Merge branch 'AtlasOfLivingAustralia:master' into master

biodiversitydata-se · Apr 3, 2024 · c7abb4f · c7abb4f
2 parents 3332f54 + e952295
commit c7abb4f
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Showing 8 changed files with 108 additions and 62 deletions.
diff --git a/build.gradle b/build.gradle
@@ -1,32 +1,23 @@
 buildscript {
-    repositories {
-        mavenLocal()
-        maven { url "https://nexus.ala.org.au/content/groups/public/" }
-        maven { url "https://repo.grails.org/grails/core" }
-    }
-    dependencies {
-        classpath "org.grails:grails-gradle-plugin:$grailsVersion"
-        classpath "gradle.plugin.com.github.erdi.webdriver-binaries:webdriver-binaries-gradle-plugin:$webdriverBinariesVersion"
-        classpath "com.bertramlabs.plugins:asset-pipeline-gradle:3.4.6"
-    }
+    version "4.1.0"
+    group "au.org.ala"
 }
 
 plugins {
-    id "com.gorylenko.gradle-git-properties" version "2.4.1"
-}
-
+    id "groovy"
+    id "org.grails.grails-gsp"
+    id "org.grails.grails-web"
+    id "com.github.erdi.webdriver-binaries" version "3.0"
+    id "war"
+    id "idea"
+    id "com.bertramlabs.asset-pipeline"
+    id "application"
+    id "eclipse"
 
-version "4.0.0"
-group "au.org.ala"
+    id "com.gorylenko.gradle-git-properties" version "2.4.1"
 
-apply plugin:"eclipse"
-apply plugin:"idea"
-apply plugin:"war"
-apply plugin:"org.grails.grails-web"
-apply plugin:"com.github.erdi.webdriver-binaries"
-apply plugin:"com.bertramlabs.asset-pipeline"
-apply plugin:"org.grails.grails-gsp"
-apply plugin:"maven-publish"
+    id "maven-publish"
+}
 
 publishing {
     repositories {
@@ -63,6 +54,7 @@ java {
 repositories {
     mavenLocal()
     maven { url "https://nexus.ala.org.au/content/groups/public/" }
+    mavenCentral()
     maven { url "https://repo.grails.org/grails/core" }
 }
 

diff --git a/grails-app/assets/javascripts/species.show.js b/grails-app/assets/javascripts/species.show.js
@@ -13,8 +13,6 @@
  * rights and limitations under the License.
  */
 
-var IMAGE_FILTER = '&fq=spatiallyValid:true&fq=-user_assertions:50001&fq=-user_assertions:50005'
-
 function showSpeciesPage(traitsTabSet) {
     //console.log("Starting show species page");
 
@@ -268,7 +266,7 @@ function loadAusTraits() {
 
     $.ajax({url: SHOW_CONF.ausTraitsCountUrl}).done(function (data) {
         if (data[0] && data[0]["summary"] && data[0]["AusTraits"] && data[0]["taxon"]) {
-            let htmlContent = "<span> There are " + data[0]["summary"] + " available for <span class='scientific-name rank-" + SHOW_CONF.rankString + "'><span class='name'>" + data[0]["taxon"] + "</span></span>  with data for " + data[0]["AusTraits"] +
+            let htmlContent = "<span> There are " + data[0]["summary"] + " traits available for <span class='scientific-name rank-" + SHOW_CONF.rankString + "'><span class='name'>" + data[0]["taxon"] + "</span></span>  with data for " + data[0]["AusTraits"] +
                 " further traits in the <a  target='_blank' href='" + SHOW_CONF.ausTraitsHomeUrl + "'>AusTraits</a> database. These are accessible via the download CSV button or alternatively the entire database can be accessed at  <a target='_blank' href='" + SHOW_CONF.ausTraitsSourceUrl + "'>" + SHOW_CONF.ausTraitsSourceUrl + "</a>. </span>"
             $('#traits-description').html(htmlContent);
         }
@@ -327,34 +325,71 @@ function loadDataProviders() {
             }
 
             $('.datasetCount').html(datasetCount);
+
+            var uidList = []
+            var facetMap = {}
             $.each(data.facetResults[0].fieldResult, function (idx, facetValue) {
                 if (facetValue.count > 0) {
 
                     var uid = facetValue.fq.replace(/data_resource_uid:/, '').replace(/[\\"]*/, '').replace(/[\\"]/, '');
-                    var dataResourceUrl = SHOW_CONF.collectoryUrl + "/public/show/" + uid;
                     var tableRowPlaceholder = "<tr id='dataset_" + uid + "'></tr>"
 
                     $('#data-providers-list tbody').append(tableRowPlaceholder);
 
-                    var tableRow = "<td><a href='" + dataResourceUrl + "'><span class='data-provider-name'>" + facetValue.label + "</span></a>";
-
-                    $.ajax({
-                        url: SHOW_CONF.collectoryServiceUrl + "/ws/dataResource/" + uid,
-                        dataType: 'json',
-                        success: function (collectoryData) {
-                            if (collectoryData.provider) {
-                                tableRow += "<br/><small><a href='" + SHOW_CONF.collectoryUrl + '/public/show/' + uid + "'>" + collectoryData.provider.name + "</a></small>";
-                            }
-                            tableRow += "</td>";
-                            tableRow += "<td>" + collectoryData.licenseType + "</td>";
+                    uidList.push(uid)
+                    facetMap[uid] = facetValue
+                }
+            });
 
-                            var queryUrl = uiUrl + "&fq=" + facetValue.fq;
-                            tableRow += "</td><td><a href='" + queryUrl + "'><span class='record-count'>" + facetValue.count + "</span></a></td>"
-                            $('#dataset_' + collectoryData.uid).html(tableRow);
+            $.post({
+                url: SHOW_CONF.collectoryServiceUrl + "/ws/find/dataResource",
+                data: JSON.stringify(uidList),
+                contentType : 'application/json',
+                dataType: 'json',
+                success: function (dataList) {
+                    $.each(dataList, function(idx, d) {
+                        var collectoryData = JSON.parse(d)
+                        var dataResourceUrl = SHOW_CONF.collectoryUrl + "/public/show/" + collectoryData.uid;
+                        var tableRow = "<td><a href='" + dataResourceUrl + "'><span class='data-provider-name'>" + facetMap[collectoryData.uid].label + "</span></a>";
+
+                        if (collectoryData.provider) {
+                            tableRow += "<br/><small><a href='" + SHOW_CONF.collectoryUrl + '/public/show/' + collectoryData.uid + "'>" + collectoryData.provider.name + "</a></small>";
                         }
-                    });
+                        tableRow += "</td>";
+                        tableRow += "<td>" + collectoryData.licenseType + "</td>";
+
+                        var queryUrl = uiUrl + "&fq=" + facetMap[collectoryData.uid].fq;
+                        tableRow += "</td><td><a href='" + queryUrl + "'><span class='record-count'>" + facetMap[collectoryData.uid].count + "</span></a></td>"
+                        $('#dataset_' + collectoryData.uid).html(tableRow);
+                    })
                 }
-            });
+            }).fail(function () {
+                // fallback to the method used pre collectory 5.1.0
+                $.each(data.facetResults[0].fieldResult, function (idx, facetValue) {
+                    if (facetValue.count > 0) {
+                        var uid = facetValue.fq.replace(/data_resource_uid:/, '').replace(/[\\"]*/, '').replace(/[\\"]/, '');
+
+                        var dataResourceUrl = SHOW_CONF.collectoryUrl + "/public/show/" + uid;
+                        var tableRow = "<td><a href='" + dataResourceUrl + "'><span class='data-provider-name'>" + facetValue.label + "</span></a>";
+
+                        $.ajax({
+                            url: SHOW_CONF.collectoryServiceUrl + "/ws/dataResource/" + uid,
+                            dataType: 'json',
+                            success: function (collectoryData) {
+                                if (collectoryData.provider) {
+                                    tableRow += "<br/><small><a href='" + SHOW_CONF.collectoryUrl + '/public/show/' + uid + "'>" + collectoryData.provider.name + "</a></small>";
+                                }
+                                tableRow += "</td>";
+                                tableRow += "<td>" + collectoryData.licenseType + "</td>";
+
+                                var queryUrl = uiUrl + "&fq=" + facetValue.fq;
+                                tableRow += "</td><td><a href='" + queryUrl + "'><span class='record-count'>" + facetValue.count + "</span></a></td>"
+                                $('#dataset_' + collectoryData.uid).html(tableRow);
+                            }
+                        });
+                    }
+                })
+            })
         }
     });
 }
@@ -427,7 +462,7 @@ function loadIndigenousData() {
     });
 }
 
-function showWikipediaData(data, testPage) {
+function showWikipediaData(data, testPage, targetName) {
     var node = $(data)
     node.find('[role="note"]').remove()
 
@@ -446,7 +481,7 @@ function showWikipediaData(data, testPage) {
                 var redirectItem = redirect[0].href.replace(/^.*\//, "")
                 var url = "/externalSite/wikipedia?name=" + encodeURI(redirectItem)
                 $.ajax({url: url}).done(function (data) {
-                    showWikipediaData(data, testPage)
+                    showWikipediaData(data, testPage, redirectItem)
                 });
                 return
             }
@@ -508,7 +543,7 @@ function showWikipediaData(data, testPage) {
             $description.css({'display': 'block'});
 
             // set the source of this description
-            var sourceHtml = "<a href='https://wikipedia.org/wiki/" + encodeURI(SHOW_CONF.scientificName) + "' target='wikipedia'>Wikipedia</a>&nbsp;" + jQuery.i18n.prop("wikipedia.licence.comment")
+            var sourceHtml = "<a href='https://wikipedia.org/wiki/" + encodeURI(targetName) + "' target='wikipedia'>Wikipedia</a>&nbsp;" + jQuery.i18n.prop("wikipedia.licence.comment")
             $description.find(".sourceText").html(sourceHtml);
 
             // hide unused properties of this description
@@ -532,12 +567,12 @@ function loadExternalSources() {
 
             var url = "/externalSite/wikipedia?name=" + encodeURI(name)
             $.ajax({url: url}).done(function (data) {
-                showWikipediaData(data, false)
+                showWikipediaData(data, false, name)
             });
         } else {
             var url = "/externalSite/wikipedia?name=" + encodeURI(name)
             $.ajax({url: url}).done(function (data) {
-                showWikipediaData(data, true)
+                showWikipediaData(data, true, name)
             });
         }
     }
@@ -643,7 +678,7 @@ function loadOverviewImages() {
         var imageIds = SHOW_CONF.preferredImageId.split(',')
         $.each(imageIds, function(idx, imageId) {
             var prefUrl = SHOW_CONF.biocacheServiceUrl +
-                '/occurrences/search?q=images:' + imageId + IMAGE_FILTER +
+                '/occurrences/search?q=images:' + imageId + SHOW_CONF.imageFilter +
                 '&im=true&facet=off&pageSize=1&start=0';
             $.ajax({
                 url: prefUrl,
@@ -658,6 +693,7 @@ function loadOverviewImages() {
                     }
                     if (data && data.totalRecords > 0) {
                         record.uuid = data.occurrences[0].uuid;
+                        record.imageMetadata = data.occurrences[0].imageMetadata
                     }
 
                     if (countPreferredImages == 0) {
@@ -674,7 +710,7 @@ function loadOverviewImages() {
     var url = SHOW_CONF.biocacheServiceUrl +
         '/occurrences/search?q=lsid:' +
         SHOW_CONF.guid +
-        '&fq=multimedia:"Image"&im=true&facet=off&pageSize=5&start=0' + IMAGE_FILTER;
+        '&fq=multimedia:"Image"&im=true&facet=off&pageSize=5&start=0' + SHOW_CONF.imageFilter;
 
     $.getJSON(url, function (data) {
         if (data && data.totalRecords > 0) {
@@ -889,7 +925,7 @@ function loadGalleryType(category, start) {
         '/occurrences/search?q=lsid:' +
         SHOW_CONF.guid +
         '&fq=multimedia:"Image"&pageSize=' + pageSize +
-        '&facet=off&start=' + start + imageCategoryParams[category] + '&im=true' + IMAGE_FILTER;
+        '&facet=off&start=' + start + imageCategoryParams[category] + '&im=true' + SHOW_CONF.imageFilter;
 
     $.getJSON(url, function (data) {
 
@@ -975,17 +1011,24 @@ function getImageTitleFromOccurrence(el) {
         briefHtml += ((el.typeStatus) ? ' | ' : br) + el.institutionName;
     }
 
-    if (el.imageMetadata && el.imageMetadata.length > 0 && el.imageMetadata[0].creator != null) {
-        if (briefHtml.length > 0) briefHtml += br;
-        briefHtml += "Photographer: " + el.imageMetadata[0].creator;
-    } else if (el.imageMetadata && el.imageMetadata.length > 0 && el.imageMetadata[0].rightsHolder != null) {
-        if (briefHtml.length > 0) briefHtml += br;
-        briefHtml += "Rights holder: " + el.imageMetadata[0].rightsHolder;
+    if (el.imageMetadata && el.imageMetadata.length > 0) {
+        $.each(el.imageMetadata, function (idx, im) {
+            if (im.imageId == el.image) {
+                if (im.creator != null) {
+                    if (briefHtml.length > 0) briefHtml += br;
+                    briefHtml += "Photographer: " + im.creator;
+                } else if (im.rightsHolder != null) {
+                    if (briefHtml.length > 0) briefHtml += br;
+                    briefHtml += "Rights holder: " + im.rightsHolder;
+                }
+            }
+        })
     } else if (el.collector) {
         if (briefHtml.length > 0) briefHtml += br;
         briefHtml += "Supplied by: " + el.collector;
     }
 
+
     return briefHtml;
 }
 

diff --git a/grails-app/conf/application.yml b/grails-app/conf/application.yml
@@ -158,7 +158,7 @@ ausTraits:
     baseURL: http://traitdata.austraits.cloud.edu.au
     homeURL: https://austraits.org/
     sourceURL: https://doi.org/10.5281/zenodo.3568417
-    definitionsURL: https://traitecoevo.github.io/austraits.build/articles/trait_definitions.html
+    definitionsURL: https://w3id.org/APD
 alaCitingURL: https://support.ala.org.au/support/solutions/articles/6000261662-citing-the-ala#website
 speciesList:
     baseURL: https://lists.ala.org.au
@@ -285,3 +285,6 @@ springcache:
 # sitemap proxied and edited from bie-index
 sitemap:
     enabled: true
+
+# filter applied to occurrence search requests that fetch images for the gallery
+imageFilter: '&fq=spatiallyValid:true&fq=-user_assertions:50001&fq=-user_assertions:50005&fq=-duplicate_status:ASSOCIATED&fq=-duplicateType:DIFFERENT_DATASET'
diff --git a/grails-app/controllers/au/org/ala/bie/ExternalSiteController.groovy b/grails-app/controllers/au/org/ala/bie/ExternalSiteController.groovy
@@ -174,7 +174,7 @@ class ExternalSiteController {
      *
      */
     def proxyAutocomplete = {
-        URL url = ( "${grailsApplication.config.getProperty("bie.index.url")}/search/auto.json" + params.toQueryString() ).toURL()
+        URL url = ( "${grailsApplication.config.getProperty("bie.index.url")}/search/auto" + params.toQueryString() ).toURL()
         StringBuilder content = new StringBuilder()
         BufferedReader bufferedReader
 

diff --git a/grails-app/i18n/messages.properties b/grails-app/i18n/messages.properties
@@ -202,6 +202,8 @@ idxtype.LAYER=Spatial layer
 idxtype.COMMON=Common Name
 idxtype.COMMON.formatted={0} Name
 idxtype.IDENTIFIER=Species Identifier
+idxtype.BIOCOLLECT=Biodiversity Science project
+idxtype.SPECIESLIST=Species list
 
 region.Australia=AU
 region.Australian\ Government=AU

diff --git a/grails-app/services/au/org/ala/bie/BieService.groovy b/grails-app/services/au/org/ala/bie/BieService.groovy
@@ -61,7 +61,7 @@ class BieService {
         if (!guid && guid != "undefined") {
             return null
         }
-        def json = webClientService.get(grailsApplication.config.bie.index.url + "/taxon/" + guid.replaceAll(/\s+/,'+'))
+        def json = webClientService.get(grailsApplication.config.bie.index.url + "/species/" + guid.replaceAll(/\s+/,'+'))
         //log.debug "ETC json: " + json
         try{
             JSON.parse(json)

diff --git a/grails-app/views/species/search.gsp b/grails-app/views/species/search.gsp
@@ -322,6 +322,11 @@
                                 <g:if test="${result.content}">
                                     <p>${result.content.trimLength(500)}</p>
                                 </g:if>
+                                <g:if test="${result.image}">
+                                    <div class="result-thumbnail">
+                                        <img src="${result.image}" alt="">
+                                    </div>
+                                </g:if>
                             </g:elseif>
                             <g:elseif test="${result.has("acronym") && result.get("acronym")}">
                                 <h4><g:message code="idxtype.${result.idxtype}"/>:

diff --git a/grails-app/views/species/show.gsp b/grails-app/views/species/show.gsp
@@ -33,7 +33,7 @@
 <g:else>
     <g:set var="tabs" value="${grailsApplication.config.show.tabs.replace('ausTraits':'').split(',')}"/>
 </g:else>
-<g:set var="jsonLink" value="${grailsApplication.config.bie.index.url}/species/${tc?.taxonConcept?.guid}.json"/>
+<g:set var="jsonLink" value="${grailsApplication.config.bie.index.url}/species/${tc?.taxonConcept?.guid}"/>
 <g:set var="sciNameFormatted"><bie:formatSciName rankId="${tc?.taxonConcept?.rankID}"
                                                  nameFormatted="${tc?.taxonConcept?.nameFormatted}"
                                                  nameComplete="${tc?.taxonConcept?.nameComplete}"
@@ -464,7 +464,8 @@
         ausTraitsCountUrl: "${raw(createLink(controller: 'externalSite', action: 'ausTraitsCount', params: [s: tc?.taxonConcept?.nameString ?: '', guid: guid]))}",
         ausTraitsHomeUrl: "${grailsApplication.config.ausTraits.homeURL}",
         ausTraitsSourceUrl:"${grailsApplication.config.ausTraits.sourceURL}",
-        showHiddenImages: false
+        showHiddenImages: false,
+        imageFilter: "${raw(grailsApplication.config.imageFilter)}"
     };
 
     $(function(){