interim commit for meta anno pred integrated

CogStack · Aug 18, 2024 · 0fb9ae8 · 0fb9ae8
1 parent 3938c4a
commit 0fb9ae8
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Showing 6 changed files with 59 additions and 20 deletions.
diff --git a/webapp/api/api/utils.py b/webapp/api/api/utils.py
@@ -14,7 +14,7 @@
 from medcat.vocab import Vocab
 
 from .models import Entity, AnnotatedEntity, ProjectAnnotateEntities, \
-    ConceptDB, MetaAnnotation
+    ConceptDB, MetaAnnotation, MetaTask
 
 log = logging.getLogger('trainer')
 
@@ -41,6 +41,19 @@ def add_annotations(spacy_doc, user, project, document, existing_annotations, ca
     tkns_in = []
     ents = []
     existing_annos_intervals = [(ann.start_ind, ann.end_ind) for ann in existing_annotations]
+    # all MetaTasks and associated values
+    # that can be produced are expected to have available models
+    try:
+        metatask2obj = {task_name: MetaTask.objects.get(name=task_name)
+                        for task_name in spacy_doc._.ents[0]._.meta_anns.keys()}
+        metataskvals2obj = {task_name: {v.name: v for v in MetaTask.objects.get(name=task_name).values.all()}
+                            for task_name in spacy_doc._.ents[0]._.meta_anns.keys()}
+    except AttributeError:
+        # ignore meta_anns that are not present - i.e. non model pack preds,
+        # or model pack preds with no meta_anns
+        metatask2obj = {}
+        metataskvals2obj = {}
+        pass
 
     def check_ents(ent):
         return any((ea[0] < ent.start_char < ea[1]) or
@@ -56,10 +69,6 @@ def check_ents(ent):
                 for tkn in ent:
                     tkns_in.append(tkn)
                 ents.append(ent)
-        # check the ent._.meta_anns if it exists
-        # meta_anno_objs = MetaAnnotation.objects
-        # for meta_ann in ent._.meta_anns:
-        #     MetaAnnotation.objects.filter(meta_ann)
 
     for ent in ents:
         label = ent._.cui
@@ -72,10 +81,11 @@ def check_ents(ent):
         else:
             entity = Entity.objects.get(label=label)
 
-        if AnnotatedEntity.objects.filter(project=project,
-                                          document=document,
-                                          start_ind=ent.start_char,
-                                          end_ind=ent.end_char).count() == 0:
+        ann_ent = AnnotatedEntity.objects.filter(project=project,
+                                                  document=document,
+                                                  start_ind=ent.start_char,
+                                                  end_ind=ent.end_char).first()
+        if ann_ent is None:
             # If this entity doesn't exist already
             ann_ent = AnnotatedEntity()
             ann_ent.user = user
@@ -94,6 +104,19 @@ def check_ents(ent):
 
             ann_ent.save()
 
+        # check the ent._.meta_anns if it exists
+        for meta_ann_task, pred in ent._.meta_anns.items():
+            # raise exception here if got here with no metatask2obj or vals present
+            meta_anno_obj = MetaAnnotation.objects.filter(annotated_entity=ann_ent,
+                                                          meta_task=metatask2obj[meta_ann_task]).first()
+            if meta_anno_obj is None or not meta_anno_obj.validated:
+                meta_anno_obj = MetaAnnotation()
+                meta_anno_obj.meta_task = metatask2obj[meta_ann_task]
+                meta_anno_obj.annotated_entity = ann_ent
+                meta_anno_obj.meta_task_value = metataskvals2obj[meta_ann_task][pred['value']]
+                meta_anno_obj.acc = pred['confidence']
+                meta_anno_obj.save()
+
 
 def get_create_cdb_infos(cdb, concept, cui, cui_info_prop, code_prop, desc_prop, model_clazz):
     codes = [c[code_prop] for c in cdb.cui2info.get(cui, {}).get(cui_info_prop, []) if code_prop in c]

diff --git a/webapp/frontend/src/components/usecases/MetaAnnotationTask.vue b/webapp/frontend/src/components/usecases/MetaAnnotationTask.vue
@@ -3,7 +3,8 @@
     <div class="task-name">{{task.name}}</div>
     <div class="task-description">{{task.description}}</div>
     <div class="task-values-container">
-      <button class="btn btn-outline-primary task-value" :class="{'selected': task.value === option.id}"
+      <button class="btn btn-outline-primary task-value"
+              :class="optionStyle(option)"
               v-for="option of task.options" :key="option.id"
               @click="selectTaskValue(option)">{{option.name}}</button>
     </div>
@@ -19,6 +20,12 @@ export default {
   methods: {
     selectTaskValue (option) {
       this.$emit('select:metaAnno', this.task, option)
+    },
+    optionStyle (option) {
+      return {
+        'selected': this.task.value === option.id && this.task.validated,
+        'unvalidated': this.task.value === option.id && !this.task.validated
+      }
     }
   }
 }
@@ -45,8 +52,13 @@ export default {
 
 .selected {
   color: #fff;
-  background-color: #005EB8;
-  border-color: #005EB8;
+  background-color: $primary-alt;
+  border-color: $primary-alt;
+}
+
+.unvalidated {
+  background: lightgrey;
+  border: 1px solid lightgrey;
 }
 
 .task-values-container {

diff --git a/webapp/frontend/src/components/usecases/MetaAnnotationTaskContainer.vue b/webapp/frontend/src/components/usecases/MetaAnnotationTaskContainer.vue
@@ -19,6 +19,7 @@ export default {
   },
   mixins: [MetaAnnotationService],
   props: {
+    modelPackSet: Boolean,
     taskIDs: Array,
     selectedEnt: {
       type: Object,
@@ -64,13 +65,15 @@ export default {
     const that = this
     this.fetchMetaTasks(this.taskIDs, () => {
       if (that.selectedEnt) {
-        that.fetchMetaAnnotations(that.selectedEnt)
+        that.fetchMetaAnnotations(that.selectedEnt, !this.modelPackSet)
       }
     })
   },
   watch: {
     'taskIDs': 'fetchMetaTasks',
-    'selectedEnt': 'fetchMetaAnnotations'
+    'selectedEnt': function() {
+      this.fetchMetaAnnotations(this.selectedEnt, !this.modelPackSet)
+    }
   }
 }
 </script>

diff --git a/webapp/frontend/src/mixins/MetaAnnotationService.js b/webapp/frontend/src/mixins/MetaAnnotationService.js
@@ -43,10 +43,7 @@ export default {
       }
       return this.$http.post(`/api/meta-annotations/`, payload)
     },
-    fetchMetaAnnotations (selectedEnt, callback, useDefault) {
-      if (useDefault === undefined) {
-        useDefault = true
-      }
+    fetchMetaAnnotations (selectedEnt, useDefault, callback) {
       if (this.tasks.length > 0 && selectedEnt !== null) {
         for (let t of this.tasks) {
           t.value = null
@@ -61,6 +58,8 @@ export default {
               let r = savedTask[0]
               task.value = r.meta_task_value
               task.annotation_id = r.id
+              task.validated = r.validated
+              task.acc = r.acc
               taskValues.push(task)
             } else if (useDefault && task.default) {
               // no annotation exists, should be validated and set as default value

diff --git a/webapp/frontend/src/styles/_variables.scss b/webapp/frontend/src/styles/_variables.scss
@@ -6,14 +6,15 @@
 
 $theme-colors: (
     "primary": #0072CE, //NHS Bright Blue
-    //"primary": #005EB8, //NHS Blue
     "danger": #DA291C, //NHS Emergency Services Red
     "warning": #768692, // NHS Mid Grey
     "info": #E8EDEE, // NHS Pale Grey
     "success": #009639, // NHS Green
     "light-success": #32ab60 // slightly lighter than NHS Green
 );
 
+$primary-alt: #005EB8;  //NHS Blue
+
 $navbar-bg: #0072CE; // NHS Bright Blue
 
 // colour palette - for backgrounds, borders, text-color etc.

diff --git a/webapp/frontend/src/views/TrainAnnotations.vue b/webapp/frontend/src/views/TrainAnnotations.vue
@@ -76,7 +76,8 @@
             </b-tabs>
           </transition>
           <transition name="slide-left">
-            <meta-annotation-task-container v-if="metaAnnotate" :taskIDs="hasMetaTasks"
+            <meta-annotation-task-container v-if="metaAnnotate" :model-pack-set="!!project.model_pack"
+                                            :taskIDs="hasMetaTasks"
                                             :selectedEnt="currentEnt">
             </meta-annotation-task-container>
           </transition>