diff --git a/pages/_predicted-structure-bak.vue b/pages/_predicted-structure-bak.vue
deleted file mode 100644
index b783a347255709e715bf9bb0fa23d63bef50c25b..0000000000000000000000000000000000000000
--- a/pages/_predicted-structure-bak.vue
+++ /dev/null
@@ -1,105 +0,0 @@
-<script setup lang="ts">
-import { useRuntimeConfig, useFetch, type MaybeRefOrGetter, ref, computed, toValue, type Ref } from '#imports'
-
-import JsonCSV from 'vue-json-csv'
-import { useDisplay } from "vuetify";
-import { useFacetsStore, type Facets } from '~~/stores/facets'
-
-
-const facetStore = useFacetsStore()
-
-const { height } = useDisplay();
-const minTableHeight = ref(400)
-const computedTableHeight = computed(() => {
- const computedHeight = height.value - 500
- return computedHeight > minTableHeight.value ? computedHeight : minTableHeight.value
-})
-
-
-// SORTING
-const sortBy: Ref<{ key: string, order: string }[]> = ref([{ key: 'system', order: "asc" }])
-const msSortBy = computed(() => {
- if (sortBy.value.length > 0) {
- return sortBy.value.map((curr) => {
- if (curr?.key && curr?.order) {
- return `${curr.key}:${curr.order}`
- }
- else { return "" }
- })
- } else { return [""] }
-})
-
-
-
-const itemValue = ref("id");
-const search: Ref<string> = ref("");
-const filter: Ref<string> = ref('')
-const hitsPerPage: Ref<number> = ref(25)
-const limit: Ref<number> = ref(500000)
-const facets = ref(["system"])
-const page = ref(1)
-const headers: Ref<Object[]> = ref([
- { title: "System", key: "system" },
- { title: "Completed", key: "completed" },
- { title: "Predition type", key: "prediction_type" },
- { title: "Num of genes", key: "system_number_of_genes" },
- { title: "pLDDT", key: "plddts" },
- { title: "Type", key: "type" }
-])
-const {
- hits: items,
- pending,
- totalHits: itemsLength,
- filterError,
- facetDistribution
-} = useFetchMsDocument(
- "structure", search, filter, limit, hitsPerPage, page, facets, msSortBy)
-
-watch(facetDistribution, (facetDistri) => {
-
- facetStore.setFacets({ facetDistribution: facetDistri, facetStat: undefined })
-})
-
-</script>
-
-<template>
- <v-card flat>
- <v-card-text>
- text here
- </v-card-text>
- <v-toolbar color="primary" density="compact">
- <v-app-bar-nav-icon></v-app-bar-nav-icon>
- <v-toolbar-title>Predicted Structures summary ({{ itemsLength }})
- </v-toolbar-title>
- <JsonCSV :data="items" name="predicted-structures-summary-defense-system.csv">
- <v-btn disabled icon>
- <v-icon icon="md:download"></v-icon>
- <v-tooltip activator="parent" location="bottom">Download {{ itemsLength }} entries</v-tooltip>
- </v-btn>
- </JsonCSV>
- </v-toolbar>
- <v-card-text>
- text here
- </v-card-text>
- <v-col>
- <v-text-field v-model="search" prepend-inner-icon="mdi-magnify"
- label="Search for defense systems predicted structures" hide-details class="mx-2"
- clearable></v-text-field></v-col>
- <v-col cols="auto">
- <v-text-field v-model="filter" prepend-inner-icon="mdi-magnify" label="Filter" hide-details="auto" class="mx-2"
- clearable :error-messages="filterError"></v-text-field></v-col>
- <v-data-table-server v-model:page="page" v-model:items-per-page="hitsPerPage" v-model:sortBy="sortBy"
- ref="datatable" fixed-header :loading="pending" :headers="headers" :items="items" :item-value="itemValue"
- :items-length="itemsLength" multi-sort density="compact" :height="computedTableHeight" class="elevation-1 mt-2">
- <!-- <template v-if="refseqData?.length >= 10000" #top>
- <v-alert type="warning" variant="tonal" title="Results table"
- text="Results won't be displayed since there is over 10000 hits"></v-alert>
- </template> -->
-
- <template #[`item.completed`]="{ item }">
- <v-icon v-if="item.completed" color="success" icon="md:check"></v-icon>
- <v-icon v-else color="warning" icon="md:dangerous"></v-icon>
- </template>
- </v-data-table-server>
- </v-card>
-</template>
\ No newline at end of file
diff --git a/pages/_refseq-bak.vue b/pages/_refseq-bak.vue
deleted file mode 100644
index ffb9fc6ae599faba5d097043c75de2b8c590c741..0000000000000000000000000000000000000000
--- a/pages/_refseq-bak.vue
+++ /dev/null
@@ -1,266 +0,0 @@
-<script setup lang="ts">
-import * as Plot from "@observablehq/plot";
-import PlotFigure from "~/components/PlotFigure";
-import { useDisplay } from "vuetify";
-import JsonCSV from 'vue-json-csv';
-import { useFacetsStore, type Facets } from '~~/stores/facets'
-
-const runtimeConfig = useRuntimeConfig();
-const facetStore = useFacetsStore()
-const { width, height } = useDisplay();
-const minTableHeight = ref(400)
-const computedTableHeight = computed(() => {
- const computedHeight = height.value - 500
- return computedHeight > minTableHeight.value ? computedHeight : minTableHeight.value
-})
-
-
-
-// SORTING
-const sortBy: Ref<{ key: string, order: string }[]> = ref([{ key: 'type', order: "asc" }])
-const msSortBy = computed(() => {
- if (sortBy.value.length > 0) {
- return sortBy.value.map((curr) => {
- if (curr?.key && curr?.order) {
- return `${curr.key}:${curr.order}`
- }
- else { return "" }
- })
- } else { return [""] }
-})
-
-
-
-
-
-const availableTaxo: Ref<string[]> = ref(["species", "genus", "family", "order", "phylum", "Superkingdom"]);
-const selectedTaxoRank = ref("phylum");
-
-
-const computedWidth = computed(() => {
- return Math.max(width.value, 550);
-});
-
-const plotHeight = computed(() => {
- return computedWidth.value / 4;
-});
-// const filterError = ref(null)
-const search: Ref<string> = ref("");
-const filter: Ref<string> = ref('')
-const hitsPerPage: Ref<number> = ref(25)
-const limit = ref(1000)
-const itemValue = ref("id");
-const facets = ref([
- "type",
- "Superkingdom",
- "phylum",
- "order",
- "family",
- "genus",
- "species",
-])
-const page = ref(1)
-const prependHeaders = ref([
- { title: "Replicon", key: "replicon" },
- {
- title: "System",
- key: "type",
- },
- {
- title: "Subtype",
- key: "subtype",
- },
-
-
-]);
-const appendHeaders = ref([
- {
- title: "Accessions",
- key: "accession_in_sys"
- }
-])
-
-
-
-function capitalize([first, ...rest]) {
- return first.toUpperCase() + rest.join('').toLowerCase();
-}
-
-
-const {
- hits: items,
- pending,
- totalHits: itemsLength,
- filterError,
- facetDistribution }
- = useFetchMsDocument(
- "refseq",
- search,
- filter,
- limit,
- hitsPerPage,
- page,
- facets,
- msSortBy
- )
-
-watch(facetDistribution, (facetDistri) => {
- facetStore.setFacets({ facetDistribution: facetDistri, facetStat: undefined })
-})
-const computedSystemDistribution = computed(() => {
- if (facetDistribution.value?.type) {
- return Object.entries(facetDistribution.value.type).map(([key, value]) => {
- return { type: key, count: value }
- }).sort()
- } else { return [] }
-
-})
-
-const computedTaxonomyDistribution = computed(() => {
- if (facetDistribution.value?.[selectedTaxoRank.value]) {
- return Object.entries(facetDistribution.value[selectedTaxoRank.value]).map(([key, value]) => {
- return { [selectedTaxoRank.value]: key, count: value }
- }).sort()
- } else { return [] }
-
-})
-
-
-const computedHeaders = computed(() => {
- return [...prependHeaders.value, ...availableTaxo.value.map(taxo => {
- return {
- title: capitalize(taxo),
- key: taxo
- }
- }), ...appendHeaders.value]
-})
-
-
-function itemToFilter(item, key) {
- const value = item[key]
- const filterToAdd = /\s/g.test(value) ? `${key}="${value}"` : `${key}=${value}`
- return filter.value === '' ? filterToAdd : `${filter.value} AND ${filterToAdd}`
-}
-
-
-const itemFilterKeys = computed(() => {
- return [...availableTaxo.value, 'type', 'subtype']
-})
-const defaultBarPlotOptions = computed(() => {
- return {
- x: { label: null, tickRotate: 70 },
- y: { nice: true, grid: true },
- color: { legend: true },
- width: computedWidth.value,
- height: plotHeight.value,
- }
-})
-const computedDistriSystemOptions = computed(() => {
- return {
- ...defaultBarPlotOptions.value,
- marginBottom: 120,
- marks: [
- // Plot.frame(),
- Plot.barY(
- toValue(computedSystemDistribution),
- {
- y: "count", x: 'type', tip: true,
- fill: "#6750a4",
- sort: { x: "-y" },
- },
-
- ),
- ],
- };
-});
-
-const computedDistriTaxoOptions = computed(() => {
- return {
- ...defaultBarPlotOptions.value,
- marginBottom: 200,
- marks: [
- Plot.barY(
- toValue(computedTaxonomyDistribution),
- {
- y: "count",
- x: selectedTaxoRank.value,
- tip: true,
- fill: "#6750a4",
- sort: { x: "-y" },
- }
- ),
- ],
- };
-});
-// const datatable = ref(null)
-const hasToGenerateDownload = ref(false)
-let itemsToDownload = ref([])
-
-watch(hasToGenerateDownload, (val) => {
- console.log(val)
- if (val === true) {
- const { hits: items, pending, totalHits: itemsLength, filterError, facetDistribution } = useFetchMsDocument("refseq", search, filter, limit, hitsPerPage, page, facets)
- itemsToDownload.value = items.value
- }
-})
-</script>
-
-<template>
- <v-card flat>
- <v-toolbar color="primary" density="compact">
- <v-app-bar-nav-icon></v-app-bar-nav-icon>
- <v-toolbar-title>RefSeq Entries ({{ itemsLength }})
- </v-toolbar-title>
- <JsonCSV :data="itemsToDownload" name="refseq-defenes-system.csv">
- <v-btn disabled icon @click="hasToGenerateDownload = true">
- <v-icon icon="md:download"></v-icon>
- <v-tooltip activator="parent" location="bottom">Download {{ itemsLength }} entries</v-tooltip>
- </v-btn>
- </JsonCSV>
- </v-toolbar>
- <!-- </template> -->
- <v-card-text>
-
- Tu peux mettre du texte ici
-
- </v-card-text>
- <v-col>
- <v-text-field v-model="search" prepend-inner-icon="mdi-magnify" label="Search for defense systems" hide-details
- class="mx-2 mb-1" clearable></v-text-field>
-
- </v-col>
- <v-col class="pt-1">
- Examples: <v-chip color="primary" @click="search = 'RADAR'">RADAR</v-chip> <v-chip color="primary"
- @click="search = 'BREX'">BREX</v-chip>
- </v-col>
- <v-col cols="auto">
- <v-text-field v-model="filter" prepend-inner-icon="mdi-magnify" label="Filter" hide-details="auto" class="mx-2"
- clearable :error-messages="filterError"></v-text-field></v-col>
- <v-data-table-server v-model:page="page" v-model:items-per-page="hitsPerPage" v-model:sortBy="sortBy" fixed-header
- :loading="pending" :headers="computedHeaders" :items="items" :items-length="itemsLength" :item-value="itemValue"
- multi-sort density="compact" :height="computedTableHeight" class="elevation-1 mt-2">
- <template #[`item.${key}`]="{ item }" v-for="key in itemFilterKeys" :key="key">
- <v-chip @click="filter = itemToFilter(item, key)">{{ item[key] }}</v-chip>
- </template>
- <template #[`item.accession_in_sys`]="{ item }">
- <accession-chips :accessions="item.accession_in_sys" baseUrl="http://toto.pasteur.cloud"></accession-chips>
- </template>
- </v-data-table-server>
-
- </v-card>
- <v-card flat class="my-3" :loading="pending">
- <v-card-title> Systems Distribution</v-card-title>
-
- <v-card-text>
- <PlotFigure :options="unref(computedDistriSystemOptions)" defer></PlotFigure>
- </v-card-text>
- </v-card>
- <v-card flat :loading="pending">
- <v-card-title> Taxonomic Distribution</v-card-title>
- <v-card-text>
- <v-select v-model="selectedTaxoRank" :items="availableTaxo" density="compact"
- label="Select taxonomic rank"></v-select>
- <PlotFigure defer :options="unref(computedDistriTaxoOptions)"></PlotFigure>
- </v-card-text>
- </v-card>
-</template>
\ No newline at end of file