Merge branch 'master' into issue-2758-disable-edits-for-existing-alleles

pombase · Sep 1, 2023 · 4a23edf · 4a23edf
2 parents c8b4e3c + 561012e
commit 4a23edf
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Showing 6 changed files with 109 additions and 60 deletions.
diff --git a/canto.yaml b/canto.yaml
@@ -25,7 +25,7 @@ header_image: logos/curation_tool.png
 
 canto_url: https://curation.pombase.org/
 
-app_version: v1762
+app_version: v1767
 
 schema_version: 35
 
@@ -1488,6 +1488,7 @@ allele_type_list:
     export_type: amino_acid_insertion
     show_description: true
     description_required: true
+    check_description_with_api: true
     allele_name_required: true
     allow_expression_change: true
     expression_required: true
@@ -1496,6 +1497,7 @@ allele_type_list:
     export_type: amino_acid_mutation
     show_description: true
     description_required: true
+    check_description_with_api: true
     allele_name_required: true
     allow_expression_change: true
     expression_required: true
@@ -1504,6 +1506,7 @@ allele_type_list:
     export_type: amino_acid_insertion_and_mutation
     show_description: true
     description_required: true
+    check_description_with_api: true
     allele_name_required: true
     allow_expression_change: true
     expression_required: true
@@ -1512,6 +1515,7 @@ allele_type_list:
     export_type: amino_acid_insertion_and_deletion
     show_description: true
     description_required: true
+    check_description_with_api: true
     allele_name_required: true
     allow_expression_change: true
     expression_required: true
@@ -1520,6 +1524,7 @@ allele_type_list:
     export_type: amino_acid_deletion_and_mutation
     show_description: true
     description_required: true
+    check_description_with_api: true
     allele_name_required: true
     allow_expression_change: true
     expression_required: true
@@ -1528,6 +1533,7 @@ allele_type_list:
     export_type: partial_amino_acid_deletion
     show_description: true
     description_required: true
+    check_description_with_api: true
     allele_name_required: true
     allow_expression_change: true
     expression_required: true
@@ -1536,6 +1542,7 @@ allele_type_list:
     export_type: nucleotide_insertion
     show_description: true
     description_required: true
+    check_description_with_api: true
     allele_name_required: true
     allow_expression_change: true
     expression_required: true
@@ -1544,6 +1551,7 @@ allele_type_list:
     export_type: nucleotide_mutation
     show_description: true
     description_required: true
+    check_description_with_api: true
     allele_name_required: true
     allow_expression_change: true
     expression_required: true
@@ -1552,6 +1560,7 @@ allele_type_list:
     export_type: partial_nucleotide_deletion
     show_description: true
     description_required: true
+    check_description_with_api: true
     allele_name_required: true
     allow_expression_change: true
     expression_required: true
@@ -1560,6 +1569,7 @@ allele_type_list:
     export_type: nucleotide_deletion_and_mutation
     show_description: true
     description_required: true
+    check_description_with_api: true
     allele_name_required: true
     allow_expression_change: true
     expression_required: true
@@ -1568,6 +1578,7 @@ allele_type_list:
     export_type: nucleotide_insertion_and_mutation
     show_description: true
     description_required: true
+    check_description_with_api: true
     allele_name_required: true
     allow_expression_change: true
     expression_required: true

diff --git a/root/curs/autohandler b/root/curs/autohandler
@@ -77,7 +77,7 @@ my $annotation_type_config_js = Data::JavaScript::Anon->anon_dump($annotation_ty
 my $multi_organism_mode = $st->{multi_organism_mode} || 0;
 my $split_genotypes_by_organism = $st->{split_genotypes_by_organism} || 0;
 my $annotation_figure_field = $st->{annotation_figure_field} || 0;
-my $allele_qc_api_url = $c->config()->{allele_qc_api_url};
+my $allele_qc_api_url = $c->config()->{webservices}->{allele_qc_api_url};
 my $show_genotype_management_genes_list = $st->{show_genotype_management_genes_list} || 0;
 my $strains_mode = $st->{strains_mode} || 0;
 my $pathogen_host_mode = $st->{pathogen_host_mode} || 0;

diff --git a/root/static/css/style.css b/root/static/css/style.css
@@ -2009,3 +2009,12 @@ dd {
 .allele-desc-problem-summ {
   margin-bottom: 1em;
 }
+
+/* override Bootstrap */
+summary {
+  display: list-item;
+}
+
+details > div {
+  margin-left: 1em;
+}
diff --git a/root/static/js/canto-modules.js b/root/static/js/canto-modules.js
@@ -4125,7 +4125,7 @@ function alleleQCCheckAllele($http, alleleQCUrl, geneSystematicId, alleleDescrip
 }
 
 var alleleEditDialogCtrl =
-  function ($scope, $uibModal, $uibModalInstance, $http, toaster, CantoConfig, args, Curs, CantoGlobals) {
+  function ($scope, $uibModal, $uibModalInstance, $http, $q, toaster, CantoConfig, args, Curs, CantoGlobals) {
     $scope.alleleData = {};
     copyObject(args.allele, $scope.alleleData);
     $scope.taxonId = args.taxonId;
@@ -4150,6 +4150,7 @@ var alleleEditDialogCtrl =
     $scope.descriptionNeedsChecking = false;
     $scope.descriptionState = 'unset';
     $scope.lastDescriptionError = '';
+    $scope.okInProgress = false;
 
     $scope.showAlleleTypeField = (
       ! $scope.lockedAlleleType && (
@@ -4239,31 +4240,25 @@ var alleleEditDialogCtrl =
       processSynonyms();
     };
 
-    $scope.updateAlleleCheckButton = function() {
+    $scope.descriptionChanged = function() {
       $scope.descriptionNeedsChecking = false;
       $scope.descriptionState = 'unset';
-
-      const description = $scope.alleleData.description.trim();
-      const alleleName = $scope.alleleData.name.trim();
-
-      if ($scope.allele_qc_api_url && $scope.userIsAdmin &&
-          alleleName.length > 0 &&
-          description.length > 0) {
-        $scope.descriptionNeedsChecking = true;
-      }
     };
 
-    $scope.$watch('alleleData.name', $scope.updateAlleleCheckButton);
-
     $scope.checkDescription = function() {
       const qcUrl = CantoGlobals.allele_qc_api_url;
 
       const alleleType = $scope.alleleData.type.trim();
 
-      if (!qcUrl || !$scope.current_type_config) {
-        return;
+      if (!qcUrl || !$scope.current_type_config ||
+          !$scope.userIsAdmin ||
+          !$scope.current_type_config.check_description_with_api) {
+        $scope.descriptionState = 'ok';
+        return $q.when(null);
       }
 
+      $scope.descriptionState = 'unset';
+
       const geneSystematicId = $scope.alleleData.gene_systematic_id;
       const alleleDescription = $scope.alleleData.description.trim();
       const alleleName = $scope.alleleData.name.trim();
@@ -4290,28 +4285,29 @@ var alleleEditDialogCtrl =
                 .map((err) => '<dt>' + err[0] + '</dt> <dd>' + err[1] + '</dd>')
                 .join("\n") + '</dl>';
 
-          let content = '';
+          let content = errorMessages;
+
           if (summaryParts.length > 0) {
-            content += '<div class="allele-desc-problem-summ">' +
+            content += '<details><summary>Details</summary><div class="allele-desc-problem-summ">' +
               summaryParts.map((part) => '<div>' + part + '</div>').join("\n") +
-              '</div>';
+              '</div></details>';
           }
 
-          content += errorMessages;
-
           openSimpleDialog($uibModal, 'Allele description problems',
                            'Allele description problems', content);
         } else {
           $scope.descriptionState = 'ok';
           $scope.lastDescriptionError = '';
 
-          toaster.pop({type: 'info', title: 'Allele description passes checks',
-                       timeout: 5000, showCloseButton: true });
+//          toaster.pop({type: 'info', title: 'Allele description passes checks',
+//                       timeout: 5000, showCloseButton: true });
         }
       })
       .finally(function () {
         loadingEnd();
       });
+
+      return promise;
     };
 
     $scope.isValidType = function () {
@@ -4345,12 +4341,40 @@ var alleleEditDialogCtrl =
       }
     };
 
+    $scope.okTitle = function() {
+      if ($scope.isExistingAllele()) {
+        return 'Finish editing this allele';
+      }
+
+      if ($scope.descriptionState == 'not-ok') {
+        return 'Fix the allele description to continue';
+      }
+
+      if (!$scope.isValidName()) {
+        return 'Set the allele name to continue';
+      }
+
+      if (!$scope.isValidType()) {
+        return 'Set the allele type to continue';
+      }
+
+      if (!$scope.isValidDescription()) {
+        return 'Set the allele description to continue';
+      }
+
+      return 'Finish editing this allele';
+    };
+
     $scope.isValid = function () {
+      if ($scope.descriptionState == 'not-ok') {
+        return false;
+      }
+
       return $scope.isValidExpression() &&
         (
           $scope.isExistingAllele() ||
-          $scope.isValidType() && $scope.isValidName() &&
-          $scope.isValidDescription()
+            $scope.isValidType() && $scope.isValidName() &&
+            $scope.isValidDescription()
         ) &&
         $scope.isValidStrain();
     };
@@ -4379,20 +4403,35 @@ var alleleEditDialogCtrl =
     }
 
     $scope.ok = function () {
-      if ($scope.isValid()) {
-        splitSynonymsForStoring($scope.alleleData, $scope.data.newSynonymsString);
-        copyObject($scope.alleleData, args.allele);
-        var strainName = null;
-        if ($scope.strainData.selectedStrain) {
-          strainName = $scope.strainData.selectedStrain.strain_name;
-        }
-        $uibModalInstance.close({
-          alleleData: args.allele,
-          strainName: strainName
-        });
-      } else {
-        toaster.pop('error', "No changes have been made");
+      if ($scope.descriptionState == 'not-ok') {
+        return;
       }
+
+      const promise = $scope.checkDescription();
+
+      promise.then(() => {
+        if ($scope.descriptionState == 'not-ok') {
+          return;
+        }
+
+        if ($scope.isValid()) {
+          $scope.okInProgress = true;
+          splitSynonymsForStoring($scope.alleleData, $scope.data.newSynonymsString);
+          copyObject($scope.alleleData, args.allele);
+          var strainName = null;
+          if ($scope.strainData.selectedStrain) {
+            strainName = $scope.strainData.selectedStrain.strain_name;
+          }
+          setTimeout(function () {
+            $uibModalInstance.close({
+              alleleData: args.allele,
+              strainName: strainName
+            });
+          }, 400);
+        } else {
+          toaster.pop('error', "No changes have been made");
+        }
+      });
     };
 
     $scope.cancel = function () {
@@ -4434,7 +4473,7 @@ var alleleEditDialogCtrl =
   };
 
 canto.controller('AlleleEditDialogCtrl',
-  ['$scope', '$uibModal', '$uibModalInstance', '$http', 'toaster', 'CantoConfig', 'args', 'Curs', 'CantoGlobals',
+  ['$scope', '$uibModal', '$uibModalInstance', '$http', '$q', 'toaster', 'CantoConfig', 'args', 'Curs', 'CantoGlobals',
     alleleEditDialogCtrl
   ]);
 
@@ -8365,14 +8404,6 @@ var annotationEditDialogCtrl =
       return countKeys(changesToStore) > 0;
     };
 
-    $scope.featureChooserTitle = function() {
-      if ($scope.featureEditable) {
-        return 'Choose a ' + $scope.annotationType.feature_type;
-      } else {
-        return 'This annotation is not editable because it has associated genetic interactions';
-      }
-    };
-
     $scope.okButtonTitleMessage = function () {
       if ($scope.isValid()) {
         if ($scope.annotationChanged()) {

diff --git a/root/static/ng_templates/allele_edit.html b/root/static/ng_templates/allele_edit.html
@@ -34,7 +34,7 @@ <h4 class="modal-title">
             </allele-name-complete>
             <input ng-if="alleleData.type == 'aberration' || alleleData.type == 'aberration wild type'" ng-model="alleleData.name"/>
             <span ng-show="!isValidName()"
-                  class="help-block">Required for this allele type</span>
+                  class="help-block">Allele name is required</span>
           </td>
         </tr>
 
@@ -58,7 +58,7 @@ <h4 class="modal-title">
           </td>
         </tr>
 
-        <tr ng-if="userIsAdmin && !!alleleData.type">
+        <tr ng-if="!!alleleData.type">
           <td>
             New synonyms:
           </td>
@@ -109,7 +109,7 @@ <h4 class="modal-title">
           </td>
           <td ng-class="{ 'has-error': !isValidDescription() }">
             <input ng-model="alleleData.description"
-                   ng-change="updateAlleleCheckButton()"
+                   ng-change="descriptionChanged()"
                    name="curs-allele-description-input" type="text" value=""
                    class="form-control" />
             <span ng-show="descriptionState == 'ok'"
@@ -118,11 +118,8 @@ <h4 class="modal-title">
             <span ng-show="descriptionState == 'not-ok'"
                   title="{{lastDescriptionError}}"
                   class="glyphicon glyphicon-remove curs-allele-desc-not-ok"></span>
-            <span ng-show="descriptionNeedsChecking" class="allele-description-check">
-              <button class="btn btn-warning" ng-click="checkDescription()">Check</button>
-            </span>
             <span ng-show="!isValidDescription()"
-                  class="help-block">Required for this allele type</span>
+                  class="help-block">Description required for this allele type</span>
           </td>
         </tr>
 
@@ -166,7 +163,7 @@ <h4 class="modal-title">
               </td>
             </tr>
 
-            <tr ng-if="userIsAdmin && !!alleleData.type">
+            <tr ng-if="!!alleleData.type">
               <td class="title">
                 New synonyms:
               </td>
@@ -240,9 +237,11 @@ <h4 class="modal-title">
       </div>
 
       <div class="modal-footer">
-        <button class="btn btn-warning" ng-click="cancel()">Cancel</button>
+        <button class="btn btn-warning" ng-click="cancel()"
+                ng-disabled="okInProgress">Cancel</button>
         <button class="btn btn-primary" ng-click="ok()" ng-alt-enter="ok()"
-                ng-disabled="!isValid()">OK</button>
+                title="{{okTitle()}}"
+                ng-disabled="okInProgress || !isValid()">OK</button>
       </div>
     </div>
   </form>