Add MCC feature to remove missing IDs (#93)

* Function to identify missing MCC IDs

Author: bbimber

mcc/resources/web/mcc/panel/MccImportPanel.js

@@ -652,6 +652,14 @@ Ext4.define('MCC.panel.MccImportPanel', {
                     parsedRows: parsedRows,
                     panel: this
                 }
+            },{
+                text: 'Process Missing IDs',
+                action: this.processMissingIds,
+                rowData: {
+                    colArray: colArray,
+                    parsedRows: parsedRows,
+                    panel: this
+                }
             }],
             columns: columns
         });
@@ -663,6 +671,143 @@ Ext4.define('MCC.panel.MccImportPanel', {
         }
     },
 
+    processMissingIds: function(e, dt, node, config) {
+        Ext4.Msg.wait('Loading...');
+
+        var idToColony = {};
+        var colonyToId = {};
+        config.rowData.parsedRows.forEach(function(row){
+            idToColony[row.Id] = row.colony;
+
+            if (!colonyToId[row.colony]) {
+                colonyToId[row.colony] = [];
+            }
+
+            colonyToId[row.colony].push(row.Id);
+        });
+
+        var missingIds = []
+        var multi = new LABKEY.MultiRequest();
+        for (var colony in colonyToId) {
+            multi.add(LABKEY.Query.selectRows, {
+                schemaName: 'study',
+                queryName: 'demographics',
+                columns: 'Id,colony,objectid,lsid,calculated_status',
+                filterArray: [
+                    LABKEY.Filter.create('colony', colony, LABKEY.Filter.Types.EQUAL),
+                    LABKEY.Filter.create('calculated_status', 'Alive', LABKEY.Filter.Types.EQUAL),
+                    LABKEY.Filter.create('Id', colonyToId[colony].join(';'), LABKEY.Filter.Types.NOT_IN)
+                ],
+                scope: this,
+                failure: LDK.Utils.getErrorCallback(),
+                success: function (results) {
+                    if (results.rows.length) {
+                        missingIds = missingIds.concat(results.rows);
+                    }
+                }
+            });
+        }
+
+        multi.send(function(){
+            Ext4.Msg.hide();
+            if (missingIds.length) {
+                Ext4.create('Ext.window.Window', {
+                    bodyStyle: 'padding: 5px;',
+                    width: 500,
+                    modal: true,
+                    title: 'Reconcile Census with Existing IDs',
+                    defaults: {
+                        labelWidth: 200,
+                        width: 450,
+                    },
+                    items: [{
+                        html: 'The following IDs are listed for the indicated colony, but were not in your census. Choose any status updates and hit submit:',
+                        border: false,
+                        style: 'padding-bottom: 10px;'
+                    },{
+                        layout: 'table',
+                        border: false,
+                        columns: 2,
+                        defaults: {
+                            border: false
+                        },
+                        items: config.rowData.panel.getAnimalRows(missingIds)
+                    }],
+                    buttons: [{
+                        text: 'Update IDs',
+                        scope: this,
+                        handler: function(btn) {
+                            var updates = []
+                            btn.up('window').query('combo').forEach(function(f){
+                                if (f.getValue() && f.getValue() !== f.sourceRecord.calculated_status) {
+                                    updates.push({
+                                        Id: f.sourceRecord.Id,
+                                        calculated_status: f.getValue(),
+                                        lsid: f.sourceRecord.lsid,
+                                        objectid: f.sourceRecord.objectid
+                                    });
+                                }
+                            });
+
+                            if (updates.length) {
+                                Ext4.Msg.wait('Saving...');
+                                LABKEY.Query.updateRows({
+                                    schemaName: 'study',
+                                    queryName: 'demographics',
+                                    rows: updates,
+                                    scope: this,
+                                    failure: LDK.Utils.getErrorCallback(),
+                                    success: function (results) {
+                                        Ext4.Msg.hide();
+                                        Ext4.Msg.alert('Success', 'Records updated', function(){
+                                            btn.up('window').close();
+                                        }, this);
+                                    }
+                                });
+                            }
+                            else {
+                                Ext4.Msg.alert('No updates', 'No changes, nothing to do');
+                                btn.up('window').close();
+                            }
+                        }
+
+                    },{
+                        text: 'Cancel',
+                        handler: function(btn) {
+                            btn.up('window').close();
+                        }
+                    }]
+                }).show();
+            }
+            else {
+                Ext4.Msg.alert('No missing IDs', 'All existing IDs from these colonies were present in this census, nothing to do');
+            }
+        }, this);
+    },
+
+    getAnimalRows: function(missingIds) {
+        var ret = [];
+        Ext4.Array.forEach(missingIds, function(r){
+            ret = ret.concat([{
+                xtype: 'displayfield',
+                width: 125,
+                value: r.Id + ' / ' + r.colony
+            },{
+                xtype: 'ldk-simplelabkeycombo',
+                schemaName: 'ehr_lookups',
+                queryName: 'calculated_status_codes',
+                displayField: 'code',
+                valueField: 'code',
+                forceSelection: true,
+                sourceRecord: r,
+                width: 100,
+                value: r.calculated_status
+            }]);
+        });
+
+        return(ret);
+    },
+
     onSubmit: function(e, dt, node, config){
         Ext4.Msg.wait('Saving...');
         var rawData = config.rowData.parsedRows;

mcc/resources/web/mcc/window/MarkShippedWindow.js

@@ -225,15 +225,16 @@ Ext4.define('MCC.window.MarkShippedWindow', {
                         }]
                     });
 
-                    // And also add an arrival record:
+                    // And also add an arrival record. NOTE: set the date after the departure to get status to update properly
+                    var arrivalDate = new Date(effectiveDate).setMinutes(effectiveDate.getMinutes() + 1);
                     commands.push({
                         command: 'insert',
                         containerPath: targetFolder,
                         schemaName: 'study',
                         queryName: 'Arrival',
                         rows: [{
                             Id: newId,
-                            date: effectiveDate,
+                            date: arrivalDate,
                             source: centerName,
                             QCState: null,
                             QCStateLabel: 'Completed',

mcc/test/src/org/labkey/test/tests/mcc/MccTest.java

@@ -58,26 +58,31 @@ public class MccTest extends BaseWebDriverTest
     @Test
     public void testMccModule() throws Exception
     {
-        //doRequestFormTest();
-        //doRequestFormTestWithFailure();
+        doRequestFormTest();
+        doRequestFormTestWithFailure();
 
-        //testInvalidId();
+        testInvalidId();
 
         testAnimalImportAndTransfer();
     }
 
+    private static final String ANIMAL_DATA_HEADER = "animal ID\tprevious IDs\tsource\t\"DOB\n(MM/DD/YYYY)\"\tsex\tmaternal ID\tpaternal ID\t\"weight(grams)\"\t\"date of weight\n(MM/DD/YY)\"\tU24 status\tavailalble to transfer\tcurrent housing status\tinfant history\tfertility status\tmedical history\n";
+
+    private static final String ANIMAL_DATA1 = "Animal1\t\t\t7/10/2011\t0 - male\tDam1\tSire1\t382.8\t5/19/2021\t0 - not assigned to U24 breeding colony\t0 - not available for transfer\t1 - natal family group\t3 - successful rearing of offspring\t2 - successful offspring produced\t0 - naive animal\n";
+
+
+    private static final String ANIMAL_DATA2 = "Animal2\t\t\t6/3/2015\t1 - female\tDam2\tSire2\t361.2\t1/28/2021\t0 - not assigned to U24 breeding colony\t0 - not available for transfer\t2 - active breeding\t3 - successful rearing of offspring\t2 - successful offspring produced\t0 - naive animal\n";
+
+    private static final String ANIMAL_DATA3 = "Animal3\t\t\t6/4/2015\t1 - female\tDam2\tSire2\t361.2\t1/28/2021\t0 - not assigned to U24 breeding colony\t0 - not available for transfer\t2 - active breeding\t3 - successful rearing of offspring\t2 - successful offspring produced\t0 - naive animal";
+
     private void testAnimalImportAndTransfer() throws Exception
     {
         beginAt(getProjectName() + "/Colonies/SNPRC/project-begin.view");
         waitAndClickAndWait(Locator.tagWithText("a", "Import Excel-Based Data"));
         waitForElement(Locator.tagWithText("label", "Paste Data Below:"));
         Ext4FieldRef.getForLabel(this, "Center/Colony Name").setValue("SNPRC");
 
-        Ext4FieldRef.getForLabel(this, "Paste Data Below").setValue(
-            "animal ID\tprevious IDs\tsource\t\"DOB\n(MM/DD/YYYY)\"\tsex\tmaternal ID\tpaternal ID\t\"weight(grams)\"\t\"date of weight\n(MM/DD/YY)\"\tU24 status\tavailalble to transfer\tcurrent housing status\tinfant history\tfertility status\tmedical history\n" +
-            "Animal1\t\t\t7/10/2011\t0 - male\tDam1\tSire1\t382.8\t5/19/2021\t0 - not assigned to U24 breeding colony\t0 - not available for transfer\t1 - natal family group\t3 - successful rearing of offspring\t2 - successful offspring produced\t0 - naive animal\n" +
-            "Animal2\t\t\t6/3/2015\t1 - female\tDam2\tSire2\t361.2\t1/28/2021\t0 - not assigned to U24 breeding colony\t0 - not available for transfer\t2 - active breeding\t3 - successful rearing of offspring\t2 - successful offspring produced\t0 - naive animal"
-        );
+        Ext4FieldRef.getForLabel(this, "Paste Data Below").setValue(ANIMAL_DATA_HEADER + ANIMAL_DATA1 + ANIMAL_DATA2 + ANIMAL_DATA3);
 
         waitAndClick(Ext4Helper.Locators.ext4Button("Preview"));
         waitForElement(Locator.tagWithText("td", "Animal2").withClass("dt-center"));
@@ -180,6 +185,35 @@ private void testAnimalImportAndTransfer() throws Exception
         srr.getRows().forEach(row -> {
             Assert.assertEquals("Incorrect QCState", "Completed", row.get("QCState/Label"));
         });
+
+        // Now check status update:
+        populateLookups("SNPRC"); //status is needed for this to work
+        beginAt(getProjectName() + "/Colonies/SNPRC/project-begin.view");
+        waitAndClickAndWait(Locator.tagWithText("a", "Import Excel-Based Data"));
+        waitForElement(Locator.tagWithText("label", "Paste Data Below:"));
+        Ext4FieldRef.getForLabel(this, "Center/Colony Name").setValue("SNPRC");
+
+        Ext4FieldRef.getForLabel(this, "Paste Data Below").setValue(ANIMAL_DATA_HEADER + ANIMAL_DATA1);
+
+        waitAndClick(Ext4Helper.Locators.ext4Button("Preview"));
+        waitForElement(Locator.tagWithText("td", "Animal1").withClass("dt-center"));
+
+        waitAndClick(getButton("Process Missing IDs"));
+        new Window.WindowFinder(getDriver()).withTitle("Reconcile Census with Existing IDs").waitFor();
+        String comboQuery = "combo[queryName='calculated_status_codes']";
+        Ext4ComboRef.waitForComponent(this, comboQuery);
+        Ext4ComboRef statusCombo = _ext4Helper.queryOne(comboQuery, Ext4ComboRef.class);
+        statusCombo.setComboByDisplayValue("Unknown");
+        waitAndClick(Ext4Helper.Locators.ext4Button("Update IDs"));
+        sleep(100);
+        new Window.WindowFinder(getDriver()).withTitle("Success").waitFor();
+        waitAndClick(Ext4Helper.Locators.ext4Button("OK"));
+
+        sr = new SelectRowsCommand("study", "demographics");
+        sr.setColumns(Arrays.asList("Id", "calculated_status"));
+        sr.setFilters(Arrays.asList(new Filter("Id", "Animal3")));
+        srr = sr.execute(createDefaultConnection(), getProjectName() + "/Colonies/SNPRC");
+        Assert.assertEquals("Incorrect status", "Unknown", srr.getRows().get(0).get("calculated_status"));
     }
 
     private static class FormElement
@@ -720,6 +754,8 @@ private void doRequestFormTestWithFailure() throws Exception
         assertElementNotPresent(getButton("Save"));
         assertElementNotPresent(getButton("Submit"));
         assertElementNotPresent(getButton("Approve Request"));
+
+        stopImpersonating();
     }
 
     private FormElement getFormElementByName(String name)
@@ -809,11 +845,19 @@ private void doSetup() throws Exception
         }
     }
 
+    private void populateLookups(String name)
+    {
+        beginAt(getProjectName() + "/Colonies/" + name + "/project-begin.view");
+        waitAndClickAndWait(Locator.tagWithText("a", "Populate Lookups"));
+        waitAndClick(Ext4Helper.Locators.ext4Button("Populate All"));
+        waitForElement(Locator.tagWithText("div", "Populate Complete"));
+    }
+
     private void testInvalidId()
     {
         beginAt("/mcc/" + getProjectName() + "/animalRequest.view?requestId=foo");
 
-        assertElementPresent(Locator.tagWithText("div", "There is no request with id: foo"));
+        waitForElement(Locator.tagWithText("div", "There is no request with id: foo"));
     }