diff --git a/.gitattributes b/.gitattributes
index 40ca7edde186cf7747ca08fac2fde1c08246d9bb..ccb58707bf8ac8d5397e3891c621cbdf553be24c 100644
--- a/.gitattributes
+++ b/.gitattributes
@@ -1,2 +1,3 @@
data/ filter=lfs diff=lfs merge=lfs -text
data/**/*.csv filter=lfs diff=lfs merge=lfs -text
+data/**/*.tsv filter=lfs diff=lfs merge=lfs -text
diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
index aa76bf3062f7ad764083d732e52dcef5bdd09e88..60d46c3f0110a7dff9533cb1881d431f689b888a 100644
--- a/.gitlab-ci.yml
+++ b/.gitlab-ci.yml
@@ -203,6 +203,15 @@ lint:
--dir content/3.defense-systems/
--pfam public/pfam-a-hmm.csv
--output data/list-systems.json
+ - df-wiki-cli meilisearch delete-all-documents refseq
+ - >
+ df-wiki-cli
+ meilisearch
+ --host ${MEILI_HOST}
+ --key ${MEILI_MASTER_KEY}
+ index-update
+ refseq
+ sys_id
- >
df-wiki-cli
meilisearch
@@ -486,7 +495,7 @@ build:prod:wiki:
deploy:dev:
extends: .deploy
rules:
- - if: $CI_COMMIT_BRANCH == "dev"
+ - if: $CI_COMMIT_BRANCH == "dev" || $CI_COMMIT_BRANCH == "refactor-facet-autocomplete"
needs:
- "build:dev:wiki"
when: manual
diff --git a/components/AutocompleteMeiliFacets.vue b/components/AutocompleteMeiliFacets.vue
new file mode 100644
index 0000000000000000000000000000000000000000..fed95eeb55847f7041b242f50a044170ded88526
--- /dev/null
+++ b/components/AutocompleteMeiliFacets.vue
@@ -0,0 +1,255 @@
+<script setup lang="ts">
+import { filter } from '@observablehq/plot'
+
+export interface FilterItem {
+ type: 'facet' | 'innerOperator' | 'outerOperator' | 'value'
+ value: string
+ title: string
+ count?: number
+ deletable: boolean
+ props: Record<string, any>
+}
+
+export interface FacetItem {
+ title: string
+ value: string
+ type: "facet"
+ icon?: string
+ count?: number
+
+}
+
+export interface OperatorItem {
+ title: string,
+ type: 'operator'
+
+}
+export interface FacetCategory {
+ title: string
+ type: "subheader"
+}
+export interface FacetDivider {
+ type: "divider"
+}
+
+export type FacetInputItem = FacetItem | FacetCategory | FacetDivider
+
+
+export interface Props {
+ db: string
+ modelValue: FilterItem[] | undefined
+ facets: MaybeRef<FacetInputItem[] | undefined>
+ facetDistribution: MaybeRef<Record<string, Record<string, number>> | undefined>
+ isValidFilters?: MaybeRef<boolean>
+ autocompleteProps?: Record<string, any>
+
+}
+
+
+const emit = defineEmits(['update:modelValue', "meiliFilters"])
+const filterId = ref<number>(0)
+const props = withDefaults(defineProps<Props>(), {
+ modelValue: undefined,
+ autocompleteProps: () => {
+ return {
+ chips: true,
+ clearable: true,
+ multiple: true,
+ "auto-select-first": true,
+ "return-object": true,
+ "prepend-inner-icon": "md:filter_alt",
+ "hide-details": "auto",
+ "item-value": "value", "item-title": "title",
+ label: "Filter results...",
+ "single-line": true,
+
+ }
+ },
+ isValidFilters: false
+});
+// const { result: msResult } = useMeiliSearch(props.db)
+const isAutocompleteFocused = ref<boolean>(false)
+// const facetDistribution: Ref<Record<string, Record<string, number>>> = useState('facetDistribution')
+
+
+
+const autocompleteProps = computed(() => {
+ return {
+ ...props.autocompleteProps,
+ items: toValue(autocompleteItems)
+ }
+})
+
+const filterStep = computed(() => {
+ const toValFilterItems = toValue(props.modelValue)
+ if (toValFilterItems !== undefined) {
+ return toValFilterItems.length % 4
+ }
+})
+
+const innerOperatorItems = ref<FilterItem[]>([
+ {
+ type: "innerOperator", value: '=', title: "is", deletable: false, props: {
+ type: "innerOperator", deletable: false
+ }
+ }, {
+ type: "innerOperator", value: '!=', title: "is not", deletable: false, props: {
+ type: "innerOperator",
+ deletable: false
+ }
+ },
+
+])
+
+const outerOperatorItems = ref<FilterItem[]>([
+ {
+ type: "outerOperator", value: 'AND', title: "AND", deletable: false, props: {
+ type: "outerOperator", deletable: false
+ }
+ }, {
+ type: "outerOperator", value: 'OR', title: "OR", deletable: false, props: {
+ type: "outerOperator",
+ deletable: false
+ }
+ },
+
+])
+
+const autocompleteItems = computed(() => {
+ const toValFilterItems = toValue(props.modelValue)
+ // const index = toValFilterItems?.length ?? 0
+ if (filterStep.value === undefined || filterStep.value === 0) {
+ filterId.value++
+ return toValue(props.facets)?.map(facetItem => {
+ switch (facetItem.type) {
+ case "facet":
+ return {
+ type: "facet",
+ value: `${facetItem.value}-${filterId.value}`,
+ title: facetItem.title,
+ deletable: false,
+ icon: facetItem?.icon,
+ count: facetItem?.count,
+ props: {
+ deletable: false,
+ type: "facet"
+ }
+ }
+ case "subheader":
+ return {
+ type: "subheader",
+ title: facetItem.title,
+ deletable: false,
+
+ props: {
+ type: "subheader"
+ }
+ }
+ case "divider":
+ return { type: "divider" }
+ default:
+ break;
+ }
+
+ })
+ }
+ if (filterStep.value === 1) {
+ filterId.value++
+ return innerOperatorItems.value.map(it => { return { ...it, value: `${it.value}-${filterId.value}`, } })
+ }
+ if (filterStep.value === 2) {
+ filterId.value++
+
+ // get the facet value
+ if (Array.isArray(toValFilterItems)) {
+ const { type, value } = toValFilterItems?.slice(-2, -1)[0]
+ const sanitizedValue = value.split("-")[0]
+ const facetDistri = toValue(props.facetDistribution)
+ return facetDistri?.[sanitizedValue] ? Object.entries(facetDistri[sanitizedValue]).map(([key, val]) => {
+ return {
+ type: "value", value: `${key}-${filterId.value}`, title: key, count: val, deletable: true, props: {
+ type: "value", count: val, deletable: true
+ }
+ }
+ }) : []
+ }
+ }
+ if (filterStep.value === 3) {
+ filterId.value++
+ return outerOperatorItems.value.map(it => { return { ...it, value: `${it.value}-${filterId.value}`, } })
+ }
+})
+
+const hasFacetDistribution = computed(() => {
+
+ const toValFacetDistribution = toValue(props.facetDistribution)
+
+ return toValFacetDistribution !== undefined && Object.keys(toValFacetDistribution).length > 0
+})
+
+function updateAutocompleteFocused(isFocused: boolean) {
+ isAutocompleteFocused.value = isFocused
+}
+
+
+function emitUpdateModelValue(filters: MaybeRef<FilterItem[] | undefined>) {
+ emit('update:modelValue', toValue(filters))
+
+}
+
+function clearFilters() {
+ emitUpdateModelValue(undefined)
+}
+function deleteOneFilter(index: number) {
+
+ const toValFilterItems = toValue(props.modelValue)
+ // check if the next item is an outeroperator
+ const nextFilterItem = toValFilterItems?.slice(index + 1, index + 2)
+ if (index + 1 === toValFilterItems?.length && toValFilterItems?.length >= 7) {
+ // need to remove the previous outer operator
+ toValFilterItems?.splice(index - 3, 4)
+ }
+ else if (nextFilterItem?.length === 1 && nextFilterItem[0].type === 'outerOperator') {
+ toValFilterItems?.splice(index - 2, 4)
+
+ }
+ else {
+ toValFilterItems?.splice(index - 2, 3)
+ }
+
+ emitUpdateModelValue(toValFilterItems)
+}
+
+function isItemFilter(type: string | undefined) {
+ return type === "facet" || type === "innerOperator" || type === "outerOperator" || type === "value"
+}
+
+const hint = ref<string>('All <span class="font-weight-bold">OR</span> in a row are grouped together. Example: <span class="font-weight-bold">brex OR avs AND Archea</span> ⇒ <span class="font-weight-bold">(brex OR avs) AND Archea</span>')
+
+</script>
+<template>
+ <v-autocomplete :model-value="props.modelValue" @click:clear="clearFilters" v-bind="autocompleteProps" :hint="hint"
+ persistent-hint @update:focused="updateAutocompleteFocused" @update:modelValue="emitUpdateModelValue"
+ :loading="!hasFacetDistribution" :disabled="!hasFacetDistribution">
+ <template #message="{ message }">
+ <span v-html="message"></span>
+ </template>
+ <template #item="{ props, item }">
+ <v-list-item v-if="isItemFilter(item?.raw?.type)" v-bind="{ ...props, active: false }" :title="item.title"
+ :prepend-icon="item?.raw?.icon ? item.raw.icon : undefined"
+ :subtitle="item.raw?.count ? item.raw.count : ''" :value="props.value">
+ </v-list-item>
+ <v-divider v-if="item.raw.type === 'divider'"></v-divider>
+ <v-list-subheader v-if="item.raw.type === 'subheader'" :title="item.raw.title"></v-list-subheader>
+ </template>
+ <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 #append>
+ <v-btn variant="text" icon="md:filter_alt" @click="emitUpdateModelValue(props.modelValue)"
+ :disabled="!isValidFilters"></v-btn>
+ </template> -->
+
+ </v-autocomplete>
+</template>
\ No newline at end of file
diff --git a/components/Nav/Navbar.vue b/components/Nav/Navbar.vue
index 3a013a447a077c4f8387dba0a4f9e46d3e777abc..e5a879a612b4b49c8d90009a22ec15c49ed4fc34 100644
--- a/components/Nav/Navbar.vue
+++ b/components/Nav/Navbar.vue
@@ -32,7 +32,7 @@ watchEffect(() => {
const sections = ref([
{
id: "webservice",
- label: "webservice",
+ label: "Webservice",
href: runtimeConfig.public.defenseFinderWebservice,
},
{ id: "wiki", label: "Wiki", to: '/', },
diff --git a/components/ServerDbTable.vue b/components/ServerDbTable.vue
index 14578f59596eabce0681816d2a3fd861ab0a59ac..f6baa3d6f04c7a029abd1885226baa505b67b8b7 100644
--- a/components/ServerDbTable.vue
+++ b/components/ServerDbTable.vue
@@ -1,13 +1,14 @@
<script setup lang="ts">
// import type { FacetDistribution } from "meilisearch";
import { useCsvDownload } from "@/composables/useCsvDownload"
+import { useMeiliFilters } from "@/composables/useMeiliFilters"
import { useSlots } from 'vue'
import { useDisplay } from "vuetify";
import { useThrottleFn } from '@vueuse/core'
-
+import type { FacetInputItem, FilterItem } from '@/components/AutocompleteMeiliFacets.vue'
import { useMeiliSearch } from "#imports"
+import type { Filter } from "meilisearch";
// import { saveAs } from "file-saver";
-import { useFileSystemAccess } from '@vueuse/core'
export interface SortItem {
key: string,
order: boolean | 'asc' | 'desc'
@@ -22,47 +23,57 @@ export interface NumericalFilter {
export interface NumericalFilterModel extends NumericalFilter {
model: [number, number]
}
+
+
+
+
+
+export interface AutocompleteMeiliFacetProps {
+ db: string
+ facets: FacetInputItem[] | undefined
+ facetDistribution: Record<string, Record<string, number>> | undefined
+
+}
export interface Props {
title?: string
- db?: string
sortBy?: SortItem[]
- facets: MaybeRef<string[]>
- numericalFilters?: MaybeRef<string | undefined>
+ numericalFilters?: Ref<string[] | undefined>
dataTableServerProps: Record<string, any>
columnsToDownload?: MaybeRef<string[] | undefined>
+ autocompleteMeiliFacetsProps: AutocompleteMeiliFacetProps
}
-export interface FilterItem {
- type: 'facet' | 'operator' | 'value' | 'text'
- value: string
- title: string
- count?: number
- deletable: boolean
- props: Record<string, any>
-}
const props = withDefaults(defineProps<Props>(), {
title: '',
- db: 'refseq',
columnsToDownload: undefined,
sortBy: () => [{ key: "type", order: "asc" }],
- numericalFilters: undefined
+ numericalFilters: () => ref(undefined),
+ autocompleteMeiliFacetsProps: () => {
+ return {
+ db: 'refseq',
+ facetDistribution: undefined,
+ facets: undefined
+ }
+ }
});
+// const facetDistribution: Ref<Record<string, Record<string, number>> | undefined> = useState(`refseqFacetDistribution`)
+
+
const slots = useSlots()
const sortByRef = toRef(props.sortBy)
-const facetsRef = toRef(props.facets)
const emit = defineEmits(["refresh:search"])
-const { search: msSearch, result: msResult } = useMeiliSearch(props.db)
+const { search: msSearch, result: msResult } = useMeiliSearch(props.autocompleteMeiliFacetsProps.db)
const search: Ref<string> = ref("");
const filterOrSearch: Ref<FilterItem[] | null> = ref(null)
const hitsPerPage: Ref<number> = ref(25)
const itemsPerPage: Ref<number[]> = ref([25, 50, 100])
const filterError: Ref<string | null> = ref(null)
-const msFilter: Ref<string | undefined> = ref(undefined)
+// const msFilter: Ref<string | undefined> = ref(undefined)
const page = ref(1)
let loading = ref(false)
const expanded = ref([])
@@ -75,6 +86,9 @@ const computedTableHeight = computed(() => {
const pendingDownloadData = ref(false)
+const toRefNumericalFilters = toRef(props.numericalFilters)
+// const meiliFilters = ref<string | undefined>(undefined)
+
const filterInputValues = computed(() => {
if (filterOrSearch.value != null) {
return filterOrSearch.value.filter(({ props }) => props.type !== 'text')
@@ -83,9 +97,6 @@ const filterInputValues = computed(() => {
}
})
-const isFilter = computed(() => {
- return Array.isArray(filterOrSearch.value)
-})
const msSortBy = computed(() => {
if (sortByRef.value.length > 0) {
@@ -114,26 +125,67 @@ const notPaginatedParams = computed(() => {
watch([paginationParams, msSortBy, page], ([newParams, newSort, newPage]) => {
- searchOrFilter()
+ if (toValue(isValidFilters)) {
+ searchOrFilter()
+ }
})
-onMounted(async () => {
+
+onBeforeMount(async () => {
searchOrFilter()
emitRefreshRes()
+
+
})
+const msFilterCompo = ref<FilterItem[] | undefined>(undefined)
+
+const computedFilterStr = computed(() => {
+ const toValFilters = toValue(msFilterCompo)
+ let filtersStr: string | undefined = undefined
+ if (toValFilters !== undefined && toValFilters.length > 0) {
+ const tmpFilterItems = [...toValFilters]
+ if (tmpFilterItems.length % 4 === 0) {
+ tmpFilterItems.splice(-1)
+ }
+ filtersStr = "(" + tmpFilterItems.map((it, index) => {
+ const sanitizedValue = it.value.split("-").slice(0, -1).join("-")
+ if ((index + 1) % 4 === 3) {
+ return `"${sanitizedValue}"`
+ } else if ((index + 1) % 4 === 0) {
+ return ` ${sanitizedValue} `
+ }
+ else {
+ return `${sanitizedValue}`
+ }
+ }).join("") + ")"
+
+ }
+
+ return [filtersStr, props.numericalFilters].filter(f => f !== undefined && f !== null).join(" AND ")
-const computedFilter = computed(() => {
- return [toValue(msFilter), props.numericalFilters].filter(f => f !== undefined).join(" AND ")
})
+const computedF = computed(() => toValue(props.numericalFilters))
+const { arrayFilters: computedFilter } = useMeiliFilters(msFilterCompo, computedF)
+// const computedFilter = computed(() => {
+// const toValFilters = toValue(msFilterCompo)
+// if (toValFilters !== undefined && toValFilters.length > 0) {
+// meiliFilterAsArray
+// }
+// })
+
+
watch(computedFilter, () => {
- searchOrFilter()
- emitRefreshRes()
+ console.log(toValue(computedFilter))
+ if (toValue(isValidFilters) && (toValue(computedFilter) !== undefined || toValue(filterInputValues) === null)) {
+ searchOrFilter()
+ emitRefreshRes()
+ }
})
@@ -147,154 +199,86 @@ const throttleSearch = useThrottleFn(async () => {
searchOrFilter()
emitRefreshRes()
}, 300)
-async function searchOrFilter() {
- // do something, it will be called at most 1 time per second
- try {
- loading.value = true
- // const q = queryInputValue.value === null ? "" : queryInputValue.value
- const q = search.value
- await msSearch(q, { ...paginationParams.value, filter: toValue(computedFilter), sort: msSortBy.value })
- } catch (error: any) {
- filterError.value = error
- console.log(error)
+
+const lastFilterItem = computed(() => {
+ const toValFilterItems = toValue(msFilterCompo)
+ if (toValFilterItems !== undefined && Array.isArray(toValFilterItems)) {
+ return toValFilterItems.slice(-1)[0]
+ }
+})
+
+const isValidFilters = computed(() => {
+ const toValFilterItems = toValue(msFilterCompo)
+ if (toValFilterItems === undefined || Array.isArray(toValFilterItems) && toValFilterItems?.length === 0) {
+ return true
}
- finally {
- loading.value = false
+ else {
+ const toValLastFilterItem = toValue(lastFilterItem)
+ if (toValLastFilterItem !== undefined) {
+ console.log(toValLastFilterItem.type)
+ console.log(toValLastFilterItem.type === 'value')
+ return toValLastFilterItem.type === 'value'
+ // && isAutocompleteFocused.value === false
+ // || (toValFilterStep === 0 && toValLastFilterItem.type === "outerOperator" && toValLastFilterItem.value.split("-")[0] === "AND")
+ }
+ }
+ return false
+})
+
+
+async function searchOrFilter() {
+ if (toValue(isValidFilters)) {
+ // do something, it will be called at most 1 time per second
+ try {
+ loading.value = true
+ // const q = queryInputValue.value === null ? "" : queryInputValue.value
+ const q = search.value
+ await msSearch(q, { ...paginationParams.value, filter: toValue(computedFilter), sort: msSortBy.value })
+ } catch (error: any) {
+ filterError.value = error
+ console.log(error)
+ }
+ finally {
+ loading.value = false
+ }
}
}
+
+
function emitRefreshRes() {
- console.log("emit refresh:search")
const q = search.value
emit("refresh:search", {
- index: props.db,
+ index: props.autocompleteMeiliFacetsProps.db,
query: q,
params: { ...notPaginatedParams.value, filter: toValue(computedFilter), sort: msSortBy.value }
})
}
-function clearFilterOrSearch() {
- filterOrSearch.value = null
- // searchOrFilter()
- // emitRefreshRes()
-
-
-}
-
-// watch(msFilter, async (fos) => {
-// searchOrFilter()
-// emitRefreshRes()
-// search.value = ''
-
-
-// })
const totalHits = computed(() => {
return toValue(msResult)?.totalHits ?? toValue(msResult)?.estimatedTotalHits ?? 0
})
-watch(filterInputValues, (newSoF) => {
- if (isFilter.value && filterInputValues.value !== null && filterInputValues.value?.length % 3 === 0) {
- msFilter.value = filterInputValues.value.map((it, index) => {
-
- const sanitizedValue = it.value.split("-").slice(0, -1).join("-")
- if (index >= 1 && (index + 1) % 3 === 1) {
- return ` AND ${sanitizedValue}`
- } else if ((index + 1) % 3 === 0) {
- return `"${sanitizedValue}"`
- } else {
- return `${sanitizedValue}`
- }
-
- }).join("")
- }
-})
watch(search, () => {
searchOrFilter()
- emitRefreshRes()
+ // emitRefreshRes()
})
-const filterStep = computed(() => {
- return filterInputValues.value !== null && filterInputValues.value.length > 0 ? filterInputValues.value?.length % 3 : null
-})
-const operatorItems = ref([
- {
- type: "operator", value: '=', title: "is", deletable: false, props: {
- type: "operator", deletable: false
- }
- }, {
- type: "operator", value: '!=', title: "is not", deletable: false, props: {
- type: "operator",
- deletable: false
- }
- },
-
-])
-
-const autocompleteItems = computed(() => {
- const index = filterOrSearch.value?.length ?? 0
- // console.log(index)
- if (filterStep.value === null || filterStep.value === 0) {
- return toValue(facetsRef).map(value => {
- return {
- type: "facet",
- value: `${value}-${index}`,
- title: value,
- deletable: false,
- props: {
- deletable: false,
- type: "facet"
- }
- }
- })
- }
- if (filterStep.value === 1) {
- return operatorItems.value.map(it => { return { ...it, value: `${it.value}-${index}`, } })
- }
- if (filterStep.value === 2) {
- // get the facet value
- if (Array.isArray(filterOrSearch.value)) {
- const { type, value } = filterOrSearch.value?.slice(-2, -1)[0]
- const sanitizedValue = value.split("-")[0]
- // console.log("compute new facets")
- const facetDistri = msResult.value?.facetDistribution
- // console.log(facetDistri)
- return facetDistri?.[sanitizedValue] ? Object.entries(facetDistri[sanitizedValue]).map(([key, val]) => {
- return {
- type: "value", value: `${key}-${index}`, title: key, count: val, deletable: true, props: {
- type: "value", count: val, deletable: true
- }
- }
- }) : []
- }
- }
-})
-
-
-
-function selectItem(item) {
- filterOrSearch.value = Array.isArray(filterOrSearch.value) ? [...filterOrSearch.value, item] : [item]
-}
-
-function deleteOneFilter(index: number) {
- if (isFilter.value) {
- filterOrSearch.value?.splice(index - 2, 2)
- }
-}
+// watch(msFilterCompo, () => {
+// searchOrFilter()
-function clearSearch() {
- search.value = ""
-}
+// })
async function downloadData() {
pendingDownloadData.value = true
try {
const { data } = await useAsyncMeiliSearch({
- index: props.db,
+ index: props.autocompleteMeiliFacetsProps.db,
params: { ...toValue(notPaginatedParams), filter: toValue(computedFilter), sort: toValue(msSortBy) },
query: toValue(search),
})
@@ -304,84 +288,50 @@ async function downloadData() {
pendingDownloadData.value = false
}
}
+
+function focusedOrBlur(isFocused: boolean) {
+
+ if (!isFocused) {
+ emitRefreshRes()
+ }
+}
+
+
+
</script>
<template>
<v-card flat color="transparent">
- <v-card-text>
- </v-card-text>
- <v-card-text>
- <slot name="numerical-filters" :search="throttleSearch"></slot>
- </v-card-text>
+ <slot name="numerical-filters" :search="throttleSearch"></slot>
<v-data-table-server v-if="!msError" v-model:page="page" color="primary" v-bind="dataTableServerProps"
v-model:items-per-page="hitsPerPage" v-model:sortBy="sortByRef" v-model:expanded="expanded" fixed-header
:loading="loading" :items="msResult?.hits ?? []" :items-length="totalHits" density="compact"
:items-per-page-options="itemsPerPage" :height="computedTableHeight" class="elevation-1 mt-2">
<template #top>
- <template v-if="mobile">
- <v-toolbar> <v-badge :content="totalHits" color="primary" class="mx-2">
- <v-btn prepend-icon="md:download" :loading="pendingDownloadData" variant="text" color="primary"
- @click="downloadData()">{{
- props.title }}
- </v-btn>
- </v-badge></v-toolbar>
- <v-toolbar><v-text-field v-model="search" label="Search..." hide-details="auto"
- prepend-inner-icon="mdi-magnify" single-line clearable class="mx-2"></v-text-field></v-toolbar>
- <v-toolbar><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" class="mx-2"
- @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-else>
- <v-toolbar>
-
+ <v-card variant="flat" color="transparent">
+ <v-card-title>
<v-badge :content="totalHits" color="primary" class="mr-3">
<v-btn prepend-icon="md:download" :loading="pendingDownloadData" variant="text" color="primary"
@click="downloadData()">{{
props.title }}
</v-btn>
</v-badge>
- <v-spacer></v-spacer>
- <v-card variant="flat" color="transparent" :min-width="400" class="mx-2" :rounded="false">
- <v-text-field v-model="search" label="Search..." hide-details="auto"
- prepend-inner-icon="mdi-magnify" single-line clearable></v-text-field>
- </v-card>
- <v-card variant="flat" color="transparent" :min-width="500" class="mx-2" :rounded="false">
- <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-card>
-
- </v-toolbar>
- </template>
+ </v-card-title>
+ <v-card-title>
+ <v-text-field v-model="search" label="Search..." hide-details="auto" :disabled="pendingDownloadData"
+ prepend-inner-icon="mdi-magnify" single-line clearable
+ @update:focused="focusedOrBlur"></v-text-field>
+ </v-card-title>
+ <v-card-title>
+ <AutocompleteMeiliFacets v-model="msFilterCompo" v-bind="props.autocompleteMeiliFacetsProps"
+ :is-valid-filters="isValidFilters">
+ </AutocompleteMeiliFacets>
+
+
+ </v-card-title>
+
+ </v-card>
</template>
<template v-for="(slot, index) of Object.keys(slots)" :key="index" v-slot:[slot]="data">
diff --git a/components/content/RefseqDb.vue b/components/content/RefseqDb.vue
index e5ef7c958dbc2e701135cb5ec788f50f770d44c7..1296f71544b80f1d775e2f9cc263dc7eb6e57320 100644
--- a/components/content/RefseqDb.vue
+++ b/components/content/RefseqDb.vue
@@ -2,36 +2,98 @@
import * as Plot from "@observablehq/plot";
import PlotFigure from "~/components/PlotFigure";
import { useDisplay } from "vuetify";
-import type { SortItem } from "@/components/ServerDbTable.vue"
+
import { ServerDbTable } from "#components"
import { useSerialize } from "@/composables/useSerialize";
import { useRasterize } from "@/composables/useRasterize";
import { useDownloadBlob } from '@/composables/useDownloadBlob';
-
+import type { SortItem, AutocompleteMeiliFacetProps } from "@/components/ServerDbTable.vue"
import type { ComponentPublicInstance } from 'vue'
const sortBy: Ref<SortItem[]> = ref([{ key: 'type', order: "asc" }])
const itemValue = ref("id");
const { width } = useDisplay();
-const scaleTransform: Ref<string[]> = ref([])
+const dbName = ref("refseq")
+
+
+
+onBeforeMount(async () => {
+ const { data } = await useAsyncMeiliSearch({
+ index: toValue(dbName), query: "", params: {
+ facets: ["*"],
+ filter: [],
+ page: 1,
+ hitsPerPage: 25,
+ }
+ })
+
+ autocompleteMeiliFacetsProps.value.facetDistribution = toValue(data)?.facetDistribution
+
+})
+onMounted(async () => {
+ const { data } = await useAsyncMeiliSearch({
+ index: toValue(dbName), query: "", params: {
+ facets: ["*"],
+ filter: [],
+ page: 1,
+ hitsPerPage: 25,
+ }
+ })
+
+ autocompleteMeiliFacetsProps.value.facetDistribution = toValue(data)?.facetDistribution
+
+})
const { serialize } = useSerialize()
const { rasterize } = useRasterize()
const { download } = useDownloadBlob()
-const facets = ref([
- "replicon",
- "type",
- "subtype",
- "Superkingdom",
- "phylum",
- "order",
- "family",
- "genus",
- "species",
-])
+const autocompleteMeiliFacetsProps = ref<AutocompleteMeiliFacetProps>({
+ db: toValue(dbName),
+ facets: [
+ { title: "Defense System", type: "subheader" },
+ { title: "System", value: "type", type: "facet", icon: "mdi-virus-outline", },
+ { title: "Subsystem", value: "subtype", type: "facet", icon: "mdi-virus-outline" },
+ { type: "divider" },
+ { title: "Taxonomy", type: "subheader" },
+ { title: "Superkingdom", value: "Superkingdom", type: "facet", icon: "mdi-family-tree" },
+ { title: "Phylum", value: "phylum", type: "facet", icon: "mdi-family-tree" },
+ { title: "Order", value: "order", type: "facet", icon: "mdi-family-tree" },
+ { title: "Family", value: "family", type: "facet", icon: "mdi-family-tree" },
+ { title: "Genus", value: "genus", type: "facet", icon: "mdi-family-tree" },
+ { title: "Species", value: "species", type: "facet", icon: "mdi-family-tree" },
+ { type: "divider" },
+ { title: "Replicon", value: "replicon", type: "facet", icon: "mdi-dna", },
+
+ ],
+ facetDistribution: undefined
+})
+const computedAutocompleteMeiliFacetsProps = computed(() => {
+ const toValFacetDistribution = toValue(autocompleteMeiliFacetsProps).facetDistribution
+ const toValFacets = toValue(autocompleteMeiliFacetsProps).facets
+ if (toValFacetDistribution !== undefined && toValFacets !== undefined) {
+ return {
+ ...toValue(autocompleteMeiliFacetsProps), facets: toValFacets.map(facet => {
+ if (facet.type === "facet") {
+ const count = toValFacetDistribution?.[facet.value] ? Object.keys(toValFacetDistribution[facet.value]).length : undefined
+
+ return count ? { ...facet, count } : { ...facet }
+ }
+ else {
+ return { ...facet }
+ }
+ })
+ }
+ }
+ else {
+ return toValue(autocompleteMeiliFacetsProps)
+ }
+
+
+})
+
const availableTaxo: Ref<string[]> = ref([
"species",
"genus",
@@ -47,11 +109,11 @@ const selectedTaxoRank = ref("phylum");
const headers = ref([
{ title: "Replicon", key: "replicon" },
{
- title: "Type",
+ title: "System",
key: "type",
},
{
- title: "Subtype",
+ title: "Subsystem",
key: "subtype",
},
{
@@ -72,7 +134,7 @@ const computedHeaders = computed(() => {
}
})]
})
-const { result: msResult } = useMeiliSearch('refseq')
+const { result: msResult } = useMeiliSearch(toValue(dbName))
const computedWidth = computed(() => {
const currentWidth = fullWidth.value ? width.value : width.value / 2
@@ -82,20 +144,11 @@ const computedWidth = computed(() => {
const allHits: Ref<Record<string, any> | undefined> = ref(undefined)
-// onMounted(async () => {
-// console.log("on mounted get all hits")
-// const params = {
-// facets: ["*"],
-// filter: undefined,
-// sort: ["type:asc"],
-// limit: 500000
-// }
-// getAllHits({ index: "refseq", params, query: "" })
-// })
+
const pendingAllHits = ref(false)
async function getAllHits(params: { index: string, params: Record<string, any>, query: string }) {
console.log(params.index)
- if (params.index === 'refseq') {
+ if (params.index === toValue(dbName)) {
console.log("get all hits in function ")
console.log(params)
pendingAllHits.value = true
@@ -112,10 +165,6 @@ async function getAllHits(params: { index: string, params: Record<string, any>,
}
-const plotHeight = computed(() => {
- return computedWidth.value / 3;
- // return 500
-});
const defaultDataTableServerProps = ref({
showExpand: false
@@ -222,7 +271,7 @@ function namesToAccessionChips(names: string[]) {
return namesToCollapsibleChips(names).map(it => {
return {
...it,
- // href: new URL(it.title, "http://toto.pasteur.cloud").toString()
+ href: new URL(it.title, "https://www.ncbi.nlm.nih.gov/protein/").toString()
}
})
}
@@ -249,10 +298,7 @@ const binPlotDataOptions = computed(() => {
type: scaleType.value,
tickFormat: '~s',
ticks: scaleType.value === 'symlog' ? 3 : 5,
- // width: 350
-
},
- // fy: { domain: groupSortDomain.value },
marks: [
Plot.cell(toValueAllHits?.hits ?? [], Plot.group({ fill: "count" }, { x: "type", y: selectedTaxoRank.value, tip: true, inset: 0.5, sort: { y: "fill" } })),
]
@@ -419,13 +465,25 @@ async function downloadPng(component: ComponentPublicInstance | null, filename:
</v-expansion-panel>
</v-expansion-panels>
- <ServerDbTable title="RefSeq" db="refseq" :sortBy="sortBy" :facets="facets"
+ <ServerDbTable title="RefSeq" :sortBy="sortBy"
+ :autocomplete-meili-facets-props="computedAutocompleteMeiliFacetsProps"
:data-table-server-props="dataTableServerProps" @refresh:search="(params) => getAllHits(params)">
<template #[`item.accession_in_sys`]="{ item }">
<CollapsibleChips :items="namesToAccessionChips(item.accession_in_sys)">
</CollapsibleChips>
</template>
+ <template #[`item.type`]="{ item }">
+ <v-chip color="info" link size="small" :to="`/defense-systems/${item.type.toLowerCase()}`" target="_blank"> {{
+ item.type }}
+ </v-chip>
+ </template>
+
+ <template #[`item.subtype`]="{ item }">
+ <v-chip color="info" link size="small" :to="`/defense-systems/${item.type.toLowerCase()}`" target="_blank"> {{
+ item.subtype }}
+ </v-chip>
+ </template>
</ServerDbTable>
diff --git a/components/content/StructureDb.vue b/components/content/StructureDb.vue
index bdbb57d54f3783c0d01f2cfebe771882e6265352..9f3c02a690cc95af299856afe83db19ab9cd8a52 100644
--- a/components/content/StructureDb.vue
+++ b/components/content/StructureDb.vue
@@ -1,15 +1,72 @@
<script setup lang="ts">
import * as Plot from "@observablehq/plot";
import PlotFigure from "~/components/PlotFigure";
-import type { SortItem } from "@/components/ServerDbTable.vue"
+import type { SortItem, AutocompleteMeiliFacetProps } from "@/components/ServerDbTable.vue"
import { useNumericalFilter } from "@/composables/useNumericalfilter"
+import type { FacetInputItem } from '@/components/AutocompleteMeiliFacets.vue'
+import { ServerDbTable } from "#components"
+
+
-import { ServerDbTable } from "#components"
const sortBy: Ref<SortItem[]> = ref([{ key: 'System', order: "asc" }])
const itemValue = ref("id");
-const facets: Ref<string[]> = ref(["System", "subtype", "gene_name", "completed", "prediction_type", "proteins_in_the_prediction", "system_genes",
-])
+const dbName = ref("structure")
+
+onBeforeMount(async () => {
+ console.log("dans le mounted refseq")
+ const { data } = await useAsyncMeiliSearch({
+ index: toValue(dbName), query: "", params: {
+ facets: ["*"],
+ filter: [],
+ page: 1,
+ hitsPerPage: 25,
+ }
+ })
+ autocompleteMeiliFacetsProps.value.facetDistribution = toValue(data)?.facetDistribution
+
+})
+
+
+const autocompleteMeiliFacetsProps = ref<AutocompleteMeiliFacetProps>({
+ db: toValue(dbName),
+ facets: [
+ { title: "Defense System", type: "subheader" },
+ { title: "System", value: "System", type: "facet", icon: "mdi-virus-outline", },
+ { title: "Subsystem", value: "subtype", type: "facet", icon: "mdi-virus-outline" },
+ { type: "divider" },
+ { title: "Gene name", value: "gene_name", type: "facet", icon: "mdi-dna" },
+ { title: "Completed", value: "completed", type: "facet", icon: "md:done" },
+ { title: "Prediction type", value: "prediction_type", type: "facet", icon: "mdi-molecule" },
+ ],
+ facetDistribution: undefined
+})
+
+
+
+const computedAutocompleteMeiliFacetsProps = computed(() => {
+ const toValFacetDistribution = toValue(autocompleteMeiliFacetsProps).facetDistribution
+ const toValFacets = toValue(autocompleteMeiliFacetsProps).facets
+ if (toValFacetDistribution !== undefined && toValFacets !== undefined) {
+ return {
+ ...toValue(autocompleteMeiliFacetsProps), facets: toValFacets.map(facet => {
+ if (facet.type === "facet") {
+ const count = toValFacetDistribution?.[facet.value] ? Object.keys(toValFacetDistribution[facet.value]).length : undefined
+
+ return count ? { ...facet, count } : { ...facet }
+ }
+ else {
+ return { ...facet }
+ }
+ })
+ }
+ }
+ else {
+ return toValue(autocompleteMeiliFacetsProps)
+ }
+})
+
+
const headers: Ref<Object[]> = ref([
{ title: 'Structure', key: 'structure', sortable: false, removable: false },
{ title: "System", key: "System", removable: false },
@@ -31,14 +88,21 @@ const headers: Ref<Object[]> = ref([
])
-const { search: msSearch, result: msResult } = useMeiliSearch('structure')
const { range: plddtsRange, stringifyFilter: plddtsFilter, reset: plddtsReset } = useNumericalFilter("plddts", 0, 100)
const { range: iptmRange, stringifyFilter: iptmFilter, reset: iptmReset } = useNumericalFilter("iptm+ptm", 0, 1)
const { range: pdockqRange, stringifyFilter: pdockqFilter, reset: pdockqReset } = useNumericalFilter("pDockQ", 0, 1)
+
+function isString(item: Ref<string | undefined>): item is Ref<string> {
+ return toValue(item) !== undefined
+
+}
+
const numericalFilters = computed(() => {
- const listFilters = [plddtsFilter, iptmFilter, pdockqFilter].map(f => toValue(f)).filter(f => f !== undefined)
- return listFilters.length > 0 ? listFilters.join(" AND ") : undefined
+ console.log("je compute mes numerical filters")
+ const listFilters = [plddtsFilter, iptmFilter, pdockqFilter].filter(isString).map(f => toValue(f))
+ console.log(listFilters)
+ return listFilters.length > 0 ? listFilters : undefined
})
const defaultDataTableServerProps = ref({
@@ -70,61 +134,55 @@ function pdbNameToCif(pdbPath: string) {
return `${cifPath}.cif`
}
-function toSystemName(rawName: string) {
- // Does it work if it's a list of system genes ?
- // split on __ for systeme_vgenes
- return rawName.split("__")[0].toLocaleLowerCase()
-
-}
-
-
-
-const plddtDistribution = computed(() => {
- if (toValue(msResult)?.facetDistribution?.plddts) {
- return Object.entries(toValue(msResult).facetDistribution.plddts).map(([key, value]) => { })
- }
-})
-
-
-
-
-
</script>
<template>
- <ServerDbTable title="Predicted Structures" db="structure" :sortBy="sortBy" :facets="facets"
- :data-table-server-props="dataTableServerProps" :numerical-filters="numericalFilters">
-
-
-
+ <ServerDbTable title="Predicted Structures" :sortBy="sortBy" :data-table-server-props="dataTableServerProps"
+ :autocomplete-meili-facets-props="computedAutocompleteMeiliFacetsProps"
+ :numerical-filters="toRef(numericalFilters)">
<template #numerical-filters="{ search }">
- <v-row>
- <v-col cols="12" md="12" lg="4">
- <v-range-slider v-model="plddtsRange" strict density="compact" hide-details="auto" label="pLDDT"
- step="0.5" :min="0" :max="100" thumb-label="always" @update:modelValue="search()">
- <template #append>
- <v-btn variant="text" icon="md:restart_alt" @click="plddtsReset()"></v-btn>
- </template>
- </v-range-slider>
- </v-col>
- <v-col cols="12" md="12" lg="4">
-
- <v-range-slider v-model="iptmRange" strict density="compact" hide-details="auto" label="iptm+ptm"
- step="0.1" :min="0" :max="1" thumb-label="always" @update:modelValue="search()">
- <template #append>
- <v-btn variant="text" icon="md:restart_alt" @click="iptmReset()"></v-btn>
- </template>
- </v-range-slider>
- </v-col>
- <!-- pdockqReset -->
- <v-col cols="12" md="12" lg="4">
- <v-range-slider v-model="pdockqRange" strict density="compact" hide-details="auto" label="pDockQ"
- step="0.1" :min="0" :max="1" thumb-label="always" @update:modelValue="search()">
- <template #append>
- <v-btn variant="text" icon="md:restart_alt" @click="pdockqReset()"></v-btn>
- </template>
- </v-range-slider>
- </v-col>
- </v-row>
+ <v-list>
+ <v-list-item>
+ <v-list-item-title class="text-subtitle-1 text-medium-emphasis">
+ pLDDT
+ </v-list-item-title>
+ <v-row>
+ <v-col class="pt-8 pl-8">
+ <v-range-slider v-model="plddtsRange" strict density="compact" hide-details="auto" step="0.5"
+ :min="0" :max="100" thumb-label="always" @update:modelValue="search()">
+ <template #append>
+ <v-btn variant="text" icon="md:restart_alt" @click="plddtsReset()"></v-btn>
+ </template>
+
+ </v-range-slider>
+ </v-col></v-row>
+ </v-list-item>
+ <v-list-item>
+ <v-list-item-title class="text-subtitle-1 text-medium-emphasis">
+ iptm+ptm
+ </v-list-item-title>
+ <v-row>
+ <v-col class="pt-8 pl-8">
+ <v-range-slider v-model="iptmRange" strict density="compact" hide-details="auto" step="0.1"
+ :min="0" :max="1" thumb-label="always" @update:modelValue="search()">
+ <template #append>
+ <v-btn variant="text" icon="md:restart_alt" @click="iptmReset()"></v-btn>
+ </template>
+ </v-range-slider>
+ </v-col></v-row>
+ </v-list-item>
+ <v-list-item>
+ <v-list-item-title class="text-subtitle-1 text-medium-emphasis">pDockQ</v-list-item-title>
+ <v-row>
+ <v-col class="pt-8 pl-8">
+ <v-range-slider v-model="pdockqRange" density="compact" strict hide-details="auto" step="0.1"
+ :min="0" :max="1" thumb-label="always" @update:modelValue="search()">
+ <template #append>
+ <v-btn variant="text" icon="md:restart_alt" @click="pdockqReset()"></v-btn>
+ </template>
+ </v-range-slider>
+ </v-col></v-row>
+ </v-list-item>
+ </v-list>
</template>
<template #[`item.proteins_in_the_prediction`]="{ item }">
diff --git a/components/content/SystemDb.vue b/components/content/SystemDb.vue
index 65e3c152f8b1ad61c37f0701272afdf07d82167d..c754d1326ba0888ffa5a489f5428b3ffd3180b91 100644
--- a/components/content/SystemDb.vue
+++ b/components/content/SystemDb.vue
@@ -1,9 +1,73 @@
<script setup lang="ts">
-import type { SortItem } from "@/components/ServerDbTable.vue"
+import type { SortItem, AutocompleteMeiliFacetProps } 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", "PFAM.DE"])
+const dbName = ref("systems")
+
+onBeforeMount(async () => {
+ const { data } = await useAsyncMeiliSearch({
+ index: toValue(dbName), query: "", params: {
+ facets: ["*"],
+ filter: [],
+ page: 1,
+ hitsPerPage: 25,
+ }
+ })
+
+ autocompleteMeiliFacetsProps.value.facetDistribution = toValue(data)?.facetDistribution
+
+})
+
+const autocompleteMeiliFacetsProps = ref<AutocompleteMeiliFacetProps>({
+ db: toValue(dbName),
+ facets: [
+ { title: "Defense System", type: "subheader" },
+ { title: 'System', value: "title", type: "facet", icon: "mdi-virus-outline" },
+
+ { type: "divider" },
+ { title: "Mechanism", type: "subheader" },
+ { title: 'Sensor', value: "Sensor", type: "facet", icon: "mdi-cog" },
+ { title: 'Effector', value: "Effector", type: "facet", icon: "mdi-cog" },
+ { title: 'Activator', value: "Activator", type: "facet", icon: "mdi-cog" },
+
+
+ { type: "divider" },
+ { title: "PFAM", type: "subheader" },
+ { title: 'Acession', value: "PFAM.AC", type: "facet", icon: "mdi-key" },
+ { title: 'Description', value: "PFAM.DE", type: "facet", icon: "md:description" },
+
+ { type: "divider" },
+ { title: 'Contributor', value: "contributors", type: "facet", icon: "md:person" },
+ ],
+ facetDistribution: undefined
+})
+
+
+const computedAutocompleteMeiliFacetsProps = computed(() => {
+ const toValFacetDistribution = toValue(autocompleteMeiliFacetsProps).facetDistribution
+ const toValFacets = toValue(autocompleteMeiliFacetsProps).facets
+ if (toValFacetDistribution !== undefined && toValFacets !== undefined) {
+ return {
+ ...toValue(autocompleteMeiliFacetsProps), facets: toValFacets.map(facet => {
+ if (facet.type === "facet") {
+ const count = toValFacetDistribution?.[facet.value] ? Object.keys(toValFacetDistribution[facet.value]).length : undefined
+
+ return count ? { ...facet, count } : { ...facet }
+ }
+ else {
+ return { ...facet }
+ }
+ })
+ }
+ }
+ else {
+ return toValue(autocompleteMeiliFacetsProps)
+ }
+
+
+})
+
const headers: Ref<Object[]> = ref([
{ title: "System", key: "title", removable: false },
{ title: "Article", key: "doi", removable: false },
@@ -16,7 +80,6 @@ const headers: Ref<Object[]> = ref([
])
-const { search: msSearch, result: msResult } = useMeiliSearch('systems')
const defaultDataTableServerProps = ref({
showExpand: false
@@ -34,7 +97,8 @@ const columnsToDownload = ref(['title', 'doi', 'Sensor', 'Activator', 'Effector'
</script>
<template>
- <ServerDbTable title="List Systems" db="systems" :sortBy="sortBy" :facets="facets"
+ <ServerDbTable title="List Systems" :db="dbName" :sortBy="sortBy"
+ :autocomplete-meili-facets-props="computedAutocompleteMeiliFacetsProps"
:data-table-server-props="dataTableServerProps" :columns-to-download="columnsToDownload">
@@ -48,8 +112,10 @@ const columnsToDownload = ref(['title', 'doi', 'Sensor', 'Activator', 'Effector'
<ArticleDoi v-if="item?.doi" :doi="item.doi" :abstract="item?.abstract" :divider="false" :enumerate="false" />
</template>
<template #[`item.PFAM`]="{ item }">
-
<pfam-chips v-if="item?.PFAM" :pfams="item.PFAM"></pfam-chips>
</template>
- </ServerDbTable>
-</template>
\ No newline at end of file
+ <template #[`item.contributors`]="{ item }">
+ <CollapsibleChips v-if="item?.contributors" :items="item.contributors.map(it => ({ title: it }))">
+ </CollapsibleChips>
+ </template>
+ </ServerDbTable></template>
\ No newline at end of file
diff --git a/composables/useFacetFilters.ts b/composables/useFacetFilters.ts
new file mode 100644
index 0000000000000000000000000000000000000000..042014f55da8656bbed20b5578cef76d0cf0ce07
--- /dev/null
+++ b/composables/useFacetFilters.ts
@@ -0,0 +1,14 @@
+export interface FilterItem {
+ type: 'facet' | 'operator' | 'value' | 'text'
+ value: string
+ title: string
+ count?: number
+ deletable: boolean
+ props: Record<string, any>
+}
+
+export function useFacetFilters(inputFilters: MaybeRef<FilterItem[] | undefined>) {
+
+
+
+}
\ No newline at end of file
diff --git a/composables/useMeiliFilters.ts b/composables/useMeiliFilters.ts
new file mode 100644
index 0000000000000000000000000000000000000000..d04ec0b186bfa30dc5587d067d3c186a0cf87d4a
--- /dev/null
+++ b/composables/useMeiliFilters.ts
@@ -0,0 +1,113 @@
+import type { FilterItem } from '@/components/AutocompleteMeiliFacets.vue'
+import { filter } from '@observablehq/plot'
+import type { Filter } from "meilisearch"
+
+export function useMeiliFilters(filters: MaybeRef<FilterItem[] | undefined>, numericalFilters: Ref<string[] | undefined>) {
+
+ const arrayFilters = ref<Filter | undefined>(undefined)
+ const nf = toRef(numericalFilters)
+
+ watch(nf, () => {
+ console.log("mon nf", nf)
+ })
+
+
+ watch(numericalFilters,() => {
+ console.log("je watch numerical filter", numericalFilters)
+ })
+
+ watchEffect(() => {
+ console.log("dans le computed de useMeilisFilter")
+ const toValFilters = toValue(filters)
+ const toValNumericalFilter = toValue(nf)
+ console.log(toValNumericalFilter)
+ let categoricalFilters: FilterItem[] | undefined = undefined
+ if (toValFilters !== undefined && toValFilters.length >= 3) {
+ const cachedFilters = [...toValFilters]
+
+ // Remove last element if it is an outerOperator
+ if (cachedFilters.length % 4 === 0 && cachedFilters.slice(-1)[0].type === 'outerOperator') {
+ cachedFilters.splice(-1)
+ }
+
+
+ let previousOperator: 'AND' | 'OR' | undefined = undefined
+ const arrayFilters = cachedFilters.reduce<FilterItem[]>((acc, curr, index) => {
+ const sanitizedValue = curr.value.split("-").slice(0, -1).join("-")
+ const position = index + 1
+ switch (position % 4) {
+ case 0:
+ // if this is the first time pass by an outeroperator
+ if (previousOperator === undefined) {
+ const newFilter = acc.splice(-3).join("")
+ console.log("newFilter: ", newFilter)
+ if (sanitizedValue === 'OR') {
+ acc = [[newFilter]]
+ }
+ else {
+ acc.push(newFilter)
+ }
+ }
+ previousOperator = sanitizedValue
+ break;
+ case 3:
+ acc.push(`'${sanitizedValue}'`)
+ const newFilter = acc.splice(-3).join("")
+ if (previousOperator === 'AND') {
+ acc.push(newFilter)
+ }
+ else {
+ const previousElem = acc.slice(-1)[0]
+ if (Array.isArray(previousElem)) {
+ acc.slice(-1)[0].push(newFilter)
+ }
+ else if (previousElem !== undefined) {
+ const previousElem = acc.splice(-1)[0]
+ console.log("previousElem: ", previousElem)
+ console.log("newFilter: ", newFilter)
+ acc.push([previousElem, newFilter])
+ }
+ else {
+ acc.push(newFilter)
+ }
+ }
+ break
+ default:
+ acc.push(sanitizedValue)
+ break;
+ }
+ return acc
+ }, [])
+ categoricalFilters = arrayFilters.length > 0 ? arrayFilters : undefined
+ }
+
+ function isFilterItem(item: FilterItem[] | string[] | undefined): item is FilterItem[] | string[] {
+ return item !== undefined
+
+ }
+ console.log(categoricalFilters)
+ const filterItemArray = [categoricalFilters, toValNumericalFilter].filter(isFilterItem).flat()
+ console.log(filterItemArray)
+ // const returnArr = filterItemArray.reduce<FilterItem | string | undefined>((acc, curr) => {
+ // const toValCurr = toValue(curr)
+ // if (toValCurr === undefined) {
+ // return acc
+ // }
+ // else {
+ // if (acc !== undefined) {
+ // return [...acc, ...toValCurr]
+ // }
+ // else { return [...toValCurr] }
+ // }
+ // }, undefined)
+ // console.log(returnArr)
+
+ // return returnArr
+ arrayFilters.value = filterItemArray
+ })
+
+ // const arrayFilters: ComputedRef<Filter | undefined> = computed(() => {
+ // })
+
+ return { arrayFilters }
+}
diff --git a/composables/useNumericalfilter.ts b/composables/useNumericalfilter.ts
index 9ee97d80a4239e558dfdea1e57e563cc500519af..8f776e3cc93168fa567c26cf1b48621ad100b576 100644
--- a/composables/useNumericalfilter.ts
+++ b/composables/useNumericalfilter.ts
@@ -6,17 +6,11 @@ export function useNumericalFilter(
const range: Ref<[number, number]> = ref([toValue(min), toValue(max)])
-
-
-
-
- const stringifyFilter: Ref<string | undefined> = ref(`${toValue(id)} ${toValue(min)} TO ${toValue(max)}`)
+ const stringifyFilter: Ref<string | undefined> = ref(undefined)
watchEffect(() => {
- console.log("watch reange")
- console.log(range.value)
if (range.value[0] === toValue(min) && range.value[1] === toValue(max)) {
stringifyFilter.value = undefined
} else {
diff --git a/content/3.defense-systems/nixi.md b/content/3.defense-systems/nixi.md
index 1e07155a975e10ddefd6efbec62f14bcea6c30fa..1341d9b0ef98b3223835d7e7763599619b810929 100644
--- a/content/3.defense-systems/nixi.md
+++ b/content/3.defense-systems/nixi.md
@@ -10,7 +10,7 @@ tableColumns:
Activator: Unknown
Effector: Nucleic acid degrading
contributors:
- - Marian Dominguez Mirazo
+ - Marian Dominguez-Mirazo
relevantAbstracts:
- doi: 10.1093/nar/gkac002
---
diff --git a/content/3.defense-systems/tiamat.md b/content/3.defense-systems/tiamat.md
index e6220d71efd3ddd389a24f496104e08c2f9784fc..4dd0e869939515c9e4f2b8096fab14f9c46c2bbe 100644
--- a/content/3.defense-systems/tiamat.md
+++ b/content/3.defense-systems/tiamat.md
@@ -11,7 +11,8 @@ tableColumns:
Effector: Unknown
PFAM: PF00656, PF13020
contributors:
- - Helena Shomar, Marie Guillaume
+ - Helena Shomar
+ - Marie Guillaume
relevantAbstracts:
- doi: 10.1016/j.chom.2022.09.017
diff --git a/data/list-systems.json b/data/list-systems.json
index d687e3b71b370263e2fb3df250064e65283c298c..1f36c55d3e4774e414cd4f913269a8cf3bf00676 100644
--- a/data/list-systems.json
+++ b/data/list-systems.json
@@ -892,7 +892,8 @@
{
"title": "Tiamat",
"contributors": [
- "Helena Shomar, Marie Guillaume"
+ "Helena Shomar",
+ "Marie Guillaume"
],
"relevantAbstracts": [
{
@@ -2412,7 +2413,7 @@
{
"title": "NixI",
"contributors": [
- "Marian Dominguez Mirazo"
+ "Marian Dominguez-Mirazo"
],
"relevantAbstracts": [
{
diff --git a/data/refseq_res.csv b/data/refseq_res.csv
index 46fbeb2e678e9473f05faac9ecedca33c7f7efcf..733fbf04e103186d499d6201405d79378c3ed802 100644
--- a/data/refseq_res.csv
+++ b/data/refseq_res.csv
@@ -1,3 +1,3 @@
version https://git-lfs.github.com/spec/v1
-oid sha256:ad4d396c49c0b602a61b50efff0d239e58f4a3ae103d36bb0cf8873b9bb6729d
-size 69374885
+oid sha256:f19dff4f92dd3ca79a66fe6835f71261b9a5264f3df176dd005490dd74aa552d
+size 64961046
diff --git a/package-lock.json b/package-lock.json
index b1474e4bb37d89f8c9c4a6e7498ff77cd8944d2d..faec1869b38d0c8695ebbbf41a28be28fc809bcb 100644
--- a/package-lock.json
+++ b/package-lock.json
@@ -1,5 +1,5 @@
{
- "name": "app",
+ "name": "wiki",
"lockfileVersion": 3,
"requires": true,
"packages": {
@@ -15,162 +15,179 @@
"yaml": "^2.3.3"
},
"devDependencies": {
- "@nuxt/content": "^2.9.0",
- "@types/node": "^20.10.4",
- "@vueuse/core": "^10.6.1",
- "@vueuse/nuxt": "^10.6.1",
+ "@nuxt/content": "^2.10.0",
+ "@types/node": "^20.10.6",
+ "@vueuse/core": "^10.7.1",
+ "@vueuse/nuxt": "^10.7.1",
"nuxt": "^3.9.0",
"nuxt-meilisearch": "^1.1.0",
- "vuetify-nuxt-module": "^0.7.3"
+ "vuetify-nuxt-module": "^0.8.0"
}
},
"node_modules/@aashutoshrathi/word-wrap": {
"version": "1.2.6",
+ "resolved": "https://registry.npmjs.org/@aashutoshrathi/word-wrap/-/word-wrap-1.2.6.tgz",
+ "integrity": "sha512-1Yjs2SvM8TflER/OD3cOjhWWOZb58A2t7wpE2S9XfBYTiIl+XFhQG2bjy4Pu1I+EAlCNUzRDYDdFwFYUKvXcIA==",
"dev": true,
- "license": "MIT",
"peer": true,
"engines": {
"node": ">=0.10.0"
}
},
"node_modules/@algolia/cache-browser-local-storage": {
- "version": "4.21.1",
+ "version": "4.22.0",
+ "resolved": "https://registry.npmjs.org/@algolia/cache-browser-local-storage/-/cache-browser-local-storage-4.22.0.tgz",
+ "integrity": "sha512-uZ1uZMLDZb4qODLfTSNHxSi4fH9RdrQf7DXEzW01dS8XK7QFtFh29N5NGKa9S+Yudf1vUMIF+/RiL4i/J0pWlQ==",
"dev": true,
- "license": "MIT",
"peer": true,
"dependencies": {
- "@algolia/cache-common": "4.21.1"
+ "@algolia/cache-common": "4.22.0"
}
},
"node_modules/@algolia/cache-common": {
- "version": "4.21.1",
+ "version": "4.22.0",
+ "resolved": "https://registry.npmjs.org/@algolia/cache-common/-/cache-common-4.22.0.tgz",
+ "integrity": "sha512-TPwUMlIGPN16eW67qamNQUmxNiGHg/WBqWcrOoCddhqNTqGDPVqmgfaM85LPbt24t3r1z0zEz/tdsmuq3Q6oaA==",
"dev": true,
- "license": "MIT",
"peer": true
},
"node_modules/@algolia/cache-in-memory": {
- "version": "4.21.1",
+ "version": "4.22.0",
+ "resolved": "https://registry.npmjs.org/@algolia/cache-in-memory/-/cache-in-memory-4.22.0.tgz",
+ "integrity": "sha512-kf4Cio9NpPjzp1+uXQgL4jsMDeck7MP89BYThSvXSjf2A6qV/0KeqQf90TL2ECS02ovLOBXkk98P7qVarM+zGA==",
"dev": true,
- "license": "MIT",
"peer": true,
"dependencies": {
- "@algolia/cache-common": "4.21.1"
+ "@algolia/cache-common": "4.22.0"
}
},
"node_modules/@algolia/client-account": {
- "version": "4.21.1",
+ "version": "4.22.0",
+ "resolved": "https://registry.npmjs.org/@algolia/client-account/-/client-account-4.22.0.tgz",
+ "integrity": "sha512-Bjb5UXpWmJT+yGWiqAJL0prkENyEZTBzdC+N1vBuHjwIJcjLMjPB6j1hNBRbT12Lmwi55uzqeMIKS69w+0aPzA==",
"dev": true,
- "license": "MIT",
"peer": true,
"dependencies": {
- "@algolia/client-common": "4.21.1",
- "@algolia/client-search": "4.21.1",
- "@algolia/transporter": "4.21.1"
+ "@algolia/client-common": "4.22.0",
+ "@algolia/client-search": "4.22.0",
+ "@algolia/transporter": "4.22.0"
}
},
"node_modules/@algolia/client-analytics": {
- "version": "4.21.1",
+ "version": "4.22.0",
+ "resolved": "https://registry.npmjs.org/@algolia/client-analytics/-/client-analytics-4.22.0.tgz",
+ "integrity": "sha512-os2K+kHUcwwRa4ArFl5p/3YbF9lN3TLOPkbXXXxOvDpqFh62n9IRZuzfxpHxMPKAQS3Et1s0BkKavnNP02E9Hg==",
"dev": true,
- "license": "MIT",
"peer": true,
"dependencies": {
- "@algolia/client-common": "4.21.1",
- "@algolia/client-search": "4.21.1",
- "@algolia/requester-common": "4.21.1",
- "@algolia/transporter": "4.21.1"
+ "@algolia/client-common": "4.22.0",
+ "@algolia/client-search": "4.22.0",
+ "@algolia/requester-common": "4.22.0",
+ "@algolia/transporter": "4.22.0"
}
},
"node_modules/@algolia/client-common": {
- "version": "4.21.1",
+ "version": "4.22.0",
+ "resolved": "https://registry.npmjs.org/@algolia/client-common/-/client-common-4.22.0.tgz",
+ "integrity": "sha512-BlbkF4qXVWuwTmYxVWvqtatCR3lzXwxx628p1wj1Q7QP2+LsTmGt1DiUYRuy9jG7iMsnlExby6kRMOOlbhv2Ag==",
"dev": true,
- "license": "MIT",
"peer": true,
"dependencies": {
- "@algolia/requester-common": "4.21.1",
- "@algolia/transporter": "4.21.1"
+ "@algolia/requester-common": "4.22.0",
+ "@algolia/transporter": "4.22.0"
}
},
"node_modules/@algolia/client-personalization": {
- "version": "4.21.1",
+ "version": "4.22.0",
+ "resolved": "https://registry.npmjs.org/@algolia/client-personalization/-/client-personalization-4.22.0.tgz",
+ "integrity": "sha512-pEOftCxeBdG5pL97WngOBi9w5Vxr5KCV2j2D+xMVZH8MuU/JX7CglDSDDb0ffQWYqcUN+40Ry+xtXEYaGXTGow==",
"dev": true,
- "license": "MIT",
"peer": true,
"dependencies": {
- "@algolia/client-common": "4.21.1",
- "@algolia/requester-common": "4.21.1",
- "@algolia/transporter": "4.21.1"
+ "@algolia/client-common": "4.22.0",
+ "@algolia/requester-common": "4.22.0",
+ "@algolia/transporter": "4.22.0"
}
},
"node_modules/@algolia/client-search": {
- "version": "4.21.1",
+ "version": "4.22.0",
+ "resolved": "https://registry.npmjs.org/@algolia/client-search/-/client-search-4.22.0.tgz",
+ "integrity": "sha512-bn4qQiIdRPBGCwsNuuqB8rdHhGKKWIij9OqidM1UkQxnSG8yzxHdb7CujM30pvp5EnV7jTqDZRbxacbjYVW20Q==",
"dev": true,
- "license": "MIT",
"peer": true,
"dependencies": {
- "@algolia/client-common": "4.21.1",
- "@algolia/requester-common": "4.21.1",
- "@algolia/transporter": "4.21.1"
+ "@algolia/client-common": "4.22.0",
+ "@algolia/requester-common": "4.22.0",
+ "@algolia/transporter": "4.22.0"
}
},
"node_modules/@algolia/events": {
"version": "4.0.1",
- "dev": true,
- "license": "MIT"
+ "resolved": "https://registry.npmjs.org/@algolia/events/-/events-4.0.1.tgz",
+ "integrity": "sha512-FQzvOCgoFXAbf5Y6mYozw2aj5KCJoA3m4heImceldzPSMbdyS4atVjJzXKMsfX3wnZTFYwkkt8/z8UesLHlSBQ==",
+ "dev": true
},
"node_modules/@algolia/logger-common": {
- "version": "4.21.1",
+ "version": "4.22.0",
+ "resolved": "https://registry.npmjs.org/@algolia/logger-common/-/logger-common-4.22.0.tgz",
+ "integrity": "sha512-HMUQTID0ucxNCXs5d1eBJ5q/HuKg8rFVE/vOiLaM4Abfeq1YnTtGV3+rFEhOPWhRQxNDd+YHa4q864IMc0zHpQ==",
"dev": true,
- "license": "MIT",
"peer": true
},
"node_modules/@algolia/logger-console": {
- "version": "4.21.1",
+ "version": "4.22.0",
+ "resolved": "https://registry.npmjs.org/@algolia/logger-console/-/logger-console-4.22.0.tgz",
+ "integrity": "sha512-7JKb6hgcY64H7CRm3u6DRAiiEVXMvCJV5gRE672QFOUgDxo4aiDpfU61g6Uzy8NKjlEzHMmgG4e2fklELmPXhQ==",
"dev": true,
- "license": "MIT",
"peer": true,
"dependencies": {
- "@algolia/logger-common": "4.21.1"
+ "@algolia/logger-common": "4.22.0"
}
},
"node_modules/@algolia/requester-browser-xhr": {
- "version": "4.21.1",
+ "version": "4.22.0",
+ "resolved": "https://registry.npmjs.org/@algolia/requester-browser-xhr/-/requester-browser-xhr-4.22.0.tgz",
+ "integrity": "sha512-BHfv1h7P9/SyvcDJDaRuIwDu2yrDLlXlYmjvaLZTtPw6Ok/ZVhBR55JqW832XN/Fsl6k3LjdkYHHR7xnsa5Wvg==",
"dev": true,
- "license": "MIT",
"peer": true,
"dependencies": {
- "@algolia/requester-common": "4.21.1"
+ "@algolia/requester-common": "4.22.0"
}
},
"node_modules/@algolia/requester-common": {
- "version": "4.21.1",
+ "version": "4.22.0",
+ "resolved": "https://registry.npmjs.org/@algolia/requester-common/-/requester-common-4.22.0.tgz",
+ "integrity": "sha512-Y9cEH/cKjIIZgzvI1aI0ARdtR/xRrOR13g5psCxkdhpgRN0Vcorx+zePhmAa4jdQNqexpxtkUdcKYugBzMZJgQ==",
"dev": true,
- "license": "MIT",
"peer": true
},
"node_modules/@algolia/requester-node-http": {
- "version": "4.21.1",
+ "version": "4.22.0",
+ "resolved": "https://registry.npmjs.org/@algolia/requester-node-http/-/requester-node-http-4.22.0.tgz",
+ "integrity": "sha512-8xHoGpxVhz3u2MYIieHIB6MsnX+vfd5PS4REgglejJ6lPigftRhTdBCToe6zbwq4p0anZXjjPDvNWMlgK2+xYA==",
"dev": true,
- "license": "MIT",
"peer": true,
"dependencies": {
- "@algolia/requester-common": "4.21.1"
+ "@algolia/requester-common": "4.22.0"
}
},
"node_modules/@algolia/transporter": {
- "version": "4.21.1",
+ "version": "4.22.0",
+ "resolved": "https://registry.npmjs.org/@algolia/transporter/-/transporter-4.22.0.tgz",
+ "integrity": "sha512-ieO1k8x2o77GNvOoC+vAkFKppydQSVfbjM3YrSjLmgywiBejPTvU1R1nEvG59JIIUvtSLrZsLGPkd6vL14zopA==",
"dev": true,
- "license": "MIT",
"peer": true,
"dependencies": {
- "@algolia/cache-common": "4.21.1",
- "@algolia/logger-common": "4.21.1",
- "@algolia/requester-common": "4.21.1"
+ "@algolia/cache-common": "4.22.0",
+ "@algolia/logger-common": "4.22.0",
+ "@algolia/requester-common": "4.22.0"
}
},
"node_modules/@algolia/ui-components-highlight-vdom": {
"version": "1.2.2",
+ "resolved": "https://registry.npmjs.org/@algolia/ui-components-highlight-vdom/-/ui-components-highlight-vdom-1.2.2.tgz",
+ "integrity": "sha512-/+7jh7cd5rR2yQC7ME4SDcnAMiD1Ofn5Qq+E7afTJx9XSMOHkLR77/o6YcuJ60TfD1S+9lr7yjBLACon8gOuzQ==",
"dev": true,
- "license": "MIT",
"dependencies": {
"@algolia/ui-components-shared": "1.2.2",
"@babel/runtime": "^7.0.0"
@@ -178,12 +195,14 @@
},
"node_modules/@algolia/ui-components-shared": {
"version": "1.2.2",
- "dev": true,
- "license": "MIT"
+ "resolved": "https://registry.npmjs.org/@algolia/ui-components-shared/-/ui-components-shared-1.2.2.tgz",
+ "integrity": "sha512-FYwEG5sbr8p4V8mqP0iUaKgmWfcrMXRXwp7e6iBuB65P/7QyL8pT4I6/iGb85Q5mNH+UtYYSmLZhKjEblllKEQ==",
+ "dev": true
},
"node_modules/@ampproject/remapping": {
"version": "2.2.1",
- "license": "Apache-2.0",
+ "resolved": "https://registry.npmjs.org/@ampproject/remapping/-/remapping-2.2.1.tgz",
+ "integrity": "sha512-lFMjJTrFL3j7L9yBxwYfCq2k6qqwHyzuUl/XBnif78PWTJYyL/dfowQHWE3sp6U6ZzqWiiIZnpTMO96zhkjwtg==",
"dependencies": {
"@jridgewell/gen-mapping": "^0.3.0",
"@jridgewell/trace-mapping": "^0.3.9"
@@ -194,15 +213,17 @@
},
"node_modules/@antfu/utils": {
"version": "0.7.7",
+ "resolved": "https://registry.npmjs.org/@antfu/utils/-/utils-0.7.7.tgz",
+ "integrity": "sha512-gFPqTG7otEJ8uP6wrhDv6mqwGWYZKNvAcCq6u9hOj0c+IKCEsY4L1oC9trPq2SaWIzAfHvqfBDxF591JkMf+kg==",
"dev": true,
- "license": "MIT",
"funding": {
"url": "https://github.com/sponsors/antfu"
}
},
"node_modules/@babel/code-frame": {
"version": "7.23.5",
- "license": "MIT",
+ "resolved": "https://registry.npmjs.org/@babel/code-frame/-/code-frame-7.23.5.tgz",
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@@ -1490,14 +1564,16 @@
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"version": "2.0.5",
- "license": "MIT",
+ "resolved": "https://registry.npmjs.org/@nodelib/fs.stat/-/fs.stat-2.0.5.tgz",
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"engines": {
"node": ">= 8"
}
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"node_modules/@nodelib/fs.walk": {
"version": "1.2.8",
- "license": "MIT",
+ "resolved": "https://registry.npmjs.org/@nodelib/fs.walk/-/fs.walk-1.2.8.tgz",
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"fastq": "^1.6.0"
@@ -1508,8 +1584,9 @@
},
"node_modules/@npmcli/agent": {
"version": "2.2.0",
+ "resolved": "https://registry.npmjs.org/@npmcli/agent/-/agent-2.2.0.tgz",
+ "integrity": "sha512-2yThA1Es98orMkpSLVqlDZAMPK3jHJhifP2gnNUdk1754uZ8yI5c+ulCoVG+WlntQA6MzhrURMXjSd9Z7dJ2/Q==",
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"http-proxy-agent": "^7.0.0",
@@ -1521,18 +1598,45 @@
"node": "^16.14.0 || >=18.0.0"
}
},
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+ "version": "7.1.0",
+ "resolved": "https://registry.npmjs.org/agent-base/-/agent-base-7.1.0.tgz",
+ "integrity": "sha512-o/zjMZRhJxny7OyEF+Op8X+efiELC7k7yOjMzgfzVqOzXqkBkWI79YoTdOtsuWd5BWhAGAuOY/Xa6xpiaWXiNg==",
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+ "dependencies": {
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+ },
+ "engines": {
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+ }
+ },
+ "node_modules/@npmcli/agent/node_modules/https-proxy-agent": {
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+ "resolved": "https://registry.npmjs.org/https-proxy-agent/-/https-proxy-agent-7.0.2.tgz",
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+ "dev": true,
+ "dependencies": {
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+ "debug": "4"
+ },
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+ }
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"node_modules/@npmcli/agent/node_modules/lru-cache": {
"version": "10.1.0",
+ "resolved": "https://registry.npmjs.org/lru-cache/-/lru-cache-10.1.0.tgz",
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"dev": true,
- "license": "ISC",
"engines": {
"node": "14 || >=16.14"
}
},
"node_modules/@npmcli/fs": {
"version": "3.1.0",
+ "resolved": "https://registry.npmjs.org/@npmcli/fs/-/fs-3.1.0.tgz",
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"dev": true,
- "license": "ISC",
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"semver": "^7.3.5"
},
@@ -1541,9 +1645,10 @@
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},
"node_modules/@npmcli/git": {
- "version": "5.0.3",
+ "version": "5.0.4",
+ "resolved": "https://registry.npmjs.org/@npmcli/git/-/git-5.0.4.tgz",
+ "integrity": "sha512-nr6/WezNzuYUppzXRaYu/W4aT5rLxdXqEFupbh6e/ovlYFQ8hpu1UUPV3Ir/YTl+74iXl2ZOMlGzudh9ZPUchQ==",
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@@ -1560,24 +1665,27 @@
},
"node_modules/@npmcli/git/node_modules/isexe": {
"version": "3.1.1",
+ "resolved": "https://registry.npmjs.org/isexe/-/isexe-3.1.1.tgz",
+ "integrity": "sha512-LpB/54B+/2J5hqQ7imZHfdU31OlgQqx7ZicVlkm9kzg9/w8GKLEcFfJl/t7DCEDueOyBAD6zCCwTO6Fzs0NoEQ==",
"dev": true,
- "license": "ISC",
"engines": {
"node": ">=16"
}
},
"node_modules/@npmcli/git/node_modules/lru-cache": {
"version": "10.1.0",
+ "resolved": "https://registry.npmjs.org/lru-cache/-/lru-cache-10.1.0.tgz",
+ "integrity": "sha512-/1clY/ui8CzjKFyjdvwPWJUYKiFVXG2I2cY0ssG7h4+hwk+XOIX7ZSG9Q7TW8TW3Kp3BUSqgFWBLgL4PJ+Blag==",
"dev": true,
- "license": "ISC",
"engines": {
"node": "14 || >=16.14"
}
},
"node_modules/@npmcli/git/node_modules/which": {
"version": "4.0.0",
+ "resolved": "https://registry.npmjs.org/which/-/which-4.0.0.tgz",
+ "integrity": "sha512-GlaYyEb07DPxYCKhKzplCWBJtvxZcZMrL+4UkrTSJHHPyZU4mYYTv3qaOe77H7EODLSSopAUFAc6W8U4yqvscg==",
"dev": true,
- "license": "ISC",
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"isexe": "^3.1.1"
},
@@ -1590,8 +1698,9 @@
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"node_modules/@npmcli/installed-package-contents": {
"version": "2.0.2",
+ "resolved": "https://registry.npmjs.org/@npmcli/installed-package-contents/-/installed-package-contents-2.0.2.tgz",
+ "integrity": "sha512-xACzLPhnfD51GKvTOOuNX2/V4G4mz9/1I2MfDoye9kBM3RYe5g2YbscsaGoTlaWqkxeiapBWyseULVKpSVHtKQ==",
"dev": true,
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@@ -1605,16 +1714,18 @@
},
"node_modules/@npmcli/node-gyp": {
"version": "3.0.0",
+ "resolved": "https://registry.npmjs.org/@npmcli/node-gyp/-/node-gyp-3.0.0.tgz",
+ "integrity": "sha512-gp8pRXC2oOxu0DUE1/M3bYtb1b3/DbJ5aM113+XJBgfXdussRAsX0YOrOhdd8WvnAR6auDBvJomGAkLKA5ydxA==",
"dev": true,
- "license": "ISC",
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"node": "^14.17.0 || ^16.13.0 || >=18.0.0"
}
},
"node_modules/@npmcli/promise-spawn": {
- "version": "7.0.0",
+ "version": "7.0.1",
+ "resolved": "https://registry.npmjs.org/@npmcli/promise-spawn/-/promise-spawn-7.0.1.tgz",
+ "integrity": "sha512-P4KkF9jX3y+7yFUxgcUdDtLy+t4OlDGuEBLNs57AZsfSfg+uV6MLndqGpnl4831ggaEdXwR50XFoZP4VFtHolg==",
"dev": true,
- "license": "ISC",
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},
@@ -1624,16 +1735,18 @@
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"node_modules/@npmcli/promise-spawn/node_modules/isexe": {
"version": "3.1.1",
+ "resolved": "https://registry.npmjs.org/isexe/-/isexe-3.1.1.tgz",
+ "integrity": "sha512-LpB/54B+/2J5hqQ7imZHfdU31OlgQqx7ZicVlkm9kzg9/w8GKLEcFfJl/t7DCEDueOyBAD6zCCwTO6Fzs0NoEQ==",
"dev": true,
- "license": "ISC",
"engines": {
"node": ">=16"
}
},
"node_modules/@npmcli/promise-spawn/node_modules/which": {
"version": "4.0.0",
+ "resolved": "https://registry.npmjs.org/which/-/which-4.0.0.tgz",
+ "integrity": "sha512-GlaYyEb07DPxYCKhKzplCWBJtvxZcZMrL+4UkrTSJHHPyZU4mYYTv3qaOe77H7EODLSSopAUFAc6W8U4yqvscg==",
"dev": true,
- "license": "ISC",
"dependencies": {
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},
@@ -1645,9 +1758,10 @@
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},
"node_modules/@npmcli/run-script": {
- "version": "7.0.2",
+ "version": "7.0.3",
+ "resolved": "https://registry.npmjs.org/@npmcli/run-script/-/run-script-7.0.3.tgz",
+ "integrity": "sha512-ZMWGLHpzMq3rBGIwPyeaoaleaLMvrBrH8nugHxTi5ACkJZXTxXPtVuEH91ifgtss5hUwJQ2VDnzDBWPmz78rvg==",
"dev": true,
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@@ -1661,16 +1775,18 @@
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"node_modules/@npmcli/run-script/node_modules/isexe": {
"version": "3.1.1",
+ "resolved": "https://registry.npmjs.org/isexe/-/isexe-3.1.1.tgz",
+ "integrity": "sha512-LpB/54B+/2J5hqQ7imZHfdU31OlgQqx7ZicVlkm9kzg9/w8GKLEcFfJl/t7DCEDueOyBAD6zCCwTO6Fzs0NoEQ==",
"dev": true,
- "license": "ISC",
"engines": {
"node": ">=16"
}
},
"node_modules/@npmcli/run-script/node_modules/which": {
"version": "4.0.0",
+ "resolved": "https://registry.npmjs.org/which/-/which-4.0.0.tgz",
+ "integrity": "sha512-GlaYyEb07DPxYCKhKzplCWBJtvxZcZMrL+4UkrTSJHHPyZU4mYYTv3qaOe77H7EODLSSopAUFAc6W8U4yqvscg==",
"dev": true,
- "license": "ISC",
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"isexe": "^3.1.1"
},
@@ -1682,15 +1798,16 @@
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"node_modules/@nuxt/content": {
- "version": "2.9.0",
+ "version": "2.10.0",
+ "resolved": "https://registry.npmjs.org/@nuxt/content/-/content-2.10.0.tgz",
+ "integrity": "sha512-HZ+1RJJc2SZc/FPYvbsME7b8++a2uf6g9JlMm+qUMDjnCWJaF38pbrsmYq2b9whXx/3WjpBmCRkWCJy6bjSP+g==",
"dev": true,
- "license": "MIT",
"dependencies": {
- "@nuxt/kit": "^3.8.0",
- "@nuxtjs/mdc": "^0.2.6",
- "@vueuse/core": "^10.5.0",
+ "@nuxt/kit": "^3.8.2",
+ "@nuxtjs/mdc": "^0.3.0",
+ "@vueuse/core": "^10.7.0",
"@vueuse/head": "^2.0.0",
- "@vueuse/nuxt": "^10.5.0",
+ "@vueuse/nuxt": "^10.7.0",
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"defu": "^6.1.3",
"destr": "^2.0.2",
@@ -1698,32 +1815,34 @@
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"listhen": "^1.5.5",
"mdast-util-to-string": "^4.0.0",
- "mdurl": "^1.0.1",
+ "mdurl": "^2.0.0",
"micromark": "^4.0.0",
"micromark-util-sanitize-uri": "^2.0.0",
"micromark-util-types": "^2.0.0",
- "minisearch": "^6.2.0",
+ "minisearch": "^6.3.0",
"ohash": "^1.1.3",
"pathe": "^1.1.1",
- "scule": "^1.0.0",
+ "scule": "^1.1.1",
"shiki-es": "^0.14.0",
"slugify": "^1.6.6",
"socket.io-client": "^4.7.2",
- "ufo": "^1.3.1",
+ "ufo": "^1.3.2",
"unist-util-stringify-position": "^4.0.0",
- "unstorage": "^1.9.0",
- "ws": "^8.14.2"
+ "unstorage": "^1.10.1",
+ "ws": "^8.15.1"
}
},
"node_modules/@nuxt/devalue": {
"version": "2.0.2",
- "dev": true,
- "license": "MIT"
+ "resolved": "https://registry.npmjs.org/@nuxt/devalue/-/devalue-2.0.2.tgz",
+ "integrity": "sha512-GBzP8zOc7CGWyFQS6dv1lQz8VVpz5C2yRszbXufwG/9zhStTIH50EtD87NmWbTMwXDvZLNg8GIpb1UFdH93JCA==",
+ "dev": true
},
"node_modules/@nuxt/devtools": {
"version": "1.0.6",
+ "resolved": "https://registry.npmjs.org/@nuxt/devtools/-/devtools-1.0.6.tgz",
+ "integrity": "sha512-3P914IHBvKl2aYSrwaCAU9E1ndVNnGJR0Jn0XKUFktsbjU5kGlwLGrtRKXAw4Yz1VNiSZPrapVrFOQWbXRGRvg==",
"dev": true,
- "license": "MIT",
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@@ -1773,8 +1892,9 @@
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"node_modules/@nuxt/devtools-kit": {
"version": "1.0.6",
+ "resolved": "https://registry.npmjs.org/@nuxt/devtools-kit/-/devtools-kit-1.0.6.tgz",
+ "integrity": "sha512-CUSE++NRTIwvBWbLsPzLZIDMpXr6oyllaWm8tOR3Wgr/04jW31uyWbXjU/fxRuDotQwZfcTe19uunRoCoBnk1Q==",
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@@ -1787,8 +1907,9 @@
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"version": "7.2.0",
+ "resolved": "https://registry.npmjs.org/execa/-/execa-7.2.0.tgz",
+ "integrity": "sha512-UduyVP7TLB5IcAQl+OzLyLcS/l32W/GLg+AhHJ+ow40FOk2U3SAllPwR44v4vmdFwIWqpdwxxpQbF1n5ta9seA==",
"dev": true,
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@@ -1809,16 +1930,18 @@
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+ "resolved": "https://registry.npmjs.org/human-signals/-/human-signals-4.3.1.tgz",
+ "integrity": "sha512-nZXjEF2nbo7lIw3mgYjItAfgQXog3OjJogSbKa2CQIIvSGWcKgeJnQlNXip6NglNzYH45nSRiEVimMvYL8DDqQ==",
"dev": true,
- "license": "Apache-2.0",
"engines": {
"node": ">=14.18.0"
}
},
"node_modules/@nuxt/devtools-kit/node_modules/is-stream": {
"version": "3.0.0",
+ "resolved": "https://registry.npmjs.org/is-stream/-/is-stream-3.0.0.tgz",
+ "integrity": "sha512-LnQR4bZ9IADDRSkvpqMGvt/tEJWclzklNgSw48V5EAaAeDd6qGvN8ei6k5p0tvxSR171VmGyHuTiAOfxAbr8kA==",
"dev": true,
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},
@@ -1828,8 +1951,9 @@
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"node_modules/@nuxt/devtools-kit/node_modules/mimic-fn": {
"version": "4.0.0",
+ "resolved": "https://registry.npmjs.org/mimic-fn/-/mimic-fn-4.0.0.tgz",
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"dev": true,
- "license": "MIT",
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},
@@ -1838,9 +1962,10 @@
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- "version": "5.1.0",
+ "version": "5.2.0",
+ "resolved": "https://registry.npmjs.org/npm-run-path/-/npm-run-path-5.2.0.tgz",
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"dev": true,
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},
@@ -1853,8 +1978,9 @@
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+ "resolved": "https://registry.npmjs.org/onetime/-/onetime-6.0.0.tgz",
+ "integrity": "sha512-1FlR+gjXK7X+AsAHso35MnyN5KqGwJRi/31ft6x0M194ht7S+rWAvd7PHss9xSKMzE0asv1pyIHaJYq+BbacAQ==",
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},
@@ -1867,8 +1993,9 @@
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"node_modules/@nuxt/devtools-kit/node_modules/path-key": {
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+ "resolved": "https://registry.npmjs.org/path-key/-/path-key-4.0.0.tgz",
+ "integrity": "sha512-haREypq7xkM7ErfgIyA0z+Bj4AGKlMSdlQE2jvJo6huWD1EdkKYV+G/T4nq0YEF2vgTT8kqMFKo1uHn950r4SQ==",
"dev": true,
- "license": "MIT",
"engines": {
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},
@@ -1878,8 +2005,9 @@
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"node_modules/@nuxt/devtools-kit/node_modules/strip-final-newline": {
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+ "resolved": "https://registry.npmjs.org/strip-final-newline/-/strip-final-newline-3.0.0.tgz",
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"dev": true,
- "license": "MIT",
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"node": ">=12"
},
@@ -1889,8 +2017,9 @@
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"node_modules/@nuxt/devtools-wizard": {
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+ "resolved": "https://registry.npmjs.org/@nuxt/devtools-wizard/-/devtools-wizard-1.0.6.tgz",
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@@ -1909,8 +2038,9 @@
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+ "resolved": "https://registry.npmjs.org/execa/-/execa-7.2.0.tgz",
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@@ -1931,16 +2061,18 @@
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+ "resolved": "https://registry.npmjs.org/human-signals/-/human-signals-4.3.1.tgz",
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"dev": true,
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"engines": {
"node": ">=14.18.0"
}
},
"node_modules/@nuxt/devtools-wizard/node_modules/is-stream": {
"version": "3.0.0",
+ "resolved": "https://registry.npmjs.org/is-stream/-/is-stream-3.0.0.tgz",
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},
@@ -1950,8 +2082,9 @@
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- "license": "MIT",
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@@ -1960,9 +2093,10 @@
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},
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},
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"dev": true,
- "license": "MIT",
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},
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- "license": "MIT",
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},
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@@ -2033,16 +2171,18 @@
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+ "resolved": "https://registry.npmjs.org/human-signals/-/human-signals-4.3.1.tgz",
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- "license": "Apache-2.0",
"engines": {
"node": ">=14.18.0"
}
},
"node_modules/@nuxt/devtools/node_modules/is-stream": {
"version": "3.0.0",
+ "resolved": "https://registry.npmjs.org/is-stream/-/is-stream-3.0.0.tgz",
+ "integrity": "sha512-LnQR4bZ9IADDRSkvpqMGvt/tEJWclzklNgSw48V5EAaAeDd6qGvN8ei6k5p0tvxSR171VmGyHuTiAOfxAbr8kA==",
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},
@@ -2052,8 +2192,9 @@
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"dev": true,
- "license": "MIT",
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},
@@ -2062,9 +2203,10 @@
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- "version": "5.1.0",
+ "version": "5.2.0",
+ "resolved": "https://registry.npmjs.org/npm-run-path/-/npm-run-path-5.2.0.tgz",
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},
@@ -2077,8 +2219,9 @@
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"node_modules/@nuxt/devtools/node_modules/onetime": {
"version": "6.0.0",
+ "resolved": "https://registry.npmjs.org/onetime/-/onetime-6.0.0.tgz",
+ "integrity": "sha512-1FlR+gjXK7X+AsAHso35MnyN5KqGwJRi/31ft6x0M194ht7S+rWAvd7PHss9xSKMzE0asv1pyIHaJYq+BbacAQ==",
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- "license": "MIT",
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},
@@ -2091,8 +2234,9 @@
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+ "resolved": "https://registry.npmjs.org/path-key/-/path-key-4.0.0.tgz",
+ "integrity": "sha512-haREypq7xkM7ErfgIyA0z+Bj4AGKlMSdlQE2jvJo6huWD1EdkKYV+G/T4nq0YEF2vgTT8kqMFKo1uHn950r4SQ==",
"dev": true,
- "license": "MIT",
"engines": {
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},
@@ -2102,8 +2246,9 @@
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"node_modules/@nuxt/devtools/node_modules/strip-final-newline": {
"version": "3.0.0",
+ "resolved": "https://registry.npmjs.org/strip-final-newline/-/strip-final-newline-3.0.0.tgz",
+ "integrity": "sha512-dOESqjYr96iWYylGObzd39EuNTa5VJxyvVAEm5Jnh7KGo75V43Hk1odPQkNDyXNmUR6k+gEiDVXnjB8HJ3crXw==",
"dev": true,
- "license": "MIT",
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"node": ">=12"
},
@@ -2113,8 +2258,9 @@
},
"node_modules/@nuxt/devtools/node_modules/which": {
"version": "3.0.1",
+ "resolved": "https://registry.npmjs.org/which/-/which-3.0.1.tgz",
+ "integrity": "sha512-XA1b62dzQzLfaEOSQFTCOd5KFf/1VSzZo7/7TUjnya6u0vGGKzU96UQBZTAThCb2j4/xjBAyii1OhRLJEivHvg==",
"dev": true,
- "license": "ISC",
"dependencies": {
"isexe": "^2.0.0"
},
@@ -2127,8 +2273,9 @@
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"node_modules/@nuxt/eslint-config": {
"version": "0.2.0",
+ "resolved": "https://registry.npmjs.org/@nuxt/eslint-config/-/eslint-config-0.2.0.tgz",
+ "integrity": "sha512-NeJX8TLcnNAjQFiDs3XhP+9CHKK8jaKsP7eUyCSrQdgY7nqWe7VJx64lwzx5FTT4cW3RHMEyH+Y0qzLGYYoa/A==",
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- "license": "MIT",
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@@ -2141,10 +2288,11 @@
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},
"node_modules/@nuxt/kit": {
- "version": "3.8.2",
- "license": "MIT",
+ "version": "3.9.0",
+ "resolved": "https://registry.npmjs.org/@nuxt/kit/-/kit-3.9.0.tgz",
+ "integrity": "sha512-XVFQihMTXM5y7Xj7EXbcDbUbxNkC8+ArQKArAH5PK1ulCWZWyP+VR94Gg2boo9vI2eNLTs+LquxnOtOHRQrg0A==",
"dependencies": {
- "@nuxt/schema": "3.8.2",
+ "@nuxt/schema": "3.9.0",
"c12": "^1.5.1",
"consola": "^3.2.3",
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@@ -2156,11 +2304,11 @@
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"pkg-types": "^1.0.3",
- "scule": "^1.1.0",
+ "scule": "^1.1.1",
"semver": "^7.5.4",
"ufo": "^1.3.2",
"unctx": "^2.3.1",
- "unimport": "^3.5.0",
+ "unimport": "^3.7.0",
"untyped": "^1.4.0"
},
"engines": {
@@ -2168,8 +2316,9 @@
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"node_modules/@nuxt/schema": {
- "version": "3.8.2",
- "license": "MIT",
+ "version": "3.9.0",
+ "resolved": "https://registry.npmjs.org/@nuxt/schema/-/schema-3.9.0.tgz",
+ "integrity": "sha512-NaRiq+g6XE4YOZLy7be2e6AmZCW0gfQWDM88TSfNr3Lypo+6PuY2VqzZLpSvOCNlW3CFj/kWtMdhool2BP0yIg==",
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"consola": "^3.2.3",
@@ -2177,10 +2326,10 @@
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"pathe": "^1.1.1",
"pkg-types": "^1.0.3",
- "scule": "^1.1.0",
- "std-env": "^3.5.0",
+ "scule": "^1.1.1",
+ "std-env": "^3.7.0",
"ufo": "^1.3.2",
- "unimport": "^3.5.0",
+ "unimport": "^3.7.0",
"untyped": "^1.4.0"
},
"engines": {
@@ -2189,8 +2338,9 @@
},
"node_modules/@nuxt/telemetry": {
"version": "2.5.3",
+ "resolved": "https://registry.npmjs.org/@nuxt/telemetry/-/telemetry-2.5.3.tgz",
+ "integrity": "sha512-Ghv2MgWbJcUM9G5Dy3oQP0cJkUwEgaiuQxEF61FXJdn0a69Q4StZEP/hLF0MWPM9m6EvAwI7orxkJHM7MrmtVg==",
"dev": true,
- "license": "MIT",
"dependencies": {
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"ci-info": "^4.0.0",
@@ -2216,8 +2366,9 @@
},
"node_modules/@nuxt/telemetry/node_modules/is-docker": {
"version": "3.0.0",
+ "resolved": "https://registry.npmjs.org/is-docker/-/is-docker-3.0.0.tgz",
+ "integrity": "sha512-eljcgEDlEns/7AXFosB5K/2nCM4P7FQPkGc/DWLy5rmFEWvZayGrik1d9/QIY5nJ4f9YsVvBkA6kJpHn9rISdQ==",
"dev": true,
- "license": "MIT",
"bin": {
"is-docker": "cli.js"
},
@@ -2230,7 +2381,8 @@
},
"node_modules/@nuxt/ui-templates": {
"version": "1.3.1",
- "license": "CC-BY-ND-4.0"
+ "resolved": "https://registry.npmjs.org/@nuxt/ui-templates/-/ui-templates-1.3.1.tgz",
+ "integrity": "sha512-5gc02Pu1HycOVUWJ8aYsWeeXcSTPe8iX8+KIrhyEtEoOSkY0eMBuo0ssljB8wALuEmepv31DlYe5gpiRwkjESA=="
},
"node_modules/@nuxt/vite-builder": {
"version": "3.9.0",
@@ -2279,70 +2431,6 @@
"vue": "^3.3.4"
}
},
- "node_modules/@nuxt/vite-builder/node_modules/@nuxt/kit": {
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- "resolved": "https://registry.npmjs.org/@nuxt/kit/-/kit-3.9.0.tgz",
- "integrity": "sha512-XVFQihMTXM5y7Xj7EXbcDbUbxNkC8+ArQKArAH5PK1ulCWZWyP+VR94Gg2boo9vI2eNLTs+LquxnOtOHRQrg0A==",
- "dev": true,
- "dependencies": {
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- "c12": "^1.5.1",
- "consola": "^3.2.3",
- "defu": "^6.1.3",
- "globby": "^14.0.0",
- "hash-sum": "^2.0.0",
- "ignore": "^5.3.0",
- "jiti": "^1.21.0",
- "knitwork": "^1.0.0",
- "mlly": "^1.4.2",
- "pathe": "^1.1.1",
- "pkg-types": "^1.0.3",
- "scule": "^1.1.1",
- "semver": "^7.5.4",
- "ufo": "^1.3.2",
- "unctx": "^2.3.1",
- "unimport": "^3.7.0",
- "untyped": "^1.4.0"
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- "engines": {
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- "node_modules/@nuxt/vite-builder/node_modules/@nuxt/schema": {
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- "resolved": "https://registry.npmjs.org/@nuxt/schema/-/schema-3.9.0.tgz",
- "integrity": "sha512-NaRiq+g6XE4YOZLy7be2e6AmZCW0gfQWDM88TSfNr3Lypo+6PuY2VqzZLpSvOCNlW3CFj/kWtMdhool2BP0yIg==",
- "dev": true,
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- "consola": "^3.2.3",
- "defu": "^6.1.3",
- "hookable": "^5.5.3",
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- "pkg-types": "^1.0.3",
- "scule": "^1.1.1",
- "std-env": "^3.7.0",
- "ufo": "^1.3.2",
- "unimport": "^3.7.0",
- "untyped": "^1.4.0"
- },
- "engines": {
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- }
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- "node_modules/@nuxt/vite-builder/node_modules/@vitejs/plugin-vue": {
- "version": "5.0.2",
- "resolved": "https://registry.npmjs.org/@vitejs/plugin-vue/-/plugin-vue-5.0.2.tgz",
- "integrity": "sha512-kEjJHrLb5ePBvjD0SPZwJlw1QTRcjjCA9sB5VyfonoXVBxTS7TMnqL6EkLt1Eu61RDeiuZ/WN9Hf6PxXhPI2uA==",
- "dev": true,
- "engines": {
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- },
- "peerDependencies": {
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- "vue": "^3.2.25"
- }
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"node_modules/@nuxt/vite-builder/node_modules/estree-walker": {
"version": "3.0.3",
"resolved": "https://registry.npmjs.org/estree-walker/-/estree-walker-3.0.3.tgz",
@@ -2352,70 +2440,16 @@
"@types/estree": "^1.0.0"
}
},
- "node_modules/@nuxt/vite-builder/node_modules/vite": {
- "version": "5.0.10",
- "resolved": "https://registry.npmjs.org/vite/-/vite-5.0.10.tgz",
- "integrity": "sha512-2P8J7WWgmc355HUMlFrwofacvr98DAjoE52BfdbwQtyLH06XKwaL/FMnmKM2crF0iX4MpmMKoDlNCB1ok7zHCw==",
- "dev": true,
- "dependencies": {
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- "postcss": "^8.4.32",
- "rollup": "^4.2.0"
- },
- "bin": {
- "vite": "bin/vite.js"
- },
- "engines": {
- "node": "^18.0.0 || >=20.0.0"
- },
- "funding": {
- "url": "https://github.com/vitejs/vite?sponsor=1"
- },
- "optionalDependencies": {
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- },
- "peerDependencies": {
- "@types/node": "^18.0.0 || >=20.0.0",
- "less": "*",
- "lightningcss": "^1.21.0",
- "sass": "*",
- "stylus": "*",
- "sugarss": "*",
- "terser": "^5.4.0"
- },
- "peerDependenciesMeta": {
- "@types/node": {
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- },
- "less": {
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- },
- "lightningcss": {
- "optional": true
- },
- "sass": {
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- },
- "stylus": {
- "optional": true
- },
- "sugarss": {
- "optional": true
- },
- "terser": {
- "optional": true
- }
- }
- },
"node_modules/@nuxtjs/mdc": {
- "version": "0.2.8",
+ "version": "0.3.0",
+ "resolved": "https://registry.npmjs.org/@nuxtjs/mdc/-/mdc-0.3.0.tgz",
+ "integrity": "sha512-WN/5OuudZwsBPBRJNHIfkJF/sPtww5ThDva7Fcs2PMl+TdDA+M38L+AeONIn7Sl2CHU7O9rf1kMHl8p7MrUZeA==",
"dev": true,
- "license": "MIT",
"dependencies": {
- "@nuxt/kit": "^3.8.0",
- "@types/hast": "^3.0.2",
- "@types/mdast": "^4.0.2",
- "@vue/compiler-core": "^3.3.7",
+ "@nuxt/kit": "^3.8.2",
+ "@types/hast": "^3.0.3",
+ "@types/mdast": "^4.0.3",
+ "@vue/compiler-core": "^3.3.13",
"consola": "^3.2.3",
"defu": "^6.1.3",
"destr": "^2.0.2",
@@ -2425,28 +2459,30 @@
"mdast-util-to-hast": "^13.0.2",
"micromark-util-sanitize-uri": "^2.0.0",
"ohash": "^1.1.3",
- "property-information": "^6.3.0",
+ "property-information": "^6.4.0",
"rehype-external-links": "^3.0.0",
- "rehype-raw": "^6.1.1",
+ "rehype-raw": "^7.0.0",
"rehype-slug": "^6.0.0",
"rehype-sort-attribute-values": "^5.0.0",
"rehype-sort-attributes": "^5.0.0",
- "remark-emoji": "^4.0.0",
- "remark-gfm": "^3.0.1",
- "remark-mdc": "^2.1.0",
- "remark-parse": "^10.0.2",
- "remark-rehype": "^10.1.0",
- "scule": "^1.1.0",
- "shikiji": "^0.6.10",
- "ufo": "^1.3.1",
- "unified": "^11.0.3",
+ "remark-emoji": "^4.0.1",
+ "remark-gfm": "^4.0.0",
+ "remark-mdc": "^3.0.0",
+ "remark-parse": "^11.0.0",
+ "remark-rehype": "^11.0.0",
+ "scule": "^1.1.1",
+ "shikiji": "^0.9.10",
+ "shikiji-transformers": "^0.9.10",
+ "ufo": "^1.3.2",
+ "unified": "^11.0.4",
"unist-builder": "^4.0.0",
"unist-util-visit": "^5.0.0"
}
},
"node_modules/@observablehq/plot": {
"version": "0.6.13",
- "license": "ISC",
+ "resolved": "https://registry.npmjs.org/@observablehq/plot/-/plot-0.6.13.tgz",
+ "integrity": "sha512-ebQS4ENodOy+O3WUjhqv9jNPZENAZRQMIdO3ziOlAKfUzSf69+gaFAqqc04SGrQA6JwJjPYnbfeN3YIpNsCF/A==",
"dependencies": {
"d3": "^7.8.0",
"interval-tree-1d": "^1.0.0",
@@ -2458,8 +2494,10 @@
},
"node_modules/@parcel/watcher": {
"version": "2.3.0",
+ "resolved": "https://registry.npmjs.org/@parcel/watcher/-/watcher-2.3.0.tgz",
+ "integrity": "sha512-pW7QaFiL11O0BphO+bq3MgqeX/INAk9jgBldVDYjlQPO4VddoZnF22TcF9onMhnLVHuNqBJeRf+Fj7eezi/+rQ==",
"dev": true,
- "license": "MIT",
+ "hasInstallScript": true,
"dependencies": {
"detect-libc": "^1.0.3",
"is-glob": "^4.0.3",
@@ -2488,16 +2526,17 @@
"@parcel/watcher-win32-x64": "2.3.0"
}
},
- "node_modules/@parcel/watcher-linux-x64-glibc": {
+ "node_modules/@parcel/watcher-android-arm64": {
"version": "2.3.0",
+ "resolved": "https://registry.npmjs.org/@parcel/watcher-android-arm64/-/watcher-android-arm64-2.3.0.tgz",
+ "integrity": "sha512-f4o9eA3dgk0XRT3XhB0UWpWpLnKgrh1IwNJKJ7UJek7eTYccQ8LR7XUWFKqw6aEq5KUNlCcGvSzKqSX/vtWVVA==",
"cpu": [
- "x64"
+ "arm64"
],
"dev": true,
- "license": "MIT",
"optional": true,
"os": [
- "linux"
+ "android"
],
"engines": {
"node": ">= 10.0.0"
@@ -2507,16 +2546,17 @@
"url": "https://opencollective.com/parcel"
}
},
- "node_modules/@parcel/watcher-linux-x64-musl": {
+ "node_modules/@parcel/watcher-darwin-arm64": {
"version": "2.3.0",
+ "resolved": "https://registry.npmjs.org/@parcel/watcher-darwin-arm64/-/watcher-darwin-arm64-2.3.0.tgz",
+ "integrity": "sha512-mKY+oijI4ahBMc/GygVGvEdOq0L4DxhYgwQqYAz/7yPzuGi79oXrZG52WdpGA1wLBPrYb0T8uBaGFo7I6rvSKw==",
"cpu": [
- "x64"
+ "arm64"
],
"dev": true,
- "license": "MIT",
"optional": true,
"os": [
- "linux"
+ "darwin"
],
"engines": {
"node": ">= 10.0.0"
@@ -2526,18 +2566,18 @@
"url": "https://opencollective.com/parcel"
}
},
- "node_modules/@parcel/watcher-wasm": {
+ "node_modules/@parcel/watcher-darwin-x64": {
"version": "2.3.0",
- "bundleDependencies": [
- "napi-wasm"
+ "resolved": "https://registry.npmjs.org/@parcel/watcher-darwin-x64/-/watcher-darwin-x64-2.3.0.tgz",
+ "integrity": "sha512-20oBj8LcEOnLE3mgpy6zuOq8AplPu9NcSSSfyVKgfOhNAc4eF4ob3ldj0xWjGGbOF7Dcy1Tvm6ytvgdjlfUeow==",
+ "cpu": [
+ "x64"
],
"dev": true,
- "license": "MIT",
- "dependencies": {
- "is-glob": "^4.0.3",
- "micromatch": "^4.0.5",
- "napi-wasm": "^1.1.0"
- },
+ "optional": true,
+ "os": [
+ "darwin"
+ ],
"engines": {
"node": ">= 10.0.0"
},
@@ -2546,15 +2586,217 @@
"url": "https://opencollective.com/parcel"
}
},
- "node_modules/@parcel/watcher-wasm/node_modules/napi-wasm": {
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"dir-glob": "^3.0.1",
@@ -3187,25 +3621,42 @@
"url": "https://github.com/sponsors/sindresorhus"
}
},
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+ "version": "9.0.3",
+ "resolved": "https://registry.npmjs.org/minimatch/-/minimatch-9.0.3.tgz",
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+ "dependencies": {
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+ },
+ "funding": {
+ "url": "https://github.com/sponsors/isaacs"
+ }
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"node_modules/@typescript-eslint/typescript-estree/node_modules/slash": {
"version": "3.0.0",
+ "resolved": "https://registry.npmjs.org/slash/-/slash-3.0.0.tgz",
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- "license": "MIT",
"engines": {
"node": ">=8"
}
},
"node_modules/@typescript-eslint/utils": {
- "version": "6.14.0",
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+ "resolved": "https://registry.npmjs.org/@typescript-eslint/utils/-/utils-6.17.0.tgz",
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},
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@@ -3220,11 +3671,12 @@
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- "license": "MIT",
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@@ -3237,13 +3689,15 @@
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- "license": "ISC"
+ "resolved": "https://registry.npmjs.org/@ungap/structured-clone/-/structured-clone-1.2.0.tgz",
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"zhead": "^2.2.4"
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},
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@@ -3289,8 +3746,9 @@
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@@ -3330,8 +3789,9 @@
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@@ -3342,8 +3802,9 @@
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@@ -3351,8 +3812,9 @@
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@@ -3370,8 +3832,9 @@
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@@ -3379,6 +3842,19 @@
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+ "resolved": "https://registry.npmjs.org/@vue/babel-plugin-jsx/-/babel-plugin-jsx-1.1.5.tgz",
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@@ -3446,33 +3925,36 @@
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}
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},
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@@ -3583,23 +4063,25 @@
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"dev": true,
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"funding": {
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}
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}
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},
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}
},
"node_modules/npm-package-arg": {
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},
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"nuxi-ng": "bin/nuxi.mjs",
@@ -11204,8 +11622,9 @@
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"node_modules/nuxt-meilisearch": {
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+ "resolved": "https://registry.npmjs.org/@nuxt/kit/-/kit-3.8.2.tgz",
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- "dev": true
+ "node_modules/nuxt/node_modules/acorn": {
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+ "resolved": "https://registry.npmjs.org/acorn/-/acorn-8.11.2.tgz",
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+ "dev": true,
+ "bin": {
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},
"node_modules/nuxt/node_modules/estree-walker": {
"version": "3.0.3",
+ "resolved": "https://registry.npmjs.org/estree-walker/-/estree-walker-3.0.3.tgz",
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}
},
"node_modules/nypm": {
- "version": "0.3.3",
- "dev": true,
- "license": "MIT",
+ "version": "0.3.4",
+ "resolved": "https://registry.npmjs.org/nypm/-/nypm-0.3.4.tgz",
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@@ -11300,8 +11726,8 @@
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- "dev": true,
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- "dev": true,
- "license": "MIT",
+ "resolved": "https://registry.npmjs.org/get-stream/-/get-stream-8.0.1.tgz",
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"node_modules/nypm/node_modules/human-signals": {
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- "dev": true,
- "license": "Apache-2.0",
+ "resolved": "https://registry.npmjs.org/human-signals/-/human-signals-5.0.0.tgz",
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}
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"version": "3.0.0",
- "dev": true,
- "license": "MIT",
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- "dev": true,
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- "dev": true,
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- "license": "MIT",
"engines": {
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}
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"dev": true,
- "license": "ISC",
"dependencies": {
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}
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"node_modules/onetime": {
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],
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"bin": {
"uuid": "dist/bin/uuid"
}
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"node_modules/yocto-queue": {
"version": "0.1.0",
+ "resolved": "https://registry.npmjs.org/yocto-queue/-/yocto-queue-0.1.0.tgz",
+ "integrity": "sha512-rVksvsnNCdJ/ohGc6xgPwyN8eheCxsiLM8mxuE/t/mOVqJewPuO1miLpTHQiRgTKCLexL4MeAFVagts7HmNZ2Q==",
"dev": true,
- "license": "MIT",
"peer": true,
"engines": {
"node": ">=10"
@@ -16180,16 +16109,18 @@
},
"node_modules/zhead": {
"version": "2.2.4",
+ "resolved": "https://registry.npmjs.org/zhead/-/zhead-2.2.4.tgz",
+ "integrity": "sha512-8F0OI5dpWIA5IGG5NHUg9staDwz/ZPxZtvGVf01j7vHqSyZ0raHY+78atOVxRqb73AotX22uV1pXt3gYSstGag==",
"dev": true,
- "license": "MIT",
"funding": {
"url": "https://github.com/sponsors/harlan-zw"
}
},
"node_modules/zip-stream": {
"version": "5.0.1",
+ "resolved": "https://registry.npmjs.org/zip-stream/-/zip-stream-5.0.1.tgz",
+ "integrity": "sha512-UfZ0oa0C8LI58wJ+moL46BDIMgCQbnsb+2PoiJYtonhBsMh2bq1eRBVkvjfVsqbEHd9/EgKPUuL9saSSsec8OA==",
"dev": true,
- "license": "MIT",
"dependencies": {
"archiver-utils": "^4.0.1",
"compress-commons": "^5.0.1",
@@ -16201,8 +16132,9 @@
},
"node_modules/zwitch": {
"version": "2.0.4",
+ "resolved": "https://registry.npmjs.org/zwitch/-/zwitch-2.0.4.tgz",
+ "integrity": "sha512-bXE4cR/kVZhKZX/RjPEflHaKVhUVl85noU3v6b8apfQEc1x4A+zBxjZ4lN8LqGd6WZ3dl98pY4o717VFmoPp+A==",
"dev": true,
- "license": "MIT",
"funding": {
"type": "github",
"url": "https://github.com/sponsors/wooorm"
diff --git a/package.json b/package.json
index 8703b4879d0275a0b1d4d34bdecdd708c7b587f7..46cfcea1f3379180042111b84a39bcf0d4caf622 100644
--- a/package.json
+++ b/package.json
@@ -7,13 +7,13 @@
"preview": "nuxt preview"
},
"devDependencies": {
- "@nuxt/content": "^2.9.0",
- "@types/node": "^20.10.4",
- "@vueuse/core": "^10.6.1",
- "@vueuse/nuxt": "^10.6.1",
+ "@nuxt/content": "^2.10.0",
+ "@types/node": "^20.10.6",
+ "@vueuse/core": "^10.7.1",
+ "@vueuse/nuxt": "^10.7.1",
"nuxt": "^3.9.0",
"nuxt-meilisearch": "^1.1.0",
- "vuetify-nuxt-module": "^0.7.3"
+ "vuetify-nuxt-module": "^0.8.0"
},
"overrides": {
"vue": "latest"
diff --git a/packages/df-wiki-cli/df_wiki_cli/content/main.py b/packages/df-wiki-cli/df_wiki_cli/content/main.py
index 1affaa6bf1c0e12ea2e6e7a5a213398ba7bcb1c9..ee09705cf6a667bf650c0267c240a94f86dcedff 100644
--- a/packages/df-wiki-cli/df_wiki_cli/content/main.py
+++ b/packages/df-wiki-cli/df_wiki_cli/content/main.py
@@ -13,6 +13,7 @@ from pydantic import BaseModel, ValidationError
import frontmatter
from enum import Enum
from rich.console import Console
+import re
console = Console()
app = typer.Typer()
@@ -216,9 +217,9 @@ def systems(
if "article" in table_data:
sanitizedMetadata["doi"] = table_data["article"]["doi"]
if "abstract" in table_data["article"]:
- sanitizedMetadata["abstract"] = table_data["article"][
- "abstract"
- ]
+ sanitizedMetadata["abstract"] = table_data[
+ "article"
+ ]["abstract"]
del table_data["article"]
if "PFAM" in table_data:
del table_data["PFAM"]
@@ -241,3 +242,35 @@ def pae2png(tsv_file, png_file):
plt.tight_layout()
plt.savefig(png_file, dpi=150, facecolor=None, transparent=True)
plt.close()
+
+
+@app.command()
+def refseq(
+ input: Annotated[
+ Path,
+ typer.Option(
+ exists=False,
+ file_okay=True,
+ writable=True,
+ ),
+ ],
+ output: Annotated[
+ Path,
+ typer.Option(
+ file_okay=True,
+ dir_okay=False,
+ writable=True,
+ resolve_path=True,
+ ),
+ ],
+):
+ with open(output, "w") as out, open(input, "r") as refseq_f:
+ reader = csv.DictReader(refseq_f)
+ fieldnames = reader.fieldnames
+ writer = csv.DictWriter(out, fieldnames=fieldnames)
+ writer.writeheader()
+ for row in reader:
+ result = re.sub(r"^(\w+)\.\d+(_.*)$", r"\1\2", row["sys_id"])
+ console.print(f"[green]{row['sys_id']} -> {result}")
+ row["sys_id"] = result
+ writer.writerow(row)
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 6b1f93ffbcd4610b601a911cd7538f9b8ab9a829..3479787cd2b5187332b02065e26547b9b5854ccd 100644
--- a/packages/df-wiki-cli/df_wiki_cli/meilisearch/__init__.py
+++ b/packages/df-wiki-cli/df_wiki_cli/meilisearch/__init__.py
@@ -5,10 +5,14 @@ import json
from typing import Annotated, List, Optional
from pydantic import BaseModel, Field, BeforeValidator
from enum import Enum
+from rich.console import Console
+
+
+console = Console()
class RefSeqCsv(BaseModel):
- id: str
+ sys_id: str
replicon: str
type: str
subtype: str
@@ -86,7 +90,9 @@ def update_refseq(
row["accession_in_sys"] = split_on_comma(row["accession_in_sys"])
doc = RefSeqCsv(**row)
documents.append(doc.model_dump(by_alias=True))
- index.add_documents_in_batches(documents, primary_key="id")
+ tasks = index.add_documents_in_batches(documents, primary_key="sys_id")
+ for task in tasks:
+ console.print(task)
index.update_pagination_settings({"maxTotalHits": 1000000})
index.update_filterable_attributes(
body=[
@@ -210,7 +216,15 @@ def update_systems(
)
print(pagination_settings_task)
attr_task = index.update_filterable_attributes(
- body=["title", "Sensor", "Activator", "Effector", "PFAM.AC", "PFAM.DE"]
+ body=[
+ "title",
+ "Sensor",
+ "Activator",
+ "Effector",
+ "PFAM.AC",
+ "PFAM.DE",
+ "contributors",
+ ]
)
params = {
"maxValuesPerFacet": 1000000,
diff --git a/packages/df-wiki-cli/df_wiki_cli/meilisearch/main.py b/packages/df-wiki-cli/df_wiki_cli/meilisearch/main.py
index 858e189d803cc336741dc29fbd0128657cfd1cdc..e7e3037766ce72d268bfdae830e4e52de3d34b03 100644
--- a/packages/df-wiki-cli/df_wiki_cli/meilisearch/main.py
+++ b/packages/df-wiki-cli/df_wiki_cli/meilisearch/main.py
@@ -5,6 +5,10 @@ from pathlib import Path
from df_wiki_cli.meilisearch import update_refseq, update_structure, update_systems
from enum import Enum
from types import SimpleNamespace
+from rich.console import Console
+
+
+console = Console()
app = typer.Typer()
@@ -66,6 +70,21 @@ def delete_all_documents(ctx: typer.Context, id: str):
index.delete_all_documents()
+@app.command()
+def indexes(ctx: typer.Context):
+ client = meilisearch.Client(ctx.obj.host, ctx.obj.key)
+ indexes = client.get_indexes()["results"]
+ for index in indexes:
+ print(index.uid)
+
+
+@app.command()
+def index_update(ctx: typer.Context, index: str, primary_key: str):
+ client = meilisearch.Client(ctx.obj.host, ctx.obj.key)
+ task = client.index(index).update(primary_key=primary_key)
+ console.print(task)
+
+
@app.command()
def task(ctx: typer.Context, id: str):
client = meilisearch.Client(ctx.obj.host, ctx.obj.key)
diff --git a/packages/df-wiki-cli/pyproject.toml b/packages/df-wiki-cli/pyproject.toml
index 538eb535c3348574c06cd5ebdaf073d7bfd119dd..22f5ffe80cd5293c84c985efe6daf7e7e3c715e5 100644
--- a/packages/df-wiki-cli/pyproject.toml
+++ b/packages/df-wiki-cli/pyproject.toml
@@ -1,6 +1,6 @@
[tool.poetry]
name = "df-wiki-cli"
-version = "0.1.4"
+version = "0.1.5"
description = ""
authors = ["Remi PLANEL <rplanel@pasteur.fr>"]
readme = "README.md"