From eb94970a1d46ff24e996878d90f23c86c4aaced8 Mon Sep 17 00:00:00 2001
From: Remi PLANEL <rplanel@pasteur.fr>
Date: Fri, 27 Oct 2023 10:33:01 +0200
Subject: [PATCH] Resolve "footnote markdown"
---
.gitlab-ci.yml | 1 -
components/Nav/Navbar.vue | 16 -----
components/content/Alert/Danger.vue | 15 +++++
components/content/Alert/ExpansionDetails.vue | 29 ++++++++++
components/content/Alert/Info.vue | 15 +++++
components/content/Alert/Tip.vue | 15 +++++
components/content/Alert/Warning.vue | 14 +++++
components/content/ArticleDoi.vue | 1 +
components/content/ArticleDoiList.vue | 24 ++++++--
components/content/Contributors.vue | 2 +-
components/content/Ref.vue | 17 ++++++
composables/useFetchArticle.ts | 2 +
content/3.defense-systems/abi2.md | 9 ++-
content/3.defense-systems/abia.md | 21 +++----
content/3.defense-systems/detocs.md | 15 +----
nuxt.config.ts | 10 ++++
server/plugins/content.ts | 58 +++++++++++--------
17 files changed, 187 insertions(+), 77 deletions(-)
create mode 100644 components/content/Alert/Danger.vue
create mode 100644 components/content/Alert/ExpansionDetails.vue
create mode 100644 components/content/Alert/Info.vue
create mode 100644 components/content/Alert/Tip.vue
create mode 100644 components/content/Alert/Warning.vue
create mode 100644 components/content/Ref.vue
diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
index d5e97b0e..29f69dff 100644
--- a/.gitlab-ci.yml
+++ b/.gitlab-ci.yml
@@ -27,7 +27,6 @@ stages:
BASE_URL: /wiki/
MEILI_HOST: "http://localhost:7700"
MEILI_API_KEY: MASTER_KEY
- CI_DEBUG_TRACE: "true"
before_script:
- i=0; while [ "$i" -lt 12 ]; do docker info && break; sleep 5; i=$(( i + 1 )) ; done
- docker login -u "$CI_REGISTRY_USER" -p "$CI_REGISTRY_PASSWORD" $CI_REGISTRY
diff --git a/components/Nav/Navbar.vue b/components/Nav/Navbar.vue
index cf7f51d2..f580e4c8 100644
--- a/components/Nav/Navbar.vue
+++ b/components/Nav/Navbar.vue
@@ -13,8 +13,6 @@ function toggleTheme() {
theme.global.name.value = theme.global.current.value.dark ? "light" : "dark";
}
-
-
const sections = ref([
{
id: "webservice",
@@ -27,20 +25,6 @@ const sections = ref([
]);
-// const computedSections = computed(() => {
-// return sections.value.map(section => {
-
-// if (section?.to) {
-// const { refinedUrl } = useRefinedUrl(section.to)
-// return { ...section, to: refinedUrl.value }
-// }
-// else {
-// return section
-// }
-
-
-// })
-// })
const drawer = ref(true);
diff --git a/components/content/Alert/Danger.vue b/components/content/Alert/Danger.vue
new file mode 100644
index 00000000..f66b8e8e
--- /dev/null
+++ b/components/content/Alert/Danger.vue
@@ -0,0 +1,15 @@
+<script setup lang="ts">
+export interface Props {
+ title?: string
+}
+
+const { title } = withDefaults(defineProps<Props>(), {
+ title: 'Danger'
+});
+</script>
+
+<template>
+ <v-alert type="error" border="start" variant="tonal" class="my-2" prominent :title="title">
+ <slot></slot>
+ </v-alert>
+</template>
diff --git a/components/content/Alert/ExpansionDetails.vue b/components/content/Alert/ExpansionDetails.vue
new file mode 100644
index 00000000..62823929
--- /dev/null
+++ b/components/content/Alert/ExpansionDetails.vue
@@ -0,0 +1,29 @@
+<script setup lang="ts">
+export interface Props {
+ title?: string
+}
+
+const { title } = withDefaults(defineProps<Props>(), {
+ title: 'Details'
+});
+
+
+import { useTheme } from "vuetify";
+const theme = useTheme();
+
+
+</script>
+<template>
+ <div>
+ <v-expansion-panels>
+ <v-expansion-panel>
+ <v-expansion-panel-title class=" text-h6">
+ {{ title }}
+ </v-expansion-panel-title>
+ <v-expansion-panel-text>
+ <slot></slot>
+ </v-expansion-panel-text>
+ </v-expansion-panel>
+ </v-expansion-panels>
+ </div>
+</template>
diff --git a/components/content/Alert/Info.vue b/components/content/Alert/Info.vue
new file mode 100644
index 00000000..4d804852
--- /dev/null
+++ b/components/content/Alert/Info.vue
@@ -0,0 +1,15 @@
+<script setup lang="ts">
+export interface Props {
+ title?: string
+}
+
+const { title } = withDefaults(defineProps<Props>(), {
+ title: 'Info'
+});
+</script>
+
+<template>
+ <v-alert type="info" border="start" variant="tonal" class="my-2" prominent :title="title">
+ <slot></slot>
+ </v-alert>
+</template>
diff --git a/components/content/Alert/Tip.vue b/components/content/Alert/Tip.vue
new file mode 100644
index 00000000..f9e390e2
--- /dev/null
+++ b/components/content/Alert/Tip.vue
@@ -0,0 +1,15 @@
+<script setup lang="ts">
+export interface Props {
+ title?: string
+}
+
+const { title } = withDefaults(defineProps<Props>(), {
+ title: 'Tip'
+});
+</script>
+<template>
+ <v-alert color="primary" border-color="primary" border="start" variant="tonal" class="my-2" prominent :title="title"
+ icon="md:lightbulb">
+ <slot></slot>
+ </v-alert>
+</template>
diff --git a/components/content/Alert/Warning.vue b/components/content/Alert/Warning.vue
new file mode 100644
index 00000000..c5fc34a2
--- /dev/null
+++ b/components/content/Alert/Warning.vue
@@ -0,0 +1,14 @@
+<script setup lang="ts">
+export interface Props {
+ title?: string
+}
+
+const { title } = withDefaults(defineProps<Props>(), {
+ title: 'Warning'
+});
+</script>
+<template>
+ <v-alert type="warning" border="start" variant="tonal" class="my-2" prominent :title="title">
+ <slot></slot>
+ </v-alert>
+</template>
diff --git a/components/content/ArticleDoi.vue b/components/content/ArticleDoi.vue
index 3cd6c619..ea79d240 100644
--- a/components/content/ArticleDoi.vue
+++ b/components/content/ArticleDoi.vue
@@ -28,6 +28,7 @@ const articleAbstract = computed(() => {
<template>
<v-list-item
:href="article?.href"
+ :id="props.doi"
:target="article?.target"
density="compact"
class="px-1"
diff --git a/components/content/ArticleDoiList.vue b/components/content/ArticleDoiList.vue
index fe7727a6..357e90ee 100644
--- a/components/content/ArticleDoiList.vue
+++ b/components/content/ArticleDoiList.vue
@@ -1,11 +1,25 @@
<script setup lang="ts">
-const props = defineProps<{
- items: { doi: string, title?: string, divider: boolean, abstract?: string }[];
-}>();
+import ProseH2 from '~/components/content/ProseH2'
+// const props = defineProps<{
+// items: { doi: string; title?: string; divider: boolean; abstract?: string }[];
+// }>();
+
+const { page } = useContent();
+const computedDois = computed(() => {
+ if (page.value?.relevantAbstracts) {
+ return page.value.relevantAbstracts;
+ } else {
+ return [];
+ }
+});
</script>
<template>
+ <div v-if="computedDois?.length > 0">
+ <ProseH2 id="relevant-abstracts">Relevant abstracts</ProseH2>
+
<v-list density="compact">
- <ArticleDoi v-for="item, index in props.items" :key="item.doi" :index="index + 1" :doi="item.doi"
- :title="item?.title" :divider="item.divider" :abstract="item?.abstract" />
+ <ArticleDoi v-for="(item, index) in computedDois" :key="item.doi" :index="index + 1" :doi="item.doi"
+ :title="item?.title" :divider="item.divider" :abstract="item?.abstract" />
</v-list>
+ </div>
</template>
\ No newline at end of file
diff --git a/components/content/Contributors.vue b/components/content/Contributors.vue
index 5c173d62..e7906086 100644
--- a/components/content/Contributors.vue
+++ b/components/content/Contributors.vue
@@ -9,6 +9,6 @@ const contributorsString = computed(() => {
</script>
<template>
- <div v-if="contributorsString" class="mt-n6 mb-6 text-subtitle-1 text-info">Contributors: {{ contributorsString }}
+ <div v-if="contributorsString" class="mt-n5 mb-6 text-subtitle-1 text-info">Contributors: {{ contributorsString }}
</div>
</template>
\ No newline at end of file
diff --git a/components/content/Ref.vue b/components/content/Ref.vue
new file mode 100644
index 00000000..006afc08
--- /dev/null
+++ b/components/content/Ref.vue
@@ -0,0 +1,17 @@
+<script setup lang="ts">
+export interface Props {
+ doi: string;
+}
+const props = withDefaults(defineProps<Props>(), {});
+const { article } = useFetchArticle(props.doi);
+</script>
+<template>
+ <v-chip
+ v-if="article"
+ variant="text"
+ :href="`#${props.doi}`"
+ class="pa-0 text-caption font-italic"
+ >({{ article?.author[0]?.family ?? "test" }} et al,
+ {{ article?.year }})</v-chip
+ >
+</template>
\ No newline at end of file
diff --git a/composables/useFetchArticle.ts b/composables/useFetchArticle.ts
index 63439bd4..a829bc4a 100644
--- a/composables/useFetchArticle.ts
+++ b/composables/useFetchArticle.ts
@@ -25,6 +25,7 @@ export interface Article {
DOI: string
title: string
subtitle: string
+ author: Array<{ family: string; given: string }>
containerTitle: string
abstract: string
year: string
@@ -74,6 +75,7 @@ export function useFetchArticle(doi: string) {
DOI,
title: sanitizedTitle,
subtitle: toAuthorsString(author || []),
+ author,
containerTitle: sanitizedContainerTitle,
abstract: sanitizedAbstract,
year: published?.["date-parts"][0][0] ?? issued?.["date-parts"][0][0] ?? '',
diff --git a/content/3.defense-systems/abi2.md b/content/3.defense-systems/abi2.md
index 808a7367..7e1d4617 100644
--- a/content/3.defense-systems/abi2.md
+++ b/content/3.defense-systems/abi2.md
@@ -9,6 +9,8 @@ tableColumns:
Activator: ''
Effector: ''
PFAM: PF07751
+relevantAbstracts:
+ - doi: 10.1016/j.mib.2005.06.006
---
# Abi2
@@ -17,7 +19,7 @@ The Abi2 system is composed of one protein: Abi_2.
Here is an example found in the RefSeq database:
-{max-width=750px}
+
Abi2 system in the genome of *Clostridium butyricum* (GCF_014131795.1) is composed of 1 protein: Abi_2 (WP_035763709.1).
@@ -27,10 +29,7 @@ The Abi2 system is present in a total of 176 different species.
Among the 22k complete genomes of RefSeq, this system is present in 1210 genomes (5.3 %).
-{max-width=750px}
+
*Proportion of genome encoding the Abi2 system for the 14 phyla with more than 50 genomes in the RefSeq database.*
-## Relevant abstracts
-
-
diff --git a/content/3.defense-systems/abia.md b/content/3.defense-systems/abia.md
index 3e5d554c..3de86ab7 100644
--- a/content/3.defense-systems/abia.md
+++ b/content/3.defense-systems/abia.md
@@ -9,9 +9,14 @@ tableColumns:
Activator: Unknown
Effector: Unknown
PFAM: PF00078, PF18160, PF18732
+relevantAbstracts:
+ - doi: 10.1023/A:1002027321171
+ - doi: 10.1016/j.mib.2005.06.006
+ - doi: 10.1093/nar/gkac467
---
-# AbiA
+# AbiA
+
The AbiA system have been describe in a total of 2 subsystems.
Here is some example found in the RefSeq database:
@@ -24,10 +29,12 @@ AbiA_large subsystem in the genome of *Lactobacillus amylovorus* (GCF_002706375.
AbiA_small subsystem in the genome of *Mesobacillus foraminis* (GCF_003667765.1) is composed of 2 proteins: AbiA_small (WP_121614402.1)and, AbiA_SLATT (WP_121614403.1).
-## Distribution of the system among prokaryotes
+## Distribution of the system among prokaryotes
The AbiA system is present in a total of 35 different species.
+
+
Among the 22k complete genomes of RefSeq, this system is present in 50 genomes (0.2 %).
{max-width=750px}
@@ -67,15 +74,5 @@ AbiA systems were experimentally validated using:
A system from *lactococcal plasmid* in *lactococci* has an anti-phage effect against 936, c2, P335 (Chopin et al., 2005)
-## Relevant abstracts
-::article-doi-list
----
-items:
- - doi: 10.1023/A:1002027321171
- - doi: 10.1016/j.mib.2005.06.006
- - doi: 10.1093/nar/gkac467
-
----
-::
diff --git a/content/3.defense-systems/detocs.md b/content/3.defense-systems/detocs.md
index b715ca64..028de448 100644
--- a/content/3.defense-systems/detocs.md
+++ b/content/3.defense-systems/detocs.md
@@ -6,6 +6,8 @@ tableColumns:
abstract: |
During viral infection, cells can deploy immune strategies that deprive viruses of molecules essential for their replication. Here, we report a family of immune effectors in bacteria that, upon phage infection, degrade cellular adenosine triphosphate (ATP) and deoxyadenosine triphosphate (dATP) by cleaving the N-glycosidic bond between the adenine and sugar moieties. These ATP nucleosidase effectors are widely distributed within multiple bacterial defense systems, including cyclic oligonucleotide-based antiviral signaling systems (CBASS), prokaryotic argonautes, and nucleotide-binding leucine-rich repeat (NLR)-like proteins, and we show that ATP and dATP degradation during infection halts phage propagation. By analyzing homologs of the immune ATP nucleosidase domain, we discover and characterize Detocs, a family of bacterial defense systems with a two-component phosphotransfer-signaling architecture. The immune ATP nucleosidase domain is also encoded within diverse eukaryotic proteins with immune-like architectures, and we show biochemically that eukaryotic homologs preserve the ATP nucleosidase activity. Our findings suggest that ATP and dATP degradation is a cell-autonomous innate immune strategy conserved across the tree of life.
PFAM: PF01048, PF18742
+relevantAbstracts:
+ - doi: 10.1016/j.cell.2023.07.020
contributors:
- François Rousset
---
@@ -83,16 +85,3 @@ dataUrl: /detocs/Detocs_hydrolase__dtcC-plddts_89.47253.pdb
---
::
-## Relevant abstract
-::article-doi-list
----
-items:
- - doi: 10.1016/j.cell.2023.07.020
-
----
-::
-
-
-## References
-
-Rousset et al., A conserved family of immune effectors cleaves cellular ATP upon viral infection. Cell 186, 1–13 (2023). https://doi.org/10.1016/j.cell.2023.07.020
diff --git a/nuxt.config.ts b/nuxt.config.ts
index 2eac5520..2a61a770 100644
--- a/nuxt.config.ts
+++ b/nuxt.config.ts
@@ -11,6 +11,16 @@ export default defineNuxtConfig({
content: {
documentDriven: {
injectPage: false,
+ },
+ highlight: {
+ theme: {
+ // Default theme (same as single string)
+ default: 'github-light',
+ // Theme used if `html.dark`
+ dark: 'github-dark',
+ // Theme used if `html.sepia`
+ sepia: 'monokai'
+ }
}
},
vuetify: {
diff --git a/server/plugins/content.ts b/server/plugins/content.ts
index 0f843c65..19dad94f 100644
--- a/server/plugins/content.ts
+++ b/server/plugins/content.ts
@@ -4,34 +4,44 @@ export default defineNitroPlugin((nitroApp) => {
nitroApp.hooks.hook('content:file:beforeParse',
(file) => {
if (file?._id?.startsWith('content:3.defense-systems:') && file?._id?.endsWith('.md')) {
- const regexp = /(?<=---\n).*?(?=\n---)/sg;
- const match = file.body.match(regexp);
- const frontMatter = match[0]
- const parsedFrontMatter = YAML.parse(frontMatter)
- if (parsedFrontMatter?.contributors?.length > 0) {
- file.body = file.body.replace(/(^#[\s+]\w*[\s\S])/gm, "$1:contributors\n\n")
+ const frontMatterRegex = /(?<=---\n).*?(?=\n---)/sg;
+
+ const fontMatterMatch = file.body.match(frontMatterRegex);
+ if (fontMatterMatch?.length > 0) {
+ const frontMatter = fontMatterMatch[0]
+ const parsedFrontMatter = YAML.parse(frontMatter)
+ if (parsedFrontMatter?.contributors?.length > 0) {
+ file.body = file.body.replace(/(^#[\s+]\w*[\s\S])/gm, "$1\n:contributors\n\n")
+ }
+ // try to look at :ref{doi=xxxx}
+ const matchRef = file.body.match(/(?<=:ref{doi=).*(?=})/gm)
+ if (matchRef?.length > 0) {
+ if (parsedFrontMatter?.relevantAbstracts) {
+ const relevantAbstractsSet = new Set(parsedFrontMatter.relevantAbstracts.map(({ doi }: { doi: string }) => doi))
+ const filteredMatchRef = matchRef.filter((doi: string) => !relevantAbstractsSet.has(doi))
+ parsedFrontMatter.relevantAbstracts = [...parsedFrontMatter.relevantAbstracts, ...filteredMatchRef.map((doi: string) => ({ doi }))]
+ } else {
+ parsedFrontMatter.relevantAbstracts = matchRef.map((doi: string) => ({ doi }))
+ }
+ const newFrontMatterStr = YAML.stringify(parsedFrontMatter)
+ file.body = file.body.replace(/---\n(.*?)\n---/gs, `---\n${newFrontMatterStr}\n---`)
+ }
}
}
})
- // nitroApp.hooks.hook(
- // 'content:file:afterParse',
- // (file) => {
- // if (file._id.endsWith('.md')) {
-
- // file.body.children.push({
- // type: "element",
- // tag: 'article-doi-list',
- // props: {
- // items: [
- // { doi: '10.1016/j.mib.2005.06.006' },
- // { doi: '10.1016/j.mib.2005.06.006' }]
- // },
- // children: []
- // })
-
- // }
- // })
+ nitroApp.hooks.hook(
+ 'content:file:afterParse',
+ (file) => {
+ if (file?._id?.startsWith('content:3.defense-systems:') && file._id.endsWith('.md')) {
+ file.body.children.push({
+ type: "element",
+ tag: 'article-doi-list',
+ props: {},
+ children: []
+ })
+ }
+ })
})
\ No newline at end of file
--
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