diff options
| -rw-r--r-- | bh20simplewebuploader/main.py | 23 | ||||
| -rw-r--r-- | bh20simplewebuploader/static/main.js | 4 | ||||
| -rw-r--r-- | bh20simplewebuploader/templates/demo.html | 14 |
3 files changed, 41 insertions, 0 deletions
diff --git a/bh20simplewebuploader/main.py b/bh20simplewebuploader/main.py index 8f9b99b..77e345b 100644 --- a/bh20simplewebuploader/main.py +++ b/bh20simplewebuploader/main.py @@ -567,11 +567,34 @@ baseURL='http://sparql.genenetwork.org/sparql/' @app.route('/api/getCount', methods=['GET']) def getCount(): + """ + Get sequence counts from Arvados record + """ api = arvados.api(host=ARVADOS_API, token=ANONYMOUS_TOKEN, insecure=True) c = api.collections().list(filters=[["owner_uuid", "=", VALIDATED_PROJECT]], limit=1).execute() return jsonify({'sequences': c["items_available"]}) +@app.route('/api/getCountDB', methods=['GET']) +def getCountDB(): + """ + Get sequence counts from Virtuoso DB + """ + query=""" + PREFIX pubseq: <http://biohackathon.org/bh20-seq-schema#MainSchema/> + 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[ <http://edamontology.org/data_2091> ?value ]}""" diff --git a/bh20simplewebuploader/static/main.js b/bh20simplewebuploader/static/main.js index a9dfc10..751e478 100644 --- a/bh20simplewebuploader/static/main.js +++ b/bh20simplewebuploader/static/main.js @@ -89,6 +89,10 @@ let fetchCount = () => { fetchAPI("/api/getCount"); } +let fetchCountDB = () => { + fetchAPI("/api/getCountDB"); +} + let fetchSEQCountBySpecimen = () => { fetchAPIV2("/api/getSEQCountbySpecimenSource"); } diff --git a/bh20simplewebuploader/templates/demo.html b/bh20simplewebuploader/templates/demo.html index f0645b9..44aded0 100644 --- a/bh20simplewebuploader/templates/demo.html +++ b/bh20simplewebuploader/templates/demo.html @@ -5,11 +5,25 @@ {% include 'banner.html' %} {% include 'menu.html' %} {% include 'search.html' %} + <p>The Virtuoso database contains <span id="CounterDB"></span> public sequences!</p> {% include 'demo-run.html' %} {% include 'footer.html' %} <script type="text/javascript"> let scriptRoot = {{ request.script_root|tojson|safe }}; // examples + + document.addEventListener("DOMContentLoaded", function(){ + var count = fetch("/api/getCountDB") + .then((resp) => resp.json()) + .then(function (data) { + count = data["sequences"]; + console.log(count); + span = document.getElementById("CounterDB"); + txt = document.createTextNode(count); + span.appendChild(txt); + }); + }); + </script> </body> |