Implement upload of results

- runner creates three folders where the script runs, and uploads their contents as zipfiles:
  - `/user_results`: provided to user
  - `/trusted_user_results`: provided to user if they have "full results" enabled by an admin
  - `/admin_results`: only visible to admins
- admin results are always uploaded, included for failed runs (for debugging)
- user results are only provided if the run was successful
- add `PREDICTCR_RUNNER_SCRIPT_DIR` env var to docker compose to specify where script & model can be found
- add /admin/result endpoint to download admin results zipfile
- switch from micromamba to miniconda docker image
  - reticulate doesn't seem to support micromamba, at least within docker
- re-enable runner docker image CI
- update runner README.md
- resolves #6
- resolves #43

Also refactor admin views using tabs

.github/workflows/ci.yml

@@ -110,23 +110,23 @@ jobs:
     steps:
       - uses: actions/checkout@v4
       - run: docker compose build
-      # - uses: docker/login-action@v3
-      #   with:
-      #     registry: ghcr.io
-      #     username: ${{ github.actor }}
-      #     password: ${{ secrets.GITHUB_TOKEN }}
-      #   if: github.event_name == 'push' && github.ref == 'refs/heads/main'
-      # - run: |
-      #     echo $PREDICTCR_DOCKER_IMAGE_TAG
-      #     docker compose build
-      #     docker compose push
-      #   if: github.event_name == 'push' && github.ref == 'refs/heads/main'
-      #   env:
-      #     PREDICTCR_DOCKER_IMAGE_TAG: ${{ github.sha }}
-      # - run: |
-      #     echo $PREDICTCR_DOCKER_IMAGE_TAG
-      #     docker compose build
-      #     docker compose push
-      #   if: github.event_name == 'push' && github.ref == 'refs/heads/main'
-      #   env:
-      #     PREDICTCR_DOCKER_IMAGE_TAG: "latest"
+      - uses: docker/login-action@v3
+        with:
+          registry: ghcr.io
+          username: ${{ github.actor }}
+          password: ${{ secrets.GITHUB_TOKEN }}
+        if: github.event_name == 'push' && github.ref == 'refs/heads/main'
+      - run: |
+          echo $PREDICTCR_DOCKER_IMAGE_TAG
+          docker compose build
+          docker compose push
+        if: github.event_name == 'push' && github.ref == 'refs/heads/main'
+        env:
+          PREDICTCR_DOCKER_IMAGE_TAG: ${{ github.sha }}
+      - run: |
+          echo $PREDICTCR_DOCKER_IMAGE_TAG
+          docker compose build
+          docker compose push
+        if: github.event_name == 'push' && github.ref == 'refs/heads/main'
+        env:
+          PREDICTCR_DOCKER_IMAGE_TAG: "latest"

backend/src/predicTCR_server/app.py

@@ -211,7 +211,10 @@ def result():
         if not user_sample.has_results_zip:
             logger.info(f"  -> sample {sample_id} found but no results available")
             return jsonify(message="No results available"), 400
-        requested_file = user_sample.result_file_path()
+        if current_user.full_results:
+            requested_file = user_sample.trusted_user_result_file_path()
+        else:
+            requested_file = user_sample.user_result_file_path()
         if not requested_file.is_file():
             logger.info(f"  -> file {requested_file} not found")
             return jsonify(message="Results file not found"), 400
@@ -243,6 +246,26 @@ def add_sample():
             return jsonify(sample=new_sample)
         return jsonify(message=error_message), 400
 
+    @app.route("/api/admin/result", methods=["POST"])
+    @jwt_required()
+    def admin_result():
+        if not current_user.is_admin:
+            return jsonify(message="Admin account required"), 400
+        sample_id = request.json.get("sample_id", None)
+        logger.info(
+            f"User {current_user.email} requesting admin results for sample {sample_id}"
+        )
+        user_sample = db.session.get(Sample, sample_id)
+        if user_sample is None:
+            logger.info(f"  -> sample {sample_id} not found")
+            return jsonify(message="Sample not found"), 400
+        requested_file = user_sample.admin_result_file_path()
+        if not requested_file.is_file():
+            logger.info(f"  -> file {requested_file} not found")
+            return jsonify(message="Results file not found"), 400
+        logger.info(f"Returning file {requested_file}")
+        return flask.send_file(requested_file, as_attachment=True)
+
     @app.route("/api/admin/samples", methods=["GET"])
     @jwt_required()
     def admin_all_samples():
@@ -258,7 +281,8 @@ def admin_resubmit_sample(sample_id: int):
         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.user_result_file_path().unlink(missing_ok=True)
+        sample.admin_result_file_path().unlink(missing_ok=True)
         sample.has_results_zip = False
         sample.status = Status.QUEUED
         db.session.commit()
@@ -381,10 +405,14 @@ def runner_result():
             logger.info("  -> missing success key")
             return jsonify(message="Missing key: success=True/False"), 400
         success = success.lower() == "true"
-        zipfile = request.files.to_dict().get("file", None)
-        if success is True and zipfile is None:
+        user_zipfile = request.files.to_dict().get("user_results", None)
+        trusted_user_zipfile = request.files.to_dict().get("trusted_user_results", None)
+        admin_zipfile = request.files.to_dict().get("admin_results", None)
+        if success is True and (user_zipfile is None or admin_zipfile is None):
             logger.info("  -> missing zipfile")
-            return jsonify(message="Result has success=True but no file"), 400
+            return jsonify(
+                message="Result has success=True but a result zipfile is missing"
+            ), 400
         runner_hostname = form_as_dict.get("runner_hostname", "")
         logger.info(
             f"Job '{job_id}' uploaded result for '{sample_id}' from runner {current_user.email} / {runner_hostname}"
@@ -393,7 +421,13 @@ def runner_result():
         if error_message != "":
             logger.info(f"  -> error message: {error_message}")
         message, code = process_result(
-            int(job_id), int(sample_id), success, error_message, zipfile
+            int(job_id),
+            int(sample_id),
+            success,
+            error_message,
+            user_zipfile,
+            trusted_user_zipfile,
+            admin_zipfile,
         )
         return jsonify(message=message), code
 

backend/src/predicTCR_server/model.py

@@ -95,8 +95,14 @@ def input_h5_file_path(self) -> pathlib.Path:
     def input_csv_file_path(self) -> pathlib.Path:
         return self.base_path() / "input.csv"
 
-    def result_file_path(self) -> pathlib.Path:
-        return self.base_path() / "result.zip"
+    def user_result_file_path(self) -> pathlib.Path:
+        return self.base_path() / "user_results.zip"
+
+    def trusted_user_result_file_path(self) -> pathlib.Path:
+        return self.base_path() / "trusted_user_results.zip"
+
+    def admin_result_file_path(self) -> pathlib.Path:
+        return self.base_path() / "admin_results.zip"
 
 
 @dataclass
@@ -191,37 +197,43 @@ def process_result(
     sample_id: int,
     success: bool,
     error_message: str,
-    result_zip_file: FileStorage | None,
+    user_result_zip_file: FileStorage | None,
+    trusted_user_result_zip_file: FileStorage | None,
+    admin_result_zip_file: FileStorage | None,
 ) -> tuple[str, int]:
     sample = db.session.get(Sample, sample_id)
     if sample is None:
         logger.warning(f" --> Unknown sample id {sample_id}")
         return f"Unknown sample id {sample_id}", 400
+    sample.base_path().mkdir(parents=True, exist_ok=True)
     job = db.session.get(Job, job_id)
     if job is None:
         logger.warning(f" --> Unknown job id {job_id}")
         return f"Unknown job id {job_id}", 400
     job.timestamp_end = timestamp_now()
-    if success is False:
-        sample.has_results_zip = False
-        sample.status = Status.FAILED
+    if success:
+        job.status = Status.COMPLETED
+    else:
         job.status = Status.FAILED
         job.error_message = error_message
-        db.session.commit()
-        return "Result processed", 200
+    db.session.commit()
     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
-    sample.result_file_path().parent.mkdir(parents=True, exist_ok=True)
-    result_zip_file.save(sample.result_file_path())
+    if admin_result_zip_file is not None:
+        admin_result_zip_file.save(sample.admin_result_file_path())
+    if success is False:
+        sample.has_results_zip = False
+        sample.status = Status.FAILED
+        db.session.commit()
+        return "Result processed", 200
+    if user_result_zip_file is None or trusted_user_result_zip_file is None:
+        logger.warning(" --> Missing user result zipfile")
+        return "User result zip file missing", 400
+    user_result_zip_file.save(sample.user_result_file_path())
+    trusted_user_result_zip_file.save(sample.trusted_user_result_file_path())
     sample.has_results_zip = True
     sample.status = Status.COMPLETED
-    job.status = Status.COMPLETED
     db.session.commit()
     return "Result processed", 200
 

backend/tests/test_app.py

@@ -221,7 +221,9 @@ def _upload_result(client, result_zipfile: pathlib.Path, job_id: int, sample_id:
                 "job_id": job_id,
                 "sample_id": sample_id,
                 "success": True,
-                "file": (io.BytesIO(f.read()), result_zipfile.name),
+                "user_results": (io.BytesIO(f.read()), result_zipfile.name),
+                "trusted_user_results": (io.BytesIO(f.read()), result_zipfile.name),
+                "admin_results": (io.BytesIO(f.read()), result_zipfile.name),
             },
             headers=headers,
         )

frontend/src/components/SamplesTable.vue

@@ -16,6 +16,7 @@ import {
   download_input_csv_file,
   download_input_h5_file,
   download_result,
+  download_admin_result,
   logout,
 } from "@/utils/api-client";
 import type { Sample } from "@/utils/types";
@@ -82,7 +83,11 @@ function delete_current_sample() {
       <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">
+      <fwb-table-row
+        v-for="sample in samples"
+        :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>{{
           new Date(sample["timestamp"] * 1000).toLocaleDateString("de-DE")
@@ -108,13 +113,22 @@ function delete_current_sample() {
           </fwb-a>
         </fwb-table-cell>
         <fwb-table-cell>
-          <template v-if="sample.has_results_zip">
+          <template v-if="admin">
             <fwb-a
               href=""
-              @click.prevent="download_result(sample.id, sample.name)"
+              @click.prevent="download_admin_result(sample.id, sample.name)"
               >zip</fwb-a
             >
           </template>
+          <template v-else>
+            <template v-if="sample.has_results_zip">
+              <fwb-a
+                href=""
+                @click.prevent="download_result(sample.id, sample.name)"
+                >zip</fwb-a
+              >
+            </template>
+          </template>
           <template v-else> - </template>
         </fwb-table-cell>
         <fwb-table-cell v-if="admin">

frontend/src/utils/api-client.ts

@@ -67,6 +67,14 @@ export function download_result(sample_id: number, sample_name: string) {
   );
 }
 
+export function download_admin_result(sample_id: number, sample_name: string) {
+  download_file_from_endpoint(
+    "admin/result",
+    { sample_id: sample_id },
+    `${sample_name}_admin.zip`,
+  );
+}
+
 export function logout() {
   const user = useUserStore();
   user.user = null;

frontend/src/views/AdminView.vue

@@ -5,7 +5,7 @@ import UsersTable from "@/components/UsersTable.vue";
 import ListComponent from "@/components/ListComponent.vue";
 import JobsTable from "@/components/JobsTable.vue";
 import ListItem from "@/components/ListItem.vue";
-import { FwbButton } from "flowbite-vue";
+import { FwbButton, FwbTab, FwbTabs } from "flowbite-vue";
 import { ref } from "vue";
 import type { Sample } from "@/utils/types";
 import { apiClient, logout } from "@/utils/api-client";
@@ -26,6 +26,7 @@ function generate_api_token() {
   });
 }
 
+const activeTab = ref("samples");
 const samples = ref([] as Sample[]);
 
 function get_samples() {
@@ -48,39 +49,55 @@ get_samples();
 <template>
   <main>
     <div class="p-4">
-      <ListComponent>
-        <ListItem title="Settings">
-          <SettingsTable />
-        </ListItem>
-        <ListItem title="Generate runner API Token">
-          <p>
-            Here you can generate a new runner user with an API token for
-            authentication. Note the token should be kept secret! It is valid
-            for 6 months, then you will need to generate a new one:
-          </p>
-          <p>
-            <fwb-button @click="generate_api_token">
-              Generate API Token and copy to clipboard
-            </fwb-button>
-          </p>
-        </ListItem>
-        <ListItem title="Runners">
-          <UsersTable :is_runner="true"></UsersTable>
-        </ListItem>
-        <ListItem title="Users">
-          <UsersTable :is_runner="false"></UsersTable>
-        </ListItem>
-        <ListItem title="Samples">
-          <SamplesTable
-            :samples="samples"
-            :admin="true"
-            @samples-modified="get_samples"
-          ></SamplesTable>
-        </ListItem>
-        <ListItem title="Runner Jobs">
-          <JobsTable />
-        </ListItem>
-      </ListComponent>
+      <fwb-tabs v-model="activeTab" variant="underline" class="p-5">
+        <fwb-tab name="samples" title="Samples">
+          <ListComponent>
+            <ListItem title="Samples">
+              <SamplesTable
+                :samples="samples"
+                :admin="true"
+                @samples-modified="get_samples"
+              ></SamplesTable>
+            </ListItem>
+          </ListComponent>
+        </fwb-tab>
+        <fwb-tab name="users" title="Users">
+          <ListComponent>
+            <ListItem title="Users">
+              <UsersTable :is_runner="false"></UsersTable>
+            </ListItem>
+          </ListComponent>
+        </fwb-tab>
+        <fwb-tab name="runners" title="Runners">
+          <ListComponent>
+            <ListItem title="Generate runner API Token">
+              <p>
+                Here you can generate a new runner user with an API token for
+                authentication. Note the token should be kept secret! It is
+                valid for 6 months, then you will need to generate a new one:
+              </p>
+              <p>
+                <fwb-button @click="generate_api_token">
+                  Generate API Token and copy to clipboard
+                </fwb-button>
+              </p>
+            </ListItem>
+            <ListItem title="Runners">
+              <UsersTable :is_runner="true"></UsersTable>
+            </ListItem>
+            <ListItem title="Runner Jobs">
+              <JobsTable />
+            </ListItem>
+          </ListComponent>
+        </fwb-tab>
+        <fwb-tab name="settings" title="Settings">
+          <ListComponent>
+            <ListItem title="Settings">
+              <SettingsTable />
+            </ListItem>
+          </ListComponent>
+        </fwb-tab>
+      </fwb-tabs>
     </div>
   </main>
 </template>