#468 partial species-list support

Author: Adam Collins

grails-app/assets/javascripts/spApp/directive/listsList.js

@@ -27,22 +27,22 @@
                             if (data.length) {
                                 for (var i = 0; i < data.length; i++) {
                                     scope.items.push({
-                                        dataResourceUid: data[i].dataResourceUid,
-                                        listName: data[i].listName,
+                                        dataResourceUid: data[i].id || data[i].dataResourceUid,
+                                        listName: data[i].listName || data[i].title,
                                         lastUpdated: data[i].lastUpdated,
-                                        itemCount: data[i].itemCount,
-                                        fullName: data[i].fullName,
+                                        itemCount: data[i].itemCount || data[i].rowCount,
+                                        fullName: data[i].fullName || data[i].owner || data[i].authority,
                                         isAuthoritative:data[i].isAuthoritative,
                                         selected: false
                                     })
                                 }
-                            } else if (data.dataResourceUid) {
+                            } else if (data.dataResourceUid || data.id) {
                                 scope.items.push({
-                                    dataResourceUid: data.dataResourceUid,
-                                    listName: data.listName,
+                                    dataResourceUid: data.id || data.dataResourceUid,
+                                    listName: data.listName || data.title,
                                     lastUpdated: data.lastUpdated,
-                                    itemCount: data.itemCount,
-                                    fullName: data.fullName,
+                                    itemCount: data.itemCount || data.rowCount,
+                                    fullName: data.fullName || dats.owner || data[i].authority,
                                     selected: false
                                 });
                             }
@@ -70,7 +70,12 @@
                         };
 
                         scope.itemUrl = function (item) {
-                            return ListsService.url() + '/speciesListItem/list/' + item.dataResourceUid
+                            if (ListsService.urlUi()) {
+                                // new species-lists as urlUi defined
+                                return ListsService.urlUi() + '/#/list/' + item.dataResourceUid
+                            } else {
+                                return ListsService.url() + '/speciesListItem/list/' + item.dataResourceUid
+                            }
                         };
 
                         scope.add = function (item) {

grails-app/assets/javascripts/spApp/service/facetAutoCompleteService.js

@@ -170,8 +170,8 @@
                         var data = ListsService.getItemsQCached(species_list);
                         if (data === undefined) {
                             return ListsService.getItemsQ(species_list).then(function () {
-                                // species list info is now cached
-                                return scope.getFacets(dynamic, groups, species_list)
+                                // species list info is now cached so repeat the parent function
+                                return scope.getGroupedFacets(dynamic, groups, species_list)
                             })
                         } else {
                             if (data.length > 0 && data[0].kvpValues && data[0].kvpValues.length > 0) {
@@ -256,8 +256,8 @@
                         var data = ListsService.getItemsQCached(species_list);
                         if (data === undefined) {
                             return ListsService.getItemsQ(species_list).then(function () {
-                                // species list info is now cached
-                                return scope.getFacets(dynamic, groups, species_list)
+                                // species list info is now cached, so repeat the parent function
+                                return scope.getAllFacets(dynamic, list, species_list)
                             })
                         } else {
                             if (data.length > 0 && data[0].kvpValues && data[0].kvpValues.length > 0) {
@@ -347,4 +347,4 @@
 
             return scope;
         }])
-}(angular));
+}(angular));

grails-app/assets/javascripts/spApp/service/listsService.js

@@ -27,15 +27,11 @@
                 list: function (q, max, offset, sort, order, user) {
                     var params = '';
                     if (q) params += "/" + encodeURIComponent(q);
-                    //TODO: investigate paging
-//                        if(q) params += '&q=' + encodeURIComponent(q);
-//                        if(max) params += '&max=' + max;
-//                        if(offset) params += '&offset=' + offset;
-//                        if(sort) params += '&sort=' + sort;
-//                        if(order) params += '&order=' + order;
-//                        if(user) params += '&user=' + user;
-                    params += "?" + "&max=2000";
+                    // The new species-lists has separate graphql query that is more UI friendly. In the meantime,
+                    // get everything, or an approximation of everything.
+                    params += "?max=20000";
                     if ($SH.userId) {
+                        // This is not used in the new species-lists. The purpose was to put lists by the current user at the top of the list.
                         params += "&user=" + $SH.userId
                     }
                     return $http.get($SH.baseUrl + "/portal/speciesList" + params, _httpDescription('list')).then(function (response) {
@@ -74,22 +70,14 @@
                     return cache.get(listId);
                 },
                 getItemsQ: function (listId) {
-                    // TODO: use 'species_list:' after biocache-service is redeployed
-                    //return $q.when('species_list:' + listId);
-
-                    if (scope.getItemsQCached(listId)) {
-                        return $q.when(scope.listToFq(scope.getItemsQCached(listId)))
-                    } else {
-                        return scope.items(listId, {includeKVP: true}).then(function (data) {
-                            cache.put(listId, data);
-
-                            return $q.when(scope.listToFq(data));
-                        });
-                    }
+                    return $q.when('species_list:' + listId);
                 },
                 url: function () {
                     return $SH.listsUrl
                 },
+                urlUi: function () {
+                    return $SH.listsUrlUi
+                },
                 listToFq: function (data) {
                     var terms = [];
                     for (var i in data) {

grails-app/conf/application.yml

@@ -28,7 +28,7 @@ i18n:
 layersService:
     url: 'https://spatial.ala.org.au/ws'
 geoserver:
-  url: 'https://spatial.ala.org.au/geoserver/web/'
+  url: 'https://spatial.ala.org.au/geoserver'
 
 info:
     app:
@@ -205,12 +205,22 @@ skin:
 
 
 lists:
+    useListWs: false
     url: 'https://lists.ala.org.au'
     threatenedSpeciesUrl: '/ws/speciesList/?isThreatened=eq:true&isAuthoritative=eq:true'
     invasiveSpeciesUrl: '/ws/speciesList/?isInvasive=eq:true&isAuthoritative=eq:true'
     facets: true
     migratoryDR: 'dr1005'
     iconicSpeciesDR: 'dr781'
+#lists:
+#    useListWs: true
+#    url: 'http://localhost:8080'
+#    urlUi: 'http://localhost:5173'
+#    threatenedSpeciesUrl: '/speciesList/?isThreatened=true&isAuthoritative=true&pageSize=1000'
+#    invasiveSpeciesUrl: '/speciesList/?isInvasive=true&isAuthoritative=true&pageSize=1000'
+#    facets: true
+#    migratoryDR: 'dr1005'
+#    iconicSpeciesDR: 'dr781'
 
 journalmap:
     url: 'https://www.journalmap.org'

grails-app/controllers/au/org/ala/spatial/portal/PortalController.groovy

@@ -376,7 +376,24 @@ class PortalController {
 
             def url = grailsApplication.config.lists.url
 
-            def r = webService.post("${url}/ws/speciesList/", json)
+            def r
+            if (grailsApplication.config.lists.useListWs) {
+                // format input
+                /*
+                    {
+                        "listName": name,
+                        "listItems": items,
+                        "description": description,
+                        "isPrivate": makePrivate,
+                        "listType": listType
+                    }
+                 */
+                r = webService.post("${url}/upload", json, null, ContentType.APPLICATION_JSON, false, true)
+
+                r = webService.post("${url}/ingest/${speciesListID}", json, null, ContentType.APPLICATION_JSON, false, true)
+            } else {
+                r = webService.post("${url}/ws/speciesList/", json)
+            }
 
             if (r == null) {
                 def status = response.setStatus(HttpURLConnection.HTTP_INTERNAL_ERROR)
@@ -400,7 +417,12 @@ class PortalController {
         } else {
             def url = grailsApplication.config.lists.url
 
-            def r = webService.get("${url}/ws/speciesListItems/" + params.id, [:], org.apache.http.entity.ContentType.APPLICATION_JSON, false, true, [:])
+            def r
+            if (grailsApplication.config.lists.useListWs) {
+                r = webService.get("${url}/speciesListItems/" + params.id, [:], org.apache.http.entity.ContentType.APPLICATION_JSON, false, true, [:])
+            } else {
+                r = webService.get("${url}/ws/speciesListItems/" + params.id, [:], org.apache.http.entity.ContentType.APPLICATION_JSON, false, true, [:])
+            }
 
             if (r == null) {
                 def status = response.setStatus(HttpURLConnection.HTTP_INTERNAL_ERROR)
@@ -424,7 +446,12 @@ class PortalController {
         } else {
             def url = grailsApplication.config.lists.url
 
-            def r = webService.get("${url}/ws/speciesList", [user: params.user ? userId : null, max: params.max], org.apache.http.entity.ContentType.APPLICATION_JSON, false, true, [:])
+            def r
+            if (grailsApplication.config.lists.useListWs) {
+                r = webService.get("${url}/speciesList/", [pageSize: params.max, page: params.page ?: 1], org.apache.http.entity.ContentType.APPLICATION_JSON, false, true, [:])
+            } else {
+                r = webService.get("${url}/ws/speciesList", [user: params.user ? userId : null, max: params.max], org.apache.http.entity.ContentType.APPLICATION_JSON, false, true, [:])
+            }
 
             if (r == null) {
                 def status = response.setStatus(HttpURLConnection.HTTP_INTERNAL_ERROR)

grails-app/services/au/org/ala/spatial/portal/PortalService.groovy

@@ -60,15 +60,15 @@ class PortalService {
                 def threatenedUrl =
                         "${grailsApplication.config.lists.url}${grailsApplication.config.lists.threatenedSpeciesUrl}"
                 def threatened = JSON.parse(hubWebService.getUrl(threatenedUrl, null, false)) as Map
-                def threatenedJoined = threatened.lists*.dataResourceUid.join(joinStr)
+                def threatenedJoined = threatened.lists.collect { it.id ?: it.dataResourceUid }.join(joinStr)
                 def threatenedQ = "species_list_uid:(${threatenedJoined})"
                 if (threatenedJoined) {
                     grailsApplication.config.threatenedQ = threatenedQ
                 }
 
                 def invasiveUrl = "${grailsApplication.config.lists.url}${grailsApplication.config.lists.invasiveSpeciesUrl}"
                 def invasive = JSON.parse(hubWebService.getUrl(invasiveUrl, null, false)) as Map
-                def invasiveJoined = invasive.lists*.dataResourceUid.join(joinStr)
+                def invasiveJoined = invasive.lists.collect { it.id ?: it.dataResourceUid }.join(joinStr)
                 def invasiveQ = "species_list_uid:(${invasiveJoined})"
                 if (invasiveJoined) {
                     grailsApplication.config.invasiveQ = invasiveQ

grails-app/views/portal/embedExample.gsp

@@ -29,6 +29,7 @@
         layersServiceUrl: '${config.layersService.url}',
         samplingUrl: '${config.sampling.url}',
         listsUrl: '${config.lists.url}',
+        listsUrlUi: '${config.lists.urlUi}',
         sandboxUrl: '${config.sandbox.url}',
         sandboxServiceUrl: '${config.sandboxService.url}',
         sandboxUiUrl: '${config.sandbox.uiUrl}',
@@ -88,4 +89,4 @@
 <sp-app></sp-app>
 
 </body>
-</html>
+</html>

grails-app/views/portal/index.gsp

@@ -40,6 +40,7 @@
         layersServiceUrl: '${config.layersService.url}',
         samplingUrl: '${config.sampling.url}',
         listsUrl: '${config.lists.url}',
+        listsUrlUi: '${config.lists.urlUi}',
         listsFacets: ${config.lists.facets},
         sandboxUrl: '${config.sandbox.url}',
         sandboxServiceUrl: '${config.sandboxService.url}',