _ensure_valid_pattern(rule["expression"])
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165
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166 def apply(self, rule, data, sources):
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167 target = rule["target_column"]
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168 expression = rule["expression"]
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169 replacement = rule.get("replacement")
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170 group_count = rule.get("group_count")
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171
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172 return apply_regex(expression, target, data, replacement, group_count), sources
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173
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174
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175 class AddColumnRownumRuleDefinition(BaseRuleDefinition):
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176 rule_type = "add_column_rownum"
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177
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178 def validate_rule(self, rule):
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179 _ensure_rule_contains_keys(rule, {"start": int})
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180
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181 def apply(self, rule, data, sources):
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182 start = rule["start"]
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183
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184 new_rows = []
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185 for index, row in enumerate(data):
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186 new_rows.append(row + ["%d" % (index + start)])
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187
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188 return new_rows, sources
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189
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190
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191 class AddColumnValueRuleDefinition(BaseRuleDefinition):
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192 rule_type = "add_column_value"
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193
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194 def validate_rule(self, rule):
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195 _ensure_rule_contains_keys(rule, {"value": str})
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196
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197 def apply(self, rule, data, sources):
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198 value = rule["value"]
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199
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200 new_rows = []
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201 for row in data:
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202 new_rows.append(row + [str(value)])
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203
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204 return new_rows, sources
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205
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206
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207 class AddColumnSubstrRuleDefinition(BaseRuleDefinition):
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208 rule_type = "add_column_substr"
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209
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210 def validate_rule(self, rule):
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211 _ensure_rule_contains_keys(rule, {
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212 "target_column": int,
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213 "length": int,
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214 "substr_type": str,
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215 })
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216 _ensure_key_value_in(rule, "substr_type", ["keep_prefix", "drop_prefix", "keep_suffix", "drop_suffix"])
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217
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218 def apply(self, rule, data, sources):
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219 target = rule["target_column"]
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220 length = rule["length"]
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221 substr_type = rule["substr_type"]
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222
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223 def new_row(row):
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224 original_value = row[target]
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225 start = 0
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226 end = len(original_value)
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227
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228 if substr_type == "keep_prefix":
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229 end = length
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230 elif substr_type == "drop_prefix":
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231 start = length
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232 elif substr_type == "keep_suffix":
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233 start = end - length
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234 if start < 0:
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235 start = 0
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236 else:
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237 end = end - length
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238 if end < 0:
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239 end = 0
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240
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241 return row + [original_value[start:end]]
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242
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243 return list(map(new_row, data)), sources
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244
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245
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246 class RemoveColumnsRuleDefinition(BaseRuleDefinition):
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247 rule_type = "remove_columns"
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248
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249 def validate_rule(self, rule):
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250 _ensure_rule_contains_keys(rule, {
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251 "target_columns": list,
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252 })
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253
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254 def apply(self, rule, data, sources):
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255 target_columns = rule["target_columns"]
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256
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257 def new_row(row):
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258 new = []
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259 for index, val in enumerate(row):
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260 if index not in target_columns:
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261 new.append(val)
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262 return new
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263
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264 return list(map(new_row, data)), sources
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265
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266
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267 def _filter_index(func, iterable):
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268 result = []
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269 for index, x in enumerate(iterable):
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270 if func(index):
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271 result.append(x)
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272
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273 return result
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274
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275
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276 class AddFilterRegexRuleDefinition(BaseRuleDefinition):
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277 rule_type = "add_filter_regex"
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278
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279 def validate_rule(self, rule):
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280 _ensure_rule_contains_keys(rule, {
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281 "target_column": int,
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282 "invert": bool,
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283 "expression": str,
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284 })
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285 _ensure_valid_pattern(rule["expression"])
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286
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287 def apply(self, rule, data, sources):
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288 target_column = rule["target_column"]
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289 invert = rule["invert"]
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290 regex = rule["expression"]
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291
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292 def _filter(index):
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293 row = data[index]
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294 val = row[target_column]
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295 pattern = re.compile(regex)
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296 return not invert if pattern.search(val) else invert
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297
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298 return _filter_index(_filter, data), _filter_index(_filter, sources)
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299
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300
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301 class AddFilterCountRuleDefinition(BaseRuleDefinition):
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302 rule_type = "add_filter_count"
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303
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304 def validate_rule(self, rule):
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305 _ensure_rule_contains_keys(rule, {
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306 "count": int,
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307 "invert": bool,
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308 "which": str,
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309 })
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310 _ensure_key_value_in(rule, "which", ["first", "last"])
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311
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312 def apply(self, rule, data, sources):
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313 num_rows = len(data)
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314 invert = rule["invert"]
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315 n = rule["count"]
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316 which = rule["which"]
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317
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318 def _filter(index):
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319 if which == "first":
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320 matches = index >= n
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321 else:
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322 matches = index < (num_rows - n)
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323 return not invert if matches else invert
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324
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325 return _filter_index(_filter, data), _filter_index(_filter, sources)
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326
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327
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328 class AddFilterEmptyRuleDefinition(BaseRuleDefinition):
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329 rule_type = "add_filter_empty"
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330
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331 def validate_rule(self, rule):
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332 _ensure_rule_contains_keys(rule, {
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333 "target_column": int,
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334 "invert": bool
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335 })
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336
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337 def apply(self, rule, data, sources):
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338 invert = rule["invert"]
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339 target_column = rule["target_column"]
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340
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341 def _filter(index):
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342 non_empty = len(data[index][target_column]) != 0
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343 return not invert if non_empty else invert
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344
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345 return _filter_index(_filter, data), _filter_index(_filter, sources)
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346
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347
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348 class AddFilterMatchesRuleDefinition(BaseRuleDefinition):
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349 rule_type = "add_filter_matches"
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350
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351 def validate_rule(self, rule):
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352 _ensure_rule_contains_keys(rule, {
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353 "target_column": int,
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354 "invert": bool,
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355 "value": str,
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356 })
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357
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358 def apply(self, rule, data, sources):
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359 invert = rule["invert"]
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360 target_column = rule["target_column"]
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361 value = rule["value"]
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362
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363 def _filter(index):
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364 row = data[index]
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365 val = row[target_column]
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366 return not invert if val == value else invert
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367
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368 return _filter_index(_filter, data), _filter_index(_filter, sources)
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369
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370
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371 class AddFilterCompareRuleDefinition(BaseRuleDefinition):
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372 rule_type = "add_filter_compare"
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373
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374 def validate_rule(self, rule):
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375 _ensure_rule_contains_keys(rule, {
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376 "target_column": int,
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377 "value": int,
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378 "compare_type": str,
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379 })
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380 _ensure_key_value_in(rule, "compare_type", ["less_than", "less_than_equal", "greater_than", "greater_than_equal"])
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381
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382 def apply(self, rule, data, sources):
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383 target_column = rule["target_column"]
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384 value = rule["value"]
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385 compare_type = rule["compare_type"]
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386
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387 def _filter(index):
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388 row = data[index]
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389 target_value = float(row[target_column])
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shellac
parents:
diff changeset
390 if compare_type == "less_than":
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shellac
parents:
diff changeset
391 matches = target_value < value
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shellac
parents:
diff changeset
392 elif compare_type == "less_than_equal":
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shellac
parents:
diff changeset
393 matches = target_value <= value
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
394 elif compare_type == "greater_than":
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shellac
parents:
diff changeset
395 matches = target_value > value
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shellac
parents:
diff changeset
396 elif compare_type == "greater_than_equal":
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shellac
parents:
diff changeset
397 matches = target_value >= value
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shellac
parents:
diff changeset
398
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shellac
parents:
diff changeset
399 return matches
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shellac
parents:
diff changeset
400
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shellac
parents:
diff changeset
401 return _filter_index(_filter, data), _filter_index(_filter, sources)
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shellac
parents:
diff changeset
402
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shellac
parents:
diff changeset
403
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shellac
parents:
diff changeset
404 class SortRuleDefinition(BaseRuleDefinition):
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shellac
parents:
diff changeset
405 rule_type = "sort"
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shellac
parents:
diff changeset
406
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shellac
parents:
diff changeset
407 def validate_rule(self, rule):
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shellac
parents:
diff changeset
408 _ensure_rule_contains_keys(rule, {
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shellac
parents:
diff changeset
409 "target_column": int,
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shellac
parents:
diff changeset
410 "numeric": bool,
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shellac
parents:
diff changeset
411 })
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shellac
parents:
diff changeset
412
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shellac
parents:
diff changeset
413 def apply(self, rule, data, sources):
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shellac
parents:
diff changeset
414 target = rule["target_column"]
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shellac
parents:
diff changeset
415 numeric = rule["numeric"]
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shellac
parents:
diff changeset
416
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shellac
parents:
diff changeset
417 sortable = zip(data, sources)
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shellac
parents:
diff changeset
418
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shellac
parents:
diff changeset
419 def sort_func(item):
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shellac
parents:
diff changeset
420 a_val = item[0][target]
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shellac
parents:
diff changeset
421 if numeric:
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shellac
parents:
diff changeset
422 a_val = float(a_val)
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shellac
parents:
diff changeset
423 return a_val
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shellac
parents:
diff changeset
424
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shellac
parents:
diff changeset
425 sorted_data = sorted(sortable, key=sort_func)
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shellac
parents:
diff changeset
426
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shellac
parents:
diff changeset
427 new_data = []
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shellac
parents:
diff changeset
428 new_sources = []
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shellac
parents:
diff changeset
429
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shellac
parents:
diff changeset
430 for (row, source) in sorted_data:
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shellac
parents:
diff changeset
431 new_data.append(row)
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shellac
parents:
diff changeset
432 new_sources.append(source)
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shellac
parents:
diff changeset
433
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shellac
parents:
diff changeset
434 return new_data, new_sources
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shellac
parents:
diff changeset
435
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
436
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
437 class SwapColumnsRuleDefinition(BaseRuleDefinition):
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
438 rule_type = "swap_columns"
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shellac
parents:
diff changeset
439
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shellac
parents:
diff changeset
440 def validate_rule(self, rule):
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
441 _ensure_rule_contains_keys(rule, {
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
442 "target_column_0": int,
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
443 "target_column_1": int,
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shellac
parents:
diff changeset
444 })
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shellac
parents:
diff changeset
445
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shellac
parents:
diff changeset
446 def apply(self, rule, data, sources):
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
447 target_column_0 = rule["target_column_0"]
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shellac
parents:
diff changeset
448 target_column_1 = rule["target_column_1"]
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shellac
parents:
diff changeset
449
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shellac
parents:
diff changeset
450 def new_row(row):
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shellac
parents:
diff changeset
451 row_copy = row[:]
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shellac
parents:
diff changeset
452 row_copy[target_column_0] = row[target_column_1]
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
453 row_copy[target_column_1] = row[target_column_0]
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
454 return row_copy
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
455
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shellac
parents:
diff changeset
456 return list(map(new_row, data)), sources
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shellac
parents:
diff changeset
457
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
458
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
459 class SplitColumnsRuleDefinition(BaseRuleDefinition):
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
460 rule_type = "split_columns"
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
461
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shellac
parents:
diff changeset
462 def validate_rule(self, rule):
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
463 _ensure_rule_contains_keys(rule, {
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
464 "target_columns_0": list,
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
465 "target_columns_1": list,
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shellac
parents:
diff changeset
466 })
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
467
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
468 def apply(self, rule, data, sources):
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
469 target_columns_0 = rule["target_columns_0"]
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
470 target_columns_1 = rule["target_columns_1"]
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
471
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
472 def split_row(row):
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
473 new_row_0 = []
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shellac
parents:
diff changeset
474 new_row_1 = []
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
475 for index, el in enumerate(row):
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
476 if index in target_columns_0:
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
477 new_row_0.append(el)
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
478 elif index in target_columns_1:
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
479 new_row_1.append(el)
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
480 else:
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
481 new_row_0.append(el)
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
482 new_row_1.append(el)
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
483
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
484 return [new_row_0, new_row_1]
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
485
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shellac
parents:
diff changeset
486 data = flat_map(split_row, data)
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
487 sources = flat_map(lambda x: [x, x], sources)
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
488
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shellac
parents:
diff changeset
489 return data, sources
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
490
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
491
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shellac
parents:
diff changeset
492 def flat_map(f, items):
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
493 return list(itertools.chain.from_iterable(map(f, items)))
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
494
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
495
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shellac
parents:
diff changeset
496 class RuleSet:
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shellac
parents:
diff changeset
497
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shellac
parents:
diff changeset
498 def __init__(self, rule_set_as_dict):
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
499 self.raw_rules = rule_set_as_dict["rules"]
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
500 self.raw_mapping = rule_set_as_dict.get("mapping", [])
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shellac
parents:
diff changeset
501
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shellac
parents:
diff changeset
502 @property
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
503 def rules(self):
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
504 return self.raw_rules
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
505
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shellac
parents:
diff changeset
506 def _rules_with_definitions(self):
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
507 for rule in self.raw_rules:
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shellac
parents:
diff changeset
508 yield (rule, RULES_DEFINITIONS[rule["type"]])
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
509
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
510 def apply(self, data, sources):
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
511 for rule, rule_definition in self._rules_with_definitions():
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
512 rule_definition.validate_rule(rule)
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
513 data, sources = rule_definition.apply(rule, data, sources)
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
514
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shellac
parents:
diff changeset
515 return data, sources
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
516
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shellac
parents:
diff changeset
517 @property
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shellac
parents:
diff changeset
518 def has_errors(self):
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
519 errored = False
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parents:
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520 try:
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parents:
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521 for rule, rule_definition in self._rules_with_definitions():
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parents:
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522 rule_definition.validate_rule(rule)
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523 except Exception:
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parents:
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524 errored = True
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parents:
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525 return errored
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parents:
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526
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527 @property
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parents:
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528 def mapping_as_dict(self):
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529 as_dict = {}
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parents:
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530 for mapping in self.raw_mapping:
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parents:
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531 as_dict[mapping["type"]] = mapping
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parents:
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532
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parents:
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533 return as_dict
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parents:
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534
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535 # Rest of this is generic, things here are Galaxy collection specific, think about about
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parents:
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536 # subclass of RuleSet for collection creation.
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parents:
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537 @property
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parents:
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538 def identifier_columns(self):
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parents:
diff changeset
539 mapping_as_dict = self.mapping_as_dict
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parents:
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540 identifier_columns = []
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parents:
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541 if "list_identifiers" in mapping_as_dict:
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parents:
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542 identifier_columns.extend(mapping_as_dict["list_identifiers"]["columns"])
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shellac
parents:
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543 if "paired_identifier" in mapping_as_dict:
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parents:
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544 identifier_columns.append(mapping_as_dict["paired_identifier"]["columns"][0])
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parents:
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545
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parents:
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546 return identifier_columns
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parents:
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547
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parents:
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548 @property
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parents:
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549 def collection_type(self):
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parents:
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550 mapping_as_dict = self.mapping_as_dict
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parents:
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551 list_columns = mapping_as_dict.get("list_identifiers", {"columns": []})["columns"]
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parents:
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552 collection_type = ":".join(map(lambda c: "list", list_columns))
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shellac
parents:
diff changeset
553 if "paired_identifier" in mapping_as_dict:
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parents:
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554 if collection_type:
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parents:
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555 collection_type += ":paired"
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parents:
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556 else:
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parents:
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557 collection_type = "paired"
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parents:
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558 return collection_type
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parents:
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559
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parents:
diff changeset
560 @property
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561 def display(self):
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parents:
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562 message = "Rules:\n"
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parents:
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563 message += "".join("- %s\n" % r for r in self.raw_rules)
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
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parents:
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564 message += "Column Definitions:\n"
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
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parents:
diff changeset
565 message += "".join("- %s\n" % m for m in self.raw_mapping)
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
566 return message
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shellac
parents:
diff changeset
567
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shellac
parents:
diff changeset
568
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shellac
parents:
diff changeset
569 RULES_DEFINITION_CLASSES: List[Type[BaseRuleDefinition]] = [
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parents:
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570 AddColumnMetadataRuleDefinition,
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parents:
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571 AddColumnGroupTagValueRuleDefinition,
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parents:
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572 AddColumnConcatenateRuleDefinition,
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parents:
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573 AddColumnBasenameRuleDefinition,
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parents:
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574 AddColumnRegexRuleDefinition,
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
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parents:
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575 AddColumnRownumRuleDefinition,
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parents:
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576 AddColumnValueRuleDefinition,
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
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parents:
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577 AddColumnSubstrRuleDefinition,
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
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parents:
diff changeset
578 RemoveColumnsRuleDefinition,
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
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parents:
diff changeset
579 AddFilterRegexRuleDefinition,
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
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parents:
diff changeset
580 AddFilterCountRuleDefinition,
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
581 AddFilterEmptyRuleDefinition,
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
582 AddFilterMatchesRuleDefinition,
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shellac
parents:
diff changeset
583 AddFilterCompareRuleDefinition,
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
584 SortRuleDefinition,
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
585 SwapColumnsRuleDefinition,
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
586 SplitColumnsRuleDefinition,
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
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parents:
diff changeset
587 ]
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
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diff changeset
588 RULES_DEFINITIONS = {}
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
589 for rule_class in RULES_DEFINITION_CLASSES:
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shellac
parents:
diff changeset
590 RULES_DEFINITIONS[rule_class.rule_type] = rule_class()