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#! /usr/bin/env python
import re
bool_feat_re = re.compile(r"^([a-z]+)(True|False)$")
int_feat_re = re.compile(r"^([a-z]+)([0-9]+)$")
real_feat_re = re.compile(r"^([a-z]+)([0-9]+\.?[0-9]*)$")
str_feat_re = re.compile(r"^([a-z]+)([A-Z][A-Za-z_0-9]+)$")
def parse_dir_feature(feat, number):
bool_match = bool_feat_re.match(feat)
if bool_match is not None:
return (bool_match.group(1), "integer", int(bool_match.group(2) == "True"))
int_match = int_feat_re.match(feat)
if int_match is not None:
return (int_match.group(1), "integer", float(int_match.group(2)))
real_match = real_feat_re.match(feat)
if real_match is not None:
return (real_match.group(1), "real", float(real_match.group(2)))
str_match = str_feat_re.match(feat)
if str_match is not None:
return (str_match.group(1), "text", str_match.group(2))
return ("dirfeat%d" % number, "text", feat)
def larger_sql_type(type_a, type_b):
assert type_a in [None, "text", "real", "integer"]
assert type_b in [None, "text", "real", "integer"]
if type_a is None:
return type_b
if type_b is None:
return type_a
if "text" in [type_a, type_b]:
return "text"
if "real" in [type_a, type_b]:
return "real"
assert type_a == type_b == "integer"
return "integer"
def sql_type_and_value(value):
if value is None:
return None, None
elif isinstance(value, bool):
return "integer", int(value)
elif isinstance(value, int):
return "integer", value
elif isinstance(value, float):
return "real", value
else:
return "text", str(value)
def sql_type_and_value_from_str(value):
if value == "None":
return None, None
elif value in ["True", "False"]:
return "integer", value == "True"
else:
try:
return "integer", int(value)
except ValueError:
pass
try:
return "real", float(value)
except ValueError:
pass
return "text", str(value)
class FeatureGatherer:
def __init__(self, features_from_dir=False, features_file=None):
self.features_from_dir = features_from_dir
self.dir_to_features = {}
if features_file is not None:
for line in open(features_file, "r").readlines():
colon_idx = line.find(":")
assert colon_idx != -1
entries = [val.strip() for val in line[colon_idx+1:].split(",")]
features = []
for entry in entries:
equal_idx = entry.find("=")
assert equal_idx != -1
features.append((entry[:equal_idx],) +
sql_type_and_value_from_str(entry[equal_idx+1:]))
self.dir_to_features[line[:colon_idx]] = features
def get_db_features(self, dbname, logmgr):
from os.path import dirname
dn = dirname(dbname)
features = self.dir_to_features.get(dn, [])[:]
if self.features_from_dir:
features.extend(parse_dir_feature(feat, i)
for i, feat in enumerate(dn.split("-")))
for name, value in logmgr.constants.iteritems():
features.append((name,) + sql_type_and_value(value))
return features
def scan(fg, dbnames, progress=True):
features = {}
dbname_to_run_id = {}
uid_to_run_id = {}
next_run_id = 1
from pytools import ProgressBar
if progress:
pb = ProgressBar("Scanning...", len(dbnames))
for dbname in dbnames:
from pytools.log import LogManager
try:
logmgr = LogManager(dbname, "r")
except:
print "Trouble with file '%s'" % dbname
raise
unique_run_id = logmgr.constants.get("unique_run_id")
run_id = uid_to_run_id.get(unique_run_id)
if run_id is None:
run_id = next_run_id
next_run_id += 1
if unique_run_id is not None:
uid_to_run_id[unique_run_id] = run_id
dbname_to_run_id[dbname] = run_id
if progress:
pb.progress()
for fname, ftype, fvalue in fg.get_db_features(dbname, logmgr):
if fname in features:
features[fname] = larger_sql_type(ftype, features[fname])
else:
if ftype is None:
ftype = "text"
features[fname] = ftype
logmgr.close()
if progress:
pb.finished()
return features, dbname_to_run_id
def make_name_map(map_str):
import re
result = {}
if not map_str:
return result
map_re = re.compile(r"^([a-z_A-Z0-9]+)=([a-z_A-Z0-9]+)$")
for fmap_entry in map_str.split(","):
match = map_re.match(fmap_entry)
assert match is not None
result[match.group(1)] = match.group(2)
return result
def transfer_data_table(db_conn, tbl_name, data_table):
db_conn.executemany("insert into %s (%s) values (%s)" %
(tbl_name,
", ".join(data_table.column_names),
", ".join("?" * len(data_table.column_names))),
data_table.data)
def gather_single_file(outfile, infiles):
from pytools import ProgressBar
pb = ProgressBar("Importing...", len(infiles))
import sqlite3
db_conn = sqlite3.connect(outfile)
from pytools.log import _set_up_schema
_set_up_schema(db_conn)
from pickle import dumps
seen_constants = set()
seen_quantities = set()
for dbname in infiles:
pb.progress()
from pytools.log import LogManager
logmgr = LogManager(dbname, "r")
# transfer warnings
transfer_data_table(db_conn, "warnings", logmgr.get_warnings())
# transfer constants
for key, val in logmgr.constants.iteritems():
if key not in seen_constants:
db_conn.execute("insert into constants values (?,?)",
(key, buffer(dumps(val))))
seen_constants.add(key)
for qname, qdata in logmgr.quantity_data.iteritems():
db_conn.execute("""insert into quantities values (?,?,?,?)""", (
qname, qdata.unit, qdata.description,
buffer(dumps(qdata.default_aggregator))))
if qname not in seen_quantities:
db_conn.execute("""create table %s
(step integer, rank integer, value real)""" % qname)
seen_quantities.add(qname)
transfer_data_table(db_conn, qname, logmgr.get_table(qname))
logmgr.close()
pb.finished()
db_conn.commit()
db_conn.close()
def gather_multi_file(outfile, infiles, fmap, qmap, fg, features,
dbname_to_run_id):
from pytools import ProgressBar
pb = ProgressBar("Importing...", len(infiles))
import sqlite3
db_conn = sqlite3.connect(outfile)
run_columns = [
"id integer primary key",
"dirname text",
"filename text",
] + ["%s %s" % (fmap.get(fname, fname), ftype)
for fname, ftype in features.iteritems()]
db_conn.execute("create table runs (%s)" % ",".join(run_columns))
db_conn.execute("create index runs_id on runs (id)")
db_conn.execute("""create table quantities (
id integer primary key,
name text,
unit text,
description text,
rank_aggregator text
)""")
created_tables = set()
from os.path import dirname, basename
uid_to_run_id = {}
written_run_ids = set()
for dbname in infiles:
pb.progress()
run_id = dbname_to_run_id[dbname]
from pytools.log import LogManager
logmgr = LogManager(dbname, "r")
if run_id not in written_run_ids:
dbfeatures = fg.get_db_features(dbname, logmgr)
qry = "insert into runs (%s) values (%s)" % (
",".join(["id", "dirname", "filename"]
+ [fmap.get(f[0], f[0]) for f in dbfeatures]),
",".join("?" * (len(dbfeatures)+3)))
rows = db_conn.execute(qry,
[run_id, dirname(dbname), basename(dbname)]
+ [f[2] for f in dbfeatures])
written_run_ids.add(run_id)
for qname, qdat in logmgr.quantity_data.iteritems():
tgt_qname = qmap.get(qname, qname)
if not tgt_qname in created_tables:
created_tables.add(tgt_qname)
db_conn.execute("create table %s ("
"run_id integer, step integer, rank integer, value real)" % tgt_qname)
db_conn.execute("create index %s_main on %s (run_id,step,rank)" % (
tgt_qname, tgt_qname))
agg = qdat.default_aggregator
try:
agg = agg.__name__
except AttributeError:
if agg is not None:
agg = str(agg)
db_conn.execute("insert into quantities "
"(name,unit,description,rank_aggregator)"
"values (?,?,?,?)",
(tgt_qname, qdat.unit, qdat.description, agg))
cursor = logmgr.db_conn.execute("select %s,step,rank,value from %s" % (
run_id, qname))
db_conn.executemany("insert into %s values (?,?,?,?)" % tgt_qname,
cursor)
logmgr.close()
pb.finished()
db_conn.commit()
db_conn.close()
def main():
import sys
from optparse import OptionParser
parser = OptionParser(usage="%prog OUTDB DBFILES ...")
parser.add_option("-1", "--single", action="store_true",
help="Gather single-run instead of multi-run file")
parser.add_option("-s", "--show-features", action="store_true",
help="Only print the features found and quit")
parser.add_option("-d", "--dir-features", action="store_true",
help="Extract features from directory names")
parser.add_option("-f", "--file-features", default=None,
metavar="FILENAME",
help="Read additional features from file, with lines like: "
"'dirname: key=value, key=value'")
parser.add_option("-m", "--feature-map", default=None,
help="Specify a feature name map.",
metavar="F1=FNAME1,F2=FNAME2")
parser.add_option("-q", "--quantity-map", default=None,
help="Specify a quantity name map.",
metavar="Q1=QNAME1,Q2=QNAME2")
options, args = parser.parse_args()
if len(args) < 2:
parser.print_help()
sys.exit(1)
outfile = args[0]
from os.path import exists
infiles = [fn for fn in args[1:] if exists(fn)]
not_found_files = [fn for fn in args[1:] if not exists(fn)]
if not_found_files:
print "Warning: The follwing files were not found and are being ignored:"
for fn in not_found_files:
print " ", fn
# list of run features as {name: sql_type}
fg = FeatureGatherer(options.dir_features, options.file_features)
features, dbname_to_run_id = scan(fg, infiles)
fmap = make_name_map(options.feature_map)
qmap = make_name_map(options.quantity_map)
if options.show_features:
for feat_name, feat_type in features.iteritems():
print fmap.get(feat_name, feat_name), feat_type
sys.exit(0)
if options.single:
if len(set(dbname_to_run_id.values())) > 1:
raise ValueError(
"data seems to come from more than one run--"
"can't write single-run file")
gather_single_file(outfile, infiles)
else:
gather_multi_file(outfile, infiles, fmap, qmap, fg, features,
dbname_to_run_id)
if __name__ == "__main__":
main()
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