packages/df-wiki-cli/df_wiki_cli/meilisearch/__init__.py

@@ -5,10 +5,14 @@ import json
 from typing import Annotated, List, Optional
 from pydantic import BaseModel, Field, BeforeValidator
 from enum import Enum
+from rich.console import Console
+
+
+console = Console()
 
 
 class RefSeqCsv(BaseModel):
-    id: str
+    sys_id: str
     replicon: str
     type: str
     subtype: str
@@ -86,7 +90,9 @@ def update_refseq(
             row["accession_in_sys"] = split_on_comma(row["accession_in_sys"])
             doc = RefSeqCsv(**row)
             documents.append(doc.model_dump(by_alias=True))
-        index.add_documents_in_batches(documents, primary_key="id")
+        tasks = index.add_documents_in_batches(documents, primary_key="sys_id")
+        for task in tasks:
+            console.print(task)
     index.update_pagination_settings({"maxTotalHits": 1000000})
     index.update_filterable_attributes(
         body=[
@@ -210,7 +216,15 @@ def update_systems(
     )
     print(pagination_settings_task)
     attr_task = index.update_filterable_attributes(
-        body=["title", "Sensor", "Activator", "Effector", "PFAM.AC", "PFAM.DE"]
+        body=[
+            "title",
+            "Sensor",
+            "Activator",
+            "Effector",
+            "PFAM.AC",
+            "PFAM.DE",
+            "contributors",
+        ]
     )
     params = {
         "maxValuesPerFacet": 1000000,

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

@@ -5,6 +5,10 @@ from pathlib import Path
 from df_wiki_cli.meilisearch import update_refseq, update_structure, update_systems
 from enum import Enum
 from types import SimpleNamespace
+from rich.console import Console
+
+
+console = Console()
 
 app = typer.Typer()
 
@@ -66,6 +70,21 @@ def delete_all_documents(ctx: typer.Context, id: str):
     index.delete_all_documents()
 
 
+@app.command()
+def indexes(ctx: typer.Context):
+    client = meilisearch.Client(ctx.obj.host, ctx.obj.key)
+    indexes = client.get_indexes()["results"]
+    for index in indexes:
+        print(index.uid)
+
+
+@app.command()
+def index_update(ctx: typer.Context, index: str, primary_key: str):
+    client = meilisearch.Client(ctx.obj.host, ctx.obj.key)
+    task = client.index(index).update(primary_key=primary_key)
+    console.print(task)
+
+
 @app.command()
 def task(ctx: typer.Context, id: str):
     client = meilisearch.Client(ctx.obj.host, ctx.obj.key)

packages/df-wiki-cli/pyproject.toml

 [tool.poetry]
 name = "df-wiki-cli"
-version = "0.1.4"
+version = "0.1.5"
 description = ""
 authors = ["Remi  PLANEL <rplanel@pasteur.fr>"]
 readme = "README.md"

pages/foldseek.vue

+<script setup lang="ts">
+definePageMeta({
+    documentDriven: false
+})
+</script>
+
+<template>
+    <NuxtPage></NuxtPage>
+</template>
\ No newline at end of file

pages/foldseek/[system]/[fileName].vue

+<script setup lang="ts">
+import { toValue } from '@vueuse/core';
+import { withTrailingSlash, withLeadingSlash, joinURL } from 'ufo'
+
+import { useDisplay } from "vuetify"
+definePageMeta({
+    documentDriven: false
+})
+definePageMeta({
+    layout: 'foldseek'
+})
+const runtimeConfig: { public: { hostUrl: string } } = useRuntimeConfig();
+
+const { width, height } = useDisplay()
+const route = useRoute()
+
+
+const layout = ref({
+    scrollbarWidth: 15,
+    paddingLeft: 24,
+    paddingRight: 24,
+    toolbarHeight: 48,
+    containerPaddingTop: 16,
+    paddingTopCol: 16,
+    containerPaddingBottom: 10,
+    toolbarModalHeight: 48
+
+
+})
+
+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.toolbarModalHeight
+        + toValLayout.containerPaddingBottom
+        + toValLayout.containerPaddingTop
+        + toValLayout.paddingTopCol
+})
+
+const computedWidth = computed(() => {
+    return toValue(width) - toValue(xMargin)
+})
+const computedHeight = computed(() => {
+    return toValue(height) - toValue(yMargin)
+})
+
+const breadcrumbItems = computed(() => {
+    return [
+        {
+            title: 'Structures DB',
+            disabled: false,
+            to: '/structure/'
+        },
+        {
+            title: route.params.system,
+            disabled: true,
+            exact: true,
+            to: {
+                name: route.name, params: {
+                    ...route.params,
+                }
+            }
+        }
+    ]
+
+})
+
+
+const refinedFoldseekPath = computed(() => {
+    // return 'https://defense-finder.dev.pasteur.cloud/wiki/abia/AbiA_large__AbiA_large-plddts_90.82916.html'
+    const url = `/${route.params.system}/${route.params.fileName}.html`
+    console.log(useRuntimeConfig())
+    if (url?.startsWith('/') && !url.startsWith('//')) {
+        const _base = withLeadingSlash(withTrailingSlash(useRuntimeConfig().app.baseURL))
+        if (_base !== '/' && !url.startsWith(_base)) {
+            return joinURL(runtimeConfig.public.hostUrl, _base, url)
+        }
+    }
+    return url
+})
+
+
+
+const iframe = ref()
+function fullscreen() {
+    console.log(iframe.value)
+    iframe.value.requestFullscreen();
+}
+</script>
+
+<template>
+    <!-- <v-breadcrumbs :items="breadcrumbItems"></v-breadcrumbs> -->
+    <v-card variant="flat" color="transparent" class="pa-0">
+        <v-toolbar flat color="transparent" density="compact">
+            <v-spacer></v-spacer>
+            <v-btn @click="fullscreen()" icon="md:fullscreen"></v-btn>
+        </v-toolbar>
+        <iframe ref="iframe" :width="computedWidth" :height="computedHeight" allow="fullscreen" loading="lazy"
+            :src="refinedFoldseekPath"></iframe>
+    </v-card>
+</template>
\ No newline at end of file

pages/foldseek/[system]/index.vue

+<script setup lang="ts">
+import { toValue } from '@vueuse/core';
+import { withTrailingSlash, withLeadingSlash, joinURL } from 'ufo'
+
+import { useDisplay } from "vuetify"
+definePageMeta({
+    documentDriven: false
+})
+definePageMeta({
+    layout: 'foldseek'
+})
+const runtimeConfig: { public: { hostUrl: string } } = useRuntimeConfig();
+
+const { width, height } = useDisplay()
+const route = useRoute()
+
+
+const layout = ref({
+    scrollbarWidth: 15,
+    paddingLeft: 24,
+    paddingRight: 24,
+    toolbarHeight: 48,
+    containerPaddingTop: 16,
+    paddingTopCol: 16,
+    containerPaddingBottom: 10,
+    toolbarModalHeight: 48
+
+
+})
+
+const xMargin = computed(() => {
+    const toValLayout = toValue(layout)
+    console.log(route)
+    return toValLayout.scrollbarWidth + toValLayout.paddingLeft + toValLayout.paddingRight
+})
+
+const yMargin = computed(() => {
+    const toValLayout = toValue(layout)
+    return toValLayout.toolbarHeight
+        + toValLayout.toolbarModalHeight
+        + toValLayout.containerPaddingBottom
+        + toValLayout.containerPaddingTop
+        + toValLayout.paddingTopCol
+})
+
+const computedWidth = computed(() => {
+    return toValue(width) - toValue(xMargin)
+})
+const computedHeight = computed(() => {
+    return toValue(height) - toValue(yMargin)
+})
+
+const breadcrumbItems = computed(() => {
+    return [
+        {
+            title: 'Structures DB',
+            disabled: false,
+            to: '/structure/'
+        },
+        {
+            title: route.params.system,
+            disabled: true,
+            exact: true,
+            to: {
+                name: route.name, params: {
+                    ...route.params,
+                }
+            }
+        }
+    ]
+
+})
+
+
+const refinedFoldseekPath = computed(() => {
+    // return 'https://defense-finder.dev.pasteur.cloud/wiki/abia/AbiA_large__AbiA_large-plddts_90.82916.html'
+    const url = `/${route.params.system}/${route.query.html}.html`
+    console.log(useRuntimeConfig())
+    if (url?.startsWith('/') && !url.startsWith('//')) {
+        const _base = withLeadingSlash(withTrailingSlash(useRuntimeConfig().app.baseURL))
+        if (_base !== '/' && !url.startsWith(_base)) {
+            const sanitizedUrl = joinURL(runtimeConfig.public.hostUrl, _base, url)
+            console.log(sanitizedUrl)
+            return sanitizedUrl
+        }
+    }
+    return url
+})
+
+
+
+const iframe = ref()
+function fullscreen() {
+    console.log(iframe.value)
+    iframe.value.requestFullscreen();
+}
+</script>
+
+<template>
+    <!-- <v-breadcrumbs :items="breadcrumbItems"></v-breadcrumbs> -->
+    <v-card variant="flat" color="transparent" class="pa-0">
+        <v-toolbar flat color="transparent" density="compact">
+            <v-spacer></v-spacer>
+            <v-btn @click="fullscreen()" icon="md:fullscreen"></v-btn>
+        </v-toolbar>
+        <iframe ref="iframe" :width="computedWidth" :height="computedHeight" allow="fullscreen"
+            :src="refinedFoldseekPath"></iframe>
+    </v-card>
+</template>
\ No newline at end of file

pages/foldseek/index.vue

+<script setup lang="ts">
+import { toValue } from '@vueuse/core';
+import { withTrailingSlash, withLeadingSlash, joinURL } from 'ufo'
+
+import { useDisplay } from "vuetify"
+definePageMeta({
+    documentDriven: false
+})
+definePageMeta({
+    layout: 'foldseek'
+})
+const runtimeConfig: { public: { hostUrl: string } } = useRuntimeConfig();
+
+const { width, height } = useDisplay()
+const route = useRoute()
+
+
+const layout = ref({
+    scrollbarWidth: 15,
+    paddingLeft: 24,
+    paddingRight: 24,
+    toolbarHeight: 48,
+    containerPaddingTop: 16,
+    paddingTopCol: 16,
+    containerPaddingBottom: 10,
+    toolbarModalHeight: 48
+
+
+})
+
+const xMargin = computed(() => {
+    const toValLayout = toValue(layout)
+    console.log(route)
+    return toValLayout.scrollbarWidth + toValLayout.paddingLeft + toValLayout.paddingRight
+})
+
+const yMargin = computed(() => {
+    const toValLayout = toValue(layout)
+    return toValLayout.toolbarHeight
+        + toValLayout.toolbarModalHeight
+        + toValLayout.containerPaddingBottom
+        + toValLayout.containerPaddingTop
+        + toValLayout.paddingTopCol
+})
+
+const computedWidth = computed(() => {
+    return toValue(width) - toValue(xMargin)
+})
+const computedHeight = computed(() => {
+    return toValue(height) - toValue(yMargin)
+})
+
+// const breadcrumbItems = computed(() => {
+//     return [
+//         {
+//             title: 'Structures DB',
+//             disabled: false,
+//             to: '/structure/'
+//         },
+//         {
+//             title: route.params.system,
+//             disabled: true,
+//             exact: true,
+//             to: {
+//                 name: route.name, params: {
+//                     ...route.params,
+//                 }
+//             }
+//         }
+//     ]
+// })
+
+
+const refinedFoldseekPath = computed(() => {
+    // return 'https://defense-finder.dev.pasteur.cloud/wiki/abia/AbiA_large__AbiA_large-plddts_90.82916.html'
+    const url = `/${route.query.system}/${route.query.html}.html`
+    console.log(useRuntimeConfig())
+    if (url?.startsWith('/') && !url.startsWith('//')) {
+        const _base = withLeadingSlash(withTrailingSlash(useRuntimeConfig().app.baseURL))
+        if (_base !== '/' && !url.startsWith(_base)) {
+            const sanitizedUrl = joinURL(_base, url)
+            return sanitizedUrl
+        }
+    }
+    return url
+})
+
+
+
+const iframe = ref()
+function fullscreen() {
+    console.log(iframe.value)
+    iframe.value.requestFullscreen();
+}
+</script>
+
+<template>
+    <!-- <v-breadcrumbs :items="breadcrumbItems"></v-breadcrumbs> -->
+    <v-card variant="flat" color="transparent" class="pa-0">
+        <v-toolbar flat color="transparent" density="compact">
+            <v-spacer></v-spacer>
+            <v-btn @click="fullscreen()" icon="md:fullscreen"></v-btn>
+        </v-toolbar>
+        <iframe ref="iframe" :width="computedWidth" :height="computedHeight" allow="fullscreen"
+            :src="refinedFoldseekPath"></iframe>
+    </v-card>
+</template>
\ No newline at end of file

scripts/copy-structure-data.sh

 #!/bin/bash 
 
-find * -type d -exec sh -c 'for d in "$@"; do (cd "/usr/share/nginx/html/$d"; cp --archive --recursive --symbolic-link /structure-data/sanitized-dump/$d/* .) done' argv0 {} +
+# find * -type d -exec sh -c 'for d in "$@"; do (cd "/usr/src/app/public/$d"; cp --archive --recursive --symbolic-link /structure-data/sanitized-dump/$d/* .) done' argv0 {} +
+find * -type d -exec sh -c 'for d in "$@"; do (cd "/usr/share/nginx/html/$d"; cp --archive --recursive --symbolic-link /structure-data/sanitized-dump/$d/* .) done' argv0 {} +
\ No newline at end of file

uno.config.ts

+import { defineConfig, presetUno, presetIcons, presetAttributify } from 'unocss'
+
+export default defineConfig({
+  // ...UnoCSS options
+  presets: [
+    presetUno(),
+    presetAttributify(),
+    presetIcons(),
+  ]
+})
\ No newline at end of file