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Enhance tool parameter sanitization. Sanitization rules can now be defined on a per input parameter basis. Resolves ticket #38 and #142.
Sanitization now occurs as part of the InputValueWrapper logic. Previously sanitization occurred as soon as parameter values were provided by the user via form submits, causing the sanitized values to be stored in the database. Now the original user specified values are stored in the database and sanitation happens when str is called on the InputValueWrapper, i.e. during command-line generation and when generating configfiles. Abstract out param name and value translations that are performed on data source tools. This changes some of the names of the tags used for these purposes (e.g. data_type_translation becomes value_translation) to reflect this generalization. The ToolConfigSyntax wiki page has been updated with these changes. Future Enhancement: Allow methods with arguments and keywords to be specified for sanitation and translation purposes.
This commit is contained in:
Daniel Blankenberg
@@ -309,35 +309,21 @@ class Maf( Alignment ):
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return #this is not a MAF file
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dataset.metadata.species = species
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dataset.metadata.blocks = blocks
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#only overwrite the contents if our newly determined chromosomes don't match stored
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#write species chromosomes to a file
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chrom_file = dataset.metadata.species_chromosomes
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compare_chroms = {}
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if chrom_file:
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try:
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for line in open( chrom_file.file_name ):
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fields = line.split( "\t" )
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if fields:
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spec = fields.pop( 0 )
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if spec:
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compare_chroms[spec] = fields
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except:
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pass
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#write out species chromosomes again only if values are different
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if not species_chromosomes or compare_chroms != species_chromosomes:
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tmp_file = tempfile.TemporaryFile( 'w+b' )
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for spec, chroms in species_chromosomes.items():
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tmp_file.write( "%s\t%s\n" % ( spec, "\t".join( chroms ) ) )
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if not chrom_file:
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chrom_file = dataset.metadata.spec['species_chromosomes'].param.new_file( dataset = dataset )
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tmp_file.seek( 0 )
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open( chrom_file.file_name, 'wb' ).write( tmp_file.read() )
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dataset.metadata.species_chromosomes = chrom_file
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tmp_file.close()
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if not chrom_file:
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chrom_file = dataset.metadata.spec['species_chromosomes'].param.new_file( dataset = dataset )
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chrom_out = open( chrom_file.file_name, 'wb' )
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for spec, chroms in species_chromosomes.items():
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chrom_out.write( "%s\t%s\n" % ( spec, "\t".join( chroms ) ) )
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chrom_out.close()
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dataset.metadata.species_chromosomes = chrom_file
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index_file = dataset.metadata.maf_index
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if not index_file:
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index_file = dataset.metadata.spec['maf_index'].param.new_file( dataset = dataset )
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indexes.write( open( index_file.file_name, 'w' ) )
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indexes.write( open( index_file.file_name, 'wb' ) )
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dataset.metadata.maf_index = index_file
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def set_peek( self, dataset, is_multi_byte=False ):
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if not dataset.dataset.purged:
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@@ -17,6 +17,7 @@ from elementtree import ElementTree
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from parameters import *
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from parameters.grouping import *
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from parameters.validation import LateValidationError
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from parameters.input_translation import ToolInputTranslator
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from galaxy.util.expressions import ExpressionContext
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from galaxy.tools.test import ToolTestBuilder
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from galaxy.tools.actions import DefaultToolAction
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@@ -299,48 +300,11 @@ class Tool:
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self.tool_type = root.get( "tool_type", None )
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#Force history to fully refresh after job execution for this tool. Useful i.e. when an indeterminate number of outputs are created by a tool.
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self.force_history_refresh = util.string_as_bool( root.get( 'force_history_refresh', 'False' ) )
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# data_source tool
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if self.tool_type == "data_source":
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self.URL_method = root.get( "URL_method", "get" ) # get is the default
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self.param_trans_dict = {}
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req_param_trans = root.find( "request_param_translation" )
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if req_param_trans is not None:
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for req_param in req_param_trans.findall( "request_param" ):
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# req_param tags must look like <request_param galaxy_name="dbkey" remote_name="GENOME" missing="" />
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trans_list = []
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remote_name = req_param.get( "remote_name" )
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trans_list.append( req_param.get( "galaxy_name" ) )
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trans_list.append( req_param.get( "missing" ) )
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if req_param.get( "galaxy_name" ) == "data_type":
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# The req_param tag for data_type is special in that it can contain another tag set like
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# <data_type_translation>
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# <format galaxy_format="tabular" remote_format="selectedFields" />
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# </data_type_translation>
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format_trans = req_param.find( "data_type_translation" )
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if format_trans is not None:
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format_trans_dict = {}
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for format in format_trans.findall( "format" ):
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remote_format = format.get( "remote_format" )
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galaxy_format = format.get( "galaxy_format" )
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format_trans_dict[ remote_format ] = galaxy_format
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trans_list.append( format_trans_dict )
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elif req_param.get( "galaxy_name" ) == "URL":
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# Some remote data sources ( e.g., Gbrowse ) send parameters back to
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# Galaxy in the initial response that must be added to URL prior to
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# Galaxy sending the secondary request to the URL. The tag set looks
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# asomething like:
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# <add_to_url>
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# <param_from_source name="d" missing="" />
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# </add_to_url>
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add_to_url = req_param.find( "add_to_url" )
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if add_to_url is not None:
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add_to_url_dict = {}
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for param_from_source in add_to_url.findall( "param_from_source" ):
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name = param_from_source.get( "name" )
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value = param_from_source.get( "missing" ) # only used if the source doesn't send the param name
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add_to_url_dict[ name ] = value
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trans_list.append( add_to_url_dict )
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self.param_trans_dict[ remote_name ] = trans_list
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self.param_trans_dict = {} #make this a property of all Tools, so don't need to check if tool is datasource, just if it is populated
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#load input translator, used by datasource tools to change names/values of incoming parameters
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self.input_translator = root.find( "request_param_translation" )
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if self.input_translator:
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self.input_translator = ToolInputTranslator.from_element( self.input_translator )
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# Command line (template). Optional for tools that do not invoke a local program
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command = root.find("command")
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if command is not None and command.text is not None:
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@@ -7,6 +7,8 @@ from elementtree.ElementTree import XML, Element
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from galaxy import config, datatypes, util
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from galaxy.web import form_builder
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from galaxy.util.bunch import Bunch
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from galaxy.util import string_as_bool, sanitize_param
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from sanitize import ToolParameterSanitizer
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import validation, dynamic_options
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# For BaseURLToolParameter
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from galaxy.web import url_for
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@@ -28,7 +30,10 @@ class ToolParameter( object ):
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self.type = param.get("type")
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self.label = util.xml_text(param, "label")
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self.help = util.xml_text(param, "help")
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self.unsanitize = param.get( "unsanitize", None )
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self.unsanitize = param.get( "unsanitize", None ) ### This doesn't looked to be used anywhere... REMOVE ME?
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self.sanitizer = param.find( "sanitizer" )
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if self.sanitizer is not None:
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self.sanitizer = ToolParameterSanitizer.from_element( self.sanitizer )
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self.html = "no html set"
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self.repeat = param.get("repeat", None)
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self.condition = param.get( "condition", None )
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@@ -122,7 +127,13 @@ class ToolParameter( object ):
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return value
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def to_param_dict_string( self, value, other_values={} ):
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return str( value )
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value = str( value )
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if self.tool is None or self.tool.options.sanitize:
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if self.sanitizer:
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value = self.sanitizer.sanitize_param( value )
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else:
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value = sanitize_param( value )
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return value
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def validate( self, value, history=None ):
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for validator in self.validators:
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@@ -154,7 +165,7 @@ class TextToolParameter( ToolParameter ):
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self.name = elem.get( 'name' )
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self.size = elem.get( 'size' )
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self.value = elem.get( 'value' )
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self.area = str_bool( elem.get( 'area', False ) )
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self.area = string_as_bool( elem.get( 'area', False ) )
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def get_html_field( self, trans=None, value=None, other_values={} ):
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if self.area:
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return form_builder.TextArea( self.name, self.size, value or self.value )
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@@ -262,7 +273,7 @@ class BooleanToolParameter( ToolParameter ):
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self.truevalue = elem.get( 'truevalue', 'true' )
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self.falsevalue = elem.get( 'falsevalue', 'false' )
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self.name = elem.get( 'name' )
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self.checked = str_bool( elem.get( 'checked' ) )
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self.checked = string_as_bool( elem.get( 'checked' ) )
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def get_html_field( self, trans=None, value=None, other_values={} ):
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checked = self.checked
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if value:
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@@ -299,7 +310,7 @@ class FileToolParameter( ToolParameter ):
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"""
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ToolParameter.__init__( self, tool, elem )
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self.name = elem.get( 'name' )
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self.ajax = str_bool( elem.get( 'ajax-upload' ) )
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self.ajax = string_as_bool( elem.get( 'ajax-upload' ) )
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def get_html_field( self, trans=None, value=None, other_values={} ):
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return form_builder.FileField( self.name, ajax = self.ajax, value = value )
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def from_html( self, value, trans=None, other_values={} ):
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@@ -474,7 +485,7 @@ class SelectToolParameter( ToolParameter ):
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"""
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def __init__( self, tool, elem, context=None ):
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ToolParameter.__init__( self, tool, elem )
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self.multiple = str_bool( elem.get( 'multiple', False ) )
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self.multiple = string_as_bool( elem.get( 'multiple', False ) )
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self.display = elem.get( 'display', None )
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self.separator = elem.get( 'separator', ',' )
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self.legal_values = set()
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@@ -492,7 +503,7 @@ class SelectToolParameter( ToolParameter ):
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for index, option in enumerate( elem.findall( "option" ) ):
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value = option.get( "value" )
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self.legal_values.add( value )
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selected = str_bool( option.get( "selected", False ) )
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selected = string_as_bool( option.get( "selected", False ) )
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self.static_options.append( ( option.text, value, selected ) )
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self.is_dynamic = ( ( self.dynamic_options is not None ) or ( self.options is not None ) )
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def get_options( self, trans, other_values ):
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@@ -571,11 +582,19 @@ class SelectToolParameter( ToolParameter ):
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if value is None:
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return "None"
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if isinstance( value, list ):
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if not(self.repeat):
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if not( self.repeat ):
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assert self.multiple, "Multiple values provided but parameter is not expecting multiple values"
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return self.separator.join( map( str, value ) )
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value = map( str, value )
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else:
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return str(value)
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value = str( value )
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if self.tool is None or self.tool.options.sanitize:
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if self.sanitizer:
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value = self.sanitizer.sanitize_param( value )
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else:
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value = sanitize_param( value )
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if isinstance( value, list ):
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value = self.separator.join( value )
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return value
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def value_to_basic( self, value, app ):
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if isinstance( value, UnvalidatedValue ):
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return { "__class__": "UnvalidatedValue", "value": value.value }
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@@ -741,9 +760,9 @@ class ColumnListParameter( SelectToolParameter ):
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def __init__( self, tool, elem ):
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SelectToolParameter.__init__( self, tool, elem )
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self.tool = tool
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self.numerical = str_bool( elem.get( "numerical", False ))
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self.force_select = str_bool( elem.get( "force_select", True ))
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self.accept_default = str_bool( elem.get( "accept_default", False ))
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self.numerical = string_as_bool( elem.get( "numerical", False ))
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self.force_select = string_as_bool( elem.get( "force_select", True ))
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self.accept_default = string_as_bool( elem.get( "accept_default", False ))
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self.data_ref = elem.get( "data_ref", None )
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self.is_dynamic = True
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def get_column_list( self, trans, other_values ):
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@@ -894,11 +913,11 @@ class DrillDownSelectToolParameter( SelectToolParameter ):
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def __init__( self, tool, elem, context=None ):
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def recurse_option_elems( cur_options, option_elems ):
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for option_elem in option_elems:
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selected = str_bool( option_elem.get( 'selected', False ) )
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selected = string_as_bool( option_elem.get( 'selected', False ) )
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cur_options.append( { 'name':option_elem.get( 'name' ), 'value': option_elem.get( 'value'), 'options':[], 'selected':selected } )
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recurse_option_elems( cur_options[-1]['options'], option_elem.findall( 'option' ) )
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ToolParameter.__init__( self, tool, elem )
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self.multiple = str_bool( elem.get( 'multiple', False ) )
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self.multiple = string_as_bool( elem.get( 'multiple', False ) )
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self.display = elem.get( 'display', None )
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self.hierarchy = elem.get( 'hierarchy', 'exact' ) #exact or recurse
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self.separator = elem.get( 'separator', ',' )
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@@ -1019,7 +1038,13 @@ class DrillDownSelectToolParameter( SelectToolParameter ):
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if len( rval ) > 1:
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if not( self.repeat ):
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assert self.multiple, "Multiple values provided but parameter is not expecting multiple values"
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return self.separator.join( rval )
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rval = self.separator.join( rval )
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if self.tool is None or self.tool.options.sanitize:
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if self.sanitizer:
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rval = self.sanitizer.sanitize_param( rval )
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else:
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rval = sanitize_param( rval )
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return rval
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def get_initial_value( self, trans, context ):
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def recurse_options( initial_values, options ):
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@@ -1094,7 +1119,7 @@ class DataToolParameter( ToolParameter ):
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def __init__( self, tool, elem ):
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ToolParameter.__init__( self, tool, elem )
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# Add metadata validator
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if not str_bool( elem.get( 'no_validation', False ) ):
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if not string_as_bool( elem.get( 'no_validation', False ) ):
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self.validators.append( validation.MetadataValidator() )
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# Build tuple of classes for supported data formats
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formats = []
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@@ -1108,9 +1133,9 @@ class DataToolParameter( ToolParameter ):
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else:
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formats.append( tool.app.datatypes_registry.get_datatype_by_extension( extension.lower() ).__class__ )
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self.formats = tuple( formats )
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self.multiple = str_bool( elem.get( 'multiple', False ) )
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self.multiple = string_as_bool( elem.get( 'multiple', False ) )
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# Optional DataToolParameters are used in tools like GMAJ and LAJ
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self.optional = str_bool( elem.get( 'optional', False ) )
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self.optional = string_as_bool( elem.get( 'optional', False ) )
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# TODO: Enhance dynamic options for DataToolParameters. Currently,
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# only the special case key='build' of type='data_meta' is
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# a valid filter
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@@ -1366,13 +1391,4 @@ class RuntimeValue( object ):
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runtime.
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"""
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pass
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def str_bool(in_str):
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"""
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returns true/false of a string, since bool(str), always returns true if string is not empty
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default action is to return false
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"""
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if str(in_str).lower() == 'true' or str(in_str).lower() == 'yes':
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return True
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return False
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@@ -0,0 +1,106 @@
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"""
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Tool Input Translation.
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"""
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import logging
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from galaxy.util.bunch import Bunch
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log = logging.getLogger( __name__ )
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class ToolInputTranslator( object ):
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"""
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Handles Tool input translation.
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This is used for data source tools
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>>> from galaxy.util import Params
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>>> from elementtree.ElementTree import XML
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>>> translator = ToolInputTranslator.from_element( XML(
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... '''
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... <request_param_translation>
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... <request_param galaxy_name="URL_method" remote_name="URL_method" missing="post" />
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... <request_param galaxy_name="URL" remote_name="URL" missing="" >
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... <append_param separator="&" first_separator="?" join="=">
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... <value name="_export" missing="1" />
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... <value name="GALAXY_URL" missing="0" />
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... </append_param>
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... </request_param>
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... <request_param galaxy_name="dbkey" remote_name="db" missing="?" />
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... <request_param galaxy_name="organism" remote_name="org" missing="unknown species" />
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... <request_param galaxy_name="table" remote_name="hgta_table" missing="unknown table" />
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... <request_param galaxy_name="description" remote_name="hgta_regionType" missing="no description" />
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... <request_param galaxy_name="data_type" remote_name="hgta_outputType" missing="tabular" >
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... <value_translation>
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... <value galaxy_value="tabular" remote_value="primaryTable" />
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... <value galaxy_value="tabular" remote_value="selectedFields" />
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... <value galaxy_value="wig" remote_value="wigData" />
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... <value galaxy_value="interval" remote_value="tab" />
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... <value galaxy_value="html" remote_value="hyperlinks" />
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... <value galaxy_value="fasta" remote_value="sequence" />
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... </value_translation>
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... </request_param>
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... </request_param_translation>
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... ''' ) )
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>>> params = Params( { 'db':'hg17', 'URL':'URL_value', 'org':'Human', 'hgta_outputType':'primaryTable' } )
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>>> translator.translate( params )
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>>> print params
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{'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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"""
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@classmethod
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def from_element( cls, elem ):
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"""Loads the proper filter by the type attribute of elem"""
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rval = ToolInputTranslator()
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for req_param in elem.findall( "request_param" ):
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# req_param tags must look like <request_param galaxy_name="dbkey" remote_name="GENOME" missing="" />
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#trans_list = []
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remote_name = req_param.get( "remote_name" )
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galaxy_name = req_param.get( "galaxy_name" )
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missing = req_param.get( "missing" )
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value_trans = {}
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append_param = None
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||||
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value_trans_elem = req_param.find( 'value_translation' )
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if value_trans_elem:
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for value_elem in value_trans_elem.findall( 'value' ):
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remote_value = value_elem.get( "remote_value" )
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galaxy_value = value_elem.get( "galaxy_value" )
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if None not in [ remote_value, galaxy_value ]:
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value_trans[ remote_value ] = galaxy_value
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||||
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append_param_elem = req_param.find( "append_param" )
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if append_param_elem:
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separator = append_param_elem.get( 'separator', ',' )
|
||||
first_separator = append_param_elem.get( 'first_separator', None )
|
||||
join_str = append_param_elem.get( 'join', '=' )
|
||||
append_dict = {}
|
||||
for value_elem in append_param_elem.findall( 'value' ):
|
||||
value_name = value_elem.get( 'name' )
|
||||
value_missing = value_elem.get( 'missing' )
|
||||
if None not in [ value_name, value_missing ]:
|
||||
append_dict[ value_name ] = value_missing
|
||||
append_param = Bunch( separator = separator, first_separator = first_separator, join_str = join_str, append_dict = append_dict )
|
||||
|
||||
rval.param_trans_dict[ remote_name ] = Bunch( galaxy_name = galaxy_name, missing = missing, value_trans = value_trans, append_param = append_param )
|
||||
|
||||
return rval
|
||||
|
||||
def __init__( self ):
|
||||
self.param_trans_dict = {}
|
||||
|
||||
def translate( self, params ):
|
||||
"""
|
||||
update params in-place
|
||||
"""
|
||||
for remote_name, translator in self.param_trans_dict.iteritems():
|
||||
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
|
||||
value = params.get( remote_name, translator.missing ) #get value from input params, or use default value specified in tool config
|
||||
if translator.value_trans and value in translator.value_trans:
|
||||
value = translator.value_trans[ value ]
|
||||
if translator.append_param:
|
||||
for param_name, missing_value in translator.append_param.append_dict.iteritems():
|
||||
param_value = params.get( param_name, missing_value )
|
||||
if translator.append_param.first_separator and translator.append_param.first_separator not in value:
|
||||
sep = translator.append_param.first_separator
|
||||
else:
|
||||
sep = translator.append_param.separator
|
||||
value += '%s%s%s%s' % ( sep, param_name, translator.append_param.join_str, param_value )
|
||||
params.update( { galaxy_name: value } )
|
||||
@@ -0,0 +1,167 @@
|
||||
"""
|
||||
Tool Parameter specific sanitizing.
|
||||
"""
|
||||
|
||||
import logging
|
||||
import string
|
||||
import galaxy.util
|
||||
|
||||
log = logging.getLogger( __name__ )
|
||||
|
||||
class ToolParameterSanitizer( object ):
|
||||
"""
|
||||
Handles tool parameter specific sanitizing.
|
||||
|
||||
>>> from elementtree.ElementTree import XML
|
||||
>>> sanitizer = ToolParameterSanitizer.from_element( XML(
|
||||
... '''
|
||||
... <sanitizer invalid_char="">
|
||||
... <valid initial="string.letters"/>
|
||||
... </sanitizer>
|
||||
... ''' ) )
|
||||
>>> sanitizer.sanitize_param( string.printable ) == string.letters
|
||||
True
|
||||
>>> slash = chr( 92 )
|
||||
>>> sanitizer = ToolParameterSanitizer.from_element( XML(
|
||||
... '''
|
||||
... <sanitizer>
|
||||
... <valid initial="none">
|
||||
... <add preset="string.printable"/>
|
||||
... <remove value="""/>
|
||||
... <remove value="%s"/>
|
||||
... </valid>
|
||||
... <mapping initial="none">
|
||||
... <add source=""" target="%s""/>
|
||||
... <add source="%s" target="%s%s"/>
|
||||
... </mapping>
|
||||
... </sanitizer>
|
||||
... ''' % ( slash, slash, slash, slash, slash ) ) )
|
||||
>>> text = '%s"$rm&#!' % slash
|
||||
>>> [ c for c in sanitizer.sanitize_param( text ) ] == [ slash, slash, slash, '"', '$', 'r', 'm', '&', '#', '!' ]
|
||||
True
|
||||
"""
|
||||
|
||||
VALID_PRESET = { 'default':( string.letters + string.digits +" -=_.()/+*^,:?!" ), 'none':'' }
|
||||
MAPPING_PRESET = { 'default':galaxy.util.mapped_chars, 'none':{} }
|
||||
DEFAULT_INVALID_CHAR = 'X'
|
||||
|
||||
#class methods
|
||||
@classmethod
|
||||
def from_element( cls, elem ):
|
||||
"""Loads the proper filter by the type attribute of elem"""
|
||||
#TODO: Add ability to generically specify a method to use for sanitizing input via specification in tool XML
|
||||
rval = ToolParameterSanitizer()
|
||||
rval._invalid_char = elem.get( 'invalid_char', cls.DEFAULT_INVALID_CHAR )
|
||||
rval.sanitize = galaxy.util.string_as_bool( elem.get( 'sanitize', 'True' ) )
|
||||
for valid_elem in elem.findall( 'valid' ):
|
||||
rval._valid_chars = rval.get_valid_by_name( valid_elem.get( 'initial', 'default' ) )
|
||||
for action_elem in valid_elem:
|
||||
preset = rval.get_valid_by_name( action_elem.get( 'preset', 'none' ) )
|
||||
valid_value = [ val for val in action_elem.get( 'value', [] ) ]
|
||||
if action_elem.tag.lower() == 'add':
|
||||
for val in ( preset + valid_value ):
|
||||
if val not in rval._valid_chars:
|
||||
rval._valid_chars.append( val )
|
||||
elif action_elem.tag.lower() == 'remove':
|
||||
for val in ( preset + valid_value ):
|
||||
while val in rval._valid_chars:
|
||||
rval._valid_chars.remove( val )
|
||||
else:
|
||||
log.debug( 'Invalid action tag in valid: %s' % action_elem.tag )
|
||||
for mapping_elem in elem.findall( 'mapping' ):
|
||||
rval._mapped_chars = rval.get_mapping_by_name( mapping_elem.get( 'initial', 'default' ) )
|
||||
for action_elem in mapping_elem:
|
||||
map_source = action_elem.get( 'source', None )
|
||||
map_target = action_elem.get( 'target', None )
|
||||
preset = rval.get_mapping_by_name( action_elem.get( 'preset', 'none' ) )
|
||||
if action_elem.tag.lower() == 'add':
|
||||
rval._mapped_chars.update( preset )
|
||||
if None not in [ map_source, map_target ]:
|
||||
rval._mapped_chars[ map_source ] = map_target
|
||||
elif action_elem.tag.lower() == 'remove':
|
||||
for map_key in preset.keys():
|
||||
if map_key in rval._mapped_chars:
|
||||
del rval._mapped_chars[ map_key ]
|
||||
if map_source is not None and map_key in rval._mapped_chars:
|
||||
del rval._mapped_chars[ map_key ]
|
||||
else:
|
||||
log.debug( 'Invalid action tag in mapping: %s' % action_elem.tag )
|
||||
return rval
|
||||
|
||||
@classmethod
|
||||
def get_valid_by_name( cls, name ):
|
||||
rval = []
|
||||
for split_name in name.split( ',' ):
|
||||
split_name = split_name.strip()
|
||||
value = []
|
||||
if split_name.startswith( 'string.' ):
|
||||
try:
|
||||
value = eval( split_name )
|
||||
except NameError, e:
|
||||
log.debug( 'Invalid string preset specified: %s' % e )
|
||||
elif split_name in cls.VALID_PRESET:
|
||||
value = cls.VALID_PRESET[ split_name ]
|
||||
else:
|
||||
log.debug( 'Invalid preset name specified: %s' % split_name )
|
||||
rval.extend( [ val for val in value if val not in rval ] )
|
||||
return rval
|
||||
|
||||
@classmethod
|
||||
def get_mapping_by_name( cls, name ):
|
||||
rval = {}
|
||||
for split_name in name.split( ',' ):
|
||||
split_name = split_name.strip()
|
||||
if split_name in cls.MAPPING_PRESET:
|
||||
rval.update( cls.MAPPING_PRESET[ split_name ] )
|
||||
else:
|
||||
log.debug( 'Invalid preset name specified: %s' % split_name )
|
||||
return rval
|
||||
#end class methods
|
||||
|
||||
def __init__( self ):
|
||||
self._valid_chars = [] #List of valid characters
|
||||
self._mapped_chars = {} #Replace a char with a any number of characters
|
||||
self._invalid_char = self.DEFAULT_INVALID_CHAR #Replace invalid characters with this character
|
||||
self.sanitize = True #Simply pass back the passed in value
|
||||
|
||||
def restore_text( self, text ):
|
||||
"""Restores sanitized text"""
|
||||
if self.sanitize:
|
||||
for key, value in self._mapped_chars.iteritems():
|
||||
text = text.replace( value, key )
|
||||
return text
|
||||
|
||||
def restore_param( self, value ):
|
||||
if self.sanitize:
|
||||
if isinstance( value, basestring ):
|
||||
return self.restore_text( value )
|
||||
elif isinstance( value, list ):
|
||||
return map( self.restore_text, value )
|
||||
else:
|
||||
raise Exception, 'Unknown parameter type (%s:%s)' % ( type( value ), value )
|
||||
return value
|
||||
|
||||
def sanitize_text( self, text ):
|
||||
"""Restricts the characters that are allowed in a text"""
|
||||
if not self.sanitize:
|
||||
return text
|
||||
rval = []
|
||||
for c in text:
|
||||
if c in self._valid_chars:
|
||||
rval.append( c )
|
||||
elif c in self._mapped_chars:
|
||||
rval.append( self._mapped_chars[ c ] )
|
||||
else:
|
||||
rval.append( self._invalid_char )
|
||||
return ''.join( rval )
|
||||
|
||||
def sanitize_param( self, value ):
|
||||
"""Clean incoming parameters (strings or lists)"""
|
||||
if not self.sanitize:
|
||||
return value
|
||||
if isinstance( value, basestring ):
|
||||
return self.sanitize_text( value )
|
||||
elif isinstance( value, list ):
|
||||
return map( self.sanitize_text, value )
|
||||
else:
|
||||
raise Exception, 'Unknown parameter type (%s:%s)' % ( type( value ), value )
|
||||
@@ -174,70 +174,16 @@ class Params:
|
||||
[('status', 'on'), ('symbols', 'alpha'), ('symbols', '__lt____gt__'), ('symbols', 'XrmXX!')]
|
||||
"""
|
||||
|
||||
# HACK: Need top prevent sanitizing certain parameter types. The
|
||||
# better solution I think is to more responsibility for
|
||||
# sanitizing into the tool parameters themselves so that
|
||||
# different parameters can be sanitized in different ways.
|
||||
# is NEVER_SANITIZE required now that sanitizing for tool parameters can be controlled on a per parameter basis and occurs via InputValueWrappers?
|
||||
NEVER_SANITIZE = ['file_data', 'url_paste', 'URL', 'filesystem_paths']
|
||||
|
||||
def __init__( self, params, safe=True, sanitize=True, tool=None ):
|
||||
if safe:
|
||||
def __init__( self, params, sanitize=True ):
|
||||
if sanitize:
|
||||
for key, value in params.items():
|
||||
# Check to see if we should translate certain parameter names. For example,
|
||||
# in data_source tools, the external data source application may send back
|
||||
# parameter names like GENOME which is translated to dbkey in Galaxy.
|
||||
# param_trans_dict looks like { "GENOME" : [ "dbkey" "?" ] }
|
||||
new_key = key
|
||||
new_value = value
|
||||
if tool and tool.tool_type == 'data_source':
|
||||
if key in tool.param_trans_dict:
|
||||
new_key = tool.param_trans_dict[ key ][0]
|
||||
if new_key == 'data_type':
|
||||
try:
|
||||
# The Galaxy "data_type entry is special in that it can include the ability
|
||||
# to translate the format to a Galaxy supported format. In the dict, this entry
|
||||
# looks something like:
|
||||
# {'hgta_outputType': ['data_type', 'bed', {'selectedFields': 'tabular'}] }
|
||||
format_trans_dict = tool.param_trans_dict[ key ][2]
|
||||
if value in format_trans_dict:
|
||||
new_value = format_trans_dict[ value ]
|
||||
except:
|
||||
pass
|
||||
elif new_key == 'URL':
|
||||
# As above, the URL can include a set of params from the remote data source
|
||||
# that must be appended to the URL prior to the post. In this case, the
|
||||
# dict entry would look something like:
|
||||
# ['URL', '', {'q': '', 's': '', 'd': '', 'dbkey': '', 't': ''}]
|
||||
try:
|
||||
add_to_url_dict = tool.param_trans_dict[ key ][2]
|
||||
if new_value.count( '?' ) == 0:
|
||||
sep = '?'
|
||||
else:
|
||||
sep = '&'
|
||||
for param_name, missing_value in add_to_url_dict.items():
|
||||
param_value = params.get( param_name, None )
|
||||
if not param_value and missing_value:
|
||||
param_value = missing_value
|
||||
if param_value:
|
||||
new_value += '%s%s=%s' % ( sep, param_name, param_value )
|
||||
sep = '&'
|
||||
except:
|
||||
pass
|
||||
if not value and not new_value:
|
||||
new_value = tool.param_trans_dict[ key ][1]
|
||||
if sanitize and not ( key in self.NEVER_SANITIZE or True in [ key.endswith( "|%s" % nonsanitize_parameter ) for nonsanitize_parameter in self.NEVER_SANITIZE ] ): #sanitize check both ungrouped and grouped parameters by name
|
||||
self.__dict__[ new_key ] = sanitize_param( new_value )
|
||||
if key not in self.NEVER_SANITIZE and True not in [ key.endswith( "|%s" % nonsanitize_parameter ) for nonsanitize_parameter in self.NEVER_SANITIZE ]: #sanitize check both ungrouped and grouped parameters by name. Anything relying on NEVER_SANITIZE should be changed to not require this and NEVER_SANITIZE should be removed.
|
||||
self.__dict__[ key ] = sanitize_param( value )
|
||||
else:
|
||||
self.__dict__[ new_key ] = new_value
|
||||
if tool and tool.tool_type == 'data_source':
|
||||
# Add the tool's URL_method to params
|
||||
self.__dict__[ 'URL_method' ] = tool.URL_method
|
||||
for key, value in tool.param_trans_dict.items():
|
||||
# Make sure that all translated values used in Galaxy are added to the params
|
||||
galaxy_name = tool.param_trans_dict[ key ][0]
|
||||
if galaxy_name not in self.__dict__:
|
||||
# This will set the galaxy_name to the "missing" value
|
||||
self.__dict__[ galaxy_name ] = tool.param_trans_dict[ key ][1]
|
||||
self.__dict__[ key ] = value
|
||||
else:
|
||||
self.__dict__.update(params)
|
||||
|
||||
|
||||
@@ -32,7 +32,7 @@ class ASync( BaseController ):
|
||||
return trans.response.send_redirect( "/index" )
|
||||
|
||||
history = trans.get_history( create=True )
|
||||
params = util.Params(kwd, safe=False)
|
||||
params = util.Params(kwd, sanitize=False)
|
||||
STATUS = params.STATUS
|
||||
URL = params.URL
|
||||
data_id = params.data_id
|
||||
|
||||
@@ -270,7 +270,7 @@ class RootController( BaseController ):
|
||||
if trans.app.security_agent.can_access_dataset( roles, data.dataset ):
|
||||
if data.state == trans.model.Dataset.states.UPLOAD:
|
||||
return trans.show_error_message( "Please wait until this dataset finishes uploading before attempting to edit its metadata." )
|
||||
params = util.Params( kwd, safe=False )
|
||||
params = util.Params( kwd, sanitize=False )
|
||||
if params.change:
|
||||
# The user clicked the Save button on the 'Change data type' form
|
||||
if data.datatype.allow_datatype_change and trans.app.datatypes_registry.get_datatype_by_extension( params.datatype ).allow_datatype_change:
|
||||
|
||||
@@ -43,7 +43,10 @@ class ToolRunner( BaseController ):
|
||||
log.error( "index called with tool id '%s' but no such tool exists", tool_id )
|
||||
trans.log_event( "Tool id '%s' does not exist" % tool_id )
|
||||
return "Tool '%s' does not exist, kwd=%s " % (tool_id, kwd)
|
||||
params = util.Params( kwd, sanitize=tool.options.sanitize, tool=tool )
|
||||
params = util.Params( kwd, sanitize = False ) #Sanitize parameters when substituting into command line via input wrappers
|
||||
#do param translation here, used by datasource tools
|
||||
if tool.input_translator:
|
||||
tool.input_translator.translate( params )
|
||||
history = trans.get_history()
|
||||
template, vars = tool.handle_input( trans, params.__dict__ )
|
||||
if len(params) > 0:
|
||||
@@ -73,7 +76,7 @@ class ToolRunner( BaseController ):
|
||||
# Get the associated job, if any. If this hda was copied from another,
|
||||
# we need to find the job that created the origial hda
|
||||
job_hda = data
|
||||
while job_hda.copied_from_history_dataset_association:
|
||||
while job_hda.copied_from_history_dataset_association:#should this check library datasets as well?
|
||||
job_hda = job_hda.copied_from_history_dataset_association
|
||||
if not job_hda.creating_job_associations:
|
||||
error( "Could not find the job for this dataset" )
|
||||
@@ -153,7 +156,7 @@ class ToolRunner( BaseController ):
|
||||
tool = self.get_toolbox().tools_by_id.get( tool_id, None )
|
||||
if not tool:
|
||||
return False # bad tool_id
|
||||
nonfile_params = util.Params( kwd, sanitize=tool.options.sanitize, tool=tool )
|
||||
nonfile_params = util.Params( kwd, sanitize=False )
|
||||
if kwd.get( 'tool_state', None ) not in ( None, 'None' ):
|
||||
encoded_state = util.string_to_object( kwd["tool_state"] )
|
||||
tool_state = DefaultToolState()
|
||||
|
||||
+10
-10
@@ -1,10 +1,10 @@
|
||||
1 68 4.1
|
||||
2 71 4.6
|
||||
3 62 3.8
|
||||
4 75 4.4
|
||||
5 58 3.2
|
||||
6 60 3.1
|
||||
7 67 3.8
|
||||
8 68 4.1
|
||||
9 71 4.3
|
||||
10 69 3.7
|
||||
1 68 4.1
|
||||
2 71 4.6
|
||||
3 62 3.8
|
||||
4 75 4.4
|
||||
5 58 3.2
|
||||
6 60 3.1
|
||||
7 67 3.8
|
||||
8 68 4.1
|
||||
9 71 4.3
|
||||
10 69 3.7
|
||||
|
||||
@@ -7,7 +7,7 @@
|
||||
TODO: Hack to get biomart to work - the 'add_to_URL' param can be eliminated when the Biomart team encodes URL prior to sending, meanwhile
|
||||
everything including and beyond the first '&' is truncated from URL. They said they'll let us know when this is fixed at their end.
|
||||
-->
|
||||
<tool name="BioMart" id="biomart" tool_type="data_source" URL_method="get" version="1.0.1">
|
||||
<tool name="BioMart" id="biomart" tool_type="data_source" version="1.0.1">
|
||||
<description>Central server</description>
|
||||
<command interpreter="python">data_source.py $output $__app__.config.output_size_limit</command>
|
||||
<inputs action="http://www.biomart.org/biomart/martview" check_values="false" method="get" target="_top">
|
||||
@@ -16,16 +16,17 @@
|
||||
</inputs>
|
||||
<request_param_translation>
|
||||
<request_param galaxy_name="URL" remote_name="URL" missing="">
|
||||
<add_to_url>
|
||||
<param_from_source name="_export" missing="1" />
|
||||
<param_from_source name="GALAXY_URL" missing="0" />
|
||||
</add_to_url>
|
||||
<append_param separator="&" first_separator="?" join="=">
|
||||
<value name="_export" missing="1" />
|
||||
<value name="GALAXY_URL" missing="0" />
|
||||
</append_param>
|
||||
</request_param>
|
||||
<request_param galaxy_name="data_type" remote_name="exportView_outputformat" missing="tabular" >
|
||||
<data_type_translation>
|
||||
<format galaxy_format="tabular" remote_format="TSV" />
|
||||
</data_type_translation>
|
||||
<value_translation>
|
||||
<value galaxy_value="tabular" remote_value="TSV" />
|
||||
</value_translation>
|
||||
</request_param>
|
||||
<request_param galaxy_name="URL_method" remote_name="URL_method" missing="get" />
|
||||
<request_param galaxy_name="dbkey" remote_name="dbkey" missing="?" />
|
||||
<request_param galaxy_name="organism" remote_name="organism" missing="" />
|
||||
<request_param galaxy_name="table" remote_name="table" missing="" />
|
||||
|
||||
@@ -7,7 +7,7 @@
|
||||
TODO: Hack to get biomart to work - the 'add_to_URL' param can be eliminated when the Biomart team encodes URL prior to sending, meanwhile
|
||||
everything including and beyond the first '&' is truncated from URL. They said they'll let us know when this is fixed at their end.
|
||||
-->
|
||||
<tool name="BioMart" id="biomart_test" tool_type="data_source" URL_method="get" version="1.0.1">
|
||||
<tool name="BioMart" id="biomart_test" tool_type="data_source" version="1.0.1">
|
||||
<description>Test server</description>
|
||||
<command interpreter="python">data_source.py $output $__app__.config.output_size_limit</command>
|
||||
<inputs action="http://test.biomart.org/biomart/martview" check_values="false" method="get" target="_top">
|
||||
@@ -16,16 +16,17 @@
|
||||
</inputs>
|
||||
<request_param_translation>
|
||||
<request_param galaxy_name="URL" remote_name="URL" missing="">
|
||||
<add_to_url>
|
||||
<param_from_source name="_export" missing="1" />
|
||||
<param_from_source name="GALAXY_URL" missing="0" />
|
||||
</add_to_url>
|
||||
<append_param separator="&" first_separator="?" join="=">
|
||||
<value name="_export" missing="1" />
|
||||
<value name="GALAXY_URL" missing="0" />
|
||||
</append_param>
|
||||
</request_param>
|
||||
<request_param galaxy_name="data_type" remote_name="exportView_outputformat" missing="tabular" >
|
||||
<data_type_translation>
|
||||
<format galaxy_format="tabular" remote_format="TSV" />
|
||||
</data_type_translation>
|
||||
<value_translation>
|
||||
<value galaxy_value="tabular" remote_value="TSV" />
|
||||
</value_translation>
|
||||
</request_param>
|
||||
<request_param galaxy_name="URL_method" remote_name="URL_method" missing="get" />
|
||||
<request_param galaxy_name="dbkey" remote_name="dbkey" missing="?" />
|
||||
<request_param galaxy_name="organism" remote_name="organism" missing="" />
|
||||
<request_param galaxy_name="table" remote_name="table" missing="" />
|
||||
|
||||
@@ -4,7 +4,7 @@
|
||||
the initial response. If value of 'URL_method' is 'post', any additional params coming back in the
|
||||
initial response ( in addition to 'URL' ) will be encoded and appended to URL and a post will be performed.
|
||||
-->
|
||||
<tool name="EpiGRAPH" id="epigraph_import" tool_type="data_source" URL_method="get">
|
||||
<tool name="EpiGRAPH" id="epigraph_import" tool_type="data_source">
|
||||
<description> server</description>
|
||||
<command interpreter="python">data_source.py $output $__app__.config.output_size_limit</command>
|
||||
<inputs action="http://epigraph.mpi-inf.mpg.de/WebGRAPH/faces/Login.jsp" check_values="false" method="get">
|
||||
@@ -12,6 +12,7 @@
|
||||
<param name="GALAXY_URL" type="baseurl" value="/tool_runner?tool_id=epigraph_import" />
|
||||
</inputs>
|
||||
<request_param_translation>
|
||||
<request_param galaxy_name="URL_method" remote_name="URL_method" missing="get" />
|
||||
<request_param galaxy_name="URL" remote_name="URL" missing="" />
|
||||
<request_param galaxy_name="dbkey" remote_name="GENOME" missing="?" />
|
||||
<request_param galaxy_name="organism" remote_name="organism" missing="" />
|
||||
|
||||
@@ -4,7 +4,7 @@
|
||||
the initial response. If value of 'URL_method' is 'post', any additional params coming back in the
|
||||
initial response ( in addition to 'URL' ) will be encoded and appended to URL and a post will be performed.
|
||||
-->
|
||||
<tool name="EpiGRAPH" id="epigraph_import_test" tool_type="data_source" URL_method="get">
|
||||
<tool name="EpiGRAPH" id="epigraph_import_test" tool_type="data_source">
|
||||
<description> test server</description>
|
||||
<command interpreter="python">data_source.py $output $__app__.config.output_size_limit</command>
|
||||
<inputs action="http://epigraph.mpi-inf.mpg.de/WebGRAPH_Public_Test/faces/Login.jsp" check_values="false" method="get">
|
||||
@@ -12,6 +12,7 @@
|
||||
<param name="GALAXY_URL" type="baseurl" value="/tool_runner?tool_id=epigraph_import_test" />
|
||||
</inputs>
|
||||
<request_param_translation>
|
||||
<request_param galaxy_name="URL_method" remote_name="URL_method" missing="get" />
|
||||
<request_param galaxy_name="URL" remote_name="URL" missing="" />
|
||||
<request_param galaxy_name="dbkey" remote_name="GENOME" missing="?" />
|
||||
<request_param galaxy_name="organism" remote_name="organism" missing="" />
|
||||
|
||||
@@ -3,7 +3,7 @@
|
||||
the initial response. If value of 'URL_method' is 'post', any additional params coming back in the
|
||||
initial response ( in addition to 'URL' ) will be encoded and appended to URL and a post will be performed.
|
||||
-->
|
||||
<tool name="EuPathDB" id="eupathdb" tool_type="data_source" url_method="post">
|
||||
<tool name="EuPathDB" id="eupathdb" tool_type="data_source">
|
||||
<description>server</description>
|
||||
<command interpreter="python">data_source.py $output $__app__.config.output_size_limit</command>
|
||||
<inputs action="http://galaxy.eupathdb.org/eupathdb.galaxy/queries_tools.jsp" check_values="false" method="post">
|
||||
@@ -11,15 +11,16 @@
|
||||
<param name="GALAXY_URL" type="baseurl" value="/tool_runner?tool_id=eupathdb" />
|
||||
</inputs>
|
||||
<request_param_translation>
|
||||
<request_param galaxy_name="URL_method" remote_name="URL_method" missing="post" />
|
||||
<request_param galaxy_name="URL" remote_name="URL" missing="">
|
||||
<add_to_url>
|
||||
<param_from_source name="dbkey" missing="?" />
|
||||
<param_from_source name="wdk_history_id" missing="" />
|
||||
<param_from_source name="wdkReportFormat" missing="tabular" />
|
||||
<param_from_source name="selectedFields" missing="" />
|
||||
<param_from_source name="includeHeader" missing="yes" />
|
||||
<param_from_source name="downloadType" missing="plain" />
|
||||
</add_to_url>
|
||||
<append_param separator="&" first_separator="?" join="=">
|
||||
<value name="dbkey" missing="?" />
|
||||
<value name="wdk_history_id" missing="" />
|
||||
<value name="wdkReportFormat" missing="tabular" />
|
||||
<value name="selectedFields" missing="" />
|
||||
<value name="includeHeader" missing="yes" />
|
||||
<value name="downloadType" missing="plain" />
|
||||
</append_param>
|
||||
</request_param>
|
||||
<request_param galaxy_name="format" remote_name="wdkReportFormat" missing="tabular" />
|
||||
<request_param galaxy_name="dbkey" remote_name="dbkey" missing="?" />
|
||||
|
||||
@@ -4,7 +4,7 @@
|
||||
the initial response. If value of 'URL_method' is 'post', any additional params coming back in the
|
||||
initial response ( in addition to 'URL' ) will be encoded and appended to URL and a post will be performed.
|
||||
-->
|
||||
<tool name="Flymine" id="flymine" tool_type="data_source" URL_method="post">
|
||||
<tool name="Flymine" id="flymine" tool_type="data_source">
|
||||
<description>server</description>
|
||||
<command interpreter="python">data_source.py $output $__app__.config.output_size_limit</command>
|
||||
<inputs action="http://www.flymine.org" check_values="false" method="get" target="_top">
|
||||
@@ -12,6 +12,7 @@
|
||||
<param name="GALAXY_URL" type="baseurl" value="/tool_runner?tool_id=flymine" />
|
||||
</inputs>
|
||||
<request_param_translation>
|
||||
<request_param galaxy_name="URL_method" remote_name="URL_method" missing="post" />
|
||||
<request_param galaxy_name="URL" remote_name="URL" missing="" />
|
||||
<request_param galaxy_name="dbkey" remote_name="db" missing="?" />
|
||||
<request_param galaxy_name="organism" remote_name="organism" missing="" />
|
||||
|
||||
@@ -4,7 +4,7 @@
|
||||
the initial response. If value of 'URL_method' is 'post', any additional params coming back in the
|
||||
initial response ( in addition to 'URL' ) will be encoded and appended to URL and a post will be performed.
|
||||
-->
|
||||
<tool name="Flymine test" id="flymine_test" tool_type="data_source" URL_method="post">
|
||||
<tool name="Flymine test" id="flymine_test" tool_type="data_source">
|
||||
<description>server</description>
|
||||
<command interpreter="python">data_source.py $output $__app__.config.output_size_limit</command>
|
||||
<inputs action="http://preview.flymine.org/preview/begin.do" check_values="false" method="get" target="_top">
|
||||
@@ -12,6 +12,7 @@
|
||||
<param name="GALAXY_URL" type="baseurl" value="/tool_runner?tool_id=flymine" />
|
||||
</inputs>
|
||||
<request_param_translation>
|
||||
<request_param galaxy_name="URL_method" remote_name="URL_method" missing="post" />
|
||||
<request_param galaxy_name="URL" remote_name="URL" missing="" />
|
||||
<request_param galaxy_name="dbkey" remote_name="db" missing="?" />
|
||||
<request_param galaxy_name="organism" remote_name="organism" missing="" />
|
||||
|
||||
@@ -7,7 +7,7 @@
|
||||
TODO: Hack to get biomart to work - the 'add_to_URL' param can be eliminated when the Biomart team encodes URL prior to sending, meanwhile
|
||||
everything including and beyond the first '&' is truncated from URL. They said they'll let us know when this is fixed at their end.
|
||||
-->
|
||||
<tool name="GrameneMart" id="gramenemart" tool_type="data_source" URL_method="get" version="1.0.1">
|
||||
<tool name="GrameneMart" id="gramenemart" tool_type="data_source" version="1.0.1">
|
||||
<description> Central server</description>
|
||||
<command interpreter="python">data_source.py $output $__app__.config.output_size_limit</command>
|
||||
<inputs action="http://www.gramene.org/biomart/martview" check_values="false" method="get" target="_top">
|
||||
@@ -16,16 +16,17 @@
|
||||
</inputs>
|
||||
<request_param_translation>
|
||||
<request_param galaxy_name="URL" remote_name="URL" missing="">
|
||||
<add_to_url>
|
||||
<param_from_source name="_export" missing="1" />
|
||||
<param_from_source name="GALAXY_URL" missing="0" />
|
||||
</add_to_url>
|
||||
<append_param separator="&" first_separator="?" join="=">
|
||||
<value name="_export" missing="1" />
|
||||
<value name="GALAXY_URL" missing="0" />
|
||||
</append_param>
|
||||
</request_param>
|
||||
<request_param galaxy_name="data_type" remote_name="exportView_outputformat" missing="tabular">
|
||||
<data_type_translation>
|
||||
<format galaxy_format="tabular" remote_format="TSV" />
|
||||
</data_type_translation>
|
||||
<value_translation>
|
||||
<value galaxy_value="tabular" remote_value="TSV" />
|
||||
</value_translation>
|
||||
</request_param>
|
||||
<request_param galaxy_name="URL_method" remote_name="URL_method" missing="get" />
|
||||
<request_param galaxy_name="dbkey" remote_name="dbkey" missing="?" />
|
||||
<request_param galaxy_name="organism" remote_name="organism" missing="" />
|
||||
<request_param galaxy_name="table" remote_name="table" missing="" />
|
||||
|
||||
@@ -4,7 +4,7 @@
|
||||
the initial response. If value of 'URL_method' is 'post', any additional params coming back in the
|
||||
initial response ( in addition to 'URL' ) will be encoded and appended to URL and a post will be performed.
|
||||
-->
|
||||
<tool name="modMine" id="modmine" tool_type="data_source" URL_method="post">
|
||||
<tool name="modMine" id="modmine" tool_type="data_source">
|
||||
<description>server</description>
|
||||
<command interpreter="python">data_source.py $output $__app__.config.output_size_limit</command>
|
||||
<inputs action="http://intermine.modencode.org/" check_values="false" method="get" target="_top">
|
||||
@@ -12,6 +12,7 @@
|
||||
<param name="GALAXY_URL" type="baseurl" value="/tool_runner?tool_id=modmine" />
|
||||
</inputs>
|
||||
<request_param_translation>
|
||||
<request_param galaxy_name="URL_method" remote_name="URL_method" missing="post" />
|
||||
<request_param galaxy_name="URL" remote_name="URL" missing="" />
|
||||
<request_param galaxy_name="dbkey" remote_name="db" missing="?" />
|
||||
<request_param galaxy_name="organism" remote_name="organism" missing="" />
|
||||
|
||||
@@ -4,7 +4,7 @@
|
||||
the initial response. If value of 'URL_method' is 'post', any additional params coming back in the
|
||||
initial response ( in addition to 'URL' ) will be encoded and appended to URL and a post will be performed.
|
||||
-->
|
||||
<tool name="Ratmine" id="ratmine" tool_type="data_source" URL_method="post">
|
||||
<tool name="Ratmine" id="ratmine" tool_type="data_source">
|
||||
<description>server</description>
|
||||
<command interpreter="python">data_source.py $output $__app__.config.output_size_limit</command>
|
||||
<inputs action="http://ratmine.mcw.edu/ratmine/begin.do" check_values="false" method="get" target="_top">
|
||||
@@ -12,6 +12,7 @@
|
||||
<param name="GALAXY_URL" type="baseurl" value="/tool_runner?tool_id=ratmine" />
|
||||
</inputs>
|
||||
<request_param_translation>
|
||||
<request_param galaxy_name="URL_method" remote_name="URL_method" missing="post" />
|
||||
<request_param galaxy_name="URL" remote_name="URL" missing="" />
|
||||
<request_param galaxy_name="dbkey" remote_name="db" missing="?" />
|
||||
<request_param galaxy_name="organism" remote_name="organism" missing="" />
|
||||
|
||||
@@ -4,7 +4,7 @@
|
||||
the initial response. If value of 'URL_method' is 'post', any additional params coming back in the
|
||||
initial response ( in addition to 'URL' ) will be encoded and appended to URL and a post will be performed.
|
||||
-->
|
||||
<tool name="UCSC Main" id="ucsc_table_direct1" tool_type="data_source" URL_method="post">
|
||||
<tool name="UCSC Main" id="ucsc_table_direct1" tool_type="data_source">
|
||||
<description>table browser</description>
|
||||
<command interpreter="python">data_source.py $output $__app__.config.output_size_limit</command>
|
||||
<inputs action="http://genome.ucsc.edu/cgi-bin/hgTables" check_values="false" method="get">
|
||||
@@ -16,20 +16,21 @@
|
||||
<param name="hgta_outputType" type="hidden" value="bed" />
|
||||
</inputs>
|
||||
<request_param_translation>
|
||||
<request_param galaxy_name="URL_method" remote_name="URL_method" missing="post" />
|
||||
<request_param galaxy_name="URL" remote_name="URL" missing="" />
|
||||
<request_param galaxy_name="dbkey" remote_name="db" missing="?" />
|
||||
<request_param galaxy_name="organism" remote_name="org" missing="unknown species" />
|
||||
<request_param galaxy_name="table" remote_name="hgta_table" missing="unknown table" />
|
||||
<request_param galaxy_name="description" remote_name="hgta_regionType" missing="no description" />
|
||||
<request_param galaxy_name="data_type" remote_name="hgta_outputType" missing="tabular" >
|
||||
<data_type_translation>
|
||||
<format galaxy_format="tabular" remote_format="primaryTable" />
|
||||
<format galaxy_format="tabular" remote_format="selectedFields" />
|
||||
<format galaxy_format="wig" remote_format="wigData" />
|
||||
<format galaxy_format="interval" remote_format="tab" />
|
||||
<format galaxy_format="html" remote_format="hyperlinks" />
|
||||
<format galaxy_format="fasta" remote_format="sequence" />
|
||||
</data_type_translation>
|
||||
<value_translation>
|
||||
<value galaxy_value="tabular" remote_value="primaryTable" />
|
||||
<value galaxy_value="tabular" remote_value="selectedFields" />
|
||||
<value galaxy_value="wig" remote_value="wigData" />
|
||||
<value galaxy_value="interval" remote_value="tab" />
|
||||
<value galaxy_value="html" remote_value="hyperlinks" />
|
||||
<value galaxy_value="fasta" remote_value="sequence" />
|
||||
</value_translation>
|
||||
</request_param>
|
||||
</request_param_translation>
|
||||
<uihints minwidth="800"/>
|
||||
|
||||
@@ -4,7 +4,7 @@
|
||||
the initial response. If value of 'URL_method' is 'post', any additional params coming back in the
|
||||
initial response ( in addition to 'URL' ) will be encoded and appended to URL and a post will be performed.
|
||||
-->
|
||||
<tool name="UCSC Archaea" id="ucsc_table_direct_archaea1" tool_type="data_source" URL_method="post">
|
||||
<tool name="UCSC Archaea" id="ucsc_table_direct_archaea1" tool_type="data_source">
|
||||
<description>table browser</description>
|
||||
<command interpreter="python">data_source.py $output $__app__.config.output_size_limit</command>
|
||||
<inputs action="http://archaea.ucsc.edu/cgi-bin/hgTables" check_values="false" method="get">
|
||||
@@ -16,20 +16,21 @@
|
||||
<param name="hgta_outputType" type="hidden" value="bed" />
|
||||
</inputs>
|
||||
<request_param_translation>
|
||||
<request_param galaxy_name="URL_method" remote_name="URL_method" missing="post" />
|
||||
<request_param galaxy_name="URL" remote_name="URL" missing="" />
|
||||
<request_param galaxy_name="dbkey" remote_name="db" missing="?" />
|
||||
<request_param galaxy_name="organism" remote_name="org" missing="unknown species" />
|
||||
<request_param galaxy_name="table" remote_name="hgta_track" missing="" />
|
||||
<request_param galaxy_name="description" remote_name="hgta_regionType" missing="" />
|
||||
<request_param galaxy_name="table" remote_name="hgta_table" missing="unknown table" />
|
||||
<request_param galaxy_name="description" remote_name="hgta_regionType" missing="no description" />
|
||||
<request_param galaxy_name="data_type" remote_name="hgta_outputType" missing="tabular" >
|
||||
<data_type_translation>
|
||||
<format galaxy_format="tabular" remote_format="primaryTable" />
|
||||
<format galaxy_format="tabular" remote_format="selectedFields" />
|
||||
<format galaxy_format="wig" remote_format="wigdata" />
|
||||
<format galaxy_format="interval" remote_format="tab" />
|
||||
<format galaxy_format="html" remote_format="hyperlinks" />
|
||||
<format galaxy_format="fasta" remote_format="sequence" />
|
||||
</data_type_translation>
|
||||
<value_translation>
|
||||
<value galaxy_value="tabular" remote_value="primaryTable" />
|
||||
<value galaxy_value="tabular" remote_value="selectedFields" />
|
||||
<value galaxy_value="wig" remote_value="wigData" />
|
||||
<value galaxy_value="interval" remote_value="tab" />
|
||||
<value galaxy_value="html" remote_value="hyperlinks" />
|
||||
<value galaxy_value="fasta" remote_value="sequence" />
|
||||
</value_translation>
|
||||
</request_param>
|
||||
</request_param_translation>
|
||||
<uihints minwidth="800"/>
|
||||
|
||||
@@ -4,7 +4,7 @@
|
||||
the initial response. If value of 'URL_method' is 'post', any additional params coming back in the
|
||||
initial response ( in addition to 'URL' ) will be encoded and appended to URL and a post will be performed.
|
||||
-->
|
||||
<tool name="UCSC Test" id="ucsc_table_direct_test1" tool_type="data_source" URL_method="post">
|
||||
<tool name="UCSC Test" id="ucsc_table_direct_test1" tool_type="data_source">
|
||||
<description>table browser</description>
|
||||
<command interpreter="python">data_source.py $output $__app__.config.output_size_limit</command>
|
||||
<inputs action="http://genome-test.cse.ucsc.edu/cgi-bin/hgTables" check_values="false" method="get">
|
||||
@@ -16,20 +16,21 @@
|
||||
<param name="hgta_outputType" type="hidden" value="bed" />
|
||||
</inputs>
|
||||
<request_param_translation>
|
||||
<request_param galaxy_name="URL_method" remote_name="URL_method" missing="post" />
|
||||
<request_param galaxy_name="URL" remote_name="URL" missing="" />
|
||||
<request_param galaxy_name="dbkey" remote_name="db" missing="?" />
|
||||
<request_param galaxy_name="organism" remote_name="org" missing="unknown species" />
|
||||
<request_param galaxy_name="table" remote_name="hgta_track" missing="" />
|
||||
<request_param galaxy_name="description" remote_name="hgta_regionType" missing="" />
|
||||
<request_param galaxy_name="table" remote_name="hgta_table" missing="unknown table" />
|
||||
<request_param galaxy_name="description" remote_name="hgta_regionType" missing="no description" />
|
||||
<request_param galaxy_name="data_type" remote_name="hgta_outputType" missing="tabular" >
|
||||
<data_type_translation>
|
||||
<format galaxy_format="tabular" remote_format="primaryTable" />
|
||||
<format galaxy_format="tabular" remote_format="selectedFields" />
|
||||
<format galaxy_format="wig" remote_format="wigdata" />
|
||||
<format galaxy_format="interval" remote_format="tab" />
|
||||
<format galaxy_format="html" remote_format="hyperlinks" />
|
||||
<format galaxy_format="fasta" remote_format="sequence" />
|
||||
</data_type_translation>
|
||||
<value_translation>
|
||||
<value galaxy_value="tabular" remote_value="primaryTable" />
|
||||
<value galaxy_value="tabular" remote_value="selectedFields" />
|
||||
<value galaxy_value="wig" remote_value="wigData" />
|
||||
<value galaxy_value="interval" remote_value="tab" />
|
||||
<value galaxy_value="html" remote_value="hyperlinks" />
|
||||
<value galaxy_value="fasta" remote_value="sequence" />
|
||||
</value_translation>
|
||||
</request_param>
|
||||
</request_param_translation>
|
||||
<uihints minwidth="800"/>
|
||||
|
||||
@@ -1,5 +1,5 @@
|
||||
<?xml version="1.0"?>
|
||||
<tool name="Wormbase" id="wormbase" tool_type="data_source" URL_method="post">
|
||||
<tool name="Wormbase" id="wormbase" tool_type="data_source">
|
||||
<description>server</description>
|
||||
<command interpreter="python">data_source.py $output $__app__.config.output_size_limit</command>
|
||||
<inputs action="http://www.wormbase.org/db/seq/gbgff/c_elegans/" check_values="false" target="_top">
|
||||
@@ -8,14 +8,15 @@
|
||||
</inputs>
|
||||
<request_param_translation>
|
||||
<request_param galaxy_name="URL" remote_name="URL" missing="">
|
||||
<add_to_url>
|
||||
<param_from_source name="d" missing="" />
|
||||
<param_from_source name="dbkey" missing="" />
|
||||
<param_from_source name="q" missing="" />
|
||||
<param_from_source name="s" missing="" />
|
||||
<param_from_source name="t" missing="" />
|
||||
</add_to_url>
|
||||
<append_param separator="&" first_separator="?" join="=">
|
||||
<value name="d" missing="" />
|
||||
<value name="dbkey" missing="" />
|
||||
<value name="q" missing="" />
|
||||
<value name="s" missing="" />
|
||||
<value name="t" missing="" />
|
||||
</append_param>
|
||||
</request_param>
|
||||
<request_param galaxy_name="URL_method" remote_name="URL_method" missing="post" />
|
||||
<request_param galaxy_name="data_type" remote_name="data_type" missing="txt" />
|
||||
</request_param_translation>
|
||||
<uihints minwidth="800"/>
|
||||
|
||||
@@ -1,5 +1,5 @@
|
||||
<?xml version="1.0"?>
|
||||
<tool name="Wormbase" id="wormbase_test" tool_type="data_source" URL_method="post">
|
||||
<tool name="Wormbase" id="wormbase_test" tool_type="data_source">
|
||||
<description>test server</description>
|
||||
<command interpreter="python">data_source.py $output $__app__.config.output_size_limit</command>
|
||||
<inputs action="http://dev.wormbase.org/db/seq/gbrowse/c_elegans/" check_values="false" target="_top">
|
||||
@@ -8,14 +8,15 @@
|
||||
</inputs>
|
||||
<request_param_translation>
|
||||
<request_param galaxy_name="URL" remote_name="URL" missing="">
|
||||
<add_to_url>
|
||||
<param_from_source name="d" missing="" />
|
||||
<param_from_source name="dbkey" missing="" />
|
||||
<param_from_source name="q" missing="" />
|
||||
<param_from_source name="s" missing="" />
|
||||
<param_from_source name="t" missing="" />
|
||||
</add_to_url>
|
||||
<append_param separator="&" first_separator="?" join="=">
|
||||
<value name="d" missing="" />
|
||||
<value name="dbkey" missing="" />
|
||||
<value name="q" missing="" />
|
||||
<value name="s" missing="" />
|
||||
<value name="t" missing="" />
|
||||
</append_param>
|
||||
</request_param>
|
||||
<request_param galaxy_name="URL_method" remote_name="URL_method" missing="post" />
|
||||
<request_param galaxy_name="data_type" remote_name="data_type" missing="txt" />
|
||||
</request_param_translation>
|
||||
<uihints minwidth="800"/>
|
||||
|
||||
@@ -1,12 +1,20 @@
|
||||
<tool id="EMBOSS: fuzznuc37" name="fuzznuc" version="5.0.0">
|
||||
<tool id="EMBOSS: fuzznuc37" name="fuzznuc" version="5.0.1">
|
||||
<description>Nucleic acid pattern search</description>
|
||||
<command>fuzznuc -sequence $input1 -outfile $out_file1 -pattern "$pattern" -pmismatch $mismatch -complement $complement -rformat2 $out_format1 -auto</command>
|
||||
<command>fuzznuc -sequence $input1 -outfile $out_file1 -pattern '$pattern' -pmismatch $mismatch -complement $complement -rformat2 $out_format1 -auto</command>
|
||||
<inputs>
|
||||
<param format="fasta" name="input1" type="data">
|
||||
<label>Sequences</label>
|
||||
</param>
|
||||
<param name="pattern" size="5" type="text" value="">
|
||||
<label>Search pattern</label>
|
||||
<sanitizer>
|
||||
<valid initial="string.printable">
|
||||
<remove value="'"/>
|
||||
</valid>
|
||||
<mapping initial="none">
|
||||
<add source="'" target=""/>
|
||||
</mapping>
|
||||
</sanitizer>
|
||||
</param>
|
||||
<param name="mismatch" size="5" type="text" value="0">
|
||||
<label>Number of mismatches</label>
|
||||
|
||||
+27
-14
@@ -13,9 +13,11 @@
|
||||
# -v true or false (output NON-matching lines)
|
||||
|
||||
import sys
|
||||
import os
|
||||
import re
|
||||
import string
|
||||
import commands
|
||||
from tempfile import NamedTemporaryFile
|
||||
|
||||
# This function is exceedingly useful, perhaps package for reuse?
|
||||
def getopts(argv):
|
||||
@@ -72,17 +74,15 @@ def main():
|
||||
'[' :'__ob__',
|
||||
']' :'__cb__',
|
||||
'{' :'__oc__',
|
||||
'}' :'__cc__',
|
||||
|
||||
'}' :'__cc__'
|
||||
}
|
||||
|
||||
|
||||
#with new sanitizing we only need to replace for single quote, but this needs to remain for backwards compatibility
|
||||
for key, value in mapped_chars.items():
|
||||
pattern = pattern.replace(value, key)
|
||||
|
||||
pattern = pattern.replace('\'', '')
|
||||
|
||||
fileRegEx = re.compile("^[A-Za-z0-9./\-_]+$")
|
||||
invertRegEx = re.compile("(true)|(false)")
|
||||
|
||||
fileRegEx = re.compile("^[A-Za-z0-9./\-_]+$") #why?
|
||||
invertRegEx = re.compile("(true)|(false)") #why?
|
||||
|
||||
if not fileRegEx.match(outputfile):
|
||||
print "Illegal output filename."
|
||||
@@ -94,16 +94,29 @@ def main():
|
||||
print "Illegal invert option."
|
||||
return -7
|
||||
|
||||
# grep
|
||||
# invert grep search?
|
||||
if invert == "true":
|
||||
invertflag = " -v"
|
||||
invertflag = " -v"
|
||||
print "Not matching pattern: %s" % pattern
|
||||
else:
|
||||
invertflag = ""
|
||||
|
||||
commandline = "grep -E"+invertflag+" '"+pattern+"' "+inputfile+" > "+outputfile
|
||||
|
||||
invertflag = ""
|
||||
print "Matching pattern: %s" % pattern
|
||||
|
||||
#Create temp file holding pattern
|
||||
#By using a file to hold the pattern, we don't have worry about sanitizing grep commandline and can include single quotes in pattern
|
||||
pattern_file_name = NamedTemporaryFile().name
|
||||
open( pattern_file_name, 'w' ).write( pattern )
|
||||
|
||||
#generate grep command
|
||||
commandline = "grep -E %s -f %s %s > %s" % ( invertflag, pattern_file_name, inputfile, outputfile )
|
||||
|
||||
#run grep
|
||||
errorcode, stdout = commands.getstatusoutput(commandline)
|
||||
|
||||
#remove temp pattern file
|
||||
os.unlink( pattern_file_name )
|
||||
|
||||
#return error code
|
||||
return errorcode
|
||||
|
||||
if __name__ == "__main__":
|
||||
|
||||
+11
-2
@@ -1,4 +1,4 @@
|
||||
<tool id="Grep1" name="Select">
|
||||
<tool id="Grep1" name="Select" version="1.0.1">
|
||||
<description>lines that match an expression</description>
|
||||
<command interpreter="python">grep.py -i $input -o $out_file1 -pattern '$pattern' -v $invert</command>
|
||||
<inputs>
|
||||
@@ -7,7 +7,16 @@
|
||||
<option value="false">Matching</option>
|
||||
<option value="true">NOT Matching</option>
|
||||
</param>
|
||||
<param name="pattern" size="40" type="text" value="^chr([0-9A-Za-z])+" label="the pattern" help="here you can enter text or regular expression (for syntax check lower part of this frame)"/>
|
||||
<param name="pattern" size="40" type="text" value="^chr([0-9A-Za-z])+" label="the pattern" help="here you can enter text or regular expression (for syntax check lower part of this frame)">
|
||||
<sanitizer>
|
||||
<valid initial="string.printable">
|
||||
<remove value="'"/>
|
||||
</valid>
|
||||
<mapping initial="none">
|
||||
<add source="'" target="__sq__"/>
|
||||
</mapping>
|
||||
</sanitizer>
|
||||
</param>
|
||||
</inputs>
|
||||
<outputs>
|
||||
<data format="input" name="out_file1" metadata_source="input"/>
|
||||
|
||||
@@ -1,4 +1,4 @@
|
||||
<tool id="join1" name="Join two Queries" version="2.0.1">
|
||||
<tool id="join1" name="Join two Queries" version="2.0.2">
|
||||
<description>side by side on a specified field</description>
|
||||
<command interpreter="python">join.py $input1 $input2 $field1 $field2 $out_file1 $unmatched $partial --index_depth=3 --buffer=50000000 --fill_options_file=$fill_options_file</command>
|
||||
<inputs>
|
||||
|
||||
@@ -94,9 +94,7 @@
|
||||
<outputs>
|
||||
<data format="pdf" name="out_file1" />
|
||||
</outputs>
|
||||
<!--
|
||||
TODO: figure out how to change the submit_form() method to correctly handle refreshing the
|
||||
form when the input for refresh is within a repeat construct ( like this tool )
|
||||
|
||||
<tests>
|
||||
<test>
|
||||
<param name="main" value="Example XY Plot"/>
|
||||
@@ -106,13 +104,12 @@
|
||||
<param name="xcol" value="1"/>
|
||||
<param name="ycol" value="2"/>
|
||||
<param name="type" value="line"/>
|
||||
<param name="lty" value="dashed"/>
|
||||
<param name="lty" value="2"/>
|
||||
<param name="col" value="2"/>
|
||||
<param name="lwd" value="1.0"/>
|
||||
<output name="out_file1" file="XY_Plot_1_out.pdf"/>
|
||||
</test>
|
||||
</tests>
|
||||
-->
|
||||
<help>
|
||||
.. class:: infomark
|
||||
|
||||
|
||||
Reference in New Issue
Block a user