diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
index 9fd01a308b4556bb00d617623068afc9734154d7..7292c2cabca2555b1c5b8415aeed636a71b8bc0a 100644
--- a/.gitlab-ci.yml
+++ b/.gitlab-ci.yml
@@ -12,7 +12,7 @@ workflow:
# Functions that should be executed before the build script is run
variables:
- HELM_VERSION: "3.9.3"
+ HELM_VERSION: "3.13.3"
IMAGE_NAME: "df-wiki"
# dev
HOST_DEV: 'defense-finder.dev.pasteur.cloud'
@@ -31,6 +31,7 @@ cache:
stages:
+
- delete-release
- build-df-cli
- lint
@@ -39,9 +40,9 @@ stages:
- update-meilisearch-indexes
- get-meili-key
- build
- - build-wiki
+ # - build-wiki
- deploy
-
+ # - load-website
.docker-login: &docker-login
- i=0; while [ "$i" -lt 12 ]; do docker info && break; sleep 5; i=$(( i + 1 )) ; done
@@ -353,25 +354,94 @@ 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}')
-build-wiki:
- stage: build-wiki
- 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
-
+# - 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 ${WIKI_POD} -- bash -c 'cd /structure-data/sanitized-dump && bash copy-structure-data.sh'
@@ -397,6 +467,16 @@ build-wiki:
--set env="${ENV:-development}"
--values deploy/df-wiki/values.yaml
--values deploy/df-wiki/values.${ENV:-development}.yaml
+ after_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} cp .output/public/ ${WIKI_POD}:/website
+ - kubectl --namespace ${KUBE_NAMESPACE} cp scripts/copy-structure-data.sh ${WIKI_POD}:/structure-data/sanitized-dump
+ - kubectl --namespace ${KUBE_NAMESPACE} exec ${WIKI_POD} -- bash -c 'cd /structure-data/sanitized-dump && bash copy-structure-data.sh'
+
+
deploy:dev:
extends: .deploy
@@ -464,3 +544,5 @@ delete-helm-release:prod:
script:
- echo "Removing $CI_PROJECT_NAME-$CI_ENVIRONMENT_NAME"
- helm delete -n ${NAMESPACE} $CI_PROJECT_NAME-$CI_ENVIRONMENT_NAME
+
+
diff --git a/components/ServerDbTable.vue b/components/ServerDbTable.vue
index 4850583886fa8991795d8593645e192358e19bd7..66a56ee6c6b6851004bcd82c81e6a36e43bedf4e 100644
--- a/components/ServerDbTable.vue
+++ b/components/ServerDbTable.vue
@@ -1,23 +1,38 @@
<script setup lang="ts">
// import type { FacetDistribution } from "meilisearch";
+import { useCsvDownload } from "@/composables/useCsvDownload"
import { useSlots } from 'vue'
import { useDisplay } from "vuetify";
import * as Plot from "@observablehq/plot";
import PlotFigure from "~/components/PlotFigure";
-import * as d3 from "d3";
import { useThrottleFn } from '@vueuse/core'
+
+import * as d3 from "d3";
import { useMeiliSearch } from "#imports"
+// import { saveAs } from "file-saver";
+import { useFileSystemAccess } from '@vueuse/core'
export interface SortItem {
key: string,
order: boolean | 'asc' | 'desc'
}
+export interface NumericalFilter {
+ id: string
+ name: string
+ range: [number, number]
+}
+
+export interface NumericalFilterModel extends NumericalFilter {
+ model: [number, number]
+}
export interface Props {
title?: string
db?: string
sortBy?: SortItem[]
facets: MaybeRef<string[]>
+ numericalFilters?: MaybeRef<string | undefined>
dataTableServerProps: Record<string, any>
+ columnsToDownload?: MaybeRef<string[] | undefined>
}
export interface FilterItem {
@@ -32,7 +47,10 @@ export interface FilterItem {
const props = withDefaults(defineProps<Props>(), {
title: '',
db: 'refseq',
+ columnsToDownload: undefined,
sortBy: () => [{ key: "type", order: "asc" }],
+ numericalFilters: undefined
+
});
@@ -51,18 +69,16 @@ const msFilter: Ref<string | undefined> = ref(undefined)
const page = ref(1)
let loading = ref(false)
const expanded = ref([])
-const { height } = useDisplay();
+const { height, mobile } = useDisplay();
const minTableHeight = ref(400)
const computedTableHeight = computed(() => {
const computedHeight = height.value - 350
return computedHeight > minTableHeight.value ? computedHeight : minTableHeight.value
})
-const plddtRange = ref([0, 100])
-// const { pending: pendingDownloadData, downloadCsv } = useCsvDownload(props.db, `df-${props.db}`)
+const pendingDownloadData = ref(false)
const filterInputValues = computed(() => {
- // console.log("recompouted FILTER value")
if (filterOrSearch.value != null) {
return filterOrSearch.value.filter(({ props }) => props.type !== 'text')
} else {
@@ -70,24 +86,6 @@ const filterInputValues = computed(() => {
}
})
-// const queryInputValue = computed(() => {
-// if (filterOrSearch.value !== null) {
-// const phrase = filterOrSearch.value
-// .filter((f) => {
-// return f.props.type === 'text'
-// })
-// .map((f) => {
-// return f.value
-// })
-// if (phrase.length > 1) {
-// return `${phrase.join(" ")}`
-// }
-// else { return phrase[0] }
-// } else {
-// return null
-// }
-// })
-
const isFilter = computed(() => {
return Array.isArray(filterOrSearch.value)
})
@@ -127,39 +125,18 @@ onMounted(async () => {
searchOrFilter()
})
-const hasPlddt = computed(() => props.db === 'structure')
-
-// Fetch results
-const plddtFilter = computed(() => {
- const plddtRangeValue = plddtRange.value
- if (hasPlddt.value && plddtRangeValue?.length === 2 && (plddtRangeValue[0] !== 0 || plddtRangeValue[1] !== 100)) {
- return `plddts ${plddtRangeValue[0]} TO ${plddtRangeValue[1]}`
- } else {
- return undefined
- }
-})
const computedFilter = computed(() => {
- if (toValue(msFilter)) {
- if (toValue(plddtFilter)) {
- return `${toValue(msFilter)} AND ${toValue(plddtFilter)}`
- }
- else {
- return toValue(msFilter)
- }
- } else {
- if (toValue(plddtFilter)) {
- return `${toValue(plddtFilter)}`
- }
- else {
- return undefined
- }
- }
+ return [toValue(msFilter), props.numericalFilters].filter(f => f !== undefined).join(" AND ")
})
+watch(computedFilter, () => {
+ searchOrFilter()
+})
+
const msError = computed(() => {
if (filterError.value?.type && filterError.value?.message) {
@@ -167,8 +144,9 @@ const msError = computed(() => {
} else { return false }
})
-const throttleSearch = useThrottleFn(async () => { searchOrFilter() }, 300)
-
+const throttleSearch = useThrottleFn(async () => {
+ searchOrFilter()
+}, 300)
async function searchOrFilter(pagination = true) {
// do something, it will be called at most 1 time per second
@@ -292,13 +270,7 @@ const autocompleteItems = computed(() => {
}
})
-// const canAddTextSearch = computed(() => {
-// if (filterOrSearch.value !== null && filterOrSearch.value.length > 0) {
-// const lastItem = filterOrSearch.value.slice(-1)[0]
-// return lastItem?.props.type === 'value' || lastItem?.props.type === "text"
-// }
-// return true
-// })
+
function selectItem(item) {
filterOrSearch.value = Array.isArray(filterOrSearch.value) ? [...filterOrSearch.value, item] : [item]
@@ -314,28 +286,45 @@ function clearSearch() {
search.value = ""
}
+async function downloadData() {
+ pendingDownloadData.value = true
+ try {
+ const { data } = await useAsyncMeiliSearch({
+ index: props.db,
+ params: { ...toValue(notPaginatedParams), filter: toValue(computedFilter), sort: toValue(msSortBy) },
+ query: toValue(search),
+ })
-
-
-// const groupSortDomain = computed(() => {
-// console.log(msResult.value)
-// return msResult.value ? d3.groupSort(msResult.value?.hits?.filter((d) => d.phylum), (g) => d3.median(g, (d) => d.phylum), (d) => d.type) : []
-// })
-
-
-
+ useCsvDownload(data, props.columnsToDownload, props.title)
+ } finally {
+ pendingDownloadData.value = false
+ }
+}
</script>
<template>
<v-card flat color="transparent">
<v-card-text>
</v-card-text>
<v-card-text>
- <v-row>
- <v-col cols="5">
- <v-text-field v-model="search" label="Search..." hide-details prepend-inner-icon="mdi-magnify"
- single-line clearable></v-text-field>
- </v-col>
- <v-col>
+ <slot name="numerical-filters" :search="throttleSearch"></slot>
+ </v-card-text>
+ <v-toolbar flat color="transparent"> </v-toolbar>
+ <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>
+ <v-toolbar floating><v-toolbar-title class="text-capitalize">
+ <v-badge :content="totalHits" color="primary" inline>
+ <v-btn prepend-icon="md:download" :loading="pendingDownloadData" variant="text" color="primary"
+ @click="downloadData()">{{
+ props.title }}
+ </v-btn>
+ </v-badge>
+ </v-toolbar-title>
+ <v-text-field v-model="search" label="Search..." hide-details="auto" prepend-inner-icon="mdi-magnify"
+ single-line clearable class="mr-2"></v-text-field>
<v-autocomplete ref="autocompleteInput" hide-details v-model:model-value="filterOrSearch"
auto-select-first chips clearable label="Filter results..." :items="autocompleteItems" single-line
item-value="value" item-title="title" multiple return-object prepend-inner-icon="md:search"
@@ -352,29 +341,9 @@ function clearSearch() {
</v-list-item>
</template>
</v-autocomplete>
- </v-col>
- </v-row>
- <v-row v-if="props.db === 'structure'">
- <v-col>
- <v-range-slider v-model="plddtRange" density="compact" hide-details="auto" label="pLDDT" step="0.1"
- @update:modelValue="throttleSearch()">
- <template v-slot:prepend>
- <span hide-details single-line type="number" variant="outlined" density="compact"
- style="width: 70px">{{ plddtRange[0] }}</span>
- </template>
- <template v-slot:append>
- <span hide-details single-line type="number" variant="outlined" style="width: 70px"
- density="compact">{{ plddtRange[1] }}</span>
- </template>
- </v-range-slider>
- </v-col>
- </v-row>
- </v-card-text>
- <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">
+ </v-toolbar>
+ </template>
<template v-for="(slot, index) of Object.keys(slots)" :key="index" v-slot:[slot]="data">
<slot :name="slot" v-bind="data"></slot>
diff --git a/components/content/ListSystems.vue b/components/content/ListSystems.vue
deleted file mode 100644
index ed19ba4b3731bf747e0580b70e1c212341c8af9e..0000000000000000000000000000000000000000
--- a/components/content/ListSystems.vue
+++ /dev/null
@@ -1,66 +0,0 @@
-<script setup lang="ts">
-import { usePfamStore } from "@/stores/pfam";
-
-export interface Props {
- headers: Array<Object>;
- systems: Array<Object>;
- height?: number;
-}
-
-const props = withDefaults(defineProps<Props>(), {
- height: 800,
-});
-
-const itemsPerParge = ref(25);
-const search = ref("");
-const sortBy = ref([{ key: "system", order: "asc" }]);
-const expanded = ref([]);
-
-function filterOnlyCapsText(value, query, item) {
- if (value != null && query != null) {
- if (typeof value === "string") {
- return value.toString().toLowerCase().indexOf(query.toLowerCase()) !== -1;
- }
- if (typeof value == "object") {
- if (value?.name) {
- return (
- value.name.toString().toLowerCase().indexOf(query.toLowerCase()) !==
- -1
- );
- }
- }
- }
- return false;
-}
-const { initPfam } = usePfamStore();
-onMounted(() => {
- initPfam();
-})
-</script>
-<template>
- <v-card>
- <v-toolbar density="compact">
- <v-toolbar-title>Defense Systems</v-toolbar-title>
-
- <v-text-field v-model="search" density="compact" variant="underlined" prepend-inner-icon="mdi-magnify"
- label="Search for defense systems" single-line hide-details class="mx-2" clearable></v-text-field>
- </v-toolbar>
- <v-data-table-virtual fixed-header :height="height" :items-per-page="itemsPerParge" v-model:sort-by="sortBy"
- :headers="props.headers" density="compact" :custom-filter="filterOnlyCapsText" :items="props.systems"
- :search="search" item-value="system.name">
- <template #[`item.system`]="{ item }">
- <v-chip variant="text" link :to="item?.system?.path ? `${item?.system?.path}` : null">{{
- item?.system?.name ?? 'None'
- }}</v-chip>
- </template>
- <template #[`item.article`]="{ item }">
- <ArticleDoi v-if="item?.article" :doi="item.article.doi" :title="item.article?.title"
- :abstract="item.article?.abstract" :divider="false" :enumerate="false" />
- </template>
- <template #[`item.PFAM`]="{ item }">
-
- <pfam-chips v-if="item?.PFAM" :pfam-string="item.PFAM"></pfam-chips>
- </template>
- </v-data-table-virtual>
- </v-card>
-</template>
\ No newline at end of file
diff --git a/components/content/Mermaid.vue b/components/content/Mermaid.vue
index c747d1f5827731593d1744e6ce5650111a1a6879..aa40306337a254d04b3673364a35c87e574fdefe 100644
--- a/components/content/Mermaid.vue
+++ b/components/content/Mermaid.vue
@@ -10,7 +10,7 @@
<script setup lang="ts">
const slot = useSlots()
-const el = ref(null)
+const el: Ref<HTMLElement | null> = ref(null)
const rendered = ref(false)
async function render() {
diff --git a/components/content/MolstarPdbePlugin.vue b/components/content/MolstarPdbePlugin.vue
index 5f1570b7e066d4767a41b54fc4397bfb8b15c017..87903b6fd7767210e53a536cbd224e98234098cd 100644
--- a/components/content/MolstarPdbePlugin.vue
+++ b/components/content/MolstarPdbePlugin.vue
@@ -105,86 +105,43 @@ useHead({
const pdbeMolstarComponent = ref(null)
// const selectedPdb = ref("/wiki/avs/AVAST_I,AVAST_I__Avs1A,0,V-plddts_85.07081.pdb")
const selectedPdb: Ref<string | null> = ref(null)
-
+const structureToDownload: Ref<string | null> = ref(null)
const selectedPaePath = computed(() => {
return selectedPdb.value ? `${selectedPdb.value.split(".").slice(0, -1).join('.')}.png` : null
})
-// const paeData = ref([])
-// watch(selectedPaePath, async (newPaePath) => {
-// if (newPaePath !== null) {
-// try {
-// const data = await d3.tsv(newPaePath);
-// if (data.length > 500) {
-// paeError.value = `The PAE is too large to be displayed (${data.length} residus)`
-// paeData.value = []
-// }
-// else if (data?.[0]?.[0] === undefined) {
-// paeError.value = "The PAE cannot be downloaded"
-// paeData.value = []
-// }
-// else {
-// paeData.value = data
-// paeError.value = null
-// }
-
-// }
-// catch (error) {
-// console.log(error)
-// }
-// } else {
-// paeData.value = []
-// }
-
-// })
-
-// const sanitizedPaeData = computed(() => {
-// return paeData.value.reduce((acc, curr, index) => {
-// const scoredResidue = index
-// // let newAcc = [...acc]
-// for (const [alignedResidue, value] of Object.entries(curr)) {
-// // console.log(value)
-// acc.push({ alignedResidue: parseInt(alignedResidue), scoredResidue: parseInt(scoredResidue), value: parseFloat(value) })
-// // newAcc = [...newAcc, ...[{ alignedResidue: parseInt(alignedResidue), scoredResidue: parseInt(scoredResidue), value: parseFloat(value) }]]
-// }
-
-// return acc
-// }, [])
-// })
-
-
-// const plotPaeOptions = computed(() => {
-// return {
-// width: 640,
-// height: 640,
-// color: { scheme: "Greens", legend: true, reverse: true, label: "Expected position error (Ångströms)" },
-// y: { reverse: true },
-// marks: [
-// Plot.dot(sanitizedPaeData.value, { x: "scoredResidue", y: "alignedResidue", stroke: "value" })
-// ]
-// }
-// })
-
watch(selectedPdb, (newSelectedPdb, prevSelectPdb) => {
viewPdb(newSelectedPdb)
+ structureToDownload.value = newSelectedPdb
})
+onMounted(() => {
+ const urls = toValue(refinedDataUrls)
+ if (props.uniq && urls.length >= 1) {
+ structureToDownload.value = urls[0]
+
+ }
+})
function viewPdb(pdbPath: string | null) {
if (pdbPath !== null) {
dialog.value = true
const format = toValue(pdbPath)?.split(".").slice(-1)[0]?.toLowerCase() ?? "pdb"
moleculeFormat.value = format
if (pdbeMolstarComponent.value?.viewerInstance) {
- console.log(pdbeMolstarComponent.value)
const viewerInstance = pdbeMolstarComponent.value.viewerInstance
const customData = { url: pdbPath, format: format, binary: false }
viewerInstance.visual.update({ customData })
-
+
}
}
}
+
+
+
+
+
function setSelectedPdbToFirst() {
const urls = toValue(refinedDataUrls)
if (urls.length >= 1) {
@@ -200,107 +157,116 @@ const moleculeFormat: Ref<string> = ref("pdb")
<template>
- <span class="d-flex flex-wrap align-center justify-center">
+ <template v-if="uniq">
+ <v-row>
+ <v-btn size="x-small" variant="tonal" icon="md:visibility" @click="setSelectedPdbToFirst()"></v-btn>
+ <v-btn :disabled="!structureToDownload" size="x-small" variant="tonal" icon="md:download" class="ml-1"
+ :href="structureToDownload"></v-btn>
+ </v-row>
+ </template>
+ <v-row v-else>
<v-col>
- <v-btn v-if="uniq" size="x-small" variant="tonal" icon="md:visibility" @click="setSelectedPdbToFirst()"></v-btn>
- <v-select v-else v-model="selectedPdb" label="Select PDB" :items="refinedDataUrls" hide-details="auto">
- </v-select>
+ <span class="d-flex flex-wrap align-center justify-center">
+ <v-select v-model="selectedPdb" label="Select PDB" :items="refinedDataUrls" hide-details="auto">
+ </v-select>
+ </span>
</v-col>
-
- <v-dialog v-model="dialog" transition="dialog-bottom-transition" fullscreen :scrim="false">
- <v-card flat :rounded="false">
- <v-toolbar>
- <v-toolbar-title>Structures</v-toolbar-title>
- <v-select v-model="selectedPdb" label="Select PDB" :items="refinedDataUrls"
- hide-details="auto"></v-select>
- <v-spacer></v-spacer>
-
- <v-btn :disabled="!selectedPdb" icon="md:download" :href="selectedPdb"></v-btn>
- <v-btn icon @click="closeStructure">
- <v-icon>mdi-close</v-icon>
- </v-btn>
-
- </v-toolbar>
- <v-card-text>
- <v-row>
- <v-col :cols="mobile ? 12 : 'auto'">
- <v-sheet v-if="selectedPdb"
- class="d-flex align-center justify-center flex-wrap text-center mx-auto px-4 my-3"
- :height="computedHeight" :width="computedWidth" position="relative">
- <pdbe-molstar ref="pdbeMolstarComponent" hide-controls="true" landscape="true"
- :custom-data-url="selectedPdb" alphafold-view="true"
- :custom-data-format="moleculeFormat"></pdbe-molstar>
- </v-sheet>
- </v-col>
- <v-col :cols="mobile ? 12 : undefined">
- <v-img :src="selectedPaePath"></v-img>
-
- <!-- <PlotFigure v-if="sanitizedPaeData?.length > 0 && paeError === null" defer
+ </v-row>
+ <v-dialog v-model="dialog" transition="dialog-bottom-transition" fullscreen :scrim="false">
+ <v-card flat :rounded="false">
+ <v-toolbar>
+ <v-toolbar-title>Structures</v-toolbar-title>
+ <v-select v-model="selectedPdb" label="Select PDB" :items="refinedDataUrls" hide-details="auto"></v-select>
+ <v-spacer></v-spacer>
+
+ <v-btn :disabled="!selectedPdb" icon="md:download" :href="structureToDownload"></v-btn>
+ <v-btn icon @click="closeStructure">
+ <v-icon>mdi-close</v-icon>
+ </v-btn>
+
+ </v-toolbar>
+ <v-card-text>
+ <v-row>
+ <v-col :cols="mobile ? 12 : 'auto'">
+ <v-sheet v-if="selectedPdb"
+ class="d-flex align-center justify-center flex-wrap text-center mx-auto px-4 my-3"
+ :height="computedHeight" :width="computedWidth" position="relative">
+ <pdbe-molstar ref="pdbeMolstarComponent" landscape :custom-data-url="selectedPdb"
+ alphafold-view="true" :custom-data-format="moleculeFormat"></pdbe-molstar>
+ </v-sheet>
+ </v-col>
+ <v-col :cols="mobile ? 12 : undefined">
+ <v-img :src="selectedPaePath"></v-img>
+
+ <!-- <PlotFigure v-if="sanitizedPaeData?.length > 0 && paeError === null" defer
:options="plotPaeOptions"></PlotFigure>
<v-alert v-else type="warning" variant="tonal">{{ paeError }}</v-alert> -->
- <v-card flat color="transparent">
- <v-card-title>Model Confidence</v-card-title>
- <v-card-text>
- AlphaFold produces a per-residue model
- confidence score (pLDDT) between 0 and 100. Some regions below 50 pLDDT may be
- unstructured
- in isolation.
- </v-card-text>
- <v-list>
- <v-list-item>
- <template #prepend>
- <div class="legendColor mr-2" style="background-color: rgb(0, 83, 214);">
- </div>
- </template>
- <v-list-item-title>
- Very high (pLDDT > 90)
- </v-list-item-title>
-
- </v-list-item>
- <v-list-item>
- <template #prepend>
- <div class="legendColor mr-2" style="background-color: rgb(101, 203, 243);">
- </div>
- </template>
- <v-list-item-title>
- High (90 > pLDDT > 70)
- </v-list-item-title>
-
- </v-list-item>
- <v-list-item>
- <template #prepend>
- <div class="legendColor mr-2" style="background-color: rgb(255, 219, 19);">
- </div>
- </template>
- <v-list-item-title>
- Low (70 > pLDDT > 50) </v-list-item-title>
-
- </v-list-item>
- <v-list-item>
- <template #prepend>
- <div class="legendColor mr-2" style="background-color: rgb(255, 125, 69);">
- </div>
- </template>
- <v-list-item-title>
- Very low (pLDDT < 50) </v-list-item-title>
-
- </v-list-item>
- </v-list>
- </v-card>
- </v-col>
- </v-row>
- </v-card-text>
- </v-card>
- </v-dialog>
- </span>
+ <v-card flat color="transparent">
+ <v-card-title>Model Confidence</v-card-title>
+ <v-card-text>
+ AlphaFold produces a per-residue model
+ confidence score (pLDDT) between 0 and 100. Some regions below 50 pLDDT may be
+ unstructured
+ in isolation.
+ </v-card-text>
+ <v-list>
+ <v-list-item>
+ <template #prepend>
+ <div class="legendColor mr-2" style="background-color: rgb(0, 83, 214);">
+ </div>
+ </template>
+ <v-list-item-title>
+ Very high (pLDDT > 90)
+ </v-list-item-title>
+
+ </v-list-item>
+ <v-list-item>
+ <template #prepend>
+ <div class="legendColor mr-2" style="background-color: rgb(101, 203, 243);">
+ </div>
+ </template>
+ <v-list-item-title>
+ High (90 > pLDDT > 70)
+ </v-list-item-title>
+
+ </v-list-item>
+ <v-list-item>
+ <template #prepend>
+ <div class="legendColor mr-2" style="background-color: rgb(255, 219, 19);">
+ </div>
+ </template>
+ <v-list-item-title>
+ Low (70 > pLDDT > 50) </v-list-item-title>
+
+ </v-list-item>
+ <v-list-item>
+ <template #prepend>
+ <div class="legendColor mr-2" style="background-color: rgb(255, 125, 69);">
+ </div>
+ </template>
+ <v-list-item-title>
+ Very low (pLDDT < 50) </v-list-item-title>
+
+ </v-list-item>
+ </v-list>
+ </v-card>
+ </v-col>
+ </v-row>
+ </v-card-text>
+ </v-card>
+ </v-dialog>
</template>
-<style scoped>
+<style>
.msp-plugin .msp-plugin-content {
color: black !important;
}
+div.msp-plugin-content.msp-layout-expanded {
+ z-index: 99 !important
+}
+
.legendColor {
height: 16px;
width: 16px;
diff --git a/components/content/RefseqDb.vue b/components/content/RefseqDb.vue
index ee4e713bbcd0f8a247d5283afe1a40fa7230f3a9..38260b1fb067278cddf555a49412b847f18253ea 100644
--- a/components/content/RefseqDb.vue
+++ b/components/content/RefseqDb.vue
@@ -11,6 +11,8 @@ const itemValue = ref("id");
const { width } = useDisplay();
const scaleTransform: Ref<string[]> = ref([])
+
+
const facets = ref([
"replicon",
"type",
@@ -80,10 +82,7 @@ onMounted(async () => {
async function getAllHits(params) {
if (params.index === 'refseq') {
- console.log(params.index)
const { data, error } = await useAsyncMeiliSearch(params)
- console.log(error.value)
- console.log(data.value)
allHits.value = data.value
}
}
@@ -207,7 +206,8 @@ const binPlotOptions = ref({
})
const binPlotDataOptions = computed(() => {
- return allHits.value?.hits?.length > 0 ? {
+ const toValueAllHits = toValue(allHits)
+ return toValueAllHits?.hits?.length > 0 ? {
...binPlotOptions.value,
color: {
...binPlotOptions.value.color,
@@ -215,7 +215,7 @@ const binPlotDataOptions = computed(() => {
},
// fy: { domain: groupSortDomain.value },
marks: [
- Plot.cell(allHits.value?.hits ?? [], Plot.group({ fill: "count" }, { x: "type", y: selectedTaxoRank.value, tip: true, inset: 0.5, sort: { y: "fill" } })),
+ Plot.cell(toValueAllHits?.hits ?? [], Plot.group({ fill: "count" }, { x: "type", y: selectedTaxoRank.value, tip: true, inset: 0.5, sort: { y: "fill" } })),
]
} : null
@@ -282,13 +282,7 @@ const scaleType = ref("linear")
<ServerDbTable title="RefSeq" db="refseq" :sortBy="sortBy" :facets="facets"
:data-table-server-props="dataTableServerProps" @refresh:search="getAllHits">
- <template #top>
- <v-toolbar><v-toolbar-title class="text-capitalize">
- RefSeq
- </v-toolbar-title><v-spacer></v-spacer>
- </v-toolbar>
- </template>
<template #[`item.accession_in_sys`]="{ item }">
<CollapsibleChips :items="namesToAccessionChips(item.accession_in_sys)">
</CollapsibleChips>
diff --git a/components/content/StructureDb.vue b/components/content/StructureDb.vue
index 711accda2a6ebdde83b6545beb50a1b957f8bc8e..e80e1719eaf4927c49185454b60e92a57858a0f7 100644
--- a/components/content/StructureDb.vue
+++ b/components/content/StructureDb.vue
@@ -2,6 +2,9 @@
import * as Plot from "@observablehq/plot";
import PlotFigure from "~/components/PlotFigure";
import type { SortItem } from "@/components/ServerDbTable.vue"
+import { useNumericalFilter } from "@/composables/useNumericalfilter"
+
+
import { ServerDbTable } from "#components"
const sortBy: Ref<SortItem[]> = ref([{ key: 'system', order: "asc" }])
const itemValue = ref("id");
@@ -24,7 +27,16 @@ const headers: Ref<Object[]> = ref([
// { title: "Type", key: "type", removable: true },
])
+
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)
+
+const numericalFilters = computed(() => {
+ const listFilters = [plddtsFilter, iptmFilter, pdockqFilter].map(f => toValue(f)).filter(f => f !== undefined)
+ return listFilters.length > 0 ? listFilters.join(" AND ") : undefined
+})
const defaultDataTableServerProps = ref({
showExpand: false
@@ -41,6 +53,7 @@ const dataTableServerProps = computed(() => {
+
function namesToCollapsibleChips(names: string[], file: string | null = null) {
if (file === null) {
return names.filter((it) => it !== "").map(it => ({ title: it.split("__")[1] }))
@@ -69,21 +82,46 @@ const plddtDistribution = computed(() => {
}
})
-function remove(key) {
- headers.value = headers.value.filter(header => header.key !== key)
-}
+
+
+
</script>
<template>
<ServerDbTable title="Predicted Structures" db="structure" :sortBy="sortBy" :facets="facets"
- :data-table-server-props="dataTableServerProps">
-
- <template #top>
- <v-toolbar><v-toolbar-title class="text-capitalize">
- Predicted Structures
- </v-toolbar-title><v-spacer></v-spacer>
-
- </v-toolbar>
+ :data-table-server-props="dataTableServerProps" :numerical-filters="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>
</template>
<template #[`item.proteins_in_the_prediction`]="{ item }">
@@ -97,9 +135,9 @@ function remove(key) {
<MolstarPdbePlugin v-if="item?.pdb && item.pdb !== 'na'"
:data-urls="[`/${toSystemName(item.system_genes)}/${pdbNameToCif(item.pdb)}`]" uniq>
</MolstarPdbePlugin>
- <span v-else class="d-flex flex-wrap align-center justify-center">
- <v-icon color="warning" icon="md:dangerous"></v-icon>
- </span>
+
+ <!-- <v-icon v-else color="warning" icon="md:dangerous"></v-icon> -->
+
</template>
<template #[`item.completed`]="{ item }">
<v-icon v-if="item.completed" color="success" icon="md:check"></v-icon>
diff --git a/components/content/SystemDb.vue b/components/content/SystemDb.vue
index 72d1642f4e757b4da5e2a7b1881039bf534d7ec6..65e3c152f8b1ad61c37f0701272afdf07d82167d 100644
--- a/components/content/SystemDb.vue
+++ b/components/content/SystemDb.vue
@@ -3,7 +3,7 @@ import type { SortItem } from "@/components/ServerDbTable.vue"
import { ServerDbTable } from "#components"
const sortBy: Ref<SortItem[]> = ref([{ key: 'title', order: "asc" }])
const itemValue = ref("title");
-const facets: Ref<string[]> = ref(["title", "Sensor", "Effector", "Activator", "PFAM.AC"])
+const facets: Ref<string[]> = ref(["title", "Sensor", "Effector", "Activator", "PFAM.AC", "PFAM.DE"])
const headers: Ref<Object[]> = ref([
{ title: "System", key: "title", removable: false },
{ title: "Article", key: "doi", removable: false },
@@ -30,16 +30,13 @@ const dataTableServerProps = computed(() => {
}
})
+const columnsToDownload = ref(['title', 'doi', 'Sensor', 'Activator', 'Effector', 'PFAM', 'contributors',])
+
</script>
<template>
- <ServerDbTable title="systems" db="systems" :sortBy="sortBy" :facets="facets"
- :data-table-server-props="dataTableServerProps">
+ <ServerDbTable title="List Systems" db="systems" :sortBy="sortBy" :facets="facets"
+ :data-table-server-props="dataTableServerProps" :columns-to-download="columnsToDownload">
- <template #top>
- <v-toolbar><v-toolbar-title class="text-capitalize">
- List Systems </v-toolbar-title><v-spacer></v-spacer>
- </v-toolbar>
- </template>
<template #[`item.title`]="{ item }">
<v-chip color="info" link :to="`/defense-systems/${item.title.toLowerCase()}`">{{
diff --git a/composables/useCsvDownload.ts b/composables/useCsvDownload.ts
index 9534544a1654e9d66d4bf0888787fa55152ed0b0..a84e6ad90db80aaf3a27d3f9c0acef621fc25b26 100644
--- a/composables/useCsvDownload.ts
+++ b/composables/useCsvDownload.ts
@@ -1,48 +1,40 @@
-import { ref } from 'vue';
import Papa from 'papaparse';
-import { saveAs } from "file-saver";
+// import { saveAs } from "file-saver";
-export function useCsvDownload(index: MaybeRef<string>, baseName: MaybeRef<string> = "df"
+export function useCsvDownload(
+ rawData: MaybeRef<Record<string, any>>,
+ columns: MaybeRef<string[] | undefined> = undefined,
+ baseName: MaybeRef<string> = 'data'
) {
- const pending = ref(false)
- const { search: msSearch, result: msResult } = useMeiliSearch(toValue(index))
- const filename = ref(`${toValue(baseName)}-data.csv`)
- const downloadCsv = async (
-
- query: MaybeRef<string>,
- filter: MaybeRef<string>,
- sortBy: MaybeRef<string[]>,
- params: MaybeRef<Record<string, any>>,
- ) => {
-
-
- filename.value = `${toValue(baseName)}-${toValue(filter)}.csv`
- pending.value = true
- try {
- await msSearch(
- toValue(query),
- {
- ...toValue(params),
- filter: toValue(filter),
- sort: toValue(sortBy)
- })
- const csvContent = Papa.unparse(toValue(msResult).hits);
- // console.log(csvContent)
- const blob = new Blob([csvContent], { type: 'text/csv;charset=utf-8;' });
- saveAs(blob, `${toValue(filename)}`);
- } finally {
- pending.value = false
- }
-
+ const filename = ref(`df-${toValue(baseName)}.csv`)
+ const data = ref()
+ const blob = ref()
+ if (toValue(rawData)?.hits?.length > 0) {
+ data.value = toValue(rawData).hits.map(row => {
+ let sanitizedRow = { ...row }
+ if (sanitizedRow?.PFAM?.length > 0) {
+ sanitizedRow = {
+ ...sanitizedRow,
+ PFAM: sanitizedRow.PFAM.map(({ AC }) => AC).join(", ")
+ }
+ }
+ if (sanitizedRow?.contributors?.length > 0) {
+ sanitizedRow = {
+ ...sanitizedRow,
+ contributors: sanitizedRow.contributors.join(", ")
+ }
+ }
+ return sanitizedRow
+
+ })
+ const csvContent = Papa.unparse(toValue(data), { columns: toValue(columns) });
+ blob.value = new Blob([csvContent], { type: "text/csv" });
+ var a = document.createElement("a");
+ a.href = URL.createObjectURL(blob.value);
+ a.download = filename.value;
+ a.click();
+ URL.revokeObjectURL(a.href);
}
- // watch(msResult, (newRes) => {
- // console.log("save file !!!!!!")
-
-
- // })
-
- return {
- pending, downloadCsv,
- };
+ return { data, filename }
}
diff --git a/composables/useNumericalfilter.ts b/composables/useNumericalfilter.ts
new file mode 100644
index 0000000000000000000000000000000000000000..9ee97d80a4239e558dfdea1e57e563cc500519af
--- /dev/null
+++ b/composables/useNumericalfilter.ts
@@ -0,0 +1,41 @@
+export function useNumericalFilter(
+ id: MaybeRef<string>,
+ min: MaybeRef<number>,
+ max: MaybeRef<number>,
+) {
+
+
+ const range: Ref<[number, number]> = ref([toValue(min), toValue(max)])
+
+
+
+
+ const stringifyFilter: Ref<string | undefined> = ref(`${toValue(id)} ${toValue(min)} TO ${toValue(max)}`)
+
+
+
+ watchEffect(() => {
+ console.log("watch reange")
+ console.log(range.value)
+ if (range.value[0] === toValue(min) && range.value[1] === toValue(max)) {
+ stringifyFilter.value = undefined
+ } else {
+ stringifyFilter.value = `'${toValue(id)}' ${range.value[0]} TO ${range.value[1]}`
+ }
+ })
+ function reset() {
+ range.value = [toValue(min), toValue(max)]
+ }
+ // watch(() => range, () => {
+ // console.log("watch reange")
+ // console.log(range)
+ // if (range.value[0] === toValue(min) && range.value[1] === toValue(max)) {
+ // stringifyFilter.value = undefined
+ // } else {
+ // stringifyFilter.value = `${toValue(id)} ${toValue(min)} TO ${toValue(max)}`
+ // }
+ // }, { deep: true })
+
+
+ return { range, stringifyFilter, reset }
+}
\ No newline at end of file
diff --git a/content/5.structure.md b/content/5.structure.md
index 923ce4a93f5dcaef3fff697cbbf03112275a0d52..a21e7e49c3db8db7c3b1ff6c281bb25c02ae321b 100644
--- a/content/5.structure.md
+++ b/content/5.structure.md
@@ -5,7 +5,7 @@ navigation:
icon: "mdi-database"
---
-# Structures' prediction DB
+# Structure's prediction DB
In the following tables are various structures that were generated by Alphafold for all monomers, hetero- and homo-dimers for a given system.
In the page for each system is the structure for the monomers and real structure when it exists.
diff --git a/deploy/df-wiki/templates/deployment.yaml b/deploy/df-wiki/templates/deployment.yaml
index c9f378b1571e9f9bf6fbb75b877e346c7450ddcc..8a362cad8a72b65dfe00b6f95f9772857141c70b 100644
--- a/deploy/df-wiki/templates/deployment.yaml
+++ b/deploy/df-wiki/templates/deployment.yaml
@@ -56,7 +56,9 @@ spec:
mountPath: /etc/nginx/conf.d/
- name: structure-data-pvc
mountPath: /structure-data
-
+ - name: website-pvc
+ mountPath: /website
+
{{- with .Values.nodeSelector }}
nodeSelector:
@@ -79,3 +81,6 @@ spec:
- name: structure-data-pvc
persistentVolumeClaim:
claimName: structure-data-pvc
+ - name: website-pvc
+ persistentVolumeClaim:
+ claimName: website-pvc
diff --git a/deploy/df-wiki/templates/pvc-structure.yaml b/deploy/df-wiki/templates/pvc-structure.yaml
index acbe7073e7a77902ee95ab2b60fcbede0353a6f4..29334d59b0efa7867b171bd746ac6a536615d267 100644
--- a/deploy/df-wiki/templates/pvc-structure.yaml
+++ b/deploy/df-wiki/templates/pvc-structure.yaml
@@ -9,6 +9,6 @@ spec:
- ReadWriteMany
resources:
requests:
- storage: 30Gi
+ storage: 35Gi
storageClassName: isilon
volumeMode: Filesystem
\ No newline at end of file
diff --git a/deploy/df-wiki/templates/pvc-website.yaml b/deploy/df-wiki/templates/pvc-website.yaml
new file mode 100644
index 0000000000000000000000000000000000000000..ee06f21b7a4d30247da089bccdd9ae81bc5be921
--- /dev/null
+++ b/deploy/df-wiki/templates/pvc-website.yaml
@@ -0,0 +1,14 @@
+apiVersion: v1
+kind: PersistentVolumeClaim
+metadata:
+ name: website-pvc
+ annotations:
+ "helm.sh/resource-policy": keep
+spec:
+ accessModes:
+ - ReadWriteMany
+ resources:
+ requests:
+ storage: 1Gi
+ storageClassName: isilon
+ volumeMode: Filesystem
\ No newline at end of file
diff --git a/package-lock.json b/package-lock.json
index db81ba7dee9d57a906c9b44fd256bcc57aa1be44..7253b32debde86f4054e4bc8a765f1cf55c099b9 100644
--- a/package-lock.json
+++ b/package-lock.json
@@ -8,7 +8,6 @@
"@observablehq/plot": "^0.6.13",
"@pinia/nuxt": "^0.5.1",
"d3": "^7.8.5",
- "file-saver": "^2.0.5",
"meilisearch": "^0.36.0",
"mermaid": "^10.6.1",
"papaparse": "^5.4.1",
@@ -5704,10 +5703,6 @@
"node": "^10.12.0 || >=12.0.0"
}
},
- "node_modules/file-saver": {
- "version": "2.0.5",
- "license": "MIT"
- },
"node_modules/file-uri-to-path": {
"version": "1.0.0",
"dev": true,
diff --git a/package.json b/package.json
index a45f22d73d4c9a0b78363f37736be7080d390062..d1dcd76fdcd518f015043bf684e1d0776ba82c8c 100644
--- a/package.json
+++ b/package.json
@@ -22,7 +22,6 @@
"@observablehq/plot": "^0.6.13",
"@pinia/nuxt": "^0.5.1",
"d3": "^7.8.5",
- "file-saver": "^2.0.5",
"meilisearch": "^0.36.0",
"mermaid": "^10.6.1",
"papaparse": "^5.4.1",
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 b3ec461a9fc5d686aae9b8b60c4f63c03e7a87b2..4ab37da8982f27631c916cdcd21a98295fd92039 100644
--- a/packages/df-wiki-cli/df_wiki_cli/meilisearch/__init__.py
+++ b/packages/df-wiki-cli/df_wiki_cli/meilisearch/__init__.py
@@ -61,6 +61,7 @@ class StrucutreStatistics(BaseModel):
iptm_ptm: NaFloat = Field(..., alias="iptm+ptm")
pDockQ: Optional[NaFloat]
plddts: Optional[NaFloat]
+ Foldseek_name: Optional[str]
def update_refseq(
@@ -193,7 +194,7 @@ def update_systems(
)
print(pagination_settings_task)
attr_task = index.update_filterable_attributes(
- body=["title", "Sensor", "Activator", "Effector", "PFAM.AC"]
+ body=["title", "Sensor", "Activator", "Effector", "PFAM.AC", "PFAM.DE"]
)
params = {
"maxValuesPerFacet": 1000000,
diff --git a/scripts/copy-structure-data.sh b/scripts/copy-structure-data.sh
new file mode 100644
index 0000000000000000000000000000000000000000..424beb09227f423d91788d0f355e503f1b4e4132
--- /dev/null
+++ b/scripts/copy-structure-data.sh
@@ -0,0 +1,3 @@
+#!/bin/bash
+
+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 {} +