Merge pull request #691 from mpi2/idg-page-publications

IDG page publications

utilities/src/main/java/org/mousephenotype/cda/common/Constants.java

@@ -103,6 +103,8 @@ public class Constants {
     // PDF thumbnail icon (so PDFs show a PDF icon.
     public static final String PDF_THUMBNAIL_RELATIVE_URL = "img/filetype_pdf.png";
 
+    public static final List<String> IDG_PUBLICATION_LIST= Arrays.asList("23504326", "23929668", "23934124", "24244016", "24284070", "25242043", "25298527", "25320282", "26197390", "27313209", "27445138", "27677211", "27693579", "27759003", "27866947", "28051178", "28461138", "28702328", "28719620", "28817564", "28894906", "29034508", "29056298", "29098359", "29282304", "29290552", "29386186", "29391390", "29481883", "29625592", "29899413", "30157172", "30291131", "30532139", "30651631", "31050055", "31135881", "31285284", "31480808", "31495563", "31509750", "31621579", "31628323", "31730008", "31941358", "31943058", "32163033", "32242025", "32381600", "32439758", "32576659", "32751134", "32758357", "32868297", "33382037", "33623007", "33753942", "33806166", "34001891", "34026458", "34273979", "34544832", "34615877");
+
 
 
 }

web/src/main/java/uk/ac/ebi/phenotype/web/controller/SecondaryProjectController.java

@@ -30,13 +30,19 @@
 import org.springframework.web.bind.annotation.RequestMethod;
 import uk.ac.ebi.phenotype.chart.PieChartCreator;
 import uk.ac.ebi.phenotype.chart.UnidimensionalChartAndTableProvider;
+import uk.ac.ebi.phenotype.util.PublicationFetcher;
+import uk.ac.ebi.phenotype.web.dao.ReferenceService;
+import uk.ac.ebi.phenotype.web.dto.AlleleRef;
+import uk.ac.ebi.phenotype.web.dto.Publication;
 
 import javax.servlet.http.HttpServletRequest;
 import javax.validation.constraints.NotNull;
 import java.io.IOException;
 import java.util.*;
 import java.util.stream.Collectors;
 
+import static org.mousephenotype.cda.common.Constants.IDG_PUBLICATION_LIST;
+
 @Controller
 public class SecondaryProjectController {
 
@@ -45,13 +51,15 @@ public class SecondaryProjectController {
     private GeneService geneService;
     private UnidimensionalChartAndTableProvider chartProvider;
     private GenesSecondaryProjectServiceIdg idg;
+    private ReferenceService referenceService;
 
     public SecondaryProjectController(
             @NotNull GeneService geneService,
-            //@NotNull EssentialGeneService essentialGeneService,
+            @NotNull ReferenceService referenceService,
             @NotNull UnidimensionalChartAndTableProvider chartProvider,
             @NotNull GenesSecondaryProjectServiceIdg idg) {
         this.geneService = geneService;
+        this.referenceService = referenceService;
         this.chartProvider = chartProvider;
         this.idg = idg;
     }
@@ -68,6 +76,13 @@ public String idgProjectPage(HttpServletRequest request,
                 .stream()
                 .map(GenesSecondaryProject::getMgiGeneAccessionId)
                 .collect(Collectors.toSet());
+        List<GeneDTO> geneDTOList = geneService.getGenesByMgiIds(new ArrayList<>(accessions));
+        Set<String> alleleSymbols = new HashSet<>();
+        geneDTOList.stream().filter(g -> g.getAlleleName() != null).forEach(g -> g.getAlleleName().forEach(aName -> alleleSymbols.add(g.getMarkerSymbol() + "<" + aName + ">")));
+        Set<String> symbols = geneDTOList
+                .stream()
+                .map(GeneDTO::getMarkerSymbol)
+                .collect(Collectors.toSet());
 
         Map<String, Long> geneStatus = geneService.getStatusCount(accessions, GeneDTO.ES_CELL_PRODUCTION_STATUS);
         Map<String, Long> mouseStatus = geneService.getStatusCount(accessions, GeneDTO.MOUSE_PRODUCTION_STATUS);
@@ -136,6 +151,14 @@ public String idgProjectPage(HttpServletRequest request,
         model.addAttribute("gpcrMiceProduced", gpcrRows.stream().filter(x -> x.getMiceProduced().contains("Mice")).count());
         model.addAttribute("gpcrPhenotypesProduced", gpcrRows.stream().filter(x -> x.getMiceProduced().contains("Phenotype data")).count());
 
+        /*
+        PUBLICATIONS
+         */
+
+        // Filter out publications not directly related to this gene
+        final List<Publication> publications = referenceService.getReviewedByPmidList(new ArrayList<>(IDG_PUBLICATION_LIST));
+        model.addAttribute("publications", publications);
+
         return "idg";
 
 

web/src/main/java/uk/ac/ebi/phenotype/web/dao/ReferenceRepository.java

@@ -9,12 +9,16 @@
 import org.springframework.stereotype.Repository;
 import uk.ac.ebi.phenotype.web.dto.Publication;
 
+import java.util.List;
+
 
 @Repository
 public interface ReferenceRepository extends MongoRepository<Publication, ObjectId>, ReferenceRepositoryCustom  {
 
     Page<Publication> findAllByStatusIs(Pageable pageable, String status);
 
+    List<Publication> findPublicationsByPmidIsInOrderByFirstPublicationDate(List<String> pmids);
+
     int countAllByStatusIs(String status);
 
     final String reviewedContainsQuery =
@@ -32,9 +36,26 @@ public interface ReferenceRepository extends MongoRepository<Publication, Object
       +   "{status: 'reviewed'}"
       +  "]"
     + " }";
+
+    final String reviewedContainsGeneQuery =
+            " {$and: "
+                    +  "["
+                    +    "{$or: "
+                    +      "["
+                    +        "{'alleles.alleleSymbol': {$regex : ?0, '$options' : 'i' }},"
+                    +        "{'alleles.geneSymbol':   {$regex : ?0, '$options' : 'i' }}"
+                    +      "]"
+                    +    "},"
+                    +   "{status: 'reviewed'}"
+                    +  "]"
+                    + " }";
+
     @Query(reviewedContainsQuery)
     Page<Publication> findReviewedContains(String filter, Pageable pageable);
 
+    @Query(reviewedContainsGeneQuery)
+    Page<Publication> findReviewedContainsGene(String genes, Pageable pageable);
+
     @CountQuery(reviewedContainsQuery)
     int countReviewedContains(String filter);
 

web/src/main/java/uk/ac/ebi/phenotype/web/dao/ReferenceService.java

@@ -9,6 +9,7 @@
 public interface ReferenceService {
 
     List<Publication> getAllReviewed(String filter, int start, int length, String orderBy, String sortOrder);
+    List<Publication> getReviewedByPmidList(List<String> pmidList);
     int countReviewed();
     int countFiltered(String filter);
 

web/src/main/java/uk/ac/ebi/phenotype/web/dao/ReferenceServiceImpl.java

@@ -2,6 +2,7 @@
 
 import org.springframework.beans.factory.annotation.Autowired;
 import org.springframework.data.domain.PageRequest;
+import org.springframework.data.domain.Pageable;
 import org.springframework.data.domain.Sort;
 import org.springframework.stereotype.Service;
 import uk.ac.ebi.phenotype.web.dto.Publication;
@@ -10,6 +11,8 @@
 import java.util.List;
 import java.util.TreeMap;
 
+import static org.mousephenotype.cda.common.Constants.IDG_PUBLICATION_LIST;
+
 @Service
 public class ReferenceServiceImpl implements ReferenceService {
 
@@ -36,6 +39,16 @@ public List<Publication> getAllReviewed(String filter, int start, int length, St
         }
     }
 
+    @Override
+    public List<Publication> getReviewedByPmidList(List<String> pmidList) {
+
+        if(pmidList == null || pmidList.isEmpty()) {
+            return referenceRepository.findAllByStatusIs(Pageable.unpaged(), "reviewed").getContent();
+        } else {
+            return referenceRepository.findPublicationsByPmidIsInOrderByFirstPublicationDate(IDG_PUBLICATION_LIST);
+        }
+    }
+
     @Override
     public int countReviewed() {
         return referenceRepository.countAllByStatusIs("reviewed");

web/src/main/webapp/WEB-INF/views/idg.jsp

@@ -4,6 +4,7 @@
 <%@ taglib prefix="c" uri="http://java.sun.com/jsp/jstl/core" %>
 <%@ taglib prefix="t" tagdir="/WEB-INF/tags" %>
 <%@ taglib prefix='fn' uri='http://java.sun.com/jsp/jstl/functions' %>
+<%@taglib prefix = "fmt" uri = "http://java.sun.com/jsp/jstl/fmt" %>
 
 <t:genericpage-landing>
 
@@ -43,6 +44,7 @@
                 //$( '#spinner'+ id ).html('');
 
             });
+            $('#publications_table').bootstrapTable({ classes: 'table'});
         </script>
 
     </jsp:attribute>
@@ -264,6 +266,73 @@
                 </div>
             </div>
 
+        <%-- PUBLICATIONS SECTION --%>
+        <div class="container white-bg-small" id="publications-section">
+            <div class="row pb-5">
+                <div class="col-12 col-md-12">
+                    <div class="pre-content clear-bg">
+                        <div class="page-content p-5">
+                            <div class="mb-5">
+                                <h2>
+                                    IMPC related publications
+                                    <a href="${cmsBaseUrl}/help/data-visualization/gene-pages/publications/" title="Go to publication help">
+                                        <i class="fal fa-question-circle fa-xs text-muted align-middle" style="font-size: 20px;"></i>
+                                    </a>
+                                </h2>
+                                <p>
+                                    The table below lists publications which used either products generated by the IMPC or data produced by the phenotyping efforts of the IMPC. These publications have also been associated to genes listed on the IDG project.
+                                </p>
+                            </div>
+                            <div>
+                                <div class="row">
+                                    <div class="col-12">
+                                        <c:choose>
+                                            <c:when test="${fn:length(publications) != 0}">
+                                                <p class="alert alert-info">There are <b>${fn:length(publications)} publication<c:if test="${fn:length(publications)!=1}">s</c:if> which use IMPC produced mice or data.</b></p>
+                                                <table id="publications_table"
+                                                       data-pagination="true"
+                                                       data-mobile-responsive="true"
+                                                       data-sortable="true">
+                                                    <thead>
+                                                    <tr>
+                                                        <th data-width="300">Title</th>
+                                                        <th>Journal</th>
+                                                        <th>IMPC Allele</th>
+                                                        <th data-width="160" data-halign="center" data-align="center">PubMed&nbsp;ID</th>
+                                                    </tr>
+                                                    </thead>
+                                                    <tbody>
+                                                    <c:forEach items="${publications}" var="publication" varStatus="loop">
+                                                        <tr id="publicationRow${loop.index}" data-link="publication" data-shown="false">
+                                                            <td><a href="https://www.doi.org/${publication.doi}">${publication.title}</a></td>
+                                                            <td>${publication.journalInfo.journal.title} (<fmt:formatDate value="${publication.firstPublicationDate}" pattern="MMMM yyyy" />)</td>
+                                                            <td><c:forEach items="${publication.alleles}" var="allele" varStatus="allele_loop">
+                                                                <t:formatAllele>${allele.alleleSymbol}</t:formatAllele>
+                                                            </c:forEach>
+                                                            </td>
+                                                            <td><c:choose>
+                                                                <c:when test="${fn:length(publication.pmcid) > 0}"><a href="https://www.ncbi.nlm.nih.gov/pmc/articles/${publication.pmcid}">${publication.pmcid}</a></c:when>
+                                                                <c:when test="${fn:length(publication.pmid) > 0}"><a href="https://pubmed.ncbi.nlm.nih.gov/${publication.pmid}/">${publication.pmid}</a></c:when>
+                                                            </c:choose>
+                                                            </td>
+                                                        </tr>
+                                                    </c:forEach>
+                                                    </tbody>
+                                                </table>
+                                            </c:when>
+                                            <c:when test="${fn:length(publications) == 0}">No publications found that use IMPC mice or data for ${gene.markerSymbol}.</c:when>
+                                        </c:choose>
+                                    </div>
+                                </div>
+                            </div>
+                        </div>
+                    </div>
+                </div>
+            </div>
+        </div>
+
+
+
     </jsp:body>