fix(medcat-trainer): Add annotation / add concept fixes.

medcat-trainer/webapp/api/api/model_cache.py

@@ -167,6 +167,9 @@ def get_medcat(project,
                cdb_map: Dict[str, CDB]=CDB_MAP,
                vocab_map: Dict[str, Vocab]=VOCAB_MAP,
                cat_map: Dict[str, CAT]=CAT_MAP):
+    cat = get_cached_medcat(project, cat_map)
+    if cat is not None:
+        return cat
     try:
         if project.model_pack is None:
             cat = get_medcat_from_cdb_vocab(project, cdb_map, vocab_map, cat_map)

medcat-trainer/webapp/api/api/solr_utils.py

@@ -165,7 +165,7 @@ def drop_collection(cdb_model: ConceptDB):
 
 def ensure_concept_searchable(cui, cdb: CDB, cdb_model: ConceptDB):
     """
-    Adds a single cui and associated metadata is available in the assocaited solr search index.
+    Adds a single cui and associated metadata is available in the associated solr search index.
     Args:
         cui: concept unique identifier of the concept to make searchable
         cdb: the MedCAT CDB where the cui can be found

medcat-trainer/webapp/api/api/utils.py

@@ -237,7 +237,6 @@ def get_create_cdb_infos(cdb, concept, cui, cui_info_prop, code_prop, desc_prop,
     return model_clazz.objects.filter(code__in=codes)
 
 
-
 def create_annotation(source_val: str, selection_occurrence_index: int, cui: str, user: User,
                       project: ProjectAnnotateEntities, document: Document):
     text = document.text

medcat-trainer/webapp/api/api/views.py

@@ -435,30 +435,44 @@ def add_concept(request):
 
     cat = get_medcat(project=project)
 
-    if cui in cat.cdb.cui2names:
-        err_msg = f'Cannot add a concept "{name}" with cui:{cui}. CUI already linked to {cat.cdb.cui2names[cui]}'
+    if cui in cat.cdb.cui2info:
+        err_msg = f'Cannot add a concept "{name}" with cui:{cui}. CUI already linked to {cat.cdb.cui2info[cui]["preferred_name"]}'
         logger.error(err_msg)
         return Response({'err': err_msg}, 400)
 
     spacy_doc = cat(document.text)
     spacy_entity = None
     if source_val in spacy_doc.text:
-        start = spacy_doc.text.index(source_val)
-        end = start + len(source_val)
-        spacy_entity = [tkn for tkn in spacy_doc if tkn.idx >= start and tkn.idx <= end]
-
+        # Find all occurrences of source_val in the text
+        all_occurrences_start_idxs = []
+        idx = 0
+        while idx != -1:
+            idx = spacy_doc.text.find(source_val, idx)
+            if idx != -1:
+                all_occurrences_start_idxs.append(idx)
+                idx += len(source_val)
+
+        # Use selection_idx to get the correct occurrence
+        if sel_occur_idx < len(all_occurrences_start_idxs):
+            start = all_occurrences_start_idxs[sel_occur_idx]
+            end = start + len(source_val)
+            # Find tokens that overlap with the span [start, end)
+            # A token overlaps if: token_start < end AND token_end > start
+            spacy_entity = [tkn for tkn in spacy_doc if tkn.char_index < end and (tkn.char_index + len(tkn.text)) > start]
+    # if len(spacy_entity) == 0:
+    #     spacy_entity = None
     cat.trainer.add_and_train_concept(cui=cui, name=name, name_status='P', mut_doc=spacy_doc, mut_entity=spacy_entity)
 
+
     id = create_annotation(source_val=source_val,
                            selection_occurrence_index=sel_occur_idx,
                            cui=cui,
                            user=user,
                            project=project,
-                           document=document,
-                           cat=cat)
+                           document=document)
 
     # ensure new concept detail is available in SOLR search service
-    ensure_concept_searchable(cui, cat.cdb, project.concept_db)
+    ensure_concept_searchable(cui, cat.cdb, project.cdb_search_filter.first())
 
     # add to project cuis if required.
     if (project.cuis or project.cuis_file) and project.restrict_concept_lookup:

medcat-trainer/webapp/frontend/src/components/anns/AddAnnotation.vue

@@ -125,16 +125,14 @@ export default {
         cui: this.selectedCUI.cui
       }
       this.loading = true
-      this.$http.get(`/api/cache-model/${this.project.id}/`).then(_ => {
+      this.$http.post('/api/add-annotation/', payload).then(resp => {
         this.loading = false
-        this.$http.post('/api/add-annotation/', payload).then(resp => {
-          this.$emit('request:addAnnotationComplete', resp.data.id)
-          this.selectedCUI = null
-        })
+        this.$emit('request:addAnnotationComplete', resp.data.id)
+        this.selectedCUI = null
       }).catch(err => {
+        this.loading = false
         this.errorMessage = err.response.data.message || 'Error loading model.'
       })
-
     },
     cancel () {
       this.$emit('request:addAnnotationComplete')

medcat-trainer/webapp/frontend/src/components/common/AddNewConcept.vue

@@ -41,8 +41,16 @@
       </tbody>
     </table>
     <div class="footer action-buttons">
-      <button class="btn btn-primary" :disabled="!addConceptEnabled()"
-              @click="addConcept">Add Concept</button>
+      <button class="btn btn-primary" :disabled="!addConceptEnabled() || loading"
+              @click="addConcept">
+        <font-awesome-icon v-if="!loading" icon="plus"></font-awesome-icon>
+        <font-awesome-icon v-if="loading" icon="spinner" spin size="xs" />
+        Add Concept
+      </button>
+    </div>
+    <div class="alert alert-info" role="alert" v-if="loading">
+      <font-awesome-icon icon="spinner" spin size="xs" />
+      Caching model, please wait...
     </div>
     <div class="alert alert-danger" role="alert" v-if="addConceptErr">
       {{addConceptErr}}
@@ -73,7 +81,8 @@ export default {
         cui: '',
         synonyms: ''
       },
-      addConceptErr: false
+      addConceptErr: false,
+      loading: false
     }
   },
   methods: {
@@ -96,23 +105,35 @@ export default {
       let nextCtx = this.selection.nextText.slice(0, 30).split(' ').slice(0, -1)
       payload['context'] = `${this.selection.prevText}${this.selection.selStr}${nextCtx}`
 
-      this.$http.post(`/api/add-concept/`, payload).then(resp => {
-        this.$emit('request:addConceptComplete', resp.data.id)
+      this.loading = true
+      this.$http.get(`/api/cache-model/${this.project.id}/`).then(_ => {
+        this.$http.post(`/api/add-concept/`, payload).then(resp => {
+          this.loading = false
+          this.$emit('request:addConceptComplete', resp.data.id)
+        }).catch(err => {
+          this.loading = false
+          if (err.code === 400) {
+            this.addConceptErr = 'Invalid CUI value. CUI already exists in MedCAT.'
+            let that = this
+            setTimeout(function () {
+              that.addConceptErr = false
+            }, 5000)
+          } else {
+            this.addConceptErr = `Error adding concept:${(err.response.data || {}).err || 'Unknown error: more info in the console'}`
+            console.error(err)
+            let that = this
+            setTimeout(function () {
+              that.addConceptErr = false
+            }, 5000)
+          }
+        })
       }).catch(err => {
-        if (err.code === 400) {
-          this.addConceptErr = 'Invalid CUI value. CUI already exists in MedCAT.'
-          let that = this
-          setTimeout(function () {
-            that.addConceptErr = false
-          }, 5000)
-        } else {
-          this.addConceptErr = `Error adding concept:${(err.response.data || {}).err || 'Unknown error: more info in the console'}`
-          console.error(err)
-          let that = this
-          setTimeout(function () {
-            that.addConceptErr = false
-          }, 5000)
-        }
+        this.loading = false
+        this.addConceptErr = err.response?.data?.message || 'Error loading model.'
+        let that = this
+        setTimeout(function () {
+          that.addConceptErr = false
+        }, 5000)
       })
     }
   }