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-rw-r--r--bh20simplewebuploader/main.py37
-rw-r--r--bh20simplewebuploader/static/main.js6
-rw-r--r--bh20simplewebuploader/templates/about.html13
-rw-r--r--bh20simplewebuploader/templates/blog.html13
-rw-r--r--bh20simplewebuploader/templates/demo.html6
-rw-r--r--bh20simplewebuploader/templates/download.html13
-rw-r--r--bh20simplewebuploader/templates/map.html13
7 files changed, 42 insertions, 59 deletions
diff --git a/bh20simplewebuploader/main.py b/bh20simplewebuploader/main.py
index 9132453..8a6794e 100644
--- a/bh20simplewebuploader/main.py
+++ b/bh20simplewebuploader/main.py
@@ -47,6 +47,7 @@ def type_to_heading(type_name):
Turn a type name like "sampleSchema" from the metadata schema into a human-readable heading.
"""
+ print(type_name,file=sys.stderr)
# Remove camel case
decamel = re.sub('([A-Z])', r' \1', type_name)
# Split
@@ -227,8 +228,13 @@ def generate_form(schema, options):
# At startup, we need to load the metadata schema from the uploader module, so we can make a form for it
-METADATA_SCHEMA = yaml.safe_load(pkg_resources.resource_stream("bh20sequploader", "bh20seq-schema.yml"))
-METADATA_OPTION_DEFINITIONS = yaml.safe_load(pkg_resources.resource_stream("bh20sequploader", "bh20seq-options.yml"))
+if os.path.isfile("bh20sequploader/bh20seq-schema.yml"):
+ METADATA_SCHEMA = yaml.safe_load(open("bh20sequploader/bh20seq-schema.yml","r").read())
+ METADATA_OPTION_DEFINITIONS = yaml.safe_load(open("bh20sequploader/bh20seq-options.yml","r").read())
+else:
+ METADATA_SCHEMA = yaml.safe_load(pkg_resources.resource_stream("bh20sequploader", "bh20seq-schema.yml"))
+ METADATA_OPTION_DEFINITIONS = yaml.safe_load(pkg_resources.resource_stream("bh20sequploader", "bh20seq-options.yml"))
+# print(METADATA_SCHEMA,file=sys.stderr)
FORM_ITEMS = generate_form(METADATA_SCHEMA, METADATA_OPTION_DEFINITIONS)
@app.route('/')
@@ -505,7 +511,7 @@ def status_page():
Processing status
"""
- api = arvados.api(host=ARVADOS_API, token=ANONYMOUS_TOKEN)
+ api = arvados.api(host=ARVADOS_API, token=ANONYMOUS_TOKEN, insecure=True)
pending = arvados.util.list_all(api.collections().list, filters=[["owner_uuid", "=", UPLOADER_PROJECT]])
out = []
status = {}
@@ -567,11 +573,34 @@ baseURL='http://sparql.genenetwork.org/sparql/'
@app.route('/api/getCount', methods=['GET'])
def getCount():
- api = arvados.api(host=ARVADOS_API, token=ANONYMOUS_TOKEN)
+ """
+ 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..4703047 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");
}
@@ -191,7 +195,7 @@ function addField(e) {
// Increment the number and use the keypath and number to set IDs and cross
// references.
// TODO: Heavily dependent on the form field HTML. Maybe we want custom
- // elements for the labeled controlsd that know how to be list items?
+ // elements for the labeled controls that know how to be list items?
fieldNumber++
newField.dataset.number = fieldNumber
let newID = keypath + '[' + fieldNumber + ']'
diff --git a/bh20simplewebuploader/templates/about.html b/bh20simplewebuploader/templates/about.html
index 07b6951..4bd238e 100644
--- a/bh20simplewebuploader/templates/about.html
+++ b/bh20simplewebuploader/templates/about.html
@@ -11,19 +11,6 @@
<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>
</body>
diff --git a/bh20simplewebuploader/templates/blog.html b/bh20simplewebuploader/templates/blog.html
index 8f8ab66..dbc0b99 100644
--- a/bh20simplewebuploader/templates/blog.html
+++ b/bh20simplewebuploader/templates/blog.html
@@ -73,19 +73,6 @@
<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>
</body>
diff --git a/bh20simplewebuploader/templates/demo.html b/bh20simplewebuploader/templates/demo.html
index 76c19c4..44aded0 100644
--- a/bh20simplewebuploader/templates/demo.html
+++ b/bh20simplewebuploader/templates/demo.html
@@ -5,6 +5,7 @@
{% 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' %}
@@ -12,16 +13,17 @@
let scriptRoot = {{ request.script_root|tojson|safe }}; // examples
document.addEventListener("DOMContentLoaded", function(){
- var count = fetch("/api/getCount")
+ var count = fetch("/api/getCountDB")
.then((resp) => resp.json())
.then(function (data) {
count = data["sequences"];
console.log(count);
- span = document.getElementById("Counter");
+ span = document.getElementById("CounterDB");
txt = document.createTextNode(count);
span.appendChild(txt);
});
});
+
</script>
</body>
diff --git a/bh20simplewebuploader/templates/download.html b/bh20simplewebuploader/templates/download.html
index 07b6951..4bd238e 100644
--- a/bh20simplewebuploader/templates/download.html
+++ b/bh20simplewebuploader/templates/download.html
@@ -11,19 +11,6 @@
<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>
</body>
diff --git a/bh20simplewebuploader/templates/map.html b/bh20simplewebuploader/templates/map.html
index 6d63c3c..595af0c 100644
--- a/bh20simplewebuploader/templates/map.html
+++ b/bh20simplewebuploader/templates/map.html
@@ -16,19 +16,6 @@
<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 -->
generated by cgit v1.2.3 (git 2.45.0) at 2024-07-08 23:45:52 +0000