[bot] Merge 25.7 to 25.11

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()))
@@ -7007,12 +7012,10 @@ public void validateCommand(PublicationDetailsForm form, Errors errors)
                         return;
                     }
                 }
-                if (!form.hasNewPublicationDetails(_copiedExperiment))
-                {
-                    errors.reject(ERROR_MSG, String.format("Publication details are the same as the ones associated with the data on %s at %s",
-                            _journal.getName(), _copiedExperiment.getShortUrl().renderShortURL()));
-                    return;
-                }
+                // Validation removed: no need to ensure that publication details entered in the form differ from the
+                // publication details already associated with the experiment. The user may have entered the
+                // correct PubMedID etc. when submitting but forgot to make the data public.
+                // (See commit history for the original logic.)
             }
             else if (_copiedExperiment.isPublic())
             {
@@ -7356,13 +7359,6 @@ public boolean hasLinkAndCitation()
         {
             return !(StringUtils.isBlank(_link) || StringUtils.isBlank(_citation));
         }
-
-        public boolean hasNewPublicationDetails(ExperimentAnnotations copiedExperiment)
-        {
-            return !(Objects.equals(_pubmedId, copiedExperiment.getPubmedId())
-                    && Objects.equals(_link, copiedExperiment.getPublicationLink())
-                    && Objects.equals(_citation, copiedExperiment.getCitation()));
-        }
     }
 
     public static abstract class PanoramaPublicExperimentAction<T extends ExperimentIdForm> extends FormViewAction<T>
@@ -9849,7 +9845,7 @@ private MessageExampleBean createExampleMessage(List<Integer> experimentIds, Pan
                 {
                     continue;
                 }
-                Announcement announcement = announcementSvc.getAnnouncement(announcementsContainer, getUser(), submission.getAnnouncementId());
+                Announcement announcement = submission.getAnnouncement(announcementSvc, announcementsContainer, getUser());
                 if (announcement == null)
                 {
                     continue; // old data before we started posting submission requests to a message board

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/src/org/labkey/panoramapublic/model/ExperimentAnnotations.java

@@ -224,6 +224,11 @@ public List<String> getInstruments()
         return instruments;
     }
 
+    public String getInstrumentsCommaSeparated()
+    {
+        return StringUtils.join(getInstruments(), ", ");
+    }
+
     public void setInstrument(String instrument)
     {
         _instrument = instrument;
@@ -504,12 +509,12 @@ public DataLicense getDataLicense()
 
     /**
      * Returns true if the experiment is in an 'Experimental Data' folder that is public and the experiment is
-     * associated with a published paper.
+     * associated with a peer-reviewed paper (excludes biorxiv and medrxiv preprint servers).
      */
     public boolean isFinal()
     {
         TargetedMSService.FolderType folderType = TargetedMSService.get().getFolderType(getContainer());
-        return Experiment.equals(folderType) && isPublic() && isPublished();
+        return Experiment.equals(folderType) && isPublic() && isPeerReviewed();
     }
 
     public boolean hasCompletePublicationInfo()

panoramapublic/src/org/labkey/panoramapublic/model/JournalSubmission.java

@@ -2,6 +2,10 @@
 
 import org.jetbrains.annotations.NotNull;
 import org.jetbrains.annotations.Nullable;
+import org.labkey.api.announcements.api.Announcement;
+import org.labkey.api.announcements.api.AnnouncementService;
+import org.labkey.api.data.Container;
+import org.labkey.api.security.User;
 import org.labkey.api.view.ShortURLRecord;
 import org.labkey.panoramapublic.query.SubmissionManager;
 
@@ -69,11 +73,20 @@ public int getModifiedBy()
         return _journalExperiment.getModifiedBy();
     }
 
-    public Integer getAnnouncementId()
+    public @Nullable Integer getAnnouncementId()
     {
         return _journalExperiment.getAnnouncementId();
     }
 
+    public @Nullable Announcement getAnnouncement(@NotNull AnnouncementService announcementSvc,
+                                                                @NotNull Container announcementsContainer,
+                                                                @NotNull User user)
+    {
+        return (getAnnouncementId() != null)
+                ? announcementSvc.getAnnouncement(announcementsContainer, user, getAnnouncementId())
+                : null; // old data before we started posting submission requests to a message board
+    }
+
     public Integer getReviewerId()
     {
         return _journalExperiment.getReviewer();

panoramapublic/src/org/labkey/panoramapublic/pipeline/PostPanoramaPublicMessageJob.java

@@ -102,7 +102,8 @@ private void postMessage()
                     continue;
                 }
 
-                Announcement announcement = announcementSvc.getAnnouncement(announcementsContainer, getUser(), submission.getAnnouncementId());
+                Announcement announcement = submission.getAnnouncement(announcementSvc, announcementsContainer, getUser());
+
                 if (announcement == null)
                 {
                     getLogger().error("Could not find the message thread for experiment Id: " + experimentAnnotationsId

panoramapublic/src/org/labkey/panoramapublic/pipeline/PrivateDataReminderJob.java

@@ -100,6 +100,13 @@ private static ReminderDecision getReminderDecision(@NotNull ExperimentAnnotatio
             return ReminderDecision.skip("Not the current version of the experiment");
         }
 
+        // Make sure the data does not have a pending re-submission request
+        JournalSubmission journalSubmission = SubmissionManager.getSubmissionForJournalCopy(exptAnnotations);
+        if (journalSubmission != null && journalSubmission.hasPendingSubmission())
+        {
+            return ReminderDecision.skip("Data has a pending re-submission request");
+        }
+
         DatasetStatus datasetStatus = DatasetStatusManager.getForExperiment(exptAnnotations);
         if (datasetStatus != null)
         {
@@ -244,7 +251,7 @@ private void processExperiment(Integer experimentAnnotationsId, ProcessingContex
         }
 
         Container announcementsFolder = context.getAnnouncementsFolder();
-        Announcement announcement = context.getAnnouncementService().getAnnouncement(announcementsFolder, getUser(), submission.getAnnouncementId());
+        Announcement announcement = submission.getAnnouncement(context.getAnnouncementService(), context.getAnnouncementsFolder(), getUser());
         if (announcement == null)
         {
             processingResults.addAnnouncementNotFound(experimentAnnotationsId, submission, announcementsFolder);

panoramapublic/src/org/labkey/panoramapublic/proteomexchange/PxHtmlWriter.java

@@ -301,7 +301,7 @@ void writePublicationList(ExperimentAnnotations experimentAnnotations)
         HtmlList publicationList = new HtmlList();
         if(experimentAnnotations.isPublished())
         {
-            publicationList.addItem("Link: ", experimentAnnotations.getPublicationLink(), false);
+            publicationList.addItem("Link", experimentAnnotations.getPublicationLink(), false);
 
             if(experimentAnnotations.hasPubmedId())
             {

panoramapublic/src/org/labkey/panoramapublic/view/expannotations/experimentDetails.jsp

@@ -337,7 +337,7 @@
  <li><strong>Organism:</strong> <%=h(annot.getOrganismsNoTaxId())%></li>
     <%}%>
     <%if(annot.getInstrument() != null){%>
- <li><strong>Instrument:</strong> <%=h(annot.getInstrument())%></li>
+ <li><strong>Instrument:</strong> <%=h(annot.getInstrumentsCommaSeparated())%></li>
     <%}%>
     <%if(annot.getSpikeIn() != null){%>
  <li><strong>SpikeIn:</strong>

panoramapublic/src/org/labkey/panoramapublic/view/publish/dataDownloadInfo.jsp

@@ -23,17 +23,20 @@
 %>
 <p>
     Select one or more files or folders in the browser above and click the download icon ( <span class="fa fa-download"></span> ).
+    <br/>
+    <br/>
     Data can also be downloaded by mapping this folder as a network drive in Windows Explorer, or by using a
     <%=simpleLink("WebDAV", "https://en.wikipedia.org/wiki/WebDAV")%>
     client such as <span class="nobr"><%=simpleLink("CyberDuck", "https://cyberduck.io")%></span>
     or <span class="nobr"><%=simpleLink("WinSCP", "https://winscp.net/eng/docs/introduction")%></span>.
-    For details look at <%=simpleLink("Download data from Panorama Public", downloadDataDocHref)%>.
-    Use the following URL, login email and password to connect to this folder:
-    <br/>
+    WebDAV downloads require an account on the PanoramaWeb server. Information on obtaining an account and other download options
+    is available on the <%=simpleLink("Download data from Panorama Public", downloadDataDocHref)%> help page.
+    Use the following URL to connect to this folder for WebDAV downloads:
     <br/>
     URL: <b class="bold"><span class="nobr" id="webdav_url_link"><%=h(webdavUrl)%></span></b>
     <br/>
-    Login email: <b class="bold"><%=h(publicDataUser.getEmail())%></b>
     <br/>
-    Password: <b class="bold"><%=h(publicDataUser.getPassword())%></b>
+    <b class="bold">Note: </b> If you plan to download large volumes of data or datasets from multiple projects via WebDAV,
+    please contact the PanoramaWeb team in advance so that we can coordinate the download to minimize load on the server
+    and ensure reliable access.
 </p>

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");