Merge branch 'ZFIN:main' into main

rtaylorzfin · Apr 18, 2023 · 82a8e82 · 82a8e82
2 parents bfc5abd + 6db2f9c
commit 82a8e82
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Showing 14 changed files with 68 additions and 9 deletions.
diff --git a/home/WEB-INF/jsp/ontology/term-view.jsp b/home/WEB-INF/jsp/ontology/term-view.jsp
@@ -14,11 +14,12 @@
 <c:set var="GENES_INVOLVED" value="${NavigationMenuOptions.GENES_INVOLVED.value}"/>
 <c:set var="ZEBRAFISH_MODELS" value="${NavigationMenuOptions.ZEBRAFISH_MODELS.value}"/>
 <c:set var="EXPRESSION" value="${NavigationMenuOptions.EXPRESSION.value}"/>
+<c:set var="OTHER_PAGES" value="${NavigationMenuOptions.OTHER_PAGE.value}"/>
 <c:set var="CITATIONS" value="${NavigationMenuOptions.CITATION.value}"/>
 
 <c:set var="secs"/>
 
-<z:dataPage sections="${[]}" navigationMenu="${navigationMenu}">
+<z:dataPage sections="${[]}" navigationMenu="${navigationMenu}" additionalBodyClass="term-view nav-title-wrap-break-word">
 
     <jsp:attribute name="entityName">
        ${term.termName}

diff --git a/home/css/datapage.scss b/home/css/datapage.scss
@@ -392,6 +392,13 @@ table.lab-view-summary-table dd a, table.company-view-summary-table dd a {
     word-break: break-all; /* <-- remove for ellipses truncation */
 }
 
+/* Wrap the page title as it appears in the left navigation menu and break on word separators */
+.nav-title-wrap-break-word a.back-to-top-link {
+    display: inline;
+    white-space: normal;
+    word-break: break-word;
+}
+
 /* Set margin for figure component on publication view page */
 .publication-view #xpresimg_control_box {
     margin-top: 20px;

diff --git a/home/javascript/react/containers/ChebiModifiedPhenotypeTable.js b/home/javascript/react/containers/ChebiModifiedPhenotypeTable.js
@@ -56,7 +56,11 @@ const ChebiModifiedPhenotypeTable = ({termId, directAnnotationOnly, endpointUrl
         },
         {
             label: 'Term',
-            content: ({term}) => <a href={'/' + term.zdbID}>{term.termName}</a>,
+            content: ({allChebiTerms}) => <CommaSeparatedList>
+                {allChebiTerms.map(term => {
+                    return <a href={'/' + term.zdbID} key={Math.random()}>{term.termName}</a>
+                })}
+            </CommaSeparatedList>,
             filterName: 'termName',
             width: '120px',
         },

diff --git a/home/javascript/react/containers/ChebiPhenotypeTable.js b/home/javascript/react/containers/ChebiPhenotypeTable.js
@@ -50,7 +50,11 @@ const ChebiPhenotypeTable = ({termId, directAnnotationOnly, endpointUrl = 'pheno
         },
         {
             label: 'Term',
-            content: ({term}) => <a href={'/' + term.zdbID}>{term.termName}</a>,
+            content: ({allChebiTerms}) => <CommaSeparatedList>
+                {allChebiTerms.map(term => {
+                    return <a href={'/' + term.zdbID} key={Math.random()}>{term.termName}</a>
+                })}
+            </CommaSeparatedList>,
             filterName: 'termName',
             width: '120px',
         },

diff --git a/source/org/zfin/db/postGmakePostloaddb/1143/ZFIN-8504.sql b/source/org/zfin/db/postGmakePostloaddb/1143/ZFIN-8504.sql
@@ -0,0 +1,4 @@
+--liquibase formatted sql
+--changeset cmpich:ZFIN-8504.sql
+
+alter table UI.CHEBI_PHENOTYPE_DISPLAY add COLUMN cpd_exp_condition_chebi_search text;
diff --git a/source/org/zfin/db/postGmakePostloaddb/1143/db.changelog.master.xml b/source/org/zfin/db/postGmakePostloaddb/1143/db.changelog.master.xml
@@ -10,6 +10,7 @@
     <include file="source/org/zfin/db/postGmakePostloaddb/1143/ZFIN-8519.sql" />
     <include file="source/org/zfin/db/postGmakePostloaddb/1143/ZFIN-8520.sql" />
     <include file="source/org/zfin/db/postGmakePostloaddb/1143/ZFIN-8531-construct-relationship.sql" />
+    <include file="source/org/zfin/db/postGmakePostloaddb/1143/ZFIN-8504.sql" />
 
 
 </databaseChangeLog>
diff --git a/source/org/zfin/framework/presentation/DiseaseNavigationMenu.java b/source/org/zfin/framework/presentation/DiseaseNavigationMenu.java
@@ -3,6 +3,9 @@
 
 import lombok.Getter;
 import lombok.Setter;
+import org.zfin.framework.featureflag.FeatureFlagEnum;
+
+import static org.zfin.framework.featureflag.FeatureFlags.isFlagEnabled;
 
 @Getter
 @Setter
@@ -16,9 +19,11 @@ public DiseaseNavigationMenu() {
         super(
             title(NavigationMenuOptions.SUMMARY).showCount(false),
             title(NavigationMenuOptions.RELATIONSHIPS).showCount(false),
+            title(NavigationMenuOptions.OTHER_PAGE).showCount(false),
             title(NavigationMenuOptions.GENES_INVOLVED).showCount(false),
             title(NavigationMenuOptions.ZEBRAFISH_MODELS).showCount(false),
-            title(NavigationMenuOptions.ALLELE).showCount(false)
+            isFlagEnabled(FeatureFlagEnum.SHOW_ALLIANCE_DATA) ?
+                title(NavigationMenuOptions.ALLELE).showCount(false) : null
         );
     }
 

diff --git a/source/org/zfin/framework/presentation/NavigationMenu.java b/source/org/zfin/framework/presentation/NavigationMenu.java
@@ -5,6 +5,7 @@
 
 import java.util.ArrayList;
 import java.util.List;
+import java.util.Objects;
 import java.util.stream.Stream;
 
 /**
@@ -22,14 +23,15 @@ public class NavigationMenu {
 
     public NavigationMenu(NavigationItem.NavigationItemBuilder ...navigationItemBuilders) {
         this.navigationItems = Stream.of(navigationItemBuilders)
+                .filter(Objects::nonNull)
                 .map(NavigationItem.NavigationItemBuilder::build)
                 .toList();
     }
 
     /**
      * Set the hidden attribute for the NavigationItem in this menu matching the given title
-     * @param title
-     * @param value
+     * @param title title of the item we are looking for (enum)
+     * @param value true if the item should be hidden
      */
     public void setHidden(NavigationMenuOptions title, boolean value) {
         for(NavigationItem item : navigationItems) {

diff --git a/source/org/zfin/framework/presentation/NavigationMenuOptions.java b/source/org/zfin/framework/presentation/NavigationMenuOptions.java
@@ -8,6 +8,7 @@ public enum NavigationMenuOptions {
     EFGs("Engineered Foreign Genes"),
     ERRATA("Errata / Notes"),
     EXPRESSION("Expression"),
+    OTHER_PAGE("Other Pages"),
     FIGURES("Figures"),
     FISH("Fish"),
     GENES("Genes / Markers"),

diff --git a/source/org/zfin/indexer/TermPageIndexer.java b/source/org/zfin/indexer/TermPageIndexer.java
@@ -40,6 +40,7 @@ public class TermPageIndexer {
     public static void main(String[] args) throws NoSuchFieldException {
         TermPageIndexer indexer = new TermPageIndexer();
         indexer.init();
+
         indexer.publicationExpressions();
         indexer.runFishModels();
         indexer.runGenesInvolved();
@@ -227,6 +228,11 @@ private void runChebiPhenotype() throws NoSuchFieldException {
                 display.setPhenotypeStatementSearch(phenotypeStatementWarehouses.stream().map(PhenotypeStatementWarehouse::getDisplayName).collect(Collectors.joining("|")));
                 display.setGeneSymbolSearch(fish.getAffectedGenes().stream().map(Marker::getAbbreviation).sorted().collect(Collectors.joining("|")));
                 display.setConditionSearch(experiment.getDisplayAllConditions());
+                display.setExpConditionChebiSearch(experiment.getExperimentConditions().stream()
+                    .filter(experimentCondition -> experimentCondition.getChebiTerm() != null)
+                    .map(ExperimentCondition::getChebiTerm)
+                    .map(GenericTerm::getTermName)
+                    .collect(Collectors.joining("|")));
                 HibernateUtil.currentSession().save(display);
             });
         }));

diff --git a/source/org/zfin/mutant/presentation/ChebiPhenotypeDisplay.java b/source/org/zfin/mutant/presentation/ChebiPhenotypeDisplay.java
@@ -4,6 +4,7 @@
 import lombok.Getter;
 import lombok.Setter;
 import org.zfin.expression.Experiment;
+import org.zfin.expression.ExperimentCondition;
 import org.zfin.expression.Figure;
 import org.zfin.framework.api.View;
 import org.zfin.mutant.Fish;
@@ -13,6 +14,8 @@
 
 import javax.persistence.*;
 import java.util.List;
+import java.util.Set;
+import java.util.TreeSet;
 
 /**
  * class to retrieve chebi term page - phenotype
@@ -85,6 +88,10 @@ public class ChebiPhenotypeDisplay {
     @Column(name = "cpd_ameliorated_exacerbated_phenotype_search")
     private String amelioratedExacerbatedPhenoSearch;
 
+    @JsonView(View.API.class)
+    @Column(name = "cpd_exp_condition_chebi_search")
+    private String expConditionChebiSearch;
+
     @Transient
     private boolean includeSubstructures;
 
@@ -100,4 +107,19 @@ public Fish getFish() {
         return fish;
     }
 
+    @JsonView(View.API.class)
+    public Set<GenericTerm> getAllChebiTerms() {
+        Set<GenericTerm> allTerms = new TreeSet<>();
+        allTerms.add(term);
+        allTerms.addAll(experiment.getExperimentConditions()
+            .stream()
+            .filter(experimentCondition -> experimentCondition.getChebiTerm() != null)
+            .map(ExperimentCondition::getChebiTerm)
+            .sorted()
+            .toList());
+        return allTerms;
+    }
+
+    public void setAllChebiTerms(Set<GenericTerm> terms) {
+    }
 }
diff --git a/source/org/zfin/mutant/repository/HibernateMutantRepository.java b/source/org/zfin/mutant/repository/HibernateMutantRepository.java
@@ -1885,9 +1885,10 @@ public Fish getFishByGenoStr(Fish fish) {
         Query<Fish> query = session.createQuery(hql, Fish.class);
         query.setParameter("genotype", fish.getGenotype());
         if (strsAvailable) {
-            query.setParameter("numberOfStrs", fish.getStrList().size());
+            Long numberOfStrs = Long.valueOf(fish.getStrList().size());
+            query.setParameter("numberOfStrs", numberOfStrs);
         } else {
-            query.setParameter("numberOfStrs", 0);
+            query.setParameter("numberOfStrs", 0L);
         }
         if (strsAvailable) {
             int index = 0;

diff --git a/source/org/zfin/ontology/presentation/OntologyTermDetailController.java b/source/org/zfin/ontology/presentation/OntologyTermDetailController.java
@@ -252,6 +252,7 @@ protected String termDetailPagePrototype(@PathVariable String termID,
         boolean isChebi = term.getOntology().equals(Ontology.CHEBI);
         model.addAttribute("isChebiTerm", isChebi);
         model.addAttribute("showPhenotypeSection", !term.getOntology().equals(Ontology.ECO));
+        form.setAgrDiseaseLinks(OntologyService.getAGRLinks(term));
 
         NavigationMenu menu = new DefaultTermNavigationMenu();
         if (isChebi) {

diff --git a/source/org/zfin/ontology/presentation/TermAPIController.java b/source/org/zfin/ontology/presentation/TermAPIController.java
@@ -236,7 +236,7 @@ public JsonResultResponse<ChebiPhenotypeDisplay> getPhenotypeChebi(@PathVariable
             pagination.addToFilterMap("chebiPhenotype.phenotypeStatementSearch", filterPhenotype);
         }
         if (StringUtils.isNotEmpty(filterTermName)) {
-            pagination.addToFilterMap("chebiPhenotype.term.termName", filterTermName);
+            pagination.addToFilterMap("chebiPhenotype.expConditionChebiSearch", filterTermName);
         }
 
         PaginationResult<ChebiPhenotypeDisplay> genesInvolvedForDiseaseDirect = getDiseasePageRepository().getPhenotypeChebi(term, pagination, false);