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  • mdm-lab/wiki
  • hvaysset/wiki
  • jsousa/wiki
  • tclabby/wiki
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with 1665 additions and 345 deletions
.gitattributes
View file @ 9fd810f9
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
View file @ 9fd810f9
......@@ -319,7 +319,7 @@ get-zotero:
variables:
CONTEXT: "."
DOCKERFILE: "Dockerfile"
BASE_URL: /wiki/
BASE_URL: /
MEILI_HOST: "http://localhost:7700"
before_script:
- *docker-login
......@@ -328,7 +328,7 @@ get-zotero:
docker buildx build --pull -t "$CI_REGISTRY_IMAGE/$IMAGE_NAME:$CI_COMMIT_SHORT_SHA"
--build-arg "BASE_URL=$BASE_URL"
--build-arg "MEILI_HOST=$MEILI_HOST"
--build-arg "MEILI_API_KEY=$MEILI_API_KEY"
--build-arg "MEILI_API_KEY=$MEILI_API_KEY"
-f $DOCKERFILE $CONTEXT
- docker push "$CI_REGISTRY_IMAGE/$IMAGE_NAME:$CI_COMMIT_SHORT_SHA"
......@@ -341,6 +341,7 @@ build:dev:wiki:
# - get-pfam
variables:
BASE_URL: /wiki/
HOST_URL: https://${HOST_DEV}
before_script:
- *docker-login
# - "sed -i 's/MEILISEARCH_API_KEY/${$MEILI_API_KEY}/g' nuxt.config.ts"
......@@ -356,6 +357,8 @@ build:prod:wiki:
# - get-pfam
variables:
BASE_URL: /wiki/
HOST_URL: https://${HOST_PROD}
rules:
- if: $CI_COMMIT_BRANCH == "main"
......@@ -486,7 +489,7 @@ build:prod:wiki:
deploy:dev:
extends: .deploy
rules:
- if: $CI_COMMIT_BRANCH == "dev"
- if: $CI_COMMIT_BRANCH == "dev" || $CI_COMMIT_BRANCH == "foldseek-pages"
needs:
- "build:dev:wiki"
when: manual
......
Dockerfile
View file @ 9fd810f9
......@@ -15,14 +15,14 @@ FROM node:21.1-bookworm-slim as dev
ARG BASE_URL=/
ARG MEILI_HOST=http://localhost:7700
ARG MEILI_API_KEY=api_key
ARG HOST_URL
ENV NUXT_APP_BASE_URL=${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}
ENV NUXT_PUBLIC_HOST_URL=${HOST_URL}
# ENV NUXT_PUBLIC_MEILI_HOST=${MEILI_HOST}
# ENV NUXT_PUBLIC_MEILI_API_KEY=${MEILI_API_KEY}
WORKDIR /usr/src/app
......@@ -43,10 +43,21 @@ RUN npm run build
### STAGE: serve ###
FROM node:21.1-bookworm-slim as serve
ARG BASE_URL=/
ARG MEILI_HOST=http://localhost:7700
ARG MEILI_API_KEY
ARG HOST_URL
WORKDIR /usr/src/app
COPY --from=build /usr/src/app/.output ./
ENV NUXT_APP_BASE_URL=${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_HOST_URL=${HOST_URL}
WORKDIR /usr/src/app
COPY --chown=node:node --from=build /usr/src/app/.output ./
USER node
CMD [ "node", "server/index.mjs"]
......@@ -55,6 +66,7 @@ FROM node:21.1-bookworm-slim as generate
ARG BASE_URL=/
ARG MEILI_HOST=http://localhost:7700
ARG MEILI_API_KEY
ARG HOST_URL
ENV NODE_OPTIONS=--max_old_space_size=12288
ENV NUXT_APP_BASE_URL=${BASE_URL}
......@@ -62,9 +74,11 @@ 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=${MEILI_API_KEY}
ENV NUXT_PUBLIC_HOST_URL=${HOST_URL}
ENV NUXT_PUBLIC_MEILI_HOST=${MEILI_HOST}
ENV NUXT_PUBLIC_MEILI_API_KEY=${MEILI_API_KEY}
# ENV NUXT_PUBLIC_MEILI_HOST=${MEILI_HOST}
# ENV NUXT_PUBLIC_MEILI_API_KEY=${MEILI_API_KEY}
WORKDIR /usr/src/app
......
LICENSE 0 → 100644
View file @ 9fd810f9
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13. Use with the GNU Affero General Public License.
Notwithstanding any other provision of this License, you have
permission to link or combine any covered work with a work licensed
under version 3 of the GNU Affero General Public License into a single
combined work, and to convey the resulting work. The terms of this
License will continue to apply to the part which is the covered work,
but the special requirements of the GNU Affero General Public License,
section 13, concerning interaction through a network will apply to the
combination as such.
14. Revised Versions of this License.
The Free Software Foundation may publish revised and/or new versions of
the GNU General Public License from time to time. Such new versions will
be similar in spirit to the present version, but may differ in detail to
address new problems or concerns.
Each version is given a distinguishing version number. If the
Program specifies that a certain numbered version of the GNU General
Public License "or any later version" applies to it, you have the
option of following the terms and conditions either of that numbered
version or of any later version published by the Free Software
Foundation. If the Program does not specify a version number of the
GNU General Public License, you may choose any version ever published
by the Free Software Foundation.
If the Program specifies that a proxy can decide which future
versions of the GNU General Public License can be used, that proxy's
public statement of acceptance of a version permanently authorizes you
to choose that version for the Program.
Later license versions may give you additional or different
permissions. However, no additional obligations are imposed on any
author or copyright holder as a result of your choosing to follow a
later version.
15. Disclaimer of Warranty.
THERE IS NO WARRANTY FOR THE PROGRAM, TO THE EXTENT PERMITTED BY
APPLICABLE LAW. EXCEPT WHEN OTHERWISE STATED IN WRITING THE COPYRIGHT
HOLDERS AND/OR OTHER PARTIES PROVIDE THE PROGRAM "AS IS" WITHOUT WARRANTY
OF ANY KIND, EITHER EXPRESSED OR IMPLIED, INCLUDING, BUT NOT LIMITED TO,
THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
PURPOSE. THE ENTIRE RISK AS TO THE QUALITY AND PERFORMANCE OF THE PROGRAM
IS WITH YOU. SHOULD THE PROGRAM PROVE DEFECTIVE, YOU ASSUME THE COST OF
ALL NECESSARY SERVICING, REPAIR OR CORRECTION.
16. Limitation of Liability.
IN NO EVENT UNLESS REQUIRED BY APPLICABLE LAW OR AGREED TO IN WRITING
WILL ANY COPYRIGHT HOLDER, OR ANY OTHER PARTY WHO MODIFIES AND/OR CONVEYS
THE PROGRAM AS PERMITTED ABOVE, BE LIABLE TO YOU FOR DAMAGES, INCLUDING ANY
GENERAL, SPECIAL, INCIDENTAL OR CONSEQUENTIAL DAMAGES ARISING OUT OF THE
USE OR INABILITY TO USE THE PROGRAM (INCLUDING BUT NOT LIMITED TO LOSS OF
DATA OR DATA BEING RENDERED INACCURATE OR LOSSES SUSTAINED BY YOU OR THIRD
PARTIES OR A FAILURE OF THE PROGRAM TO OPERATE WITH ANY OTHER PROGRAMS),
EVEN IF SUCH HOLDER OR OTHER PARTY HAS BEEN ADVISED OF THE POSSIBILITY OF
SUCH DAMAGES.
17. Interpretation of Sections 15 and 16.
If the disclaimer of warranty and limitation of liability provided
above cannot be given local legal effect according to their terms,
reviewing courts shall apply local law that most closely approximates
an absolute waiver of all civil liability in connection with the
Program, unless a warranty or assumption of liability accompanies a
copy of the Program in return for a fee.
END OF TERMS AND CONDITIONS
How to Apply These Terms to Your New Programs
If you develop a new program, and you want it to be of the greatest
possible use to the public, the best way to achieve this is to make it
free software which everyone can redistribute and change under these terms.
To do so, attach the following notices to the program. It is safest
to attach them to the start of each source file to most effectively
state the exclusion of warranty; and each file should have at least
the "copyright" line and a pointer to where the full notice is found.
<one line to give the program's name and a brief idea of what it does.>
Copyright (C) 2024 Remi PLANEL
This program is free software: you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
the Free Software Foundation, either version 3 of the License, or
(at your option) any later version.
This program is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
GNU General Public License for more details.
You should have received a copy of the GNU General Public License
along with this program. If not, see <https://www.gnu.org/licenses/>.
Also add information on how to contact you by electronic and paper mail.
If the program does terminal interaction, make it output a short
notice like this when it starts in an interactive mode:
<program> Copyright (C) 2024 Remi PLANEL
This program comes with ABSOLUTELY NO WARRANTY; for details type `show w'.
This is free software, and you are welcome to redistribute it
under certain conditions; type `show c' for details.
The hypothetical commands `show w' and `show c' should show the appropriate
parts of the General Public License. Of course, your program's commands
might be different; for a GUI interface, you would use an "about box".
You should also get your employer (if you work as a programmer) or school,
if any, to sign a "copyright disclaimer" for the program, if necessary.
For more information on this, and how to apply and follow the GNU GPL, see
<https://www.gnu.org/licenses/>.
The GNU General Public License does not permit incorporating your program
into proprietary programs. If your program is a subroutine library, you
may consider it more useful to permit linking proprietary applications with
the library. If this is what you want to do, use the GNU Lesser General
Public License instead of this License. But first, please read
<https://www.gnu.org/licenses/why-not-lgpl.html>.
assets/foldseek.png 0 → 100644
View file @ 9fd810f9
assets/foldseek.png

142 KiB

components/AutocompleteMeiliFacets.vue 0 → 100644
View file @ 9fd810f9
<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/EditGitlab.vue
View file @ 9fd810f9
<template>
<v-row>
<v-col>
<v-btn prepend-icon="mdi-gitlab" variant="text" size="small" :href="path" target="_blank">Edit on gitlab</v-btn>
<v-btn prepend-icon="i-vscode-icons:file-type-gitlab" variant="text" size="small" :href="path" target="_blank">Edit on gitlab</v-btn>
<v-divider> </v-divider>
</v-col>
</v-row>
......
components/FoldseekDialog.vue 0 → 100644
View file @ 9fd810f9
<script setup lang="ts">
interface Props {
foldseekPath: string
title: string
}
const props = withDefaults(defineProps<Props>(), { title: "Result of Foldseek search" });
const { width, height } = useDisplay()
const dialog = ref(false)
const iframe = ref()
const layout = ref({
scrollbarWidth: 15,
paddingLeft: 24,
paddingRight: 24,
toolbarHeight: 48,
containerPaddingTop: 16,
containerPaddingBottom: 10
})
const xMargin = computed(() => {
const toValLayout = toValue(layout)
return toValLayout.scrollbarWidth + toValLayout.paddingLeft + toValLayout.paddingRight
})
const yMargin = computed(() => {
const toValLayout = toValue(layout)
return toValLayout.toolbarHeight + toValLayout.containerPaddingBottom + toValLayout.containerPaddingTop
})
const computedWidth = computed(() => {
return toValue(width) - toValue(xMargin)
})
const computedHeight = computed(() => {
return toValue(height) - toValue(yMargin)
})
function fullscreen() {
console.log(iframe.value)
iframe.value.requestFullscreen();
}
</script>
<template>
<v-dialog v-model="dialog" fullscreen transition="dialog-bottom-transition">
<template v-slot:activator="{ props }">
<v-avatar>
<v-img src="~/assets/foldseek.png" alt="Foldseek results" v-bind="props" class="cursor-pointer"></v-img>
<!-- <v-btn color="primary" dark v-bind="props">
<v-img src="~/assets/foldseek.png" alt="Foldseek results"></v-img>
</v-btn> -->
</v-avatar>
</template>
<v-card variant="flat">
<v-toolbar flat color="transparent" density="compact">
<v-btn variant="text" color="primary" prepend-icon="mdi-arrow-left" @click="dialog = false">
Return to structure list
</v-btn>
<v-divider vertical inset></v-divider>
<v-toolbar-title> {{ props.title }}</v-toolbar-title>
<v-spacer></v-spacer>
<v-toolbar-items>
<v-btn @click="fullscreen()" icon="md:fullscreen"></v-btn>
</v-toolbar-items>
</v-toolbar>
<v-card-text>
<iframe ref="iframe" :width="computedWidth" :height="computedHeight" allow="fullscreen" loading="eager"
:src="props.foldseekPath"></iframe>
</v-card-text>
</v-card>
</v-dialog>
</template>
<style scoped>
.cursor-pointer {
cursor: pointer
}
</style>
\ No newline at end of file
components/LayoutWrapper.vue
View file @ 9fd810f9
......@@ -9,6 +9,7 @@ export interface Props {
edit?: boolean
navDrawer?: boolean
title?: string
density?: 'compact' | 'prominent'
}
const props = withDefaults(defineProps<Props>(), {
......@@ -16,15 +17,31 @@ const props = withDefaults(defineProps<Props>(), {
toc: true,
edit: true,
navDrawer: true,
title: null
title: "",
density: undefined
});
const drawer = ref(true);
const { page } = useContent();
const scrollThreshold = ref(200)
const density = ref<'compact' | 'prominent'>("prominent")
onMounted(() => {
if (props?.density) {
density.value = props.density
} else {
density.value = "prominent"
}
})
function onScroll() {
if (window.scrollY > scrollThreshold.value) {
if (props?.density) {
return props.density
}
else if (window.scrollY > scrollThreshold.value) {
density.value = "compact"
}
else { density.value = "prominent" }
......@@ -36,9 +53,9 @@ function onScroll() {
<v-main style="min-height: 300px">
<v-container v-scroll="onScroll" :fluid="fluid">
<v-row justify="center">
<v-col cols="auto">
<v-col cols="auto" class="pa-0">
<v-card flat color="transparent" :min-width="mobile ? undefined : 900" :max-width="fluid ? undefined : 1500">
<v-card-text>
<v-card-text class="pa-0">
<slot />
</v-card-text>
<EditGitlab v-if="edit" />
......@@ -48,6 +65,10 @@ function onScroll() {
</v-row>
</v-container>
<!-- <Footer></Footer> -->
<!-- <div class="i-ph-anchor-simple-thin d-none" />
<div class="i-tabler:database d-none" />
<div class="i-mdi:book-education-outline d-none" />
<div class="i-tabler:help d-none" /> -->
</v-main>
<NavNavbar v-model:drawer="drawer" :title="title !== null ? title : undefined" :density="density"
:drawer-enabled="navDrawer" />
......
components/Nav/Navbar.vue
View file @ 9fd810f9
......@@ -32,7 +32,7 @@ watchEffect(() => {
const sections = ref([
{
id: "webservice",
label: "webservice",
label: "Webservice",
href: runtimeConfig.public.defenseFinderWebservice,
},
{ id: "wiki", label: "Wiki", to: '/', },
......
components/ServerDbTable.vue
View file @ 9fd810f9
<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";
import { useFileSystemAccess } from '@vueuse/core'
export interface SortItem {
key: string,
order: boolean | 'asc' | 'desc'
......@@ -22,47 +23,57 @@ export interface NumericalFilter {
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
db?: string
sortBy?: SortItem[]
facets: MaybeRef<string[]>
numericalFilters?: MaybeRef<string | undefined>
numericalFilters?: Ref<string[] | undefined>
dataTableServerProps: Record<string, any>
columnsToDownload?: MaybeRef<string[] | undefined>
autocompleteMeiliFacetsProps: AutocompleteMeiliFacetProps
}
export interface FilterItem {
type: 'facet' | 'operator' | 'value' | 'text'
value: string
title: string
count?: number
deletable: boolean
props: Record<string, any>
}
const props = withDefaults(defineProps<Props>(), {
title: '',
db: 'refseq',
columnsToDownload: undefined,
sortBy: () => [{ key: "type", order: "asc" }],
numericalFilters: undefined
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 facetsRef = toRef(props.facets)
const emit = defineEmits(["refresh:search"])
const { search: msSearch, result: msResult } = useMeiliSearch(props.db)
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 msFilter: Ref<string | undefined> = ref(undefined)
const page = ref(1)
let loading = ref(false)
const expanded = ref([])
......@@ -75,6 +86,9 @@ const computedTableHeight = computed(() => {
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')
......@@ -83,9 +97,6 @@ const filterInputValues = computed(() => {
}
})
const isFilter = computed(() => {
return Array.isArray(filterOrSearch.value)
})
const msSortBy = computed(() => {
if (sortByRef.value.length > 0) {
......@@ -114,26 +125,67 @@ const notPaginatedParams = computed(() => {
watch([paginationParams, msSortBy, page], ([newParams, newSort, newPage]) => {
searchOrFilter()
if (toValue(isValidFilters)) {
searchOrFilter()
}
})
onMounted(async () => {
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 computedFilter = computed(() => {
return [toValue(msFilter), props.numericalFilters].filter(f => f !== undefined).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, () => {
searchOrFilter()
emitRefreshRes()
console.log(toValue(computedFilter))
if (toValue(isValidFilters) && (toValue(computedFilter) !== undefined || toValue(filterInputValues) === null)) {
searchOrFilter()
emitRefreshRes()
}
})
......@@ -147,154 +199,86 @@ const throttleSearch = useThrottleFn(async () => {
searchOrFilter()
emitRefreshRes()
}, 300)
async function searchOrFilter() {
// 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)
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
}
finally {
loading.value = false
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() {
console.log("emit refresh:search")
const q = search.value
emit("refresh:search", {
index: props.db,
index: props.autocompleteMeiliFacetsProps.db,
query: q,
params: { ...notPaginatedParams.value, filter: toValue(computedFilter), sort: msSortBy.value }
})
}
function clearFilterOrSearch() {
filterOrSearch.value = null
// searchOrFilter()
// emitRefreshRes()
}
// watch(msFilter, async (fos) => {
// searchOrFilter()
// emitRefreshRes()
// search.value = ''
// })
const totalHits = computed(() => {
return toValue(msResult)?.totalHits ?? toValue(msResult)?.estimatedTotalHits ?? 0
})
watch(filterInputValues, (newSoF) => {
if (isFilter.value && filterInputValues.value !== null && filterInputValues.value?.length % 3 === 0) {
msFilter.value = filterInputValues.value.map((it, index) => {
const sanitizedValue = it.value.split("-").slice(0, -1).join("-")
if (index >= 1 && (index + 1) % 3 === 1) {
return ` AND ${sanitizedValue}`
} else if ((index + 1) % 3 === 0) {
return `"${sanitizedValue}"`
} else {
return `${sanitizedValue}`
}
}).join("")
}
})
watch(search, () => {
searchOrFilter()
emitRefreshRes()
// emitRefreshRes()
})
const filterStep = computed(() => {
return filterInputValues.value !== null && filterInputValues.value.length > 0 ? filterInputValues.value?.length % 3 : null
})
const operatorItems = ref([
{
type: "operator", value: '=', title: "is", deletable: false, props: {
type: "operator", deletable: false
}
}, {
type: "operator", value: '!=', title: "is not", deletable: false, props: {
type: "operator",
deletable: false
}
},
])
const autocompleteItems = computed(() => {
const index = filterOrSearch.value?.length ?? 0
// console.log(index)
if (filterStep.value === null || filterStep.value === 0) {
return toValue(facetsRef).map(value => {
return {
type: "facet",
value: `${value}-${index}`,
title: value,
deletable: false,
props: {
deletable: false,
type: "facet"
}
}
})
}
if (filterStep.value === 1) {
return operatorItems.value.map(it => { return { ...it, value: `${it.value}-${index}`, } })
}
if (filterStep.value === 2) {
// get the facet value
if (Array.isArray(filterOrSearch.value)) {
const { type, value } = filterOrSearch.value?.slice(-2, -1)[0]
const sanitizedValue = value.split("-")[0]
// console.log("compute new facets")
const facetDistri = msResult.value?.facetDistribution
// console.log(facetDistri)
return facetDistri?.[sanitizedValue] ? Object.entries(facetDistri[sanitizedValue]).map(([key, val]) => {
return {
type: "value", value: `${key}-${index}`, title: key, count: val, deletable: true, props: {
type: "value", count: val, deletable: true
}
}
}) : []
}
}
})
function selectItem(item) {
filterOrSearch.value = Array.isArray(filterOrSearch.value) ? [...filterOrSearch.value, item] : [item]
}
function deleteOneFilter(index: number) {
if (isFilter.value) {
filterOrSearch.value?.splice(index - 2, 2)
}
}
// watch(msFilterCompo, () => {
// searchOrFilter()
function clearSearch() {
search.value = ""
}
// })
async function downloadData() {
pendingDownloadData.value = true
try {
const { data } = await useAsyncMeiliSearch({
index: props.db,
index: props.autocompleteMeiliFacetsProps.db,
params: { ...toValue(notPaginatedParams), filter: toValue(computedFilter), sort: toValue(msSortBy) },
query: toValue(search),
})
......@@ -304,84 +288,50 @@ async function downloadData() {
pendingDownloadData.value = false
}
}
function focusedOrBlur(isFocused: boolean) {
if (!isFocused) {
emitRefreshRes()
}
}
</script>
<template>
<v-card flat color="transparent">
<v-card-text>
</v-card-text>
<v-card-text>
<slot name="numerical-filters" :search="throttleSearch"></slot>
</v-card-text>
<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>
<template v-if="mobile">
<v-toolbar> <v-badge :content="totalHits" color="primary" class="mx-2">
<v-btn prepend-icon="md:download" :loading="pendingDownloadData" variant="text" color="primary"
@click="downloadData()">{{
props.title }}
</v-btn>
</v-badge></v-toolbar>
<v-toolbar><v-text-field v-model="search" label="Search..." hide-details="auto"
prepend-inner-icon="mdi-magnify" single-line clearable class="mx-2"></v-text-field></v-toolbar>
<v-toolbar><v-autocomplete ref="autocompleteInput" hide-details v-model:model-value="filterOrSearch"
auto-select-first chips clearable label="Filter results..." :items="autocompleteItems"
single-line item-value="value" item-title="title" multiple return-object
prepend-inner-icon="md:search" @click:appendInner="searchOrFilter" class="mx-2"
@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 === deleteOneFilter(index)"></v-chip>
</template>
<template #item="{ props, item }">
<v-list-item v-bind="{ ...props, active: false, onClick: () => selectItem(item) }"
:title="item.title" :subtitle="item.raw?.count ? item.raw.count : ''"
:value="props.value">
</v-list-item>
</template>
</v-autocomplete></v-toolbar>
</template>
<template v-else>
<v-toolbar>
<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-spacer></v-spacer>
<v-card variant="flat" color="transparent" :min-width="400" class="mx-2" :rounded="false">
<v-text-field v-model="search" label="Search..." hide-details="auto"
prepend-inner-icon="mdi-magnify" single-line clearable></v-text-field>
</v-card>
<v-card variant="flat" color="transparent" :min-width="500" class="mx-2" :rounded="false">
<v-autocomplete ref="autocompleteInput" hide-details v-model:model-value="filterOrSearch"
auto-select-first chips clearable label="Filter results..." :items="autocompleteItems"
single-line item-value="value" item-title="title" multiple return-object
prepend-inner-icon="md:search" @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 === deleteOneFilter(index)"></v-chip>
</template>
<template #item="{ props, item }">
<v-list-item v-bind="{ ...props, active: false, onClick: () => selectItem(item) }"
:title="item.title" :subtitle="item.raw?.count ? item.raw.count : ''"
:value="props.value">
</v-list-item>
</template>
</v-autocomplete>
</v-card>
</v-toolbar>
</template>
</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">
......
components/content/MolstarPdbePlugin.vue
View file @ 9fd810f9
......@@ -107,7 +107,7 @@ const pdbeMolstarComponent = 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` : null
return selectedPdb.value ? `${selectedPdb.value.split(".").slice(0, -1).join('.')}.png` : undefined
})
watch(selectedPdb, (newSelectedPdb, prevSelectPdb) => {
......@@ -190,10 +190,9 @@ const moleculeFormat: Ref<string> = ref("pdb")
<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" position="relative">
<pdbe-molstar ref="pdbeMolstarComponent" landscape="true" hide-controls="true"
:custom-data-url="selectedPdb" alphafold-view="true"
:custom-data-format="moleculeFormat"></pdbe-molstar>
: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">
......@@ -272,4 +271,4 @@ div.msp-plugin-content.msp-layout-expanded {
height: 16px;
width: 16px;
}
</style>
\ No newline at end of file
</style>
components/content/RefseqDb.vue
View file @ 9fd810f9
......@@ -2,36 +2,98 @@
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"
import { useSerialize } from "@/composables/useSerialize";
import { useRasterize } from "@/composables/useRasterize";
import { useDownloadBlob } from '@/composables/useDownloadBlob';
import type { SortItem, AutocompleteMeiliFacetProps } from "@/components/ServerDbTable.vue"
import type { ComponentPublicInstance } from 'vue'
const sortBy: Ref<SortItem[]> = ref([{ key: 'type', order: "asc" }])
const itemValue = ref("id");
const { width } = useDisplay();
const scaleTransform: Ref<string[]> = ref([])
const dbName = ref("refseq")
onBeforeMount(async () => {
const { data } = await useAsyncMeiliSearch({
index: toValue(dbName), query: "", params: {
facets: ["*"],
filter: [],
page: 1,
hitsPerPage: 25,
}
})
autocompleteMeiliFacetsProps.value.facetDistribution = toValue(data)?.facetDistribution
})
onMounted(async () => {
const { data } = await useAsyncMeiliSearch({
index: toValue(dbName), query: "", params: {
facets: ["*"],
filter: [],
page: 1,
hitsPerPage: 25,
}
})
autocompleteMeiliFacetsProps.value.facetDistribution = toValue(data)?.facetDistribution
})
const { serialize } = useSerialize()
const { rasterize } = useRasterize()
const { download } = useDownloadBlob()
const facets = ref([
"replicon",
"type",
"subtype",
"Superkingdom",
"phylum",
"order",
"family",
"genus",
"species",
])
const autocompleteMeiliFacetsProps = ref<AutocompleteMeiliFacetProps>({
db: toValue(dbName),
facets: [
{ title: "Defense System", type: "subheader" },
{ title: "System", value: "type", type: "facet", icon: "i-tabler:virus-off", },
{ title: "Subsystem", value: "subtype", type: "facet", icon: "i-tabler:virus-off" },
{ type: "divider" },
{ title: "Taxonomy", type: "subheader" },
{ title: "Superkingdom", value: "Superkingdom", type: "facet", icon: "i-tabler:binary-tree" },
{ title: "Phylum", value: "phylum", type: "facet", icon: "i-tabler:binary-tree" },
{ title: "Order", value: "order", type: "facet", icon: "i-tabler:binary-tree" },
{ title: "Family", value: "family", type: "facet", icon: "i-tabler:binary-tree" },
{ title: "Genus", value: "genus", type: "facet", icon: "i-tabler:binary-tree" },
{ title: "Species", value: "species", type: "facet", icon: "i-tabler:binary-tree" },
{ type: "divider" },
{ title: "Replicon", value: "replicon", type: "facet", icon: "mdi-dna", },
],
facetDistribution: undefined
})
const computedAutocompleteMeiliFacetsProps = computed(() => {
const toValFacetDistribution = toValue(autocompleteMeiliFacetsProps).facetDistribution
const toValFacets = toValue(autocompleteMeiliFacetsProps).facets
if (toValFacetDistribution !== undefined && toValFacets !== undefined) {
return {
...toValue(autocompleteMeiliFacetsProps), facets: toValFacets.map(facet => {
if (facet.type === "facet") {
const count = toValFacetDistribution?.[facet.value] ? Object.keys(toValFacetDistribution[facet.value]).length : undefined
return count ? { ...facet, count } : { ...facet }
}
else {
return { ...facet }
}
})
}
}
else {
return toValue(autocompleteMeiliFacetsProps)
}
})
const availableTaxo: Ref<string[]> = ref([
"species",
"genus",
......@@ -42,16 +104,16 @@ const availableTaxo: Ref<string[]> = ref([
]);
const scaleTypes = ref<string[]>(['linear', 'sqrt', 'log', 'symlog'])
const selectedTaxoRank = ref("phylum");
const selectedTaxoRank = ref("Superkingdom");
const headers = ref([
{ title: "Replicon", key: "replicon" },
{
title: "Type",
title: "System",
key: "type",
},
{
title: "Subtype",
title: "Subsystem",
key: "subtype",
},
{
......@@ -72,7 +134,7 @@ const computedHeaders = computed(() => {
}
})]
})
const { result: msResult } = useMeiliSearch('refseq')
const { result: msResult } = useMeiliSearch(toValue(dbName))
const computedWidth = computed(() => {
const currentWidth = fullWidth.value ? width.value : width.value / 2
......@@ -82,20 +144,11 @@ const computedWidth = computed(() => {
const allHits: Ref<Record<string, any> | undefined> = ref(undefined)
// onMounted(async () => {
// console.log("on mounted get all hits")
// const params = {
// facets: ["*"],
// filter: undefined,
// sort: ["type:asc"],
// limit: 500000
// }
// getAllHits({ index: "refseq", params, query: "" })
// })
const pendingAllHits = ref(false)
async function getAllHits(params: { index: string, params: Record<string, any>, query: string }) {
console.log(params.index)
if (params.index === 'refseq') {
if (params.index === toValue(dbName)) {
console.log("get all hits in function ")
console.log(params)
pendingAllHits.value = true
......@@ -112,10 +165,6 @@ async function getAllHits(params: { index: string, params: Record<string, any>,
}
const plotHeight = computed(() => {
return computedWidth.value / 3;
// return 500
});
const defaultDataTableServerProps = ref({
showExpand: false
......@@ -222,7 +271,7 @@ function namesToAccessionChips(names: string[]) {
return namesToCollapsibleChips(names).map(it => {
return {
...it,
// href: new URL(it.title, "http://toto.pasteur.cloud").toString()
href: new URL(it.title, "https://www.ncbi.nlm.nih.gov/protein/").toString()
}
})
}
......@@ -235,7 +284,7 @@ const binPlotOptions = ref({
grid: true,
x: { tickRotate: 90, tip: true, label: "Systems" },
// y: { tickFormat: 's' },
color: { scheme: "turbo", legend: true },
color: { scheme: "plasma", legend: true },
})
const binPlotDataOptions = computed(() => {
......@@ -249,10 +298,7 @@ const binPlotDataOptions = computed(() => {
type: scaleType.value,
tickFormat: '~s',
ticks: scaleType.value === 'symlog' ? 3 : 5,
// width: 350
},
// fy: { domain: groupSortDomain.value },
marks: [
Plot.cell(toValueAllHits?.hits ?? [], Plot.group({ fill: "count" }, { x: "type", y: selectedTaxoRank.value, tip: true, inset: 0.5, sort: { y: "fill" } })),
]
......@@ -419,13 +465,25 @@ async function downloadPng(component: ComponentPublicInstance | null, filename:
</v-expansion-panel>
</v-expansion-panels>
<ServerDbTable title="RefSeq" db="refseq" :sortBy="sortBy" :facets="facets"
<ServerDbTable title="RefSeq" :sortBy="sortBy"
:autocomplete-meili-facets-props="computedAutocompleteMeiliFacetsProps"
:data-table-server-props="dataTableServerProps" @refresh:search="(params) => getAllHits(params)">
<template #[`item.accession_in_sys`]="{ item }">
<CollapsibleChips :items="namesToAccessionChips(item.accession_in_sys)">
</CollapsibleChips>
</template>
<template #[`item.type`]="{ item }">
<v-chip color="info" link size="small" :to="`/defense-systems/${item.type.toLowerCase()}`" target="_blank"> {{
item.type }}
</v-chip>
</template>
<template #[`item.subtype`]="{ item }">
<v-chip color="info" link size="small" :to="`/defense-systems/${item.type.toLowerCase()}`" target="_blank"> {{
item.subtype }}
</v-chip>
</template>
</ServerDbTable>
......
components/content/StructureDb.vue
View file @ 9fd810f9
<script setup lang="ts">
import * as Plot from "@observablehq/plot";
import PlotFigure from "~/components/PlotFigure";
import type { SortItem } from "@/components/ServerDbTable.vue"
import type { SortItem, AutocompleteMeiliFacetProps } from "@/components/ServerDbTable.vue"
import { useNumericalFilter } from "@/composables/useNumericalfilter"
import { useRefinedUrl } from "@/composables/useRefinedUrl"
import { ServerDbTable } from "#components"
import { withQuery, joinURL, withTrailingSlash } from 'ufo'
import { ServerDbTable } from "#components"
interface Item {
Foldseek_name: string
System_name_ok: string
}
const sortBy: Ref<SortItem[]> = ref([{ key: 'System', order: "asc" }])
const itemValue = ref("id");
const facets: Ref<string[]> = ref(["System", "subtype", "gene_name", "completed", "prediction_type", "proteins_in_the_prediction", "system_genes",
])
const dbName = ref("structure")
onBeforeMount(async () => {
console.log("dans le mounted refseq")
const { data } = await useAsyncMeiliSearch({
index: toValue(dbName), query: "", params: {
facets: ["*"],
filter: [],
page: 1,
hitsPerPage: 25,
}
})
autocompleteMeiliFacetsProps.value.facetDistribution = toValue(data)?.facetDistribution
})
const autocompleteMeiliFacetsProps = ref<AutocompleteMeiliFacetProps>({
db: toValue(dbName),
facets: [
{ title: "Defense System", type: "subheader" },
{ title: "System", value: "System", type: "facet", icon: "i-tabler:virus-off", },
{ title: "Subsystem", value: "subtype", type: "facet", icon: "i-tabler:virus-off" },
{ type: "divider" },
{ title: "Gene name", value: "gene_name", type: "facet", icon: "mdi-dna" },
{ title: "Completed", value: "completed", type: "facet", icon: "md:done" },
{ title: "Prediction type", value: "prediction_type", type: "facet", icon: "i-gravity-ui:molecule" },
],
facetDistribution: undefined
})
const computedAutocompleteMeiliFacetsProps = computed(() => {
const toValFacetDistribution = toValue(autocompleteMeiliFacetsProps).facetDistribution
const toValFacets = toValue(autocompleteMeiliFacetsProps).facets
if (toValFacetDistribution !== undefined && toValFacets !== undefined) {
return {
...toValue(autocompleteMeiliFacetsProps), facets: toValFacets.map(facet => {
if (facet.type === "facet") {
const count = toValFacetDistribution?.[facet.value] ? Object.keys(toValFacetDistribution[facet.value]).length : undefined
return count ? { ...facet, count } : { ...facet }
}
else {
return { ...facet }
}
})
}
}
else {
return toValue(autocompleteMeiliFacetsProps)
}
})
const headers: Ref<Object[]> = ref([
{ title: 'Structure', key: 'structure', sortable: false, removable: false },
{ title: 'Foldseek', key: 'Foldseek_name', sortable: false },
{ title: "System", key: "System", removable: false },
{ title: "Gene name", key: "gene_name", removable: false },
{ title: "Subtype", key: "subtype", removable: false },
......@@ -31,14 +93,19 @@ const headers: Ref<Object[]> = ref([
])
const { search: msSearch, result: msResult } = useMeiliSearch('structure')
const { range: plddtsRange, stringifyFilter: plddtsFilter, reset: plddtsReset } = useNumericalFilter("plddts", 0, 100)
const { range: iptmRange, stringifyFilter: iptmFilter, reset: iptmReset } = useNumericalFilter("iptm+ptm", 0, 1)
const { range: pdockqRange, stringifyFilter: pdockqFilter, reset: pdockqReset } = useNumericalFilter("pDockQ", 0, 1)
function isString(item: Ref<string | undefined>): item is Ref<string> {
return toValue(item) !== undefined
}
const numericalFilters = computed(() => {
const listFilters = [plddtsFilter, iptmFilter, pdockqFilter].map(f => toValue(f)).filter(f => f !== undefined)
return listFilters.length > 0 ? listFilters.join(" AND ") : undefined
const listFilters = [plddtsFilter, iptmFilter, pdockqFilter].filter(isString).map(f => toValue(f))
return listFilters.length > 0 ? listFilters : undefined
})
const defaultDataTableServerProps = ref({
......@@ -55,6 +122,12 @@ const dataTableServerProps = computed(() => {
function toFolseekUrl(item: Item) {
const url = joinURL("/" + item.System_name_ok, item.Foldseek_name)
const { refinedUrl } = useRefinedUrl(url)
console.log(toValue(refinedUrl))
return toValue(refinedUrl)
}
function namesToCollapsibleChips(names: string[], systemDir: string, file: string | null = null) {
......@@ -70,63 +143,64 @@ function pdbNameToCif(pdbPath: string) {
return `${cifPath}.cif`
}
function toSystemName(rawName: string) {
// Does it work if it's a list of system genes ?
// split on __ for systeme_vgenes
return rawName.split("__")[0].toLocaleLowerCase()
}
const plddtDistribution = computed(() => {
if (toValue(msResult)?.facetDistribution?.plddts) {
return Object.entries(toValue(msResult).facetDistribution.plddts).map(([key, value]) => { })
}
})
</script>
<template>
<ServerDbTable title="Predicted Structures" db="structure" :sortBy="sortBy" :facets="facets"
:data-table-server-props="dataTableServerProps" :numerical-filters="numericalFilters">
<ServerDbTable title="Predicted Structures" :sortBy="sortBy" :data-table-server-props="dataTableServerProps"
:autocomplete-meili-facets-props="computedAutocompleteMeiliFacetsProps"
:numerical-filters="toRef(numericalFilters)">
<template #numerical-filters="{ search }">
<v-row>
<v-col cols="12" md="12" lg="4">
<v-range-slider v-model="plddtsRange" strict density="compact" hide-details="auto" label="pLDDT"
step="0.5" :min="0" :max="100" thumb-label="always" @update:modelValue="search()">
<template #append>
<v-btn variant="text" icon="md:restart_alt" @click="plddtsReset()"></v-btn>
</template>
</v-range-slider>
</v-col>
<v-col cols="12" md="12" lg="4">
<v-range-slider v-model="iptmRange" strict density="compact" hide-details="auto" label="iptm+ptm"
step="0.1" :min="0" :max="1" thumb-label="always" @update:modelValue="search()">
<template #append>
<v-btn variant="text" icon="md:restart_alt" @click="iptmReset()"></v-btn>
</template>
</v-range-slider>
</v-col>
<!-- pdockqReset -->
<v-col cols="12" md="12" lg="4">
<v-range-slider v-model="pdockqRange" strict density="compact" hide-details="auto" label="pDockQ"
step="0.1" :min="0" :max="1" thumb-label="always" @update:modelValue="search()">
<template #append>
<v-btn variant="text" icon="md:restart_alt" @click="pdockqReset()"></v-btn>
</template>
</v-range-slider>
</v-col>
</v-row>
<v-list>
<v-list-item>
<v-list-item-title class="text-subtitle-1 text-medium-emphasis">
pLDDT
</v-list-item-title>
<v-row>
<v-col class="pt-8 pl-8" :lg="8">
<v-range-slider v-model="plddtsRange" strict density="compact" hide-details="auto" step="0.5"
:min="0" :max="100" thumb-label="always" @update:modelValue="search()">
<template #append>
<v-btn variant="text" icon="md:restart_alt" @click="plddtsReset()"></v-btn>
</template>
</v-range-slider>
</v-col></v-row>
</v-list-item>
<v-list-item>
<v-list-item-title class="text-subtitle-1 text-medium-emphasis">
iptm+ptm
</v-list-item-title>
<v-row>
<v-col class="pt-8 pl-8" :lg="8">
<v-range-slider v-model="iptmRange" strict density="compact" hide-details="auto" step="0.1"
:min="0" :max="1" thumb-label="always" @update:modelValue="search()">
<template #append>
<v-btn variant="text" icon="md:restart_alt" @click="iptmReset()"></v-btn>
</template>
</v-range-slider>
</v-col></v-row>
</v-list-item>
<v-list-item>
<v-list-item-title class="text-subtitle-1 text-medium-emphasis">pDockQ</v-list-item-title>
<v-row>
<v-col class="pt-8 pl-8" :lg="8">
<v-range-slider v-model="pdockqRange" density="compact" strict hide-details="auto" step="0.1"
:min="0" :max="1" thumb-label="always" @update:modelValue="search()">
<template #append>
<v-btn variant="text" icon="md:restart_alt" @click="pdockqReset()"></v-btn>
</template>
</v-range-slider>
</v-col></v-row>
</v-list-item>
</v-list>
</template>
<template #[`item.Foldseek_name`]="{ item }">
<FoldseekDialog v-if="item.Foldseek_name !== 'na'" :foldseek-path="toFolseekUrl(item)"></FoldseekDialog>
<!-- <NuxtLink v-if="item.Foldseek_name !== 'na'" :to="toFolseekUrl(item)" :external="false">
<v-avatar>
<v-img src="~/assets/foldseek.png" alt="Foldseek results"></v-img>
</v-avatar>
</NuxtLink> -->
</template>
<template #[`item.proteins_in_the_prediction`]="{ item }">
<CollapsibleChips
:items="namesToCollapsibleChips(item.proteins_in_the_prediction, item.System_name_ok, item.fasta_file)">
......
components/content/SystemDb.vue
View file @ 9fd810f9
<script setup lang="ts">
import type { SortItem } from "@/components/ServerDbTable.vue"
import type { SortItem, AutocompleteMeiliFacetProps } from "@/components/ServerDbTable.vue"
import { ServerDbTable } from "#components"
const sortBy: Ref<SortItem[]> = ref([{ key: 'title', order: "asc" }])
const itemValue = ref("title");
const facets: Ref<string[]> = ref(["title", "Sensor", "Effector", "Activator", "PFAM.AC", "PFAM.DE"])
const dbName = ref("systems")
onBeforeMount(async () => {
const { data } = await useAsyncMeiliSearch({
index: toValue(dbName), query: "", params: {
facets: ["*"],
filter: [],
page: 1,
hitsPerPage: 25,
}
})
autocompleteMeiliFacetsProps.value.facetDistribution = toValue(data)?.facetDistribution
})
const autocompleteMeiliFacetsProps = ref<AutocompleteMeiliFacetProps>({
db: toValue(dbName),
facets: [
{ title: "Defense System", type: "subheader" },
{ title: 'System', value: "title", type: "facet", icon: "i-tabler:virus-off" },
{ type: "divider" },
{ title: "Mechanism", type: "subheader" },
{ title: 'Sensor', value: "Sensor", type: "facet", icon: "i-tabler:shield-cog" },
{ title: 'Effector', value: "Effector", type: "facet", icon: "i-tabler:shield-cog" },
{ title: 'Activator', value: "Activator", type: "facet", icon: "i-tabler:shield-cog" },
{ type: "divider" },
{ title: "PFAM", type: "subheader" },
{ title: 'Acession', value: "PFAM.AC", type: "facet", icon: "i-tabler:circle-key" },
{ title: 'Description', value: "PFAM.DE", type: "facet", icon: "i-tabler:file-description" },
{ type: "divider" },
{ title: 'Contributor', value: "contributors", type: "facet", icon: "i-tabler:user-heart" },
],
facetDistribution: undefined
})
const computedAutocompleteMeiliFacetsProps = computed(() => {
const toValFacetDistribution = toValue(autocompleteMeiliFacetsProps).facetDistribution
const toValFacets = toValue(autocompleteMeiliFacetsProps).facets
if (toValFacetDistribution !== undefined && toValFacets !== undefined) {
return {
...toValue(autocompleteMeiliFacetsProps), facets: toValFacets.map(facet => {
if (facet.type === "facet") {
const count = toValFacetDistribution?.[facet.value] ? Object.keys(toValFacetDistribution[facet.value]).length : undefined
return count ? { ...facet, count } : { ...facet }
}
else {
return { ...facet }
}
})
}
}
else {
return toValue(autocompleteMeiliFacetsProps)
}
})
const headers: Ref<Object[]> = ref([
{ title: "System", key: "title", removable: false },
{ title: "Article", key: "doi", removable: false },
......@@ -16,7 +80,6 @@ const headers: Ref<Object[]> = ref([
])
const { search: msSearch, result: msResult } = useMeiliSearch('systems')
const defaultDataTableServerProps = ref({
showExpand: false
......@@ -34,7 +97,8 @@ const columnsToDownload = ref(['title', 'doi', 'Sensor', 'Activator', 'Effector'
</script>
<template>
<ServerDbTable title="List Systems" db="systems" :sortBy="sortBy" :facets="facets"
<ServerDbTable title="List Systems" :db="dbName" :sortBy="sortBy"
:autocomplete-meili-facets-props="computedAutocompleteMeiliFacetsProps"
:data-table-server-props="dataTableServerProps" :columns-to-download="columnsToDownload">
......@@ -48,8 +112,11 @@ const columnsToDownload = ref(['title', 'doi', 'Sensor', 'Activator', 'Effector'
<ArticleDoi v-if="item?.doi" :doi="item.doi" :abstract="item?.abstract" :divider="false" :enumerate="false" />
</template>
<template #[`item.PFAM`]="{ item }">
<pfam-chips v-if="item?.PFAM" :pfams="item.PFAM"></pfam-chips>
</template>
<template #[`item.contributors`]="{ item }">
<CollapsibleChips v-if="item?.contributors" :items="item.contributors.map(it => ({ title: it }))">
</CollapsibleChips>
</template>
</ServerDbTable>
</template>
\ No newline at end of file
composables/useFacetFilters.ts 0 → 100644
View file @ 9fd810f9
export interface FilterItem {
type: 'facet' | 'operator' | 'value' | 'text'
value: string
title: string
count?: number
deletable: boolean
props: Record<string, any>
}
export function useFacetFilters(inputFilters: MaybeRef<FilterItem[] | undefined>) {
}
\ No newline at end of file
composables/useFetchMsDocument.ts
View file @ 9fd810f9
......@@ -17,8 +17,8 @@ export async function useFetchMsDocument(
const runtimeConfig = useRuntimeConfig();
const client = new MeiliSearch({
host: runtimeConfig.public.meiliHost,
apiKey: runtimeConfig.public.meiliApiKey
host: runtimeConfig.public.meilisearchClient.hostUrl,
apiKey: runtimeConfig.public.meilisearchClient.searchApiKey
})
const pending = ref(false)
const filterError: Ref<string | null> = ref(null)
......
composables/useMeiliFilters.ts 0 → 100644
View file @ 9fd810f9
import type { FilterItem } from '@/components/AutocompleteMeiliFacets.vue'
import { filter } from '@observablehq/plot'
import type { Filter } from "meilisearch"
export function useMeiliFilters(filters: MaybeRef<FilterItem[] | undefined>, numericalFilters: Ref<string[] | undefined>) {
const arrayFilters = ref<Filter | undefined>(undefined)
const nf = toRef(numericalFilters)
watch(nf, () => {
console.log("mon nf", nf)
})
watch(numericalFilters,() => {
console.log("je watch numerical filter", numericalFilters)
})
watchEffect(() => {
console.log("dans le computed de useMeilisFilter")
const toValFilters = toValue(filters)
const toValNumericalFilter = toValue(nf)
console.log(toValNumericalFilter)
let categoricalFilters: FilterItem[] | undefined = undefined
if (toValFilters !== undefined && toValFilters.length >= 3) {
const cachedFilters = [...toValFilters]
// Remove last element if it is an outerOperator
if (cachedFilters.length % 4 === 0 && cachedFilters.slice(-1)[0].type === 'outerOperator') {
cachedFilters.splice(-1)
}
let previousOperator: 'AND' | 'OR' | undefined = undefined
const arrayFilters = cachedFilters.reduce<FilterItem[]>((acc, curr, index) => {
const sanitizedValue = curr.value.split("-").slice(0, -1).join("-")
const position = index + 1
switch (position % 4) {
case 0:
// if this is the first time pass by an outeroperator
if (previousOperator === undefined) {
const newFilter = acc.splice(-3).join("")
console.log("newFilter: ", newFilter)
if (sanitizedValue === 'OR') {
acc = [[newFilter]]
}
else {
acc.push(newFilter)
}
}
previousOperator = sanitizedValue
break;
case 3:
acc.push(`'${sanitizedValue}'`)
const newFilter = acc.splice(-3).join("")
if (previousOperator === 'AND') {
acc.push(newFilter)
}
else {
const previousElem = acc.slice(-1)[0]
if (Array.isArray(previousElem)) {
acc.slice(-1)[0].push(newFilter)
}
else if (previousElem !== undefined) {
const previousElem = acc.splice(-1)[0]
console.log("previousElem: ", previousElem)
console.log("newFilter: ", newFilter)
acc.push([previousElem, newFilter])
}
else {
acc.push(newFilter)
}
}
break
default:
acc.push(sanitizedValue)
break;
}
return acc
}, [])
categoricalFilters = arrayFilters.length > 0 ? arrayFilters : undefined
}
function isFilterItem(item: FilterItem[] | string[] | undefined): item is FilterItem[] | string[] {
return item !== undefined
}
console.log(categoricalFilters)
const filterItemArray = [categoricalFilters, toValNumericalFilter].filter(isFilterItem).flat()
console.log(filterItemArray)
// const returnArr = filterItemArray.reduce<FilterItem | string | undefined>((acc, curr) => {
// const toValCurr = toValue(curr)
// if (toValCurr === undefined) {
// return acc
// }
// else {
// if (acc !== undefined) {
// return [...acc, ...toValCurr]
// }
// else { return [...toValCurr] }
// }
// }, undefined)
// console.log(returnArr)
// return returnArr
arrayFilters.value = filterItemArray
})
// const arrayFilters: ComputedRef<Filter | undefined> = computed(() => {
// })
return { arrayFilters }
}
composables/useNumericalfilter.ts
View file @ 9fd810f9
......@@ -6,17 +6,11 @@ export function useNumericalFilter(
const range: Ref<[number, number]> = ref([toValue(min), toValue(max)])
const stringifyFilter: Ref<string | undefined> = ref(`${toValue(id)} ${toValue(min)} TO ${toValue(max)}`)
const stringifyFilter: Ref<string | undefined> = ref(undefined)
watchEffect(() => {
console.log("watch reange")
console.log(range.value)
if (range.value[0] === toValue(min) && range.value[1] === toValue(max)) {
stringifyFilter.value = undefined
} else {
......
content/1.help/2.Contributing-Wiki.md
View file @ 9fd810f9
---
title: Contributing to the Wiki
layout: article
navigation:
---
# Contributing to the Wiki
......