[bot] Merge 25.3 to develop

ehr/resources/web/ehr/panel/GeneticCalculationSettingsPanel.js

@@ -7,6 +7,7 @@ Ext4.define('EHR.panel.GeneticCalculationSettingsPanel', {
     extend: 'Ext.panel.Panel',
 
     initComponent: function(){
+        Ext4.QuickTips.init();
         Ext4.apply(this, {
             //width: 550,
             border: false,
@@ -48,6 +49,15 @@ Ext4.define('EHR.panel.GeneticCalculationSettingsPanel', {
                 fieldLabel: 'Hour Of Day',
                 itemId: 'hourOfDay',
                 width: 400
+            },{
+                xtype: 'numberfield',
+                hideTrigger: true,
+                fieldLabel: 'Day of Week',
+                itemId: 'dayOfWeek',
+                helpPopup: 'If provided, the job will run on the specified day of the week (1-7 or Sun-Sat). If blank, it will run each day.',
+                width: 400,
+                minValue: 1,
+                maxValue: 7
             },{
                 xtype: 'textfield',
                 fieldLabel: 'Container Path',
@@ -96,6 +106,7 @@ Ext4.define('EHR.panel.GeneticCalculationSettingsPanel', {
         this.down('#isScheduled').setValue(results.isScheduled);
         this.down('#enabled').setValue(results.enabled);
         this.down('#hourOfDay').setValue(results.hourOfDay);
+        this.down('#dayOfWeek').setValue(results.dayOfWeek);
         this.down('#containerPath').setValue(results.containerPath);
         this.down('#kinshipValidation').setValue(results.kinshipValidation);
         this.down('#allowImportDuringBusinessHours').setValue(results.allowImportDuringBusinessHours)
@@ -109,6 +120,7 @@ Ext4.define('EHR.panel.GeneticCalculationSettingsPanel', {
                 containerPath: this.down('#containerPath').getValue(),
                 enabled: this.down('#enabled').getValue(),
                 hourOfDay: this.down('#hourOfDay').getValue(),
+                dayOfWeek: this.down('#dayOfWeek').getValue(),
                 kinshipValidation: this.down('#kinshipValidation').getValue(),
                 allowImportDuringBusinessHours: this.down('#allowImportDuringBusinessHours').getValue()
             },

ehr/src/org/labkey/ehr/EHRController.java

@@ -640,7 +640,7 @@ public ApiResponse execute(ScheduleGeneticCalculationForm form, BindException er
                 errors.reject(ERROR_MSG, "Unable to find container for path: " + form.getContainerPath());
                 return null;
             }
-            GeneticCalculationsJob.setProperties(form.isEnabled(), c, form.getHourOfDay(), form.isKinshipValidation(), form.isAllowImportDuringBusinessHours());
+            GeneticCalculationsJob.setProperties(form.isEnabled(), c, form.getHourOfDay(), form.getDayOfWeek(), form.isKinshipValidation(), form.isAllowImportDuringBusinessHours());
 
             return new ApiSimpleResponse("success", true);
         }
@@ -758,6 +758,7 @@ public static class ScheduleGeneticCalculationForm
         private boolean _enabled;
         private String containerPath;
         private int hourOfDay;
+        private Integer dayOfWeek;
 
         private boolean _kinshipValidation;
         private boolean _allowImportDuringBusinessHours;
@@ -792,6 +793,16 @@ public void setHourOfDay(int hourOfDay)
             this.hourOfDay = hourOfDay;
         }
 
+        public Integer getDayOfWeek()
+        {
+            return dayOfWeek;
+        }
+
+        public void setDayOfWeek(Integer dayOfWeek)
+        {
+            this.dayOfWeek = dayOfWeek;
+        }
+
         public boolean isKinshipValidation()
         {
             return _kinshipValidation;
@@ -828,6 +839,7 @@ public ApiResponse execute(ScheduleGeneticCalculationForm form, BindException er
             ret.put("isScheduled", GeneticCalculationsJob.isScheduled());
             ret.put("enabled", GeneticCalculationsJob.isEnabled());
             ret.put("hourOfDay", GeneticCalculationsJob.getHourOfDay());
+            ret.put("dayOfWeek", GeneticCalculationsJob.getDayOfWeek());
             ret.put("kinshipValidation", GeneticCalculationsJob.isKinshipValidation());
             ret.put("allowImportDuringBusinessHours", GeneticCalculationsJob.isAllowImportDuringBusinessHours());
 

ehr/src/org/labkey/ehr/pipeline/GeneticCalculationsImportTask.java

@@ -307,6 +307,14 @@ else if (kinshipTable.getSqlDialect().isPostgreSQL())
                     if (lineNum % 250000 == 0)
                     {
                         log.info("imported " + String.format("%,d", lineNum) + " rows");
+                        if (job != null)
+                        {
+                            job.updateStatusForTask();
+                            if (job.isCancelled())
+                            {
+                                throw new CancelledException();
+                            }
+                        }
                     }
                 }
 

ehr/src/org/labkey/ehr/pipeline/GeneticCalculationsJob.java

@@ -97,13 +97,15 @@ public static void schedule()
         if (hour == null)
             hour = 2;
 
+        Integer day = getDayOfWeek();
+
         JobDetail job = JobBuilder.newJob(GeneticCalculationsJob.class)
                 .withIdentity(GeneticCalculationsJob.class.getCanonicalName())
                 .build();
 
         Trigger trigger = TriggerBuilder.newTrigger()
                 .withIdentity(GeneticCalculationsJob.class.getCanonicalName())
-                .withSchedule(CronScheduleBuilder.dailyAtHourAndMinute(hour, 0))
+                .withSchedule(day == null ? CronScheduleBuilder.dailyAtHourAndMinute(hour, 0) : CronScheduleBuilder.weeklyOnDayAndHourAndMinute(day, hour, 0))
                 .forJob(job)
                 .build();
 
@@ -174,12 +176,23 @@ public static Integer getHourOfDay()
         return null;
     }
 
-    public static void setProperties(Boolean isEnabled, Container c, Integer hourOfDay, Boolean isKinshipValidation, Boolean allowImportDuringBusinessHours)
+    public static Integer getDayOfWeek()
+    {
+        Map<String, String> saved = PropertyManager.getProperties(GENETICCALCULATIONS_PROPERTY_DOMAIN);
+
+        if (saved.containsKey("dayOfWeek") & saved.get("dayOfWeek") != null)
+            return Integer.parseInt(saved.get("dayOfWeek"));
+
+        return null;
+    }
+
+    public static void setProperties(Boolean isEnabled, Container c, Integer hourOfDay, @Nullable Integer dayOfWeek, Boolean isKinshipValidation, Boolean allowImportDuringBusinessHours)
     {
         WritablePropertyMap props = PropertyManager.getWritableProperties(GENETICCALCULATIONS_PROPERTY_DOMAIN, true);
         props.put("enabled", isEnabled.toString());
         props.put("container", c.getId());
         props.put("hourOfDay", hourOfDay.toString());
+        props.put("dayOfWeek", dayOfWeek == null ?  null : dayOfWeek.toString());
         props.put("kinshipValidation", isKinshipValidation.toString());
         props.put("allowImportDuringBusinessHours", allowImportDuringBusinessHours.toString());
         props.save();

ehr/test/src/org/labkey/test/util/ehr/EHRTestHelper.java

@@ -230,13 +230,31 @@ public void applyTemplate(Ext4GridRef grid, String templateName, boolean bulkEdi
         }
     }
 
+    public Locator.XPathLocator openBulkEdit(Ext4GridRef grid)
+    {
+        grid.clickTbarButton("More Actions");
+        _test.waitAndClick(Locator.tag("span").withText("Bulk Edit"));
+        Locator.XPathLocator bulkEditWindow = Ext4Helper.Locators.window("Bulk Edit");
+        _test.waitForElement(bulkEditWindow);
+        return bulkEditWindow;
+    }
+
+    // This method toggles the bulk edit field that CONTAINS the label parameter in the label
     public void toggleBulkEditField(String label)
     {
         Locator.XPathLocator l = Ext4Helper.Locators.window("Bulk Edit").append(Locator.tagContainingText("label", label + ":").withClass("x4-form-item-label"));
         _test.shortWait().until(ExpectedConditions.numberOfElementsToBe(l, 1)).get(0).click();
         _test.waitForElement(l.enabled());
     }
 
+    // This method toggles the bulk edit field that has the exact label
+    public void toggleBulkEditExactField(String label)
+    {
+        Locator.XPathLocator l = Ext4Helper.Locators.window("Bulk Edit").append(Locator.tagWithText("label", label + ":").withClass("x4-form-item-label"));
+        _test.shortWait().until(ExpectedConditions.numberOfElementsToBe(l, 1)).get(0).click();
+        _test.waitForElement(l.enabled());
+    }
+
     public void discardForm()
     {
         WebElement dataEntryButton = getDataEntryButton("More Actions").findElement(_test.getDriver());

snd/test/src/org/labkey/test/tests/snd/SNDTest.java

@@ -1048,6 +1048,7 @@ public void preTest()
         //TODO: once exp tables are exposed - do a full cleanup from snd.pkgs, exp.DomainDescriptor, exp.PropertyDomain, exp.PropertyDescriptor
     }
 
+    @SuppressWarnings("JUnit3StyleTestMethodInJUnit4Class") // Explicitly called as part of setup
     public void testSNDImport()
     {
         //go to SND Project
@@ -1264,7 +1265,7 @@ public void cloneDraftPackage()
         assertEquals("2", fairReviewRow.getMin());
         assertEquals("7", fairReviewRow.getMax());
         assertEquals(":-)", fairReviewRow.getDefault());
-        assertEquals(true, fairReviewRow.getRequired());
+        assertTrue(fairReviewRow.getRequired());
         assertEquals("lol", fairReviewRow.getRedactedText());
     }
 
@@ -1404,7 +1405,7 @@ public void saveNewPackage()
         assertEquals("2", reviewRow.getMin());
         assertEquals("7", reviewRow.getMax());
         assertEquals("men", reviewRow.getDefault());
-        assertEquals(true, reviewRow.getRequired());
+        assertTrue(reviewRow.getRequired());
         assertEquals("and women", reviewRow.getRedactedText());
     }
 
@@ -1545,11 +1546,11 @@ public void editCategories() throws Exception
 
         CategoryEditRow surgeryRowCat = catPage.getCategory("Surgery");
         assertNotNull("Surgery category should exist", surgeryRowCat);
-        assertEquals("Surgery category should be active", true, surgeryRowCat.getIsActive());
+        assertTrue("Surgery category should be active", surgeryRowCat.getIsActive());
 
         CategoryEditRow ourCat = catPage.getCategory(editedCategory);
         assertNotNull("test edit category should exist", ourCat);
-        assertEquals("test edit category should be inactive", false, ourCat.getIsActive());
+        assertFalse("test edit category should be inactive", ourCat.getIsActive());
         assertEquals("test edit category should have new description", editedCategory, ourCat.getDescription());
 
         SelectRowsCommand catsCmd = new SelectRowsCommand("snd", "PkgCategories");
@@ -1803,12 +1804,17 @@ public void testProjectApis() throws Exception
     public void testSuperPackageApis() throws Exception
     {
         goToProjectHome();
-        goToSchemaBrowser();
 
         //insert super package
         runScript(SAVEPACKAGEAPI_CHILDREN);
         goToSchemaBrowser();
-        viewQueryData("snd", "SuperPkgs");
+        selectQuery("snd", "SuperPkgs");
+        // Issue 52277: Be sure that the call to analyze the query has completed by waiting for the dependency report,
+        // ensuring it won't be chosen as a deadlock victim
+        waitForText("Dependency Report");
+        Locator viewData = Locator.linkWithText("view data");
+        waitAndClickAndWait(viewData);
+
         assertTextPresent(TEST_SUPER_PKG_DESCRIPTION_1, 1);
         checkResults(TEST_SUPER_PKG_DESCRIPTION_1,
                 Arrays.asList(TEST_SUPER_PKG_START_ID1 + 1,  // top-level super package is the + 0, so start at + 1
@@ -1818,8 +1824,7 @@ public void testSuperPackageApis() throws Exception
 
         //update super package without cloning, with children
         runScript(UPDATESUPERPACKAGEAPI_CHILDREN);
-        goToSchemaBrowser();
-        viewQueryData("snd", "SuperPkgs");
+        refresh();
         assertTextPresent(TEST_SUPER_PKG_DESCRIPTION_2, 1);
         assertTextNotPresent(TEST_SUPER_PKG_DESCRIPTION_1);
         checkResults(TEST_SUPER_PKG_DESCRIPTION_2,
@@ -1832,8 +1837,7 @@ public void testSuperPackageApis() throws Exception
 
         //update super package with cloning
         runScript(UPDATESUPERPACKAGEAPI_CLONE);
-        goToSchemaBrowser();
-        viewQueryData("snd", "SuperPkgs");
+        refresh();
         assertTextPresent(TEST_SUPER_PKG_DESCRIPTION_3, 1);
         assertTextPresent(TEST_SUPER_PKG_DESCRIPTION_2, 1);
         checkResults(TEST_SUPER_PKG_DESCRIPTION_3,
@@ -1846,8 +1850,7 @@ public void testSuperPackageApis() throws Exception
 
         //update super package without cloning, without children
         runScript(UPDATESUPERPACKAGEAPI_NOCHILDREN);
-        goToSchemaBrowser();
-        viewQueryData("snd", "SuperPkgs");
+        refresh();
         assertTextPresent(TEST_SUPER_PKG_DESCRIPTION_4, 1);
         assertTextPresent(TEST_SUPER_PKG_DESCRIPTION_3, 1);
         assertTextNotPresent(TEST_SUPER_PKG_DESCRIPTION_2);
@@ -2170,7 +2173,7 @@ public void categoryPermissionsUI() throws Exception
             {
                 value = getPermissionTableValue(i, 1);
                 assertNotNull(value);
-                assertTrue(value.equals("None"));
+                assertEquals("None", value);
                 categoryRows.add(i);
             }
         }
@@ -2182,7 +2185,7 @@ public void categoryPermissionsUI() throws Exception
         {
             value = getPermissionTableValue(r, 1);
             assertNotNull(value);
-            assertTrue(value.equals("SND Reader"));
+            assertEquals("SND Reader", value);
         }
 
         findButton("Clear All").click();
@@ -2192,7 +2195,7 @@ public void categoryPermissionsUI() throws Exception
         {
             value = getPermissionTableValue(categoryRows.get(k), 1);
             assertNotNull(value);
-            assertTrue(value.equals("None"));
+            assertEquals("None", value);
             click(getSimpleTableCell(Locator.id("category-security"), categoryRows.get(k), 1));
             clickRoleInOpenDropDown(permissions.get(k));
         }
@@ -2203,7 +2206,7 @@ public void categoryPermissionsUI() throws Exception
         {
             value = getPermissionTableValue(categoryRows.get(j), 1);
             assertNotNull(value);
-            assertTrue(value.equals(permissions.get(j)));
+            assertEquals(value, permissions.get(j));
         }
 
     }