Item 7348 : Front Page, ETL & Breadcrumbs on Reports (#272)

- Feature Request 39428: Modify home page to clarify for HIV: Font updates. - Feature Request 36306: Update virus metadata in Learn - Assays: ETL file name change from VirusPanel_Metadata.txt to VirusPanel.txt, and PK updates to cds.import_nabantigen and cds.nabantigen tables. - Feature Request 39429: Enable more than 2 reports in MAB section: add breadcrumbs on reports page. - Secure Issue 40526: Invalid param value for 'study' throws NPE : show error message instead of NPE.
LabKey · May 31, 2020 · e77083a · e77083a
1 parent 155678e
commit e77083a
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Showing 20 changed files with 216 additions and 53 deletions.
diff --git a/resources/schemas/dbscripts/postgresql/cds-20.003-20.004.sql b/resources/schemas/dbscripts/postgresql/cds-20.003-20.004.sql
@@ -0,0 +1,5 @@
+ALTER TABLE cds.import_nabantigen DROP CONSTRAINT import_nabantigen_pkey;
+ALTER TABLE cds.import_nabantigen ADD PRIMARY KEY (container, assay_identifier, cds_virus_id);
+
+ALTER TABLE cds.nabantigen DROP CONSTRAINT nabantigen_pkey;
+ALTER TABLE cds.nabantigen ADD PRIMARY KEY (container, assay_identifier, cds_virus_id);
diff --git a/src/org/labkey/cds/CDSController.java b/src/org/labkey/cds/CDSController.java
@@ -1036,7 +1036,6 @@ else if (isPost())
     @RequiresPermission(ReadPermission.class)
     public static class GetStudyDocumentAction extends SimpleViewAction<StudyDocumentForm>
     {
-        @Override
         public NavTree appendNavTrail(NavTree root)
         {
             return null;
@@ -1067,7 +1066,12 @@ public ModelAndView getView(StudyDocumentForm form, BindException errors) throws
 
             if (!errors.hasErrors() && !StringUtils.isBlank(filename))
             {
-                if (form.isPublicAccess() || CDSManager.get().isStudyDocumentAccessible(form.getStudy(), form.getDocumentId(), getUser(), getContainer()))
+                //fix for Secure Issue 40526: Invalid param value for 'study' throws NPE
+                if (null != form.getStudy() && null != form.getDocumentId() && !CDSManager.get().isParamValueValid(form.getStudy(), form.getDocumentId(), getUser(), getContainer()))
+                {
+                    errors.reject(ERROR_MSG, "Invalid parameter value(s) for 'study' and/or 'documentId'.");
+                }
+                else if (form.isPublicAccess() || CDSManager.get().isStudyDocumentAccessible(form.getStudy(), form.getDocumentId(), getUser(), getContainer()))
                 {
                     WebdavService service = ServiceRegistry.get().getService(WebdavService.class);
                     WebdavResource resource = service.lookup(Path.parse(basePath + filename));

diff --git a/src/org/labkey/cds/CDSManager.java b/src/org/labkey/cds/CDSManager.java
@@ -17,6 +17,7 @@
 package org.labkey.cds;
 
 import org.apache.commons.lang3.StringUtils;
+import org.jetbrains.annotations.NotNull;
 import org.labkey.api.data.Container;
 import org.labkey.api.data.ContainerManager;
 import org.labkey.api.data.CoreSchema;
@@ -244,16 +245,32 @@ public void setActiveUserProperties(User user, Container container, Map<String,
     }
 
     public boolean isStudyDocumentAccessible(String studyName, String docId, User user, Container container)
+    {
+        TableSelector selector = getDocumentsForStudiesTableSelector(studyName, docId, user, container);
+        return selector.getObject(Boolean.class);
+    }
+
+    @NotNull
+    private TableSelector getDocumentsForStudiesTableSelector(String studyName, String docId, User user, Container container)
     {
         TableInfo tableInfo = getCDSQueryTableInfo("learn_documentsforstudies", user, container);
         SimpleFilter filter = new SimpleFilter();
         filter.addCondition(FieldKey.fromParts("prot"), studyName);
         filter.addCondition(FieldKey.fromParts("document_id"), docId);
 
-        TableSelector selector = new TableSelector(tableInfo, Collections.singleton("accessible"), filter, null);
-        return selector.getObject(Boolean.class);
+        return new TableSelector(tableInfo, Collections.singleton("accessible"), filter, null);
     }
 
+    public boolean isParamValueValid(String studyName, String docId, User user, Container container)
+    {
+        TableSelector selector = getDocumentsForStudiesTableSelector(studyName, docId, user, container);
+
+        if (null == selector.getObject(Boolean.class))
+        {
+            return false;
+        }
+        return selector.getObject(Boolean.class);
+    }
 
     public static TableInfo getCDSQueryTableInfo(String queryName, User user, Container container)
     {

diff --git a/src/org/labkey/cds/CDSModule.java b/src/org/labkey/cds/CDSModule.java
@@ -170,7 +170,7 @@ public String getName()
     @Override
     public @Nullable Double getSchemaVersion()
     {
-        return 20.003;
+        return 20.004;
     }
 
     @Override

diff --git a/src/org/labkey/cds/data/steps/CDSImportTask.java b/src/org/labkey/cds/data/steps/CDSImportTask.java
@@ -93,7 +93,7 @@ public class CDSImportTask extends TaskRefTaskImpl
         new TSVCopyConfig("NAbAntigen", "AssayNABAntigen_Metadata"),
         new TSVCopyConfig("BAMAAntigen", "AssayBAMAAntigen_Metadata"),
         new TSVCopyConfig("antigenPanel", "AntigenPanel_Metadata"),
-        new TSVCopyConfig("virusPanel", "VirusPanel_Metadata"),
+        new TSVCopyConfig("virusPanel", "VirusPanel"),
 
         // Datasets
         new TSVCopyConfig("ICS", "AssayICS"),

diff --git a/src/org/labkey/cds/view/template/FrontPage.jsp b/src/org/labkey/cds/view/template/FrontPage.jsp
@@ -536,11 +536,16 @@
                 <span>Don't have an account?</span>
                 <a href="#" class="register-modal-trigger front-page-button">Register Here</a>
             </div>
-            <div class="welcome">
-                <div class="title">
+            <div class="welcome" style="margin-bottom: unset">
+                <div class="title" style="margin-bottom: unset">
+                    <h1></h1>
                     <h1>Welcome to the</h1>
                     <h1>CAVD DataSpace</h1>
-                    <h1>A data sharing and discovery tool for HIV vaccine research</h1>
+                </div>
+            </div>
+            <div class="learn-more" style="max-width:unset;">
+                <div class="container" style="margin-top: unset;">
+                    <h3>A data sharing and discovery tool for HIV vaccine research</h3>
                 </div>
             </div>
             <div class="video-container">

diff --git a/...taspace/cdsimport/VirusPanel_Metadata.txt → ...ledata/dataspace/cdsimport/VirusPanel.txt b/...taspace/cdsimport/VirusPanel_Metadata.txt → ...ledata/dataspace/cdsimport/VirusPanel.txt
diff --git a/test/src/org/labkey/test/tests/cds/CDSMAbTest.java b/test/src/org/labkey/test/tests/cds/CDSMAbTest.java
@@ -22,19 +22,24 @@
 import org.junit.experimental.categories.Category;
 import org.junit.rules.Timeout;
 import org.labkey.test.Locator;
+import org.labkey.test.TestFileUtils;
 import org.labkey.test.pages.cds.AntigenFilterPanel;
 import org.labkey.test.pages.cds.CDSExport;
 import org.labkey.test.pages.cds.InfoPane;
 import org.labkey.test.pages.cds.MAbDataGrid;
 import org.labkey.test.util.cds.CDSHelper;
 import org.openqa.selenium.WebElement;
 
+import java.io.File;
 import java.io.IOException;
 import java.util.ArrayList;
 import java.util.Arrays;
 import java.util.List;
 import java.util.concurrent.TimeUnit;
 
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertFalse;
+import static org.junit.Assert.assertTrue;
 import static org.labkey.test.pages.cds.MAbDataGrid.ANTIGEN_BINDING_COL;
 import static org.labkey.test.pages.cds.MAbDataGrid.CLADES_COL;
 import static org.labkey.test.pages.cds.MAbDataGrid.GEOMETRIC_MEAN_IC50_COL;
@@ -227,7 +232,7 @@ public void testMAbSearchFilter()
     }
 
     @Test
-    public void testMAbReports()
+    public void testMAbReports() throws IOException
     {
         CDSHelper.NavigationLink.MABGRID.makeNavigationSelection(this);
         MAbDataGrid grid = new MAbDataGrid(getGridEl(), this, this);
@@ -284,6 +289,42 @@ public void testMAbReports()
         log("Verify the 2nd R report");
         grid.openIC50Report();
         Assert.assertTrue("Report image is not rendered", isElementPresent(grid.getReportImageOut()));
+
+        verifyBreadCrumbs(grid);
+    }
+
+    private void verifyBreadCrumbs(MAbDataGrid grid) throws IOException
+    {
+        log("Verify header breadcrumbs from the Reports view");
+        clickExportCSVBreadCrumb();
+        clickExportExcelBreadCrumb();
+        clickViewGrid(grid);
+    }
+
+    private void clickViewGrid(MAbDataGrid grid)
+    {
+        log("Verify 'View Grid' button takes user back to MAb grid.");
+        Locator.XPathLocator viewGridBtn = Locator.tagWithId("a", "mabgridcolumnsbtn-breadcrumb");
+        click(viewGridBtn);
+        assertTrue("Unable to get back to the grid, MAb report buttons not present",
+                isElementPresent(grid.getDilutionReportBtn()) && isElementPresent(grid.getIC50ReportBtn()));
+    }
+
+    private void clickExportExcelBreadCrumb()
+    {
+        log("Verify 'Export CSV' button downloads the zip from Reports view.");
+        Locator.XPathLocator exportExcelBtn = Locator.tagWithId("a", "gridexportexcelbtn-breadcrumb");
+        File exceldownload = clickAndWaitForDownload(exportExcelBtn);
+        String fileContents = TestFileUtils.getFileContents(exceldownload);
+        assertTrue("Empty file", fileContents.length() > 0);
+    }
+
+    private void clickExportCSVBreadCrumb() throws IOException
+    {
+        Locator.XPathLocator exportCSVBtn = Locator.tagWithId("a", "gridexportcsvbtn-breadcrumb");
+        File csvZipArchive = clickAndWaitForDownload(exportCSVBtn);
+        assertEquals("Zip archive file count mismatch (expected these files in the zip archive: Assays.csv, MAbs.csv, Metadata.txt, NAB MAB.csv, Studies.csv, Study and MAbs.csv, Variable definitions.csv)", 7,
+                TestFileUtils.getFilesInZipArchive(csvZipArchive).size());
     }
 
     private void verifyReportContent(List<String> expectedContent, String reportContent)

diff --git a/test/src/org/labkey/test/tests/cds/CDSTestLearnAbout.java b/test/src/org/labkey/test/tests/cds/CDSTestLearnAbout.java
@@ -1136,7 +1136,8 @@ private void verifyNonIntegratedDetailFieldValues(String value, String suffix)
     private void verifyNonIntegratedDownloadLink(String altText, String documentName)
     {
         Locator.XPathLocator downloadLinkLocator = Locator.tagWithAttributeContaining("img", "alt", altText);
-        File downloadedFile = clickAndWaitForDownload(downloadLinkLocator, 1)[0];
+        scrollIntoView(downloadLinkLocator);
+        File downloadedFile = clickAndWaitForDownload(downloadLinkLocator);
         assertTrue(downloadedFile + " not downloaded.", downloadedFile.getName().contains(documentName));
     }
 
@@ -1149,7 +1150,7 @@ private void verifyNonIntegratedDataHeader(String studyName)
 
         verifySectionHeaders("Non-integrated data");
 
-        Locator.XPathLocator nonIntegratedDataElement = Locator.tagWithAttributeContaining("div", "id", "nonintegrateddataavailability");
+        Locator.XPathLocator nonIntegratedDataElement = Locator.tagWithAttributeContaining("div", "id", "studynonintegrateddata");
         assertElementPresent(nonIntegratedDataElement);
 
         Locator.XPathLocator instructions = nonIntegratedDataElement.withDescendant(Locator.tag("p")).containing("Download individual files");
@@ -1676,18 +1677,21 @@ public void validateReportsDocumentLinks()
         documentLink = CDSHelper.Locators.studyReportLink("Epitope Mapping Results Summary").findElement(getDriver());
         assertTrue("Was not able to find link to the Powerpoint document for study '" + studyName + "'.", documentLink != null);
         documentName = "cvd260_CAVIMC 031 Linear Epitope Mapping_BaselineSubtracted-3.pptx";
+        scrollIntoView(documentLink);
         cds.validateDocLink(documentLink, documentName);
 
         log("Now check the Excel link.");
         documentLink = CDSHelper.Locators.studyReportLink("NAB Data Summary 2").findElement(getDriver());
         assertTrue("Was not able to find link to the Excel document for study '" + studyName + "'.", documentLink != null);
         documentName = "cvd260_CAVIMC-031 Neutralization Data with AUC 3 May 2011-6.xlsx";
+        scrollIntoView(documentLink);
         cds.validateDocLink(documentLink, documentName);
 
         log("Finally for this study validate the pdf file.");
         documentLink = CDSHelper.Locators.studyReportLink("NAB Data Summary 1").findElement(getDriver());
         assertTrue("Was not able to find link to the PDF document for study '" + studyName + "'.", documentLink != null);
         documentName = "cvd260_McElrath_Seder_Antibody Responses 1.1 01Jun11.pdf";
+        scrollIntoView(documentLink);
         cds.validatePDFLink(documentLink, documentName);
 
         cds.viewLearnAboutPage("Studies");
@@ -1706,12 +1710,14 @@ public void validateReportsDocumentLinks()
         documentLink = CDSHelper.Locators.studyReportLink("CFSE Results Summary").findElement(getDriver());
         assertTrue("Was not able to find link to the Word Document document for study '" + studyName + "'.", documentLink != null);
         documentName = "cvd264_DCVax001_CFSE_Memo_JUL13_v4.docx";
+        scrollIntoView(documentLink);
         cds.validateDocLink(documentLink, documentName);
 
         log("Now check one of the PDF link.");
         documentLink = CDSHelper.Locators.studyReportLink("ICS Data Summary").findElement(getDriver());
         assertTrue("Was not able to find link to the PDF document for study '" + studyName + "'.", documentLink != null);
         documentName = "cvd264_ICS_LAB_REPORT_19APR13_n24fcm_fh_IL2_CD154_MIMOSA.pdf";
+        scrollIntoView(documentLink);
         cds.validatePDFLink(documentLink, documentName);
 
         cds.viewLearnAboutPage("Studies");

diff --git a/webapp/Connector/src/app/store/Publication.js b/webapp/Connector/src/app/store/Publication.js
@@ -151,7 +151,7 @@ Ext.define('Connector.app.store.Publication', {
             }, this);
 
             // map the docs to each publication
-            let publicationMap = {};
+            var publicationMap = {};
             Ext.each(documents, function (doc) {
                 publicationMap[doc.publication_id] = publicationMap[doc.publication_id] || [];
                 publicationMap[doc.publication_id].push(doc);

diff --git a/webapp/Connector/src/app/view/module/NonIntegratedDataAvailability.js b/webapp/Connector/src/app/view/module/NonIntegratedDataAvailability.js
@@ -18,7 +18,7 @@ Ext.define('Connector.view.module.NonIntegratedDataAvailability', {
 
     initComponent : function() {
 
-        const data = this.getData();
+        var data = this.getData();
         if (data.length > 0) {
             var docIsValidAction = function(doc, status) {
                 doc.isLinkValid = status;
@@ -62,7 +62,7 @@ Ext.define('Connector.view.module.NonIntegratedDataAvailability', {
                 width: '90%',
                 sortable: false,
                 menuDisabled: true,
-                tpl:  this.getColTemplate(),
+                tpl:  this.getColTemplate()
             }],
             listeners : {
                 'itemmouseenter' : function(view, record, item, index, evt) {
@@ -268,7 +268,7 @@ Ext.define('Connector.view.module.PublicationNonIntegratedData', {
     },
 
     getStore : function(data) {
-        let config =  {
+        var config =  {
             fields: ['publication_id', 'document_id', 'label', 'fileName', 'filePath', 'docType', 'isLinkValid', 'suffix'],
             data: data,
             storeId: 'PublicationNonIntegratedDataStore'

diff --git a/webapp/Connector/src/component/Started.js b/webapp/Connector/src/component/Started.js
@@ -153,7 +153,7 @@ Ext.define('Connector.component.Started', {
                         me.loadHelpFile();
                     }
                 }
-            }],
+            }]
         };
         Connector.panel.HelpCenter.displayWikiWindow(target, config);
     },

diff --git a/webapp/Connector/src/controller/AbstractGridController.js b/webapp/Connector/src/controller/AbstractGridController.js
@@ -67,5 +67,5 @@ Ext.define('Connector.controller.AbstractGridController', {
 
     onViewActivate : function() {},
 
-    onViewDeactivate : function() {},
+    onViewDeactivate : function() {}
 });
diff --git a/webapp/Connector/src/ext-patches.js b/webapp/Connector/src/ext-patches.js
@@ -76,7 +76,7 @@ Ext.override(Ext.grid.View, {
 });
 
 Ext.override(Ext.util.Format, {
-    date(v, format){
+    date : function(v, format){
         if (!v) {
             return "";
         }

diff --git a/webapp/Connector/src/panel/HelpCenter.js b/webapp/Connector/src/panel/HelpCenter.js
@@ -27,7 +27,7 @@ Ext.define('Connector.panel.HelpCenter', {
                         },
                         scope: this
                     }
-                }],
+                }]
             };
             Connector.panel.HelpCenter.displayWikiWindow(animateTarget, config);
         },

diff --git a/webapp/Connector/src/panel/ToolsAndLinks.js b/webapp/Connector/src/panel/ToolsAndLinks.js
@@ -21,7 +21,7 @@ Ext.define('Connector.panel.ToolsAndLinks', {
                 id: 'toolspopup',
                 items: [{
                     xtype: 'toolslinks'
-                }],
+                }]
             };
             Connector.panel.HelpCenter.displayWikiWindow(animateTarget, config);
         }

diff --git a/webapp/Connector/src/view/Grid.js b/webapp/Connector/src/view/Grid.js
@@ -91,7 +91,7 @@ Ext.define('Connector.view.Grid', {
                 xtype: 'container',
                 items: [this.getSourceTabHeader(), this.getSelectColumnsButton()],
                 layout: {
-                    type: 'hbox',
+                    type: 'hbox'
                 }
             }]
         }];