Merge pull request #126 from CogStack/more-search-improvements

More search improvements
CogStack · Mar 3, 2023 · 3d544e6 · 3d544e6
2 parents 5355a6b + 3d84b5e
commit 3d544e6
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Showing 9 changed files with 74 additions and 40 deletions.
diff --git a/webapp/Dockerfile b/webapp/Dockerfile
@@ -1,4 +1,4 @@
-FROM python:3.9
+FROM python:3.10
 
 # Update and upgrade everything
 RUN apt-get -y update && \

diff --git a/webapp/api/api/admin.py b/webapp/api/api/admin.py
@@ -26,6 +26,7 @@
 
 _dt_fmt = '%Y-%m-%d %H:%M:%S.%f'
 
+
 def reset_project(modeladmin, request, queryset):
     if not request.user.is_staff:
         raise PermissionDenied

diff --git a/webapp/api/api/solr_utils.py b/webapp/api/api/solr_utils.py
@@ -1,7 +1,7 @@
 import json
 import logging
 import re
-from typing import List
+from typing import List, Dict
 
 import requests
 from django.http import HttpResponseServerError
@@ -43,11 +43,29 @@ def collections_available(cdbs: List[int]):
         return HttpResponseServerError('Error requesting solr concept search collection list')
 
 
+def _process_result_repsonse(resp: Dict):
+    uniq_results_map = {}
+    docs = [d for d in resp['response']['docs']]
+    for d in docs:
+        if d['cui'][0] not in uniq_results_map:
+            parsed_doc = {
+                'cui': str(d['cui'][0]),
+                'pretty_name': d['pretty_name'][0],
+                'type_ids': d.get('type_ids', []),
+                'synonyms': d['synonyms']
+            }
+            if d.get('icd10'):
+                parsed_doc['icd10'] = d['icd10'][0]
+            if d.get('opcs4'):
+                parsed_doc['opcs4'] = d['opcs4'][0]
+            uniq_results_map[d['cui'][0]] = parsed_doc
+    return uniq_results_map
+
+
 def search_collection(cdbs: List[int], raw_query: str):
     query = raw_query.strip().replace(r'\s+', r'\s').split(' ')
     if len(query) == 1 and query[0] == '':
         return Response({'results': []})
-
     res = []
     if len(cdbs) > 0:
         uniq_results_map = {}
@@ -69,24 +87,20 @@ def search_collection(cdbs: List[int], raw_query: str):
             solr_url = f'http://{SOLR_HOST}:{SOLR_PORT}/solr/{collection_name}/select?q.op=OR&q={query_str}&rows=15'
             logger.info(f'Searching solr collection: {solr_url}')
             resp = json.loads(requests.get(solr_url).text)
+
             if 'error' in resp:
                 return HttpResponseServerError(f'Concept Search Index {collection_name} not available, '
                                                f'import concept DB first before trying to search it.')
+            elif len(resp['response']['docs']) == 0:
+                # try with wildcards at the end of the entire query, rather than each token
+                fallback_query = f'name:{" ".join(query)}* synonyms:{" ".join(query)}*'
+                solr_url = f'http://{SOLR_HOST}:{SOLR_PORT}/solr/{collection_name}/select?q.op=OR&q={fallback_query}&rows=15'
+                logger.info(f'Searching solr collection with fall back query at url: {solr_url}')
+                resp = json.loads(requests.get(solr_url).text)
+                uniq_results_map.update(_process_result_repsonse(resp))
             else:
-                docs = [d for d in resp['response']['docs']]
-                for d in docs:
-                    if d['cui'][0] not in uniq_results_map:
-                        parsed_doc = {
-                            'cui': str(d['cui'][0]),
-                            'pretty_name': d['pretty_name'][0],
-                            'type_ids': d.get('type_ids', []),
-                            'synonyms': d['synonyms']
-                        }
-                        if d.get('icd10'):
-                            parsed_doc['icd10'] = d['icd10'][0]
-                        if d.get('opcs4'):
-                            parsed_doc['opcs4'] = d['opcs4'][0]
-                        uniq_results_map[d['cui'][0]] = parsed_doc
+                uniq_results_map.update(_process_result_repsonse(resp))
+
         res = sorted(uniq_results_map.values(), key=lambda r: len(r['pretty_name']))
     return Response({'results': res})
 

diff --git a/webapp/frontend/src/components/anns/AddAnnotation.vue b/webapp/frontend/src/components/anns/AddAnnotation.vue
@@ -16,7 +16,8 @@
         <tr @keyup.stop>
           <td>Concept Lookup</td>
           <td>
-            <concept-picker :project="project" :selection="name" @pickedResult:concept="enrichCUI">
+            <concept-picker :project="project" :selection="name" @pickedResult:concept="enrichCUI"
+                            @picker:opened="conceptPickerState(true)" @picker:closed="conceptPickerState(false)">
             </concept-picker>
           </td>
         </tr>
@@ -110,7 +111,8 @@ export default {
       name: this.selection.selStr,
       prevText: this.selection.prevText,
       nextText: this.selection.nextText,
-      selectedCUI: null
+      selectedCUI: null,
+      conceptPickerOpen: false
     }
   },
   methods: {
@@ -148,11 +150,19 @@ export default {
     cancel () {
       this.$emit('request:addAnnotationComplete')
     },
-    keyup (e) {
-      if (e.keyCode === 27) {
+    keydown (e) {
+      if (e.keyCode === 27) { // esc key
         this.cancel()
+      } else if (e.keyCode === 13 && !this.conceptPickerOpen) { // enter key
+        this.submit()
       }
     },
+    conceptPickerState (val) {
+      const that = this
+      window.setTimeout(function () {
+        that.conceptPickerOpen = val
+      }, 100)
+    },
     newConceptSelected () {
       this.selectedCUI = null
     },
@@ -161,10 +171,10 @@ export default {
     }
   },
   mounted () {
-    window.addEventListener('keyup', this.keyup)
+    window.addEventListener('keydown', this.keydown)
   },
   beforeDestroy () {
-    window.removeEventListener('keyup', this.keyup)
+    window.removeEventListener('keydown', this.keydown)
   }
 }
 </script>

diff --git a/webapp/frontend/src/components/anns/TaskBar.vue b/webapp/frontend/src/components/anns/TaskBar.vue
@@ -29,7 +29,8 @@ export default {
     submitLocked: Boolean,
     altSearch: Boolean,
     terminateEnabled: Boolean,
-    irrelevantEnabled: Boolean
+    irrelevantEnabled: Boolean,
+    conceptSelection: Object
   },
   watch: {
     'submitLocked' (oldVal, newVal) {
@@ -67,8 +68,8 @@ export default {
       }
       return true
     },
-    keyup  (e) {
-      if (e.keyCode === 13) {
+    keydown (e) {
+      if (e.keyCode === 13 && !this.conceptSelection) {
         if (!this.submitDisabled()) {
           this.ignoreSubmit()
           this.submit()
@@ -100,10 +101,10 @@ export default {
       }
     },
     listenSubmit () {
-      window.addEventListener('keyup', this.keyup)
+      window.addEventListener('keydown', this.keydown)
     },
     ignoreSubmit () {
-      window.removeEventListener('keyup', this.keyup)
+      window.removeEventListener('keydown', this.keydown)
     }
   },
   mounted () {

diff --git a/webapp/frontend/src/components/common/ClinicalText.vue b/webapp/frontend/src/components/common/ClinicalText.vue
@@ -121,7 +121,7 @@ export default {
       const anchor = selection.anchorNode
       const focus = selection.focusNode
 
-      if (selStr.length > 0 && focus !== null) {
+      if (selStr.length > 0 && focus !== null && focus.data) {
         let nextText = focus.data.slice(selection.focusOffset)
         let nextSibling = focus.nextSibling || focus.parentElement.nextSibling
         let priorText = anchor.data.slice(0, selection.anchorOffset)

diff --git a/webapp/frontend/src/components/common/ConceptPicker.vue b/webapp/frontend/src/components/common/ConceptPicker.vue
@@ -6,7 +6,9 @@
             :appendToBody="true"
             :options="searchResults"
             :loading="loadingResults"
-            label="cui">
+            label="cui"
+            @open="$emit('picker:opened')"
+            @close="$emit('picker:closed')">
     <template v-slot:option="option">
       <span class="select-option">{{option.name}}</span>
       <span class="select-option-cui"> - {{option.cui}}</span>
@@ -34,7 +36,7 @@ export default {
       el.focus()
       el.value = that.selection
       that.searchCUI(that.selection)
-    }, 500)
+    }, 150)
   },
   data () {
     return {

diff --git a/webapp/frontend/src/components/common/ConceptSummary.vue b/webapp/frontend/src/components/common/ConceptSummary.vue
@@ -203,7 +203,8 @@ export default {
         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) {
-              that.searchFilterDBIndex = `${resp.data.name}_id_${that.project.cdb_search_filter}`
+              // 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()
               })

diff --git a/webapp/frontend/src/views/TrainAnnotations.vue b/webapp/frontend/src/views/TrainAnnotations.vue
@@ -2,9 +2,7 @@
   <div @click="selectRelation(null)" class="container-fluid app-container">
     <div class="app-header">
       <div class="project-name">
-        <span>
-          <h4>{{ project === null ? '' : project.name }}</h4>
-        </span>
+        <h4>{{ project === null ? '' : project.name }}</h4>
       </div>
 
       <div class="meta">
@@ -37,12 +35,14 @@
                            :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"
-                           @select:concept="selectEntity" @select:addSynonym="addSynonym"></clinical-text>
+                           @select:concept="selectEntity" @select:addSynonym="addSynonym"
+                           @pick:concept="conceptPickerState"></clinical-text>
             <div class="taskbar">
               <nav-bar class="nav" :ents="ents" :currentEnt="currentEnt" @select:next="next" @select:back="back"></nav-bar>
               <task-bar class="tasks" :taskLocked="taskLocked" :ents="ents" :altSearch="altSearch"
                         :submitLocked="docToSubmit !== null" :terminateEnabled="(project || {}).terminate_available"
                         :irrelevantEnabled="(project || {}).irrelevant_available"
+                        :conceptSelection="conceptSynonymSelection"
                         @select:remove="markRemove" @select:correct="markCorrect"
                         @select:kill="markKill" @select:alternative="toggleAltSearch"
                         @select:irrelevant="markIrrelevant" @submit="submitDoc"></task-bar>
@@ -325,6 +325,7 @@ export default {
       helpModal: false,
       projectCompleteModal: false,
       resetModal: false,
+      conceptPickerOpen: true,
       errors: {
         modal: false,
         message: '',
@@ -606,12 +607,14 @@ export default {
         that.metaAnnotate = false
       }, 50)
     },
+    conceptPickerState (val) {
+      this.conceptPickerOpen = val
+    },
     next () {
       this.selectEntity(this.ents.indexOf(this.currentEnt) + 1)
     },
     back () {
       this.selectEntity(this.ents.indexOf(this.currentEnt) - 1)
-      this.selectEntity(this.ents.indexOf(this.currentEnt) - 1)
     },
     submitDoc (docId) {
       if (this.docToSubmit === null) {
@@ -703,16 +706,18 @@ export default {
         })
       }
     },
-    keyup (e) {
+    keydown (e) {
       if (e.keyCode === 13 && this.docToSubmit && !this.submitConfirmedLoading) {
         this.submitConfirmed()
+      } else if (e.keyCode === 27 && this.docToSubmit) {
+        this.docToSubmit = null
       }
     },
     confirmSubmitListenerRemove () {
-      window.removeEventListener('keyup', this.keyup)
+      window.removeEventListener('keydown', this.keydown)
     },
     confirmSubmitListenerAdd () {
-      window.addEventListener('keyup', this.keyup)
+      window.addEventListener('keydown', this.keydown)
     },
     confirmReset () {
       this.loadingDoc = true