Merge branch 'develop' into fb_pipelineFileLike

Author: labkey-jeckels

data/qc/noopTransform.R

@@ -0,0 +1,9 @@
+all.lines = readLines("${runInfo}")
+runDataFile.line = grep("^runDataFile", all.lines, value = TRUE);
+runDataFile.props <- strsplit(runDataFile.line, "\t")[[1]]
+run.data.file = runDataFile.props[2];
+run.output.file = runDataFile.props[4];
+
+run.data = read.delim(run.data.file, header=TRUE, sep="\t", quote="", check.names=FALSE);
+run.data$TransformType = "${transformOperation}";
+write.table(run.data, file=run.output.file, sep="\t", na="", row.names=FALSE, quote=TRUE, qmethod="double");

modules/editableModule/src/org/labkey/editablemodule/EditableModuleContainerListener.java

@@ -52,8 +52,6 @@ protected void init()
     @Override
     public void doStartup(ModuleContext moduleContext)
     {
-        // add a container listener so we'll know when our container is deleted:
-        ContainerManager.addContainerListener(new EditableModuleContainerListener());
     }
 
     @Override

modules/editableModule/src/org/labkey/editablemodule/EditableModuleModule.java

@@ -1252,6 +1252,12 @@ public DomainFieldRow setSampleType(String sampleTypeName)
         return this;
     }
 
+    public List<String> getAvailableSampleTypes()
+    {
+        expand();
+        return elementCache().getLookupSampleTypeSelect().getOptions().stream().map(WebElement::getText).collect(Collectors.toList());
+    }
+
     public DomainFieldRow setAliquotOption(ExpSchema.DerivationDataScopeType option)
     {
         expand();

src/org/labkey/test/components/domain/DomainFieldRow.java

@@ -4,6 +4,7 @@
  */
 package org.labkey.test.components.ui.grids;
 
+import org.awaitility.Awaitility;
 import org.jetbrains.annotations.Nullable;
 import org.labkey.remoteapi.query.Filter;
 import org.labkey.test.Locator;
@@ -26,6 +27,7 @@
 import org.openqa.selenium.interactions.Actions;
 import org.openqa.selenium.support.ui.ExpectedConditions;
 
+import java.time.Duration;
 import java.util.ArrayList;
 import java.util.Arrays;
 import java.util.Collection;
@@ -357,20 +359,16 @@ public void editColumnLabel(CharSequence columnIdentifier, String newColumnLabel
                 .keyUp(Keys.SHIFT)
                 .perform();
 
-        // Enter the new text.
-        textEdit.sendKeys(newColumnLabel, Keys.RETURN);
+        doAndWaitForUpdate(()-> {
+            textEdit.sendKeys(newColumnLabel, Keys.RETURN);
 
-        getWrapper().shortWait()
+            getWrapper().shortWait()
                 .withMessage("Column label edit text box did not go away.")
                 .until(ExpectedConditions.stalenessOf(textEdit));
 
-        doAndWaitForUpdate(()->
-                WebDriverWrapper.waitFor(()-> WebElementUtils.getTextContent(headerCell).equals(newColumnLabel),
-                        "Column header not updated.", 1_000)
-        );
-        waitForLoaded();
-        clearElementCache();
-
+            Awaitility.await().atMost(Duration.ofSeconds(1)).untilAsserted(() -> assertEquals("Column label",
+                newColumnLabel, WebElementUtils.getTextContent(headerCell)));
+        });
     }
 
     /**

src/org/labkey/test/components/ui/grids/ResponsiveGrid.java

@@ -8,6 +8,7 @@
 import org.labkey.test.BaseWebDriverTest;
 import org.labkey.test.Locator;
 import org.labkey.test.categories.Daily;
+import org.labkey.test.util.WebServicesUtil;
 
 import java.util.List;
 
@@ -53,7 +54,10 @@ public void testLinkedReportToExternalURL()
         waitAndClick(Locator.linkWithText(REPORT_NAME));
         switchToWindow(1);
 
-        waitForElement(Locator.linkWithText("Get a Demo"));
+        if (!WebServicesUtil.isLabKeyDotOrgMaintenance(getDriver()))
+        {
+            waitForElement(Locator.linkWithText("Get a Demo"));
+        }
         Assert.assertEquals("Linked report navigated to incorrect external link", LINK_REPORT_URL, getDriver().getCurrentUrl());
     }
 }

src/org/labkey/test/tests/LinkedReportTest.java

@@ -32,6 +32,7 @@
 import org.labkey.test.util.DataRegionTable;
 import org.labkey.test.util.PortalHelper;
 import org.labkey.test.util.URLBuilder;
+import org.labkey.test.util.WebServicesUtil;
 import org.openqa.selenium.WebElement;
 
 import java.io.IOException;
@@ -764,6 +765,7 @@ public void testScopeFromSiteToSubFolder() throws IOException, CommandException
                 WebElement banner = Locator.tagWithText("h3", "Date & Number Display Formats").refindWhenNeeded(getDriver());
                 checker().withScreenshot()
                         .verifyTrue("'Click here' link did not navigate as expected.",
+                            WebServicesUtil.isLabKeyDotOrgMaintenance(getDriver()) ||
                                 waitFor(banner::isDisplayed, 1_000));
                 closeExtraWindows();
             }

src/org/labkey/test/tests/NonStandardDateAndTimeFormatTest.java

@@ -165,7 +165,7 @@ private void createSmallSampleType() throws IOException, CommandException
                             FILTER_INT_COL.getName(), TestDataGenerator.randomInt(1, INT_MAX),
                             FILTER_STRING_COL.getName(), stringSets.get(setIndex++),
                             FILTER_DATE_COL.getName(), sampleSetDataGenerator.randomDateString(DateUtils.addWeeks(new Date(), -25), new Date()),
-                            FILTER_BOOL_COL.getName(), sampleSetDataGenerator.randomBoolean())
+                            FILTER_BOOL_COL.getName(), TestDataGenerator.randomBoolean())
             );
         }
 

src/org/labkey/test/tests/component/GridPanelTest.java

@@ -469,7 +469,7 @@ private Supplier<Object> getDefaultDataSupplier(PropertyDescriptor propertyDescr
                     case "double":
                         return () -> randomDouble(0, 20);
                     case "boolean":
-                        return this::randomBoolean;
+                        return TestDataGenerator::randomBoolean;
                     case "date":
                     case "datetime":
                         return () -> randomDateString(DateUtils.addWeeks(new Date(), -39), new Date());
@@ -797,7 +797,7 @@ public String randomDateString(String dateFormat, Date min, Date max)
         return new SimpleDateFormat(dateFormat).format(date);
     }
 
-    public boolean randomBoolean()
+    public static boolean randomBoolean()
     {
         return ThreadLocalRandom.current().nextBoolean();
     }

src/org/labkey/test/util/TestDataGenerator.java

@@ -15,10 +15,14 @@
  */
 package org.labkey.test.util;
 
+import org.openqa.selenium.WebDriver;
+
 import java.io.IOException;
 import java.net.InetAddress;
 import java.net.InetSocketAddress;
 import java.net.Socket;
+import java.net.URL;
+import java.util.Objects;
 
 import static org.junit.Assert.assertTrue;
 
@@ -91,4 +95,27 @@ static public Socket openSocket(String hostIp, int port) throws IOException
         socket.connect(new InetSocketAddress(hostIp, port), 2000);
         return socket;
     }
+
+    /**
+     * Checks whether the current page is the maintenance page for labkey.org.
+     * This is usually indicated by a {@code 502}-{@code 504} status code.
+     * Allows tests that check links to labkey.org to not fail during maintenance periods.
+     *
+     * @param driver The WebDriver instance to check
+     * @return true if the current page is the maintenance page for labkey.org, false otherwise.
+     */
+    public static boolean isLabKeyDotOrgMaintenance(WebDriver driver)
+    {
+        try
+        {
+            URL url = new URL(Objects.requireNonNull(driver.getCurrentUrl()));
+            String title = driver.getTitle();
+            int responseCode = Integer.parseInt(Objects.requireNonNull(title).substring(0, 3));
+            return url.getHost().endsWith("labkey.org") && 502 <= responseCode && responseCode <= 504;
+        }
+        catch (Exception e)
+        {
+            return false;
+        }
+    }
 }