def taxonomy(request, job):
jobtitle = job_name(job)
service = 'taxonomy'
servicename = 'taxonomic groups'
taxfilters = controls.run_script("", job, "taxonomy")
treedata = controls.run_script("", job, "get_taxonomy")
if request.method == 'POST':
print(request.POST['jsfilters'])
newfilters = controls.run_script(
"newfilters=" +
urllib.parse.unquote_plus(request.POST['jsfilters']), job,
"taxonomy")
taxfilters = newfilters.replace("u'", "'")
pfilters = json.loads(taxfilters)
pfkeys = list(pfilters.keys())
pfkeys.remove("none")
template = loader.get_template('taxonomy.html')
context = {
'job': job,
'title': jobtitle,
'service': service,
'servicename': servicename,
'taxfilters': taxfilters,
'pfkeys': pfkeys,
'treedata': treedata,
'jscripts': ["d3.v3.min.js"]
}
return HttpResponse(template.render(context, request))
def tags(request, job):
jobtitle = job_name(job)
service = 'tags'
servicename = 'subsets of samples'
tags = controls.run_script("", job, "tags")
if request.method == 'POST':
re_pattern = re.compile('[^\u0000-\uD7FF\uE000-\uFFFF]', re.UNICODE)
ntstr = re_pattern.sub(
'_', ''.join([urllib.parse.unquote_plus(request.POST['jstags'])]))
ntstr = "".join([
uc if uc < "\u00ff" else "_"
for uc in urllib.parse.unquote_plus(request.POST['jstags'])
])
print(ntstr)
newtags = controls.run_script("newtags=" + ntstr, job, "tags")
tags = newtags.replace("u'", "'")
ptags = json.loads(tags)
ptkeys = list(ptags.keys())
ptkeys.remove("name")
ptkeys.remove("none")
volumes = ptags['name']
template = loader.get_template('tags.html')
context = {
'job': job,
'title': jobtitle,
'service': service,
'servicename': servicename,
'tags': tags,
'ptkeys': ptkeys,
'volumes': json.dumps(volumes),
'pvolumes': volumes
}
return HttpResponse(template.render(context, request))
def summary(request, job):
summary = json.loads(controls.run_script("", job, "summary"))
tags = json.loads(controls.run_script("", job, "tags"))
jobtitle = summary['name']
template = loader.get_template('summary.html')
vollist = ", ".join(summary['volumes'])
result = '<br>'.join([
"maxlevel: " + str(summary['maxlevel']),
"taxonomy type: " + summary['taxtype'],
"num_volumes: " + str(summary['numvolumes']),
"num_records: " + str(summary['numrecords']), "volumes: " + vollist
])
context = {
'job': job,
'title': jobtitle,
'service': 'summary',
'servicename': 'summary of the dataset',
'result': result
}
return HttpResponse(template.render(context, request))
def generic_view(request, job, service, formclass, **kwargs):
jobtitle = job_name(job)
jscripts = kwargs.get('jscripts', [])
servicename = kwargs.get('servicename', service)
script = kwargs.get('script', service)
template = kwargs.get(
'template',
"default_service" if len(jscripts) == 0 else "default_chart")
outname = jobtitle + "_" + service
result = "select parameters and press <i>Submit</i><br>"
tags = controls.run_script("", job, "tags")
if request.method == 'POST':
form = formclass(request.POST,
request.FILES,
job_id=job,
tags_dict=tags)
if not service in ["indices", "summary", "anova"]:
outname += "_" + form.data['level']
if "command" in form.data and form.data["command"] != "Submit":
host = "http://secure.bri-shur.com:%s/static" % request.META[
'SERVER_PORT']
print(form.data["command"])
#host = "http://bri-shur.com/javascripts"
if form.data["command"] == "Download as PNG":
pngres = controls.render_png(format_params(form), job, script,
host, jscripts)
if len(pngres) > 0:
response = HttpResponse(pngres, content_type="image/png")
response[
'Content-Disposition'] = 'attachment; filename="%s.png"' % outname.replace(
"\n", "_")
return response
if form.data["command"] == "Download as SVG":
svgres = controls.render_svg(format_params(form), job, script,
host, jscripts)
if len(svgres) > 0:
response = HttpResponse(svgres,
content_type="image/svg+xml")
response[
'Content-Disposition'] = 'attachment; filename="%s.svg"' % outname.replace(
"\n", "_")
return response
print(script)
result = run_script(form, job, script)
else:
form = formclass(job_id=job, tags_dict=tags)
template = loader.get_template(template + '.html')
context = {
'job': job,
'title': jobtitle,
'service': service,
'servicename': servicename,
'result': result,
'form': form,
'outname': outname,
'jscripts': jscripts,
'tags': tags
}
if service == "venn" and request.method == 'POST' and form.data[
"ptype"] == "interactive-presence":
context['extracss'] = jvenn_css
context['extrascripts'] = jvenn_js
return HttpResponse(template.render(context, request))
def job_name(job):
summary = json.loads(controls.run_script("", job, "summary"))
return summary['name']
def run_script(form, job, script):
return controls.run_script(format_params(form), job, script)
def __init__(self, *args, **kwargs):
job_id = kwargs.pop('job_id')
tags = json.loads(kwargs.pop('tags_dict'))
super(GenericForm, self).__init__(*args, **kwargs)
summary = json.loads(controls.run_script("", job_id, "summary"))
#tags = json.loads( controls.run_script( "", job_id, "tags" ) )
taxfilters = json.loads(controls.run_script("", job_id, "taxonomy"))
cvolumes = [(v, v) for v in summary['volumes']]
levelnames = {
"qiime": [
"Kingdom", "Phylum", "Class", "Order", "Family", "Genus",
"Species", "OTU"
]
}
if summary["taxtype"] != "none":
clevels = [
(str(k),
levelnames[summary["taxtype"]][k - 1] + " (" + str(k) + ")")
for k in range(1, summary['maxlevel'] + 1)
]
else:
clevels = [(str(k), str(k))
for k in range(1, summary['maxlevel'] + 1)]
ctags = [(v, v) for v in list(tags.keys())]
ctaxfilters = [(v, v) for v in list(taxfilters.keys())]
distmeasures = [
"Pearson", "Kendall", "Spearman", "Euclidean", "Bray-Curtis",
"Jaccard", "Morisita-Horn", "Unifrac-unweighted",
"Unifrac-weighted"
]
cdmeasures = [(v, v) for v in distmeasures]
if 'level' in self.fields:
self.fields['level'].widget.choices += clevels
self.initial['level'] = [
clevels[min(summary['maxlevel'] - 1, 3)][0]
]
#self.fields[ 'level' ].widget.initial = [ clevels[ min( summary[ 'maxlevel' ], 3 ) ][1] ]
for fieldname in ['dorder', 'volume']:
if fieldname in self.fields:
self.fields[fieldname].widget.choices += cvolumes
for fieldname in ['dmethod']:
if fieldname in self.fields:
self.fields[fieldname].widget.choices += cdmeasures
for fieldname in [
'dfilter', 'color', 'shape', 'dgroup', 'order1', 'order2',
'labels', 'shisttag'
]:
if fieldname in self.fields:
self.fields[fieldname].widget.choices += ctags
if fieldname in ['labels']:
self.initial[fieldname] = ['name']
else:
self.initial[fieldname] = ['none']
for fieldname in ['spfilter', 'spshow']:
if fieldname in self.fields:
self.initial[fieldname] = ['none']
self.fields[fieldname].widget.choices += ctaxfilters
if 'samples' in self.fields:
ctag = 'name'
if len(args) > 0:
post = args[0]
if 'dgroup' in post:
ctag = post['dgroup']
if ctag == 'none':
ctag = 'name'
snames = set(tags[ctag])
print(snames)
self.fields['samples'].widget.choices = [(v, v) for v in snames]
self.initial['dgroup'] = ['name']