[ENH] in the review interface, it is possible to toggle, if only conflicting entries are shown

Author: anastasia-escher

svip-o-vue/src/components/widgets/review/VariantDisease.vue

@@ -1,5 +1,20 @@
 <template>
     <div :key="renderKey">
+        <div v-if="review_cycle > 1">
+            <br />
+            <b-form-checkbox
+                id="checkbox-1"
+                v-model="only_conflicting"
+                name="checkbox-1"
+                value="yes"
+                unchecked-value="no">
+                Show only conflicting entries
+            </b-form-checkbox>
+
+            <br />
+
+        </div>
+
         <div v-for="(submissionEntry, idx) in submissionEntries" :key="submissionEntry[0] + idx">
             <b-card class="shadow-sm mb-3" align="left" no-body>
                 <h6 class="bg-primary text-light unwrappable-header p-2 m-0">
@@ -11,14 +26,25 @@
                     <b-card-body class="p-0">
                         <transition name="slide-fade">
                             <div v-if="expander_array[idx].disease">
-                                <b-card-text class="p-2 m-0">
+                                <b-card-text
+                                    class="p-2 m-0"
+                                    :class="
+                                        only_conflicting === 'yes' && !type.if_conflicting_reviews
+                                            ? 'hidden'
+                                            : ''
+                                    ">
                                     <b-row align-v="center">
                                         <b-col align="left" cols="2">
                                             <div class="ml-1">
                                                 <expander
                                                     v-model="expander_array[idx].curation_entries[index]" />
                                                 {{ type.type_of_evidence }}
                                                 {{ type.drug && ` - ${type.drug}` }}
+                                                <br />
+
+                                                <p style="color: red" v-if="type.if_conflicting_reviews">
+                                                    Conflicting entry!
+                                                </p>
                                             </div>
                                         </b-col>
                                         <b-col cols="2">
@@ -324,6 +350,7 @@ export default {
     props: ['variant_id', 'gene_id'],
     data() {
         return {
+            only_conflicting: 'no',
             renderKey: 0,
             submissionEntries: [],
             selfReviewedEvidences: {},
@@ -343,22 +370,29 @@ export default {
             },
             draft: false,
             showOnlyOwnReviewStatus: true,
+            review_cycle: 0,
         };
     },
     created() {
         // Watch if user is going to leave the page
         window.addEventListener('beforeunload', this.beforeWindowUnload);
 
+        if (this.variant.submission_entries.length > 0) {
+            this.review_cycle = this.variant.submission_entries[0].review_cycle;
+        }
+
         this.submissionEntries = Object.entries(
             groupBy(
-                this.variant.submission_entries.filter(i =>
-                    ['Prognostic', 'Diagnostic', 'Predictive / Therapeutic'].includes(i.type_of_evidence)
-                ),
+                this.variant.submission_entries //
+                    .filter(i =>
+                        ['Prognostic', 'Diagnostic', 'Predictive / Therapeutic'].includes(i.type_of_evidence)
+                    ),
                 item => {
                     return item.disease && item.disease.name ? item.disease.name : 'Unspecified';
                 }
             )
         );
+
         this.getExpanderArray();
 
         // Check that this page is appropriate regarding current review stage of variant
@@ -390,6 +424,19 @@ export default {
     },
 
     methods: {
+        // groupSubmissionsEntries(submissionEntriesUngrouped) {
+        //     return Object.entries(
+        //         groupBy(
+        //             submissionEntriesUngrouped.filter(i =>
+        //                 ['Prognostic', 'Diagnostic', 'Predictive / Therapeutic'].includes(i.type_of_evidence)
+        //             ),
+        //             item => {
+        //                 return item.disease && item.disease.name ? item.disease.name : 'Unspecified';
+        //             }
+        //         )
+        //     );
+        // },
+
         numberOfEmptySquares(length) {
             switch (length) {
                 case 0:
@@ -644,4 +691,8 @@ export default {
 .alert-border {
     border-color: red;
 }
+
+.hidden {
+    visibility: hidden;
+}
 </style>

svip_api/api/migrations/0168_submissionentry_if_conflicting_reviews.py

@@ -0,0 +1,18 @@
+# Generated by Django 2.2.28 on 2022-12-12 17:25
+
+from django.db import migrations, models
+
+
+class Migration(migrations.Migration):
+
+    dependencies = [
+        ('api', '0167_submissionentry_review_cycle'),
+    ]
+
+    operations = [
+        migrations.AddField(
+            model_name='submissionentry',
+            name='if_conflicting_reviews',
+            field=models.BooleanField(default=False),
+        ),
+    ]

svip_api/api/migrations/0169_remove_submissionentry_if_conflicting_reviews.py

@@ -0,0 +1,17 @@
+# Generated by Django 2.2.28 on 2022-12-12 17:29
+
+from django.db import migrations
+
+
+class Migration(migrations.Migration):
+
+    dependencies = [
+        ('api', '0168_submissionentry_if_conflicting_reviews'),
+    ]
+
+    operations = [
+        migrations.RemoveField(
+            model_name='submissionentry',
+            name='if_conflicting_reviews',
+        ),
+    ]

svip_api/api/migrations/0170_submissionentry_if_conflicting_reviews.py

@@ -0,0 +1,18 @@
+# Generated by Django 2.2.28 on 2022-12-12 17:33
+
+from django.db import migrations, models
+
+
+class Migration(migrations.Migration):
+
+    dependencies = [
+        ('api', '0169_remove_submissionentry_if_conflicting_reviews'),
+    ]
+
+    operations = [
+        migrations.AddField(
+            model_name='submissionentry',
+            name='if_conflicting_reviews',
+            field=models.BooleanField(default=False),
+        ),
+    ]

svip_api/api/models/svip.py

@@ -248,6 +248,7 @@ class SubmissionEntry(models.Model):
     effect = models.TextField(default="Not yet annotated")
     tier = models.TextField(default="Not yet annotated")
     review_cycle = models.IntegerField(default=1)
+    if_conflicting_reviews = models.BooleanField(default=False)
 
 
 class CURATION_STATUS(ModelChoice):

svip_api/api/serializers/svip.py

@@ -552,6 +552,8 @@ class Meta:
 
 
 class SubmissionEntrySerializer(serializers.ModelSerializer):
+
+
     variant = SimpleVariantSerializer()
     curation_entries = CurationEntrySerializer(
         many=True, required=False, source='curationentry_set')
@@ -567,6 +569,8 @@ class Meta:
         read_only_fields = ['id']
 
 
+
+
 # ================================================================================================================
 # === SVIP Variant Submission
 # ================================================================================================================

svip_api/api/views/svip.py

@@ -316,6 +316,30 @@ def perform_create(self, serializer):
         """Create a new recipe."""
         serializer.save(user=self.request.user)
 
+    @action(detail=False, methods=['POST'])
+    def bulk_submit_test(self, request):
+        if isinstance(request.data, dict) and request.data['update']:
+            for entry in request.data['data']:
+                submission_entry = SubmissionEntry.objects.filter(pk=entry['id'])
+                for id in entry['curation_reviews']:
+                    curation_review = CurationReview.objects.get(pk=id)
+                    print(entry['effect'], curation_review.annotated_effect, entry['tier'], curation_review.annotated_tier)
+                    print(entry['effect'] == curation_review.annotated_effect and entry['tier'] == curation_review.annotated_tier)
+                    print('\n' * 5)
+                submission_entry = submission_entry[0]
+                print([review.acceptance for review in submission_entry.curation_reviews.all()])
+                print(all(review.acceptance for review in submission_entry.curation_reviews.all()))
+                return JsonResponse({
+                    "message": "pi pa po",
+                })
+
+        return JsonResponse({
+            "message": "pi pa po",
+        })
+
+
+
+
     @action(detail=False, methods=['POST'])
     def bulk_submit(self, request):
 
@@ -326,8 +350,25 @@ def bulk_submit(self, request):
                                         review_cycle=submission_entry[0].review_cycle + 1)
                 for id in entry['curation_entries']:
                     CurationEntry.objects.filter(pk=id).update(status='resubmitted')
+
+                for id in entry['curation_reviews']:
+                    curation_review = CurationReview.objects.get(pk=id)
+                    if entry['effect'] == curation_review.annotated_effect and entry['tier'] == curation_review.annotated_tier:
+                        curation_review.acceptance = True
+                    else:
+                        curation_review.acceptance = False
+                    curation_review.save()
+
+                submission_entry = submission_entry[0]
+                if not all(review.acceptance for review in submission_entry.curation_reviews.all()):
+                    submission_entry.if_conflicting_reviews = True
+                else:
+                    submission_entry.if_conflicting_reviews = False
+                submission_entry.save()
+
                 for id in entry['curation_reviews']:
                     CurationReview.objects.get(pk=id).delete()
+
             return JsonResponse({
                 "message": "Your annotation  was successfully saved!",
 
@@ -367,7 +408,8 @@ def __save_review_obj(self, obj):
             review = CurationReview.objects.get(id=obj['id'])
         else:
             review = CurationReview()
-        review.submission_entry = SubmissionEntry.objects.get(id=obj['submission_entry'])
+        submission_entry = SubmissionEntry.objects.get(id=obj['submission_entry'])
+        review.submission_entry = submission_entry
         review.annotated_effect = obj['effect']
         review.annotated_tier = obj['tier']
         review.comment = obj['comment']