def report_progress():
"""
Generates URLs from report names and validates them.
"""
req = request.get_json()
current_status = list(
trait.select(trait.status)
.join(report)
.filter(
trait.trait_slug == req["trait_slug"],
(report.report_slug == req["report_slug"]) | (report.report_hash == req["report_slug"]),
)
.dicts()
.execute()
)[0]["status"]
return json.dumps(current_status)
def statistics():
title = "Site Statistics"
bcs = OrderedDict([("About", url_for("about")), ("Statistics", None)])
# Number of reports
n_reports = report.select().count()
n_traits = trait.select().count()
n_significant_mappings = mapping.select().count()
n_distinct_strains = strain.select(strain.strain).distinct().count()
n_distinct_isotypes = strain.select(strain.isotype).filter(strain.isotype != None).distinct().count()
# Collection dates
collection_dates = list(strain.select().filter(
strain.isotype != None, strain.isolation_date != None).order_by(strain.isolation_date).execute())
return render_template('statistics.html', **locals())
def public_mapping():
query = request.args.get("query")
if query is not None:
bcs = OrderedDict([("Public Mappings", url_for("public_mapping")), ("Search", None)])
title = "Search: " + query
subtitle = "results"
q = "%" + query + "%"
results = (
trait.select(report, trait, mapping)
.filter(trait.status == "complete", report.release == 0)
.join(mapping)
.join(report)
.dicts()
.filter(
(trait.trait_slug % q) | (trait.trait_name % q) | (report.report_name % q) | (report.report_slug % q)
)
.order_by(mapping.log10p.desc())
)
search_results = list(results.dicts().execute())
search = True
return render_template("public_mapping.html", **locals())
title = "Perform Mapping"
results = (
trait.select(
report.release,
report.report_name,
report.report_slug,
trait.trait_name,
trait.trait_slug,
trait.status,
trait.submission_complete,
trait.submission_date,
mapping,
)
.filter(trait.status == "complete", report.release == 0)
.join(mapping, JOIN.LEFT_OUTER)
.switch(trait)
.join(report)
.distinct()
.dicts()
.order_by(trait.submission_complete.desc())
.execute()
)
date_set = dict(
Counter([time.mktime((x["submission_date"] + relativedelta(hours=+6)).timetuple()) for x in results])
)
wdata = Counter([(x["submission_date"] + relativedelta(hours=+6)).date().isoformat() for x in results])
waffle_date_set = [{"date": x, "count": y} for x, y in wdata.items()]
# added in here waffle_date_set should be filtered by month instead of time stamp. Then could be used for the waffle plot
# submission date is a datetime object
# waffle_date_set=[]
# sum=0
# current_month=results[0]["submission_date"].month
# for x in results:
# if x["submission_date"].month==current_month:
# sum++
# else:
# waffle_date_set.append(("month": current_month, "total": sum)) #appending a tuple
# sum=1
# current_month=x["submission_date"].month
recent_results = list(results)[0:20]
bcs = OrderedDict([("Public", None)])
title = "Public Mappings"
pub_mappings = list(
mapping.select(mapping, report, trait).join(trait).join(report).filter(report.release == 0).dicts().execute()
)
return render_template("public_mapping.html", **locals())