Merge branch 'master' into feature-display-uri-descriptions-2

PavlidisLab · Jun 20, 2024 · 03f242d · 03f242d
2 parents 913ce4d + e3a0c3f
commit 03f242d
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diff --git a/src/components/CodeSnippet.vue b/src/components/CodeSnippet.vue
@@ -96,7 +96,7 @@ export default {
         {
           label: "gemma.R",
           language: "r",
-          instructions: `Install the [gemma.R](https://github.com/PavlidisLab/gemma.R) package from GitHub and run the following code in an R console:`
+          instructions: `Install the [gemma.R](https://bioconductor.org/packages/release/bioc/html/gemma.R.html) package from GitHub and run the following code in an R console:`
         },
         {
           label: "curl",
@@ -142,19 +142,11 @@ export default {
         if (sort !== undefined) {
           queryGemmapy.push(`, sort=${this.escapePythonString(sort)}`);
         }
-        queryGemmapy.push(", offset=offset, limit=limit)");
 
         queryGemmapy.unshift(`import gemmapy\n` +
-          `api_instance = gemmapy.GemmaPy()\n` +
-          `all_datasets = []\n` +
-          `limit = ${MAX_DATASETS}\n` +
-          `for offset in range(0, ${this.totalNumberOfExpressionExperiments}, limit):\n` +
-          `\tapi_response = api_instance.get_datasets_by_ids([], `);
-        queryGemmapy.push(`)\n` +
-          `\tif api_response.data:\n` +
-          `\t\tall_datasets.extend(api_response.data)\n` +
-          `\telse:\n` +
-          `\t\tbreak`);
+          `api = gemmapy.GemmaPy()\n` +
+          `data = api.get_all_pages(api.get_datasets,`);
+        queryGemmapy.push(`)\n`)
       }
       tabs[0].content = queryGemmapy.join("");
 
@@ -173,7 +165,7 @@ export default {
         if (sort !== undefined) {
           queryGemmaR.push(`, sort = ${this.escapeRString(sort)}`);
         }
-        queryGemmaR.unshift(`devtools::install_github("PavlidisLab/gemma.R")\n` +
+        queryGemmaR.unshift(`BiocManager::install("gemma.R")\n` +
           `library(gemma.R)\n` +
           `library(dplyr)\n` +
           `data <- get_datasets(`);

diff --git a/src/components/DatasetPreview.vue b/src/components/DatasetPreview.vue
@@ -1,6 +1,6 @@
 <template>
     <div class="py-3">
-        <h3> <a v-bind:href="datasetUrl">{{ dataset.shortName }}</a>: {{ dataset.name }}</h3>
+        <h3> <a v-bind:href="datasetUrl" target="_blank">{{ dataset.shortName }}</a>: {{ dataset.name }}</h3>
         <v-chip v-for="term in includedTerms" :key="getId(term)"
                 @[getClickEventName(term)]="handleChipClick(term)"
                 small :color="getChipColor(term.objectClass)"
@@ -123,8 +123,10 @@ export default {
     getTitle(term) {
       let n = this.getNumberOfExpressionExperiments(term);
       if (term.termUri !== null) { // if the term is not free text
-        if (n > 0) {
+        if (n > 0 && this.isSelectable(term)) {
           return `${term.className.charAt(0).toUpperCase() + term.className.slice(1)}: ${term.termUri} via ${term.objectClass}; click to add terms to filter (associated with ${n} datasets)`;
+        } else if (n > 0 && this.isUnselectable(term)){
+          return `${term.className.charAt(0).toUpperCase() + term.className.slice(1)}: ${term.termUri} via ${term.objectClass}; click to remove terms from filter (associated with ${n} datasets)`;
         } else {
           return `${term.className.charAt(0).toUpperCase() + term.className.slice(1)}: ${term.termUri} via ${term.objectClass}`;
         }

diff --git a/src/components/PlatformSelector.vue b/src/components/PlatformSelector.vue
diff --git a/src/components/SearchSettings.vue b/src/components/SearchSettings.vue
@@ -37,9 +37,10 @@
                 class="mb-1"/>
         <TechnologyTypeSelector
                 v-if="searchSettings.resultTypes.indexOf(platformResultType) === -1"
-                v-model="searchSettings.platforms"
+                v-model="selectedTech"
                 :platforms="platforms"
-                :selected-technology-types.sync="searchSettings.technologyTypes"
+                :selectedPlatforms.sync="searchSettings.platforms"
+                :selectedTechnologyTypes.sync="searchSettings.technologyTypes"
                 :disabled="platformDisabled"
                 :loading="platformLoading"
                 class="mb-1"/>
@@ -108,6 +109,7 @@ export default {
   emits: ["input"],
   data() {
     return {
+      selectedTech: [],
       searchSettings: this.value,
       platformResultType: ArrayDesignType,
       selectedTaxa: this.value ? [this.value] : []
@@ -134,10 +136,9 @@ export default {
   },
   methods: {
     clearAllSelections() {
+      this.selectedTech = []
       this.searchSettings.annotations = [];
-      this.searchSettings.platforms = [];
       this.searchSettings.taxon = []; 
-      this.searchSettings.technologyTypes = [];
       this.searchSettings.query = undefined;
     }
   },

diff --git a/src/components/TechnologyTypeSelector.vue b/src/components/TechnologyTypeSelector.vue
@@ -35,15 +35,8 @@
 import { chain, isEqual } from "lodash";
 import { formatNumber } from "@/lib/utils";
 import { mapState } from "vuex";
+import { TECHNOLOGY_TYPES, TOP_TECHNOLOGY_TYPES} from "@/lib/platformConstants";
 
-const MICROARRAY_TECHNOLOGY_TYPES = ["ONECOLOR", "TWOCOLOR", "DUALMODE"];
-const RNA_SEQ_TECHNOLOGY_TYPES = ["SEQUENCING"];
-const OTHER_TECHNOLOGY_TYPES = ["GENELIST", "OTHER"];
-const TECHNOLOGY_TYPES = MICROARRAY_TECHNOLOGY_TYPES + RNA_SEQ_TECHNOLOGY_TYPES + OTHER_TECHNOLOGY_TYPES;
-const TOP_TECHNOLOGY_TYPES = [
-  ["RNA_SEQ", "RNA-Seq", RNA_SEQ_TECHNOLOGY_TYPES],
-  ["MICROARRAY", "Microarray", MICROARRAY_TECHNOLOGY_TYPES],
-  ["OTHER", "Other", OTHER_TECHNOLOGY_TYPES]];
 
 export default {
   name: "TechnologyTypeSelector",
@@ -59,10 +52,18 @@ export default {
   events: ["input"],
   data() {
     return {
-      selectedValues: this.value.map(t => t.id)
     };
   },
   computed: {
+    selectedValues:
+    {
+      get(){
+        return this.value
+      },
+      set(val){
+        this.$emit('input',val)
+      }
+    },
     technologyTypes() {
       return TOP_TECHNOLOGY_TYPES
         .filter(([id]) => id !== "OTHER" || this.debug)
@@ -104,9 +105,6 @@ export default {
     }
   },
   watch: {
-    value(newVal) {
-      this.selectedValues = newVal.map(t => t.id);
-    },
     selectedValues(newVal, oldVal) {
       let ids = new Set(newVal.filter(id => !TECHNOLOGY_TYPES.includes(id)));
       let selectedTechnologyTypes = this.computeSelectedTechnologyTypes(ids);
@@ -115,7 +113,7 @@ export default {
       let oldSelectedTechnologyTypes = this.computeSelectedTechnologyTypes(oldIds);
       let oldSelectedPlatforms = this.computeSelectedPlatforms(oldIds, oldSelectedTechnologyTypes);
       if (!isEqual(selectedPlatforms.map(p => p.id), oldSelectedPlatforms.map(p => p.id))) {
-        this.$emit("input", selectedPlatforms);
+        this.$emit("update:selectedPlatforms", selectedPlatforms);
       }
       if (!isEqual(selectedTechnologyTypes, oldSelectedTechnologyTypes)) {
         this.$emit("update:selectedTechnologyTypes", selectedTechnologyTypes);

diff --git a/src/lib/filter.js b/src/lib/filter.js
@@ -1,6 +1,10 @@
 import { SearchSettings } from "@/lib/models";
 import { chain, sumBy } from "lodash";
 import { getCategoryId, pluralize } from "@/lib/utils";
+import { MICROARRAY_TECHNOLOGY_TYPES, RNA_SEQ_TECHNOLOGY_TYPES, OTHER_TECHNOLOGY_TYPES} from "@/lib/platformConstants";
+
+
+
 
 const MAX_URIS_IN_CLAUSE = 200;
 
@@ -159,10 +163,10 @@ export function generateFilterDescription(searchSettings,inferredTermLabelsByCat
   }
   if (searchSettings.platforms.length > 0 || searchSettings.technologyTypes.length > 0) {
     const platformValues = searchSettings.platforms.map(platforms => platforms.name);
-    if (searchSettings.technologyTypes && searchSettings.technologyTypes.includes("RNASEQ")) {
+    if (searchSettings.technologyTypes && RNA_SEQ_TECHNOLOGY_TYPES.every(tech=>searchSettings.technologyTypes.includes(tech))) {
       platformValues.unshift("RNA-Seq");
     }
-    if (searchSettings.technologyTypes && searchSettings.technologyTypes.length >= 3 && searchSettings.platforms.length === 0) {
+    if (searchSettings.technologyTypes && MICROARRAY_TECHNOLOGY_TYPES.every(tech=>searchSettings.technologyTypes.includes(tech))) {
       platformValues.unshift("Microarray");
     }
     filter.push({ key: "Platforms", value: platformValues });

diff --git a/src/lib/platformConstants.js b/src/lib/platformConstants.js
@@ -0,0 +1,11 @@
+const MICROARRAY_TECHNOLOGY_TYPES = ["ONECOLOR", "TWOCOLOR", "DUALMODE"];
+const RNA_SEQ_TECHNOLOGY_TYPES = ["SEQUENCING"];
+const OTHER_TECHNOLOGY_TYPES = ["GENELIST", "OTHER"];
+const TECHNOLOGY_TYPES = MICROARRAY_TECHNOLOGY_TYPES + RNA_SEQ_TECHNOLOGY_TYPES + OTHER_TECHNOLOGY_TYPES;
+const TOP_TECHNOLOGY_TYPES = [
+  ["RNA_SEQ", "RNA-Seq", RNA_SEQ_TECHNOLOGY_TYPES],
+  ["MICROARRAY", "Microarray", MICROARRAY_TECHNOLOGY_TYPES],
+  ["OTHER", "Other", OTHER_TECHNOLOGY_TYPES]];
+
+
+export {MICROARRAY_TECHNOLOGY_TYPES, RNA_SEQ_TECHNOLOGY_TYPES, OTHER_TECHNOLOGY_TYPES, TECHNOLOGY_TYPES, TOP_TECHNOLOGY_TYPES}
diff --git a/src/views/Browser.vue b/src/views/Browser.vue
@@ -49,7 +49,7 @@
                     <span v-else :key="h.value">{{ h.text }}</span>
                 </template>
                 <template v-slot:item.shortName="{item}">
-                    <a :href="getUrl(item)">
+                    <a :href="getUrl(item)" target="_blank">
                         {{ item.shortName }}
                     </a>
                 </template>