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https://github.com/galaxyproject/galaxy.git
synced 2026-09-24 16:30:27 +08:00
- Fixed the MetadataMissingValidator and added a new UnspecifiedBuildValidator.
- Added the UnspecifiedBuildValidator to several tools. - Added is_dynamic and get_dependencies() to DataToolParameter.
This commit is contained in:
Greg Von Kuster
@@ -769,7 +769,7 @@ class Tool:
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errors[ input.name ] = old_errors[ input.name ]
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else:
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incoming_value = incoming.get( key, None )
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if ( incoming_value == 'None' or incoming_value == '?' ) and isinstance( input, SelectToolParameter ) and input.is_dynamic:
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if ( incoming_value == 'None' or incoming_value == '?' ) and ( isinstance( input, SelectToolParameter ) or isinstance( input, DataToolParameter ) ) and input.is_dynamic:
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# FIXME: This is a HACK, but is necessary because the
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# values in incoming are not yet set by the user when
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# the select list is dynamically generated.
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@@ -746,7 +746,8 @@ class DataToolParameter( ToolParameter ):
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if options is None:
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self.options = None
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else:
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self.options = dynamic_options.DynamicOptions( options, parameter_type = type( self ) )
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self.options = dynamic_options.DynamicOptions( options, parameter_type=type( self ) )
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self.is_dynamic = self.options is not None
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def get_html_field( self, trans=None, value=None, other_values={} ):
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filter_key = filter_value = None
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@@ -756,7 +757,8 @@ class DataToolParameter( ToolParameter ):
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history = trans.history
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assert history is not None, "DataToolParameter requires a history"
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if value is not None:
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if type( value ) != list: value = [ value ]
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if type( value ) != list:
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value = [ value ]
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field = form_builder.SelectField( self.name, self.multiple, None, self.refresh_on_change )
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# CRUCIAL: the dataset_collector function needs to be local to DataToolParameter.get_html_field()
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def dataset_collector( datasets, parent_hid ):
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@@ -775,13 +777,11 @@ class DataToolParameter( ToolParameter ):
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dataset_collector( history.datasets, None )
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some_data = bool( field.options )
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if some_data:
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if value is None:
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if value is None or len( field.options ) == 1:
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# Ensure that the last item is always selected
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a, b, c = field.options[-1]; field.options[-1] = a, b, True
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else:
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# HACK: we should just disable the form or something
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field.add_option( "no data has the proper type", '' )
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if self.optional == True:
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a, b, c = field.options[-1]
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field.options[-1] = a, b, True
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elif self.optional:
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field.add_option( "Selection is Optional", 'None', True )
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return field
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@@ -823,7 +823,7 @@ class DataToolParameter( ToolParameter ):
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if trans.workflow_building_mode:
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return None
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if not value:
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raise ValueError( "A data of the appropriate type is required" )
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raise ValueError( "History does not include a dataset of the required format / build" )
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if value in [None, "None"]:
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temp_data = trans.app.model.Dataset( extension = 'data' )
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temp_data.state = temp_data.states.OK
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@@ -864,6 +864,15 @@ class DataToolParameter( ToolParameter ):
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else:
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return "No dataset"
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def get_dependencies( self ):
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"""
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Get the *names* of the other params this param depends on.
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"""
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if self.options:
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return self.options.get_dependency_names()
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else:
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return []
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# class RawToolParameter( ToolParameter ):
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# """
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# Completely nondescript parameter, HTML representation is provided as text
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@@ -146,9 +146,35 @@ class MetadataValidator( Validator ):
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"""
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Validator that checks for missing metadata
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"""
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def __init__( self, message=None ):
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self.message = message
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@classmethod
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def from_element( cls, elem ):
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return cls( elem.get( 'message', None ) )
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def validate( self, value, history=None ):
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if value and value.missing_meta():
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raise ValueError( "Metadata missing, click the pencil icon in the history item to edit / save the metadata attributes" )
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if self.message is None:
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self.message = "Metadata missing, click the pencil icon in the history item to edit / save the metadata attributes"
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raise ValueError( self.message )
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class UnspecifiedBuildValidator( Validator ):
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"""
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Validator that checks for missing metadata
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"""
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def __init__( self, message=None ):
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self.message = message
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@classmethod
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def from_element( cls, elem ):
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return cls( elem.get( 'message', None ) )
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def validate( self, value, history=None ):
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if value:
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dbkey = value.metadata.dbkey
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if isinstance( dbkey, list ):
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dbkey = dbkey[0]
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if dbkey == '?':
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if self.message is None:
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self.message = "Unspecified genome build, click the pencil icon in the history item to set the genome build"
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raise ValueError( self.message )
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class MetadataInFileColumnValidator( Validator ):
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"""
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@@ -185,6 +211,7 @@ validator_types = dict( expression=ExpressionValidator,
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in_range=InRangeValidator,
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length=LengthValidator,
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metadata=MetadataValidator,
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unspecified_build=UnspecifiedBuildValidator,
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dataset_metadata_in_file=MetadataInFileColumnValidator )
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def get_suite():
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@@ -2,7 +2,9 @@
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<description>create a random set of intervals</description>
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<command interpreter="python2.4">random_intervals_no_bits.py $regions $input2 $input1 $out_file1 $input2_chromCol $input2_startCol $input2_endCol $input1_chromCol $input1_startCol $input1_endCol $input1_strandCol $use_mask $strand_overlaps</command>
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<inputs>
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<param name="input1" type="data" format="interval" label="File to Mimick"/>
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<param name="input1" type="data" format="interval" label="File to Mimick">
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<validator type="unspecified_build" message="Unspecified build, this tool works with data from genome builds hg16 or hg17. Click the pencil icon in your history item to set the genome build."/>
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</param>
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<param name="input2" type="data" format="interval" label="Intervals to Mask"/>
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<param name="use_mask" type="select" label="Use mask">
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<option value="no_mask">No</option>
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@@ -4,6 +4,7 @@
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<inputs>
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<param format="interval" name="input" type="data" label="Between regions of Query"/>
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<param name="species" type="select" label="and one of these genomes">
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<validator type="unspecified_build" />
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<options from_file="/depot/data2/galaxy/alignseq.loc" >
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<filter type="data_meta" data_ref="input" key="build" />
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<filter type="column" name="build_col" value="0" />
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@@ -2,7 +2,9 @@
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<description> between assemblies and genomes</description>
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<command interpreter="python">liftOver_wrapper.py $input "$out_file1" "$out_file2" $dbkey $to_dbkey</command>
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<inputs>
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<param format="bed" name="input" type="data" label="Convert co-ordinates of" />
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<param format="bed" name="input" type="data" label="Convert co-ordinates of">
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<validator type="unspecified_build" />
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</param>
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<param name="to_dbkey" type="select" label="To">
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<options from_file="/depot/data2/galaxy/liftOver.loc">
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<filter type="data_meta" data_ref="input" key="build" />
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@@ -2,7 +2,9 @@
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<description>for each interval</description>
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<command interpreter="python2.4">get_scores_galaxy.py $per_col ${score_file}.h5 ${score_file}.mapping.bed $input $output $input_chromCol $input_startCol $input_endCol</command>
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<inputs>
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<param format="interval" name="input" type="data" label="Interval file"/>
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<param format="interval" name="input" type="data" label="Interval file">
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<validator type="unspecified_build" message="Unspecified build, this tool works with data from genome builds hg17. Click the pencil icon in your history item to set the genome build."/>
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</param>
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<param name="score_file" type="select" label="Available datasets">
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<options from_file="/depot/data2/galaxy/phastOdds.loc" >
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<filter type="data_meta" data_ref="input" key="build" />
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@@ -5,7 +5,9 @@
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#end if
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</command>
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<inputs>
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<param name="input1" type="data" format="bed" label="Gene BED File"/>
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<param name="input1" type="data" format="bed" label="Gene BED File">
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<validator type="unspecified_build" />
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</param>
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<conditional name="maf_source_type">
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<param name="maf_source" type="select" label="MAF Source">
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<option value="cached" selected="true">Locally Cached Alignments</option>
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@@ -6,7 +6,9 @@
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#end if
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</command>
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<inputs>
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<param format="interval" name="input1" type="data" label="Choose intervals"/>
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<param format="interval" name="input1" type="data" label="Choose intervals">
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<validator type="unspecified_build" />
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</param>
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<conditional name="maf_source_type">
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<param name="maf_source" type="select" label="MAF Source">
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<option value="cached" selected="true">Locally Cached Alignments</option>
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@@ -2,7 +2,9 @@
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<description>given a set of genomic intervals</description>
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<command interpreter="python2.4">interval2maf.py --dbkey=$input1_dbkey --chromCol=$input1_chromCol --startCol=$input1_startCol --endCol=$input1_endCol --strandCol=$input1_strandCol --mafType=$mafType --interval_file=$input1 --output_file=$out_file1 --indexLocation=/depot/data2/galaxy/maf_pairwise.loc</command>
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<inputs>
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<param name="input1" type="data" format="interval" label="Interval File"/>
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<param name="input1" type="data" format="interval" label="Interval File">
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<validator type="unspecified_build" />
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</param>
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<param name="mafType" type="select" label="Choose MAF source">
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<options from_file="/depot/data2/galaxy/maf_pairwise.loc">
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<filter type="data_meta" data_ref="input1" key="build" />
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@@ -6,7 +6,9 @@
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</command>
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<inputs>
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<page>
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<param format="interval" name="input1" type="data" label="Choose intervals"/>
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<param format="interval" name="input1" type="data" label="Choose intervals">
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<validator type="unspecified_build" />
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</param>
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<conditional name="maf_source_type">
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<param name="maf_source" type="select" label="MAF Source">
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<option value="cached" selected="true">Locally Cached Alignments</option>
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@@ -9,7 +9,9 @@
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#end if
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</command>
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<inputs>
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<param format="interval" name="input1" label="Interval File" type="data"/>
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<param format="interval" name="input1" label="Interval File" type="data">
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<validator type="unspecified_build" />
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</param>
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<conditional name="maf_source_type">
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<param name="maf_source" type="select" label="MAF Source">
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<option value="cached" selected="true">Locally Cached Alignments</option>
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+3
-1
@@ -6,7 +6,9 @@
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#end if
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</command>
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<inputs>
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<param format="interval" name="input1" type="data" label="Interval file"/>
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<param format="interval" name="input1" type="data" label="Interval file">
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<validator type="unspecified_build" message="Unspecified build, this tool works with data from genome builds hg16, hg17 or hg18. Click the pencil icon in your history item to set the genome build."/>
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</param>
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<conditional name="score_source_type">
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<param name="score_source" type="select" label="Score Source">
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<option value="cached" selected="true">Locally Cached Scores</option>
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