Should fix compilation website

components/Nav/Drawer.vue

@@ -10,21 +10,19 @@ 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(() => {
-//     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"
-//         // })
+//         .filter((item: { layout: string }) => {
+//             if (item?.layout === "db") {
+//                 console.log(item)
+//                 return false
+//             }
+//             return true
+//             // return item?.layout !== "db"
+//         })
 
 // });
 </script>

components/Nav/Navbar.vue

@@ -9,7 +9,6 @@ export interface Props {
 }
 const runtimeConfig = useRuntimeConfig();
 
-const { navigation } = useContent();
 const { mobile } = useDisplay();
 const theme = useTheme();
 
@@ -36,17 +35,10 @@ const sections = ref([
   },
   { id: "wiki", label: "Wiki", to: '/', },
   { id: "refseq", label: "RefSeq DB", to: '/refseq/' },
-  { id: "structure", label: "Structures DB", to: '/predicted-structure/' },
+  { id: "structure", label: "Structures DB", to: '/structure/' },
   { id: "help", label: "Help", to: '/help/' },
 ]);
 
-const computedNavigation = computed(() => {
-  return navigation.value
-    .filter(({ _path }) => {
-      return _path !== "/refseq";
-    })
-});
-
 
 function toggleDrawer() {
   emit('update:drawer', !props.drawer)

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/ServerDbTable.vue

@@ -2,11 +2,11 @@
 // import type { FacetDistribution } from "meilisearch";
 import { useSlots } from 'vue'
 import { useDisplay } from "vuetify";
-import { useFacetsStore, type Facets } from '~~/stores/facets'
+import { useFacetsStore } from '~~/stores/facets'
 
 
 import { useMeiliSearch } from "#imports"
-interface SortItem {
+export interface SortItem {
     key: string,
     order: boolean | 'asc' | 'desc'
 }
@@ -15,8 +15,8 @@ export interface Props {
     title?: string
     db?: string
     sortBy?: SortItem[]
-    facets: string[]
-    dataTableServerProps: { [key: string]: any; }
+    facets: MaybeRef<string[]>
+    dataTableServerProps: Record<string, any>
 }
 
 export interface FilterItem {
@@ -25,12 +25,7 @@ export interface FilterItem {
     title: string
     count?: number
     deletable: boolean
-    props: {
-        [key: string]: any
-        // title: string
-        // value: any
-    }
-    // raw?: any
+    props: Record<string, any>
 }
 
 const props = withDefaults(defineProps<Props>(), {
@@ -38,17 +33,20 @@ const props = withDefaults(defineProps<Props>(), {
     db: 'refseq',
     sortBy: () => [{ key: "type", order: "asc" }],
 });
+
+
+
+console.log(props.dataTableServerProps)
+
 const slots = useSlots()
-console.log(slots)
-const sortByRef = ref(toValue(props.sortBy))
-const facetsRef = toRef(() => props.facets)
+const sortByRef = toRef(props.sortBy)
+const facetsRef = toRef(props.facets)
 
 const { search: msSearch, result: msResult } = useMeiliSearch(props.db)
 const facetStore = useFacetsStore()
 const search: Ref<string> = ref("");
 const filterOrSearch: Ref<FilterItem[] | null> = ref(null)
 const hitsPerPage: Ref<number> = ref(25)
-const limit = ref(1000)
 const filterError: Ref<string | null> = ref(null)
 const msFilter: Ref<string | undefined> = ref(undefined)
 const page = ref(1)
@@ -61,7 +59,7 @@ const computedTableHeight = computed(() => {
     return computedHeight > minTableHeight.value ? computedHeight : minTableHeight.value
 })
 
-const { pending: pendingDownloadData, downloadCsv } = useCsvDownload(props.db, `df-${props.db}`)
+// const { pending: pendingDownloadData, downloadCsv } = useCsvDownload(props.db, `df-${props.db}`)
 
 const filterInputValues = computed(() => {
     // console.log("recompouted FILTER value")
@@ -72,25 +70,23 @@ const filterInputValues = computed(() => {
     }
 })
 
-const queryInputValue = computed(() => {
-    // console.log("recompouted TEXT value")
-
-    if (filterOrSearch.value !== null) {
-        const phrase = filterOrSearch.value
-            .filter((f) => {
-                return f.props.type === 'text'
-            })
-            .map((f) => {
-                return f.value
-            })
-        if (phrase.length > 1) {
-            return `${phrase.join(" ")}`
-        }
-        else { return phrase[0] }
-    } else {
-        return null
-    }
-})
+// const queryInputValue = computed(() => {
+//     if (filterOrSearch.value !== null) {
+//         const phrase = filterOrSearch.value
+//             .filter((f) => {
+//                 return f.props.type === 'text'
+//             })
+//             .map((f) => {
+//                 return f.value
+//             })
+//         if (phrase.length > 1) {
+//             return `${phrase.join(" ")}`
+//         }
+//         else { return phrase[0] }
+//     } else {
+//         return null
+//     }
+// })
 
 const isFilter = computed(() => {
     return Array.isArray(filterOrSearch.value)
@@ -172,8 +168,6 @@ watch(msFilter, async (fos) => {
 })
 
 watch(msResult, (newRes) => {
-    // console.log(msResult)
-    // console.log(newRes)
     facetStore.setFacets({ facetDistribution: newRes.facetDistribution, facetStat: newRes.facetStat })
 }, { deep: true })
 
@@ -223,7 +217,7 @@ const autocompleteItems = computed(() => {
     const index = filterOrSearch.value?.length ?? 0
     // console.log(index)
     if (filterStep.value === null || filterStep.value === 0) {
-        return props.facets.map(value => {
+        return toValue(facetsRef).map(value => {
             return {
                 type: "facet",
                 value: `${value}-${index}`,
@@ -258,80 +252,52 @@ const autocompleteItems = computed(() => {
     }
 })
 
-const canAddTextSearch = computed(() => {
-    if (filterOrSearch.value !== null && filterOrSearch.value.length > 0) {
-        const lastItem = filterOrSearch.value.slice(-1)[0]
-        return lastItem?.props.type === 'value' || lastItem?.props.type === "text"
-    }
-    return true
-})
+// const canAddTextSearch = computed(() => {
+//     if (filterOrSearch.value !== null && filterOrSearch.value.length > 0) {
+//         const lastItem = filterOrSearch.value.slice(-1)[0]
+//         return lastItem?.props.type === 'value' || lastItem?.props.type === "text"
+//     }
+//     return true
+// })
 
 function selectItem(item) {
     filterOrSearch.value = Array.isArray(filterOrSearch.value) ? [...filterOrSearch.value, item] : [item]
 }
 
 function deleteOneFilter(index: number) {
-    // 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)
-
     }
-
 }
 
-function deleteTextFilter(index: number) {
-    // 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)
-
-    }
-
-}
-
-
 function clearSearch() {
     search.value = ""
 }
 
 
 
-function runTextSearch() {
-    if (canAddTextSearch) {
-        const item: FilterItem = reactive({
-            type: 'text', title: search.value, value: search.value, deletable: true, props: { type: "text", deletable: true, }
-        })
-        if (Array.isArray(filterOrSearch.value)) {
-            filterOrSearch.value = [
-                ...filterOrSearch.value, item
+// function runTextSearch() {
+//     if (canAddTextSearch) {
+//         const item: FilterItem = reactive({
+//             type: 'text', title: search.value, value: search.value, deletable: true, props: { type: "text", deletable: true, }
+//         })
+//         if (Array.isArray(filterOrSearch.value)) {
+//             filterOrSearch.value = [
+//                 ...filterOrSearch.value, item
 
-            ]
-        } else {
-            filterOrSearch.value = [item]
-        }
-        search.value = ""
-        searchOrFilter()
-    }
-}
+//             ]
+//         } else {
+//             filterOrSearch.value = [item]
+//         }
+//         search.value = ""
+//         searchOrFilter()
+//     }
+// }
 
 
-function downloadData() {
-    downloadCsv(search, msFilter, msSortBy, notPaginatedParams)
-}
+// function downloadData() {
+//     downloadCsv(search, msFilter, msSortBy, notPaginatedParams)
+// }
 
 </script>
 <template>
@@ -349,13 +315,8 @@ function downloadData() {
                         @click:appendInner="searchOrFilter" @click:clear="clearFilterOrSearch"
                         @update:modelValue="() => clearSearch()">
                         <template #chip="{ props, item, index }">
-
-
                             <v-chip v-bind="props" :text="item.raw.title" :closable="item.props.deletable"
-                                @click:close="item.props.type === 'text' ? deleteTextFilter(index) : deleteOneFilter(index)"></v-chip>
-                            <!-- <v-chip v-if="(index + 1) % 3 === 0" v-bind="props" :text="item.raw.title" closable
-                        @click:close="deleteOneFilter(index)"></v-chip>
-                    <v-chip v-else v-bind="props" :text="item.raw.title"></v-chip> -->
+                                @click:close="item.props.type === deleteOneFilter(index)"></v-chip>
                         </template>
                         <template #item="{ props, item }">
                             <v-list-item v-bind="{ ...props, active: false, onClick: () => selectItem(item) }"
@@ -363,10 +324,6 @@ function downloadData() {
 
                             </v-list-item>
                         </template>
-                        <!-- <template #no-data></template>
-                <template #prepend-item>
-                    <v-list-item v-if="canAddTextSearch" :title="`Text search: ${search}`" @click="runTextSearch"> </v-list-item>
-                </template> -->
                     </v-autocomplete>
                 </v-col>
             </v-row>
@@ -381,10 +338,10 @@ function downloadData() {
                     </v-toolbar-title><v-spacer></v-spacer>
 
 
-                    <v-btn :loading="pendingDownloadData" :disabled="totalHits > 10000" @click="downloadData" icon
+                    <!-- <v-btn :loading="pendingDownloadData" :disabled="totalHits > 10000" @click="downloadData" icon
                         variant="text" class="text-none mr-15">
                         <v-badge :content="totalHits" color="info" floating>
-                            <v-icon>md:download</v-icon></v-badge></v-btn>
+                            <v-icon>md:download</v-icon></v-badge></v-btn> -->
                 </v-toolbar>
             </template>
             <template v-for="(slot, index) of Object.keys(slots)" :key="index" v-slot:[slot]="data">

components/content/RefseqDb.vue

@@ -3,11 +3,12 @@ import { useFacetsStore } from '~~/stores/facets'
 import * as Plot from "@observablehq/plot";
 import PlotFigure from "~/components/PlotFigure";
 import { useDisplay } from "vuetify";
-
+import type { SortItem } from "@/components/ServerDbTable.vue"
+import { ServerDbTable } from "#components"
 
 const facetStore = useFacetsStore()
 
-const sortBy: Ref<{ key: string, order: string }[]> = ref([{ key: 'type', order: "asc" }])
+const sortBy: Ref<SortItem[]> = ref([{ key: 'type', order: "asc" }])
 const itemValue = ref("id");
 const { width } = useDisplay();
 const distriTool: Ref<string[]> = ref([])
@@ -157,7 +158,8 @@ const computedDistriTaxoOptions = computed(() => {
         ],
     };
 });
-function capitalize([first, ...rest]) {
+function capitalize(name: string) {
+    const [first, ...rest] = name
     return first.toUpperCase() + rest.join('').toLowerCase();
 }
 
@@ -209,7 +211,6 @@ function namesToAccessionChips(names: string[]) {
             </v-col>
         </v-row>
     </v-card>
-
     <ServerDbTable title="RefSeq" db="refseq" :sortBy="sortBy" :facets="facets"
         :data-table-server-props="dataTableServerProps">
         <template #[`item.accession_in_sys`]="{ item }">

components/content/StructureDb.vue

 <script setup lang="ts">
-const sortBy: Ref<{ key: string, order: string }[]> = ref([{ key: 'system', order: "asc" }])
+import type { SortItem } from "@/components/ServerDbTable.vue"
+import { ServerDbTable } from "#components"
+const sortBy: Ref<SortItem[]> = ref([{ key: 'system', order: "asc" }])
 const itemValue = ref("id");
 const facets: Ref<string[]> = ref(["system", "completed",
     "plddts",])
@@ -26,9 +28,9 @@ const defaultDataTableServerProps = ref({
 
 const dataTableServerProps = computed(() => {
     return {
-        ...defaultDataTableServerProps.value,
-        headers: headers.value,
-        itemValue: itemValue.value
+        ...toValue(defaultDataTableServerProps),
+        headers: toValue(headers),
+        itemValue: toValue(itemValue)
     }
 })
 

content/2.general-concepts/0.index.md

 ---
 title: General Concepts
-toc: true
 layout: article
 ---
 

content/2.general-concepts/1.abortive-infection.md

 ---
 title: Abortive Infection
 layout: article
-toc: true
 ---
 
 

content/2.general-concepts/2.defense-islands.md

 ---
 title: Defense Islands
+layout: article
 ---
 
 

content/2.general-concepts/3.phage_trigger.md

@@ -2,6 +2,7 @@
 title: Defense system triggers
 contributors: 
     - Avigail Stokar-Avihail
+layout: article
 ---
 
 # How anti-phage systems sense invading phages

content/4.refseq.md

 ---
+title: RefSeq DB
 layout: db
-navigation: false
+navigation: true
 ---
 
 

content/5.predicted-structure.md → content/5.structure.md

 ---
+title: Structures DB
 layout: db
-navigation: false
+navigation: true
 ---
 
+
 ::structure-db
 ::
\ No newline at end of file

nuxt.config.ts

@@ -19,7 +19,6 @@ export default defineNuxtConfig({
         'sh',
       ]
     },
-    layoutFallbacks: ['article'],
   },
   vuetify: {
     vuetifyOptions: {
@@ -53,6 +52,7 @@ export default defineNuxtConfig({
       meiliApiKey: 'api_key'
     }
   },
+
   vue: {
     compilerOptions: {
       isCustomElement: (tag) => ['pdbe-molstar'].includes(tag),

packages/df-wiki-cli/df_wiki_cli/content/main.py

@@ -27,10 +27,10 @@ class TableArticle(BaseModel):
 
 class TableColumns(BaseModel):
     article: TableArticle
-    Sensor: str
-    Activator: str
-    Effector: str
-    PFAM: str
+    Sensor: Optional[str] = None
+    Activator: Optional[str] = None
+    Effector: Optional[str] = None
+    PFAM: Optional[str] = None
 
 
 class RelevantAbstract(BaseModel):
@@ -64,10 +64,6 @@ def lint(
         try:
             FrontMatter.model_validate(metadata)
         except ValidationError as exc:
-            # print(repr(exc.errors()[0]["type"]))
-            # print(repr(exc))
-            # print(exc.errors())
-            # pprint(exc.errors(), expand_all=True)
             for err in exc.errors():
                 console.print(
                     f"[red]{err['msg']} : {err['type']} {' -> '.join([str(l) for l in err['loc']])}"

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