From dfd5230d23b2fa7da164d35524aaccdfcc9e62f5 Mon Sep 17 00:00:00 2001
From: Ryan Taylor <90803397+rtaylorzfin@users.noreply.github.com>
Date: Fri, 15 Nov 2024 08:00:16 -0800
Subject: [PATCH] ZFIN-9405: SEO: Handle error "Duplicate without user-selected
 canonical" (#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
---
 home/WEB-INF/tags/layout/page.tag             |   1 +
 home/WEB-INF/tld/zfin-fn.tld                  |  12 +
 home/robots.txt                               |   8 +
 .../ExpressionSearchController.java           |   8 +-
 .../ExpressionSearchCriteria.java             | 218 +-----------------
 .../service/ExpressionSearchService.java      |   7 +
 .../presentation/FigureViewController.java    |   6 -
 .../presentation/FishPhenotypeController.java |   2 +-
 .../presentation/ZfinJSPFunctions.java        |  22 ++
 .../seo/CanonicalLinkConfig.java              |  92 ++++++++
 .../service/RequestService.java               |  25 ++
 .../presentation/MappingDetailController.java |   1 -
 .../presentation/CloneViewController.java     |   3 -
 .../presentation/GeneViewController.java      |   3 +
 ...equenceTargetingReagentViewController.java |   4 +-
 .../TranscriptViewController.java             |   3 -
 .../NomenclatureSubmissionController.java     |  14 +-
 .../presentation/ImageViewController.java     |   2 +-
 .../PublicationViewController.java            |   3 -
 19 files changed, 194 insertions(+), 240 deletions(-)
 create mode 100644 source/org/zfin/infrastructure/seo/CanonicalLinkConfig.java
 create mode 100644 source/org/zfin/infrastructure/service/RequestService.java

diff --git a/home/WEB-INF/tags/layout/page.tag b/home/WEB-INF/tags/layout/page.tag
index 57a46ecdf8..a4e97b0c4b 100644
--- 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
index 7c83c24282..43340d3b0e 100644
--- 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
index 701c9bd4f7..ae7b4d60b4 100644
--- 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
index 3ff588ed17..c4f8e9cbb0 100644
--- 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
index 3fdf9ddf55..021c646a81 100644
--- 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
index ee1d24530b..8f9c9fc42c 100644
--- 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
index 9577dc1e8f..a1dabb700d 100644
--- 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
index 8c9cb8c108..4ce5178df1 100644
--- 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";
     }
 }
\ No newline at end of file
diff --git a/source/org/zfin/framework/presentation/ZfinJSPFunctions.java b/source/org/zfin/framework/presentation/ZfinJSPFunctions.java
index 70e9600104..d0458d9932 100644
--- a/source/org/zfin/framework/presentation/ZfinJSPFunctions.java
+++ b/source/org/zfin/framework/presentation/ZfinJSPFunctions.java
@@ -27,6 +27,8 @@
 import org.zfin.ontology.Term;
 import org.zfin.profile.Person;
 import org.zfin.profile.UserService;
+import org.zfin.properties.ZfinProperties;
+import org.zfin.properties.ZfinPropertiesEnum;
 import org.zfin.repository.RepositoryFactory;
 import org.zfin.sequence.blast.Database;
 import org.zfin.util.DateUtil;
@@ -39,6 +41,10 @@
 import java.lang.management.ThreadMXBean;
 import java.util.*;
 
+import static org.zfin.infrastructure.seo.CanonicalLinkConfig.getCanonicalIfFound;
+import static org.zfin.infrastructure.service.RequestService.getRequestedForwardedUrl;
+import static org.zfin.infrastructure.service.RequestService.getRequestedUrlPath;
+
 /**
  * Class that is called from JSP through a function call.
  */
@@ -420,7 +426,23 @@ public static String getAssetPath(String name) {
         } catch (IOException e) {
             return "";
         }
+    }
+
+    public static String getProperty(String name) {
+        ZfinPropertiesEnum property = ZfinPropertiesEnum.valueOf(name);
+        return property == null ? "" : property.toString();
+    }
 
+    public static String getCanonical() {
+        String canonical = getCanonicalIfFound(getRequestedForwardedUrl());
+        if (StringUtils.isEmpty(canonical)) {
+            return "";
+        }
+        return """
+                <link rel="canonical" href="https://%s" />
+                """
+                .formatted(ZfinPropertiesEnum.DOMAIN_NAME + canonical )
+                .trim();
     }
 
     public static String getTruncatedName(String name, Integer length) {
diff --git a/source/org/zfin/infrastructure/seo/CanonicalLinkConfig.java b/source/org/zfin/infrastructure/seo/CanonicalLinkConfig.java
new file mode 100644
index 0000000000..da7116934c
--- /dev/null
+++ b/source/org/zfin/infrastructure/seo/CanonicalLinkConfig.java
@@ -0,0 +1,92 @@
+package org.zfin.infrastructure.seo;
+
+import org.springframework.ui.Model;
+
+import java.util.HashMap;
+import java.util.List;
+import java.util.Map;
+import java.util.regex.Pattern;
+
+import static org.zfin.infrastructure.service.RequestService.getRequestedUrlPath;
+
+public class CanonicalLinkConfig {
+
+    /**
+     * URL patterns and their replacement formats
+     *
+     *    based on contents of view-page-url-map.txt:
+     *     ALT	/action/feature/view/ZDB-ALT
+     *     ANAT	/action/ontology/term/ZDB-ANAT
+     *     ATB	/action/antibody/view/ZDB-ATB
+     *     BAC	/action/marker/clone/view/ZDB-BAC
+     *     ...
+     *
+     * @return Map of URL patterns and their replacement formats
+     */
+    public static Map<Pattern, String> urlPatterns() {
+        Map<Pattern, String> patterns = new HashMap<>();
+        String zdbIDPattern = "ZDB-[A-Z_]+-\\d{6}-\\d+";
+        List<String> zdbURLs = List.of(
+    "/action/antibody/view/",
+//                "/action/data/alias/", //not needed since it is a redirect
+                "/action/feature/view/",
+                "/action/figure/view/",
+                "/action/fish/",
+                "/action/genotype/view/",
+                "/action/image/view/",
+                "/action/mapping/linkage/",
+                "/action/mapping/panel-detail/",
+                "/action/marker/clone/view/",
+                "/action/marker/construct/view/",
+                "/action/marker/efg/view/",
+                "/action/marker/eregion/view/",
+                "/action/marker/gene/view/",
+                "/action/marker/generic/view/",
+                "/action/marker/pseudogene/view/",
+                "/action/marker/region/view/",
+                "/action/marker/snp/view/",
+                "/action/marker/str/view/",
+                "/action/marker/transcript/view/",
+                "/action/nomenclature/view/", //eg. ZDB-NOMEN-230912-3
+                "/action/ontology/term/",
+                "/action/profile/view/",
+                "/action/publication/",
+                "/action/publication/journal/"
+        );
+        zdbURLs.forEach(url -> patterns.put(Pattern.compile(url + "(" + zdbIDPattern + ")$"), "/$1"));
+        patterns.put(Pattern.compile("/action/publication/journal/(" + zdbIDPattern + ")$"), "/$1");
+
+        String termIDPattern = "[^/]+"; //every character other than a forward slash
+        List<String> termPrefixes = List.of("BSPO", "CHEBI", "DOID", "ECO", "GO", "MMO", "MPATH", "NBO", "NBO", "NCBITaxon", "OBI", "PATO", "RO", "SO", "ZECO", "ZFA", "ZFS");
+        termPrefixes.forEach(prefix ->
+                patterns.put(Pattern.compile("/action/ontology/term/(" + prefix + termIDPattern + ")$"), "/$1"));
+
+        return patterns;
+    }
+
+    public static String match(String url) {
+        Map<Pattern, String> urlPatterns = urlPatterns();
+        for (Map.Entry<Pattern, String> entry : urlPatterns.entrySet()) {
+            if (entry.getKey().matcher(url).matches()) {
+                return entry.getKey().matcher(url).replaceAll(entry.getValue());
+            }
+        }
+        return null;
+    }
+
+
+    public static void addCanonicalIfFound(Model model) {
+        String canonicalUrl = match(getRequestedUrlPath());
+        if (canonicalUrl != null) {
+            model.addAttribute("canonicalUrl", canonicalUrl);
+        }
+    }
+
+    public static String getCanonicalIfFound(String url) {
+        String canonicalUrl = match(url);
+        if (canonicalUrl != null) {
+            return canonicalUrl;
+        }
+        return "";
+    }
+}
diff --git a/source/org/zfin/infrastructure/service/RequestService.java b/source/org/zfin/infrastructure/service/RequestService.java
new file mode 100644
index 0000000000..80370cb9e5
--- /dev/null
+++ b/source/org/zfin/infrastructure/service/RequestService.java
@@ -0,0 +1,25 @@
+package org.zfin.infrastructure.service;
+
+import org.springframework.web.context.request.RequestAttributes;
+import org.springframework.web.context.request.RequestContextHolder;
+import org.springframework.web.context.request.ServletRequestAttributes;
+
+import javax.servlet.http.HttpServletRequest;
+
+
+public class RequestService {
+    public static HttpServletRequest getCurrentRequest() {
+        ServletRequestAttributes requestAttributes = (ServletRequestAttributes) RequestContextHolder.currentRequestAttributes();
+        return requestAttributes.getRequest();
+    }
+
+    public static String getRequestedUrlPath() {
+        HttpServletRequest request = getCurrentRequest();
+        return request.getRequestURI();
+    }
+
+    public static String getRequestedForwardedUrl() {
+        HttpServletRequest request = getCurrentRequest();
+        return request.getAttribute("javax.servlet.forward.request_uri").toString();
+    }
+}
\ No newline at end of file
diff --git a/source/org/zfin/mapping/presentation/MappingDetailController.java b/source/org/zfin/mapping/presentation/MappingDetailController.java
index 9b151f7dd2..106a864705 100644
--- a/source/org/zfin/mapping/presentation/MappingDetailController.java
+++ b/source/org/zfin/mapping/presentation/MappingDetailController.java
@@ -15,7 +15,6 @@
 import org.zfin.framework.presentation.LookupStrings;
 import org.zfin.gbrowse.GBrowseService;
 import org.zfin.genomebrowser.presentation.GenomeBrowserFactory;
-import org.zfin.genomebrowser.presentation.GenomeBrowserImage;
 import org.zfin.gwt.curation.dto.FeatureMarkerRelationshipTypeEnum;
 import org.zfin.gwt.root.util.StringUtils;
 import org.zfin.infrastructure.ActiveData;
diff --git a/source/org/zfin/marker/presentation/CloneViewController.java b/source/org/zfin/marker/presentation/CloneViewController.java
index 5e9a88eaa6..488403ce3c 100644
--- a/source/org/zfin/marker/presentation/CloneViewController.java
+++ b/source/org/zfin/marker/presentation/CloneViewController.java
@@ -1,6 +1,5 @@
 package org.zfin.marker.presentation;
 
-import org.apache.commons.collections4.CollectionUtils;
 import org.apache.logging.log4j.LogManager;
 import org.apache.logging.log4j.Logger;
 import org.springframework.beans.factory.annotation.Autowired;
@@ -14,9 +13,7 @@
 import org.zfin.framework.HibernateUtil;
 import org.zfin.framework.presentation.Area;
 import org.zfin.framework.presentation.LookupStrings;
-import org.zfin.genomebrowser.GenomeBrowserTrack;
 import org.zfin.genomebrowser.presentation.GenomeBrowserFactory;
-import org.zfin.mapping.MarkerGenomeLocation;
 import org.zfin.marker.Clone;
 import org.zfin.marker.Marker;
 import org.zfin.marker.MarkerNotFoundException;
diff --git a/source/org/zfin/marker/presentation/GeneViewController.java b/source/org/zfin/marker/presentation/GeneViewController.java
index a8b7497ce7..9ed957e58b 100644
--- a/source/org/zfin/marker/presentation/GeneViewController.java
+++ b/source/org/zfin/marker/presentation/GeneViewController.java
@@ -304,6 +304,7 @@ public String phenotypeSummary(Model model
         //retrieveMutantData(term, form, true);
         //model.addAttribute(LookupStrings.FORM_BEAN, form);
         model.addAttribute("marker", marker);
+        model.addAttribute("title", "ZFIN Phenotype Figure Summary for Marker " + marker.getAbbreviation());
         return "marker/phenotype-summary";
     }
 
@@ -317,6 +318,7 @@ public String getExpression(Model model, @PathVariable String geneID) {
 
         String searchLink = new ExpressionSearchService.LinkBuilder()
             .gene(marker)
+            .title("Expression for Marker " + marker.getAbbreviation())
             .build();
         return "forward:" + searchLink;
     }
@@ -332,6 +334,7 @@ public String getWildtypeExpression(Model model, @PathVariable String geneID) {
         String searchLink = new ExpressionSearchService.LinkBuilder()
             .wildtypeOnly(true)
             .gene(marker)
+            .title("Wildtype Expression for Marker " + marker.getAbbreviation())
             .build();
         return "forward:" + searchLink;
     }
diff --git a/source/org/zfin/marker/presentation/SequenceTargetingReagentViewController.java b/source/org/zfin/marker/presentation/SequenceTargetingReagentViewController.java
index 9e1c276a7e..664c71c597 100644
--- a/source/org/zfin/marker/presentation/SequenceTargetingReagentViewController.java
+++ b/source/org/zfin/marker/presentation/SequenceTargetingReagentViewController.java
@@ -1,14 +1,14 @@
 package org.zfin.marker.presentation;
 
 import org.apache.commons.collections4.CollectionUtils;
-import org.apache.logging.log4j.LogManager; import org.apache.logging.log4j.Logger;
+import org.apache.logging.log4j.LogManager;
+import org.apache.logging.log4j.Logger;
 import org.springframework.beans.factory.annotation.Autowired;
 import org.springframework.stereotype.Controller;
 import org.springframework.ui.Model;
 import org.springframework.web.bind.annotation.*;
 import org.zfin.database.InformixUtil;
 import org.zfin.expression.ExpressionFigureStage;
-import org.zfin.expression.ExpressionResult;
 import org.zfin.expression.presentation.ExpressionDisplay;
 import org.zfin.expression.repository.ExpressionRepository;
 import org.zfin.expression.service.ExpressionService;
diff --git a/source/org/zfin/marker/presentation/TranscriptViewController.java b/source/org/zfin/marker/presentation/TranscriptViewController.java
index 299e992a74..1cb657e087 100644
--- a/source/org/zfin/marker/presentation/TranscriptViewController.java
+++ b/source/org/zfin/marker/presentation/TranscriptViewController.java
@@ -10,14 +10,12 @@
 import org.zfin.framework.HibernateUtil;
 import org.zfin.framework.presentation.Area;
 import org.zfin.framework.presentation.LookupStrings;
-import org.zfin.framework.presentation.PublicationNavigationMenu;
 import org.zfin.framework.presentation.TranscriptNavigationMenu;
 import org.zfin.marker.Marker;
 import org.zfin.marker.Transcript;
 import org.zfin.marker.TranscriptType;
 import org.zfin.marker.repository.MarkerRepository;
 import org.zfin.marker.service.MarkerService;
-import org.zfin.mutant.Genotype;
 import org.zfin.repository.RepositoryFactory;
 import org.zfin.sequence.DBLink;
 import org.zfin.sequence.DisplayGroup;
@@ -30,7 +28,6 @@
 import java.util.List;
 
 import static org.zfin.profile.UserService.isRootUser;
-import static org.zfin.repository.RepositoryFactory.getMarkerRepository;
 
 @Controller
 @RequestMapping("/marker")
diff --git a/source/org/zfin/nomenclature/presentation/NomenclatureSubmissionController.java b/source/org/zfin/nomenclature/presentation/NomenclatureSubmissionController.java
index 1c0a81a6cc..20d471869e 100644
--- a/source/org/zfin/nomenclature/presentation/NomenclatureSubmissionController.java
+++ b/source/org/zfin/nomenclature/presentation/NomenclatureSubmissionController.java
@@ -1,10 +1,9 @@
 package org.zfin.nomenclature.presentation;
 
-import com.fasterxml.jackson.core.JsonProcessingException;
-import com.fasterxml.jackson.databind.ObjectWriter;
 import org.apache.commons.collections4.CollectionUtils;
 import org.apache.commons.lang3.StringUtils;
-import org.apache.logging.log4j.LogManager; import org.apache.logging.log4j.Logger;
+import org.apache.logging.log4j.LogManager;
+import org.apache.logging.log4j.Logger;
 import org.hibernate.HibernateException;
 import org.hibernate.Transaction;
 import org.springframework.stereotype.Controller;
@@ -17,19 +16,20 @@
 import org.zfin.gwt.root.dto.PublicationDTO;
 import org.zfin.gwt.root.server.DTOConversionService;
 import org.zfin.infrastructure.PublicationAttribution;
+import org.zfin.infrastructure.seo.CanonicalLinkConfig;
 import org.zfin.marker.Marker;
 import org.zfin.marker.MarkerHistory;
-import org.zfin.marker.MarkerHistoryDTO;
 import org.zfin.nomenclature.*;
 import org.zfin.properties.ZfinPropertiesEnum;
 import org.zfin.publication.Publication;
 import org.zfin.repository.RepositoryFactory;
 
-import java.util.*;
-import java.util.stream.Collectors;
+import java.util.ArrayList;
+import java.util.Arrays;
+import java.util.Collection;
+import java.util.List;
 
 import static org.zfin.repository.RepositoryFactory.*;
-import com.fasterxml.jackson.databind.ObjectMapper;
 
 @Controller
 @RequestMapping("/nomenclature")
diff --git a/source/org/zfin/publication/presentation/ImageViewController.java b/source/org/zfin/publication/presentation/ImageViewController.java
index 1c7c70d718..3c611188c8 100644
--- a/source/org/zfin/publication/presentation/ImageViewController.java
+++ b/source/org/zfin/publication/presentation/ImageViewController.java
@@ -15,13 +15,13 @@
 import org.zfin.figure.presentation.FigureFromPublicationLink;
 import org.zfin.figure.presentation.FigureGalleryImagePresentation;
 import org.zfin.figure.presentation.FigurePhenotypeSummary;
-import org.zfin.publication.Publication;
 import org.zfin.figure.service.FigureViewService;
 import org.zfin.framework.presentation.ImageNavigationMenu;
 import org.zfin.framework.presentation.LookupStrings;
 import org.zfin.marker.Clone;
 import org.zfin.ontology.GenericTerm;
 import org.zfin.ontology.repository.OntologyRepository;
+import org.zfin.publication.Publication;
 import org.zfin.publication.repository.PublicationRepository;
 import org.zfin.repository.RepositoryFactory;
 import org.zfin.search.Category;
diff --git a/source/org/zfin/publication/presentation/PublicationViewController.java b/source/org/zfin/publication/presentation/PublicationViewController.java
index f4013c83a4..f9f05cdfb8 100644
--- a/source/org/zfin/publication/presentation/PublicationViewController.java
+++ b/source/org/zfin/publication/presentation/PublicationViewController.java
@@ -18,8 +18,6 @@
 import org.zfin.figure.service.FigureViewService;
 import org.zfin.framework.ComparatorCreator;
 import org.zfin.framework.api.Pagination;
-import org.zfin.framework.featureflag.FeatureFlagEnum;
-import org.zfin.framework.featureflag.FeatureFlags;
 import org.zfin.framework.presentation.*;
 import org.zfin.infrastructure.repository.InfrastructureRepository;
 import org.zfin.marker.Clone;
@@ -58,7 +56,6 @@
 import static org.zfin.repository.RepositoryFactory.getFigureRepository;
 import static org.zfin.repository.RepositoryFactory.getPublicationPageRepository;
 import static org.zfin.util.ZfinStringUtils.objectToJson;
-import static org.zfin.util.servlet.ServletService.isAuthenticated;
 
 @Controller
 @RequestMapping("/publication")