From f0e36f69ad474e3c327fc3e6863a90b6d3fd18e4 Mon Sep 17 00:00:00 2001
From: Remi PLANEL <rplanel@pasteur.fr>
Date: Wed, 20 Mar 2024 09:36:31 +0100
Subject: [PATCH] Error msg when galaxy instance not running
---
backend/analysis/api.py | 26 +++++++++-
backend/analysis/models.py | 6 +--
deploy/charts/nuxt/templates/deployment.yaml | 4 +-
frontend/components/AnalysisList.vue | 50 ++++++++++----------
frontend/components/ErrorAlert.vue | 36 ++++++++++++++
frontend/components/Main.vue | 2 -
frontend/components/SubmitAnalysis.vue | 8 ++++
frontend/components/UppyGenomeUpload.vue | 8 ++--
frontend/composables/isGalaxyOffline.ts | 18 +++++++
frontend/composables/useFetchAnalyses.ts | 7 +--
frontend/error.vue | 2 +
frontend/middleware/maintenance.global.ts | 6 ---
frontend/pages/analyses/index.vue | 14 +-----
frontend/pages/index.vue | 13 +----
frontend/plugins/api.ts | 1 +
frontend/server/api/probe.get.ts | 3 ++
16 files changed, 132 insertions(+), 72 deletions(-)
create mode 100644 frontend/components/ErrorAlert.vue
create mode 100644 frontend/composables/isGalaxyOffline.ts
create mode 100644 frontend/server/api/probe.get.ts
diff --git a/backend/analysis/api.py b/backend/analysis/api.py
index a481fde..984063d 100644
--- a/backend/analysis/api.py
+++ b/backend/analysis/api.py
@@ -4,6 +4,9 @@ from django.conf import settings
from ninja import Router, File
from ninja.files import UploadedFile
+
+from django_to_galaxy.models import GalaxyInstance
+
from analysis.models import (
Analysis,
AnalysisWorkflow,
@@ -38,6 +41,14 @@ def csrf(request):
return JsonResponse({"token": token})
+@router.get("is-galaxy-online")
+def is_galaxy_online(request):
+
+ gi = GalaxyInstance.objects.get(name=settings.GALAXY_INSTANCE_NAME)
+
+ return JsonResponse({"is_online": gi.is_online()})
+
+
@router.get("login")
def login(request):
if not request.session.session_key:
@@ -49,7 +60,7 @@ def login(request):
)
-@router.post("add", response=AnalysisOutSchema)
+@router.post("add", response={200: AnalysisOutSchema, 503: Error})
def add(
request,
genomefile: UploadedFile = File(...),
@@ -71,6 +82,12 @@ def add(
session = Session.objects.get(session_key=session_key)
aw = AnalysisWorkflow.objects.get(galaxy_id=settings.GALAXY_WORKFLOW_ID)
+
+ # check if Galaxy online
+
+ is_galaxy_online = aw.analysis_owner.galaxy_instance.is_online()
+ if not is_galaxy_online:
+ return 503, {"message": "The Galaxy instance is offline"}
input_files = [
genome_path,
]
@@ -80,11 +97,16 @@ def add(
return analysis
-@router.get("/", response=list[AnalysisOutSchema])
+@router.get("/", response={200: list[AnalysisOutSchema], 503: Error})
def list(request):
session_key = request.session.session_key
if session_key:
session = Session.objects.get(session_key=session_key)
+ gi = GalaxyInstance.objects.get(name=settings.GALAXY_INSTANCE_NAME)
+ # check if Galaxy online
+ is_galaxy_online = gi.is_online()
+ if not is_galaxy_online:
+ return 503, {"message": "The Galaxy instance is offline"}
return Analysis.objects.filter(analysis_history__session=session)
else:
return []
diff --git a/backend/analysis/models.py b/backend/analysis/models.py
index 6418f16..3793948 100644
--- a/backend/analysis/models.py
+++ b/backend/analysis/models.py
@@ -2,16 +2,14 @@ import csv
import tarfile
from typing import Any
from django.db import models
-from django_to_galaxy.utils import enabled_cache
from django.contrib.sessions.models import Session
from tempfile import mkstemp
from django.conf import settings
from Bio import SeqIO
from pathlib import Path
from rich.console import Console
-from typing import List, Dict
+from typing import Dict
-console = Console()
# from galaxy.models import WorkflowInvocation
@@ -31,6 +29,8 @@ from .schemas import GeneEntry, HmmerEntry, ProteinEntry, SystemEntry
# Create your models here.
+console = Console()
+
class AnalysisGalaxyUser(GalaxyUser):
def create_history(self, session, name=None):
diff --git a/deploy/charts/nuxt/templates/deployment.yaml b/deploy/charts/nuxt/templates/deployment.yaml
index ca6d250..38819ab 100644
--- a/deploy/charts/nuxt/templates/deployment.yaml
+++ b/deploy/charts/nuxt/templates/deployment.yaml
@@ -48,11 +48,11 @@ spec:
value: {{ .Values.dfApiPrefix }}
livenessProbe:
httpGet:
- path: /
+ path: /api/probe
port: 3000
readinessProbe:
httpGet:
- path: /
+ path: /api/probe
port: 3000
resources:
{{- toYaml .Values.resources | nindent 12 }}
diff --git a/frontend/components/AnalysisList.vue b/frontend/components/AnalysisList.vue
index 8180e81..8ec5158 100644
--- a/frontend/components/AnalysisList.vue
+++ b/frontend/components/AnalysisList.vue
@@ -3,19 +3,13 @@ import { computed } from 'vue'
import { usePolling } from "../composables/useFetchAnalyses";
import type { Analysis } from '~/types';
import { joinURL } from "ufo";
-// import { useIsGalaxyOffline } from '~/composables/isGalaxyOffline';
const runtimeConfig = useRuntimeConfig()
const sessionExpiryDate = useState('sessionExpiryDate')
const toEdit: Ref<number | null> = ref(null)
const newTitle: Ref<string | null> = ref(null)
-
-
-
const sanitizedAnalyses = computed(() => {
return data !== null ? data.value?.map(a => {
-
const createTimeDate = new Date(a.create_time)
-
return {
...a,
create_time: createTimeDate.toLocaleString()
@@ -29,13 +23,17 @@ function getResultArchiveUrl(analysisId: number) {
async function deleteAnalysis(analysisId: number) {
// if (csrfToken.value) {
- const { error } = await useAPI<null>(`/analysis/${analysisId}`,
- {
- method: "DELETE",
- }
- )
- if (error.value) throw createError(`Cannot delete analysis ${analysisId}`)
- refresh()
+ try {
+ await useNuxtApp().$api<null>(`/analysis/${analysisId}`,
+ {
+ method: "DELETE",
+ }
+ )
+ await refreshNuxtData()
+ } catch (error) {
+ throw createError(`Cannot delete analysis ${analysisId}`)
+ }
+
}
function editionMode(analysisId: number, name: string) {
@@ -44,14 +42,14 @@ function editionMode(analysisId: number, name: string) {
}
async function editAnalysis(analysisId: number) {
// if (csrfToken.value) {
- await useAPI<null>(`/analysis/${analysisId}`,
+ await useNuxtApp().$api<null>(`/analysis/${analysisId}`,
{
method: "PUT",
body: {
name: newTitle.value
},
onResponse() {
- refresh().finally(() => {
+ refreshNuxtData().finally(() => {
toEdit.value = null
newTitle.value = null
})
@@ -76,27 +74,31 @@ const options = computed(() => {
}
})
-
-
-
const { data, refresh, pending, error } = await useAPI<Analysis[]>('/analysis/', {
key: "analyses-list",
});
-
usePolling(options)
-
-
if (error.value) {
+ console.log(error.value)
const toValError = toValue(error)
- if (toValError !== null) {
+
+ if (toValError?.data) {
throw createError({
statusCode: toValError.statusCode,
- message: "Error while getting the list of analysis"
-
+ statusMessage: toValError.statusMessage,
+ message: toValError?.message,
+ data: toValError?.data ?? ""
})
+ } else {
+ console.log(error.value)
+ throw createError("Unable to get the analysis")
+
}
+
+
+ // }
}
diff --git a/frontend/components/ErrorAlert.vue b/frontend/components/ErrorAlert.vue
new file mode 100644
index 0000000..582fd1d
--- /dev/null
+++ b/frontend/components/ErrorAlert.vue
@@ -0,0 +1,36 @@
+<script setup lang="ts">
+import { useIsGalaxyOffline } from '~/composables/isGalaxyOffline';
+import type { FetchError } from "ofetch"
+
+defineEmits(['clearError'])
+
+export interface Props {
+ error?: MaybeRef<Error | FetchError | null | undefined>
+}
+const props = withDefaults(defineProps<Props>(), {
+ error: undefined,
+});
+
+const { message, isGalaxyOffline } = useIsGalaxyOffline({ error: props.error })
+
+
+
+</script>
+
+<template>
+ <v-alert type="error" variant="tonal" prominent>
+ <v-card flat color="transparent">
+ <v-card-text v-if="isGalaxyOffline">
+ {{ message }}
+ </v-card-text>
+ <v-card-text v-else>
+ {{ error }}
+ </v-card-text>
+ <v-card-actions>
+ <v-btn color="currentColor" prepend-icon="md:home" variant="text" @click="$emit('clearError')">
+ Back home
+ </v-btn>
+ </v-card-actions>
+ </v-card>
+ </v-alert>
+</template>
\ No newline at end of file
diff --git a/frontend/components/Main.vue b/frontend/components/Main.vue
index 47949bd..9d21eae 100644
--- a/frontend/components/Main.vue
+++ b/frontend/components/Main.vue
@@ -8,8 +8,6 @@ export interface Props {
const props = withDefaults(defineProps<Props>(), {
fluid: true
});
-const sessionExpiryDate = useState('sessionExpiryDate', () => "")
-// const { csrfToken } = useCsrfToken()
const maxWidth = ref(1300)
const minWidth = ref(900)
const computedMinWidth = computed(() => {
diff --git a/frontend/components/SubmitAnalysis.vue b/frontend/components/SubmitAnalysis.vue
index f50afc0..b538d0f 100644
--- a/frontend/components/SubmitAnalysis.vue
+++ b/frontend/components/SubmitAnalysis.vue
@@ -14,6 +14,14 @@ const { meta, handleSubmit } = useForm({
const files = useField("files");
+const { data, error } = await useAPI<{ is_online: boolean }>("/analysis/is-galaxy-online", {
+ onRequest({ request }) {
+ }
+})
+
+if (data.value !== null && !data.value.is_online) {
+ throw createError("The galaxy instance is offline")
+}
</script>
<template>
diff --git a/frontend/components/UppyGenomeUpload.vue b/frontend/components/UppyGenomeUpload.vue
index 76d380c..848b5b9 100644
--- a/frontend/components/UppyGenomeUpload.vue
+++ b/frontend/components/UppyGenomeUpload.vue
@@ -53,10 +53,10 @@ const uppyCovar = new Uppy({
const emitObject = (files.length === 0) ? undefined : files
emit('update:modelValue', emitObject)
})
- .on("error", (error) => {
- console.log(error)
- throw createError("uppy error")
- });
+ // .on("error", (error) => {
+ // console.log(error)
+ // throw createError("uppy error")
+ // });
const themeUppy = computed(() => {
diff --git a/frontend/composables/isGalaxyOffline.ts b/frontend/composables/isGalaxyOffline.ts
new file mode 100644
index 0000000..6dbb86a
--- /dev/null
+++ b/frontend/composables/isGalaxyOffline.ts
@@ -0,0 +1,18 @@
+import type { FetchError } from "ofetch"
+
+export const useIsGalaxyOffline = ({ error }: {
+ error: MaybeRef<Error | FetchError | null | undefined>
+}) => {
+ const message = ref<string>("The Galaxy instance used to run the analyses is currently offline. It is probably a maintenance ")
+ const isGalaxyOffline = ref<boolean>(false)
+ const toValError = toValue(error)
+ console.dir(toValError)
+ if (toValError && "data" in toValError) {
+ if (toValError?.statusCode === 503 && toValError.data?.message === "The Galaxy instance is offline") {
+ isGalaxyOffline.value = true
+ }
+
+ }
+
+ return { message, isGalaxyOffline }
+}
diff --git a/frontend/composables/useFetchAnalyses.ts b/frontend/composables/useFetchAnalyses.ts
index ee4ee5c..bfac4b2 100644
--- a/frontend/composables/useFetchAnalyses.ts
+++ b/frontend/composables/useFetchAnalyses.ts
@@ -1,18 +1,13 @@
import { useIntervalFn } from "@vueuse/core";
import { NON_TERMINAL_STATE, type JobState, type AnalysesPollingOptions, type Analysis } from "~/types";
-
-
-
-
-export function usePolling( options: MaybeRef<AnalysesPollingOptions> = { interval: 5000, refresh: null, data: ref(null), pending: ref(false) }) {
+export function usePolling(options: MaybeRef<AnalysesPollingOptions> = { interval: 5000, refresh: null, data: ref(null), pending: ref(false) }) {
const nonTerminalState = computed(() => {
return new Set<JobState>(NON_TERMINAL_STATE)
})
const { interval, refresh, pending, data } = toValue(options)
const { pause, resume, isActive } = useIntervalFn(() => {
- console.log("je suis dans le polling")
if (!pending.value) {
console.log(
`pending ${pending.value
diff --git a/frontend/error.vue b/frontend/error.vue
index a42e825..645b210 100644
--- a/frontend/error.vue
+++ b/frontend/error.vue
@@ -1,4 +1,5 @@
<script setup lang="ts">
+
const error = useError()
function handleError() {
clearError({ redirect: '/' })
@@ -7,6 +8,7 @@ function handleError() {
<template>
<div>
<NuxtLayout>
+ <!-- <div v-if="isGalaxyOffline">galaxy offfline</div> -->
<v-alert type="error" variant="tonal" prominent>
<v-card flat color="transparent">
<v-card-title v-if="error && error?.statusCode">
diff --git a/frontend/middleware/maintenance.global.ts b/frontend/middleware/maintenance.global.ts
index 4e10edf..e1469c6 100644
--- a/frontend/middleware/maintenance.global.ts
+++ b/frontend/middleware/maintenance.global.ts
@@ -7,10 +7,4 @@ export default defineNuxtRouteMiddleware((to, from) => {
if (isMaintenance && to.name !== "maintenance") {
return navigateTo('/maintenance')
}
- // else { return }
-
-
-
-
-
})
diff --git a/frontend/pages/analyses/index.vue b/frontend/pages/analyses/index.vue
index beda58b..dcf62b3 100644
--- a/frontend/pages/analyses/index.vue
+++ b/frontend/pages/analyses/index.vue
@@ -27,19 +27,9 @@ function resetError(error) {
<v-card flat color="transparent">
<v-breadcrumbs :items="breadcrumbItems"></v-breadcrumbs>
<NuxtErrorBoundary>
- <analysis-list> </analysis-list>
+ <AnalysisList></AnalysisList>
<template #error="{ error }">
- <v-alert type="error" variant="tonal" prominent>
- <v-card flat color="transparent">
- <v-card-text>
- {{ error }}
- </v-card-text>
- <v-card-actions>
- <v-btn color="currentColor" prepend-icon="md:home" variant="outlined"
- @click="resetError(error)">Back home</v-btn>
- </v-card-actions>
- </v-card>
- </v-alert>
+ <ErrorAlert :error="error" @clear-error="resetError(error)"></ErrorAlert>
</template>
</NuxtErrorBoundary>
</v-card>
diff --git a/frontend/pages/index.vue b/frontend/pages/index.vue
index b9ccb96..82f4e13 100644
--- a/frontend/pages/index.vue
+++ b/frontend/pages/index.vue
@@ -82,17 +82,8 @@ function resetError(error) {
<NuxtErrorBoundary>
<SubmitAnalysis></SubmitAnalysis>
<template #error="{ error }">
- <v-alert type="error" variant="tonal" prominent>
- <v-card flat color="transparent">
- <v-card-text>
- {{ error }}
- </v-card-text>
- <v-card-actions>
- <v-btn color="currentColor" prepend-icon="md:home" variant="outlined" @click="resetError(error)">Back
- home</v-btn>
- </v-card-actions>
- </v-card>
- </v-alert></template>
+ <ErrorAlert :error="error"></ErrorAlert>
+ </template>
</NuxtErrorBoundary>
</v-card>
</v-col>
diff --git a/frontend/plugins/api.ts b/frontend/plugins/api.ts
index 8d66b65..57f7964 100644
--- a/frontend/plugins/api.ts
+++ b/frontend/plugins/api.ts
@@ -5,6 +5,7 @@ export default defineNuxtPlugin(() => {
const $api = $fetch.create({
baseURL: "/dfapi",
async onRequest({ request, options, error }) {
+ console.log("dans le on request du create")
const { data } = await useFetch("/api/auth", { headers })
const toValToken = toValue(csrfToken)
if (toValToken !== undefined) {
diff --git a/frontend/server/api/probe.get.ts b/frontend/server/api/probe.get.ts
new file mode 100644
index 0000000..a5cd75e
--- /dev/null
+++ b/frontend/server/api/probe.get.ts
@@ -0,0 +1,3 @@
+export default defineEventHandler((event) => {
+ return 'ok'
+})
--
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