.gitlab-ci.yml

-# The Docker image that will be used to build your app
-image: node:19.5-bullseye-slim
 # Functions that should be executed before the build script is run
 
+variables:
+  HELM_VERSION: "3.9.3"
+  IMAGE_NAME: "df-wiki"
+
 cache:
   paths:
     - node_modules/
@@ -10,28 +12,89 @@ stages:
   - build
   - deploy
 
-build:
+.build:
   stage: build
+  image: docker:24
+  variables:
+    CONTEXT: "."
+    DOCKERFILE: "Dockerfile"
+    BASE_URL: /wiki/
   before_script:
-    - npm ci
+    - 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" $CI_REGISTRY
   script:
-    - NUXT_APP_BASE_URL=/wiki/ npm run generate
-  artifacts:
-    paths:
-      - .output/public
-    untracked: false
-    when: on_success
-    expire_in: "30 days"
-
-pages:
+    - docker build --pull -t "$CI_REGISTRY_IMAGE/$IMAGE_NAME:$CI_COMMIT_SHORT_SHA" --build-arg "BASE_URL=$BASE_URL" -f $DOCKERFILE $CONTEXT
+    - docker push "$CI_REGISTRY_IMAGE/$IMAGE_NAME:$CI_COMMIT_SHORT_SHA"
+
+# build:
+#   stage: build
+#   before_script:
+#     - npm ci
+#   script:
+#     - NUXT_APP_BASE_URL=/wiki/ npm run generate
+#   artifacts:
+#     paths:
+#       - .output/public
+#     untracked: false
+#     when: on_success
+#     expire_in: "30 days"
+
+build:dev:
+  extends: .build
+  rules:
+    - if: $CI_COMMIT_BRANCH != "main"
+
+.deploy:
+  stage: deploy
+  image: harbor.pasteur.fr/kube-system/helm-kubectl:$HELM_VERSION
+  variables:
+    CI_DEBUG_TRACE: "true"
+    TEAM_ID: "df"
+  script:
+    - >
+      helm upgrade --install $CI_PROJECT_NAME-$CI_ENVIRONMENT_NAME ./deploy/df-wiki --namespace=${KUBE_NAMESPACE}
+      --set registry.image=${CI_REGISTRY_IMAGE}
+      --set registry.username=${DEPLOY_USER}
+      --set registry.password=${DEPLOY_TOKEN}
+      --set registry.host=${CI_REGISTRY}
+      --set imagePullSecrets[0].name="registry-pull-secret-${CI_COMMIT_REF_SLUG}"
+      --set image.repository="$CI_REGISTRY_IMAGE/$IMAGE_NAME"
+      --set image.tag="$CI_COMMIT_SHORT_SHA"
+      --set image.pullPolicy='Always'
+      --set env="$ENV"
+
+deploy:dev:
+  extends: .deploy
+  rules:
+    - if: $CI_COMMIT_BRANCH != "main"
+  needs:
+    - "build:dev"
+  variables:
+    NODE_ENV: "development"
+    KUBE_NAMESPACE: "defense-finder-dev"
+    PUBLIC_URL: "defense-finder.dev.pasteur.cloud"
+    INGRESS_CLASS: "internal"
+    AUTOSCALE: "true"
+    AUTSCALING_MIN_REPLICAS: "1"
+    AUTSCALING_MAX_REPLICAS: "4"
+    ENV: "development"
+  environment:
+    name: k8sdev-01
+    url: "https://defense-finder.dev.pasteur.cloud"
+
+
+delete-helm-release:
+  except:
+    - master
   stage: deploy
-  only:
-    - main
+  when: manual
+  image: harbor.pasteur.fr/kube-system/helm-kubectl:$HELM_VERSION
+  variables:
+    GIT_STRATEGY: none # important to not checkout source when branch is deleted
+    NAMESPACE: "defense-finder-dev"
+  environment:
+    name: "k8sdev-01"
+    action: stop
   script:
-    - NUXT_APP_BASE_URL=/wiki npm run generate
-    - rm -rf public
-    - mv .output/public public
-  artifacts:
-    paths:
-      # The folder that contains the files to be exposed at the Page URL
-      - public
+    - echo "Removing $CI_PROJECT_NAME-$CI_ENVIRONMENT_NAME"
+    - helm delete -n ${NAMESPACE} $CI_PROJECT_NAME-$CI_ENVIRONMENT_NAME

Dockerfile

 ### Stage Install ###
 FROM node:19.5-bullseye-slim as install
 
-RUN mkdir /usr/src/app
+
+
 WORKDIR /usr/src/app
 ENV PATH /usr/src/app/node_modules/.bin:$PATH
 COPY package*.json ./
@@ -22,13 +23,34 @@ CMD ["npm", "run", "dev"]
 ### STAGE: Build ###
 FROM node:19.5-bullseye-slim as build
 
+WORKDIR /usr/src/app
+COPY --from=install /usr/src/app ./
+COPY . /usr/src/app
+RUN npm run build
+
+### STAGE: serve ###
+FROM node:19.5-bullseye-slim as serve
+
+WORKDIR /usr/src/app
+COPY --from=build /usr/src/app/.output ./
+
+CMD [ "node", "server/index.mjs"]
+
+
+### STAGE: Generate ###
+FROM node:19.5-bullseye-slim as generate
+ARG BASE_URL=/
+
+ENV NUXT_APP_BASE_URL=${BASE_URL}
+
 WORKDIR /usr/src/app
 COPY --from=install /usr/src/app ./
 COPY . /usr/src/app
 RUN npm run generate
 
 ### STAGE: NGINX ###
-FROM nginx:stable-alpine
-COPY --from=build /usr/src/app/dist /usr/share/nginx/html
-EXPOSE 80
+FROM nginxinc/nginx-unprivileged:1.25
+# RUN rm -rf /usr/share/nginx/html/*
+COPY nginx.conf /etc/nginx/conf.d/default.conf
+COPY --from=generate /usr/src/app/.output/public /etc/nginx/html
 CMD ["nginx", "-g", "daemon off;"]
\ No newline at end of file

components/content/ListSystems.vue

 <script setup lang="ts">
-
 const props = defineProps<{
-    systems: any;
+    headers: Array<Object>
+    systems: Array<Object>
+
 }>();
 const itemsPerParge = ref(25)
 const search = ref('')
 const sortBy = ref([{ key: 'system', order: 'asc' }])
-const headers = ref([{
-    title: "Systems",
-    key: "system"
-}, { title: "Articles", key: "dois" }
-])
 
+function filterOnlyCapsText(value, query, item) {
+    if (value != null && query != null) {
+        if (typeof value === 'string') {
+            return value.toString().toLowerCase().indexOf(query.toLowerCase()) !== -1
+        }
+        if (typeof value == 'object') {
+            if (value?.name) {
+                return value.name.toString().toLowerCase().indexOf(query.toLowerCase()) !== -1
+            }
+        }
+    }
+    return false
+}
 </script>
 <template>
     <v-card flat color="transparent" class="my-5">
         <v-toolbar>
             <v-toolbar-title>Defense Systems</v-toolbar-title>
 
-            <v-text-field v-model="search" density="compact" variant="underlined" append-inner-icon="mdi-magnify"
-                label="Search" single-line hide-details class="mx-2"></v-text-field>
+            <v-text-field v-model="search" density="compact" variant="underlined" prepend-inner-icon="mdi-magnify"
+                label="Search for defense systems" single-line hide-details class="mx-2" clearable></v-text-field>
         </v-toolbar>
-        <v-data-table :items-per-page="itemsPerParge" v-model:sort-by="sortBy" :headers="headers" :items="props.systems"
-            :search="search">
+        <v-data-table :items-per-page="itemsPerParge" v-model:sort-by="sortBy" :headers="props.headers"
+            :custom-filter="filterOnlyCapsText" :items="props.systems" :search="search">
             <template #[`item.system`]="{ item }">
-                <v-chip variant="text" link :to="`/defense-systems/${item.columns.system.toLowerCase()}`">{{
-                    item.columns.system }}</v-chip>
+                <v-chip variant="text" link :to="`${item.columns.system.path}`">{{
+                    item.columns.system.name }}</v-chip>
             </template>
-            <template #[`item.dois`]="{ item }">
-                <ArticleDoiList :items="item.columns.dois" :divider="false" />
+            <template #[`item.doi`]="{ item }">
+                <ArticleDoiList v-if="item.columns?.doi" :items="[item.columns.doi]" :divider="false" />
             </template>
         </v-data-table>
     </v-card>

content/2.defense-systems/0.index.md

@@ -11,23 +11,7 @@ The knowledge of anti-phage defense systems is ever expanding. The spectacular i
 
 
 
-::list-systems
----
-systems:
-    - system: Paris
-      dois: 
-        - 10.1101/2021.01.21.427644
-    - system: AbiE
-      dois: 
-        - 10.1093/nar/gkt1419
-    - system: AVAST
-      dois: 
-        - 10.1126/science.aba0372
-    - system: RM
-      dois:
-        - 10.1093/nar/gku734
----
-::
+
 
 
 

content/2.defense-systems/abi2.md

 ---
 title: Abi2
+tableColumns:
+    doi: 10.1016/j.mib.2005.06.006
 ---
 
 The Abi2 system is composed of one protein: Abi_2.

content/2.defense-systems/abia.md

 ---
 title: AbiA
+tableColumns:
+    doi: 10.1016/j.mib.2005.06.006
 ---
 
 The AbiA system have been describe in a total of 2 subsystems.

content/2.defense-systems/abib.md

 ---
 title: AbiB
+tableColumns:
+    doi: 10.1016/j.mib.2005.06.006
 ---
 
 The AbiB system is composed of one protein: AbiB.

content/2.defense-systems/abic.md

 ---
 title: AbiC
+tableColumns:
+    doi: 10.1016/j.mib.2005.06.006
 ---
 
 The AbiC system is composed of one protein: AbiC.

content/2.defense-systems/abid.md

 ---
 title: AbiD
+tableColumns:
+    doi: 10.1016/j.mib.2005.06.006
 ---
 
 The AbiD system is composed of one protein: AbiD.

content/2.defense-systems/abie.md

 ---
 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. 

content/2.defense-systems/abig.md

 ---
 title: AbiG
+tableColumns:
+    doi: 10.1016/j.mib.2005.06.006
 ---
 
 The AbiG system is composed of 2 proteins: AbiGi and, AbiGii.

content/2.defense-systems/abih.md

 ---
 title: AbiH
+tableColumns:
+    doi: 10.1111/j.1574-6968.1996.tb08446.x
 ---
 
 ## Example of genomic structure

content/2.defense-systems/abiv.md

 ---
 title: AbiV
+tableColumns:
+    doi: 10.1128/AEM.00780-08
 ---
 
 ## Example of genomic structure

content/2.defense-systems/brex.md

@@ -4,13 +4,13 @@ title: BREX
 
 ## Description
 
-BREX (for Bacteriophage Exclusion) is a family of anti-phage defense systems. BREX systems are active against both lytic and lysogenic phages. They allow phage adsorption but block phage DNA replication, and are considered to be [RM](/list_defense_systems/RM)-like systems (1,2). BREX systems are found in around 10% of sequenced microbial genomes (1).
+BREX (for Bacteriophage Exclusion) is a family of anti-phage defense systems. BREX systems are active against both lytic and lysogenic phages. They allow phage adsorption but block phage DNA replication, and are considered to be [RM](/defense-systems/rm)-like systems (1,2). BREX systems are found in around 10% of sequenced microbial genomes (1).
 
 BREX systems can be divided into six subtypes, and are encoded by 4 to 8 genes, some of these genes being mandatory while others are subtype-specific (1).
 
 ## Molecular mechanism
 
-*B. cereus* BREX Type 1 system was reported to methylate target motifs in the bacterial genome (1). The methylation activity of this system has been hypothesized to allow for self from non-self discrimination, as it is the case for Restriction-Modification ([RM)](/list_defense_systems/RM) systems. 
+*B. cereus* BREX Type 1 system was reported to methylate target motifs in the bacterial genome (1). The methylation activity of this system has been hypothesized to allow for self from non-self discrimination, as it is the case for Restriction-Modification ([RM)](/defense-systems/rm) systems. 
 
 However, the mechanism through which BREX Type 1 systems defend against phages is distinct from RM systems, and does not seem to degrade phage nucleic acids (1). 
 

content/2.defense-systems/disarm.md

@@ -6,7 +6,7 @@ title: DISARM
 
 DISARM (Defense Island System Associated with Restriction-Modification) is a defense system widespread in prokaryotes, encoded by a 5-gene cassette. DISARM provides broad protection against double-stranded DNA phages, including siphophages, myophages, and podophages (1,3).
 
- It was reported to restrict incoming phage DNA and methylate the bacterial host DNA, which could be responsible for self from non-self discrimination (1). This suggests a [Restriction-Modification](/list_defense_systems/RM)-like (RM-like) mechanism, yet some pieces of experimental evidence hint that DISARM actually acts through a novel and uncharacterized molecular mechanism (1,2).
+ It was reported to restrict incoming phage DNA and methylate the bacterial host DNA, which could be responsible for self from non-self discrimination (1). This suggests a [Restriction-Modification](/defense-systems/rm)-like (RM-like) mechanism, yet some pieces of experimental evidence hint that DISARM actually acts through a novel and uncharacterized molecular mechanism (1,2).
 
 ## Molecular mechanism
 

content/2.defense-systems/rst_paris.md

 ---
 title: Rst_PARIS
+tableColumns:
+    doi: https://doi.org/10.1101/2021.01.21.427644
 ---
 
 ## Description
 
 PARIS (for Phage Anti-Restriction-Induced System) is a novel anti-phage system. PARIS is found in 4% of prokaryotic genomes. It comprises an ATPase associated with a DUF4435 protein, which can be found either as a two-gene cassette or a single-gene fusion (1).
 
-This system relies on an unknown [Abortive infection](/general_concepts/Abi) mechanism to trigger growth arrest upon sensing a phage-encoded protein (Ocr). Interestingly, the Ocr protein has been found to inhibit R-M systems and BREX systems, making PARIS a suitable defense mechanism against RM resistant and/or BREX resistant phages (1, 2, 3). 
+This system relies on an unknown [Abortive infection](/general-concepts/abortive-infection) mechanism to trigger growth arrest upon sensing a phage-encoded protein (Ocr). Interestingly, the Ocr protein has been found to inhibit R-M systems and BREX systems, making PARIS a suitable defense mechanism against RM resistant and/or BREX resistant phages (1, 2, 3). 
 
 ## Example of genomic structure
 

deploy/df-wiki/.helmignore

+# Patterns to ignore when building packages.
+# This supports shell glob matching, relative path matching, and
+# negation (prefixed with !). Only one pattern per line.
+.DS_Store
+# Common VCS dirs
+.git/
+.gitignore
+.bzr/
+.bzrignore
+.hg/
+.hgignore
+.svn/
+# Common backup files
+*.swp
+*.bak
+*.tmp
+*.orig
+*~
+# Various IDEs
+.project
+.idea/
+*.tmproj
+.vscode/

deploy/df-wiki/Chart.yaml

+apiVersion: v2
+name: df-wiki
+description: A Helm chart for Kubernetes
+
+# A chart can be either an 'application' or a 'library' chart.
+#
+# Application charts are a collection of templates that can be packaged into versioned archives
+# to be deployed.
+#
+# Library charts provide useful utilities or functions for the chart developer. They're included as
+# a dependency of application charts to inject those utilities and functions into the rendering
+# pipeline. Library charts do not define any templates and therefore cannot be deployed.
+type: application
+
+# This is the chart version. This version number should be incremented each time you make changes
+# to the chart and its templates, including the app version.
+# Versions are expected to follow Semantic Versioning (https://semver.org/)
+version: 0.1.0
+
+# This is the version number of the application being deployed. This version number should be
+# incremented each time you make changes to the application. Versions are not expected to
+# follow Semantic Versioning. They should reflect the version the application is using.
+# It is recommended to use it with quotes.
+appVersion: "1.16.0"

deploy/df-wiki/templates/NOTES.txt

+1. Get the application URL by running these commands:
+{{- if .Values.ingress.enabled }}
+{{- range $host := .Values.ingress.hosts }}
+  {{- range .paths }}
+  http{{ if $.Values.ingress.tls }}s{{ end }}://{{ $host.host }}{{ .path }}
+  {{- end }}
+{{- end }}
+{{- else if contains "NodePort" .Values.service.type }}
+  export NODE_PORT=$(kubectl get --namespace {{ .Release.Namespace }} -o jsonpath="{.spec.ports[0].nodePort}" services {{ include "df-wiki.fullname" . }})
+  export NODE_IP=$(kubectl get nodes --namespace {{ .Release.Namespace }} -o jsonpath="{.items[0].status.addresses[0].address}")
+  echo http://$NODE_IP:$NODE_PORT
+{{- else if contains "LoadBalancer" .Values.service.type }}
+     NOTE: It may take a few minutes for the LoadBalancer IP to be available.
+           You can watch the status of by running 'kubectl get --namespace {{ .Release.Namespace }} svc -w {{ include "df-wiki.fullname" . }}'
+  export SERVICE_IP=$(kubectl get svc --namespace {{ .Release.Namespace }} {{ include "df-wiki.fullname" . }} --template "{{"{{ range (index .status.loadBalancer.ingress 0) }}{{.}}{{ end }}"}}")
+  echo http://$SERVICE_IP:{{ .Values.service.port }}
+{{- else if contains "ClusterIP" .Values.service.type }}
+  export POD_NAME=$(kubectl get pods --namespace {{ .Release.Namespace }} -l "app.kubernetes.io/name={{ include "df-wiki.name" . }},app.kubernetes.io/instance={{ .Release.Name }}" -o jsonpath="{.items[0].metadata.name}")
+  export CONTAINER_PORT=$(kubectl get pod --namespace {{ .Release.Namespace }} $POD_NAME -o jsonpath="{.spec.containers[0].ports[0].containerPort}")
+  echo "Visit http://127.0.0.1:8080 to use your application"
+  kubectl --namespace {{ .Release.Namespace }} port-forward $POD_NAME 8080:$CONTAINER_PORT
+{{- end }}

deploy/df-wiki/templates/_helpers.tpl

+{{/*
+Expand the name of the chart.
+*/}}
+{{- define "df-wiki.name" -}}
+{{- default .Chart.Name .Values.nameOverride | trunc 63 | trimSuffix "-" }}
+{{- end }}
+
+{{/*
+Create a default fully qualified app name.
+We truncate at 63 chars because some Kubernetes name fields are limited to this (by the DNS naming spec).
+If release name contains chart name it will be used as a full name.
+*/}}
+{{- define "df-wiki.fullname" -}}
+{{- if .Values.fullnameOverride }}
+{{- .Values.fullnameOverride | trunc 63 | trimSuffix "-" }}
+{{- else }}
+{{- $name := default .Chart.Name .Values.nameOverride }}
+{{- if contains $name .Release.Name }}
+{{- .Release.Name | trunc 63 | trimSuffix "-" }}
+{{- else }}
+{{- printf "%s-%s" .Release.Name $name | trunc 63 | trimSuffix "-" }}
+{{- end }}
+{{- end }}
+{{- end }}
+
+{{/*
+Create chart name and version as used by the chart label.
+*/}}
+{{- define "df-wiki.chart" -}}
+{{- printf "%s-%s" .Chart.Name .Chart.Version | replace "+" "_" | trunc 63 | trimSuffix "-" }}
+{{- end }}
+
+{{/*
+Common labels
+*/}}
+{{- define "df-wiki.labels" -}}
+helm.sh/chart: {{ include "df-wiki.chart" . }}
+{{ include "df-wiki.selectorLabels" . }}
+{{- if .Chart.AppVersion }}
+app.kubernetes.io/version: {{ .Chart.AppVersion | quote }}
+{{- end }}
+app.kubernetes.io/managed-by: {{ .Release.Service }}
+{{- end }}
+
+{{/*
+Selector labels
+*/}}
+{{- define "df-wiki.selectorLabels" -}}
+app.kubernetes.io/name: {{ include "df-wiki.name" . }}
+app.kubernetes.io/instance: {{ .Release.Name }}
+{{- end }}
+
+{{/*
+Create the name of the service account to use
+*/}}
+{{- define "df-wiki.serviceAccountName" -}}
+{{- if .Values.serviceAccount.create }}
+{{- default (include "df-wiki.fullname" .) .Values.serviceAccount.name }}
+{{- else }}
+{{- default "default" .Values.serviceAccount.name }}
+{{- end }}
+{{- end }}