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