From 99af299197dfc527155cd3257388b784810518c4 Mon Sep 17 00:00:00 2001
From: Peter Amstutz
Date: Wed, 8 Jul 2020 00:16:23 -0400
Subject: Split upload tab. Add upload status tab.
Add more direct links on download page.
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <peter.amstutz@curii.com>
---
bh20simplewebuploader/templates/resource.html | 26 ++++++++++++++++++++++++++
1 file changed, 26 insertions(+)
create mode 100644 bh20simplewebuploader/templates/resource.html
(limited to 'bh20simplewebuploader/templates/resource.html')
diff --git a/bh20simplewebuploader/templates/resource.html b/bh20simplewebuploader/templates/resource.html
new file mode 100644
index 0000000..e0d344f
--- /dev/null
+++ b/bh20simplewebuploader/templates/resource.html
@@ -0,0 +1,26 @@
+<!DOCTYPE html>
+<html>
+ {% include 'header.html' %}
+ <body>
+ {% include 'banner.html' %}
+ {% include 'menu.html' %}
+
+ <div class="status">
+ <p><img src="https://workbench.lugli.arvadosapi.com/collections/lugli-4zz18-z513nlpqm03hpca/relabeledSeqs_dedup_relabeledSeqs_dedup.png" height="300px"></p>
+ <p><a href="https://workbench.lugli.arvadosapi.com/collections/lugli-4zz18-z513nlpqm03hpca/relabeledSeqs_dedup.fasta">All sequences (FASTA) relabled and deduplicated</a></p>
+ <p><a href="https://workbench.lugli.arvadosapi.com/collections/lugli-4zz18-z513nlpqm03hpca/mergedmetadata.ttl">Metadata (RDF) for all sequences</a></p>
+ <p><a href="https://workbench.lugli.arvadosapi.com/collections/lugli-4zz18-z513nlpqm03hpca/relabeledSeqs_dedup_relabeledSeqs_dedup.gfa">All sequences in Graphical Fragment Assembly (GFA)</a> - <a href="https://github.com/GFA-spec/GFA-spec">More about GFA</a></p>
+ <p><a href="https://workbench.lugli.arvadosapi.com/collections/lugli-4zz18-z513nlpqm03hpca/relabeledSeqs_dedup_relabeledSeqs_dedup.gfa">All sequences in Optimized Dynamic Genome/Graph Implementation (ODGI)</a> - <a href="https://github.com/vgteam/odgi">More about ODGI</a></p>
+ <p><a href="https://workbench.lugli.arvadosapi.com/collections/lugli-4zz18-z513nlpqm03hpca/relabeledSeqs_dedup_relabeledSeqs_dedup.ttl.xz">All sequences in RDF using spodgi</a> - <a href="https://github.com/pangenome/spodgi">More about spodgi</a></p>
+
+
+ <p><a href="http://sparql.genenetwork.org/sparql/">SPARQL endpoint</a> - <a href="http://sparql.genenetwork.org/sparql/?default-graph-uri=&query=SELECT+DISTINCT+%3Ffasta+%3Fvalue+WHERE+%7B%3Ffasta+%3Fx%5B+%3Chttp%3A%2F%2Fedamontology.org%2Fdata_2091%3E+%3Fvalue+%5D%7D%0D%0A&format=text%2Fhtml&timeout=0&debug=on&run=+Run+Query+">Sample query for accessions</a>
+
+ {{ embed|safe }}
+
+ </div>
+
+{% include 'footer.html' %}
+
+ </body>
+</html>
--
cgit v1.2.3
From cbb191cb23f4e40b1a1d3024401960939fda9bc3 Mon Sep 17 00:00:00 2001
From: Peter Amstutz
Date: Wed, 8 Jul 2020 14:02:11 -0400
Subject: Get count from arvados
Separate pending/rejected tables
"Lastest results" is latest successful run.
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <peter.amstutz@curii.com>
---
bh20seqanalyzer/main.py | 10 +--
bh20simplewebuploader/main.py | 93 +++++++++++++++++----------
bh20simplewebuploader/templates/resource.html | 1 +
3 files changed, 65 insertions(+), 39 deletions(-)
(limited to 'bh20simplewebuploader/templates/resource.html')
diff --git a/bh20seqanalyzer/main.py b/bh20seqanalyzer/main.py
index 1746587..ce9a723 100644
--- a/bh20seqanalyzer/main.py
+++ b/bh20seqanalyzer/main.py
@@ -187,14 +187,15 @@ def get_workflow_output_from_project(api, uuid):
cr = api.container_requests().list(filters=[['owner_uuid', '=', uuid],
["requesting_container_uuid", "=", None]]).execute()
if cr["items"] and cr["items"][0]["output_uuid"]:
- return cr["items"][0]
- else:
- return None
+ container = api.containers().get(uuid=cr["items"][0]["container_uuid"]).execute()
+ if container["state"] == "Complete" and container["exit_code"] == 0:
+ return cr["items"][0]
+ return None
def copy_most_recent_result(api, analysis_project, latest_result_uuid):
most_recent_analysis = api.groups().list(filters=[['owner_uuid', '=', analysis_project]],
- order="created_at desc", limit=1).execute()
+ order="created_at desc").execute()
for m in most_recent_analysis["items"]:
wf = get_workflow_output_from_project(api, m["uuid"])
if wf:
@@ -220,6 +221,7 @@ def move_fastq_to_fasta_results(api, analysis_project, uploader_project):
body={"owner_uuid": uploader_project}).execute()
p["properties"]["moved_output"] = True
api.groups().update(uuid=p["uuid"], body={"properties": p["properties"]}).execute()
+ break
def upload_schema(api, workflow_def_project):
diff --git a/bh20simplewebuploader/main.py b/bh20simplewebuploader/main.py
index d602288..d4adbda 100644
--- a/bh20simplewebuploader/main.py
+++ b/bh20simplewebuploader/main.py
@@ -20,6 +20,7 @@ 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__ )
@@ -457,6 +458,47 @@ def download_page():
buf = get_html_body('doc/web/download.html')
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():
"""
@@ -477,27 +519,18 @@ def status_page():
status[prop["status"]] = status.get(prop["status"], 0) + 1
output = io.StringIO()
- for s in status:
- output.write("<p>%s sequences %s QC</p>" % (status[s], s))
- output.write(
-"""
-<table>
-<tr><th>Collection</th>
-<th>Sequence label</th>
-<th>Status</th>
-<th>Errors</th></tr>
-""")
- for r in out:
- 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>%s</td>" % r["status"])
- output.write("<td><pre>%s</pre></td>" % Markup.escape("\n".join(r.get("errors", []))))
- output.write("</tr>")
- output.write(
-"""
-</table>
-""")
+
+ 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')
@@ -534,20 +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():
diff --git a/bh20simplewebuploader/templates/resource.html b/bh20simplewebuploader/templates/resource.html
index e0d344f..91b6c20 100644
--- a/bh20simplewebuploader/templates/resource.html
+++ b/bh20simplewebuploader/templates/resource.html
@@ -7,6 +7,7 @@
<div class="status">
<p><img src="https://workbench.lugli.arvadosapi.com/collections/lugli-4zz18-z513nlpqm03hpca/relabeledSeqs_dedup_relabeledSeqs_dedup.png" height="300px"></p>
+ <p><a href="https://workbench.lugli.arvadosapi.com/projects/lugli-j7d0g-5ct8p1i1wrgyjvp#Data_collections">All sequences project</a></p>
<p><a href="https://workbench.lugli.arvadosapi.com/collections/lugli-4zz18-z513nlpqm03hpca/relabeledSeqs_dedup.fasta">All sequences (FASTA) relabled and deduplicated</a></p>
<p><a href="https://workbench.lugli.arvadosapi.com/collections/lugli-4zz18-z513nlpqm03hpca/mergedmetadata.ttl">Metadata (RDF) for all sequences</a></p>
<p><a href="https://workbench.lugli.arvadosapi.com/collections/lugli-4zz18-z513nlpqm03hpca/relabeledSeqs_dedup_relabeledSeqs_dedup.gfa">All sequences in Graphical Fragment Assembly (GFA)</a> - <a href="https://github.com/GFA-spec/GFA-spec">More about GFA</a></p>
--
cgit v1.2.3