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-rw-r--r--bh20simplewebuploader/main.py51
-rw-r--r--bh20simplewebuploader/static/main.js37
-rw-r--r--bh20simplewebuploader/templates/demo-run.html1
-rw-r--r--bh20simplewebuploader/templates/map.html46
-rwxr-xr-xscripts/update_virtuoso/check_for_updates.py11
5 files changed, 143 insertions, 3 deletions
diff --git a/bh20simplewebuploader/main.py b/bh20simplewebuploader/main.py
index b67e1bf..40046c8 100644
--- a/bh20simplewebuploader/main.py
+++ b/bh20simplewebuploader/main.py
@@ -459,6 +459,13 @@ def about_page():
buf = get_html_body('doc/web/about.html')
return render_template('about.html',menu='ABOUT',embed=buf)
+##
+@app.route('/map')
+def map_page():
+ return render_template('map.html',menu='DEMO')
+
+
+
## Dynamic API functions starting here
## This is quick and dirty for now, just to get something out and demonstrate the queries
## Feel free to rename the functions/endpoints, feel free to process result so we get nicer JSON
@@ -522,10 +529,10 @@ def getCountByGPS():
payload = {'query': query, 'format': 'json'}
r = requests.get(baseURL, params=payload)
result = r.json()['results']['bindings']
- return jsonify([{'Fasta Count': x['fastaCount']['value'],
+ return jsonify([{'count': x['fastaCount']['value'],
'Location': x['location']['value'],
'LocationLabel': x['location_label']['value'],
- 'GPS' :x['GPS']['value']} for x in result])
+ 'GPS' :x['GPS']['value'][6:-1]} for x in result])
@app.route('/api/getSEQCountbytech', methods=['GET'])
@@ -587,6 +594,46 @@ def getSEQCountbyLocation():
'label': x['geoLocation_label']['value']} for x in result])
+@app.route('/api/getSEQCountbyContinent', methods=['GET'])
+def getSEQCountbyContinent():
+ query="""SELECT DISTINCT ?continent ?continent_label (count(?fasta) as ?fastaCount) WHERE {
+ ?fasta ?x[ <http://purl.obolibrary.org/obo/GAZ_00000448> ?location] .
+ ?location <http://www.wikidata.org/prop/direct/P30> ?continent .
+ OPTIONAL { ?continent rdfs:label ?key_tmp_label }
+ BIND(IF(BOUND(?key_tmp_label),?key_tmp_label, ?location) as ?continent_label)
+ }
+ GROUP BY ?continent ?continent_label
+ """
+ payload = {'query': query, 'format': 'json'}
+ r = requests.get(baseURL, params=payload)
+ result = r.json()['results']['bindings']
+ return jsonify([{'count': x['fastaCount']['value'],
+ 'key': x['continent']['value'],
+ 'label': x['continent_label']['value']} for x in result])
+
+
+
+@app.route('/api/getSEQCountbyCountryContinent', methods=['GET'])
+def getSEQCountbyCountryContinent():
+ query="""SELECT DISTINCT ?location ?location_label (count(?fasta) as ?fastaCount) WHERE {
+ ?fasta ?x[ <http://purl.obolibrary.org/obo/GAZ_00000448> ?location] .
+ ?location <http://www.wikidata.org/prop/direct/P30> <placeholder> .
+ OPTIONAL { ?location rdfs:label ?key_tmp_label }
+ BIND(IF(BOUND(?key_tmp_label),?key_tmp_label, ?location) as ?location_label)
+ }
+ GROUP BY ?location ?location_label
+ """
+ continent = request.args.get('continent')
+ query = query.replace("placeholder", continent)
+ payload = {'query': query, 'format': 'json'}
+ r = requests.get(baseURL, params=payload)
+ result = r.json()['results']['bindings']
+ return jsonify([{'count': x['fastaCount']['value'],
+ 'key': x['location']['value'],
+ 'label': x['location_label']['value']} for x in result])
+
+
+
@app.route('/api/getSEQCountbySpecimenSource', methods=['GET'])
def getSEQCountbySpecimenSource():
query="""SELECT ?specimen_source ?specimen_source_label (count(?fasta) as ?fastaCount) WHERE
diff --git a/bh20simplewebuploader/static/main.js b/bh20simplewebuploader/static/main.js
index 149eb3c..f2e5d99 100644
--- a/bh20simplewebuploader/static/main.js
+++ b/bh20simplewebuploader/static/main.js
@@ -56,6 +56,7 @@ function fetchAPI(apiEndPoint) {
}
+// Copy from function above but now added as table instead of plain json
function fetchAPIV2(apiEndPoint) {
fetch(scriptRoot + apiEndPoint)
.then(response => {
@@ -115,6 +116,9 @@ let fetchSEQByLocation = () => {
console.log("Missing - set parameter for request, retrieve data")
};
+let fetchSEQCountbyContinent = () => {
+ fetchAPIV2("/api/getSEQCountbyContinent");
+}
/*
@@ -243,3 +247,36 @@ function on_submit_button() {
return false;
}
}
+
+
+
+//
+
+function drawMap(){
+
+// initialize the map on the "map" div with a given center and zoom
+var mymap = L.map('mapid').setView([51.505, -0.09], 1);
+
+L.tileLayer('https://{s}.tile.openstreetmap.org/{z}/{x}/{y}.png', {
+ attribution: '&copy; <a href="https://www.openstreetmap.org/copyright">OpenStreetMap</a> contributors'
+}).addTo(mymap);
+
+fetch(scriptRoot + "api/getCountByGPS")
+ .then(response => {
+ console.log(response)
+ return response.json();
+ })
+ .then(data => {
+
+ for (var i=0; i<data.length;i++) {
+ gps=data[i]["GPS"].split(" ")
+ var circle = L.circle([gps[1], gps[0]], {
+ color: 'red',
+ fillColor: '#f03',
+ fillOpacity: 0.5,
+ radius: parseInt(data[i]["count"]) //not working for whatever reason
+ }).addTo(mymap);
+ }
+
+ });
+} \ No newline at end of file
diff --git a/bh20simplewebuploader/templates/demo-run.html b/bh20simplewebuploader/templates/demo-run.html
index a5b4150..a8f9edc 100644
--- a/bh20simplewebuploader/templates/demo-run.html
+++ b/bh20simplewebuploader/templates/demo-run.html
@@ -6,6 +6,7 @@
<button class="button" onclick="fetchSEQCountByLocation()">Count by Location</button>
<button class="button" onclick="fetchSEQCountByTech()">Count by Sequencer</button>
<button class="button" onclick="fetchAllaccessions()">Show All accessions</button>
+ <button class="button" onclick="fetchSEQCountbyContinent()">Count by Continent</button>
<button class="button" onclick="fetchCountByGPS()">Map</button>
</div>
diff --git a/bh20simplewebuploader/templates/map.html b/bh20simplewebuploader/templates/map.html
new file mode 100644
index 0000000..6d63c3c
--- /dev/null
+++ b/bh20simplewebuploader/templates/map.html
@@ -0,0 +1,46 @@
+<!DOCTYPE html>
+<html>
+ {% include 'header.html' %}
+<link rel="stylesheet" href="https://unpkg.com/leaflet@1.6.0/dist/leaflet.css"
+ integrity="sha512-xwE/Az9zrjBIphAcBb3F6JVqxf46+CDLwfLMHloNu6KEQCAWi6HcDUbeOfBIptF7tcCzusKFjFw2yuvEpDL9wQ=="
+ crossorigin=""/>
+
+ {% include 'banner.html' %}
+ {% include 'menu.html' %}
+ <div id="mapid" style="height: 500px;"></div>
+
+ {% include 'footer.html' %}
+
+
+
+
+ <script type="text/javascript">
+ let scriptRoot = {{ request.script_root|tojson|safe }}; // examples
+
+ document.addEventListener("DOMContentLoaded", function(){
+ var count = fetch("/api/getCount")
+ .then((resp) => resp.json())
+ .then(function (data) {
+ count = data["sequences"];
+ console.log(count);
+ span = document.getElementById("Counter");
+ txt = document.createTextNode(count);
+ span.appendChild(txt);
+ });
+ });
+
+ </script>
+
+<!-- Make sure you put this AFTER Leaflet's CSS -->
+ <script src="https://unpkg.com/leaflet@1.6.0/dist/leaflet.js"
+ integrity="sha512-gZwIG9x3wUXg2hdXF6+rVkLF/0Vi9U8D2Ntg4Ga5I5BZpVkVxlJWbSQtXPSiUTtC0TjtGOmxa1AJPuV0CPthew=="
+ crossorigin=""></script>
+
+ <script>
+ //drawMap
+ drawMap()
+ </script>
+
+ </body>
+
+</html>
diff --git a/scripts/update_virtuoso/check_for_updates.py b/scripts/update_virtuoso/check_for_updates.py
index 81496ce..d5eee14 100755
--- a/scripts/update_virtuoso/check_for_updates.py
+++ b/scripts/update_virtuoso/check_for_updates.py
@@ -29,7 +29,7 @@ def upload(fn):
# cmd = ("curl --digest --user dba:%s --verbose --url -G http://sparql.genenetwork.org/sparql-graph-crud-auth --data-urlencode graph=http://covid-19.genenetwork.org/graph -X DELETE" % pwd).split(" ")
print("UPLOAD "+fn)
- cmd = ("curl -X PUT --digest -u dba:%s -H Content-Type:text/turtle -T %s -G http://sparql.genenetwork.org/sparql-graph-crud-auth --data-urlencode graph=http://covid-19.genenetwork.org/graph/%s" % (pwd, fn, fn) ).split(" ")
+ cmd = ("curl -X PUT --digest -u dba:%s -H Content-Type:text/turtle -T %s -G http://sparql.genenetwork.org/sparql-graph-crud-auth --data-urlencode graph=http://covid-19.genenetwork.org/graph/%s" % (pwd, fn, os.path.basename(fn)) ).split(" ")
print(cmd)
p = subprocess.Popen(cmd)
output = p.communicate()[0]
@@ -56,6 +56,15 @@ if os.path.isfile(fn):
file.close
if stamp != last_modified_str:
+ print("Delete graphs")
+ for graph in ["labels.ttl", "metadata.ttl", "countries.ttl" ""]:
+ cmd = ("curl --digest -u dba:%s --verbose --url http://127.0.0.1:8890/sparql-graph-crud-auth?graph=http://covid-19.genenetwork.org/graph/%s -X DELETE" % (pwd, graph))
+ print(cmd)
+ p = subprocess.Popen(cmd.split(" "))
+ output = p.communicate()[0]
+ print(output)
+ # assert(p.returncode == 0) -> may prevent update
+
upload(basedir+"/semantic_enrichment/labels.ttl")
upload(basedir+"/semantic_enrichment/countries.ttl")
generated by cgit v1.2.3 (git 2.44.0) at 2024-05-20 04:51:30 +0000