- Fix: Do not send private data reminders for datasets that may have been resubmitted and are pending copy.

- Include experiment title in the private data reminder message
- Updated PanoramaPublicMakePublicTest to verify that data pending copy cannot be made public by entering the MakePublicAction URL in the browser.

Author: vagisha

panoramapublic/src/org/labkey/panoramapublic/PanoramaPublicController.java

@@ -6876,6 +6876,11 @@ private ExperimentAnnotations getCopiedExperimentFor(ExperimentAnnotations expAn
                     return null;
                 }
 
+                if (_journalSubmission.hasPendingSubmission())
+                {
+                    errors.reject(ERROR_MSG, String.format("There is a pending re-submit request for this experiment on '%s'", _journal.getName()));
+                    return null;
+                }
                 if (expAnnot.isJournalCopy())
                 {
                     if (!_journalSubmission.isLatestExperimentCopy(_expAnnot.getId()))
@@ -6894,11 +6899,6 @@ private ExperimentAnnotations getCopiedExperimentFor(ExperimentAnnotations expAn
                         errors.reject(ERROR_MSG, String.format("Cannot find a copy of experiment Id %d on '%s'", expAnnot.getId(), _journal.getName()));
                         return null;
                     }
-                    if (submission.isPending())
-                    {
-                        errors.reject(ERROR_MSG, String.format("There is a pending re-submit request for experiment Id %d on '%s'", expAnnot.getId(), _journal.getName()));
-                        return null;
-                    }
                     return copiedExperiment;
                 }
             }

panoramapublic/src/org/labkey/panoramapublic/PanoramaPublicNotification.java

@@ -396,14 +396,15 @@ public static String getDataStatusReminderMessage(@NotNull ExperimentAnnotations
         message.append("Dear ").append(getUserName(submitter)).append(",").append(NL2)
                 .append("We are reaching out regarding your data on Panorama Public (").append(shortUrl).append("), which has been private since ")
                 .append(dateString).append(".")
-                .append("\n\n**Is the paper associated with this work already published?**")
-                .append("\n- If yes: Please make your data public by clicking the \"Make Public\" button in your folder or by clicking this link: ")
+                .append(NL2).append(bold("Title:")).append(" ").append(escape(exptAnnotations.getTitle()))
+                .append(NL2).append(bold("Is the paper associated with this work already published?"))
+                .append(NL).append("- If yes: Please make your data public by clicking the \"Make Public\" button in your folder or by clicking this link: ")
                 .append(bold(link("Make Data Public", makePublicLink)))
                 .append(". This helps ensure that your valuable research is easily accessible to the community.")
-                .append("\n- If not: You have a couple of options:")
-                .append("\n  - **Request an Extension** - If your paper is still under review, or you need additional time, please let us know by clicking ")
+                .append(NL).append("- If not: You have a couple of options:")
+                .append(NL).append("  - ").append(bold("Request an Extension")).append(" - If your paper is still under review, or you need additional time, please let us know by clicking ")
                 .append(bold(link("Request Extension", requestExtensionUrl.getURIString()))).append(".")
-                .append("\n  - **Delete from Panorama Public** - If you no longer wish to host your data on Panorama Public, please click ")
+                .append(NL).append("  - ").append(bold("Delete from Panorama Public")).append(" - If you no longer wish to host your data on Panorama Public, please click ")
                 .append(bold(link("Request Deletion", requesDeletionUrl.getURIString()))).append(". ")
                 .append("We will remove your data from Panorama Public.");
         if (sourceExperiment != null)
@@ -413,9 +414,9 @@ public static String getDataStatusReminderMessage(@NotNull ExperimentAnnotations
                     .append(") will remain intact, allowing you to resubmit your data in the future if you wish.");
         }
 
-        message.append("\n\nIf you have any questions or need further assistance, please do not hesitate to respond to this message by ")
+        message.append(NL2).append("If you have any questions or need further assistance, please do not hesitate to respond to this message by ")
         .append(bold(link("clicking here", respondToMessageUrl.getURIString()))).append(".")
-        .append("\n\nThank you for sharing your research on Panorama Public. We appreciate your commitment to open science and your contributions to the research community.")
+        .append(NL2).append("Thank you for sharing your research on Panorama Public. We appreciate your commitment to open science and your contributions to the research community.")
         .append(NL2).append("Best regards,")
         .append(NL).append(getUserName(journalAdmin));
         return message.toString();

panoramapublic/test/src/org/labkey/test/components/panoramapublic/TargetedMsExperimentWebPart.java

@@ -2,10 +2,16 @@
 
 import org.labkey.test.BaseWebDriverTest;
 import org.labkey.test.Locator;
+import org.labkey.test.WebTest;
+import org.labkey.test.WebTestHelper;
 import org.labkey.test.components.BodyWebPart;
 import org.labkey.test.util.DataRegionTable;
 import org.openqa.selenium.WebElement;
 
+import java.net.MalformedURLException;
+import java.net.URL;
+import java.util.Map;
+
 import static org.junit.Assert.assertNotNull;
 import static org.junit.Assert.assertNull;
 import static org.junit.Assert.assertTrue;
@@ -83,6 +89,24 @@ public void clickMakePublic()
         clickLink(elementCache().makePublicButton, "Expected to see a \"Make Public\" button");
     }
 
+    public Integer getExperimentAnnotationsId()
+    {
+        WebElement moreDetailsLink = elementCache().moreDetailsLink;
+        if (moreDetailsLink != null)
+        {
+            String href = moreDetailsLink.getAttribute("href");
+            try
+            {
+                return Integer.parseInt(WebTestHelper.parseUrlQuery(new URL(href)).get("id"));
+            }
+            catch (MalformedURLException e)
+            {
+                throw new RuntimeException(e);
+            }
+        }
+        return null;
+    }
+
     public void clickAddPublication()
     {
         clickLink(elementCache().addPublicationButton, "Expected to see a \"Add Publication\" button");

panoramapublic/test/src/org/labkey/test/tests/panoramapublic/PanoramaPublicMakePublicTest.java

@@ -18,11 +18,13 @@
 import org.openqa.selenium.NoSuchElementException;
 import org.openqa.selenium.WebElement;
 
+import java.util.Map;
 import java.util.regex.Matcher;
 import java.util.regex.Pattern;
 
 import static org.junit.Assert.assertEquals;
 import static org.junit.Assert.assertFalse;
+import static org.junit.Assert.assertNotNull;
 import static org.junit.Assert.assertTrue;
 
 @Category({External.class, MacCossLabModules.class})
@@ -45,24 +47,38 @@ public void testExperimentCopy()
         verifyIsPublicColumn(PANORAMA_PUBLIC, experimentTitle, false);
         verifyPermissions(projectName, folderName, PANORAMA_PUBLIC, targetFolder);
 
-        // Verify that the submitter can make the data public
-        verifyMakePublic(PANORAMA_PUBLIC, targetFolder, SUBMITTER, true);
         // Verify that a folder admin in the source folder, who is not the submitter or lab head will not see the
         // "Make Public" button in the Panorama Public copy.
-        verifyMakePublic(PANORAMA_PUBLIC, targetFolder, ADMIN_2, false);
+        verifyMakePublicButtonIsNotVisible(PANORAMA_PUBLIC, targetFolder, ADMIN_2,
+                "Make Public button should not be visible to a non-submitter and non-lab head user in the Panorama Public copy");
+
+        // Verify that the submitter can make the data public
+        verifyMakePublic(PANORAMA_PUBLIC, targetFolder, SUBMITTER, true);
 
         // Resubmit the folder.  This is still possible since the Panorama Public copy is not yet associated with a publication.
         resubmitFolder(projectName, folderName, SUBMITTER, true);
 
+        // Data copy is pending. Verify that the "Make Public" button in not available in the source folder or the copied folder
+        verifyMakePublicButtonIsNotVisible(PANORAMA_PUBLIC, targetFolder, SUBMITTER,
+                "Make Public button should not be visible in the Panorama Public copy for submitter if data copy is pending");
+        verifyMakePublicButtonIsNotVisible(projectName, folderName, SUBMITTER,
+                "Make Public button should not be visible in the Panorama Public copy for submitter if data copy is pending");
+
+        // Verify that the submitter cannot enter the MakePublicAction URL in the browser to make the data public
+        verifyCannotMakePublicPendingResubmit(PANORAMA_PUBLIC, targetFolder, SUBMITTER); // In the target folder
+        verifyCannotMakePublicPendingResubmit(projectName, folderName, SUBMITTER); // In the source folder
+
         // Re-copy the experiment to the Panorama Public project. Do not delete the previous copy
         makeCopy(shortAccessUrl, experimentTitle, targetFolder, true, false);
 
         // Verify that the "Make Public button is not visible in the older copy of the data.
         String v1Folder = targetFolder + " V.1";
-        verifyMakePublic(PANORAMA_PUBLIC, v1Folder, SUBMITTER, true);
-        // Verify that the submitter can make data public, and add publication details
+        verifyMakePublicButtonIsNotVisible(PANORAMA_PUBLIC, v1Folder, SUBMITTER,
+                "Make Public button should not be visible in an older copy of the data");
+        verifyCannotMakePublicOldCopy(PANORAMA_PUBLIC, v1Folder, SUBMITTER);
+
+        // Verify that the submitter can make the latest copy of the data public, and add publication details
         verifyMakePublic(PANORAMA_PUBLIC, targetFolder, SUBMITTER, true, true);
-        verifyMakePublic(PANORAMA_PUBLIC, v1Folder, ADMIN_2, false);
 
         verifyIsPublicColumn(PANORAMA_PUBLIC, experimentTitle, true);
 
@@ -281,6 +297,64 @@ private void verifyMakePublic(String projectName, String folderName, String user
         stopImpersonating();
     }
 
+    private void verifyMakePublicButtonVisible(boolean visible, String projectName, String folderName, String user, String errorMessage)
+    {
+        if (isImpersonating())
+        {
+            stopImpersonating(true);
+        }
+        goToProjectFolder(projectName, folderName);
+        impersonate(user);
+        goToDashboard();
+        TargetedMsExperimentWebPart expWebPart = new TargetedMsExperimentWebPart(this);
+
+        if (visible)
+        {
+            assertTrue(errorMessage, expWebPart.hasMakePublicButton());
+        }
+        else
+        {
+            assertFalse(errorMessage, expWebPart.hasMakePublicButton());
+        }
+    }
+
+    private void verifyMakePublicButtonIsVisible(String projectName, String folderName, String user, String errorMessage)
+    {
+        verifyMakePublicButtonVisible(true, projectName, folderName, user, errorMessage);
+    }
+
+    private void verifyMakePublicButtonIsNotVisible(String projectName, String folderName, String user, String errorMessage)
+    {
+        verifyMakePublicButtonVisible(false, projectName, folderName, user, errorMessage);
+    }
+
+    private void verifyCannotMakePublicOldCopy(String projectName, String folderName, String user)
+    {
+        verifyCannotMakePublic(projectName, folderName, user, "not the most recent copy of the data");
+    }
+
+    private void verifyCannotMakePublicPendingResubmit(String projectName, String folderName, String user)
+    {
+        verifyCannotMakePublic(projectName, folderName, user, "There is a pending re-submit request for this experiment");
+    }
+
+    private void verifyCannotMakePublic(String projectName, String folderName, String user, String expectedMessage)
+    {
+        if (isImpersonating())
+        {
+            stopImpersonating(true);
+        }
+        goToProjectFolder(projectName, folderName);
+        impersonate(user);
+        goToDashboard();
+        TargetedMsExperimentWebPart expWebPart = new TargetedMsExperimentWebPart(this);
+        Integer expAnnotationsId = expWebPart.getExperimentAnnotationsId();
+        assertNotNull(expAnnotationsId);
+        beginAt(WebTestHelper.buildURL("panoramapublic", getCurrentContainerPath(), "makePublic", Map.of("id", expAnnotationsId)));
+        waitForText(expectedMessage);
+    }
+
+
     private void makeDataPublic()
     {
         makeDataPublic(true);