diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
index 0c2205e49335079feb61abb6ce37da576c40a9a8..acd89d16cabf4b48ba4fcf363e823d12b6ad5a7c 100644
--- a/.gitlab-ci.yml
+++ b/.gitlab-ci.yml
@@ -1,13 +1,8 @@
workflow:
- rules:
- - if: '$CI_PIPELINE_SOURCE == "merge_request_event"'
- when: never
- - when: always
-
-
-
-
-
+ rules:
+ - if: '$CI_PIPELINE_SOURCE == "merge_request_event"'
+ when: never
+ - when: always
# Functions that should be executed before the build script is run
@@ -31,8 +26,6 @@ cache:
stages:
-
-
- zotero
- get-meili-key
- build
@@ -43,7 +36,7 @@ stages:
- deploy-meilisearch
- update-meilisearch-indexes
- deploy
- # - load-website
+ - post-deploy
.docker-login: &docker-login
- i=0; while [ "$i" -lt 12 ]; do docker info && break; sleep 5; i=$(( i + 1 )) ; done
@@ -199,6 +192,12 @@ lint:
MEILI_HOST: "http://localhost:7700"
script:
# - rm data/list-systems.json
+ - >
+ df-wiki-cli
+ meilisearch
+ --host ${MEILI_HOST}
+ --key ${MEILI_MASTER_KEY}
+ delete-all-documents refseq
- >
df-wiki-cli
content systems
@@ -213,6 +212,14 @@ lint:
update
--file data/refseq_res.csv
--document refseq
+ - >
+ df-wiki-cli
+ meilisearch
+ --host ${MEILI_HOST}
+ --key ${MEILI_MASTER_KEY}
+ update
+ --file data/refseq_res.csv
+ --document refseqtaxo
- >
df-wiki-cli
meilisearch
@@ -229,6 +236,8 @@ lint:
update
--file data/list-systems.json
--document systems
+
+
allow_failure: false
when: manual
@@ -360,96 +369,6 @@ build:prod:wiki:
- if: $CI_COMMIT_BRANCH == "main"
-# build-wiki:dev:
-# stage: build-wiki
-# needs:
-# - set-meili-env:dev
-# rules:
-# - if: $CI_COMMIT_BRANCH != "main"
-# image: node:21.1-bookworm-slim
-# variables:
-# NODE_OPTIONS: --max_old_space_size=12288
-# NUXT_APP_BASE_URL: /wiki/
-# NUXT_PUBLIC_MEILISEARCH_CLIENT_HOST_URL: ${MEILI_HOST}
-# NUXT_PUBLIC_MEILISEARCH_CLIENT_SEARCH_API_KEY: ${MEILI_API_KEY}
-# NUXT_PUBLIC_MEILI_HOST: ${MEILI_HOST}
-# NUXT_PUBLIC_MEILI_API_KEY: ${MEILI_API_KEY}
-# before_script:
-# - npm install
-# script:
-# - npm run generate
-# artifacts:
-# paths:
-# - .output/public
-
-# build-wiki:prod:
-# stage: build-wiki
-# rules:
-# - if: $CI_COMMIT_BRANCH == "main"
-# needs:
-# - set-meili-env:prod
-# - get-zotero
-# image: node:21.1-bookworm-slim
-# variables:
-# NODE_OPTIONS: --max_old_space_size=12288
-# NUXT_APP_BASE_URL: /wiki/
-# NUXT_PUBLIC_MEILISEARCH_CLIENT_HOST_URL: ${MEILI_HOST}
-# NUXT_PUBLIC_MEILISEARCH_CLIENT_SEARCH_API_KEY: ${MEILI_API_KEY}
-# NUXT_PUBLIC_MEILI_HOST: ${MEILI_HOST}
-# NUXT_PUBLIC_MEILI_API_KEY: ${MEILI_API_KEY}
-# before_script:
-# - npm install
-# script:
-# - npm run generate
-# artifacts:
-# paths:
-# - .output/public
-
-
-# load-website:dev:
-# image: harbor.pasteur.fr/kube-system/helm-kubectl:$HELM_VERSION
-# stage: load-website
-# needs:
-# - build-wiki:dev
-# - deploy:dev
-# variables:
-# NAMESPACE: "defense-finder-dev"
-# environment:
-# name: "k8sdev-01"
-# rules:
-# - if: $CI_COMMIT_BRANCH != "main"
-# script:
-# - kubectl --namespace ${NAMESPACE} wait pod -l "app.kubernetes.io/name=df-wiki" --for condition=Ready --timeout=600s
-# - echo "Le pod est ready"
-# - WIKI_POD=$(kubectl --namespace ${NAMESPACE} get pods -l "app.kubernetes.io/name=df-wiki" --output jsonpath='{.items[0].metadata.name}')
-# - kubectl --namespace ${NAMESPACE} cp .output/public/ ${WIKI_POD}:/website
-# - |
-# kubectl --namespace ${NAMESPACE}
-# exec ${WIKI_POD} -- bash -c 'cd /structure-data/sanitized-dump && find * -type d -exec sh -c "for d in "$@"; do (cd "/usr/share/nginx/html/$d"; cp --archive --recursive --symbolic-link /structure-data/sanitized-dump/$d/* .) done" argv0 {} +'
-
-
-# load-website:prod:
-# image: harbor.pasteur.fr/kube-system/helm-kubectl:$HELM_VERSION
-# stage: load-website
-# needs:
-# - build-wiki:prod
-# - deploy:prod
-# environment:
-# name: "k8sprod-02"
-# variables:
-# NAMESPACE: "defense-finder-prod"
-# rules:
-# - if: $CI_COMMIT_BRANCH == "main"
-# script:
-# - kubectl --namespace ${NAMESPACE} wait pod -l "app.kubernetes.io/name=df-wiki" --for condition=Ready --timeout=600s
-# - echo "Le pod est ready"
-# - WIKI_POD=$(kubectl --namespace ${NAMESPACE} get pods -l "app.kubernetes.io/name=df-wiki" --output jsonpath='{.items[0].metadata.name}')
-
-# - kubectl --namespace ${NAMESPACE} cp .output/public/ ${WIKI_POD}:/website
-# - kubectl --namespace ${NAMESPACE} cp scripts/copy-structure-data.sh ${WIKI_POD}:/structure-data/sanitized-dump
-# - kubectl --namespace ${NAMESPACE} exec ${WIKI_POD} -- bash -c 'cd /structure-data/sanitized-dump && bash copy-structure-data.sh'
-
-
################ DEPLOY ##########################
@@ -474,11 +393,11 @@ build:prod:wiki:
--values deploy/df-wiki/values.yaml
--values deploy/df-wiki/values.${ENV:-development}.yaml
after_script:
+ - sleep 30
- kubectl --namespace ${KUBE_NAMESPACE} wait pod -l "app.kubernetes.io/name=df-wiki" --for condition=Ready --timeout=600s
- echo "Wiki pod is ready"
- WIKI_POD=$(kubectl --namespace ${KUBE_NAMESPACE} get pods -l "app.kubernetes.io/name=df-wiki" --output jsonpath='{.items[0].metadata.name}')
- echo ${WIKI_POD}
- # - kubectl --namespace ${KUBE_NAMESPACE} cp scripts/copy-structure-data.sh ${WIKI_POD}:/structure-data/sanitized-dump
- kubectl --namespace ${KUBE_NAMESPACE} exec ${WIKI_POD} -- rsync -avz /public-website/ /usr/share/nginx/html/
@@ -486,7 +405,7 @@ build:prod:wiki:
deploy:dev:
extends: .deploy
rules:
- - if: $CI_COMMIT_BRANCH == "dev" || $CI_COMMIT_BRANCH == "public-as-mount-volume"
+ - if: $CI_COMMIT_BRANCH == "dev" || $CI_COMMIT_BRANCH == "refseq-no-sys"
needs:
- "build:dev:wiki"
when: manual
@@ -551,3 +470,34 @@ delete-helm-release:prod:
- helm delete -n ${NAMESPACE} $CI_PROJECT_NAME-$CI_ENVIRONMENT_NAME
+
+.post-deploy:
+ stage: post-deploy
+ image: harbor.pasteur.fr/kube-system/helm-kubectl:$HELM_VERSION
+ when: manual
+ variables:
+ CI_DEBUG_TRACE: "false"
+ TEAM_ID: "df"
+ script:
+ - kubectl --namespace ${KUBE_NAMESPACE} wait pod -l "app.kubernetes.io/name=df-wiki" --for condition=Ready --timeout=600s
+ - echo "Wiki pod is ready"
+ - WIKI_POD=$(kubectl --namespace ${KUBE_NAMESPACE} get pods -l "app.kubernetes.io/name=df-wiki" --output jsonpath='{.items[0].metadata.name}')
+ - echo ${WIKI_POD}
+ # - kubectl --namespace ${KUBE_NAMESPACE} exec ${WIKI_POD} -- rsync -avz /public-website/ /usr/share/nginx/html/
+ - kubectl --namespace ${KUBE_NAMESPACE} exec ${WIKI_POD} -- bash -c "cd /usr/share/nginx/html/ && find ./ -name '*.pdb' -exec tar -czvf /usr/share/nginx/html/df-all-pdbs.tar.gz {} +"
+ - kubectl --namespace ${KUBE_NAMESPACE} exec ${WIKI_POD} -- bash -c "cd /usr/share/nginx/html/ && find ./ -name '*.cif' -exec tar -czvf /usr/share/nginx/html/df-all-cifs.tar.gz {} +"
+
+
+post-deploy:dev:
+ extends: .post-deploy
+ needs:
+ - "deploy:dev"
+ variables:
+ NODE_ENV: "development"
+ KUBE_NAMESPACE: "defense-finder-dev"
+ PUBLIC_URL: "${HOST_DEV}"
+ CI_DEBUG_TRACE: "true"
+ ENV: "development"
+ environment:
+ name: k8sdev-01
+ url: "https://${HOST_DEV}"
diff --git a/components/LayoutWrapper.vue b/components/LayoutWrapper.vue
index 547650d6201a558a91ef66e5cf68582572c3c42f..60f8f7a6e72e561c9e157bbc75657e115303efa2 100644
--- a/components/LayoutWrapper.vue
+++ b/components/LayoutWrapper.vue
@@ -54,7 +54,7 @@ function onScroll() {
<v-container v-scroll="onScroll" :fluid="fluid">
<v-row justify="center">
<v-col cols="auto" class="pa-0">
- <v-card flat color="transparent" :min-width="mobile ? undefined : 900" :max-width="fluid ? undefined : 1500">
+ <v-card flat color="transparent" :min-width="mobile ? undefined : 900" :max-width="fluid ? undefined : 1280">
<v-card-text class="pa-0">
<slot />
</v-card-text>
diff --git a/components/ServerDbTable.vue b/components/ServerDbTable.vue
index f6baa3d6f04c7a029abd1885226baa505b67b8b7..bb510c498a2994965c9b484ce0519098bced9c06 100644
--- a/components/ServerDbTable.vue
+++ b/components/ServerDbTable.vue
@@ -309,26 +309,28 @@ function focusedOrBlur(isFocused: boolean) {
<template #top>
<v-card variant="flat" color="transparent">
- <v-card-title>
- <v-badge :content="totalHits" color="primary" class="mr-3">
+ <v-card-text class="d-flex flex-row">
+ <v-badge :content="totalHits" color="primary" class="me-auto">
<v-btn prepend-icon="md:download" :loading="pendingDownloadData" variant="text" color="primary"
@click="downloadData()">{{
props.title }}
</v-btn>
</v-badge>
- </v-card-title>
- <v-card-title>
+ <slot name="toolbar-items"></slot>
+
+ </v-card-text>
+ <v-card-text>
<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>
+ </v-card-text>
+ <v-card-text>
<AutocompleteMeiliFacets v-model="msFilterCompo" v-bind="props.autocompleteMeiliFacetsProps"
:is-valid-filters="isValidFilters">
</AutocompleteMeiliFacets>
- </v-card-title>
+ </v-card-text>
</v-card>
diff --git a/components/content/MolstarPdbePlugin.vue b/components/content/MolstarPdbePlugin.vue
index 03689717de70342291bb98dbeb82650fbcb2b809..82f8db51cd1b8741ccde6b7ff2e503ac872cbf74 100644
--- a/components/content/MolstarPdbePlugin.vue
+++ b/components/content/MolstarPdbePlugin.vue
@@ -13,6 +13,7 @@ export interface Props {
dataUrls?: string[]
dataUrl?: string
uniq?: boolean
+ format?: "pdb" | "cif"
}
const { mobile } = useDisplay()
@@ -52,7 +53,8 @@ const refinedDataUrls = computed(() => {
// const selectedPdb = ref(refinedDataUrls.value?.length > 0 ? refinedDataUrls.value[0] : null)
const props = withDefaults(defineProps<Props>(), {
height: 600,
- uniq: false
+ uniq: false,
+ format: 'pdb'
})
const { width, height } = useDisplay()
@@ -158,10 +160,23 @@ const moleculeFormat: Ref<string> = ref("pdb")
<template>
<template v-if="uniq">
- <v-row>
- <v-btn size="x-small" variant="text" icon="md:visibility" @click="setSelectedPdbToFirst()"></v-btn>
- <v-btn :disabled="!structureToDownload" size="x-small" variant="text" icon="md:download" class="ml-1"
- :href="structureToDownload"></v-btn>
+ <v-row justify="space-between" dense no-gutters align="center">
+ <v-col>
+ <v-btn size="x-small" variant="text" icon="md:visibility" @click="setSelectedPdbToFirst()"></v-btn>
+ </v-col>
+ <v-col>
+ <v-menu>
+ <template v-slot:activator="{ props }">
+ <v-btn :disabled="refinedDataUrls?.length < 1" size="x-small" variant="text" icon="md:download"
+ class="ml-1" v-bind="props"></v-btn>
+ </template>
+ <v-list>
+ <v-list-item v-for="(item, index) in refinedDataUrls" :key="index" :value="index" :href="item">
+ <v-list-item-title>{{ item.split('.').slice(-1)[0] }}</v-list-item-title>
+ </v-list-item>
+ </v-list>
+ </v-menu>
+ </v-col>
</v-row>
</template>
<v-row v-else>
@@ -195,7 +210,7 @@ const moleculeFormat: Ref<string> = ref("pdb")
sequence-panel="true" landscape="false" :custom-data-format="moleculeFormat"></pdbe-molstar>
</v-sheet>
</v-col>
- <v-col :cols="mobile ? 12 : undefined">
+ <v-col v-if="moleculeFormat === 'cif'" :cols="mobile ? 12 : undefined">
<v-img :src="selectedPaePath"></v-img>
<!-- <PlotFigure v-if="sanitizedPaeData?.length > 0 && paeError === null" defer
diff --git a/components/content/RefseqDb.vue b/components/content/RefseqDb.vue
index 4056d43c96cf82ff27325ab12acce526f2dca17f..9f4a2cdd1f1cd2a153a57aca9f7618334187afbd 100644
--- a/components/content/RefseqDb.vue
+++ b/components/content/RefseqDb.vue
@@ -1,4 +1,6 @@
<script setup lang="ts">
+import * as d3 from "d3";
+
import * as Plot from "@observablehq/plot";
import PlotFigure from "~/components/PlotFigure";
import { useDisplay } from "vuetify";
@@ -25,24 +27,49 @@ onBeforeMount(async () => {
filter: [],
page: 1,
hitsPerPage: 25,
+
}
})
autocompleteMeiliFacetsProps.value.facetDistribution = toValue(data)?.facetDistribution
-
+ // allHitsDb.value = toValue(data)?.hits
+ const { data: taxo } = await useAsyncMeiliSearch({
+ index: toValue("refseqtaxo"), query: "", params: {
+ facets: ["*"],
+ filter: [],
+ page: 1,
+ hitsPerPage: 25,
+ }
+ })
+ taxonomyFacet.value = toValue(taxo)?.facetDistribution
})
-
+const taxonomyFacet = ref<Record<string, any> | undefined>(undefined)
+// const allHitsDb = ref<Record<string, any>[] | undefined>(undefined)
onMounted(async () => {
+
const { data } = await useAsyncMeiliSearch({
index: toValue(dbName), query: "", params: {
facets: ["*"],
filter: [],
page: 1,
hitsPerPage: 25,
+ // limit: 500000,
+ // sort: ["type:asc"]
}
})
autocompleteMeiliFacetsProps.value.facetDistribution = toValue(data)?.facetDistribution
+ // allHitsDb.value = toValue(data)?.hits
+
+ const { data: taxo } = await useAsyncMeiliSearch({
+ index: toValue("refseqtaxo"), query: "", params: {
+ facets: ["*"],
+ filter: [],
+ page: 1,
+ hitsPerPage: 25,
+ }
+ })
+ taxonomyFacet.value = toValue(taxo)?.facetDistribution
})
@@ -99,19 +126,22 @@ const availableTaxo: Ref<string[]> = ref([
"genus",
"family",
"order",
+ "class",
"phylum",
"Superkingdom"
]);
const scaleTypes = ref<string[]>(['linear', 'sqrt', 'log', 'symlog'])
-const selectedTaxoRank = ref("Superkingdom");
+const selectedTaxoRank = ref<"species" | "genus" | "family" | "order" | "class" | "phylum" | "Superkingdom">("Superkingdom");
const headers = ref([
- { title: "Replicon", key: "replicon" },
{
title: "System",
key: "type",
+ fixed: true
},
+ { title: "Assembly", key: "Assembly" },
+ { title: "Replicon", key: "replicon" },
{
title: "Subsystem",
key: "subtype",
@@ -145,15 +175,25 @@ const computedWidth = computed(() => {
const allHits: Ref<Record<string, any> | undefined> = ref(undefined)
+
const pendingAllHits = ref(false)
async function getAllHits(params: { index: string, params: Record<string, any>, query: string }) {
- console.log(params.index)
+ if (!params?.params?.filter || params?.params?.filter?.length === 0) {
+ selectedTaxoRank.value = "Superkingdom"
+
+ }
if (params.index === toValue(dbName)) {
- console.log("get all hits in function ")
- console.log(params)
+
pendingAllHits.value = true
try {
- const { data, error } = await useAsyncMeiliSearch(params)
+ console.log(params.params.filter)
+ const { data, error } = await useAsyncMeiliSearch({
+ ...params,
+ params: {
+ ...params.params,
+ 'attributesToRetrieve': ['type', 'Assembly', ...toValue(availableTaxo)]
+ }
+ })
allHits.value = data.value
console.log(error.value)
} finally {
@@ -203,6 +243,8 @@ const computedSystemDistribution = computed(() => {
})
const computedDistriSystemOptions = computed(() => {
+ // const toValNormalizePerAssembly = toValue(normalizePerAssembly)
+
return {
...defaultBarPlotOptions.value,
marginBottom: 100,
@@ -226,10 +268,12 @@ const computedDistriSystemOptions = computed(() => {
// Taxo distri
const computedTaxonomyDistribution = computed(() => {
- if (toValue(msResult)?.facetDistribution?.[selectedTaxoRank.value]) {
- return Object.entries(toValue(msResult).facetDistribution[selectedTaxoRank.value]).map(([key, value]) => {
+ const toValSelectedTaxoRank = toValue(selectedTaxoRank)
+ const toValFacetsPerRank = toValue(msResult)?.facetDistribution?.[toValSelectedTaxoRank]
+ if (toValFacetsPerRank) {
+ return Object.entries(toValFacetsPerRank).map(([key, value]) => {
return {
- [selectedTaxoRank.value]: key,
+ [toValSelectedTaxoRank]: key,
count: value
}
}).sort()
@@ -246,6 +290,7 @@ const computedDistriTaxoOptions = computed(() => {
width: computedWidth.value,
marks: [
Plot.barY(
+
toValue(computedTaxonomyDistribution),
{
y: "count",
@@ -277,18 +322,54 @@ function namesToAccessionChips(names: string[]) {
}
const systemPanel: Ref<string[]> = ref([])
const layoutPlot: Ref<string> = ref("grid")
-const binPlotOptions = ref({
- marginLeft: 150,
- marginBottom: 200,
- padding: 0,
- grid: true,
- x: { tickRotate: 90, tip: true, label: "Systems" },
- // y: { tickFormat: 's' },
- color: { scheme: "plasma", legend: true },
+const binPlotOptions = computed(() => {
+ return {
+ marginLeft: 150,
+ marginBottom: 200,
+ padding: 0,
+ grid: true,
+ x: { tickRotate: 90, label: "Systems" },
+ // y: { tickFormat: 's' },
+ color: { scheme: "plasma", legend: true, label: `Proportion of genomes with defense system X for a given ${selectedTaxoRank.value} clade`, domain: [0, 100] },
+ }
+})
+
+
+const binPlotGroup = computed(() => {
+ return Plot.group(
+ {
+ label: (d) => d.fill,
+ fill: {
+ reduceIndex: function (I, X) {
+ const toValTaxonomyFacet = toValue(taxonomyFacet)
+ if (toValTaxonomyFacet !== undefined) {
+ const clade = X[I[0]][selectedTaxoRank.value]
+ const system = X[I[0]].type
+ // Get the list of item for this group
+ const itemsPerGroup = d3.rollup(I.map(index => {
+ return X[index]
+ }), D => D.length, d => d.type, d => d.Assembly)
+ const countForClade = toValTaxonomyFacet[selectedTaxoRank.value][clade]
+ console.log(`${itemsPerGroup.get(system).size} / ${countForClade}`)
+ const frequency = (itemsPerGroup.get(system).size / countForClade) * 100
+ return frequency
+ }
+ return I.length
+ }
+ }
+ },
+ {
+ x: "type",
+ y: selectedTaxoRank.value,
+ tip: true,
+ inset: 0.5,
+ sort: { y: "fill" }
+ })
})
const binPlotDataOptions = computed(() => {
const toValueAllHits = toValue(allHits)
+ const data = toValueAllHits?.hits ?? []
return toValueAllHits?.hits?.length > 0 ? {
...binPlotOptions.value,
width: width.value,
@@ -298,14 +379,16 @@ const binPlotDataOptions = computed(() => {
type: scaleType.value,
tickFormat: '~s',
ticks: scaleType.value === 'symlog' ? 3 : 5,
+
},
marks: [
- Plot.cell(toValueAllHits?.hits ?? [], Plot.group({ fill: "count" }, { x: "type", y: selectedTaxoRank.value, tip: true, inset: 0.5, sort: { y: "fill" } })),
+ Plot.cell(data, toValue(binPlotGroup)),
]
} : null
-
})
+
+
const scaleType = ref("linear")
const systemsDistributionPlot = ref<ComponentPublicInstance | null>(null)
const taxonomicDistributionPlot = ref<ComponentPublicInstance | null>(null)
@@ -464,7 +547,6 @@ async function downloadPng(component: ComponentPublicInstance | null, filename:
</v-expansion-panel-text>
</v-expansion-panel>
</v-expansion-panels>
-
<ServerDbTable title="RefSeq" :sortBy="sortBy"
:autocomplete-meili-facets-props="computedAutocompleteMeiliFacetsProps"
:data-table-server-props="dataTableServerProps" @refresh:search="(params) => getAllHits(params)">
@@ -474,14 +556,29 @@ async function downloadPng(component: ComponentPublicInstance | null, filename:
</CollapsibleChips>
</template>
<template #[`item.type`]="{ item }">
- <v-chip color="info" link size="small" :to="`/defense-systems/${item.type.toLowerCase()}`" target="_blank"> {{
- item.type }}
+ <v-chip color="info" link size="small" :to="`/defense-systems/${item.type.toLowerCase()}`"
+ target="_blank"> {{
+ item.type }}
+ </v-chip>
+ </template>
+ <template #[`item.Assembly`]="{ item }">
+ <v-chip color="info" link size="small"
+ :href="`https://www.ncbi.nlm.nih.gov/datasets/genome/${item.Assembly}`" target="_blank"> {{
+ item.Assembly }}
+ </v-chip>
+ </template>
+ <template #[`item.replicon`]="{ item }">
+ <v-chip color="info" link size="small" :href="`https://www.ncbi.nlm.nih.gov/nuccore/${item.replicon}`"
+ target="_blank"> {{
+ item.replicon }}
</v-chip>
</template>
+ <!-- -->
<template #[`item.subtype`]="{ item }">
- <v-chip color="info" link size="small" :to="`/defense-systems/${item.type.toLowerCase()}`" target="_blank"> {{
- item.subtype }}
+ <v-chip color="info" link size="small" :to="`/defense-systems/${item.type.toLowerCase()}`"
+ target="_blank"> {{
+ item.subtype }}
</v-chip>
</template>
</ServerDbTable>
diff --git a/components/content/StructureDb.vue b/components/content/StructureDb.vue
index c0c5324b868a615f7a621d818b8edef56d533be2..10805d568c65dada00ca0c9bd0703226607ccd78 100644
--- a/components/content/StructureDb.vue
+++ b/components/content/StructureDb.vue
@@ -18,7 +18,6 @@ const itemValue = ref("id");
const dbName = ref("structure")
onBeforeMount(async () => {
- console.log("dans le mounted refseq")
const { data } = await useAsyncMeiliSearch({
index: toValue(dbName), query: "", params: {
facets: ["*"],
@@ -72,7 +71,7 @@ const computedAutocompleteMeiliFacetsProps = computed(() => {
const headers: Ref<Object[]> = ref([
- { title: 'Structure', key: 'structure', sortable: false, removable: false },
+ { title: 'Structure', key: 'structure', sortable: false, removable: false, fixed: true, minWidth: "110px" },
{ title: 'Foldseek', key: 'Foldseek_name', sortable: false },
{ title: "System", key: "System", removable: false },
{ title: "Gene name", key: "gene_name", removable: false },
@@ -125,7 +124,6 @@ const dataTableServerProps = computed(() => {
function toFolseekUrl(item: Item) {
const url = joinURL("/" + item.System_name_ok, item.Foldseek_name)
const { refinedUrl } = useRefinedUrl(url)
- console.log(toValue(refinedUrl))
return toValue(refinedUrl)
}
@@ -143,6 +141,9 @@ function pdbNameToCif(pdbPath: string) {
return `${cifPath}.cif`
}
+const { refinedUrl: downloadAllPdbUrl } = useRefinedUrl("/df-all-pdbs.tar.gz")
+const { refinedUrl: downloadAllCifUrl } = useRefinedUrl("/df-all-cifs.tar.gz")
+
</script>
<template>
<ServerDbTable title="Predicted Structures" :sortBy="sortBy" :data-table-server-props="dataTableServerProps"
@@ -210,9 +211,18 @@ function pdbNameToCif(pdbPath: string) {
<CollapsibleChips :items="namesToCollapsibleChips(item.system_genes, item.System_name_ok)"></CollapsibleChips>
</template>
<template #[`item.structure`]="{ item }">
- <MolstarPdbePlugin v-if="item?.pdb && item.pdb !== 'na'"
- :data-urls="[`/${item.System_name_ok}/${pdbNameToCif(item.pdb)}`]" uniq>
- </MolstarPdbePlugin>
+ <v-row no-gutters align="center">
+ <MolstarPdbePlugin v-if="item?.pdb && item.pdb !== 'na'"
+ :data-urls="[`/${item.System_name_ok}/${pdbNameToCif(item.pdb)}`, `/${item.System_name_ok}/${item.pdb}`]" uniq format="cif">
+ </MolstarPdbePlugin>
+ </v-row>
+ <!-- <v-row no-gutters align="center">
+ <MolstarPdbePlugin v-if="item?.pdb && item.pdb !== 'na'"
+ :data-urls="[`/${item.System_name_ok}/${item.pdb}`]" uniq format="pdb">
+ </MolstarPdbePlugin>
+ </v-row> -->
+
+
<!-- <v-icon v-else color="warning" icon="md:dangerous"></v-icon> -->
@@ -221,5 +231,22 @@ function pdbNameToCif(pdbPath: string) {
<v-icon v-if="item.completed" color="success" icon="md:check"></v-icon>
<v-icon v-else color="warning" icon="md:dangerous"></v-icon>
</template>
+ <template #toolbar-items>
+ <v-menu>
+ <template v-slot:activator="{ props }">
+ <!-- <v-tooltip activator="parent" location="top">Download all structures</v-tooltip> -->
+ <v-btn class="align-self-end" v-bind="props" icon="md:download">
+ </v-btn>
+ </template>
+ <v-list>
+ <v-list-item value="pdb" :href="downloadAllPdbUrl">
+ <v-list-item-title>all pdbs</v-list-item-title>
+ </v-list-item>
+ <v-list-item value="cif" :href="downloadAllCifUrl">
+ <v-list-item-title>all cifs</v-list-item-title>
+ </v-list-item>
+ </v-list>
+ </v-menu>
+ </template>
</ServerDbTable>
</template>
\ No newline at end of file
diff --git a/data/refseq_res.csv b/data/refseq_res.csv
index 733fbf04e103186d499d6201405d79378c3ed802..becb696192d60bc89a646284da9d6d86ba120069 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:f19dff4f92dd3ca79a66fe6835f71261b9a5264f3df176dd005490dd74aa552d
-size 64961046
+oid sha256:1a7d382a7f767718dc48aa49ae3dd9b0159fdffd96e48946c7a167bcbc516deb
+size 68772089
diff --git a/deploy/meilisearch/values.development.yaml b/deploy/meilisearch/values.development.yaml
index de47d7f485b092bb1e144cb1ec61031a48822912..2d19040e8755916814dee3d7ec5a163074cb2c6f 100644
--- a/deploy/meilisearch/values.development.yaml
+++ b/deploy/meilisearch/values.development.yaml
@@ -9,7 +9,7 @@ meilisearch:
persistence:
enabled: true
storageClass: isilon
- size: "1Gi"
+ size: "4Gi"
resources:
limits:
cpu: 2000m
diff --git a/deploy/meilisearch/values.production.yaml b/deploy/meilisearch/values.production.yaml
index d22b8e5a25595bf1358470bbf14da4a9f5db99d2..fc8654b1c48f6adcca361f96c7d379ed83beb32a 100644
--- a/deploy/meilisearch/values.production.yaml
+++ b/deploy/meilisearch/values.production.yaml
@@ -11,7 +11,7 @@ meilisearch:
path: /
persistence:
enabled: true
- storageClass: isilon
+ storageClass: ceph-block
size: "10Gi"
resources:
limits:
diff --git a/nuxt.config.ts b/nuxt.config.ts
index e38c481ea0fe8575999dff66dcbef191bdce4a15..8ca24b3f4dc6a230b5b2e70c479151d690d6292a 100644
--- a/nuxt.config.ts
+++ b/nuxt.config.ts
@@ -10,6 +10,24 @@ export default defineNuxtConfig({
'nuxt-meilisearch',
'@nuxtjs/plausible',
],
+ app: {
+ head: {
+ script: [
+ {
+ defer: true,
+ "data-domaim": "defense-finder.dev.pasteur.cloud",
+ src: "https://plausible.dev.pasteur.cloud/js/script.js"
+ },
+ {
+ defer: true,
+ "data-domaim": "defense-finder.dev.pasteur.cloud",
+ src: "https://plausible.pasteur.cloud/js/script.js"
+ }
+
+
+ ]
+ }
+ },
content: {
documentDriven: {
injectPage: false,
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 ee09705cf6a667bf650c0267c240a94f86dcedff..17b7865777a7117790fa90495b7ddd602bc903f7 100644
--- a/packages/df-wiki-cli/df_wiki_cli/content/main.py
+++ b/packages/df-wiki-cli/df_wiki_cli/content/main.py
@@ -270,6 +270,8 @@ def refseq(
writer = csv.DictWriter(out, fieldnames=fieldnames)
writer.writeheader()
for row in reader:
+ if row["sys_id"] == "":
+ row["sys_id"] = f'{row["Assembly"]}_{row["replicon"]}'
result = re.sub(r"^(\w+)\.\d+(_.*)$", r"\1\2", row["sys_id"])
console.print(f"[green]{row['sys_id']} -> {result}")
row["sys_id"] = result
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 3479787cd2b5187332b02065e26547b9b5854ccd..1111225625f07cbc4584ae571646350cbe00a998 100644
--- a/packages/df-wiki-cli/df_wiki_cli/meilisearch/__init__.py
+++ b/packages/df-wiki-cli/df_wiki_cli/meilisearch/__init__.py
@@ -11,15 +11,22 @@ from rich.console import Console
console = Console()
+def emptyStringToNone(val: str) -> None | int:
+ if val == "":
+ return None
+ return int(float(val))
+
+
class RefSeqCsv(BaseModel):
sys_id: str
+ Assembly: str
replicon: str
type: str
subtype: str
sys_beg: str
sys_end: str
protein_in_syst: List[str]
- genes_count: int
+ genes_count: Annotated[int | None, BeforeValidator(emptyStringToNone)]
name_of_profiles_in_sys: List[str]
accession_in_sys: List[str]
Superkingdom: str
@@ -71,6 +78,66 @@ class StrucutreStatistics(BaseModel):
Foldseek_name: Optional[str]
+def update_refseqtaxo(host: str, key: str, file: Path, document: str):
+ client = meilisearch.Client(host, key)
+ index = client.index(document.lower())
+ documents = []
+ with open(file, "r") as csvfile:
+ csvreader = csv.DictReader(csvfile)
+ assembly = {}
+ for row in csvreader:
+ assembly_id = row["Assembly"]
+ assembly[row["Assembly"]] = {
+ k: row[k]
+ for k in (
+ "Superkingdom",
+ "phylum",
+ "class",
+ "order",
+ "family",
+ "genus",
+ "species",
+ "Assembly",
+ )
+ if k in row
+ }
+ assembly[assembly_id]["Assembly"] = assembly[assembly_id]["Assembly"].split('.')[0]
+ for item in assembly.values():
+ documents.append(item)
+ tasks = index.add_documents_in_batches(documents, primary_key="Assembly")
+ print(tasks)
+ index.update_pagination_settings({"maxTotalHits": 1000000})
+ index.update_filterable_attributes(
+ body=[
+ "Superkingdom",
+ "phylum",
+ "class",
+ "order",
+ "family",
+ "genus",
+ "species",
+ "Assembly",
+ ]
+ )
+ index.update_sortable_attributes(
+ [
+ "Superkingdom",
+ "phylum",
+ "class",
+ "order",
+ "family",
+ "genus",
+ "species",
+ "Assembly",
+ ]
+ )
+ params = {
+ "maxValuesPerFacet": 1000000,
+ "sortFacetValuesBy": {"*": "count"},
+ }
+ index.update_faceting_settings(params)
+
+
def update_refseq(
host: str,
key: str,
@@ -97,10 +164,12 @@ def update_refseq(
index.update_filterable_attributes(
body=[
"replicon",
+ "Assembly",
"type",
"subtype",
"Superkingdom",
"phylum",
+ "class",
"order",
"family",
"genus",
@@ -110,10 +179,12 @@ def update_refseq(
index.update_sortable_attributes(
[
"replicon",
+ "Assembly",
"type",
"subtype",
"Superkingdom",
"phylum",
+ "class",
"order",
"family",
"genus",
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 e7e3037766ce72d268bfdae830e4e52de3d34b03..f32ac8c3af221457efe03522b7e0bdf206f0c610 100644
--- a/packages/df-wiki-cli/df_wiki_cli/meilisearch/main.py
+++ b/packages/df-wiki-cli/df_wiki_cli/meilisearch/main.py
@@ -2,7 +2,12 @@ import typer
import meilisearch
from typing_extensions import Annotated
from pathlib import Path
-from df_wiki_cli.meilisearch import update_refseq, update_structure, update_systems
+from df_wiki_cli.meilisearch import (
+ update_refseq,
+ update_structure,
+ update_systems,
+ update_refseqtaxo,
+)
from enum import Enum
from types import SimpleNamespace
from rich.console import Console
@@ -14,6 +19,7 @@ app = typer.Typer()
class Documents(str, Enum):
+ refseqtaxo = "refseqtaxo"
refseq = "refseq"
structure = "structure"
systems = "systems"
@@ -55,6 +61,8 @@ def update(
] = Documents.refseq,
content_type: Annotated[str, typer.Option(help="Content-Type header")] = "text/csv",
):
+ if document == "refseqtaxo":
+ update_refseqtaxo(ctx.obj.host, ctx.obj.key, file, document)
if document == "refseq":
update_refseq(ctx.obj.host, ctx.obj.key, file, document)
if document == "structure":