From c5c010d00ffa54181a0950211ad409ab56713742 Mon Sep 17 00:00:00 2001
From: Remi PLANEL <rplanel@pasteur.fr>
Date: Wed, 13 Dec 2023 13:27:50 +0100
Subject: [PATCH] Should fix compilation website
---
components/Nav/Drawer.vue | 20 +--
components/Nav/Navbar.vue | 10 +-
components/Nav/Navigation.vue | 2 +-
components/ServerDbTable.vue | 163 +++++++-----------
components/content/RefseqDb.vue | 9 +-
components/content/StructureDb.vue | 10 +-
content/2.general-concepts/0.index.md | 1 -
.../1.abortive-infection.md | 1 -
.../2.general-concepts/2.defense-islands.md | 1 +
content/2.general-concepts/3.phage_trigger.md | 1 +
content/4.refseq.md | 3 +-
content/5.predicted-structure.md | 7 -
content/5.structure.md | 9 +
nuxt.config.ts | 2 +-
.../df-wiki-cli/df_wiki_cli/content/main.py | 12 +-
pages/predicted-structure.vue | 3 -
pages/refseq.vue | 3 -
17 files changed, 100 insertions(+), 157 deletions(-)
delete mode 100644 content/5.predicted-structure.md
create mode 100644 content/5.structure.md
delete mode 100644 pages/predicted-structure.vue
delete mode 100644 pages/refseq.vue
diff --git a/components/Nav/Drawer.vue b/components/Nav/Drawer.vue
index 4234bd99..645e512f 100644
--- a/components/Nav/Drawer.vue
+++ b/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>
diff --git a/components/Nav/Navbar.vue b/components/Nav/Navbar.vue
index 0f19d827..271dc77a 100644
--- a/components/Nav/Navbar.vue
+++ b/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)
diff --git a/components/Nav/Navigation.vue b/components/Nav/Navigation.vue
index 6bc1162f..2d98ea9a 100644
--- a/components/Nav/Navigation.vue
+++ b/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>
diff --git a/components/ServerDbTable.vue b/components/ServerDbTable.vue
index 2bc7a684..b85e8eeb 100644
--- a/components/ServerDbTable.vue
+++ b/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">
diff --git a/components/content/RefseqDb.vue b/components/content/RefseqDb.vue
index caa8f067..87f1ba6a 100644
--- a/components/content/RefseqDb.vue
+++ b/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 }">
diff --git a/components/content/StructureDb.vue b/components/content/StructureDb.vue
index 93ecadf1..4757a267 100644
--- a/components/content/StructureDb.vue
+++ b/components/content/StructureDb.vue
@@ -1,5 +1,7 @@
<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)
}
})
diff --git a/content/2.general-concepts/0.index.md b/content/2.general-concepts/0.index.md
index e172046e..255c3d7f 100644
--- a/content/2.general-concepts/0.index.md
+++ b/content/2.general-concepts/0.index.md
@@ -1,6 +1,5 @@
---
title: General Concepts
-toc: true
layout: article
---
diff --git a/content/2.general-concepts/1.abortive-infection.md b/content/2.general-concepts/1.abortive-infection.md
index 2e5c1975..dfea3e89 100644
--- a/content/2.general-concepts/1.abortive-infection.md
+++ b/content/2.general-concepts/1.abortive-infection.md
@@ -1,7 +1,6 @@
---
title: Abortive Infection
layout: article
-toc: true
---
diff --git a/content/2.general-concepts/2.defense-islands.md b/content/2.general-concepts/2.defense-islands.md
index 82062efe..cc7d3012 100644
--- a/content/2.general-concepts/2.defense-islands.md
+++ b/content/2.general-concepts/2.defense-islands.md
@@ -1,5 +1,6 @@
---
title: Defense Islands
+layout: article
---
diff --git a/content/2.general-concepts/3.phage_trigger.md b/content/2.general-concepts/3.phage_trigger.md
index 17be0ed6..da335edb 100644
--- a/content/2.general-concepts/3.phage_trigger.md
+++ b/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
diff --git a/content/4.refseq.md b/content/4.refseq.md
index a93eeb2e..5f47b8c5 100644
--- a/content/4.refseq.md
+++ b/content/4.refseq.md
@@ -1,6 +1,7 @@
---
+title: RefSeq DB
layout: db
-navigation: false
+navigation: true
---
diff --git a/content/5.predicted-structure.md b/content/5.predicted-structure.md
deleted file mode 100644
index 72f24e20..00000000
--- a/content/5.predicted-structure.md
+++ /dev/null
@@ -1,7 +0,0 @@
----
-layout: db
-navigation: false
----
-
-::structure-db
-::
\ No newline at end of file
diff --git a/content/5.structure.md b/content/5.structure.md
new file mode 100644
index 00000000..7fdd6f72
--- /dev/null
+++ b/content/5.structure.md
@@ -0,0 +1,9 @@
+---
+title: Structures DB
+layout: db
+navigation: true
+---
+
+
+::structure-db
+::
\ No newline at end of file
diff --git a/nuxt.config.ts b/nuxt.config.ts
index 57f09717..0b414ce8 100644
--- a/nuxt.config.ts
+++ b/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),
diff --git a/packages/df-wiki-cli/df_wiki_cli/content/main.py b/packages/df-wiki-cli/df_wiki_cli/content/main.py
index b869c668..015ec277 100644
--- a/packages/df-wiki-cli/df_wiki_cli/content/main.py
+++ b/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']])}"
diff --git a/pages/predicted-structure.vue b/pages/predicted-structure.vue
deleted file mode 100644
index b05e520f..00000000
--- a/pages/predicted-structure.vue
+++ /dev/null
@@ -1,3 +0,0 @@
-<template>
- <ContentDoc></ContentDoc>
-</template>
\ No newline at end of file
diff --git a/pages/refseq.vue b/pages/refseq.vue
deleted file mode 100644
index b05e520f..00000000
--- a/pages/refseq.vue
+++ /dev/null
@@ -1,3 +0,0 @@
-<template>
- <ContentDoc></ContentDoc>
-</template>
\ No newline at end of file
--
GitLab