Unverified Commit 8edced97 authored by Nicola Soranzo's avatar Nicola Soranzo Committed by GitHub
Browse files

Merge pull request #19819 from mvdbeek/default_tool_test_timeout 

[24.2] Reduce default framework tool test timeout to 60 seconds
parents 6a610a1b a19e4eb0

lib/galaxy/config/sample/datatypes_conf.xml.sample

+1 −1
Original line number Diff line number Diff line
@@ -532,7 +532,7 @@ 
    <datatype extension="juicer_medium_tabix.gz" type="galaxy.datatypes.interval:JuicerMediumTabix" mimetype="application/octet-stream" display_in_upload="true"/>

    <datatype extension="bed_tabix.gz" type="galaxy.datatypes.interval:BedTabix" mimetype="application/octet-stream" display_in_upload="true"/>

    <datatype extension="gff_tabix.gz" type="galaxy.datatypes.interval:GffTabix" mimetype="application/octet-stream" display_in_upload="true"/>

    <datatype extension="bgzip" type="galaxy.datatypes.binary:Binary" subclass="true" display_in_upload="true"/>

    <datatype extension="bgzip" type="galaxy.datatypes.binary:CompressedArchive" subclass="true" display_in_upload="true"/>

    <datatype extension="vcf_bgzip" type="galaxy.datatypes.tabular:VcfGz" display_in_upload="true">

      <display file="igv/vcf.xml"/>

      <converter file="vcf_bgzip_to_tabix_converter.xml" target_datatype="tabix"/>

lib/galaxy/datatypes/converters/interval_to_tabix_converter.xml

+16 −43
Original line number Diff line number Diff line
@@ -42,11 +42,6 @@ 
        <test>

            <param name="input1" ftype="bed" value="droPer1.bed" />

            <param name="bgzip" ftype="bgzip" value="droPer1.bed.gz" />

            <output name="output1" ftype="tabix">

                <assert_contents>

                    <has_size value="133"/>

                </assert_contents>

            </output>

            <assert_command>

                <has_text text="-p bed"/>

            </assert_command>
@@ -57,11 +52,6 @@ 
        <test>

            <param name="input1" ftype="encodepeak" value="encode.broad.peak" />

            <param name="bgzip" ftype="bgzip" value="encode.broad.peak.gz" />

            <output name="output1" ftype="tabix">

                <assert_contents>

                    <has_size value="110" delta="10"/>

                </assert_contents>

            </output>

            <assert_command>

                <has_text text="-p" negate="true"/>

            </assert_command>
@@ -72,11 +62,6 @@ 
        <test>

            <param name="input1" ftype="gff" value="gff_filter_by_feature_count_out2.gff" />

            <param name="bgzip" ftype="bgzip" value="gff_filter_by_feature_count_out2.gff.gz" />

            <output name="output1" ftype="tabix">

                <assert_contents>

                    <has_size value="120"/>

                </assert_contents>

            </output>

            <assert_command>

                <has_text text="-p gff"/>

            </assert_command>
@@ -87,11 +72,6 @@ 
        <test>

            <param name="input1" ftype="interval" value="2.interval" />

            <param name="bgzip" ftype="bgzip" value="2.interval.gz" />

            <output name="output1" ftype="tabix">

                <assert_contents>

                    <has_size value="247"/>

                </assert_contents>

            </output>

            <assert_command>

                <has_text text="-p" negate="true"/>

            </assert_command>
@@ -102,11 +82,6 @@ 
        <test>

            <param name="input1" ftype="vcf" value="vcf_to_maf_in.vcf" />

            <param name="bgzip" ftype="bgzip" value="vcf_to_maf_in.vcf.gz" />

            <output name="output1" ftype="tabix">

                <assert_contents>

                    <has_size value="143"/>

                </assert_contents>

            </output>

            <assert_command>

                <has_text text="-p vcf"/>

            </assert_command>
@@ -117,14 +92,12 @@ 
        <test>

            <param name="input1" ftype="gtf" value="cufflinks_out1.gtf" />

            <param name="bgzip" ftype="bgzip" value="cufflinks_out1.gtf.gz" />

            <output name="output1" ftype="tabix">

                <assert_contents>

                    <has_size value="125"/>

                </assert_contents>

            </output>

            <assert_command>

                <has_text text="-p gff" />

            </assert_command>

            <assert_stdout>

                <has_line line="test_chromosome" />

            </assert_stdout>

        </test>

    </tests>

    <help>

lib/galaxy/datatypes/converters/neostorezip_to_neostore_converter.xml

+3 −1
Original line number Diff line number Diff line
@@ -15,7 +15,9 @@ 
  <tests>

    <test>

      <!-- TODO mock test? $output1 should be the html primary file? -->

      <param name="input1" ftype="neostore.zip" value="neostore.zip"/>

      <param name="input1" value="" ftype="neostore.zip">

        <composite_data value="neostore.zip" />

      </param>

      <output name="output1" ftype="neostore">

        <assert_contents>

          <has_n_lines n="2"/>

lib/galaxy_test/driver/driver_util.py

+7 −0
Original line number Diff line number Diff line
@@ -66,6 +66,7 @@ FRAMEWORK_DATATYPES_CONF = os.path.join(FRAMEWORK_TOOLS_DIR, "sample_datatypes_c 
MIGRATED_TOOL_PANEL_CONFIG = "config/migrated_tools_conf.xml"

INSTALLED_TOOL_PANEL_CONFIGS = [os.environ.get("GALAXY_TEST_SHED_TOOL_CONF", "config/shed_tool_conf.xml")]

DEFAULT_LOCALES = "en"

DEFAULT_TOOL_TEST_WAIT: int = int(os.environ.get("GALAXY_TEST_DEFAULT_WAIT", 60))



log = logging.getLogger("test_driver")
@@ -862,6 +863,7 @@ class GalaxyTestDriver(TestDriver): 
        self.allow_tool_conf_override = allow_tool_conf_override

        self.default_tool_conf = default_tool_conf

        self.datatypes_conf_override = datatypes_conf_override

        self.maxseconds = getattr(config_object, "maxseconds", DEFAULT_TOOL_TEST_WAIT)



    def setup(self, config_object=None):

        """Setup a Galaxy server for functional test (if needed).
@@ -961,12 +963,17 @@ class GalaxyTestDriver(TestDriver): 
            "keep_outputs_dir": None,

        }

        galaxy_interactor = GalaxyInteractorApi(**galaxy_interactor_kwds)

        # Cut down default timeout to 60 seconds within tests run via

        # GalaxyTestDriver. Does not affect tests run via galaxy-tool-util,

        # which use a much longer timeout.

        maxseconds = kwd.pop("maxseconds", self.maxseconds)

        verify_tool(

            tool_id=tool_id,

            test_index=index,

            galaxy_interactor=galaxy_interactor,

            resource_parameters=resource_parameters,

            test_data_resolver=TestDataResolver(),

            maxseconds=maxseconds,

            **kwd,

        )

test/integration/resubmission_pulsar_job_conf.xml

+4 −2
Original line number Diff line number Diff line
@@ -5,7 +5,9 @@ 
<job_conf>

    <plugins>

        <plugin id="local" type="runner" load="galaxy.jobs.runners.local:LocalJobRunner" workers="1"/>

        <plugin id="pulsar_rest" type="runner" load="galaxy.jobs.runners.pulsar:PulsarRESTJobRunner"/>

        <plugin id="pulsar_rest" type="runner" load="galaxy.jobs.runners.pulsar:PulsarRESTJobRunner">

            <param id="transport_timeout">10</param>

        </plugin>

    </plugins>



    <destinations default="initial_pulsar">