From a66740765d2c92b8149da4b7c0b114acfb7bd5c7 Mon Sep 17 00:00:00 2001
From: Remi PLANEL <rplanel@pasteur.fr>
Date: Mon, 18 Sep 2023 20:18:19 +0200
Subject: [PATCH] optional title and abstract
---
components/content/ArticleDoi.vue | 9 ++++++---
components/content/ListSystems.vue | 5 +++--
content/2.defense-systems/abi2.md | 5 ++++-
content/2.defense-systems/abia.md | 5 ++++-
content/2.defense-systems/abib.md | 5 ++++-
content/2.defense-systems/abic.md | 3 +--
content/2.defense-systems/abid.md | 3 +--
content/2.defense-systems/abie.md | 3 +--
content/2.defense-systems/abig.md | 3 +--
content/2.defense-systems/abih.md | 5 ++++-
content/2.defense-systems/abiv.md | 3 ++-
content/2.defense-systems/rst_paris.md | 5 ++---
12 files changed, 33 insertions(+), 21 deletions(-)
diff --git a/components/content/ArticleDoi.vue b/components/content/ArticleDoi.vue
index f453ffe4..fdfe831e 100644
--- a/components/content/ArticleDoi.vue
+++ b/components/content/ArticleDoi.vue
@@ -11,6 +11,9 @@ const { article } = useFetchArticle(props.doi)
const show = ref(false)
console.log(article)
+const articleTitle = computed(() => { return props?.title ?? article.value?.title ?? props.doi })
+const articleAbstract = computed(() => { return props.abstract ?? article.value?.abstract })
+
</script>
<template>
<v-list-item :href="article?.href" :target="article?.target">
@@ -22,13 +25,13 @@ console.log(article)
<v-card flat color="transparent" density="compact">
<v-card-item density="compact">
- <v-card-title><span class="text-subtitle-1 font-weight-bold">{{ article?.title ?? props?.title ?? props.doi
+ <v-card-title><span class="text-subtitle-1 font-weight-bold">{{ articleTitle
}}</span></v-card-title>
<v-card-subtitle> {{ article?.subtitle ?? "no subtitle" }}</v-card-subtitle>
<v-card-subtitle> {{ article?.containerTitle ?? "no containerTitle" }} ({{ article?.year
}})</v-card-subtitle>
</v-card-item>
- <v-card-actions v-if="article?.abstract ?? props.abstract" density="compact">
+ <v-card-actions v-if="articleAbstract" density="compact">
<v-btn size="x-small" variant="outlined" :append-icon="show ? 'mdi-chevron-up' : 'mdi-chevron-down'"
@click.stop.prevent="show = !show">Abstract</v-btn>
</v-card-actions>
@@ -36,7 +39,7 @@ console.log(article)
<v-expand-transition>
<v-card v-show="show" flat color="transparent">
<v-card-text>
- {{ article?.abstract ?? props.abstract }}
+ {{ articleAbstract }}
</v-card-text>
</v-card>
diff --git a/components/content/ListSystems.vue b/components/content/ListSystems.vue
index beb7ef11..0831ea2b 100644
--- a/components/content/ListSystems.vue
+++ b/components/content/ListSystems.vue
@@ -36,8 +36,9 @@ function filterOnlyCapsText(value, query, item) {
<v-chip variant="text" link :to="`${item.columns.system.path}`">{{
item.columns.system.name }}</v-chip>
</template>
- <template #[`item.doi`]="{ item }">
- <ArticleDoiList v-if="item.columns?.doi" :items="[item.columns.doi]" :divider="false" />
+ <template #[`item.article`]="{ item }">
+ <ArticleDoi v-if="item.columns?.article" :doi="item.columns.article.doi"
+ :title="item.columns.article?.title" :abstract="item.columns.article?.abstract" :divider="false" />
</template>
</v-data-table>
</v-card>
diff --git a/content/2.defense-systems/abi2.md b/content/2.defense-systems/abi2.md
index b7f40795..d1307292 100644
--- a/content/2.defense-systems/abi2.md
+++ b/content/2.defense-systems/abi2.md
@@ -1,7 +1,10 @@
---
title: Abi2
tableColumns:
- doi: 10.1016/j.mib.2005.06.006
+ article:
+ 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.
---
The Abi2 system is composed of one protein: Abi_2.
diff --git a/content/2.defense-systems/abia.md b/content/2.defense-systems/abia.md
index fd1b4e47..0874239e 100644
--- a/content/2.defense-systems/abia.md
+++ b/content/2.defense-systems/abia.md
@@ -1,7 +1,10 @@
---
title: AbiA
tableColumns:
- doi: 10.1016/j.mib.2005.06.006
+ article:
+ 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.
---
The AbiA system have been describe in a total of 2 subsystems.
diff --git a/content/2.defense-systems/abib.md b/content/2.defense-systems/abib.md
index 0428f535..1ed106de 100644
--- a/content/2.defense-systems/abib.md
+++ b/content/2.defense-systems/abib.md
@@ -1,7 +1,10 @@
---
title: AbiB
tableColumns:
- doi: 10.1016/j.mib.2005.06.006
+ article:
+ 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.
---
The AbiB system is composed of one protein: AbiB.
diff --git a/content/2.defense-systems/abic.md b/content/2.defense-systems/abic.md
index 26d4e748..6c9ca705 100644
--- a/content/2.defense-systems/abic.md
+++ b/content/2.defense-systems/abic.md
@@ -1,7 +1,6 @@
---
title: AbiC
-tableColumns:
- doi: 10.1016/j.mib.2005.06.006
+
---
The AbiC system is composed of one protein: AbiC.
diff --git a/content/2.defense-systems/abid.md b/content/2.defense-systems/abid.md
index 6b1230e0..f01d7a28 100644
--- a/content/2.defense-systems/abid.md
+++ b/content/2.defense-systems/abid.md
@@ -1,7 +1,6 @@
---
title: AbiD
-tableColumns:
- doi: 10.1016/j.mib.2005.06.006
+
---
The AbiD system is composed of one protein: AbiD.
diff --git a/content/2.defense-systems/abie.md b/content/2.defense-systems/abie.md
index b83cbadb..0111e34c 100644
--- a/content/2.defense-systems/abie.md
+++ b/content/2.defense-systems/abie.md
@@ -1,7 +1,6 @@
---
title: AbiE
-tableColumns:
- doi: 10.1016/j.mib.2005.06.006
+
---
AbiE is a family of an anti-phage defense systems. They act through a Toxin-Antitoxin mechanism, and are comprised of a pair of genes, with one gene being toxic while the other confers immunity to this toxicity.Â
diff --git a/content/2.defense-systems/abig.md b/content/2.defense-systems/abig.md
index b21a9877..f6945753 100644
--- a/content/2.defense-systems/abig.md
+++ b/content/2.defense-systems/abig.md
@@ -1,7 +1,6 @@
---
title: AbiG
-tableColumns:
- doi: 10.1016/j.mib.2005.06.006
+
---
The AbiG system is composed of 2 proteins: AbiGi and, AbiGii.
diff --git a/content/2.defense-systems/abih.md b/content/2.defense-systems/abih.md
index 32d4ddc2..76c6e630 100644
--- a/content/2.defense-systems/abih.md
+++ b/content/2.defense-systems/abih.md
@@ -1,7 +1,10 @@
---
title: AbiH
tableColumns:
- doi: 10.1111/j.1574-6968.1996.tb08446.x
+ article:
+ doi: 10.1111/j.1574-6968.1996.tb08446.x
+ abstract: |
+ A gene which encodes resistance by abortive infection (Abi+) to bacteriophage was cloned from Lactococcus lactis ssp. lactis biovar. diacetylactis S94. This gene was found to confer a reduction in efficiency of plating and plaque size for prolate-headed bacteriophage φ53 (group I of homology) and total resistance to the small isometric-headed bacteriophage φ59 (group III of homology). The cloned gene is predicted to encode a polypeptide of 346 amino acid residues with a deduced molecular mass of 41 455 Da. No homology with any previously described genes was found. A probe was used to determine the presence of this gene in two strains on 31 tested.
---
## Example of genomic structure
diff --git a/content/2.defense-systems/abiv.md b/content/2.defense-systems/abiv.md
index 162b5edd..96f646c4 100644
--- a/content/2.defense-systems/abiv.md
+++ b/content/2.defense-systems/abiv.md
@@ -1,7 +1,8 @@
---
title: AbiV
tableColumns:
- doi: 10.1128/AEM.00780-08
+ article:
+ doi: 10.1128/AEM.00780-08
---
## Example of genomic structure
diff --git a/content/2.defense-systems/rst_paris.md b/content/2.defense-systems/rst_paris.md
index acdd06f1..2cee1158 100644
--- a/content/2.defense-systems/rst_paris.md
+++ b/content/2.defense-systems/rst_paris.md
@@ -1,7 +1,6 @@
---
title: Rst_PARIS
-tableColumns:
- doi: https://doi.org/10.1101/2021.01.21.427644
+
---
## Description
@@ -56,7 +55,7 @@ Subsystem Paris 2 with a system from *Escherichia coli (P4 loci)* in *Escherichi
---
items:
- doi: 10.1016/j.chom.2022.02.018
-
+
---
::
--
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