root/galaxy-central/lib/galaxy/tools/parameters/input_translation.py

リビジョン 2, 5.6 KB (コミッタ: hatakeyama, 14 年 前)

import galaxy-central

行番号 
1"""
2Tool Input Translation.
3"""
4
5import logging
6from galaxy.util.bunch import Bunch
7
8log = logging.getLogger( __name__ )
9
10class ToolInputTranslator( object ):
11    """
12    Handles Tool input translation.
13    This is used for data source tools
14   
15    >>> from galaxy.util import Params
16    >>> from elementtree.ElementTree import XML
17    >>> translator = ToolInputTranslator.from_element( XML(
18    ... '''
19    ... <request_param_translation>
20    ...  <request_param galaxy_name="URL_method" remote_name="URL_method" missing="post" />
21    ...  <request_param galaxy_name="URL" remote_name="URL" missing="" >
22    ...     <append_param separator="&amp;" first_separator="?" join="=">
23    ...         <value name="_export" missing="1" />
24    ...         <value name="GALAXY_URL" missing="0" />
25    ...     </append_param>
26    ...  </request_param>
27    ...  <request_param galaxy_name="dbkey" remote_name="db" missing="?" />
28    ...  <request_param galaxy_name="organism" remote_name="org" missing="unknown species" />
29    ...  <request_param galaxy_name="table" remote_name="hgta_table" missing="unknown table" />
30    ...  <request_param galaxy_name="description" remote_name="hgta_regionType" missing="no description" />
31    ...  <request_param galaxy_name="data_type" remote_name="hgta_outputType" missing="tabular" >
32    ...   <value_translation>
33    ...    <value galaxy_value="tabular" remote_value="primaryTable" />
34    ...    <value galaxy_value="tabular" remote_value="selectedFields" />
35    ...    <value galaxy_value="wig" remote_value="wigData" />
36    ...    <value galaxy_value="interval" remote_value="tab" />
37    ...    <value galaxy_value="html" remote_value="hyperlinks" />
38    ...    <value galaxy_value="fasta" remote_value="sequence" />
39    ...   </value_translation>
40    ...  </request_param>
41    ... </request_param_translation>
42    ... ''' ) )
43    >>> params = Params( { 'db':'hg17', 'URL':'URL_value', 'org':'Human', 'hgta_outputType':'primaryTable'  } )
44    >>> translator.translate( params )
45    >>> print params
46    {'hgta_outputType': 'primaryTable', 'data_type': 'tabular', 'table': 'unknown table', 'URL': 'URL_value?GALAXY_URL=0&_export=1', 'org': 'Human', 'URL_method': 'post', 'db': 'hg17', 'organism': 'Human', 'dbkey': 'hg17', 'description': 'no description'}
47    """
48    @classmethod
49    def from_element( cls, elem ):
50        """Loads the proper filter by the type attribute of elem"""
51        rval = ToolInputTranslator()
52        for req_param in elem.findall( "request_param" ):
53            # req_param tags must look like <request_param galaxy_name="dbkey" remote_name="GENOME" missing="" />
54            #trans_list = []
55            remote_name = req_param.get( "remote_name" )
56            galaxy_name = req_param.get( "galaxy_name" )
57            missing = req_param.get( "missing" )
58            value_trans = {}
59            append_param = None
60           
61            value_trans_elem = req_param.find( 'value_translation' )
62            if value_trans_elem:
63                for value_elem in value_trans_elem.findall( 'value' ):
64                    remote_value = value_elem.get( "remote_value" )
65                    galaxy_value = value_elem.get( "galaxy_value" )
66                    if None not in [ remote_value, galaxy_value ]:
67                        value_trans[ remote_value ] = galaxy_value
68           
69            append_param_elem = req_param.find( "append_param" )
70            if append_param_elem:
71                separator = append_param_elem.get( 'separator', ',' )
72                first_separator = append_param_elem.get( 'first_separator', None )
73                join_str = append_param_elem.get( 'join', '=' )
74                append_dict = {}
75                for value_elem in append_param_elem.findall( 'value' ):
76                    value_name = value_elem.get( 'name' )
77                    value_missing = value_elem.get( 'missing' )
78                    if None not in [ value_name, value_missing ]:
79                        append_dict[ value_name ] = value_missing
80                append_param = Bunch( separator = separator, first_separator = first_separator, join_str = join_str, append_dict = append_dict )
81           
82            rval.param_trans_dict[ remote_name ] = Bunch( galaxy_name = galaxy_name, missing = missing, value_trans = value_trans, append_param = append_param  )
83       
84        return rval
85   
86    def __init__( self ):
87        self.param_trans_dict = {}
88
89    def translate( self, params ):
90        """
91        update params in-place
92        """
93        for remote_name, translator in self.param_trans_dict.iteritems():
94            galaxy_name = translator.galaxy_name #NB: if a param by name galaxy_name is provided, it is always thrown away unless galaxy_name == remote_name
95            value = params.get( remote_name, translator.missing ) #get value from input params, or use default value specified in tool config
96            if translator.value_trans and value in translator.value_trans:
97                value = translator.value_trans[ value ]
98            if translator.append_param:
99                for param_name, missing_value in translator.append_param.append_dict.iteritems():
100                    param_value = params.get( param_name, missing_value )
101                    if translator.append_param.first_separator and translator.append_param.first_separator not in value:
102                        sep = translator.append_param.first_separator
103                    else:
104                        sep = translator.append_param.separator
105                    value += '%s%s%s%s' % ( sep, param_name, translator.append_param.join_str, param_value )
106            params.update( { galaxy_name: value } )
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