Add a timeout for runner jobs

backend/src/predicTCR_server/app.py

@@ -160,7 +160,7 @@ def get_settings():
     def input_h5_file():
         sample_id = request.json.get("sample_id", None)
         logger.info(
-            f"User {current_user.email} requesting results for sample {sample_id}"
+            f"User {current_user.email} requesting h5 file for sample {sample_id}"
         )
         filters = {"id": sample_id}
         if not current_user.is_admin and not current_user.is_runner:
@@ -178,7 +178,7 @@ def input_h5_file():
     def input_csv_file():
         sample_id = request.json.get("sample_id", None)
         logger.info(
-            f"User {current_user.email} requesting results for sample {sample_id}"
+            f"User {current_user.email} requesting csv file for sample {sample_id}"
         )
         filters = {"id": sample_id}
         if not current_user.is_admin and not current_user.is_runner:
@@ -321,6 +321,8 @@ def runner_request_job():
         new_job = Job(
             id=None,
             sample_id=sample_id,
+            runner_id=current_user.id,
+            runner_hostname=runner_hostname,
             timestamp_start=timestamp_now(),
             timestamp_end=0,
             status=Status.RUNNING,
@@ -376,6 +378,7 @@ def runner_result():
                     tumor_types="Lung;Breast;Other",
                     sources="TIL;PMBC;Other",
                     csv_required_columns="barcode;cdr3;chain",
+                    runner_job_timeout_mins=60,
                 )
             )
             db.session.commit()

backend/src/predicTCR_server/model.py

@@ -52,6 +52,7 @@ class Settings(db.Model):
     tumor_types: Mapped[str] = mapped_column(String, nullable=False)
     sources: Mapped[str] = mapped_column(String, nullable=False)
     csv_required_columns: Mapped[str] = mapped_column(String, nullable=False)
+    runner_job_timeout_mins: Mapped[int] = mapped_column(Integer, nullable=False)
 
     def as_dict(self):
         return {c: getattr(self, c) for c in inspect(self).attrs.keys()}
@@ -61,6 +62,8 @@ def as_dict(self):
 class Job(db.Model):
     id: Mapped[int] = mapped_column(Integer, primary_key=True)
     sample_id: Mapped[int] = mapped_column(Integer, nullable=False)
+    runner_id: Mapped[int] = mapped_column(Integer, nullable=False)
+    runner_hostname: Mapped[str] = mapped_column(String, nullable=False)
     timestamp_start: Mapped[int] = mapped_column(Integer, nullable=False)
     timestamp_end: Mapped[int] = mapped_column(Integer, nullable=False)
     status: Mapped[Status] = mapped_column(Enum(Status), nullable=False)
@@ -78,6 +81,7 @@ class Sample(db.Model):
     tumor_type: Mapped[str] = mapped_column(String(128), nullable=False)
     source: Mapped[str] = mapped_column(String(128), nullable=False)
     timestamp: Mapped[int] = mapped_column(Integer, nullable=False)
+    timestamp_results: Mapped[int] = mapped_column(Integer, nullable=False)
     status: Mapped[Status] = mapped_column(Enum(Status), nullable=False)
     has_results_zip: Mapped[bool] = mapped_column(Boolean, nullable=False)
 
@@ -145,7 +149,26 @@ def get_samples(email: str | None = None) -> list[Sample]:
 
 
 def request_job() -> int | None:
-    # todo: go through running jobs and reset to queued if they have been running for more than e.g. 2 hrs
+    job_timeout_minutes = db.session.get(Settings, 1).runner_job_timeout_mins
+    sample_to_resubmit = (
+        db.session.execute(
+            db.select(Sample).filter(
+                (Sample.status == Status.RUNNING)
+                & (
+                    timestamp_now() - Sample.timestamp_results
+                    > job_timeout_minutes * 60
+                )
+            )
+        )
+        .scalars()
+        .first()
+    )
+    if sample_to_resubmit is not None:
+        logger.info(
+            f"Sample {sample_to_resubmit.id} has been running for more than {job_timeout_minutes} minutes - putting back in queue"
+        )
+        sample_to_resubmit.status = Status.QUEUED
+        db.session.commit()
     selected_samples = (
         db.select(Sample)
         .filter(Sample.status == Status.QUEUED)
@@ -157,6 +180,7 @@ def request_job() -> int | None:
         return None
     else:
         logger.info(f"  --> sample id {sample.id}")
+        sample.timestamp_results = timestamp_now()
         sample.status = Status.RUNNING
         db.session.commit()
         return sample.id
@@ -185,6 +209,11 @@ def process_result(
         job.error_message = error_message
         db.session.commit()
         return "Result processed", 200
+    if sample.has_results_zip:
+        logger.warning(f" --> Sample {sample_id} already has results")
+        job.status = Status.COMPLETED
+        db.session.commit()
+        return f"Sample {sample_id} already has results", 400
     if result_zip_file is None:
         logger.warning(" --> No zipfile")
         return "Zip file missing", 400
@@ -455,6 +484,7 @@ def add_new_sample(
         tumor_type=tumor_type,
         source=source,
         timestamp=timestamp_now(),
+        timestamp_results=0,
         status=Status.QUEUED,
         has_results_zip=False,
     )

backend/tests/helpers/flask_test_utils.py

@@ -53,6 +53,7 @@ def add_test_samples(app, data_path: pathlib.Path):
                 tumor_type=f"tumor_type{sample_id}",
                 source=f"source{sample_id}",
                 timestamp=sample_id,
+                timestamp_results=0,
                 status=Status.QUEUED,
                 has_results_zip=False,
             )

backend/tests/test_app.py

@@ -141,6 +141,7 @@ def test_get_settings_valid(client):
         "id": 1,
         "sources": "TIL;PMBC;Other",
         "tumor_types": "Lung;Breast;Other",
+        "runner_job_timeout_mins": 60,
     }
 
 
@@ -154,6 +155,7 @@ def test_update_settings_valid(client):
         "id": 1,
         "sources": "a;b;g",
         "tumor_types": "1;2;6",
+        "runner_job_timeout_mins": 12,
         "invalid-key": "invalid",
     }
     response = client.post("/api/admin/settings", headers=headers, json=new_settings)

frontend/src/components/JobsTable.vue

@@ -28,13 +28,22 @@ function get_jobs() {
 }
 
 get_jobs();
+
+function get_runtime_minutes(job: Job): number {
+  if (job.status === "running") {
+    return Math.ceil((Date.now() / 1000 - job.timestamp_start) / 60);
+  }
+  return Math.ceil((job.timestamp_end - job.timestamp_start) / 60);
+}
 </script>
 
 <template>
   <fwb-table aria-label="Runner jobs">
     <fwb-table-head>
-      <fwb-table-head-cell>Id</fwb-table-head-cell>
+      <fwb-table-head-cell>JobId</fwb-table-head-cell>
       <fwb-table-head-cell>SampleId</fwb-table-head-cell>
+      <fwb-table-head-cell>RunnerId</fwb-table-head-cell>
+      <fwb-table-head-cell>Hostname</fwb-table-head-cell>
       <fwb-table-head-cell>Start</fwb-table-head-cell>
       <fwb-table-head-cell>Runtime</fwb-table-head-cell>
       <fwb-table-head-cell>Status</fwb-table-head-cell>
@@ -48,12 +57,12 @@ get_jobs();
       >
         <fwb-table-cell>{{ job.id }}</fwb-table-cell>
         <fwb-table-cell>{{ job.sample_id }}</fwb-table-cell>
+        <fwb-table-cell>{{ job.runner_id }}</fwb-table-cell>
+        <fwb-table-cell>{{ job.runner_hostname }}</fwb-table-cell>
         <fwb-table-cell>{{
           new Date(job.timestamp_start * 1000).toISOString()
         }}</fwb-table-cell>
-        <fwb-table-cell
-          >{{ (job.timestamp_end - job.timestamp_start) / 60 }}m</fwb-table-cell
-        >
+        <fwb-table-cell>{{ get_runtime_minutes(job) }}m</fwb-table-cell>
         <fwb-table-cell>{{ job.status }}</fwb-table-cell>
         <fwb-table-cell>{{ job.error_message }}</fwb-table-cell>
       </fwb-table-row>

frontend/src/components/RefreshButton.vue

@@ -0,0 +1,25 @@
+<script setup lang="ts">
+import { FwbButton } from "flowbite-vue";
+</script>
+
+<template>
+  <fwb-button>
+    <svg
+      class="w-6 h-6 text-gray-800 dark:text-white"
+      aria-hidden="true"
+      xmlns="http://www.w3.org/2000/svg"
+      width="24"
+      height="24"
+      fill="none"
+      viewBox="0 0 24 24"
+    >
+      <path
+        stroke="currentColor"
+        stroke-linecap="round"
+        stroke-linejoin="round"
+        stroke-width="2"
+        d="M17.651 7.65a7.131 7.131 0 0 0-12.68 3.15M18.001 4v4h-4m-7.652 8.35a7.13 7.13 0 0 0 12.68-3.15M6 20v-4h4"
+      />
+    </svg>
+  </fwb-button>
+</template>

frontend/src/components/SettingsTable.vue

@@ -78,6 +78,14 @@ function update_settings() {
       class="mb-2"
       label="Required columns in CSV file (separated by ;)"
     ></fwb-input>
+    <fwb-range
+      v-model="settings.runner_job_timeout_mins"
+      :steps="1"
+      :min="1"
+      :max="360"
+      :label="`Timeout for runner jobs: ${settings.runner_job_timeout_mins} minutes`"
+      class="mb-2"
+    />
     <fwb-button @click="update_settings" color="green">
       Save settings</fwb-button
     >

frontend/src/utils/types.ts

@@ -5,6 +5,7 @@ export type Sample = {
   tumor_type: string;
   source: number;
   timestamp: number;
+  timestamp_results: number;
   status: string;
   has_results_zip: boolean;
 };
@@ -30,11 +31,14 @@ export type Settings = {
   tumor_types: string;
   sources: string;
   csv_required_columns: string;
+  runner_job_timeout_mins: number;
 };
 
 export type Job = {
   id: number;
   sample_id: number;
+  runner_id: number;
+  runner_hostname: string;
   timestamp_start: number;
   timestamp_end: number;
   status: string;

frontend/src/views/SamplesView.vue

@@ -147,12 +147,13 @@
 
 const submit_message = ref("");
 
-let update_submit_message_timer = setInterval(() => {
+let update_data = setInterval(() => {
+  update_samples();
   update_submit_message();
 }, 30000);
 
 onUnmounted(() => {
-  clearInterval(update_submit_message_timer);
+  clearInterval(update_data);
 });
 
 function update_submit_message() {
@@ -185,7 +186,7 @@
         "Content-Type": "multipart/form-data",
       },
     })
     .then((response) => {
       update_samples();
       update_submit_message();
       new_sample_error_message.value = "";

runner/scripts/script.sh

@@ -4,9 +4,9 @@
 
 echo "Starting fake analysis..."
 
-echo "Sleeping for 1 minute..."
+echo "Sleeping for 5 minutes..."
 
-sleep 60
+sleep 300
 
 ls > result.zip