diff --git a/components/Nav/Navbar.vue b/components/Nav/Navbar.vue
index f580e4c8b290b5f5cb7b42c13076cc062341253c..e870e4c8e67b244773a9a8d18c84a93861e49191 100644
--- a/components/Nav/Navbar.vue
+++ b/components/Nav/Navbar.vue
@@ -38,7 +38,7 @@ const computedNavigation = computed(() => {
});
</script>
<template>
- <v-app-bar :elevation="0" border density="prominent" scroll-behavior="hide">
+ <v-app-bar :elevation="0" border density="prominent" scroll-behavior="hide" scroll-threshold="150">
<template #prepend>
<v-app-bar-nav-icon @click.stop="drawer = !drawer"></v-app-bar-nav-icon>
<!-- <Logo height="45px" /> -->
diff --git a/content/3.defense-systems/abi2.md b/content/3.defense-systems/abi2.md
index af6bebe3d5c3ac8c5dfe4a5a5f1467adf986ef71..f7175bc53060f9e8a09c7c1f3b17316661531f5d 100644
--- a/content/3.defense-systems/abi2.md
+++ b/content/3.defense-systems/abi2.md
@@ -18,7 +18,8 @@ relevantAbstracts:
The Abi2 system is composed of one protein: Abi_2.
-Here is an example found in the RefSeq database:
+Here is an example found in the RefSeq database:
+
diff --git a/content/3.defense-systems/abia.md b/content/3.defense-systems/abia.md
index fc0a3f645015dab1a552bd7302a14a3093e96339..82ca565193c97af2731ff427a6b1ae179251d533 100644
--- a/content/3.defense-systems/abia.md
+++ b/content/3.defense-systems/abia.md
@@ -19,8 +19,6 @@ relevantAbstracts:
# AbiA
-:ref{doi=10.1093/nar/gkac467}
-
The AbiA system have been describe in a total of 2 subsystems.
Here is some example found in the RefSeq database:
diff --git a/content/3.defense-systems/avs.md b/content/3.defense-systems/avs.md
index f0595e0552767458e4fc42f557bd693e1dc21a2f..06614abfcfd0e683c957686a97c8d0b8648ff456 100644
--- a/content/3.defense-systems/avs.md
+++ b/content/3.defense-systems/avs.md
@@ -11,6 +11,9 @@ tableColumns:
Effector: Diverse effectors (Nucleic acid degrading, putative Nucleotide modifying, putative Membrane disrupting)
PFAM: PF00753, PF13289, PF13365
+relevantAbstracts:
+ - doi: 10.1126/science.aba0372
+ - doi: 10.1126/science.abm4096
---
# Avs
@@ -173,12 +176,4 @@ Subsystem CcAvs4 with a system from *Corallococcus coralloides* in *Escherichia
## Relevant abstracts
-::relevant-abstracts
----
-items:
- - doi: 10.1126/science.aba0372
- - doi: 10.1126/science.abm4096
-
----
-::
-
+
diff --git a/package-lock.json b/package-lock.json
index 484806b25bc89ba9105f0198aec73bacc0b5943f..eb72b2f9a328342a1546f57261da38ee4fccf69e 100644
--- a/package-lock.json
+++ b/package-lock.json
@@ -7,6 +7,7 @@
"dependencies": {
"@observablehq/plot": "^0.6.11",
"@pinia/nuxt": "^0.4.11",
+ "d3": "^7.8.5",
"meilisearch": "^0.35.0",
"pinia": "^2.1.6",
"vue-json-csv": "^2.1.0",
@@ -2625,7 +2626,8 @@
},
"node_modules/d3": {
"version": "7.8.5",
- "license": "ISC",
+ "resolved": "https://registry.npmjs.org/d3/-/d3-7.8.5.tgz",
+ "integrity": "sha512-JgoahDG51ncUfJu6wX/1vWQEqOflgXyl4MaHqlcSruTez7yhaRKR9i8VjjcQGeS2en/jnFivXuaIMnseMMt0XA==",
"dependencies": {
"d3-array": "3",
"d3-axis": "3",
diff --git a/package.json b/package.json
index fc09b4037ca9d62846fdf2b53f4302e39a8cf9a8..a438a08f64d2d78a897db005c41a56bfe2bbfef0 100644
--- a/package.json
+++ b/package.json
@@ -20,9 +20,10 @@
"dependencies": {
"@observablehq/plot": "^0.6.11",
"@pinia/nuxt": "^0.4.11",
- "yaml": "^2.3.3",
+ "d3": "^7.8.5",
"meilisearch": "^0.35.0",
"pinia": "^2.1.6",
- "vue-json-csv": "^2.1.0"
+ "vue-json-csv": "^2.1.0",
+ "yaml": "^2.3.3"
}
}
diff --git a/server/plugins/content.ts b/server/plugins/content.ts
index f20c59b59606f25a79a0a46618bf5dbad6e1bc06..878a8d231c136c40b6ea15379a9727a6569ac4b2 100644
--- a/server/plugins/content.ts
+++ b/server/plugins/content.ts
@@ -1,4 +1,8 @@
import YAML from 'yaml'
+import * as d3 from "d3";
+
+
+
export default defineNitroPlugin((nitroApp) => {
nitroApp.hooks.hook('content:file:beforeParse',
@@ -11,19 +15,8 @@ export default defineNitroPlugin((nitroApp) => {
const frontMatter = fontMatterMatch[0]
const parsedFrontMatter = YAML.parse(frontMatter)
if (parsedFrontMatter?.contributors?.length > 0) {
- file.body = file.body.replace(/(^#[\s+]\w*[\s\S])/gm, "$1\n:contributors\n\n")
+ // file.body = file.body.replace(/(^#[\s+]\w*[\s\S])/gm, "$1\n:contributors\n\n")
}
- // try to look at :ref{doi=xxxx}
- // const matchRef = file.body.match(/(?<=:ref{doi=).*(?=})/gm)
- // if (matchRef?.length > 0) {
-
- // // put the ref found in references list
- // const filteredMatchRef = Array.from(new Set(matchRef)).map((doi: string) => ({ doi }))
- // parsedFrontMatter.references = filteredMatchRef
- // const newFrontMatterStr = YAML.stringify(parsedFrontMatter)
- // file.body = file.body.replace(/---\n(.*?)\n---/gs, `---\n${newFrontMatterStr}\n---`)
- // }
-
}
}
})
@@ -33,44 +26,55 @@ export default defineNitroPlugin((nitroApp) => {
'content:file:afterParse',
(file) => {
if (file?._id?.startsWith('content:3.defense-systems:') && file._id.endsWith('.md')) {
-
if (file?.body?.children?.length > 0) {
- // console.log("====================")
- // console.log(file.contributors)
- // console.log("dans after")
- // console.log(file._id)
- // console.log(file?.title)
- // console.log(file?.layout)
-
- // get the ref tags
- // console.log(file.body.children.length)
- const refTags = file.body.children
- .filter(({ tag, props }) => tag === "ref" && props?.doi)
- .reduce((acc, curr) => {
- // console.log(curr)
- // console.log(acc)
- acc.add(curr.props.doi)
- return acc
- }, new Set())
- // console.log(refTags)
- if (refTags.size > 0) file.references = Array.from(refTags).map(doi => ({ doi }))
-
- // console.log(file.references)
- // console.log(file.body.children.slice(4))}
- file.body.children.push({
- type: "element",
- tag: 'relevant-abstracts',
- props: {},
- children: []
- })
+ // has contributors
+ if (file?.contributors?.length > 0) {
+ console.log("has contributors")
+ console.log(file.body.children.slice(0, 2))
+ const h1Index = file.body.children.findIndex(({ tag }) => tag === "h1")
+ if (h1Index >= 0) {
+ file.body.children.splice(h1Index + 1, 0, {
+ type: "element",
+ tag: 'contributors',
+ props: {},
+ children: []
+ })
+ }
+ }
- file.body.children.push({
- type: "element",
- tag: 'references',
- props: {},
- children: []
+ const root = d3.hierarchy(file.body)
+ const refNodes = []
+ root.eachAfter(({ data }) => {
+ if (data?.tag === 'ref') refNodes.push(data)
})
+ const refTags = new Set(
+ refNodes
+ .map(({ props }) => props?.doi ?? null)
+ .filter(doi => doi !== null)
+ )
+ if (refTags.size > 0) file.references = Array.from(refTags).map(doi => ({ doi }))
+ // Update the TOC
+ // if relevant abstract available
+ if (file?.relevantAbstracts?.length > 0) {
+ // check if relevant Abstracts exists
+ file.body.toc.links.push({ id: "relevant-abstracts", depth: 2, text: 'Relevant abstracts' })
+ file.body.children.push({
+ type: "element",
+ tag: 'relevant-abstracts',
+ props: {},
+ children: []
+ })
+ }
+ if (file?.references?.length > 0) {
+ file.body.toc.links.push({ id: "references", depth: 2, text: 'References' })
+ file.body.children.push({
+ type: "element",
+ tag: 'references',
+ props: {},
+ children: []
+ })
+ }
}
}
})