def main():
print "This line will be printed."
request = "35872"
pop = "ALL"
#reference = request.args.get('reference', False)
print 'pop: ' + pop
print 'request: ' + request
snplst = tmp_dir+'snps'+request+'.txt'
print 'snplst: '+snplst
file = "meta_assoc.meta"
region = "variant"
args = {}
args["origin"] = "rs1231"
print args
try:
out_json = calculate_hap(snplst,pop,request, false)
#out_json = calculate_assoc(file,region,pop,request,args)
except:
return sendTraceback()
#copy_output_files(reference)
return sendJSON(out_json)
def ldhap():
isProgrammatic = False
print 'Execute ldhap'
print 'working'
print 'Gathering Variables from url'
snps = request.args.get('snps', False)
pop = request.args.get('pop', False)
if request.args.get('reference', False):
reference = request.args.get('reference', False)
else:
reference = str(time.strftime("%I%M%S")) + ` random.randint(0, 10000) `
isProgrammatic = True
print 'snps: ' + snps
print 'pop: ' + pop
print 'request: ' + str(reference)
if reference is False:
reference = str(time.strftime("%I%M%S")) + ` random.randint(0, 10000) `
snplst = tmp_dir + 'snps' + reference + '.txt'
print 'snplst: ' + snplst
f = open(snplst, 'w')
f.write(snps)
f.close()
try:
out_json = calculate_hap(snplst, pop, reference)
if isProgrammatic:
resultFile = ""
resultFile1 = "./tmp/snps_" + reference + ".txt"
resultFile2 = "./tmp/haplotypes_" + reference + ".txt"
fp = open(resultFile1, "r")
content1 = fp.read()
fp.close()
fp = open(resultFile2, "r")
content2 = fp.read()
fp.close()
return content1 + "\n" + "#####################################################################################" + "\n\n" + content2
except:
return sendTraceback()
return sendJSON(out_json)
def ldhap():
print
print 'Execute ldhap'
print 'Gathering Variables from url'
snps = request.args.get('snps', False)
pop = request.args.get('pop', False)
reference = request.args.get('reference', False)
print 'snps: ' + snps
print 'pop: ' + pop
print 'request: ' + reference
snplst = tmp_dir+'snps'+reference+'.txt'
print 'snplst: '+snplst
f = open(snplst, 'w')
f.write(snps)
f.close()
out_json = calculate_hap(snplst,pop,reference)
copy_output_files(reference)
return out_json
def ldhap():
print 'Execute ldhap.'
# print 'Request User Agent: ', request.user_agent
# print 'Request User Agent Platform: ', request.user_agent.platform
# print 'Request User Agent Browser: ', request.user_agent.browser
snps = request.args.get('snps', False)
pop = request.args.get('pop', False)
token = request.args.get('token', False)
print 'snps: ' + snps
print 'pop: ' + pop
web = False
# differentiate web or api request
if 'LDlinkRestWeb' in request.path:
# WEB REQUEST
if request.user_agent.browser is not None:
web = True
reference = request.args.get('reference', False)
print 'request: ' + str(reference)
snplst = tmp_dir + 'snps' + reference + '.txt'
with open(snplst, 'w') as f:
f.write(snps.lower())
try:
out_json = calculate_hap(snplst, pop, reference, web)
except:
return sendTraceback(None)
else:
return sendJSON(
"This web API route does not support programmatic access. Please use the API routes specified on the API Access web page."
)
else:
# API REQUEST
web = False
reference = str(time.strftime("%I%M%S")) + ` random.randint(0, 10000) `
print 'request: ' + str(reference)
snplst = tmp_dir + 'snps' + reference + '.txt'
with open(snplst, 'w') as f:
f.write(snps.lower())
try:
# lock token preventing concurrent requests
toggleLocked(token, 1)
out_json = calculate_hap(snplst, pop, reference, web)
# display api out
try:
# unlock token then display api output
resultFile1 = "./tmp/snps_" + reference + ".txt"
resultFile2 = "./tmp/haplotypes_" + reference + ".txt"
with open(resultFile1, "r") as fp:
content1 = fp.read()
with open(resultFile2, "r") as fp:
content2 = fp.read()
toggleLocked(token, 0)
return content1 + "\n" + "#####################################################################################" + "\n\n" + content2
except:
# unlock token then display error message
output = json.loads(out_json)
toggleLocked(token, 0)
return sendTraceback(output["error"])
except:
# unlock token if internal error w/ calculation
toggleLocked(token, 0)
return sendTraceback(None)
return sendJSON(out_json)