def run_rscript(request):
user = request.user
datapath = "media/server/%s/" % user
if os.path.exists(datapath + "study.txt") == False:
return render(request, 'server/error.html', {'message': "No study"})
f = open(datapath + "study.txt", 'r')
study = f.read()
f.close()
datapath += study
target = ""
try:
with open(datapath + "/target.csv", newline='') as csvfile:
spamreader = csv.reader(csvfile, delimiter=';', quotechar='|')
for row in spamreader:
target = row
break
except:
return render(request, 'server/error.html', {'message': "No target"})
message = "Results of user %s on " % user
message += "Date: " + datetime.datetime.now().strftime("%y-%m-%d %H:%M")
message += ", Target: " + target[0]
message += ", Study: " + study
message += '\n'
if os.path.exists(datapath + "/data.csv") == False:
return render(request, 'server/error.html',
{'message': "No data file"})
r = R(use_numpy=True)
r("datadir2<-\"" + datapath +
"\"; source('server/r_files/globaltest-przyklad-kodnaserwer.r')")
del (r)
filename = "static/server/%s_message.txt" % user
f = open(filename, "w")
f.write(message)
f.close()
filename = "static/server/%s_testowy.pdf" % user
if os.path.exists(filename) == True:
os.remove(filename)
while os.path.exists("static/server/testowy.pdf") == False:
continue
os.rename("static/server/testowy.pdf", filename)
filename = "media/server/{0}/{1}/{0}_out.txt".format(user, study)
if os.path.exists(filename) == True:
os.remove(filename)
while os.path.exists("static/server/out.txt") == False:
continue
os.rename("static/server/out.txt", filename)
#os.system("Rscript server/r_files/globaltest-przyklad-kodnaserwer.r")
return render(request, 'server/results.html', {'study': study})
def __init__(self, dataFileName, alpha=1.0, numtopics=5, eta=0.1, logistic=True, lamda=1.0, e_iter=10, m_iter=4, variance=0.25):
model_filename = "%s/model_%s.RDS" % (os.getcwd(), dataFileName)
topic_filename = "%s/topics_%s.RDS" % (os.getcwd(), dataFileName)
vocab_filename = "%s/vocabulary_%s.RDS" % (os.getcwd(), dataFileName)
self.params = {
"numtopics": numtopics,
"alpha": alpha,
"eta": eta,
"logistic": logistic,
"lambda": lamda,
"e_iter": e_iter,
"m_iter": m_iter,
"variance": variance
"dataFiles": dataFileName,
"model_filename": model_filename,
"topic_filename": topic_filename,
"vocab_filename": vocab_filename
}
self.r = R(use_pandas=True, use_numpy=True)
self.assign_R_params()
def __init__(self, dataFileName, alpha=1.0, numtopics=5, eta=0.1, logistic=True, lamda=1.0, e_iter=10, m_iter=4, variance=0.25, cutoff=0.25):
model_filename = 'model_%s.RDS' % dataFileName
vocab_filename = 'vocabulary_%s.RDS' % dataFileName
fullpath = os.path.realpath(__file__)
(path, files) = os.path.split(fullpath)
self.path = path
self.params = {
'numtopics': numtopics,
'alpha': alpha,
'eta': eta,
'logistic': logistic,
'lambda': lamda,
'e_iter': e_iter,
'm_iter': m_iter,
'variance': variance,
'OutputName': dataFileName,
'model_filename': model_filename,
'vocab_filename': vocab_filename,
'test_cutoff': cutoff,
}
self.r = R(use_pandas=True, use_numpy=True)
self.assign_R_params()
def read_comets_input():
try:
input_file = request.files['inputFile']
original_filename = input_file.filename
filename = save_input_file(input_file)
filepath = os.path.join('tmp', filename)
app.logger.info("Successfully Uploaded: %s", filename)
r = R()
r.filename = filepath
r.cohort = request.form['cohortSelection']
r(''' source("./cometsWrapper.R")
output_file = checkIntegrity(filename, cohort) ''')
with open(r.output_file) as f:
result = json.load(f)
os.remove(r.output_file)
os.remove(filepath)
del r
app.logger.info("Finished integrity check for: %s", filename)
if ('error' in result):
return buildFailure(result['error'])
else:
result = result['saveValue']
result['filename'] = filename
result['originalFilename'] = original_filename
return buildSuccess(result)
except Exception as e:
app.logger.error(traceback.format_exc())
return buildFailure({
"status": False,
"integritymessage": "An unknown error occurred"
})
def r_connection_initialized(initialization_string):
r = R(RCMD=R_PATH)
r(initialization_string)
yield r
r.prog.terminate()
def r_connection():
r = R(RCMD=R_PATH)
yield r
r.prog.terminate()
### R_test.py
#!/usr/bin/env python
import os, sys, string, inspect
currentdir = os.path.dirname(
os.path.abspath(inspect.getfile(inspect.currentframe())))
parentdir = os.path.dirname(currentdir)
parentdir = os.path.dirname(parentdir)
sys.path.insert(0, parentdir)
from pyper import R
import unique
if 'darwin' in sys.platform:
try:
path = unique.filepath("AltDatabase/tools/R/Mac/R")
r = R(RCMD=path, use_numpy=True)
#print '1'
except Exception:
#print '2'
r = R(use_numpy=True)
elif os.name == 'nt':
try:
path = unique.filepath("AltDatabase/tools/R/PC/bin/x64/R.exe")
r = R(RCMD=path, use_numpy=True)
except Exception:
r = R(use_numpy=True)
else:
#print '3'
r = R(use_numpy=True)
print_out = r('library("Biobase")')
from pyper import R
from pysmac.optimize import fmin
import sys
args = sys.argv[1]
r = R()
r('r_args_list <- eval(parse(text="%s"))' % args.replace('[CRLF]', '\n'))
r('eval(r_args_list$init_rcode)')
r('r_objective <- r_args_list$objective')
r('grid <- r_args_list$grid')
# kwargs examples
# {'x': array([ 5.22359753, 0.526101 ])}
# {'x': array([ 0.5]), 'x_int': array([4])}
def fill_objective_args(args_map):
r('objective_args <- list()')
pyr_type_map = {'x': 'continuous', 'x_int': 'discrete'}
for key in args_map:
assert key in pyr_type_map.keys()
r.cur_r_type = pyr_type_map[key]
r('cur_names <- names(Filter(function(x) x$type == cur_r_type, grid))')
r.cur_values = args_map[key]
r('cur_values <- as.list(cur_values)')
r('names(cur_values) <- cur_names')
r('objective_args <- append(objective_args, cur_values)')
def py_wrap_objective(**kwargs):
fill_objective_args(kwargs)
return r['do.call(r_objective, args=objective_args)']
def correlate():
try:
if not os.path.exists(app.tmp):
os.makedirs(app.tmp)
parameters = dict(request.form)
print(parameters)
for field in parameters:
parameters[field] = parameters[field][0].decode()
if ('outcome' in parameters):
parameters['outcome'] = json.loads(parameters['outcome'])
if (len(parameters['outcome']) == 0):
parameters['outcome'] = None
if ('exposure' in parameters):
parameters['exposure'] = json.loads(parameters['exposure'])
if (len(parameters['exposure']) == 0):
parameters['exposure'] = None
if ('covariates' in parameters):
parameters['covariates'] = json.loads(parameters['covariates'])
if (len(parameters['covariates']) == 0):
parameters['covariates'] = None
if ('strata' in parameters):
if (len(parameters['strata']) == 0):
parameters['strata'] = None
else:
parameters['strata'] = [parameters['strata']]
if ('whereQuery' in parameters):
parameters['whereQuery'] = json.loads(parameters['whereQuery'])
if (len(parameters['whereQuery']) == 0):
parameters['whereQuery'] = None
if (parameters['methodSelection'] == "All"):
filename = save_input_file(request.files['inputFile'])
filepath = os.path.join('tmp', filename)
parameters['filename'] = filename
parameters['filepath'] = filepath
queueFile(parameters)
os.remove(filepath)
app.logger.info("Queued file %s", filepath)
return buildFailure({
'status':
'info',
'statusMessage':
"The results will be emailed to you."
})
else:
r = R()
r('source("./cometsWrapper.R")')
r.parameters = json.dumps(parameters)
r('output_file = runModel(parameters)')
with open(r.output_file) as f:
result = json.load(f)
os.remove(r.output_file)
del r
if ("error" in result):
return buildFailure(result['error'])
else:
if ('warnings' in result):
result['saveValue']['warnings'] = result['warnings']
return buildSuccess(result['saveValue'])
app.logger.info("Finished running model")
except Exception:
app.logger.error(traceback.format_exc())
return buildFailure({
"status": False,
"statusMessage": "An unknown error has occurred."
})