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Commit 90f52fd0 authored by Remi PLANEL's avatar Remi PLANEL
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Merge branch 'zotero-generated-json' into 'dev' 

Resolve "Use a zotero generated json instead of crossref api"

Closes #129

See merge request !8
parents 00aa09cf ff3a9f5b
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1 merge request!8Resolve "Use a zotero generated json instead of crossref api"
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components/Logo.vue 0 → 100644
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View file @ 90f52fd0
<script setup lang="ts">
interface Props {
height: string
}
const props = defineProps<Props>()
</script>
<template>
<svg :height="height" xmlns="http://www.w3.org/2000/svg" version="1.1" viewBox="0 0 1210 515">
<g>
<title>Defense Finder</title>
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\ No newline at end of file
components/Nav/Navbar.vue
+ 18
− 8
View file @ 90f52fd0
<template> <template>
<v-app-bar> <v-app-bar :elevation="0" border>
<v-app-bar-nav-icon variant="text" @click.stop="drawer = !drawer"></v-app-bar-nav-icon> <template #prepend>
<v-toolbar-title>DefenseFinder Wiki</v-toolbar-title> <v-app-bar-nav-icon @click.stop="drawer = !drawer"></v-app-bar-nav-icon>
<v-btn icon="mdi-theme-light-dark" @click="toggle()"> </template>
<v-app-bar-title>
<Logo height="45px" />
</v-app-bar-title>
<template #append v-if="!mobile">
<v-btn v-for="section in sections" :key="section.id" color="primary" :href="section.href">
{{ section.label }}
</v-btn> </v-btn>
</template>
</v-app-bar> </v-app-bar>
<v-navigation-drawer v-model="drawer" :border="0"> <v-navigation-drawer v-model="drawer" :border="0">
<v-card flat> <v-card flat>
...@@ -16,10 +23,13 @@ ...@@ -16,10 +23,13 @@
<script setup lang="ts"> <script setup lang="ts">
import { useCustomTheme } from '~/composables/useCustomTheme' import { useCustomTheme } from '~/composables/useCustomTheme'
const runtimeConfig = useRuntimeConfig()
const { toggle } = useCustomTheme() const { toggle } = useCustomTheme()
const { navigation } = useContent();
const { mobile } = useDisplay();
const { navigation, page, surround, globals } = useContent(); const sections = ref([
{ id: "webservice", label: "webservice", href: runtimeConfig.public.defenseFinderWebservice }
])
const drawer = ref(true); const drawer = ref(true);
</script> </script>
components/content/ReferencesList.vue
+ 0
− 2
View file @ 90f52fd0
...@@ -49,12 +49,10 @@ const computedItems = computed(() => { ...@@ -49,12 +49,10 @@ const computedItems = computed(() => {
published, published,
...rest ...rest
} = doi.message; } = doi.message;
console.log(abstract)
let sanitizedAbstract = abstract let sanitizedAbstract = abstract
if (sanitizedAbstract) { if (sanitizedAbstract) {
sanitizedAbstract = /\<jats\:p\>(.*)\<\/jats\:p\>/.exec(sanitizedAbstract)?.[1] ?? '' sanitizedAbstract = /\<jats\:p\>(.*)\<\/jats\:p\>/.exec(sanitizedAbstract)?.[1] ?? ''
} }
console.log(sanitizedAbstract)
return { return {
DOI, DOI,
title: title[0], title: title[0],
......
composables/useFetchArticle.ts
+ 60
− 21
View file @ 90f52fd0
import { useArticlesStore } from '@/stores/articles'
import { ref, computed, watchEffect, queryContent } from '#imports'
import { CslJson } from '@/stores/articles'
export interface ArticleMessage { export interface ArticleMessage {
DOI: string; DOI: string;
issue: number; issue: number;
title: string; title: string | string[];
author: Array<{ family: string; given: string }>; author: Array<{ family: string; given: string }>;
"container-title-short": string; "container-title-short": string;
"container-title": string; "container-title": string;
...@@ -9,9 +14,13 @@ export interface ArticleMessage { ...@@ -9,9 +14,13 @@ export interface ArticleMessage {
published: { published: {
"date-parts": string[]; "date-parts": string[];
}; };
issued: {
"date-parts": string[];
};
} }
export interface Article { export interface Article {
DOI: string DOI: string
title: string title: string
...@@ -28,54 +37,84 @@ export interface RawArticle { ...@@ -28,54 +37,84 @@ export interface RawArticle {
} }
type SrcArticle = ArticleMessage | CslJson
export function useFetchArticle(doi: string) { export function useFetchArticle(doi: string) {
// const article = ref<Article>()
const article = ref<Article | null>(null) // const rawArticle = ref<RawArticle>()
const srcArticle = ref<SrcArticle | null>(null)
const store = useArticlesStore()
const pending = ref(false) const pending = ref(false)
const doiBaseUrl = ref(new URL("https://doi.org/")); const doiBaseUrl = ref(new URL("https://doi.org/"));
const url = ref(new URL(`/works/${doi}`, " https://api.crossref.org/").href); const url = ref(new URL(`/works/${doi}`, " https://api.crossref.org/").href);
console.log("dans useFetchArticle") console.log("dans useFetchArticle")
console.log(url.value) console.log(url.value)
watchEffect(async () => {
console.log("dans watch effect") const article = computed(() => {
article.value = null if (srcArticle.value != undefined) {
const { data, pending: pendingUseFetch, error, refresh } = await useFetch<RawArticle>(toValue(url), {
lazy: true, server: false,
})
console.log(data)
if (data.value?.message) {
const { const {
DOI, DOI,
title, title,
"container-title-short": cts, "container-title-short": cts,
"container-title": ct, "container-title": ct,
journalAbbreviation,
abstract, abstract,
published, published,
issued,
author, author,
...rest ...rest
} = data.value.message; } = srcArticle.value;
let sanitizedAbstract = abstract let sanitizedAbstract = abstract
console.log(DOI)
if (sanitizedAbstract) { if (sanitizedAbstract) {
sanitizedAbstract = /\<jats\:p\>(.*)\<\/jats\:p\>/.exec(sanitizedAbstract)?.[1] ?? ''
sanitizedAbstract = /(?:\<jats\:p\>)?(.*)(?:\<\/jats\:p\>)?/.exec(sanitizedAbstract)?.[1] ?? ''
} }
article.value = {
const sanitizedTitle = (Array.isArray(title)) ? title[0] : title
const sanitizedContainerTitle = (Array.isArray(ct)) ? cts?.length > 0 ? cts[0] : ct?.length > 0 ? ct[0] : "" : journalAbbreviation || ct
return {
DOI, DOI,
title: title[0], title: sanitizedTitle,
subtitle: toAuthorsString(author || []), subtitle: toAuthorsString(author || []),
containerTitle: cts?.length > 0 ? cts[0] : ct?.length > 0 ? ct[0] : "", containerTitle: sanitizedContainerTitle,
abstract: sanitizedAbstract, abstract: sanitizedAbstract,
year: published["date-parts"][0][0], year: published?.["date-parts"][0][0] ?? issued?.["date-parts"][0][0] ?? '',
href: getReferenceUrl(DOI), href: getReferenceUrl(DOI),
target: "_blank", target: "_blank",
prependIcon: "mdi-newspaper-variant-outline", prependIcon: "mdi-newspaper-variant-outline",
} }
console.log(article.value)
} else { return srcArticle.value }
})
watchEffect(async () => {
if (store.articles.size === 0) {
const localArticles = await queryContent('/_partial/articles').where({ _partial: true }).findOne()
console.log("aritcles in json csl")
console.log(localArticles)
if (localArticles.body && store.articles.size <= 0) {
for (const article of localArticles.body) {
store.add(article)
} }
pending.value = pendingUseFetch.value }
}
if (store.articles.has(doi)) {
console.log("dans l state")
srcArticle.value = store.articles.get(doi)
console.log(srcArticle.value)
return
} else {
const { data, pending: pendingUseFetch, error, refresh } = await useFetch<RawArticle>(toValue(url), {
lazy: true, server: false,
})
if (data.value?.message) {
srcArticle.value = data.value.message
}
pending.value = pendingUseFetch.value
}
}) })
function toAuthorsString(authors: Array<{ family: string; given: string }>) { function toAuthorsString(authors: Array<{ family: string; given: string }>) {
......
content/2.defense-systems/abia.md
+ 0
− 3
View file @ 90f52fd0
...@@ -41,10 +41,7 @@ A system from *lactococcal plasmid* in *lactococci* has an anti-phage effect aga ...@@ -41,10 +41,7 @@ A system from *lactococcal plasmid* in *lactococci* has an anti-phage effect aga
--- ---
items: items:
- doi: 10.1023/A:1002027321171 - doi: 10.1023/A:1002027321171
title: Bacteriophage defence systems in lactic acid bacteria
- doi: 10.1016/j.mib.2005.06.006 - doi: 10.1016/j.mib.2005.06.006
abstract: |
Abortive infection (Abi) systems, also called phage exclusion, block phage multiplication and cause premature bacterial cell death upon phage infection. This decreases the number of progeny particles and limits their spread to other cells allowing the bacterial population to survive. Twenty Abi systems have been isolated in Lactococcus lactis, a bacterium used in cheese-making fermentation processes, where phage attacks are of economical importance. Recent insights in their expression and mode of action indicate that, behind diverse phenotypic and molecular effects, lactococcal Abis share common traits with the well-studied Escherichia coli systems Lit and Prr. Abis are widespread in bacteria, and recent analysis indicates that Abis might have additional roles other than conferring phage resistance.
- doi: 10.1093/nar/gkac467 - doi: 10.1093/nar/gkac467
--- ---
......
content/_partial/articles.json 0 → 100644
+ 5298
− 0
View file @ 90f52fd0
This diff is collapsed.
layouts/custom.vue
+ 0
− 2
View file @ 90f52fd0
...@@ -15,7 +15,5 @@ ...@@ -15,7 +15,5 @@
import { useCustomTheme } from '~/composables/useCustomTheme' import { useCustomTheme } from '~/composables/useCustomTheme'
const { isDark } = useCustomTheme() const { isDark } = useCustomTheme()
const { navigation } = useContent();
const drawer = ref(true);
</script> </script>
nginx.conf
+ 1
− 1
View file @ 90f52fd0
...@@ -2,7 +2,7 @@ server_tokens off; ...@@ -2,7 +2,7 @@ server_tokens off;
server { server {
listen 8080; listen 8080;
server_name localhost; server_name localhost;
location /wiki { location /wiki/ {
alias /etc/nginx/html/; alias /etc/nginx/html/;
index index.html index.htm; index index.html index.htm;
......
nuxt.config.ts
+ 11
− 5
View file @ 90f52fd0
// https://v3.nuxtjs.org/api/configuration/nuxt.config // https://v3.nuxtjs.org/api/configuration/nuxt.config
export default defineNuxtConfig({ export default defineNuxtConfig({
modules: ['@nuxt/content', 'vuetify-nuxt-module', '@vueuse/nuxt'], modules: [
'@nuxt/content',
'vuetify-nuxt-module',
'@vueuse/nuxt',
'@pinia/nuxt'
],
content: { content: {
documentDriven: { documentDriven: {
injectPage: false, injectPage: false,
...@@ -14,8 +19,9 @@ export default defineNuxtConfig({ ...@@ -14,8 +19,9 @@ export default defineNuxtConfig({
devtools: { devtools: {
enabled: false enabled: false
}, },
// app: { runtimeConfig: {
// baseURL: '/wiki', public: {
// } defenseFinderWebservice: '/'
}
},
}) })
package-lock.json
+ 284
− 462
View file @ 90f52fd0
This diff is collapsed.
package.json
+ 7
− 0
View file @ 90f52fd0
...@@ -13,5 +13,12 @@ ...@@ -13,5 +13,12 @@
"@vueuse/nuxt": "^10.4.1", "@vueuse/nuxt": "^10.4.1",
"nuxt": "^3.7.0", "nuxt": "^3.7.0",
"vuetify-nuxt-module": "^0.5.7" "vuetify-nuxt-module": "^0.5.7"
},
"overrides": {
"vue": "latest"
},
"dependencies": {
"@pinia/nuxt": "^0.4.11",
"pinia": "^2.1.6"
} }
} }
pages/defense-systems.vue
+ 34
− 0
View file @ 90f52fd0
<script setup lang="ts"> <script setup lang="ts">
import { useArticlesStore } from '@/stores/articles'
// const store = useArticlesStore()
// const { data: localArticles } = await useAsyncData('local-articles', () => queryContent('/_partial/articles').where({ _partial: true }).findOne())
// console.log(localArticles.value)
// const localArticleMap = computed(() => {
// if (localArticles.value?.body) {
// return new Map(localArticles.value.body.map(article => {
// // console.log(article)
// // return article
// return [article.DOI, article]
// }))
// }
// else {
// return []
// }
// })
// watchEffect(() => {
// if (localArticles.value?.body && store.articles.size <= 0) {
// for (const article of localArticles.value.body) {
// store.add(article)
// }
// }
// })
const { data, error, pending } = await useAsyncData( const { data, error, pending } = await useAsyncData(
'list-defense-systems', 'list-defense-systems',
() => queryContent('/defense-systems').find() () => queryContent('/defense-systems').find()
......
stores/articles.ts 0 → 100644
+ 32
− 0
View file @ 90f52fd0
import { defineStore } from 'pinia'
import { ref } from 'vue'
export interface CslJson {
id: string
type: string
title: string
"container-title": string
page: string,
volume: string,
abstract: string
URL: string
DOI: string
journalAbbreviation: string
language: string
author: Array<{ family: string, given: string }>
issued: {
"date-parts": Array<string>
},
}
export const useArticlesStore = defineStore('articles', () => {
const articles = ref(new Map<string, CslJson>())
function add(article: CslJson) {
const doi = article.DOI
if (articles.value.has(doi)) return
articles.value.set(article.DOI, article)
}
return { articles, add }
})
\ No newline at end of file
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