- Include the PubMedId in the make public URL included in the "found publication" message.

- Improve author match and title match logic

Author: vagisha

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

@@ -6951,7 +6951,6 @@ public ModelAndView getView(PublicationDetailsForm form, boolean reshow, BindExc
                 return new SimpleErrorView(errors);
             }
 
-            form.setPubmedId(_copiedExperiment.getPubmedId());
             form.setLink(_copiedExperiment.getPublicationLink());
             form.setCitation(_copiedExperiment.getCitation());
             return getPublicationDetailsView(form, errors);

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

@@ -410,7 +410,12 @@ public static String getDataStatusReminderMessage(@NotNull ExperimentAnnotations
                                                       @Nullable PublicationMatch articleMatch)
     {
         String shortUrl = exptAnnotations.getShortUrl().renderShortURL();
-        String makePublicLink = PanoramaPublicController.getMakePublicUrl(exptAnnotations.getId(), exptAnnotations.getContainer()).getURIString();
+        ActionURL makePublicUrl = PanoramaPublicController.getMakePublicUrl(exptAnnotations.getId(), exptAnnotations.getContainer());
+        if (articleMatch != null && articleMatch.isPubMed() && articleMatch.getPublicationId() != null)
+        {
+            makePublicUrl.replaceParameter("pubmedId", articleMatch.getPublicationId());
+        }
+        String makePublicLink = makePublicUrl.getURIString();
         String dateString = DateUtil.formatDateTime(js.getLatestSubmission().getCreated(), PrivateDataReminderSettings.DATE_FORMAT_PATTERN);
 
         ActionURL viewMessageUrl = new ActionURL("announcements", "thread", announcementContainer)
@@ -446,6 +451,7 @@ public static String getDataStatusReminderMessage(@NotNull ExperimentAnnotations
                     .append(NL2).append("If this is indeed your paper, congratulations! We encourage you to make your data public so the research community can access it alongside your paper. ")
                     .append("You can do this by clicking the \"Make Public\" button in your data folder or by clicking this link: ")
                     .append(bold(link("Make Data Public", makePublicLink))).append(".")
+                    .append(articleMatch.isPubMed() ? " Please enter " + articleMatch.getPublicationId() + " in the PubMed ID field." : "")
                     .append(NL2).append("If this paper is not associated with your data please let us know by clicking ")
                     .append(bold(link("Dismiss Publication Suggestion", dismissPublicationUrl.getURIString())));
         }

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

@@ -3,7 +3,6 @@
 import org.jetbrains.annotations.Nullable;
 import org.json.JSONArray;
 import org.json.JSONObject;
-import org.labkey.panoramapublic.ncbi.NcbiConstants.DB;
 
 import java.io.IOException;
 import java.util.ArrayList;
@@ -14,13 +13,12 @@
 /**
  * Mock implementation of {@link NcbiPublicationSearchService} that returns canned data registered by tests.
  * Used by Selenium tests when running on TeamCity.
- * Extends {@link NcbiPublicationSearchServiceImpl} and only overrides the two methods that make HTTP calls
- * to NCBI: {@link #getJson(String)} (used by ESearch/ESummary) and {@link #getCitation(String, DB)}
- * (used for the Citation Exporter API). All search logic, filtering, author/title verification, and
- * priority filtering run through the real implementation code.
+ * Extends {@link NcbiPublicationSearchServiceImpl} and only overrides {@link #getString(String)},
+ * the single method that makes HTTP calls to NCBI. All search logic, filtering, author/title
+ * verification, citation parsing, and priority filtering run through the real implementation code.
  * Tests register mock articles via {@link #register}, providing the database, ID, search key,
  * metadata fields, and citation. The mock builds internal lookup maps from this data and returns
- * appropriate JSON responses when the real search logic calls {@code getJson()} or {@code getCitation()}.
+ * appropriate responses when the real search logic calls {@code getString()}.
  */
 public class MockNcbiPublicationSearchService extends NcbiPublicationSearchServiceImpl
 {
@@ -37,7 +35,7 @@ public class MockNcbiPublicationSearchService extends NcbiPublicationSearchServi
 
     /**
      * Register a mock article. The mock stores the data in internal lookup maps used by
-     * {@link #getJson(String)} and {@link #getCitation(String, DB)}.
+     * {@link #getString(String)}.
      * @param database     "pmc" or "pubmed" — the NCBI database this article is in
      * @param id           the article ID in the given database (numeric ID for pmc or pubmed)
      * @param searchKey    what ESearch query term finds this article (e.g. PXD ID for PMC, author last name for PubMed)
@@ -115,31 +113,27 @@ public void register(String database, String id, String searchKey,
     }
 
     /**
-     * Returns canned JSON for NCBI ESearch and ESummary API requests based on registered mock data.
+     * Returns canned responses for NCBI API requests based on registered mock data.
+     * Handles ESearch, ESummary, and Citation Exporter URLs.
      */
     @Override
-    protected JSONObject getJson(String url) throws IOException
+    protected String getString(String url) throws IOException
     {
         if (url.contains("esearch.fcgi"))
         {
-            return handleESearch(url);
+            return handleESearch(url).toString();
         }
         else if (url.contains("esummary.fcgi"))
         {
-            return handleESummary(url);
+            return handleESummary(url).toString();
+        }
+        else if (url.contains("lit/ctxp"))
+        {
+            return handleCitation(url).toString();
         }
         throw new IOException("MockNcbiPublicationSearchService: unexpected URL: " + url);
     }
 
-    /**
-     * Returns the registered citation for the given PubMed ID, or null if not registered.
-     */
-    @Override
-    public @Nullable String getCitation(String pubMedId, DB database)
-    {
-        return _citations.get(pubMedId);
-    }
-
     private JSONObject handleESearch(String url)
     {
         boolean isPmc = url.contains("db=pmc");
@@ -175,4 +169,33 @@ private JSONObject handleESummary(String url)
 
         return new JSONObject().put("result", result);
     }
+
+    /**
+     * Build a citation JSON response matching the NCBI Literature Citation Exporter format.
+     * The real API returns {@code {"nlm":{"orig":"citation text..."}}}.
+     * If no citation is registered for the ID, returns an empty JSON object.
+     */
+    private JSONObject handleCitation(String url)
+    {
+        // Extract the publication ID from the URL (last segment after "id=")
+        String id = null;
+        int idIdx = url.indexOf("id=");
+        if (idIdx >= 0)
+        {
+            id = url.substring(idIdx + 3);
+            // Remove any trailing query parameters
+            int ampIdx = id.indexOf('&');
+            if (ampIdx >= 0)
+            {
+                id = id.substring(0, ampIdx);
+            }
+        }
+
+        String citation = id != null ? _citations.get(id) : null;
+        if (citation != null)
+        {
+            return new JSONObject().put("nlm", new JSONObject().put("orig", citation));
+        }
+        return new JSONObject();
+    }
 }