From 9454e8fc5cf6120e134f1b22e1abf75d5a9a0659 Mon Sep 17 00:00:00 2001
From: Remi PLANEL <rplanel@pasteur.fr>
Date: Thu, 11 Apr 2024 19:41:29 +0200
Subject: [PATCH] update
---
components/OperonStructure.vue | 175 ++
components/content/ArticleStructure.vue | 41 +-
.../{pdockqMatrix.vue => PdockqMatrix.vue} | 26 +-
components/content/StructureDb.vue | 16 +-
components/content/SystemOperonStructure.vue | 42 +-
content/3.defense-systems/avs.md | 11 -
content/3.defense-systems/brex.md | 6 +
data/all_predictions_statistics.csv | 3 -
data/all_predictions_statistics.tsv | 3 +
data/all_predictions_statistics_clean.csv | 3 -
package-lock.json | 1421 +++++++++++++++--
.../df-wiki-cli/df_wiki_cli/content/main.py | 51 +-
.../df_wiki_cli/meilisearch/__init__.py | 427 -----
.../df_wiki_cli/meilisearch/main.py | 45 -
.../df_wiki_cli/meilisearch/update/main.py | 56 +-
packages/df-wiki-cli/poetry.lock | 173 +-
packages/df-wiki-cli/pyproject.toml | 1 +
.../scripts/fill-local-meilisearch.sh | 6 +-
types/plot.ts | 15 +
19 files changed, 1777 insertions(+), 744 deletions(-)
create mode 100644 components/OperonStructure.vue
rename components/content/{pdockqMatrix.vue => PdockqMatrix.vue} (84%)
delete mode 100644 data/all_predictions_statistics.csv
create mode 100644 data/all_predictions_statistics.tsv
delete mode 100644 data/all_predictions_statistics_clean.csv
create mode 100644 types/plot.ts
diff --git a/components/OperonStructure.vue b/components/OperonStructure.vue
new file mode 100644
index 00000000..ca56049b
--- /dev/null
+++ b/components/OperonStructure.vue
@@ -0,0 +1,175 @@
+<script setup lang="ts">
+import { useElementSize } from '@vueuse/core'
+import * as d3 from "d3";
+import type { PlotMargin, StructureOperonGene } from "../types/plot";
+
+
+
+interface Props {
+ genes: StructureOperonGene[] | null
+}
+
+const props = withDefaults(defineProps<Props>(), {
+ genes: null
+});
+const height = ref<number>(75)
+const svgRef = ref(null)
+
+
+
+const margin = ref<PlotMargin>({
+ marginTop: 10,
+ marginRight: 0,
+ marginBottom: 20,
+ marginLeft: 0,
+})
+
+const plotHeight = computed(() => {
+ const { marginTop, marginBottom } = toValue(margin)
+ return toValue(height) + marginTop + marginBottom
+})
+
+const xScale = ref(
+ d3.scaleBand().paddingInner(0.1)
+);
+const yScale = ref(d3.scaleBand()
+ .domain(['1'])
+ .range([toValue(margin).marginTop, toValue(height)]));
+const gbContainer = ref(null)
+const gbContainerWidth = ref(useElementSize(gbContainer, { width: 500, height: 0 }, { box: 'border-box' }).width)
+
+const computedWidth = computed(() => {
+ return gbContainerWidth.value
+})
+
+
+
+onMounted(() => {
+ draw()
+})
+
+const computedGenes = computed(() => {
+ const genes = toValue(props.genes)
+ if (genes !== null) {
+ return genes.map(d => {
+ return {
+ ...d,
+ }
+ })
+ }
+ else { return [] }
+})
+watch(computedGenes, () => {
+ const genes = toValue(computedGenes)
+ console.log(genes)
+ const domain = genes?.map(d => { return d.gene })
+ console.log(domain)
+ xScale.value.domain(domain)
+ .range([0, computedWidth.value])
+})
+
+
+
+const genesWithCoord = computed(() => {
+ const genes = toValue(computedGenes)
+ const xScaleVal = toValue(xScale)
+ const yScaleVal = toValue(yScale)
+ if (genes !== null) {
+ return genes.map(d => {
+ return {
+ ...d,
+ width: xScaleVal.bandwidth(),
+ x: xScaleVal(d.gene),
+ y: yScaleVal('1'),
+ height: yScaleVal.bandwidth()
+ }
+ })
+ }
+ else { return [] }
+})
+
+watch(genesWithCoord, () => {
+ draw()
+})
+
+function createOrSelect(container, tag, selectionClass) {
+ let selection = container.select(`${tag}.${selectionClass}`)
+ if (selection.empty()) {
+ selection = container.append(tag).classed(selectionClass, true)
+ }
+ return selection
+}
+
+function draw() {
+ const svg = d3.select(svgRef.value);
+ const { marginLeft, marginRight } = toValue(margin)
+ const xAxis = d3.axisBottom(xScale.value)
+ const gx = createOrSelect(svg, 'g', 'x-axis')
+
+ gx
+ .attr("transform", `translate(${marginLeft},${toValue(height)})`)
+ .call(xAxis)
+
+ const gxTitle = createOrSelect(gx, "text", "x-axis-title")
+ gxTitle.attr("text-anchor", "end")
+ .attr("fill", "currentColor")
+
+ gxTitle
+ .attr("x", computedWidth.value - marginLeft - marginRight)
+ .attr("y", - 10)
+
+
+ let gGenes = createOrSelect(svg, "g", "genes")
+ gGenes.call(drawGenes, xScale, yScale)
+}
+
+function drawGenes(genesGroup) {
+ console.log(toValue(genesWithCoord))
+ const genesSelection = genesGroup
+ .selectAll("g.gene") // get all "existing" lines in svg
+ .data(toValue(genesWithCoord)) // sync them with our data
+ .join(
+ enter => {
+ const g = enter.append("g")
+ .classed("gene", true);
+ g.append("path").classed("gene", true)
+ g.append("text")
+ // .attr("fill", "white")
+ .classed("gene-label", true)
+ .attr("fill", "currentColor")
+ .attr("dominant-baseline", "middle")
+ g.append("title")
+ return g
+ },
+ update => update,
+ exit => exit.remove()
+ )
+ genesSelection.attr("transform", d => `translate(${d.x},${d.y})`)
+ genesSelection.select("path.gene")
+ .attr("d", d => drawGene(d).toString())
+}
+
+function drawGene({ width, height }) {
+ console.log("dans le draw gene")
+ console.log(width)
+ console.log(height)
+ const context = d3.path()
+ context.moveTo(0, 0)
+ context.lineTo(width, 0)
+ context.lineTo(width, height)
+ context.lineTo(0, height)
+ context.closePath()
+
+ return context
+}
+
+</script>
+<template>
+ <div ref="gbContainer">
+ <v-card flat color="transparent">
+ <svg ref="svgRef" :width="computedWidth" :height="plotHeight">
+ <g class="x-axis" />
+ </svg>
+ </v-card>
+ </div>
+</template>
\ No newline at end of file
diff --git a/components/content/ArticleStructure.vue b/components/content/ArticleStructure.vue
index 76dabe6d..8fb4be2f 100644
--- a/components/content/ArticleStructure.vue
+++ b/components/content/ArticleStructure.vue
@@ -1,6 +1,8 @@
<script setup lang="ts">
import { toValue } from '@vueuse/core';
// import MolstarPdbePlugin from './MolstarPdbePlugin.vue';
+import * as d3 from "d3";
+import SystemOperonStructure from './SystemOperonStructure.vue';
const { page } = useContent();
@@ -14,9 +16,9 @@ const stuctureUrls = ref<string[] | undefined>(undefined)
const headers = ref<Record<string, any>[]>([
{ title: 'Structure', key: 'structure', sortable: false, removable: false, fixed: true, minWidth: "110px" },
- { title: " System", key: "System" },
+ { title: "System", key: "system" },
{ title: "Gene name", key: "gene_name", removable: false },
- { title: "Subtype", key: "subtype", removable: false },
+ { title: "Subtype", key: "subsystem", removable: false },
{ title: "Proteins in structure", key: 'proteins_in_the_prediction', sortable: false, removable: true },
{ title: "System genes", key: "system_genes", sortable: false, removable: true },
{ title: "Prediction type", key: "prediction_type", removable: true },
@@ -27,7 +29,7 @@ const headers = ref<Record<string, any>[]>([
])
const groupBy = ref([
{
- key: 'subtype',
+ key: 'subsystem',
order: 'asc',
},
])
@@ -53,7 +55,7 @@ function pdbNameToCif(pdbPath: string) {
}
function displayStructure(item) {
stuctureUrls.value = item.structuresUrls
- structureTitle.value = `${item.subtype} - ${item.gene_name}`
+ structureTitle.value = `${item.subsystem} - ${item.gene_name}`
}
@@ -64,7 +66,7 @@ const sanitizedStructures = computed(() => {
return toValStructures.hits.map(item => {
return {
- ...item, structuresUrls: [`/${item.System_name_ok}/${pdbNameToCif(item.pdb)}`, `/${item.System_name_ok}/${item.pdb}`]
+ ...item, structuresUrls: [`/${item.system}/${pdbNameToCif(item.pdb)}`, `/${item.system}/${item.pdb}`]
.map(url => {
return toValue(useRefinedUrl(url).refinedUrl)
})
@@ -72,20 +74,28 @@ const sanitizedStructures = computed(() => {
})
}
return []
-
})
+const perSubsystemStructures = computed(() => {
+ const toValStructures = toValue(sanitizedStructures)
+ if (toValStructures?.length > 0) {
+ return d3.groups(toValStructures, d => d.subsystem)
+ }
+ else { return [] }
+})
+
// ==================================================================================
// ASYNC PART
async function fetchStructures() {
+
try {
const d = await client.index(toValue(msIndexName)).search("", {
facets: ["*"],
- filter: [`System='${toValue(computedSystem)}'`, "completed='true'"],
+ filter: [`system='${toValue(computedSystem)}'`, "completed='true'"],
})
structures.value = d
} catch (error) {
@@ -96,14 +106,27 @@ async function fetchStructures() {
</script>
<template>
<v-card flat>
+ <template v-for="[subsystem, structures] in perSubsystemStructures" :key="subsystem[0]">
+ <ProseH3>{{ computedSystem }} - {{ subsystem }}</ProseH3>
+ <v-row align="end">
+ <v-col cols="6">
+ <SystemOperonStructure :system="computedSystem" :subsystem="subsystem" />
+ </v-col>
+ <v-col cols="6">
+ <PdockqMatrix :subsystem="subsystem" />
+ </v-col>
+ </v-row>
+ </template>
+
+ <ProseH3>Summary</ProseH3>
<v-data-table :headers="headers" :items="sanitizedStructures" :group-by="groupBy">
<template #[`item.proteins_in_the_prediction`]="{ item }">
<CollapsibleChips
- :items="namesToCollapsibleChips(item.proteins_in_the_prediction, item.System_name_ok, item.fasta_file)">
+ :items="namesToCollapsibleChips(item.proteins_in_the_prediction, item.system, item.fasta_file)">
</CollapsibleChips>
</template>
<template #[`item.system_genes`]="{ item }">
- <CollapsibleChips :items="namesToCollapsibleChips(item.system_genes, item.System_name_ok)">
+ <CollapsibleChips :items="namesToCollapsibleChips(item.system_genes, item.system)">
</CollapsibleChips>
</template>
diff --git a/components/content/pdockqMatrix.vue b/components/content/PdockqMatrix.vue
similarity index 84%
rename from components/content/pdockqMatrix.vue
rename to components/content/PdockqMatrix.vue
index a76433c7..c03dce96 100644
--- a/components/content/pdockqMatrix.vue
+++ b/components/content/PdockqMatrix.vue
@@ -7,10 +7,12 @@ import type { SearchResponse } from 'meilisearch'
import { useRefinedUrl } from "@/composables/useRefinedUrl"
import { useDisplay } from "vuetify";
-
-
+interface Props {
+ subsystem: string
+}
+const { subsystem } = withDefaults(defineProps<Props>(), {
+});
const { mobile } = useDisplay();
-
const { page } = useContent();
const dbName = "structure"
const filterBase = ref<string[]>([
@@ -19,6 +21,7 @@ const filterBase = ref<string[]>([
])
const structureTitle = ref("Structure")
const structureUrls = ref<string[] | undefined>(undefined)
+const matrixElemSize = ref(50)
export interface PlotMargin {
marginTop: number,
@@ -42,7 +45,7 @@ onMounted(async () => {
const d = await client.index(toValue(dbName)).search("", {
facets: ["*"],
filter: [
- `System='${toValue(computedSystem)}'`,
+ `system='${toValue(computedSystem)}' AND subsystem='${subsystem}'`,
...toValue(filterBase)
],
})
@@ -70,7 +73,7 @@ const groupedPdocks = computed(() => {
}
}
if (toValData?.hits) {
- return d3.groups(toValData.hits.flatMap(({ System_name_ok, pDockQ, pdb, nb_sys, proteins_in_the_prediction, system_genes }) => {
+ return d3.groups(toValData.hits.flatMap(({ system, pDockQ, pdb, nb_sys, proteins_in_the_prediction, system_genes }) => {
if (proteins_in_the_prediction.length === 2) {
const sanitizedSystemGenes = system_genes.map(getSeqName)
const sanitizedProteins = proteins_in_the_prediction.map(getSeqName)
@@ -79,15 +82,15 @@ const groupedPdocks = computed(() => {
if (setProteins.size === 2) {
return sanitizedProteins.map((prot, i) => {
if (i === 0) {
- return { key, System_name_ok, system_genes: sanitizedSystemGenes, pDockQ, pdb, nb_sys, proteins_in_the_prediction: sanitizedProteins, protX: prot, protY: sanitizedProteins[i + 1] }
+ return { key, system, system_genes: sanitizedSystemGenes, pDockQ, pdb, nb_sys, proteins_in_the_prediction: sanitizedProteins, protX: prot, protY: sanitizedProteins[i + 1] }
}
else {
- return { key, System_name_ok, system_genes: sanitizedSystemGenes, pDockQ, pdb, nb_sys, proteins_in_the_prediction: sanitizedProteins, protX: prot, protY: sanitizedProteins[i - 1] }
+ return { key, system, system_genes: sanitizedSystemGenes, pDockQ, pdb, nb_sys, proteins_in_the_prediction: sanitizedProteins, protX: prot, protY: sanitizedProteins[i - 1] }
}
})
} else {
- return { key, System_name_ok, system_genes: sanitizedSystemGenes, pDockQ, pdb, nb_sys, proteins_in_the_prediction: sanitizedProteins, protX: sanitizedProteins[0], protY: sanitizedProteins[1] }
+ return { key, system, system_genes: sanitizedSystemGenes, pDockQ, pdb, nb_sys, proteins_in_the_prediction: sanitizedProteins, protX: sanitizedProteins[0], protY: sanitizedProteins[1] }
}
} else {
throw createError(`More than 2 proteins in a dimer structure for system ${computedSystem.value} !`)
@@ -102,11 +105,12 @@ const computedPDocksMatrixPlotOptions = computed(() => {
const range = domain.map(d => {
return d3.interpolatePlasma(scaleLinear(d))
})
+ const matrixElemSizeVal = toValue(matrixElemSize)
const { marginBottom, marginLeft, marginRight, marginTop } = toValue(margin)
return toValue(groupedPdocks).map((matrix) => {
return {
- width: matrix[1][0].system_genes.length * 75 + marginLeft + marginRight,
- height: matrix[1][0].system_genes.length * 75 + marginTop + marginBottom,
+ width: matrix[1][0].system_genes.length * matrixElemSizeVal + marginLeft + marginRight,
+ height: matrix[1][0].system_genes.length * matrixElemSizeVal + marginTop + marginBottom,
title: matrix[0],
padding: 0,
marginTop,
@@ -175,7 +179,7 @@ function pdbNameToCif(pdbPath: string) {
return `${cifPath}.cif`
}
function buildStructureUrl(item) {
- return [`/${item.System_name_ok}/${pdbNameToCif(item.pdb)}`, `/${item.System_name_ok}/${item.pdb}`]
+ return [`/${item.system}/${pdbNameToCif(item.pdb)}`, `/${item.system}/${item.pdb}`]
}
function displayStructure(item) {
diff --git a/components/content/StructureDb.vue b/components/content/StructureDb.vue
index 28232eb7..86b68c47 100644
--- a/components/content/StructureDb.vue
+++ b/components/content/StructureDb.vue
@@ -8,7 +8,7 @@ import { withQuery, joinURL, withTrailingSlash } from 'ufo'
interface Item {
Foldseek_name: string
- System_name_ok: string
+ system: string
}
@@ -132,7 +132,7 @@ const dataTableServerProps = computed(() => {
function toFolseekUrl(item: Item) {
- const url = joinURL("/" + item.System_name_ok, item.Foldseek_name)
+ const url = joinURL("/" + item.system, item.Foldseek_name)
const { refinedUrl } = useRefinedUrl(url)
return toValue(refinedUrl)
}
@@ -153,7 +153,7 @@ function pdbNameToCif(pdbPath: string) {
function buildStructureUrl(item) {
- return [`/${item.System_name_ok}/${pdbNameToCif(item.pdb)}`, `/${item.System_name_ok}/${item.pdb}`]
+ return [`/${item.system}/${pdbNameToCif(item.pdb)}`, `/${item.system}/${item.pdb}`]
}
function displayStructure(item) {
@@ -237,11 +237,11 @@ const { refinedUrl: downloadAllCifUrl } = useRefinedUrl("/df-all-cifs.tar.gz")
</template>
<template #[`item.proteins_in_the_prediction`]="{ item }">
<CollapsibleChips
- :items="namesToCollapsibleChips(item.proteins_in_the_prediction, item.System_name_ok, item.fasta_file)">
+ :items="namesToCollapsibleChips(item.proteins_in_the_prediction, item.system, item.fasta_file)">
</CollapsibleChips>
</template>
<template #[`item.system_genes`]="{ item }">
- <CollapsibleChips :items="namesToCollapsibleChips(item.system_genes, item.System_name_ok)">
+ <CollapsibleChips :items="namesToCollapsibleChips(item.system_genes, item.system)">
</CollapsibleChips>
</template>
<template #[`item.structure`]="{ item }">
@@ -265,12 +265,6 @@ const { refinedUrl: downloadAllCifUrl } = useRefinedUrl("/df-all-cifs.tar.gz")
</v-menu>
</v-col>
</v-row>
- <!-- <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> -->
</template>
<template #[`item.completed`]="{ item }">
<v-icon v-if="item.completed" color="success" icon="md:check"></v-icon>
diff --git a/components/content/SystemOperonStructure.vue b/components/content/SystemOperonStructure.vue
index bfa0430b..2a5004a4 100644
--- a/components/content/SystemOperonStructure.vue
+++ b/components/content/SystemOperonStructure.vue
@@ -1,28 +1,27 @@
<script setup lang="ts">
-import * as d3 from "d3";
+import type { StructureOperonGene } from "../../types/plot";
+import type { SearchResponse } from "meilisearch";
+
+interface Props {
+ system: string
+ subsystem: string
+}
+
+
+const { system, subsystem } = withDefaults(defineProps<Props>(), {
+});
const client = useMeiliSearchRef()
-const { page } = useContent();
const pending = ref<boolean>(false)
const msIndexName = ref<'systemoperonstruct'>("systemoperonstruct")
-const msResponse = ref()
-const systemName = computed(() => {
- const toValPage = toValue(page)
- return toValPage?.system ?? toValPage?.title ?? undefined
-})
+const msResponse = ref<SearchResponse<StructureOperonGene> | undefined>(undefined)
-const systemGroupedBySubtype = computed(() => {
- return d3.groups(sanitizedHits.value, d => d.subsystem)
-})
-
const sanitizedHits = computed(() => {
const toValMsResponse = toValue(msResponse)
- console.log(toValMsResponse)
- if (toValMsResponse?.hits?.length > 0) {
+ if (toValMsResponse && toValMsResponse?.hits?.length > 0) {
return toValMsResponse.hits.map(hit => {
- console.log(hit)
return { ...hit, gene: hit.gene.split("__")[1] }
})
} else {
@@ -38,32 +37,25 @@ onMounted(() => {
async function fetchOperonStructure() {
try {
pending.value = true
- const data = await client.index(toValue(msIndexName)).search("", {
+ const data = await client.index(toValue(msIndexName)).search<StructureOperonGene>("", {
facets: ["*"],
- filter: [`system = '${toValue(systemName)}'`],
+ filter: [`system='${system}' AND subsystem='${subsystem}'`],
limit: 500000,
})
msResponse.value = data
} catch (error) {
- throw createError(`Cannot get hits on refseq for system: ${toValue(systemName)} `)
+ throw createError(`Cannot get hits on refseq for system: ${system} `)
} finally {
pending.value = false
}
}
-
-
-
-
</script>
<template>
<v-card flat>
- <v-list-item v-for="s in sanitizedHits" :key="s.id">
- {{ s.gene }} - {{ s.subsystem }}
- </v-list-item>
- <pre>{{ systemGroupedBySubtype }}</pre>
+ <OperonStructure :genes="sanitizedHits" />
</v-card>
</template>
\ No newline at end of file
diff --git a/content/3.defense-systems/avs.md b/content/3.defense-systems/avs.md
index 479c6527..f18121d5 100644
--- a/content/3.defense-systems/avs.md
+++ b/content/3.defense-systems/avs.md
@@ -79,17 +79,6 @@ Proportion of genome encoding the Avs system for the 14 phyla with more than 50
## Structure
-::system-operon-structure
-::
-
-
-### matrix
-
-::pdockq-matrix
-::
-
-### List
-
::article-structure
::
diff --git a/content/3.defense-systems/brex.md b/content/3.defense-systems/brex.md
index 4b7c3d7d..015028c9 100644
--- a/content/3.defense-systems/brex.md
+++ b/content/3.defense-systems/brex.md
@@ -86,6 +86,12 @@ Proportion of genome encoding the BREX system for the 14 phyla with more than 50
## Structure
+
+
+::article-structure
+::
+
+
### BREX_II
##### Example 1
diff --git a/data/all_predictions_statistics.csv b/data/all_predictions_statistics.csv
deleted file mode 100644
index 7403c25d..00000000
--- a/data/all_predictions_statistics.csv
+++ /dev/null
@@ -1,3 +0,0 @@
-version https://git-lfs.github.com/spec/v1
-oid sha256:e94119ef1fa73e1b0d2da1e070f27d1576901f53504e7b4c0f6aa2532762dc1b
-size 556202
diff --git a/data/all_predictions_statistics.tsv b/data/all_predictions_statistics.tsv
new file mode 100644
index 00000000..08320223
--- /dev/null
+++ b/data/all_predictions_statistics.tsv
@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:eade182c1e7173dfe7f63bfce768d38a050377d221bc91d08c1c2371a5f3a3d4
+size 547149
diff --git a/data/all_predictions_statistics_clean.csv b/data/all_predictions_statistics_clean.csv
deleted file mode 100644
index 8ade3e63..00000000
--- a/data/all_predictions_statistics_clean.csv
+++ /dev/null
@@ -1,3 +0,0 @@
-version https://git-lfs.github.com/spec/v1
-oid sha256:09bae9951cf2a86917f3a65ebd9bc2eb1e37c7fd342104b4442076aacb68a133
-size 593832
diff --git a/package-lock.json b/package-lock.json
index 1808619b..88c9197d 100644
--- a/package-lock.json
+++ b/package-lock.json
@@ -16,6 +16,7 @@
"yaml": "^2.3.3"
},
"devDependencies": {
+ "@antfu/eslint-config": "^2.12.2",
"@iconify-json/game-icons": "^1.1.7",
"@iconify-json/gravity-ui": "^1.1.1",
"@iconify-json/material-symbols": "^1.1.69",
@@ -29,11 +30,13 @@
"@nuxtjs/seo": "^2.0.0-rc.9",
"@types/d3": "^7.4.3",
"@types/node": "^20.11.0",
+ "@unocss/eslint-plugin": "^0.59.0",
"@unocss/nuxt": "^0.58.3",
"@unocss/preset-icons": "^0.58.3",
"@vueuse/core": "^10.7.1",
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"node": ">=6.0.0"
}
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+ "vue-eslint-parser": "^9.4.2",
+ "yaml-eslint-parser": "^1.2.2",
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+ "bin": {
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+ },
+ "funding": {
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+ },
+ "peerDependencies": {
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+ "eslint-plugin-astro": {
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+ "eslint-plugin-react": {
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+ "eslint-plugin-react-hooks": {
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+ "eslint-plugin-react-refresh": {
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+ "eslint-plugin-solid": {
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+ "eslint-plugin-svelte": {
+ "optional": true
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+ "prettier-plugin-astro": {
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+ "prettier-plugin-slidev": {
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+ "svelte-eslint-parser": {
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+ "dev": true,
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+ "funding": {
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+ "dev": true,
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+ "is-stream": "^3.0.0",
+ "merge-stream": "^2.0.0",
+ "npm-run-path": "^5.1.0",
+ "onetime": "^6.0.0",
+ "signal-exit": "^4.1.0",
+ "strip-final-newline": "^3.0.0"
+ },
+ "engines": {
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+ },
+ "funding": {
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+ }
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+ "node_modules/@antfu/eslint-config/node_modules/get-stream": {
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+ "resolved": "https://registry.npmjs.org/get-stream/-/get-stream-8.0.1.tgz",
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+ "dev": true,
+ "engines": {
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+ "funding": {
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+ }
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+ "node_modules/@antfu/eslint-config/node_modules/human-signals": {
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+ "resolved": "https://registry.npmjs.org/human-signals/-/human-signals-5.0.0.tgz",
+ "integrity": "sha512-AXcZb6vzzrFAUE61HnN4mpLqd/cSIwNQjtNWR0euPm6y0iqx3G4gOXaIDdtdDwZmhwe82LA6+zinmW4UBWVePQ==",
+ "dev": true,
+ "engines": {
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+ }
+ },
+ "node_modules/@antfu/eslint-config/node_modules/signal-exit": {
+ "version": "4.1.0",
+ "resolved": "https://registry.npmjs.org/signal-exit/-/signal-exit-4.1.0.tgz",
+ "integrity": "sha512-bzyZ1e88w9O1iNJbKnOlvYTrWPDl46O1bG0D3XInv+9tkPrxrN8jUUTiFlDkkmKWgn1M6CfIA13SuGqOa9Korw==",
+ "dev": true,
+ "engines": {
+ "node": ">=14"
+ },
+ "funding": {
+ "url": "https://github.com/sponsors/isaacs"
+ }
+ },
"node_modules/@antfu/install-pkg": {
"version": "0.1.1",
"resolved": "https://registry.npmjs.org/@antfu/install-pkg/-/install-pkg-0.1.1.tgz",
@@ -1088,6 +1259,43 @@
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},
+ "node_modules/@clack/core": {
+ "version": "0.3.4",
+ "resolved": "https://registry.npmjs.org/@clack/core/-/core-0.3.4.tgz",
+ "integrity": "sha512-H4hxZDXgHtWTwV3RAVenqcC4VbJZNegbBjlPvzOzCouXtS2y3sDvlO3IsbrPNWuLWPPlYVYPghQdSF64683Ldw==",
+ "dev": true,
+ "dependencies": {
+ "picocolors": "^1.0.0",
+ "sisteransi": "^1.0.5"
+ }
+ },
+ "node_modules/@clack/prompts": {
+ "version": "0.7.0",
+ "resolved": "https://registry.npmjs.org/@clack/prompts/-/prompts-0.7.0.tgz",
+ "integrity": "sha512-0MhX9/B4iL6Re04jPrttDm+BsP8y6mS7byuv0BvXgdXhbV5PdlsHt55dvNsuBCPZ7xq1oTAOOuotR9NFbQyMSA==",
+ "bundleDependencies": [
+ "is-unicode-supported"
+ ],
+ "dev": true,
+ "dependencies": {
+ "@clack/core": "^0.3.3",
+ "is-unicode-supported": "*",
+ "picocolors": "^1.0.0",
+ "sisteransi": "^1.0.5"
+ }
+ },
+ "node_modules/@clack/prompts/node_modules/is-unicode-supported": {
+ "version": "1.3.0",
+ "dev": true,
+ "inBundle": true,
+ "license": "MIT",
+ "engines": {
+ "node": ">=12"
+ },
+ "funding": {
+ "url": "https://github.com/sponsors/sindresorhus"
+ }
+ },
"node_modules/@cloudflare/kv-asset-handler": {
"version": "0.3.1",
"resolved": "https://registry.npmjs.org/@cloudflare/kv-asset-handler/-/kv-asset-handler-0.3.1.tgz",
@@ -1392,6 +1600,24 @@
"node": ">= 10"
}
},
+ "node_modules/@dprint/formatter": {
+ "version": "0.2.1",
+ "resolved": "https://registry.npmjs.org/@dprint/formatter/-/formatter-0.2.1.tgz",
+ "integrity": "sha512-GCzgRt2o4mhZLy8L47k2A+q9EMG/jWhzZebE29EqKsxmjDrSfv2VisEj/Q+39OOf04jTkEfB/TRO+IZSyxHdYg==",
+ "dev": true
+ },
+ "node_modules/@dprint/markdown": {
+ "version": "0.16.4",
+ "resolved": "https://registry.npmjs.org/@dprint/markdown/-/markdown-0.16.4.tgz",
+ "integrity": "sha512-WjsC4yLybR5/76+d/2s36nOBGjETe+jJR//ddFHohDXKdis+FTUv7dJ00kmd6g0AKQwDITayM1Nid10gFNG0Yg==",
+ "dev": true
+ },
+ "node_modules/@dprint/toml": {
+ "version": "0.5.4",
+ "resolved": "https://registry.npmjs.org/@dprint/toml/-/toml-0.5.4.tgz",
+ "integrity": "sha512-d+5GwwzztZD0QixmOBhaO6nWVLsAeYsJ1HJYNxDoDRbASFCpza9BBVshG5ctBRXCkkIHhD9BO1SnbOoRQltUQw==",
+ "dev": true
+ },
"node_modules/@es-joy/jsdoccomment": {
"version": "0.42.0",
"resolved": "https://registry.npmjs.org/@es-joy/jsdoccomment/-/jsdoccomment-0.42.0.tgz",
@@ -3613,6 +3839,18 @@
"node": ">=14"
}
},
+ "node_modules/@pkgr/core": {
+ "version": "0.1.1",
+ "resolved": "https://registry.npmjs.org/@pkgr/core/-/core-0.1.1.tgz",
+ "integrity": "sha512-cq8o4cWH0ibXh9VGi5P20Tu9XF/0fFXl9EUinr9QfTM7a7p0oTA4iJRCQWppXR1Pg8dSM0UCItCkPwsk9qWWYA==",
+ "dev": true,
+ "engines": {
+ "node": "^12.20.0 || ^14.18.0 || >=16.0.0"
+ },
+ "funding": {
+ "url": "https://opencollective.com/unts"
+ }
+ },
"node_modules/@polka/url": {
"version": "1.0.0-next.25",
"resolved": "https://registry.npmjs.org/@polka/url/-/url-1.0.0-next.25.tgz",
@@ -4060,6 +4298,7 @@
"cpu": [
"arm"
],
+ "dev": true,
"optional": true,
"os": [
"android"
@@ -4072,6 +4311,7 @@
"cpu": [
"arm64"
],
+ "dev": true,
"optional": true,
"os": [
"android"
@@ -4084,6 +4324,7 @@
"cpu": [
"arm64"
],
+ "dev": true,
"optional": true,
"os": [
"darwin"
@@ -4096,6 +4337,7 @@
"cpu": [
"x64"
],
+ "dev": true,
"optional": true,
"os": [
"darwin"
@@ -4108,6 +4350,7 @@
"cpu": [
"arm"
],
+ "dev": true,
"optional": true,
"os": [
"linux"
@@ -4120,6 +4363,7 @@
"cpu": [
"arm64"
],
+ "dev": true,
"optional": true,
"os": [
"linux"
@@ -4132,6 +4376,7 @@
"cpu": [
"arm64"
],
+ "dev": true,
"optional": true,
"os": [
"linux"
@@ -4144,6 +4389,7 @@
"cpu": [
"ppc64le"
],
+ "dev": true,
"optional": true,
"os": [
"linux"
@@ -4156,6 +4402,7 @@
"cpu": [
"riscv64"
],
+ "dev": true,
"optional": true,
"os": [
"linux"
@@ -4168,6 +4415,7 @@
"cpu": [
"s390x"
],
+ "dev": true,
"optional": true,
"os": [
"linux"
@@ -4180,6 +4428,7 @@
"cpu": [
"x64"
],
+ "dev": true,
"optional": true,
"os": [
"linux"
@@ -4192,6 +4441,7 @@
"cpu": [
"x64"
],
+ "dev": true,
"optional": true,
"os": [
"linux"
@@ -4204,6 +4454,7 @@
"cpu": [
"arm64"
],
+ "dev": true,
"optional": true,
"os": [
"win32"
@@ -4216,6 +4467,7 @@
"cpu": [
"ia32"
],
+ "dev": true,
"optional": true,
"os": [
"win32"
@@ -4228,6 +4480,7 @@
"cpu": [
"x64"
],
+ "dev": true,
"optional": true,
"os": [
"win32"
@@ -5174,22 +5427,22 @@
"dev": true
},
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- "integrity": "sha512-HpqNTH8Du34nLxbKgVMGljZMG0rJd2O9ecvr2QLYp+7512ty1j42KnsFwspPXg1Vh8an9YImf6CokUBltisZFQ==",
+ "version": "7.6.0",
+ "resolved": "https://registry.npmjs.org/@typescript-eslint/eslint-plugin/-/eslint-plugin-7.6.0.tgz",
+ "integrity": "sha512-gKmTNwZnblUdnTIJu3e9kmeRRzV2j1a/LUO27KNNAnIC5zjy1aSvXSRp4rVNlmAoHlQ7HzX42NbKpcSr4jF80A==",
"dev": true,
"dependencies": {
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- "@typescript-eslint/scope-manager": "7.5.0",
- "@typescript-eslint/type-utils": "7.5.0",
- "@typescript-eslint/utils": "7.5.0",
- "@typescript-eslint/visitor-keys": "7.5.0",
+ "@eslint-community/regexpp": "^4.10.0",
+ "@typescript-eslint/scope-manager": "7.6.0",
+ "@typescript-eslint/type-utils": "7.6.0",
+ "@typescript-eslint/utils": "7.6.0",
+ "@typescript-eslint/visitor-keys": "7.6.0",
"debug": "^4.3.4",
"graphemer": "^1.4.0",
- "ignore": "^5.2.4",
+ "ignore": "^5.3.1",
"natural-compare": "^1.4.0",
- "semver": "^7.5.4",
- "ts-api-utils": "^1.0.1"
+ "semver": "^7.6.0",
+ "ts-api-utils": "^1.3.0"
},
"engines": {
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@@ -5209,15 +5462,15 @@
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- "integrity": "sha512-cj+XGhNujfD2/wzR1tabNsidnYRaFfEkcULdcIyVBYcXjBvBKOes+mpMBP7hMpOyk+gBcfXsrg4NBGAStQyxjQ==",
+ "version": "7.6.0",
+ "resolved": "https://registry.npmjs.org/@typescript-eslint/parser/-/parser-7.6.0.tgz",
+ "integrity": "sha512-usPMPHcwX3ZoPWnBnhhorc14NJw9J4HpSXQX4urF2TPKG0au0XhJoZyX62fmvdHONUkmyUe74Hzm1//XA+BoYg==",
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- "@typescript-eslint/typescript-estree": "7.5.0",
- "@typescript-eslint/visitor-keys": "7.5.0",
+ "@typescript-eslint/scope-manager": "7.6.0",
+ "@typescript-eslint/types": "7.6.0",
+ "@typescript-eslint/typescript-estree": "7.6.0",
+ "@typescript-eslint/visitor-keys": "7.6.0",
"debug": "^4.3.4"
},
"engines": {
@@ -5236,15 +5489,41 @@
}
}
},
+ "node_modules/@typescript-eslint/parser/node_modules/@typescript-eslint/types": {
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+ "resolved": "https://registry.npmjs.org/@typescript-eslint/types/-/types-7.6.0.tgz",
+ "integrity": "sha512-h02rYQn8J+MureCvHVVzhl69/GAfQGPQZmOMjG1KfCl7o3HtMSlPaPUAPu6lLctXI5ySRGIYk94clD/AUMCUgQ==",
+ "dev": true,
+ "engines": {
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+ },
+ "funding": {
+ "type": "opencollective",
+ "url": "https://opencollective.com/typescript-eslint"
+ }
+ },
"node_modules/@typescript-eslint/scope-manager": {
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- "resolved": "https://registry.npmjs.org/@typescript-eslint/scope-manager/-/scope-manager-7.5.0.tgz",
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+ "version": "7.6.0",
+ "resolved": "https://registry.npmjs.org/@typescript-eslint/scope-manager/-/scope-manager-7.6.0.tgz",
+ "integrity": "sha512-ngttyfExA5PsHSx0rdFgnADMYQi+Zkeiv4/ZxGYUWd0nLs63Ha0ksmp8VMxAIC0wtCFxMos7Lt3PszJssG/E6w==",
"dev": true,
"dependencies": {
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- "@typescript-eslint/visitor-keys": "7.5.0"
+ "@typescript-eslint/types": "7.6.0",
+ "@typescript-eslint/visitor-keys": "7.6.0"
+ },
+ "engines": {
+ "node": "^18.18.0 || >=20.0.0"
},
+ "funding": {
+ "type": "opencollective",
+ "url": "https://opencollective.com/typescript-eslint"
+ }
+ },
+ "node_modules/@typescript-eslint/scope-manager/node_modules/@typescript-eslint/types": {
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+ "resolved": "https://registry.npmjs.org/@typescript-eslint/types/-/types-7.6.0.tgz",
+ "integrity": "sha512-h02rYQn8J+MureCvHVVzhl69/GAfQGPQZmOMjG1KfCl7o3HtMSlPaPUAPu6lLctXI5ySRGIYk94clD/AUMCUgQ==",
+ "dev": true,
"engines": {
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@@ -5254,15 +5533,15 @@
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+ "version": "7.6.0",
+ "resolved": "https://registry.npmjs.org/@typescript-eslint/type-utils/-/type-utils-7.6.0.tgz",
+ "integrity": "sha512-NxAfqAPNLG6LTmy7uZgpK8KcuiS2NZD/HlThPXQRGwz6u7MDBWRVliEEl1Gj6U7++kVJTpehkhZzCJLMK66Scw==",
"dev": true,
"dependencies": {
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- "@typescript-eslint/utils": "7.5.0",
+ "@typescript-eslint/typescript-estree": "7.6.0",
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"debug": "^4.3.4",
- "ts-api-utils": "^1.0.1"
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@@ -5294,19 +5573,19 @@
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+ "version": "7.6.0",
+ "resolved": "https://registry.npmjs.org/@typescript-eslint/typescript-estree/-/typescript-estree-7.6.0.tgz",
+ "integrity": "sha512-+7Y/GP9VuYibecrCQWSKgl3GvUM5cILRttpWtnAu8GNL9j11e4tbuGZmZjJ8ejnKYyBRb2ddGQ3rEFCq3QjMJw==",
"dev": true,
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- "@typescript-eslint/visitor-keys": "7.5.0",
+ "@typescript-eslint/types": "7.6.0",
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+ "node_modules/eslint-plugin-perfectionist/node_modules/slash": {
+ "version": "3.0.0",
+ "resolved": "https://registry.npmjs.org/slash/-/slash-3.0.0.tgz",
+ "integrity": "sha512-g9Q1haeby36OSStwb4ntCGGGaKsaVSjQ68fBxoQcutl5fS1vuY18H3wSt3jFyFtrkx+Kz0V1G85A4MyAdDMi2Q==",
"dev": true,
- "dependencies": {
- "@typescript-eslint/utils": "^7.4.0",
- "debug": "^4.3.4",
- "doctrine": "^3.0.0",
- "eslint-import-resolver-node": "^0.3.9",
- "get-tsconfig": "^4.7.3",
- "is-glob": "^4.0.3",
- "minimatch": "^9.0.3",
- "semver": "^7.6.0"
- },
"engines": {
- "node": ">=16"
- },
- "peerDependencies": {
- "eslint": "^8.56.0 || ^9.0.0-0"
+ "node": ">=8"
}
},
- "node_modules/eslint-plugin-jsdoc": {
- "version": "48.2.3",
- "resolved": "https://registry.npmjs.org/eslint-plugin-jsdoc/-/eslint-plugin-jsdoc-48.2.3.tgz",
- "integrity": "sha512-r9DMAmFs66VNvNqRLLjHejdnJtILrt3xGi+Qx0op0oRfFGVpOR1Hb3BC++MacseHx93d8SKYPhyrC9BS7Os2QA==",
+ "node_modules/eslint-plugin-toml": {
+ "version": "0.11.0",
+ "resolved": "https://registry.npmjs.org/eslint-plugin-toml/-/eslint-plugin-toml-0.11.0.tgz",
+ "integrity": "sha512-sau+YvPU4fWTjB+qtBt3n8WS87aoDCs+BVbSUAemGaIsRNbvR9uEk+Tt892iLHTGvp/DPWYoCX4/8DoyAbB+sQ==",
"dev": true,
"dependencies": {
- "@es-joy/jsdoccomment": "~0.42.0",
- "are-docs-informative": "^0.0.2",
- "comment-parser": "1.4.1",
- "debug": "^4.3.4",
- "escape-string-regexp": "^4.0.0",
- "esquery": "^1.5.0",
- "is-builtin-module": "^3.2.1",
- "semver": "^7.6.0",
- "spdx-expression-parse": "^4.0.0"
+ "debug": "^4.1.1",
+ "eslint-compat-utils": "^0.5.0",
+ "lodash": "^4.17.19",
+ "toml-eslint-parser": "^0.9.0"
},
"engines": {
- "node": ">=18"
+ "node": "^12.22.0 || ^14.17.0 || >=16.0.0"
+ },
+ "funding": {
+ "url": "https://github.com/sponsors/ota-meshi"
},
"peerDependencies": {
- "eslint": "^7.0.0 || ^8.0.0 || ^9.0.0"
+ "eslint": ">=6.0.0"
}
},
"node_modules/eslint-plugin-unicorn": {
@@ -9580,10 +10533,55 @@
"eslint": ">=8.56.0"
}
},
+ "node_modules/eslint-plugin-unused-imports": {
+ "version": "3.1.0",
+ "resolved": "https://registry.npmjs.org/eslint-plugin-unused-imports/-/eslint-plugin-unused-imports-3.1.0.tgz",
+ "integrity": "sha512-9l1YFCzXKkw1qtAru1RWUtG2EVDZY0a0eChKXcL+EZ5jitG7qxdctu4RnvhOJHv4xfmUf7h+JJPINlVpGhZMrw==",
+ "dev": true,
+ "dependencies": {
+ "eslint-rule-composer": "^0.3.0"
+ },
+ "engines": {
+ "node": "^12.22.0 || ^14.17.0 || >=16.0.0"
+ },
+ "peerDependencies": {
+ "@typescript-eslint/eslint-plugin": "6 - 7",
+ "eslint": "8"
+ },
+ "peerDependenciesMeta": {
+ "@typescript-eslint/eslint-plugin": {
+ "optional": true
+ }
+ }
+ },
+ "node_modules/eslint-plugin-vitest": {
+ "version": "0.5.1",
+ "resolved": "https://registry.npmjs.org/eslint-plugin-vitest/-/eslint-plugin-vitest-0.5.1.tgz",
+ "integrity": "sha512-g137wC+LCq2N+tfqK39Nl6Rs2N9u+zu6lWxaVgpN3wX+Kq6zSyxjPSI/ZBXUjP+qandT3z1DM5wK5IjD4XrAIw==",
+ "dev": true,
+ "dependencies": {
+ "@typescript-eslint/utils": "^7.6.0"
+ },
+ "engines": {
+ "node": "^18.0.0 || >= 20.0.0"
+ },
+ "peerDependencies": {
+ "eslint": "^8.57.0 || ^9.0.0",
+ "vitest": "*"
+ },
+ "peerDependenciesMeta": {
+ "@typescript-eslint/eslint-plugin": {
+ "optional": true
+ },
+ "vitest": {
+ "optional": true
+ }
+ }
+ },
"node_modules/eslint-plugin-vue": {
- "version": "9.24.0",
- "resolved": "https://registry.npmjs.org/eslint-plugin-vue/-/eslint-plugin-vue-9.24.0.tgz",
- "integrity": "sha512-9SkJMvF8NGMT9aQCwFc5rj8Wo1XWSMSHk36i7ZwdI614BU7sIOR28ZjuFPKp8YGymZN12BSEbiSwa7qikp+PBw==",
+ "version": "9.24.1",
+ "resolved": "https://registry.npmjs.org/eslint-plugin-vue/-/eslint-plugin-vue-9.24.1.tgz",
+ "integrity": "sha512-wk3SuwmS1pZdcuJlokGYEi/buDOwD6KltvhIZyOnpJ/378dcQ4zchu9PAMbbLAaydCz1iYc5AozszcOOgZIIOg==",
"dev": true,
"dependencies": {
"@eslint-community/eslint-utils": "^4.4.0",
@@ -9599,7 +10597,7 @@
"node": "^14.17.0 || >=16.0.0"
},
"peerDependencies": {
- "eslint": "^6.2.0 || ^7.0.0 || ^8.0.0"
+ "eslint": "^6.2.0 || ^7.0.0 || ^8.0.0 || ^9.0.0"
}
},
"node_modules/eslint-plugin-vue/node_modules/globals": {
@@ -9629,6 +10627,50 @@
"url": "https://github.com/sponsors/sindresorhus"
}
},
+ "node_modules/eslint-plugin-yml": {
+ "version": "1.14.0",
+ "resolved": "https://registry.npmjs.org/eslint-plugin-yml/-/eslint-plugin-yml-1.14.0.tgz",
+ "integrity": "sha512-ESUpgYPOcAYQO9czugcX5OqRvn/ydDVwGCPXY4YjPqc09rHaUVUA6IE6HLQys4rXk/S+qx3EwTd1wHCwam/OWQ==",
+ "dev": true,
+ "dependencies": {
+ "debug": "^4.3.2",
+ "eslint-compat-utils": "^0.5.0",
+ "lodash": "^4.17.21",
+ "natural-compare": "^1.4.0",
+ "yaml-eslint-parser": "^1.2.1"
+ },
+ "engines": {
+ "node": "^14.17.0 || >=16.0.0"
+ },
+ "funding": {
+ "url": "https://github.com/sponsors/ota-meshi"
+ },
+ "peerDependencies": {
+ "eslint": ">=6.0.0"
+ }
+ },
+ "node_modules/eslint-processor-vue-blocks": {
+ "version": "0.1.1",
+ "resolved": "https://registry.npmjs.org/eslint-processor-vue-blocks/-/eslint-processor-vue-blocks-0.1.1.tgz",
+ "integrity": "sha512-9+dU5lU881log570oBwpelaJmOfOzSniben7IWEDRYQPPWwlvaV7NhOtsTuUWDqpYT+dtKKWPsgz4OkOi+aZnA==",
+ "dev": true,
+ "funding": {
+ "url": "https://github.com/sponsors/antfu"
+ },
+ "peerDependencies": {
+ "@vue/compiler-sfc": "^3.3.0",
+ "eslint": "^8.50.0"
+ }
+ },
+ "node_modules/eslint-rule-composer": {
+ "version": "0.3.0",
+ "resolved": "https://registry.npmjs.org/eslint-rule-composer/-/eslint-rule-composer-0.3.0.tgz",
+ "integrity": "sha512-bt+Sh8CtDmn2OajxvNO+BX7Wn4CIWMpTRm3MaiKPCQcnnlm0CS2mhui6QaoeQugs+3Kj2ESKEEGJUdVafwhiCg==",
+ "dev": true,
+ "engines": {
+ "node": ">=4.0.0"
+ }
+ },
"node_modules/eslint-scope": {
"version": "7.2.2",
"resolved": "https://registry.npmjs.org/eslint-scope/-/eslint-scope-7.2.2.tgz",
@@ -10019,6 +11061,12 @@
"integrity": "sha512-f3qQ9oQy9j2AhBe/H9VC91wLmKBCCU/gDOnKNAYG5hswO7BLKj09Hc5HYNz9cGI++xlpDCIgDaitVs03ATR84Q==",
"dev": true
},
+ "node_modules/fast-diff": {
+ "version": "1.3.0",
+ "resolved": "https://registry.npmjs.org/fast-diff/-/fast-diff-1.3.0.tgz",
+ "integrity": "sha512-VxPP4NqbUjj6MaAOafWeUn2cXWLcCtljklUtZf0Ind4XQ+QPtmA0b18zZy0jIQx+ExRVCR/ZQpBmik5lXshNsw==",
+ "dev": true
+ },
"node_modules/fast-fifo": {
"version": "1.3.2",
"resolved": "https://registry.npmjs.org/fast-fifo/-/fast-fifo-1.3.2.tgz",
@@ -11723,6 +12771,24 @@
"node": ">=6"
}
},
+ "node_modules/jsonc-eslint-parser": {
+ "version": "2.4.0",
+ "resolved": "https://registry.npmjs.org/jsonc-eslint-parser/-/jsonc-eslint-parser-2.4.0.tgz",
+ "integrity": "sha512-WYDyuc/uFcGp6YtM2H0uKmUwieOuzeE/5YocFJLnLfclZ4inf3mRn8ZVy1s7Hxji7Jxm6Ss8gqpexD/GlKoGgg==",
+ "dev": true,
+ "dependencies": {
+ "acorn": "^8.5.0",
+ "eslint-visitor-keys": "^3.0.0",
+ "espree": "^9.0.0",
+ "semver": "^7.3.5"
+ },
+ "engines": {
+ "node": "^12.22.0 || ^14.17.0 || >=16.0.0"
+ },
+ "funding": {
+ "url": "https://github.com/sponsors/ota-meshi"
+ }
+ },
"node_modules/jsonc-parser": {
"version": "3.2.1",
"resolved": "https://registry.npmjs.org/jsonc-parser/-/jsonc-parser-3.2.1.tgz",
@@ -17194,6 +18260,33 @@
"node": ">= 0.8.0"
}
},
+ "node_modules/prettier": {
+ "version": "3.2.5",
+ "resolved": "https://registry.npmjs.org/prettier/-/prettier-3.2.5.tgz",
+ "integrity": "sha512-3/GWa9aOC0YeD7LUfvOG2NiDyhOWRvt1k+rcKhOuYnMY24iiCphgneUfJDyFXd6rZCAnuLBv6UeAULtrhT/F4A==",
+ "dev": true,
+ "bin": {
+ "prettier": "bin/prettier.cjs"
+ },
+ "engines": {
+ "node": ">=14"
+ },
+ "funding": {
+ "url": "https://github.com/prettier/prettier?sponsor=1"
+ }
+ },
+ "node_modules/prettier-linter-helpers": {
+ "version": "1.0.0",
+ "resolved": "https://registry.npmjs.org/prettier-linter-helpers/-/prettier-linter-helpers-1.0.0.tgz",
+ "integrity": "sha512-GbK2cP9nraSSUF9N2XwUwqfzlAFlMNYYl+ShE/V+H8a9uNl/oUqB1w2EL54Jh0OlyRSd8RfWYJ3coVS4TROP2w==",
+ "dev": true,
+ "dependencies": {
+ "fast-diff": "^1.1.2"
+ },
+ "engines": {
+ "node": ">=6.0.0"
+ }
+ },
"node_modules/pretty-bytes": {
"version": "6.1.1",
"resolved": "https://registry.npmjs.org/pretty-bytes/-/pretty-bytes-6.1.1.tgz",
@@ -19346,6 +20439,22 @@
"url": "https://opencollective.com/svgo"
}
},
+ "node_modules/synckit": {
+ "version": "0.9.0",
+ "resolved": "https://registry.npmjs.org/synckit/-/synckit-0.9.0.tgz",
+ "integrity": "sha512-7RnqIMq572L8PeEzKeBINYEJDDxpcH8JEgLwUqBd3TkofhFRbkq4QLR0u+36avGAhCRbk2nnmjcW9SE531hPDg==",
+ "dev": true,
+ "dependencies": {
+ "@pkgr/core": "^0.1.0",
+ "tslib": "^2.6.2"
+ },
+ "engines": {
+ "node": "^14.18.0 || >=16.0.0"
+ },
+ "funding": {
+ "url": "https://opencollective.com/unts"
+ }
+ },
"node_modules/system-architecture": {
"version": "0.1.0",
"resolved": "https://registry.npmjs.org/system-architecture/-/system-architecture-0.1.0.tgz",
@@ -19558,6 +20667,21 @@
"node": ">=0.6"
}
},
+ "node_modules/toml-eslint-parser": {
+ "version": "0.9.3",
+ "resolved": "https://registry.npmjs.org/toml-eslint-parser/-/toml-eslint-parser-0.9.3.tgz",
+ "integrity": "sha512-moYoCvkNUAPCxSW9jmHmRElhm4tVJpHL8ItC/+uYD0EpPSFXbck7yREz9tNdJVTSpHVod8+HoipcpbQ0oE6gsw==",
+ "dev": true,
+ "dependencies": {
+ "eslint-visitor-keys": "^3.0.0"
+ },
+ "engines": {
+ "node": "^12.22.0 || ^14.17.0 || >=16.0.0"
+ },
+ "funding": {
+ "url": "https://github.com/sponsors/ota-meshi"
+ }
+ },
"node_modules/totalist": {
"version": "3.0.1",
"resolved": "https://registry.npmjs.org/totalist/-/totalist-3.0.1.tgz",
@@ -21364,6 +22488,23 @@
"node": ">= 14"
}
},
+ "node_modules/yaml-eslint-parser": {
+ "version": "1.2.2",
+ "resolved": "https://registry.npmjs.org/yaml-eslint-parser/-/yaml-eslint-parser-1.2.2.tgz",
+ "integrity": "sha512-pEwzfsKbTrB8G3xc/sN7aw1v6A6c/pKxLAkjclnAyo5g5qOh6eL9WGu0o3cSDQZKrTNk4KL4lQSwZW+nBkANEg==",
+ "dev": true,
+ "dependencies": {
+ "eslint-visitor-keys": "^3.0.0",
+ "lodash": "^4.17.21",
+ "yaml": "^2.0.0"
+ },
+ "engines": {
+ "node": "^14.17.0 || >=16.0.0"
+ },
+ "funding": {
+ "url": "https://github.com/sponsors/ota-meshi"
+ }
+ },
"node_modules/yargs": {
"version": "17.7.2",
"resolved": "https://registry.npmjs.org/yargs/-/yargs-17.7.2.tgz",
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 9202e8a3..bc669941 100644
--- a/packages/df-wiki-cli/df_wiki_cli/content/main.py
+++ b/packages/df-wiki-cli/df_wiki_cli/content/main.py
@@ -115,7 +115,7 @@ def structure(
count_row = 0
for row in reader:
count_row += 1
- system_dir_name = row["System_name_ok"]
+ system_dir_name = row["system"]
pdb_path_file = Path(row["pdb"])
foldseek_html_file = Path(str(pdb_path_file).split(".pdb")[0] + ".html")
png_structure = Path(str(pdb_path_file).split(".pdb")[0] + ".png")
@@ -255,11 +255,12 @@ def system_operon_structure(
),
] = "./system-structures.csv",
version: Annotated[str, typer.Option(help="Defense finder model")] = "v1.2.4",
+ tag: Annotated[str, typer.Option(help="Defense finder model")] = "1.2.4",
):
# get defense finder model from github
- df_model_url = f"https://github.com/mdmparis/defense-finder-models/releases/download/{version}/defense-finder-models-{version}.tar.gz"
+ df_model_url = f"https://github.com/mdmparis/defense-finder-models/releases/download/{tag}/defense-finder-models-{version}.tar.gz"
_, tmp_path = tempfile.mkstemp()
tmp_root_dir = tempfile.gettempdir()
df_model_dir = Path(f"{tmp_root_dir}/defense-finder-models-{version}")
@@ -281,33 +282,39 @@ def system_operon_structure(
for child in df_model_definitions_dir.iterdir():
for system_path in child.iterdir():
system = system_path.name
- console.rule(system)
+ # console.rule(system)
subsystem_list = (
s for s in system_path.iterdir() if str(s).endswith(".xml")
)
for subsystem in subsystem_list:
susbsystem_name = subsystem.stem
console.print(susbsystem_name)
+ in_exchangeables = False
+ current_gene = {}
+ exchangeables = []
+
with open(subsystem) as file:
- tree = ET.parse(file)
- root = tree.getroot()
- current_gene = {}
- for child in root.iter():
- if child.tag == "gene":
- current_gene = {
- "system": system,
- "subsystem": susbsystem_name,
- "gene": child.attrib["name"],
- "exchangeables": None,
- }
- system_genes.append(current_gene)
- if child.tag == "exchangeables":
- exchangeables = []
- for ex_gene in child.iter():
- if ex_gene.tag == "gene":
- exchangeables.append(ex_gene.attrib["name"])
- current_gene["exchangeables"] = ",".join(exchangeables)
- current_gene = {}
+ for event, elem in ET.iterparse(file, events=("start", "end")):
+ if event == "start":
+ if elem.tag == "gene" and not in_exchangeables:
+ current_gene = {
+ "system": system,
+ "subsystem": susbsystem_name,
+ "gene": elem.attrib["name"],
+ "exchangeables": None,
+ }
+ system_genes.append(current_gene)
+ if elem.tag == "gene" and in_exchangeables:
+ exchangeables.append(elem.attrib["name"])
+ if elem.tag == "exchangeables":
+ in_exchangeables = True
+ exchangeables = []
+ elif event == "end":
+ if elem.tag == "exchangeables":
+ in_exchangeables = False
+ current_gene["exchangeables"] = ",".join(exchangeables)
+ exchangeables = []
+
with open(output, "w") as f:
fieldnames = ["id", "system", "subsystem", "gene", "exchangeables"]
writer = csv.DictWriter(f, fieldnames=fieldnames)
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 52668833..e69de29b 100644
--- a/packages/df-wiki-cli/df_wiki_cli/meilisearch/__init__.py
+++ b/packages/df-wiki-cli/df_wiki_cli/meilisearch/__init__.py
@@ -1,427 +0,0 @@
-import meilisearch
-from pathlib import Path
-import csv
-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()
-
-
-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: Annotated[int | None, BeforeValidator(emptyStringToNone)]
- name_of_profiles_in_sys: List[str]
- accession_in_sys: List[str]
- Superkingdom: str
- phylum: str
- class_: str = Field(..., alias="class")
- order: str
- family: str
- genus: str
- species: str
-
-
-class RefSeqTaxo(BaseModel):
- index: int
- Assembly: str
- Superkingdom: str
- phylum: str
- class_: str = Field(..., alias="class")
- order: str
- family: str
- genus: str
- species: str
- size: int
-
-
-class RefSeqTaxoType(RefSeqTaxo):
- type: str
-
-
-class RefSeqTypeCount(BaseModel):
- type: str
- size: int
-
-
-class StructureTypes(str, Enum):
- Validated = "Validated"
- DF = "DF"
- na = "na"
-
-
-def na_to_none(v: Optional[float]) -> Optional[float]:
- if v == "na":
- return None
- else:
- return v
-
-
-NaFloat = Annotated[Optional[float], BeforeValidator(na_to_none)]
-
-
-class StrucutreStatistics(BaseModel):
- id: int
- System_name_ok: str
- System: str
- gene_name: str
- subtype: str
- proteins_in_the_prediction: List[str]
- prediction_type: str
- batch: int
- nb_sys: str
- type: StructureTypes
- system_number_of_genes: int
- system_genes: List[str]
- pdb: str
- pae_table: str
- plddt_table: str
- fasta_file: str
- completed: bool
- iptm_ptm: NaFloat = Field(..., alias="iptm+ptm")
- pDockQ: Optional[NaFloat]
- plddts: Optional[NaFloat]
- 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)
- for row in csvreader:
- doc = RefSeqTaxo(**row)
- documents.append(doc.model_dump(by_alias=True))
- tasks = index.add_documents_in_batches(documents, primary_key="Assembly")
- for task in tasks:
- console.print(task)
- 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",
- "size",
- ]
- )
- params = {
- "maxValuesPerFacet": 1000000,
- "sortFacetValuesBy": {"*": "count"},
- }
- index.update_faceting_settings(params)
-
-
-def update_refseqtaxotype(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)
- for row in csvreader:
- doc = RefSeqTaxoType(**row)
- documents.append(doc.model_dump(by_alias=True))
- tasks = index.add_documents_in_batches(documents, primary_key="index")
- for task in tasks:
- console.print(task)
- 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",
- "type",
- "size",
- ]
- )
- params = {
- "maxValuesPerFacet": 1000000,
- "sortFacetValuesBy": {"*": "count"},
- }
- index.update_faceting_settings(params)
-
-
-def update_refseqtypecount(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)
- for row in csvreader:
- doc = RefSeqTypeCount(**row)
- documents.append(doc.model_dump(by_alias=True))
- tasks = index.add_documents_in_batches(documents, primary_key="type")
- for task in tasks:
- console.print(task)
- index.update_pagination_settings({"maxTotalHits": 1000000})
- index.update_filterable_attributes(body=["type"])
- index.update_sortable_attributes(
- [
- "type",
- "size",
- ]
- )
- params = {
- "maxValuesPerFacet": 1000000,
- "sortFacetValuesBy": {"*": "count"},
- }
- index.update_faceting_settings(params)
-
-
-def update_refseq(
- 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)
- for row in csvreader:
- row["protein_in_syst"] = split_on_comma(row["protein_in_syst"])
- row["name_of_profiles_in_sys"] = split_on_comma(
- row["name_of_profiles_in_sys"]
- )
- row["accession_in_sys"] = split_on_comma(row["accession_in_sys"])
- doc = RefSeqCsv(**row)
- documents.append(doc.model_dump(by_alias=True))
- 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=[
- "replicon",
- "Assembly",
- "type",
- "subtype",
- "Superkingdom",
- "phylum",
- "class",
- "order",
- "family",
- "genus",
- "species",
- ]
- )
- index.update_sortable_attributes(
- [
- "replicon",
- "Assembly",
- "type",
- "subtype",
- "Superkingdom",
- "phylum",
- "class",
- "order",
- "family",
- "genus",
- "species",
- ]
- )
- params = {
- "maxValuesPerFacet": 1000000,
- "sortFacetValuesBy": {"*": "count"},
- }
- index.update_faceting_settings(params)
- index.update_typo_tolerance(
- {
- "enabled": False
- # "minWordSizeForTypos": {"oneTypo": 50, "twoTypos": 100}
- }
- )
-
-
-def update_structure(
- 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)
- for id, row in enumerate(csvreader):
- row["proteins_in_the_prediction"] = split_on_comma(
- row["proteins_in_the_prediction"]
- )
- row["system_genes"] = split_on_comma(row["system_genes"])
- doc = StrucutreStatistics(**row, id=id)
- documents.append(doc.model_dump(by_alias=True))
- tasks = index.add_documents_in_batches(documents, primary_key="id")
- for task in tasks:
- print(task)
- pagination_settings_task = index.update_pagination_settings(
- {"maxTotalHits": 100000}
- )
- print(pagination_settings_task)
- attr_task = index.update_filterable_attributes(
- body=[
- "System",
- "gene_name",
- "subtype",
- "completed",
- "prediction_type",
- "plddts",
- "iptm+ptm",
- "proteins_in_the_prediction",
- "system_genes",
- "pDockQ",
- ]
- )
- params = {
- "maxValuesPerFacet": 1000000,
- "sortFacetValuesBy": {"*": "count"},
- }
- index.update_faceting_settings(params)
-
- print(attr_task)
- index.update_sortable_attributes(
- [
- "System_name_ok",
- "System",
- "gene_name",
- "subtype",
- "completed",
- "plddts",
- "nb_sys",
- "completed",
- "prediction_type",
- "system_number_of_genes",
- "iptm+ptm",
- "pDockQ",
- ]
- )
- index.update_typo_tolerance({"enabled": False})
-
-
-def update_systems(
- host: str,
- key: str,
- file: Path,
- document: str,
-):
- client = meilisearch.Client(host, key)
- index = client.index(document.lower())
- with open(file, "r") as jsonfile:
- json_object = json.load(jsonfile)
- tasks = index.add_documents_in_batches(json_object, primary_key="title")
- for task in tasks:
- print(task)
- pagination_settings_task = index.update_pagination_settings(
- {"maxTotalHits": 100000}
- )
- print(pagination_settings_task)
- attr_task = index.update_filterable_attributes(
- body=[
- "title",
- "Sensor",
- "Activator",
- "Effector",
- "PFAM.AC",
- "PFAM.DE",
- "contributors",
- ]
- )
- params = {
- "maxValuesPerFacet": 1000000,
- "sortFacetValuesBy": {"*": "count"},
- }
- index.update_faceting_settings(params)
-
- print(attr_task)
- index.update_sortable_attributes(["title", "Sensor", "Activator", "Effector"])
- index.update_typo_tolerance({"enabled": False})
-
-
-def update_articles(
- host: str,
- key: str,
- file: Path,
- document: str,
-):
- client = meilisearch.Client(host, key)
- index = client.index(document.lower())
- with open(file, "r") as jsonfile:
- json_object = json.load(jsonfile)
- for obj in json_object:
- obj["ms_id"] = obj["id"].replace("/", "_")
- tasks = index.add_documents_in_batches(json_object, primary_key="ms_id")
- for task in tasks:
- print(task)
-
- pagination_settings_task = index.update_pagination_settings(
- {"maxTotalHits": 100000}
- )
- print(pagination_settings_task)
- attr_task = index.update_filterable_attributes(
- body=[
- "DOI",
- ]
- )
- params = {
- "maxValuesPerFacet": 1000000,
- "sortFacetValuesBy": {"*": "count"},
- }
- index.update_faceting_settings(params)
-
- print(attr_task)
-
-
-def split_on_comma(str_val: str) -> List[str]:
- for val in str_val.split(","):
- yield val.strip()
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 ea904573..b7bbffdb 100644
--- a/packages/df-wiki-cli/df_wiki_cli/meilisearch/main.py
+++ b/packages/df-wiki-cli/df_wiki_cli/meilisearch/main.py
@@ -5,16 +5,6 @@ from pathlib import Path
from df_wiki_cli.meilisearch.update import main as update_main
-# from df_wiki_cli.meilisearch import update
-from df_wiki_cli.meilisearch import (
- update_refseqtaxo,
- update_articles,
- update_refseq,
- update_refseqtaxotype,
- update_refseqtypecount,
- update_structure,
- update_systems,
-)
from enum import Enum
from types import SimpleNamespace
@@ -58,41 +48,6 @@ def main(
# ctx.obj = SimpleNamespace()
-# @app.command()
-# def update(
-# ctx: typer.Context,
-# file: Annotated[
-# Path,
-# typer.Option(
-# exists=False,
-# file_okay=True,
-# writable=True,
-# ),
-# ],
-# document: Annotated[
-# Documents, typer.Option(case_sensitive=False)
-# ] = 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":
-# update_structure(ctx.obj.host, ctx.obj.key, file, document)
-# if document == "systems":
-# update_systems(ctx.obj.host, ctx.obj.key, file, document)
-# if document == "article":
-# update_articles(ctx.obj.host, ctx.obj.key, file, document)
-# if document == "refseqtaxotype":
-# update_refseqtaxotype(ctx.obj.host, ctx.obj.key, file, document)
-# if document == "refseqsanitized":
-# update_refseq(ctx.obj.host, ctx.obj.key, file, document)
-# if document == "refseqtypecount":
-# update_refseqtypecount(ctx.obj.host, ctx.obj.key, file, document)
-
-
@app.command()
def delete_all_documents(ctx: typer.Context, id: str):
client = meilisearch.Client(ctx.obj.host, ctx.obj.key)
diff --git a/packages/df-wiki-cli/df_wiki_cli/meilisearch/update/main.py b/packages/df-wiki-cli/df_wiki_cli/meilisearch/update/main.py
index 24a6290b..02f3965a 100644
--- a/packages/df-wiki-cli/df_wiki_cli/meilisearch/update/main.py
+++ b/packages/df-wiki-cli/df_wiki_cli/meilisearch/update/main.py
@@ -81,7 +81,9 @@ NaFloat = Annotated[Optional[float], BeforeValidator(na_to_none)]
class StrucutreStatistics(BaseModel):
id: int
+ structure_system: str
system: str
+ subsystem: str
proteins_in_the_prediction: Optional[List[str]]
prediction_type: str
batch: int
@@ -97,6 +99,9 @@ class StrucutreStatistics(BaseModel):
iptm_ptm: NaFloat = Field(..., alias="iptm+ptm")
pDockQ: Optional[NaFloat]
plddts: Optional[NaFloat]
+ Abi2: str
+ OrbA: str
+ Anti_BREX: str
class SystemOperonStructure(BaseModel):
@@ -312,53 +317,31 @@ def structure(
index = client.index(document.lower())
documents = []
with open(file, "r") as csvfile:
- csvreader = csv.DictReader(csvfile)
+ csvreader = csv.DictReader(csvfile, delimiter="\t")
for id, row in enumerate(csvreader):
row["proteins_in_the_prediction"] = split_on_comma(
row["proteins_in_the_prediction"]
)
row["system_genes"] = split_on_comma(row["system_genes"])
- # get info from systemoperonstruct
-
- search_subtype = re.split(r"-\d+$", row["system"])[0]
- # search_subtype = row["system"].split("-")[0]
- console.print(search_subtype)
- res = client.index("systemoperonstruct").search(
- "",
- {
- "filter": f"subsystem = '{search_subtype}'",
- },
+ doc = StrucutreStatistics(
+ **row,
+ id=id,
)
- if len(res["hits"]) < 1:
-
- # raise RuntimeError("do not find hits for " + search_subtype)
- console.print(f"[red] no hits for {search_subtype}")
- # else:
- # console.print(res["hits"])
- # group data per subtype
-
- # create a set of list of gene
-
- # compare with the one defined in system_genes=
-
- # if it is the same, set subtype
-
- doc = StrucutreStatistics(**row, id=id)
# console.print(doc)
documents.append(doc.model_dump(by_alias=True))
- # tasks = index.add_documents_in_batches(documents, primary_key="id")
- # for task in tasks:
- # print(task)
+ tasks = index.add_documents_in_batches(documents, primary_key="id")
+ for task in tasks:
+ print(task)
pagination_settings_task = index.update_pagination_settings(
{"maxTotalHits": 100000}
)
print(pagination_settings_task)
attr_task = index.update_filterable_attributes(
body=[
- "System",
+ "system",
+ "subsystem",
"gene_name",
- "subtype",
"completed",
"prediction_type",
"plddts",
@@ -366,6 +349,9 @@ def structure(
"proteins_in_the_prediction",
"system_genes",
"pDockQ",
+ "Abi2",
+ "OrbA",
+ "Anti_BREX",
]
)
params = {
@@ -377,10 +363,9 @@ def structure(
print(attr_task)
index.update_sortable_attributes(
[
- "System_name_ok",
- "System",
+ "system",
+ "subsystem",
"gene_name",
- "subtype",
"completed",
"plddts",
"nb_sys",
@@ -389,6 +374,9 @@ def structure(
"system_number_of_genes",
"iptm+ptm",
"pDockQ",
+ "Abi2",
+ "OrbA",
+ "Anti_BREX",
]
)
index.update_typo_tolerance({"enabled": False})
diff --git a/packages/df-wiki-cli/poetry.lock b/packages/df-wiki-cli/poetry.lock
index 34991255..391b6c00 100644
--- a/packages/df-wiki-cli/poetry.lock
+++ b/packages/df-wiki-cli/poetry.lock
@@ -570,6 +570,177 @@ files = [
{file = "kiwisolver-1.4.5.tar.gz", hash = "sha256:e57e563a57fb22a142da34f38acc2fc1a5c864bc29ca1517a88abc963e60d6ec"},
]
+[[package]]
+name = "lxml"
+version = "5.2.1"
+description = "Powerful and Pythonic XML processing library combining libxml2/libxslt with the ElementTree API."
+optional = false
+python-versions = ">=3.6"
+files = [
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+ {file = "lxml-5.2.1-cp310-cp310-macosx_10_9_x86_64.whl", hash = "sha256:6cc6ee342fb7fa2471bd9b6d6fdfc78925a697bf5c2bcd0a302e98b0d35bfad3"},
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+ {file = "lxml-5.2.1.tar.gz", hash = "sha256:3f7765e69bbce0906a7c74d5fe46d2c7a7596147318dbc08e4a2431f3060e306"},
+]
+
+[package.extras]
+cssselect = ["cssselect (>=0.7)"]
+html-clean = ["lxml-html-clean"]
+html5 = ["html5lib"]
+htmlsoup = ["BeautifulSoup4"]
+source = ["Cython (>=3.0.10)"]
+
[[package]]
name = "markdown-it-py"
version = "3.0.0"
@@ -1452,4 +1623,4 @@ testing = ["big-O", "jaraco.functools", "jaraco.itertools", "more-itertools", "p
[metadata]
lock-version = "2.0"
python-versions = ">=3.11,<3.13"
-content-hash = "8834fc25ed4a598a81158cb81ef55d0fb6d950ee29a02caa62e3241dcefc3ca0"
+content-hash = "e869e30378379cbc207695da4dede924c88dad26782577ce3d6c0d8948911e2a"
diff --git a/packages/df-wiki-cli/pyproject.toml b/packages/df-wiki-cli/pyproject.toml
index 421d54c8..27dd969e 100644
--- a/packages/df-wiki-cli/pyproject.toml
+++ b/packages/df-wiki-cli/pyproject.toml
@@ -20,6 +20,7 @@ python-frontmatter = "^1.0.1"
matplotlib = "^3.8.2"
habanero = "^1.2.6"
biopython = "^1.83"
+lxml = "^5.2.1"
[tool.poetry.group.dev.dependencies]
diff --git a/packages/df-wiki-cli/scripts/fill-local-meilisearch.sh b/packages/df-wiki-cli/scripts/fill-local-meilisearch.sh
index 2fabe8ea..588c51ff 100755
--- a/packages/df-wiki-cli/scripts/fill-local-meilisearch.sh
+++ b/packages/df-wiki-cli/scripts/fill-local-meilisearch.sh
@@ -6,7 +6,8 @@ PUBLIC_DIR=../../../public
# system operon structure
-df-wiki-cli content system-operon-structure --version "1.2.3" --output ${DATA_DIR}/system-structures.csv
+df-wiki-cli meilisearch delete-all-documents system-operon-structure
+df-wiki-cli content system-operon-structure --tag "1.2.2" --version "1.2.2" --output ${DATA_DIR}/system-structures.csv
df-wiki-cli meilisearch update system-operon-structure --file ${DATA_DIR}/system-structures.csv
@@ -38,7 +39,8 @@ df-wiki-cli content systems --dir ${CONTENT_DIR}/3.defense-systems/ --pfam ${PUB
df-wiki-cli meilisearch update systems --file /tmp/list-systems.json
# STRUCTURE
-df-wiki-cli meilisearch update structure --file ${DATA_DIR}/all_predictions_statistics.csv
+df-wiki-cli meilisearch delete-all-documents structure
+df-wiki-cli meilisearch update structure --file ${DATA_DIR}/all_predictions_statistics.tsv
# ARTICLES
# df-wiki-cli meilisearch delete-all-documents article
diff --git a/types/plot.ts b/types/plot.ts
new file mode 100644
index 00000000..483cd6bf
--- /dev/null
+++ b/types/plot.ts
@@ -0,0 +1,15 @@
+export interface PlotMargin {
+ marginTop: number
+ marginRight: number
+ marginBottom: number
+ marginLeft: number
+}
+
+
+
+export interface StructureOperonGene {
+ gene: string
+ id: number
+ subsystem: string
+ system: string
+}
\ No newline at end of file
--
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