Merge pull request #686 from AtlasOfLivingAustralia/dev

Merge 2.4 from dev to master
AtlasOfLivingAustralia · May 13, 2019 · ba2f767 · ba2f767
2 parents 47d0d8e + 4af4631
commit ba2f767
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diff --git a/application.properties b/application.properties
@@ -2,4 +2,4 @@
 #Wed Dec 21 11:09:46 AEDT 2016
 app.grails.version=2.5.6
 app.name=profile-hub
-app.version=2.3
+app.version=2.4
diff --git a/grails-app/assets/javascripts/profileEditor/controllers/CreateProfileController.js b/grails-app/assets/javascripts/profileEditor/controllers/CreateProfileController.js
@@ -1,7 +1,7 @@
 /**
  * Controller for handling creating a new profile (via a modal popup)
  */
-profileEditor.controller('CreateProfileController', function (profileService, $modalInstance, opusId, duplicateExisting) {
+profileEditor.controller('CreateProfileController', function (profileService, messageService, $modalInstance, opusId, duplicateExisting) {
     var self = this;
 
     self.opusId = opusId;
@@ -44,14 +44,18 @@ profileEditor.controller('CreateProfileController', function (profileService, $m
     };
 
     self.searchByScientificName = function () {
-        var searchResult = profileService.profileSearch(self.opusId, self.profileToCopy, true);
-        searchResult.then(function (data) {
-                self.profiles = data;
-            },
-            function () {
-                messageService.alert("Failed to perform search for '" + self.searchTerm + "'.");
-            }
-        );
+        if (!self.profileToCopy || self.profileToCopy === undefined || self.profileToCopy.length <= 0) {
+            self.profiles = [];
+        } else {
+            var searchResult = profileService.profileSearch(self.opusId, self.profileToCopy, true);
+            searchResult.then(function (data) {
+                    self.profiles = data;
+                },
+                function () {
+                    messageService.alert("Failed to perform search for '" + self.searchTerm + "'.");
+                }
+            );
+        }
     };
 
     self.valid = function() {

diff --git a/grails-app/assets/javascripts/profileEditor/controllers/MapController.js b/grails-app/assets/javascripts/profileEditor/controllers/MapController.js
@@ -303,7 +303,8 @@ profileEditor.controller('MapController', function ($scope, profileService, util
                     point: {
                         colour: self.opus.mapConfig.mapPointColour,
                         mapAttribution: self.opus.mapConfig.mapAttribution
-                    }
+                    },
+                    facetGroupUrl: config.facetGroupUrl
                 }
             );
 

diff --git a/grails-app/assets/javascripts/profileEditor/controllers/PublicationController.js b/grails-app/assets/javascripts/profileEditor/controllers/PublicationController.js
@@ -25,7 +25,7 @@ profileEditor.controller('PublicationController', function (profileService, util
             promise.then(function () {
                 loadPublications();
             }, function () {
-                messageService.alert("An error occurred while creating the snapshot.");
+                messageService.alertStayOn("An error occurred while creating the snapshot. The error might be due to profile not having an author.");
             });
         });
     };

diff --git a/grails-app/assets/javascripts/profileEditor/directives/masterList.js b/grails-app/assets/javascripts/profileEditor/directives/masterList.js
@@ -75,6 +75,7 @@
 
         function checkMasterlistSyncStatus() {
             $log.debug("Chceking masterlist sync status");
+            if (!self.opus.uuid) return;
             profileService.isMasterListSyncing(self.opus.uuid)
                 .then(function(res) {
                     self.isMasterListSyncing = res.response;

diff --git a/grails-app/assets/javascripts/profileEditor/directives/vocabularyEditor.js b/grails-app/assets/javascripts/profileEditor/directives/vocabularyEditor.js
@@ -49,7 +49,8 @@ profileEditor.directive('vocabularyEditor', function ($browser) {
             $scope.removeVocabTerm = function (index, form) {
                 var promise = profileService.findUsagesOfVocabTerm($scope.opusId, $scope.vocabId, $scope.vocabulary.terms[index].termId);
                 promise.then(function (data) {
-                        if (data.usageCount == 0) {
+                        if (data.usageCount == 0 &&
+                                $filter('filter')($scope.replacements, {'newTermName':$scope.vocabulary.terms[index].name}).length == 0) {
                             var deletedItemOrder = $scope.vocabulary.terms[index].order;
                             $scope.vocabulary.terms.splice(index, 1);
 
@@ -85,9 +86,15 @@ profileEditor.directive('vocabularyEditor', function ($browser) {
                             return $scope.vocabulary.terms[existingTermIndex];
                         },
                         terms: function() {
-                            var terms = angular.copy($scope.vocabulary.terms);
-                            var deletedItemOrder = terms[existingTermIndex].order;
-                            terms.splice(existingTermIndex, 1);
+                            var terms = [];
+                            var itemToDel = $scope.vocabulary.terms[existingTermIndex];
+                            var deletedItemOrder = $scope.vocabulary.terms[existingTermIndex].order;
+                            angular.forEach($scope.vocabulary.terms, function(term) {
+                                if ($filter('filter')($scope.replacements, {'existingTermId':term.termId}).length == 0 &&
+                                    term.termId != itemToDel.termId) {
+                                    terms.push(term);
+                                }
+                            });
 
                             angular.forEach(terms, function(term) {
                                 if (term.order > deletedItemOrder) {

diff --git a/grails-app/assets/javascripts/profileEditor/templates/commentContent.tpl.htm b/grails-app/assets/javascripts/profileEditor/templates/commentContent.tpl.htm
@@ -9,11 +9,12 @@
         </div>
 
         <!-- config is on root scope -->
-        <div ng-if="config.isOpusReviewer && (config.isOpusAuthor || comment.author.userId == config.currentUserId)"
-             class="col-md-4">
-            <button class="btn btn-link fa fa-trash-o color--red" ng-click="commentCtrl.deleteComment(path)"
+        <div class="col-md-4">
+            <button ng-if="config.isALAAdmin || config.isOpusAdmin"
+                    class="btn btn-link fa fa-trash-o color--red" ng-click="commentCtrl.deleteComment(path)"
                     title="Delete comment"></button>
-            <button class="btn btn-link fa fa-edit" ng-click="commentCtrl.editComment(path)"
+            <button ng-if="config.isOpusAdmin || config.isOpusEditor || config.isOpusAuthor || (config.isOpusReviewer && comment.author.userId == config.currentUserId)"
+                    class="btn btn-link fa fa-edit" ng-click="commentCtrl.editComment(path)"
                     title="Edit comment"></button>
         </div>
     </div>

diff --git a/grails-app/assets/javascripts/profileEditor/templates/nomenclature.tpl.htm b/grails-app/assets/javascripts/profileEditor/templates/nomenclature.tpl.htm
@@ -28,8 +28,8 @@
 
     <!-- readonly view -->
     <div class="col-md-12 nomenclature" ng-show="selectedReference && readonly">
-        <a href="" class="btn btn-link btn-sm" ng-click="toggleSynonomy()"><span class="fa" ng-class="showSynonomy ? 'fa-angle-double-up' : 'fa-angle-double-down'"></span>&nbsp;
-            <div class="concept" data-ng-bind-html="selectedReference.formattedName | sanitizeHtml"></div>
+        <a href="" class="btn btn-link btn-sm"  ng-click="toggleSynonomy()"><span class="fa" ng-class="showSynonomy ? 'fa-angle-double-up' : 'fa-angle-double-down'"></span>&nbsp;
+            <span class="concept" data-ng-bind-html="selectedReference.formattedName | sanitizeHtml"></span>
         </a>
 
         <div class="apc" ng-show="selectedReference.apcReference"

diff --git a/grails-app/assets/javascripts/profileEditor/templates/removeTermPopup.tpl.htm b/grails-app/assets/javascripts/profileEditor/templates/removeTermPopup.tpl.htm
@@ -4,12 +4,16 @@ <h4 class="modal-title">Remove vocabulary term</h4>
 </div>
 
 <div class="modal-body">
-    <p>
+    <p ng-hide="removeTermCtrl.usageCount == '0'" >
         The vocabulary term {{removeTermCtrl.existingTerm.name}} is being used in {{removeTermCtrl.usageCount}}
         profile(s).
         You must either select a replacement term or manually find and remove all usages before you can delete
         the term.
     </p>
+    <p ng-show="removeTermCtrl.usageCount == '0'" >
+        The vocabulary term {{removeTermCtrl.existingTerm.name}} is being selected as a replacement term.
+        You must either select another replacement term or remove all usages before you can delete the term.
+    </p>
 
     <div class="form-horizontal">
         <div class="form-group">

diff --git a/grails-app/assets/stylesheets/mergedProfilesThemeColour.scss b/grails-app/assets/stylesheets/mergedProfilesThemeColour.scss
@@ -1349,7 +1349,11 @@ hr.comment-divider {
 
 .nomenclature .concept {
   font-weight: bold;
-  display: inline-block;
+}
+
+.nomenclature .btn {
+  white-space: normal;
+  text-align: start;
 }
 
 .nomenclature a, .nomenclature a:focus, .nomenclature a:hover {

diff --git a/grails-app/assets/thirdparty/ckeditor/ng-ckeditor-0.2.1.js b/grails-app/assets/thirdparty/ckeditor/ng-ckeditor-0.2.1.js
@@ -140,7 +140,10 @@
               onUpdateModelData(true);
             });
 
-            instance.document.on('keyup', setModelData);
+            // This fixes a bug in ng-ckeditor that caused #627.
+            // Previously listener was incorrectly configured. Function setModelData was called on a keystroke
+            // anywhere on the page.
+            instance.on('key', setModelData);
           });
           instance.on('customConfigLoaded', function() {
             configLoaderDef.resolve();

diff --git a/grails-app/conf/BuildConfig.groovy b/grails-app/conf/BuildConfig.groovy
@@ -85,7 +85,7 @@ grails.project.dependency.resolution = {
         compile ":cache:1.1.8"
         compile ":cors:1.1.6"
         compile ":csv:0.3.1"
-        compile(":ala-map:2.0.4") {
+        compile(":ala-map:2.1.8-SNAPSHOT") {
             excludes "resources"
         }
         compile(":ala-ws-plugin:1.6.1") {

diff --git a/grails-app/conf/UrlMappings.groovy b/grails-app/conf/UrlMappings.groovy
@@ -223,6 +223,7 @@ class UrlMappings {
         "/opus/$opusId/profile/$profileId/image/$imageId/tile/$zoom/$x/$y" controller: "image", action: [GET: "getTile"]
 
         "/stylesheet/$id?" controller: "stylesheet", action: "opus"
+        "/facets" controller: "resource", action: "facets"
         if (Environment.current == Environment.DEVELOPMENT) {
             "/console/$action?/$id?(.$format)?" controller: 'console'
         }

diff --git a/grails-app/conf/au/org/ala/profile/filter/AccessControlFilters.groovy b/grails-app/conf/au/org/ala/profile/filter/AccessControlFilters.groovy
@@ -81,10 +81,10 @@ class AccessControlFilters {
                                                     authorised = params.isOpusAdmin
                                                     log.debug "Action ${actionFullName} requires ROLE_PROFILE_ADMIN. User ${request.userPrincipal?.name} has it? ${authorised}"
                                                 } else if (requiredRole == Role.ROLE_PROFILE_EDITOR.toString()) {
-                                                    authorised = params.isOpusAdmin || params.isOpusEditor
+                                                    authorised = params.isOpusAdmin || params.isOpusAuthor || params.isOpusEditor
                                                     log.debug "Action ${actionFullName} requires ${requiredRole}. User ${request.userPrincipal?.name} has it? ${authorised}"
                                                 } else if (requiredRole == Role.ROLE_PROFILE_AUTHOR.toString()) {
-                                                    authorised = params.isOpusAdmin || params.isOpusAuthor || params.isOpusEditor
+                                                    authorised = params.isOpusAdmin || params.isOpusAuthor
                                                     log.debug "Action ${actionFullName} requires ${requiredRole}. User ${request.userPrincipal?.name} has it? ${authorised}"
                                                 } else if (requiredRole == Role.ROLE_PROFILE_REVIEWER.toString()) {
                                                     authorised = params.isOpusAdmin || params.isOpusAuthor || params.isOpusReviewer || params.isOpusEditor
@@ -122,6 +122,8 @@ class AccessControlFilters {
                         response.status = HttpStatus.SC_FORBIDDEN
                         response.sendError(HttpStatus.SC_FORBIDDEN)
                     }
+
+                    return authorised
                 } else {
                     boolean authenticated = authService.getDisplayName() != null
                     params.isOpusAdmin = authenticated
@@ -130,6 +132,7 @@ class AccessControlFilters {
                     params.isOpusReviewer = authenticated
                     params.isOpusUser = authenticated
                     log.warn "**** Authorisation has been disabled! ****"
+                    return true
                 }
             }
             after = { Map model ->

diff --git a/grails-app/conf/grouped_facets_ala.json b/grails-app/conf/grouped_facets_ala.json
@@ -0,0 +1,115 @@
+[
+  {
+    "title":"Taxon",
+    "facets":[
+      {
+        "sort":"index",
+        "field":"taxon_name"
+      },
+      {
+        "sort":"index",
+        "field":"subspecies_name"
+      },
+      {
+        "sort":"index",
+        "field":"species"
+      },
+      {
+        "sort":"index",
+        "field":"genus"
+      },
+      {
+        "sort":"index",
+        "field":"family"
+      },
+      {
+        "sort":"index",
+        "field":"order"
+      },
+      {
+        "sort":"index",
+        "field":"class"
+      },
+      {
+        "sort":"index",
+        "field":"phylum"
+      },
+      {
+        "sort":"index",
+        "field":"kingdom"
+      },
+      {
+        "sort":"index",
+        "field":"common_name"
+      },
+      {
+        "sort":"count",
+        "field":"species_subgroup"
+      }
+    ]
+  },
+  {
+    "title":"Occurrence",
+    "facets":[
+      {
+        "sort":"index",
+        "field":"month"
+      },
+      {
+        "sort":"index",
+        "field":"year"
+      }
+    ]
+  },
+  {
+    "title":"Location",
+    "facets":[
+      {
+        "sort":"index",
+        "field":"country"
+      },
+      {
+        "sort":"count",
+        "field":"state"
+      },
+      {
+        "sort":"count",
+        "field": "cl1048"
+      },
+      {
+        "sort":"count",
+        "field": "cl1049"
+      }
+    ]
+  },
+  {
+    "title":"Record",
+    "facets":[
+      {
+        "sort":"index",
+        "field":"basis_of_record"
+      },
+      {
+        "sort":"count",
+        "field":"multimedia"
+      },
+      {
+        "sort":"index",
+        "field":"occurrence_status"
+      }
+    ]
+  },
+  {
+    "title":"Attribution",
+    "facets":[
+      {
+        "sort":"count",
+        "field":"alau_user_id"
+      },
+      {
+        "sort":"count",
+        "field":"data_resource_uid"
+      }
+    ]
+  }
+]
diff --git a/grails-app/conf/reports/profiles/PROFILES_detail.jrxml b/grails-app/conf/reports/profiles/PROFILES_detail.jrxml
@@ -238,6 +238,7 @@
 				<reportElement positionType="Float" x="0" y="86" width="515" height="15" uuid="6c27bf88-e8a0-4428-b155-5ec3610add41">
 					<property name="com.jaspersoft.studio.unit.width" value="pixel"/>
 					<property name="com.jaspersoft.studio.unit.height" value="pixel"/>
+					<printWhenExpression><![CDATA[Boolean.valueOf($P{PROFILES_REPORT_OPTIONS}.map)]]></printWhenExpression>
 				</reportElement>
 				<subreportParameter name="REPORT_TEMPLATES">
 					<subreportParameterExpression><![CDATA[(java.util.Collection<net.sf.jasperreports.engine.JRTemplate>)$P{REPORT_TEMPLATES}]]></subreportParameterExpression>

diff --git a/grails-app/controllers/au/org/ala/profile/hub/CommentController.groovy b/grails-app/controllers/au/org/ala/profile/hub/CommentController.groovy
@@ -48,16 +48,14 @@ class CommentController extends BaseController {
         }
     }
 
-    @Secured(role = Role.ROLE_PROFILE_REVIEWER)
+    @Secured(role = Role.ROLE_PROFILE_ADMIN)
     def deleteComment() {
         if (!params.commentId) {
             badRequest()
-        } else if (checkCommentPermissions(params.profileId, params.commentId)) {
+        } else {
             def response = profileService.deleteComment(params.opusId, params.profileId, params.commentId)
 
             handle response
-        } else {
-            notAuthorised()
         }
     }
 

diff --git a/grails-app/controllers/au/org/ala/profile/hub/OpusController.groovy b/grails-app/controllers/au/org/ala/profile/hub/OpusController.groovy
@@ -9,7 +9,6 @@ import org.springframework.web.multipart.MultipartFile
 import org.springframework.web.multipart.MultipartHttpServletRequest
 import org.springframework.web.multipart.support.DefaultMultipartHttpServletRequest
 
-import static au.org.ala.profile.hub.Utils.encPath
 import static au.org.ala.profile.hub.util.HubConstants.*
 import static au.org.ala.profile.security.Role.ROLE_ADMIN
 import static au.org.ala.profile.security.Role.ROLE_PROFILE_ADMIN
@@ -104,6 +103,7 @@ class OpusController extends OpusBaseController {
         }
     }
 
+    @Secured(role = ROLE_PROFILE_ADMIN)
     def reports() {
         def opus = profileService.getOpus(params.opusId as String)