diff --git a/lib/galaxy/tools/parameters.py b/lib/galaxy/tools/parameters.py
index 38c2ae8b73a..69d5b4571f8 100644
--- a/lib/galaxy/tools/parameters.py
+++ b/lib/galaxy/tools/parameters.py
@@ -4,15 +4,23 @@ Classes encapsulating tool parameters
import logging, string, sys
from galaxy import config, datatypes, util
+from galaxy.datatypes.tabular import *
import validation
from elementtree.ElementTree import XML, Element
# For BaseURLToolParameter
from galaxy.web import url_for
from galaxy.web import form_builder
+from galaxy.model import Dataset
log = logging.getLogger(__name__)
+class NoProperDataError( Exception ):
+ def __init__(self, value):
+ self.value = value
+ def __str__(self):
+ return repr(self.value)
+
class ToolParameter( object ):
"""
Describes a parameter accepted by a tool. This is just a simple stub at the
@@ -510,6 +518,92 @@ class GenomeBuildParameter( SelectToolParameter ):
def get_legal_values( self, other_values ):
return set( dbkey for dbkey, _ in util.dbnames )
+class ColumnListParameter( SelectToolParameter ):
+ """
+ Select list that consists of either the total number of columns or only
+ those columns that contain numerical values in the associated DataToolParameter.
+
+ # TODO: we need better testing here, but not sure how to associate a DatatoolParameter with a ColumnListParameter
+ # from a twill perspective...
+
+ >>> # Mock up a history (not connected to database)
+ >>> from galaxy.model import History, Dataset
+ >>> from galaxy.util.bunch import Bunch
+ >>> hist = History()
+ >>> hist.flush()
+ >>> hist.add_dataset( Dataset( id=1, extension='interval' ) )
+ >>> dtp = DataToolParameter( None, XML( '' ) )
+ >>> print dtp.name
+ blah
+ >>> clp = ColumnListParameter ( None, XML( '' ) )
+ >>> print clp.name
+ numerical_column
+ """
+ def __init__( self, tool, elem ):
+ SelectToolParameter.__init__( self, tool, elem )
+
+ self.tool = tool
+ self.numerical = elem.get( "numerical", False )
+ self.assoc_dataset = elem.get( "assoc_dataset", None )
+
+ def get_options( self, trans, other_values ):
+ columnList = []
+ dataset_id = 0
+ dataset = None
+ assoc_dataset = self.tool.get_param( self.assoc_dataset )
+
+ assert assoc_dataset is not None, "Tools that include a ColumnListParameter must also include a DataToolParameter"
+
+ if len( self.tool.updated_params ) == 0:
+ """
+ This will execute when the tool page is initially loading and the
+ user has not yet manually selected a dataset. In this case, ad_val
+ will be a DataToolParameter.
+ """
+ field = assoc_dataset.get_html_field(trans, assoc_dataset, other_values )
+
+ """We need to make sure there is a dataset of the proper format in the history."""
+ if len( field.options ) == 0:
+ raise NoProperDataError( ",".join( param.extensions ))
+
+ if dataset_id == 0:
+ for txt, val, selected in field.options:
+ if selected:
+ dataset_id = val
+ break
+ if dataset_id == 0:
+ """This should be the latest dataset in the history"""
+ dataset_id = str(field.options[-1][1])
+
+ dataset = assoc_dataset.from_html(dataset_id, trans, other_values )
+
+ else:
+ """
+ This will execute whenever the user selects a dataset from the input data
+ select list. Doing this results in executing the tool's update_state function,
+ so we can retrieve the selected dataset from the tool.
+ """
+ dataset = self.tool.updated_params[self.assoc_dataset]
+
+ assert dataset is not None, "Error retrieving required dataset for ColumnListParameter"
+
+ if dataset.missing_meta():
+ """Just to be safe..."""
+ Tabular().set_meta(dataset)
+
+ if self.numerical:
+ for i, col in enumerate( dataset.metadata.column_types ):
+ if col == 'int' or col == 'float':
+ self.legal_values.add(str( i+1 ))
+ option = 'c' + str( i+1 )
+ columnList.append((option,str( i+1 ),False))
+ else:
+ for col in range (0, dataset.metadata.columns):
+ self.legal_values.add(str(col+1))
+ option = 'c' + str(col+1)
+ columnList.append((option,str(col+1),False))
+
+ return columnList
class DataToolParameter( ToolParameter ):
"""
@@ -542,8 +636,8 @@ class DataToolParameter( ToolParameter ):
ToolParameter.__init__( self, tool, elem )
# Build tuple of classes for supported data formats
formats = []
- extensions = elem.get( 'format', 'data' ).split( "," )
- for extension in extensions:
+ self.extensions = elem.get( 'format', 'data' ).split( "," )
+ for extension in self.extensions:
extension = extension.strip()
if tool is None:
#This occurs for things such as unit tests
@@ -554,6 +648,7 @@ class DataToolParameter( ToolParameter ):
self.formats = tuple( formats )
self.multiple = str_bool( elem.get( 'multiple', False ) )
self.optional = str_bool( elem.get( 'optional', False ) )
+ self.refresh_on_change = str_bool( elem.get( "refresh_on_change", False ))
self.dynamic_options = elem.get( "dynamic_options", None )
def get_html_field( self, trans=None, value=None, other_values={} ):
@@ -562,15 +657,12 @@ class DataToolParameter( ToolParameter ):
assert history is not None, "DataToolParameter requires a history"
if value is not None:
if type( value ) != list: value = [ value ]
- field = form_builder.SelectField( self.name, self.multiple )
+ field = form_builder.SelectField( self.name, self.multiple, None, self.refresh_on_change )
if self.dynamic_options:
- # Dynamic options for a DataToolParameter specify limits on
- # acceptrable build, id, or extension
+ """Dynamic options for a DataToolParameter specify limits on acceptrable build, id, or extension"""
option_build, option_id, option_extension = \
eval( self.dynamic_options, self.tool.code_namespace, other_values )
- """
- CRUCIAL: the dataset_collector function needs to be local to DataToolParameter.get_html_field()
- """
+ """CRUCIAL: the dataset_collector function needs to be local to DataToolParameter.get_html_field()"""
def dataset_collector( datasets, parent_hid ):
for i, data in enumerate( datasets ):
if parent_hid is not None:
@@ -606,7 +698,7 @@ class DataToolParameter( ToolParameter ):
def from_html( self, value, trans, other_values={} ):
if not value:
- raise ValueError( "A data of the appropriate type is required" )
+ raise NoProperDataError( ",".join( self.extensions ))
if value in [None, "None"]:
temp_data = trans.app.model.Dataset()
temp_data.state = temp_data.states.FAKE
@@ -692,6 +784,7 @@ parameter_types = dict( text = TextToolParameter,
boolean = BooleanToolParameter,
genomebuild = GenomeBuildParameter,
select = SelectToolParameter,
+ columnlist = ColumnListParameter,
hidden = HiddenToolParameter,
baseurl = BaseURLToolParameter,
file = FileToolParameter,
diff --git a/lib/galaxy/web/controllers/tool_runner.py b/lib/galaxy/web/controllers/tool_runner.py
index 08f0dac8ee1..1a7a0fc29ad 100644
--- a/lib/galaxy/web/controllers/tool_runner.py
+++ b/lib/galaxy/web/controllers/tool_runner.py
@@ -3,6 +3,7 @@ Upload class
"""
from galaxy.web.base.controller import *
+from galaxy.tools.parameters import NoProperDataError
import logging
log = logging.getLogger( __name__ )
@@ -36,7 +37,10 @@ class ToolRunner( BaseController ):
params = util.Params(kwd, sanitize = tool.options.sanitize)
history = trans.get_history()
trans.ensure_valid_galaxy_session()
- template, vars = tool.handle_input( trans, params.__dict__ )
+ try:
+ template, vars = tool.handle_input( trans, params.__dict__ )
+ except NoProperDataError, exc:
+ return trans.fill_template( 'no_proper_data.tmpl', error_msg=exc.value )
if len(params) > 0:
trans.log_event( "Tool params: %s" % (str(params)), tool_id=tool_id )
return trans.fill_template( template, history=history, toolbox=toolbox, tool=tool, util=util, **vars )
\ No newline at end of file
diff --git a/templates/no_proper_data.tmpl b/templates/no_proper_data.tmpl
new file mode 100644
index 00000000000..865a6a4c770
--- /dev/null
+++ b/templates/no_proper_data.tmpl
@@ -0,0 +1,18 @@
+
+
+
+No Proper Query
+
+
+
+
+
+
No Proper Query
+
+ Your history does not contain a query of the required format for this tool.
+ #if $getVar( 'error_msg', None )
+ Query formats required: $error_msg.
+ #end if
+