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Add a make_dict_copy method to Tool.execute so that when wrapping the tool's inputs to display output labels and such, we are not overwriting the incoming param dictionary. Also, yet another fix for tranlsating EOL to <br/> so they can be displayed in the data.info in the histoy.

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This commit is contained in:
Greg Von Kuster
2009-01-26 14:41:00 -05:00
parent c998a43692
commit c09f6759ab
2 changed files with 25 additions and 10 deletions
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lib/galaxy/datatypes/data.py
+8 -7
View File
@@ -137,13 +137,14 @@ class Data( object ):
"""Returns formatted html of dataset info"""
try:
# Change new line chars to html
if dataset.info.find( '\r\n' ) >= 0:
dataset.info = dataset.info.replace( '\r\n', '<br/>' )
if dataset.info.find( '\r' ) >= 0:
dataset.info = dataset.info.replace( '\r', '<br/>' )
if dataset.info.find( '\n' ) >= 0:
dataset.info = dataset.info.replace( '\n', '<br/>' )
return escape( dataset.info )
info = escape( dataset.info )
if info.find( '\r\n' ) >= 0:
info = info.replace( '\r\n', '<br/>' )
if info.find( '\r' ) >= 0:
info = info.replace( '\r', '<br/>' )
if info.find( '\n' ) >= 0:
info = info.replace( '\n', '<br/>' )
return info
except:
return "info unavailable"
def validate(self, dataset):
lib/galaxy/tools/actions/__init__.py
+17 -3
View File
@@ -6,6 +6,7 @@ from galaxy.util.none_like import NoneDataset
from galaxy.web import url_for
from galaxy.jobs import JOB_OK
import galaxy.tools
from types import *
import logging
log = logging.getLogger( __name__ )
@@ -65,8 +66,21 @@ class DefaultToolAction( object ):
param_values[input.name] = input_datasets[ prefix + input.name ]
tool.visit_inputs( param_values, visitor )
return input_datasets
def execute(self, tool, trans, incoming={}, set_output_hid=True ):
def make_dict_copy( from_dict ):
"""
Makes a copy of input dictionary from_dict such that all values that are dictionaries
result in creation of a new dictionary ( a sort of deepcopy ). We may need to handle
other complex types ( e.g., lists, etc ), but not sure...
"""
copy_from_dict = {}
for key, value in from_dict.items():
if type( value ).__name__ == 'dict':
copy_from_dict[ key ] = make_dict_copy( value )
else:
copy_from_dict[ key ] = value
return copy_from_dict
def wrap_values( inputs, input_values ):
# Wrap tool inputs as necessary
for input in inputs.itervalues():
@@ -75,7 +89,7 @@ class DefaultToolAction( object ):
wrap_values( input.inputs, d )
elif isinstance( input, Conditional ):
values = input_values[ input.name ]
current = values["__current_case__"]
current = values[ "__current_case__" ]
wrap_values( input.cases[current].inputs, values )
elif isinstance( input, DataToolParameter ):
input_values[ input.name ] = \
@@ -172,7 +186,7 @@ class DefaultToolAction( object ):
data.blurb = "queued"
# Set output label
if output.label:
params = dict( incoming )
params = make_dict_copy( incoming )
# wrapping the params allows the tool config to contain things like
# <outputs>
# <data format="input" name="output" label="Blat on ${<input_param>.name}" />