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Test that metadata validators work

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This commit is contained in:
mvdbeek
2022-06-25 12:55:51 +02:00
parent 8178178736
commit df6551da78
2 changed files with 35 additions and 3 deletions
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lib/galaxy_test/api/test_tools.py
+34 -2
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@@ -2738,13 +2738,45 @@ class ToolsTestCase(ApiTestCase, TestsTools):
inputs = {"input_bam": dataset_to_param(details), "ref_names": "chrM"}
run_response = self.dataset_populator.run_tool(tool_id="metadata_bam", inputs=inputs, history_id=history_id)
output = run_response["outputs"][0]
details = self.dataset_populator.get_history_dataset_details(
output_details = self.dataset_populator.get_history_dataset_details(
history_id, dataset=output, wait=True, assert_ok=True
)
assert details["state"] == "ok"
assert output_details["state"] == "ok"
output_content = self.dataset_populator.get_history_dataset_content(history_id, dataset=output)
assert output_content.startswith("chrM")
@skip_without_tool("pileup")
@uses_test_history(require_new=False)
def test_metadata_validator_on_deferred_input(self, history_id):
deferred_bam_details = self.dataset_populator.create_deferred_hda(
history_id, "https://raw.githubusercontent.com/galaxyproject/galaxy/dev/test-data/1.bam", ext="bam"
)
fasta1_contents = open(self.get_filename("1.fasta")).read()
fasta = self.dataset_populator.new_dataset(history_id, content=fasta1_contents)
inputs = {"input1": dataset_to_param(deferred_bam_details), "reference": dataset_to_param(fasta)}
run_response = self.dataset_populator.run_tool(tool_id="pileup", inputs=inputs, history_id=history_id)
self.dataset_populator.wait_for_job(run_response["jobs"][0]["id"], assert_ok=True)
@pytest.mark.xfail
@skip_without_tool("pileup")
@uses_test_history(require_new=False)
def test_metadata_validator_can_fail_on_deferred_input(self, history_id):
# This test fails because we just skip the validator
# Fixing this is a TODO
deferred_bam_details = self.dataset_populator.create_deferred_hda(
history_id,
"https://github.com/galaxyproject/galaxy/blob/dev/test-data/3unsorted.bam?raw=true",
ext="unsorted.bam",
)
fasta1_contents = open(self.get_filename("1.fasta")).read()
fasta = self.dataset_populator.new_dataset(history_id, content=fasta1_contents)
inputs = {"input1": dataset_to_param(deferred_bam_details), "reference": dataset_to_param(fasta)}
run_response = self.dataset_populator.run_tool(tool_id="pileup", inputs=inputs, history_id=history_id)
self.dataset_populator.wait_for_job(run_response["jobs"][0]["id"], assert_ok=False)
job_id = run_response["jobs"][0]["id"]
job_details = self.dataset_populator.get_job_details(job_id=job_id).json()
assert job_details["state"] == "failed"
@skip_without_tool("cat1")
@uses_test_history(require_new=False)
def test_run_deferred_mapping(self, history_id: str):
test/functional/tools/for_workflows/pileup.xml
+1 -1
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@@ -3,7 +3,7 @@
printf 'Summary' > '$out_file1'
]]></command>
<inputs>
<param name="input1" type="data" format="bam" multiple="true" min="1" label="BAM Inputs">
<param name="input1" type="data" format="unsorted.bam" multiple="true" min="1" label="BAM Inputs">
<validator check="bam_index" message="Metadata missing, click the pencil icon in the history item and use the auto-detect feature to correct this issue." type="metadata" />
</param>
<param name="reference" type="data" format="fasta" label="Fasta Input"/>