def row_iter(rows, reader):
for row in rows:
yield quoteRow(row,
take,
map_column2type,
options.missing_values,
null=options.null,
string_value=options.string_value)
for data in reader:
yield quoteRow(IOTools.convertDictionary(data, map=options.map),
take,
map_column2type,
options.missing_values,
null=options.null,
string_value=options.string_value)
def main(argv=None):
"""script main.
parses command line options in sys.argv, unless *argv* is given.
"""
if argv is None:
argv = sys.argv
parser = E.OptionParser(
version="%prog version: $Id$")
parser.add_option(
"-s", "--method=sort --sort-order", dest="sort", type="string",
help="fields to take (in sorted order).")
(options, args) = E.start(parser, add_csv_options=True)
reader = csv.DictReader(E.stdin, dialect=options.csv_dialect)
if options.sort:
fields = options.sort.split(",")
else:
fields = None
writer = csv.DictWriter(E.stdout,
fields,
dialect=options.csv_dialect,
lineterminator=options.csv_lineterminator,
extrasaction='ignore')
E.stdout.write("\t".join(fields) + "\n")
for row in reader:
row = IOTools.convertDictionary(row)
writer.writerow(row)
E.stop()
def run(infile, options, report_step=10000):
options.tablename = quoteTableName(options.tablename,
backend=options.backend)
if options.map:
m = {}
for x in options.map:
f, t = x.split(":")
m[f] = t
options.map = m
else:
options.map = {}
existing_tables = set()
quick_import_separator = "\t"
if options.database_backend == "postgres":
import psycopg2
raise NotImplementedError("needs refactoring for commandline options")
dbhandle = psycopg2.connect(options.psql_connection)
error = psycopg2.Error
options.null = "NULL"
options.string_value = "'%s'"
options.text = "TEXT"
options.index = "TEXT"
if options.insert_quick:
raise ValueError("quick import not implemented.")
elif options.database_backend == "mysql":
import MySQLdb
dbhandle = MySQLdb.connect(host=options.database_host,
user=options.database_username,
passwd=options.database_password,
port=options.database_port,
db=options.database_name)
error = Exception
options.null = "NULL"
options.string_value = "%s"
options.text = "TEXT"
options.index = "VARCHAR(40)"
if options.insert_quick:
raise ValueError("quick import not implemented.")
elif options.backend == "sqlite":
import sqlite3
dbhandle = sqlite3.connect(options.database_name)
try:
os.chmod(options.database_name, 0o664)
except OSError as msg:
E.warn("could not change permissions of database: %s" % msg)
# Avoid the following error:
# sqlite3.ProgrammingError: You must not use 8-bit bytestrings
# unless you use a text_factory that can interpret 8-bit
# bytestrings (like text_factory = str). It is highly
# recommended that you instead just switch your application
# to Unicode strings
# Note: might be better to make csv2db unicode aware.
dbhandle.text_factory = str
error = sqlite3.OperationalError
options.insert_many = True # False
options.null = None # "NULL"
options.text = "TEXT"
options.index = "TEXT"
options.string_value = "%s" # "'%s'"
statement = "SELECT name FROM sqlite_master WHERE type='table'"
cc = executewait(dbhandle, statement, error, options.retry)
existing_tables = set([x[0] for x in cc])
cc.close()
# use , as separator
quick_import_statement = \
"sqlite3 %s '.import %%s %s'" % \
(options.database_name, options.tablename)
quick_import_separator = "|"
if options.header is not None:
options.header = [x.strip() for x in options.header.split(",")]
if options.utf:
reader = CSV.UnicodeDictReader(infile,
dialect=options.dialect,
fieldnames=options.header)
else:
reader = csv.DictReader(CSV.CommentStripper(infile),
dialect=options.dialect,
fieldnames=options.header)
if options.replace_header:
try:
next(reader)
except StopIteration:
pass
E.info("reading %i columns to guess column types" % options.guess_size)
rows = []
for row in reader:
if None in row:
raise ValueError("undefined columns in input file at row: %s" %
row)
try:
rows.append(IOTools.convertDictionary(row, map=options.map))
except TypeError as msg:
E.warn("incomplete line? Type error in conversion: "
"'%s' with data: %s" % (msg, str(row)))
except ValueError as msg:
E.warn("incomplete line? Type error in conversion: "
"'%s' with data: %s" % (msg, str(row)))
if len(rows) >= options.guess_size:
break
E.info("read %i rows for type guessing" % len(rows))
E.info("creating table")
if len(rows) == 0:
if options.allow_empty:
if not reader.fieldnames:
E.warn("no data - no table created")
else:
# create empty table and exit
take, map_column2type, ignored = createTable(
dbhandle,
error,
options.tablename,
options,
retry=options.retry,
headers=reader.fieldnames,
ignore_empty=options.ignore_empty,
ignore_columns=options.ignore_columns,
rename_columns=options.rename_columns,
lowercase=options.lowercase,
ignore_duplicates=options.ignore_duplicates,
indices=options.indices,
first_column=options.first_column,
existing_tables=existing_tables,
append=options.append)
E.info("empty table created")
return
else:
raise ValueError("empty table")
else:
take, map_column2type, ignored = createTable(
dbhandle,
error,
options.tablename,
options,
rows=rows,
retry=options.retry,
headers=reader.fieldnames,
ignore_empty=options.ignore_empty,
ignore_columns=options.ignore_columns,
rename_columns=options.rename_columns,
lowercase=options.lowercase,
ignore_duplicates=options.ignore_duplicates,
indices=options.indices,
first_column=options.first_column,
existing_tables=existing_tables,
append=options.append)
def row_iter(rows, reader):
for row in rows:
yield quoteRow(row,
take,
map_column2type,
options.missing_values,
null=options.null,
string_value=options.string_value)
for data in reader:
yield quoteRow(IOTools.convertDictionary(data, map=options.map),
take,
map_column2type,
options.missing_values,
null=options.null,
string_value=options.string_value)
ninput = 0
E.info("inserting data")
if options.insert_quick:
E.info("using quick insert")
outfile, filename = tempfile.mkstemp()
E.debug("dumping data into %s" % filename)
for d in row_iter(rows, reader):
ninput += 1
os.write(
outfile,
quick_import_separator.join([str(d[x]) for x in take]) + "\n")
if ninput % report_step == 0:
E.info("iteration %i\n" % ninput)
os.close(outfile)
statement = quick_import_statement % filename
E.debug(statement)
# infinite loop possible
while 1:
retcode = E.run(statement, cwd=os.getcwd(), close_fds=True)
if retcode != 0:
E.warn("import error using statement: %s" % statement)
if not options.retry:
raise ValueError("import error using statement: %s" %
statement)
time.sleep(5)
continue
break
os.remove(filename)
# there is no way to insert NULL values into sqlite. The only
# solution is to update all colums.
for column in take:
executewait(
dbhandle, "UPDATE %s SET %s = NULL WHERE %s = 'None'" %
(options.tablename, column, column), error, options.retry)
elif options.insert_many:
data = []
for d in row_iter(rows, reader):
ninput += 1
data.append([d[x] for x in take])
if ninput % report_step == 0:
E.info("iteration %i" % ninput)
statement = "INSERT INTO %s VALUES (%s)" % (options.tablename,
",".join("?" * len(take)))
E.info("inserting %i rows" % len(data))
E.debug("multiple insert:\n# %s" % statement)
while 1:
try:
dbhandle.executemany(statement, data)
except error as msg:
E.warn("import failed: msg=%s, statement=\n %s" %
(msg, statement))
# TODO: check for database locked msg
if not options.retry:
raise error(msg)
if not re.search("locked", str(msg)):
raise error(msg)
time.sleep(5)
continue
break
else:
# insert line by line (could not figure out how to do bulk loading with
# subprocess and COPY FROM STDIN)
statement = "INSERT INTO %s VALUES (%%(%s)s)" % (options.tablename,
')s, %('.join(take))
# output data used for guessing:
for d in row_iter(rows, reader):
ninput += 1
E.debug("single insert:\n# %s" % (statement % d))
cc = executewait(dbhandle,
statement,
error,
retry=options.retry,
args=d)
cc.close()
if ninput % report_step == 0:
E.info("iteration %i" % ninput)
E.info("building indices")
nindex = 0
for index in options.indices:
nindex += 1
try:
statement = "CREATE INDEX %s_index%i ON %s (%s)" % (
options.tablename, nindex, options.tablename, index)
cc = executewait(dbhandle, statement, error, options.retry)
cc.close()
E.info("added index on column %s" % (index))
except error as msg:
E.info("adding index on column %s failed: %s" % (index, msg))
statement = "SELECT COUNT(*) FROM %s" % (options.tablename)
cc = executewait(dbhandle, statement, error, options.retry)
result = cc.fetchone()
cc.close()
noutput = result[0]
E.info("ninput=%i, noutput=%i, nskipped_columns=%i" %
(ninput, noutput, len(ignored)))
dbhandle.commit()
def main(argv=None):
"""script main.
parses command line options in sys.argv, unless *argv* is given.
"""
if argv is None:
argv = sys.argv
parser = E.OptionParser(version="%prog version: $Id$",
usage=globals()["__doc__"])
parser.add_option("-o",
"--outfile=",
dest="output_filename",
type="string",
help="write to output filename.")
parser.set_defaults(output_filename=None, )
(options, args) = E.start(parser, add_csv_options=True)
if not options.output_filename:
raise ValueError("please specify an output filename.")
w = openpyxl.Workbook(optimized_write=True)
for filename in args:
lines = [
x for x in IOTools.open_file(filename, "r").readlines()
if x[0] != "#"
]
if len(lines) == 0:
continue
if options.loglevel >= 2:
print("# read %i rows" % len(lines))
sys.stdout.flush()
headers = lines[0][:-1].split("\t")
ws = w.add_sheet(os.path.basename(filename))
cur_row = 0
ws.append(headers)
cur_row += 1
reader = csv.DictReader(lines, dialect=options.csv_dialect)
for row in reader:
row = IOTools.convertDictionary(row)
data = [row.get(headers[x], "") for x in range(len(headers))]
ws.append(data)
cur_row += 1
w.save(options.output_filename)
E.stop()
def main(argv=None):
"""script main.
parses command line options in sys.argv, unless *argv* is given.
"""
if argv is None:
argv = sys.argv
parser = E.OptionParser(
version="%prog version: $Id: csv_intersection.py 2782 2009-09-10 11:40:29Z andreas $")
parser.add_option("-u", "--unique", dest="unique", action="store_true",
help="output rows are uniq.")
parser.set_defaults(
remove=False,
unique=False,
)
(options, args) = E.start(parser, add_csv_options=True)
if len(args) != 2:
raise ValueError("please specify two files to join")
options.filename1, options.filename2 = args
table1 = CSV.readTable(IOTools.open_file(options.filename1, "r"))
table2 = CSV.readTable(IOTools.open_file(options.filename2, "r"))
if options.unique:
outfile = UniqueBuffer(sys.stdout)
else:
outfile = options.stdout
# build new field list
new_fields = []
for x in options.join_fields1:
new_fields.append(x)
for x in fields1:
if x not in options.join_fields1:
new_fields.append(x)
if x not in options.join_fields2:
new_fields.append(x)
writer = csv.DictWriter(outfile,
fields,
dialect=options.csv_dialect,
lineterminator=options.csv_lineterminator,
extrasaction='ignore')
if len(lines) > 0:
old_fields = lines[0][:-1].split("\t")
if options.remove:
fields = []
for x in old_fields:
if x not in input_fields:
fields.append(x)
else:
fields = input_fields
reader = csv.DictReader(lines,
dialect=options.csv_dialect)
print("\t".join(fields))
first_row = True
for row in reader:
row = IOTools.convertDictionary(row)
writer.writerow(row)
E.stop()