Merge pull request #68 from ssciwr/fix_58_add_platform_to_sample

Add platform to Sample

README_DEPLOYMENT.md

@@ -9,10 +9,11 @@ To deploy the latest version on a virtual machine with docker compose installed,
 download [docker-compose.yml](https://raw.githubusercontent.com/ssciwr/predicTCR/main/docker-compose.yml), then do
 
 ```
-sudo docker compose pull
-sudo docker compose up -d
+sudo docker compose pull && sudo docker compose up -d && sudo docker system prune -af
 ```
 
+The same command can be used to update the running website to use the latest available docker images.
+
 The location of data directory, SSL keys and secret key should be set
 either in env vars or in a file `.env` in the same location as the docker compose.yml.
 
@@ -60,9 +61,11 @@ sudo sqlite3 docker_volume/predicTCR.db
 sqlite> UPDATE user SET is_admin=true WHERE email='[email protected]';
 sqlite> .quit
 ```
+
 ### Visitor count
 
 To get a count of the unique visitor IPs from the nginx logs:
+
 ```
 sudo docker compose logs frontend --no-log-prefix | grep "GET" | awk '{print $1}' | sort | uniq | wc -l
 ```

backend/src/predicTCR_server/app.py

@@ -234,11 +234,12 @@ def add_sample():
         name = form_as_dict.get("name", "")
         tumor_type = form_as_dict.get("tumor_type", "")
         source = form_as_dict.get("source", "")
+        platform = form_as_dict.get("platform", "")
         h5_file = request.files.get("h5_file")
         csv_file = request.files.get("csv_file")
         logger.info(f"Adding sample {name} from {email}")
         new_sample, error_message = add_new_sample(
-            email, name, tumor_type, source, h5_file, csv_file
+            email, name, tumor_type, source, platform, h5_file, csv_file
         )
         if new_sample is not None:
             logger.info("  - > success")
@@ -443,6 +444,7 @@ def runner_result():
                     global_quota=1000,
                     tumor_types="Lung;Breast;Other",
                     sources="TIL;PMBC;Other",
+                    platforms="Illumina;Other",
                     csv_required_columns="barcode;cdr3;chain",
                     runner_job_timeout_mins=60,
                     max_filesize_h5_mb=50,

backend/src/predicTCR_server/model.py

@@ -51,6 +51,7 @@ class Settings(db.Model):
     global_quota: Mapped[int] = mapped_column(Integer, nullable=False)
     tumor_types: Mapped[str] = mapped_column(String, nullable=False)
     sources: Mapped[str] = mapped_column(String, nullable=False)
+    platforms: 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)
     max_filesize_h5_mb: Mapped[int] = mapped_column(Integer, nullable=False)
@@ -83,6 +84,7 @@ class Sample(db.Model):
     name: Mapped[str] = mapped_column(String(128), nullable=False)
     tumor_type: Mapped[str] = mapped_column(String(128), nullable=False)
     source: Mapped[str] = mapped_column(String(128), nullable=False)
+    platform: Mapped[str] = mapped_column(String(128), nullable=False)
     timestamp: 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)
@@ -488,6 +490,7 @@ def add_new_sample(
     name: str,
     tumor_type: str,
     source: str,
+    platform: str,
     h5_file: FileStorage,
     csv_file: FileStorage,
 ) -> tuple[Sample | None, str]:
@@ -504,6 +507,7 @@ def add_new_sample(
         name=name,
         tumor_type=tumor_type,
         source=source,
+        platform=platform,
         timestamp=timestamp_now(),
         timestamp_job_start=0,
         timestamp_job_end=0,

backend/tests/helpers/flask_test_utils.py

@@ -53,6 +53,7 @@ def add_test_samples(app, data_path: pathlib.Path):
                 name=name,
                 tumor_type=f"tumor_type{sample_id}",
                 source=f"source{sample_id}",
+                platform=f"platform{sample_id}",
                 timestamp=sample_id,
                 timestamp_job_start=0,
                 timestamp_job_end=0,

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",
+        "platforms": "Illumina;Other",
         "runner_job_timeout_mins": 60,
         "max_filesize_h5_mb": 50,
         "max_filesize_csv_mb": 10,
@@ -158,6 +159,7 @@ def test_update_settings_valid(client):
         "id": 1,
         "sources": "a;b;g",
         "tumor_types": "1;2;6",
+        "platforms": "Alpha;Beta;Other",
         "runner_job_timeout_mins": 12,
         "max_filesize_h5_mb": 77,
         "max_filesize_csv_mb": 12,

frontend/src/components/SamplesTable.vue

@@ -84,9 +84,10 @@ function job_runtime(sample: Sample): string {
 }
 
 function download_samples_as_csv() {
-  let csv = "Id,Date,Email,SampleName,TumorType,Source,Status,Runtime\n";
+  let csv =
+    "Id,Date,Email,SampleName,TumorType,Source,Platform,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`;
+    csv += `${sample.id},${timestamp_to_date(sample.timestamp)},${sample.email},${sample.name},${sample.tumor_type},${sample.source},${sample.platform},${sample.status},${job_runtime(sample)}\n`;
   }
   download_string_as_file("samples.csv", csv);
 }
@@ -101,6 +102,7 @@ function download_samples_as_csv() {
       <fwb-table-head-cell>Sample Name</fwb-table-head-cell>
       <fwb-table-head-cell>Tumor type</fwb-table-head-cell>
       <fwb-table-head-cell>Source</fwb-table-head-cell>
+      <fwb-table-head-cell>Platform</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>
@@ -122,6 +124,7 @@ function download_samples_as_csv() {
         <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.platform }}</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>

frontend/src/components/SettingsTable.vue

@@ -57,6 +57,11 @@ function update_settings() {
       class="mb-2"
       label="Sources (separated by ;)"
     ></fwb-input>
+    <fwb-input
+      v-model="settingsStore.settings.platforms"
+      class="mb-2"
+      label="Platforms (separated by ;)"
+    ></fwb-input>
     <fwb-input
       v-model="settingsStore.settings.csv_required_columns"
       class="mb-2"

frontend/src/stores/settings.ts

@@ -11,6 +11,7 @@ export const useSettingsStore = defineStore("settings", () => {
     global_quota: 1,
     tumor_types: "",
     sources: "",
+    platforms: "",
     csv_required_columns: "",
     runner_job_timeout_mins: 1,
     about_md: "",

frontend/src/utils/types.ts

@@ -3,7 +3,8 @@ export type Sample = {
   email: string;
   name: string;
   tumor_type: string;
-  source: number;
+  source: string;
+  platform: string;
   timestamp: number;
   timestamp_job_start: number;
   timestamp_job_end: number;
@@ -32,6 +33,7 @@ export type Settings = {
   global_quota: number;
   tumor_types: string;
   sources: string;
+  platforms: string;
   csv_required_columns: string;
   runner_job_timeout_mins: number;
   about_md: string;

frontend/src/views/ActivateView.vue

@@ -11,7 +11,6 @@ const icon = ref("bi-person-exclamation");
 apiClient
   .get(`activate/${props.activation_token}`)
   .then((response) => {
-    console.log(response);
     message.value = response.data.message;
     icon.value = "bi-person-check";
     title.value =

frontend/src/views/ResetPasswordView.vue

@@ -39,7 +39,6 @@ function reset_password() {
       new_password: new_password.value,
     })
     .then((response) => {
-      console.log(response);
       message.value = response.data.message;
       icon.value = "bi-person-check";
       title.value = "Password reset successful";

frontend/src/views/SamplesView.vue

@@ -4,7 +4,7 @@ import SamplesTable from "@/components/SamplesTable.vue";
 import ListComponent from "@/components/ListComponent.vue";
 import ListItem from "@/components/ListItem.vue";
 import { apiClient, logout } from "@/utils/api-client";
-import type { Sample, Settings } from "@/utils/types";
+import type { Sample } from "@/utils/types";
 import {
   FwbButton,
   FwbSelect,
@@ -24,6 +24,7 @@ type OptionsType = {
 
 const tumor_types = ref([] as Array<OptionsType>);
 const sources = ref([] as Array<OptionsType>);
+const platforms = ref([] as Array<OptionsType>);
 const required_columns = ref([] as Array<string>);
 
 function closeModalSubmit() {
@@ -39,6 +40,7 @@ const agree_to_conditions = ref(false);
 const sample_name = ref("");
 const tumor_type = ref("");
 const source = ref("");
+const platform = ref("");
 const selected_h5_file = ref(null as null | File);
 const h5_file_input_key = ref(0);
 const selected_csv_file = ref(null as null | File);
@@ -68,10 +70,8 @@ async function validate_csv_file(file: File) {
   const lines = text.split(/\n/);
   if (lines.length >= 1) {
     const columns = lines[0].split(/,/);
-    console.log(columns);
     for (const required_column of required_columns.value) {
       if (!columns.includes(required_column)) {
-        console.log(`Missing header: ${required_column}`);
         return false;
       }
     }
@@ -110,6 +110,7 @@ function string_to_options(str: string): Array<OptionsType> {
 
 tumor_types.value = string_to_options(settingsStore.settings.tumor_types);
 sources.value = string_to_options(settingsStore.settings.sources);
+platforms.value = string_to_options(settingsStore.settings.platforms);
 required_columns.value = settingsStore.settings.csv_required_columns.split(";");
 
 const samples = ref([] as Sample[]);
@@ -119,7 +120,6 @@ function update_samples() {
     .get("samples")
     .then((response) => {
       samples.value = response.data;
-      console.log(samples.value);
     })
     .catch((error) => {
       if (error.response.status > 400) {
@@ -144,7 +144,6 @@ onUnmounted(() => {
 });
 
 function update_submit_message() {
-  console.log("update_submit_message");
   apiClient
     .get("user_submit_message")
     .then((response) => {
@@ -165,6 +164,7 @@ function add_sample() {
   formData.append("name", sample_name.value);
   formData.append("tumor_type", tumor_type.value);
   formData.append("source", source.value);
+  formData.append("platform", platform.value);
   formData.append("h5_file", selected_h5_file.value as File);
   formData.append("csv_file", selected_csv_file.value as File);
   apiClient
@@ -225,6 +225,13 @@ function add_sample() {
               label="Source"
               class="mb-2"
             />
+            <fwb-select
+              v-model="platform"
+              :options="platforms"
+              id="platform"
+              label="Platform"
+              class="mb-2"
+            />
             <fwb-file-input
               type="file"
               id="input_h5_file"