def run_for_file(filein, location, solver, restrict):
data_in = read_file(os.path.join(location, filein))
output_folder = get_output_folder(filein, "output_files", restrict)
t_start = datetime.datetime.utcnow()
if solver in solvers_7rules:
output_file = os.path.join(output_folder, prettyprint_solver(solver) + '.txt')
file_handler = write_file_header(output_file, False)
for (mass, tolerance) in data_in:
t1 = datetime.datetime.utcnow()
formulas = solver.search(mass, tolerance, delta, restrict)
t2 = datetime.datetime.utcnow()
write_file_formulas(file_handler, formulas, mass, tolerance, t2 - t1)
file_handler.close()
elif solver in solvers_basic:
output_file = os.path.join(output_folder, prettyprint_solver(solver) + '.txt')
output_file_filtered = os.path.join(output_folder, prettyprint_solver(solver) + '_post_7rules.txt')
file_handler = write_file_header(output_file, False)
file_handler_filtered = write_file_header(output_file_filtered, True)
for (mass, tolerance) in data_in:
t1 = datetime.datetime.utcnow()
formulas = solver.search(mass, tolerance, delta, restrict)
t2 = datetime.datetime.utcnow()
formulas_filtered = the_7rules.filter_all(formulas, restrict)
t3 = datetime.datetime.utcnow()
write_file_formulas(file_handler, formulas, mass, tolerance, t2 - t1)
write_file_formulas(file_handler_filtered, formulas_filtered, mass, tolerance, t3 - t1)
file_handler.close()
file_handler_filtered.close()
t_end = datetime.datetime.utcnow()
print prettyprint_solver(solver) + " processed " + filein + " in " + str(t_end - t_start)
def run_locally():
"""
Run from console
Enter manually: 1 mass and 1 tolerance (in ppm)
:return: print formulas
"""
# message for run_locally
incorrect_input = "\n The input was not correctly formatted \n restarting..."
try:
# display algorithms
i = 1
for solver in solvers_basic:
print str(i) + " " + prettyprint_solver(solver)
i += 1
for solver in solvers_7rules:
print str(i) + " " + prettyprint_solver(solver)
i += 1
print
# get input from user
algorithm = int(input("Enter number for your choice: "))
mass = float(input("Enter a mass: "))
tolerance = float(input("Enter a tolerance (in ppm): ")) / 1000000
if algorithm <= len(solvers_basic):
function = solvers_basic[algorithm - 1]
else:
function = solvers_7rules[algorithm - len(solvers_basic) - 1]
print
print "Would you like to restrict the search to CHNOPS? (recommended)"
choice = raw_input("Enter y/n: ")
restrict = False
if choice == 'y':
restrict = True
print
# perform search using input
t1 = datetime.datetime.utcnow()
formulas = function.search(mass, tolerance, delta, restrict)
t2 = datetime.datetime.utcnow()
for formula in formulas:
print get_formula_string(formula)
if len(formulas) == 0:
print "No results"
print "Search time: " + str(t2 - t1)
print
# get input for filtering and proceed as required
print "Would you like to filter these? "
choice = raw_input("Enter y/n: ")
if choice == 'y':
t1 = datetime.datetime.utcnow()
formulas_filtered = the_7rules.filter_all(formulas, restrict)
for formula in formulas_filtered:
print get_formula_string(formula)
if len(formulas_filtered) == 0:
print "No results"
t2 = datetime.datetime.utcnow()
print "Filter time: " + str(t2 - t1)
print
# ask if to terminate
print "This iteration is done, would you like to go again? "
choice = raw_input("Enter y/n: ")
if choice == 'y':
run_locally()
except SyntaxError as se:
print incorrect_input
run_locally()
except NameError as ne:
print incorrect_input
run_locally()
except IndexError as ie:
print incorrect_input
run_locally()
