- Reset settings after test

- Fixed citation retrieval through mock service
- Fixed confirm messages

Author: vagisha

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

@@ -10457,7 +10457,7 @@ public abstract static class UpdateDatasetStatusAction extends ConfirmAction<Sho
         protected abstract void updateDatasetStatus(DatasetStatus datasetStatus);
         protected abstract void postNotification();
         protected abstract String getConfirmViewTitle();
-        protected abstract HtmlString getConfirmViewMessage();
+        protected abstract Renderable getConfirmViewMessage();
 
         @Override
         public ModelAndView getConfirmView(ShortUrlForm shortUrlForm, BindException errors) throws Exception
@@ -10534,9 +10534,9 @@ protected String getConfirmViewTitle()
         }
 
         @Override
-        protected HtmlString getConfirmViewMessage()
+        protected Renderable getConfirmViewMessage()
         {
-            return HtmlString.of("You are requesting an extension for the private data on Panorama Public at " + _exptAnnotations.getShortUrl().renderShortURL());
+            return DIV("You are requesting an extension for the private data on Panorama Public at ", _exptAnnotations.getShortUrl().renderShortURL());
         }
 
         @Override
@@ -10598,9 +10598,9 @@ protected String getConfirmViewTitle()
         }
 
         @Override
-        protected HtmlString getConfirmViewMessage()
+        protected Renderable getConfirmViewMessage()
         {
-            return HtmlString.of("You are requesting deletion of the private data on Panorama Public at " + _exptAnnotations.getShortUrl().renderShortURL());
+            return DIV("You are requesting deletion of the private data on Panorama Public at ",  _exptAnnotations.getShortUrl().renderShortURL());
         }
 
         @Override
@@ -10656,15 +10656,17 @@ protected String getConfirmViewTitle()
         }
 
         @Override
-        protected HtmlString getConfirmViewMessage()
+        protected Renderable getConfirmViewMessage()
         {
             String publicationRef = _publicationMatch.getCitation() != null
                     ? _publicationMatch.getCitation()
                     : _publicationMatch.getPublicationIdLabel();
-            return HtmlString.of("You are dismissing the publication suggestion for your data on Panorama Public at "
-                    + _exptAnnotations.getShortUrl().renderShortURL() +
-                    ". We will no longer suggest the following publication for this dataset - " +
-                    HtmlString.BR +  publicationRef);
+            return DIV("You are dismissing the publication suggestion for your data on Panorama Public at "
+                    , _exptAnnotations.getShortUrl().renderShortURL()
+                    , BR()
+                    , "We will no longer suggest the following publication for this dataset - "
+                    , BR(),
+                    publicationRef);
         }
 
         @Override
@@ -10712,7 +10714,6 @@ public ModelAndView getSuccessView(ShortUrlForm shortUrlForm)
         {
             setTitle("Publication Suggestion Dismissed");
             return new HtmlView(DIV("The publication suggestion has been dismissed for the data at " + _exptAnnotations.getShortUrl().renderShortURL(),
-                    DIV("We will no longer suggest this publication for your dataset."),
                     BR(),
                     DIV(
                             LinkBuilder.labkeyLink("Data Folder", PageFlowUtil.urlProvider(ProjectUrls.class).getBeginURL(_exptAnnotations.getContainer()))

panoramapublic/src/org/labkey/panoramapublic/ncbi/MockNcbiPublicationSearchService.java

@@ -98,10 +98,16 @@ public void register(String database, String id, String searchKey,
             _pubmedMetadata.put(id, metadata);
         }
 
-        // Store citation keyed by PMID
-        if (citation != null && pmid != null)
+        // Store citation keyed by PMID.
+        // For PMC articles, the PMID is in the pmid parameter.
+        // For PubMed articles, the id parameter is already the PMID.
+        if (citation != null)
         {
-            _citations.put(pmid, citation);
+            String citationKey = isPmc ? pmid : id;
+            if (citationKey != null)
+            {
+                _citations.put(citationKey, citation);
+            }
         }
     }
 

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

@@ -1,5 +1,6 @@
 package org.labkey.test.tests.panoramapublic;
 
+import org.junit.After;
 import org.junit.Test;
 import org.junit.experimental.categories.Category;
 import org.labkey.remoteapi.CommandException;
@@ -238,7 +239,7 @@ private void setupMockNcbiService()
         boolean useMockNcbiService = TestProperties.isTestRunningOnTeamCity();
         if (useMockNcbiService)
         {
-            installMockNcbiService();
+            initMockNcbiService();
         }
         else
         {
@@ -247,7 +248,7 @@ private void setupMockNcbiService()
         }
     }
 
-    private void installMockNcbiService()
+    private void initMockNcbiService()
     {
         try
         {
@@ -367,8 +368,8 @@ private void restoreNcbiService()
         }
     }
 
-    @Override
-    protected void doCleanup(boolean afterTest) throws TestTimeoutException
+    @After
+    public void resetAfterTest()
     {
         if (_useMockNcbi)
         {
@@ -383,7 +384,11 @@ protected void doCleanup(boolean afterTest) throws TestTimeoutException
                     _originalReminderSettings.get("reminderFrequency"),
                     Boolean.parseBoolean(_originalReminderSettings.get("enablePublicationSearch")));
         }
+    }
 
+    @Override
+    protected void doCleanup(boolean afterTest) throws TestTimeoutException
+    {
         _userHelper.deleteUsers(false, SUBMITTER_1, SUBMITTER_2, ADMIN_USER);
         super.doCleanup(afterTest);
     }