From 2d201e156d530e5e912252c4300245da382b846e Mon Sep 17 00:00:00 2001
From: Pjotr Prins
Date: Sat, 16 May 2020 10:14:13 -0500
Subject: Counting number of sequences
---
bh20simplewebuploader/main.py | 17 +++++++++++++++++
bh20simplewebuploader/static/main.js | 5 ++++-
bh20simplewebuploader/templates/form.html | 21 +++++++++++++++++----
doc/blog/using-covid-19-pubseq-part1.org | 31 +++++++++++++++++++++++++++----
4 files changed, 65 insertions(+), 9 deletions(-)
diff --git a/bh20simplewebuploader/main.py b/bh20simplewebuploader/main.py
index 1dff207..0ba43fd 100644
--- a/bh20simplewebuploader/main.py
+++ b/bh20simplewebuploader/main.py
@@ -424,6 +424,23 @@ def receive_files():
## but most likley you don't want to touch the queries, Cheers.
baseURL='http://sparql.genenetwork.org/sparql/'
+@app.route('/api/getCount', methods=['GET'])
+def getCount():
+ query="""
+PREFIX pubseq:
+select (COUNT(distinct ?dataset) as ?num)
+{
+ ?dataset pubseq:submitter ?id .
+ ?id ?p ?submitter
+}
+"""
+ payload = {'query': query, 'format': 'json'}
+ r = requests.get(baseURL, params=payload)
+ result = r.json()['results']['bindings']
+ # [{'num': {'type': 'typed-literal', 'datatype': 'http://www.w3.org/2001/XMLSchema#integer', 'value': '1352'}}]
+ # print(result, file=sys.stderr)
+ return jsonify({'sequences': int(result[0]["num"]["value"])})
+
@app.route('/api/getAllaccessions', methods=['GET'])
def getAllaccessions():
query="""SELECT DISTINCT ?fasta ?value WHERE {?fasta ?x[ ?value ]}"""
diff --git a/bh20simplewebuploader/static/main.js b/bh20simplewebuploader/static/main.js
index 7084e1f..bf95832 100644
--- a/bh20simplewebuploader/static/main.js
+++ b/bh20simplewebuploader/static/main.js
@@ -18,6 +18,10 @@ let search = () => {
fetchAPI(scriptRoot + "/api/getDetailsForSeq?seq=" + encodeURIComponent(m));
}
+let fetchCount = () => {
+ fetchAPI("/api/getCount");
+}
+
let fetchSEQBySpecimen = () => {
fetchAPI("/api/getSEQCountbySpecimenSource");
}
@@ -160,7 +164,6 @@ for (let button of document.getElementsByClassName('remove-field')) {
}
// Change the submit button after hitting
-
function on_submit_button() {
var elem = document.getElementById("submit");
elem.value = "Submitting...";
diff --git a/bh20simplewebuploader/templates/form.html b/bh20simplewebuploader/templates/form.html
index 7d7cef8..2cbaf62 100644
--- a/bh20simplewebuploader/templates/form.html
+++ b/bh20simplewebuploader/templates/form.html
@@ -6,13 +6,14 @@
Web uploader for Public SARS-CoV-2 Sequence Resource
+
@@ -209,9 +210,21 @@
-
-
+ 