def tbimport():
t = db.study
key = "uploaded_nexml_%s" % auth.user.id
contributor = "%s %s" % (auth.user.first_name, auth.user.last_name)
status = None
tbid = request.args(0)
if tbid:
try:
e = treebase.fetch_study(tbid)
nexml = treebase.parse_nexml(e)
except:
nexml = {}
status = "Valid study id required"
if nexml:
nexml.meta['contributor'] = contributor
cache.ram.clear(key)
x = cache.ram(key, lambda: nexml, time_expire=10000)
redirect(URL('study', 'tbimport2', args=tbid))
uploadfolder = request.folder + 'uploads'
fields = [
Field("study_id", "string", default=tbid),
Field("nexml_file", "upload", uploadfolder=uploadfolder)
]
form = SQLFORM.factory(*fields)
if form.accepts(request.vars, session, dbio=False):
if form.vars.study_id:
try:
e = treebase.fetch_study(form.vars.study_id)
nexml = treebase.parse_nexml(e)
except:
nexml = {}
status = "Valid study id required"
elif form.vars.nexml_file:
## print form.vars.nexml_file
path = os.path.join(uploadfolder, form.vars.nexml_file)
## form.vars.nexml_file_newfilename)
nexml = treebase.parse_nexml(path)
os.remove(path)
else:
nexml = {}
request.flash = "Valid study id or nexml file required"
if nexml:
nexml.meta['contributor'] = contributor
cache.ram.clear(key)
x = cache.ram(key, lambda: nexml, time_expire=10000)
redirect(URL('study', 'tbimport2', args=tbid))
return dict(form=form, status=status)
def tbimport():
t = db.study
key = "uploaded_nexml_%s" % auth.user.id
contributor = "%s %s" % (auth.user.first_name, auth.user.last_name)
status = None
tbid = request.args(0)
if tbid:
try:
e = treebase.fetch_study(tbid)
nexml = treebase.parse_nexml(e)
except:
nexml = { }
status = "Valid study id required"
if nexml:
nexml.meta['contributor'] = contributor
cache.ram.clear(key)
x = cache.ram(key, lambda:nexml, time_expire=10000)
redirect(URL('study','tbimport2',args=tbid))
uploadfolder = request.folder+'uploads'
fields = [Field("study_id", "string", default=tbid),
Field("nexml_file", "upload", uploadfolder=uploadfolder)]
form = SQLFORM.factory(*fields)
if form.accepts(request.vars, session, dbio=False):
if form.vars.study_id:
try:
e = treebase.fetch_study(form.vars.study_id)
nexml = treebase.parse_nexml(e)
except:
nexml = { }
status = "Valid study id required"
elif form.vars.nexml_file:
## print form.vars.nexml_file
path = os.path.join(uploadfolder,
form.vars.nexml_file)
## form.vars.nexml_file_newfilename)
nexml = treebase.parse_nexml(path)
os.remove(path)
else:
nexml = {}
request.flash = "Valid study id or nexml file required"
if nexml:
nexml.meta['contributor'] = contributor
cache.ram.clear(key)
x = cache.ram(key, lambda:nexml, time_expire=10000)
redirect(URL('study','tbimport2',args=tbid))
return dict(form=form, status=status )
def fetch_treebase_nexml():
sid = request.args(0)
e = treebase.fetch_study(sid)
response.headers["Content-Type"] = "text/xml"
s = "attachment; filename=TB-study-%s.nexml" % sid
response.headers["Content-Disposition"] = s
buf = StringIO()
e.write(buf, pretty_print=True)
return buf.getvalue()
def fetch_treebase_nexml():
sid = request.args(0)
e = treebase.fetch_study(sid)
response.headers["Content-Type"] = "text/xml"
s = "attachment; filename=TB-study-%s.nexml" % sid
response.headers["Content-Disposition"] = s
buf = StringIO()
e.write(buf, pretty_print=True)
return buf.getvalue()