Merge pull request #144 from CogStack/model-caching

Model caching

webapp/api/api/views.py

@@ -602,24 +602,6 @@ def search_solr(request):
     return search_collection(cdbs, query)
 
 
-@api_view(http_method_names=['DELETE', 'POST'])
-def cache_model(request, p_id):
-    method = request.method
-    project = ProjectAnnotateEntities.objects.get(id=p_id)
-    cat = get_cached_medcat(CAT_MAP=CAT_MAP, project=project)
-    if method == 'POST':
-        if cat is None:
-            get_medcat(CDB_MAP=CDB_MAP, VOCAB_MAP=VOCAB_MAP,
-                       CAT_MAP=CAT_MAP, project=project)
-            return Response({'result': f'Successfully loaded model for project:{p_id}'})
-        else:
-            return Response({'result': f'Model already loaded for project:{p_id}'})
-    else:
-        clear_cached_medcat(CAT_MAP, project)
-        logger.info(f'Cleared cached model{p_id}')
-        return Response({'result': f'Cleared cached model:{p_id}'})
-
-
 @api_view(http_method_names=['POST'])
 def upload_deployment(request):
     deployment_upload = request.data
@@ -628,15 +610,20 @@ def upload_deployment(request):
     return Response("successfully uploaded", 200)
 
 
-@api_view(http_method_names=['GET'])
-def cache_model(_, cdb_id):
-    get_cached_cdb(cdb_id, CDB_MAP)
-    return Response("success", 200)
+@api_view(http_method_names=['GET', 'DELETE'])
+def cache_model(request, cdb_id):
+    if request.method == 'GET':
+        get_cached_cdb(cdb_id, CDB_MAP)
+    elif request.method == 'DELETE' and cdb_id in CDB_MAP:
+        del CDB_MAP[cdb_id]
+    else:
+        return Response(f'Invalid method or cdb_id:{cdb_id} is invalid / not loaded', 400)
+    return Response('success', 200)
 
 
 @api_view(http_method_names=['GET'])
 def model_loaded(_):
-    return Response({p.id: get_cached_medcat(CAT_MAP, p) is not None
+    return Response({p.id: False if not p.concept_db else p.concept_db.id in CDB_MAP
                      for p in ProjectAnnotateEntities.objects.all()})
 
 

webapp/api/core/urls.py

@@ -59,7 +59,7 @@
     path('api/version/', api.views.version),
     path('api/concept-db-search-index-created/', api.views.concept_search_index_available),
     path('api/model-loaded/', api.views.model_loaded),
-    path('api/cache_model/<int:cdb_id>', api.views.cache_model),
+    path('api/cache-model/<int:cdb_id>/', api.views.cache_model),
     path('api/upload-deployment/', api.views.upload_deployment),
     path('api/model-concept-children/<int:cdb_id>/', api.views.cdb_cui_children),
     path('api/metrics/', api.views.metrics),

webapp/frontend/src/components/common/ClinicalText.vue

@@ -1,7 +1,7 @@
 <template>
   <div class="note-container">
-    <loading-overlay :loading="loading">
-      <div slot="message">Preparing Document...</div>
+    <loading-overlay :loading="loading !== null">
+      <div slot="message">{{loading}}</div>
     </loading-overlay>
     <div v-if="!loading" class="clinical-note">
       <v-runtime-template ref="clinicalText" :template="formattedText"></v-runtime-template>
@@ -34,10 +34,20 @@ export default {
     taskValues: Array,
     task: Object,
     ents: Array,
-    loading: Boolean,
+    loading: String,
     currentEnt: Object,
-    currentRelStartEnt: Object,
-    currentRelEndEnt: Object,
+    currentRelStartEnt: {
+      default () {
+        return {}
+      },
+      type: Object,
+    },
+    currentRelEndEnt: {
+      default () {
+        return {}
+      },
+      type: Object,
+    },
     addAnnos: Boolean
   },
   data () {
@@ -73,9 +83,9 @@ export default {
           styleClass = `highlight-task-${btnIndex}`
         }
 
-        if ((this.ents[i] === this.currentRelStartEnt) || (this.ents[i].id === (this.currentRelStartEnt || {}).id)) {
+        if (this.ents[i] === this.currentRelStartEnt) {
           styleClass += ' current-rel-start'
-        } else if ((this.ents[i] === this.currentRelEndEnt) || (this.ents[i].id === (this.currentRelEndEnt || {}).id)) {
+        } else if (this.ents[i] === this.currentRelEndEnt) {
           styleClass += ' current-rel-end'
         }
 

webapp/frontend/src/components/common/ConceptSummary.vue

@@ -200,22 +200,6 @@ export default {
         })
       },
       deep: true
-    },
-    'project': {
-      handler () {
-        let that = this
-        if (this.project.cdb_search_filter.length > 0) {
-          this.$http.get(`/api/concept-dbs/${this.project.cdb_search_filter[0]}/`).then(resp => {
-            if (resp.data) {
-              // this is a bit hacky - backend should just return the correct CDB search filter
-              that.$set(that, 'searchFilterDBIndex', `${resp.data.name}_id_${that.project.cdb_search_filter}`)
-              this.fetchDetail(this.selectedEnt, this.searchFilterDBIndex, () => {
-                that.cleanProps()
-              })
-            }
-          })
-        }
-      }
     }
   }
 }

webapp/frontend/src/views/Demo.vue

@@ -18,21 +18,17 @@
           <textarea v-model="cuiFilters" class="form-control" name="cui"
                     rows="3" placeholder="Comma separated list: S-91175000, S-84757009"></textarea>
         </div>
-        <div class="form-group">
-          <label>Type IDs Filter</label>
-          <textarea v-model="typeIDsFilters" class="form-control" name="type_ids"
-                    rows="3" placeholder="Comma separated list: T-00010, T00020"></textarea>
-        </div>
         <button @click="annotate()" class="btn btn-primary">Annotate</button>
       </form>
     </div>
     <div class="view-port">
       <div class="clinical-text">
-        <clinical-text :loading="loadingDoc" :text="annotatedText" :ents="ents"
+        <clinical-text :loading="loadingMsg" :text="annotatedText" :ents="ents"
                        :taskName="task" :taskValues="taskValues" @select:concept="selectEntity"></clinical-text>
       </div>
       <div class="sidebar">
-        <concept-summary :selectedEnt="currentEnt" :project="selectedProject"></concept-summary>
+        <concept-summary :selectedEnt="currentEnt" :project="selectedProject"
+                         :searchFilterDBIndex="searchFilterDBIndex"></concept-summary>
       </div>
     </div>
   </div>
@@ -57,13 +53,13 @@ export default {
       projects: [],
       selectedProject: {},
       cuiFilters: '',
-      typeIDsFilters: '',
       ents: [],
       currentEnt: {},
       annotatedText: '',
-      loadingDoc: false,
+      loadingMsg: null,
       task: TASK_NAME,
-      taskValues: VALUES
+      taskValues: VALUES,
+      searchFilterDBIndex: null
     }
   },
   created () {
@@ -89,11 +85,10 @@ export default {
         project_id: this.selectedProject.id,
         message: this.exampleText,
         cuis: this.cuiFilters,
-        tuis: this.tuiFilters
       }
-      this.loadingDoc = true
+      this.loadingMsg = 'Annotating Text...'
       this.$http.post('/api/annotate-text/', payload).then(resp => {
-        this.loadingDoc = false
+        this.loadingMsg = null
         this.ents = resp.data['entities'].map(e => {
           e.assignedValues = {}
           e.assignedValues[this.task] = this.taskValues[0]
@@ -105,6 +100,22 @@ export default {
     },
     selectEntity (entIndex) {
       this.currentEnt = this.ents[entIndex]
+    },
+    fetchCDBSearchIndex () {
+      if (this.selectedProject.cdb_search_filter.length > 0) {
+        this.$http.get(`/api/concept-dbs/${this.selectedProject.cdb_search_filter[0]}/`).then(resp => {
+          if (resp.data) {
+            this.searchFilterDBIndex = `${resp.data.name}_id_${this.selectedProject.cdb_search_filter}`
+          }
+        })
+      }
+    }
+  },
+  watch: {
+    'selectedProject': {
+      handler () {
+        this.fetchCDBSearchIndex()
+      }
     }
   }
 }

webapp/frontend/src/views/Home.vue

@@ -93,14 +93,14 @@
         <template #cell(model_loaded)="data">
           <div v-if="cdbLoaded[data.item.id]">
             <button class="btn btn-outline-success model-up">
-              <font-awesome-icon icon="times" class="clear-model-cache" @click="clearLoadedModel(data.item.id)"></font-awesome-icon>
+              <font-awesome-icon icon="times" class="clear-model-cache" @click="clearLoadedModel(data.item.concept_db)"></font-awesome-icon>
               <font-awesome-icon icon="fa-cloud-arrow-up"></font-awesome-icon>
             </button>
           </div>
           <div v-if="!cdbLoaded[data.item.id]">
-            <button class="btn btn-outline-secondary" @click="loadProjectCDB(data.item.id)">
-              <font-awesome-icon v-if="loadingModel !== data.item.id" icon="fa-cloud-arrow-up"></font-awesome-icon>
-              <font-awesome-icon v-if="loadingModel === data.item.id" icon="spinner" spin></font-awesome-icon>
+            <button class="btn btn-outline-secondary" @click="loadProjectCDB(data.item.concept_db)">
+              <font-awesome-icon v-if="loadingModel !== data.item.concept_db" icon="fa-cloud-arrow-up"></font-awesome-icon>
+              <font-awesome-icon v-if="loadingModel === data.item.concept_db" icon="spinner" spin></font-awesome-icon>
             </button>
           </div>
         </template>
@@ -125,13 +125,18 @@
       <transition name="alert"><div class="alert alert-danger" v-if="modelCacheLoadError" role="alert">Error loading MedCAT model for project</div></transition>
       <transition name="alert"><div class="alert alert-danger" v-if="projectLockedWarning" role="alert">Unable load a locked project. Contact your CogStack administrator to unlock</div></transition>
     </div>
+
     <modal v-if="clearModelModal" :closable="true" @modal:close="clearModelModal = false">
       <div slot="header">
         <h3>Confirm Clear Cached Model State</h3>
       </div>
       <div slot="body">
-        Confirm clearing cached MedCAT Model for Project {{clearModelModal}} (any other Projects that use this model). This will remove any interim training
-        done (if any). To recover the cached model, re-open the project(s), and re-submit all documents. If you're unsure you should not clear the model state.
+        <p>Confirm clearing cached MedCAT Model for Concept DB {{clearModelModal}} (and any other Projects that use this model). </p>
+        <p>
+          This will remove any interim training done (if any).
+          To recover the cached model, re-open the project(s), and re-submit all documents.
+          If you're unsure you should not clear the model state.
+        </p>
       </div>
       <div slot="footer">
         <button class="btn btn-primary" @click="confirmClearLoadedModel(clearModelModal)">Confirm</button>
@@ -267,18 +272,18 @@ export default {
         this.cdbLoaded = resp.data
       })
     },
-    clearLoadedModel (projId) {
-      this.clearModelModal = projId
+    clearLoadedModel (cdbId) {
+      this.clearModelModal = cdbId
     },
-    confirmClearLoadedModel (projId) {
+    confirmClearLoadedModel (cdbId) {
       this.clearModelModal = false
-      this.$http.delete(`/api/cache-model/${projId}/`).then(_ => {
+      this.$http.delete(`/api/cache-model/${cdbId}/`).then(_ => {
         this.fetchCDBsLoaded()
       })
     },
-    loadProjectCDB (projId) {
-      this.loadingModel = projId
-      this.$http.post(`api/cache-model/${projId}/`).then(_ => {
+    loadProjectCDB (cdbId) {
+      this.loadingModel = cdbId
+      this.$http.get(`/api/cache-model/${cdbId}/`).then(_ => {
         this.loadingModel = false
         this.fetchCDBsLoaded()
       }).catch(_ => {

webapp/frontend/src/views/TrainAnnotations.vue

@@ -28,10 +28,10 @@
         <div class="app-main">
           <document-summary :docs="docs" :moreDocs="nextDocSetUrl !== null"
                             :validatedDocIds="validatedDocuments"
-                            :selectedDocId="currentDoc !== null ? currentDoc.id : null" :loadingDoc="loadingDoc"
+                            :selectedDocId="currentDoc !== null ? currentDoc.id : null" :loadingDoc="loadingMsg !== null"
                             @request:nextDocSet="fetchDocuments()" @request:loadDoc="loadDoc"></document-summary>
           <div class="main-viewport">
-            <clinical-text :loading="loadingDoc" :text="currentDoc !== null ? currentDoc.text : null"
+            <clinical-text :loading="loadingMsg" :text="currentDoc !== null ? currentDoc.text : null"
                            :current-ent="currentEnt" :ents="ents" :task-name="taskName" :task-values="taskValues"
                            :addAnnos="true" :current-rel-start-ent="(currentRel || {}).start_entity"
                            :current-rel-end-ent="(currentRel || {}).end_entity"
@@ -319,7 +319,7 @@ export default {
       currentDoc: null,
       currentEnt: null,
       currentRel: null,
-      loadingDoc: false,
+      loadingMsg: null,
       resubmittingAllDocs: false,
       resubmitSuccess: false,
       helpModal: false,
@@ -425,25 +425,32 @@ export default {
       this.prepareDoc()
     },
     prepareDoc () {
-      this.loadingDoc = true
-      let payload = {
-        project_id: this.project.id,
-        document_ids: [this.currentDoc.id]
-      }
-      if (this.validatedDocuments.indexOf(this.currentDoc.id) === -1) {
-        payload['update'] = 1
-      }
-      this.$http.post('/api/prepare-documents/', payload).then(_ => {
-        // assuming a 200 is fine here.
-        this.fetchEntities()
-      }).catch(err => {
-        this.errors.modal = true
-        if (err.response) {
-          this.errors.message = err.response.data.message || 'Internal Server Error.'
-          this.errors.description = err.response.data.description || ''
-          this.errors.stacktrace = err.response.data.stacktrace
+      this.loadingMsg = "Loading MedCAT model..."
+      this.$http.get(`/api/cache-model/${this.project.concept_db}/`).then(_ => {
+        this.loadingMsg = "Preparing Document..."
+        let payload = {
+          project_id: this.project.id,
+          document_ids: [this.currentDoc.id]
         }
+        if (this.validatedDocuments.indexOf(this.currentDoc.id) === -1) {
+          payload['update'] = 1
+        }
+        this.$http.post('/api/prepare-documents/', payload).then(_ => {
+          // assuming a 200 is fine here.
+          this.fetchEntities()
+        }).catch(err => {
+          this.errors.modal = true
+          if (err.response) {
+            this.errors.message = err.response.data.message || 'Internal Server Error.'
+            this.errors.description = err.response.data.description || ''
+            this.errors.stacktrace = err.response.data.stacktrace
+          }
+        })
+      }).catch(_ => {
+        this.errors.modal = true
+        this.errors.mesasge = "Internal server error - cannot load MedCAT model. Contact your MedCAT admin quoting this project ID"
       })
+
     },
     fetchEntities (selectedEntId) {
       let params = this.nextEntSetUrl === null ? `?project=${this.projectId}&document=${this.currentDoc.id}`
@@ -484,7 +491,7 @@ export default {
             : this.ents[0]
           this.metaAnnotate = this.currentEnt && (this.currentEnt.assignedValues[TASK_NAME] === CONCEPT_ALTERNATIVE ||
             this.currentEnt.assignedValues[TASK_NAME] === CONCEPT_CORRECT)
-          this.loadingDoc = false
+          this.loadingMsg = null
           if (this.$route.query.annoStart && this.$route.query.annoEnd) {
             const ent = _.find(this.ents, e => {
               return Number(this.$route.query.annoStart) === e.start_ind &
@@ -709,18 +716,18 @@ export default {
         }
         subPromises.push(this.$http.post(`/api/submit-document/`, payload))
         this.resubmittingAllDocs = true
-        this.loadingDoc = true
+        this.loadingMsg = "Submitting document annotations..."
         Promise.all(subPromises).then(_ => {
           this.resubmitSuccess = true
-          this.loadingDoc = false
+          this.loadingMsg = null
           this.resubmittingAllDocs = false
           const that = this
           setTimeout(function () {
             that.resubmitSuccess = false
           }, 10000)
         }).catch(() => {
           this.resubmittingAllDocs = true
-          this.loadingDoc = false
+          this.loadingMsg = null
           this.errors.modal = true
           this.errors.message = 'Failure re-submitting all validated documents: Refresh Project'
         })
@@ -740,7 +747,7 @@ export default {
       window.addEventListener('keydown', this.keydown)
     },
     confirmReset () {
-      this.loadingDoc = true
+      this.loadingMsg = "Resetting document annotations..."
       const payload = {
         project_id: this.project.id,
         document_ids: [this.currentDoc.id],
@@ -749,7 +756,7 @@ export default {
       this.$http.post('/api/prepare-documents/', payload).then(_ => {
         this.fetchEntities()
         this.resetModal = false
-        this.loadingDoc = false
+        this.loadingMsg = null
       }).catch(err => {
         this.resetModal = false
         this.errors.modal = true