def main(argv=None):
"""The main() function processes the command-line arguments and then
converts the simulation results."""
if argv is None:
argv = sys.argv
try:
try:
o_short = "o:t:h"
o_long = ["output=", "time=", "help"]
opts, args = getopt.getopt(argv[1:], o_short, o_long)
except getopt.error, msg:
raise Usage(msg)
# The default output file.
out_file = 'results.csv'
# Which snapshot to record.
nth_time = 4
for o, a in opts:
if o in ("-h", "--help"):
print __doc__
return 2
elif o in ("-o", "--output"):
out_file = a
elif o in ("-t", "--time"):
nth_time = int(a) - 1
if len(args) != 1 or nth_time < 0 or nth_time > 4:
print __doc__
return 2
p_interest = par_list().index('VV9') + 1
v_interest = var_list().index('GFR') + 1
p_name = lambda n: "p_" + n
v_name = lambda n: "v_" + n
p_names = map(p_name, par_list()[0:p_interest])
v_names = map(v_name, var_list()[0:v_interest])
with open(out_file, 'wb') as output:
writer = csv.writer(output, delimiter=',')
writer.writerow(p_names + v_names)
settings = (writer, p_interest, v_interest, nth_time)
with open(args[0]) as results:
count = parse(results, convert, settings, warn=True)
print count, "simulations were converted."
def get_metrics(dirname):
package_file = open('pypi_list.txt')
exec(package_file) #package_list is name of the master list of public python modules
std_package_file = open('std_packages.txt')
exec(std_package_file) #std_package_list
babies = crawl_dir(dirname)
filenames = []
excluded=[]
all_imports = {}
for (root,f) in babies:
print f,"hihi"
file_imports = ip.parse(root+"/"+f)
filenames.append(f[:-3])
for m in file_imports.keys():
if m in package_list or m in std_package_list:
if m in all_imports:
all_imports[m] += file_imports[m]
else:
all_imports[m] = file_imports[m]
else:
excluded.append(m)
return all_imports
def connect_and_import(results_file, tags, host=None, user=None, password=None,
log_per=500):
"""Records the simulation results stored in results_file."""
# Extract the database name from psql_conf.sh (this bit isn't pretty)
p = subprocess.Popen(
"grep '^DBNAME=' psql_conf.sh | sed 's/DBNAME/dbname/'",
shell=True, stdout=subprocess.PIPE)
conn_strs = map(lambda s: s.strip(), p.stdout.readlines())
if host is not None:
conn_strs.append("host='%s'" % (host,))
if user is not None:
conn_strs.append("user='******'" % (user,))
if password is not None:
conn_strs.append("password='******'" % (password,))
conn_string = " ".join(conn_strs)
try:
conn = psycopg2.connect(conn_string)
# The default isolation level is READ_COMMITTED, which is perfect
cursor = conn.cursor()
# TODO -- allow the model to be specified on the command line
model_ID = 1
# Retrieve parameter IDs
param_IDs = {}
cursor.execute("SELECT parameter.name, parameter.id "
"FROM parameter INNER JOIN defined_for "
"ON (defined_for.model = %s)", (model_ID,))
for (p_name, p_id) in cursor:
param_IDs[p_name] = p_id
# Retrieve variable IDs
var_IDs = {}
cursor.execute("SELECT name, id FROM variable")
for (v_name, v_id) in cursor:
var_IDs[v_name] = v_id
# Retrieve tag IDs, creating tags where necessary
tag_IDs = {}
if 'Perturbation' not in tags:
tags.append('Perturbation')
for tag_name in tags:
cursor.execute("SELECT id FROM tag WHERE name = %s", (tag_name,))
result = cursor.fetchone()
if result is None or len(result) < 1:
print >> sys.stderr, ("Creating tag '%s'" % (tag_name,))
cursor.execute("INSERT INTO tag (name, description) "
"VALUES (%s, %s) RETURNING id", (tag_name, ''))
tag_id = cursor.fetchone()[0]
else:
tag_id = result[0]
tag_IDs[tag_name] = tag_id
info = (cursor, conn, model_ID, param_IDs, var_IDs, tag_IDs, log_per)
with open(results_file) as results:
count = parse(results, import_result, info, warn=True)
print count, "simulations were imported."
conn.commit()
except:
exceptionType, exceptionValue, exceptionTraceback = sys.exc_info()
sys.exit("%s" % (exceptionValue))
finally:
if locals().has_key('conn'):
conn.close()