Skip to content
Snippets Groups Projects

Compare revisions

Changes are shown as if the source revision was being merged into the target revision. Learn more about comparing revisions.

Source

Select target project
No results found

Target

Select target project
  • mdm-lab/wiki
  • hvaysset/wiki
  • jsousa/wiki
  • tclabby/wiki
4 results
Show changes
Expand all Hide whitespace changes
Inline Side-by-side
package-lock.json
View file @ c382702a
This diff is collapsed.
package.json
View file @ c382702a
......@@ -12,6 +12,7 @@
"@vueuse/core": "^10.6.1",
"@vueuse/nuxt": "^10.6.1",
"nuxt": "^3.8.1",
"nuxt-meilisearch": "^1.1.0",
"vuetify-nuxt-module": "^0.6.7"
},
"overrides": {
......
packages/df-wiki-cli/df_wiki_cli/meilisearch/__init__.py
View file @ c382702a
......@@ -108,6 +108,18 @@ def update_refseq(
"species",
]
)
params = {
"maxValuesPerFacet": 1000000,
"sortFacetValuesBy": {"*": "count"},
}
index.update_faceting_settings(params)
print("typo toler")
index.update_typo_tolerance(
{
"enabled": False
# "minWordSizeForTypos": {"oneTypo": 50, "twoTypos": 100}
}
)
def update_structure(
......@@ -150,6 +162,7 @@ def update_structure(
"plddts",
]
)
index.update_typo_tolerance({"enabled": False})
def split_on_comma(str_val: str) -> List[str]:
......
pages/[...slug].vue
View file @ c382702a
<template>
<v-row justify="center">
<v-col cols="auto">
<v-card flat color="transparent" max-width="1280">
<v-card-text>
<ContentDoc />
</v-card-text>
</v-card></v-col>
</v-row>
<v-card-text>
<ContentDoc />
</v-card-text>
</template>
pages/predicted-structure.vue deleted 100644 → 0
View file @ 6df21164
<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
pages/refseq.vue deleted 100644 → 0
View file @ 6df21164
<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
stores/articles.ts
View file @ c382702a
import { defineStore } from 'pinia'
import { ref } from 'vue'
// import jsonArticles from '@/assets/articles.json'
export interface CslJson {
id: string
// id: string
type: string
title: string
"container-title": string
page: string,
volume: string,
// page: string,
// volume: string,
abstract: string
URL: string
// URL: string
DOI: string
journalAbbreviation: string
language: string
// journalAbbreviation: string
// language: string
author: Array<{ family: string, given: string }>
issued: {
"date-parts": Array<string>
......@@ -21,12 +21,15 @@ export interface CslJson {
}
export const useArticlesStore = defineStore('articles', () => {
const articles = ref(new Map<string, CslJson>())
const articleMap = new Map([])
const articles = ref(articleMap)
function add(article: CslJson) {
const doi = article.DOI
if (articles.value.has(doi)) return
articles.value.set(article.DOI, article)
}
return { articles, add }
})
\ No newline at end of file
stores/facets.ts
View file @ c382702a
......@@ -14,7 +14,10 @@ export const useFacetsStore = defineStore('facets', () => {
function setFacets(newFacets: Facets) {
console.log("start set facets")
console.log(newFacets)
facets.value = newFacets
console.log("end set facets")
}
......