Unverified Commit df6551da authored by mvdbeek's avatar mvdbeek
Browse files

Test that metadata validators work

parent 81781787

lib/galaxy_test/api/test_tools.py

+34 −2
Original line number Diff line number Diff line
@@ -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
Original line number Diff line number Diff line
@@ -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"/>