diff --git a/microsetta_admin/server.py b/microsetta_admin/server.py index c949a29..8f0788a 100644 --- a/microsetta_admin/server.py +++ b/microsetta_admin/server.py @@ -1,3 +1,5 @@ +import csv +import tempfile import jwt from flask import render_template, Flask, request, session, send_file, url_for import secrets @@ -512,35 +514,100 @@ def new_kits(): **build_login_variables()) elif request.method == 'POST': - num_kits = int(request.form['num_kits']) - num_samples = int(request.form['num_samples']) prefix = request.form['prefix'] selected_project_ids = request.form.getlist('project_ids') - payload = {'number_of_kits': num_kits, - 'number_of_samples': num_samples, - 'project_ids': selected_project_ids} + num_kits = int(request.form['number_of_kits']) + num_samples = int(request.form['number_of_samples']) + + generate_barcodes = [] + i = 1 + while i <= num_samples: + barcode = request.form.get(f'generate_barcodes_sample_{i}') + if barcode: + generate_barcodes.append([barcode] * num_kits) + else: + generate_barcodes.append([]) + i += 1 + + user_barcodes = [] + total_provided_samples = 0 + + for i in range(0, 25): + barcode_file = request.files.get(f'upload_csv_{i}') + if barcode_file: + barcode_file = barcode_file.read().decode('utf-8') + new_barcodes = [line.split(',')[0].strip('\ufeff\r') + for line in barcode_file.split('\n') + if line.strip()] + if len(new_barcodes) != num_kits: + if len(new_barcodes) > num_kits: + error_message = (f'Too many barcodes provided in ' + f'file {barcode_file}.') + else: + error_message = (f'Not enough barcodes provided in ' + f'file {barcode_file}.') + return render_template('create_kits.html', + error_message=error_message, + projects=projects, + **build_login_variables()) + + user_barcodes.append(new_barcodes) + total_provided_samples += len(new_barcodes) + + # Calculate remaining samples to be generated + total_needed_samples = num_kits * num_samples + remaining_samples_to_generate = total_needed_samples - \ + total_provided_samples + + if remaining_samples_to_generate < 0: + error_message = (f'Too many samples provided ' + f'({total_provided_samples}) ' + f'for the specified number of kits and samples ' + f'({total_needed_samples}).') + return render_template('create_kits.html', + error_message=error_message, + projects=projects, + **build_login_variables()) + + payload = { + 'action': 'create' if not user_barcodes else 'insert', + 'project_ids': selected_project_ids, + 'number_of_kits': num_kits, + 'number_of_samples': num_samples, + 'generate_barcodes': generate_barcodes, + 'user_barcodes': user_barcodes + } + if prefix: payload['kit_id_prefix'] = prefix - status, result = APIRequest.post( - '/api/admin/create/kits', - json=payload) + status, result = APIRequest.post('/api/admin/create/kits', + json=payload) if status != 201: + start_index = result.find("Key") + if start_index != -1: + error_message = result[start_index:] + error_message = error_message[:44] + else: + error_message = "Error message not found in the results." + return render_template('create_kits.html', - error_message='Failed to create kits', + error_message=error_message, projects=projects, **build_login_variables()) - # StringIO/BytesIO based off https://stackoverflow.com/a/45111660 buf = io.StringIO() payload = io.BytesIO() - # explicitly expand out the barcode detail kits = pd.DataFrame(result['created']) - for i in range(num_samples): - kits['barcode_%d' % (i+1)] = [r['sample_barcodes'][i] - for _, r in kits.iterrows()] + + for kit_index, row in kits.iterrows(): + sample_barcodes = row['sample_barcodes'] + for sample_index in range(len(sample_barcodes)): + kits.at[kit_index, f'barcode_{sample_index + 1}'] = \ + sample_barcodes[sample_index] + kits.drop(columns='sample_barcodes', inplace=True) kits.to_csv(buf, sep=',', index=False, header=True) @@ -556,6 +623,125 @@ def new_kits(): mimetype='text/csv') +def _read_csv_file(file): + content = file.read().decode('utf-8-sig') + return [row[0] for row in csv.reader(io.StringIO(content), + skipinitialspace=True) + if row] + + +def _handle_add_barcodes_api_request(payload): + status, result = APIRequest.post('/api/admin/add_barcodes', + json=payload) + if status != 200 and status != 204: + return render_template('add_barcode_to_kit.html', + error_message=result, + **build_login_variables()), status + return result + + +def _save_and_send_csv(kit_ids, barcodes): + with tempfile.NamedTemporaryFile(mode='w', + delete=False, + newline='') as file: + writer = csv.writer(file) + writer.writerow(['Kit IDs', 'Barcode']) + writer.writerows(zip(kit_ids, barcodes)) + filename = file.name + + stamp = datetime.now().strftime('%d%b%Y-%H%M') + fname = f'kits-{stamp}.csv' + return send_file(filename, + as_attachment=True, + download_name=fname) + + +@app.route('/add_barcode_to_kit', methods=['GET', 'POST']) +def new_barcode_kit(): + if request.method == 'GET': + return render_template('add_barcode_to_kit.html', + **build_login_variables()) + + kit_ids = [] + barcodes = [] + + if 'kit_ids' in request.form: + kit_ids = request.form['kit_ids'] + + if 'user_barcode' in request.form: + user_barcode = request.form['user_barcode'] + barcodes.append(user_barcode) + else: + user_barcode = None + + generate_barcode_single = \ + request.form.get('generate_barcode_single') + generate_barcodes_multiple = \ + request.form.get('generate_barcodes_multiple') + + if 'kit_ids' in request.files: + kit_ids_file = request.files['kit_ids'] + kit_ids = _read_csv_file(kit_ids_file) + + if 'barcodes_file' in request.files: + barcodes_file = request.files['barcodes_file'] + barcodes = _read_csv_file(barcodes_file) + + if generate_barcode_single or user_barcode: + if not user_barcode: + payload = { + 'action': 'create', + 'kit_ids': kit_ids, + 'generate_barcode_single': generate_barcode_single + } + barcodes = _handle_add_barcodes_api_request(payload) + if isinstance(barcodes, tuple): + return barcodes + + payload = { + "action": "insert", + "barcodes": barcodes, + "kit_ids": kit_ids + } + result = _handle_add_barcodes_api_request(payload) + if isinstance(result, tuple): + return result + + return render_template('add_barcode_to_kit.html', + barcodes=barcodes, + kit_id=kit_ids, + **build_login_variables()) + + if generate_barcodes_multiple: + payload = { + 'action': 'create', + 'kit_ids': kit_ids, + 'generate_barcodes_multiple': generate_barcodes_multiple + } + barcodes = _handle_add_barcodes_api_request(payload) + if isinstance(barcodes, tuple): + return barcodes + + if len(kit_ids) != len(barcodes): + error_message = f'The number of kit IDs ({len(kit_ids)}) '\ + f'does not match the number of barcodes '\ + f'({len(barcodes)}).' + return render_template('add_barcode_to_kit.html', + error_message=error_message, + **build_login_variables()), 400 + + payload = { + "action": "insert", + "barcodes": barcodes, + "kit_ids": kit_ids + } + result = _handle_add_barcodes_api_request(payload) + if isinstance(result, tuple): + return result + + return _save_and_send_csv(kit_ids, barcodes) + + def _check_sample_status(extended_barcode_info): warning = None in_microsetta_project = any( diff --git a/microsetta_admin/templates/add_barcode_to_kit.html b/microsetta_admin/templates/add_barcode_to_kit.html new file mode 100644 index 0000000..5b4bbf9 --- /dev/null +++ b/microsetta_admin/templates/add_barcode_to_kit.html @@ -0,0 +1,172 @@ +{% extends "sitebase.html" %} +{% block head %} + + + +{% endblock %} + +{% block content %} +

Add Barcode to Kit(s)

+ +
+ {% if error_message %} +

+ {{ error_message |e }} +

+ {% endif %} + + + + + + {% if barcodes %} + + {% endif %} + +
+{% endblock %} diff --git a/microsetta_admin/templates/create_kits.html b/microsetta_admin/templates/create_kits.html index 90ede1a..606fecb 100644 --- a/microsetta_admin/templates/create_kits.html +++ b/microsetta_admin/templates/create_kits.html @@ -1,86 +1,135 @@ {% extends "sitebase.html" %} {% block head %} - - -{% endblock %} -{% block content %} -

Microsetta Create Kits

-
+{% endblock %} +{% block content %} +

Microsetta Create Kits

+
{% if error_message %}

{{ error_message |e }}

{% endif %} -
+ - - + + - - + + - + - - - -
- {% if search_error %} -

- {{search_error |e}} -

- {% endif %} - +
+
+
+
-{{blob}} {% endblock %} diff --git a/microsetta_admin/templates/sitebase.html b/microsetta_admin/templates/sitebase.html index 50e24ac..38ac8bd 100644 --- a/microsetta_admin/templates/sitebase.html +++ b/microsetta_admin/templates/sitebase.html @@ -47,11 +47,17 @@

Microsetta Utilities

  • Manage Projects
  • Account Summaries
  • Create Kit
    • +
  • Add Barcode to Kit
  • Scan Barcode
  • Retrieve Metadata
  • Sample Summaries
  • Submit Daklapack Order
    • -
  • Log Out
    ({{email |e}})
    • +
  • + + Log Out ({{email |e}}) + +
    • {% else %}
  • Log In
    • {% endif %} diff --git a/microsetta_admin/tests/test_routes.py b/microsetta_admin/tests/test_routes.py index 14cc30b..1c385ab 100644 --- a/microsetta_admin/tests/test_routes.py +++ b/microsetta_admin/tests/test_routes.py @@ -1,5 +1,7 @@ +import csv import json from copy import deepcopy +import tempfile from microsetta_admin.tests.base import TestBase @@ -399,6 +401,53 @@ def test_create_project_fail(self): self.assertEqual(response.status_code, 200) self.assertIn(b'Unable to create project.', response.data) + def test_insert_barcode_success(self): + self.mock_post.return_value = DummyResponse(201, {}) + + response = self.app.post('/add_barcode_to_kit', + data={'kit_id': 'test', + 'user_barcode': 'X64444485'}, + follow_redirects=True) + self.assertEqual(response.status_code, 201) + + def test_insert_barcode_from_csv(self): + self.mock_post.return_value = DummyResponse(201, {}) + + with tempfile.NamedTemporaryFile(mode='w', delete=False) as temp_file: + csv_writer = csv.writer(temp_file) + csv_writer.writerow(['X11204416']) + + with open(temp_file.name, 'rb') as f: + response = self.app.post('/add_barcode_to_kit', + data={'kit_ids': 'test', + 'barcodes_file': (f, 'test.csv')}, + follow_redirects=True) + self.assertEqual(response.status_code, 400) + + def test_insert_barcode_fail_kit_id(self): + self.mock_post.return_value = DummyResponse(404, {}) + + response = self.app.post('/add_barcode_to_kit', + data={'kit_ids': 'alpha9', + 'generate_barcode_single': 'on'}, + follow_redirects=True) + self.assertEqual(response.status_code, 404) + + def test_insert_barcode_fail_csv_mismatch(self): + self.mock_post.return_value = DummyResponse(201, {}) + + with tempfile.NamedTemporaryFile(mode='w', delete=False) as temp_file: + csv_writer = csv.writer(temp_file) + csv_writer.writerow(['X11204415']) + csv_writer.writerow(['X11204416']) + + with open(temp_file.name, 'rb') as f: + response = self.app.post('/add_barcode_to_kit', + data={'kit_ids': 'test', + 'barcodes_file': (f, 'test.csv')}, + follow_redirects=True) + self.assertEqual(response.status_code, 400) + def test_update_project_success(self): self.mock_put.return_value = DummyResponse(204, {}) self.mock_get.return_value = DummyResponse(200, self.PROJ_LIST)