From 792aae69c0e8ce23ef6aa63cfef116ee0d454abd Mon Sep 17 00:00:00 2001
From: Simon Bear <simon.bear@csiro.au>
Date: Mon, 16 Nov 2020 18:01:48 +1100
Subject: [PATCH 01/22] Increment version number for next development iteration

---
 build.gradle | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/build.gradle b/build.gradle
index 516297c26..99c9346ae 100644
--- a/build.gradle
+++ b/build.gradle
@@ -10,7 +10,7 @@ buildscript {
     }
 }
 
-version "3.0.0.DQ"
+version "3.0.1.DQ-SNAPSHOT"
 group "au.org.ala.plugins.grails"
 
 apply plugin:"eclipse"

From d287374e886e59faec8ecc522c231b66c988e7d4 Mon Sep 17 00:00:00 2001
From: Simon Bear <simon.bear@csiro.au>
Date: Fri, 27 Nov 2020 10:35:34 +1100
Subject: [PATCH 02/22] AtlasOfLivingAustralia/DataQuality#182 Add duplicate
 assertion type to flag an issue

---
 grails-app/assets/javascripts/show.js         | 69 ++++++++++++++++++-
 .../biocache/hubs/AssertionsController.groovy |  8 ++-
 .../biocache/hubs/OccurrenceController.groovy | 13 ++++
 grails-app/i18n/messages_en.properties        |  1 +
 .../biocache/hubs/WebServicesService.groovy   |  3 +-
 .../views/occurrence/_recordSidebar.gsp       | 11 ++-
 grails-app/views/occurrence/show.gsp          |  4 ++
 7 files changed, 105 insertions(+), 4 deletions(-)

diff --git a/grails-app/assets/javascripts/show.js b/grails-app/assets/javascripts/show.js
index f651f2c48..f4cb14ffb 100644
--- a/grails-app/assets/javascripts/show.js
+++ b/grails-app/assets/javascripts/show.js
@@ -26,6 +26,65 @@ $(document).ready(function() {
         $('.missingPropResult').toggle();
     });
 
+    $('#copyRecordIdToClipboard').on('click', function(e) {
+        var copyText = document.querySelector("#hidden-uuid");
+        copyText.type = 'text';
+        copyText.select();
+        document.execCommand("copy");
+        copyText.type = 'hidden';
+        var $parent = $('#copyRecordIdToClipboard-parent');
+        $parent.tooltip('show');
+        setTimeout(function() {
+            $parent.tooltip('hide');
+        }, 1000);
+        // alert("Copied");
+    });
+    $('#issue').on('change', function(e) {
+        var $this = $(this);
+        var val = $this.val();
+        var $submit = $('#issueForm input[type=submit]');
+        var $p = $('#related-record-p');
+        if (val == '20020') {
+            $('#relatedRecordId').val('');
+            $submit.prop('disabled', true);
+            $p.show();
+        } else {
+            $submit.prop('disabled', false);
+            $p.hide();
+            $('#related-record-id-not-found').hide();
+            $('#related-record-id-found').hide();
+            $('#related-record-id-loading').hide();
+        }
+    });
+    $('#relatedRecordId').on('change', function(e) {
+        var $this = $(this);
+        var $submit = $('#issueForm input[type=submit]');
+        var val = $this.val().trim();
+        if (val == OCC_REC.recordUuid) {
+            alert("You can't mark this record as a duplicate of itself!");
+        } else if (val == '') {
+            $('#related-record-id-not-found').hide();
+            $('#related-record-id-found').hide();
+            $('#related-record-id-loading').hide();
+            $submit.prop('disabled', true);
+        } else {
+
+            $('#related-record-id-loading').show();
+            $.get( OCC_REC.contextPath + "/occurrence/exists/" + val, function(data) {
+                $('#related-record-id-not-found').hide();
+                $('#related-record-id-found').text(data).show();
+                $('#related-record-id-loading').hide();
+                $submit.prop('disabled', false);
+            }).error(function () {
+                $('#related-record-id-not-found').show();
+                $('#related-record-id-found').hide();
+                $('#related-record-id-loading').hide();
+                $submit.prop('disabled', true);
+            });
+        }
+
+    });
+
     jQuery.i18n.properties({
         name: 'messages',
         path: OCC_REC.contextPath + '/messages/i18n/',
@@ -43,6 +102,7 @@ $(document).ready(function() {
         e.preventDefault();
         var comment = $("#issueComment").val();
         var code = $("#issue").val();
+        var relatedRecordId = $('#relatedRecordId').val();
         var userDisplayName = OCC_REC.userDisplayName //'${userDisplayName}';
         var recordUuid = OCC_REC.recordUuid //'${ala:escapeJS(record.raw.rowKey)}';
         if(code!=""){
@@ -63,6 +123,12 @@ $(document).ready(function() {
                 if (bPreventAddingIssue) {
                     alert("You cannot flag an issue with the same type that has already been verified.");
                     return;
+                } else if (code == '20020' && !relatedRecordId) {
+                    alert("You must provide a duplicate record id to mark this as a duplicate");
+                    return;
+                } else if (code == '20020' && relatedRecordId == recordUuid) {
+                    alert("You can't mark a record as a duplicate of itself");
+                    return;
                 } else {
 
                     $.post(OCC_REC.contextPath + "/occurrences/assertions/add",
@@ -72,7 +138,8 @@ $(document).ready(function() {
                             comment: comment,
                             userAssertionStatus: 'Open issue',
                             userId: OCC_REC.userId,
-                            userDisplayName: userDisplayName
+                            userDisplayName: userDisplayName,
+                            relatedRecordId: relatedRecordId
                         },
                         function (data) {
                             $('#assertionSubmitProgress').css({'display': 'none'});
diff --git a/grails-app/controllers/au/org/ala/biocache/hubs/AssertionsController.groovy b/grails-app/controllers/au/org/ala/biocache/hubs/AssertionsController.groovy
index 12e4dba41..8da413570 100644
--- a/grails-app/controllers/au/org/ala/biocache/hubs/AssertionsController.groovy
+++ b/grails-app/controllers/au/org/ala/biocache/hubs/AssertionsController.groovy
@@ -40,11 +40,17 @@ class AssertionsController {
         String comment = params.comment?:''
         String userAssertionStatus = params.userAssertionStatus?: ""
         String assertionUuid = params.assertionUuid?: ""
+        String relatedRecordId = params.relatedRecordId ?: ''
         UserDetails userDetails = authService?.userDetails() // will return null if not available/not logged in
 
         if (recordUuid && code && userDetails) {
+
+            if (code == '20020' && !relatedRecordId) {
+                render(status: 400, text: 'Duplicate record id not provided')
+            }
+
             log.info("Adding assertion to UUID: ${recordUuid}, code: ${code}, comment: ${comment}, userAssertionStatus: ${userAssertionStatus}, userId: ${userDetails.userId}, userEmail: ${userDetails.email}")
-            Map postResponse = webServicesService.addAssertion(recordUuid, code, comment, userDetails.userId, userDetails.displayName, userAssertionStatus, assertionUuid)
+            Map postResponse = webServicesService.addAssertion(recordUuid, code, comment, userDetails.userId, userDetails.displayName, userAssertionStatus, assertionUuid, relatedRecordId)
 
             if (postResponse.statusCode == 201) {
                 log.info("Called REST service. Assertion should be added" )
diff --git a/grails-app/controllers/au/org/ala/biocache/hubs/OccurrenceController.groovy b/grails-app/controllers/au/org/ala/biocache/hubs/OccurrenceController.groovy
index 4db6d6fd6..a0a527ed5 100644
--- a/grails-app/controllers/au/org/ala/biocache/hubs/OccurrenceController.groovy
+++ b/grails-app/controllers/au/org/ala/biocache/hubs/OccurrenceController.groovy
@@ -25,9 +25,12 @@ import org.grails.web.json.JSONArray
 import org.grails.web.json.JSONElement
 import org.grails.web.json.JSONObject
 
+import javax.servlet.http.HttpServletResponse
 import java.text.SimpleDateFormat
 
 import static au.org.ala.biocache.hubs.TimingUtils.time
+import static javax.servlet.http.HttpServletResponse.SC_NOT_FOUND
+import static javax.servlet.http.HttpServletResponse.SC_NO_CONTENT
 
 /**
  * Controller for occurrence searches and records
@@ -602,6 +605,16 @@ class OccurrenceController {
         render webServicesService.facetCSVDownload(requestParams), contentType: 'text/csv', fileName: 'data.csv'
     }
 
+    def exists(String id) {
+        def record = webServicesService.getRecord(id, false)
+        if (record.keySet()) {
+            log.error("{}", record)
+            render text: record?.processed?.classification?.vernacularName ?: record?.raw?.classification?.vernacularName ?: record?.processed?.classification?.scientificName ?: record?.raw?.classification?.scientificName
+        } else {
+            render status: SC_NOT_FOUND, text: ''
+        }
+    }
+
     /**
      * JSON webservices for debugging/testing
      */
diff --git a/grails-app/i18n/messages_en.properties b/grails-app/i18n/messages_en.properties
index 8e4b8954d..2e289ab85 100644
--- a/grails-app/i18n/messages_en.properties
+++ b/grails-app/i18n/messages_en.properties
@@ -133,6 +133,7 @@ show.loginorflag.div01.navigator = Click here
 show.loginorflag.div02.label = You are logged in as
 show.issueform.label01 = Issue type:
 show.issueform.label02 = Comment:
+show.issueform.label03 = Duplicate Record ID:
 show.issueform.button.submit = Submit
 show.issueform.button.cancel = Cancel
 show.issueform.button.close = Close
diff --git a/grails-app/services/au/org/ala/biocache/hubs/WebServicesService.groovy b/grails-app/services/au/org/ala/biocache/hubs/WebServicesService.groovy
index 0350cb27b..ccaba2c43 100644
--- a/grails-app/services/au/org/ala/biocache/hubs/WebServicesService.groovy
+++ b/grails-app/services/au/org/ala/biocache/hubs/WebServicesService.groovy
@@ -182,13 +182,14 @@ class WebServicesService {
      * @return Map postResponse
      */
     Map addAssertion(String recordUuid, String code, String comment, String userId, String userDisplayName,
-                         String userAssertionStatus, String assertionUuid) {
+                         String userAssertionStatus, String assertionUuid, String relatedRecordId) {
         Map postBody =  [
                 recordUuid: recordUuid,
                 code: code,
                 comment: comment,
                 userAssertionStatus: userAssertionStatus,
                 assertionUuid: assertionUuid,
+                relatedRecordId: relatedRecordId,
                 userId: userId,
                 userDisplayName: userDisplayName,
                 apiKey: grailsApplication.config.biocache.apiKey
diff --git a/grails-app/views/occurrence/_recordSidebar.gsp b/grails-app/views/occurrence/_recordSidebar.gsp
index 6a3c078cf..6ef5c65ff 100644
--- a/grails-app/views/occurrence/_recordSidebar.gsp
+++ b/grails-app/views/occurrence/_recordSidebar.gsp
@@ -319,12 +319,21 @@
                         <form id="issueForm">
                             <p style="margin-top:20px;">
                                 <label for="issue"><g:message code="show.issueform.label01" default="Issue type:"/></label>
-                                <select name="issue" id="issue">
+                                <select name="issue" id="issue" autocomplete="off">
                                     <g:each in="${errorCodes}" var="code">
                                         <option value="${code.code}"><g:message code="${code.name}" default="${code.name}"/></option>
                                     </g:each>
                                 </select>
                             </p>
+                            <p id="related-record-p" style="display: none; margin-top:30px;">
+                                <label for="relatedRecordId" style="vertical-align:top;"><g:message code="show.issueform.label03" default="Duplicate Record ID:"/><span style="color: red;">*</span></label>
+                                <input type="text" name="relatedRecordId" id="relatedRecordId" placeholder="Paste the duplicate record id here" style="width:380px;"/>
+                                <p class="help-block">
+                                    <span style="display: none; color:red;" id="related-record-id-not-found">The record id can't be found.</span>
+                                    <span style="display: none;" id="related-record-id-loading"><i class="fa fa-gear fa-spin"></i></span>
+                                    <span style="display: none; color:green;" id="related-record-id-found">The record id can be found.</span>
+                                </p>
+                            </p>
                             <p style="margin-top:30px;">
                                 <label for="issueComment" style="vertical-align:top;"><g:message code="show.issueform.label02" default="Comment:"/></label>
                                 <textarea name="comment" id="issueComment" style="width:380px;height:150px;" placeholder="Please add a comment here..."></textarea>
diff --git a/grails-app/views/occurrence/show.gsp b/grails-app/views/occurrence/show.gsp
index e092f1365..7465e7804 100644
--- a/grails-app/views/occurrence/show.gsp
+++ b/grails-app/views/occurrence/show.gsp
@@ -176,6 +176,10 @@
                 </div><!-- end div#SidebarBox -->
                 <div id="" class="col-md-8">
                     <div class="text-right">
+                        <input id="hidden-uuid" type="hidden" value="${uuid}">
+                        <span id="copyRecordIdToClipboard-parent" data-toggle="tooltip" data-trigger="manual" data-title="${uuid} copied!">
+                            <button class="btn btn-default" id="copyRecordIdToClipboard" role="button" title="Copy this record's id to the clipboard"><g:message code="show.sidebar02.copyrecordid" default="Copy record id" /></button>
+                        </span>
                         <button href="#processedVsRawView" class="btn btn-default" id="showRawProcessed" role="button" data-toggle="modal"
                                 title="Table showing both original and processed record values">
                             <span id="processedVsRawViewSpan" href="#processedVsRawView" title=""><i class="glyphicon glyphicon-transfer"></i>

From 419e47054c453eed236e91d7caddff7bb564be7c Mon Sep 17 00:00:00 2001
From: Simon Bear <simon.bear@csiro.au>
Date: Mon, 30 Nov 2020 10:28:23 +1100
Subject: [PATCH 03/22] AtlasOfLivingAustralia/DataQuality#208 Add duplicate
 user assertion support to user assertion UI

---
 grails-app/assets/javascripts/show.js  | 10 ++++++++++
 grails-app/i18n/messages_en.properties |  3 +++
 grails-app/views/occurrence/show.gsp   | 10 ++++++++++
 3 files changed, 23 insertions(+)

diff --git a/grails-app/assets/javascripts/show.js b/grails-app/assets/javascripts/show.js
index f4cb14ffb..2264ddac2 100644
--- a/grails-app/assets/javascripts/show.js
+++ b/grails-app/assets/javascripts/show.js
@@ -415,6 +415,16 @@ function refreshUserAnnotations(){
                 $clone.find('.userRole').text(userAssertion.userRole != null ? userAssertion.userRole : '');
                 $clone.find('.userEntity').text(userAssertion.userEntityName != null ? userAssertion.userEntityName : '');
                 $clone.find('.created').text('Date created: ' + (moment(userAssertion.created, "YYYY-MM-DDTHH:mm:ssZ").format('YYYY-MM-DD HH:mm:ss')));
+                if (userAssertion.relatedRecordId) {
+                    $clone.find('.related-record').show();
+                    var href = $clone.find('.related-record-link').attr('href');
+                    $clone.find('.related-record-link').attr('href', href.replace('replace-me', userAssertion.relatedRecordId));
+                    if (userAssertion.code == 20020) {
+                        $clone.find('.related-record-span-user-duplicate').show();
+                    } else {
+                        $clone.find('.related-record-span-default').show();
+                    }
+                }
                 if (userAssertion.userRole != null) {
                     $clone.find('.userRole').text(', ' + userAssertion.userRole);
                 }
diff --git a/grails-app/i18n/messages_en.properties b/grails-app/i18n/messages_en.properties
index 2e289ab85..fe696efc8 100644
--- a/grails-app/i18n/messages_en.properties
+++ b/grails-app/i18n/messages_en.properties
@@ -199,6 +199,8 @@ show.userannotationtemplate.p01.navigator = View more with this annotation
 show.userannotationtemplate.p02.navigator = Delete this annotation
 show.userannotationtemplate.p03.navigator = Verify this annotation
 show.userannotationtemplate.p04.navigator = Delete this verification
+show.userannotationtemplate.relatedrecord.userduplicate.a = View duplicated record
+show.userannotationtemplate.relatedrecord.default.a = View related record
 show.headingbar02.title = Record Not Found
 show.headingbar02.p01 = The requested record ID
 show.headingbar02.p02 = was not found
@@ -822,6 +824,7 @@ unrecognisedCollectionCode=Collection code not recognised
 unrecognisedInstitutionCode=Institution code not recognised
 invalidImageUrl=Image URL invalid
 temporalIssue=Temporal issue
+userDuplicateRecord=Duplicate record
 idPreOccurrence=Identification date before occurrence date
 georefPostDate=Georeferenced after occurrence date
 firstOfMonth=First of the month
diff --git a/grails-app/views/occurrence/show.gsp b/grails-app/views/occurrence/show.gsp
index 7465e7804..faae37ddb 100644
--- a/grails-app/views/occurrence/show.gsp
+++ b/grails-app/views/occurrence/show.gsp
@@ -700,6 +700,16 @@
         <ul style="display:none;">
             <li id="userAnnotationTemplate" class="userAnnotationTemplate well well-sm">
                 <h4><span class="issue"></span> - <g:message code="show.userannotationtemplate.title" default="flagged by"/> <span class="user"></span><span class="userRole"></span><span class="userEntity"></span></h4>
+                <p class="related-record" style="display:none;">
+                    <g:link class="related-record-link" controller="occurrence" action="show" id="replace-me">
+                        <span class="related-record-span-user-duplicate" style="display:none;">
+                            <g:message code="show.userannotationtemplate.relatedrecord.userduplicate.a" default="View duplicated record"/>
+                        </span>
+                        <span class="related-record-span-default" style="display:none;">
+                            <g:message code="show.userannotationtemplate.relatedrecord.default.a" default="View related record"/>
+                        </span>
+                    </g:link>
+                </p>
                 <p class="comment"></p>
                 <p class="hide userDisplayName"></p>
                 <p class="created small"></p>

From 3af21a1f9a8e67e123cfcfb16c033965d74a2204 Mon Sep 17 00:00:00 2001
From: Simon Bear <simon.bear@csiro.au>
Date: Tue, 1 Dec 2020 13:06:00 +1100
Subject: [PATCH 04/22] AtlasOfLivingAustralia/DataQuality#187 Add duplicate
 reason to duplicate record assertion

---
 grails-app/assets/javascripts/show.js         | 42 ++++++++++++++-----
 .../biocache/hubs/AssertionsController.groovy |  7 +++-
 grails-app/i18n/messages_en.properties        |  3 ++
 .../biocache/hubs/WebServicesService.groovy   |  4 +-
 .../views/occurrence/_recordSidebar.gsp       |  9 ++++
 5 files changed, 53 insertions(+), 12 deletions(-)

diff --git a/grails-app/assets/javascripts/show.js b/grails-app/assets/javascripts/show.js
index 2264ddac2..1c3281c9a 100644
--- a/grails-app/assets/javascripts/show.js
+++ b/grails-app/assets/javascripts/show.js
@@ -39,50 +39,67 @@ $(document).ready(function() {
         }, 1000);
         // alert("Copied");
     });
+    var recordIdValid = false;
+    function validateIssueForm() {
+        var issueCode = $('#issue').val();
+        var relatedRecordReason = $('#relatedRecordReason').val();
+        if (issueCode == '20020') {
+            return recordIdValid && relatedRecordReason;
+        }
+        return true;
+    }
+    function setIssueFormButtonState() {
+        $('#issueForm input[type=submit]').prop('disabled', !validateIssueForm());
+    }
     $('#issue').on('change', function(e) {
         var $this = $(this);
         var val = $this.val();
         var $submit = $('#issueForm input[type=submit]');
-        var $p = $('#related-record-p');
+        var $p = $('#related-record-p, #related-record-reason-p');
         if (val == '20020') {
             $('#relatedRecordId').val('');
-            $submit.prop('disabled', true);
+            recordIdValid = false;
             $p.show();
         } else {
-            $submit.prop('disabled', false);
             $p.hide();
             $('#related-record-id-not-found').hide();
             $('#related-record-id-found').hide();
             $('#related-record-id-loading').hide();
         }
+        setIssueFormButtonState();
     });
+    $('#relatedRecordReason').on('change', function(e) {
+        setIssueFormButtonState();
+    })
     $('#relatedRecordId').on('change', function(e) {
         var $this = $(this);
         var $submit = $('#issueForm input[type=submit]');
         var val = $this.val().trim();
         if (val == OCC_REC.recordUuid) {
             alert("You can't mark this record as a duplicate of itself!");
+            recordIdValid = false;
         } else if (val == '') {
             $('#related-record-id-not-found').hide();
             $('#related-record-id-found').hide();
             $('#related-record-id-loading').hide();
-            $submit.prop('disabled', true);
+            recordIdValid = false;
         } else {
-
             $('#related-record-id-loading').show();
-            $.get( OCC_REC.contextPath + "/occurrence/exists/" + val, function(data) {
+            $.get( OCC_REC.contextPath + "/occurrence/exists/" + val).success(function(data) {
                 $('#related-record-id-not-found').hide();
                 $('#related-record-id-found').text(data).show();
                 $('#related-record-id-loading').hide();
-                $submit.prop('disabled', false);
+                recordIdValid = true;
             }).error(function () {
                 $('#related-record-id-not-found').show();
                 $('#related-record-id-found').hide();
                 $('#related-record-id-loading').hide();
-                $submit.prop('disabled', true);
+                recordIdValid = false;
+            }).always(function() {
+                setIssueFormButtonState();
             });
         }
-
+        setIssueFormButtonState();
     });
 
     jQuery.i18n.properties({
@@ -103,6 +120,7 @@ $(document).ready(function() {
         var comment = $("#issueComment").val();
         var code = $("#issue").val();
         var relatedRecordId = $('#relatedRecordId').val();
+        var relatedRecordReason = $('#relatedRecordReason').val();
         var userDisplayName = OCC_REC.userDisplayName //'${userDisplayName}';
         var recordUuid = OCC_REC.recordUuid //'${ala:escapeJS(record.raw.rowKey)}';
         if(code!=""){
@@ -126,6 +144,9 @@ $(document).ready(function() {
                 } else if (code == '20020' && !relatedRecordId) {
                     alert("You must provide a duplicate record id to mark this as a duplicate");
                     return;
+                } else if (code == '20020' && !relatedRecordReason) {
+                    alert("You must select a reason to mark this record as a duplicate");
+                    return;
                 } else if (code == '20020' && relatedRecordId == recordUuid) {
                     alert("You can't mark a record as a duplicate of itself");
                     return;
@@ -139,7 +160,8 @@ $(document).ready(function() {
                             userAssertionStatus: 'Open issue',
                             userId: OCC_REC.userId,
                             userDisplayName: userDisplayName,
-                            relatedRecordId: relatedRecordId
+                            relatedRecordId: relatedRecordId,
+                            relatedRecordReason: relatedRecordReason,
                         },
                         function (data) {
                             $('#assertionSubmitProgress').css({'display': 'none'});
diff --git a/grails-app/controllers/au/org/ala/biocache/hubs/AssertionsController.groovy b/grails-app/controllers/au/org/ala/biocache/hubs/AssertionsController.groovy
index 8da413570..58cc5690f 100644
--- a/grails-app/controllers/au/org/ala/biocache/hubs/AssertionsController.groovy
+++ b/grails-app/controllers/au/org/ala/biocache/hubs/AssertionsController.groovy
@@ -41,6 +41,7 @@ class AssertionsController {
         String userAssertionStatus = params.userAssertionStatus?: ""
         String assertionUuid = params.assertionUuid?: ""
         String relatedRecordId = params.relatedRecordId ?: ''
+        String relatedRecordReason = params.relatedRecordReason ?: ''
         UserDetails userDetails = authService?.userDetails() // will return null if not available/not logged in
 
         if (recordUuid && code && userDetails) {
@@ -49,8 +50,12 @@ class AssertionsController {
                 render(status: 400, text: 'Duplicate record id not provided')
             }
 
+            if (code == '20020' && !relatedRecordReason) {
+                render(status: 400, text: 'Duplicate record reason not provided')
+            }
+
             log.info("Adding assertion to UUID: ${recordUuid}, code: ${code}, comment: ${comment}, userAssertionStatus: ${userAssertionStatus}, userId: ${userDetails.userId}, userEmail: ${userDetails.email}")
-            Map postResponse = webServicesService.addAssertion(recordUuid, code, comment, userDetails.userId, userDetails.displayName, userAssertionStatus, assertionUuid, relatedRecordId)
+            Map postResponse = webServicesService.addAssertion(recordUuid, code, comment, userDetails.userId, userDetails.displayName, userAssertionStatus, assertionUuid, relatedRecordId, relatedRecordReason)
 
             if (postResponse.statusCode == 201) {
                 log.info("Called REST service. Assertion should be added" )
diff --git a/grails-app/i18n/messages_en.properties b/grails-app/i18n/messages_en.properties
index fe696efc8..99282a06e 100644
--- a/grails-app/i18n/messages_en.properties
+++ b/grails-app/i18n/messages_en.properties
@@ -1149,3 +1149,6 @@ dq.warning.dataprofile.content.line1 = Search results are now filtered by defaul
 dq.warning.dataprofile.buttonleft.text = Learn More
 dq.warning.dataprofile.buttonright.text = Got it
 
+related.record.reason.sameoccurence=Same occurence
+related.record.reason.tissuesample=Tissue sample
+related.record.reason.splitspecimen=Split specimen
\ No newline at end of file
diff --git a/grails-app/services/au/org/ala/biocache/hubs/WebServicesService.groovy b/grails-app/services/au/org/ala/biocache/hubs/WebServicesService.groovy
index ccaba2c43..1dcb6b42c 100644
--- a/grails-app/services/au/org/ala/biocache/hubs/WebServicesService.groovy
+++ b/grails-app/services/au/org/ala/biocache/hubs/WebServicesService.groovy
@@ -182,7 +182,8 @@ class WebServicesService {
      * @return Map postResponse
      */
     Map addAssertion(String recordUuid, String code, String comment, String userId, String userDisplayName,
-                         String userAssertionStatus, String assertionUuid, String relatedRecordId) {
+                         String userAssertionStatus, String assertionUuid, String relatedRecordId,
+                         String relatedRecordReason) {
         Map postBody =  [
                 recordUuid: recordUuid,
                 code: code,
@@ -190,6 +191,7 @@ class WebServicesService {
                 userAssertionStatus: userAssertionStatus,
                 assertionUuid: assertionUuid,
                 relatedRecordId: relatedRecordId,
+                relatedRecordReason: relatedRecordReason,
                 userId: userId,
                 userDisplayName: userDisplayName,
                 apiKey: grailsApplication.config.biocache.apiKey
diff --git a/grails-app/views/occurrence/_recordSidebar.gsp b/grails-app/views/occurrence/_recordSidebar.gsp
index 6ef5c65ff..a1c016e80 100644
--- a/grails-app/views/occurrence/_recordSidebar.gsp
+++ b/grails-app/views/occurrence/_recordSidebar.gsp
@@ -334,6 +334,15 @@
                                     <span style="display: none; color:green;" id="related-record-id-found">The record id can be found.</span>
                                 </p>
                             </p>
+                            <p id="related-record-reason-p" style="display: none; margin-top:30px;">
+                                <label for="relatedRecordId" style="vertical-align:top;"><g:message code="show.issueform.label03" default="Duplicate Record ID:"/><span style="color: red;">*</span></label>
+                                <select name="relatedRecordReason" id="relatedRecordReason" autocomplete="off">
+                                    <option value=""><g:message code="related.record.reason.select" default="-- Select a reason --" /></option>
+                                    <option value="sameoccurence"><g:message code="related.record.reason.sameoccurence" default="Same occurence"/></option>
+                                    <option value="tissuesample"><g:message code="related.record.reason.tissuesample" default="Tissue sample"/></option>
+                                    <option value="splitspecimen"><g:message code="related.record.reason.splitspecimen" default="Split specimen"/></option>
+                                </select>
+                            </p>
                             <p style="margin-top:30px;">
                                 <label for="issueComment" style="vertical-align:top;"><g:message code="show.issueform.label02" default="Comment:"/></label>
                                 <textarea name="comment" id="issueComment" style="width:380px;height:150px;" placeholder="Please add a comment here..."></textarea>

From 1e4bd595fcba16a138e1b57eb204005bc5bc568f Mon Sep 17 00:00:00 2001
From: Simon Bear <simon.bear@csiro.au>
Date: Tue, 1 Dec 2020 13:07:25 +1100
Subject: [PATCH 05/22] AtlasOfLivingAustralia/DataQuality#208 Add duplicate
 reason display

---
 grails-app/assets/javascripts/show.js | 4 ++++
 grails-app/views/occurrence/show.gsp  | 1 +
 2 files changed, 5 insertions(+)

diff --git a/grails-app/assets/javascripts/show.js b/grails-app/assets/javascripts/show.js
index 1c3281c9a..2e93fb8eb 100644
--- a/grails-app/assets/javascripts/show.js
+++ b/grails-app/assets/javascripts/show.js
@@ -447,6 +447,10 @@ function refreshUserAnnotations(){
                         $clone.find('.related-record-span-default').show();
                     }
                 }
+                if (userAssertion.relatedRecordReason) {
+                    $clone.find('.related-record-reason').show();
+                    $clone.find('.related-record-reason-span').text(jQuery.i18n.prop('related.record.reason.'+userAssertion.relatedRecordReason));
+                }
                 if (userAssertion.userRole != null) {
                     $clone.find('.userRole').text(', ' + userAssertion.userRole);
                 }
diff --git a/grails-app/views/occurrence/show.gsp b/grails-app/views/occurrence/show.gsp
index faae37ddb..e385bf0da 100644
--- a/grails-app/views/occurrence/show.gsp
+++ b/grails-app/views/occurrence/show.gsp
@@ -700,6 +700,7 @@
         <ul style="display:none;">
             <li id="userAnnotationTemplate" class="userAnnotationTemplate well well-sm">
                 <h4><span class="issue"></span> - <g:message code="show.userannotationtemplate.title" default="flagged by"/> <span class="user"></span><span class="userRole"></span><span class="userEntity"></span></h4>
+                <p class="related-record-reason" style="display:none;"><g:message code="show.userannotationtemplate.relatedrecord.reason.label" default="Reason:"/> <span class="related-record-reason-span"></span></p>
                 <p class="related-record" style="display:none;">
                     <g:link class="related-record-link" controller="occurrence" action="show" id="replace-me">
                         <span class="related-record-span-user-duplicate" style="display:none;">

From 34c49b7b1da53e1d724c868624ff0d3474fe37b8 Mon Sep 17 00:00:00 2001
From: Simon Bear <simon.bear@csiro.au>
Date: Tue, 1 Dec 2020 14:38:03 +1100
Subject: [PATCH 06/22] AtlasOfLivingAustralia/DataQuality#187 Lower logging
 level for exists action

---
 .../au/org/ala/biocache/hubs/OccurrenceController.groovy        | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/grails-app/controllers/au/org/ala/biocache/hubs/OccurrenceController.groovy b/grails-app/controllers/au/org/ala/biocache/hubs/OccurrenceController.groovy
index a0a527ed5..bcfa7f21d 100644
--- a/grails-app/controllers/au/org/ala/biocache/hubs/OccurrenceController.groovy
+++ b/grails-app/controllers/au/org/ala/biocache/hubs/OccurrenceController.groovy
@@ -608,7 +608,7 @@ class OccurrenceController {
     def exists(String id) {
         def record = webServicesService.getRecord(id, false)
         if (record.keySet()) {
-            log.error("{}", record)
+            log.trace("{}", record)
             render text: record?.processed?.classification?.vernacularName ?: record?.raw?.classification?.vernacularName ?: record?.processed?.classification?.scientificName ?: record?.raw?.classification?.scientificName
         } else {
             render status: SC_NOT_FOUND, text: ''

From cf43901c08b345cf1c14b2e68607c5483049e356 Mon Sep 17 00:00:00 2001
From: Simon Bear <simon.bear@csiro.au>
Date: Fri, 4 Dec 2020 10:54:36 +1100
Subject: [PATCH 07/22] AtlasOfLivingAustralia/DataQuality#214 preview record
 when flagging a duplicate record

---
 grails-app/assets/javascripts/show.js                       | 3 ++-
 .../au/org/ala/biocache/hubs/OccurrenceController.groovy    | 3 ++-
 grails-app/i18n/messages_en.properties                      | 2 ++
 grails-app/views/occurrence/_recordSidebar.gsp              | 6 +++++-
 4 files changed, 11 insertions(+), 3 deletions(-)

diff --git a/grails-app/assets/javascripts/show.js b/grails-app/assets/javascripts/show.js
index 2e93fb8eb..6ebac7dc4 100644
--- a/grails-app/assets/javascripts/show.js
+++ b/grails-app/assets/javascripts/show.js
@@ -87,7 +87,8 @@ $(document).ready(function() {
             $('#related-record-id-loading').show();
             $.get( OCC_REC.contextPath + "/occurrence/exists/" + val).success(function(data) {
                 $('#related-record-id-not-found').hide();
-                $('#related-record-id-found').text(data).show();
+                $('#related-record-id-found').show();
+                $('#related-record-id-found-other').text(data);
                 $('#related-record-id-loading').hide();
                 recordIdValid = true;
             }).error(function () {
diff --git a/grails-app/controllers/au/org/ala/biocache/hubs/OccurrenceController.groovy b/grails-app/controllers/au/org/ala/biocache/hubs/OccurrenceController.groovy
index bcfa7f21d..4452b5db5 100644
--- a/grails-app/controllers/au/org/ala/biocache/hubs/OccurrenceController.groovy
+++ b/grails-app/controllers/au/org/ala/biocache/hubs/OccurrenceController.groovy
@@ -609,7 +609,8 @@ class OccurrenceController {
         def record = webServicesService.getRecord(id, false)
         if (record.keySet()) {
             log.trace("{}", record)
-            render text: record?.processed?.classification?.vernacularName ?: record?.raw?.classification?.vernacularName ?: record?.processed?.classification?.scientificName ?: record?.raw?.classification?.scientificName
+            def result = "${record?.processed?.classification?.scientificName ?: record?.raw?.classification?.scientificName ?: ''}, ${record?.processed?.location?.stateProvince ?: record?.raw?.location?.stateProvince ?: ''}, ${record?.processed?.location?.decimalLongitude ?: record?.raw?.location?.decimalLongitude ?: ''}, ${record?.processed?.location?.decimalLatitude ?: record?.raw?.location?.decimalLatitude ?: ''}, ${record?.processed?.event?.eventDate ?: record?.raw?.event?.eventDate ?: ''}"
+            render text: result
         } else {
             render status: SC_NOT_FOUND, text: ''
         }
diff --git a/grails-app/i18n/messages_en.properties b/grails-app/i18n/messages_en.properties
index 99282a06e..839283691 100644
--- a/grails-app/i18n/messages_en.properties
+++ b/grails-app/i18n/messages_en.properties
@@ -134,6 +134,8 @@ show.loginorflag.div02.label = You are logged in as
 show.issueform.label01 = Issue type:
 show.issueform.label02 = Comment:
 show.issueform.label03 = Duplicate Record ID:
+show.issueform.relatedrecord.found.this = You are indicating this record (the one you are viewing):
+show.issueform.relatedrecord.found.other = is a duplicate of this record (the id you provided):
 show.issueform.button.submit = Submit
 show.issueform.button.cancel = Cancel
 show.issueform.button.close = Close
diff --git a/grails-app/views/occurrence/_recordSidebar.gsp b/grails-app/views/occurrence/_recordSidebar.gsp
index a1c016e80..de47dce47 100644
--- a/grails-app/views/occurrence/_recordSidebar.gsp
+++ b/grails-app/views/occurrence/_recordSidebar.gsp
@@ -331,7 +331,11 @@
                                 <p class="help-block">
                                     <span style="display: none; color:red;" id="related-record-id-not-found">The record id can't be found.</span>
                                     <span style="display: none;" id="related-record-id-loading"><i class="fa fa-gear fa-spin"></i></span>
-                                    <span style="display: none; color:green;" id="related-record-id-found">The record id can be found.</span>
+                                    <span style="display: none;" id="related-record-id-found">
+                                        <g:message code="show.issueform.relatedrecord.found.this" default="You are indicating this record (the one you are viewing):"/> <span id="related-record-id-found-this">${record?.processed?.classification?.scientificName ?: record?.raw?.classification?.scientificName ?: ''}, ${record?.processed?.location?.stateProvince ?: record?.raw?.location?.stateProvince ?: ''}, ${record?.processed?.location?.decimalLongitude ?: record?.raw?.location?.decimalLongitude ?: ''}, ${record?.processed?.location?.decimalLatitude ?: record?.raw?.location?.decimalLatitude ?: ''}, ${record?.processed?.event?.eventDate ?: record?.raw?.event?.eventDate ?: ''}</span>
+                                        <br/>
+                                        <g:message code="show.issueform.relatedrecord.found.other" default="is a duplicate of this record (the id you provided):"/> <span id="related-record-id-found-other"></span>
+                                    </span>
                                 </p>
                             </p>
                             <p id="related-record-reason-p" style="display: none; margin-top:30px;">

From b313e76b75894f3dcd3fe9196a91cccfba98ff25 Mon Sep 17 00:00:00 2001
From: Simon Bear <simon.bear@csiro.au>
Date: Mon, 14 Dec 2020 17:46:20 +1100
Subject: [PATCH 08/22] AtlasOfLivingAustralia/DataQuality#187 Review feedback

---
 grails-app/i18n/messages_en.properties         | 1 +
 grails-app/views/occurrence/_recordSidebar.gsp | 4 ++--
 2 files changed, 3 insertions(+), 2 deletions(-)

diff --git a/grails-app/i18n/messages_en.properties b/grails-app/i18n/messages_en.properties
index 839283691..1c8d74379 100644
--- a/grails-app/i18n/messages_en.properties
+++ b/grails-app/i18n/messages_en.properties
@@ -134,6 +134,7 @@ show.loginorflag.div02.label = You are logged in as
 show.issueform.label01 = Issue type:
 show.issueform.label02 = Comment:
 show.issueform.label03 = Duplicate Record ID:
+show.issueform.label04 = Duplicate Reason:
 show.issueform.relatedrecord.found.this = You are indicating this record (the one you are viewing):
 show.issueform.relatedrecord.found.other = is a duplicate of this record (the id you provided):
 show.issueform.button.submit = Submit
diff --git a/grails-app/views/occurrence/_recordSidebar.gsp b/grails-app/views/occurrence/_recordSidebar.gsp
index de47dce47..36479f7f2 100644
--- a/grails-app/views/occurrence/_recordSidebar.gsp
+++ b/grails-app/views/occurrence/_recordSidebar.gsp
@@ -339,8 +339,8 @@
                                 </p>
                             </p>
                             <p id="related-record-reason-p" style="display: none; margin-top:30px;">
-                                <label for="relatedRecordId" style="vertical-align:top;"><g:message code="show.issueform.label03" default="Duplicate Record ID:"/><span style="color: red;">*</span></label>
-                                <select name="relatedRecordReason" id="relatedRecordReason" autocomplete="off">
+                                <label for="relatedRecordId" style="vertical-align:top;"><g:message code="show.issueform.label04" default="Duplicate Reason:"/><span style="color: red;">*</span></label>
+                                <select name="relatedRecordReason" id="relatedRecordReason" autocomplete="off
                                     <option value=""><g:message code="related.record.reason.select" default="-- Select a reason --" /></option>
                                     <option value="sameoccurence"><g:message code="related.record.reason.sameoccurence" default="Same occurence"/></option>
                                     <option value="tissuesample"><g:message code="related.record.reason.tissuesample" default="Tissue sample"/></option>

From df1e332a52cb5ef05c7ac86e08b211794258b132 Mon Sep 17 00:00:00 2001
From: "alex.huang" <HUA091@csiro.au>
Date: Tue, 15 Dec 2020 10:49:18 +1100
Subject: [PATCH 09/22] Feature my annotations (#391)

* initial commit

* updated API calls to get/add/delete alerts

* updated API calls to get/add/delete alerts

* use logged in user id when get/add/delete alerts

* removed useless config

* update subscribe/un-subscribe my annotations

* parameterise the alert name we want to subscribe for my annotation

* code style per code review

* init myannotations before every call

Co-authored-by: Simon Bear <simon.bear@csiro.au>
---
 grails-app/assets/javascripts/show.js         | 51 ++++++++++++++++++-
 grails-app/conf/plugin.groovy                 |  1 +
 .../hubs/BiocacheHubsUrlMappings.groovy       |  3 ++
 .../biocache/hubs/OccurrenceController.groovy | 31 ++++++++++-
 grails-app/i18n/messages_en.properties        |  1 +
 .../biocache/hubs/WebServicesService.groovy   | 26 +++++++++-
 .../views/occurrence/_recordSidebar.gsp       |  5 ++
 grails-app/views/occurrence/show.gsp          |  3 +-
 8 files changed, 115 insertions(+), 6 deletions(-)

diff --git a/grails-app/assets/javascripts/show.js b/grails-app/assets/javascripts/show.js
index 6ebac7dc4..03597f2ce 100644
--- a/grails-app/assets/javascripts/show.js
+++ b/grails-app/assets/javascripts/show.js
@@ -152,7 +152,6 @@ $(document).ready(function() {
                     alert("You can't mark a record as a duplicate of itself");
                     return;
                 } else {
-
                     $.post(OCC_REC.contextPath + "/occurrences/assertions/add",
                         {
                             recordUuid: recordUuid,
@@ -165,6 +164,18 @@ $(document).ready(function() {
                             relatedRecordReason: relatedRecordReason,
                         },
                         function (data) {
+                            // when add assertion succeeds, we update alert settings
+                            if (myAnnotationQueryId) {
+                                var orig_state = $('#notifyChangeCheckbox').prop('data-origstate');
+                                var new_state = $('#notifyChangeCheckbox').prop('checked');
+
+                                // only update when user changed preference
+                                if (orig_state !== new_state) {
+                                    var actionpath = new_state ? ("/occurrences/addAlert?queryId=" + myAnnotationQueryId) : ("/occurrences/deleteAlert?queryId=" + myAnnotationQueryId)
+                                    $.post(OCC_REC.contextPath + actionpath)
+                                }
+                            }
+
                             $('#assertionSubmitProgress').css({'display': 'none'});
                             $("#submitSuccess").html("Thanks for flagging the problem!");
                             $("#issueFormSubmit").hide();
@@ -197,6 +208,43 @@ $(document).ready(function() {
         $(el).html(replaceURLWithHTMLLinks(html)); // convert it
     });
 
+    var myAnnotationQueryId = null
+
+    $('#assertionButton').click(function (e) {
+        var getAlerts = OCC_REC.contextPath + "/occurrences/alerts";
+        // hide check box until we get user alerts settings
+        $("#notifyChange").hide();
+
+        $.getJSON(getAlerts, function (data) {
+            // init status
+            myAnnotationQueryId = null
+            var myAnnotationEnabled = false
+            if (data.enabledQueries) {
+                for (var i = 0; i < data.enabledQueries.length; i++) {
+                    if (data.enabledQueries[i].name.indexOf(OCC_REC.alertName) !== -1) {
+                        myAnnotationEnabled = true;
+                        myAnnotationQueryId = data.enabledQueries[i].id
+                    }
+                }
+            }
+
+            if (data.disabledQueries) {
+                for (var i = 0; i < data.disabledQueries.length; i++) {
+                    if (data.disabledQueries[i].name.indexOf(OCC_REC.alertName) !== -1) {
+                        myAnnotationEnabled = false;
+                        myAnnotationQueryId = data.disabledQueries[i].id
+                    }
+                }
+            }
+
+            // if find 'my annotation' show the check box
+            if (myAnnotationQueryId !== null) {
+                $("#notifyChange").show();
+                $("#notifyChangeCheckbox").prop('checked', myAnnotationEnabled);
+                $("#notifyChangeCheckbox").prop('data-origstate', myAnnotationEnabled);
+            }
+        })
+    })
 
     // bind to form "close" button TODO
     $("input#close").on("click", function(e) {
@@ -598,7 +646,6 @@ function updateConfirmVerificationEvents(occUuid, assertionUuid, userDisplayName
         }
 
         console.log("Submitting an assertion with userAssertionStatus: " + userAssertionStatus)
-
         $.post(OCC_REC.contextPath + "/occurrences/assertions/add",
             { recordUuid: occUuid,
                 code: code,
diff --git a/grails-app/conf/plugin.groovy b/grails-app/conf/plugin.groovy
index 3446b61da..4b3575609 100644
--- a/grails-app/conf/plugin.groovy
+++ b/grails-app/conf/plugin.groovy
@@ -143,6 +143,7 @@ alwaysshow.imagetab = false
 
 facets.defaultSelected = "data_resource_uid,taxon_name,year,multimedia"
 
+myannotation.name="My Annotations"
 mapdownloads {
     baseLayers {
         default_layer {
diff --git a/grails-app/controllers/au/org/ala/biocache/hubs/BiocacheHubsUrlMappings.groovy b/grails-app/controllers/au/org/ala/biocache/hubs/BiocacheHubsUrlMappings.groovy
index 49f0f4e23..2e9b8b646 100644
--- a/grails-app/controllers/au/org/ala/biocache/hubs/BiocacheHubsUrlMappings.groovy
+++ b/grails-app/controllers/au/org/ala/biocache/hubs/BiocacheHubsUrlMappings.groovy
@@ -24,6 +24,9 @@ class BiocacheHubsUrlMappings {
         "/occurrences/next"(controller: 'occurrence', action: 'next')
         "/occurrences/previous"(controller: 'occurrence', action: 'previous')
         "/occurrences/dataQualityExcludeCounts"(controller: 'occurrence', action: 'dataQualityExcludeCounts')
+        "/occurrences/alerts"(controller: 'occurrence', action: [GET: 'getAlerts'])
+        "/occurrences/addAlert"(controller: 'occurrence', action: [POST: 'addAlert'])
+        "/occurrences/deleteAlert"(controller: 'occurrence', action: [POST: 'deleteAlert'])
         "/occurrences/$id"(controller: 'occurrence', action: 'show')
         "/occurrence/$id"(controller: 'occurrence', action: 'show')
         "/assertions/$id"(controller: 'assertions', action: 'assertions')
diff --git a/grails-app/controllers/au/org/ala/biocache/hubs/OccurrenceController.groovy b/grails-app/controllers/au/org/ala/biocache/hubs/OccurrenceController.groovy
index 4452b5db5..b31c993f6 100644
--- a/grails-app/controllers/au/org/ala/biocache/hubs/OccurrenceController.groovy
+++ b/grails-app/controllers/au/org/ala/biocache/hubs/OccurrenceController.groovy
@@ -17,7 +17,6 @@ package au.org.ala.biocache.hubs
 
 import au.org.ala.dataquality.model.QualityProfile
 import au.org.ala.web.CASRoles
-import com.google.common.base.Stopwatch
 import com.maxmind.geoip2.record.Location
 import grails.converters.JSON
 import groovy.util.logging.Slf4j
@@ -639,4 +638,34 @@ class OccurrenceController {
         data.count = qualityService.getExcludeCount(params.categoryLabel, profile.getCategories(), requestParams)
         render data as JSON
     }
+
+    def getAlerts() {
+        String userId = authService?.getUserId()
+        if (userId == null) {
+            response.status = 404
+            render ([error: 'userId must be supplied to get alerts'] as JSON)
+        } else {
+            render webServicesService.getAlerts(userId) as JSON
+        }
+    }
+
+    def addAlert() {
+        String userId = authService?.getUserId()
+        if (userId == null) {
+            response.status = 404
+            render ([error: 'userId must be supplied to add alert'] as JSON)
+        } else {
+            render webServicesService.addAlert(userId, params.queryId) as JSON
+        }
+    }
+
+    def deleteAlert() {
+        String userId = authService?.getUserId()
+        if (userId == null) {
+            response.status = 404
+            render ([error: 'userId must be supplied to delete alert'] as JSON)
+        } else {
+            render webServicesService.deleteAlert(userId, params.queryId) as JSON
+        }
+    }
 }
diff --git a/grails-app/i18n/messages_en.properties b/grails-app/i18n/messages_en.properties
index 1c8d74379..8f6509d65 100644
--- a/grails-app/i18n/messages_en.properties
+++ b/grails-app/i18n/messages_en.properties
@@ -135,6 +135,7 @@ show.issueform.label01 = Issue type:
 show.issueform.label02 = Comment:
 show.issueform.label03 = Duplicate Record ID:
 show.issueform.label04 = Duplicate Reason:
+show.issueform.notifyme = Notify me when records I have annotated are updated
 show.issueform.relatedrecord.found.this = You are indicating this record (the one you are viewing):
 show.issueform.relatedrecord.found.other = is a duplicate of this record (the id you provided):
 show.issueform.button.submit = Submit
diff --git a/grails-app/services/au/org/ala/biocache/hubs/WebServicesService.groovy b/grails-app/services/au/org/ala/biocache/hubs/WebServicesService.groovy
index 1dcb6b42c..7034056c9 100644
--- a/grails-app/services/au/org/ala/biocache/hubs/WebServicesService.groovy
+++ b/grails-app/services/au/org/ala/biocache/hubs/WebServicesService.groovy
@@ -100,6 +100,21 @@ class WebServicesService {
         getJsonElements(url)
     }
 
+    def getAlerts(String userId) {
+        def url = "${grailsApplication.config.alerts.baseURL}" + "/api/alerts/user/" + userId
+        return getJsonElements(url, "${grailsApplication.config.alerts.apiKey}")
+    }
+
+    def addAlert(String userId, String queryId) {
+        String url = "${grailsApplication.config.alerts.baseURL}" + "/api/alerts/user/" + userId + "/subscribe/" + queryId
+        postFormData(url, [:], grailsApplication.config.alerts.apiKey as String)
+    }
+
+    def deleteAlert(String userId, String queryId) {
+        String url = "${grailsApplication.config.alerts.baseURL}" + "/api/alerts/user/" + userId + "/unsubscribe/" + queryId
+        postFormData(url, [:], grailsApplication.config.alerts.apiKey as String)
+    }
+
     def JSONObject getDuplicateRecordDetails(JSONObject record) {
         log.debug "getDuplicateRecordDetails -> ${record?.processed?.occurrence?.associatedOccurrences}"
         if (record?.processed?.occurrence?.associatedOccurrences) {
@@ -401,12 +416,15 @@ class WebServicesService {
      * @param url
      * @return
      */
-    JSONElement getJsonElements(String url) {
+    JSONElement getJsonElements(String url, String apiKey = null) {
         log.debug "(internal) getJson URL = " + url
         def conn = new URL(url).openConnection()
         try {
             conn.setConnectTimeout(10000)
             conn.setReadTimeout(50000)
+            if (apiKey != null) {
+                conn.setRequestProperty('apiKey', apiKey)
+            }
             return JSON.parse(conn.getInputStream(), "UTF-8")
         } catch (Exception e) {
             def error = "Failed to get json from web service (${url}). ${e.getClass()} ${e.getMessage()}, ${e}"
@@ -445,13 +463,17 @@ class WebServicesService {
      * @param postParams
      * @return postResponse (Map with keys: statusCode (int) and statusMsg (String)
      */
-    def Map postFormData(String uri, Map postParams) {
+    def Map postFormData(String uri, Map postParams, String apiKey = null) {
         HTTPBuilder http = new HTTPBuilder(uri)
         log.debug "POST (form encoded) to ${http.uri}"
         Map postResponse = [:]
 
         http.request( Method.POST ) {
 
+            if (apiKey != null) {
+                headers.'apiKey' = apiKey
+            }
+
             send ContentType.URLENC, postParams
 
             response.success = { resp ->
diff --git a/grails-app/views/occurrence/_recordSidebar.gsp b/grails-app/views/occurrence/_recordSidebar.gsp
index 36479f7f2..5a2565613 100644
--- a/grails-app/views/occurrence/_recordSidebar.gsp
+++ b/grails-app/views/occurrence/_recordSidebar.gsp
@@ -351,6 +351,11 @@
                                 <label for="issueComment" style="vertical-align:top;"><g:message code="show.issueform.label02" default="Comment:"/></label>
                                 <textarea name="comment" id="issueComment" style="width:380px;height:150px;" placeholder="Please add a comment here..."></textarea>
                             </p>
+
+                            <p style="margin-top:30px;">
+                                <label style="width:100%" id="notifyChange"><input type="checkbox" id="notifyChangeCheckbox" name="notifyChange" value="">&nbsp;<g:message code="show.issueform.notifyme" default="Notify me when records I have annotated are updated"/></label>
+                            </p>
+
                             <p style="margin-top:20px;">
                                 <input id="issueFormSubmit" type="submit" value="<g:message code="show.issueform.button.submit" default="Submit"/>" class="btn btn-primary" />
                                 <input type="reset" value="<g:message code="show.issueform.button.cancel" default="Cancel"/>" class="btn btn-default" onClick="$('#loginOrFlag').modal('hide');"/>
diff --git a/grails-app/views/occurrence/show.gsp b/grails-app/views/occurrence/show.gsp
index e385bf0da..e85deb52f 100644
--- a/grails-app/views/occurrence/show.gsp
+++ b/grails-app/views/occurrence/show.gsp
@@ -59,7 +59,8 @@
                    status="s">'${sds}': '${grailsApplication.config.sensitiveDatasets[sds]}'${s < (sensitiveDatasets.size() - 1) ? ',' : ''}
                 </g:each>
             },
-            hasGoogleKey: ${grailsApplication.config.google.apikey as Boolean}
+            hasGoogleKey: ${grailsApplication.config.google.apikey as Boolean},
+            alertName: "${grailsApplication.config.myannotation.name}"
         }
 
         // Google charts

From e4c4e1dbda9a9e617becd277bf41fa2af68673a8 Mon Sep 17 00:00:00 2001
From: alexhuang091 <hua091@csiro.au>
Date: Mon, 21 Dec 2020 10:41:22 +1100
Subject: [PATCH 10/22] removed unused param from processUserFQInteraction

---
 .../au/org/ala/biocache/hubs/OccurrenceController.groovy        | 2 +-
 .../au/org/ala/biocache/hubs/PostProcessingService.groovy       | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/grails-app/controllers/au/org/ala/biocache/hubs/OccurrenceController.groovy b/grails-app/controllers/au/org/ala/biocache/hubs/OccurrenceController.groovy
index b31c993f6..e7106e02a 100644
--- a/grails-app/controllers/au/org/ala/biocache/hubs/OccurrenceController.groovy
+++ b/grails-app/controllers/au/org/ala/biocache/hubs/OccurrenceController.groovy
@@ -168,7 +168,7 @@ class OccurrenceController {
             def groupedEnabledFilters = time("get grouped enabled filters") { qualityService.getGroupedEnabledFilters(requestParams.qualityProfile) }
             def qualityFilterDescriptionsByLabel = groupedEnabledFilters.collectEntries {[(it.key) : it.value*.description.join(' and ')] }
 
-            def (fqInteract, dqInteract, UserFQColors, DQColors) = time("process user fq interactions") { postProcessingService.processUserFQInteraction(requestParams, searchResults?.activeFacetObj) }
+            def (fqInteract, dqInteract, UserFQColors, DQColors) = time("process user fq interactions") { postProcessingService.processUserFQInteraction(requestParams) }
 
             def messagePropertiesFile = time("message properties file") { webServicesService.getMessagesPropertiesFile() }
             def assertionCodeMap = time("assertionCodeMap") { webServicesService.getAssertionCodeMap() }
diff --git a/grails-app/services/au/org/ala/biocache/hubs/PostProcessingService.groovy b/grails-app/services/au/org/ala/biocache/hubs/PostProcessingService.groovy
index 657c784ea..b3e3e7452 100644
--- a/grails-app/services/au/org/ala/biocache/hubs/PostProcessingService.groovy
+++ b/grails-app/services/au/org/ala/biocache/hubs/PostProcessingService.groovy
@@ -504,7 +504,7 @@ class PostProcessingService {
         layerObjects
     }
 
-    def processUserFQInteraction(SpatialSearchRequestParams requestParams, activeFacetObj) {
+    def processUserFQInteraction(SpatialSearchRequestParams requestParams) {
         def disabled = requestParams.disableQualityFilter as Set
 
         // map from category label to filter names

From 1feef6fafbf557771c40bcc363fa7eda81469e92 Mon Sep 17 00:00:00 2001
From: alexhuang091 <hua091@csiro.au>
Date: Tue, 22 Dec 2020 16:02:37 +1100
Subject: [PATCH 11/22] updated biocache-hubs to use dq-client 1.1.0 with user
 profile feature

---
 build.gradle                                  |  2 +-
 .../biocache/hubs/OccurrenceController.groovy |  4 +--
 .../ala/biocache/hubs/QualityService.groovy   | 26 +++++++++++--------
 .../biocache/hubs/WebServicesService.groovy   |  4 +--
 4 files changed, 20 insertions(+), 16 deletions(-)

diff --git a/build.gradle b/build.gradle
index 99c9346ae..d92a43007 100644
--- a/build.gradle
+++ b/build.gradle
@@ -76,7 +76,7 @@ dependencies {
     //compile 'com.google.guava:guava:19.0' // replaces ehcache
     compile "com.googlecode.owasp-java-html-sanitizer:owasp-java-html-sanitizer:20180219.1"
 
-    compile "au.org.ala:data-quality-filter-service-client:1.0.0", noCache
+    compile "au.org.ala:data-quality-filter-service-client:1.1.0", noCache
 
     //plugins
     //compile 'org.grails.plugins:cache-ehcache:3.0.0.M1'
diff --git a/grails-app/controllers/au/org/ala/biocache/hubs/OccurrenceController.groovy b/grails-app/controllers/au/org/ala/biocache/hubs/OccurrenceController.groovy
index e7106e02a..06ab92425 100644
--- a/grails-app/controllers/au/org/ala/biocache/hubs/OccurrenceController.groovy
+++ b/grails-app/controllers/au/org/ala/biocache/hubs/OccurrenceController.groovy
@@ -65,7 +65,7 @@ class OccurrenceController {
     def list(SpatialSearchRequestParams requestParams) {
         def start = System.currentTimeMillis()
 
-        def activeProfile = time("active profile") { qualityService.activeProfile(requestParams.qualityProfile) }
+        def activeProfile = time("active profile") { qualityService.activeProfile(requestParams.qualityProfile, authService?.getUserId()) }
 
         normaliseRequestParams(requestParams)
 
@@ -217,7 +217,7 @@ class OccurrenceController {
                     UserFQColors: UserFQColors,
                     DQColors: DQColors,
                     activeProfile: activeProfile,
-                    qualityProfiles: time("findAllEnabledProfiles") { qualityService.findAllEnabledProfiles(true) },
+                    qualityProfiles: time("findAllEnabledProfiles") { qualityService.findAllEnabledProfiles(true, authService?.getUserId()) },
                     inverseFilters: inverseFilters
             ]
 
diff --git a/grails-app/services/au/org/ala/biocache/hubs/QualityService.groovy b/grails-app/services/au/org/ala/biocache/hubs/QualityService.groovy
index e8c5d1833..38471dd94 100644
--- a/grails-app/services/au/org/ala/biocache/hubs/QualityService.groovy
+++ b/grails-app/services/au/org/ala/biocache/hubs/QualityService.groovy
@@ -25,6 +25,9 @@ class QualityService {
     @Value('${dataquality.baseUrl}')
     def dataQualityBaseUrl
 
+    @Value('${dataquality.apiKey}')
+    String dataQualityAPIKey
+
     @Value('${dataquality.recordCountCacheSpec}')
     String recordCountCacheSpec
 
@@ -39,6 +42,7 @@ class QualityService {
     def init() {
         if (dataQualityEnabled) {
             def apiClient = new ApiClient()
+            apiClient.setApiKey(dataQualityAPIKey)
             apiClient.adapterBuilder.baseUrl(dataQualityBaseUrl)
             apiClient.okBuilder.addInterceptor { chain ->
                 def request = chain.request().newBuilder().addHeader('User-Agent', "${grailsApplication.config.info.app.name}/${grailsApplication.config.info.app.version}").build()
@@ -50,9 +54,9 @@ class QualityService {
         recordCountCache = CacheBuilder.from(recordCountCacheSpec).build { webServicesService.fullTextSearch(it)?.totalRecords }
     }
 
-    Map<String, String> getEnabledFiltersByLabel(String profileName) {
+    Map<String, String> getEnabledFiltersByLabel(String profileName, userId = null) {
         if (dataQualityEnabled) {
-            return responseOrThrow(api.getEnabledFiltersByLabel(profileName))
+            return responseOrThrow(api.getEnabledFiltersByLabel(profileName, userId))
         } else {
             return [:]
         }
@@ -66,26 +70,26 @@ class QualityService {
         }
     }
 
-    Map<String, List<QualityFilter>> getGroupedEnabledFilters(String profileName) {
+    Map<String, List<QualityFilter>> getGroupedEnabledFilters(String profileName, String userId = null) {
         if (dataQualityEnabled) {
-            return responseOrThrow(api.getGroupedEnabledFilters(profileName))
+            return responseOrThrow(api.getGroupedEnabledFilters(profileName, userId))
         } else {
             return [:]
         }
-
     }
 
-    List<QualityCategory> findAllEnabledCategories(String profileName) {
+    List<QualityCategory> findAllEnabledCategories(String profileName, String userId = null) {
         if (dataQualityEnabled) {
-            return responseOrThrow(api.findAllEnabledCategories(profileName))
+            return responseOrThrow(api.findAllEnabledCategories(profileName, userId))
         } else {
             return []
         }
     }
 
-    QualityProfile activeProfile(String profileName) {
+    QualityProfile activeProfile(String profileName, String userId = null) {
         if (dataQualityEnabled) {
-            return responseOrThrow(api.activeProfile(profileName))
+            QualityProfile qp = responseOrThrow(api.activeProfile(profileName, userId))
+            return qp
         } else {
             return null
         }
@@ -115,9 +119,9 @@ class QualityService {
         }
     }
 
-    List<QualityProfile> findAllEnabledProfiles(boolean enabled) {
+    List<QualityProfile> findAllEnabledProfiles(boolean enabled, String userId = null) {
         if (dataQualityEnabled) {
-            return responseOrThrow(dataProfilesApi.dataProfiles(null, null, null, null, enabled, null, null))
+            return responseOrThrow(dataProfilesApi.dataProfiles(null, null, null, null, enabled, null, null, userId))
         } else {
             return []
         }
diff --git a/grails-app/services/au/org/ala/biocache/hubs/WebServicesService.groovy b/grails-app/services/au/org/ala/biocache/hubs/WebServicesService.groovy
index 7034056c9..9bfb9f5ae 100644
--- a/grails-app/services/au/org/ala/biocache/hubs/WebServicesService.groovy
+++ b/grails-app/services/au/org/ala/biocache/hubs/WebServicesService.groovy
@@ -29,7 +29,7 @@ class WebServicesService {
 
     public static final String ENVIRONMENTAL = "Environmental"
     public static final String CONTEXTUAL = "Contextual"
-    def grailsApplication, facetsCacheServiceBean
+    def grailsApplication, facetsCacheServiceBean, authService
     QualityService qualityService
 
     @Value('${dataquality.enabled}')
@@ -665,7 +665,7 @@ class WebServicesService {
     def populateProfile(requestParams) {
         // force set the profile if none provided
         if (dataQualityEnabled && !requestParams.qualityProfile && !requestParams.disableAllQualityFilters) {
-            def activeProfile = qualityService.activeProfile(requestParams.qualityProfile)
+            def activeProfile = qualityService.activeProfile(requestParams.qualityProfile, authService?.getUserId())
             requestParams.qualityProfile = activeProfile?.shortName
         }
     }

From a787499f537fb8a4dd1170987508928734801948 Mon Sep 17 00:00:00 2001
From: alexhuang091 <hua091@csiro.au>
Date: Wed, 23 Dec 2020 16:47:28 +1100
Subject: [PATCH 12/22] changes needed for my annotation changes on alerts side

---
 grails-app/assets/javascripts/show.js         | 31 ++++++-------------
 .../hubs/BiocacheHubsUrlMappings.groovy       |  4 +--
 .../biocache/hubs/OccurrenceController.groovy | 10 +++---
 .../biocache/hubs/WebServicesService.groovy   |  8 ++---
 4 files changed, 20 insertions(+), 33 deletions(-)

diff --git a/grails-app/assets/javascripts/show.js b/grails-app/assets/javascripts/show.js
index 03597f2ce..5906a7327 100644
--- a/grails-app/assets/javascripts/show.js
+++ b/grails-app/assets/javascripts/show.js
@@ -165,14 +165,14 @@ $(document).ready(function() {
                         },
                         function (data) {
                             // when add assertion succeeds, we update alert settings
-                            if (myAnnotationQueryId) {
+                            if (myAnnotationAvailable) {
                                 var orig_state = $('#notifyChangeCheckbox').prop('data-origstate');
                                 var new_state = $('#notifyChangeCheckbox').prop('checked');
 
                                 // only update when user changed preference
                                 if (orig_state !== new_state) {
-                                    var actionpath = new_state ? ("/occurrences/addAlert?queryId=" + myAnnotationQueryId) : ("/occurrences/deleteAlert?queryId=" + myAnnotationQueryId)
-                                    $.post(OCC_REC.contextPath + actionpath)
+                                    var actionpath = new_state ? "/occurrences/addMyAnnotationAlert" : "/occurrences/deleteMyAnnotationAlert";
+                                    $.post(OCC_REC.contextPath + actionpath);
                                 }
                             }
 
@@ -208,7 +208,7 @@ $(document).ready(function() {
         $(el).html(replaceURLWithHTMLLinks(html)); // convert it
     });
 
-    var myAnnotationQueryId = null
+    var myAnnotationAvailable = false
 
     $('#assertionButton').click(function (e) {
         var getAlerts = OCC_REC.contextPath + "/occurrences/alerts";
@@ -217,28 +217,17 @@ $(document).ready(function() {
 
         $.getJSON(getAlerts, function (data) {
             // init status
-            myAnnotationQueryId = null
+            myAnnotationAvailable = false
             var myAnnotationEnabled = false
-            if (data.enabledQueries) {
-                for (var i = 0; i < data.enabledQueries.length; i++) {
-                    if (data.enabledQueries[i].name.indexOf(OCC_REC.alertName) !== -1) {
-                        myAnnotationEnabled = true;
-                        myAnnotationQueryId = data.enabledQueries[i].id
-                    }
-                }
-            }
-
-            if (data.disabledQueries) {
-                for (var i = 0; i < data.disabledQueries.length; i++) {
-                    if (data.disabledQueries[i].name.indexOf(OCC_REC.alertName) !== -1) {
-                        myAnnotationEnabled = false;
-                        myAnnotationQueryId = data.disabledQueries[i].id
-                    }
+            if (data && data.myannotation) {
+                myAnnotationAvailable = true
+                if (data.myannotation.length > 0) {
+                    myAnnotationEnabled = true
                 }
             }
 
             // if find 'my annotation' show the check box
-            if (myAnnotationQueryId !== null) {
+            if (myAnnotationAvailable) {
                 $("#notifyChange").show();
                 $("#notifyChangeCheckbox").prop('checked', myAnnotationEnabled);
                 $("#notifyChangeCheckbox").prop('data-origstate', myAnnotationEnabled);
diff --git a/grails-app/controllers/au/org/ala/biocache/hubs/BiocacheHubsUrlMappings.groovy b/grails-app/controllers/au/org/ala/biocache/hubs/BiocacheHubsUrlMappings.groovy
index 2e9b8b646..92c3471a5 100644
--- a/grails-app/controllers/au/org/ala/biocache/hubs/BiocacheHubsUrlMappings.groovy
+++ b/grails-app/controllers/au/org/ala/biocache/hubs/BiocacheHubsUrlMappings.groovy
@@ -25,8 +25,8 @@ class BiocacheHubsUrlMappings {
         "/occurrences/previous"(controller: 'occurrence', action: 'previous')
         "/occurrences/dataQualityExcludeCounts"(controller: 'occurrence', action: 'dataQualityExcludeCounts')
         "/occurrences/alerts"(controller: 'occurrence', action: [GET: 'getAlerts'])
-        "/occurrences/addAlert"(controller: 'occurrence', action: [POST: 'addAlert'])
-        "/occurrences/deleteAlert"(controller: 'occurrence', action: [POST: 'deleteAlert'])
+        "/occurrences/addMyAnnotationAlert"(controller: 'occurrence', action: [POST: 'addMyAnnotationAlert'])
+        "/occurrences/deleteMyAnnotationAlert"(controller: 'occurrence', action: [POST: 'deleteMyAnnotationAlert'])
         "/occurrences/$id"(controller: 'occurrence', action: 'show')
         "/occurrence/$id"(controller: 'occurrence', action: 'show')
         "/assertions/$id"(controller: 'assertions', action: 'assertions')
diff --git a/grails-app/controllers/au/org/ala/biocache/hubs/OccurrenceController.groovy b/grails-app/controllers/au/org/ala/biocache/hubs/OccurrenceController.groovy
index e7106e02a..232057467 100644
--- a/grails-app/controllers/au/org/ala/biocache/hubs/OccurrenceController.groovy
+++ b/grails-app/controllers/au/org/ala/biocache/hubs/OccurrenceController.groovy
@@ -24,12 +24,10 @@ import org.grails.web.json.JSONArray
 import org.grails.web.json.JSONElement
 import org.grails.web.json.JSONObject
 
-import javax.servlet.http.HttpServletResponse
 import java.text.SimpleDateFormat
 
 import static au.org.ala.biocache.hubs.TimingUtils.time
 import static javax.servlet.http.HttpServletResponse.SC_NOT_FOUND
-import static javax.servlet.http.HttpServletResponse.SC_NO_CONTENT
 
 /**
  * Controller for occurrence searches and records
@@ -649,23 +647,23 @@ class OccurrenceController {
         }
     }
 
-    def addAlert() {
+    def addMyAnnotationAlert() {
         String userId = authService?.getUserId()
         if (userId == null) {
             response.status = 404
             render ([error: 'userId must be supplied to add alert'] as JSON)
         } else {
-            render webServicesService.addAlert(userId, params.queryId) as JSON
+            render webServicesService.addMyAnnotationAlert(userId) as JSON
         }
     }
 
-    def deleteAlert() {
+    def deleteMyAnnotationAlert() {
         String userId = authService?.getUserId()
         if (userId == null) {
             response.status = 404
             render ([error: 'userId must be supplied to delete alert'] as JSON)
         } else {
-            render webServicesService.deleteAlert(userId, params.queryId) as JSON
+            render webServicesService.deleteMyAnnotationAlert(userId) as JSON
         }
     }
 }
diff --git a/grails-app/services/au/org/ala/biocache/hubs/WebServicesService.groovy b/grails-app/services/au/org/ala/biocache/hubs/WebServicesService.groovy
index 7034056c9..8b86700a5 100644
--- a/grails-app/services/au/org/ala/biocache/hubs/WebServicesService.groovy
+++ b/grails-app/services/au/org/ala/biocache/hubs/WebServicesService.groovy
@@ -105,13 +105,13 @@ class WebServicesService {
         return getJsonElements(url, "${grailsApplication.config.alerts.apiKey}")
     }
 
-    def addAlert(String userId, String queryId) {
-        String url = "${grailsApplication.config.alerts.baseURL}" + "/api/alerts/user/" + userId + "/subscribe/" + queryId
+    def addMyAnnotationAlert(String userId) {
+        String url = "${grailsApplication.config.alerts.baseURL}" + "/api/alerts/user/" + userId + "/addMyAnnotationAlert"
         postFormData(url, [:], grailsApplication.config.alerts.apiKey as String)
     }
 
-    def deleteAlert(String userId, String queryId) {
-        String url = "${grailsApplication.config.alerts.baseURL}" + "/api/alerts/user/" + userId + "/unsubscribe/" + queryId
+    def deleteMyAnnotationAlert(String userId) {
+        String url = "${grailsApplication.config.alerts.baseURL}" + "/api/alerts/user/" + userId + "/deleteMyAnnotationAlert"
         postFormData(url, [:], grailsApplication.config.alerts.apiKey as String)
     }
 

From 1157eae6238c0e6405c1c0535681161f027e1dec Mon Sep 17 00:00:00 2001
From: alexhuang091 <hua091@csiro.au>
Date: Thu, 7 Jan 2021 20:43:44 +1100
Subject: [PATCH 13/22] to use dq-service-client 1.2.0-SNAPSHOT for
 user-specific profile

---
 build.gradle                                  |  2 +-
 .../ala/biocache/hubs/QualityService.groovy   | 25 ++++++++++++-------
 .../biocache/hubs/WebServicesService.groovy   |  2 +-
 3 files changed, 18 insertions(+), 11 deletions(-)

diff --git a/build.gradle b/build.gradle
index d92a43007..5b5371d22 100644
--- a/build.gradle
+++ b/build.gradle
@@ -76,7 +76,7 @@ dependencies {
     //compile 'com.google.guava:guava:19.0' // replaces ehcache
     compile "com.googlecode.owasp-java-html-sanitizer:owasp-java-html-sanitizer:20180219.1"
 
-    compile "au.org.ala:data-quality-filter-service-client:1.1.0", noCache
+    compile "au.org.ala:data-quality-filter-service-client:1.2.0-SNAPSHOT", noCache
 
     //plugins
     //compile 'org.grails.plugins:cache-ehcache:3.0.0.M1'
diff --git a/grails-app/services/au/org/ala/biocache/hubs/QualityService.groovy b/grails-app/services/au/org/ala/biocache/hubs/QualityService.groovy
index 38471dd94..a233c113a 100644
--- a/grails-app/services/au/org/ala/biocache/hubs/QualityService.groovy
+++ b/grails-app/services/au/org/ala/biocache/hubs/QualityService.groovy
@@ -54,9 +54,9 @@ class QualityService {
         recordCountCache = CacheBuilder.from(recordCountCacheSpec).build { webServicesService.fullTextSearch(it)?.totalRecords }
     }
 
-    Map<String, String> getEnabledFiltersByLabel(String profileName, userId = null) {
+    Map<String, String> getEnabledFiltersByLabel(String profileName) {
         if (dataQualityEnabled) {
-            return responseOrThrow(api.getEnabledFiltersByLabel(profileName, userId))
+            return responseOrThrow(api.getEnabledFiltersByLabel(profileName))
         } else {
             return [:]
         }
@@ -70,26 +70,33 @@ class QualityService {
         }
     }
 
-    Map<String, List<QualityFilter>> getGroupedEnabledFilters(String profileName, String userId = null) {
+    Map<String, List<QualityFilter>> getGroupedEnabledFilters(String profileName) {
         if (dataQualityEnabled) {
-            return responseOrThrow(api.getGroupedEnabledFilters(profileName, userId))
+            return responseOrThrow(api.getGroupedEnabledFilters(profileName))
         } else {
             return [:]
         }
     }
 
-    List<QualityCategory> findAllEnabledCategories(String profileName, String userId = null) {
+    List<QualityCategory> findAllEnabledCategories(String profileName) {
         if (dataQualityEnabled) {
-            return responseOrThrow(api.findAllEnabledCategories(profileName, userId))
+            return responseOrThrow(api.findAllEnabledCategories(profileName))
         } else {
             return []
         }
     }
 
-    QualityProfile activeProfile(String profileName, String userId = null) {
+    QualityProfile activeProfile(String profileName = null, String userId = null) {
         if (dataQualityEnabled) {
-            QualityProfile qp = responseOrThrow(api.activeProfile(profileName, userId))
-            return qp
+            return responseOrThrow(api.activeProfile(profileName, userId))
+        } else {
+            return null
+        }
+    }
+
+    QualityProfile getDefaultProfile(String userId = null) {
+        if (dataQualityEnabled) {
+            return responseOrThrow(api.getDefaultProfile(userId))
         } else {
             return null
         }
diff --git a/grails-app/services/au/org/ala/biocache/hubs/WebServicesService.groovy b/grails-app/services/au/org/ala/biocache/hubs/WebServicesService.groovy
index b0a7dfa2d..2ebbd353d 100644
--- a/grails-app/services/au/org/ala/biocache/hubs/WebServicesService.groovy
+++ b/grails-app/services/au/org/ala/biocache/hubs/WebServicesService.groovy
@@ -665,7 +665,7 @@ class WebServicesService {
     def populateProfile(requestParams) {
         // force set the profile if none provided
         if (dataQualityEnabled && !requestParams.qualityProfile && !requestParams.disableAllQualityFilters) {
-            def activeProfile = qualityService.activeProfile(requestParams.qualityProfile, authService?.getUserId())
+            def activeProfile = qualityService.getDefaultProfile(authService?.getUserId())
             requestParams.qualityProfile = activeProfile?.shortName
         }
     }

From a037da34a46e26ef55db804235ae16074455e503 Mon Sep 17 00:00:00 2001
From: alexhuang091 <hua091@csiro.au>
Date: Fri, 8 Jan 2021 15:55:05 +1100
Subject: [PATCH 14/22] Refined the way apiKey is set in ApiClient

---
 .../ala/biocache/hubs/OccurrenceController.groovy    |  2 +-
 .../ala/biocache/hubs/PostProcessingService.groovy   |  2 +-
 .../au/org/ala/biocache/hubs/QualityService.groovy   | 12 +++++++++++-
 3 files changed, 13 insertions(+), 3 deletions(-)

diff --git a/grails-app/controllers/au/org/ala/biocache/hubs/OccurrenceController.groovy b/grails-app/controllers/au/org/ala/biocache/hubs/OccurrenceController.groovy
index 979b1cc4a..c76cee203 100644
--- a/grails-app/controllers/au/org/ala/biocache/hubs/OccurrenceController.groovy
+++ b/grails-app/controllers/au/org/ala/biocache/hubs/OccurrenceController.groovy
@@ -632,7 +632,7 @@ class OccurrenceController {
 
     def getExcluded(SpatialSearchRequestParams requestParams) {
         def data = [:]
-        QualityProfile profile = qualityService.activeProfile(requestParams.qualityProfile)
+        QualityProfile profile = qualityService.activeProfile(requestParams.qualityProfile, authService?.getUserId())
         data.count = qualityService.getExcludeCount(params.categoryLabel, profile.getCategories(), requestParams)
         render data as JSON
     }
diff --git a/grails-app/services/au/org/ala/biocache/hubs/PostProcessingService.groovy b/grails-app/services/au/org/ala/biocache/hubs/PostProcessingService.groovy
index b3e3e7452..c7df4360d 100644
--- a/grails-app/services/au/org/ala/biocache/hubs/PostProcessingService.groovy
+++ b/grails-app/services/au/org/ala/biocache/hubs/PostProcessingService.groovy
@@ -522,7 +522,7 @@ class PostProcessingService {
             }
         }
 
-        def profile = qualityService.activeProfile(requestParams.qualityProfile)
+        def profile = qualityService.getProfile(requestParams.qualityProfile)
         // label to name map
         def labelToNameMap = profile?.categories?.collectEntries{ [(it.label): it.name] } ?: [:]
 
diff --git a/grails-app/services/au/org/ala/biocache/hubs/QualityService.groovy b/grails-app/services/au/org/ala/biocache/hubs/QualityService.groovy
index a233c113a..4eb9665d6 100644
--- a/grails-app/services/au/org/ala/biocache/hubs/QualityService.groovy
+++ b/grails-app/services/au/org/ala/biocache/hubs/QualityService.groovy
@@ -3,6 +3,7 @@ package au.org.ala.biocache.hubs
 import au.org.ala.dataquality.api.DataProfilesApi
 import au.org.ala.dataquality.api.QualityServiceRpcApi
 import au.org.ala.dataquality.client.ApiClient
+import au.org.ala.dataquality.client.auth.ApiKeyAuth
 import au.org.ala.dataquality.model.QualityCategory
 import au.org.ala.dataquality.model.QualityFilter
 import au.org.ala.dataquality.model.QualityProfile
@@ -42,8 +43,9 @@ class QualityService {
     def init() {
         if (dataQualityEnabled) {
             def apiClient = new ApiClient()
-            apiClient.setApiKey(dataQualityAPIKey)
             apiClient.adapterBuilder.baseUrl(dataQualityBaseUrl)
+            apiClient.addAuthorization('apiKeyAuth', new ApiKeyAuth('header', 'apiKey'))
+            apiClient.setApiKey(dataQualityAPIKey)
             apiClient.okBuilder.addInterceptor { chain ->
                 def request = chain.request().newBuilder().addHeader('User-Agent', "${grailsApplication.config.info.app.name}/${grailsApplication.config.info.app.version}").build()
                 chain.proceed(request)
@@ -94,6 +96,14 @@ class QualityService {
         }
     }
 
+    QualityProfile getProfile(String profileName) {
+        if (dataQualityEnabled) {
+            return responseOrThrow(dataProfilesApi.dataProfilesId(profileName))
+        } else {
+            return null
+        }
+    }
+
     QualityProfile getDefaultProfile(String userId = null) {
         if (dataQualityEnabled) {
             return responseOrThrow(api.getDefaultProfile(userId))

From 72bc1367fa6abeadeb44a4dfab5ed1553a5285dd Mon Sep 17 00:00:00 2001
From: alexhuang091 <hua091@csiro.au>
Date: Wed, 20 Jan 2021 09:42:03 +1100
Subject: [PATCH 15/22] removed 'myannotation.name' which is never used.

---
 grails-app/conf/plugin.groovy        | 1 -
 grails-app/views/occurrence/show.gsp | 1 -
 2 files changed, 2 deletions(-)

diff --git a/grails-app/conf/plugin.groovy b/grails-app/conf/plugin.groovy
index 4b3575609..3446b61da 100644
--- a/grails-app/conf/plugin.groovy
+++ b/grails-app/conf/plugin.groovy
@@ -143,7 +143,6 @@ alwaysshow.imagetab = false
 
 facets.defaultSelected = "data_resource_uid,taxon_name,year,multimedia"
 
-myannotation.name="My Annotations"
 mapdownloads {
     baseLayers {
         default_layer {
diff --git a/grails-app/views/occurrence/show.gsp b/grails-app/views/occurrence/show.gsp
index e85deb52f..41ccb14ab 100644
--- a/grails-app/views/occurrence/show.gsp
+++ b/grails-app/views/occurrence/show.gsp
@@ -60,7 +60,6 @@
                 </g:each>
             },
             hasGoogleKey: ${grailsApplication.config.google.apikey as Boolean},
-            alertName: "${grailsApplication.config.myannotation.name}"
         }
 
         // Google charts

From b9fad6d89bff02e7710f311e05765d7eb53d3f59 Mon Sep 17 00:00:00 2001
From: alexhuang091 <hua091@csiro.au>
Date: Mon, 1 Feb 2021 14:31:41 +1100
Subject: [PATCH 16/22] fixed an issue when disableAllQualityFilters = true

when disableAllQualityFilters == true, requestParams.qualityProfile won't be populated so it could be null.

When it's null, lots existing calls to dq-service failed since dq-service expects not-null profileName
---
 .../biocache/hubs/OccurrenceController.groovy | 25 +++++++++++++------
 .../hubs/PostProcessingService.groovy         | 16 ++++++------
 2 files changed, 27 insertions(+), 14 deletions(-)

diff --git a/grails-app/controllers/au/org/ala/biocache/hubs/OccurrenceController.groovy b/grails-app/controllers/au/org/ala/biocache/hubs/OccurrenceController.groovy
index c76cee203..9ebd9ad10 100644
--- a/grails-app/controllers/au/org/ala/biocache/hubs/OccurrenceController.groovy
+++ b/grails-app/controllers/au/org/ala/biocache/hubs/OccurrenceController.groovy
@@ -160,14 +160,25 @@ class OccurrenceController {
                 hasImages = true
             }
 
-            def qualityCategories = time("quality categories") { qualityService.findAllEnabledCategories(requestParams.qualityProfile) }
-            def qualityFiltersByLabel = time("quality filters by label") { qualityService.getEnabledFiltersByLabel(requestParams.qualityProfile) }
-            def qualityTotalCount = time("quality total count") { qualityService.countTotalRecords(requestParams) }
-            def groupedEnabledFilters = time("get grouped enabled filters") { qualityService.getGroupedEnabledFilters(requestParams.qualityProfile) }
-            def qualityFilterDescriptionsByLabel = groupedEnabledFilters.collectEntries {[(it.key) : it.value*.description.join(' and ')] }
-
-            def (fqInteract, dqInteract, UserFQColors, DQColors) = time("process user fq interactions") { postProcessingService.processUserFQInteraction(requestParams) }
+            def qualityCategories = []
+            def qualityFiltersByLabel = [:]
+            def groupedEnabledFilters = [:]
+            def qualityFilterDescriptionsByLabel = [:]
+            def fqInteract = [:]
+            def dqInteract = [:]
+            def UserFQColors = [:]
+            def DQColors = [:]
+
+            // if disable all quality filters, we don't need to retrieve them, it saves time
+            if (!requestParams.disableAllQualityFilters) {
+                qualityCategories = time("quality categories") { qualityService.findAllEnabledCategories(requestParams.qualityProfile) }
+                qualityFiltersByLabel = time("quality filters by label") { qualityService.getEnabledFiltersByLabel(requestParams.qualityProfile) }
+                groupedEnabledFilters = time("get grouped enabled filters") { qualityService.getGroupedEnabledFilters(requestParams.qualityProfile) }
+                qualityFilterDescriptionsByLabel = groupedEnabledFilters.collectEntries { [(it.key): it.value*.description.join(' and ')] }
+                (fqInteract, dqInteract, UserFQColors, DQColors) = time("process user fq interactions") { postProcessingService.processUserFQInteraction(requestParams) }
+            }
 
+            def qualityTotalCount = time("quality total count") { qualityService.countTotalRecords(requestParams) }
             def messagePropertiesFile = time("message properties file") { webServicesService.getMessagesPropertiesFile() }
             def assertionCodeMap = time("assertionCodeMap") { webServicesService.getAssertionCodeMap() }
             def translatedFilterMap = postProcessingService.translateValues(groupedEnabledFilters, messagePropertiesFile, assertionCodeMap)
diff --git a/grails-app/services/au/org/ala/biocache/hubs/PostProcessingService.groovy b/grails-app/services/au/org/ala/biocache/hubs/PostProcessingService.groovy
index c7df4360d..477e76413 100644
--- a/grails-app/services/au/org/ala/biocache/hubs/PostProcessingService.groovy
+++ b/grails-app/services/au/org/ala/biocache/hubs/PostProcessingService.groovy
@@ -505,6 +505,10 @@ class PostProcessingService {
     }
 
     def processUserFQInteraction(SpatialSearchRequestParams requestParams) {
+        if (requestParams.disableAllQualityFilters) {
+            return [[:], [:], [:], [:]]
+        }
+
         def disabled = requestParams.disableQualityFilter as Set
 
         // map from category label to filter names
@@ -513,13 +517,11 @@ class PostProcessingService {
         // This means a user filter can interact with a DQ filter even when its exclude count == 0
         def categoryToKeyMap = [:]
 
-        if (!requestParams.disableAllQualityFilters) {
-            categoryToKeyMap = qualityService.getGroupedEnabledFilters(requestParams.qualityProfile).findAll { label, list ->
-                !disabled.contains(label)
-            }.collectEntries { label, list ->
-                def keys = list*.filter.collect { getKeysFromFilter(it) }.flatten()
-                keys.isEmpty() ? [:] : [(label): keys as Set]
-            }
+        categoryToKeyMap = qualityService.getGroupedEnabledFilters(requestParams.qualityProfile).findAll { label, list ->
+            !disabled.contains(label)
+        }.collectEntries { label, list ->
+            def keys = list*.filter.collect { getKeysFromFilter(it) }.flatten()
+            keys.isEmpty() ? [:] : [(label): keys as Set]
         }
 
         def profile = qualityService.getProfile(requestParams.qualityProfile)

From bebd0213c1ff0dcc53a8cf50e0c9d3ae50eeae30 Mon Sep 17 00:00:00 2001
From: alexhuang091 <hua091@csiro.au>
Date: Wed, 3 Feb 2021 16:08:18 +1100
Subject: [PATCH 17/22] UI update for flag a duplicate record & DQ#217

DQ#217 formatting duplicate record preview
---
 grails-app/assets/javascripts/show.js         | 43 ++++++++++++++++---
 .../biocache/hubs/OccurrenceController.groovy | 12 ++++--
 grails-app/i18n/messages_en.properties        | 11 +++--
 .../views/occurrence/_recordSidebar.gsp       | 34 ++++++++++++---
 4 files changed, 82 insertions(+), 18 deletions(-)

diff --git a/grails-app/assets/javascripts/show.js b/grails-app/assets/javascripts/show.js
index 5906a7327..5dcce3366 100644
--- a/grails-app/assets/javascripts/show.js
+++ b/grails-app/assets/javascripts/show.js
@@ -56,7 +56,8 @@ $(document).ready(function() {
         var val = $this.val();
         var $submit = $('#issueForm input[type=submit]');
         var $p = $('#related-record-p, #related-record-reason-p');
-        if (val == '20020') {
+        // if duplicate record
+        if (val === '20020') {
             $('#relatedRecordId').val('');
             recordIdValid = false;
             $p.show();
@@ -65,37 +66,67 @@ $(document).ready(function() {
             $('#related-record-id-not-found').hide();
             $('#related-record-id-found').hide();
             $('#related-record-id-loading').hide();
+            // hide the records table
+            $('#records_comparison_table').hide();
+            $('#records_comparison_heading').hide();
         }
         setIssueFormButtonState();
     });
+
     $('#relatedRecordReason').on('change', function(e) {
+        var col_reason = $('#col_duplicate_reason');
+        var relatedRecordReason = $('#relatedRecordReason').val();
+        if (relatedRecordReason === '') {
+            $(col_reason).text('');
+        } else if (relatedRecordReason === 'sameoccurence') {
+            $(col_reason).text(jQuery.i18n.prop('related.record.reason.sameoccurrence.description'));
+        } else if (relatedRecordReason === 'tissuesample') {
+            $(col_reason).text(jQuery.i18n.prop('related.record.reason.tissuesample.description'));
+        } else if (relatedRecordReason === 'splitspecimen') {
+            $(col_reason).text(jQuery.i18n.prop('related.record.reason.splitspecimen.description'));
+        }
         setIssueFormButtonState();
     })
+
     $('#relatedRecordId').on('change', function(e) {
         var $this = $(this);
         var $submit = $('#issueForm input[type=submit]');
         var val = $this.val().trim();
-        if (val == OCC_REC.recordUuid) {
+        if (val === OCC_REC.recordUuid) {
             alert("You can't mark this record as a duplicate of itself!");
             recordIdValid = false;
-        } else if (val == '') {
+        } else if (val === '') {
             $('#related-record-id-not-found').hide();
             $('#related-record-id-found').hide();
             $('#related-record-id-loading').hide();
+            $('#records_comparison_table').hide();
+            $('#records_comparison_heading').hide();
+            $('#relatedRecordReason').val("");
+            $('#col_duplicate_reason').text('');
             recordIdValid = false;
         } else {
             $('#related-record-id-loading').show();
             $.get( OCC_REC.contextPath + "/occurrence/exists/" + val).success(function(data) {
+                $('#related-record-id-loading').hide();
                 $('#related-record-id-not-found').hide();
                 $('#related-record-id-found').show();
-                $('#related-record-id-found-other').text(data);
-                $('#related-record-id-loading').hide();
+                $('#records_comparison_table').show();
+                $('#records_comparison_heading').show();
+                // populate the table
+                $('#t_scientificName').text(data.scientificName ? data.scientificName : '');
+                $('#t_stateProvince').text(data.stateProvince ? data.stateProvince : '');
+                $('#t_decimalLongitude').text(data.decimalLongitude ? data.decimalLongitude : '');
+                $('#t_decimalLatitude').text(data.decimalLatitude ? data.decimalLatitude : '');
+                $('#t_eventDate').text(data.eventDate ? data.eventDate : '');
                 recordIdValid = true;
             }).error(function () {
                 $('#related-record-id-not-found').show();
                 $('#related-record-id-found').hide();
                 $('#related-record-id-loading').hide();
-                recordIdValid = false;
+                $('#records_comparison_table').hide();
+                $('#records_comparison_heading').hide();
+                $('#relatedRecordReason').val("");
+                $('#col_duplicate_reason').text('');
             }).always(function() {
                 setIssueFormButtonState();
             });
diff --git a/grails-app/controllers/au/org/ala/biocache/hubs/OccurrenceController.groovy b/grails-app/controllers/au/org/ala/biocache/hubs/OccurrenceController.groovy
index 9ebd9ad10..81fffad98 100644
--- a/grails-app/controllers/au/org/ala/biocache/hubs/OccurrenceController.groovy
+++ b/grails-app/controllers/au/org/ala/biocache/hubs/OccurrenceController.groovy
@@ -616,14 +616,18 @@ class OccurrenceController {
     def exists(String id) {
         def record = webServicesService.getRecord(id, false)
         if (record.keySet()) {
-            log.trace("{}", record)
-            def result = "${record?.processed?.classification?.scientificName ?: record?.raw?.classification?.scientificName ?: ''}, ${record?.processed?.location?.stateProvince ?: record?.raw?.location?.stateProvince ?: ''}, ${record?.processed?.location?.decimalLongitude ?: record?.raw?.location?.decimalLongitude ?: ''}, ${record?.processed?.location?.decimalLatitude ?: record?.raw?.location?.decimalLatitude ?: ''}, ${record?.processed?.event?.eventDate ?: record?.raw?.event?.eventDate ?: ''}"
-            render text: result
+            def rslt = [:]
+            rslt.scientificName = record?.processed?.classification?.scientificName ?: (record?.raw?.classification?.scientificName ?: '')
+            rslt.stateProvince = record?.processed?.location?.stateProvince ?: (record?.raw?.location?.stateProvince ?: '')
+            rslt.decimalLongitude = record?.processed?.location?.decimalLongitude ?: (record?.raw?.location?.decimalLongitude ?: '')
+            rslt.decimalLatitude = record?.processed?.location?.decimalLatitude ?: (record?.raw?.location?.decimalLatitude ?: '')
+            rslt.eventDate = record?.processed?.event?.eventDate ?: (record?.raw?.event?.eventDate ?: '')
+            render rslt as JSON
         } else {
             render status: SC_NOT_FOUND, text: ''
         }
     }
-
+    
     /**
      * JSON webservices for debugging/testing
      */
diff --git a/grails-app/i18n/messages_en.properties b/grails-app/i18n/messages_en.properties
index 8f6509d65..ff8b72227 100644
--- a/grails-app/i18n/messages_en.properties
+++ b/grails-app/i18n/messages_en.properties
@@ -136,8 +136,6 @@ show.issueform.label02 = Comment:
 show.issueform.label03 = Duplicate Record ID:
 show.issueform.label04 = Duplicate Reason:
 show.issueform.notifyme = Notify me when records I have annotated are updated
-show.issueform.relatedrecord.found.this = You are indicating this record (the one you are viewing):
-show.issueform.relatedrecord.found.other = is a duplicate of this record (the id you provided):
 show.issueform.button.submit = Submit
 show.issueform.button.cancel = Cancel
 show.issueform.button.close = Close
@@ -1153,6 +1151,13 @@ dq.warning.dataprofile.content.line1 = Search results are now filtered by defaul
 dq.warning.dataprofile.buttonleft.text = Learn More
 dq.warning.dataprofile.buttonright.text = Got it
 
+record.compare_table.heading = You are indicating that
+record.compare_table.source_record.heading = This record you are viewing
+record.compare_table.target_record.heading = This record ID provided
+related.record.reason.select=-- Select a reason --
 related.record.reason.sameoccurence=Same occurence
 related.record.reason.tissuesample=Tissue sample
-related.record.reason.splitspecimen=Split specimen
\ No newline at end of file
+related.record.reason.splitspecimen=Split specimen
+related.record.reason.sameoccurrence.description=Is the same occurrence as
+related.record.reason.tissuesample.description=Is a tissue sample of
+related.record.reason.splitspecimen.description=Is a duplicate specimen of
diff --git a/grails-app/views/occurrence/_recordSidebar.gsp b/grails-app/views/occurrence/_recordSidebar.gsp
index 5a2565613..1bd21067c 100644
--- a/grails-app/views/occurrence/_recordSidebar.gsp
+++ b/grails-app/views/occurrence/_recordSidebar.gsp
@@ -332,15 +332,39 @@
                                     <span style="display: none; color:red;" id="related-record-id-not-found">The record id can't be found.</span>
                                     <span style="display: none;" id="related-record-id-loading"><i class="fa fa-gear fa-spin"></i></span>
                                     <span style="display: none;" id="related-record-id-found">
-                                        <g:message code="show.issueform.relatedrecord.found.this" default="You are indicating this record (the one you are viewing):"/> <span id="related-record-id-found-this">${record?.processed?.classification?.scientificName ?: record?.raw?.classification?.scientificName ?: ''}, ${record?.processed?.location?.stateProvince ?: record?.raw?.location?.stateProvince ?: ''}, ${record?.processed?.location?.decimalLongitude ?: record?.raw?.location?.decimalLongitude ?: ''}, ${record?.processed?.location?.decimalLatitude ?: record?.raw?.location?.decimalLatitude ?: ''}, ${record?.processed?.event?.eventDate ?: record?.raw?.event?.eventDate ?: ''}</span>
-                                        <br/>
-                                        <g:message code="show.issueform.relatedrecord.found.other" default="is a duplicate of this record (the id you provided):"/> <span id="related-record-id-found-other"></span>
+                                        <span style="display: none;" id="records_comparison_heading"><g:message code="record.compare_table.heading" default="You are indicating that"/>:</span>
+                                        <table style="display: none;" id='records_comparison_table' class="table table-bordered table-condensed table-striped scrollTable">
+                                            <tr>
+                                                <th width="35%"><g:message code="record.compare_table.source_record.heading" default="This record you are viewing"/></th>
+                                                <th rowspan="6" id="col_duplicate_reason"></th>
+                                                <th width="35%"><g:message code="record.compare_table.target_record.heading" default="This record ID provided"/></th></tr>
+                                            <tr>
+                                                <td>${record?.processed?.classification?.scientificName ?: record?.raw?.classification?.scientificName ?: ''}</td>
+                                                <td id="t_scientificName"></td>
+                                            </tr>
+                                            <tr>
+                                                <td>${record?.processed?.location?.stateProvince ?: record?.raw?.location?.stateProvince ?: ''}</td>
+                                                <td id="t_stateProvince"></td>
+                                            </tr>
+                                            <tr>
+                                                <td>${record?.processed?.location?.decimalLongitude ?: record?.raw?.location?.decimalLongitude ?: ''}</td>
+                                                <td id="t_decimalLongitude"></td>
+                                            </tr>
+                                            <tr>
+                                                <td>${record?.processed?.location?.decimalLatitude ?: record?.raw?.location?.decimalLatitude ?: ''}</td>
+                                                <td id="t_decimalLatitude"></td>
+                                            </tr>
+                                            <tr>
+                                                <td>${record?.processed?.event?.eventDate ?: record?.raw?.event?.eventDate ?: ''}</td>
+                                                <td id="t_eventDate"></td>
+                                            </tr>
+                                        </table>
                                     </span>
                                 </p>
                             </p>
                             <p id="related-record-reason-p" style="display: none; margin-top:30px;">
                                 <label for="relatedRecordId" style="vertical-align:top;"><g:message code="show.issueform.label04" default="Duplicate Reason:"/><span style="color: red;">*</span></label>
-                                <select name="relatedRecordReason" id="relatedRecordReason" autocomplete="off
+                                <select name="relatedRecordReason" id="relatedRecordReason" autocomplete="off">
                                     <option value=""><g:message code="related.record.reason.select" default="-- Select a reason --" /></option>
                                     <option value="sameoccurence"><g:message code="related.record.reason.sameoccurence" default="Same occurence"/></option>
                                     <option value="tissuesample"><g:message code="related.record.reason.tissuesample" default="Tissue sample"/></option>
@@ -358,7 +382,7 @@
 
                             <p style="margin-top:20px;">
                                 <input id="issueFormSubmit" type="submit" value="<g:message code="show.issueform.button.submit" default="Submit"/>" class="btn btn-primary" />
-                                <input type="reset" value="<g:message code="show.issueform.button.cancel" default="Cancel"/>" class="btn btn-default" onClick="$('#loginOrFlag').modal('hide');"/>
+                                <input type="button" value="<g:message code="show.issueform.button.cancel" default="Cancel"/>" class="btn btn-default" onClick="$('#loginOrFlag').modal('hide');"/>
                                 <input type="button" id="close" value="<g:message code="show.issueform.button.close" default="Close"/>" class="btn btn-default" style="display:none;"/>
                                 <span id="submitSuccess"></span>
                             </p>

From 12e7113001085d0711513a1d51f3e81f33290ff3 Mon Sep 17 00:00:00 2001
From: alexhuang091 <hua091@csiro.au>
Date: Fri, 5 Feb 2021 13:59:22 +1100
Subject: [PATCH 18/22] DQ#217, handle 'user input id retrieves more than 1
 record'

---
 grails-app/assets/javascripts/show.js         | 35 ++++++++++++-------
 .../biocache/hubs/OccurrenceController.groovy |  6 +++-
 2 files changed, 28 insertions(+), 13 deletions(-)

diff --git a/grails-app/assets/javascripts/show.js b/grails-app/assets/javascripts/show.js
index 5dcce3366..789d54b3b 100644
--- a/grails-app/assets/javascripts/show.js
+++ b/grails-app/assets/javascripts/show.js
@@ -108,19 +108,30 @@ $(document).ready(function() {
             $('#related-record-id-loading').show();
             $.get( OCC_REC.contextPath + "/occurrence/exists/" + val).success(function(data) {
                 $('#related-record-id-loading').hide();
-                $('#related-record-id-not-found').hide();
-                $('#related-record-id-found').show();
-                $('#records_comparison_table').show();
-                $('#records_comparison_heading').show();
-                // populate the table
-                $('#t_scientificName').text(data.scientificName ? data.scientificName : '');
-                $('#t_stateProvince').text(data.stateProvince ? data.stateProvince : '');
-                $('#t_decimalLongitude').text(data.decimalLongitude ? data.decimalLongitude : '');
-                $('#t_decimalLatitude').text(data.decimalLatitude ? data.decimalLatitude : '');
-                $('#t_eventDate').text(data.eventDate ? data.eventDate : '');
-                recordIdValid = true;
+                if (data.error) {
+                    // show error
+                    $('#related-record-id-not-found').text('More than 1 record found with specified id, please use a more specific id').show();
+                    // hide compare table
+                    $('#records_comparison_heading').hide();
+                    $('#records_comparison_table').hide();
+                    recordIdValid = false;
+                } else {
+                    // hide error
+                    $('#related-record-id-not-found').hide();
+                    // show compare table
+                    $('#related-record-id-found').show();
+                    $('#records_comparison_table').show();
+                    $('#records_comparison_heading').show();
+                    // populate the table
+                    $('#t_scientificName').text(data.scientificName ? data.scientificName : '');
+                    $('#t_stateProvince').text(data.stateProvince ? data.stateProvince : '');
+                    $('#t_decimalLongitude').text(data.decimalLongitude ? data.decimalLongitude : '');
+                    $('#t_decimalLatitude').text(data.decimalLatitude ? data.decimalLatitude : '');
+                    $('#t_eventDate').text(data.eventDate ? data.eventDate : '');
+                    recordIdValid = true;
+                }
             }).error(function () {
-                $('#related-record-id-not-found').show();
+                $('#related-record-id-not-found').text("The record id can't be found.").show();
                 $('#related-record-id-found').hide();
                 $('#related-record-id-loading').hide();
                 $('#records_comparison_table').hide();
diff --git a/grails-app/controllers/au/org/ala/biocache/hubs/OccurrenceController.groovy b/grails-app/controllers/au/org/ala/biocache/hubs/OccurrenceController.groovy
index 81fffad98..3765642ec 100644
--- a/grails-app/controllers/au/org/ala/biocache/hubs/OccurrenceController.groovy
+++ b/grails-app/controllers/au/org/ala/biocache/hubs/OccurrenceController.groovy
@@ -614,8 +614,12 @@ class OccurrenceController {
     }
 
     def exists(String id) {
+        // getRecord can return either 1 record or a list of records
+        // if a list returned, asking user to be more specific
         def record = webServicesService.getRecord(id, false)
-        if (record.keySet()) {
+        if (record.occurrences) {
+            render ([error: 'id not unique'] as JSON)
+        } else if (record.keySet()) {
             def rslt = [:]
             rslt.scientificName = record?.processed?.classification?.scientificName ?: (record?.raw?.classification?.scientificName ?: '')
             rslt.stateProvince = record?.processed?.location?.stateProvince ?: (record?.raw?.location?.stateProvince ?: '')

From 3db615c3c3a11e45ff63f93794a4e0e2a65f66ad Mon Sep 17 00:00:00 2001
From: alexhuang091 <hua091@csiro.au>
Date: Mon, 8 Feb 2021 09:59:24 +1100
Subject: [PATCH 19/22] fixed an issue in displaying comment.

Old code displayed 'undefined' when comment is empty.
---
 grails-app/assets/javascripts/show.js | 8 ++++++--
 1 file changed, 6 insertions(+), 2 deletions(-)

diff --git a/grails-app/assets/javascripts/show.js b/grails-app/assets/javascripts/show.js
index 789d54b3b..390a475ab 100644
--- a/grails-app/assets/javascripts/show.js
+++ b/grails-app/assets/javascripts/show.js
@@ -490,7 +490,9 @@ function refreshUserAnnotations(){
             var $clone = $('#userAnnotationTemplate').clone();
             $clone.find('.issue').text(data.assertionQueries[i].assertionType);
             $clone.find('.user').text(data.assertionQueries[i].userName);
-            $clone.find('.comment').text('Comment: ' + data.assertionQueries[i].comment);
+            if (data.assertionQueries[i].hasOwnProperty('comment')) {
+                $clone.find('.comment').text('Comment: ' + data.assertionQueries[i].comment);
+            }
             $clone.find('.created').text('Date created: ' + (moment(data.assertionQueries[i].createdDate).format('YYYY-MM-DD')));
             if(data.assertionQueries[i].recordCount > 1){
                 $clone.find('.viewMore').css({display:'block'});
@@ -513,7 +515,9 @@ function refreshUserAnnotations(){
                 $clone.prop('id', "userAnnotation_" + userAssertion.uuid);
                 $clone.find('.issue').text(jQuery.i18n.prop(userAssertion.name));
                 $clone.find('.user').text(userAssertion.userDisplayName);
-                $clone.find('.comment').text('Comment: ' + userAssertion.comment);
+                if (userAssertion.hasOwnProperty('comment')) {
+                    $clone.find('.comment').text('Comment: ' + userAssertion.comment);
+                }
                 $clone.find('.userRole').text(userAssertion.userRole != null ? userAssertion.userRole : '');
                 $clone.find('.userEntity').text(userAssertion.userEntityName != null ? userAssertion.userEntityName : '');
                 $clone.find('.created').text('Date created: ' + (moment(userAssertion.created, "YYYY-MM-DDTHH:mm:ssZ").format('YYYY-MM-DD HH:mm:ss')));

From fed9e317c5c019f3b10dcc734ddd173fd28cc2dd Mon Sep 17 00:00:00 2001
From: alexhuang091 <HUA091@csiro.au>
Date: Thu, 8 Apr 2021 15:08:24 +1000
Subject: [PATCH 20/22] do alerts related url mappings conditionally

---
 .../ala/biocache/hubs/BiocacheHubsUrlMappings.groovy |  3 ---
 grails-app/init/biocache/hubs/BootStrap.groovy       | 12 ++++++++++++
 2 files changed, 12 insertions(+), 3 deletions(-)

diff --git a/grails-app/controllers/au/org/ala/biocache/hubs/BiocacheHubsUrlMappings.groovy b/grails-app/controllers/au/org/ala/biocache/hubs/BiocacheHubsUrlMappings.groovy
index 92c3471a5..49f0f4e23 100644
--- a/grails-app/controllers/au/org/ala/biocache/hubs/BiocacheHubsUrlMappings.groovy
+++ b/grails-app/controllers/au/org/ala/biocache/hubs/BiocacheHubsUrlMappings.groovy
@@ -24,9 +24,6 @@ class BiocacheHubsUrlMappings {
         "/occurrences/next"(controller: 'occurrence', action: 'next')
         "/occurrences/previous"(controller: 'occurrence', action: 'previous')
         "/occurrences/dataQualityExcludeCounts"(controller: 'occurrence', action: 'dataQualityExcludeCounts')
-        "/occurrences/alerts"(controller: 'occurrence', action: [GET: 'getAlerts'])
-        "/occurrences/addMyAnnotationAlert"(controller: 'occurrence', action: [POST: 'addMyAnnotationAlert'])
-        "/occurrences/deleteMyAnnotationAlert"(controller: 'occurrence', action: [POST: 'deleteMyAnnotationAlert'])
         "/occurrences/$id"(controller: 'occurrence', action: 'show')
         "/occurrence/$id"(controller: 'occurrence', action: 'show')
         "/assertions/$id"(controller: 'assertions', action: 'assertions')
diff --git a/grails-app/init/biocache/hubs/BootStrap.groovy b/grails-app/init/biocache/hubs/BootStrap.groovy
index 78264cd69..f410236a9 100644
--- a/grails-app/init/biocache/hubs/BootStrap.groovy
+++ b/grails-app/init/biocache/hubs/BootStrap.groovy
@@ -3,8 +3,20 @@ package biocache.hubs
 class BootStrap {
     def messageSource
     def application
+    def grailsApplication
+    def grailsUrlMappingsHolder
 
     def init = { servletContext ->
+
+        // if my annotation feature turned on, add url mapping to handle add/remove my annotation alert requests
+        if (grailsApplication.config.getProperty('alerts.myannotation.enabled', Boolean, false)) {
+            grailsUrlMappingsHolder.addMappings({
+                "/occurrences/alerts"(controller: 'occurrence', action: [GET: 'getAlerts'])
+                "/occurrences/addMyAnnotationAlert"(controller: 'occurrence', action: [POST: 'addMyAnnotationAlert'])
+                "/occurrences/deleteMyAnnotationAlert"(controller: 'occurrence', action: [POST: 'deleteMyAnnotationAlert'])
+            })
+        }
+
         messageSource.setBasenames(
                 "file:///var/opt/atlas/i18n/downloads-plugin/messages",
                 "file:///opt/atlas/i18n/downloads-plugin/messages",

From 9e244592dcdf496017eeb4b50f07fd4eb72bba16 Mon Sep 17 00:00:00 2001
From: alexhuang091 <HUA091@csiro.au>
Date: Fri, 9 Apr 2021 12:17:33 +1000
Subject: [PATCH 21/22] fixed typo

---
 grails-app/assets/javascripts/show.js              | 14 +++++---------
 .../ala/biocache/hubs/WebServicesService.groovy    |  6 +++---
 grails-app/views/occurrence/_recordSidebar.gsp     |  2 +-
 3 files changed, 9 insertions(+), 13 deletions(-)

diff --git a/grails-app/assets/javascripts/show.js b/grails-app/assets/javascripts/show.js
index 0257fe6a1..43ef12f3d 100644
--- a/grails-app/assets/javascripts/show.js
+++ b/grails-app/assets/javascripts/show.js
@@ -199,20 +199,15 @@ $(document).ready(function() {
                         function (data) {
                             // when add assertion succeeds, we update alert settings (only when myannotation is enabled)
                             if (OCC_REC.myAnnotationEnabled) {
-                                var orig_state = $('#notifyChangeCheckbox').prop('data-origstate');
                                 var new_state = $('#notifyChangeCheckbox').prop('checked');
-
-                                // only update when user changed preference
-                                if (orig_state !== new_state) {
-                                    var actionpath = new_state ? "/occurrences/addMyAnnotationAlert" : "/occurrences/deleteMyAnnotationAlert";
-                                    $.post(OCC_REC.contextPath + actionpath);
-                                }
+                                var actionpath = new_state ? "/occurrences/addMyAnnotationAlert" : "/occurrences/deleteMyAnnotationAlert";
+                                $.post(OCC_REC.contextPath + actionpath);
                             }
 
                             $('#assertionSubmitProgress').css({'display': 'none'});
                             $("#submitSuccess").html("Thanks for flagging the problem!");
                             $("#issueFormSubmit").hide();
-                            $("input:reset").hide();
+                            $("input#cancel").hide();
                             $("input#close").show();
                             //retrieve all assertions
                             $.get(OCC_REC.contextPath + '/assertions/' + OCC_REC.recordUuid, function (data) { // recordUuid=${record.raw.uuid}
@@ -244,11 +239,12 @@ $(document).ready(function() {
     $('#assertionButton').click(function (e) {
         // if myannotation enabled, to retrieve current settings
         if (OCC_REC.myAnnotationEnabled) {
+            // by default off
+            $("#notifyChangeCheckbox").prop('checked', false);
             var getAlerts = OCC_REC.contextPath + "/occurrences/alerts";
             $.getJSON(getAlerts, function (data) {
                 var myAnnotationEnabled =  data && data.myannotation && data.myannotation.length > 0;
                 $("#notifyChangeCheckbox").prop('checked', myAnnotationEnabled);
-                $("#notifyChangeCheckbox").prop('data-origstate', myAnnotationEnabled);
             })
         }
     })
diff --git a/grails-app/services/au/org/ala/biocache/hubs/WebServicesService.groovy b/grails-app/services/au/org/ala/biocache/hubs/WebServicesService.groovy
index b2532177e..b23995ded 100644
--- a/grails-app/services/au/org/ala/biocache/hubs/WebServicesService.groovy
+++ b/grails-app/services/au/org/ala/biocache/hubs/WebServicesService.groovy
@@ -113,17 +113,17 @@ class WebServicesService {
     }
 
     def getAlerts(String userId) {
-        def url = "${grailsApplication.config.alerts.baseURL}" + "/api/alerts/user/" + userId
+        def url = "${grailsApplication.config.alerts.baseUrl}" + "/api/alerts/user/" + userId
         return getJsonElements(url, "${grailsApplication.config.alerts.apiKey}")
     }
 
     def addMyAnnotationAlert(String userId) {
-        String url = "${grailsApplication.config.alerts.baseURL}" + "/api/alerts/user/" + userId + "/addMyAnnotationAlert"
+        String url = "${grailsApplication.config.alerts.baseUrl}" + "/api/alerts/user/" + userId + "/addMyAnnotationAlert"
         postFormData(url, [:], grailsApplication.config.alerts.apiKey as String)
     }
 
     def deleteMyAnnotationAlert(String userId) {
-        String url = "${grailsApplication.config.alerts.baseURL}" + "/api/alerts/user/" + userId + "/deleteMyAnnotationAlert"
+        String url = "${grailsApplication.config.alerts.baseUrl}" + "/api/alerts/user/" + userId + "/deleteMyAnnotationAlert"
         postFormData(url, [:], grailsApplication.config.alerts.apiKey as String)
     }
 
diff --git a/grails-app/views/occurrence/_recordSidebar.gsp b/grails-app/views/occurrence/_recordSidebar.gsp
index 48d98a90e..abed77be5 100644
--- a/grails-app/views/occurrence/_recordSidebar.gsp
+++ b/grails-app/views/occurrence/_recordSidebar.gsp
@@ -384,7 +384,7 @@
 
                             <p style="margin-top:20px;">
                                 <input id="issueFormSubmit" type="submit" value="<g:message code="show.issueform.button.submit" default="Submit"/>" class="btn btn-primary" />
-                                <input type="button" value="<g:message code="show.issueform.button.cancel" default="Cancel"/>" class="btn btn-default" onClick="$('#loginOrFlag').modal('hide');"/>
+                                <input type="button" id="cancel" value="<g:message code="show.issueform.button.cancel" default="Cancel"/>" class="btn btn-default" onClick="$('#loginOrFlag').modal('hide');"/>
                                 <input type="button" id="close" value="<g:message code="show.issueform.button.close" default="Close"/>" class="btn btn-default" style="display:none;"/>
                                 <span id="submitSuccess"></span>
                             </p>

From 5bb0a83474d9a68b2fbbd75d38692e28b64ec44f Mon Sep 17 00:00:00 2001
From: alexhuang091 <HUA091@csiro.au>
Date: Mon, 12 Apr 2021 14:43:54 +1000
Subject: [PATCH 22/22] alerts API names changed so we need to update
 accordingly

---
 grails-app/assets/javascripts/show.js                     | 2 +-
 .../au/org/ala/biocache/hubs/OccurrenceController.groovy  | 8 ++++----
 grails-app/init/biocache/hubs/BootStrap.groovy            | 4 ++--
 .../au/org/ala/biocache/hubs/WebServicesService.groovy    | 8 ++++----
 4 files changed, 11 insertions(+), 11 deletions(-)

diff --git a/grails-app/assets/javascripts/show.js b/grails-app/assets/javascripts/show.js
index 43ef12f3d..83f86132c 100644
--- a/grails-app/assets/javascripts/show.js
+++ b/grails-app/assets/javascripts/show.js
@@ -200,7 +200,7 @@ $(document).ready(function() {
                             // when add assertion succeeds, we update alert settings (only when myannotation is enabled)
                             if (OCC_REC.myAnnotationEnabled) {
                                 var new_state = $('#notifyChangeCheckbox').prop('checked');
-                                var actionpath = new_state ? "/occurrences/addMyAnnotationAlert" : "/occurrences/deleteMyAnnotationAlert";
+                                var actionpath = new_state ? "/occurrences/subscribeMyAnnotation" : "/occurrences/unsubscribeMyAnnotation";
                                 $.post(OCC_REC.contextPath + actionpath);
                             }
 
diff --git a/grails-app/controllers/au/org/ala/biocache/hubs/OccurrenceController.groovy b/grails-app/controllers/au/org/ala/biocache/hubs/OccurrenceController.groovy
index 7e30b9355..4c2ecc683 100644
--- a/grails-app/controllers/au/org/ala/biocache/hubs/OccurrenceController.groovy
+++ b/grails-app/controllers/au/org/ala/biocache/hubs/OccurrenceController.groovy
@@ -736,23 +736,23 @@ class OccurrenceController {
         }
     }
 
-    def addMyAnnotationAlert() {
+    def subscribeMyAnnotation() {
         String userId = authService?.getUserId()
         if (userId == null) {
             response.status = 404
             render ([error: 'userId must be supplied to add alert'] as JSON)
         } else {
-            render webServicesService.addMyAnnotationAlert(userId) as JSON
+            render webServicesService.subscribeMyAnnotation(userId) as JSON
         }
     }
 
-    def deleteMyAnnotationAlert() {
+    def unsubscribeMyAnnotation() {
         String userId = authService?.getUserId()
         if (userId == null) {
             response.status = 404
             render ([error: 'userId must be supplied to delete alert'] as JSON)
         } else {
-            render webServicesService.deleteMyAnnotationAlert(userId) as JSON
+            render webServicesService.unsubscribeMyAnnotation(userId) as JSON
         }
     }
 }
diff --git a/grails-app/init/biocache/hubs/BootStrap.groovy b/grails-app/init/biocache/hubs/BootStrap.groovy
index f410236a9..8df5a2a0a 100644
--- a/grails-app/init/biocache/hubs/BootStrap.groovy
+++ b/grails-app/init/biocache/hubs/BootStrap.groovy
@@ -12,8 +12,8 @@ class BootStrap {
         if (grailsApplication.config.getProperty('alerts.myannotation.enabled', Boolean, false)) {
             grailsUrlMappingsHolder.addMappings({
                 "/occurrences/alerts"(controller: 'occurrence', action: [GET: 'getAlerts'])
-                "/occurrences/addMyAnnotationAlert"(controller: 'occurrence', action: [POST: 'addMyAnnotationAlert'])
-                "/occurrences/deleteMyAnnotationAlert"(controller: 'occurrence', action: [POST: 'deleteMyAnnotationAlert'])
+                "/occurrences/subscribeMyAnnotation"(controller: 'occurrence', action: [POST: 'subscribeMyAnnotation'])
+                "/occurrences/unsubscribeMyAnnotation"(controller: 'occurrence', action: [POST: 'unsubscribeMyAnnotation'])
             })
         }
 
diff --git a/grails-app/services/au/org/ala/biocache/hubs/WebServicesService.groovy b/grails-app/services/au/org/ala/biocache/hubs/WebServicesService.groovy
index b23995ded..434f3f53e 100644
--- a/grails-app/services/au/org/ala/biocache/hubs/WebServicesService.groovy
+++ b/grails-app/services/au/org/ala/biocache/hubs/WebServicesService.groovy
@@ -117,13 +117,13 @@ class WebServicesService {
         return getJsonElements(url, "${grailsApplication.config.alerts.apiKey}")
     }
 
-    def addMyAnnotationAlert(String userId) {
-        String url = "${grailsApplication.config.alerts.baseUrl}" + "/api/alerts/user/" + userId + "/addMyAnnotationAlert"
+    def subscribeMyAnnotation(String userId) {
+        String url = "${grailsApplication.config.alerts.baseUrl}" + "/api/alerts/user/" + userId + "/subscribeMyAnnotation"
         postFormData(url, [:], grailsApplication.config.alerts.apiKey as String)
     }
 
-    def deleteMyAnnotationAlert(String userId) {
-        String url = "${grailsApplication.config.alerts.baseUrl}" + "/api/alerts/user/" + userId + "/deleteMyAnnotationAlert"
+    def unsubscribeMyAnnotation(String userId) {
+        String url = "${grailsApplication.config.alerts.baseUrl}" + "/api/alerts/user/" + userId + "/unsubscribeMyAnnotation"
         postFormData(url, [:], grailsApplication.config.alerts.apiKey as String)
     }