diff --git a/build.gradle b/build.gradle index 883a3813..08843bad 100644 --- a/build.gradle +++ b/build.gradle @@ -12,7 +12,7 @@ buildscript { } } -version "2.0.0" +version "2.1.0" group "au.org.ala" apply plugin:"eclipse" @@ -105,9 +105,10 @@ dependencies { exclude group: 'org.slf4j', module: 'slf4j-nop' } implementation "org.grails.plugins:ala-admin-plugin:2.3.0" - implementation "org.grails.plugins:ala-auth:6.0.0" + implementation "org.grails.plugins:ala-auth:$alaSecurityLibsVersion" + implementation "org.grails.plugins:ala-ws-plugin:$alaSecurityLibsVersion" - implementation "org.grails.plugins:ala-bootstrap3:4.1.0" + implementation "org.grails.plugins:ala-bootstrap3:4.4.0" implementation "au.org.ala.plugins.grails:ala-charts-plugin:2.3.0-ANGULAR-SNAPSHOT" runtimeOnly 'org.grails.plugins:sandbox-hub:1.0' diff --git a/gradle.properties b/gradle.properties index 0506158a..00c1447e 100644 --- a/gradle.properties +++ b/gradle.properties @@ -9,4 +9,5 @@ seleniumVersion=3.14.0 webdriverBinariesVersion=2.6 #chromeDriverVersion=2.45.0 geckodriverVersion=0.24.0 -seleniumSafariDriverVersion=3.14.0 \ No newline at end of file +seleniumSafariDriverVersion=3.14.0 +alaSecurityLibsVersion=6.2.0 diff --git a/grails-app/assets/compile/spAppModules.js b/grails-app/assets/compile/spAppModules.js index 6a8ae6fd..0ae47478 100644 --- a/grails-app/assets/compile/spAppModules.js +++ b/grails-app/assets/compile/spAppModules.js @@ -1,2 +1,2 @@ /* Do not edit. This file built at compile by _Events.groovy */ -$spAppModules = ["tool-add-layer-service","tool-export-checklist-service","sandbox-service","lists-service","layers-service","http-service","colour-service","i18n-service","tool-export-sample-service","species-auto-complete-service","logger-service","menu-service","doi-service","tool-export-doi-service","layout-service","tool-add-facet-service","phylo-service","url-params-service","popup-service","facet-auto-complete-service","tool-export-area-service","gaz-auto-complete-service","layer-distances-service","keep-alive-service","tool-area-report-service","poi-service","bie-service","event-service","predefined-layer-lists-service","sessions-service","tool-add-species-service","tools-service","predefined-areas-service","tool-export-map-service","biocache-service","flickr-service","workflow-service","map-service","select-area-directive","facet-editor-directive","select-date-range-directive","i18n-directive","sp-percent-directive","sp-options-directive","sp-legend-directive","layer-list-upload-directive","lists-list-directive","species-auto-complete-directive","envelope-directive","select-multiple-area-directive","nearest-locality-directive","sp-menu-directive","sandbox-list-directive","http-ui-directive","draw-area-directive","workflow-annotation-directive","point-comparison-directive","species-options-directive","leaflet-quick-links-directive","select-phylo-directive","doi-auto-complete-directive","google-places-directive","lifeform-select-directive","playback-directive","layer-auto-complete-directive","layer-list-select-directive","select-facet-directive","select-species-directive","workflow-item-directive","area-list-select-directive","sp-map-directive","select-layers-directive","biocache-chart-directive","gaz-auto-complete-directive","modal-iframe-instance-ctrl","species-info-ctrl","facet-ctrl","workflow-ctrl","add-d-o-i-ctrl","tabulate-ctrl","layout-ctrl","area-report-ctrl","add-w-m-s-ctrl","tool-ctrl","leaflet-map-controller","sand-box-ctrl","sessions-ctrl","create-species-list-ctrl","csv-ctrl","facet-editor-modal-ctrl","add-area-ctrl","log-ctrl","analysis-ctrl","export-bccvl-ctrl"]; \ No newline at end of file +$spAppModules = ["tool-add-layer-service","tool-export-checklist-service","sandbox-service","lists-service","layers-service","http-service","colour-service","i18n-service","tool-export-sample-service","species-auto-complete-service","logger-service","menu-service","doi-service","tool-export-doi-service","layout-service","tool-add-facet-service","url-params-service","popup-service","facet-auto-complete-service","tool-export-area-service","gaz-auto-complete-service","layer-distances-service","keep-alive-service","tool-area-report-service","poi-service","bie-service","event-service","predefined-layer-lists-service","sessions-service","tool-add-species-service","tools-service","predefined-areas-service","tool-export-map-service","biocache-service","flickr-service","workflow-service","map-service","select-area-directive","facet-editor-directive","select-date-range-directive","i18n-directive","sp-percent-directive","sp-options-directive","sp-legend-directive","layer-list-upload-directive","lists-list-directive","species-auto-complete-directive","envelope-directive","select-multiple-area-directive","nearest-locality-directive","sp-menu-directive","sandbox-list-directive","http-ui-directive","draw-area-directive","workflow-annotation-directive","point-comparison-directive","species-options-directive","leaflet-quick-links-directive","doi-auto-complete-directive","google-places-directive","lifeform-select-directive","playback-directive","layer-auto-complete-directive","layer-list-select-directive","select-facet-directive","select-species-directive","workflow-item-directive","area-list-select-directive","sp-map-directive","select-layers-directive","biocache-chart-directive","gaz-auto-complete-directive","modal-iframe-instance-ctrl","species-info-ctrl","facet-ctrl","workflow-ctrl","add-d-o-i-ctrl","tabulate-ctrl","layout-ctrl","area-report-ctrl","add-w-m-s-ctrl","tool-ctrl","leaflet-map-controller","sand-box-ctrl","sessions-ctrl","create-species-list-ctrl","csv-ctrl","facet-editor-modal-ctrl","add-area-ctrl","log-ctrl","analysis-ctrl"]; \ No newline at end of file diff --git a/grails-app/assets/javascripts/spApp/controller/addAreaCtrl.js b/grails-app/assets/javascripts/spApp/controller/addAreaCtrl.js index afe6f839..c128f975 100644 --- a/grails-app/assets/javascripts/spApp/controller/addAreaCtrl.js +++ b/grails-app/assets/javascripts/spApp/controller/addAreaCtrl.js @@ -379,6 +379,7 @@ if (data.data === undefined || data.data.id === undefined || !data.data.indb) { LayersService.getWkt(pid).then(function (wkt) { $scope.selectedArea.wkt = wkt.data + $scope.selectedArea.obj.wkt = wkt.data if (mapNow) { $scope.addToMapAndClose(); } @@ -426,4 +427,4 @@ $scope.isLoggedIn = $scope.isLoggedIn = $SH.userId !== undefined && $SH.userId !== null && $SH.userId.length > 0; $scope.isNotLoggedIn = !$scope.isLoggedIn; }]) -}(angular)); \ No newline at end of file +}(angular)); diff --git a/grails-app/assets/javascripts/spApp/controller/areaReportCtrl.js b/grails-app/assets/javascripts/spApp/controller/areaReportCtrl.js index d45d23bf..c46d392f 100644 --- a/grails-app/assets/javascripts/spApp/controller/areaReportCtrl.js +++ b/grails-app/assets/javascripts/spApp/controller/areaReportCtrl.js @@ -262,7 +262,7 @@ name: $i18n(365, "Number of species - spatially valid only"), query: {q: areaQ.q, bs: areaQ.bs, ws: areaQ.ws, wkt: areaQ.wkt, qid: areaQ.qid}, map: false, - extraQ: ["geospatial_kosher:true"] + extraQ: ["spatiallyValid:true"] }, { name: $i18n(366, "Number of endemic species"), @@ -275,7 +275,7 @@ endemic: true, query: {q: areaQ.q, bs: areaQ.bs, ws: areaQ.ws, wkt: areaQ.wkt, qid: areaQ.qid}, map: false, - extraQ: ["geospatial_kosher:true"] + extraQ: ["spatiallyValid:true"] }]; // TODO: move this into config and retrieve from $SH @@ -289,7 +289,7 @@ name: $i18n(368, "Occurrences - spatially valid only"), query: {q: areaQ.q, bs: areaQ.bs, ws: areaQ.ws, wkt: areaQ.wkt, qid: areaQ.qid}, occurrences: true, - extraQ: ["geospatial_kosher:true"] + extraQ: ["spatiallyValid:true"] }, { name: $i18n(356, "Expert distributions"), @@ -512,8 +512,8 @@ overrideValues: { ToolExportSampleService: { input: { - species: {constraints: {'default': query, disable: true}}, - area: {constraints: {'default': area, disable: true}} + species: {constraints: {'defaultValue': query, disable: true}}, + area: {constraints: {'defaultValue': area, disable: true}} } } }, diff --git a/grails-app/assets/javascripts/spApp/controller/createSpeciesListCtrl.js b/grails-app/assets/javascripts/spApp/controller/createSpeciesListCtrl.js index 094aa5bc..03497ced 100644 --- a/grails-app/assets/javascripts/spApp/controller/createSpeciesListCtrl.js +++ b/grails-app/assets/javascripts/spApp/controller/createSpeciesListCtrl.js @@ -47,7 +47,7 @@ $scope.newListName = $i18n(375, "My species list"); $scope.newListDescription = ''; $scope.newItems = ''; - $scope.makePrivate = false; + $scope.makePrivate = true; // new lists are private by default $scope.newListType = $scope.listTypes[0] $scope.selectedQ = { @@ -227,4 +227,4 @@ }]) -}(angular)); \ No newline at end of file +}(angular)); diff --git a/grails-app/assets/javascripts/spApp/controller/exportBccvlCtrl.js b/grails-app/assets/javascripts/spApp/controller/exportBccvlCtrl.js deleted file mode 100644 index f89e11eb..00000000 --- a/grails-app/assets/javascripts/spApp/controller/exportBccvlCtrl.js +++ /dev/null @@ -1,122 +0,0 @@ -(function (angular) { - 'use strict'; - /** - * @memberof spApp - * @ngdoc controller - * @name ExportBccvlCtrl - * @description - * Manage export of occurrence layers to BCCVL - */ - angular.module('export-bccvl-ctrl', ['map-service']).controller('ExportBccvlCtrl', ['$scope', 'MapService', - '$timeout', 'LayoutService', 'BiocacheService', '$window', '$uibModalInstance', 'SessionsService', '$http', - '$q', 'LoggerService', 'data', - function ($scope, MapService, $timeout, LayoutService, BiocacheService, $window, $uibModalInstance, - SessionsService, $http, $q, LoggerService, config) { - - $scope.stepNames = ['Select species']; - - $scope.isSpeciesList = false; - $scope.includeSpeciesList = true; - - $scope._httpDescription = function (method, httpconfig) { - if (httpconfig === undefined) { - httpconfig = {}; - } - httpconfig.service = 'ExportBccvlCtrl'; - httpconfig.method = method; - - return httpconfig; - }; - - if (config && config.selectedQ) { - $scope.selectedQs = config.selectedQs - } else { - $scope.selectedQs = [] - } - - if (config && config.step) { - $scope.step = config.step - } else { - $scope.step = 1 - } - - $scope.bccvlOpenUrl = ''; - - LayoutService.addToSave($scope); - - $scope.setQ = function (query) { - if (query.species_list) { - $scope.isSpeciesList = true; - } - }; - - $scope.ok = function () { - if ($scope.step === 1) { - $scope.step = $scope.step + 1 - } else if ($scope.step === 2) { - var promises = []; - var url = $SH.bccvlPostUrl; - var data = []; - $.each($scope.selectedQs, function (i) { - var q = $scope.selectedQs[i]; - promises.push(BiocacheService.registerQuery(q).then(function (response) { - if (response == null) { - return $q.when(false) - } - return BiocacheService.facet('taxon_name', response).then(function (facets) { - if ($scope.includeSpeciesList && q.species_list) { - var species = []; - facets && facets.forEach(function (facet) { - if (facet && facet.count > 0 && facet.name) { - speices.push(facet.name) - } - }); - - data.push({ - name: q.name, - query: response.qid, - url: q.bs, - trait: q.species_list, - species_list: species - }); - } else { - data.push({name: q.name, query: response.qid, url: q.bs}); - } - - return true - }) - })); - }); - $q.all(promises).then(function () { - var authorizationToken = "Bearer " + window.location.hash.split('&')[0].split('=')[1]; - var config = {headers: {Accept: 'application/json', Authorization: authorizationToken}}; - - $http.post(url, {data: data}, $scope._httpDescription('export', config)).then(function (response) { - $scope.bccvlOpenUrl = response.headers('location'); - - LoggerService.log('Export', 'exportBccvl', JSON.stringify({ - data: data, - bccvlOpenUrl: $scope.bccvlOpenUrl - })) - }); - }); - $scope.step = $scope.step + 1 - } - }; - - $scope.isDisabled = function () { - return $scope.selectedQs.length === 0; - }; - - $scope.bccvlLogin = function () { - var bccvlExportTool = encodeURIComponent("&tool=exportBccvl&toolParameters=" + encodeURIComponent('{"step":2}')); - - //save session and open BCCVL login page - SessionsService.saveAndLogin(SessionsService.current(), $SH.bccvlLoginUrl + '$url' + bccvlExportTool, true, true) - }; - - if ($scope.step === 1) { - $scope.bccvlLogin() - } - }]) -}(angular)); \ No newline at end of file diff --git a/grails-app/assets/javascripts/spApp/controller/leafletMapController.js b/grails-app/assets/javascripts/spApp/controller/leafletMapController.js index f1baf505..561cf084 100644 --- a/grails-app/assets/javascripts/spApp/controller/leafletMapController.js +++ b/grails-app/assets/javascripts/spApp/controller/leafletMapController.js @@ -484,7 +484,7 @@ if (data[pt] instanceof Array) { g = [data[pt][1], data[pt][2]]; } else { - g = data[pt].geometry.replace("POINT(", "").replace(")", "").split(" "); + g = data[pt].geometry.replace("POINT (", "").replace(")", "").split(" "); } var m = L.marker([g[1], g[0]]) .bindLabel(data[pt].name, {noHide: true}); @@ -772,4 +772,4 @@ }, 0) }]) -}(angular)); \ No newline at end of file +}(angular)); diff --git a/grails-app/assets/javascripts/spApp/controller/toolCtrl.js b/grails-app/assets/javascripts/spApp/controller/toolCtrl.js index a1f5059e..968b8d8b 100644 --- a/grails-app/assets/javascripts/spApp/controller/toolCtrl.js +++ b/grails-app/assets/javascripts/spApp/controller/toolCtrl.js @@ -159,7 +159,6 @@ selected: false }) } - // } else if (value.type === 'phylogeneticTree') { // } else if (value.type === 'text') { } else if (value.type === 'speciesOptions') { if (value.constraints['areaIncludes'] === undefined) value.constraints['areaIncludes'] = false; @@ -211,12 +210,12 @@ if (value.constraints['defaultToWorld'] === undefined) value.constraints['defaultToWorld'] = true; if (value.constraints['max'] === undefined) value.constraints['max'] = 1000; - if (value.constraints['default'] !== undefined) { + if (value.constraints['defaultValue'] !== undefined) { // getInputs returns the .area array which is inconsistent with the value - if (value.constraints['default'] instanceof Array) { - v = {area: value.constraints['default']} + if (value.constraints['defaultValue'] instanceof Array) { + v = {area: value.constraints['defaultValue']} } else { - v = value.constraints['default'] + v = value.constraints['defaultValue'] } } else { v = {area: []} @@ -234,7 +233,7 @@ if (value.constraints['searchSpecies'] === undefined) value.constraints['searchSpecies'] = true; if (value.constraints['allSpecies'] === undefined) value.constraints['allSpecies'] = true; - if (value.constraints['default'] !== undefined) v = value.constraints['default']; + if (value.constraints['defaultValue'] !== undefined) v = value.constraints['defaultValue']; else if (value.constraints['speciesOption'] === 'allSpecies') { //specify allSpecies default v = { @@ -253,50 +252,47 @@ } else if (value.type === 'date') { v = {fq: []} } else if (value.type === 'layer') { - if (value.constraints['default'] !== undefined) { + if (value.constraints['defaultValue'] !== undefined) { // getInputs returns the .area array which is inconsistent with the value - if (value.constraints['default'] instanceof Array) { + if (value.constraints['defaultValue'] instanceof Array) { v = {layers: []}; - $.map(value.constraints['default'], function (layer) { + $.map(value.constraints['defaultValue'], function (layer) { v.layers.push(LayersService.getLayer(layer)) }) } else { - v = LayersService.getLayer(value.constraints['default']); + v = LayersService.getLayer(value.constraints['defaultValue']); } } else v = {layers: []} } else if (value.type === 'boolean') { - v = value.constraints['default'] + v = value.constraints['defaultValue'] } else if (value.type === 'int') { - v = value.constraints['default'] + v = value.constraints['defaultValue'] } else if (value.type === 'double') { - v = value.constraints['default'] + v = value.constraints['defaultValue'] } else if (value.type === 'list') { if (value.constraints.selection !== 'single') { - v = value.constraints['default']; + v = value.constraints['defaultValue']; if (v == undefined) { v = []; } } else { - v = value.constraints['default']; + v = value.constraints['defaultValue']; } - } else if (value.type === 'phylogeneticTree') { - if (value.constraints['default'] !== undefined) v = value.constraints['default']; - else v = [] } else if (value.type === 'text') { - v = value.constraints['default'] + v = value.constraints['defaultValue'] } else if (value.type === 'speciesOptions') { if (value.constraints['areaIncludes'] === undefined) value.constraints['areaIncludes'] = false; if (value.constraints['kosherIncludes'] === undefined) value.constraints['kosherIncludes'] = true; if (value.constraints['endemicIncludes'] === undefined) value.constraints['endemicIncludes'] = false; - if (value.constraints['default'] !== undefined) v = value.constraints['default']; + if (value.constraints['defaultValue'] !== undefined) v = value.constraints['defaultValue']; else v = {} } else if (value.type === 'facet') { - if (value.constraints['default'] !== undefined) v = value.constraints['default']; + if (value.constraints['defaultValue'] !== undefined) v = value.constraints['defaultValue']; else v = [] - } else if (value.constraints !== undefined && value.constraints['default'] !== undefined) { - v = value.constraints['default'] + } else if (value.constraints !== undefined && value.constraints['defaultValue'] !== undefined) { + v = value.constraints['defaultValue'] } else { v = null } @@ -351,8 +347,6 @@ return $scope.values[i] === undefined } else if (value.type === 'list' && value.constraints.selection !== 'single') { return $scope.values[i].length === 0 - } else if (value.type === 'phylogeneticTree') { - return $scope.values[i].length === 0 } else if (value.type === 'text') { return $scope.values[i] < value.constraints.min || $scope.values[i] > value.constraints.max } else if (value.type === 'speciesOptions') { @@ -523,4 +517,4 @@ } }]) -}(angular)); \ No newline at end of file +}(angular)); diff --git a/grails-app/assets/javascripts/spApp/controller/workflowCtrl.js b/grails-app/assets/javascripts/spApp/controller/workflowCtrl.js index 2a86fd91..3a1df05c 100644 --- a/grails-app/assets/javascripts/spApp/controller/workflowCtrl.js +++ b/grails-app/assets/javascripts/spApp/controller/workflowCtrl.js @@ -170,7 +170,7 @@ var input = [] $.map(item.data, function (v, k) { - input[k] = {constraints: {default: v}} + input[k] = {constraints: {defaultValue: v}} }) var ov = {}; @@ -366,4 +366,4 @@ $scope.editing = -1; } }]) -}(angular)); \ No newline at end of file +}(angular)); diff --git a/grails-app/assets/javascripts/spApp/directive/envelope.js b/grails-app/assets/javascripts/spApp/directive/envelope.js index 64ff0b37..ee059abd 100644 --- a/grails-app/assets/javascripts/spApp/directive/envelope.js +++ b/grails-app/assets/javascripts/spApp/directive/envelope.js @@ -38,7 +38,7 @@ input: { envelope: { constraints: { - 'default': scope.getFq() + 'defaultValue': scope.getFq() } } } @@ -192,4 +192,4 @@ }; }]) -}(angular)); \ No newline at end of file +}(angular)); diff --git a/grails-app/assets/javascripts/spApp/directive/leafletQuickLinks.js b/grails-app/assets/javascripts/spApp/directive/leafletQuickLinks.js index 20a85ad9..d7a0e815 100644 --- a/grails-app/assets/javascripts/spApp/directive/leafletQuickLinks.js +++ b/grails-app/assets/javascripts/spApp/directive/leafletQuickLinks.js @@ -11,7 +11,7 @@ * IS" basis, WITHOUT WARRANTY OF ANY KIND, either express or * implied. See the License for the specific language governing * rights and limitations under the License. - * + * * Created by Temi on 8/09/2016. */ (function (angular) { @@ -45,7 +45,7 @@ if (data.overrideValues.input === undefined) data.overrideValues.input = {}; if (data.overrideValues.input[key] === undefined) data.overrideValues.input[key] = {}; if (data.overrideValues.input[key].constraints === undefined) data.overrideValues.input[key].constraints = {}; - data.overrideValues.input[key].constraints['default'] = value; + data.overrideValues.input[key].constraints['defaultValue'] = value; }; $scope.open = function (name, data, includeSpecies, includeArea) { @@ -227,4 +227,4 @@ }] } }]) -}(angular)); \ No newline at end of file +}(angular)); diff --git a/grails-app/assets/javascripts/spApp/directive/nearestLocality.js b/grails-app/assets/javascripts/spApp/directive/nearestLocality.js index 491ea1ad..14d7b2c1 100644 --- a/grails-app/assets/javascripts/spApp/directive/nearestLocality.js +++ b/grails-app/assets/javascripts/spApp/directive/nearestLocality.js @@ -128,7 +128,7 @@ var header = $i18n(409, "Longitude") + "," + scope.point.longitude + "\n" + $i18n(410, "Latitude") + "," + scope.point.latitude + "\n\n" + - $i18n(160, "Feature") + "," + $i18n(161, "Location") + "," + $i18n(162, "Distance (km)") + "," + $i18n(163, "Heading (deg)"); + $i18n(160, "Feature") + "," + $i18n(161, "Location") + "," + $i18n(162, "Distance (m)") + "," + $i18n(163, "Heading (deg)"); var blob = new Blob([header + rows], {type: 'text/plain'}); scope.exportUrl = (window.URL || window.webkitURL).createObjectURL(blob); @@ -173,4 +173,4 @@ } } }]) -}(angular)); \ No newline at end of file +}(angular)); diff --git a/grails-app/assets/javascripts/spApp/directive/selectArea.js b/grails-app/assets/javascripts/spApp/directive/selectArea.js index a3c8488e..c8f3d87d 100644 --- a/grails-app/assets/javascripts/spApp/directive/selectArea.js +++ b/grails-app/assets/javascripts/spApp/directive/selectArea.js @@ -17,7 +17,8 @@ _selectedArea: '=selectedArea', _includeDefaultAreas: '=includeDefaultAreas', _uniqueId: '=uniqueId', - _defaultToWorld: '=?defaultToWorld' + _defaultToWorld: '=?defaultToWorld', + _excludeWorld: '=?excludeWorld' }, link: function (scope, element, attrs) { @@ -63,7 +64,7 @@ scope.defaultAreas = []; if (scope._includeDefaultAreas !== false) { - scope.defaultAreas = $.map(PredefinedAreasService.getList(), function (x, idx) { + scope.defaultAreas = $.map(PredefinedAreasService.getList(scope._excludeWorld), function (x, idx) { return x }) } @@ -115,4 +116,4 @@ } }]) -}(angular)); \ No newline at end of file +}(angular)); diff --git a/grails-app/assets/javascripts/spApp/directive/selectFacet.js b/grails-app/assets/javascripts/spApp/directive/selectFacet.js index 10a88965..6fcba39c 100644 --- a/grails-app/assets/javascripts/spApp/directive/selectFacet.js +++ b/grails-app/assets/javascripts/spApp/directive/selectFacet.js @@ -34,16 +34,16 @@ }); //Watch special options update - //fq=geospatial_kosher:true&fq=-occurrence_status:absent + //fq=spatiallyValid:true&fq=-occurrence_status:absent scope.$on("speciesOptionsChange",function (event, value) { scope.fqsOfSpeciesOptions = []; /* - spatially-valid = geospatial_kosher:true - spatially-suspect = geospatial_kosher:false - spatially-unknown = -geospatial_kosher:* + spatially-valid = spatiallyValid:true + spatially-suspect = spatiallyValid:false + spatially-unknown = -spatiallyValid:* If we want include VALID and MISSING(UNKNOWN) spatial data - fq=(geospatial_kosher:true OR -geospatial_kosher:*) BS(solr) does not support '-' in complicated query + fq=(spatiallyValid:true OR -spatiallyValid:*) BS(solr) does not support '-' in complicated query */ if (value.spatiallyUnknown) { //include UNKNOWN (MISSING) spatial data records @@ -53,20 +53,20 @@ } else if (value.spatiallyValid) { //spatially-unknown && spatiallyValid //-> rule out of spatiallySuspect - scope.fqsOfSpeciesOptions.push('-geospatial_kosher:false'); + scope.fqsOfSpeciesOptions.push('-spatiallyValid:false'); }else if (value.spatiallySuspect) { //spatially-unknown && spatiallySuspect //-> rule out of spatiallyValid - scope.fqsOfSpeciesOptions.push('-geospatial_kosher:true'); + scope.fqsOfSpeciesOptions.push('-spatiallyValid:true'); } } else { //spatially-valid and spatially-suspect if (value.spatiallyValid && value.spatiallySuspect) { - scope.fqsOfSpeciesOptions.push('geospatial_kosher:*'); + scope.fqsOfSpeciesOptions.push('spatiallyValid:*'); } else if (value.spatiallyValid) { - scope.fqsOfSpeciesOptions.push('geospatial_kosher:true'); + scope.fqsOfSpeciesOptions.push('spatiallyValid:true'); } else if (value.spatiallySuspect) { - scope.fqsOfSpeciesOptions.push('geospatial_kosher:false'); + scope.fqsOfSpeciesOptions.push('spatiallyValid:false'); } } @@ -413,4 +413,4 @@ } } }]) -}(angular)); \ No newline at end of file +}(angular)); diff --git a/grails-app/assets/javascripts/spApp/directive/selectMultipleArea.js b/grails-app/assets/javascripts/spApp/directive/selectMultipleArea.js index 24166598..c7dd7ae2 100644 --- a/grails-app/assets/javascripts/spApp/directive/selectMultipleArea.js +++ b/grails-app/assets/javascripts/spApp/directive/selectMultipleArea.js @@ -103,11 +103,29 @@ a.splice(i, 1); } } + scope.pickInOutLayerName = ""; + scope.pickInOutLayerVisible = true; }; + scope.updatePickInOutLayer = function () { + if (!scope.pickInOutLayer) { + scope.removeInOutLayer() + } + } + + scope.updatePickContextualLayer = function () { + if (!scope.pickContextualLayer) { + scope.removeContextualLayer() + } + } + + scope.removeInOut = true scope.$watch('selectedInOutLayer.layers.length', function (newValue, oldValue) { //remove all inOutLayers - scope.removeInOutLayer(); + if (scope.removeInOut) { + scope.removeInOutLayer(); + } + scope.removeInOut = true; //add selected var a = scope.selectedInOutLayer.layers; @@ -134,19 +152,19 @@ }; scope._selectedArea.area.push(areaOut); + scope.removeInOut = false scope.selectedInOutLayer.layers.splice(0, scope.selectedInOutLayer.layers.length); } }); scope.updateSelection = function (area) { - if (!area) { - if (!scope.pickInOutLayer) { - scope.removeInOutLayer(); - } - if (!scope.pickContextualLayer) { - scope.removeContextualLayer(); - } - } else { + if (!scope.pickInOutLayer) { + scope.removeInOutLayer(); + } + if (!scope.pickContextualLayer) { + scope.removeContextualLayer(); + } + if (area) { if (area.selected) { scope._selectedArea.area.push(area) } else { @@ -172,11 +190,17 @@ a.splice(i, 1); } } + scope.pickContextualLayerName = ""; + scope.pickContextualLayerVisible = true; }; + scope.removeContextual = true scope.$watch('selectedLayer.layers.length', function (newValue, oldValue) { //remove all inOutLayers - scope.removeContextualLayer(); + if (scope.removeContextual) { + scope.removeContextualLayer(); + } + scope.removeContextual = true; //add selected var a = scope.selectedLayer.layers; @@ -196,6 +220,7 @@ //TODO: Make the corresponding spatial-service change to recognise this aggregation. scope._selectedArea.area.push(area); + scope.removeContextual = false scope.selectedLayer.layers.splice(0, scope.selectedLayer.layers.length); } }); @@ -227,4 +252,4 @@ } }]) -}(angular)); \ No newline at end of file +}(angular)); diff --git a/grails-app/assets/javascripts/spApp/directive/selectPhylo.js b/grails-app/assets/javascripts/spApp/directive/selectPhylo.js deleted file mode 100644 index 87f8afd3..00000000 --- a/grails-app/assets/javascripts/spApp/directive/selectPhylo.js +++ /dev/null @@ -1,83 +0,0 @@ -(function (angular) { - 'use strict'; - /** - * @memberof spApp - * @ngdoc directive - * @name selectPhylo - * @description - * Table with selectable phylogenetic trees from phylolink - */ - angular.module('select-phylo-directive', ['phylo-service']) - .directive('selectPhylo', ['$http', 'PhyloService', 'LayoutService', '$timeout', - function ($http, PhyloService, LayoutService, $timeout) { - - return { - templateUrl: '/spApp/selectPhyloCtrl.htm', - scope: { - _selection: "=selectedPhylo" - }, - link: function (scope, element, attrs) { - - scope.name = 'selectPhylo'; - LayoutService.addToSave(scope); - - scope.trees = []; - scope.loading = true; - - scope.change = function (tree) { - if (tree.checked) { - var found = false; - for (var k in scope._selection) { - if (scope._selection.hasOwnProperty(k)) { - if (scope._selection[k].id === tree.id) { - found = true - } - } - } - if (!found) scope._selection.push(tree.id) - } else { - for (k in scope._selection) { - if (scope._selection.hasOwnProperty(k)) { - if (scope._selection[k].id === tree.id) { - scope._selection.splice(k, 1) - } - } - } - } - }; - - scope.clearSelection = function () { - for (var i in scope.trees) { - scope.trees[i].selected = false - } - while (scope._selection.length) { - scope._selection.pop() - } - }; - - - scope.init = function () { - PhyloService.getExpertTrees().then(function (data) { - for (var k in data.data) { - if (data.data.hasOwnProperty(k)) { - scope.trees.push({ - id: data.data[k].studyId, - group: data.data[k].focalClade, - name: data.data[k].studyName, - leaves: data.data[k].numberOfLeaves, - checked: false - }) - } - } - }).finally(function () { - scope.loading = false; - }); - - }; - - $timeout(scope.init, 0); - } - } - }]) -}(angular)); - diff --git a/grails-app/assets/javascripts/spApp/directive/selectSpecies.js b/grails-app/assets/javascripts/spApp/directive/selectSpecies.js index 6eea7e59..175ee5b4 100644 --- a/grails-app/assets/javascripts/spApp/directive/selectSpecies.js +++ b/grails-app/assets/javascripts/spApp/directive/selectSpecies.js @@ -236,12 +236,12 @@ if (pos >= 0) query.q.splice(pos, 1) } /* - spatially-valid = geospatial_kosher:true - spatially-suspect = geospatial_kosher:false - spatially-unknown = -geospatial_kosher:* + spatially-valid = spatiallyValid:true + spatially-suspect = spatiallyValid:false + spatially-unknown = -spatiallyValid:* If we want include VALID and MISSING(UNKNOWN) spatial data - fq=(geospatial_kosher:true OR -geospatial_kosher:*) BS(solr) does not support '-' in complicated query + fq=(spatiallyValid:true OR -spatiallyValid:*) BS(solr) does not support '-' in complicated query */ var gs = ["-*:*"]; // select nothing if (scope.spatiallyUnknown) { //include UNKNOWN (MISSING) spatial data records @@ -251,23 +251,23 @@ } else if (scope.spatiallyValid) { // spatially-unknown && spatiallyValid // Solution -> rule out of spatiallySuspect - gs = ['-geospatial_kosher:false']; + gs = ['-spatiallyValid:false']; } else if (scope.spatiallySuspect) { // spatially-unknown && spatiallySuspect // -> rule out of spatiallyValid - gs = ['-geospatial_kosher:true']; + gs = ['-spatiallyValid:true']; } else { //return records without spatial - gs = ['-geospatial_kosher:*']; + gs = ['-spatiallyValid:*']; } } else { //spatially-valid and spatially-suspect if (scope.spatiallyValid && scope.spatiallySuspect) { - gs = ['geospatial_kosher:*']; + gs = ['spatiallyValid:*']; } else if (scope.spatiallyValid){ - gs = ['geospatial_kosher:true']; + gs = ['spatiallyValid:true']; } else if (scope.spatiallySuspect){ - gs = ['geospatial_kosher:false']; + gs = ['spatiallyValid:false']; } else { // No records returned by default } @@ -490,4 +490,4 @@ } }]) -}(angular)); \ No newline at end of file +}(angular)); diff --git a/grails-app/assets/javascripts/spApp/directive/spLegend.js b/grails-app/assets/javascripts/spApp/directive/spLegend.js index e1f49b8a..57b2880f 100644 --- a/grails-app/assets/javascripts/spApp/directive/spLegend.js +++ b/grails-app/assets/javascripts/spApp/directive/spLegend.js @@ -302,7 +302,7 @@ var selectedStyle = currentLayer.style //Raster style - if(selectedStyle == 'non-linear') selectedStyle = currentLayer.defaultStyle //e.g geomacs_gmean + if (selectedStyle == 'non-linear') selectedStyle = currentLayer.defaultStyle //e.g geomacs_gmean if (selectedStyle == 'linear') selectedStyle = currentLayer.defaultStyle + '_linear' //Vector sytle if (selectedStyle == 'default') selectedStyle = currentLayer.defaultStyle //e.g cl1084 @@ -1287,4 +1287,4 @@ } }]) -}(angular)); \ No newline at end of file +}(angular)); diff --git a/grails-app/assets/javascripts/spApp/directive/spMenu.js b/grails-app/assets/javascripts/spApp/directive/spMenu.js index 5dd03f42..3d3f19ee 100644 --- a/grails-app/assets/javascripts/spApp/directive/spMenu.js +++ b/grails-app/assets/javascripts/spApp/directive/spMenu.js @@ -70,7 +70,7 @@ scope.exportMap = function () { scope.open('tool', { processName: 'ToolExportMapService', - overrideValues: {ToolExportMapService: {input: {caption: {constraints: {default: (new Date())}}}}} + overrideValues: {ToolExportMapService: {input: {caption: {constraints: {defaultValue: (new Date())}}}}} }) }; @@ -79,4 +79,4 @@ } }; }]) -}(angular)); \ No newline at end of file +}(angular)); diff --git a/grails-app/assets/javascripts/spApp/service/biocacheService.js b/grails-app/assets/javascripts/spApp/service/biocacheService.js index e86caa7a..17452443 100644 --- a/grails-app/assets/javascripts/spApp/service/biocacheService.js +++ b/grails-app/assets/javascripts/spApp/service/biocacheService.js @@ -38,7 +38,7 @@ * "ws": "https://biocache.ala.org.au" * } * - fqs - * ["geospatial_kosher:true"] + * ["spatiallyValid:true"] * * Ouput: * 10 @@ -74,7 +74,7 @@ * "ws": "https://biocache.ala.org.au" * } * - fqs - * ["geospatial_kosher:true"] + * ["spatiallyValid:true"] * * Ouput: * 2 @@ -115,7 +115,7 @@ * "ws": "https://biocache.ala.org.au" * } * - fqs - * ["geospatial_kosher:true"] + * ["spatiallyValid:true"] * - config * Ouput: * "names_and_lsid","Species Name","Scientific Name Authorship","Taxon Rank","Kingdom","Phylum","Class","Order","Family","Genus","Vernacular Name","Number of records","Conservation","Invasive" @@ -148,10 +148,10 @@ * "ws": "https://biocache.ala.org.au" * } * - fqs - * ["geospatial_kosher:true"] + * ["spatiallyValid:true"] * * Output: - * "https://biocache-ws.ala.org.au/ws/occurrences/facets/download?facets=names_and_lsid&lookup=true&count=true&lists=true&q=Macropus&fq=geospatial_kosher:true" + * "https://biocache-ws.ala.org.au/ws/occurrences/facets/download?facets=names_and_lsid&lookup=true&count=true&lists=true&q=Macropus&fq=spatiallyValid:true" */ speciesListUrl: function (query, fqs) { var fqList = (fqs === undefined ? '' : '&fq=' + this.joinAndEncode(fqs)); @@ -178,7 +178,7 @@ * "ws": "https://biocache.ala.org.au" * } * - fqs - * ["geospatial_kosher:true"] + * ["spatiallyValid:true"] * * Output: * ``` @@ -213,7 +213,7 @@ * "ws": "https://biocache.ala.org.au" * } * - fqs - * ["geospatial_kosher:true"] + * ["spatiallyValid:true"] * * Output: * "http://biocache.ala.org.au/ws/explore/endemic/species/1234.csv?facets=names_and_lsid&lookup=true&count=true&lists=true" @@ -251,7 +251,7 @@ * "ws": "https://biocache.ala.org.au" * } * - fqs - * ["geospatial_kosher:true"] + * ["spatiallyValid:true"] * * Output: * [] @@ -284,7 +284,7 @@ * "ws": "https://biocache.ala.org.au" * } * - fqs - * ["geospatial_kosher:true"] + * ["spatiallyValid:true"] * * Output: * 500 @@ -322,7 +322,7 @@ * "ws": "https://biocache.ala.org.au" * } * - fqs - * ["geospatial_kosher:true"] + * ["spatiallyValid:true"] * * Output: * "Macropus" @@ -364,10 +364,10 @@ * "ws": "https://biocache.ala.org.au" * } * - fqs - * ["geospatial_kosher:true"] + * ["spatiallyValid:true"] * * Output: - * "http://biocache-ws.ala.org.au/ws/occurrences/search?q=Macropus&fq=geospatial_kosher:true&pageSize=1&offset=0&facet=false" + * "http://biocache-ws.ala.org.au/ws/occurrences/search?q=Macropus&fq=spatiallyValid:true&pageSize=1&offset=0&facet=false" */ constructSearchResultUrl: function (query, fqs, pageSize, offset, facet) { facet = facet || false; diff --git a/grails-app/assets/javascripts/spApp/service/flickrService.js b/grails-app/assets/javascripts/spApp/service/flickrService.js index 00db59d6..60b1d4f2 100644 --- a/grails-app/assets/javascripts/spApp/service/flickrService.js +++ b/grails-app/assets/javascripts/spApp/service/flickrService.js @@ -21,15 +21,16 @@ return { getPhotos: function (bbox) { var url = $SH.flickrUrl + $SH.flickrSearchPhotos - + '&api_key=' + $SH.flickrApiKey + '&extras=' + encodeURIComponent($SH.flickrExtra) - + '&tags=' + encodeURIComponent($SH.flickrTags) - + '&geo_context=' + encodeURIComponent($SH.flickrGeoContext) - + '&content_type=' + encodeURIComponent($SH.flickrContentType) - + $SH.flickrFilter + + '&api_key=' + $SH.flickrApiKey + '&per_page=' + $SH.flickrNbrOfPhotosToDisplay - + '&format=json&nojsoncallback=1&bbox='; + + '&format=json&nojsoncallback=1&bbox=' + bbox; + if ($SH.flickrExtra != '') url += '&extras=' + encodeURIComponent($SH.flickrExtra) + if ($SH.flickrTags != '') url += '&tags=' + encodeURIComponent($SH.flickrTags) + if ($SH.flickrGeoContext != '') url += '&geo_context=' + encodeURIComponent($SH.flickrGeoContext) + if ($SH.flickrContentType != '') url += '&content_type=' + encodeURIComponent($SH.flickrContentType) + if ($SH.flickrFilter != '') url += $SH.flickrFilter - return $http.get(url + bbox, _httpDescription('getPhotos')).then(function (response) { + return $http.get(url, _httpDescription('getPhotos')).then(function (response) { return response.data; }); }, diff --git a/grails-app/assets/javascripts/spApp/service/layersService.js b/grails-app/assets/javascripts/spApp/service/layersService.js index 2faa6705..9961e79d 100644 --- a/grails-app/assets/javascripts/spApp/service/layersService.js +++ b/grails-app/assets/javascripts/spApp/service/layersService.js @@ -561,4 +561,4 @@ return thiz; }]) -}(angular)); \ No newline at end of file +}(angular)); diff --git a/grails-app/assets/javascripts/spApp/service/mapService.js b/grails-app/assets/javascripts/spApp/service/mapService.js index 9250af8d..537a1f97 100644 --- a/grails-app/assets/javascripts/spApp/service/mapService.js +++ b/grails-app/assets/javascripts/spApp/service/mapService.js @@ -731,9 +731,12 @@ var url = layer.layer.displaypath url = url.replace(/\?.*/, '') + var source = 'analysis' if (layer.id.startsWith("el") || id.layertype == 'gridAsContextual') { + source = 'environmental' id.defaultStyle = layer.layer.name } else if (layer.id.startsWith("cl")) { + source = 'contextual' id.defaultStyle = layer.id } @@ -751,14 +754,17 @@ opacity: id.opacity / 100.0, url: url, layertype: id.layertype, + source: source, layerParams: { opacity: id.opacity / 100.0, layers: 'ALA:' + layer.layer.name, format: 'image/png', - transparent: true, - styles: style + transparent: true } }; + if (source != 'analysis' && !style) { + newLayer.layerParams.styles = style || id.id + } if (id.layertype === 'scatterplotEnvelope') { var layer2 = LayersService.getLayer(id.layer2); @@ -1014,4 +1020,4 @@ return MapService }]) -}(angular)); \ No newline at end of file +}(angular)); diff --git a/grails-app/assets/javascripts/spApp/service/phyloService.js b/grails-app/assets/javascripts/spApp/service/phyloService.js deleted file mode 100644 index a0647e0f..00000000 --- a/grails-app/assets/javascripts/spApp/service/phyloService.js +++ /dev/null @@ -1,58 +0,0 @@ -(function (angular) { - 'use strict'; - /** - * @memberof spApp - * @ngdoc service - * @name PhyloService - * @description - * Access to phylolink services - */ - angular.module('phylo-service', []) - .factory('PhyloService', ['$http', function ($http) { - - var _httpDescription = function (method, httpconfig) { - if (httpconfig === undefined) { - httpconfig = {}; - } - httpconfig.service = 'PhyloService'; - httpconfig.method = method; - - return httpconfig; - }; - - return { - /** - * Get phylolink tree list - * - * @memberof PhyloService - * @returns {List} list of public expert trees - * - * @example: - * Output: - * [{ - "studyId": 92, - "focalClade": "Acacia", - "treeFormat": "newick", - "studyName": "Miller, J. T., Murphy, D. J., Brown, G. K., Richardson, D. M. and González-Orozco, C. E. (2011), The evolution and phylogenetic placement of invasive Australian Acacia species. Diversity and Distributions, 17: 848–860. doi: 10.1111/j.1472-4642.2011.00780.x", - "year": 2011, - "authors": "Acacia – Miller et al 2012", - "doi": "http://onlinelibrary.wiley.com/doi/10.1111/j.1472-4642.2011.00780.x/full", - "numberOfLeaves": 510, - "numberOfInternalNodes": 509, - "treeId": null, - "notes": null, - "treeViewUrl": "http://phylolink.ala.org.au/phylo/getTree?studyId=92&treeId=null" - }] - */ - getExpertTrees: function () { - //TODO: add parameter to exclude "tree" - var url = $SH.phylolinkUrl + "/phylo/getExpertTrees?noTreeText=true"; - return $http.get(url, _httpDescription('search', { - headers: { - 'Content-Type': 'application/json' - } - })) - } - }; - }]) -}(angular)); \ No newline at end of file diff --git a/grails-app/assets/javascripts/spApp/service/predefinedAreasService.js b/grails-app/assets/javascripts/spApp/service/predefinedAreasService.js index 2fb967da..e029d5b9 100644 --- a/grails-app/assets/javascripts/spApp/service/predefinedAreasService.js +++ b/grails-app/assets/javascripts/spApp/service/predefinedAreasService.js @@ -15,13 +15,13 @@ * * @returns {Array.} list of default areas. */ - getList: function () { + getList: function (excludeWorld) { var extents = MapService.getExtents(); var defaultAreas = []; for (var i in $SH.defaultAreas) { - if ($SH.defaultAreas.hasOwnProperty(i)) { + if ($SH.defaultAreas.hasOwnProperty(i) && (!excludeWorld || $SH.defaultAreas[i].name != 'World')) { var area = $SH.defaultAreas[i]; var geoArea = undefined if (area.areaSqKm) { @@ -53,4 +53,4 @@ } }]) -}(angular)); \ No newline at end of file +}(angular)); diff --git a/grails-app/assets/javascripts/spApp/service/predefinedLayerListsService.js b/grails-app/assets/javascripts/spApp/service/predefinedLayerListsService.js index 4edca5a0..ecd446b9 100644 --- a/grails-app/assets/javascripts/spApp/service/predefinedLayerListsService.js +++ b/grails-app/assets/javascripts/spApp/service/predefinedLayerListsService.js @@ -16,17 +16,9 @@ { label: "BIOCLIM 1960 best 5", value: "el882,el889,el887,el894,el865" - }, - { - label: "Williams 1960 best 5", - value: "el720,el726,el718,el766,el708" - }, - { - label: "Williams 2030 best 5", - value: "el1002,el1019,el1037,el1036,el1013" } ] } } }]) -}(angular)); \ No newline at end of file +}(angular)); diff --git a/grails-app/assets/javascripts/spApp/service/toolAddFacetService.js b/grails-app/assets/javascripts/spApp/service/toolAddFacetService.js index 102686b1..7fbdd5ca 100644 --- a/grails-app/assets/javascripts/spApp/service/toolAddFacetService.js +++ b/grails-app/assets/javascripts/spApp/service/toolAddFacetService.js @@ -52,12 +52,12 @@ var q = facet; if (speciesOptions.spatiallyUnknown) { if (speciesOptions.spatiallyValid && speciesOptions.spatiallySuspect) { /* do nothing */ - } else if (speciesOptions.spatiallyValid) q.push('-geospatial_kosher:false'); - else if (speciesOptions.spatiallySuspect) q.push('-geospatial_kosher:true'); + } else if (speciesOptions.spatiallyValid) q.push('-spatiallyValid:false'); + else if (speciesOptions.spatiallySuspect) q.push('-spatiallyValid:true'); } else { - if (speciesOptions.spatiallyValid && speciesOptions.spatiallySuspect) q.push('geospatial_kosher:*'); - else if (speciesOptions.spatiallyValid) q.push('geospatial_kosher:true'); - else if (speciesOptions.spatiallySuspect) q.push('geospatial_kosher:false'); + if (speciesOptions.spatiallyValid && speciesOptions.spatiallySuspect) q.push('spatiallyValid:*'); + else if (speciesOptions.spatiallyValid) q.push('spatiallyValid:true'); + else if (speciesOptions.spatiallySuspect) q.push('spatiallyValid:false'); } if (!speciesOptions.includeAbsences) { diff --git a/grails-app/assets/javascripts/spApp/service/toolAreaReportService.js b/grails-app/assets/javascripts/spApp/service/toolAreaReportService.js index e1c85200..589a702f 100644 --- a/grails-app/assets/javascripts/spApp/service/toolAreaReportService.js +++ b/grails-app/assets/javascripts/spApp/service/toolAreaReportService.js @@ -20,7 +20,8 @@ "constraints": { "min": 1, "max": 1, - "optional": false + "optional": false, + "excludeWorld": true } }], "description": $i18n("Area Report") diff --git a/grails-app/assets/javascripts/spApp/service/toolExportAreaService.js b/grails-app/assets/javascripts/spApp/service/toolExportAreaService.js index 2c3aff34..b7117efc 100644 --- a/grails-app/assets/javascripts/spApp/service/toolExportAreaService.js +++ b/grails-app/assets/javascripts/spApp/service/toolExportAreaService.js @@ -28,7 +28,7 @@ "description": $i18n(421,"Filetype."), "type": "list", "constraints": { - "default": "Shapefile", + "defaultValue": "Shapefile", "selection": "single", "content": [ "Shapefile", diff --git a/grails-app/assets/javascripts/spApp/service/toolExportChecklistService.js b/grails-app/assets/javascripts/spApp/service/toolExportChecklistService.js index 86042ced..571f2d81 100644 --- a/grails-app/assets/javascripts/spApp/service/toolExportChecklistService.js +++ b/grails-app/assets/javascripts/spApp/service/toolExportChecklistService.js @@ -8,8 +8,8 @@ * Client side tool to export list of species in an occurrence layer */ angular.module('tool-export-checklist-service', []) - .factory("ToolExportChecklistService", ["$http", "$q", "MapService", "BiocacheService", "LayoutService", - function ($http, $q, MapService, BiocacheService, LayoutService) { + .factory("ToolExportChecklistService", ["$http", "$q", "MapService", "BiocacheService", "LayoutService", "LayersService", + function ($http, $q, MapService, BiocacheService, LayoutService, LayersService) { var _this = { // Override text with view-config.json spec: { @@ -52,19 +52,25 @@ var wkt = undefined; if (area[0].q && (area[0].q.length > 0)) { q = area[0].q - } else if (area[0].wkt.length > 0) { + } else if (area[0].wkt && area[0].wkt.length > 0) { q = ['*:*']; wkt = area[0].wkt; + } else { + LayersService.getWkt(area[0].pid).then(function (wkt) { + inputs[0][0].wkt = wkt.data + _this.execute(inputs) + }) + return } if (speciesOptions.spatiallyUnknown) { if (speciesOptions.spatiallyValid && speciesOptions.spatiallySuspect) { /* do nothing */ - } else if (speciesOptions.spatiallyValid) q.push('-geospatial_kosher:false'); - else if (speciesOptions.spatiallySuspect) q.push('-geospatial_kosher:true'); + } else if (speciesOptions.spatiallyValid) q.push('-spatiallyValid:false'); + else if (speciesOptions.spatiallySuspect) q.push('-spatiallyValid:true'); } else { - if (speciesOptions.spatiallyValid && speciesOptions.spatiallySuspect) q.push('geospatial_kosher:*'); - else if (speciesOptions.spatiallyValid) q.push('geospatial_kosher:true'); - else if (speciesOptions.spatiallySuspect) q.push('geospatial_kosher:false'); + if (speciesOptions.spatiallyValid && speciesOptions.spatiallySuspect) q.push('spatiallyValid:*'); + else if (speciesOptions.spatiallyValid) q.push('spatiallyValid:true'); + else if (speciesOptions.spatiallySuspect) q.push('spatiallyValid:false'); } if (!speciesOptions.includeAbsences) { diff --git a/grails-app/assets/javascripts/spApp/service/toolExportMapService.js b/grails-app/assets/javascripts/spApp/service/toolExportMapService.js index 3e7fecc0..cc4cbfb5 100644 --- a/grails-app/assets/javascripts/spApp/service/toolExportMapService.js +++ b/grails-app/assets/javascripts/spApp/service/toolExportMapService.js @@ -28,7 +28,7 @@ "description": "Select an image format.", "type": "list", "constraints": { - "default": "png", + "defaultValue": "png", "selection": "single", "content": [ "png", @@ -88,13 +88,13 @@ data.overrideValues = { MapImage: { input: { - outputType: {constraints: {'default': outputType}}, - resolution: {constraints: {'default': resolution}}, - bbox: {constraints: {'default': bbox}}, - windowSize: {constraints: {'default': windowSize}}, - comment: {constraints: {'default': comment}}, - baseMap: {constraints: {'default': baseMap}}, - mapLayers: {constraints: {'default': mapLayers}} + outputType: {constraints: {'defaultValue': outputType}}, + resolution: {constraints: {'defaultValue': resolution}}, + bbox: {constraints: {'defaultValue': bbox}}, + windowSize: {constraints: {'defaultValue': windowSize}}, + comment: {constraints: {'defaultValue': comment}}, + baseMap: {constraints: {'defaultValue': baseMap}}, + mapLayers: {constraints: {'defaultValue': mapLayers}} } }, 'stage': 'execute' diff --git a/grails-app/assets/javascripts/spApp/service/toolExportSampleService.js b/grails-app/assets/javascripts/spApp/service/toolExportSampleService.js index 4e702026..969d741b 100644 --- a/grails-app/assets/javascripts/spApp/service/toolExportSampleService.js +++ b/grails-app/assets/javascripts/spApp/service/toolExportSampleService.js @@ -73,7 +73,7 @@ //include redirect to biocache-service/occurrences/search page var sampleUrl = _this.species.ws + '/download/options1?searchParams=' + - encodeURIComponent('q=' + query.qid) + + encodeURIComponent('?q=' + encodeURIComponent(query.qid)) + "&targetUri=/occurrences/search%3F&downloadType=records"; if (_this.layers && (_this.layers.length > 0)) { diff --git a/grails-app/assets/javascripts/spApp/service/toolsService.js b/grails-app/assets/javascripts/spApp/service/toolsService.js index 5f0e8970..00caee9f 100644 --- a/grails-app/assets/javascripts/spApp/service/toolsService.js +++ b/grails-app/assets/javascripts/spApp/service/toolsService.js @@ -213,7 +213,7 @@ displayname: name } }); - } else if (d.name === 'area') { + } else if (d.name === 'area' || d.name === 'AREA') { if (d.file.indexOf("{") === 0) { // parse JSON response // ENVELOPE is the only output of this type @@ -239,7 +239,7 @@ return MapService.add(data.data) })) } - } else if (d.name === 'species') { + } else if (d.name === 'species' || d.name === 'SPECIES') { var q = jQuery.parseJSON(d.file); if (!q.qid) { @@ -252,7 +252,7 @@ q.log = false // The task is logged, no need to log adding the layer promises.push(MapService.add(q)) - } else if (d.name === 'nextprocess') { + } else if (d.name === 'nextprocess' || d.name === 'NEXTPROCESS') { var nextinput = jQuery.parseJSON(d.file); // format 'nextprocess' output for LayoutService.openModal diff --git a/grails-app/assets/javascripts/spApp/service/urlParamsService.js b/grails-app/assets/javascripts/spApp/service/urlParamsService.js index 661df53b..0f34f321 100644 --- a/grails-app/assets/javascripts/spApp/service/urlParamsService.js +++ b/grails-app/assets/javascripts/spApp/service/urlParamsService.js @@ -22,17 +22,17 @@ * - ```ws```: biocache-hub URL for any layers added with this method. e.g. ```ws=https://biocache.ala.org.au``` * - ```bs```: biocache-service URL for any layers added with this method. e.g. ```bs=https://biocache.ala.org.au/ws``` * * Global to the whole session - * - ```wmscache```: ON/OFF for the current session (TODO: implement this) + * - ```wmscache```: ON/OFF for the current session * * Map control * - ```bbox```: zoom to this area with Min Lng, Min Lat, Max Lng, Max Lat. e.g. ```bbox=112,-42,154,-9``` * * Open a tool - * - ```tool```: name of tool to open. This can be any client side or spatial-service tool (TODO: support more than phylogeneticdiversity and exportBCCVL). e.g. ```tool=exportBCCVL``` + * - ```tool```: name of tool to open. This can be any client side or spatial-service tool * - ```toolParameters```: JSON Map of inputName:value for 'tool'. e.g. ```toolParameters={}``` * * Add one species layer * - ```qname```: display name for the 'q' layer. e.g. ```qname=My URL layer``` * - ```q```: biocache-service q term for occurrences layer to add. e.g. ```q=state:Queensland``` * - ```species_lsid```: LSID for occurrences layer to add. e.g. ```species_lsid=urn:lsid:biodiversity.org.au:afd.taxon:e6aff6af-ff36-4ad5-95f2-2dfdcca8caff``` - * - ```fq```: biocache-service fq term for occurrences layer to add. e.g. ```fq=geospatial_kosher:true``` + * - ```fq```: biocache-service fq term for occurrences layer to add. e.g. ```fq=spatiallyValid:true``` * - ```qc```: biocache-service fq term for occurrences layer to add. e.g. ```qc=data_hub_uid:dh1``` * - ```qualityProfile```: biocache-service qualityProfile param for data quality profile to apply * - ```disableAllQualityFilters```: biocache-service disableAllQualityFilters param to disable all data quality filters on this request @@ -275,9 +275,6 @@ var parameters = {}; if (toolParameters) parameters = JSON.parse(toolParameters); - if (tool === 'phylogeneticdiversity') { - //TODO: translate SpatialPortal phylogenetic diversity input parameters to SpatialHub format - } if (LayoutService.isPanel(tool)) { // is panel @@ -400,4 +397,4 @@ return _this; }]) -}(angular)); \ No newline at end of file +}(angular)); diff --git a/grails-app/assets/javascripts/spApp/templates/exportBccvlContent.tpl.htm b/grails-app/assets/javascripts/spApp/templates/exportBccvlContent.tpl.htm deleted file mode 100644 index c560c6d0..00000000 --- a/grails-app/assets/javascripts/spApp/templates/exportBccvlContent.tpl.htm +++ /dev/null @@ -1,53 +0,0 @@ -
- -

Export to BCCVL

-
- -
- -
-
-
- -
- -
- 1. {{stepNames[0]}} - - - - -
- -
- Include species traits (if available) -
-
- Export Status -
exporting to BCCVL ...
-
Finished uploading to BCCVL
-
- -
-
-
-
-
- -
- - - - - -
\ No newline at end of file diff --git a/grails-app/assets/javascripts/spApp/templates/legendContent.tpl.htm b/grails-app/assets/javascripts/spApp/templates/legendContent.tpl.htm index 14428831..2c14a786 100644 --- a/grails-app/assets/javascripts/spApp/templates/legendContent.tpl.htm +++ b/grails-app/assets/javascripts/spApp/templates/legendContent.tpl.htm @@ -26,12 +26,13 @@ -
- - -
+ + + + + + +
+ ng-show="selected.layer.layertype == 'grid' && selected.layer.id.startsWith('el')"> (2 areas) In/Out of a contextual layer + (2 areas) In/Out of a contextual layer
@@ -32,26 +32,27 @@ unique-id="inout">
-
-
-
-
- -
-

{{pickContextualLayerName}}

-
-
-
+ + + + + + + + + + + + + + + + +


-
\ No newline at end of file + diff --git a/grails-app/assets/javascripts/spApp/templates/selectPhyloCtrl.tpl.htm b/grails-app/assets/javascripts/spApp/templates/selectPhyloCtrl.tpl.htm deleted file mode 100644 index 650cd817..00000000 --- a/grails-app/assets/javascripts/spApp/templates/selectPhyloCtrl.tpl.htm +++ /dev/null @@ -1,22 +0,0 @@ -Loading... - - - - - - - - - - - - - - - - - - - -
Group# LeavesStudy nameStudy Id
{{tree.group}}{{tree.leaves}}{{tree.name}}{{tree.id}}
\ No newline at end of file diff --git a/grails-app/assets/javascripts/spApp/templates/selectSpeciesCtrl.tpl.htm b/grails-app/assets/javascripts/spApp/templates/selectSpeciesCtrl.tpl.htm index 74f71091..50e8bc49 100644 --- a/grails-app/assets/javascripts/spApp/templates/selectSpeciesCtrl.tpl.htm +++ b/grails-app/assets/javascripts/spApp/templates/selectSpeciesCtrl.tpl.htm @@ -17,7 +17,7 @@ -

Minimum one spatially related option is required! See this support article for more information

+

Minimum one spatially related option is required! See this support article for more information

diff --git a/grails-app/assets/javascripts/spApp/templates/speciesOptionsContent.tpl.htm b/grails-app/assets/javascripts/spApp/templates/speciesOptionsContent.tpl.htm index f719b696..6bbb42c8 100644 --- a/grails-app/assets/javascripts/spApp/templates/speciesOptionsContent.tpl.htm +++ b/grails-app/assets/javascripts/spApp/templates/speciesOptionsContent.tpl.htm @@ -18,7 +18,7 @@ -

Minimum one spatially related option is required! See this support article for more information

+

Minimum one spatially related option is required! See this support article for more information

@@ -56,4 +56,4 @@
- \ No newline at end of file + diff --git a/grails-app/assets/javascripts/spApp/templates/toolContent.tpl.htm b/grails-app/assets/javascripts/spApp/templates/toolContent.tpl.htm index 6d8c348d..2797bb57 100644 --- a/grails-app/assets/javascripts/spApp/templates/toolContent.tpl.htm +++ b/grails-app/assets/javascripts/spApp/templates/toolContent.tpl.htm @@ -32,7 +32,8 @@

{{stepCount[idx - 1] + $index + 1}}. {{sv.name !== u
+ default-to-world="v.constraints.defaultToWorld" + exclude-world="v.constraints.excludeWorld">
{{stepCount[idx - 1] + $index + 1}}. {{sv.name !== u
-
-
-
@@ -179,4 +176,4 @@

{{stepCount[idx - 1] + $index + 1}}. {{sv.name !== u -

\ No newline at end of file + diff --git a/grails-app/conf/application.yml b/grails-app/conf/application.yml index 365fc2c7..5aecf85e 100644 --- a/grails-app/conf/application.yml +++ b/grails-app/conf/application.yml @@ -129,12 +129,12 @@ endpoints: security: cas: uriFilterPattern: ['/alaAdmin/*', '/'] - casServerName: 'https://auth-dev.ala.org.au' + casServerName: 'https://auth-test.ala.org.au' uriExclusionFilterPattern: ['/portal/q/.*','/portal/messages/.*','/portal/sessionCache/.*','/static/.*','/assets/.*'] authenticateOnlyIfCookieFilterPattern: ['/portal/config/*','/portal/i18n/*','/hub/*', '/log/*'] - loginUrl: 'https://auth-dev.ala.org.au/cas/login' - logoutUrl: 'https://auth-dev.ala.org.au/cas/logout' - casServerUrlPrefix: 'https://auth-dev.ala.org.au/cas' + loginUrl: 'https://auth-test.ala.org.au/cas/login' + logoutUrl: 'https://auth-test.ala.org.au/cas/logout' + casServerUrlPrefix: 'https://auth-test.ala.org.au/cas' bypass: false # set to true for non-ALA deployment ignoreCase: true renew: false @@ -142,16 +142,18 @@ security: enabled: false oidc: enabled: true - discovery-uri: 'https://auth-dev.ala.org.au/cas/oidc/.well-known' + discovery-uri: 'https://auth-test.ala.org.au/cas/oidc/.well-known' clientId: 'change me' secret: 'change me' allowUnsignedIdTokens: true scope: 'openid profile email ala roles' jwt: enabled: true - discoveryUri: https://auth-dev.ala.org.au/cas/oidc/.well-known + discoveryUri: https://auth-test.ala.org.au/cas/oidc/.well-known fallbackToLegacyBehaviour: true + + autocompleteUrl: 'https://bie.ala.org.au/ws/search/auto.jsonp' auth: @@ -217,10 +219,10 @@ gazField: 'cl915' userObjectsField: 'cl1082' biocache: - url: 'https://biocache.ala.org.au' + url: 'https://biocache-databox.ala.org.au' biocacheService: - url: 'https://biocache.ala.org.au/ws' + url: 'https://biocache-ws-test.ala.org.au/ws' #Facets to ignore in the biocache grouped/facets service default_facets_ignored: 'data_resource_uid,data_provider_uid,species,collection_uid,institution_code_name,institution_uid,uncertainty' custom_facets: @@ -272,6 +274,8 @@ user_roles: # When using skin.layout='portal' enable google analytics by setting the googleAnalyticsId googleAnalyticsId: +# When using skin.layout='portal' enable fathom analytics by setting the fathomId +fathomId: speciesDotSize: 5 @@ -393,7 +397,7 @@ defaultareas: areaSqKm: 16322156.76 bbox: [112, -44, 154, -9] - name: 'World' - fqs: [] + fqs: ['*:*'] wkt: 'POLYGON((-179.9999 -89.9999,179.9999 -89.9999,179.9999 89.9999,-179.9999 89.9999,-179.9999 -89.9999))' areaSqKm: 510000000 bbox: [-180, -90, 180, 90] @@ -641,11 +645,12 @@ environments: port: 8087 use-forward-headers: true grails: - serverURL: "http://devt.ala.org.au:8087" + serverURL: "http://local.ala.org.au:8087" layersService: - url: "https://spatial-test.ala.org.au/ws" + url: "http://localhost:8081/ws" +# url: "https://spatial.ala.org.au/ws" geoserver: - url: 'https://spatial-test.ala.org.au/geoserver' + url: 'http://localhost:8079/geoserver' test: production: assets: diff --git a/grails-app/conf/logback.xml b/grails-app/conf/logback.xml index 2ff44dd5..721e225c 100644 --- a/grails-app/conf/logback.xml +++ b/grails-app/conf/logback.xml @@ -12,7 +12,10 @@ + + + - \ No newline at end of file + diff --git a/grails-app/conf/menu-config.json b/grails-app/conf/menu-config.json index 07f651b9..bed4aa93 100644 --- a/grails-app/conf/menu-config.json +++ b/grails-app/conf/menu-config.json @@ -94,10 +94,6 @@ "name": "Classify", "open": "Classification" }, - { - "name": "Phylogenetic Diversity", - "open": "PhylogeneticDiversity" - }, { "name": "Nearest Locality", "open": "nearestLocality" @@ -175,14 +171,6 @@ { "name": "Areas", "open": "ToolExportAreaService" - }, - { - "name": "DOI", - "open": "ToolExportDoiService" - }, - { - "name": "Points to BCCVL", - "open": "exportBccvl" } ] }, @@ -212,4 +200,4 @@ } ] } -] \ No newline at end of file +] diff --git a/grails-app/conf/view-config.json b/grails-app/conf/view-config.json index 5473d696..7e0af419 100644 --- a/grails-app/conf/view-config.json +++ b/grails-app/conf/view-config.json @@ -128,30 +128,6 @@ } ] }, - "PhylogeneticDiversity": { - "download": false, - "view": [ - { - "name": "Apply to an area", - "inputs": [ - "area" - ] - }, - { - "name": "Select Phylogenetic trees", - "inputs": [ - "phylo" - ] - } - ], - "input": { - "species": { - "constraints": { - "speciesOption": "allSpecies" - } - } - } - }, "Classification": { "download": true, "view": [ @@ -328,6 +304,15 @@ "description": "Select 1 layer" } } + }, + "AreaReport": { + "input": { + "area": { + "constraints": { + "excludeWorld": true + } + } + } } } diff --git a/grails-app/controllers/au/org/ala/spatial/portal/PortalController.groovy b/grails-app/controllers/au/org/ala/spatial/portal/PortalController.groovy index 81835806..2692a310 100644 --- a/grails-app/controllers/au/org/ala/spatial/portal/PortalController.groovy +++ b/grails-app/controllers/au/org/ala/spatial/portal/PortalController.groovy @@ -1,5 +1,6 @@ package au.org.ala.spatial.portal +import au.org.ala.ws.service.WebService import grails.converters.JSON import grails.util.Holders import grails.web.http.HttpHeaders @@ -7,6 +8,7 @@ import org.apache.commons.httpclient.methods.StringRequestEntity import org.apache.commons.lang.StringUtils import org.apache.http.client.methods.HttpGet import org.apache.http.client.methods.HttpPost +import org.apache.http.entity.ContentType import org.jasig.cas.client.util.CommonUtils import org.springframework.web.multipart.MultipartFile import org.springframework.web.multipart.MultipartHttpServletRequest @@ -19,6 +21,8 @@ import java.util.zip.ZipInputStream */ class PortalController { + WebService webService + def propertiesService private def defaultConfigLabel() { @@ -107,7 +111,8 @@ class PortalController { userDetails: authService.userDetails(), sessionId : sessionService.newId(userId), messagesAge: messageService.messagesAge, - hub : hub]) + hub : hub, + custom_facets: toMapOfLists(config.biocacheService.custom_facets)]) } else if (!authDisabled && userId == null) { login() } else { @@ -255,13 +260,11 @@ class PortalController { if (!userId) { notAuthorised() } else { - 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, - new StringRequestEntity((json as JSON).toString())) - response.status = r.statusCode - render JSON.parse(new String(r?.text ?: "")) as JSON + + webService.proxyPostRequest(response, url, json.toString(), ContentType.APPLICATION_JSON, false, true) + response.contentType = ContentType.APPLICATION_JSON } } @@ -288,7 +291,7 @@ class PortalController { } else { def type = id MultipartFile mFile = ((MultipartHttpServletRequest) request).getFile('shapeFile') - def settings = [api_key: grailsApplication.config.api_key] + def settings = [apiKey: grailsApplication.config.api_key] String ce = grailsApplication.config.character.encoding @@ -376,6 +379,7 @@ class PortalController { def header = [:] if (Holders.config.security.oidc.enabled) { header.put("userId", userId) + header.put("X-ALA-userId", userId) header.put("apiKey", grailsApplication.config.api_key) //header.put('Cookie', 'ALA-Auth=' + URLEncoder.encode(authService.email, 'UTF-8')) } @@ -629,4 +633,78 @@ class PortalController { def embedExample() { render(view: 'embedExample') } + + private def toList(Object o) { + if (o == null || org.apache.commons.lang3.StringUtils.isEmpty(o.toString())) { + return [] + } else if (o instanceof List) { + return o + } else if (o.toString().startsWith("[")) { + // JSON list + return JSON.parse(o.toString()) + } else { + // comma delimited + return Arrays.asList(o.toString().split(",")) + } + } + + private def toListOfMaps(Object o) { + if (o == null || o.toString().isEmpty()) { + return new ArrayList() + } + + def listOfMaps = toList(o) + + for (def i = 0; i < listOfMaps.size(); i++) { + listOfMaps.set(i, toMap(listOfMaps.get(i))) + } + + return listOfMaps + } + + private def toMap(Object o) { + if (o == null || o.toString().isEmpty()) { + return new HashMap() + } + + def map = o + + if (!(map instanceof Map)) { + map = JSON.parse(map.toString()) + } + + return map + } + + private def toMapOfMaps(Object o) { + if (o == null || o.toString().isEmpty()) { + return new HashMap() + } + + def mapOfMaps = toMap(o) + + for (def key : mapOfMaps.keySet) { + mapOfMaps[key] = toMap(mapOfMaps[key]) + } + + return mapOfMaps + } + + private def toMapOfLists(Object o) { + if (o == null || o.toString().isEmpty()) { + return new HashMap() + } + + def mapOfLists = toMap(o) + + def result = [:] + mapOfLists.each { k, v -> + if (!k.contains('[')) { // exclude odd artifacts + result[k] = toList(v) + } + } + + + return result + } } diff --git a/grails-app/i18n/messages.properties b/grails-app/i18n/messages.properties index c30e3346..16d40b62 100644 --- a/grails-app/i18n/messages.properties +++ b/grails-app/i18n/messages.properties @@ -222,7 +222,7 @@ Area\ Report\ -\ interactive=Area Report - interactive 159=Latitude:  160=Feature 161=Location -162=Distance (km) +162=Distance (m) 163=Heading (deg) 164=Select the base map type. 165=Add WMS Layer diff --git a/grails-app/init/au/org/ala/spatial/portal/BootStrap.groovy b/grails-app/init/au/org/ala/spatial/portal/BootStrap.groovy index 02f9fbf2..b92e62bd 100644 --- a/grails-app/init/au/org/ala/spatial/portal/BootStrap.groovy +++ b/grails-app/init/au/org/ala/spatial/portal/BootStrap.groovy @@ -243,10 +243,14 @@ class BootStrap { def mapOfLists = toMap(o) - for (def key : mapOfLists.keySet) { - mapOfLists[key] = toList(mapOfLists[key]) + def result = [:] + mapOfLists.each { k, v -> + if (!k.contains('[')) { // exclude odd artifacts + result[k] = toList(v) + } } - return mapOfLists + + return result } } diff --git a/grails-app/views/layouts/portal.gsp b/grails-app/views/layouts/portal.gsp index acf7655c..603c86d9 100644 --- a/grails-app/views/layouts/portal.gsp +++ b/grails-app/views/layouts/portal.gsp @@ -17,6 +17,9 @@ <g:layoutTitle/> + + + @@ -391,7 +394,7 @@ - +