ZFIN-9405: SEO: Handle error "Duplicate without user-selected canonic…

…al" (ZFIN#1195) * ZFIN-9405: Add canonical URLs for entities * ZFIN-9405: Add title for fish phenotype pages * ZFIN-9405: Remove user agent * Move logic for resolving canonical URLs into the JSP function
rtaylorzfin · Nov 15, 2024 · dfd5230 · dfd5230
1 parent 66c6a6d
commit dfd5230
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Showing 19 changed files with 194 additions and 240 deletions.
diff --git a/home/WEB-INF/tags/layout/page.tag b/home/WEB-INF/tags/layout/page.tag
@@ -32,6 +32,7 @@
 
         <title>${title}</title>
 
+        ${zfn:getCanonical()}
         <link rel="stylesheet" href="${zfn:getAssetPath("style.css")}">
 
         <!-- jquery is loaded via CDN here instead being part of the webpack bundle so that

diff --git a/home/WEB-INF/tld/zfin-fn.tld b/home/WEB-INF/tld/zfin-fn.tld
@@ -360,6 +360,18 @@
         <function-signature>java.lang.String getAssetPath(java.lang.String)</function-signature>
     </function>
 
+    <function>
+        <name>getProperty</name>
+        <function-class>org.zfin.framework.presentation.ZfinJSPFunctions</function-class>
+        <function-signature>java.lang.String getProperty(java.lang.String)</function-signature>
+    </function>
+
+    <function>
+        <name>getCanonical</name>
+        <function-class>org.zfin.framework.presentation.ZfinJSPFunctions</function-class>
+        <function-signature>java.lang.String getCanonical()</function-signature>
+    </function>
+
     <function>
         <name>isFlagEnabled</name>
         <function-class>org.zfin.framework.featureflag.FeatureFlags</function-class>

diff --git a/home/robots.txt b/home/robots.txt
@@ -43,6 +43,14 @@ Disallow: /cgi-bin/webdriver?MIval=aa-your_input_welcome.apg
 Disallow: /action/phenotype/statement/
 Disallow: /action/phenotype/statement-popup/
 
+#More popups:
+Disallow: /action/api/marker/ZDB-*/citations.tsv
+Disallow: /action/api/marker/ZDB-*/citations.tsv
+Disallow: /action/expression/experiment-popup/
+Disallow: /action/fish/fish-detail-popup/
+Disallow: /action/ontology/term-detail-popup/
+Disallow: /action/marker/gene-product-description/ZDB-*
+
 Disallow: /downloads/archive
 Disallow: /downloads/archive/*
 

diff --git a/source/org/zfin/expression/presentation/ExpressionSearchController.java b/source/org/zfin/expression/presentation/ExpressionSearchController.java
@@ -105,7 +105,13 @@ public String results(Model model, @ModelAttribute("criteria") ExpressionSearchC
         }
 
         model.addAttribute("criteria", criteria);
-        model.addAttribute(LookupStrings.DYNAMIC_TITLE, "Expression Search Results");
+
+        if (criteria.getTitle() != null) {
+            model.addAttribute(LookupStrings.DYNAMIC_TITLE, criteria.getTitle());
+        } else {
+            model.addAttribute(LookupStrings.DYNAMIC_TITLE, "Expression Search Results");
+        }
+
         return "expression/results";
     }
 

diff --git a/source/org/zfin/expression/presentation/ExpressionSearchCriteria.java b/source/org/zfin/expression/presentation/ExpressionSearchCriteria.java
@@ -1,12 +1,16 @@
 package org.zfin.expression.presentation;
 
 
+import lombok.Getter;
+import lombok.Setter;
 import org.zfin.marker.Marker;
 
 import java.util.Arrays;
 import java.util.List;
 import java.util.Map;
 
+@Setter
+@Getter
 public class ExpressionSearchCriteria {
 
     private String authorField;
@@ -40,223 +44,13 @@ public class ExpressionSearchCriteria {
     private String linkWithImagesOnly;
     private boolean hasMatchingText;
 
+    private String title;
+
     public List<String> getAnatomy() {
         if (anatomyTermNames == null || anatomyTermNames.equals("")) { return null; }
         return Arrays.asList(anatomyTermNames.split("\\|"));
     }
 
-    public String getAuthorField() {
-        return authorField;
-    }
-
-    public void setAuthorField(String authorField) {
-        this.authorField = authorField;
-    }
-
-    public JournalTypeOption getJournalType() {
-        return journalType;
-    }
-
-    public void setJournalType(JournalTypeOption journalType) {
-        this.journalType = journalType;
-    }
-
-    public boolean isOnlyReporter() {
-        return onlyReporter;
-    }
-
-    public void setOnlyReporter(boolean onlyReporter) {
-        this.onlyReporter = onlyReporter;
-    }
-
-    public String getGeneField() {
-        return geneField;
-    }
-
-    public void setGeneField(String geneField) {
-        this.geneField = geneField;
-    }
-
-    public void setGeneZdbID(String geneZdbID) {
-        this.geneZdbID = geneZdbID;
-    }
-
-    public String getGeneZdbID() {
-        return geneZdbID;
-    }
-
-    public void setGeneZdbId(String geneZdbID) {
-        this.geneZdbID = geneZdbID;
-    }
-
-    public Marker getGene() {
-        return gene;
-    }
-
-    public void setGene(Marker gene) {
-        this.gene = gene;
-    }
-
-    public String getTargetGeneField() {
-        return targetGeneField;
-    }
-
-    public void setTargetGeneField(String targetGeneField) {
-        this.targetGeneField = targetGeneField;
-    }
-
-    public boolean isOnlyFiguresWithImages() {
-        return onlyFiguresWithImages;
-    }
-
-    public void setOnlyFiguresWithImages(boolean onlyFiguresWithImages) {
-        this.onlyFiguresWithImages = onlyFiguresWithImages;
-    }
-
-    public boolean isOnlyWildtype() {
-        return onlyWildtype;
-    }
-
-    public void setOnlyWildtype(boolean onlyWildtype) {
-        this.onlyWildtype = onlyWildtype;
-    }
-
-    public Map<String, String> getStages() {
-        return stages;
-    }
-
-    public void setStages(Map<String, String> stages) {
-        this.stages = stages;
-    }
-
-    public String getStartStageId() {
-        return startStageId;
-    }
-
-    public void setStartStageId(String startStageId) {
-        this.startStageId = startStageId;
-    }
-
-    public String getEndStageId() {
-        return endStageId;
-    }
-
-    public void setEndStageId(String endStageId) {
-        this.endStageId = endStageId;
-    }
-
-    public String getAssayName() {
-        return assayName;
-    }
-
-    public void setAssayName(String assayName) {
-        this.assayName = assayName;
-    }
-
-    public String getFish() {
-        return fish;
-    }
-
-    public void setFish(String fish) {
-        this.fish = fish;
-    }
-
-    public String getAnatomyTermNames() {
-        return anatomyTermNames;
-    }
-
-    public void setAnatomyTermNames(String anatomyTermNames) {
-        this.anatomyTermNames = anatomyTermNames;
-    }
-
-    public String getAnatomyTermIDs() {
-        return anatomyTermIDs;
-    }
-
-    public void setAnatomyTermIDs(String anatomyTermIDs) {
-        this.anatomyTermIDs = anatomyTermIDs;
-    }
-
-    public boolean isIncludeSubstructures() {
-        return includeSubstructures;
-    }
-
-    public void setIncludeSubstructures(boolean includeSubstructures) {
-        this.includeSubstructures = includeSubstructures;
-    }
-
-    public List<GeneResult> getGeneResults() {
-        return geneResults;
-    }
-
-    public void setGeneResults(List<GeneResult> geneResults) {
-        this.geneResults = geneResults;
-    }
-
-    public List<FigureResult> getFigureResults() {
-        return figureResults;
-    }
-
-    public void setFigureResults(List<FigureResult> figureResults) {
-        this.figureResults = figureResults;
-    }
-
-    public List<ImageResult> getImageResults() {
-        return imageResults;
-    }
-
-    public void setImageResults(List<ImageResult> imageResults) {
-        this.imageResults = imageResults;
-    }
-
-    public long getNumFound() {
-        return numFound;
-    }
-
-    public void setNumFound(long numFound) {
-        this.numFound = numFound;
-    }
-
-    public long getPubCount() {
-        return pubCount;
-    }
-
-    public void setPubCount(long pubCount) {
-        this.pubCount = pubCount;
-    }
-
-    public Integer getRows() {
-        return rows;
-    }
-
-    public void setRows(Integer rows) {
-        this.rows = rows;
-    }
-
-    public Integer getPage() {
-        return page;
-    }
-
-    public void setPage(Integer page) {
-        this.page = page;
-    }
-
-    public String getLinkWithImagesOnly() {
-        return linkWithImagesOnly;
-    }
-
-    public void setLinkWithImagesOnly(String linkWithImagesOnly) {
-        this.linkWithImagesOnly = linkWithImagesOnly;
-    }
-
-    public boolean isHasMatchingText() {
-        return hasMatchingText;
-    }
-
-    public void setHasMatchingText(boolean hasMatchingText) {
-        this.hasMatchingText = hasMatchingText;
-    }
-
     public enum JournalTypeOption {
         DIRECT("Show only direct submission data"),
         PUBLISHED("Show only published literature"),

diff --git a/source/org/zfin/expression/service/ExpressionSearchService.java b/source/org/zfin/expression/service/ExpressionSearchService.java
@@ -555,6 +555,7 @@ public static class LinkBuilder {
         private ExpressionSearchCriteria.JournalTypeOption journalType = ExpressionSearchCriteria.JournalTypeOption.ALL;
         private boolean onlyFiguresWithImages;
         private boolean onlyReporter;
+        private String title;
 
         public LinkBuilder gene(Marker gene) {
             this.gene = gene;
@@ -645,6 +646,11 @@ public LinkBuilder author(String author) {
             return this;
         }
 
+        public LinkBuilder title(String title) {
+            this.title = title;
+            return this;
+        }
+
         public String build() {
             URLCreator url = new URLCreator("/action/expression/results");
             addIfNotNull(url, "geneField", geneField);
@@ -674,6 +680,7 @@ public String build() {
             addIfTrue(url, "onlyWildtype", wildtypeOnly);
             addIfTrue(url, "onlyReporter", onlyReporter);
             addIfTrue(url, "onlyFiguresWithImages", onlyFiguresWithImages);
+            addIfNotNull(url, "title", title);
             return url.getURL();
         }
 

diff --git a/source/org/zfin/figure/presentation/FigureViewController.java b/source/org/zfin/figure/presentation/FigureViewController.java
@@ -1,12 +1,10 @@
 package org.zfin.figure.presentation;
 
-import org.apache.commons.lang3.StringUtils;
 import org.springframework.beans.factory.annotation.Autowired;
 import org.springframework.stereotype.Controller;
 import org.springframework.ui.Model;
 import org.springframework.web.bind.annotation.PathVariable;
 import org.springframework.web.bind.annotation.RequestMapping;
-import org.springframework.web.bind.annotation.RequestParam;
 import org.zfin.expression.Figure;
 import org.zfin.expression.FigureService;
 import org.zfin.figure.repository.FigureRepository;
@@ -15,14 +13,10 @@
 import org.zfin.marker.Clone;
 import org.zfin.marker.presentation.OrganizationLink;
 import org.zfin.mutant.PhenotypeWarehouse;
-import org.zfin.publication.Publication;
 import org.zfin.publication.repository.PublicationRepository;
 import org.zfin.repository.RepositoryFactory;
 
-import java.util.HashMap;
 import java.util.List;
-import java.util.Map;
-import java.util.stream.Collectors;
 
 import static org.zfin.repository.RepositoryFactory.getPhenotypeRepository;
 

diff --git a/source/org/zfin/fish/presentation/FishPhenotypeController.java b/source/org/zfin/fish/presentation/FishPhenotypeController.java
@@ -50,7 +50,7 @@ protected String showPhenotypeSummary(@RequestParam(value = "fishID", required =
         model.addAttribute("phenotypeSummaryCriteria", summaryCriteria);
         Fish fish = getMutantRepository().getFish(fishID);
         model.addAttribute("fish", fish);
-        model.addAttribute(LookupStrings.DYNAMIC_TITLE, "Phenotype Summary");
+        model.addAttribute(LookupStrings.DYNAMIC_TITLE, "Phenotype Summary: " + fish.getName());
         return "fish/fish-phenotype-figure-summary";
     }
 }