Merge pull request #526 from brucehyslop/develop

Pre-grails4 branch changes

README.md

@@ -1,4 +1,4 @@
-# biocache-hubs [![Build Status](https://travis-ci.com/AtlasOfLivingAustralia/biocache-hubs.svg?branch=master)](https://travis-ci.com/AtlasOfLivingAustralia/biocache-hubs) 
+# biocache-hubs [![Build Status](https://travis-ci.com/AtlasOfLivingAustralia/biocache-hubs.svg?branch=develop)](https://travis-ci.com/AtlasOfLivingAustralia/biocache-hubs) 
 
 **biocache-hubs** is a Grails plugin that provides the core functionality for the _Atlas of Living Australia_ (ALA) [Occurrence search portal](https://biocache.ala.org.au/search) (Biocache) front-end.
 

build.gradle

@@ -10,7 +10,7 @@ buildscript {
  }
 }
 
-version "3.0.6-SNAPSHOT"
+version "3.0.9-SNAPSHOT"
 group "au.org.ala.plugins.grails"
 
 apply plugin:"eclipse"
@@ -44,6 +44,7 @@ dependencies {
  def noCache = {
  exclude group: 'org.grails.plugins', module: 'cache'
  exclude group: 'org.ehcache', module: 'ehcache'
+ exclude group: 'org.grails.plugins', module: 'cache-ehcache'
  }
 
  compile "org.springframework.boot:spring-boot-starter-logging"
@@ -53,7 +54,8 @@ dependencies {
  compile "org.springframework.boot:spring-boot-starter-tomcat"
  compile "org.grails:grails-dependencies"
  compile "org.grails:grails-web-boot"
- compile "org.grails.plugins:cache"
+ compile "org.grails.plugins:cache:4.0.0"
+ compile "org.grails.plugins:cache-ehcache:3.0.0"
  compile "org.grails.plugins:scaffolding"
  console "org.grails:grails-console"
  profile "org.grails.profiles:web-plugin"

grails-app/assets/javascripts/bieAutocomplete.js → grails-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) );
  }
  } );
  }

grails-app/assets/javascripts/biocache-hubs.js

@@ -4,7 +4,6 @@
 /************************************************************\
  * i18n
  \************************************************************/
-//= require jquery_i18n
 if (typeof BC_CONF != 'undefined' && BC_CONF.hasOwnProperty('contextPath')) {
  jQuery.i18n.properties({
  name: 'messages',

grails-app/assets/javascripts/exploreYourArea.js

@@ -451,8 +451,7 @@ function loadRecordsLayer(retry) {
  }, true);
 
  // records popups need to know the species group
- MAP_VAR.removeFqs = "&fq=species_group:" + (speciesGroup == "ALL_SPECIES" ? "*" : speciesGroup) + "&fq=taxon_name:" + (taxon ? taxon : "*");
-
+ MAP_VAR.removeFqs = "&fq=species_group:" + (speciesGroup === "ALL_SPECIES" ? "*" : speciesGroup) + "&fq=taxon_name:" + (taxon ? ("\"" + taxon + "\""): "*");
  // console.log("alaParams = ", alaParams, speciesGroupParam);
 
  var alaMapUrl = MAP_VAR.biocacheServiceUrl + "/ogc/wms/reflect?" + alaParams;
@@ -627,20 +626,22 @@ function groupClicked(el) {
  if (MAP_VAR.map) loadRecordsLayer();
  // AJAX...
  var uri = MAP_VAR.biocacheServiceUrl + "/explore/group/"+speciesGroup+".json";
+ var sortField = "count"
  var params = {
  lat: $('#latitude').val(),
  lon: $('#longitude').val(),
  radius: $('#radius').val(),
  fq: "geospatial_kosher:true",
  qc: MAP_VAR.queryContext,
- sort: "count",
+ sort: sortField,
  pageSize: 50
  };
  //var params = "?latitude=${latitude}&longitude=${longitude}&radius=${radius}&taxa="+taxa+"&rank="+rank;
  $('#taxaDiv').html('[loading...]');
+ $("div#rightList").data("sort", sortField); // save 'sort' value to the DOM
  $.getJSON(uri, params, function(data) {
  // process JSON data from request
- if (data) processSpeciesJsonData(data);
+ if (data) processSpeciesJsonData(data, false);
  });
 }
 
@@ -748,7 +749,7 @@ function processSpeciesJsonData(data, appendResults) {
  taxa = []; // array of taxa
  taxa = (thisTaxon.indexOf("|") > 0) ? thisTaxon.split("|") : thisTaxon;
  var start = $(this).attr('href');
- var sortOrder = $(this).data("sort") ? $(this).data("sort") : "index";
+ var sortOrder = $(this).data("sort") ? $(this).data("sort") : "count";
  var sortParam = sortOrder;
  var commonName = false;
  if (sortOrder == "common") {

grails-app/assets/javascripts/leafletPlugins.js

@@ -1,4 +1,4 @@
-//= require jquery_i18n
+
 //= require leaflet/leaflet-src.js
 //= require leaflet-fullscreen.js
 //= require leaflet-plugins/layer/tile/Google.js

grails-app/assets/javascripts/search.js

@@ -29,9 +29,14 @@ $(document).ready(function() {
  $('.exclude-loader').hide();
  for (var key in data) {
  var categoryEnabled = $('.exclude-count-label[data-category='+key+']').data('enabled')
- data[key] = categoryEnabled ? (new Intl.NumberFormat()).format(parseInt(data[key])) : 0
+ data[key] = categoryEnabled ? (new Intl.NumberFormat()).format(parseInt(data[key])) : '0';
  $('.exclude-count-label[data-category='+key+']').text(data[key]).show();
- $('.exclude-count-facet[data-category='+key+']').text("-("+data[key]+")").show();
+
+ if (data[key] === '0') {
+ $('.exclude-count-facet[data-category=' + key + ']').text('(' + data[key] + ')').show();
+ } else {
+ $('.exclude-count-facet[data-category=' + key + ']').text('(-' + data[key] + ')').show();
+ }
  }
  excludeCounts = data;
  });
@@ -165,7 +170,8 @@ $(document).ready(function() {
 
  //Check user has selected at least 1 facet
  if (selectedFacets.length > 0 && selectedFacets.length <= BC_CONF.maxFacets) {
- // save facets to the user_facets cookie
+ // save facets to the user_facets cookie as string
+ $.cookie.json = false;
  $.cookie("user_facets", selectedFacets, { expires: 7 });
  // reload page
  document.location.reload(true);
@@ -242,8 +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/>";
  });
  }
  });
@@ -349,13 +355,19 @@ $(document).ready(function() {
  loadMoreFacets(facetName, displayName, null);
  });
 
+ $('#profiles-selection').click(function(e) {
+ e.preventDefault();
+ $('#active-profile-name').text(e.target.innerText)
+ window.location.href = e.target.href
+ })
+
  // When user clicks the 'view profile description' icon next to profiles selection drop-down
  $('.DQProfileDetailsLink').click(function() {
  $.each($(".cat-table"), function(idx, el) {
- var filters = $(el).data('filters');
 
- var filterlist = filters.split(' AND ');
+ var filterlist = $(el).data('filters');
  var keys = [];
+
  for (var i = 0; i < filterlist.length; i++) {
  var val = parseFilter(filterlist[i]);
  if (val.length > 0) {
@@ -416,8 +428,8 @@ $(document).ready(function() {
  // when use clicks <i/> to view details of a category
  $('.DQCategoryDetailsLink').click(function() {
  var link = this;
+ var filters = $(link).data("filters");
  var fq = $(link).data("fq");
- var fqs = fq.split(' AND ')
 
  var description = $(link).data("description");
  var dqCategoryLabel = $(link).data('categorylabel')
@@ -430,10 +442,10 @@ $(document).ready(function() {
  $('#DQDetailsModal .modal-body #filter-value').html("<b>Filter applied: </b><i>fq=" + fq + "</i>");
  $("#view-excluded").attr('href', dqInverse);
 
- if (excludeCounts[dqCategoryLabel]) {
+ if (excludeCounts[dqCategoryLabel] !== '0') {
  $("#excluded .exclude-count-label").text(excludeCounts[dqCategoryLabel]).removeData('category').removeAttr('category');
  } else {
- $("#excluded .exclude-count-label").text('').data('category', dqCategoryLabel).attr('data-category', dqCategoryLabel);
+ $("#excluded .exclude-count-label").text(excludeCounts[dqCategoryLabel]).data('category', dqCategoryLabel).attr('data-category', dqCategoryLabel);
  }
 
  var pos = 0;
@@ -495,10 +507,9 @@ $(document).ready(function() {
  }
  })
 
- var descs = description.split(' and ')
  var valuesHtml = ""
 
- $.each(fqs, function(idx, el) {
+ $.each(filters, function(idx, el) {
  var vals = parseFilter(el);
  if (vals.length > 0) {
  var key = vals[0];
@@ -515,10 +526,11 @@ $(document).ready(function() {
  wiki = replaceURL(map.get(key)[1], 'Link');
  }
 
- // make sure no beak between '-' and key
- var els = el.split(':');
- el = '<span style="white-space: nowrap;">' + els[0] + '</span>:' + els[1];
- valuesHtml += '<tr><td style=\"word-break: break-word\">' + replaceURL(descs[idx]) + '</td><td style=\"word-break: normal\">' + el + '</td><td>' + wiki + '</td></tr>';
+ valuesHtml += '<tr>'
+ valuesHtml += '<td class="filter-description" style="word-break: break-word">' + replaceURL(description[idx]) + '</td>'
+ valuesHtml += '<td class="filter-value" style="word-break: normal"><span style="white-space: nowrap;">' + el + '</span></td>'
+ valuesHtml += '<td class="filter-wiki">' + wiki + '</td>'
+ valuesHtml += '</tr>'
  }
  })
 
@@ -633,6 +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');
@@ -1173,7 +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'
  },

grails-app/assets/javascripts/show.js

@@ -11,18 +11,42 @@
 //= 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();
  });
 
+ $('#showPassedPropResult').on('click', function(e){
+ $('.passedPropResult').toggle();
+ });
+
  $('#showMissingPropResult').on('click', function(e){
  $('.missingPropResult').toggle();
  });
@@ -196,7 +220,7 @@ $(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/subscribeMyAnnotation" : "/occurrences/unsubscribeMyAnnotation";
+ var actionpath = new_state ? "/api/subscribeMyAnnotation" : "/api/unsubscribeMyAnnotation";
  $.post(OCC_REC.contextPath + actionpath);
  }
 
@@ -216,7 +240,7 @@ $(document).ready(function() {
  }
  ).error(function () {
  $('#assertionSubmitProgress').css({'display': 'none'});
- $("#submitSuccess").html("There was problem flagging the issue. Please try again later.");
+ $("#submitSuccess").html(jQuery.i18n.prop('show.issueform.flagfail.message'));
  });
  }
 
@@ -237,7 +261,7 @@ $(document).ready(function() {
  if (OCC_REC.myAnnotationEnabled) {
  // by default off
  $("#notifyChangeCheckbox").prop('checked', false);
- var getAlerts = OCC_REC.contextPath + "/occurrences/alerts";
+ var getAlerts = OCC_REC.contextPath + "/api/alerts";
  $.getJSON(getAlerts, function (data) {
  var myAnnotationEnabled = data && data.myannotation && data.myannotation.length > 0;
  $("#notifyChangeCheckbox").prop('checked', myAnnotationEnabled);
@@ -477,7 +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);
@@ -529,8 +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);
@@ -571,7 +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')));
@@ -720,7 +744,7 @@ function getDataQualityItem(code) {
  url: url,
  dataType: 'json',
  success: function(data) {
- if (data && data[1]) {
+ if (data) {
  $.each(data, function(key, val) {
  //console.log("data", key, val);
  dataQualityItems[key] = val;