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sample summary report expansion #106

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merged 6 commits into from
Oct 29, 2024
Merged

sample summary report expansion #106

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4da7caa
added new fields to sample summary
ayobi Oct 3, 2024
0df4dd1
lint
ayobi Oct 3, 2024
15c020c
add csv handling for sample summaries
ayobi Oct 21, 2024
8a1d7c3
changes based on feedback
ayobi Oct 28, 2024
d4b815f
update naming
ayobi Oct 28, 2024
d23cd5c
Apply suggestions from code review
cassidysymons Oct 29, 2024
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113 changes: 65 additions & 48 deletions microsetta_admin/server.py
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Original file line number Diff line number Diff line change
@@ -1,3 +1,4 @@
import csv
import jwt
from flask import render_template, Flask, request, session, send_file, url_for
import secrets
Expand Down Expand Up @@ -401,63 +402,79 @@ def per_sample_summary():
projects=projects,
error_message=result,
**build_login_variables())

# if we are here then the user is querying using barcodes and we
# simply need to set up the query below to perform.
sample_barcodes = [sample_barcode, ]
else:
# assume POST, since there are only two methods defined in route.
# if we are here, it is because the user is querying using an uploaded
# file containing sample names.
sample_barcodes, err = upload_util.parse_request_csv_col(request,
'file',
'sample_name')
if err is not None:
# there was an error. abort early.
return render_template('per_sample_summary.html',
resource=None,
projects=projects,
**build_login_variables(),
search_error=[{'error': err}])
search_field = request.form.get('search_field')
search_value = request.form.get('single_search')
uploaded_file = request.files.get('upload_list')

# perform the main query.
payload = {'sample_barcodes': sample_barcodes}
status, result = APIRequest.post('/api/admin/account_barcode_summary?stri'
'p_sampleid=%s' % str(strip_sampleid),
json=payload)
search_values = []

if status == 200:
if result['partial_result'] is True:
unprocessed_barcodes = result['unprocessed_barcodes']
if uploaded_file:
file_content = io.TextIOWrapper(uploaded_file,
encoding='utf-8-sig')
csv_reader = csv.reader(file_content)

for row in csv_reader:
search_values.extend(row)
else:
unprocessed_barcodes = None
resource = pd.DataFrame(result['samples'])
order = ['sampleid', 'project', 'account-email',
'source-type', 'site-sampled', 'sample-date',
'sample-time', 'sample-status', 'sample-received',
'ffq-taken', 'ffq-complete', 'vioscreen_username']
order.extend(sorted(set(resource.columns) - set(order)))
resource = resource[order]
search_values = [search_value] if search_value else []

if unprocessed_barcodes:
return render_template('per_sample_summary.html',
resource=resource,
projects=projects,
error_message="Too many barcodes. S"
"erver processed only"
" the first 1000.",
**build_login_variables())
payload = {}
payload[search_field] = search_values

# perform the main query.
status, result = APIRequest.post('/api/admin/account_barcode_summary?'
'strip_sampleid=%s' %
str(strip_sampleid),
json=payload)

if status == 200:
if result['partial_result'] is True:
unprocessed_barcodes = result['unprocessed_barcodes']
else:
unprocessed_barcodes = None
resource = pd.DataFrame(result['samples'])
if not resource.empty:
order = ['sampleid', 'project', 'account-email',
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'source-type', 'site-sampled', 'sample-date',
'sample-time', 'sample-status', 'sample-received',
'first-scan-status', 'first-scan-timestamp',
'latest-scan-status', 'latest-scan-timestamp',
'sample-has-inconsistencies', 'sample-is-valid',
'no-associated-source', 'no-collection-info',
'no-registered-account', 'received-unknown-validity',
'ffq-taken', 'ffq-complete', 'vioscreen_username',
'kit-id', 'outbound-tracking',
'inbound-tracking'
]
order.extend(sorted(set(resource.columns) - set(order)))
resource = resource[order]
else:
return render_template('per_sample_summary.html',
resource=resource,
projects=projects,
error_message="No sample found",
**build_login_variables())

if unprocessed_barcodes:
return render_template('per_sample_summary.html',
resource=resource,
projects=projects,
error_message="Too many barcodes. S"
"erver processed only"
" the first 1000.",
**build_login_variables())
else:
return render_template('per_sample_summary.html',
resource=resource,
projects=projects,
**build_login_variables())
else:
return render_template('per_sample_summary.html',
resource=resource,
resource=None,
projects=projects,
error_message=result,
**build_login_variables())
else:
return render_template('per_sample_summary.html',
resource=None,
projects=projects,
error_message=result,
**build_login_variables())


def _get_by_sample_barcode(sample_barcodes, strip_sampleid, projects):
Expand Down
81 changes: 57 additions & 24 deletions microsetta_admin/templates/per_sample_summary.html
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Original file line number Diff line number Diff line change
Expand Up @@ -11,6 +11,25 @@
block.innerHTML = "";
}
};

function handleFormSubmit(event) {
var uploadList = document.getElementById('upload_list');
var singleSearch = document.getElementById('single_search');

if (uploadList.files.length > 0 && singleSearch.value.trim() !== "") {
alert("Please provide either a text input or a file, not both.");
event.preventDefault();
return false;
} else if (uploadList.files.length === 0 && singleSearch.value.trim() === "") {
alert("Please provide either a text input or a file.");
event.preventDefault();
return false;
} else {
remove_error_messages();
return true;
}
}

$(document).ready(function() {
{% if resource is not none %}
$('#search_results').DataTable({
Expand All @@ -27,36 +46,50 @@
{% block content %}
<h3>Sample Summaries</h3>
<hr class="dashed">
<h5>Retrieve summary for a single sample</h5>
{% if error_message %}
<p style="color:red">
{{ error_message |e }}
</p>
{% endif %}
<div style="height: 400px; width: 400px">
{% if error_message %}
<p style="color:red">
{{ error_message |e }}
</p>
{% endif %}
<form name="search_form" id="search_form" method="GET">
<table width=100% border=0>
<tr>
<td colspan=3 style="text-align:left;padding:4px"> <input type="text" name="sample_barcode" placeholder="Enter barcode here" id="sample_barcode" {% if info %} value="{{info.barcode}}"{% endif %}> </td>
<td colspan=1 style="text-align:right;padding:4px"> <input type="submit" value="Retrieve"> </td>
</tr>
</table>
<script> document.search_form.sample_barcode.focus() </script>
</form>
<hr class="dashed">
<h5>Retrieve summaries using a csv file</h5>
<form name="upload_csv" id="search_csv" method="POST" enctype="multipart/form-data" onsubmit="return remove_error_messages()">
<h5>Retrieve summary for a sample</h5>
<form name="search_form" id="search_form" method="POST" enctype="multipart/form-data" onsubmit="return handleFormSubmit(event)">
<table width=100% border=0>
<tr>
<td colspan=3 style="text-align:left;padding:4px"><input type=file name=file></td>
<td colspan=1 style="text-align:right;padding:4px"><input type=submit value=Upload></td>
<td colspan=4 style="text-align:left;padding:4px">
<label for="search_field">Select search field:</label>
<select id="search_field" name="search_field">
<option value="sample_barcodes">Barcode</option>
<option value="kit_ids">Kit ID</option>
<option value="emails">Email</option>
<option value="outbound_tracking_numbers">Outbound Tracking Number</option>
<option value="inbound_tracking_numbers">Inbound Tracking Number</option>
</select>
</td>
</tr>
<tr><td colspan=4>&nbsp;</td></tr>
<tr>
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<td colspan=4 style="text-align:left;padding:4px">
Single Value Search: <input type="text" name="single_search" placeholder="Enter value here" id="single_search">
</td>
</tr>
<tr><td colspan=4 style="text-align: center; padding: 4px">-- OR --</td></tr>
<tr>
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<td colspan=4 style="text-align:left;padding:4px">
Upload List: <input type="file" name="upload_list" id="upload_list">
</td>
</tr>
<tr>
<td colspan=4 style="text-align:right;padding:4px">
<input type="submit" value="Retrieve">
</td>
</tr>
<tr><td colspan=4></td></tr>
<tr><td colspan=4 style="text-align:center;padding:4px"><i>Barcodes must be listed in column "sample_name"<br>(max: 1000)</i> </td></tr>
<tr><td colspan=4></td></tr>
<tr>
<td colspan=3> <label for="strip_sampleid"> Check to remove sample IDs from summary</label> </td>
<td colspan=1 style="text-align:center;padding:4px"> <input type="checkbox" id="strip_sampleid" name="strip_sampleid"> </td>
<td colspan=3><label for="strip_sampleid">Check to remove sample IDs from summary</label></td>
<td colspan=1 style="text-align:center;padding:4px">
<input type="checkbox" id="strip_sampleid" name="strip_sampleid">
</td>
</tr>
</table>
</form>
Expand Down
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