Merge pull request #48 from ssciwr/fix_47_add_job_runtime_to_sample

Add job runtime info to sample

backend/src/predicTCR_server/model.py

@@ -81,7 +81,8 @@ 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)
+    timestamp_job_start: Mapped[int] = mapped_column(Integer, nullable=False)
+    timestamp_job_end: 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)
 
@@ -161,7 +162,7 @@ def request_job() -> int | None:
             db.select(Sample).filter(
                 (Sample.status == Status.RUNNING)
                 & (
-                    timestamp_now() - Sample.timestamp_results
+                    timestamp_now() - Sample.timestamp_job_start
                     > job_timeout_minutes * 60
                 )
             )
@@ -186,7 +187,8 @@ def request_job() -> int | None:
         return None
     else:
         logger.info(f"  --> sample id {sample.id}")
-        sample.timestamp_results = timestamp_now()
+        sample.timestamp_job_start = timestamp_now()
+        sample.timestamp_job_end = 0
         sample.status = Status.RUNNING
         db.session.commit()
         return sample.id
@@ -210,6 +212,7 @@ def process_result(
     if job is None:
         logger.warning(f" --> Unknown job id {job_id}")
         return f"Unknown job id {job_id}", 400
+    sample.timestamp_job_end = timestamp_now()
     job.timestamp_end = timestamp_now()
     if success:
         job.status = Status.COMPLETED
@@ -496,7 +499,8 @@ def add_new_sample(
         tumor_type=tumor_type,
         source=source,
         timestamp=timestamp_now(),
-        timestamp_results=0,
+        timestamp_job_start=0,
+        timestamp_job_end=0,
         status=Status.QUEUED,
         has_results_zip=False,
     )

backend/tests/helpers/flask_test_utils.py

@@ -54,7 +54,8 @@ 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,
+                timestamp_job_start=0,
+                timestamp_job_end=0,
                 status=status,
                 has_results_zip=False,
             )

frontend/src/App.vue

@@ -44,7 +44,7 @@ const login_title = computed(() => {
       </fwb-navbar-collapse>
     </template>
   </fwb-navbar>
-  <div class="flex flex-col items-center justify-center">
+  <div class="flex flex-col items-stretch justify-center">
     <RouterView />
   </div>
 </template>

frontend/src/components/SamplesTable.vue

@@ -18,11 +18,12 @@ import {
   download_result,
   download_admin_result,
   logout,
+  download_string_as_file,
 } from "@/utils/api-client";
 import type { Sample } from "@/utils/types";
 import { ref } from "vue";
 
-defineProps<{
+const props = defineProps<{
   samples: Sample[];
   admin: boolean;
 }>();
@@ -66,6 +67,29 @@ function delete_current_sample() {
       console.log(error);
     });
 }
+
+function timestamp_to_date(timestamp_secs: number): string {
+  const secs_to_ms = 1000;
+  return new Date(timestamp_secs * secs_to_ms).toLocaleDateString("de-DE");
+}
+
+function job_runtime(sample: Sample): string {
+  // returns job runtime as hh::mm::ss
+  const runtime_secs = sample.timestamp_job_end - sample.timestamp_job_start;
+  const secs_to_ms = 1000;
+  if (runtime_secs <= 0) {
+    return "-";
+  }
+  return new Date(runtime_secs * secs_to_ms).toISOString().slice(11, 19);
+}
+
+function download_samples_as_csv() {
+  let csv = "Id,Date,Email,SampleName,TumorType,Source,Status,Runtime\n";
+  for (const sample of props.samples) {
+    csv += `${sample.id},${timestamp_to_date(sample.timestamp)},${sample.email},${sample.name},${sample.tumor_type},${sample.source},${sample.status},${job_runtime(sample)}\n`;
+  }
+  download_string_as_file("samples.csv", csv);
+}
 </script>
 
 <template>
@@ -78,6 +102,7 @@ function delete_current_sample() {
       <fwb-table-head-cell>Tumor type</fwb-table-head-cell>
       <fwb-table-head-cell>Source</fwb-table-head-cell>
       <fwb-table-head-cell>Status</fwb-table-head-cell>
+      <fwb-table-head-cell v-if="admin">Runtime</fwb-table-head-cell>
       <fwb-table-head-cell>Inputs</fwb-table-head-cell>
       <fwb-table-head-cell>Results</fwb-table-head-cell>
       <fwb-table-head-cell v-if="admin">Actions</fwb-table-head-cell>
@@ -88,15 +113,16 @@ function delete_current_sample() {
         :key="sample.id"
         :class="sample.status === 'failed' ? '!bg-red-200' : '!bg-slate-50'"
       >
-        <fwb-table-cell v-if="admin">{{ sample["id"] }}</fwb-table-cell>
+        <fwb-table-cell v-if="admin">{{ sample.id }}</fwb-table-cell>
         <fwb-table-cell>{{
-          new Date(sample["timestamp"] * 1000).toLocaleDateString("de-DE")
+          timestamp_to_date(sample.timestamp)
         }}</fwb-table-cell>
-        <fwb-table-cell v-if="admin">{{ sample["email"] }}</fwb-table-cell>
-        <fwb-table-cell>{{ sample["name"] }}</fwb-table-cell>
-        <fwb-table-cell>{{ sample["tumor_type"] }}</fwb-table-cell>
-        <fwb-table-cell>{{ sample["source"] }}</fwb-table-cell>
-        <fwb-table-cell>{{ sample["status"] }}</fwb-table-cell>
+        <fwb-table-cell v-if="admin">{{ sample.email }}</fwb-table-cell>
+        <fwb-table-cell>{{ sample.name }}</fwb-table-cell>
+        <fwb-table-cell>{{ sample.tumor_type }}</fwb-table-cell>
+        <fwb-table-cell>{{ sample.source }}</fwb-table-cell>
+        <fwb-table-cell>{{ sample.status }}</fwb-table-cell>
+        <fwb-table-cell v-if="admin">{{ job_runtime(sample) }}</fwb-table-cell>
         <fwb-table-cell>
           <fwb-a
             href=""
@@ -151,6 +177,9 @@ function delete_current_sample() {
       </fwb-table-row>
     </fwb-table-body>
   </fwb-table>
+  <fwb-button v-if="admin" class="mt-2" @click="download_samples_as_csv"
+    >Download as CSV</fwb-button
+  >
 
   <fwb-modal size="lg" v-if="show_resubmit_modal" @close="close_modals">
     <template #header>

frontend/src/components/SettingsTable.vue

@@ -86,7 +86,7 @@ function update_settings() {
       :label="`Timeout for runner jobs: ${settings.runner_job_timeout_mins} minutes`"
       class="mb-2"
     />
-    <fwb-button @click="update_settings" color="green">
+    <fwb-button @click="update_settings" class="mt-2" color="green">
       Save settings</fwb-button
     >
   </div>

frontend/src/components/UsersTable.vue

@@ -12,7 +12,7 @@ import {
   FwbRange,
 } from "flowbite-vue";
 import type { User } from "@/utils/types";
-import { apiClient, logout } from "@/utils/api-client";
+import { apiClient, download_string_as_file, logout } from "@/utils/api-client";
 import { ref, computed } from "vue";
 
 const props = defineProps<{
@@ -63,6 +63,17 @@ function update_user() {
       console.log(error);
     });
 }
+
+function download_users_as_csv() {
+  let csv =
+    "Id,Email,Activated,Enabled,FullResults,Quota,SubmissionIntervalMinutes,Admin\n";
+  for (const user of users.value) {
+    if (!user.is_runner) {
+      csv += `${user.id},${user.email},${user.activated},${user.enabled},${user.full_results},${user.quota},${user.submission_interval_minutes},${user.is_admin}\n`;
+    }
+  }
+  download_string_as_file("users.csv", csv);
+}
 </script>
 
 <template>
@@ -114,6 +125,9 @@ function update_user() {
       </fwb-table-row>
     </fwb-table-body>
   </fwb-table>
+  <fwb-button class="mt-2" @click="download_users_as_csv"
+    >Download as CSV</fwb-button
+  >
 
   <fwb-modal size="lg" v-if="show_modal" @close="close_modal">
     <template #header>

frontend/src/utils/api-client.ts

@@ -80,3 +80,12 @@ export function logout() {
   user.user = null;
   user.token = "";
 }
+
+export function download_string_as_file(filename: string, str: string) {
+  const link = document.createElement("a");
+  const file = new Blob([str], { type: "text/plain" });
+  link.href = URL.createObjectURL(file);
+  link.download = filename;
+  link.click();
+  URL.revokeObjectURL(link.href);
+}

frontend/src/utils/types.ts

@@ -5,7 +5,8 @@ export type Sample = {
   tumor_type: string;
   source: number;
   timestamp: number;
-  timestamp_results: number;
+  timestamp_job_start: number;
+  timestamp_job_end: number;
   status: string;
   has_results_zip: boolean;
 };

frontend/src/views/AboutView.vue

@@ -23,7 +23,7 @@ function openModalSignup() {
 </script>
 
 <template>
-  <main>
+  <main class="flex flex-col items-center justify-center">
     <fwb-jumbotron
       header-text="predicTCR v2"
       header-classes="text-slate-100"

frontend/src/views/ActivateView.vue

@@ -29,7 +29,7 @@ apiClient
 </script>
 
 <template>
-  <main>
+  <main class="flex flex-col items-center justify-center">
     <CardComponent :title="title">
       <p>{{ message }}</p>
       <p>Go to <RouterLink to="/login">login</RouterLink> page.</p>

frontend/src/views/LoginView.vue

@@ -8,7 +8,7 @@ const userStore = useUserStore();
 </script>
 
 <template>
-  <main>
+  <main class="flex flex-col items-center justify-center">
     <template v-if="userStore.user !== null">
       <AccountComponent></AccountComponent>
     </template>

frontend/src/views/ResetPasswordView.vue

@@ -62,7 +62,7 @@ function reset_password() {
 </script>
 
 <template>
-  <main>
+  <main class="flex flex-col items-center justify-center">
     <CardComponent :title="title" :icon="icon">
       <form @submit.prevent="reset_password" v-if="show_form">
         <p>

frontend/src/views/SamplesView.vue

@@ -207,7 +207,7 @@ function add_sample() {
 </script>
 
 <template>
-  <main>
+  <main class="flex flex-col items-center justify-center">
     <ListComponent>
       <ListItem title="Submit a sample">
         <template v-if="submit_message.length > 0">