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-rw-r--r--bh20simplewebuploader/main.py231
-rw-r--r--bh20simplewebuploader/static/image/curii.logo.ai.pngbin0 -> 16739 bytes
-rw-r--r--bh20simplewebuploader/static/image/curii.logo.ai.svg3
-rw-r--r--bh20simplewebuploader/static/main.css24
-rw-r--r--bh20simplewebuploader/static/main.js149
-rw-r--r--bh20simplewebuploader/static/map.js50
-rw-r--r--bh20simplewebuploader/templates/blog.html8
-rw-r--r--bh20simplewebuploader/templates/demo-run.html26
-rw-r--r--bh20simplewebuploader/templates/demo.html49
-rw-r--r--bh20simplewebuploader/templates/error.html2
-rw-r--r--bh20simplewebuploader/templates/footer.html8
-rw-r--r--bh20simplewebuploader/templates/header.html18
-rw-r--r--bh20simplewebuploader/templates/home.html15
-rw-r--r--bh20simplewebuploader/templates/map.html33
-rw-r--r--bh20simplewebuploader/templates/mapheader.html16
-rw-r--r--bh20simplewebuploader/templates/search.html10
-rw-r--r--bh20simplewebuploader/templates/status.html3
-rw-r--r--bh20simplewebuploader/templates/success.html2
-rw-r--r--bh20simplewebuploader/templates/validated.html17
19 files changed, 380 insertions, 284 deletions
diff --git a/bh20simplewebuploader/main.py b/bh20simplewebuploader/main.py
index 77b3832..206f884 100644
--- a/bh20simplewebuploader/main.py
+++ b/bh20simplewebuploader/main.py
@@ -8,7 +8,7 @@ import os
import sys
import re
import string
-import yaml
+import ruamel.yaml as yaml
import pkg_resources
from flask import Flask, request, redirect, send_file, send_from_directory, render_template, jsonify
import os.path
@@ -16,6 +16,9 @@ import requests
import io
import arvados
from markupsafe import Markup
+from schema_salad.sourceline import add_lc_filename
+from schema_salad.schema import shortname
+from typing import MutableSequence, MutableMapping
ARVADOS_API = 'lugli.arvadosapi.com'
ANONYMOUS_TOKEN = '5o42qdxpxp5cj15jqjf7vnxx5xduhm4ret703suuoa3ivfglfh'
@@ -47,6 +50,8 @@ def type_to_heading(type_name):
Turn a type name like "sampleSchema" from the metadata schema into a human-readable heading.
"""
+ type_name = shortname(type_name)
+
print(type_name,file=sys.stderr)
# Remove camel case
decamel = re.sub('([A-Z])', r' \1', type_name)
@@ -78,7 +83,7 @@ def is_iri(string):
return string.startswith('http')
-def generate_form(schema, options):
+def generate_form(components, options):
"""
Linearize the schema into a list of dicts.
@@ -101,9 +106,6 @@ def generate_form(schema, options):
IRI.
"""
- # Get the list of form components, one of which is the root
- components = schema.get('$graph', [])
-
# Find the root
root_name = None
# And also index components by type name
@@ -131,55 +133,54 @@ def generate_form(schema, options):
# First make a heading, if we aren't the very root of the form
yield {'heading': type_to_heading(type_name)}
- for field_name, field_type in by_name.get(type_name, {}).get('fields', {}).items():
+ for field in by_name.get(type_name, {}).get('fields', []):
+ field_name = shortname(field["name"])
+ field_type = field["type"]
# For each field
ref_iri = None
docstring = None
- if not isinstance(field_type, str):
- # If the type isn't a string
-
- # It may have documentation
- docstring = field_type.get('doc', None)
-
- # See if it has a more info/what goes here URL
- predicate = field_type.get('jsonldPredicate', {})
- # Predicate may be a URL, a dict with a URL in _id, maybe a
- # dict with a URL in _type, or a dict with _id and _type but no
- # URLs anywhere. Some of these may not technically be allowed
- # by the format, but if they occur, we might as well try to
- # handle them.
- if isinstance(predicate, str):
- if is_iri(predicate):
- ref_iri = predicate
- else:
- # Assume it's a dict. Look at the fields we know about.
- for field in ['_id', 'type']:
- field_value = predicate.get(field, None)
- if isinstance(field_value, str) and is_iri(field_value) and ref_iri is None:
- # Take the first URL-looking thing we find
- ref_iri = field_value
- break
-
- # Now overwrite the field type with the actual type string
- field_type = field_type.get('type', '')
-
- # Decide if the field is optional (type ends in ?)
optional = False
- if field_type.endswith('?'):
- # It's optional
- optional = True
- # Drop the ?
- field_type = field_type[:-1]
-
- # Decide if the field is a list (type ends in [])
is_list = False
- if field_type.endswith('[]'):
- # It's a list
- is_list = True
- # Reduce to the normal type
- field_type = field_type[:-2]
+
+ # It may have documentation
+ docstring = field.get('doc', None)
+
+ # See if it has a more info/what goes here URL
+ predicate = field.get('jsonldPredicate', {})
+ # Predicate may be a URL, a dict with a URL in _id, maybe a
+ # dict with a URL in _type, or a dict with _id and _type but no
+ # URLs anywhere. Some of these may not technically be allowed
+ # by the format, but if they occur, we might as well try to
+ # handle them.
+ if isinstance(predicate, str):
+ if is_iri(predicate):
+ ref_iri = predicate
+ else:
+ # Assume it's a dict. Look at the fields we know about.
+ for field in ['_id', 'type']:
+ field_value = predicate.get(field, None)
+ if isinstance(field_value, str) and is_iri(field_value) and ref_iri is None:
+ # Take the first URL-looking thing we find
+ ref_iri = field_value
+ break
+
+ if isinstance(field_type, MutableSequence):
+ if field_type[0] == "null" and len(field_type) == 2:
+ optional = True
+ field_type = field_type[1]
+ else:
+ raise Exception("Can't handle it")
+
+ if isinstance(field_type, MutableMapping):
+ if field_type["type"] == "array":
+ # Now replace the field type with the actual type string
+ is_list = True
+ field_type = field_type.get('items', '')
+ else:
+ field_type = field_type.get('type', '')
+ pass
if field_type in by_name:
# This is a subrecord. We need to recurse
@@ -227,15 +228,24 @@ def generate_form(schema, options):
return list(walk_fields(root_name))
-# At startup, we need to load the metadata schema from the uploader module, so we can make a form for it
-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)
+import schema_salad.schema
+def load_schema_generate_form():
+ # At startup, we need to load the metadata schema from the uploader module, so we can make a form for it
+ if os.path.isfile("bh20sequploader/bh20seq-schema.yml"):
+ METADATA_SCHEMA = yaml.round_trip_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.round_trip_load(pkg_resources.resource_stream("bh20sequploader", "bh20seq-schema.yml"))
+ METADATA_OPTION_DEFINITIONS = yaml.safe_load(pkg_resources.resource_stream("bh20sequploader", "bh20seq-options.yml"))
+
+ METADATA_SCHEMA["name"] = "bh20seq-schema.yml"
+ add_lc_filename(METADATA_SCHEMA, "bh20seq-schema.yml")
+ metaschema_names, _metaschema_doc, metaschema_loader = schema_salad.schema.get_metaschema()
+ schema_doc, schema_metadata = metaschema_loader.resolve_ref(METADATA_SCHEMA, "")
+
+ return generate_form(schema_doc, METADATA_OPTION_DEFINITIONS)
+
+FORM_ITEMS = load_schema_generate_form()
@app.route('/')
def send_home():
@@ -243,7 +253,7 @@ def send_home():
Send the front page.
"""
- return render_template('home.html', menu='HOME')
+ return render_template('home.html', menu='HOME', load_map=True)
@app.route('/upload')
@@ -435,12 +445,12 @@ def receive_files():
if result.returncode != 0:
# It didn't work. Complain.
- error_message="Uploader returned value {} and said:".format(result.returncode) + str(result.stderr.decode('utf-8'))
+ error_message="Uploader returned value {} and said:\n".format(result.returncode) + str(result.stderr.decode('utf-8'))
print(error_message, file=sys.stderr)
return (render_template('error.html', error_message=error_message), 403)
else:
# It worked. Say so.
- return render_template('success.html', log=result.stdout.decode('utf-8', errors='replace'))
+ return render_template('success.html', log=result.stderr.decode('utf-8', errors='replace'))
finally:
shutil.rmtree(dest_dir)
@@ -479,10 +489,13 @@ def pending_table(output, items):
for r in items:
if r["status"] != "pending":
continue
- output.write("<tr>")
- output.write("<td><a href='https://workbench.lugli.arvadosapi.com/collections/%s'>%s</a></td>" % (r["uuid"], r["uuid"]))
- output.write("<td>%s</td>" % Markup.escape(r["sequence_label"]))
- output.write("</tr>")
+ try:
+ output.write("<tr>")
+ output.write("<td><a href='https://workbench.lugli.arvadosapi.com/collections/%s'>%s</a></td>" % (r["uuid"], r["uuid"]))
+ output.write("<td>%s</td>" % Markup.escape(r.get("sequence_label")))
+ output.write("</tr>")
+ except:
+ pass
output.write(
"""
</table>
@@ -497,18 +510,69 @@ def rejected_table(output, items):
<th>Errors</th></tr>
""")
for r in items:
- if r["status"] != "rejected":
- continue
+ try:
+ if r["status"] != "rejected":
+ continue
+ output.write("<tr>")
+ output.write("<td><a href='https://workbench.lugli.arvadosapi.com/collections/%s'>%s</a></td>" % (r["uuid"], r["uuid"]))
+ output.write("<td>%s</td>" % Markup.escape(r.get("sequence_label")))
+ output.write("<td><pre>%s</pre></td>" % Markup.escape("\n".join(r.get("errors", []))))
+ output.write("</tr>")
+ except:
+ pass
+ output.write(
+"""
+</table>
+""")
+
+def workflows_table(output, items):
+ output.write(
+"""
+<table>
+<tr>
+<th>Name</th>
+<th>Sample id</th>
+<th>Started</th>
+<th>Container request</th>
+</tr>
+""")
+ for r in items:
output.write("<tr>")
- output.write("<td><a href='https://workbench.lugli.arvadosapi.com/collections/%s'>%s</a></td>" % (r["uuid"], r["uuid"]))
- output.write("<td>%s</td>" % Markup.escape(r["sequence_label"]))
- output.write("<td><pre>%s</pre></td>" % Markup.escape("\n".join(r.get("errors", []))))
+ try:
+ sid = r["mounts"]["/var/lib/cwl/cwl.input.json"]["content"]["sample_id"]
+ output.write("<td>%s</td>" % Markup.escape(r["name"]))
+ output.write("<td>%s</td>" % Markup.escape(sid))
+ output.write("<td>%s</td>" % Markup.escape(r["created_at"]))
+ output.write("<td><a href='https://workbench.lugli.arvadosapi.com/container_requests/%s'>%s</a></td>" % (r["uuid"], r["uuid"]))
+ except:
+ pass
output.write("</tr>")
output.write(
"""
</table>
""")
+def validated_table(output, items):
+ output.write(
+"""
+<table>
+<tr>
+<th>Collection</th>
+<th>Sequence label</th>
+</tr>
+""")
+ for r in items:
+ try:
+ output.write("<tr>")
+ output.write("<td><a href='https://workbench.lugli.arvadosapi.com/collections/%s'>%s</a></td>" % (r["uuid"], r["uuid"]))
+ output.write("<td>%s</td>" % Markup.escape(r["properties"].get("sequence_label")))
+ output.write("</tr>")
+ except:
+ pass
+ output.write(
+"""
+</table>
+""")
@app.route('/status')
def status_page():
@@ -529,25 +593,42 @@ def status_page():
prop["uuid"] = p["uuid"]
status[prop["status"]] = status.get(prop["status"], 0) + 1
+ workflows = arvados.util.list_all(api.container_requests().list,
+ filters=[["name", "in", ["fastq2fasta.cwl"]], ["state", "=", "Committed"]],
+ order="created_at asc")
+
output = io.StringIO()
validated = api.collections().list(filters=[["owner_uuid", "=", VALIDATED_PROJECT]], limit=1).execute()
status["passed"] = validated["items_available"]
- for s in (("passed", "/download"), ("pending", "#pending"), ("rejected", "#rejected")):
+ for s in (("passed", "/validated"), ("pending", "#pending"), ("rejected", "#rejected")):
output.write("<p><a href='%s'>%s sequences QC %s</a></p>" % (s[1], status.get(s[0], 0), s[0]))
- output.write("<a id='pending'><h1>Pending</h1>")
+ output.write("<p><a href='%s'>%s analysis workflows running</a></p>" % ('#workflows', len(workflows)))
+
+ output.write("<a id='pending'><h1>Pending</h1></a>")
pending_table(output, out)
- output.write("<a id='rejected'><h1>Rejected</h1>")
+ output.write("<a id='rejected'><h1>Rejected</h1></a>")
rejected_table(output, out)
+ output.write("<a id='workflows'><h1>Running Workflows</h1></a>")
+ workflows_table(output, workflows)
+
return render_template('status.html', table=Markup(output.getvalue()), menu='STATUS')
+@app.route('/validated')
+def validated_page():
+ api = arvados.api(host=ARVADOS_API, token=ANONYMOUS_TOKEN, insecure=True)
+ output = io.StringIO()
+ validated = arvados.util.list_all(api.collections().list, filters=[["owner_uuid", "=", VALIDATED_PROJECT]])
+ validated_table(output, validated)
+ return render_template('validated.html', table=Markup(output.getvalue()), menu='STATUS')
+
@app.route('/demo')
def demo_page():
- return render_template('demo.html',menu='DEMO')
+ return render_template('demo.html',menu='DEMO',load_map=True)
@app.route('/blog',methods=['GET'])
def blog_page():
@@ -563,12 +644,6 @@ def about_page():
buf = get_html_body('doc/web/about.html','https://github.com/arvados/bh20-seq-resource/blob/master/doc/web/about.org')
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
diff --git a/bh20simplewebuploader/static/image/curii.logo.ai.png b/bh20simplewebuploader/static/image/curii.logo.ai.png
new file mode 100644
index 0000000..401afad
--- /dev/null
+++ b/bh20simplewebuploader/static/image/curii.logo.ai.png
Binary files differ
diff --git a/bh20simplewebuploader/static/image/curii.logo.ai.svg b/bh20simplewebuploader/static/image/curii.logo.ai.svg
new file mode 100644
index 0000000..e87ea05
--- /dev/null
+++ b/bh20simplewebuploader/static/image/curii.logo.ai.svg
@@ -0,0 +1,3 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!-- Created with Inkscape (http://www.inkscape.org/) -->
+<svg width="1333.3" height="1333.3" version="1.1" viewBox="0 0 1333.3 1333.3" xml:space="preserve" xmlns="http://www.w3.org/2000/svg" xmlns:cc="http://creativecommons.org/ns#" xmlns:dc="http://purl.org/dc/elements/1.1/" xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"><metadata><rdf:RDF><cc:Work rdf:about=""><dc:format>image/svg+xml</dc:format><dc:type rdf:resource="http://purl.org/dc/dcmitype/StillImage"/><dc:title/></cc:Work></rdf:RDF></metadata><defs><clipPath id="clipPath18"><path d="m0 1e3h1e3v-1e3h-1e3z"/></clipPath></defs><g transform="matrix(1.3333 0 0 -1.3333 0 1333.3)"><g clip-path="url(#clipPath18)"><g transform="translate(473.7 553.52)"><path d="m0 0c-23.91 0-41.063-17.932-41.063-44.182 0-26.251 17.153-44.179 41.063-44.179 17.414 0 31.448 5.714 40.805 16.63l16.63-16.63c-12.476-16.377-32.488-25.735-58.734-25.735-41.063 0-69.653 28.329-69.653 69.914 0 41.843 28.59 70.428 69.653 70.428 24.95 0 44.439-8.053 57.174-22.611l-16.37-19.229c-9.619 9.876-22.875 15.851-39.505 15.594" fill="#008a82"/></g><g transform="translate(681.34 578.73)"><path d="m0 0v-138.26h-29.889v27.029c-9.355-19.232-26.765-27.806-49.377-28.07-31.707 0-50.676 20.276-50.676 53.281v86.022h29.884v-77.707c0-20.792 12.216-33.526 32.228-33.526 23.911 0.523 37.941 18.972 37.941 43.143v68.09z" fill="#008a82"/></g><g transform="translate(796.73 579.77)"><path d="m0 0v-28.585c-27.809 1.556-45.481-14.815-47.818-38.468v-72.248h-29.887v138.26h29.887v-27.546c9.356 18.71 25.99 28.585 47.818 28.585" fill="#008a82"/></g><g transform="translate(847.15 618.24)"><path d="m0 0c0-10.136-7.54-17.673-17.412-17.673-9.877 0-17.413 7.537-17.413 17.673 0 10.396 7.536 17.933 17.413 17.933 9.872 0 17.412-7.537 17.412-17.933" fill="#f15a29"/></g><path d="m844.54 440.47h-29.625v138.26h29.625z" fill="#008a82"/><g transform="translate(914.46 618.24)"><path d="m0 0c0-10.136-7.541-17.673-17.413-17.673-9.876 0-17.413 7.537-17.413 17.673 0 10.396 7.537 17.933 17.413 17.933 9.872 0 17.413-7.537 17.413-17.933" 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62.177 14.151 70.26 48.559 4.169 17.775 3.976 36.163 0.456 54.069-2.558 13.035-7.277 26.098-9.819 39.366" fill="#008a82"/></g><g transform="translate(312.28 562.6)"><path d="m0 0c-9.515 0-17.227 7.709-17.227 17.228 0 9.514 7.712 17.227 17.227 17.227 9.519 0 17.228-7.713 17.228-17.227 0-9.519-7.709-17.228-17.228-17.228m-87.342 118.87-2.248-58.267c4.425-1.198 7.753-4.685 8.799-9.009l56.965 0.679c7.689 4.574 16.285 7.993 25.578 9.991 2.66 0.576 4.931-0.281 6.548-1.786l-2.677 1.573c-28.575-13.342-42.238-34.715-48.462-48.807-2.258-4.6-3.79-9.265-4.739-13.983-0.01-0.048-0.03-0.179-0.03-0.179-1.08-5.452-1.428-10.967-1.175-16.536 30.725 3.518 70.847-3.875 96.101 16.526-12.633 65.686-68.086 114.92-134.66 119.8" fill="#f15a29"/></g></g></g></svg> \ No newline at end of file
diff --git a/bh20simplewebuploader/static/main.css b/bh20simplewebuploader/static/main.css
index 47fb408..6e651a4 100644
--- a/bh20simplewebuploader/static/main.css
+++ b/bh20simplewebuploader/static/main.css
@@ -47,7 +47,7 @@ h2 > svg {
float: right;
}
-#map {
+#mapid {
width: 800px;
height: 440px;
border: 1px solid #AAA;
@@ -178,7 +178,7 @@ span.dropt:hover {text-decoration: none; background: #ffffff; z-index: 6; }
.about {
display: grid;
- grid-template-columns: repeat(2, 1fr);
+ grid-template-columns: 1fr 1fr;
grid-auto-flow: row;
}
@@ -229,7 +229,7 @@ a {
#metadata_fill_form {
column-count: 4;
margin-top: 0.5em;
- column-width: 250px;
+ column-width: 15em;
}
.record, .record .field-group, .record .field-group .field {
@@ -238,6 +238,8 @@ a {
-webkit-column-break-inside: avoid; /* Chrome, Safari, Opera */
page-break-inside: avoid; /* Firefox */
break-inside: avoid;
+ display: block;
+ width: 90%;
}
.record {
@@ -258,6 +260,10 @@ a {
width: max-content;
}
+.control {
+ width: 100%;
+}
+
.filter-options {
width: 100%;
}
@@ -304,9 +310,10 @@ footer {
}
.sponsors img {
- width: 80%;
- display:block;
- margin:auto;
+ width: auto;
+ display: block;
+ margin: auto;
+ height: 4em;
}
.loader {
@@ -378,6 +385,11 @@ div.status {
border-bottom: 1px solid #ddd;
}
+.map {
+ padding: 20px 32px;
+ // display: inline-block;
+}
+
.editbutton {
float: right;
text-align: right;
diff --git a/bh20simplewebuploader/static/main.js b/bh20simplewebuploader/static/main.js
index 4703047..1633c25 100644
--- a/bh20simplewebuploader/static/main.js
+++ b/bh20simplewebuploader/static/main.js
@@ -13,70 +13,41 @@ function myFunction() {
}
}
-let map = L.map( 'map', {
- center: [37.0902, -95.7129], // Default to U.S.A
- minZoom: 3,
- zoom: 0
-});
-L.tileLayer( 'http://{s}.tile.openstreetmap.org/{z}/{x}/{y}.png', {
- attribution: '&copy; <a href="https://www.openstreetmap.org/copyright">OpenStreetMap</a>',
- subdomains: ['a','b','c']
-}).addTo( map );
-
-let markers = L.markerClusterGroup().addTo(map)
-
-
function fetchAPI(apiEndPoint) {
- fetch(scriptRoot + apiEndPoint)
- .then(response => {
- return response.json();
- })
- .then(data => {
- console.log(data);
- markers.clearLayers();
- document.getElementById("results").classList.remove("invisible");
- document.getElementById("loader").classList.add("invisible");
- if (!(apiEndPoint === "/api/getAllaccessions")) {
- for (let i = 0; i < data.length; i++) {
- let {"count": fastaCount, GPS, LocationLabel: label } = data[i];
- let coordinates = GPS.split(" ");
- if (!(coordinates == null)) {
- let lat, lon;
- [lon, lat] = coordinates.map(parseFloat);
- let point = L.point()
- let marker = L.marker([lat, lon]);
- marker.bindPopup("<b>" + label + "</b><br/>" + "FastaCount: " +fastaCount);
- markers.addLayer(marker)
- }}
- }
- // Reload the map
- map.invalidateSize();
- });
- document.getElementById("results").classList.add("invisible");
- document.getElementById("loader").classList.remove("invisible");
-
-}
-
-// Copy from function above but now added as table instead of plain json
-function fetchAPIV2(apiEndPoint) {
- fetch(scriptRoot + apiEndPoint)
- .then(response => {
- return response.json();
- })
- .then(data => {
- console.log(data)
- htmlString="<table>"
-
- // Depending on what we want to explore we'd have to call a different function ....? But how to Include that?
- for (var i=0; i<data.length;i++) {
- htmlString=htmlString+"<tr><td><a href='#' onclick='fetchSEQByLocation(\""+data[i]["key"]+"\");'>"+data[i]["label"]+"</a></td><td>"+data[i]["count"]+"<td></tr>"
- }
- htmlString=htmlString+"</table>"
-
- document.getElementById("table").innerHTML = htmlString
- });
-
- document.getElementById("results").classList.add("invisible");
+ fetch(scriptRoot + apiEndPoint)
+ .then(response => {
+ return response.json();
+ })
+ .then(data => {
+ console.log(data);
+ });
+ document.getElementById("map_view").classList.add("invisible");
+ document.getElementById("loader").classList.remove("invisible");
+}
+
+// Copy from function above but now output HTML table instead of plain json
+function fetchHTMLTable(apiEndPoint) {
+ fetch(scriptRoot + apiEndPoint)
+ .then(response => {
+ return response.json();
+ })
+ .then(data => {
+ console.log(data)
+ htmlString="<table>"
+
+ // Depending on what we want to explore we'd have to call a different function ....? But how to Include that?
+ /*
+ for (var i=0; i<data.length;i++) {
+ htmlString=htmlString+"<tr><td><a href='#' onclick='fetchSEQByLocation(\""+data[i]["key"]+"\");'>"+data[i]["label"]+"</a></td><td>"+data[i]["count"]+"<td></tr>"
+ }
+*/
+ for (var i=0; i<data.length;i++) {
+ htmlString=htmlString+"<tr><td>"+data[i]["label"]+"</td><td>"+data[i]["count"]+"<td></tr>"
+ }
+ htmlString=htmlString+"</table>"
+
+ document.getElementById("table").innerHTML = htmlString
+ });
}
@@ -85,36 +56,39 @@ let search = () => {
fetchAPI(scriptRoot + "/api/getDetailsForSeq?seq=" + encodeURIComponent(m));
}
+// Get count from Arvados
let fetchCount = () => {
fetchAPI("/api/getCount");
}
+// Get count from Virtuoso
let fetchCountDB = () => {
fetchAPI("/api/getCountDB");
}
let fetchSEQCountBySpecimen = () => {
- fetchAPIV2("/api/getSEQCountbySpecimenSource");
+ fetchHTMLTable("/api/getSEQCountbySpecimenSource");
}
let fetchSEQCountByLocation = () => {
- fetchAPIV2("/api/getSEQCountbyLocation");
+ fetchHTMLTable("/api/getSEQCountbyLocation");
}
let fetchSEQCountByTech = () => {
- fetchAPIV2("/api/getSEQCountbytech");
+ fetchHTMLTable("/api/getSEQCountbytech");
}
let fetchAllaccessions = () => {
- fetchAPI("/api/getAllaccessions");
+ fetchHTMLTable("/api/getAllaccessions");
};
-let fetchCountByGPS = () => {
- fetchAPI("/api/getCountByGPS");
+let fetchMap = () => {
+ fetchAPI("/api/getCountByGPS");
+ updateMapMarkers();
};
let fetchSEQCountbyLocation = () => {
- fetchAPIV2("/api/getSEQCountbyLocation");
+ fetchHTMLTable("/api/getSEQCountbyLocation");
};
let fetchSEQByLocation = () => {
@@ -122,7 +96,7 @@ let fetchSEQByLocation = () => {
};
let fetchSEQCountbyContinent = () => {
- fetchAPIV2("/api/getSEQCountbyContinent");
+ fetchHTMLTable("/api/getSEQCountbyContinent");
}
@@ -252,36 +226,3 @@ 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);
- }
-
- });
-}
diff --git a/bh20simplewebuploader/static/map.js b/bh20simplewebuploader/static/map.js
new file mode 100644
index 0000000..1003f7d
--- /dev/null
+++ b/bh20simplewebuploader/static/map.js
@@ -0,0 +1,50 @@
+
+var map = L.map( 'mapid', {
+ center: [51.505, -0.09], // Default to U.S.A
+ minZoom: 2,
+ zoom: 0
+});
+
+L.tileLayer( 'http://{s}.tile.openstreetmap.org/{z}/{x}/{y}.png', {
+ attribution: '&copy; <a href="https://www.openstreetmap.org/copyright">OpenStreetMap</a> | <a href="http://covid19.genenetwork.org/">COVID-19 PubSeq</a>',
+ subdomains: ['a','b','c']
+}).addTo(map);
+
+
+function drawMap(){
+ var mymap = map;
+
+ fetch(scriptRoot + "api/getCountByGPS")
+ .then(response => {
+ console.log(response)
+ return response.json();
+ })
+ .then(data => {
+ updateMapMarkers(data);
+
+ });
+ document.getElementById("map_view").classList.remove("invisible");
+ map.invalidateSize();
+}
+
+
+
+/* This function updates the map with markers
+ *
+*/
+function updateMapMarkers(data) {
+ let markers = L.markerClusterGroup();
+ for (let i = 0; i < data.length; i++) {
+ let {"count": fastaCount, GPS, LocationLabel: label } = data[i];
+ let coordinates = GPS.split(" ");
+ if (!(coordinates == null)) {
+ let lat, lon;
+ [lon, lat] = coordinates.map(parseFloat);
+ let point = L.point()
+ marker = (L.marker([lat, lon]));
+ marker.bindPopup("<b>" + label + "</b><br/>" + "SARS-CoV-2<br/>sequences: " +fastaCount);
+ markers.addLayer(marker);
+ }
+ }
+ map.addLayer(markers);
+}
diff --git a/bh20simplewebuploader/templates/blog.html b/bh20simplewebuploader/templates/blog.html
index 823f8a1..f4c2a85 100644
--- a/bh20simplewebuploader/templates/blog.html
+++ b/bh20simplewebuploader/templates/blog.html
@@ -63,6 +63,14 @@
We explore the Arvados command line and API
</div>
</div>
+ <div class="blog-table-row">
+ <div class="blog-table-cell">
+ <a href="/blog?id=using-covid-19-pubseq-part6">Prepare for uploading to EBI/ENA</a>
+ </div>
+ <div class="blog-table-cell">
+ Generate the files needed for uploading to EBI/ENA
+ </div>
+ </div>
</div>
</div>
</section>
diff --git a/bh20simplewebuploader/templates/demo-run.html b/bh20simplewebuploader/templates/demo-run.html
deleted file mode 100644
index a8f9edc..0000000
--- a/bh20simplewebuploader/templates/demo-run.html
+++ /dev/null
@@ -1,26 +0,0 @@
-<section class="search-section">
- <div class="filter-options" action="#">
- <p>[Demo] Display content sequences by: </p>
- <div>
- <button class="button" onclick="fetchSEQCountBySpecimen()">Count by Specimen source</button>
- <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>
-
- </div>
-
-</section>
-<div id="loader" class="loader invisible">
-</div>
-
-<section id="results" class="invisible">
- <div id="map"></div>
-</section>
-
- <section>
- <div id="table"></div>
- </section>
diff --git a/bh20simplewebuploader/templates/demo.html b/bh20simplewebuploader/templates/demo.html
index 44aded0..75bc0e2 100644
--- a/bh20simplewebuploader/templates/demo.html
+++ b/bh20simplewebuploader/templates/demo.html
@@ -1,13 +1,51 @@
<!DOCTYPE html>
<html>
{% include 'header.html' %}
+ {% include 'mapheader.html' %}
<body>
{% 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' %}
+
+ <p>The Virtuoso database contains <span id="CounterDB"></span> public sequences!</p>
+
+ <!--
+ <div class="search">
+ <input id="search-input" type="search" placeholder="FASTA uri" required>
+ <button class="button search-button" type="submit" onclick="search()">
+ <span class="icon ion-search">
+ <span class="sr-only">Search</span>
+ </span>
+ </button>
+ <span class="dropt" title="http://collections.lugli.arvadosapi.com/c=00fede2c6f52b053a14edca01cfa02b7+126/sequence.fasta">(example)<span style="width:500px;"></span></span>
+ </div>
+ -->
+
+ <section class="search-section">
+ <div class="filter-options" action="#">
+ <p>[Demo] Display content sequences by: </p>
+ <div>
+ <button class="button" onclick="fetchSEQCountBySpecimen()">Count by Specimen source</button>
+ <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>
+ </div>
+
+ </div>
+
+ </section>
+ <div id="loader" class="loader invisible">
+ </div>
+
+ <section id="map_view" class="map">
+ <div id="mapid"></div>
+ </section>
+
+ <section>
+ <div id="table"></div>
+ </section>
+
+ {% include 'footer.html' %}
<script type="text/javascript">
let scriptRoot = {{ request.script_root|tojson|safe }}; // examples
@@ -24,7 +62,10 @@
});
});
+ drawMap()
+
</script>
+
</body>
</html>
diff --git a/bh20simplewebuploader/templates/error.html b/bh20simplewebuploader/templates/error.html
index b1d9402..fc08aed 100644
--- a/bh20simplewebuploader/templates/error.html
+++ b/bh20simplewebuploader/templates/error.html
@@ -15,7 +15,7 @@
</pre>
</p>
<p>
- <a href="/">Click here to try again.</a>
+ <a href="/upload">Click here to try again.</a>
</p>
<hr>
</body>
diff --git a/bh20simplewebuploader/templates/footer.html b/bh20simplewebuploader/templates/footer.html
index 37a6b64..f84cef5 100644
--- a/bh20simplewebuploader/templates/footer.html
+++ b/bh20simplewebuploader/templates/footer.html
@@ -21,12 +21,15 @@
<img src="static/image/covid19biohackathon.png"></a>
</div>
<div class="sponsorimg">
- <a href="https://www.commonwl.org/"><img src="static/image/CWL.png"></a>
+ <a href="https://www.curii.com/"><img src="static/image/curii.logo.ai.png"></a>
</div>
<div class="sponsorimg">
<a href="https://arvados.org/"><img src="static/image/arvados-logo.png"></a>
</div>
<div class="sponsorimg">
+ <a href="https://www.commonwl.org/"><img src="static/image/CWL.png"></a>
+ </div>
+ <div class="sponsorimg">
<a href="https://uthsc.edu/"><img src="static/image/UTHSC-primary-stacked-logo-4c.png"></a>
</div>
<div class="sponsorimg">
@@ -44,6 +47,9 @@
</center>
</div>
</section>
+{% if load_map %}
+<script type="text/javascript" src="/static/map.js"></script>
+{% endif %}
<script type="text/javascript" src="/static/main.js"></script>
<script type="text/javascript">
diff --git a/bh20simplewebuploader/templates/header.html b/bh20simplewebuploader/templates/header.html
index 0ac5157..1d66590 100644
--- a/bh20simplewebuploader/templates/header.html
+++ b/bh20simplewebuploader/templates/header.html
@@ -6,22 +6,4 @@
{% if blog %}
<link rel="Blog stylesheet" type="text/css" href="/static/blog.css" />
{% endif %}
- <link rel="stylesheet" href="https://unpkg.com/leaflet@1.6.0/dist/leaflet.css"
- integrity="sha512-xwE/Az9zrjBIphAcBb3F6JVqxf46+CDLwfLMHloNu6KEQCAWi6HcDUbeOfBIptF7tcCzusKFjFw2yuvEpDL9wQ=="
- crossorigin=""/>
- <link rel="stylesheet" href="https://unpkg.com/leaflet.markercluster@1.4.1/dist/MarkerCluster.css"
- integrity="sha512-RLEjtaFGdC4iQMJDbMzim/dOvAu+8Qp9sw7QE4wIMYcg2goVoivzwgSZq9CsIxp4xKAZPKh5J2f2lOko2Ze6FQ=="
- crossorigin=""/>
-
- <link rel="stylesheet" href="https://unpkg.com/leaflet.markercluster@1.4.1/dist/MarkerCluster.Default.css"
- integrity="sha512-BBToHPBStgMiw0lD4AtkRIZmdndhB6aQbXpX7omcrXeG2PauGBl2lzq2xUZTxaLxYz5IDHlmneCZ1IJ+P3kYtQ=="
- crossorigin=""/>
-
- <script src="https://unpkg.com/leaflet@1.6.0/dist/leaflet.js"
- integrity="sha512-gZwIG9x3wUXg2hdXF6+rVkLF/0Vi9U8D2Ntg4Ga5I5BZpVkVxlJWbSQtXPSiUTtC0TjtGOmxa1AJPuV0CPthew=="
- crossorigin=""></script>
-
- <script src="https://unpkg.com/leaflet.markercluster@1.4.1/dist/leaflet.markercluster.js"
- integrity="sha512-MQlyPV+ol2lp4KodaU/Xmrn+txc1TP15pOBF/2Sfre7MRsA/pB4Vy58bEqe9u7a7DczMLtU5wT8n7OblJepKbg=="
- crossorigin=""></script>
</head>
diff --git a/bh20simplewebuploader/templates/home.html b/bh20simplewebuploader/templates/home.html
index b90a18d..bede611 100644
--- a/bh20simplewebuploader/templates/home.html
+++ b/bh20simplewebuploader/templates/home.html
@@ -1,6 +1,7 @@
<!DOCTYPE html>
<html>
{% include 'header.html' %}
+ {% include 'mapheader.html' %}
<body>
{% include 'banner.html' %}
{% include 'menu.html' %}
@@ -44,7 +45,19 @@
</div>
</section>
-{% include 'footer.html' %}
+ <section id="map_view" class="map">
+ <div id="mapid"></div>
+ </section>
+
+ {% include 'footer.html' %}
+
+
+ <script type="text/javascript">
+ let scriptRoot = {{ request.script_root|tojson|safe }}; // examples
+
+ drawMap()
+
+ </script>
</body>
</html>
diff --git a/bh20simplewebuploader/templates/map.html b/bh20simplewebuploader/templates/map.html
deleted file mode 100644
index 595af0c..0000000
--- a/bh20simplewebuploader/templates/map.html
+++ /dev/null
@@ -1,33 +0,0 @@
-<!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
- </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/bh20simplewebuploader/templates/mapheader.html b/bh20simplewebuploader/templates/mapheader.html
new file mode 100644
index 0000000..ca62051
--- /dev/null
+++ b/bh20simplewebuploader/templates/mapheader.html
@@ -0,0 +1,16 @@
+ <link rel="stylesheet" href="https://unpkg.com/leaflet@1.6.0/dist/leaflet.css"
+ integrity="sha512-xwE/Az9zrjBIphAcBb3F6JVqxf46+CDLwfLMHloNu6KEQCAWi6HcDUbeOfBIptF7tcCzusKFjFw2yuvEpDL9wQ=="
+ crossorigin=""/>
+ <link rel="stylesheet" href="https://unpkg.com/leaflet.markercluster@1.4.1/dist/MarkerCluster.css"
+ integrity="sha512-RLEjtaFGdC4iQMJDbMzim/dOvAu+8Qp9sw7QE4wIMYcg2goVoivzwgSZq9CsIxp4xKAZPKh5J2f2lOko2Ze6FQ=="
+ crossorigin=""/>
+ <link rel="stylesheet" href="https://unpkg.com/leaflet.markercluster@1.4.1/dist/MarkerCluster.Default.css"
+ integrity="sha512-BBToHPBStgMiw0lD4AtkRIZmdndhB6aQbXpX7omcrXeG2PauGBl2lzq2xUZTxaLxYz5IDHlmneCZ1IJ+P3kYtQ=="
+ crossorigin=""/>
+
+ <script src="https://unpkg.com/leaflet@1.6.0/dist/leaflet.js"
+ integrity="sha512-gZwIG9x3wUXg2hdXF6+rVkLF/0Vi9U8D2Ntg4Ga5I5BZpVkVxlJWbSQtXPSiUTtC0TjtGOmxa1AJPuV0CPthew=="
+ crossorigin=""></script>
+ <script src="https://unpkg.com/leaflet.markercluster@1.4.1/dist/leaflet.markercluster.js"
+ integrity="sha512-MQlyPV+ol2lp4KodaU/Xmrn+txc1TP15pOBF/2Sfre7MRsA/pB4Vy58bEqe9u7a7DczMLtU5wT8n7OblJepKbg=="
+ crossorigin=""></script>
diff --git a/bh20simplewebuploader/templates/search.html b/bh20simplewebuploader/templates/search.html
index dbdca90..e69de29 100644
--- a/bh20simplewebuploader/templates/search.html
+++ b/bh20simplewebuploader/templates/search.html
@@ -1,10 +0,0 @@
-<div class="search">
- <input id="search-input" type="search" placeholder="FASTA uri" required>
- <button class="button search-button" type="submit" onclick="search()">
- <span class="icon ion-search">
- <span class="sr-only">Search</span>
- </span>
- </button>
- <span class="dropt" title="http://collections.lugli.arvadosapi.com/c=00fede2c6f52b053a14edca01cfa02b7+126/sequence.fasta">(example)<span style="width:500px;"></span></span>
-</div>
-
diff --git a/bh20simplewebuploader/templates/status.html b/bh20simplewebuploader/templates/status.html
index a1cf28f..e89437e 100644
--- a/bh20simplewebuploader/templates/status.html
+++ b/bh20simplewebuploader/templates/status.html
@@ -7,7 +7,8 @@
<h1>Sequence upload processing status</h1>
- <div class="status">
+ <div class="status">
+
{{ table }}
</div>
diff --git a/bh20simplewebuploader/templates/success.html b/bh20simplewebuploader/templates/success.html
index 9f0987c..c2302fa 100644
--- a/bh20simplewebuploader/templates/success.html
+++ b/bh20simplewebuploader/templates/success.html
@@ -9,7 +9,7 @@
<h1>Upload Successful</h1>
<hr>
<p>
- Your files have been uploaded. They should soon appear as output of the <a href="/download">Public SARS-CoV-2 Sequence Resource</a>.
+ Your files have been uploaded. You can track their <a href="/status">QC status</a>, once validated they will be part of the <a href="/download">Public SARS-CoV-2 Sequence Resource</a>.
</p>
<p>
The upload log was:
diff --git a/bh20simplewebuploader/templates/validated.html b/bh20simplewebuploader/templates/validated.html
new file mode 100644
index 0000000..cee94bd
--- /dev/null
+++ b/bh20simplewebuploader/templates/validated.html
@@ -0,0 +1,17 @@
+<!DOCTYPE html>
+<html>
+ {% include 'header.html' %}
+ <body>
+ {% include 'banner.html' %}
+ {% include 'menu.html' %}
+
+ <h1>Validated sequences</h1>
+
+ <div class="status">
+ {{ table }}
+ </div>
+
+{% include 'footer.html' %}
+
+ </body>
+</html>