Merge branch 'develop'

# Conflicts: # build.gradle
AtlasOfLivingAustralia · Apr 10, 2022 · 20f3619 · 20f3619
2 parents 5c2ab47 + 34448a1
commit 20f3619
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diff --git a/.gitignore b/.gitignore
@@ -13,3 +13,4 @@ out/
 /node_modules/
 /grails-app/assets/node_modules/
 /grails-app/assets/node_modules/
+/package-lock.json
diff --git a/README.md b/README.md
@@ -254,6 +254,7 @@ Layers required to be imported to Spatial Service:
     Temperature - annual mean (Bio01)
     GEOMACS - geometric mean
     ASGS Australian States and Territories
+    IBRA 7 Subregions
 
 Williams 2030 best 5  - for predict and classify
 

diff --git a/build.gradle b/build.gradle
@@ -11,11 +11,7 @@ buildscript {
     }
 }
 
-plugins {
-    id 'war'
-}
-
-version "1.0.1"
+version "1.0.2"
 group "au.org.ala"
 
 apply plugin:"eclipse"

diff --git a/grails-app/assets/javascripts/spApp/controller/createSpeciesListCtrl.js b/grails-app/assets/javascripts/spApp/controller/createSpeciesListCtrl.js
@@ -155,7 +155,7 @@
 
                 $scope.addNewSpecies = function () {
                     ListsService.createList($scope.newListName, $scope.newListDescription, $scope.matchedGuids(), $scope.makePrivate, $scope.newListType.id).then(function (resp) {
-                        if (resp.status === 200) {
+                        if (resp.status >= 200 && resp.status < 300) {
                             var json = JSON.parse(resp.data.text);
                             var druid = json.druid;
 

diff --git a/grails-app/assets/javascripts/spApp/directive/listsList.js b/grails-app/assets/javascripts/spApp/directive/listsList.js
@@ -32,6 +32,7 @@
                                         lastUpdated: data[i].lastUpdated,
                                         itemCount: data[i].itemCount,
                                         fullName: data[i].fullName,
+                                        isAuthoritative:data[i].isAuthoritative,
                                         selected: false
                                     })
                                 }
@@ -79,13 +80,33 @@
                                 found.selected = true;
                                 scope.selection = found;
 
-                                ListsService.getItemsQ(found.dataResourceUid).then(function (data) {
+                                //If the list is authoritative, Biocache builds index against species_list_uid (over night)
+                                //We should use q=species_list_uid:drxxxx
+                                if (found.isAuthoritative) {
+
                                     scope._custom()({
-                                        q: [data],
+                                        q: ["species_list_uid:" + found.dataResourceUid],
                                         name: found.listName,
                                         species_list: found.dataResourceUid
                                     })
-                                })
+                                } else {
+                                    //q=qid:xxxxxxxxxx
+                                    ListsService.getItemsQ(found.dataResourceUid).then(function (data) {
+                                        //example: (lsid:xxxx OR lsid:xxxx)
+                                        var items = data.split(" OR ");
+                                        var query = data;
+                                        var limit = 200;
+                                        if (items.length > limit ) {
+                                            alert("Note: only the first 200 names will be used when when adding species to the map (for user-uploaded checklists)");
+                                            query = items.slice(0,limit).join(" OR ") +")";
+                                        }
+                                        scope._custom()({
+                                            q: [query],
+                                            name: found.listName,
+                                            species_list: found.dataResourceUid
+                                        })
+                                    })
+                                }
 
                             }
                         };

diff --git a/grails-app/assets/javascripts/spApp/service/layersService.js b/grails-app/assets/javascripts/spApp/service/layersService.js
@@ -241,7 +241,7 @@
                             name: name,
                             description: description,
                             user_id: $SH.userId
-                        }, _httpDescription('createFromWkt'))
+                        })
                 },
                 /**
                  * Get object information

diff --git a/grails-app/assets/javascripts/spApp/service/listsService.js b/grails-app/assets/javascripts/spApp/service/listsService.js
@@ -57,8 +57,8 @@
                     };
                     return $http.post($SH.baseUrl + "/portal/postSpeciesList", list, _httpDescription('createList', {withCredentials: true})).then(function (resp) {
                         return resp;
-                    }, function (resp) {
-                        return resp;
+                    }, function (error) {
+                        return error;
                     });
                 },
                 items: function (listId, params) {

diff --git a/grails-app/assets/javascripts/spApp/service/toolExportSampleService.js b/grails-app/assets/javascripts/spApp/service/toolExportSampleService.js
@@ -23,7 +23,7 @@
                         "input": [
                             {
                                 "name": "area",
-                                "description": $i18n(382,"Select area."),
+                                "description": $i18n(420,"Select area."),
                                 "type": "area",
                                 "constraints": {
                                     "min": 1,

diff --git a/grails-app/assets/javascripts/spApp/spApp.js b/grails-app/assets/javascripts/spApp/spApp.js
@@ -104,27 +104,28 @@ spApp.config(['$httpProvider', function ($httpProvider) {
                     var $http = angular.element(document.querySelector('sp-app')).injector().get('$http');
                     rejection.config.retried = true;
                     return $http(rejection.config);
-                }
-
-                var httpService = angular.element(document.querySelector('sp-app')).injector().get('HttpService');
-                if (httpService) httpService.pop(rejection, 'responseError');
-
-                if ( rejection.status == 403 || rejection.status == 401) {
-                    bootbox.alert("Authentication failed or login session expired, Please login again!")
-                    rejection.handled = true;
-                } else if (rejection.status == -1) {
-                    // urls not accessible are ignored.
-                    // Mainly caused by network/connection, or CORS
-                    console.log("Cannot connect to: " + rejection.config.url +" due to network/connection problems, for example: CORS")
-                } else if (rejection.status === 0) {
-                    if (window.isInWrapper) {
-                        //Logout if in an app;
-                        window.location.href = 'ios:logout';
-                    } else {
-                        window.location.reload();
+                } else {
+                    var httpService = angular.element(document.querySelector('sp-app')).injector().get('HttpService');
+                    if (httpService) httpService.pop(rejection, 'responseError');
+
+                    if ( rejection.status == 403 || rejection.status == 401) {
+                        bootbox.alert("Authentication failed or login session expired, Please login again!")
+                        rejection.handled = true;
+                    } else if (rejection.status == -1) {
+                        // urls not accessible are ignored.
+                        // Mainly caused by network/connection, or CORS
+                        console.log("Cannot connect to: " + rejection.config.url +" due to network/connection problems, for example: CORS")
+                    } else if (rejection.status === 0) {
+                        if (window.isInWrapper) {
+                            //Logout if in an app;
+                            window.location.href = 'ios:logout';
+                        } else {
+                            window.location.reload();
+                        }
                     }
+                    return $q.reject(rejection);
                 }
-                return $q.reject(rejection);
+
             }
         };
     });

diff --git a/grails-app/assets/javascripts/spApp/templates/listsList.tpl.htm b/grails-app/assets/javascripts/spApp/templates/listsList.tpl.htm
@@ -1,13 +1,13 @@
 <div class="">
     <div class="">
         <div class="">
-            <table class="table table-striped fixed-head layers-table" style="width:430px">
+            <table class="table table-striped fixed-head layers-table" style="width:480px" name="speciesList">
                 <caption>
                     <div class="row">
                         <div class="col-sm-6">
                             <div class="input-group">
                                 <input type="text" class="form-control" placeholder="Filter"
-                                       ng-model="searchLists">
+                                       ng-model="searchLists" name="searchInSpeciesList">
                                 <div class="input-group-addon"><i class="fa fa-search"></i></div>
                             </div>
                         </div>
@@ -47,7 +47,7 @@
                     <td style="width:10px" class="td-vertical-align text-center"><input type="checkbox"
                                                                                         ng-model="item.selected"
                                                                                         ng-click="select(item)"></td>
-                    <td class="td-vertical-align table-text-ellipsis" style="width:300px"><a target="_blank"
+                    <td class="td-vertical-align table-text-ellipsis" style="width:300px"><span title="Authoritative list" ng-show="item.isAuthoritative" class="glyphicon glyphicon-ok-circle"></span><a target="_blank"
                                                                                              href="{{ itemUrl(item) }}">{{
                         item.listName }}</a></td>
                     <td style="width:100px" class="td-vertical-align text-right">{{ item.lastUpdated | date: short}}

diff --git a/grails-app/assets/stylesheets/application.css b/grails-app/assets/stylesheets/application.css
@@ -21,4 +21,5 @@
 *= require commonui-bs3-2019/css/ala-styles.css
 *= require spatial-hub.css
 *= require commonui-bs3-2019.css
+*= require flag-icons-master/css/flag-icon.css
 */
diff --git a/grails-app/assets/stylesheets/spatial-hub.css b/grails-app/assets/stylesheets/spatial-hub.css
@@ -1116,3 +1116,9 @@ ul.errors {
     padding-top: 20px;
     font-style: italic;
 }
+
+#lang {
+    color: #FFFFFF;
+    background-color: #000000;
+    border-width: 0;
+}
diff --git a/grails-app/conf/application.yml b/grails-app/conf/application.yml
@@ -22,6 +22,8 @@ grails:
         upload:
             maxFileSize: 10000000
             maxRequestSize: 10000000
+i18n:
+  region: 'default'
 
 layersService:
     url: 'https://spatial.ala.org.au/ws'
@@ -127,16 +129,14 @@ endpoints:
 security:
     cas:
         casServerName: 'https://auth.ala.org.au'
-        uriFilterPattern: '/alaAdmin,/alaAdmin.*'
-        uriExclusionFilterPattern: '/portal/q.*,/portal/messages.*,/portal/sessionCache.*,/static.*,/assets.*'
-        authenticateOnlyIfLoggedInPattern: '/portal.*,/,/portal/config.*,/portal/i18n.*,/hub/[a-zA-Z0-9]+'
+        uriFilterPattern: ['/alaAdmin/?.*']
+        uriExclusionFilterPattern: ['/portal/q/*','/portal/messages/*','/portal/sessionCache/*','/static/*','/assets/*']
+        authenticateOnlyIfLoggedInPattern: ['/portal/*','/','/portal/config/*','/portal/i18n/*','/hub/[a-zA-Z0-9]+']
         loginUrl: 'https://auth.ala.org.au/cas/login'
         logoutUrl: 'https://auth.ala.org.au/cas/logout'
-        gateway: false
         casServerUrlPrefix: 'https://auth.ala.org.au/cas'
         bypass: false # set to true for non-ALA deployment
         disableCAS: false
-        roleAttribute: authority
         ignoreCase: true
         authCookieName: ALA-Auth
 
@@ -178,8 +178,6 @@ skin:
   orgNameLong: 'Atlas of Living Australia'
   favicon: 'https://www.ala.org.au/app/uploads/2019/01/cropped-favicon-32x32.png'
 
-layersService:
-    url: 'https://spatial.ala.org.au/ws/'
 
 lists:
     url: 'https://lists.ala.org.au'

diff --git a/grails-app/controllers/au/org/ala/spatial/portal/PortalController.groovy b/grails-app/controllers/au/org/ala/spatial/portal/PortalController.groovy
@@ -151,7 +151,12 @@ class PortalController {
                     config.spApp.each { k, v ->
                         spApp.put(k, v.class.newInstance(params.get(k, v)))
                     }
-                    config.spApp = spApp
+                    if (params.get("lang")) {
+                        config.i18n?.currentRegion = params.get("lang")
+                    } else {
+                        config.i18n?.currentRegion = null;
+                    }
+
 
                     render(view: 'index',
                             model: [config     : config,
@@ -322,7 +327,7 @@ class PortalController {
         if (!userId) {
             notAuthorised()
         } else {
-            Map headers = [apiKey: grailsApplication.config.api_key]
+            Map headers = [apiKey: grailsApplication.config.api_key, Accept: 'application/json']
             def json = request.JSON as Map
             def url = "${grailsApplication.config.layersService.url}/shape/upload/wkt"
             def r = hubWebService.urlResponse(HttpPost.METHOD_NAME, url, null, headers,
@@ -453,13 +458,14 @@ class PortalController {
             if (r == null) {
                 def status = response.setStatus(HttpURLConnection.HTTP_INTERNAL_ERROR)
                 r = [status: status, error: 'Unknown error when creating list']
-            } else if (r.error) {
-                response.setStatus((int) r.statusCode)
-            } else {
-                response.setStatus(HttpURLConnection.HTTP_OK)
             }
 
-            render r as JSON
+            def status = r.statusCode
+            if (r.statusCode < 200 || r.statusCode > 300) {
+                r = [error: r.text  ]
+            }
+
+            render status: status, r as JSON
         }
     }
 

diff --git a/grails-app/i18n/messages_de.properties b/grails-app/i18n/messages_de.properties
@@ -400,6 +400,10 @@ typeMismatch.java.math.BigInteger=Die Eigenschaft {0} muss eine gültige Zahl se
 354=Gebiet
 355=Die Befehl konnte nicht gefunden werden
 356=Wissenschaftliche Verbreitung
+357=JournalMap articles
+358=Checklist species distributions
+359=Checklist areas
+360=Gazetteer Points
 361=Sehenswürdigkeiten
 362=https\://www.ala.org.au/spatial-portal-help/note-area-sq-km/
 363=Info
@@ -432,7 +436,9 @@ typeMismatch.java.math.BigInteger=Die Eigenschaft {0} muss eine gültige Zahl se
 390=Oktober
 391=November
 392=Dezember
+393=expert distribution(s)
 394=Checkliste(n)
+395=track(s)
 396=gefunden
 397=Metadaten-URL
 398=Sammlung von Flächen aus Layer
@@ -461,6 +467,7 @@ typeMismatch.java.math.BigInteger=Die Eigenschaft {0} muss eine gültige Zahl se
 421=Dateityp.
 422=Flächen zum Exportieren auswählen.
 423=Dateityp auswählen.
+424=Number of groups and Shapefile generation
 425=Flächen exportieren.
 426=Eine Artenliste exportieren.
 427=Endemisch
@@ -470,4 +477,85 @@ typeMismatch.java.math.BigInteger=Die Eigenschaft {0} muss eine gültige Zahl se
 431=Datum
 432=Aktionstyp
 433=Daten
-434=Anzahl der Aktionen
+434=Anzahl der Aktionen
+435=Suche im ALA DOI-Dienst nach Datensätzen für Arten
+436=Nach Lizenz
+450=(ausgewählt)
+451=Slider help
+452=Use the slider to select facet classes. All facet classes falling in between the range selector are selected. Selections falling outside the range are cleared.
+453=Diagramme
+454=view in larger window
+455=Diagramm
+456=Tabelle
+457=Facet classes for 
+458=Aktualisieren
+459=My workflow
+460=Workflow Saved
+461=Aus DOI hinzufügen
+462=Kein Datensatz ausgewählt
+463=Search returned with no results
+464=Metadaten anzeigen
+465=DOI
+466=Arten
+467=Datenanzahl
+468=Department
+469=Modeller
+470=Datum
+471=SDM available
+472=No data was able to be extracted from the selected DOI
+473=Select by clicking label or bar
+474=Nicht angegeben
+475=No occurrences mapped for this layer and applied filters.
+476=Die hochgeladene Datei ist zu groß. Maximale Dateigröße\:
+477=Upload fehlgeschlagen.
+478=Failed to register query. Try again later.
+479=Ungültiger WKT
+480=Display facet class in
+481=Auswahl löschen
+482=Search CSDM dataset by species, department or modeller
+483=Absenden
+484=Workflow Name
+485=ist privat
+486=Id
+487=Ist privat
+488=bearbeiten
+489=Anhand eines Zeitraums begrenzen
+490=Zeitraum
+491=TO
+492=Listentyp\:
+493=Radius (km)&nbsp;
+494=Draw polyline with buffer
+495=Datenprovider\:
+496=Add occurrences to adhoc
+497=Artenmerkmale mit einschließen (falls verfügbar)
+498=Annotating your workflow will allow other users to assess the suitability of the dataset for their purposes and make it reusable.
+499=User
+500=Organsation
+501=General annotation of the dataset
+502=Workflow annotation
+503=Search facets...
+504=--- Aktive Filter ---
+505=Facet begins with (case sensitive)\:
+506=Available Workflows
+507=Laden
+508=Bearbeitung läuft...
+509=Speichern
+510=Ausführen
+511=Kartenprojektion
+512=Filter entfernen
+513=Räumlich-unbekannte Daten berücksichtigen
+514=Abwesenheiten (Absences) berücksichtigen
+515=Verlauf
+516=Actions
+517=Sessions
+518=Zoom to Localities
+519=Select Facet
+520=Filter löschen
+521=Aktiviert
+522=Kategorie
+523=facets selected
+524=Weiter
+525=Räumlich-undefinierte Daten berücksichtigen
+526=(kann Artenmerkmale enthalten)
+527=Keine weiteren Arten
+528=Lebensform