[2] | 1 | """ |
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| 2 | Basic tool parameters. |
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| 3 | """ |
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| 4 | |
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| 5 | import logging, string, sys, os, os.path |
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| 6 | from elementtree.ElementTree import XML, Element |
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| 7 | from galaxy import config, datatypes, util |
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| 8 | from galaxy.web import form_builder |
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| 9 | from galaxy.util.bunch import Bunch |
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| 10 | from galaxy.util import string_as_bool, sanitize_param |
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| 11 | from sanitize import ToolParameterSanitizer |
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| 12 | import validation, dynamic_options |
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| 13 | # For BaseURLToolParameter |
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| 14 | from galaxy.web import url_for |
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| 15 | import galaxy.model |
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| 16 | |
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| 17 | log = logging.getLogger(__name__) |
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| 18 | |
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| 19 | class ToolParameter( object ): |
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| 20 | """ |
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| 21 | Describes a parameter accepted by a tool. This is just a simple stub at the |
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| 22 | moment but in the future should encapsulate more complex parameters (lists |
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| 23 | of valid choices, validation logic, ...) |
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| 24 | """ |
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| 25 | def __init__( self, tool, param, context=None ): |
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| 26 | self.tool = tool |
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| 27 | self.refresh_on_change = False |
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| 28 | self.refresh_on_change_values = [] |
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| 29 | self.name = param.get("name") |
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| 30 | self.type = param.get("type") |
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| 31 | self.label = util.xml_text(param, "label") |
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| 32 | self.help = util.xml_text(param, "help") |
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| 33 | self.sanitizer = param.find( "sanitizer" ) |
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| 34 | if self.sanitizer is not None: |
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| 35 | self.sanitizer = ToolParameterSanitizer.from_element( self.sanitizer ) |
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| 36 | self.html = "no html set" |
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| 37 | self.repeat = param.get("repeat", None) |
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| 38 | self.condition = param.get( "condition", None ) |
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| 39 | self.validators = [] |
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| 40 | for elem in param.findall("validator"): |
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| 41 | self.validators.append( validation.Validator.from_element( self, elem ) ) |
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| 42 | |
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| 43 | def get_label( self ): |
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| 44 | """Return user friendly name for the parameter""" |
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| 45 | if self.label: return self.label |
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| 46 | else: return self.name |
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| 47 | |
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| 48 | def get_html_field( self, trans=None, value=None, other_values={} ): |
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| 49 | raise TypeError( "Abstract Method" ) |
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| 50 | |
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| 51 | def get_html( self, trans=None, value=None, other_values={}): |
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| 52 | """ |
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| 53 | Returns the html widget corresponding to the parameter. |
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| 54 | Optionally attempt to retain the current value specific by 'value' |
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| 55 | """ |
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| 56 | return self.get_html_field( trans, value, other_values ).get_html() |
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| 57 | |
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| 58 | def from_html( self, value, trans=None, other_values={} ): |
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| 59 | """ |
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| 60 | Convert a value from an HTML POST into the parameters preferred value |
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| 61 | format. |
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| 62 | """ |
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| 63 | return value |
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| 64 | |
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| 65 | def get_initial_value( self, trans, context ): |
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| 66 | """ |
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| 67 | Return the starting value of the parameter |
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| 68 | """ |
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| 69 | return None |
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| 70 | |
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| 71 | def get_required_enctype( self ): |
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| 72 | """ |
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| 73 | If this parameter needs the form to have a specific encoding |
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| 74 | return it, otherwise return None (indicating compatibility with |
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| 75 | any encoding) |
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| 76 | """ |
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| 77 | return None |
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| 78 | |
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| 79 | def get_dependencies( self ): |
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| 80 | """ |
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| 81 | Return the names of any other parameters this parameter depends on |
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| 82 | """ |
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| 83 | return [] |
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| 84 | |
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| 85 | def filter_value( self, value, trans=None, other_values={} ): |
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| 86 | """ |
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| 87 | Parse the value returned by the view into a form usable by the tool OR |
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| 88 | raise a ValueError. |
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| 89 | """ |
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| 90 | return value |
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| 91 | |
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| 92 | def to_string( self, value, app ): |
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| 93 | """Convert a value to a string representation suitable for persisting""" |
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| 94 | return str( value ) |
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| 95 | |
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| 96 | def to_python( self, value, app ): |
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| 97 | """Convert a value created with to_string back to an object representation""" |
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| 98 | return value |
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| 99 | |
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| 100 | def value_to_basic( self, value, app ): |
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| 101 | if isinstance( value, RuntimeValue ): |
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| 102 | return { "__class__": "RuntimeValue" } |
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| 103 | return self.to_string( value, app ) |
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| 104 | |
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| 105 | def value_from_basic( self, value, app, ignore_errors=False ): |
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| 106 | # HACK: Some things don't deal with unicode well, psycopg problem? |
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| 107 | if type( value ) == unicode: |
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| 108 | value = str( value ) |
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| 109 | # Handle Runtime values (valid for any parameter?) |
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| 110 | if isinstance( value, dict ) and '__class__' in value and value['__class__'] == "RuntimeValue": |
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| 111 | return RuntimeValue() |
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| 112 | # Delegate to the 'to_python' method |
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| 113 | if ignore_errors: |
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| 114 | try: |
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| 115 | return self.to_python( value, app ) |
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| 116 | except: |
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| 117 | return value |
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| 118 | else: |
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| 119 | return self.to_python( value, app ) |
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| 120 | |
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| 121 | def value_to_display_text( self, value, app ): |
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| 122 | """ |
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| 123 | Convert a value to a text representation suitable for displaying to |
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| 124 | the user |
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| 125 | """ |
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| 126 | return value |
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| 127 | |
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| 128 | def to_param_dict_string( self, value, other_values={} ): |
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| 129 | value = str( value ) |
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| 130 | if self.tool is None or self.tool.options.sanitize: |
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| 131 | if self.sanitizer: |
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| 132 | value = self.sanitizer.sanitize_param( value ) |
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| 133 | else: |
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| 134 | value = sanitize_param( value ) |
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| 135 | return value |
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| 136 | |
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| 137 | def validate( self, value, history=None ): |
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| 138 | for validator in self.validators: |
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| 139 | validator.validate( value, history ) |
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| 140 | |
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| 141 | @classmethod |
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| 142 | def build( cls, tool, param ): |
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| 143 | """Factory method to create parameter of correct type""" |
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| 144 | param_type = param.get("type") |
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| 145 | if not param_type or param_type not in parameter_types: |
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| 146 | raise ValueError( "Unknown tool parameter type '%s'" % param_type ) |
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| 147 | else: |
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| 148 | return parameter_types[param_type]( tool, param ) |
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| 149 | |
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| 150 | class TextToolParameter( ToolParameter ): |
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| 151 | """ |
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| 152 | Parameter that can take on any text value. |
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| 153 | |
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| 154 | >>> p = TextToolParameter( None, XML( '<param name="blah" type="text" size="4" value="default" />' ) ) |
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| 155 | >>> print p.name |
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| 156 | blah |
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| 157 | >>> print p.get_html() |
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| 158 | <input type="text" name="blah" size="4" value="default"> |
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| 159 | >>> print p.get_html( value="meh" ) |
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| 160 | <input type="text" name="blah" size="4" value="meh"> |
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| 161 | """ |
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| 162 | def __init__( self, tool, elem ): |
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| 163 | ToolParameter.__init__( self, tool, elem ) |
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| 164 | self.size = elem.get( 'size' ) |
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| 165 | self.value = elem.get( 'value' ) |
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| 166 | self.area = string_as_bool( elem.get( 'area', False ) ) |
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| 167 | def get_html_field( self, trans=None, value=None, other_values={} ): |
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| 168 | if self.area: |
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| 169 | return form_builder.TextArea( self.name, self.size, value or self.value ) |
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| 170 | else: |
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| 171 | return form_builder.TextField( self.name, self.size, value or self.value ) |
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| 172 | def get_initial_value( self, trans, context ): |
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| 173 | return self.value |
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| 174 | |
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| 175 | class IntegerToolParameter( TextToolParameter ): |
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| 176 | """ |
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| 177 | Parameter that takes an integer value. |
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| 178 | |
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| 179 | >>> p = IntegerToolParameter( None, XML( '<param name="blah" type="integer" size="4" value="10" />' ) ) |
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| 180 | >>> print p.name |
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| 181 | blah |
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| 182 | >>> print p.get_html() |
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| 183 | <input type="text" name="blah" size="4" value="10"> |
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| 184 | >>> type( p.from_html( "10" ) ) |
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| 185 | <type 'int'> |
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| 186 | >>> type( p.from_html( "bleh" ) ) |
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| 187 | Traceback (most recent call last): |
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| 188 | ... |
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| 189 | ValueError: An integer is required |
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| 190 | """ |
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| 191 | def __init__( self, tool, elem ): |
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| 192 | TextToolParameter.__init__( self, tool, elem ) |
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| 193 | if self.value: |
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| 194 | try: |
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| 195 | int( self.value ) |
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| 196 | except: |
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| 197 | raise ValueError( "An integer is required" ) |
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| 198 | elif self.value is None: |
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| 199 | raise ValueError( "The settings for this field require a 'value' setting and optionally a default value which must be an integer" ) |
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| 200 | def get_html_field( self, trans=None, value=None, other_values={} ): |
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| 201 | if isinstance( value, int ): |
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| 202 | value = str( value ) |
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| 203 | return super( IntegerToolParameter, self ).get_html_field( trans=trans, value=value, other_values=other_values ) |
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| 204 | def from_html( self, value, trans=None, other_values={} ): |
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| 205 | try: |
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| 206 | return int( value ) |
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| 207 | except: |
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| 208 | raise ValueError( "An integer is required" ) |
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| 209 | def to_python( self, value, app ): |
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| 210 | return int( value ) |
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| 211 | def get_initial_value( self, trans, context ): |
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| 212 | if self.value: |
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| 213 | return int( self.value ) |
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| 214 | else: |
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| 215 | return None |
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| 216 | |
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| 217 | class FloatToolParameter( TextToolParameter ): |
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| 218 | """ |
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| 219 | Parameter that takes a real number value. |
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| 220 | |
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| 221 | >>> p = FloatToolParameter( None, XML( '<param name="blah" type="float" size="4" value="3.141592" />' ) ) |
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| 222 | >>> print p.name |
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| 223 | blah |
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| 224 | >>> print p.get_html() |
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| 225 | <input type="text" name="blah" size="4" value="3.141592"> |
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| 226 | >>> type( p.from_html( "36.1" ) ) |
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| 227 | <type 'float'> |
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| 228 | >>> type( p.from_html( "bleh" ) ) |
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| 229 | Traceback (most recent call last): |
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| 230 | ... |
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| 231 | ValueError: A real number is required |
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| 232 | """ |
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| 233 | def __init__( self, tool, elem ): |
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| 234 | TextToolParameter.__init__( self, tool, elem ) |
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| 235 | if self.value: |
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| 236 | try: |
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| 237 | float( self.value ) |
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| 238 | except: |
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| 239 | raise ValueError( "A real number is required" ) |
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| 240 | elif self.value is None: |
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| 241 | raise ValueError( "The settings for this field require a 'value' setting and optionally a default value which must be a real number" ) |
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| 242 | def get_html_field( self, trans=None, value=None, other_values={} ): |
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| 243 | if isinstance( value, float ): |
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| 244 | value = str( value ) |
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| 245 | return super( FloatToolParameter, self ).get_html_field( trans=trans, value=value, other_values=other_values ) |
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| 246 | def from_html( self, value, trans=None, other_values={} ): |
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| 247 | try: |
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| 248 | return float( value ) |
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| 249 | except: |
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| 250 | raise ValueError( "A real number is required" ) |
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| 251 | def to_python( self, value, app ): |
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| 252 | return float( value ) |
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| 253 | def get_initial_value( self, trans, context ): |
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| 254 | try: |
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| 255 | return float( self.value ) |
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| 256 | except: |
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| 257 | return None |
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| 258 | |
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| 259 | class BooleanToolParameter( ToolParameter ): |
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| 260 | """ |
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| 261 | Parameter that takes one of two values. |
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| 262 | |
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| 263 | >>> p = BooleanToolParameter( None, XML( '<param name="blah" type="boolean" checked="yes" truevalue="bulletproof vests" falsevalue="cellophane chests" />' ) ) |
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| 264 | >>> print p.name |
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| 265 | blah |
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| 266 | >>> print p.get_html() |
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| 267 | <input type="checkbox" name="blah" value="true" checked><input type="hidden" name="blah" value="true"> |
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| 268 | >>> print p.from_html( ["true","true"] ) |
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| 269 | True |
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| 270 | >>> print p.to_param_dict_string( True ) |
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| 271 | bulletproof vests |
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| 272 | >>> print p.from_html( ["true"] ) |
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| 273 | False |
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| 274 | >>> print p.to_param_dict_string( False ) |
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| 275 | cellophane chests |
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| 276 | """ |
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| 277 | def __init__( self, tool, elem ): |
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| 278 | ToolParameter.__init__( self, tool, elem ) |
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| 279 | self.truevalue = elem.get( 'truevalue', 'true' ) |
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| 280 | self.falsevalue = elem.get( 'falsevalue', 'false' ) |
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| 281 | self.checked = string_as_bool( elem.get( 'checked' ) ) |
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| 282 | def get_html_field( self, trans=None, value=None, other_values={} ): |
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| 283 | checked = self.checked |
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| 284 | if value: |
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| 285 | checked = form_builder.CheckboxField.is_checked( value ) |
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| 286 | return form_builder.CheckboxField( self.name, checked ) |
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| 287 | def from_html( self, value, trans=None, other_values={} ): |
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| 288 | return form_builder.CheckboxField.is_checked( value ) |
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| 289 | def to_python( self, value, app ): |
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| 290 | return ( value == 'True' ) |
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| 291 | def get_initial_value( self, trans, context ): |
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| 292 | return self.checked |
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| 293 | def to_param_dict_string( self, value, other_values={} ): |
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| 294 | if value: |
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| 295 | return self.truevalue |
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| 296 | else: |
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| 297 | return self.falsevalue |
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| 298 | |
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| 299 | class FileToolParameter( ToolParameter ): |
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| 300 | """ |
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| 301 | Parameter that takes an uploaded file as a value. |
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| 302 | |
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| 303 | >>> p = FileToolParameter( None, XML( '<param name="blah" type="file"/>' ) ) |
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| 304 | >>> print p.name |
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| 305 | blah |
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| 306 | >>> print p.get_html() |
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| 307 | <input type="file" name="blah"> |
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| 308 | >>> p = FileToolParameter( None, XML( '<param name="blah" type="file" ajax-upload="true"/>' ) ) |
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| 309 | >>> print p.get_html() |
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| 310 | <input type="file" name="blah" galaxy-ajax-upload="true"> |
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| 311 | """ |
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| 312 | def __init__( self, tool, elem ): |
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| 313 | """ |
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| 314 | Example: C{<param name="bins" type="file" />} |
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| 315 | """ |
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| 316 | ToolParameter.__init__( self, tool, elem ) |
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| 317 | self.ajax = string_as_bool( elem.get( 'ajax-upload' ) ) |
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| 318 | def get_html_field( self, trans=None, value=None, other_values={} ): |
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| 319 | return form_builder.FileField( self.name, ajax = self.ajax, value = value ) |
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| 320 | def from_html( self, value, trans=None, other_values={} ): |
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| 321 | # Middleware or proxies may encode files in special ways (TODO: this |
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| 322 | # should be pluggable) |
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| 323 | if type( value ) == dict: |
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| 324 | upload_store = self.tool.app.config.nginx_upload_store |
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| 325 | assert upload_store, \ |
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| 326 | "Request appears to have been processed by nginx_upload_module \ |
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| 327 | but Galaxy is not configured to recognize it" |
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| 328 | # Check that the file is in the right location |
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| 329 | local_filename = os.path.abspath( value['path'] ) |
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| 330 | assert local_filename.startswith( upload_store ), \ |
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| 331 | "Filename provided by nginx is not in correct directory" |
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| 332 | value = dict( |
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| 333 | filename = value["name"], |
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| 334 | local_filename = local_filename |
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| 335 | ) |
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| 336 | return value |
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| 337 | def get_required_enctype( self ): |
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| 338 | """ |
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| 339 | File upload elements require the multipart/form-data encoding |
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| 340 | """ |
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| 341 | return "multipart/form-data" |
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| 342 | def to_string( self, value, app ): |
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| 343 | if value in [ None, '' ]: |
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| 344 | return None |
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| 345 | elif isinstance( value, unicode ) or isinstance( value, str ): |
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| 346 | return value |
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| 347 | elif isinstance( value, dict ): |
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| 348 | # or should we jsonify? |
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| 349 | try: |
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| 350 | return value['local_filename'] |
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| 351 | except: |
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| 352 | return None |
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| 353 | raise Exception( "FileToolParameter cannot be persisted" ) |
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| 354 | def to_python( self, value, app ): |
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| 355 | if value is None: |
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| 356 | return None |
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| 357 | elif isinstance( value, unicode ) or isinstance( value, str ): |
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| 358 | return value |
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| 359 | else: |
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| 360 | raise Exception( "FileToolParameter cannot be persisted" ) |
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| 361 | def get_initial_value( self, trans, context ): |
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| 362 | return None |
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| 363 | |
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| 364 | class HiddenToolParameter( ToolParameter ): |
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| 365 | """ |
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| 366 | Parameter that takes one of two values. |
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| 367 | |
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| 368 | FIXME: This seems hacky, parameters should only describe things the user |
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| 369 | might change. It is used for 'initializing' the UCSC proxy tool |
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| 370 | |
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| 371 | >>> p = HiddenToolParameter( None, XML( '<param name="blah" type="hidden" value="wax so rockin"/>' ) ) |
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| 372 | >>> print p.name |
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| 373 | blah |
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| 374 | >>> print p.get_html() |
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| 375 | <input type="hidden" name="blah" value="wax so rockin"> |
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| 376 | """ |
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| 377 | def __init__( self, tool, elem ): |
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| 378 | ToolParameter.__init__( self, tool, elem ) |
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| 379 | self.value = elem.get( 'value' ) |
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| 380 | def get_html_field( self, trans=None, value=None, other_values={} ): |
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| 381 | return form_builder.HiddenField( self.name, self.value ) |
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| 382 | def get_initial_value( self, trans, context ): |
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| 383 | return self.value |
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| 384 | def get_label( self ): |
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| 385 | return None |
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| 386 | |
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| 387 | ## This is clearly a HACK, parameters should only be used for things the user |
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| 388 | ## can change, there needs to be a different way to specify this. I'm leaving |
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| 389 | ## it for now to avoid breaking any tools. |
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| 390 | |
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| 391 | class BaseURLToolParameter( ToolParameter ): |
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| 392 | """ |
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| 393 | Returns a parameter the contains its value prepended by the |
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| 394 | current server base url. Used in all redirects. |
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| 395 | """ |
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| 396 | def __init__( self, tool, elem ): |
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| 397 | ToolParameter.__init__( self, tool, elem ) |
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| 398 | self.value = elem.get( 'value', '' ) |
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| 399 | def get_value( self, trans ): |
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| 400 | # url = trans.request.base + self.value |
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| 401 | url = url_for( self.value, qualified=True ) |
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| 402 | return url |
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| 403 | def get_html_field( self, trans=None, value=None, other_values={} ): |
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| 404 | return form_builder.HiddenField( self.name, self.get_value( trans ) ) |
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| 405 | def get_initial_value( self, trans, context ): |
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| 406 | return self.value |
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| 407 | def get_label( self ): |
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| 408 | # BaseURLToolParameters are ultimately "hidden" parameters |
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| 409 | return None |
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| 410 | |
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| 411 | class SelectToolParameter( ToolParameter ): |
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| 412 | """ |
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| 413 | Parameter that takes on one (or many) or a specific set of values. |
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| 414 | |
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| 415 | >>> p = SelectToolParameter( None, XML( |
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| 416 | ... ''' |
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| 417 | ... <param name="blah" type="select"> |
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| 418 | ... <option value="x">I am X</option> |
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| 419 | ... <option value="y" selected="true">I am Y</option> |
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| 420 | ... <option value="z">I am Z</option> |
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| 421 | ... </param> |
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| 422 | ... ''' ) ) |
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| 423 | >>> print p.name |
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| 424 | blah |
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| 425 | >>> print p.get_html() |
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| 426 | <select name="blah" last_selected_value="y"> |
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| 427 | <option value="x">I am X</option> |
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| 428 | <option value="y" selected>I am Y</option> |
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| 429 | <option value="z">I am Z</option> |
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| 430 | </select> |
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| 431 | >>> print p.get_html( value="z" ) |
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| 432 | <select name="blah" last_selected_value="z"> |
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| 433 | <option value="x">I am X</option> |
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| 434 | <option value="y">I am Y</option> |
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| 435 | <option value="z" selected>I am Z</option> |
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| 436 | </select> |
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| 437 | >>> print p.filter_value( "y" ) |
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| 438 | y |
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| 439 | |
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| 440 | >>> p = SelectToolParameter( None, XML( |
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| 441 | ... ''' |
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| 442 | ... <param name="blah" type="select" multiple="true"> |
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| 443 | ... <option value="x">I am X</option> |
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| 444 | ... <option value="y" selected="true">I am Y</option> |
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| 445 | ... <option value="z" selected="true">I am Z</option> |
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| 446 | ... </param> |
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| 447 | ... ''' ) ) |
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| 448 | >>> print p.name |
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| 449 | blah |
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| 450 | >>> print p.get_html() |
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| 451 | <select name="blah" multiple last_selected_value="z"> |
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| 452 | <option value="x">I am X</option> |
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| 453 | <option value="y" selected>I am Y</option> |
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| 454 | <option value="z" selected>I am Z</option> |
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| 455 | </select> |
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| 456 | >>> print p.get_html( value=["x","y"]) |
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| 457 | <select name="blah" multiple last_selected_value="y"> |
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| 458 | <option value="x" selected>I am X</option> |
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| 459 | <option value="y" selected>I am Y</option> |
---|
| 460 | <option value="z">I am Z</option> |
---|
| 461 | </select> |
---|
| 462 | >>> print p.to_param_dict_string( ["y", "z"] ) |
---|
| 463 | y,z |
---|
| 464 | |
---|
| 465 | >>> p = SelectToolParameter( None, XML( |
---|
| 466 | ... ''' |
---|
| 467 | ... <param name="blah" type="select" multiple="true" display="checkboxes"> |
---|
| 468 | ... <option value="x">I am X</option> |
---|
| 469 | ... <option value="y" selected="true">I am Y</option> |
---|
| 470 | ... <option value="z" selected="true">I am Z</option> |
---|
| 471 | ... </param> |
---|
| 472 | ... ''' ) ) |
---|
| 473 | >>> print p.name |
---|
| 474 | blah |
---|
| 475 | >>> print p.get_html() |
---|
| 476 | <div class="checkUncheckAllPlaceholder" checkbox_name="blah"></div> |
---|
| 477 | <div><input type="checkbox" name="blah" value="x">I am X</div> |
---|
| 478 | <div class="odd_row"><input type="checkbox" name="blah" value="y" checked>I am Y</div> |
---|
| 479 | <div><input type="checkbox" name="blah" value="z" checked>I am Z</div> |
---|
| 480 | >>> print p.get_html( value=["x","y"]) |
---|
| 481 | <div class="checkUncheckAllPlaceholder" checkbox_name="blah"></div> |
---|
| 482 | <div><input type="checkbox" name="blah" value="x" checked>I am X</div> |
---|
| 483 | <div class="odd_row"><input type="checkbox" name="blah" value="y" checked>I am Y</div> |
---|
| 484 | <div><input type="checkbox" name="blah" value="z">I am Z</div> |
---|
| 485 | >>> print p.to_param_dict_string( ["y", "z"] ) |
---|
| 486 | y,z |
---|
| 487 | """ |
---|
| 488 | def __init__( self, tool, elem, context=None ): |
---|
| 489 | ToolParameter.__init__( self, tool, elem ) |
---|
| 490 | self.multiple = string_as_bool( elem.get( 'multiple', False ) ) |
---|
| 491 | self.display = elem.get( 'display', None ) |
---|
| 492 | self.separator = elem.get( 'separator', ',' ) |
---|
| 493 | self.legal_values = set() |
---|
| 494 | # TODO: the <dynamic_options> tag is deprecated and should be replaced with the <options> tag. |
---|
| 495 | self.dynamic_options = elem.get( "dynamic_options", None ) |
---|
| 496 | options = elem.find( 'options' ) |
---|
| 497 | if options is None: |
---|
| 498 | self.options = None |
---|
| 499 | else: |
---|
| 500 | self.options = dynamic_options.DynamicOptions( options, self ) |
---|
| 501 | for validator in self.options.validators: |
---|
| 502 | self.validators.append( validator ) |
---|
| 503 | if self.dynamic_options is None and self.options is None: |
---|
| 504 | self.static_options = list() |
---|
| 505 | for index, option in enumerate( elem.findall( "option" ) ): |
---|
| 506 | value = option.get( "value" ) |
---|
| 507 | self.legal_values.add( value ) |
---|
| 508 | selected = string_as_bool( option.get( "selected", False ) ) |
---|
| 509 | self.static_options.append( ( option.text, value, selected ) ) |
---|
| 510 | self.is_dynamic = ( ( self.dynamic_options is not None ) or ( self.options is not None ) ) |
---|
| 511 | def get_options( self, trans, other_values ): |
---|
| 512 | if self.options: |
---|
| 513 | return self.options.get_options( trans, other_values ) |
---|
| 514 | elif self.dynamic_options: |
---|
| 515 | return eval( self.dynamic_options, self.tool.code_namespace, other_values ) |
---|
| 516 | else: |
---|
| 517 | return self.static_options |
---|
| 518 | def get_legal_values( self, trans, other_values ): |
---|
| 519 | def _get_UnvalidatedValue_value( value ): |
---|
| 520 | if isinstance( value, UnvalidatedValue ): |
---|
| 521 | return value.value |
---|
| 522 | return value |
---|
| 523 | if self.options: |
---|
| 524 | return map( _get_UnvalidatedValue_value, set( v for _, v, _ in self.options.get_options( trans, other_values ) ) ) |
---|
| 525 | elif self.dynamic_options: |
---|
| 526 | return set( v for _, v, _ in eval( self.dynamic_options, self.tool.code_namespace, other_values ) ) |
---|
| 527 | else: |
---|
| 528 | return self.legal_values |
---|
| 529 | def get_html_field( self, trans=None, value=None, context={} ): |
---|
| 530 | # Dynamic options are not yet supported in workflow, allow |
---|
| 531 | # specifying the value as text for now. |
---|
| 532 | if self.need_late_validation( trans, context ): |
---|
| 533 | assert isinstance( value, UnvalidatedValue ) |
---|
| 534 | value = value.value |
---|
| 535 | if self.multiple: |
---|
| 536 | if value is None: |
---|
| 537 | value = "" |
---|
| 538 | else: |
---|
| 539 | value = "\n".join( value ) |
---|
| 540 | return form_builder.TextArea( self.name, value=value ) |
---|
| 541 | else: |
---|
| 542 | return form_builder.TextField( self.name, value=(value or "") ) |
---|
| 543 | if value is not None: |
---|
| 544 | if not isinstance( value, list ): value = [ value ] |
---|
| 545 | field = form_builder.SelectField( self.name, self.multiple, self.display, self.refresh_on_change, refresh_on_change_values = self.refresh_on_change_values ) |
---|
| 546 | options = self.get_options( trans, context ) |
---|
| 547 | for text, optval, selected in options: |
---|
| 548 | if isinstance( optval, UnvalidatedValue ): |
---|
| 549 | optval = optval.value |
---|
| 550 | text = "%s (unvalidated)" % text |
---|
| 551 | if value: |
---|
| 552 | selected = ( optval in value ) |
---|
| 553 | field.add_option( text, optval, selected ) |
---|
| 554 | return field |
---|
| 555 | def from_html( self, value, trans=None, context={} ): |
---|
| 556 | if self.need_late_validation( trans, context ): |
---|
| 557 | if self.multiple: |
---|
| 558 | # While it is generally allowed that a select value can be '', |
---|
| 559 | # we do not allow this to be the case in a dynamically |
---|
| 560 | # generated multiple select list being set in workflow building |
---|
| 561 | # mode we instead treat '' as 'No option Selected' (None) |
---|
| 562 | if value == '': |
---|
| 563 | value = None |
---|
| 564 | else: |
---|
| 565 | if not isinstance( value, list ): |
---|
| 566 | value = value.split( "\n" ) |
---|
| 567 | return UnvalidatedValue( value ) |
---|
| 568 | legal_values = self.get_legal_values( trans, context ) |
---|
| 569 | if isinstance( value, list ): |
---|
| 570 | if not(self.repeat): |
---|
| 571 | assert self.multiple, "Multiple values provided but parameter is not expecting multiple values" |
---|
| 572 | rval = [] |
---|
| 573 | for v in value: |
---|
| 574 | v = util.restore_text( v ) |
---|
| 575 | if v not in legal_values: |
---|
| 576 | raise ValueError( "An invalid option was selected, please verify" ) |
---|
| 577 | rval.append( v ) |
---|
| 578 | return rval |
---|
| 579 | else: |
---|
| 580 | value = util.restore_text( value ) |
---|
| 581 | if value not in legal_values: |
---|
| 582 | raise ValueError( "An invalid option was selected, please verify" ) |
---|
| 583 | return value |
---|
| 584 | def to_param_dict_string( self, value, other_values={} ): |
---|
| 585 | if value is None: |
---|
| 586 | return "None" |
---|
| 587 | if isinstance( value, list ): |
---|
| 588 | if not( self.repeat ): |
---|
| 589 | assert self.multiple, "Multiple values provided but parameter is not expecting multiple values" |
---|
| 590 | value = map( str, value ) |
---|
| 591 | else: |
---|
| 592 | value = str( value ) |
---|
| 593 | if self.tool is None or self.tool.options.sanitize: |
---|
| 594 | if self.sanitizer: |
---|
| 595 | value = self.sanitizer.sanitize_param( value ) |
---|
| 596 | else: |
---|
| 597 | value = sanitize_param( value ) |
---|
| 598 | if isinstance( value, list ): |
---|
| 599 | value = self.separator.join( value ) |
---|
| 600 | return value |
---|
| 601 | def value_to_basic( self, value, app ): |
---|
| 602 | if isinstance( value, UnvalidatedValue ): |
---|
| 603 | return { "__class__": "UnvalidatedValue", "value": value.value } |
---|
| 604 | elif isinstance( value, RuntimeValue ): |
---|
| 605 | # Need to handle runtime value's ourself since delegating to the |
---|
| 606 | # parent method causes the value to be turned into a string, which |
---|
| 607 | # breaks multiple selection |
---|
| 608 | return { "__class__": "RuntimeValue" } |
---|
| 609 | return value |
---|
| 610 | def value_from_basic( self, value, app, ignore_errors=False ): |
---|
| 611 | if isinstance( value, dict ) and value["__class__"] == "UnvalidatedValue": |
---|
| 612 | return UnvalidatedValue( value["value"] ) |
---|
| 613 | return super( SelectToolParameter, self ).value_from_basic( value, app ) |
---|
| 614 | def need_late_validation( self, trans, context ): |
---|
| 615 | """ |
---|
| 616 | Determine whether we need to wait to validate this parameters value |
---|
| 617 | given the current state. For parameters with static options this is |
---|
| 618 | always false (can always validate immediately). For parameters with |
---|
| 619 | dynamic options, we need to check whether the other parameters which |
---|
| 620 | determine what options are valid have been set. For the old style |
---|
| 621 | dynamic options which do not specify dependencies, this is always true |
---|
| 622 | (must valiate at runtime). |
---|
| 623 | """ |
---|
| 624 | # Option list is statically defined, never need late validation |
---|
| 625 | if not self.is_dynamic: |
---|
| 626 | return False |
---|
| 627 | # Old style dynamic options, no dependency information so there isn't |
---|
| 628 | # a lot we can do: if we're dealing with workflows, have to assume |
---|
| 629 | # late validation no matter what. |
---|
| 630 | if self.dynamic_options is not None: |
---|
| 631 | return ( trans is None or trans.workflow_building_mode ) |
---|
| 632 | # If we got this far, we can actually look at the dependencies |
---|
| 633 | # to see if their values will not be available until runtime. |
---|
| 634 | for dep_name in self.get_dependencies(): |
---|
| 635 | dep_value = context[ dep_name ] |
---|
| 636 | # Dependency on a dataset that does not yet exist |
---|
| 637 | if isinstance( dep_value, DummyDataset ): |
---|
| 638 | return True |
---|
| 639 | # Dependency on a value that has not been checked |
---|
| 640 | if isinstance( dep_value, UnvalidatedValue ): |
---|
| 641 | return True |
---|
| 642 | # Dependency on a value that does not yet exist |
---|
| 643 | if isinstance( dep_value, RuntimeValue ): |
---|
| 644 | return True |
---|
| 645 | # Dynamic, but all dependenceis are known and have values |
---|
| 646 | return False |
---|
| 647 | def get_initial_value( self, trans, context ): |
---|
| 648 | # More working around dynamic options for workflow |
---|
| 649 | if self.need_late_validation( trans, context ): |
---|
| 650 | # Really the best we can do? |
---|
| 651 | return UnvalidatedValue( None ) |
---|
| 652 | options = list( self.get_options( trans, context ) ) |
---|
| 653 | value = [ optval for _, optval, selected in options if selected ] |
---|
| 654 | if len( value ) == 0: |
---|
| 655 | if not self.multiple and options: |
---|
| 656 | # Nothing selected, but not a multiple select, with some values, |
---|
| 657 | # so we have to default to something (the HTML form will anyway) |
---|
| 658 | # TODO: deal with optional parameters in a better way |
---|
| 659 | value = options[0][1] |
---|
| 660 | else: |
---|
| 661 | value = None |
---|
| 662 | elif len( value ) == 1: |
---|
| 663 | value = value[0] |
---|
| 664 | return value |
---|
| 665 | def value_to_display_text( self, value, app ): |
---|
| 666 | if isinstance( value, UnvalidatedValue ): |
---|
| 667 | suffix = "\n(value not yet validated)" |
---|
| 668 | value = value.value |
---|
| 669 | else: |
---|
| 670 | suffix = "" |
---|
| 671 | if not isinstance( value, list ): |
---|
| 672 | value = [ value ] |
---|
| 673 | # FIXME: Currently only translating values back to labels if they |
---|
| 674 | # are not dynamic |
---|
| 675 | if self.is_dynamic: |
---|
| 676 | rval = map( str, value ) |
---|
| 677 | else: |
---|
| 678 | options = list( self.static_options ) |
---|
| 679 | rval = [] |
---|
| 680 | for t, v, s in options: |
---|
| 681 | if v in value: |
---|
| 682 | rval.append( t ) |
---|
| 683 | return "\n".join( rval ) + suffix |
---|
| 684 | def get_dependencies( self ): |
---|
| 685 | """ |
---|
| 686 | Get the *names* of the other params this param depends on. |
---|
| 687 | """ |
---|
| 688 | if self.options: |
---|
| 689 | return self.options.get_dependency_names() |
---|
| 690 | else: |
---|
| 691 | return [] |
---|
| 692 | |
---|
| 693 | class GenomeBuildParameter( SelectToolParameter ): |
---|
| 694 | """ |
---|
| 695 | Select list that sets the last used genome build for the current history |
---|
| 696 | as "selected". |
---|
| 697 | |
---|
| 698 | >>> # Create a mock transcation with 'hg17' as the current build |
---|
| 699 | >>> from galaxy.util.bunch import Bunch |
---|
| 700 | >>> trans = Bunch( history=Bunch( genome_build='hg17' ), db_builds=util.dbnames ) |
---|
| 701 | |
---|
| 702 | >>> p = GenomeBuildParameter( None, XML( |
---|
| 703 | ... ''' |
---|
| 704 | ... <param name="blah" type="genomebuild" /> |
---|
| 705 | ... ''' ) ) |
---|
| 706 | >>> print p.name |
---|
| 707 | blah |
---|
| 708 | |
---|
| 709 | >>> # hg17 should be selected by default |
---|
| 710 | >>> print p.get_html( trans ) # doctest: +ELLIPSIS |
---|
| 711 | <select name="blah" last_selected_value="hg17"> |
---|
| 712 | <option value="?">unspecified (?)</option> |
---|
| 713 | ... |
---|
| 714 | <option value="hg18">Human Mar. 2006 (NCBI36/hg18) (hg18)</option> |
---|
| 715 | <option value="hg17" selected>Human May 2004 (NCBI35/hg17) (hg17)</option> |
---|
| 716 | ... |
---|
| 717 | </select> |
---|
| 718 | |
---|
| 719 | >>> # If the user selected something else already, that should be used |
---|
| 720 | >>> # instead |
---|
| 721 | >>> print p.get_html( trans, value='hg18' ) # doctest: +ELLIPSIS |
---|
| 722 | <select name="blah" last_selected_value="hg18"> |
---|
| 723 | <option value="?">unspecified (?)</option> |
---|
| 724 | ... |
---|
| 725 | <option value="hg18" selected>Human Mar. 2006 (NCBI36/hg18) (hg18)</option> |
---|
| 726 | <option value="hg17">Human May 2004 (NCBI35/hg17) (hg17)</option> |
---|
| 727 | ... |
---|
| 728 | </select> |
---|
| 729 | |
---|
| 730 | >>> print p.filter_value( "hg17" ) |
---|
| 731 | hg17 |
---|
| 732 | """ |
---|
| 733 | def get_options( self, trans, other_values ): |
---|
| 734 | last_used_build = trans.history.genome_build |
---|
| 735 | for dbkey, build_name in trans.db_builds: |
---|
| 736 | yield build_name, dbkey, ( dbkey == last_used_build ) |
---|
| 737 | def get_legal_values( self, trans, other_values ): |
---|
| 738 | return set( dbkey for dbkey, _ in trans.db_builds ) |
---|
| 739 | |
---|
| 740 | class ColumnListParameter( SelectToolParameter ): |
---|
| 741 | """ |
---|
| 742 | Select list that consists of either the total number of columns or only |
---|
| 743 | those columns that contain numerical values in the associated DataToolParameter. |
---|
| 744 | |
---|
| 745 | # TODO: we need better testing here, but not sure how to associate a DatatoolParameter with a ColumnListParameter |
---|
| 746 | # from a twill perspective... |
---|
| 747 | |
---|
| 748 | >>> # Mock up a history (not connected to database) |
---|
| 749 | >>> from galaxy.model import History, HistoryDatasetAssociation |
---|
| 750 | >>> from galaxy.util.bunch import Bunch |
---|
| 751 | >>> from galaxy.model.mapping import context as sa_session |
---|
| 752 | >>> hist = History() |
---|
| 753 | >>> sa_session.add( hist ) |
---|
| 754 | >>> sa_session.flush() |
---|
| 755 | >>> hist.add_dataset( HistoryDatasetAssociation( id=1, extension='interval', create_dataset=True, sa_session=sa_session ) ) |
---|
| 756 | >>> dtp = DataToolParameter( None, XML( '<param name="blah" type="data" format="interval"/>' ) ) |
---|
| 757 | >>> print dtp.name |
---|
| 758 | blah |
---|
| 759 | >>> clp = ColumnListParameter ( None, XML( '<param name="numerical_column" type="data_column" data_ref="blah" numerical="true"/>' ) ) |
---|
| 760 | >>> print clp.name |
---|
| 761 | numerical_column |
---|
| 762 | """ |
---|
| 763 | def __init__( self, tool, elem ): |
---|
| 764 | SelectToolParameter.__init__( self, tool, elem ) |
---|
| 765 | self.tool = tool |
---|
| 766 | self.numerical = string_as_bool( elem.get( "numerical", False )) |
---|
| 767 | self.force_select = string_as_bool( elem.get( "force_select", True )) |
---|
| 768 | self.accept_default = string_as_bool( elem.get( "accept_default", False )) |
---|
| 769 | self.data_ref = elem.get( "data_ref", None ) |
---|
| 770 | self.default_value = elem.get( "default_value", None ) |
---|
| 771 | self.is_dynamic = True |
---|
| 772 | def from_html( self, value, trans=None, context={} ): |
---|
| 773 | """ |
---|
| 774 | Label convention prepends column number with a 'c', but tool uses the integer. This |
---|
| 775 | removes the 'c' when entered into a workflow. |
---|
| 776 | """ |
---|
| 777 | def _strip_c( column ): |
---|
| 778 | column = column.strip().lower() |
---|
| 779 | if column.startswith( 'c' ): |
---|
| 780 | column = column[1:] |
---|
| 781 | return column |
---|
| 782 | if self.multiple: |
---|
| 783 | #split on newline and , |
---|
| 784 | if value: |
---|
| 785 | column_list = [] |
---|
| 786 | if not isinstance( value, list ): |
---|
| 787 | value = value.split( '\n' ) |
---|
| 788 | for column in value: |
---|
| 789 | for column2 in column.split( ',' ): |
---|
| 790 | column2 = column2.strip() |
---|
| 791 | if column2: |
---|
| 792 | column_list.append( column2 ) |
---|
| 793 | value = map( _strip_c, column_list ) |
---|
| 794 | else: |
---|
| 795 | value = [] |
---|
| 796 | else: |
---|
| 797 | if value: |
---|
| 798 | value = _strip_c( value ) |
---|
| 799 | else: |
---|
| 800 | value = None |
---|
| 801 | return super( ColumnListParameter, self ).from_html( value, trans, context ) |
---|
| 802 | def get_column_list( self, trans, other_values ): |
---|
| 803 | """ |
---|
| 804 | Generate a select list containing the columns of the associated |
---|
| 805 | dataset (if found). |
---|
| 806 | """ |
---|
| 807 | column_list = [] |
---|
| 808 | # No value indicates a configuration error, the named DataToolParameter |
---|
| 809 | # must preceed this parameter in the config |
---|
| 810 | assert self.data_ref in other_values, "Value for associated DataToolParameter not found" |
---|
| 811 | # Get the value of the associated DataToolParameter (a dataset) |
---|
| 812 | dataset = other_values[ self.data_ref ] |
---|
| 813 | # Check if a dataset is selected |
---|
| 814 | if dataset is None or dataset == '': |
---|
| 815 | # NOTE: Both of these values indicate that no dataset is selected. |
---|
| 816 | # However, 'None' indicates that the dataset is optional |
---|
| 817 | # while '' indicates that it is not. Currently column |
---|
| 818 | # parameters do not work well with optional datasets |
---|
| 819 | return column_list |
---|
| 820 | # Generate options |
---|
| 821 | if not dataset.metadata.columns: |
---|
| 822 | if self.accept_default: |
---|
| 823 | column_list.append( self.default_value or '1' ) |
---|
| 824 | return column_list |
---|
| 825 | if not self.force_select: |
---|
| 826 | column_list.append( 'None' ) |
---|
| 827 | if self.numerical: |
---|
| 828 | # If numerical was requsted, filter columns based on metadata |
---|
| 829 | for i, col in enumerate( dataset.metadata.column_types ): |
---|
| 830 | if col == 'int' or col == 'float': |
---|
| 831 | column_list.append( str( i + 1 ) ) |
---|
| 832 | else: |
---|
| 833 | for i in range(0, dataset.metadata.columns): |
---|
| 834 | column_list.append( str( i + 1 ) ) |
---|
| 835 | return column_list |
---|
| 836 | def get_options( self, trans, other_values ): |
---|
| 837 | options = [] |
---|
| 838 | column_list = self.get_column_list( trans, other_values ) |
---|
| 839 | if len( column_list ) > 0 and not self.force_select: |
---|
| 840 | options.append( ('?', 'None', False) ) |
---|
| 841 | for col in column_list: |
---|
| 842 | if col != 'None': |
---|
| 843 | options.append( ( 'c' + col, col, False ) ) |
---|
| 844 | return options |
---|
| 845 | def get_initial_value( self, trans, context ): |
---|
| 846 | if self.default_value is not None: |
---|
| 847 | # dataset not ready / in workflow / etc |
---|
| 848 | if self.need_late_validation( trans, context ): |
---|
| 849 | return UnvalidatedValue( self.default_value ) |
---|
| 850 | return self.default_value |
---|
| 851 | return SelectToolParameter.get_initial_value( self, trans, context ) |
---|
| 852 | def get_legal_values( self, trans, other_values ): |
---|
| 853 | return set( self.get_column_list( trans, other_values ) ) |
---|
| 854 | def get_dependencies( self ): |
---|
| 855 | return [ self.data_ref ] |
---|
| 856 | def need_late_validation( self, trans, context ): |
---|
| 857 | if super( ColumnListParameter, self ).need_late_validation( trans, context ): |
---|
| 858 | return True |
---|
| 859 | # Get the selected dataset if selected |
---|
| 860 | dataset = context[ self.data_ref ] |
---|
| 861 | if dataset: |
---|
| 862 | # Check if the dataset does not have the expected metadata for columns |
---|
| 863 | if not dataset.metadata.columns: |
---|
| 864 | # Only allow late validation if the dataset is not yet ready |
---|
| 865 | # (since we have reason to expect the metadata to be ready eventually) |
---|
| 866 | if dataset.is_pending: |
---|
| 867 | return True |
---|
| 868 | # No late validation |
---|
| 869 | return False |
---|
| 870 | |
---|
| 871 | |
---|
| 872 | class DrillDownSelectToolParameter( SelectToolParameter ): |
---|
| 873 | """ |
---|
| 874 | Parameter that takes on one (or many) of a specific set of values. |
---|
| 875 | Creating a hierarchical select menu, which allows users to 'drill down' a tree-like set of options. |
---|
| 876 | |
---|
| 877 | >>> p = DrillDownSelectToolParameter( None, XML( |
---|
| 878 | ... ''' |
---|
| 879 | ... <param name="some_name" type="drill_down" display="checkbox" hierarchy="recurse" multiple="true"> |
---|
| 880 | ... <options> |
---|
| 881 | ... <option name="Heading 1" value="heading1"> |
---|
| 882 | ... <option name="Option 1" value="option1"/> |
---|
| 883 | ... <option name="Option 2" value="option2"/> |
---|
| 884 | ... <option name="Heading 1" value="heading1"> |
---|
| 885 | ... <option name="Option 3" value="option3"/> |
---|
| 886 | ... <option name="Option 4" value="option4"/> |
---|
| 887 | ... </option> |
---|
| 888 | ... </option> |
---|
| 889 | ... <option name="Option 5" value="option5"/> |
---|
| 890 | ... </options> |
---|
| 891 | ... </param> |
---|
| 892 | ... ''' ) ) |
---|
| 893 | >>> print p.get_html() |
---|
| 894 | <div><ul class="toolParameterExpandableCollapsable"> |
---|
| 895 | <li><span class="toolParameterExpandableCollapsable">[+]</span><input type="checkbox" name="some_name" value="heading1"">Heading 1 |
---|
| 896 | <ul class="toolParameterExpandableCollapsable" default_state="collapsed"> |
---|
| 897 | <li><input type="checkbox" name="some_name" value="option1"">Option 1 |
---|
| 898 | </li> |
---|
| 899 | <li><input type="checkbox" name="some_name" value="option2"">Option 2 |
---|
| 900 | </li> |
---|
| 901 | <li><span class="toolParameterExpandableCollapsable">[+]</span><input type="checkbox" name="some_name" value="heading1"">Heading 1 |
---|
| 902 | <ul class="toolParameterExpandableCollapsable" default_state="collapsed"> |
---|
| 903 | <li><input type="checkbox" name="some_name" value="option3"">Option 3 |
---|
| 904 | </li> |
---|
| 905 | <li><input type="checkbox" name="some_name" value="option4"">Option 4 |
---|
| 906 | </li> |
---|
| 907 | </ul> |
---|
| 908 | </li> |
---|
| 909 | </ul> |
---|
| 910 | </li> |
---|
| 911 | <li><input type="checkbox" name="some_name" value="option5"">Option 5 |
---|
| 912 | </li> |
---|
| 913 | </ul></div> |
---|
| 914 | >>> p = DrillDownSelectToolParameter( None, XML( |
---|
| 915 | ... ''' |
---|
| 916 | ... <param name="some_name" type="drill_down" display="radio" hierarchy="recurse" multiple="false"> |
---|
| 917 | ... <options> |
---|
| 918 | ... <option name="Heading 1" value="heading1"> |
---|
| 919 | ... <option name="Option 1" value="option1"/> |
---|
| 920 | ... <option name="Option 2" value="option2"/> |
---|
| 921 | ... <option name="Heading 1" value="heading1"> |
---|
| 922 | ... <option name="Option 3" value="option3"/> |
---|
| 923 | ... <option name="Option 4" value="option4"/> |
---|
| 924 | ... </option> |
---|
| 925 | ... </option> |
---|
| 926 | ... <option name="Option 5" value="option5"/> |
---|
| 927 | ... </options> |
---|
| 928 | ... </param> |
---|
| 929 | ... ''' ) ) |
---|
| 930 | >>> print p.get_html() |
---|
| 931 | <div><ul class="toolParameterExpandableCollapsable"> |
---|
| 932 | <li><span class="toolParameterExpandableCollapsable">[+]</span><input type="radio" name="some_name" value="heading1"">Heading 1 |
---|
| 933 | <ul class="toolParameterExpandableCollapsable" default_state="collapsed"> |
---|
| 934 | <li><input type="radio" name="some_name" value="option1"">Option 1 |
---|
| 935 | </li> |
---|
| 936 | <li><input type="radio" name="some_name" value="option2"">Option 2 |
---|
| 937 | </li> |
---|
| 938 | <li><span class="toolParameterExpandableCollapsable">[+]</span><input type="radio" name="some_name" value="heading1"">Heading 1 |
---|
| 939 | <ul class="toolParameterExpandableCollapsable" default_state="collapsed"> |
---|
| 940 | <li><input type="radio" name="some_name" value="option3"">Option 3 |
---|
| 941 | </li> |
---|
| 942 | <li><input type="radio" name="some_name" value="option4"">Option 4 |
---|
| 943 | </li> |
---|
| 944 | </ul> |
---|
| 945 | </li> |
---|
| 946 | </ul> |
---|
| 947 | </li> |
---|
| 948 | <li><input type="radio" name="some_name" value="option5"">Option 5 |
---|
| 949 | </li> |
---|
| 950 | </ul></div> |
---|
| 951 | >>> print p.options |
---|
| 952 | [{'selected': False, 'name': 'Heading 1', 'value': 'heading1', 'options': [{'selected': False, 'name': 'Option 1', 'value': 'option1', 'options': []}, {'selected': False, 'name': 'Option 2', 'value': 'option2', 'options': []}, {'selected': False, 'name': 'Heading 1', 'value': 'heading1', 'options': [{'selected': False, 'name': 'Option 3', 'value': 'option3', 'options': []}, {'selected': False, 'name': 'Option 4', 'value': 'option4', 'options': []}]}]}, {'selected': False, 'name': 'Option 5', 'value': 'option5', 'options': []}] |
---|
| 953 | """ |
---|
| 954 | def __init__( self, tool, elem, context=None ): |
---|
| 955 | def recurse_option_elems( cur_options, option_elems ): |
---|
| 956 | for option_elem in option_elems: |
---|
| 957 | selected = string_as_bool( option_elem.get( 'selected', False ) ) |
---|
| 958 | cur_options.append( { 'name':option_elem.get( 'name' ), 'value': option_elem.get( 'value'), 'options':[], 'selected':selected } ) |
---|
| 959 | recurse_option_elems( cur_options[-1]['options'], option_elem.findall( 'option' ) ) |
---|
| 960 | ToolParameter.__init__( self, tool, elem ) |
---|
| 961 | self.multiple = string_as_bool( elem.get( 'multiple', False ) ) |
---|
| 962 | self.display = elem.get( 'display', None ) |
---|
| 963 | self.hierarchy = elem.get( 'hierarchy', 'exact' ) #exact or recurse |
---|
| 964 | self.separator = elem.get( 'separator', ',' ) |
---|
| 965 | from_file = elem.get( 'from_file', None ) |
---|
| 966 | if from_file: |
---|
| 967 | if not os.path.isabs( from_file ): |
---|
| 968 | from_file = os.path.join( tool.app.config.tool_data_path, from_file ) |
---|
| 969 | elem = XML( "<root>%s</root>" % open( from_file ).read() ) |
---|
| 970 | self.is_dynamic = False |
---|
| 971 | self.dynamic_options = None #backwards compatibility with SelectToolParameter's old dynamic options and late validation |
---|
| 972 | self.options = [] |
---|
| 973 | self.filtered = {} |
---|
| 974 | if elem.find( 'filter' ): |
---|
| 975 | self.is_dynamic = True |
---|
| 976 | for filter in elem.findall( 'filter' ): |
---|
| 977 | #currently only filtering by metadata key matching input file is allowed |
---|
| 978 | if filter.get( 'type' ) == 'data_meta': |
---|
| 979 | if filter.get( 'data_ref' ) not in self.filtered: |
---|
| 980 | self.filtered[filter.get( 'data_ref' )] = {} |
---|
| 981 | if filter.get( 'meta_key' ) not in self.filtered[filter.get( 'data_ref' )]: |
---|
| 982 | self.filtered[filter.get( 'data_ref' )][filter.get( 'meta_key' )] = {} |
---|
| 983 | if filter.get( 'value' ) not in self.filtered[filter.get( 'data_ref' )][filter.get( 'meta_key' )]: |
---|
| 984 | self.filtered[filter.get( 'data_ref' )][filter.get( 'meta_key' )][filter.get( 'value' )] = [] |
---|
| 985 | recurse_option_elems( self.filtered[filter.get( 'data_ref' )][filter.get( 'meta_key' )][filter.get( 'value' )], filter.find( 'options' ).findall( 'option' ) ) |
---|
| 986 | else: |
---|
| 987 | recurse_option_elems( self.options, elem.find( 'options' ).findall( 'option' ) ) |
---|
| 988 | |
---|
| 989 | def get_options( self, trans=None, value=None, other_values={} ): |
---|
| 990 | if self.is_dynamic: |
---|
| 991 | options = [] |
---|
| 992 | for filter_key, filter_value in self.filtered.iteritems(): |
---|
| 993 | dataset = other_values[filter_key] |
---|
| 994 | if dataset.__class__.__name__.endswith( "DatasetFilenameWrapper" ): #this is a bad way to check for this, but problems importing class ( due to circular imports? ) |
---|
| 995 | dataset = dataset.dataset |
---|
| 996 | if dataset: |
---|
| 997 | for meta_key, meta_dict in filter_value.iteritems(): |
---|
| 998 | check_meta_val = dataset.metadata.spec[meta_key].param.to_string( dataset.metadata.get( meta_key ) ) |
---|
| 999 | if check_meta_val in meta_dict: |
---|
| 1000 | options.extend( meta_dict[check_meta_val] ) |
---|
| 1001 | return options |
---|
| 1002 | return self.options |
---|
| 1003 | |
---|
| 1004 | def get_legal_values( self, trans, other_values ): |
---|
| 1005 | def recurse_options( legal_values, options ): |
---|
| 1006 | for option in options: |
---|
| 1007 | legal_values.append( option['value'] ) |
---|
| 1008 | recurse_options( legal_values, option['options'] ) |
---|
| 1009 | legal_values = [] |
---|
| 1010 | recurse_options( legal_values, self.get_options( trans=trans, other_values=other_values ) ) |
---|
| 1011 | return legal_values |
---|
| 1012 | |
---|
| 1013 | def get_html( self, trans=None, value=None, other_values={} ): |
---|
| 1014 | """ |
---|
| 1015 | Returns the html widget corresponding to the paramter. |
---|
| 1016 | Optionally attempt to retain the current value specific by 'value' |
---|
| 1017 | """ |
---|
| 1018 | return self.get_html_field( trans, value, other_values ).get_html() |
---|
| 1019 | |
---|
| 1020 | def get_html_field( self, trans=None, value=None, other_values={} ): |
---|
| 1021 | # Dynamic options are not yet supported in workflow, allow |
---|
| 1022 | # specifying the value as text for now. |
---|
| 1023 | if self.need_late_validation( trans, other_values ): |
---|
| 1024 | if value is not None: |
---|
| 1025 | assert isinstance( value, UnvalidatedValue ) |
---|
| 1026 | value = value.value |
---|
| 1027 | if self.multiple: |
---|
| 1028 | if value is None: |
---|
| 1029 | value = "" |
---|
| 1030 | else: |
---|
| 1031 | value = "\n".join( value ) |
---|
| 1032 | return form_builder.TextArea( self.name, value=value ) |
---|
| 1033 | else: |
---|
| 1034 | return form_builder.TextField( self.name, value=(value or "") ) |
---|
| 1035 | return form_builder.DrillDownField( self.name, self.multiple, self.display, self.refresh_on_change, self.get_options( trans, value, other_values ), value, refresh_on_change_values = self.refresh_on_change_values ) |
---|
| 1036 | |
---|
| 1037 | def from_html( self, value, trans=None, other_values={} ): |
---|
| 1038 | if self.need_late_validation( trans, other_values ): |
---|
| 1039 | if self.multiple: |
---|
| 1040 | if value == '': #No option selected |
---|
| 1041 | value = None |
---|
| 1042 | else: |
---|
| 1043 | value = value.split( "\n" ) |
---|
| 1044 | return UnvalidatedValue( value ) |
---|
| 1045 | if not value: return None |
---|
| 1046 | if not isinstance( value, list ): |
---|
| 1047 | value = [value] |
---|
| 1048 | if not( self.repeat ) and len( value ) > 1: |
---|
| 1049 | assert self.multiple, "Multiple values provided but parameter is not expecting multiple values" |
---|
| 1050 | rval = [] |
---|
| 1051 | for val in value: |
---|
| 1052 | if val not in self.get_legal_values( trans, other_values ): raise ValueError( "An invalid option was selected, please verify" ) |
---|
| 1053 | rval.append( util.restore_text( val ) ) |
---|
| 1054 | return rval |
---|
| 1055 | |
---|
| 1056 | def to_param_dict_string( self, value, other_values={} ): |
---|
| 1057 | def get_options_list( value ): |
---|
| 1058 | def get_base_option( value, options ): |
---|
| 1059 | for option in options: |
---|
| 1060 | if value == option['value']: |
---|
| 1061 | return option |
---|
| 1062 | rval = get_base_option( value, option['options'] ) |
---|
| 1063 | if rval: return rval |
---|
| 1064 | return None #not found |
---|
| 1065 | def recurse_option( option_list, option ): |
---|
| 1066 | if not option['options']: |
---|
| 1067 | option_list.append( option['value'] ) |
---|
| 1068 | else: |
---|
| 1069 | for opt in option['options']: |
---|
| 1070 | recurse_option( option_list, opt ) |
---|
| 1071 | rval = [] |
---|
| 1072 | recurse_option( rval, get_base_option( value, self.get_options( other_values = other_values ) ) ) |
---|
| 1073 | return rval or [value] |
---|
| 1074 | |
---|
| 1075 | if value is None: return "None" |
---|
| 1076 | rval = [] |
---|
| 1077 | if self.hierarchy == "exact": |
---|
| 1078 | rval = value |
---|
| 1079 | else: |
---|
| 1080 | for val in value: |
---|
| 1081 | options = get_options_list( val ) |
---|
| 1082 | rval.extend( options ) |
---|
| 1083 | if len( rval ) > 1: |
---|
| 1084 | if not( self.repeat ): |
---|
| 1085 | assert self.multiple, "Multiple values provided but parameter is not expecting multiple values" |
---|
| 1086 | rval = self.separator.join( rval ) |
---|
| 1087 | if self.tool is None or self.tool.options.sanitize: |
---|
| 1088 | if self.sanitizer: |
---|
| 1089 | rval = self.sanitizer.sanitize_param( rval ) |
---|
| 1090 | else: |
---|
| 1091 | rval = sanitize_param( rval ) |
---|
| 1092 | return rval |
---|
| 1093 | |
---|
| 1094 | def get_initial_value( self, trans, context ): |
---|
| 1095 | def recurse_options( initial_values, options ): |
---|
| 1096 | for option in options: |
---|
| 1097 | if option['selected']: |
---|
| 1098 | initial_values.append( option['value'] ) |
---|
| 1099 | recurse_options( initial_values, option['options'] ) |
---|
| 1100 | # More working around dynamic options for workflow |
---|
| 1101 | if self.need_late_validation( trans, context ): |
---|
| 1102 | # Really the best we can do? |
---|
| 1103 | return UnvalidatedValue( None ) |
---|
| 1104 | initial_values = [] |
---|
| 1105 | recurse_options( initial_values, self.get_options( trans=trans, other_values=context ) ) |
---|
| 1106 | return initial_values |
---|
| 1107 | |
---|
| 1108 | def value_to_display_text( self, value, app ): |
---|
| 1109 | def get_option_display( value, options ): |
---|
| 1110 | for option in options: |
---|
| 1111 | if value == option['value']: |
---|
| 1112 | return option['name'] |
---|
| 1113 | rval = get_option_display( value, option['options'] ) |
---|
| 1114 | if rval: return rval |
---|
| 1115 | return None #not found |
---|
| 1116 | |
---|
| 1117 | if isinstance( value, UnvalidatedValue ): |
---|
| 1118 | suffix = "\n(value not yet validated)" |
---|
| 1119 | value = value.value |
---|
| 1120 | else: |
---|
| 1121 | suffix = "" |
---|
| 1122 | if not value: |
---|
| 1123 | value = [] |
---|
| 1124 | elif not isinstance( value, list ): |
---|
| 1125 | value = [ value ] |
---|
| 1126 | # FIXME: Currently only translating values back to labels if they |
---|
| 1127 | # are not dynamic |
---|
| 1128 | if self.is_dynamic: |
---|
| 1129 | if value: |
---|
| 1130 | if isinstance( value, list ): |
---|
| 1131 | rval = value |
---|
| 1132 | else: |
---|
| 1133 | rval = [ value ] |
---|
| 1134 | else: |
---|
| 1135 | rval = [] |
---|
| 1136 | else: |
---|
| 1137 | rval = [] |
---|
| 1138 | for val in value: |
---|
| 1139 | rval.append( get_option_display( val, self.options ) or val ) |
---|
| 1140 | return "\n".join( rval ) + suffix |
---|
| 1141 | |
---|
| 1142 | def get_dependencies( self ): |
---|
| 1143 | """ |
---|
| 1144 | Get the *names* of the other params this param depends on. |
---|
| 1145 | """ |
---|
| 1146 | return self.filtered.keys() |
---|
| 1147 | |
---|
| 1148 | class DummyDataset( object ): |
---|
| 1149 | pass |
---|
| 1150 | |
---|
| 1151 | class DataToolParameter( ToolParameter ): |
---|
| 1152 | # TODO, Nate: Make sure the following unit tests appropriately test the dataset security |
---|
| 1153 | # components. Add as many additional tests as necessary. |
---|
| 1154 | """ |
---|
| 1155 | Parameter that takes on one (or many) or a specific set of values. |
---|
| 1156 | |
---|
| 1157 | TODO: There should be an alternate display that allows single selects to be |
---|
| 1158 | displayed as radio buttons and multiple selects as a set of checkboxes |
---|
| 1159 | |
---|
| 1160 | TODO: The following must be fixed to test correctly for the new security_check tag in the DataToolParameter ( the last test below is broken ) |
---|
| 1161 | Nate's next passs at the dataset security stuff will dramatically alter this anyway. |
---|
| 1162 | """ |
---|
| 1163 | |
---|
| 1164 | def __init__( self, tool, elem ): |
---|
| 1165 | ToolParameter.__init__( self, tool, elem ) |
---|
| 1166 | # Add metadata validator |
---|
| 1167 | if not string_as_bool( elem.get( 'no_validation', False ) ): |
---|
| 1168 | self.validators.append( validation.MetadataValidator() ) |
---|
| 1169 | # Build tuple of classes for supported data formats |
---|
| 1170 | formats = [] |
---|
| 1171 | self.extensions = elem.get( 'format', 'data' ).split( "," ) |
---|
| 1172 | for extension in self.extensions: |
---|
| 1173 | extension = extension.strip() |
---|
| 1174 | if tool is None: |
---|
| 1175 | #This occurs for things such as unit tests |
---|
| 1176 | import galaxy.datatypes.registry |
---|
| 1177 | formats.append( galaxy.datatypes.registry.Registry().get_datatype_by_extension( extension.lower() ).__class__ ) |
---|
| 1178 | else: |
---|
| 1179 | formats.append( tool.app.datatypes_registry.get_datatype_by_extension( extension.lower() ).__class__ ) |
---|
| 1180 | self.formats = tuple( formats ) |
---|
| 1181 | self.multiple = string_as_bool( elem.get( 'multiple', False ) ) |
---|
| 1182 | # Optional DataToolParameters are used in tools like GMAJ and LAJ |
---|
| 1183 | self.optional = string_as_bool( elem.get( 'optional', False ) ) |
---|
| 1184 | # TODO: Enhance dynamic options for DataToolParameters. Currently, |
---|
| 1185 | # only the special case key='build' of type='data_meta' is |
---|
| 1186 | # a valid filter |
---|
| 1187 | options = elem.find( 'options' ) |
---|
| 1188 | if options is None: |
---|
| 1189 | self.options = None |
---|
| 1190 | else: |
---|
| 1191 | self.options = dynamic_options.DynamicOptions( options, self ) |
---|
| 1192 | self.is_dynamic = self.options is not None |
---|
| 1193 | # Load conversions required for the dataset input |
---|
| 1194 | self.conversions = [] |
---|
| 1195 | for conv_elem in elem.findall( "conversion" ): |
---|
| 1196 | name = conv_elem.get( "name" ) #name for commandline substitution |
---|
| 1197 | conv_extensions = conv_elem.get( "type" ) #target datatype extension |
---|
| 1198 | # FIXME: conv_extensions should be able to be an ordered list |
---|
| 1199 | assert None not in [ name, type ], 'A name (%s) and type (%s) are required for explicit conversion' % ( name, type ) |
---|
| 1200 | conv_types = tool.app.datatypes_registry.get_datatype_by_extension( conv_extensions.lower() ).__class__ |
---|
| 1201 | self.conversions.append( ( name, conv_extensions, conv_types ) ) |
---|
| 1202 | |
---|
| 1203 | def get_html_field( self, trans=None, value=None, other_values={} ): |
---|
| 1204 | filter_value = None |
---|
| 1205 | if self.options: |
---|
| 1206 | try: |
---|
| 1207 | filter_value = self.options.get_options( trans, other_values )[0][0] |
---|
| 1208 | except IndexError: |
---|
| 1209 | pass #no valid options |
---|
| 1210 | assert trans is not None, "DataToolParameter requires a trans" |
---|
| 1211 | history = trans.get_history() |
---|
| 1212 | assert history is not None, "DataToolParameter requires a history" |
---|
| 1213 | if value is not None: |
---|
| 1214 | if type( value ) != list: |
---|
| 1215 | value = [ value ] |
---|
| 1216 | field = form_builder.SelectField( self.name, self.multiple, None, self.refresh_on_change, refresh_on_change_values = self.refresh_on_change_values ) |
---|
| 1217 | # CRUCIAL: the dataset_collector function needs to be local to DataToolParameter.get_html_field() |
---|
| 1218 | def dataset_collector( hdas, parent_hid ): |
---|
| 1219 | current_user_roles = trans.get_current_user_roles() |
---|
| 1220 | for i, hda in enumerate( hdas ): |
---|
| 1221 | if len( hda.name ) > 30: |
---|
| 1222 | hda_name = '%s..%s' % ( hda.name[:17], hda.name[-11:] ) |
---|
| 1223 | else: |
---|
| 1224 | hda_name = hda.name |
---|
| 1225 | if parent_hid is not None: |
---|
| 1226 | hid = "%s.%d" % ( parent_hid, i + 1 ) |
---|
| 1227 | else: |
---|
| 1228 | hid = str( hda.hid ) |
---|
| 1229 | if not hda.dataset.state in [galaxy.model.Dataset.states.ERROR, galaxy.model.Dataset.states.DISCARDED] and \ |
---|
| 1230 | hda.visible and \ |
---|
| 1231 | trans.app.security_agent.can_access_dataset( current_user_roles, hda.dataset ): |
---|
| 1232 | # If we are sending data to an external application, then we need to make sure there are no roles |
---|
| 1233 | # associated with the dataset that restrict it's access from "public". |
---|
| 1234 | if self.tool and self.tool.tool_type == 'data_destination' and not trans.app.security_agent.dataset_is_public( hda.dataset ): |
---|
| 1235 | continue |
---|
| 1236 | if self.options and hda.get_dbkey() != filter_value: |
---|
| 1237 | continue |
---|
| 1238 | if isinstance( hda.datatype, self.formats): |
---|
| 1239 | selected = ( value and ( hda in value ) ) |
---|
| 1240 | field.add_option( "%s: %s" % ( hid, hda_name ), hda.id, selected ) |
---|
| 1241 | else: |
---|
| 1242 | target_ext, converted_dataset = hda.find_conversion_destination( self.formats, converter_safe = self.converter_safe( other_values, trans ) ) |
---|
| 1243 | if target_ext: |
---|
| 1244 | if converted_dataset: |
---|
| 1245 | hda = converted_dataset |
---|
| 1246 | if not trans.app.security_agent.can_access_dataset( current_user_roles, hda.dataset ): |
---|
| 1247 | continue |
---|
| 1248 | selected = ( value and ( hda in value ) ) |
---|
| 1249 | field.add_option( "%s: (as %s) %s" % ( hid, target_ext, hda_name ), hda.id, selected ) |
---|
| 1250 | # Also collect children via association object |
---|
| 1251 | dataset_collector( hda.children, hid ) |
---|
| 1252 | dataset_collector( history.active_datasets, None ) |
---|
| 1253 | some_data = bool( field.options ) |
---|
| 1254 | if some_data: |
---|
| 1255 | if value is None or len( field.options ) == 1: |
---|
| 1256 | # Ensure that the last item is always selected |
---|
| 1257 | a, b, c = field.options[-1] |
---|
| 1258 | if self.optional: |
---|
| 1259 | field.options[-1] = a, b, False |
---|
| 1260 | else: |
---|
| 1261 | field.options[-1] = a, b, True |
---|
| 1262 | if self.optional: |
---|
| 1263 | if not value: |
---|
| 1264 | field.add_option( "Selection is Optional", 'None', True ) |
---|
| 1265 | else: |
---|
| 1266 | field.add_option( "Selection is Optional", 'None', False ) |
---|
| 1267 | return field |
---|
| 1268 | |
---|
| 1269 | def get_initial_value( self, trans, context ): |
---|
| 1270 | """ |
---|
| 1271 | NOTE: This is wasteful since dynamic options and dataset collection |
---|
| 1272 | happens twice (here and when generating HTML). |
---|
| 1273 | """ |
---|
| 1274 | # Can't look at history in workflow mode |
---|
| 1275 | if trans.workflow_building_mode: |
---|
| 1276 | return DummyDataset() |
---|
| 1277 | assert trans is not None, "DataToolParameter requires a trans" |
---|
| 1278 | history = trans.get_history() |
---|
| 1279 | assert history is not None, "DataToolParameter requires a history" |
---|
| 1280 | if self.optional: |
---|
| 1281 | return None |
---|
| 1282 | most_recent_dataset = [None] |
---|
| 1283 | filter_value = None |
---|
| 1284 | if self.options: |
---|
| 1285 | try: |
---|
| 1286 | filter_value = self.options.get_options( trans, context )[0][0] |
---|
| 1287 | except IndexError: |
---|
| 1288 | pass #no valid options |
---|
| 1289 | def dataset_collector( datasets ): |
---|
| 1290 | def is_convertable( dataset ): |
---|
| 1291 | target_ext, converted_dataset = dataset.find_conversion_destination( self.formats, converter_safe = self.converter_safe( None, trans ) ) |
---|
| 1292 | if target_ext is not None: |
---|
| 1293 | return True |
---|
| 1294 | return False |
---|
| 1295 | for i, data in enumerate( datasets ): |
---|
| 1296 | if data.visible and not data.deleted and data.state not in [data.states.ERROR, data.states.DISCARDED] and ( isinstance( data.datatype, self.formats) or is_convertable( data ) ): |
---|
| 1297 | if self.options and data.get_dbkey() != filter_value: |
---|
| 1298 | continue |
---|
| 1299 | most_recent_dataset[0] = data |
---|
| 1300 | # Also collect children via association object |
---|
| 1301 | dataset_collector( data.children ) |
---|
| 1302 | dataset_collector( history.datasets ) |
---|
| 1303 | most_recent_dataset = most_recent_dataset.pop() |
---|
| 1304 | if most_recent_dataset is not None: |
---|
| 1305 | return most_recent_dataset |
---|
| 1306 | else: |
---|
| 1307 | return '' |
---|
| 1308 | |
---|
| 1309 | def from_html( self, value, trans, other_values={} ): |
---|
| 1310 | # Can't look at history in workflow mode, skip validation and such, |
---|
| 1311 | # although, this should never be called in workflow mode right? |
---|
| 1312 | if trans.workflow_building_mode: |
---|
| 1313 | return None |
---|
| 1314 | if not value: |
---|
| 1315 | raise ValueError( "History does not include a dataset of the required format / build" ) |
---|
| 1316 | if value in [None, "None"]: |
---|
| 1317 | return None |
---|
| 1318 | if isinstance( value, list ): |
---|
| 1319 | return [ trans.sa_session.query( trans.app.model.HistoryDatasetAssociation ).get( v ) for v in value ] |
---|
| 1320 | elif isinstance( value, trans.app.model.HistoryDatasetAssociation ): |
---|
| 1321 | return value |
---|
| 1322 | else: |
---|
| 1323 | return trans.sa_session.query( trans.app.model.HistoryDatasetAssociation ).get( value ) |
---|
| 1324 | |
---|
| 1325 | def to_string( self, value, app ): |
---|
| 1326 | if value is None or isinstance( value, str ): |
---|
| 1327 | return value |
---|
| 1328 | elif isinstance( value, DummyDataset ): |
---|
| 1329 | return None |
---|
| 1330 | return value.id |
---|
| 1331 | |
---|
| 1332 | def to_python( self, value, app ): |
---|
| 1333 | # Both of these values indicate that no dataset is selected. However, 'None' |
---|
| 1334 | # indicates that the dataset is optional, while '' indicates that it is not. |
---|
| 1335 | if value is None or value == '' or value == 'None': |
---|
| 1336 | return value |
---|
| 1337 | return app.model.context.query( app.model.HistoryDatasetAssociation ).get( int( value ) ) |
---|
| 1338 | |
---|
| 1339 | def to_param_dict_string( self, value, other_values={} ): |
---|
| 1340 | if value is None: return "None" |
---|
| 1341 | return value.file_name |
---|
| 1342 | |
---|
| 1343 | def value_to_display_text( self, value, app ): |
---|
| 1344 | if value: |
---|
| 1345 | return "%s: %s" % ( value.hid, value.name ) |
---|
| 1346 | else: |
---|
| 1347 | return "No dataset" |
---|
| 1348 | |
---|
| 1349 | def get_dependencies( self ): |
---|
| 1350 | """ |
---|
| 1351 | Get the *names* of the other params this param depends on. |
---|
| 1352 | """ |
---|
| 1353 | if self.options: |
---|
| 1354 | return self.options.get_dependency_names() |
---|
| 1355 | else: |
---|
| 1356 | return [] |
---|
| 1357 | |
---|
| 1358 | def converter_safe( self, other_values, trans ): |
---|
| 1359 | if self.tool is None or self.tool.has_multiple_pages or not hasattr( trans, 'workflow_building_mode' ) or trans.workflow_building_mode: |
---|
| 1360 | return False |
---|
| 1361 | if other_values is None: |
---|
| 1362 | return True # we don't know other values, so we can't check, assume ok |
---|
| 1363 | converter_safe = [True] |
---|
| 1364 | def visitor( prefix, input, value, parent = None ): |
---|
| 1365 | if isinstance( input, SelectToolParameter ) and self.name in input.get_dependencies(): |
---|
| 1366 | if input.is_dynamic and ( input.dynamic_options or ( not input.dynamic_options and not input.options ) or not input.options.converter_safe ): |
---|
| 1367 | converter_safe[0] = False #This option does not allow for conversion, i.e. uses contents of dataset file to generate options |
---|
| 1368 | self.tool.visit_inputs( other_values, visitor ) |
---|
| 1369 | return False not in converter_safe |
---|
| 1370 | |
---|
| 1371 | # class RawToolParameter( ToolParameter ): |
---|
| 1372 | # """ |
---|
| 1373 | # Completely nondescript parameter, HTML representation is provided as text |
---|
| 1374 | # contents. |
---|
| 1375 | # |
---|
| 1376 | # >>> p = RawToolParameter( None, XML( |
---|
| 1377 | # ... ''' |
---|
| 1378 | # ... <param name="blah" type="raw"> |
---|
| 1379 | # ... <![CDATA[<span id="$name">Some random stuff</span>]]> |
---|
| 1380 | # ... </param> |
---|
| 1381 | # ... ''' ) ) |
---|
| 1382 | # >>> print p.name |
---|
| 1383 | # blah |
---|
| 1384 | # >>> print p.get_html().strip() |
---|
| 1385 | # <span id="blah">Some random stuff</span> |
---|
| 1386 | # """ |
---|
| 1387 | # def __init__( self, tool, elem ): |
---|
| 1388 | # ToolParameter.__init__( self, tool, elem ) |
---|
| 1389 | # self.template = string.Template( elem.text ) |
---|
| 1390 | # def get_html( self, prefix="" ): |
---|
| 1391 | # context = dict( self.__dict__ ) |
---|
| 1392 | # context.update( dict( prefix=prefix ) ) |
---|
| 1393 | # return self.template.substitute( context ) |
---|
| 1394 | |
---|
| 1395 | # class HistoryIDParameter( ToolParameter ): |
---|
| 1396 | # """ |
---|
| 1397 | # Parameter that takes a name value, makes history.id available. |
---|
| 1398 | # |
---|
| 1399 | # FIXME: This is a hack (esp. if hidden params are a hack) but in order to |
---|
| 1400 | # have the history accessable at the job level, it is necessary |
---|
| 1401 | # I also probably wrote this docstring test thing wrong. |
---|
| 1402 | # |
---|
| 1403 | # >>> from galaxy.model import History |
---|
| 1404 | # >>> from galaxy.util.bunch import Bunch |
---|
| 1405 | # >>> hist = History( id=1 ) |
---|
| 1406 | # >>> p = HistoryIDParameter( None, XML( '<param name="blah" type="history"/>' ) ) |
---|
| 1407 | # >>> print p.name |
---|
| 1408 | # blah |
---|
| 1409 | # >>> html_string = '<input type="hidden" name="blah" value="%d">' % hist.id |
---|
| 1410 | # >>> assert p.get_html( trans=Bunch( history=hist ) ) == html_string |
---|
| 1411 | # """ |
---|
| 1412 | # def __init__( self, tool, elem ): |
---|
| 1413 | # ToolParameter.__init__( self, tool, elem ) |
---|
| 1414 | # def get_html( self, trans, value=None, other_values={} ): |
---|
| 1415 | # assert trans.history is not None, "HistoryIDParameter requires a history" |
---|
| 1416 | # self.html = form_builder.HiddenField( self.name, trans.history.id ).get_html() |
---|
| 1417 | # return self.html |
---|
| 1418 | |
---|
| 1419 | parameter_types = dict( text = TextToolParameter, |
---|
| 1420 | integer = IntegerToolParameter, |
---|
| 1421 | float = FloatToolParameter, |
---|
| 1422 | boolean = BooleanToolParameter, |
---|
| 1423 | genomebuild = GenomeBuildParameter, |
---|
| 1424 | select = SelectToolParameter, |
---|
| 1425 | data_column = ColumnListParameter, |
---|
| 1426 | hidden = HiddenToolParameter, |
---|
| 1427 | baseurl = BaseURLToolParameter, |
---|
| 1428 | file = FileToolParameter, |
---|
| 1429 | data = DataToolParameter, |
---|
| 1430 | drill_down = DrillDownSelectToolParameter ) |
---|
| 1431 | |
---|
| 1432 | class UnvalidatedValue( object ): |
---|
| 1433 | """ |
---|
| 1434 | Wrapper to mark a value that has not been validated |
---|
| 1435 | """ |
---|
| 1436 | def __init__( self, value ): |
---|
| 1437 | self.value = value |
---|
| 1438 | def __str__( self ): |
---|
| 1439 | return str( self.value ) |
---|
| 1440 | |
---|
| 1441 | class RuntimeValue( object ): |
---|
| 1442 | """ |
---|
| 1443 | Wrapper to note a value that is not yet set, but will be required at |
---|
| 1444 | runtime. |
---|
| 1445 | """ |
---|
| 1446 | pass |
---|
| 1447 | |
---|