Merge branch 'master' into explicite-filename

.gitlab-ci.yml

@@ -27,6 +27,8 @@ test-docker-compose:
   services:
     - registry-gitlab.pasteur.fr/dsi-tools/docker-images/docker:dind
   needs: []
+  when: delayed
+  start_in: 3 minutes
   stage: test
   script:
   - apk update && apk upgrade && apk add jq bash curl

chart/templates/deployment-celery-worker.yaml → chart/templates/celery-worker.yaml

+apiVersion: v1
+kind: Service
+metadata:
+  name: {{ printf "%s-%s" .Release.Name "celery-worker-svc" }}
+  labels:
+    {{- include "chart.labels" . | nindent 4 }}
+    app: celery-worker-svc
+spec:
+  ports:
+  - port: 80
+    name: web
+  clusterIP: None
+  selector:
+    {{- include "chart.labels" . | nindent 4 }}
+    app: celery-worker
+---
 apiVersion: apps/v1
-kind: Deployment
+kind: StatefulSet
 metadata:
   name: {{ printf "%s-%s" .Release.Name "celery" }}
   labels:
@@ -10,8 +26,12 @@ spec:
     matchLabels:
       {{- include "chart.selectorLabels" . | nindent 6 }}
       app: celery-worker
-  strategy:
-    type: Recreate
+  serviceName: {{ printf "%s-%s" .Release.Name "celery-worker-svc" }}
+  {{- if .Values.celery.replicas }}
+  replicas: {{ .Values.celery.replicas }}
+  {{- end }}
+  updateStrategy:
+    type: RollingUpdate
   template:
     metadata:
     {{- with .Values.podAnnotations }}

client/pages/phenotypes.vue

@@ -33,7 +33,7 @@ Please select the traits you want to analyze jointly with the Omnibus test. A re
         </template>
         </v-data-table>
         <div align="left" justify="start">
-          <v-btn depressed color="primary" v-on:click="runAnalysis()">
+          <v-btn depressed color="primary" v-on:click="runAnalysis()" :disabled="selectedRows.length <=1">
             Launch analysis
           </v-btn>
         </div>

client/pages/projects/_id.vue

@@ -29,6 +29,13 @@
         <strong style="color:white; text-transform:capitalize;">{{progress}} %</strong>
       </v-progress-linear>
     </v-col>
+    <v-col
+      class="text-subtitle-1 text-center"
+      cols="12"
+      v-if="(activeTask == 0) || (pendingTask != 0)"
+    >
+      Task: {{activeTask}} running and {{pendingTask}} pending.
+    </v-col>
   </v-row>
   <v-row v-show="isready" align="center">
 
@@ -297,6 +304,8 @@ export default {
       isready: false,
       isready2: false,
       progress:0,
+      activeTask: 1,
+      pendingTask: 0,
       gencov:null,
       metadata:{"nb_phenotypes":0,"nb_snps":0},
       summary:{"JASSSignif":{"MinUnivNotSignif":0,"MinUnivSignif":0},"JASSNotSignif":{"MinUnivNotSignif":0,"MinUnivSignif":0}},
@@ -562,6 +571,12 @@ methods:{
 
     async getStatus(){
 
+      await this.$axios.$get('/queue_status').then((function (resultStatus) {
+          console.log(resultStatus);
+          this.activeTask = resultStatus.active;
+          this.pendingTask = resultStatus.reserved;
+      }).bind(this));
+
 
       await this.$axios.$get('/projects/'+this.project.id).then((async function (result) {
             console.log(result.status.worktable);

jass/server.py

@@ -6,14 +6,14 @@ from json import JSONDecodeError
 from pathlib import Path
 from typing import List
 
-from starlette.responses import RedirectResponse
+from starlette.responses import RedirectResponse, JSONResponse
 
 from jass import util
 from jass.config import config
 from jass.models.phenotype import Phenotype, get_available_phenotypes, PhenotypeIdList
 from jass.models.inittable import get_inittable_meta
 from jass.models.project import GlobalProject, load_project as project__load_project
-from jass.tasks import create_project, run_project_analysis_if_needed
+from jass.tasks import create_project, run_project_analysis_if_needed, get_queue_status
 
 from fastapi import FastAPI, HTTPException
 from fastapi.responses import Response, FileResponse
@@ -169,6 +169,11 @@ def get_manhattan(project_id: str, selected_chr: str, selected_region: str):
     )
 
 
+@app.get("/api/queue_status")
+def queue_status():
+    return JSONResponse(get_queue_status())
+
+
 
 
 # @blp_inittable.route("")

jass/tasks.py

@@ -84,14 +84,31 @@ def dummy_task():
     print("This task to nothing, but help the chain to have a valid status")
 
 
+def get_queue_status():
+    inspect = celery.control.inspect()
+    workers = set()
+    ret = {'active': 0, 'reserved': 0}
+    for k in ['active', 'reserved']:
+        try:
+            for worker, queue in getattr(inspect, k)().items():
+                ret[k] += len(queue)
+                workers.add(worker)
+        except (
+                AttributeError,  # when no worker
+                ConnectionResetError,  # when rabbitMQ went down
+                TimeoutError,  # when rabbitMQ is not reachable
+        ):
+            pass
+    ret['worker'] = len(workers)
+    return ret
+
+
 def run_project_analysis_if_needed(project):
     if project.has_computation_going_on():
         return
     tasks = []
     post_worktable_tasks = []
 
-    tasks.append(ensure_space_in_project_dir_task.si(project.id))
-
     if not os.path.exists(project.get_worktable_path()):
         tasks.append(create_project_worktable.si(project.id))
 
@@ -110,7 +127,11 @@ def run_project_analysis_if_needed(project):
     if len(tasks) + len(post_worktable_tasks) == 0:
         return
     main_wf = chain(
+        # first we check again that there is enough disk space
+        ensure_space_in_project_dir_task.si(project.id),
+        # we run the main task(s)
         *tasks,
+        # we then compute the missing charts
         group(post_worktable_tasks),
         # it is mandatory to add a task that do nothing if group is used in order to have a success/failure status
         dummy_task.si(),