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Merge pull request #10434 from jmchilton/sort_by

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[20.09] Rework new collection order testing in 20.09.
This commit is contained in:
Marius van den Beek
2020-10-23 13:01:47 +02:00
committed by GitHub
parent aec21e6786 4c3932df60
commit dfb2288281
5 changed files with 96 additions and 37 deletions
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lib/galaxy/tool_util/parser/xml.py
+15 -12
View File
@@ -513,7 +513,8 @@ class XmlToolSource(ToolSource):
if tests_elem is not None:
for i, test_elem in enumerate(tests_elem.findall("test")):
tests.append(_test_elem_to_dict(test_elem, i))
profile = self.parse_profile()
tests.append(_test_elem_to_dict(test_elem, i, profile))
return rval
@@ -533,10 +534,10 @@ class XmlToolSource(ToolSource):
return python_template_version
def _test_elem_to_dict(test_elem, i):
def _test_elem_to_dict(test_elem, i, profile=None):
rval = dict(
outputs=__parse_output_elems(test_elem),
output_collections=__parse_output_collection_elems(test_elem),
output_collections=__parse_output_collection_elems(test_elem, profile=profile),
inputs=__parse_input_elems(test_elem, i),
expect_num_outputs=test_elem.get("expect_num_outputs"),
command=__parse_assert_list_from_elem(test_elem.find("assert_command")),
@@ -579,36 +580,38 @@ def __parse_command_elem(test_elem):
return __parse_assert_list_from_elem(assert_elem)
def __parse_output_collection_elems(test_elem):
def __parse_output_collection_elems(test_elem, profile=None):
output_collections = []
for output_collection_elem in test_elem.findall("output_collection"):
output_collection_def = __parse_output_collection_elem(output_collection_elem)
output_collection_def = __parse_output_collection_elem(output_collection_elem, profile=profile)
output_collections.append(output_collection_def)
return output_collections
def __parse_output_collection_elem(output_collection_elem):
def __parse_output_collection_elem(output_collection_elem, profile=None):
attrib = dict(output_collection_elem.attrib)
name = attrib.pop('name', None)
if name is None:
raise Exception("Test output collection does not have a 'name'")
element_tests = __parse_element_tests(output_collection_elem)
element_tests = __parse_element_tests(output_collection_elem, profile=profile)
return TestCollectionOutputDef(name, attrib, element_tests).to_dict()
def __parse_element_tests(parent_element):
def __parse_element_tests(parent_element, profile=None):
element_tests = {}
for idx, element in enumerate(parent_element.findall("element")):
element_attrib = dict(element.attrib)
identifier = element_attrib.pop('name', None)
if identifier is None:
raise Exception("Test primary dataset does not have a 'identifier'")
element_tests[identifier] = __parse_test_attributes(element, element_attrib, parse_elements=True)
element_tests[identifier][1]["element_index"] = idx
element_tests[identifier] = __parse_test_attributes(element, element_attrib, parse_elements=True, profile=profile)
if profile and profile >= "20.09":
element_tests[identifier][1]["expected_sort_order"] = idx
return element_tests
def __parse_test_attributes(output_elem, attrib, parse_elements=False, parse_discovered_datasets=False):
def __parse_test_attributes(output_elem, attrib, parse_elements=False, parse_discovered_datasets=False, profile=None):
assert_list = __parse_assert_list(output_elem)
# Allow either file or value to specify a target file to compare result with
@@ -638,7 +641,7 @@ def __parse_test_attributes(output_elem, attrib, parse_elements=False, parse_dis
checksum = attrib.get("checksum", None)
element_tests = {}
if parse_elements:
element_tests = __parse_element_tests(output_elem)
element_tests = __parse_element_tests(output_elem, profile=profile)
primary_datasets = {}
if parse_discovered_datasets:
lib/galaxy/tool_util/verify/interactor.py
+31 -23
View File
@@ -724,36 +724,29 @@ def verify_collection(output_collection_def, data_collection, verify_dataset):
message = template % (name, expected_element_count, actual_element_count)
raise AssertionError(message)
def get_element(elements, id):
for element in elements:
if element["element_identifier"] == id:
return element
return False
def verify_elements(element_objects, element_tests):
sorted_test_ids = [None] * len(element_tests)
# sorted_test_ids = [None] * len(element_tests)
expected_sort_order = []
eo_ids = [_["element_identifier"] for _ in element_objects]
for element_identifier, element_test in element_tests.items():
if isinstance(element_test, dict):
element_outfile, element_attrib = None, element_test
else:
element_outfile, element_attrib = element_test
sorted_test_ids[element_attrib["element_index"]] = element_identifier
if 'expected_sort_order' in element_attrib:
expected_sort_order.append(element_identifier)
i = 0
for element_identifier in sorted_test_ids:
element_test = element_tests[element_identifier]
if isinstance(element_test, dict):
element_outfile, element_attrib = None, element_test
else:
element_outfile, element_attrib = element_test
element = None
while i < len(element_objects):
if element_objects[i]["element_identifier"] == element_identifier:
element = element_objects[i]
i += 1
break
i += 1
if element is None:
template = "Failed to find identifier '%s' of test collection %s in the tool generated collection elements %s (at the correct position)"
eo_ids = [_["element_identifier"] for _ in element_objects]
message = template % (element_identifier, sorted_test_ids,
eo_ids)
element = get_element(element_objects, element_identifier)
if not element:
template = "Failed to find identifier '%s' in the tool generated collection elements %s"
message = template % (element_identifier, eo_ids)
raise AssertionError(message)
element_type = element["element_type"]
@@ -763,6 +756,21 @@ def verify_collection(output_collection_def, data_collection, verify_dataset):
elements = element["object"]["elements"]
verify_elements(elements, element_attrib.get("elements", {}))
if len(expected_sort_order) > 0:
i = 0
for element_identifier in expected_sort_order:
element = None
while i < len(element_objects):
if element_objects[i]["element_identifier"] == element_identifier:
element = element_objects[i]
i += 1
break
i += 1
if element is None:
template = "Collection identifier '%s' found out of order, expected order of %s for the tool generated collection elements %s"
message = template % (element_identifier, expected_sort_order, eo_ids)
raise AssertionError(message)
verify_elements(data_collection["elements"], output_collection_def.element_tests)
lib/galaxy/tool_util/xsd/galaxy.xsd
+7 -1
View File
@@ -1507,7 +1507,7 @@ Note that this tool uses ``assign_primary_output="true"`` for ``<discover_data_s
<xs:annotation>
<xs:documentation xml:lang="en"><![CDATA[
Define tests for extra files corresponding to an output collection.
Define tests for extra datasets and metadata corresponding to an output collection.
``output_collection`` directives should specify a ``name`` and ``type``
attribute to describe the expected output collection as a whole.
@@ -1516,6 +1516,12 @@ Expectations about collection contents are described using child ``element``
directives. For nested collections, these child ``element`` directives may
themselves contain children.
For tools marked as having profile 20.09 or newer, the order of elements within
an ``output_collection`` declaration are meaningful. The test definition may
omit any number of elements from a collection, but the ones that are specified
will be checked against the actual resulting collection from the tool run and the
order within the collection verified.
### Examples
The [genetrack](https://github.com/galaxyproject/tools-iuc/blob/master/tools/genetrack/genetrack.xml)
test/functional/tools/discover_sort_by.xml
+1 -1
View File
@@ -1,4 +1,4 @@
<tool id="discover_sort_by" name="discover_sort_by" version="0.1.0">
<tool id="discover_sort_by" name="discover_sort_by" version="0.1.0" profile="20.09">
<command><![CDATA[
for i in \$(seq 1 10);
do
test/functional/tools/discover_sort_by_legacy_test.xml
+42
View File
@@ -0,0 +1,42 @@
<tool id="discover_sort_by_legacy_test" name="discover_sort_by_legacy_test" version="0.1.0" profile="20.05">
<!-- same as discover_sort_by but with tests not ordered correctly, this would cause
failure in profile 20.09 or newer.
-->
<command><![CDATA[
for i in \$(seq 1 10);
do
echo "\$i" > \$i.txt;
done
]]></command>
<inputs/>
<outputs>
<collection name="collection_numeric_name" type="list" label="num">
<discover_datasets pattern="__name_and_ext__" sort_by="numeric_name"/>
</collection>
<collection name="collection_rev_numeric_name" type="list" label="num rev">
<discover_datasets pattern="__name_and_ext__" sort_by="reverse_numeric_name"/>
</collection>
<collection name="collection_lexical_name" type="list" label="num">
<discover_datasets pattern="__name_and_ext__" sort_by="lexical_name" />
</collection>
<data name="data_reverse_lexical_name">
<discover_datasets pattern="__name_and_ext__" format="txt" assign_primary_output="true" sort_by="reverse_lexical_name" visible="true"/>
</data>
</outputs>
<tests>
<test expect_num_outputs="4">
<param name="input1" value="tinywga.fam" />
<output_collection name="collection_numeric_name" type="list" count="10">
<element name="2">
<assert_contents><has_text_matching expression="^.*$"/></assert_contents>
</element>
<element name="1">
<assert_contents><has_text_matching expression="^.*$"/></assert_contents>
</element>
<element name="10">
<assert_contents><has_text_matching expression="^.*$"/></assert_contents>
</element>
</output_collection>
</test>
</tests>
</tool>