Merge branch 'develop' into epic/grails4/develop

* develop: (51 commits) Revert "Merge branch 'develop' into epic/develop-branch-fix" cherry pick of commit brucehyslop@646c31f Translation of Map legend button and pagination next and previous button 3.0.6-SNAPSHOT release 3.0.5 (#449) #379 Records from DigiVol don't show "Flag an issue" button #443 fixes for flash.message exposing apiKey 3.0.5-SNAPSHOT Release/3.0.4 (#442) Fix jquery.i18n load errors Feature my annotation (#435) #434 fix duplicate record facet labels version to 3.0.4-SNAPSHOT release 3.0.3 (#432) enhanced duplicate record flag (#431) Feature/duplicate record (#429) updated version to 3.0.3-SNAPSHOT for next iteration Issue 245 - enhancement to batch taxon search tab (#523) added biosecurity user assertion biocache-hubs change due to backend changes (#521) ... # Conflicts: # grails-app/controllers/au/org/ala/biocache/hubs/ProxyController.groovy
AtlasOfLivingAustralia · Jan 12, 2022 · 60f14bd · 60f14bd
2 parents e66f790 + d59e4e4
commit 60f14bd
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diff --git a/...app/assets/javascripts/bieAutocomplete.js → ...ls-app/assets/javascripts/autocomplete.js b/...app/assets/javascripts/bieAutocomplete.js → ...ls-app/assets/javascripts/autocomplete.js
@@ -21,10 +21,15 @@
  */
 jQuery(document).ready(function() {
     // Autocomplete
-    var bieBaseUrl = BC_CONF.bieWebServiceUrl;
-    var bieParams = { limit: 20 };
-    var autoHints = BC_CONF.autocompleteHints; // expects { fq: "kingdom:Plantae" }
-    $.extend( bieParams, autoHints ); // merge autoHints into bieParams
+    var autocompleteUrl = BC_CONF.autocompleteUrl;
+    var params = {};
+    if (BC_CONF.autocompleteUseBie) {
+        $.extend(params, {limit: 20});
+        var autoHints = BC_CONF.autocompleteHints; // expects { fq: "kingdom:Plantae" }
+        $.extend(params, autoHints); // merge autoHints into params
+    } else {
+        $.extend(params, {pageSize: 20});
+    }
 
     function getMatchingName(item) {
         if (item.scientificNameMatches && item.scientificNameMatches.length) {
@@ -34,7 +39,7 @@ jQuery(document).ready(function() {
         } else {
             return item.name;
         }
-    };
+    }
 
     function formatAutocompleteList(list) {
         var results = [];
@@ -46,17 +51,17 @@ jQuery(document).ready(function() {
         }
 
         return results;
-    };
+    }
 
     $.ui.autocomplete({
         source: function (request, response) {
-            bieParams.q = request.term;
+            params.q = request.term;
             $.ajax( {
-                url: bieBaseUrl + '/search/auto.json',
+                url: autocompleteUrl,
                 dataType: "json",
-                data: bieParams,
+                data: params,
                 success: function( data ) {
-                    response( formatAutocompleteList(data.autoCompleteList) );
+                    response( formatAutocompleteList(BC_CONF.autocompleteUseBie ? data.autoCompleteList : data.searchResults.results) );
                 }
             } );
         }

diff --git a/grails-app/assets/javascripts/search.js b/grails-app/assets/javascripts/search.js
@@ -248,8 +248,8 @@ $(document).ready(function() {
                         synListSize++;
                         synList1 += "<input type='checkbox' name='raw_taxon_guid' id='rawTaxon_" + index + "_" + j +
                             "' class='rawTaxonCheckBox' value='" + el1.label + "'/>&nbsp;" +
-                            "<a href='" + BC_CONF.contextPath + "/occurrences/search?q=raw_taxon_name:%22" + el1.label +
-                            "%22'>" + el1.label + "</a> (" + el1.count + ")<br/>";
+                            "<a href=\"" + BC_CONF.contextPath + "/occurrences/search?q=raw_taxon_name:%22" + encodeURIComponent(el1.label) +
+                            "%22\">" + el1.label + "</a> (" + el1.count + ")<br/>";
                     });
                 }
             });
@@ -645,6 +645,25 @@ $(document).ready(function() {
         window.location.href = BC_CONF.serverName + "/occurrences/facets/download" + BC_CONF.facetDownloadQuery + '&facets=' + facetName;
     });
 
+    $('#copy-al4r').on('click', function() {
+        var input = document.querySelector('#al4rcode');
+        navigator.clipboard.writeText(input.value)
+            .then(() => {
+                $(this).qtip({
+                    content: jQuery.i18n.prop('list.copylinks.tooltip.copied'),
+                    show: true,
+                    hide: { when: { event: 'mouseout'} }
+                })})
+            .catch((error) => { alert(jQuery.i18n.prop('list.copylinks.alert.failed') + error) })
+    });
+
+    $('#copy-al4r').on('mouseleave', function() {
+        $(this).qtip({
+            content: jQuery.i18n.prop('list.copylinks.tooltip.copytoclipboard'),
+            show: { when: { event: 'mouseover'} }
+        })
+    })
+
     // when open the user preference dlg
     $('.DQPrefSettingsLink').click(function() {
         var prefSettings = $('#DQPrefSettings');
@@ -1185,7 +1204,7 @@ $(document).ready(function() {
     });
 
     // user preference settings and download link tooltips will be above the control
-    $("#usersettings, a.newDownload").qtip({
+    $("#usersettings, a.copyLink").qtip({
         style: {
             classes: 'ui-tooltip-rounded ui-tooltip-shadow'
         },

diff --git a/grails-app/assets/javascripts/show.js b/grails-app/assets/javascripts/show.js
@@ -11,13 +11,33 @@
 //= require linkifyjs/linkify-jquery.js
 //= require leaflet/leaflet.js
 //= require leaflet-plugins/layer/tile/Google.js
-//= require biocache-hubs.js
 //= require_self
  */
 /**
  * JQuery on document ready callback
  */
+
+function updatei18n() {
+    $('.i8nupdate').each(function() {
+        var key = $(this).attr('i18nkey')
+        if (key !== undefined) {
+            $(this).text(jQuery.i18n.prop(key));
+        }
+    });
+}
+
 $(document).ready(function() {
+    if (typeof BC_CONF != 'undefined' && BC_CONF.hasOwnProperty('contextPath')) {
+        jQuery.i18n.properties({
+            name: 'messages',
+            path: BC_CONF.contextPath + '/messages/i18n/',
+            mode: 'map',
+            async: true,
+            cache: true,
+            language: BC_CONF.locale, // default is to use browser specified locale
+            callback: updatei18n
+        });
+    }
 
     $('#showUncheckedTests').on('click', function(e){
         $('.uncheckTestResult').toggle();
@@ -481,7 +501,7 @@ function refreshUserAnnotations(){
             // if the code == 50000, then we have verification - so don't display here
             if (userAssertion.code != 50000) {
                 $clone.prop('id', "userAnnotation_" + userAssertion.uuid);
-                $clone.find('.issue').text(jQuery.i18n.prop(userAssertion.name));
+                $clone.find('.issue').text(jQuery.i18n.prop(userAssertion.name)).attr('i18nkey', userAssertion.name);
                 $clone.find('.user').text(userAssertion.userDisplayName);
                 if (userAssertion.hasOwnProperty('comment')) {
                     $clone.find('.comment').text('Comment: ' + userAssertion.comment);
@@ -533,8 +553,8 @@ function refreshUserAnnotations(){
                 }
                 if (userAssertion.relatedRecordReason) {
                     $clone.find('.related-record-reason').show();
-                    $clone.find('.related-record-reason-span').text(jQuery.i18n.prop('related.record.reason.' + userAssertion.relatedRecordReason));
-                    $clone.find('.related-record-reason-explanation').text(jQuery.i18n.prop('related.record.reason.explanation.' + userAssertion.relatedRecordReason)).show();
+                    $clone.find('.related-record-reason-span').text(jQuery.i18n.prop('related.record.reason.' + userAssertion.relatedRecordReason)).attr('i18nkey', 'related.record.reason.' + userAssertion.relatedRecordReason);
+                    $clone.find('.related-record-reason-explanation').text(jQuery.i18n.prop('related.record.reason.explanation.' + userAssertion.relatedRecordReason)).attr('i18nkey', 'related.record.reason.explanation.' + userAssertion.relatedRecordReason).show();
                 }
                 if (userAssertion.userRole != null) {
                     $clone.find('.userRole').text(', ' + userAssertion.userRole);
@@ -575,7 +595,7 @@ function refreshUserAnnotations(){
             var $clone = $('#userVerificationTemplate').clone();
             $clone.prop('id', "userVerificationAnnotation_" + sortedVerifiedAssertion[i].uuid);
             var qaStatusMessage = jQuery.i18n.prop("user_assertions." + sortedVerifiedAssertion[i].qaStatus);
-            $clone.find('.qaStatus').text(qaStatusMessage);
+            $clone.find('.qaStatus').text(qaStatusMessage).attr('i18nkey', "user_assertions." + sortedVerifiedAssertion[i].qaStatus);
             $clone.find('.comment').text(sortedVerifiedAssertion[i].comment);
             $clone.find('.userDisplayName').text(sortedVerifiedAssertion[i].userDisplayName);
             $clone.find('.created').text((moment(sortedVerifiedAssertion[i].created, "YYYY-MM-DDTHH:mm:ssZ").format('YYYY-MM-DD HH:mm:ss')));

diff --git a/grails-app/assets/stylesheets/search.css b/grails-app/assets/stylesheets/search.css
@@ -1097,3 +1097,80 @@ a.leaflet-control-zoom-fullscreen + a.leaflet-control-zoom-fullscreen {
     font-style: normal;
     font-weight: bold;
 }
+
+#dq-collapse-caret {
+    color: black;
+}
+
+#DQProfileDetails .filter-description {
+    word-break: break-word;
+}
+
+#DQProfileDetails .filter-value {
+    word-break: keep-all;
+}
+
+#DQProfileDetails .filter-value span{
+    white-space: nowrap;
+}
+
+#DQManageFilters .expand {
+    vertical-align: middle;
+    margin: 0;
+    padding: 0;
+    text-decoration: none;
+    font-size: 14px
+}
+
+#DQManageFilters .expanded {
+    vertical-align: middle;
+    margin: 0;
+    font-style: italic;
+}
+
+.valign-middle {
+    vertical-align: middle;
+}
+
+.DQPrefSettingsLink {
+    float: right;
+}
+
+.DQPrefSettingsLink span {
+    color: black;
+}
+
+#excluded, #filter-value {
+    margin-bottom: 0
+}
+
+#view-excluded, #expandfilters {
+    text-decoration: none;
+    padding: 0;
+}
+
+#DQDetailsTable {
+    margin-top: 20px;
+}
+
+#fqdetail-heading-description {
+    font-style: italic;
+}
+
+#download-button-area {
+    padding-right: 5px;
+}
+
+a.copyLink {
+    border-color: black;
+    color: black
+}
+
+#copy-al4r {
+    border-color: black;
+}
+
+#content .tooltip-inner {
+    word-break: break-word;
+    white-space: normal;
+}
diff --git a/grails-app/conf/plugin.groovy b/grails-app/conf/plugin.groovy
@@ -90,7 +90,7 @@ test.var = "test"
 // used to link temporary data resources back to an originating sandbox.
 sandbox.uploadSource=''
 advancedTaxaField = "taxa" // used in advanced form for the 4 taxa query inputs
-
+alerts.myannotation.enabled = false
 clubRoleForHub = "ROLE_ADMIN"
 // whether map or list is the default tab to show - empty for list and "mapView" for map
 defaultListView = "" //  'mapView' or 'listView'

diff --git a/grails-app/controllers/au/org/ala/biocache/hubs/AdminController.groovy b/grails-app/controllers/au/org/ala/biocache/hubs/AdminController.groovy
@@ -31,8 +31,8 @@ class AdminController {
 
     def clearAllCaches() {
         def message = doClearAllCaches()
-        flash.message = message.replaceAll("\n","<br/>")
-        redirect(action:'index')
+        flash.message = message.replaceAll("\n", "<br/>")
+        redirect(action: 'index')
     }
 
     private String doClearAllCaches() {
@@ -47,22 +47,22 @@ class AdminController {
 
     def clearCollectoryCache() {
         flash.message = webServicesService.doClearCollectoryCache()
-        redirect(action:'index')
+        redirect(action: 'index')
     }
 
     def clearLongTermCache() {
         flash.message = webServicesService.doClearLongTermCache()
-        redirect(action:'index')
+        redirect(action: 'index')
     }
 
     def clearFacetsCache() {
         flash.message = doClearFacetsCache()
-        redirect(action:'index')
+        redirect(action: 'index')
     }
 
     def clearPropertiesCache() {
         flash.message = doClearPropertiesCache()
-        redirect(action:'index')
+        redirect(action: 'index')
     }
 
     def clearRecordCountCache() {

diff --git a/grails-app/controllers/au/org/ala/biocache/hubs/AdminInterceptor.groovy b/grails-app/controllers/au/org/ala/biocache/hubs/AdminInterceptor.groovy
@@ -29,8 +29,8 @@ class AdminInterceptor {
             // old-style AUTH config - bypass
             true
         } else if (!authService?.userInRole(grailsApplication.config.getProperty("auth.admin_role", String, "ROLE_ADMIN"))) {
-            log.debug "User not authorised to access the page: ${params.controller}/${params.action?:''}. Redirecting to index."
-            flash.message = "You are not authorised to access the page: ${params.controller}/${params.action?:''}."
+            log.debug "User not authorised to access the page: ${params.controller}/${params.action ?: ''}. Redirecting to index."
+            flash.message = "You are not authorised to access the page: ${params.controller}/${params.action ?: ''}."
             redirect(controller: "home", action: "index")
             false
         } else {

diff --git a/grails-app/controllers/au/org/ala/biocache/hubs/AssertionsController.groovy b/grails-app/controllers/au/org/ala/biocache/hubs/AssertionsController.groovy
@@ -37,7 +37,7 @@ class AssertionsController {
         JSONArray qualityAssertions = webServicesService.getQueryAssertions(id)
         Boolean hasClubView = request.isUserInRole("${grailsApplication.config.clubRoleForHub}")
         String userAssertionStatus = webServicesService.getRecord(id, hasClubView)?.raw.userAssertionStatus
-        Map combined = [userAssertions: userAssertions?:[], assertionQueries: qualityAssertions?:[], userAssertionStatus: userAssertionStatus?:"" ]
+        Map combined = [userAssertions: userAssertions ?: [], assertionQueries: qualityAssertions ?: [], userAssertionStatus: userAssertionStatus ?: ""]
         render combined as JSON
     }
 
@@ -49,9 +49,9 @@ class AssertionsController {
     def addAssertion() {
         String recordUuid = params.recordUuid
         String code = params.code
-        String comment = params.comment?:''
-        String userAssertionStatus = params.userAssertionStatus?: ""
-        String assertionUuid = params.assertionUuid?: ""
+        String comment = params.comment ?: ''
+        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
@@ -70,8 +70,8 @@ class AssertionsController {
             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" )
-                render(status: postResponse.statusCode, text:'Assertion added')
+                log.info("Called REST service. Assertion should be added")
+                render(status: postResponse.statusCode, text: 'Assertion added')
             } else {
                 log.error "Unexpected error: ${postResponse.statusCode} (${postResponse.statusCode.class.name}) : ${postResponse.statusMsg}"
                 render(status: postResponse.statusCode, text: postResponse.statusMsg)
@@ -80,9 +80,9 @@ class AssertionsController {
             def errorMsg = (!userDetails) ?
                     "User details not found" :
                     "Required parameters not provided: ${(!recordUuid) ? 'recordUuid' : ''} ${(!code) ? 'code' : ''}"
-            log.warn("Unable to add assertions. ${errorMsg}." )
+            log.warn("Unable to add assertions. ${errorMsg}.")
 
-            render(status:400, text: errorMsg)
+            render(status: 400, text: errorMsg)
         }
     }
 
@@ -100,17 +100,17 @@ class AssertionsController {
             Map postResponse = webServicesService.deleteAssertion(recordUuid, assertionUuid)
 
             if (postResponse.statusCode == 200) {
-                log.info("Called REST service. Assertion should be deleted" )
-                render(status: postResponse.statusCode, text:'Assertion deleted')
+                log.info("Called REST service. Assertion should be deleted")
+                render(status: postResponse.statusCode, text: 'Assertion deleted')
             } else {
                 log.error "Unexpected error: ${postResponse.statusCode} (${postResponse.statusCode.class.name}) : ${postResponse.statusMsg}"
                 render(status: postResponse.statusCode, text: postResponse.statusMsg)
             }
         } else {
             def errorMsg = "Required parameters not provided: ${(!recordUuid) ? 'recordUuid' : ''} ${(!assertionUuid) ? 'assertionUuid' : ''}"
-            log.warn("Unable to add assertions. ${errorMsg}." )
+            log.warn("Unable to add assertions. ${errorMsg}.")
 
-            render(status:400, text: errorMsg)
+            render(status: 400, text: errorMsg)
         }
     }
 }
diff --git a/grails-app/controllers/au/org/ala/biocache/hubs/BiocacheHubsUrlMappings.groovy b/grails-app/controllers/au/org/ala/biocache/hubs/BiocacheHubsUrlMappings.groovy
@@ -31,6 +31,7 @@ class BiocacheHubsUrlMappings {
         "/explore/your-area"(controller: 'occurrence', action: 'exploreYourArea')
         "/search"(controller: 'home')
         "/advancedSearch"(controller: 'home', action: 'advancedSearch')
+        "/simpleSearch"(controller: 'home', action: 'simpleSearch')
         "/proxy/$path**" (controller: 'proxy'){
             action = [POST:'doPost']
         }

diff --git a/grails-app/controllers/au/org/ala/biocache/hubs/DataQualityController.groovy b/grails-app/controllers/au/org/ala/biocache/hubs/DataQualityController.groovy
@@ -28,7 +28,7 @@ class DataQualityController {
     def webServicesService
 
     static responseFormats = [
-            list: ['json']
+        list: ['json']
     ]
 
     def index() {
@@ -38,5 +38,4 @@ class DataQualityController {
     def allCodes() {
         render webServicesService.getAllCodes() as JSON
     }
-
 }
diff --git a/grails-app/controllers/au/org/ala/biocache/hubs/HelpController.groovy b/grails-app/controllers/au/org/ala/biocache/hubs/HelpController.groovy
@@ -7,6 +7,8 @@ class HelpController {
     }
 
     def help() {}
+
     def data() {}
+
     def termsOfUse() {}
 }