Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Add Barcodes to Existing Kits #110

Open
wants to merge 18 commits into
base: master
Choose a base branch
from
Open

Add Barcodes to Existing Kits #110

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
18 commits
Select commit Hold shift + click to select a range
bfdc545
add barcodes to existing kits
ayobi Mar 8, 2024
251b322
Merge branch 'biocore:master' into generate_barcodes_for_exisiting_kits
ayobi Mar 8, 2024
94020c2
added user barcode for create kits
ayobi Mar 25, 2024
a2f7b2d
improvements per suggestions
ayobi Jun 21, 2024
579ac0a
Merge branch 'biocore:master' into generate_barcodes_for_exisiting_kits
ayobi Jun 25, 2024
c143b03
fixed test
ayobi Jun 25, 2024
27d0c79
changes per suggestions
ayobi Aug 6, 2024
1e9c6e0
lint
ayobi Aug 6, 2024
8d448fb
fixed post for create/kits
ayobi Aug 7, 2024
9e3914b
fixes and improvements
ayobi Aug 15, 2024
21161ba
fixes
ayobi Aug 20, 2024
7fe1546
fix create kits for sample slots
ayobi Aug 23, 2024
6408f7d
changes based on latest feedback
ayobi Aug 30, 2024
be86573
Merge branch 'biocore:master' into generate_barcodes_for_exisiting_kits
ayobi Oct 2, 2024
a739b84
Merge pull request #108 from ayobi/generate_barcodes_for_exisiting_kits
cassidysymons Oct 15, 2024
d5da7f1
Add barcodes to kits
cassidysymons Dec 16, 2024
2a7fd1a
Merge branch 'master' into csymons_add_barcodes
cassidysymons Dec 16, 2024
130d4c9
Lint
cassidysymons Dec 16, 2024
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
132 changes: 118 additions & 14 deletions microsetta_admin/server.py
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -1,4 +1,5 @@
import csv
import tempfile
import jwt
from flask import render_template, Flask, request, session, send_file, url_for
import secrets
Expand Down Expand Up @@ -539,35 +540,64 @@ def new_kits():
**build_login_variables())

elif request.method == 'POST':
num_kits = int(request.form['num_kits'])
num_samples = int(request.form['num_samples'])
num_kits = int(request.form['number_of_kits'])
num_samples = int(request.form['number_of_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}

barcodes_container = []

# Determine if each sample slot was provided or is to be generated.
# We default to generating novel barcodes.
for i in range(1, num_samples+1):
barcode_file = request.files.get(f'upload_csv_{i}')
if barcode_file:
# Barcodes provided for this slot
barcodes = _read_csv_file(barcode_file)
else:
# Generate barcodes for this slot
barcodes = []

# Add this slot's barcodes (or empty list) to the container
barcodes_container.append(barcodes)

payload = {
'number_of_kits': num_kits,
'number_of_samples': num_samples,
'project_ids': selected_project_ids,
'barcodes': barcodes_container
}

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 = result

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)
Expand All @@ -583,6 +613,80 @@ 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]


@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())

elif request.method == 'POST':
if 'add_single_barcode' in request.form:
kit_ids = [request.form['kit_id']]
if 'user_barcode' in request.form:
# User provided a barcode
barcodes = [request.form['user_barcode']]
generate_barcodes = False
else:
# Generate barcode
barcodes = []
generate_barcodes = True

elif 'add_multiple_barcodes' in request.form:
kit_ids_file = request.files['kit_ids']
kit_ids = _read_csv_file(kit_ids_file)
if 'barcodes_file' in request.files:
# User provided barcodes
barcodes = _read_csv_file(request.files['barcodes_file'])
generate_barcodes = False
else:
# Generate barcodes
barcodes = []
generate_barcodes = True

payload = {
'kit_ids': kit_ids,
'barcodes': barcodes,
'generate_barcodes': generate_barcodes
}

status, result = APIRequest.post(
'/api/admin/add_barcodes_to_kits',
json=payload
)

if status != 201:
return render_template(
'add_barcode_to_kit.html',
error_message=result,
**build_login_variables()
)

with tempfile.NamedTemporaryFile(
mode='w',
delete=False,
newline=''
) as file:
writer = csv.writer(file)
writer.writerow(['Kit ID', 'Barcode'])
writer.writerows(result)
filename = file.name

timestamp = datetime.now().strftime('%d%b%Y-%H%M')
fname = f'kit_ids-barcodes-{timestamp}.csv'
return send_file(
filename,
as_attachment=True,
download_name=fname
)


def _check_sample_status(extended_barcode_info):
warning = None
in_microsetta_project = any(
Expand Down
221 changes: 221 additions & 0 deletions microsetta_admin/templates/add_barcode_to_kit.html
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -0,0 +1,221 @@
{% extends "sitebase.html" %}
{% block head %}
<script src="/static/vendor/js/jquery.validate.min.js"></script>
<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery.form/4.3.0/jquery.form.min.js"></script>
<script>
$(document).ready(function(){
// Initialize form validation
$("form[name='single_kit_form']").validate({
rules: {
kit_id: "required",
user_barcode: {
required: function(element) {
return !$("#generate_barcode_single").is(':checked');
}
}
},
submitHandler: function (form) {
form.submit();
}
});

$("form[name='multiple_kits_form']").validate({
rules: {
kit_ids: "required",
barcodes_file: {
required: function(element) {
return !$("#generate_barcodes_multiple").is(':checked');
}
}
},
submitHandler: function (form) {
form.submit();
}
});

function clearMessages() {
$('#error_message').text("");
$('#success_message').empty();
}

// Toggle form visibility
$('#single_kit_button').click(function() {
$('#single_kit_form').show();
$('#multiple_kits_form').hide();
clearMessages();
});
$('#multiple_kits_button').click(function() {
$('#multiple_kits_form').show();
$('#single_kit_form').hide();
clearMessages();
});

$("#generate_barcode_single").on("change", function() {
if ($(this).is(":checked")) {
$("#user_barcode").prop("disabled", true);
} else {
$("#user_barcode").prop("disabled", false);
}
});

$("#user_barcode").on("input", function() {
if ($(this).val().length > 0) {
$("#generate_barcode_single").prop("disabled", true);
} else {
$("#generate_barcode_single").prop("disabled", false);
}
});

$("#generate_barcodes_multiple").on("change", function() {
if ($(this).is(":checked")) {
$("#barcodes_file").prop("disabled", true);
} else {
$("#barcodes_file").prop("disabled", false);
}
});

$("#barcodes_file").on("change", function() {
if ($(this).val()) {
$("#generate_barcodes_multiple").prop("disabled", true);
} else {
$("#generate_barcodes_multiple").prop("disabled", false);
}
});

$("input[type='submit']").click(function() {
$("input[type='submit']", $(this).parents("form")).removeAttr("clicked");
$(this).attr("clicked", "true");
});
});
</script>
{% endblock %}

{% block content %}
<h3>Add Barcode(s) to Kit(s)</h3>
<div style="height: 335px;">
{% if error_message %}
<p id="error_message" style="color:red">
{{ error_message |e }}
</p>
{% endif %}

<button id="single_kit_button">Add Barcode to Single Kit</button>
<button id="multiple_kits_button">Add Barcodes to Multiple Kits</button>

<form name="single_kit_form" id="single_kit_form" method="POST" style="display:none;">
<table>
<tr>
<td colspan="2">
<br />
</td>
</tr>
<tr>
<td>
<label for="kit_id" style="margin: auto;">Kit ID: </label>
</td>
<td>
<input type="text" name="kit_id" id="kit_id" required>
</td>
</tr>
<tr>
<td colspan="2">
<hr style="width: 100%" />
</td>
</tr>
<tr>
<td>
<label for="user_barcode" style="margin: auto;">Enter Barcode: </label>
</td>
<td>
<input type="text" name="user_barcode" id="user_barcode">
</td>
</tr>
<tr>
<td colspan="2" style="text-align: center; padding-top: 10px; padding-bottom: 10px;">
-- OR --
</td>
</tr>
<tr>
<td>
<label for="generate_barcode_single" style="margin: auto;">Generate Barcode: </label>
</td>
<td>
<input type="checkbox" name="generate_barcode_single" id="generate_barcode_single">
</td>
</tr>
<tr>
<td colspan="2">
<hr style="width: 100%" />
</td>
</tr>
<tr>
<td colspan="2" style="text-align: center;">
<input type="submit" name="add_single_barcode" value="Add Barcode">
</td>
</tr>
</table>
</form>
{% if barcodes %}
<ul id="success_message">
{% for barcode in barcodes %}
<span>You added {{ barcode }} to Kit ID {{ kit_id }}</span><br>
{% endfor %}
</ul>
{% endif %}
<form name="multiple_kits_form" id="multiple_kits_form" method="POST" enctype="multipart/form-data" style="display:none;">
<table>
<tr>
<td colspan="2">
<br />
Upload comma-separated value file(s) (CSV)
<br /><br />
</td>
</tr>
<tr>
<td>
<label for="kit_ids" style="margin: auto;">Kit IDs: </label>
</td>
<td>
<input type="file" name="kit_ids" id="kit_ids" required>
</td>
</tr>
<tr>
<td colspan="2">
<hr style="width: 100%" />
</td>
</tr>
<tr>
<td>
<label for="barcodes_file" style="margin: auto;">Barcodes: </label>
</td>
<td>
<input type="file" name="barcodes_file" id="barcodes_file">
</td>
</tr>
<tr>
<td colspan="2" style="text-align: center; padding-top: 10px; padding-bottom: 10px;">
-- OR --
</td>
</tr>
<tr>
<td>
<label for="generate_barcodes_multiple" style="margin: auto;">Generate Barcodes: </label>
</td>
<td>
<input type="checkbox" name="generate_barcodes_multiple" id="generate_barcodes_multiple">
</td>
</tr>
<tr>
<td colspan="2">
<hr style="width: 100%" />
</td>
</tr>
<tr>
<td colspan="2" style="text-align: center;">
<input type="submit" name="add_multiple_barcodes" value="Add Barcodes">
</td>
</tr>
</table>
</form>
</div>
{% endblock %}
Loading
Loading