Release 2025.0.0

package.json

@@ -1,6 +1,6 @@
 {
   "name": "mavedb-ui",
-  "version": "2024.4.2",
+  "version": "2025.0.0",
   "private": true,
   "scripts": {
     "build": "vite build --mode=${MODE=live}",

src/components/screens/HomeScreen.vue

@@ -69,21 +69,6 @@
         <HighlightsView model="Target"></HighlightsView>
       </div>
       <div class="col-4">
-        <Card>
-          <template #title>Citation</template>
-          <template #content>
-            <p>
-              MaveDB: an open-source platform to distribute and interpret data from multiplexed assays of variant Effect
-            </p>
-            <p>
-              Daniel Esposito, Jochen Weile, Jay Shendure, Lea M Starita, Anthony T Papenfuss, Frederick P Roth, Douglas M Fowler, Alan F Rubin
-            </p>
-            <p>
-              Genome Biol 20, 223 (2019) <a href="https://doi.org/10.1186/s13059-019-1845-6">doi:10.1186/s13059-019-1845-6</a>
-            </p>
-          </template>
-        </Card>
-        <br />
         <Card>
           <template #title>News</template>
           <template #content>
@@ -109,6 +94,26 @@
           </template>
         </Card>
       </div>
+      <div class="col-12">
+        <Card>
+          <template #title>Citing MaveDB</template>
+          <template #content>
+            <p>
+              To cite MaveDB, please cite our most recent publication:
+            </p>
+            <blockquote>
+                Rubin, A.F., Stone, J., Bianchi, A.H. <i>et al.</i> MaveDB 2024: a curated community database with over seven million variant effects
+                from multiplexed functional assays. <i>Genome Biol</i> <b>26</b>, 13 (2025). <a href=https://doi.org/10.1186/s13059-025-03476-y>https://doi.org/10.1186/s13059-025-03476-y</a>
+            </blockquote>
+            Previous MaveDB publications are listed below:
+            <blockquote>
+              Daniel Esposito, Jochen Weile, Jay Shendure, Lea M Starita, Anthony T Papenfuss, Frederick P Roth, Douglas M Fowler, Alan F Rubin.
+              MaveDB: an open-source platform to distribute and interpret data from multiplexed assays of variant effect.
+              <i>Genome Biol</i> <b>20</b>, 223 (2019). <a href="https://doi.org/10.1186/s13059-019-1845-6">https://doi.org/10.1186/s13059-019-1845-6</a>
+            </blockquote>
+          </template>
+        </Card>
+      </div>
     </div>
   </DefaultLayout>
 </template>

src/components/screens/ScoreSetCreator.vue

@@ -106,7 +106,7 @@
                             style="width: 100%;"
                           >
                             <template #option="slotProps">
-                              {{slotProps.option.urn}}: {{slotProps.option.title}}
+                              {{ slotProps.option.urn }}: {{ slotProps.option.title }}
                             </template>
                             <template #empty>
                               <div style="padding: 10px; text-align:center;">
@@ -1224,15 +1224,6 @@ export default {
   },
 
   setup: () => {
-    const editableExperiments = useItems({
-      itemTypeName: 'experiment',
-      options: {
-        filter: {
-          query: { l: { path: 'something' }, r: { constant: 'value' } }
-        }
-      }
-    })
-
     const publicationIdentifierSuggestions = useItems({ itemTypeName: 'publication-identifier-search' })
     const externalPublicationIdentifierSuggestions = useItems({ itemTypeName: 'external-publication-identifier-search' })
 
@@ -1253,7 +1244,7 @@ export default {
 
       ...useFormatters(),
       ...useItem({ itemTypeName: 'scoreSet' }),
-      editableExperiments: editableExperiments.items,
+      editableExperiments: ref([]),
       licenses: licenses.items,
       publicationIdentifierSuggestions: publicationIdentifierSuggestions.items,
       setPublicationIdentifierSearch: (text) => publicationIdentifierSuggestions.setRequestBody({ text }),
@@ -1570,6 +1561,10 @@ export default {
     }
   },
 
+  mounted: async function() {
+    await this.loadEditableExperiment()
+  },
+
   methods: {
     //////////////////////////////////////////////////////////////////////////////////////////////////////////////////
     // Contributors
@@ -1811,7 +1806,7 @@ export default {
         this.$toast.add({ severity: 'info', summary: `${currentTargetGene.targetAccession.accession} is already a protein accession.`, life: 3000 })
         return
       }
-      const url = `${config.apiBaseUrl}/hgvs/transcripts/protein/${currentTargetGene.targetAccession.accession}`
+      const url = `${config.apiBaseUrl}/hgvs/protein/${currentTargetGene.targetAccession.accession}`
       try {
         const response = await axios.get(
           url,
@@ -1853,7 +1848,7 @@ export default {
     },
 
     fetchTargetAccessionsByGene: async function (gene) {
-      const url = `${config.apiBaseUrl}/hgvs/transcripts/gene/${gene.trim()}`
+      const url = `${config.apiBaseUrl}/hgvs/gene/${gene.trim()}`
       try {
         const response = await axios.get(
           url,
@@ -1895,6 +1890,16 @@ export default {
     // Form fields
     ////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////
 
+    loadEditableExperiment: async function() {
+      try {
+        const response = await axios.post(`${config.apiBaseUrl}/me/experiments/search`, {metaAnalysis: false})
+        this.editableExperiments = response.data
+      } catch (error) {
+        console.error("Error loading experiments:", error)
+        this.editableExperiments = [] // Reset in case of an error
+      }
+    },
+
     populateExperimentMetadata: function (event) {
       this.abstractText = event.value.abstractText
       this.contributors = event.value.contributors || []

src/components/screens/ScoreSetEditor.vue

@@ -787,14 +787,6 @@ import { TARGET_GENE_CATEGORIES, textForTargetGeneCategory } from '@/lib/target-
     components: { AutoComplete, Button, Card, Chips, Column, Checkbox, DataTable, DefaultLayout, Dropdown, EmailPrompt, EntityLink, FileUpload, InputGroup, InputGroupAddon, InputNumber, InputText, Message, Multiselect, ProgressSpinner, SelectButton, TabPanel, TabView, Textarea },
 
     setup: () => {
-      const editableExperiments = useItems({
-        itemTypeName: 'experiment',
-        options: {
-          filter: {
-            query: { l: { path: 'something' }, r: { constant: 'value' } }
-          }
-        }
-      })
       const publicationIdentifierSuggestions = useItems({ itemTypeName: 'publication-identifier-search' })
       const externalPublicationIdentifierSuggestions = useItems({ itemTypeName: 'external-publication-identifier-search' })
       const targetGeneIdentifierSuggestions = {}
@@ -812,7 +804,7 @@ import { TARGET_GENE_CATEGORIES, textForTargetGeneCategory } from '@/lib/target-
       return {
         ...useFormatters(),
         ...useItem({ itemTypeName: 'scoreSet' }),
-        editableExperiments: editableExperiments.items,
+        editableExperiments: ref([]),
         licenses: licenses.items,
         publicationIdentifierSuggestions: publicationIdentifierSuggestions.items,
         setPublicationIdentifierSearch: (text) => publicationIdentifierSuggestions.setRequestBody({ text }),
@@ -1056,6 +1048,10 @@ import { TARGET_GENE_CATEGORIES, textForTargetGeneCategory } from '@/lib/target-
       },
     },
 
+    mounted: async function() {
+      await this.loadEditableExperiment()
+    },
+
     methods: {
       //////////////////////////////////////////////////////////////////////////////////////////////////////////////////
       // Contributors
@@ -1205,7 +1201,7 @@ import { TARGET_GENE_CATEGORIES, textForTargetGeneCategory } from '@/lib/target-
       },
 
       fetchTargetAccessionsByGene: async function (gene) {
-        const url = `${config.apiBaseUrl}/hgvs/transcripts/gene/${gene}`
+        const url = `${config.apiBaseUrl}/hgvs/gene/${gene}`
         try {
           const response = await axios.get(
             url,
@@ -1235,7 +1231,7 @@ import { TARGET_GENE_CATEGORIES, textForTargetGeneCategory } from '@/lib/target-
           this.$toast.add({ severity: 'info', summary: `${this.targetGene.targetAccession.accession} is already a protein accession.`, life: 3000 })
           return
         }
-        const url = `${config.apiBaseUrl}/hgvs/transcripts/protein/${this.targetGene.targetAccession.accession}`
+        const url = `${config.apiBaseUrl}/hgvs/protein/${this.targetGene.targetAccession.accession}`
         try {
           const response = await axios.get(
             url,
@@ -1291,6 +1287,16 @@ import { TARGET_GENE_CATEGORIES, textForTargetGeneCategory } from '@/lib/target-
       // Form fields
       ////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////
 
+      loadEditableExperiment: async function() {
+        try {
+          const response = await axios.post(`${config.apiBaseUrl}/me/experiments/search`, {metaAnalysis: false})
+          this.editableExperiments = response.data
+        } catch (error) {
+          console.error("Error loading experiments:", error)
+          this.editableExperiments = [] // Reset in case of an error
+        }
+      },
+
       populateExperimentMetadata: function (event) {
         this.doiIdentifiers = event.value.doiIdentifiers
         this.publicationIdentifiers = _.concat(event.value.primaryPublicationIdentifiers, event.value.secondaryPublicationIdentifiers)