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Fix bugs in test and code introduced in PR #1113.

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This commit is contained in:
Nicola Soranzo
2015-11-23 15:18:57 +00:00
parent 11f9fed4ac
commit b6451d0be6
3 changed files with 6 additions and 5 deletions
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lib/galaxy/tools/actions/__init__.py
+3 -2
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@@ -602,11 +602,12 @@ def determine_output_format(output, parameter_context, input_datasets, input_dat
if collection_name in input_dataset_collections:
try:
input_collection = input_dataset_collections[collection_name]
input_collection = input_dataset_collections[collection_name][0]
input_dataset = input_collection.collection[element_index].element_object
input_extension = input_dataset.ext
ext = input_extension
except Exception:
except Exception, e:
log.debug("Exception while trying to determine format_source: %s", e)
pass
# process change_format tags
test/functional/tools/output_format_collection.xml
+2 -2
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@@ -8,9 +8,9 @@
</inputs>
<outputs>
<!-- Access by element name (for paired data) -->
<data format="txt" from_work_dir="1" name="format_source_1_output" format_source="input_collection['forward']" />
<data from_work_dir="1" name="format_source_1_output" format_source="input_collection['forward']" />
<!-- Access by element index (for any collection) -->
<data format="txt" from_work_dir="2" name="format_source_2_output" format_source="input_collection[0]" />
<data from_work_dir="2" name="format_source_2_output" format_source="input_collection[0]" />
</outputs>
<tests>
<test>
test/unit/tools/test_actions.py
+1 -1
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@@ -212,7 +212,7 @@ def __assert_output_format_is( expected, output, input_extensions=[], param_cont
dce2 = model.DatasetCollectionElement(collection=c1, element=hda_reverse, element_identifier="reverse", element_index=1)
c1.elements = [dce1, dce2]
input_collections["hdcai"] = hc1
input_collections["hdcai"] = (hc1, False)
actual_format = determine_output_format( output, param_context, inputs, input_collections, last_ext )
assert actual_format == expected, "Actual format %s, does not match expected %s" % (actual_format, expected)