From 7e9f161046c993fb2a773fdec46eebf39edf9c28 Mon Sep 17 00:00:00 2001
From: Remi PLANEL <rplanel@pasteur.fr>
Date: Thu, 21 Dec 2023 12:54:52 +0100
Subject: [PATCH] Can download data server
---
components/ServerDbTable.vue | 69 ++++++++++---------
components/content/RefseqDb.vue | 14 ++--
components/content/StructureDb.vue | 4 +-
components/content/SystemDb.vue | 13 ++--
composables/useCsvDownload.ts | 43 +++++++++---
content/5.structure.md | 2 +-
.../df_wiki_cli/meilisearch/__init__.py | 2 +-
7 files changed, 84 insertions(+), 63 deletions(-)
diff --git a/components/ServerDbTable.vue b/components/ServerDbTable.vue
index cb80b6d8..b6acb9c4 100644
--- a/components/ServerDbTable.vue
+++ b/components/ServerDbTable.vue
@@ -18,6 +18,7 @@ export interface Props {
sortBy?: SortItem[]
facets: MaybeRef<string[]>
dataTableServerProps: Record<string, any>
+ columnsToDownload: MaybeRef<string[]>
}
export interface FilterItem {
@@ -324,44 +325,20 @@ const { pending: pendingDownloadData, downloadCsv } = useCsvDownload(props.db)
// })
-
+function downloadData() {
+ downloadCsv(
+ props.db,
+ toValue(search), { ...toValue(notPaginatedParams), filter: toValue(computedFilter), sort: toValue(msSortBy) },
+ props.columnsToDownload
+
+ )
+}
</script>
<template>
<v-card flat color="transparent">
<v-card-text>
</v-card-text>
<v-card-text>
- <v-row>
- <v-col :cols="mobile ? 12 : 5">
- <v-text-field v-model="search" label="Search..." hide-details prepend-inner-icon="mdi-magnify"
- single-line clearable></v-text-field>
- </v-col>
- <v-col :cols="mobile ? 12 : 6">
- <v-autocomplete ref="autocompleteInput" hide-details v-model:model-value="filterOrSearch"
- auto-select-first chips clearable label="Filter results..." :items="autocompleteItems" single-line
- item-value="value" item-title="title" multiple return-object prepend-inner-icon="md:search"
- @click:appendInner="searchOrFilter" @click:clear="clearFilterOrSearch"
- @update:modelValue="() => clearSearch()">
- <template #chip="{ props, item, index }">
- <v-chip v-bind="props" :text="item.raw.title" :closable="item.props.deletable"
- @click:close="item.props.type === deleteOneFilter(index)"></v-chip>
- </template>
- <template #item="{ props, item }">
- <v-list-item v-bind="{ ...props, active: false, onClick: () => selectItem(item) }"
- :title="item.title" :subtitle="item.raw?.count ? item.raw.count : ''" :value="props.value">
-
- </v-list-item>
- </template>
- </v-autocomplete>
- </v-col>
- <v-col :cols="mobile ? 'auto' : 1">
- <v-badge :content="totalHits" color="primary">
- <v-btn icon="md:download"
- @click="downloadCsv(props.db, toValue(search), { ...notPaginatedParams.value, filter: toValue(computedFilter), sort: msSortBy.value })">
- </v-btn>
- </v-badge>
- </v-col>
- </v-row>
<v-row v-if="props.db === 'structure'">
<v-col>
@@ -386,7 +363,35 @@ const { pending: pendingDownloadData, downloadCsv } = useCsvDownload(props.db)
:loading="loading" :items="msResult?.hits ?? []" :items-length="totalHits" density="compact"
:items-per-page-options="itemsPerPage" :height="computedTableHeight" class="elevation-1 mt-2">
+ <template #top>
+ <v-toolbar floating><v-toolbar-title class="text-capitalize">
+ <v-badge :content="totalHits" color="primary" inline>
+ <v-btn prepend-icon="md:download" variant="text" color="primary" @click="downloadData()">{{
+ props.title }}
+ </v-btn>
+ </v-badge>
+ </v-toolbar-title>
+ <v-text-field v-model="search" label="Search..." hide-details="auto" prepend-inner-icon="mdi-magnify"
+ single-line clearable class="mr-2"></v-text-field>
+ <v-autocomplete ref="autocompleteInput" hide-details v-model:model-value="filterOrSearch"
+ auto-select-first chips clearable label="Filter results..." :items="autocompleteItems" single-line
+ item-value="value" item-title="title" multiple return-object prepend-inner-icon="md:search"
+ @click:appendInner="searchOrFilter" @click:clear="clearFilterOrSearch"
+ @update:modelValue="() => clearSearch()">
+ <template #chip="{ props, item, index }">
+ <v-chip v-bind="props" :text="item.raw.title" :closable="item.props.deletable"
+ @click:close="item.props.type === deleteOneFilter(index)"></v-chip>
+ </template>
+ <template #item="{ props, item }">
+ <v-list-item v-bind="{ ...props, active: false, onClick: () => selectItem(item) }"
+ :title="item.title" :subtitle="item.raw?.count ? item.raw.count : ''" :value="props.value">
+ </v-list-item>
+ </template>
+ </v-autocomplete>
+
+ </v-toolbar>
+ </template>
<template v-for="(slot, index) of Object.keys(slots)" :key="index" v-slot:[slot]="data">
<slot :name="slot" v-bind="data"></slot>
diff --git a/components/content/RefseqDb.vue b/components/content/RefseqDb.vue
index fc3fa610..38260b1f 100644
--- a/components/content/RefseqDb.vue
+++ b/components/content/RefseqDb.vue
@@ -206,7 +206,8 @@ const binPlotOptions = ref({
})
const binPlotDataOptions = computed(() => {
- return allHits.value?.hits?.length > 0 ? {
+ const toValueAllHits = toValue(allHits)
+ return toValueAllHits?.hits?.length > 0 ? {
...binPlotOptions.value,
color: {
...binPlotOptions.value.color,
@@ -214,7 +215,7 @@ const binPlotDataOptions = computed(() => {
},
// fy: { domain: groupSortDomain.value },
marks: [
- Plot.cell(allHits.value?.hits ?? [], Plot.group({ fill: "count" }, { x: "type", y: selectedTaxoRank.value, tip: true, inset: 0.5, sort: { y: "fill" } })),
+ Plot.cell(toValueAllHits?.hits ?? [], Plot.group({ fill: "count" }, { x: "type", y: selectedTaxoRank.value, tip: true, inset: 0.5, sort: { y: "fill" } })),
]
} : null
@@ -280,13 +281,8 @@ const scaleType = ref("linear")
</v-expansion-panels>
<ServerDbTable title="RefSeq" db="refseq" :sortBy="sortBy" :facets="facets"
- :data-table-server-props="dataTableServerProps">
- <template #top>
- <v-toolbar><v-toolbar-title class="text-capitalize">
- RefSeq
- </v-toolbar-title><v-spacer></v-spacer>
- </v-toolbar>
- </template>
+ :data-table-server-props="dataTableServerProps" @refresh:search="getAllHits">
+
<template #[`item.accession_in_sys`]="{ item }">
<CollapsibleChips :items="namesToAccessionChips(item.accession_in_sys)">
</CollapsibleChips>
diff --git a/components/content/StructureDb.vue b/components/content/StructureDb.vue
index 6fc5a9c8..a02fc2c5 100644
--- a/components/content/StructureDb.vue
+++ b/components/content/StructureDb.vue
@@ -76,13 +76,13 @@ function remove(key) {
<ServerDbTable title="Predicted Structures" db="structure" :sortBy="sortBy" :facets="facets"
:data-table-server-props="dataTableServerProps">
- <template #top>
+ <!-- <template #top>
<v-toolbar><v-toolbar-title class="text-capitalize">
Predicted Structures
</v-toolbar-title><v-spacer></v-spacer>
</v-toolbar>
- </template>
+ </template> -->
<template #[`item.proteins_in_the_prediction`]="{ item }">
<CollapsibleChips :items="namesToCollapsibleChips(item.proteins_in_the_prediction, item.fasta_file)">
diff --git a/components/content/SystemDb.vue b/components/content/SystemDb.vue
index 72d1642f..65e3c152 100644
--- a/components/content/SystemDb.vue
+++ b/components/content/SystemDb.vue
@@ -3,7 +3,7 @@ import type { SortItem } from "@/components/ServerDbTable.vue"
import { ServerDbTable } from "#components"
const sortBy: Ref<SortItem[]> = ref([{ key: 'title', order: "asc" }])
const itemValue = ref("title");
-const facets: Ref<string[]> = ref(["title", "Sensor", "Effector", "Activator", "PFAM.AC"])
+const facets: Ref<string[]> = ref(["title", "Sensor", "Effector", "Activator", "PFAM.AC", "PFAM.DE"])
const headers: Ref<Object[]> = ref([
{ title: "System", key: "title", removable: false },
{ title: "Article", key: "doi", removable: false },
@@ -30,16 +30,13 @@ const dataTableServerProps = computed(() => {
}
})
+const columnsToDownload = ref(['title', 'doi', 'Sensor', 'Activator', 'Effector', 'PFAM', 'contributors',])
+
</script>
<template>
- <ServerDbTable title="systems" db="systems" :sortBy="sortBy" :facets="facets"
- :data-table-server-props="dataTableServerProps">
+ <ServerDbTable title="List Systems" db="systems" :sortBy="sortBy" :facets="facets"
+ :data-table-server-props="dataTableServerProps" :columns-to-download="columnsToDownload">
- <template #top>
- <v-toolbar><v-toolbar-title class="text-capitalize">
- List Systems </v-toolbar-title><v-spacer></v-spacer>
- </v-toolbar>
- </template>
<template #[`item.title`]="{ item }">
<v-chip color="info" link :to="`/defense-systems/${item.title.toLowerCase()}`">{{
diff --git a/composables/useCsvDownload.ts b/composables/useCsvDownload.ts
index 88589b8f..3ce2d7cd 100644
--- a/composables/useCsvDownload.ts
+++ b/composables/useCsvDownload.ts
@@ -1,6 +1,7 @@
import { ref } from 'vue';
import Papa from 'papaparse';
import { saveAs } from "file-saver";
+import { column } from '@observablehq/plot';
export function useCsvDownload(baseName: MaybeRef<string> = "df"
) {
@@ -12,33 +13,55 @@ export function useCsvDownload(baseName: MaybeRef<string> = "df"
index: MaybeRef<string>,
query: MaybeRef<string>,
params: MaybeRef<Record<string, any>>,
+ columns: MaybeRef<string[] | undefined> = undefined
) => {
- filename.value = `${toValue(baseName)}-${toValue(params).filter}.csv`
+ const toValueParams = toValue(params)
+ const filterName = toValueParams?.filter ? toValueParams.filter.replaceAll('\"', "") : ''
+ filename.value = `${toValue(baseName)}-${filterName}.csv`
pending.value = true
+
try {
const { data, error } = await useAsyncMeiliSearch({
index: toValue(index),
- params: toValue(params),
+ params: toValueParams,
query: toValue(query)
})
- const csvContent = Papa.unparse(toValue(data).hits);
- // console.log(csvContent)
- const blob = new Blob([csvContent], { type: 'text/csv;charset=utf-8;' });
- saveAs(blob, `${toValue(filename)}`);
+ if (toValue(data)?.hits?.length > 0) {
+ const sanitizedData = toValue(data).hits.map(row => {
+ let sanitizedRow = { ...row }
+ if (sanitizedRow?.PFAM?.length > 0) {
+ sanitizedRow = {
+ ...sanitizedRow,
+ PFAM: sanitizedRow.PFAM.map(({ AC }) => AC).join(", ")
+ }
+
+ }
+ if (sanitizedRow?.contributors?.length > 0) {
+ sanitizedRow = {
+ ...sanitizedRow,
+ contributors: sanitizedRow.contributors.join(", ")
+ }
+ }
+ return sanitizedRow
+
+ })
+
+
+ console.log(sanitizedData)
+ const csvContent = Papa.unparse(sanitizedData, { columns: toValue(columns) });
+ const blob = new Blob([csvContent], { type: 'text/csv;charset=utf-8;' });
+ saveAs(blob, `${toValue(filename)}`);
+ }
} finally {
pending.value = false
}
}
- // watch(msResult, (newRes) => {
- // console.log("save file !!!!!!")
-
- // })
return {
pending, downloadCsv,
diff --git a/content/5.structure.md b/content/5.structure.md
index 923ce4a9..a21e7e49 100644
--- a/content/5.structure.md
+++ b/content/5.structure.md
@@ -5,7 +5,7 @@ navigation:
icon: "mdi-database"
---
-# Structures' prediction DB
+# Structure's prediction DB
In the following tables are various structures that were generated by Alphafold for all monomers, hetero- and homo-dimers for a given system.
In the page for each system is the structure for the monomers and real structure when it exists.
diff --git a/packages/df-wiki-cli/df_wiki_cli/meilisearch/__init__.py b/packages/df-wiki-cli/df_wiki_cli/meilisearch/__init__.py
index b3ec461a..eb98e990 100644
--- a/packages/df-wiki-cli/df_wiki_cli/meilisearch/__init__.py
+++ b/packages/df-wiki-cli/df_wiki_cli/meilisearch/__init__.py
@@ -193,7 +193,7 @@ def update_systems(
)
print(pagination_settings_task)
attr_task = index.update_filterable_attributes(
- body=["title", "Sensor", "Activator", "Effector", "PFAM.AC"]
+ body=["title", "Sensor", "Activator", "Effector", "PFAM.AC" , "PFAM.DE"]
)
params = {
"maxValuesPerFacet": 1000000,
--
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