From 91aa2a2feba7103faf89979a476de1cc32a1db79 Mon Sep 17 00:00:00 2001
From: Guillaume Poirier-Morency <guillaumepoiriermorency@gmail.com>
Date: Thu, 7 Sep 2023 10:40:48 -0700
Subject: [PATCH 1/2] Limit to 50 platforms and 20 terms/category in
 development mode

---
 src/views/Browser.vue | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/src/views/Browser.vue b/src/views/Browser.vue
index 050eb1d..5b257f4 100644
--- a/src/views/Browser.vue
+++ b/src/views/Browser.vue
@@ -120,8 +120,8 @@ import Error from "@/components/Error.vue";
 import { mapMutations, mapState } from "vuex";
 
 const MAX_URIS_IN_CLAUSE = 200;
-const MAX_TERMS_PER_CATEGORY = 200;
-const MAX_PLATFORMS = 200;
+const MAX_TERMS_PER_CATEGORY = process.env.NODE_ENV !== "production" ? 20 : 200;;
+const MAX_PLATFORMS = process.env.NODE_ENV !== "production" ? 50 : 200;
 
 function quoteIfNecessary(s) {
   if (s.match(/[(), "]/) || s.length === 0) {

From c1e80ecb3d0381630f3bf9464a2f362c92db0647 Mon Sep 17 00:00:00 2001
From: Guillaume Poirier-Morency <guillaumepoiriermorency@gmail.com>
Date: Thu, 7 Sep 2023 10:42:01 -0700
Subject: [PATCH 2/2] Allow selection of any dataset annotation

---
 src/components/AnnotationSelector.vue | 14 ++++----
 src/components/DatasetPreview.vue     | 47 ++++++++++++++++++---------
 src/views/Browser.vue                 | 40 ++++++++++++++++++-----
 3 files changed, 68 insertions(+), 33 deletions(-)

diff --git a/src/components/AnnotationSelector.vue b/src/components/AnnotationSelector.vue
index ec75a6c..054293d 100644
--- a/src/components/AnnotationSelector.vue
+++ b/src/components/AnnotationSelector.vue
@@ -229,17 +229,15 @@ export default {
      */
     computeSelectedAnnotations(newVal, selectedCategories) {
       let sc = new Set(selectedCategories.map(sc => getCategoryId(sc)));
-      let selectedAnnotations = newVal
+      return newVal
         // exclude annotations from selected categories
         .filter(a => !sc.has(a.split(SEPARATOR, 2)[0]))
-        .map(a => this.annotationById[a]);
-        selectedAnnotations.forEach(a => {
-          if (!a) {
-            console.warn('Term is not selectable');
-          }
+        .map(a => this.annotationById[a] || {
+          classUri: a.split(SEPARATOR, 2)[0],
+          className: "",
+          termUri: a.split(SEPARATOR, 2)[1],
+          termName: ""
         });
-
-        return selectedAnnotations.filter(a => a)
     },
     /**
      * Selected categories.
diff --git a/src/components/DatasetPreview.vue b/src/components/DatasetPreview.vue
index 72ef8a7..bb80152 100644
--- a/src/components/DatasetPreview.vue
+++ b/src/components/DatasetPreview.vue
@@ -2,20 +2,15 @@
     <div class="py-3">
         <h3>{{ dataset.name }}</h3>
         <template v-for="term in includedTerms">
-            <v-chip v-if="isClickable(term)"
+            <v-chip
                     :key="getId(term)"
-                    @click="isClickable(term) && handleChipClick(term) || null"
+                    @click="handleChipClick(term)"
                     small :color="getChipColor(term.objectClass)"
                     :title="getTitle(term)"
-                    class="mb-1 mr-1">
-                {{ term.termName }}
-                <v-icon v-if="isClickable(term)" right>mdi-plus</v-icon>
-            </v-chip>
-            <v-chip v-else :key="getId(term)"
-                    small :color="getChipColor(term.objectClass)"
-                    :title="getTitle(term)"
-                    class="mb-1 mr-1">
+                    class="text-capitalize mb-1 mr-1">
                 {{ term.termName }}
+                <v-icon v-if="isSelectable(term)" right>mdi-plus</v-icon>
+                <v-icon v-else-if="isUnselectable(term)" right>mdi-minus</v-icon>
             </v-chip>
         </template>
         <div v-html="this.description"></div>
@@ -51,6 +46,7 @@ export default {
     selectedAnnotations: Array,
     availableAnnotations: Array
   },
+  events: ["annotation-selected", "annotation-unselected"],
   data() {
     return {
       includedTerms: []
@@ -126,13 +122,20 @@ export default {
      * @param term
      * @returns {boolean}
      */
-    isClickable(term) {
-      return this.availableAnnotationIds.has(this.getId(term))
-        && !this.selectedCategoryIds.has(getCategoryId(term))
-        && !this.selectedAnnotationIds.has(this.getId(term));
+    isSelectable(term) {
+      return !this.selectedCategoryIds.has(getCategoryId(term)) && !this.selectedAnnotationIds.has(this.getId(term));
+    },
+    isUnselectable(term) {
+      return this.selectedAnnotationIds.has(this.getId(term));
     },
     handleChipClick(term) {
-      this.$emit("chip-clicked", term);
+      if (this.isSelectable(term)) {
+        this.$emit("annotation-selected", term);
+      } else if (this.isUnselectable(term)) {
+        this.$emit("annotation-unselected", term);
+      } else {
+        console.warn(`Term ${term} cannot be unselected.`, term);
+      }
     },
     getChipColor(objectClass) {
       return this.chipColorMap[objectClass] || "orange";
@@ -144,7 +147,19 @@ export default {
     updateTerms() {
       this.includedTerms = [];
       this.getTerms().then(terms => {
-        this.includedTerms = terms.sort((a, b) => OBJECT_CLASS_PRIORITY[a.objectClass] - OBJECT_CLASS_PRIORITY[b.objectClass]);
+        // we don't display the same term from different object classes
+        let seenIds = new Set();
+        this.includedTerms = terms
+          .sort((a, b) => OBJECT_CLASS_PRIORITY[a.objectClass] - OBJECT_CLASS_PRIORITY[b.objectClass])
+          .filter(term => {
+            let id = this.getId(term);
+            if (seenIds.has(id)) {
+              console.log("Skipped already seen term");
+              return true;
+            }
+            seenIds.add(id);
+            return true;
+          });
       });
     }
   },
diff --git a/src/views/Browser.vue b/src/views/Browser.vue
index 5b257f4..42ac645 100644
--- a/src/views/Browser.vue
+++ b/src/views/Browser.vue
@@ -70,7 +70,8 @@
                                         :selected-categories="searchSettings.categories"
                                         :selected-annotations="searchSettings.annotations"
                                         :available-annotations="datasetsAnnotations"
-                                        @chip-clicked="handleChipClicked"></DatasetPreview>
+                                        @annotation-selected="selectTerm"
+                                        @annotation-unselected="unselectTerm"/>
                     </td>
                 </template>
                 <template v-slot:footer.prepend>
@@ -101,7 +102,7 @@
 <script>
 import SearchSettings from "@/components/SearchSettings";
 import { ExpressionExperimentType, SearchSettings as SearchSettingsModel } from "@/models";
-import { baseUrl, excludedCategories, excludedTerms, marked, HIGHLIGHT_LABELS } from "@/config/gemma";
+import { baseUrl, excludedCategories, excludedTerms, HIGHLIGHT_LABELS, marked } from "@/config/gemma";
 import { chain, debounce, escapeRegExp, isEqual, sumBy } from "lodash";
 import DatasetPreview from "@/components/DatasetPreview.vue";
 import { highlight } from "@/search-utils";
@@ -564,8 +565,16 @@ export default {
       let mFilter = filter;
       if (mFilter) {
         mFilter = mFilter.map(clause => clause
-          .filter(subClause => !disallowedPrefixes.some(p => subClause.startsWith(p))))
-          .filter(clause => clause.length > 0);
+          .map(subClause => {
+            for (let p of disallowedPrefixes) {
+              if (subClause.startsWith(p)) {
+                // this will render the clause always true and preserve the term URI for retainMentionedTerms to work
+                subClause = `${subClause} or ${p}id > 0`;
+                break;
+              }
+            }
+            return subClause;
+          }));
       }
       return compressFilter(mFilter).then(compressedFilter => {
         let payload = {
@@ -580,6 +589,7 @@ export default {
         if (excludedTerms !== undefined) {
           payload["excludedTerms"] = excludedTerms;
         }
+        payload["retainMentionedTerms"] = true;
         if (this.myself) {
           payload["gid"] = this.myself.group;
         }
@@ -706,12 +716,24 @@ export default {
         .join(" ");
     },
     ...mapMutations(["setTitle", "setFilterSummary", "setFilterDescription", "setLastError"]),
-    handleChipClicked(previewTerm) {
-     this.searchSettings.annotations.push({
-        classUri: previewTerm.classUri, 
+    selectTerm(previewTerm) {
+      this.searchSettings.annotations.push({
+        classUri: previewTerm.classUri,
         className: previewTerm.className,
-        termUri: previewTerm.termUri, 
-        termName: previewTerm.termName})
+        termUri: previewTerm.termUri,
+        termName: previewTerm.termName
+      });
+    },
+    unselectTerm(previewTerm) {
+      let categoryId = getCategoryId(previewTerm);
+      let termId = getTermId(previewTerm);
+      for (let [i, a] of this.searchSettings.annotations.entries()) {
+        if (getCategoryId(a) === categoryId && getTermId(a) === termId) {
+          this.searchSettings.annotations.splice(i, 1);
+          return;
+        }
+      }
+      console.warn(`${previewTerm} is not selected and thus cannot be unselected.`);
     }
   },
   created() {