.gitattributes

 data/ filter=lfs diff=lfs merge=lfs -text
 data/**/*.csv filter=lfs diff=lfs merge=lfs -text
+data/**/*.tsv filter=lfs diff=lfs merge=lfs -text

.gitlab-ci.yml

@@ -4,10 +4,15 @@ workflow:
       when: never
     - when: always
 
+
+
+
+
+
 # Functions that should be executed before the build script is run
 
 variables:
-  HELM_VERSION: "3.9.3"
+  HELM_VERSION: "3.13.3"
   IMAGE_NAME: "df-wiki"
   # dev
   HOST_DEV: 'defense-finder.dev.pasteur.cloud'
@@ -15,6 +20,8 @@ variables:
   # prod
   HOST_PROD: 'defense-finder.pasteur.cloud'
   MEILI_HOST_PROD: 'defense-finder-meilisearch.pasteur.cloud'
+  PIP_CACHE_DIR: "$CI_PROJECT_DIR/.cache/pip"
+
 
 
 cache:
@@ -24,15 +31,18 @@ cache:
     
 
 stages:
+ 
   - delete-release
   - build-df-cli
+  - lint
   - get-data
   - deploy-meilisearch
   - update-meilisearch-indexes
   - get-meili-key
   - build
+  # - build-wiki
   - deploy
-
+  # - load-website
 
 .docker-login: &docker-login
   - i=0; while [ "$i" -lt 12 ]; do docker info && break; sleep 5; i=$(( i + 1 )) ; done
@@ -43,9 +53,17 @@ stages:
 # Build df-wiki-cli package
 
 
+.df-wiki-cli-run:
+  image: python:3.11-bullseye
+  cache:                      # Pip's cache doesn't store the python packages
+    paths:                    # https://pip.pypa.io/en/stable/topics/caching/
+      - .cache/pip
+  before_script:
+    - pip install df-wiki-cli --index-url https://gitlab-ci-token:${CI_JOB_TOKEN}@gitlab.pasteur.fr/api/v4/projects/5222/packages/pypi/simple
+
 build:df-wiki-cli:
-  stage: build-df-cli
   image: python:3.11-bullseye
+  stage: build-df-cli
   before_script:
     - cd packages/df-wiki-cli/
     - pip install poetry
@@ -61,9 +79,7 @@ build:df-wiki-cli:
     - echo "Build done ..."
     - poetry publish --repository gitlab --skip-existing
     - echo "Publishing done!"
-  rules:
-    - changes:
-      - packages/df-wiki-cli/**/*.{py, toml} # ... or whatever your file extension is
+  when: manual
   allow_failure: true
 ################ DEPLOY MEILISEARCH #################
 
@@ -88,14 +104,14 @@ build:df-wiki-cli:
       --values deploy/meilisearch/values.yaml
       --values deploy/meilisearch/values.${ENV:-development}.yaml
     # wait for it to start
-    - MEILI_POD=$(kubectl -n=${KUBE_NAMESPACE} get po -l app.kubernetes.io\/instance=${CI_PROJECT_NAME}-${CI_ENVIRONMENT_NAME}-meilisearch,app.kubernetes.io\/name=meilisearch --output jsonpath='{.items[0].metadata.name}')
-    - |
-      until kubectl -n=${KUBE_NAMESPACE} wait --for=condition=ready pod ${MEILI_POD} --timeout=1s
-      do
-        date
-        sleep 1
-        kubectl -n=${KUBE_NAMESPACE} get po
-      done
+    # - MEILI_POD=$(kubectl -n=${KUBE_NAMESPACE} get po -l app.kubernetes.io\/instance=${CI_PROJECT_NAME}-${CI_ENVIRONMENT_NAME}-meilisearch,app.kubernetes.io\/name=meilisearch --output jsonpath='{.items[0].metadata.name}')
+    # - |
+    #   until kubectl -n=${KUBE_NAMESPACE} wait --for=condition=ready pod ${MEILI_POD} --timeout=1s
+    #   do
+    #     date
+    #     sleep 1
+    #     kubectl -n=${KUBE_NAMESPACE} get po
+    #   done
 
 
 deploy:meilisearch:dev:
@@ -163,16 +179,39 @@ delete-meili-helm-release:prod:
     - helm delete -n ${NAMESPACE} ${CI_PROJECT_NAME}-${CI_ENVIRONMENT_NAME}-meilisearch 
 
 
-# Update Meili search indexes
+# lint
 
+lint:
+  extends: .df-wiki-cli-run
+  stage: lint
+  script:
+    - cd content/3.defense-systems
+    - find . -name '*.md' ! -name '0.index.md' | sort | xargs -I {} df-wiki-cli content lint --file {}
+  when: manual
+
+# Update Meili search indexes + generate some file that goes to meilisearch
 .update-meilisearch-index:
+  extends: .df-wiki-cli-run
   stage: update-meilisearch-indexes
-  image: python:3.11-bullseye
   variables:
     MEILI_HOST: "http://localhost:7700"
-  before_script:
-    - pip install df-wiki-cli --index-url https://gitlab-ci-token:${CI_JOB_TOKEN}@gitlab.pasteur.fr/api/v4/projects/5222/packages/pypi/simple
   script:
+    # - rm data/list-systems.json
+    - >
+      df-wiki-cli 
+      content systems 
+      --dir content/3.defense-systems/ 
+      --pfam public/pfam-a-hmm.csv 
+      --output data/list-systems.json
+    - df-wiki-cli meilisearch delete-all-documents refseq  
+    - >
+      df-wiki-cli
+      meilisearch 
+      --host ${MEILI_HOST} 
+      --key ${MEILI_MASTER_KEY}
+      index-update 
+      refseq 
+      sys_id
     - >
       df-wiki-cli
       meilisearch 
@@ -187,8 +226,18 @@ delete-meili-helm-release:prod:
       --host ${MEILI_HOST} 
       --key ${MEILI_MASTER_KEY}
       update
-      --file data/all_predictions_statistics.csv
+      --file data/all_predictions_statistics_clean.csv
       --document structure
+    - >
+      df-wiki-cli
+      meilisearch 
+      --host ${MEILI_HOST} 
+      --key ${MEILI_MASTER_KEY}
+      update
+      --file data/list-systems.json
+      --document systems
+  allow_failure: false
+
 
 update-meilisearch-index:dev:
   rules:
@@ -212,12 +261,10 @@ update-meilisearch-index:prod:
 ############# get-meili-key ###############
 
 .set-meili-env:
-  image: python:3.11-bullseye
+  extends: .df-wiki-cli-run
   stage: get-meili-key
   variables:
     MEILI_HOST: "http://localhost:7700"
-  before_script:
-    - pip install df-wiki-cli --index-url https://gitlab-ci-token:${CI_JOB_TOKEN}@gitlab.pasteur.fr/api/v4/projects/5222/packages/pypi/simple
   script:
     - > 
       df-wiki-cli 
@@ -229,6 +276,7 @@ update-meilisearch-index:prod:
   artifacts:
       reports:
         dotenv: build.env
+  allow_failure: false
 
 
 set-meili-env:dev:
@@ -249,28 +297,24 @@ set-meili-env:prod:
 
 ##############################
 get-zotero:
-  image: python:3.11-bullseye
+  extends: .df-wiki-cli-run
   stage: get-data
-  before_script:
-    - pip install df-wiki-cli --index-url https://gitlab-ci-token:${CI_JOB_TOKEN}@gitlab.pasteur.fr/api/v4/projects/5222/packages/pypi/simple
   script:
-    - df-wiki-cli articles --key ${ZOTERO_API_KEY} --output public/articles.json
+    - df-wiki-cli articles --key ${ZOTERO_API_KEY} --output content/_data/_articles.json
   artifacts:
     paths:
-      - public/articles.json
+      - content/_data/_articles.json
   rules:
     - if: $CI_COMMIT_BRANCH == "main"
 
-get-pfam:
-  image: python:3.11-bullseye
-  stage: get-data
-  before_script:
-    - pip install df-wiki-cli --index-url https://gitlab-ci-token:${CI_JOB_TOKEN}@gitlab.pasteur.fr/api/v4/projects/5222/packages/pypi/simple
-  script:
-    - df-wiki-cli pfam --output public/pfam-a-hmm.csv
-  artifacts:
-    paths:
-      - public/pfam-a-hmm.csv
+# get-pfam:
+#   extends: .df-wiki-cli-run
+#   stage: get-data
+#   script:
+#     - df-wiki-cli pfam --output public/pfam-a-hmm.csv
+#   artifacts:
+#     paths:
+#       - public/pfam-a-hmm.csv
   # rules:
   #   - if: $CI_COMMIT_BRANCH == "main"
 
@@ -303,9 +347,12 @@ build:dev:wiki:
   extends: .build
   needs:
     - set-meili-env:dev
-    - get-pfam
+    # - get-pfam
   variables:
     BASE_URL: /wiki/
+  before_script:
+    - *docker-login
+    # - "sed -i 's/MEILISEARCH_API_KEY/${$MEILI_API_KEY}/g' nuxt.config.ts"
   rules:
     - if: $CI_COMMIT_BRANCH != "main"  
 
@@ -315,13 +362,105 @@ build:prod:wiki:
   needs:
     - set-meili-env:prod
     - get-zotero
-    - get-pfam
+    # - get-pfam
   variables:
     BASE_URL: /wiki/
   rules:
     - if: $CI_COMMIT_BRANCH == "main"  
 
 
+# build-wiki:dev:
+#   stage: build-wiki
+#   needs:
+#     - set-meili-env:dev
+#   rules:
+#     - if: $CI_COMMIT_BRANCH != "main"    
+#   image: node:21.1-bookworm-slim
+#   variables:
+#     NODE_OPTIONS: --max_old_space_size=12288
+#     NUXT_APP_BASE_URL: /wiki/
+#     NUXT_PUBLIC_MEILISEARCH_CLIENT_HOST_URL: ${MEILI_HOST}
+#     NUXT_PUBLIC_MEILISEARCH_CLIENT_SEARCH_API_KEY: ${MEILI_API_KEY}
+#     NUXT_PUBLIC_MEILI_HOST: ${MEILI_HOST}
+#     NUXT_PUBLIC_MEILI_API_KEY: ${MEILI_API_KEY}
+#   before_script:
+#     - npm install
+#   script:
+#     - npm run generate
+#   artifacts:
+#     paths:
+#       - .output/public
+
+# build-wiki:prod:
+#   stage: build-wiki
+#   rules:
+#     - if: $CI_COMMIT_BRANCH == "main"
+#   needs:
+#     - set-meili-env:prod
+#     - get-zotero
+#   image: node:21.1-bookworm-slim
+#   variables:
+#     NODE_OPTIONS: --max_old_space_size=12288
+#     NUXT_APP_BASE_URL: /wiki/
+#     NUXT_PUBLIC_MEILISEARCH_CLIENT_HOST_URL: ${MEILI_HOST}
+#     NUXT_PUBLIC_MEILISEARCH_CLIENT_SEARCH_API_KEY: ${MEILI_API_KEY}
+#     NUXT_PUBLIC_MEILI_HOST: ${MEILI_HOST}
+#     NUXT_PUBLIC_MEILI_API_KEY: ${MEILI_API_KEY}
+#   before_script:
+#     - npm install
+#   script:
+#     - npm run generate
+#   artifacts:
+#     paths:
+#       - .output/public
+
+
+# load-website:dev:
+#   image: harbor.pasteur.fr/kube-system/helm-kubectl:$HELM_VERSION
+#   stage: load-website
+#   needs: 
+#     - build-wiki:dev
+#     - deploy:dev
+#   variables:
+#     NAMESPACE: "defense-finder-dev"
+#   environment:
+#     name: "k8sdev-01"
+#   rules:
+#     - if: $CI_COMMIT_BRANCH != "main"
+#   script:
+#     - kubectl --namespace ${NAMESPACE} wait pod -l "app.kubernetes.io/name=df-wiki" --for condition=Ready --timeout=600s 
+#     - echo "Le pod est ready"
+#     - WIKI_POD=$(kubectl --namespace ${NAMESPACE} get pods -l "app.kubernetes.io/name=df-wiki" --output jsonpath='{.items[0].metadata.name}')
+#     - kubectl --namespace ${NAMESPACE} cp .output/public/ ${WIKI_POD}:/website
+#     - |
+#       kubectl --namespace ${NAMESPACE}
+#       exec ${WIKI_POD} -- bash -c 'cd /structure-data/sanitized-dump && find * -type d -exec sh -c "for d in "$@"; do (cd "/usr/share/nginx/html/$d"; cp --archive --recursive --symbolic-link /structure-data/sanitized-dump/$d/* .) done" argv0 {} +'
+
+
+# load-website:prod:
+#   image: harbor.pasteur.fr/kube-system/helm-kubectl:$HELM_VERSION
+#   stage: load-website
+#   needs: 
+#     - build-wiki:prod
+#     - deploy:prod
+#   environment:
+#     name: "k8sprod-02"
+#   variables: 
+#     NAMESPACE: "defense-finder-prod"
+#   rules:
+#     - if: $CI_COMMIT_BRANCH == "main"
+#   script:
+#     - kubectl --namespace ${NAMESPACE} wait pod -l "app.kubernetes.io/name=df-wiki" --for condition=Ready --timeout=600s 
+#     - echo "Le pod est ready"
+#     - WIKI_POD=$(kubectl --namespace ${NAMESPACE} get pods -l "app.kubernetes.io/name=df-wiki" --output jsonpath='{.items[0].metadata.name}')
+
+#     - kubectl --namespace ${NAMESPACE} cp .output/public/ ${WIKI_POD}:/website
+#     - kubectl --namespace ${NAMESPACE} cp scripts/copy-structure-data.sh ${WIKI_POD}:/structure-data/sanitized-dump
+#     - kubectl --namespace ${NAMESPACE} exec ${WIKI_POD} -- bash -c 'cd /structure-data/sanitized-dump && bash copy-structure-data.sh'
+
+
+
+
 ################ DEPLOY ##########################
 .deploy:
   stage: deploy
@@ -343,11 +482,20 @@ build:prod:wiki:
       --set env="${ENV:-development}"
       --values deploy/df-wiki/values.yaml
       --values deploy/df-wiki/values.${ENV:-development}.yaml
+  after_script:
+    - kubectl --namespace ${KUBE_NAMESPACE} wait pod -l "app.kubernetes.io/name=df-wiki" --for condition=Ready --timeout=600s 
+    - echo "Wiki pod is ready"
+    - WIKI_POD=$(kubectl --namespace ${KUBE_NAMESPACE} get pods -l "app.kubernetes.io/name=df-wiki" --output jsonpath='{.items[0].metadata.name}')
+    - echo ${WIKI_POD}
+    - kubectl --namespace ${KUBE_NAMESPACE} cp scripts/copy-structure-data.sh ${WIKI_POD}:/structure-data/sanitized-dump
+    - kubectl --namespace ${KUBE_NAMESPACE} exec ${WIKI_POD} -- bash -c 'cd /structure-data/sanitized-dump && bash copy-structure-data.sh'
+    
+    
 
 deploy:dev:
   extends: .deploy
   rules:
-    - if: $CI_COMMIT_BRANCH != "main"
+    - if: $CI_COMMIT_BRANCH == "dev" || $CI_COMMIT_BRANCH == "refactor-facet-autocomplete"
   needs:
     - "build:dev:wiki"
   when: manual
@@ -410,3 +558,5 @@ delete-helm-release:prod:
   script:
     - echo "Removing $CI_PROJECT_NAME-$CI_ENVIRONMENT_NAME"
     - helm delete -n ${NAMESPACE} $CI_PROJECT_NAME-$CI_ENVIRONMENT_NAME
+
+

Dockerfile

@@ -17,6 +17,10 @@ ARG MEILI_HOST=http://localhost:7700
 ARG MEILI_API_KEY=api_key
 
 ENV NUXT_APP_BASE_URL=${BASE_URL}
+# nuxt module
+ENV NUXT_PUBLIC_MEILISEARCH_CLIENT_HOST_URL=${MEILI_HOST}
+ENV NUXT_PUBLIC_MEILISEARCH_CLIENT_SEARCH_API_KEY=${MEILI_API_KEY}
+
 ENV NUXT_PUBLIC_MEILI_HOST=${MEILI_HOST}
 ENV NUXT_PUBLIC_MEILI_API_KEY=${MEILI_API_KEY}
 
@@ -24,6 +28,7 @@ ENV NUXT_PUBLIC_MEILI_API_KEY=${MEILI_API_KEY}
 WORKDIR /usr/src/app
 COPY --from=install /usr/src/app ./
 COPY . /usr/src/app
+
 EXPOSE 3000 24678 4000
 CMD ["npm", "run", "dev"]
 
@@ -51,8 +56,13 @@ ARG BASE_URL=/
 ARG MEILI_HOST=http://localhost:7700
 ARG MEILI_API_KEY
 
-ENV NODE_OPTIONS=--max_old_space_size=8192
+ENV NODE_OPTIONS=--max_old_space_size=12288
 ENV NUXT_APP_BASE_URL=${BASE_URL}
+
+# nuxt module
+ENV NUXT_PUBLIC_MEILISEARCH_CLIENT_HOST_URL=${MEILI_HOST}
+ENV NUXT_PUBLIC_MEILISEARCH_CLIENT_SEARCH_API_KEY=${MEILI_API_KEY}
+
 ENV NUXT_PUBLIC_MEILI_HOST=${MEILI_HOST}
 ENV NUXT_PUBLIC_MEILI_API_KEY=${MEILI_API_KEY}
 
@@ -60,11 +70,16 @@ ENV NUXT_PUBLIC_MEILI_API_KEY=${MEILI_API_KEY}
 WORKDIR /usr/src/app
 COPY --from=install /usr/src/app ./
 COPY . /usr/src/app
+
 RUN npm run generate
 
 ### STAGE: NGINX ###
-FROM nginxinc/nginx-unprivileged:1.25
+FROM nginx:1.25-bookworm
 # 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
+RUN apt update -y && apt install rsync -y
+COPY nginx.conf /etc/nginx/nginx.conf
+RUN chown nginx:nginx /usr/share/nginx/html
+COPY --chown=nginx:nginx --from=generate /usr/src/app/.output/public /usr/share/nginx/html
+# RUN chmod -R nginx:nginx /usr/share/nginx/html/
+USER nginx
 CMD ["nginx", "-g", "daemon off;"]
\ No newline at end of file

components/AutocompleteMeiliFacets.vue

+<script setup lang="ts">
+import { filter } from '@observablehq/plot'
+
+export interface FilterItem {
+    type: 'facet' | 'innerOperator' | 'outerOperator' | 'value'
+    value: string
+    title: string
+    count?: number
+    deletable: boolean
+    props: Record<string, any>
+}
+
+export interface FacetItem {
+    title: string
+    value: string
+    type: "facet"
+    icon?: string
+    count?: number
+
+}
+
+export interface OperatorItem {
+    title: string,
+    type: 'operator'
+
+}
+export interface FacetCategory {
+    title: string
+    type: "subheader"
+}
+export interface FacetDivider {
+    type: "divider"
+}
+
+export type FacetInputItem = FacetItem | FacetCategory | FacetDivider
+
+
+export interface Props {
+    db: string
+    modelValue: FilterItem[] | undefined
+    facets: MaybeRef<FacetInputItem[] | undefined>
+    facetDistribution: MaybeRef<Record<string, Record<string, number>> | undefined>
+    isValidFilters?: MaybeRef<boolean>
+    autocompleteProps?: Record<string, any>
+
+}
+
+
+const emit = defineEmits(['update:modelValue', "meiliFilters"])
+const filterId = ref<number>(0)
+const props = withDefaults(defineProps<Props>(), {
+    modelValue: undefined,
+    autocompleteProps: () => {
+        return {
+            chips: true,
+            clearable: true,
+            multiple: true,
+            "auto-select-first": true,
+            "return-object": true,
+            "prepend-inner-icon": "md:filter_alt",
+            "hide-details": "auto",
+            "item-value": "value", "item-title": "title",
+            label: "Filter results...",
+            "single-line": true,
+
+        }
+    },
+    isValidFilters: false
+});
+// const { result: msResult } = useMeiliSearch(props.db)
+const isAutocompleteFocused = ref<boolean>(false)
+// const facetDistribution: Ref<Record<string, Record<string, number>>>  = useState('facetDistribution')
+
+
+
+const autocompleteProps = computed(() => {
+    return {
+        ...props.autocompleteProps,
+        items: toValue(autocompleteItems)
+    }
+})
+
+const filterStep = computed(() => {
+    const toValFilterItems = toValue(props.modelValue)
+    if (toValFilterItems !== undefined) {
+        return toValFilterItems.length % 4
+    }
+})
+
+const innerOperatorItems = ref<FilterItem[]>([
+    {
+        type: "innerOperator", value: '=', title: "is", deletable: false, props: {
+            type: "innerOperator", deletable: false
+        }
+    }, {
+        type: "innerOperator", value: '!=', title: "is not", deletable: false, props: {
+            type: "innerOperator",
+            deletable: false
+        }
+    },
+
+])
+
+const outerOperatorItems = ref<FilterItem[]>([
+    {
+        type: "outerOperator", value: 'AND', title: "AND", deletable: false, props: {
+            type: "outerOperator", deletable: false
+        }
+    }, {
+        type: "outerOperator", value: 'OR', title: "OR", deletable: false, props: {
+            type: "outerOperator",
+            deletable: false
+        }
+    },
+
+])
+
+const autocompleteItems = computed(() => {
+    const toValFilterItems = toValue(props.modelValue)
+    // const index = toValFilterItems?.length ?? 0
+    if (filterStep.value === undefined || filterStep.value === 0) {
+        filterId.value++
+        return toValue(props.facets)?.map(facetItem => {
+            switch (facetItem.type) {
+                case "facet":
+                    return {
+                        type: "facet",
+                        value: `${facetItem.value}-${filterId.value}`,
+                        title: facetItem.title,
+                        deletable: false,
+                        icon: facetItem?.icon,
+                        count: facetItem?.count,
+                        props: {
+                            deletable: false,
+                            type: "facet"
+                        }
+                    }
+                case "subheader":
+                    return {
+                        type: "subheader",
+                        title: facetItem.title,
+                        deletable: false,
+
+                        props: {
+                            type: "subheader"
+                        }
+                    }
+                case "divider":
+                    return { type: "divider" }
+                default:
+                    break;
+            }
+
+        })
+    }
+    if (filterStep.value === 1) {
+        filterId.value++
+        return innerOperatorItems.value.map(it => { return { ...it, value: `${it.value}-${filterId.value}`, } })
+    }
+    if (filterStep.value === 2) {
+        filterId.value++
+
+        // get the facet value
+        if (Array.isArray(toValFilterItems)) {
+            const { type, value } = toValFilterItems?.slice(-2, -1)[0]
+            const sanitizedValue = value.split("-")[0]
+            const facetDistri = toValue(props.facetDistribution)
+            return facetDistri?.[sanitizedValue] ? Object.entries(facetDistri[sanitizedValue]).map(([key, val]) => {
+                return {
+                    type: "value", value: `${key}-${filterId.value}`, title: key, count: val, deletable: true, props: {
+                        type: "value", count: val, deletable: true
+                    }
+                }
+            }) : []
+        }
+    }
+    if (filterStep.value === 3) {
+        filterId.value++
+        return outerOperatorItems.value.map(it => { return { ...it, value: `${it.value}-${filterId.value}`, } })
+    }
+})
+
+const hasFacetDistribution = computed(() => {
+
+    const toValFacetDistribution = toValue(props.facetDistribution)
+
+    return toValFacetDistribution !== undefined && Object.keys(toValFacetDistribution).length > 0
+})
+
+function updateAutocompleteFocused(isFocused: boolean) {
+    isAutocompleteFocused.value = isFocused
+}
+
+
+function emitUpdateModelValue(filters: MaybeRef<FilterItem[] | undefined>) {
+    emit('update:modelValue', toValue(filters))
+
+}
+
+function clearFilters() {
+    emitUpdateModelValue(undefined)
+}
+function deleteOneFilter(index: number) {
+
+    const toValFilterItems = toValue(props.modelValue)
+    // check if the next item is an outeroperator
+    const nextFilterItem = toValFilterItems?.slice(index + 1, index + 2)
+    if (index + 1 === toValFilterItems?.length && toValFilterItems?.length >= 7) {
+        // need to remove the previous outer operator
+        toValFilterItems?.splice(index - 3, 4)
+    }
+    else if (nextFilterItem?.length === 1 && nextFilterItem[0].type === 'outerOperator') {
+        toValFilterItems?.splice(index - 2, 4)
+
+    }
+    else {
+        toValFilterItems?.splice(index - 2, 3)
+    }
+
+    emitUpdateModelValue(toValFilterItems)
+}
+
+function isItemFilter(type: string | undefined) {
+    return type === "facet" || type === "innerOperator" || type === "outerOperator" || type === "value"
+}
+
+const hint = ref<string>('All <span class="font-weight-bold">OR</span> in a row are grouped together. Example: <span class="font-weight-bold">brex OR avs AND Archea</span> &rArr; <span class="font-weight-bold">(brex OR avs) AND Archea</span>')
+
+</script>
+<template>
+    <v-autocomplete :model-value="props.modelValue" @click:clear="clearFilters" v-bind="autocompleteProps" :hint="hint"
+        persistent-hint @update:focused="updateAutocompleteFocused" @update:modelValue="emitUpdateModelValue"
+        :loading="!hasFacetDistribution" :disabled="!hasFacetDistribution">
+        <template #message="{ message }">
+            <span v-html="message"></span>
+        </template>
+        <template #item="{ props, item }">
+            <v-list-item v-if="isItemFilter(item?.raw?.type)" v-bind="{ ...props, active: false }" :title="item.title"
+                :prepend-icon="item?.raw?.icon ? item.raw.icon : undefined"
+                :subtitle="item.raw?.count ? item.raw.count : ''" :value="props.value">
+            </v-list-item>
+            <v-divider v-if="item.raw.type === 'divider'"></v-divider>
+            <v-list-subheader v-if="item.raw.type === 'subheader'" :title="item.raw.title"></v-list-subheader>
+        </template>
+        <template #chip="{ props, item, index }">
+            <v-chip v-bind="props" :text="item.raw.title" :closable="item.props.deletable"
+                @click:close="item.props.type === deleteOneFilter(index)"></v-chip>
+        </template>
+        <!-- <template #append>
+            <v-btn variant="text" icon="md:filter_alt" @click="emitUpdateModelValue(props.modelValue)"
+                :disabled="!isValidFilters"></v-btn>
+        </template> -->
+
+    </v-autocomplete>
+</template>
\ No newline at end of file

components/AccessionChips.vue → components/CollapsibleChips.vue

 <script setup lang="ts">
 
+
+interface item {
+    title: string;
+    href?: string | undefined
+}
+
 export interface Props {
-    accessions: string[];
+    items: item[];
     itemsToDisplay?: number;
-    baseUrl: string;
 }
 
 const props = withDefaults(defineProps<Props>(), {
-    pfamString: null,
-    itemsToDisplay: 2,
+    items: () => [],
+    itemsToDisplay: 1,
+
 });
-// const accessions = computed(() => {
-//     if (props.accessionString === null) {
-//         return [];
-//     } else {
-//         return props.accessionString.split(",").map((acc) => acc.trim());
-//     }
-// });
+
+
 const show = ref(false);
 
-function constructUrl(accession: string) {
-    return new URL(accession, props.baseUrl).toString();
-}
+
 </script>
 <template>
     <!-- class="d-inline-flex justify-start align-center" -->
 
     <span v-if="show" class="d-flex flex-wrap align-center justify-start">
-        <template v-if="accessions.length > itemsToDisplay">
-            <template v-for="(acc) in accessions" :key="acc">
-                <v-chip :href="constructUrl(acc)" target="_blank" color="info" class="mr-1 my-1 align-self-center"
-                    size="small">
-                    {{ acc }}
+        <template v-if="items.length > itemsToDisplay">
+            <template v-for="item in items" :key="item.title">
+                <v-chip :href="item?.href" :target="item?.href === undefined ? item?.href : '_blank'" color="info"
+                    class="mr-1 my-1 align-self-center" size="small">
+                    {{ item.title }}
                 </v-chip>
             </template>
         </template>
-        <v-btn v-if="itemsToDisplay < accessions.length" variant="text" :icon="'mdi-chevron-up'"
-            @click="show = !show"></v-btn>
+        <v-btn v-if="itemsToDisplay < items.length" variant="text" :icon="'mdi-chevron-up'" @click="show = !show"></v-btn>
     </span>
     <span v-else class="d-flex flex-wrap align-center justify-start">
-        <template v-for="(acc, index) in accessions" :key="acc">
-            <v-chip v-if="index < itemsToDisplay || itemsToDisplay < 0" :href="constructUrl(acc)" target="_blank"
-                color="info" class="mr-1 my-1 align-self-center" size="small">
-                {{ acc }}
+        <template v-for="(item, index) in items" :key="item.title">
+            <v-chip v-if="index < itemsToDisplay || itemsToDisplay < 0 || items.length - itemsToDisplay === 1"  :href="item?.href"
+                :target="item?.href === undefined ? item?.href : '_blank'" color="info" class="mr-1 my-1 align-self-center"
+                size="small">
+                {{ item.title }}
             </v-chip>
-            <template v-if="index === itemsToDisplay">
+            <template v-if="index === itemsToDisplay && items.length - itemsToDisplay > 1">
                 <v-chip v-if="!show" variant="text" class="text-grey text-caption align-self-center px-1"
                     @click="show = !show">
-                    (+{{ accessions.length - itemsToDisplay }} others)
+                    (+{{ items.length - itemsToDisplay }} others)
                 </v-chip>
-                <v-btn v-if="itemsToDisplay < accessions.length && !show" variant="text" :icon="'mdi-chevron-down'"
+                <v-btn v-if="itemsToDisplay < items.length && !show" variant="text" :icon="'mdi-chevron-down'"
                     @click="show = !show"></v-btn>
             </template>
         </template>

components/LayoutWrapper.vue

 <script lang="ts" setup>
+
+import { useDisplay } from 'vuetify'
+
+const { mobile } = useDisplay()
 export interface Props {
   fluid?: boolean
   toc?: boolean
   edit?: boolean
+  navDrawer?: boolean
+  title?: string
 }
 
 const props = withDefaults(defineProps<Props>(), {
   fluid: false,
   toc: true,
-  edit: true
+  edit: true,
+  navDrawer: true,
+  title: null
 });
 const drawer = ref(true);
 
@@ -21,26 +29,32 @@ function onScroll() {
   }
   else { density.value = "prominent" }
 }
-
 </script>
 
 <template>
   <VApp>
     <v-main style="min-height: 300px">
       <v-container v-scroll="onScroll" :fluid="fluid">
-        <slot />
-        <!-- </v-card-text>
-          </v-card> -->
-        <EditGitlab v-if="edit" />
-        <NavPrevNext v-if="edit" />
+        <v-row justify="center">
+          <v-col cols="auto">
+            <v-card flat color="transparent" :min-width="mobile ? undefined : 900" :max-width="fluid ? undefined : 1500">
+              <v-card-text>
+                <slot />
+              </v-card-text>
+              <EditGitlab v-if="edit" />
+              <NavPrevNext v-if="edit" />
+            </v-card>
+          </v-col>
+        </v-row>
       </v-container>
       <!-- <Footer></Footer> -->
     </v-main>
-    <NavNavbar v-model:drawer="drawer" :density="density"  />
-    <slot name="drawer" :drawer="drawer">
+    <NavNavbar v-model:drawer="drawer" :title="title !== null ? title : undefined" :density="density"
+      :drawer-enabled="navDrawer" />
+    <slot v-if="navDrawer" name="drawer" :drawer="drawer">
       <NavDrawer :drawer="drawer" />
     </slot>
-    <NavTableOfContent v-if="toc" :links="page.body.toc.links" />
+    <NavTableOfContent v-if="toc" :links="page.body.toc.links ?? []" />
     <nav-back-to-top />
   </VApp>
 </template>

components/Nav/Drawer.vue

@@ -10,13 +10,18 @@ const props = withDefaults(defineProps<Props>(), {
 // import { useCustomTheme } from '~/composables/useCustomTheme'
 import { useDisplay, useTheme } from "vuetify";
 
-const { navigation } = useContent();
+const { navigation, page } = useContent();
 // const drawer = ref(true);
 
 // const computedNavigation = computed(() => {
 //     return navigation.value
-//         .filter(({ _path }) => {
-//             return _path !== "/refseq";
+//         .filter((item: { layout: string }) => {
+//             if (item?.layout === "db") {
+//                 console.log(item)
+//                 return false
+//             }
+//             return true
+//             // return item?.layout !== "db"
 //         })
 
 // });

components/Nav/Navbar.vue

@@ -5,17 +5,20 @@ import { useDisplay, useTheme } from "vuetify";
 export interface Props {
   density: 'prominent' | 'compact'
   drawer: boolean
+  drawerEnabled: boolean
+  title?: string
 }
 const runtimeConfig = useRuntimeConfig();
 
-const { navigation } = useContent();
 const { mobile } = useDisplay();
 const theme = useTheme();
 
 const switchTheme = ref(false)
 const props = withDefaults(defineProps<Props>(), {
   density: "prominent",
-  drawer: true
+  drawer: true,
+  drawerEnabled: true,
+  title: "Knowledge database of all known defense systems"
 });
 const emit = defineEmits(['update:drawer'])
 function toggleTheme() {
@@ -29,22 +32,15 @@ watchEffect(() => {
 const sections = ref([
   {
     id: "webservice",
-    label: "webservice",
+    label: "Webservice",
     href: runtimeConfig.public.defenseFinderWebservice,
   },
   { id: "wiki", label: "Wiki", to: '/', },
   { id: "refseq", label: "RefSeq DB", to: '/refseq/' },
-  { id: "structure", label: "Structures DB", to: '/predicted-structure/' },
-  { id: "help", label: "Help", to: '/help/' },
+  { id: "structure", label: "Structures DB", to: '/structure/' },
+  { id: "help", label: "Help", to: '/help/defensefinder' },
 ]);
 
-const computedNavigation = computed(() => {
-  return navigation.value
-    .filter(({ _path }) => {
-      return _path !== "/refseq";
-    })
-});
-
 
 function toggleDrawer() {
   emit('update:drawer', !props.drawer)
@@ -52,14 +48,13 @@ function toggleDrawer() {
 </script>
 <template>
   <v-app-bar :elevation="0" border name="app-bar" :density="density" color="background">
-    <template #prepend>
-      <v-app-bar-nav-icon @click.stop="toggleDrawer"></v-app-bar-nav-icon>
+    <template v-if="drawerEnabled" #prepend>
+      <v-app-bar-nav-icon @click.stop="toggleDrawer" class="d-flex align-self-center"></v-app-bar-nav-icon>
       <!-- <Logo height="45px" /> -->
     </template>
-    <v-app-bar-title>
-      <span class="d-flex align-center">
-        Knowledge database of all known anti-phage systems
-      </span>
+    <v-app-bar-title class="d-flex align-self-center py-0">
+      <span class="">
+        {{ title }} </span>
     </v-app-bar-title>
     <template #append>
       <template v-if="!mobile">

components/Nav/Navigation.vue

@@ -16,7 +16,7 @@ const props = defineProps<{
       <Navigation :navigation="navItem.children" />
     </v-list-group>
     <template v-else>
-      <v-list-item :title="navItem.title" :value="navItem.title" :to="navItem._path"
+      <v-list-item :title="navItem?.title ?? 'no title'" :value="navItem.title" :to="navItem._path"
         :prepend-icon="navItem?.icon ? navItem.icon : null" color="primary" exact nav>
       </v-list-item>
     </template>

components/PfamChips.vue

@@ -3,21 +3,21 @@ import { usePfamStore } from "@/stores/pfam";
 
 const { pfam: pfamStore } = usePfamStore();
 export interface Props {
-  pfamString: string | null;
+  pfams: Record<string, any>[];
   itemsToDisplay?: number;
 }
 
 const props = withDefaults(defineProps<Props>(), {
-  pfamString: null,
+  pfams: [],
   itemsToDisplay: 2,
 });
-const pfams = computed(() => {
-  if (props.pfamString === null) {
-    return [];
-  } else {
-    return props.pfamString.split(",").map((pfam) => pfam.trim());
-  }
-});
+// const pfams = computed(() => {
+//   if (props.pfamString === null) {
+//     return [];
+//   } else {
+//     return props.pfamString.split(",").map((pfam) => pfam.trim());
+//   }
+// });
 const show = ref(false);
 
 const pfamBaseUrl = ref(new URL("https://www.ebi.ac.uk/interpro/entry/pfam/"));
@@ -31,11 +31,11 @@ function constructPfamUrl(pfam: string) {
     <v-col>
       <v-card flat color="transparent" density="compact" rounded="false">
         <template v-for="(pfam, index) in pfams" :key="pfam">
-          <v-chip v-if="index < itemsToDisplay || itemsToDisplay < 0" :href="constructPfamUrl(pfam)" target="_blank"
+          <v-chip v-if="index < itemsToDisplay || itemsToDisplay < 0" :href="constructPfamUrl(pfam.AC)" target="_blank"
             color="info" class="mr-1 mb-1">
-            {{ pfam }}
+            {{ pfam.DE }}
             <v-tooltip activator="parent" location="top">{{
-              pfamStore.get(pfam)?.DE ?? "none"
+              pfam.AC
             }}</v-tooltip></v-chip>
 
           <template v-if="index === itemsToDisplay">
@@ -51,11 +51,11 @@ function constructPfamUrl(pfam: string) {
         </template>
         <template v-if="pfams.length > itemsToDisplay && show">
           <template v-for="(pfam, index) in pfams" :key="pfam">
-            <v-chip v-if="index >= itemsToDisplay" :href="constructPfamUrl(pfam)" target="_blank" color="info"
+            <v-chip v-if="index >= itemsToDisplay" :href="constructPfamUrl(pfam.AC)" target="_blank" color="info"
               class="mr-1 mb-1">
-              {{ pfam }}
+              {{ pfam.DE }}
               <v-tooltip activator="parent" location="top">{{
-                pfamStore.get(pfam)?.DE ?? "none"
+                pfam.AC
               }}</v-tooltip></v-chip>
           </template>
         </template>

components/PlotFigure.js

@@ -148,7 +148,7 @@ export default {
     const options = {
       ...(method === "plot" && {
         marks: this.mark == null ? [] : [this.mark],
-        width: 688 // better default for VitePress
+        // width: 688 // better default for VitePress
       }),
       ...this.options,
       className: "plot"

components/ServerDbTable.vue

+<script setup lang="ts">
+// import type { FacetDistribution } from "meilisearch";
+import { useCsvDownload } from "@/composables/useCsvDownload"
+import { useMeiliFilters } from "@/composables/useMeiliFilters"
+import { useSlots } from 'vue'
+import { useDisplay } from "vuetify";
+import { useThrottleFn } from '@vueuse/core'
+import type { FacetInputItem, FilterItem } from '@/components/AutocompleteMeiliFacets.vue'
+import { useMeiliSearch } from "#imports"
+import type { Filter } from "meilisearch";
+// import { saveAs } from "file-saver";
+export interface SortItem {
+    key: string,
+    order: boolean | 'asc' | 'desc'
+}
+
+export interface NumericalFilter {
+    id: string
+    name: string
+    range: [number, number]
+}
+
+export interface NumericalFilterModel extends NumericalFilter {
+    model: [number, number]
+}
+
+
+
+
+
+export interface AutocompleteMeiliFacetProps {
+    db: string
+    facets: FacetInputItem[] | undefined
+    facetDistribution: Record<string, Record<string, number>> | undefined
+
+}
+export interface Props {
+    title?: string
+    sortBy?: SortItem[]
+    numericalFilters?: Ref<string[] | undefined>
+    dataTableServerProps: Record<string, any>
+    columnsToDownload?: MaybeRef<string[] | undefined>
+    autocompleteMeiliFacetsProps: AutocompleteMeiliFacetProps
+}
+
+
+const props = withDefaults(defineProps<Props>(), {
+    title: '',
+    columnsToDownload: undefined,
+    sortBy: () => [{ key: "type", order: "asc" }],
+    numericalFilters: () => ref(undefined),
+    autocompleteMeiliFacetsProps: () => {
+        return {
+            db: 'refseq',
+            facetDistribution: undefined,
+            facets: undefined
+
+        }
+    }
+});
+
+
+
+// const facetDistribution: Ref<Record<string, Record<string, number>> | undefined> = useState(`refseqFacetDistribution`)
+
+
+const slots = useSlots()
+const sortByRef = toRef(props.sortBy)
+const emit = defineEmits(["refresh:search"])
+const { search: msSearch, result: msResult } = useMeiliSearch(props.autocompleteMeiliFacetsProps.db)
+const search: Ref<string> = ref("");
+const filterOrSearch: Ref<FilterItem[] | null> = ref(null)
+const hitsPerPage: Ref<number> = ref(25)
+const itemsPerPage: Ref<number[]> = ref([25, 50, 100])
+const filterError: Ref<string | null> = ref(null)
+// const msFilter: Ref<string | undefined> = ref(undefined)
+const page = ref(1)
+let loading = ref(false)
+const expanded = ref([])
+const { height, mobile } = useDisplay();
+const minTableHeight = ref(400)
+const computedTableHeight = computed(() => {
+    const computedHeight = height.value - 350
+    return computedHeight > minTableHeight.value ? computedHeight : minTableHeight.value
+})
+
+const pendingDownloadData = ref(false)
+
+const toRefNumericalFilters = toRef(props.numericalFilters)
+// const meiliFilters = ref<string | undefined>(undefined)
+
+const filterInputValues = computed(() => {
+    if (filterOrSearch.value != null) {
+        return filterOrSearch.value.filter(({ props }) => props.type !== 'text')
+    } else {
+        return null
+    }
+})
+
+
+const msSortBy = computed(() => {
+    if (sortByRef.value.length > 0) {
+        return sortByRef.value.map((curr) => {
+            if (curr?.key && curr?.order) {
+                return `${curr.key}:${curr.order}`
+            }
+            else { return "" }
+        })
+    } else { return undefined }
+})
+
+
+const reactiveParams = reactive({
+    facets: ["*"],
+    filter: [],
+    sort: ["type:asc"],
+})
+const paginationParams = computed(() => {
+    return { ...reactiveParams, page: toValue(page), hitsPerPage: toValue(hitsPerPage), limit: 500 }
+})
+
+const notPaginatedParams = computed(() => {
+    return { ...reactiveParams, limit: 500000 }
+})
+
+
+watch([paginationParams, msSortBy, page], ([newParams, newSort, newPage]) => {
+    if (toValue(isValidFilters)) {
+        searchOrFilter()
+    }
+})
+
+
+
+onBeforeMount(async () => {
+    searchOrFilter()
+    emitRefreshRes()
+
+
+})
+
+const msFilterCompo = ref<FilterItem[] | undefined>(undefined)
+
+
+const computedFilterStr = computed(() => {
+    const toValFilters = toValue(msFilterCompo)
+    let filtersStr: string | undefined = undefined
+    if (toValFilters !== undefined && toValFilters.length > 0) {
+        const tmpFilterItems = [...toValFilters]
+        if (tmpFilterItems.length % 4 === 0) {
+            tmpFilterItems.splice(-1)
+        }
+        filtersStr = "(" + tmpFilterItems.map((it, index) => {
+            const sanitizedValue = it.value.split("-").slice(0, -1).join("-")
+            if ((index + 1) % 4 === 3) {
+                return `"${sanitizedValue}"`
+            } else if ((index + 1) % 4 === 0) {
+                return ` ${sanitizedValue} `
+            }
+            else {
+                return `${sanitizedValue}`
+            }
+
+        }).join("") + ")"
+
+    }
+
+    return [filtersStr, props.numericalFilters].filter(f => f !== undefined && f !== null).join(" AND ")
+
+})
+
+
+const computedF = computed(() => toValue(props.numericalFilters))
+const { arrayFilters: computedFilter } = useMeiliFilters(msFilterCompo, computedF)
+// const computedFilter = computed(() => {
+//     const toValFilters = toValue(msFilterCompo)
+//     if (toValFilters !== undefined && toValFilters.length > 0) {
+//         meiliFilterAsArray
+//     }
+// })
+
+
+watch(computedFilter, () => {
+    console.log(toValue(computedFilter))
+    if (toValue(isValidFilters) && (toValue(computedFilter) !== undefined || toValue(filterInputValues) === null)) {
+        searchOrFilter()
+        emitRefreshRes()
+    }
+})
+
+
+const msError = computed(() => {
+    if (filterError.value?.type && filterError.value?.message) {
+        return filterError.value?.message
+    } else { return false }
+})
+
+const throttleSearch = useThrottleFn(async () => {
+    searchOrFilter()
+    emitRefreshRes()
+}, 300)
+
+
+const lastFilterItem = computed(() => {
+    const toValFilterItems = toValue(msFilterCompo)
+    if (toValFilterItems !== undefined && Array.isArray(toValFilterItems)) {
+        return toValFilterItems.slice(-1)[0]
+    }
+})
+
+const isValidFilters = computed(() => {
+    const toValFilterItems = toValue(msFilterCompo)
+    if (toValFilterItems === undefined || Array.isArray(toValFilterItems) && toValFilterItems?.length === 0) {
+        return true
+    }
+    else {
+        const toValLastFilterItem = toValue(lastFilterItem)
+        if (toValLastFilterItem !== undefined) {
+            console.log(toValLastFilterItem.type)
+            console.log(toValLastFilterItem.type === 'value')
+            return toValLastFilterItem.type === 'value'
+            // && isAutocompleteFocused.value === false
+            // || (toValFilterStep === 0 && toValLastFilterItem.type === "outerOperator" && toValLastFilterItem.value.split("-")[0] === "AND")
+        }
+    }
+    return false
+})
+
+
+async function searchOrFilter() {
+    if (toValue(isValidFilters)) {
+        // do something, it will be called at most 1 time per second
+        try {
+            loading.value = true
+            // const q = queryInputValue.value === null ? "" : queryInputValue.value
+            const q = search.value
+            await msSearch(q, { ...paginationParams.value, filter: toValue(computedFilter), sort: msSortBy.value })
+        } catch (error: any) {
+            filterError.value = error
+            console.log(error)
+        }
+        finally {
+            loading.value = false
+        }
+    }
+
+}
+
+
+
+function emitRefreshRes() {
+    const q = search.value
+    emit("refresh:search", {
+        index: props.autocompleteMeiliFacetsProps.db,
+        query: q,
+        params: { ...notPaginatedParams.value, filter: toValue(computedFilter), sort: msSortBy.value }
+    })
+}
+
+
+
+const totalHits = computed(() => {
+    return toValue(msResult)?.totalHits ?? toValue(msResult)?.estimatedTotalHits ?? 0
+})
+
+
+watch(search, () => {
+    searchOrFilter()
+    // emitRefreshRes()
+
+})
+// watch(msFilterCompo, () => {
+//     searchOrFilter()
+
+// })
+
+async function downloadData() {
+    pendingDownloadData.value = true
+    try {
+        const { data } = await useAsyncMeiliSearch({
+            index: props.autocompleteMeiliFacetsProps.db,
+            params: { ...toValue(notPaginatedParams), filter: toValue(computedFilter), sort: toValue(msSortBy) },
+            query: toValue(search),
+        })
+
+        useCsvDownload(data, props.columnsToDownload, props.title)
+    } finally {
+        pendingDownloadData.value = false
+    }
+}
+
+function focusedOrBlur(isFocused: boolean) {
+
+    if (!isFocused) {
+        emitRefreshRes()
+    }
+}
+
+
+
+</script>
+<template>
+    <v-card flat color="transparent">
+        <slot name="numerical-filters" :search="throttleSearch"></slot>
+        <v-data-table-server v-if="!msError" v-model:page="page" color="primary" v-bind="dataTableServerProps"
+            v-model:items-per-page="hitsPerPage" v-model:sortBy="sortByRef" v-model:expanded="expanded" fixed-header
+            :loading="loading" :items="msResult?.hits ?? []" :items-length="totalHits" density="compact"
+            :items-per-page-options="itemsPerPage" :height="computedTableHeight" class="elevation-1 mt-2">
+
+            <template #top>
+                <v-card variant="flat" color="transparent">
+                    <v-card-title>
+                        <v-badge :content="totalHits" color="primary" class="mr-3">
+                            <v-btn prepend-icon="md:download" :loading="pendingDownloadData" variant="text" color="primary"
+                                @click="downloadData()">{{
+                                    props.title }}
+                            </v-btn>
+                        </v-badge>
+                    </v-card-title>
+                    <v-card-title>
+                        <v-text-field v-model="search" label="Search..." hide-details="auto" :disabled="pendingDownloadData"
+                            prepend-inner-icon="mdi-magnify" single-line clearable
+                            @update:focused="focusedOrBlur"></v-text-field>
+                    </v-card-title>
+                    <v-card-title>
+                        <AutocompleteMeiliFacets v-model="msFilterCompo" v-bind="props.autocompleteMeiliFacetsProps"
+                            :is-valid-filters="isValidFilters">
+                        </AutocompleteMeiliFacets>
+
+
+                    </v-card-title>
+
+
+                </v-card>
+            </template>
+
+            <template v-for="(slot, index) of Object.keys(slots)" :key="index" v-slot:[slot]="data">
+                <slot :name="slot" v-bind="data"></slot>
+            </template>
+
+        </v-data-table-server>
+        <v-alert v-else type="error">
+            {{ msError }}
+        </v-alert>
+    </v-card>
+</template>
\ No newline at end of file

components/content/ArticleDoi.vue

 <script setup lang="ts">
 import { useDisplay } from "vuetify";
+import { useArticlesStore } from '@/stores/articles'
 
 export interface Props {
   index?: number;
@@ -8,16 +9,21 @@ export interface Props {
   enumerate?: boolean;
   title?: string;
   abstract?: string;
+  isRelevant?: boolean;
+
 }
 
 const props = withDefaults(defineProps<Props>(), {
   enumerate: true,
   divider: false,
+  isRelevant: false,
 });
+
 const { article } = useFetchArticle(props.doi);
 const { mobile } = useDisplay();
 const show = ref(false);
 
+
 const articleTitle = computed(() => {
   return props?.title ?? article?.value?.title ?? props.doi;
 });
@@ -26,42 +32,67 @@ const articleAbstract = computed(() => {
 });
 </script>
 <template>
-  <v-list-item :href="article?.href" :id="props.doi" :target="article?.target" density="compact" color="transparent"
+  <v-list-item :href="article?.href" :id="`ref-${props.doi}`" :target="article?.target" density="compact" color="transparent"
     class="px-1">
-    <template #prepend v-if="!mobile && enumerate">
-      <v-avatar color="primary" size="small" density="compact" variant="tonal">
-        {{ props?.index ?? "#" }}
-      </v-avatar>
+    <template v-if="!mobile" #prepend>
+      <v-icon icon="md:star" :color="props.isRelevant ? 'info' : 'transparent'"></v-icon>
     </template>
-    <!-- <template #append v-if="!mobile">
-            <v-avatar>
-                <v-icon>{{ article?.prependIcon }}</v-icon>
-            </v-avatar>
-        </template> -->
-    <v-card flat color="transparent" density="compact" class="my-0">
-      <v-card-item density="compact" :class="mobile ? 'px-0 py-1' : 'py-1'">
-        <v-card-title><span class="text-subtitle-1 font-weight-bold">{{
-          articleTitle
-        }}</span></v-card-title>
-        <v-card-subtitle>
+    <!-- <template v-if="!mobile" #append>
+      <v-btn v-if="articleAbstract" size="x-small" variant="plain"
+        :append-icon="show ? 'mdi-chevron-up' : 'mdi-chevron-down'" class="px-0"
+        @click.stop.prevent="show = !show">Abstract</v-btn>
+    </template> -->
+    <v-card flat color="transparent" density="compact" class="my-0 article-ref">
+      <v-card-item density="compact" class="pa-0">
+        <v-toolbar class="py-0 d-flex align-start article-toolbar" color="transparent" :height="20">
+          <v-toolbar-title class="font-weight-bold ml-0">{{ articleTitle }}</v-toolbar-title>
+
+          <v-btn v-if="articleAbstract" size="x-small" variant="plain" color="primary"
+            :append-icon="show ? 'mdi-chevron-up' : 'mdi-chevron-down'" class="px-1 align-center"
+            @click.stop.prevent="show = !show">Abstract</v-btn>
+        </v-toolbar>
+        <!-- <v-card-title class="py-0"><span class="font-weight-bold">{{
+            articleTitle
+          }}</span></v-card-title> -->
+        <v-card-subtitle class="py-0">
           {{ article?.subtitle ?? "no authors" }}</v-card-subtitle>
-        <v-card-subtitle>
+        <v-card-subtitle class="py-0">
           {{ article?.containerTitle ?? "no containerTitle" }} ({{
             article?.year
           }})</v-card-subtitle>
       </v-card-item>
-      <v-card-item v-if="articleAbstract" density="compact" :class="mobile ? 'px-0' : 'py-1'">
-        <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-item class="pa-0">
+        <v-expand-transition>
+          <v-card v-show="show" flat color="transparent">
+            <v-card-text class="px-0">
+              {{ articleAbstract }}
+            </v-card-text>
+          </v-card>
+        </v-expand-transition>
       </v-card-item>
-      <v-expand-transition>
-        <v-card v-show="show" flat color="transparent">
-          <v-card-text>
-            {{ articleAbstract }}
-          </v-card-text>
-        </v-card>
-      </v-expand-transition>
     </v-card>
   </v-list-item>
   <v-divider v-if="props.divider" inset></v-divider>
-</template>
\ No newline at end of file
+</template>
+<style scoped>
+.article-ref .v-card-item * {
+  line-height: 1rem !important;
+}
+
+
+
+.article-ref .v-card-item .v-card-subtitle,
+
+
+.article-ref .v-card-item button.v-btn span {
+  font-size: 0.8rem !important;
+}
+
+.article-toolbar .v-toolbar-title {
+  font-size: 0.9rem !important;
+}
+
+.article-toolbar div.v-toolbar__content * {
+  align-items: flex-start;
+}
+</style>
\ No newline at end of file

components/content/ListSystems.vue

-<script setup lang="ts">
-import { usePfamStore } from "@/stores/pfam";
-
-export interface Props {
-  headers: Array<Object>;
-  systems: Array<Object>;
-  height?: number;
-}
-
-const props = withDefaults(defineProps<Props>(), {
-  height: 800,
-});
-
-const itemsPerParge = ref(25);
-const search = ref("");
-const sortBy = ref([{ key: "system", order: "asc" }]);
-const expanded = ref([]);
-
-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;
-}
-const { initPfam } = usePfamStore();
-onMounted(() => {
-  initPfam();
-})
-</script>
-<template>
-  <v-card>
-    <v-toolbar density="compact">
-      <v-toolbar-title>Defense Systems</v-toolbar-title>
-
-      <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-virtual fixed-header :height="height" :items-per-page="itemsPerParge" v-model:sort-by="sortBy"
-      :headers="props.headers" density="compact" :custom-filter="filterOnlyCapsText" :items="props.systems"
-      :search="search" item-value="system.name">
-      <template #[`item.system`]="{ item }">
-        <v-chip variant="text" link :to="item?.system?.path ? `${item?.system?.path}` : null">{{
-          item?.system?.name ?? 'None'
-        }}</v-chip>
-      </template>
-      <template #[`item.article`]="{ item }">
-        <ArticleDoi v-if="item?.article" :doi="item.article.doi" :title="item.article?.title"
-          :abstract="item.article?.abstract" :divider="false" :enumerate="false" />
-      </template>
-      <template #[`item.PFAM`]="{ item }">
-
-        <pfam-chips v-if="item?.PFAM" :pfam-string="item.PFAM"></pfam-chips>
-      </template>
-    </v-data-table-virtual>
-  </v-card>
-</template>
\ No newline at end of file

components/content/Mermaid.vue

@@ -10,7 +10,7 @@
   
 <script setup lang="ts">
 const slot = useSlots()
-const el = ref(null)
+const el: Ref<HTMLElement | null> = ref(null)
 const rendered = ref(false)
 
 async function render() {

components/content/MolstarPdbePlugin.vue

 <script setup lang="ts">
+
 import { withTrailingSlash, withLeadingSlash, joinURL } from 'ufo'
 import { useRuntimeConfig, computed } from '#imports'
+import * as d3 from "d3";
+import * as Plot from "@observablehq/plot";
+import PlotFigure from "~/components/PlotFigure";
+
+import { useDisplay } from "vuetify";
+
 export interface Props {
     height?: number
     dataUrls?: string[]
     dataUrl?: string
+    uniq?: boolean
 }
+
+const { mobile } = useDisplay()
 // const selectedPdb = ref('')
 const refinedDataUrls = computed(() => {
 
@@ -24,10 +34,15 @@ const refinedDataUrls = computed(() => {
     if (props?.dataUrls && props?.dataUrls?.length > 0) {
         urls = [...props.dataUrls.map((dataUrl) => {
             return refinedUrl(dataUrl)
+            // return dataUrl
         })]
     }
     if (props?.dataUrl) {
-        urls = [...urls, refinedUrl(props.dataUrl)]
+        urls = [
+            ...urls,
+            // props.dataUrl
+            refinedUrl(props.dataUrl)
+        ]
     }
     return urls
 
@@ -37,29 +52,30 @@ const refinedDataUrls = computed(() => {
 // const selectedPdb = ref(refinedDataUrls.value?.length > 0 ? refinedDataUrls.value[0] : null)
 const props = withDefaults(defineProps<Props>(), {
     height: 600,
+    uniq: false
 })
 
 const { width, height } = useDisplay()
 
-const maxWidth = ref(1300)
+const maxWidth = ref(1500)
 
 const dialog = ref(false)
 // const show = ref(false)
 
 const computedWidth = computed(() => {
-    if (width > maxWidth) return maxWidth
-    return width
+    // if (toValue(width) > toValue(maxWidth)) return toValue(maxWidth) / 1.5
+    return toValue(width) / 1.5
 })
 
 const computedHeight = computed(() => {
     return height.value - 250
 })
 
+const paeError: Ref<string | null> = ref(null)
+
 function closeStructure() {
     selectedPdb.value = null
     dialog.value = false
-
-
 }
 
 
@@ -67,7 +83,7 @@ useHead({
     link: [
         {
             rel: 'stylesheet',
-            href: 'https://www.ebi.ac.uk/pdbe/pdb-component-library/css/pdbe-molstar-3.1.2.css'
+            href: 'https://www.ebi.ac.uk/pdbe/pdb-component-library/css/pdbe-molstar-3.1.3.css'
         },
     ],
     script: [
@@ -80,7 +96,7 @@ useHead({
         },
         {
             type: "text/javascript",
-            src: "https://www.ebi.ac.uk/pdbe/pdb-component-library/js/pdbe-molstar-component-3.1.2.js",
+            src: "https://www.ebi.ac.uk/pdbe/pdb-component-library/js/pdbe-molstar-component-3.1.3.js",
             // tagPosition: 'bodyClose'
         }
     ]
@@ -88,65 +104,171 @@ useHead({
 
 const pdbeMolstarComponent = ref(null)
 // const selectedPdb = ref("/wiki/avs/AVAST_I,AVAST_I__Avs1A,0,V-plddts_85.07081.pdb")
-const selectedPdb = ref(null)
+const selectedPdb: Ref<string | null> = ref(null)
+const structureToDownload: Ref<string | null> = ref(null)
+const selectedPaePath = computed(() => {
+    return selectedPdb.value ? `${selectedPdb.value.split(".").slice(0, -1).join('.')}.png` : undefined
+})
+
+watch(selectedPdb, (newSelectedPdb, prevSelectPdb) => {
+    viewPdb(newSelectedPdb)
+    structureToDownload.value = newSelectedPdb
+})
+
 
-watch(selectedPdb, (selectedPdb, prevSelectPdb) => {
-    if (selectedPdb !== null) {
+onMounted(() => {
+    const urls = toValue(refinedDataUrls)
+    if (props.uniq && urls.length >= 1) {
+        structureToDownload.value = urls[0]
+
+    }
+})
+function viewPdb(pdbPath: string | null) {
+    if (pdbPath !== null) {
         dialog.value = true
+        const format = toValue(pdbPath)?.split(".").slice(-1)[0]?.toLowerCase() ?? "pdb"
+        moleculeFormat.value = format
         if (pdbeMolstarComponent.value?.viewerInstance) {
             const viewerInstance = pdbeMolstarComponent.value.viewerInstance
+            const customData = { url: pdbPath, format: format, binary: false }
+            viewerInstance.visual.update({ customData })
+
+        }
+    }
+}
 
-            // show.value = true
 
-            const customData = { url: selectedPdb, format: "pdb", binary: false }
 
-            viewerInstance.visual.update({ customData })
 
-        }
 
+
+function setSelectedPdbToFirst() {
+    const urls = toValue(refinedDataUrls)
+    if (urls.length >= 1) {
+        selectedPdb.value = urls[0]
     }
-})
+}
 
+// const moleculeFormat = computed(() => {
+//     return toValue(selectedPdb)?.split(".")?.[-1]?.toLowerCase() ?? "pdb"
+// })
+const moleculeFormat: Ref<string> = ref("pdb")
 </script>
 
 
 <template>
-    <v-row><v-col><v-select v-model="selectedPdb" label="Select PDB" :items="refinedDataUrls"
-                hide-details="auto"></v-select></v-col></v-row>
-
-    <v-row justify="center">
-        <v-dialog v-model="dialog" transition="dialog-bottom-transition" fullscreen :scrim="false">
-            <v-card flat :rounded="false">
-                <v-toolbar>
-                    <v-toolbar-title>Structures</v-toolbar-title>
-                    <v-select v-model="selectedPdb" label="Select PDB" :items="refinedDataUrls"
-                        hide-details="auto"></v-select>
-                    <v-spacer></v-spacer>
-
-                    <v-btn :disabled="!selectedPdb" icon="md:download" :href="selectedPdb"></v-btn>
-                    <v-btn icon @click="closeStructure">
-                        <v-icon>mdi-close</v-icon>
-                    </v-btn>
-
-                </v-toolbar>
-                <v-card-text>
-
-                    <v-sheet v-if="selectedPdb"
-                        class="d-flex align-center justify-center flex-wrap text-center mx-auto px-4 my-3"
-                        :height="computedHeight" :max-width="1300" :width="computedWidth" position="relative">
-                        <pdbe-molstar ref="pdbeMolstarComponent" hide-controls :custom-data-url="selectedPdb"
-                            custom-data-format="pdb"></pdbe-molstar>
-                    </v-sheet>
-                </v-card-text>
-
-            </v-card>
-        </v-dialog>
+    <template v-if="uniq">
+        <v-row>
+            <v-btn size="x-small" variant="text" icon="md:visibility" @click="setSelectedPdbToFirst()"></v-btn>
+            <v-btn :disabled="!structureToDownload" size="x-small" variant="text" icon="md:download" class="ml-1"
+                :href="structureToDownload"></v-btn>
+        </v-row>
+    </template>
+    <v-row v-else>
+        <v-col>
+            <span class="d-flex flex-wrap align-center justify-center">
+                <v-select v-model="selectedPdb" label="Select PDB" :items="refinedDataUrls" hide-details="auto">
+                </v-select>
+            </span>
+        </v-col>
     </v-row>
+    <v-dialog v-model="dialog" transition="dialog-bottom-transition" fullscreen :scrim="false">
+        <v-card flat :rounded="false">
+            <v-toolbar>
+                <v-toolbar-title>Structures</v-toolbar-title>
+                <v-select v-model="selectedPdb" label="Select PDB" :items="refinedDataUrls" hide-details="auto"></v-select>
+                <v-spacer></v-spacer>
+
+                <v-btn :disabled="!selectedPdb" icon="md:download" :href="structureToDownload"></v-btn>
+                <v-btn icon @click="closeStructure">
+                    <v-icon>mdi-close</v-icon>
+                </v-btn>
+
+            </v-toolbar>
+            <v-card-text>
+                <v-row>
+                    <v-col :cols="mobile ? 12 : 'auto'">
+                        <v-sheet v-if="selectedPdb"
+                            class="d-flex align-center justify-center flex-wrap text-center mx-auto px-4 my-3"
+                            :height="computedHeight" :width="computedWidth" style="position:relative;">
+                            <pdbe-molstar ref="pdbeMolstarComponent" :custom-data-url="selectedPdb" alphafold-view
+                                sequence-panel="true" landscape="false" :custom-data-format="moleculeFormat"></pdbe-molstar>
+                        </v-sheet>
+                    </v-col>
+                    <v-col :cols="mobile ? 12 : undefined">
+                        <v-img :src="selectedPaePath"></v-img>
+
+                        <!-- <PlotFigure v-if="sanitizedPaeData?.length > 0 && paeError === null" defer
+                                :options="plotPaeOptions"></PlotFigure>
+                            <v-alert v-else type="warning" variant="tonal">{{ paeError }}</v-alert> -->
+                        <v-card flat color="transparent">
+                            <v-card-title>Model Confidence</v-card-title>
+                            <v-card-text>
+                                AlphaFold produces a per-residue model
+                                confidence score (pLDDT) between 0 and 100. Some regions below 50 pLDDT may be
+                                unstructured
+                                in isolation.
+                            </v-card-text>
+                            <v-list>
+                                <v-list-item>
+                                    <template #prepend>
+                                        <div class="legendColor mr-2" style="background-color: rgb(0, 83, 214);">
+                                            &nbsp;</div>
+                                    </template>
+                                    <v-list-item-title>
+                                        Very high (pLDDT > 90)
+                                    </v-list-item-title>
+
+                                </v-list-item>
+                                <v-list-item>
+                                    <template #prepend>
+                                        <div class="legendColor mr-2" style="background-color: rgb(101, 203, 243);">
+                                            &nbsp;</div>
+                                    </template>
+                                    <v-list-item-title>
+                                        High (90 > pLDDT > 70)
+                                    </v-list-item-title>
+
+                                </v-list-item>
+                                <v-list-item>
+                                    <template #prepend>
+                                        <div class="legendColor mr-2" style="background-color: rgb(255, 219, 19);">
+                                            &nbsp;</div>
+                                    </template>
+                                    <v-list-item-title>
+                                        Low (70 > pLDDT > 50) </v-list-item-title>
+
+                                </v-list-item>
+                                <v-list-item>
+                                    <template #prepend>
+                                        <div class="legendColor mr-2" style="background-color: rgb(255, 125, 69);">
+                                            &nbsp;</div>
+                                    </template>
+                                    <v-list-item-title>
+                                        Very low (pLDDT &lt; 50) </v-list-item-title>
+
+                                </v-list-item>
+                            </v-list>
+                        </v-card>
+                    </v-col>
+                </v-row>
+            </v-card-text>
+        </v-card>
+    </v-dialog>
 </template>
 
 
-<style scoped>
-.msp-plugin .msp-plugin-content {
+<style>
+/* .msp-plugin .msp-plugin-content {
     color: black !important;
+} */
+
+div.msp-plugin-content.msp-layout-expanded {
+    z-index: 5 !important
+}
+
+.legendColor {
+    height: 16px;
+    width: 16px;
 }
-</style>
\ No newline at end of file
+</style>

components/content/Ref.vue

@@ -11,10 +11,8 @@ const dois = computed(() => {
 
 </script>
 <template>
-  (
-  <template v-for="doi, index in dois" :key="doi">
+  (<template v-for="doi, index in dois" :key="doi">
     <RefArticle :doi="doi"></RefArticle>
     <span v-if="index < dois.length - 1">, </span>
-  </template>
-  )
+  </template>)
 </template>
\ No newline at end of file

components/content/RefArticle.vue

 <script setup lang="ts">
+import { useTheme } from "vuetify";
+const theme = useTheme();
 export interface Props {
     doi: string;
 }
@@ -7,7 +9,17 @@ const props = withDefaults(defineProps<Props>(), {});
 const { article } = useFetchArticle(props.doi);
 </script>
 <template>
-    <v-chip v-if="article" variant="text" :href="`#ref-${props.doi}`" class="pa-0 text-caption font-italic">{{
+    <!-- <v-chip v-if="article" variant="text" :href="`#ref-${props.doi}`" class="pa-0 font-italic">{{
         article?.author[0]?.family ?? "test" }} et al,
-        {{ article?.year }}</v-chip>
-</template>
\ No newline at end of file
+        {{ article?.year }}</v-chip> -->
+    <NuxtLink v-if="article" :href="`#ref-${props.doi}`"
+        :class="theme.global.current.value.dark ? 'text-grey-lighten-1' : 'text-grey-darken-2'" class="pa-0 ">{{
+            article?.author[0]?.family ?? "test" }} et al,
+        {{ article?.year }}</NuxtLink>
+</template>
+<style scoped>
+.ref-link {
+    /* color: rgba(var(--v-theme-tertiary)); */
+    color: grey-darken-3;
+}
+</style>
\ No newline at end of file

components/content/RelevantAbstracts.vue

@@ -15,11 +15,11 @@ const computedDois = computed(() => {
 </script>
 <template>
   <div v-if="computedDois?.length > 0">
-    <ProseH2 id="relevant-abstracts">Relevant abstracts</ProseH2>
+    <ProseH2 id="references">References</ProseH2>
 
     <v-list density="compact" bg-color="transparent">
       <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" />
+        :title="item?.title" :divider="item.divider" :abstract="item?.abstract" :is-relevant="item?.isRelevant ?? false" />
     </v-list>
   </div>
 </template>
\ No newline at end of file