Fixed the private data reminder schedule and NCBI publication search failure handling

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

@@ -158,6 +158,7 @@
 import org.labkey.panoramapublic.message.PrivateDataMessageScheduler;
 import org.labkey.panoramapublic.message.PrivateDataReminderSettings;
 import org.labkey.panoramapublic.ncbi.MockNcbiPublicationSearchService;
+import org.labkey.panoramapublic.ncbi.NcbiApiKeyCheck;
 import org.labkey.panoramapublic.ncbi.NcbiPublicationSearchService;
 import org.labkey.panoramapublic.ncbi.NcbiPublicationSearchServiceImpl;
 import org.labkey.panoramapublic.ncbi.PublicationMatch;
@@ -10084,6 +10085,55 @@ public static ActionURL getViewExperimentModificationsURL(int experimentAnnotati
         return result;
     }
 
+    @RequiresPermission(AdminOperationsPermission.class)
+    public static class ValidateNcbiApiKeyAction extends MutatingApiAction<PrivateDataReminderSettingsForm>
+    {
+        @Override
+        public Object execute(PrivateDataReminderSettingsForm form, BindException errors)
+        {
+            ApiSimpleResponse response = new ApiSimpleResponse();
+            response.put("success", true);
+
+            // An empty field means check the key that is already saved, since the form never
+            // displays it.
+            boolean checkingSavedKey = StringUtils.isBlank(form.getNcbiApiKey());
+            String apiKey = checkingSavedKey
+                    ? PrivateDataReminderSettings.get().getNcbiApiKey()
+                    : form.getNcbiApiKey().trim();
+
+            if (StringUtils.isBlank(apiKey))
+            {
+                response.put("valid", false);
+                response.put("message", "Enter a key to validate, or save one first.");
+                return response;
+            }
+
+            NcbiApiKeyCheck check = NcbiPublicationSearchService.get().checkApiKey(apiKey);
+            response.put("valid", check.isValid());
+            if (check.isValid())
+            {
+                // Validating does not store anything, so say so. Otherwise "accepted" reads as
+                // confirmation that the key is now in effect.
+                response.put("message", checkingSavedKey
+                        ? "NCBI accepted the saved key."
+                        : "NCBI accepted this key. Click Save to store it.");
+                LOG.info("NCBI accepted an API key entered on the Private Data Reminder Settings page.");
+            }
+            else
+            {
+                // The short message goes beside the field. NCBI's own words are offered separately,
+                // since the admin holding the key is the one who has to act on them.
+                response.put("message", check.isRejected()
+                        ? "NCBI rejected this key."
+                        : "Could not reach NCBI to check this key.");
+                response.put("detail", check.getMessage());
+                LOG.warn("Could not confirm an API key entered on the Private Data Reminder Settings page. {}",
+                        check.getMessage());
+            }
+            return response;
+        }
+    }
+
     @RequiresPermission(AdminOperationsPermission.class)
     public static class PrivateDataReminderSettingsAction extends FormViewAction<PrivateDataReminderSettingsForm>
     {
@@ -10146,6 +10196,8 @@ public ModelAndView getView(PrivateDataReminderSettingsForm form, boolean reshow
                 form.setExtensionLength(settings.getExtensionLength());
                 form.setEnablePublicationSearch(settings.isEnablePublicationSearch());
                 form.setPublicationSearchFrequency(settings.getPublicationSearchFrequency());
+                // Do not put the saved key in the form. The JSP shows only whether one is stored.
+                form.setNcbiApiKeySet(PrivateDataReminderSettings.hasNcbiApiKey());
             }
 
             VBox view = new VBox();
@@ -10168,6 +10220,17 @@ public boolean handlePost(PrivateDataReminderSettingsForm form, BindException er
             settings.setPublicationSearchFrequency(form.getPublicationSearchFrequency());
             PrivateDataReminderSettings.save(settings);
 
+            // A blank field leaves the saved key alone, so editing the reminder schedule cannot
+            // erase it. Removing a key takes the explicit checkbox.
+            if (form.isClearNcbiApiKey())
+            {
+                PrivateDataReminderSettings.saveNcbiApiKey(null);
+            }
+            else if (!StringUtils.isBlank(form.getNcbiApiKey()))
+            {
+                PrivateDataReminderSettings.saveNcbiApiKey(form.getNcbiApiKey());
+            }
+
             PrivateDataMessageScheduler.getInstance().initialize(settings.isEnableReminders());
             return true;
         }
@@ -10205,6 +10268,9 @@ public static class PrivateDataReminderSettingsForm
         private Integer _delayUntilFirstReminder;
         private boolean _enablePublicationSearch;
         private Integer _publicationSearchFrequency;
+        private String _ncbiApiKey;
+        private boolean _clearNcbiApiKey;
+        private boolean _ncbiApiKeySet;
 
         public boolean isEnabled()
         {
@@ -10275,6 +10341,36 @@ public void setPublicationSearchFrequency(Integer publicationSearchFrequency)
         {
             _publicationSearchFrequency = publicationSearchFrequency;
         }
+
+        public String getNcbiApiKey()
+        {
+            return _ncbiApiKey;
+        }
+
+        public void setNcbiApiKey(String ncbiApiKey)
+        {
+            _ncbiApiKey = ncbiApiKey;
+        }
+
+        public boolean isClearNcbiApiKey()
+        {
+            return _clearNcbiApiKey;
+        }
+
+        public void setClearNcbiApiKey(boolean clearNcbiApiKey)
+        {
+            _clearNcbiApiKey = clearNcbiApiKey;
+        }
+
+        public boolean isNcbiApiKeySet()
+        {
+            return _ncbiApiKeySet;
+        }
+
+        public void setNcbiApiKeySet(boolean ncbiApiKeySet)
+        {
+            _ncbiApiKeySet = ncbiApiKeySet;
+        }
     }
 
     @RequiresPermission(AdminOperationsPermission.class)

panoramapublic/src/org/labkey/panoramapublic/PanoramaPublicModule.java

@@ -16,6 +16,7 @@
 
 package org.labkey.panoramapublic;
 
+import org.apache.logging.log4j.Logger;
 import org.jetbrains.annotations.NotNull;
 import org.jetbrains.annotations.Nullable;
 import org.labkey.api.admin.FolderSerializationRegistry;
@@ -34,6 +35,7 @@
 import org.labkey.api.security.roles.RoleManager;
 import org.labkey.api.settings.AdminConsole;
 import org.labkey.api.targetedms.TargetedMSService;
+import org.labkey.api.util.logging.LogHelper;
 import org.labkey.api.view.ActionURL;
 import org.labkey.api.view.BaseWebPartFactory;
 import org.labkey.api.view.HtmlView;
@@ -46,6 +48,7 @@
 import org.labkey.panoramapublic.bluesky.BlueskyApiClient;
 import org.labkey.panoramapublic.bluesky.PanoramaPublicLogoResourceType;
 import org.labkey.panoramapublic.catalog.CatalogImageAttachmentType;
+import org.labkey.panoramapublic.message.PrivateDataMessageScheduler;
 import org.labkey.panoramapublic.message.PrivateDataReminderSettings;
 import org.labkey.panoramapublic.ncbi.NcbiPublicationSearchServiceImpl;
 import org.labkey.panoramapublic.model.Journal;
@@ -82,6 +85,8 @@
 
 public class PanoramaPublicModule extends SpringModule
 {
+    private static final Logger LOG = LogHelper.getLogger(PanoramaPublicModule.class, "Panorama Public module");
+
     public static final String NAME = "PanoramaPublic";
     public static final String DOWNLOAD_DATA_INFO_WP = "Download Data";
 
@@ -151,6 +156,22 @@ protected void startupAfterSpringConfig(ModuleContext moduleContext)
         {
             fileContentService.addFileListener(new PanoramaPublicFileListener());
         }
+
+    }
+
+    @Override
+    public void startBackgroundThreads()
+    {
+        // Re-establish the reminder schedule on every startup. Reminder messages contain absolute
+        // URLs, which are only safe to build once this method is called.
+        try
+        {
+            PrivateDataMessageScheduler.getInstance().initialize(PrivateDataReminderSettings.get().isEnableReminders());
+        }
+        catch (RuntimeException e)
+        {
+            LOG.error("Failed to schedule the Panorama Public private data reminder job", e);
+        }
     }
 
     @NotNull