Merge branch 'dev' into structure-db-with-molstar

Dockerfile

@@ -76,6 +76,6 @@ RUN npm run generate
 ### STAGE: NGINX ###
 FROM nginxinc/nginx-unprivileged:1.25
 # RUN rm -rf /usr/share/nginx/html/*
-COPY nginx.conf /etc/nginx/conf.d/default.conf
+# 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/LayoutWrapper.vue

@@ -49,7 +49,7 @@ function onScroll() {
     <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?.body?.toc?.links" :links="page.body.toc.links" />
     <nav-back-to-top />
   </VApp>
 </template>

components/Nav/Drawer.vue

@@ -13,19 +13,25 @@ import { useDisplay, useTheme } from "vuetify";
 const { navigation } = useContent();
 // const drawer = ref(true);
 
-const computedNavigation = computed(() => {
-    console.log(navigation.value)
-    return navigation.value
-        .filter(({ layout }) => {
-            return layout !== "db"
-        })
+// const computedNavigation = computed(() => {
+//     console.log(page.value.title)
+//     // console.log(navigation.value)
+//     if (page.value.title === "stru") {
+//         console.log(navigation.value)
 
-});
+//     }
+//     return navigation.value
+//         // .filter((item) => {
+
+//         //     return item?.layout !== "db"
+//         // })
+
+// });
 </script>
 <template>
     <v-navigation-drawer :model-value="drawer" :border="1" color="background">
         <v-list nav density="compact" :lines="false">
-            <NavNavigation :navigation="computedNavigation" />
+            <NavNavigation :navigation="navigation" />
         </v-list>
     </v-navigation-drawer>
 </template>
\ No newline at end of file

components/ServerDbTable.vue

@@ -61,7 +61,7 @@ const computedTableHeight = computed(() => {
 
 
 const filterInputValues = computed(() => {
-    console.log("recompouted FILTER value")
+    // console.log("recompouted FILTER value")
     if (filterOrSearch.value != null) {
         return filterOrSearch.value.filter(({ props }) => props.type !== 'text')
     } else {
@@ -70,7 +70,7 @@ const filterInputValues = computed(() => {
 })
 
 const queryInputValue = computed(() => {
-    console.log("recompouted TEXT value")
+    // console.log("recompouted TEXT value")
 
     if (filterOrSearch.value !== null) {
         const phrase = filterOrSearch.value
@@ -162,8 +162,8 @@ watch(msFilter, async (fos) => {
 })
 
 watch(msResult, (newRes) => {
-    console.log(msResult)
-    console.log(newRes)
+    // console.log(msResult)
+    // console.log(newRes)
     facetStore.setFacets({ facetDistribution: newRes.facetDistribution, facetStat: newRes.facetStat })
 }, { deep: true })
 
@@ -207,7 +207,7 @@ const operatorItems = ref([
 
 const autocompleteItems = computed(() => {
     const index = filterOrSearch.value?.length ?? 0
-    console.log(index)
+    // console.log(index)
     if (filterStep.value === null || filterStep.value === 0) {
         return props.facets.map(value => {
             return {
@@ -230,9 +230,9 @@ const autocompleteItems = computed(() => {
         if (Array.isArray(filterOrSearch.value)) {
             const { type, value } = filterOrSearch.value?.slice(-2, -1)[0]
             const sanitizedValue = value.split("-")[0]
-            console.log("compute new facets")
+            // console.log("compute new facets")
             const facetDistri = facetStore.facets?.facetDistribution
-            console.log(facetDistri)
+            // console.log(facetDistri)
             return facetDistri?.[sanitizedValue] ? Object.entries(facetDistri[sanitizedValue]).map(([key, val]) => {
                 return {
                     type: "value", value: `${key}-${index}`, title: key, count: val, deletable: true, props: {
@@ -257,33 +257,33 @@ function selectItem(item) {
 }
 
 function deleteOneFilter(index: number) {
-    console.log("deleteOnefilter")
-    console.log(index)
-    console.log(isFilter.value)
-    console.log(filterOrSearch)
+    // console.log("deleteOnefilter")
+    // console.log(index)
+    // console.log(isFilter.value)
+    // console.log(filterOrSearch)
     if (isFilter.value) {
 
         filterOrSearch.value?.splice(index - 2, 2)
-        console.log(filterOrSearch.value)
+        // console.log(filterOrSearch.value)
 
     }
 
 }
 
 function deleteTextFilter(index: number) {
-    console.log("delete text filter")
-    console.log(index)
-    console.log(isFilter.value)
-    console.log(filterOrSearch)
-    console.log(filterOrSearch.value?.length)
+    // console.log("delete text filter")
+    // console.log(index)
+    // console.log(isFilter.value)
+    // console.log(filterOrSearch)
+    // console.log(filterOrSearch.value?.length)
     if (isFilter.value) {
         if (index === 0) {
             filterOrSearch.value?.shift()
         } else {
             filterOrSearch.value?.splice(index, 1)
         }
-        console.log(filterOrSearch.value?.length)
-        console.log(filterOrSearch.value)
+        // console.log(filterOrSearch.value?.length)
+        // console.log(filterOrSearch.value)
 
     }
 

components/content/StructureDb.vue

 <script setup lang="ts">
-
-import { useFacetsStore } from '~~/stores/facets'
 const sortBy: Ref<{ key: string, order: string }[]> = ref([{ key: 'system', order: "asc" }])
 const itemValue = ref("id");
-const facets = ref(["system", "completed",
+const facets: Ref<string[]> = ref(["system", "completed",
     "plddts",])
 const headers: Ref<Object[]> = ref([
     { title: "System", key: "system" },
@@ -22,7 +20,7 @@ const headers: Ref<Object[]> = ref([
 
 </script>
 <template>
-    <ServerDbTable title="Predicted Strucutres" db="structure" :sortBy="sortBy" :headers="headers" :item-value="itemValue"
+    <ServerDbTable title="Predicted Structures" db="structure" :sortBy="sortBy" :headers="headers" :item-value="itemValue"
         :facets="facets">
     </ServerDbTable>
 </template>
\ No newline at end of file

composables/useFetchMsDocument.ts

@@ -63,7 +63,7 @@ export async function useFetchMsDocument(
         pending.value = false
     }
     // })
-    console.log(hits)
+    // console.log(hits)
     return { hits, totalHits, pending, filterError, totalPages, facetDistribution }
 }
 

content/4.refseq.md

 ---
 layout: db
+navigation: false
 ---
 
 

content/5.predicted-structure.md

 ---
 layout: db
+navigation: false
 ---
 
-
 ::structure-db
 ::
\ No newline at end of file

deploy/df-wiki/templates/configmap-nginx-conf.yaml

@@ -7,7 +7,7 @@ data:
     server {
         listen 8080;
         server_name localhost;
-        location /wiki {
+        location /wiki/ {
             alias /etc/nginx/html/;
             index index.html index.htm;
             try_files $uri $uri/ $uri/index.html /index.html =404;

layouts/db.vue

-<script setup lang="ts">
 
-import { useFacetsStore, type Facets } from '~~/stores/facets'
-
-const facetStore = useFacetsStore()
-</script>
 <template>
     <LayoutWrapper :fluid="true" :toc="false" :edit="false" :nav-drawer="false">
         

package.json

@@ -8,12 +8,12 @@
   },
   "devDependencies": {
     "@nuxt/content": "^2.9.0",
-    "@types/node": "^20.10.3",
+    "@types/node": "^20.10.4",
     "@vueuse/core": "^10.6.1",
     "@vueuse/nuxt": "^10.6.1",
-    "nuxt": "^3.8.1",
+    "nuxt": "^3.8.2",
     "nuxt-meilisearch": "^1.1.0",
-    "vuetify-nuxt-module": "^0.7.2"
+    "vuetify-nuxt-module": "^0.7.3"
   },
   "overrides": {
     "vue": "latest"

pages/predicted-structure.vue

+<template>
+    <ContentDoc></ContentDoc>
+</template>
\ No newline at end of file

pages/refseq.vue

+<template>
+    <ContentDoc></ContentDoc>
+</template>
\ No newline at end of file

stores/facets.ts

@@ -14,10 +14,10 @@ export const useFacetsStore = defineStore('facets', () => {
 
 
     function setFacets(newFacets: Facets) {
-        console.log("start set facets")
-        console.log(newFacets)
+        // console.log("start set facets")
+        // console.log(newFacets)
         facets.value = newFacets
-        console.log("end set facets")
+        // console.log("end set facets")
 
     }