[2] | 1 | """ |
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| 2 | Classes related to parameter validation. |
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| 3 | """ |
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| 4 | |
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| 5 | import os, re, logging |
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| 6 | from elementtree.ElementTree import XML |
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| 7 | from galaxy import model |
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| 8 | |
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| 9 | log = logging.getLogger( __name__ ) |
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| 10 | |
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| 11 | class LateValidationError( Exception ): |
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| 12 | def __init__( self, message ): |
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| 13 | self.message = message |
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| 14 | |
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| 15 | class Validator( object ): |
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| 16 | """ |
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| 17 | A validator checks that a value meets some conditions OR raises ValueError |
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| 18 | """ |
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| 19 | @classmethod |
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| 20 | def from_element( cls, param, elem ): |
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| 21 | type = elem.get( 'type', None ) |
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| 22 | assert type is not None, "Required 'type' attribute missing from validator" |
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| 23 | return validator_types[type].from_element( param, elem ) |
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| 24 | def validate( self, value, history=None ): |
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| 25 | raise TypeError( "Abstract Method" ) |
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| 26 | |
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| 27 | class RegexValidator( Validator ): |
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| 28 | """ |
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| 29 | Validator that evaluates a regular expression |
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| 30 | |
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| 31 | >>> from galaxy.tools.parameters import ToolParameter |
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| 32 | >>> p = ToolParameter.build( None, XML( ''' |
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| 33 | ... <param name="blah" type="text" size="10" value="10"> |
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| 34 | ... <validator type="regex" message="Not gonna happen">[Ff]oo</validator> |
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| 35 | ... </param> |
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| 36 | ... ''' ) ) |
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| 37 | >>> t = p.validate( "Foo" ) |
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| 38 | >>> t = p.validate( "foo" ) |
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| 39 | >>> t = p.validate( "Fop" ) |
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| 40 | Traceback (most recent call last): |
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| 41 | ... |
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| 42 | ValueError: Not gonna happen |
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| 43 | """ |
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| 44 | @classmethod |
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| 45 | def from_element( cls, param, elem ): |
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| 46 | return cls( elem.get( 'message' ), elem.text ) |
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| 47 | def __init__( self, message, expression ): |
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| 48 | self.message = message |
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| 49 | # Compile later. RE objects used to not be thread safe. Not sure about |
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| 50 | # the sre module. |
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| 51 | self.expression = expression |
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| 52 | def validate( self, value, history=None ): |
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| 53 | if re.match( self.expression, value ) is None: |
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| 54 | raise ValueError( self.message ) |
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| 55 | |
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| 56 | class ExpressionValidator( Validator ): |
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| 57 | """ |
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| 58 | Validator that evaluates a python expression using the value |
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| 59 | |
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| 60 | >>> from galaxy.tools.parameters import ToolParameter |
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| 61 | >>> p = ToolParameter.build( None, XML( ''' |
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| 62 | ... <param name="blah" type="text" size="10" value="10"> |
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| 63 | ... <validator type="expression" message="Not gonna happen">value.lower() == "foo"</validator> |
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| 64 | ... </param> |
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| 65 | ... ''' ) ) |
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| 66 | >>> t = p.validate( "Foo" ) |
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| 67 | >>> t = p.validate( "foo" ) |
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| 68 | >>> t = p.validate( "Fop" ) |
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| 69 | Traceback (most recent call last): |
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| 70 | ... |
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| 71 | ValueError: Not gonna happen |
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| 72 | """ |
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| 73 | @classmethod |
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| 74 | def from_element( cls, param, elem ): |
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| 75 | return cls( elem.get( 'message' ), elem.text, elem.get( 'substitute_value_in_message' ) ) |
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| 76 | def __init__( self, message, expression, substitute_value_in_message ): |
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| 77 | self.message = message |
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| 78 | self.substitute_value_in_message = substitute_value_in_message |
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| 79 | # Save compiled expression, code objects are thread safe (right?) |
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| 80 | self.expression = compile( expression, '<string>', 'eval' ) |
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| 81 | def validate( self, value, history=None ): |
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| 82 | if not( eval( self.expression, dict( value=value ) ) ): |
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| 83 | message = self.message |
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| 84 | if self.substitute_value_in_message: |
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| 85 | message = message % value |
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| 86 | raise ValueError( message ) |
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| 87 | |
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| 88 | class InRangeValidator( Validator ): |
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| 89 | """ |
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| 90 | Validator that ensures a number is in a specific range |
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| 91 | |
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| 92 | >>> from galaxy.tools.parameters import ToolParameter |
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| 93 | >>> p = ToolParameter.build( None, XML( ''' |
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| 94 | ... <param name="blah" type="integer" size="10" value="10"> |
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| 95 | ... <validator type="in_range" message="Not gonna happen" min="10" max="20"/> |
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| 96 | ... </param> |
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| 97 | ... ''' ) ) |
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| 98 | >>> t = p.validate( 10 ) |
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| 99 | >>> t = p.validate( 15 ) |
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| 100 | >>> t = p.validate( 20 ) |
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| 101 | >>> t = p.validate( 21 ) |
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| 102 | Traceback (most recent call last): |
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| 103 | ... |
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| 104 | ValueError: Not gonna happen |
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| 105 | """ |
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| 106 | @classmethod |
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| 107 | def from_element( cls, param, elem ): |
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| 108 | return cls( elem.get( 'message', None ), elem.get( 'min', '-inf' ), elem.get( 'max', '+inf' ) ) |
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| 109 | def __init__( self, message, range_min, range_max ): |
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| 110 | self.min = float( range_min ) |
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| 111 | self.max = float( range_max ) |
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| 112 | self.message = message or ( "Value must be between %f and %f" % ( self.min, self.max ) ) |
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| 113 | def validate( self, value, history=None ): |
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| 114 | if not( self.min <= float( value ) <= self.max ): |
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| 115 | raise ValueError( self.message ) |
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| 116 | |
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| 117 | class LengthValidator( Validator ): |
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| 118 | """ |
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| 119 | Validator that ensures the length of the provided string (value) is in a specific range |
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| 120 | |
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| 121 | >>> from galaxy.tools.parameters import ToolParameter |
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| 122 | >>> p = ToolParameter.build( None, XML( ''' |
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| 123 | ... <param name="blah" type="text" size="10" value="foobar"> |
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| 124 | ... <validator type="length" min="2" max="8"/> |
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| 125 | ... </param> |
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| 126 | ... ''' ) ) |
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| 127 | >>> t = p.validate( "foo" ) |
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| 128 | >>> t = p.validate( "bar" ) |
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| 129 | >>> t = p.validate( "f" ) |
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| 130 | Traceback (most recent call last): |
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| 131 | ... |
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| 132 | ValueError: Must have length of at least 2 |
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| 133 | >>> t = p.validate( "foobarbaz" ) |
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| 134 | Traceback (most recent call last): |
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| 135 | ... |
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| 136 | ValueError: Must have length no more than 8 |
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| 137 | """ |
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| 138 | @classmethod |
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| 139 | def from_element( cls, param, elem ): |
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| 140 | return cls( elem.get( 'message', None ), elem.get( 'min', None ), elem.get( 'max', None ) ) |
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| 141 | def __init__( self, message, length_min, length_max ): |
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| 142 | self.message = message |
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| 143 | if length_min is not None: |
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| 144 | length_min = int( length_min ) |
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| 145 | if length_max is not None: |
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| 146 | length_max = int( length_max ) |
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| 147 | self.min = length_min |
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| 148 | self.max = length_max |
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| 149 | def validate( self, value, history=None ): |
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| 150 | if self.min is not None and len( value ) < self.min: |
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| 151 | raise ValueError( self.message or ( "Must have length of at least %d" % self.min ) ) |
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| 152 | if self.max is not None and len( value ) > self.max: |
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| 153 | raise ValueError( self.message or ( "Must have length no more than %d" % self.max ) ) |
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| 154 | |
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| 155 | class DatasetOkValidator( Validator ): |
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| 156 | """ |
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| 157 | Validator that checks if a dataset is in an 'ok' state |
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| 158 | """ |
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| 159 | def __init__( self, message=None ): |
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| 160 | self.message = message |
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| 161 | @classmethod |
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| 162 | def from_element( cls, param, elem ): |
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| 163 | return cls( elem.get( 'message', None ) ) |
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| 164 | def validate( self, value, history=None ): |
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| 165 | if value and value.state != model.Dataset.states.OK: |
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| 166 | if self.message is None: |
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| 167 | self.message = "The selected dataset is still being generated, select another dataset or wait until it is completed" |
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| 168 | raise ValueError( self.message ) |
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| 169 | |
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| 170 | class MetadataValidator( Validator ): |
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| 171 | """ |
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| 172 | Validator that checks for missing metadata |
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| 173 | """ |
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| 174 | def __init__( self, message = None, check = "", skip = "" ): |
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| 175 | self.message = message |
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| 176 | self.check = check.split( "," ) |
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| 177 | self.skip = skip.split( "," ) |
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| 178 | @classmethod |
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| 179 | def from_element( cls, param, elem ): |
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| 180 | return cls( message=elem.get( 'message', None ), check=elem.get( 'check', "" ), skip=elem.get( 'skip', "" ) ) |
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| 181 | def validate( self, value, history=None ): |
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| 182 | if value and value.missing_meta( check = self.check, skip = self.skip ): |
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| 183 | if self.message is None: |
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| 184 | self.message = "Metadata missing, click the pencil icon in the history item to edit / save the metadata attributes" |
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| 185 | raise ValueError( self.message ) |
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| 186 | |
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| 187 | class UnspecifiedBuildValidator( Validator ): |
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| 188 | """ |
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| 189 | Validator that checks for missing metadata |
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| 190 | """ |
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| 191 | def __init__( self, message=None ): |
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| 192 | if message is None: |
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| 193 | self.message = "Unspecified genome build, click the pencil icon in the history item to set the genome build" |
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| 194 | else: |
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| 195 | self.message = message |
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| 196 | @classmethod |
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| 197 | def from_element( cls, param, elem ): |
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| 198 | return cls( elem.get( 'message', None ) ) |
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| 199 | def validate( self, value, history=None ): |
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| 200 | #if value is None, we cannot validate |
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| 201 | if value: |
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| 202 | dbkey = value.metadata.dbkey |
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| 203 | if isinstance( dbkey, list ): |
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| 204 | dbkey = dbkey[0] |
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| 205 | if dbkey == '?': |
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| 206 | raise ValueError( self.message ) |
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| 207 | |
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| 208 | class NoOptionsValidator( Validator ): |
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| 209 | """Validator that checks for empty select list""" |
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| 210 | def __init__( self, message=None ): |
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| 211 | self.message = message |
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| 212 | @classmethod |
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| 213 | def from_element( cls, param, elem ): |
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| 214 | return cls( elem.get( 'message', None ) ) |
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| 215 | def validate( self, value, history=None ): |
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| 216 | if value is None: |
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| 217 | if self.message is None: |
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| 218 | self.message = "No options available for selection" |
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| 219 | raise ValueError( self.message ) |
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| 220 | |
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| 221 | class EmptyTextfieldValidator( Validator ): |
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| 222 | """Validator that checks for empty text field""" |
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| 223 | def __init__( self, message=None ): |
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| 224 | self.message = message |
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| 225 | @classmethod |
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| 226 | def from_element( cls, param, elem ): |
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| 227 | return cls( elem.get( 'message', None ) ) |
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| 228 | def validate( self, value, history=None ): |
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| 229 | if value == '': |
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| 230 | if self.message is None: |
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| 231 | self.message = "Field requires a value" |
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| 232 | raise ValueError( self.message ) |
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| 233 | |
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| 234 | class MetadataInFileColumnValidator( Validator ): |
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| 235 | """ |
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| 236 | Validator that checks if the value for a dataset's metadata item exists in a file. |
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| 237 | """ |
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| 238 | @classmethod |
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| 239 | def from_element( cls, param, elem ): |
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| 240 | filename = elem.get( "filename", None ) |
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| 241 | if filename: |
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| 242 | filename = "%s/%s" % ( param.tool.app.config.tool_data_path, filename.strip() ) |
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| 243 | metadata_name = elem.get( "metadata_name", None ) |
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| 244 | if metadata_name: |
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| 245 | metadata_name = metadata_name.strip() |
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| 246 | metadata_column = int( elem.get( "metadata_column", 0 ) ) |
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| 247 | message = elem.get( "message", "Value for metadata %s was not found in %s." % ( metadata_name, filename ) ) |
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| 248 | line_startswith = elem.get( "line_startswith", None ) |
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| 249 | if line_startswith: |
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| 250 | line_startswith = line_startswith.strip() |
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| 251 | return cls( filename, metadata_name, metadata_column, message, line_startswith ) |
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| 252 | def __init__( self, filename, metadata_name, metadata_column, message="Value for metadata not found.", line_startswith=None ): |
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| 253 | self.metadata_name = metadata_name |
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| 254 | self.message = message |
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| 255 | self.valid_values = [] |
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| 256 | for line in open( filename ): |
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| 257 | if line_startswith is None or line.startswith( line_startswith ): |
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| 258 | fields = line.split( '\t' ) |
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| 259 | if metadata_column < len( fields ): |
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| 260 | self.valid_values.append( fields[metadata_column].strip() ) |
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| 261 | def validate( self, value, history = None ): |
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| 262 | if not value: return |
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| 263 | if hasattr( value, "metadata" ): |
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| 264 | if value.metadata.spec[self.metadata_name].param.to_string( value.metadata.get( self.metadata_name ) ) in self.valid_values: |
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| 265 | return |
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| 266 | raise ValueError( self.message ) |
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| 267 | |
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| 268 | validator_types = dict( expression=ExpressionValidator, |
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| 269 | regex=RegexValidator, |
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| 270 | in_range=InRangeValidator, |
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| 271 | length=LengthValidator, |
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| 272 | metadata=MetadataValidator, |
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| 273 | unspecified_build=UnspecifiedBuildValidator, |
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| 274 | no_options=NoOptionsValidator, |
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| 275 | empty_field=EmptyTextfieldValidator, |
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| 276 | dataset_metadata_in_file=MetadataInFileColumnValidator, |
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| 277 | dataset_ok_validator=DatasetOkValidator ) |
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| 278 | |
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| 279 | def get_suite(): |
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| 280 | """Get unittest suite for this module""" |
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| 281 | import doctest, sys |
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| 282 | return doctest.DocTestSuite( sys.modules[__name__] ) |
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| 283 | |
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