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format_source in workflow editor is too restrictive.

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Case made well by @erasche on #1746, fixes #1746.

To resolve this more correctly (and many other potential type problems) - the workflow editor should be significantly reworked to track the datatype (or a range of datatypes) on each terminal (the way it does for collection mapping information). The change would be a weeks worth of development effort and inappropriate to apply to a release branch.
This commit is contained in:
John Chilton
2016-02-23 17:16:27 +00:00
parent 805b5906b2
commit b402093479
2 changed files with 3 additions and 12 deletions
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lib/galaxy/workflow/modules.py
-9
View File
@@ -983,7 +983,6 @@ class ToolModule( WorkflowModule ):
def get_data_outputs( self ):
data_outputs = []
data_inputs = None
for name, tool_output in self.tool.outputs.iteritems():
extra_kwds = {}
if tool_output.collection:
@@ -992,14 +991,6 @@ class ToolModule( WorkflowModule ):
formats = [ 'input' ] # TODO: fix
elif tool_output.format_source is not None:
formats = [ 'input' ] # default to special name "input" which remove restrictions on connections
if data_inputs is None:
data_inputs = self.get_data_inputs()
# find the input parameter referenced by format_source
for di in data_inputs:
# input names come prefixed with conditional and repeat names separated by '|'
# remove prefixes when comparing with format_source
if di['name'] is not None and di['name'].split('|')[-1] == tool_output.format_source:
formats = di['extensions']
else:
formats = [ tool_output.format ]
for change_elem in tool_output.change_format:
test/functional/tools/output_format.xml
+3 -3
View File
@@ -7,9 +7,9 @@
echo "test" > 5;
</command>
<inputs>
<param name="input_data_1" type="data" format="data" />
<param name="input_data_2" type="data" format="data" />
<param name="input_text" type="text" value="1" />
<param name="input_data_1" type="data" format="data" label="input_data_1" />
<param name="input_data_2" type="data" format="data" label="input_data_2" />
<param name="input_text" type="text" value="1" label="input_text" />
</inputs>
<outputs>
<data format="txt" from_work_dir="1" name="direct_output" />