Merge pull request #108 from ayobi/generate_barcodes_for_exisiting_kits

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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(