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Commit 7e9f1610 authored by Remi PLANEL's avatar Remi PLANEL
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Can download data server

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1 merge request!167Download server data
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components/ServerDbTable.vue
+ 37
− 32
View file @ 7e9f1610
......@@ -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>
......
components/content/RefseqDb.vue
+ 5
− 9
View file @ 7e9f1610
......@@ -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>
......
components/content/StructureDb.vue
+ 2
− 2
View file @ 7e9f1610
......@@ -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)">
......
components/content/SystemDb.vue
+ 5
− 8
View file @ 7e9f1610
......@@ -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/${item.title.toLowerCase()}`">{{
......
composables/useCsvDownload.ts
+ 33
− 10
View file @ 7e9f1610
import { ref } from 'vue';
import Papa from 'papaparse';
import { saveAs } from "file-saver";
import { column } from '@observablehq/plot';
export function useCsvDownload(baseName: MaybeRef<string> = "df"
) {
......@@ -12,33 +13,55 @@ export function useCsvDownload(baseName: MaybeRef<string> = "df"
index: MaybeRef<string>,
query: MaybeRef<string>,
params: MaybeRef<Record<string, any>>,
columns: MaybeRef<string[] | undefined> = undefined
) => {
filename.value = `${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,
......
content/5.structure.md
+ 1
− 1
View file @ 7e9f1610
......@@ -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.
......
packages/df-wiki-cli/df_wiki_cli/meilisearch/__init__.py
+ 1
− 1
View file @ 7e9f1610
......@@ -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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