Merge pull request #45 from ssciwr/fix_39_40_sample_delete_resubmit

Add admin buttons to delete and resubmit samples

backend/src/predicTCR_server/app.py

@@ -3,6 +3,7 @@
 import os
 import secrets
 import datetime
+import shutil
 import flask
 from flask import Flask
 from flask import jsonify
@@ -249,6 +250,36 @@ def admin_all_samples():
             return jsonify(message="Admin account required"), 400
         return jsonify(get_samples())
 
+    @app.route("/api/admin/resubmit-sample/<int:sample_id>", methods=["POST"])
+    @jwt_required()
+    def admin_resubmit_sample(sample_id: int):
+        if not current_user.is_admin:
+            return jsonify(message="Admin account required"), 400
+        sample = db.session.get(Sample, sample_id)
+        if sample is None:
+            return jsonify(message="Sample not found"), 404
+        sample.result_file_path().unlink(missing_ok=True)
+        sample.has_results_zip = False
+        sample.status = Status.QUEUED
+        db.session.commit()
+        return jsonify(message="Sample added to the queue")
+
+    @app.route("/api/admin/samples/<int:sample_id>", methods=["DELETE"])
+    @jwt_required()
+    def admin_delete_sample(sample_id: int):
+        if not current_user.is_admin:
+            return jsonify(message="Admin account required"), 400
+        sample = db.session.get(Sample, sample_id)
+        if sample is None:
+            return jsonify(message="Sample not found"), 404
+        try:
+            shutil.rmtree(sample.base_path())
+        except Exception as e:
+            logger.error(e)
+        db.session.delete(sample)
+        db.session.commit()
+        return jsonify(message="Sample deleted")
+
     @app.route("/api/admin/user", methods=["POST"])
     @jwt_required()
     def admin_update_user():

backend/src/predicTCR_server/model.py

@@ -85,18 +85,18 @@ class Sample(db.Model):
     status: Mapped[Status] = mapped_column(Enum(Status), nullable=False)
     has_results_zip: Mapped[bool] = mapped_column(Boolean, nullable=False)
 
-    def _base_path(self) -> pathlib.Path:
+    def base_path(self) -> pathlib.Path:
         data_path = flask.current_app.config["PREDICTCR_DATA_PATH"]
         return pathlib.Path(f"{data_path}/{self.id}")
 
     def input_h5_file_path(self) -> pathlib.Path:
-        return self._base_path() / "input.h5"
+        return self.base_path() / "input.h5"
 
     def input_csv_file_path(self) -> pathlib.Path:
-        return self._base_path() / "input.csv"
+        return self.base_path() / "input.csv"
 
     def result_file_path(self) -> pathlib.Path:
-        return self._base_path() / "result.zip"
+        return self.base_path() / "result.zip"
 
 
 @dataclass

backend/tests/helpers/flask_test_utils.py

@@ -32,14 +32,15 @@ def add_test_users(app):
 
 def add_test_samples(app, data_path: pathlib.Path):
     with app.app_context():
-        for sample_id, name in zip(
+        for sample_id, name, status in zip(
             [1, 2, 3, 4],
             [
                 "s1",
                 "s2",
                 "s3",
                 "s4",
             ],
+            [Status.QUEUED, Status.RUNNING, Status.COMPLETED, Status.FAILED],
         ):
             ref_dir = data_path / f"{sample_id}"
             ref_dir.mkdir(parents=True, exist_ok=True)
@@ -54,7 +55,7 @@ def add_test_samples(app, data_path: pathlib.Path):
                 source=f"source{sample_id}",
                 timestamp=sample_id,
                 timestamp_results=0,
-                status=Status.QUEUED,
+                status=status,
                 has_results_zip=False,
             )
             db.session.add(new_sample)

backend/tests/test_app.py

@@ -286,6 +286,34 @@ def test_admin_samples_valid(client):
     assert len(response.json) == 4
 
 
+def test_admin_delete_samples_valid_admin_user(client):
+    headers = _get_auth_headers(client, "[email protected]", "admin")
+    assert len(client.get("/api/admin/samples", headers=headers).json) == 4
+    response = client.delete("/api/admin/samples/1", headers=headers)
+    assert response.status_code == 200
+    assert len(client.get("/api/admin/samples", headers=headers).json) == 3
+    response = client.delete("/api/admin/samples/1", headers=headers)
+    assert response.status_code == 404
+    response = client.delete("/api/admin/samples/2", headers=headers)
+    assert response.status_code == 200
+    assert len(client.get("/api/admin/samples", headers=headers).json) == 2
+
+
+@pytest.mark.parametrize(
+    "index,sample_id,status",
+    [(0, 4, "failed"), (1, 3, "completed"), (2, 2, "running"), (3, 1, "queued")],
+)
+def test_admin_resubmit_samples_valid_admin_user(client, index, sample_id, status):
+    headers = _get_auth_headers(client, "[email protected]", "admin")
+    sample_before = client.get("/api/admin/samples", headers=headers).json[index]
+    assert sample_before["status"] == status
+    response = client.post(f"/api/admin/resubmit-sample/{sample_id}", headers=headers)
+    assert response.status_code == 200
+    sample_after = client.get("/api/admin/samples", headers=headers).json[index]
+    assert sample_after["status"] == "queued"
+    assert sample_after["has_results_zip"] is False
+
+
 def test_admin_runner_token_invalid(client):
     # no auth header
     response = client.get("/api/admin/runner_token")

frontend/src/components/SamplesTable.vue

@@ -2,6 +2,8 @@
 // @ts-ignore
 import {
   FwbA,
+  FwbButton,
+  FwbModal,
   FwbTable,
   FwbTableBody,
   FwbTableCell,
@@ -10,16 +12,59 @@ import {
   FwbTableRow,
 } from "flowbite-vue";
 import {
+  apiClient,
   download_input_csv_file,
   download_input_h5_file,
   download_result,
+  logout,
 } from "@/utils/api-client";
 import type { Sample } from "@/utils/types";
+import { ref } from "vue";
 
 defineProps<{
   samples: Sample[];
   admin: boolean;
 }>();
+
+const emit = defineEmits(["samplesModified"]);
+
+const current_sample_id = ref(null as number | null);
+const show_delete_modal = ref(false);
+const show_resubmit_modal = ref(false);
+function close_modals() {
+  show_resubmit_modal.value = false;
+  show_delete_modal.value = false;
+}
+
+function resubmit_current_sample() {
+  close_modals();
+  apiClient
+    .post(`admin/resubmit-sample/${current_sample_id.value}`)
+    .then(() => {
+      emit("samplesModified");
+    })
+    .catch((error) => {
+      if (error.response.status > 400) {
+        logout();
+      }
+      console.log(error);
+    });
+}
+
+function delete_current_sample() {
+  close_modals();
+  apiClient
+    .delete(`admin/samples/${current_sample_id.value}`)
+    .then(() => {
+      emit("samplesModified");
+    })
+    .catch((error) => {
+      if (error.response.status > 400) {
+        logout();
+      }
+      console.log(error);
+    });
+}
 </script>
 
 <template>
@@ -34,6 +79,7 @@ defineProps<{
       <fwb-table-head-cell>Status</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>
     </fwb-table-head>
     <fwb-table-body>
       <fwb-table-row v-for="sample in samples" :key="sample.id">
@@ -71,7 +117,63 @@ defineProps<{
           </template>
           <template v-else> - </template>
         </fwb-table-cell>
+        <fwb-table-cell v-if="admin">
+          <fwb-button
+            @click="
+              current_sample_id = sample.id;
+              show_resubmit_modal = true;
+            "
+            class="mr-2"
+            >Resubmit</fwb-button
+          >
+          <fwb-button
+            @click="
+              current_sample_id = sample.id;
+              show_delete_modal = true;
+            "
+            class="mr-2"
+            color="red"
+            >Delete</fwb-button
+          >
+        </fwb-table-cell>
       </fwb-table-row>
     </fwb-table-body>
   </fwb-table>
+
+  <fwb-modal size="lg" v-if="show_resubmit_modal" @close="close_modals">
+    <template #header>
+      <div class="flex items-center text-lg">Resubmit sample</div>
+    </template>
+    <template #body
+      >Are you sure you want to resubmit this sample (any existing results will
+      be deleted)?
+    </template>
+    <template #footer>
+      <div class="flex justify-between">
+        <fwb-button @click="close_modals" color="alternative">
+          No, cancel
+        </fwb-button>
+        <fwb-button @click="resubmit_current_sample" color="green">
+          Yes, resubmit
+        </fwb-button>
+      </div>
+    </template>
+  </fwb-modal>
+
+  <fwb-modal size="lg" v-if="show_delete_modal" @close="close_modals">
+    <template #header>
+      <div class="flex items-center text-lg">Delete sample</div>
+    </template>
+    <template #body> Are you sure you want to delete this sample? </template>
+    <template #footer>
+      <div class="flex justify-between">
+        <fwb-button @click="close_modals" color="alternative">
+          No, cancel
+        </fwb-button>
+        <fwb-button @click="delete_current_sample" color="red">
+          Yes, delete
+        </fwb-button>
+      </div>
+    </template>
+  </fwb-modal>
 </template>

frontend/src/views/AdminView.vue

@@ -71,7 +71,11 @@ get_samples();
           <UsersTable :is_runner="false"></UsersTable>
         </ListItem>
         <ListItem title="Samples">
-          <SamplesTable :samples="samples" :admin="true"></SamplesTable>
+          <SamplesTable
+            :samples="samples"
+            :admin="true"
+            @samples-modified="get_samples"
+          ></SamplesTable>
         </ListItem>
         <ListItem title="Runner Jobs">
           <JobsTable />

runner/docker-compose.yml

@@ -17,4 +17,3 @@ services:
 networks:
   predictcr-network:
     name: predictcr
-    external: true