diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
index 9fd01a308b4556bb00d617623068afc9734154d7..28412e3833b83db014269ba709e388bfb611619e 100644
--- a/.gitlab-ci.yml
+++ b/.gitlab-ci.yml
@@ -41,6 +41,7 @@ stages:
- build
- build-wiki
- deploy
+ - load-website
.docker-login: &docker-login
@@ -464,3 +465,28 @@ delete-helm-release:prod:
script:
- echo "Removing $CI_PROJECT_NAME-$CI_ENVIRONMENT_NAME"
- helm delete -n ${NAMESPACE} $CI_PROJECT_NAME-$CI_ENVIRONMENT_NAME
+
+
+load-website:dev:
+ image: harbor.pasteur.fr/kube-system/helm-kubectl:$HELM_VERSION
+ stage: load-website
+ rules:
+ - if: $CI_COMMIT_BRANCH != "main"
+ needs:
+ - "deploy:dev"
+ script:
+ - kubectl wait pods -l app.kubernetes.io/name=df-wiki --for condition=Ready --timeout=90s
+ - echo "Le pod est ready"
+
+
+
+load-website:prod:
+ image: harbor.pasteur.fr/kube-system/helm-kubectl:$HELM_VERSION
+ stage: load-website
+ rules:
+ - if: $CI_COMMIT_BRANCH == "main"
+ needs:
+ - "deploy:prod"
+ script:
+ - kubectl wait pods -l app.kubernetes.io/name=df-wiki --for condition=Ready --timeout=90s
+ - echo "Le pod est ready"
\ No newline at end of file
diff --git a/components/ServerDbTable.vue b/components/ServerDbTable.vue
index 4850583886fa8991795d8593645e192358e19bd7..95a2402f5e385fc21c7be9e0725cf64eb4a079a5 100644
--- a/components/ServerDbTable.vue
+++ b/components/ServerDbTable.vue
@@ -1,5 +1,6 @@
<script setup lang="ts">
// import type { FacetDistribution } from "meilisearch";
+import { useCsvDownload } from "@/composables/useCsvDownload"
import { useSlots } from 'vue'
import { useDisplay } from "vuetify";
import * as Plot from "@observablehq/plot";
@@ -7,6 +8,8 @@ import PlotFigure from "~/components/PlotFigure";
import * as d3 from "d3";
import { useThrottleFn } from '@vueuse/core'
import { useMeiliSearch } from "#imports"
+// import { saveAs } from "file-saver";
+import { useFileSystemAccess } from '@vueuse/core'
export interface SortItem {
key: string,
order: boolean | 'asc' | 'desc'
@@ -18,6 +21,7 @@ export interface Props {
sortBy?: SortItem[]
facets: MaybeRef<string[]>
dataTableServerProps: Record<string, any>
+ columnsToDownload: MaybeRef<string[]>
}
export interface FilterItem {
@@ -51,18 +55,16 @@ const msFilter: Ref<string | undefined> = ref(undefined)
const page = ref(1)
let loading = ref(false)
const expanded = ref([])
-const { height } = useDisplay();
+const { height, mobile } = useDisplay();
const minTableHeight = ref(400)
const computedTableHeight = computed(() => {
const computedHeight = height.value - 350
return computedHeight > minTableHeight.value ? computedHeight : minTableHeight.value
})
const plddtRange = ref([0, 100])
-
-// const { pending: pendingDownloadData, downloadCsv } = useCsvDownload(props.db, `df-${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 +72,6 @@ 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)
})
@@ -314,48 +298,29 @@ 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>
- <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-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>
@@ -371,11 +336,43 @@ function clearSearch() {
</v-col>
</v-row>
</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"
+ @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-toolbar>
+ </template>
+
<template v-for="(slot, index) of Object.keys(slots)" :key="index" v-slot:[slot]="data">
<slot :name="slot" v-bind="data"></slot>
</template>
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 5cbd960233f326669e60178dc5728741b6d36a8e..0c54ce0fad12b0a1daadc64874b65a7f6daded89 100644
--- a/components/content/StructureDb.vue
+++ b/components/content/StructureDb.vue
@@ -83,13 +83,13 @@ function remove(key) {
<ServerDbTable title="Predicted Structures" db="structure" :sortBy="sortBy" :facets="facets"
:data-table-server-props="dataTableServerProps">
- <template #top>
+ <!-- <template #top>
<v-toolbar><v-toolbar-title class="text-capitalize">
Predicted Structures
</v-toolbar-title><v-spacer></v-spacer>
</v-toolbar>
- </template>
+ </template> -->
<template #[`item.proteins_in_the_prediction`]="{ item }">
<CollapsibleChips :items="namesToCollapsibleChips(item.proteins_in_the_prediction, item.fasta_file)">
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/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/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/package-lock.json b/package-lock.json
index db81ba7dee9d57a906c9b44fd256bcc57aa1be44..4796f6d6d72f6920cc876d96509f496ae7876f09 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",
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..eb98e990dd938f46f00d6af48b977d6490045161 100644
--- a/packages/df-wiki-cli/df_wiki_cli/meilisearch/__init__.py
+++ b/packages/df-wiki-cli/df_wiki_cli/meilisearch/__init__.py
@@ -193,7 +193,7 @@ 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,