diff --git a/microsetta_admin/server.py b/microsetta_admin/server.py
index c949a29..f1530d4 100644
--- a/microsetta_admin/server.py
+++ b/microsetta_admin/server.py
@@ -1,3 +1,4 @@
+import csv
import jwt
from flask import render_template, Flask, request, session, send_file, url_for
import secrets
@@ -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',
+ '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):
diff --git a/microsetta_admin/templates/per_sample_summary.html b/microsetta_admin/templates/per_sample_summary.html
index 3b06ab1..be90368 100644
--- a/microsetta_admin/templates/per_sample_summary.html
+++ b/microsetta_admin/templates/per_sample_summary.html
@@ -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({
@@ -27,36 +46,50 @@
{% block content %}
Sample Summaries
-Retrieve summary for a single sample
+{% if error_message %}
+
+ {{ error_message |e }}
+
+{% endif %}
- {% if error_message %}
-
- {{ error_message |e }}
-
- {% endif %}
-
-
-
Retrieve summaries using a csv file
-