- Added a citation column to the DatasetStatus table so that we don't have to lookup the citation for a saved publicationId.

- Added test: running the pipeline job in "test" mode should not update rows in the DatasetStatus table
- Updated PublicationMatch constructor and fromMatchInfo method
- Fixed comments, renamed variables, class.

Author: vagisha

panoramapublic/resources/schemas/dbscripts/postgresql/panoramapublic-25.003-25.004.sql

@@ -3,4 +3,5 @@
 ALTER TABLE panoramapublic.DatasetStatus ADD COLUMN PotentialPublicationId VARCHAR(255);
 ALTER TABLE panoramapublic.DatasetStatus ADD COLUMN PublicationType VARCHAR(50);
 ALTER TABLE panoramapublic.DatasetStatus ADD COLUMN PublicationMatchInfo TEXT;
+ALTER TABLE panoramapublic.DatasetStatus ADD COLUMN Citation TEXT;
 ALTER TABLE panoramapublic.DatasetStatus ADD COLUMN UserDismissedPublication TIMESTAMP;

panoramapublic/resources/schemas/panoramapublic.xml

@@ -865,14 +865,17 @@
             <column columnName="ExtensionRequestedDate" />
             <column columnName="DeletionRequestedDate"/>
             <column columnName="PotentialPublicationId">
-                <description>Cached publication ID (PubMed ID, PMC ID etc.)</description>
+                <description>Publication ID (PubMed ID, PMC ID) suggestion based on NCBI search</description>
             </column>
             <column columnName="PublicationType">
-                <description>Type of publication ID: PMID, PMC, etc.</description>
+                <description>Type of publication ID: PMID, PMC</description>
             </column>
             <column columnName="PublicationMatchInfo">
                 <description>Information about which fields (e.g. PXD, Panorama link, title etc.) matched</description>
             </column>
+            <column columnName="Citation">
+                <description>NLM citation string for the potential publication match</description>
+            </column>
             <column columnName="UserDismissedPublication">
                 <description>Date when the user dismissed the publication suggestion for this dataset</description>
             </column>

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

@@ -159,6 +159,7 @@
 import org.labkey.panoramapublic.ncbi.NcbiPublicationSearchService;
 import org.labkey.panoramapublic.ncbi.NcbiPublicationSearchServiceImpl;
 import org.labkey.panoramapublic.ncbi.PublicationMatch;
+import org.labkey.panoramapublic.ncbi.NcbiConstants.DB;
 import org.labkey.panoramapublic.model.CatalogEntry;
 import org.labkey.panoramapublic.model.DataLicense;
 import org.labkey.panoramapublic.model.DatasetStatus;
@@ -183,7 +184,6 @@
 import org.labkey.panoramapublic.proteomexchange.ChemElement;
 import org.labkey.panoramapublic.proteomexchange.ExperimentModificationGetter;
 import org.labkey.panoramapublic.proteomexchange.Formula;
-import org.labkey.panoramapublic.ncbi.NcbiConstants.DB;
 import org.labkey.panoramapublic.proteomexchange.NcbiUtils;
 import org.labkey.panoramapublic.proteomexchange.ProteomeXchangeService;
 import org.labkey.panoramapublic.proteomexchange.ProteomeXchangeServiceException;
@@ -10300,6 +10300,7 @@ public ModelAndView getView(PrivateDataSendReminderForm form, boolean reshow, Bi
             // Initialize form with current settings on first view
             if (!reshow)
             {
+                // Check the "Search for Publications" box if enabled in the saved settings
                 PrivateDataReminderSettings settings = PrivateDataReminderSettings.get();
                 form.setSearchPublications(settings.isEnablePublicationSearch());
             }
@@ -10670,6 +10671,22 @@ public static class DismissPublicationSuggestionAction extends UpdateDatasetStat
     {
         private PublicationMatch _publicationMatch;
 
+        @Override
+        protected void doValidationForAction(Errors errors)
+        {
+            _publicationMatch = PublicationMatch.fromDatasetStatus(_datasetStatus);
+
+            if (_publicationMatch == null)
+            {
+                errors.reject(ERROR_MSG, "No publication suggestion exists for the data with short URL " + _exptAnnotations.getShortUrl().renderShortURL());
+            }
+            else if (_datasetStatus.getUserDismissedPublication() != null)
+            {
+                errors.reject(ERROR_MSG, "The publication suggestion for the data with short URL " + _exptAnnotations.getShortUrl().renderShortURL()
+                        + " has already been dismissed");
+            }
+        }
+
         @Override
         protected String getConfirmViewTitle()
         {
@@ -10691,22 +10708,6 @@ protected Renderable getConfirmViewMessage()
                     publicationRef);
         }
 
-        @Override
-        protected void doValidationForAction(Errors errors)
-        {
-            _publicationMatch = PublicationMatch.fromDatasetStatus(_datasetStatus);
-
-            if (_publicationMatch == null)
-            {
-                errors.reject(ERROR_MSG, "No publication suggestion exists for the data with short URL " + _exptAnnotations.getShortUrl().renderShortURL());
-            }
-            else if (_datasetStatus.getUserDismissedPublication() != null)
-            {
-                errors.reject(ERROR_MSG, "The publication suggestion for the data with short URL " + _exptAnnotations.getShortUrl().renderShortURL()
-                        + " has already been dismissed");
-            }
-        }
-
         // Fetch the citation from NCBI. If NCBI is unavailable, the publication ID label will be used as a fallback.
         private void fetchCitation()
         {
@@ -10756,6 +10757,21 @@ public ModelAndView getSuccessView(ShortUrlForm shortUrlForm)
         }
     }
 
+    public static class ShortUrlForm
+    {
+        private String _shortUrlEntityId;
+
+        public String getShortUrlEntityId()
+        {
+            return _shortUrlEntityId;
+        }
+
+        public void setShortUrlEntityId(String shortUrlEntityId)
+        {
+            _shortUrlEntityId = shortUrlEntityId;
+        }
+    }
+
     @RequiresPermission(AdminOperationsPermission.class)
     public static class SearchPublicationsForDatasetAction extends SimpleViewAction<ExperimentIdForm>
     {
@@ -10785,21 +10801,17 @@ public ModelAndView getView(ExperimentIdForm form, BindException errors)
             DatasetStatus datasetStatus = DatasetStatusManager.getForExperiment(_exptAnnotations);
 
             // Check if any displayed match was dismissed by the user
-            boolean showDismissedColumn = false;
+
             String dismissedPubId = null;
-            if (datasetStatus != null && datasetStatus.getUserDismissedPublication() != null
-                    && datasetStatus.getPotentialPublicationId() != null)
+            if (datasetStatus != null)
             {
-                dismissedPubId = datasetStatus.getPotentialPublicationId();
-                for (PublicationMatch match : matches)
-                {
-                    if (match.getPublicationId().equals(dismissedPubId))
-                    {
-                        showDismissedColumn = true;
-                        break;
-                    }
-                }
+                dismissedPubId = matches.stream()
+                        .map(PublicationMatch::getPublicationId)
+                        .filter(datasetStatus::isPublicationDismissed)
+                        .findFirst()
+                        .orElse(null);
             }
+            boolean showDismissedColumn = dismissedPubId != null;
 
             SearchPublicationsForDatasetBean bean = new SearchPublicationsForDatasetBean(_exptAnnotations, matches, showDismissedColumn, dismissedPubId);
             JspView<SearchPublicationsForDatasetBean> jspView = new JspView<>("/org/labkey/panoramapublic/view/searchPublicationsForDataset.jsp", bean, errors);
@@ -10891,46 +10903,8 @@ public Object execute(ExperimentIdForm form, BindException errors)
         }
     }
 
-    public static class NotifySubmitterForm extends IdForm
-    {
-        private String _publicationId;
-        private String _publicationType;
-        private String _matchInfo;
-
-        public String getPublicationId()
-        {
-            return _publicationId;
-        }
-
-        public void setPublicationId(String publicationId)
-        {
-            _publicationId = publicationId;
-        }
-
-        public String getPublicationType()
-        {
-            return _publicationType;
-        }
-
-        public void setPublicationType(String publicationType)
-        {
-            _publicationType = publicationType;
-        }
-
-        public String getMatchInfo()
-        {
-            return _matchInfo;
-        }
-
-        public void setMatchInfo(String matchInfo)
-        {
-            _matchInfo = matchInfo;
-        }
-
-    }
-
     @RequiresPermission(AdminOperationsPermission.class)
-    public static class NotifySubmitterOfPublicationsAction extends FormHandlerAction<NotifySubmitterForm>
+    public static class NotifySubmitterOfPublicationAction extends FormHandlerAction<NotifySubmitterForm>
     {
         private Container _announcementsContainer;
         private Announcement _announcement;
@@ -10960,8 +10934,7 @@ public boolean handlePost(NotifySubmitterForm form, BindException errors) throws
 
             // Check if the user has already dismissed this publication suggestion
             DatasetStatus datasetStatus = DatasetStatusManager.getForExperiment(exptAnnotations);
-            if (datasetStatus != null && datasetStatus.getUserDismissedPublication() != null
-                    && form.getPublicationId().equals(datasetStatus.getPotentialPublicationId()))
+            if (datasetStatus != null && datasetStatus.isPublicationDismissed(form.getPublicationId()))
             {
                 errors.reject(ERROR_MSG, "The user has already dismissed the publication suggestion "
                         + datasetStatus.getPublicationIdLabel()
@@ -10977,8 +10950,8 @@ public boolean handlePost(NotifySubmitterForm form, BindException errors) throws
             }
 
             // Reconstruct PublicationMatch from form fields
-            PublicationMatch selectedMatch = PublicationMatch.fromMatchInfo(form.getPublicationId(), pubType, form.getMatchInfo());
-            selectedMatch.setCitation(NcbiPublicationSearchService.get().getCitation(form.getPublicationId(), pubType));
+            String citation = NcbiPublicationSearchService.get().getCitation(form.getPublicationId(), pubType);
+            PublicationMatch selectedMatch = PublicationMatch.fromMatchInfo(form.getPublicationId(), pubType, form.getMatchInfo(), citation);
 
             // Post notification
             JournalSubmission submission = SubmissionManager.getSubmissionForExperiment(exptAnnotations);
@@ -11029,6 +11002,7 @@ journal, submission, exptAnnotations, submitter, getUser(), notifyUsers,
             datasetStatus.setPotentialPublicationId(form.getPublicationId());
             datasetStatus.setPublicationType(pubType.name());
             datasetStatus.setPublicationMatchInfo(form.getMatchInfo());
+            datasetStatus.setCitation(selectedMatch.getCitation());
             datasetStatus.setUserDismissedPublication(null);
             datasetStatus.setLastReminderDate(new Date());
 
@@ -11052,19 +11026,42 @@ public ActionURL getSuccessURL(NotifySubmitterForm form)
         }
     }
 
-    public static class ShortUrlForm
+    public static class NotifySubmitterForm extends IdForm
     {
-        private String _shortUrlEntityId;
+        private String _publicationId;
+        private String _publicationType;
+        private String _matchInfo;
 
-        public String getShortUrlEntityId()
+        public String getPublicationId()
         {
-            return _shortUrlEntityId;
+            return _publicationId;
         }
 
-        public void setShortUrlEntityId(String shortUrlEntityId)
+        public void setPublicationId(String publicationId)
         {
-            _shortUrlEntityId = shortUrlEntityId;
+            _publicationId = publicationId;
+        }
+
+        public String getPublicationType()
+        {
+            return _publicationType;
         }
+
+        public void setPublicationType(String publicationType)
+        {
+            _publicationType = publicationType;
+        }
+
+        public String getMatchInfo()
+        {
+            return _matchInfo;
+        }
+
+        public void setMatchInfo(String matchInfo)
+        {
+            _matchInfo = matchInfo;
+        }
+
     }
 
     private static ExperimentAnnotations getValidExperimentAnnotations(ShortUrlForm shortUrlForm, Errors errors)

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

@@ -16,6 +16,7 @@ public class DatasetStatus  extends DbEntity
     private String _potentialPublicationId;
     private String _publicationType;
     private String _publicationMatchInfo;
+    private String _citation;
     private Date _userDismissedPublication;
 
     public int getExperimentAnnotationsId()
@@ -101,7 +102,7 @@ public void setPublicationType(String publicationType)
     public String getPublicationIdLabel()
     {
         NcbiConstants.DB type = NcbiConstants.DB.fromString(_publicationType);
-        String label = type == null ? (_publicationType != null ? _publicationType : "") : type.getLabel();
+        String label = type == null ? (_publicationType != null ? _publicationType : "") : type.name();
         return label + " ID " + getPotentialPublicationId();
     }
 
@@ -115,6 +116,16 @@ public void setPublicationMatchInfo(String publicationMatchInfo)
         _publicationMatchInfo = publicationMatchInfo;
     }
 
+    public String getCitation()
+    {
+        return _citation;
+    }
+
+    public void setCitation(String citation)
+    {
+        _citation = citation;
+    }
+
     public Date getUserDismissedPublication()
     {
         return _userDismissedPublication;
@@ -124,4 +135,9 @@ public void setUserDismissedPublication(Date userDismissedPublication)
     {
         _userDismissedPublication = userDismissedPublication;
     }
+
+    public boolean isPublicationDismissed(String publicationId)
+    {
+        return getUserDismissedPublication() != null && publicationId != null && publicationId.equals(getPotentialPublicationId());
+    }
 }

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

@@ -46,7 +46,8 @@ public class MockNcbiPublicationSearchService extends NcbiPublicationSearchServi
      *                     Null for pubmed articles (where {@code id} is already the PMID).
      * @param title        article title
      * @param authors      comma-separated author list (e.g. "Abbatiello SE,Mani DR,Schilling B")
-     * @param pubDate      publication date string (e.g. "2013 Sep")
+     * @param pubDate      publication date in "YYYY/MM/DD HH:MM" format, matching the NCBI ESummary
+     *                     sortpubdate (PubMed) or sortdate (PMC) field that parsePublicationDate() checks first
      * @param source       journal abbreviation used as ESummary "source" field (e.g. "Mol Cell Proteomics", "bioRxiv")
      * @param journalFull  full journal name used as ESummary "fulljournalname" field
      * @param citation     NLM citation string (for getCitation, keyed by PMID; null if not applicable)
@@ -64,7 +65,9 @@ public void register(String database, String id, String searchKey,
         metadata.put("sorttitle", title.toLowerCase());
         metadata.put("source", source);
         metadata.put("fulljournalname", journalFull);
-        metadata.put("pubdate", pubDate);
+        // Real NCBI ESummary returns sortpubdate (PubMed) or sortdate (PMC) in "YYYY/MM/DD HH:MM" format.
+        // parsePublicationDate() checks these first before falling back to pubdate.
+        metadata.put(isPmc ? "sortdate" : "sortpubdate", pubDate);
 
         // Authors array
         JSONArray authorsArray = new JSONArray();

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

@@ -25,6 +25,10 @@ static NcbiPublicationSearchService get()
 
     @Nullable Pair<String, String> getPubMedLinkAndCitation(String pubmedId);
 
+    /**
+     * Searches PMC and PubMed for a publication associated with the experiment.
+     * Returns the top match (highest priority) if multiple matches are found, or null if none.
+     */
     @Nullable PublicationMatch searchForPublication(@NotNull ExperimentAnnotations expAnnotations, @Nullable Logger logger);
 
     List<PublicationMatch> searchForPublication(@NotNull ExperimentAnnotations expAnnotations, int maxResults, @Nullable Logger logger, boolean getCitations);