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labkey-jeckels merged 3 commits into from
Feb 17, 2025
Merged

Test fixes related to MS2 GWT deletion work #838

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a7afc01
Test fixes related to MS2 GWT deletion work
labkey-jeckels Feb 15, 2025
b7dc625
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labkey-jeckels Feb 15, 2025
4314965
Different redirect location
labkey-jeckels Feb 15, 2025
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26 changes: 13 additions & 13 deletions ms2/test/src/org/labkey/test/ms2/QuantitationTest.java
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Original file line number Diff line number Diff line change
Expand Up @@ -20,11 +20,14 @@
import org.labkey.test.BaseWebDriverTest;
import org.labkey.test.Locator;
import org.labkey.test.categories.Daily;
import org.labkey.test.categories.MS2;
import org.labkey.test.categories.XTandem;
import org.labkey.test.components.ui.lineage.LineageGraph;
import org.labkey.test.util.PipelineAnalysisHelper;

import java.io.File;

@Category({Daily.class})
@Category({Daily.class, MS2.class, XTandem.class})
@BaseWebDriverTest.ClassTimeout(minutes = 4)
public class QuantitationTest extends AbstractXTandemTest
{
Expand All @@ -34,6 +37,8 @@ public class QuantitationTest extends AbstractXTandemTest
"<?xml version=\"1.0\" encoding=\"UTF-8\" ?> \n" +
"<bioml>\n" +
" <note label=\"pipeline, protocol name\" type=\"input\">" + LIBRA_PROTOCOL_NAME + "</note> \n" +
" <note label=\"pipeline, database\" type=\"input\">Bovine_mini1.fasta</note>\n" +
" <note label=\"protein, cleavage site\" type=\"input\">[KR]|{P}</note>\n" +
" <note label=\"pipeline, protocol description\" type=\"input\">Search with Libra quantitation</note> \n" +
" <note label=\"pipeline prophet, min peptide probability\" type=\"input\">0</note> \n" +
" <note label=\"pipeline prophet, min protein probability\" type=\"input\">0</note> \n" +
Expand All @@ -55,20 +60,15 @@ public void testSteps()

setupEngine();

waitForElement(Locator.xpath("//select[@name='sequenceDB']/option[.='" + DATABASE1 + "']" ), WAIT_FOR_JAVASCRIPT);
log("Set analysis parameters.");
setFormElement(Locator.name("protocolName"), LIBRA_PROTOCOL_NAME);
setFormElement(Locator.name("protocolDescription"), "Search with Libra quantitation");
selectOptionByText(Locator.name("sequenceDB"), DATABASE1);
setFormElement(Locator.name("configureXml"), "");
waitAndClick(Locator.xpath("//a[@class='labkey-button']/span[text() = 'OK']"));
setFormElement(Locator.name("configureXml"), LIBRA_INPUT_XML);
clickButton("Search");
PipelineAnalysisHelper helper = new PipelineAnalysisHelper(this);
helper.waitForProtocolSelect();
helper.setProtocol(LIBRA_PROTOCOL_NAME, LIBRA_INPUT_XML);
helper.setDescription("Search with Libra quantitation");
clickButton("Analyze");

log("View the analysis log.");
// Search is submitted as AJAX, and upon success the browser is redirected to a new page. Wait for it to load
waitForElement(Locator.linkWithText("Data Pipeline"), WAIT_FOR_JAVASCRIPT);
sleep(5000); // without this sleep, some machines try to redirect back to the begin.view page after the Data Pipeline link is clicked
clickAndWait(Locator.linkWithText("Data Pipeline"));
goToModule("Pipeline");

String runDescription = SAMPLE_BASE_NAME + " (" + LIBRA_PROTOCOL_NAME + ")";
waitForPipelineJobsToComplete(1, runDescription, false);
Expand Down
6 changes: 3 additions & 3 deletions ms2/test/src/org/labkey/test/tests/ms2/XTandemTest.java
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Original file line number Diff line number Diff line change
Expand Up @@ -32,6 +32,7 @@

import java.io.File;

import static org.junit.Assert.assertFalse;
import static org.junit.Assert.assertTrue;
import static org.junit.Assert.fail;

Expand All @@ -48,7 +49,6 @@ public class XTandemTest extends AbstractXTandemTest
protected static final String SEARCH_FIND_FASTA3 = "search target ribosomal protein S16 (BS17)";
protected static final String PROTOCOL = "X!Tandem analysis";
protected static final String PEPTIDE_CROSSTAB_RADIO_PROBABILITY_ID = "peptideProphetRadioButton";
protected static final String PEPTIDE_CROSSTAB_RADIO_PROBABILITY_VALUE = "probability";
protected static final String PEPTIDE_CROSSTAB__PROBABILITY_TEXTBOX_NAME = "peptideProphetProbability";
protected static final String PEPTIDE_CROSSTAB_RADIO_NAME = "peptideFilterType";
protected static final String PEPTIDE_CROSSTAB_RADIO_VALUE_NONE = "none";
Expand All @@ -59,7 +59,7 @@ public void testSteps()
log("Verifying that pipeline files were cleaned up properly");
File test2 = new File(PIPELINE_PATH + "/bov_sample/" + SEARCH_TYPE + "/test2");
if (test2.exists())
fail("Pipeline files were not cleaned up; test2("+test2.toString()+") directory still exists");
fail("Pipeline files were not cleaned up; test2("+ test2 +") directory still exists");

basicMS2Check();
}
Expand Down Expand Up @@ -157,7 +157,7 @@ private void verifyComparePeptides()
setFormElement(Locator.name("minimumProbability"), "");
clickButton("Search");
clickAndWait(Locator.id("expandCollapse-ProteinSearchProteinMatches"), 0);
assertTrue(!(isTextPresent(SEARCH_FIND_FASTA1) || isTextPresent(SEARCH_FIND_ALT_FASTA1)));
assertFalse(isTextPresent(SEARCH_FIND_FASTA1) || isTextPresent(SEARCH_FIND_ALT_FASTA1));
assertTextNotPresent(SEARCH_FIND_FASTA1);
assertTextPresent("No data to show");

Expand Down