diff options
| -rw-r--r-- | bh20seqanalyzer/main.py | 10 | ||||
| -rw-r--r-- | bh20simplewebuploader/main.py | 93 | ||||
| -rw-r--r-- | bh20simplewebuploader/templates/resource.html | 1 |
3 files changed, 65 insertions, 39 deletions
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> |