diff options
Diffstat (limited to 'bh20simplewebuploader/main.py')
| -rw-r--r-- | bh20simplewebuploader/main.py | 119 |
1 files changed, 101 insertions, 18 deletions
diff --git a/bh20simplewebuploader/main.py b/bh20simplewebuploader/main.py index 3100dfd..9132453 100644 --- a/bh20simplewebuploader/main.py +++ b/bh20simplewebuploader/main.py @@ -13,12 +13,20 @@ import pkg_resources from flask import Flask, request, redirect, send_file, send_from_directory, render_template, jsonify import os.path import requests +import io +import arvados +from markupsafe import Markup + +ARVADOS_API = 'lugli.arvadosapi.com' +ANONYMOUS_TOKEN = '5o42qdxpxp5cj15jqjf7vnxx5xduhm4ret703suuoa3ivfglfh' +UPLOADER_PROJECT = 'lugli-j7d0g-n5clictpuvwk8aa' +VALIDATED_PROJECT = 'lugli-j7d0g-5ct8p1i1wrgyjvp' logging.basicConfig(level=logging.DEBUG) log = logging.getLogger(__name__ ) log.debug("Entering web uploader") -if not os.path.isfile('bh20sequploader/mainx.py'): +if not os.path.isfile('bh20sequploader/main.py'): print("WARNING: run FLASK from the root of the source repository!", file=sys.stderr) app = Flask(__name__, static_url_path='/static', static_folder='static') @@ -224,12 +232,21 @@ METADATA_OPTION_DEFINITIONS = yaml.safe_load(pkg_resources.resource_stream("bh20 FORM_ITEMS = generate_form(METADATA_SCHEMA, METADATA_OPTION_DEFINITIONS) @app.route('/') +def send_home(): + """ + Send the front page. + """ + + return render_template('home.html', menu='HOME') + + +@app.route('/upload') def send_form(): """ Send the file upload form/front page. """ - return render_template('form.html', fields=FORM_ITEMS, menu='HOME') + return render_template('form.html', fields=FORM_ITEMS, menu='UPLOAD') class FileTooBigError(RuntimeError): """ @@ -405,7 +422,7 @@ def receive_files(): # Try and upload files to Arvados using the sequence uploader CLI - cmd = ['python3','bh20sequploader/main.py', fasta_dest, metadata_dest] + cmd = ['python3','bh20sequploader/main.py', metadata_dest, fasta_dest] print(" ".join(cmd),file=sys.stderr) result = subprocess.run(cmd, stdout=subprocess.PIPE, stderr=subprocess.PIPE) @@ -439,7 +456,83 @@ def get_html_body(fn): @app.route('/download') def download_page(): buf = get_html_body('doc/web/download.html') - return render_template('about.html',menu='DOWNLOAD',embed=buf) + return render_template('resource.html',menu='DOWNLOAD',embed=buf) + +def pending_table(output, items): + output.write( +""" +<table> +<tr><th>Collection</th> +<th>Sequence label</th></tr> +""") + 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>") + output.write( +""" +</table> +""") + +def rejected_table(output, items): + output.write( +""" +<table> +<tr><th>Collection</th> +<th>Sequence label</th> +<th>Errors</th></tr> +""") + for r in items: + 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["sequence_label"])) + output.write("<td><pre>%s</pre></td>" % Markup.escape("\n".join(r.get("errors", [])))) + output.write("</tr>") + output.write( +""" +</table> +""") + + +@app.route('/status') +def status_page(): + """ + Processing status + """ + + api = arvados.api(host=ARVADOS_API, token=ANONYMOUS_TOKEN) + pending = arvados.util.list_all(api.collections().list, filters=[["owner_uuid", "=", UPLOADER_PROJECT]]) + out = [] + status = {} + for p in pending: + prop = p["properties"] + out.append(prop) + if "status" not in prop: + prop["status"] = "pending" + prop["created_at"] = p["created_at"] + prop["uuid"] = p["uuid"] + status[prop["status"]] = status.get(prop["status"], 0) + 1 + + 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")): + 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>") + pending_table(output, out) + + output.write("<a id='rejected'><h1>Rejected</h1>") + rejected_table(output, out) + + return render_template('status.html', table=Markup(output.getvalue()), menu='STATUS') @app.route('/demo') def demo_page(): @@ -474,20 +567,10 @@ baseURL='http://sparql.genenetwork.org/sparql/' @app.route('/api/getCount', methods=['GET']) def getCount(): - 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"])}) + api = arvados.api(host=ARVADOS_API, token=ANONYMOUS_TOKEN) + c = api.collections().list(filters=[["owner_uuid", "=", VALIDATED_PROJECT]], limit=1).execute() + + return jsonify({'sequences': c["items_available"]}) @app.route('/api/getAllaccessions', methods=['GET']) def getAllaccessions(): |