fix minor bugs

guigolab · Oct 7, 2024 · 20f69ee · 20f69ee
1 parent 9d252fa
commit 20f69ee
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Showing 11 changed files with 108 additions and 139 deletions.
diff --git a/biogenome-client/src/components/blocks/FiltersBlock.vue b/biogenome-client/src/components/blocks/FiltersBlock.vue
@@ -7,9 +7,6 @@
                 </div>
                 <div class="flex">
                     <VaMenu>
-                        <VaMenuItem icon="article" v-if="isGoaTActive" @selected="downloadGoatReport">
-                            GoaT
-                        </VaMenuItem>
                         <VaMenuItem icon="article" @selected="itemStore.showTsvModal = !itemStore.showTsvModal">
                             Report
                         </VaMenuItem>
@@ -44,8 +41,6 @@ import { useItemStore } from '../../stores/items-store'
 import { useI18n } from 'vue-i18n'
 import ExportTSV from '../modals/ExportTSV.vue'
 import CreateChart from '../modals/CreateChart.vue'
-import general from '../../../configs/general.json'
-import GoaTService from '../../services/clients/GoaTService'
 
 const { t } = useI18n()
 
@@ -70,52 +65,13 @@ const model = computed(() => {
     return itemStore.currentModel
 })
 
-const isGoaTActive = computed(() => {
-    return model.value === 'organisms' && general.goat
-})
-
 const isFiltering = computed(() => !!itemStore.stores[model.value].searchForm.filter)
 
 const total = computed(() => itemStore.stores[model.value].total)
 
 const modelFilterEntries = computed(() => Object.entries(itemStore.stores[model.value].searchForm)
     .filter(([k, v]) => !staticColumns.includes(k)))
 
-const activeFilters = computed(() => modelFilterEntries.value
-    .filter(([k, v]) => (v || v === false))
-)
-
-
-async function downloadGoatReport() {
-    try {
-        const response = await GoaTService.getGoatReport()
-        const data = response.data
-        const href = URL.createObjectURL(data);
-
-        const filename = response.headers['content-disposition']
-        const match = filename.match(/filename=([^;]+)/);
-        let name = ''
-        if (match && match[1]) {
-            name = match[1];
-        } else {
-            name = 'file.tsv'
-            console.log("Filename not found in the string.");
-        }
-        // create "a" HTML element with href to file & click
-        const link = document.createElement('a');
-        link.href = href;
-        link.setAttribute('download', name); //or any other extension
-        document.body.appendChild(link);
-        link.click();
-        // clean up "a" element & remove ObjectURL
-        document.body.removeChild(link);
-        URL.revokeObjectURL(href);
-    } catch (err) {
-        console.error(err)
-        itemStore.toast({ message: 'Error downloading Goat Report', color: 'danger' })
-    }
-
-}
 
 </script>
 <style>

diff --git a/biogenome-client/src/components/blocks/TableBlock.vue b/biogenome-client/src/components/blocks/TableBlock.vue
@@ -17,10 +17,13 @@
                     </va-avatar>
                 </template>
                 <template #cell(gff_gz_location)="{ rowData }">
-                    <VaChip :href="rowData.gff_gz_location" outline size="small">{{ t('buttons.download') }}</VaChip>
+                    <VaChip @click.stop :href="rowData.gff_gz_location" outline size="small">{{
+                        t('buttons.download') }}
+                    </VaChip>
                 </template>
                 <template #cell(tab_index_location)="{ rowData }">
-                    <VaChip :href="rowData.tab_index_location" outline size="small">{{ t('buttons.download')
+                    <VaChip @click.stop :href="rowData.tab_index_location" outline size="small">{{
+                        t('buttons.download')
                         }}</VaChip>
                 </template>
             </VaDataTable>

diff --git a/biogenome-client/src/components/maps/LeafletMap.vue b/biogenome-client/src/components/maps/LeafletMap.vue
@@ -14,7 +14,7 @@
             </div>
             <div v-if="showSampleTypeSelect" class="flex">
               <va-select preset="bordered" inner-label v-model="sampleType" label="Sample Type"
-                :options="['local_sample', 'biosamples']" />
+                :options="['local_sample', 'biosample']" />
             </div>
             <div class="flex">
               <va-button :loading="isLoading" :disabled="isSubmitDisabled" :round="false" @click="search">

diff --git a/biogenome-client/src/components/sidebar/Sidebar.vue b/biogenome-client/src/components/sidebar/Sidebar.vue
@@ -19,6 +19,13 @@
         </VaSidebarItemTitle>
       </VaSidebarItemContent>
     </VaSidebarItem>
+    <VaSidebarItem v-if="general.goat" @click="downloadGoatReport">
+      <VaSidebarItemContent>
+        <VaSidebarItemTitle>
+          GoaT Report
+        </VaSidebarItemTitle>
+      </VaSidebarItemContent>
+    </VaSidebarItem>
     <VaSidebarItem @click="globalStore.isSidebarVisible = !globalStore.isSidebarVisible"
       v-if="globalStore.isAuthenticated" :to="{ name: 'cms-organisms' }">
       <VaSidebarItemContent>
@@ -51,6 +58,11 @@ import general from '../../../configs/general.json'
 import { useGlobalStore } from '../../stores/global-store'
 import { useRoute, useRouter } from 'vue-router'
 import { useI18n } from 'vue-i18n'
+import GoaTService from '../../services/clients/GoaTService'
+import { useToast } from 'vuestic-ui/web-components'
+
+
+const { init } = useToast()
 
 const { t } = useI18n()
 const route = useRoute()
@@ -70,6 +82,37 @@ async function logout() {
   await globalStore.logout()
   router.push({ name: 'dashboard' })
 }
+
+
+async function downloadGoatReport() {
+  try {
+    const response = await GoaTService.getGoatReport()
+    const data = response.data
+    const href = URL.createObjectURL(data);
+
+    const filename = response.headers['content-disposition']
+    const match = filename.match(/filename=([^;]+)/);
+    let name = ''
+    if (match && match[1]) {
+      name = match[1];
+    } else {
+      name = 'file.tsv'
+      console.log("Filename not found in the string.");
+    }
+    // create "a" HTML element with href to file & click
+    const link = document.createElement('a');
+    link.href = href;
+    link.setAttribute('download', name); //or any other extension
+    document.body.appendChild(link);
+    link.click();
+    // clean up "a" element & remove ObjectURL
+    document.body.removeChild(link);
+    URL.revokeObjectURL(href);
+  } catch (err) {
+    console.error(err)
+    init({ message: 'Error downloading Goat Report', color: 'danger' })
+  }
+}
 </script>
 
 <style lang="scss">

diff --git a/biogenome-client/src/components/tables/RelatedDataTable.vue b/biogenome-client/src/components/tables/RelatedDataTable.vue
@@ -4,11 +4,14 @@
             {{ key.split('.').length ? key.split('.')[key.split('.').length - 1] : key }}
         </template>
         <template #cell(gff_gz_location)="{ rowData }">
-            <VaChip :href="rowData.gff_gz_location" outline size="small">{{ t('buttons.download') }}</VaChip>
+            <VaChip @click.stop :href="rowData.gff_gz_location" outline size="small">{{
+                t('buttons.download') }}
+            </VaChip>
         </template>
         <template #cell(tab_index_location)="{ rowData }">
-            <VaChip :href="rowData.tab_index_location" outline size="small">{{ t('buttons.download')
-                }}</VaChip>
+            <VaChip @click.stop :href="rowData.tab_index_location" outline size="small">{{
+                t('buttons.download')
+            }}</VaChip>
         </template>
     </VaDataTable>
 </template>
@@ -41,9 +44,12 @@ const columns = computed(() => {
     } else {
         return []
     }
-
 })
 
+const handleLinkClick = (event: MouseEvent) => {
+    event.stopPropagation(); // Prevent event from bubbling to the row
+};
+
 const handleClick = (event: any) => {
     const { item } = event
     const routeMap: Record<string, any> = {

diff --git a/biogenome-client/src/pages/cms/assembly/Assemblies.vue b/biogenome-client/src/pages/cms/assembly/Assemblies.vue
@@ -19,12 +19,12 @@
             <va-icon color="danger" name="delete" @click="deleteConfirmation(rowData)" />
         </template>
         <template #cell(chromosome_aliases)="{ rowData }">
-            <div class="row justify-space-between">
+            <div class="row">
                 <div v-if="rowData.has_chromosomes_aliases" class="flex">
                     <va-button size="small" :href="`${baseURL}/assemblies/${rowData.accession}/chr_aliases`"
                         icon="download"></va-button>
                 </div>
-                <div v-if="rowData.metadata.assembly_info.assembly_level === 'Chromosome'" class="flex">
+                <div v-if="rowData.metadata && rowData.metadata.assembly_info.assembly_level === 'Chromosome'" class="flex">
                     <va-button :to="{ name: 'chr-aliases', params: { accession: rowData.accession } }" size="small"
                         icon="add" />
                 </div>

diff --git a/biogenome-client/src/pages/cms/uploads/ChrAliasesForm.vue b/biogenome-client/src/pages/cms/uploads/ChrAliasesForm.vue
@@ -22,8 +22,11 @@ import { ref } from 'vue';
 import AuthService from '../../../services/clients/AuthService';
 import { useToast } from 'vuestic-ui/web-components';
 import { AxiosError } from 'axios';
+import { useRouter } from 'vue-router';
 
-const {init} = useToast()
+
+const router = useRouter()
+const { init } = useToast()
 const props = defineProps<{
     accession: string,
 }>()
@@ -39,11 +42,12 @@ async function handleSubmit() {
         const formData = new FormData()
         formData.append('chr_aliases', refName.value)
         const { data } = await AuthService.uploadRefNameAliases(props.accession, formData)
-        init({message: data as string, color:'success'})
+        init({ message: data as string, color: 'success' })
+        router.push({ name: 'cms-assemblies' })
     } catch (error) {
         const axiosError = error as AxiosError
-        if(axiosError.response && axiosError.response.data){
-            init({message:axiosError.response.data as string,color:'danger'})
+        if (axiosError.response && axiosError.response.data) {
+            init({ message: axiosError.response.data as string, color: 'danger' })
         }
         console.log(error)
     } finally {

diff --git a/biogenome-client/src/stores/items-store.ts b/biogenome-client/src/stores/items-store.ts
@@ -89,6 +89,32 @@ export const useItemStore = defineStore('item', {
             const model = this.currentModel
             this.stores[model].searchForm[field] = null
         },
+        catchError(error: any) {
+            console.error(error)
+            const axiosError = error as AxiosError<ErrorResponseData>
+            let message
+            if (axiosError.response && axiosError.response.data && axiosError.response.data.message) {
+                message = axiosError.response.data.message
+
+            } else {
+                message = axiosError.message
+            }
+            this.toast({ message: message, color: 'danger' })
+        },
+        downloadFile(data: any) {
+            const href = URL.createObjectURL(data);
+
+            const filename = `${this.currentModel}_report.tsv`
+            // create "a" HTML element with href to file & click
+            const link = document.createElement('a');
+            link.href = href;
+            link.setAttribute('download', filename); //or any other extension
+            document.body.appendChild(link);
+            link.click();
+            // clean up "a" element & remove ObjectURL
+            document.body.removeChild(link);
+            URL.revokeObjectURL(href);
+        },
         //incoming model may not correspond to currentModel
         async getStats(model: string, field: string) {
             try {
@@ -101,20 +127,12 @@ export const useItemStore = defineStore('item', {
                 const { data } = await StatisticsService.getModelFieldStats(model, field, query)
                 return data
             } catch (err) {
-                const axiosError = err as AxiosError<ErrorResponseData>
-                let message
-                if (axiosError.response && axiosError.response.data && axiosError.response.data.message) {
-                    message = axiosError.response.data.message
-
-                } else {
-                    message = axiosError.message
-                }
-                this.toast({ message: message, color: 'danger' })
+                this.catchError(err)
             }
         },
         async fetchItems() {
             const model = this.currentModel
-            this.stores[model].isLoading = true
+            this.isTableLoading = true
             const { searchForm, pagination } = this.stores[model]
 
             // Build the query params
@@ -127,23 +145,14 @@ export const useItemStore = defineStore('item', {
             if (this.parentTaxon) {
                 params['taxon_lineage'] = this.parentTaxon
             }
-
             try {
                 const { data } = await CommonService.getItems(`/${model}`, params)
                 this.stores[model].items = [...data.data]
                 this.stores[model].total = data.total
             } catch (err) {
-                const axiosError = err as AxiosError<ErrorResponseData>
-                let message
-                if (axiosError.response && axiosError.response.data && axiosError.response.data.message) {
-                    message = axiosError.response.data.message
-
-                } else {
-                    message = axiosError.message
-                }
-                this.toast({ message: message, color: 'danger' })
+                this.catchError(err)
             } finally {
-                this.stores[model].isLoading = false
+                this.isTableLoading = false
             }
         },
         async downloadData(fields: string[], applyFilters: boolean) {
@@ -158,25 +167,11 @@ export const useItemStore = defineStore('item', {
                 if (this.parentTaxon) {
                     requestData['taxon_lineage'] = this.parentTaxon
                 }
+                const { data } = await CommonService.getTsv(`/${model}`, requestData)
+                this.downloadFile(data)
 
-                const response = await CommonService.getTsv(`/${model}`, requestData)
-                const data = response.data
-                const href = URL.createObjectURL(data);
-
-                const filename = `${model}_report.tsv`
-                // create "a" HTML element with href to file & click
-                const link = document.createElement('a');
-                link.href = href;
-                link.setAttribute('download', filename); //or any other extension
-                document.body.appendChild(link);
-                link.click();
-                // clean up "a" element & remove ObjectURL
-                document.body.removeChild(link);
-                URL.revokeObjectURL(href);
             } catch (e) {
-                console.log(e)
-                const axiosError = e as AxiosError
-                this.toast({ message: axiosError.message, color: 'danger' })
+                this.catchError(e)
             } finally {
                 this.isTSVLoading = false
             }

diff --git a/docker-compose.yml b/docker-compose.yml