'''
file_extractor.py
'''
import fileinput
import linecache
import logging
import toml
import sys
import argparse
import numpy as np
import re
from datetime import datetime
import tools
from physical_parameter import Roscop
from notanorm import SqliteDb
# define SQL station table
table_station = """
CREATE TABLE station (
id INTEGER PRIMARY KEY,
header TEXT,
date_time TEXT NOT NULL UNIQUE,
julian_day REAL NOT NULL UNIQUE,
latitude REAL NOT NULL,
longitude REAL NOT NULL,
max_depth REAL,
bottom_depth REAL
);"""
# define the profile table
# the id is actually the rowid AUTOINCREMENT column.
table_profile = """
CREATE TABLE profile (
id INTEGER PRIMARY KEY,
station_id INTEGER,
FOREIGN KEY (station_id)
REFERENCES station (id)
); """
class FileExtractor:
'''
This class read multiple ASCII file, extract physical parameter from ROSCOP codification at the given column
and fill arrays.
Header values and 1 dimensions variables as TIME, LATITUDE and LONGITUDE are
automaticaly extracted from toml configuration file, actually bi set_regexp function, may be add inside constructor ?
Parameters
----------
fname : file, str, pathlib.Path, list of str
File, filename, or list to read.
keys: list of physical parameter to extract
separator : str, column separator, default None (blank)
'''
# constructor with values by defaul
def __init__(self, fname, roscop, keys, separator=None, dbname=":memory:"):
# attibutes
# public:
self.fname = fname
self.keys = keys
self.roscop = roscop
self.n = 0
self.m = 0
self.lineHeader = 0
self.db = SqliteDb(dbname)
# private:
self.__separator = separator
self.__header = ''
self.__data = {}
self.__regex = {}
# replace this constante with roscop fill value
#self.__FillValue = 1e36
# overloading operators
def __getitem__(self, key):
''' overload r[key] '''
if key not in self.__data:
logging.error(
" file_extractor.py: invalid key: \"{}\"".format(key))
else:
return self.__data[key]
def __str__(self):
''' overload string representation '''
return 'Class FileExtractor, file: %s, size = %d x %d' % (self.fname, self.n, self.m)
def disp(self):
# for key in keys:
# print("{}:".format(key))
# print(self.__data[key])
buf = ''
for key in self.keys:
buf += "{}:\n".format(key)
buf += "{}\n".format(self.__data[key])
return buf
def set_regex(self, cfg, ti):
''' prepare (compile) each regular expression inside toml file under section [<device>.header]
[ctd.header]
isHeader = '^[*#]'
isDevice = '^\*\s+(Sea-Bird)'
TIME = 'System UpLoad Time\s*=\s*(\w+)\s+(\d+)\s+(\d+)\s+(\d+):(\d+):(\d+)'
LATITUDE = 'NMEA\s+Latitude\s*[:=]\s*(\d+)\s+(\d+\.\d+)\s+(\w)'
LONGITUDE = 'NMEA\s+Longitude\s*[:=]\s*(\d+)\s+(\d+.\d+)\s+(\w)'
'''
# first pass on file(s)
d = cfg[ti.lower()]['header']
# fill the __regex dict with compiled regex
for key in d.keys():
self.__regex[key] = re.compile(d[key])
def read_files(self, cfg, device):
print('Create table station')
#db.query("DROP DATABASE IF EXISTS '{}'".format(fname))
self.db.query(table_station)
print('Create table profile')
self.db.query(table_profile)
for pm in self.keys:
print('\tUpdate table profile with new column {}'.format(pm))
addColumn = "ALTER TABLE profile ADD COLUMN {} REAL NOT NULL".format(pm)
self.db.query(addColumn)
# get the dictionary from toml block, device must be is in lower case
hash = cfg['split'][device.lower()]
# set separator field if declared in toml section, none by default
if 'separator' in cfg[device.lower()]:
self.__separator = cfg[device.lower()]['separator']
for file in self.fname:
with fileinput.input(
file, openhook=fileinput.hook_encoded("ISO-8859-1")) as f:
for line in f:
if self.__regex['isHeader'].match(line):
self.__header += line
continue
if self.__regex['endHeader'].match(line):
# read and decode header
#for k in self.__regex.keys():
# fake
print("insert station")
self.db.insert("station", id = 1, header = self.__header,
date_time = "2022-04-06 12:00:00.000",
julian_day = 10.5, latitude = -10.2, longitude = 23.6)
continue
print(line)
# split the line, remove leading and trailing space before
p = line.strip().split(self.__separator)
sql = 'station_id = 1'
# for key in self.keys:
# # Insert data in profile table
# sql += ", {} = {}".format(key, p[hash[key]])
# print(sql)
#sql = ', '.join(['{} = {}'.format(key, p[hash[key]]) for key in self.keys])
#print(sql)
sql = {}
#[sql[key] = p[hash[key]] for key in self.keys]
sql['station_id'] = 1
for key in self.keys:
sql[key] = p[hash[key]]
print(sql)
self.db.insert("profile", sql )
#self.db.insert("profile", station_id = 1, PRES = 1, TEMP = 20, PSAL = 35, DOX2 = 20, DENS = 30)
print('get sizes:')
st = self.db.query('SELECT COUNT(id) FROM station')
max_press = self.db.query('SELECT count(PRES) FROM profile')
print(st, max_press)
# for testing in standalone context
# ---------------------------------
if __name__ == "__main__":
# usage Unix:
# > python file_extractor.py data/CTD/cnv/dfr2900[1-3].cnv -d -i CTD
# > python file_extractor.py data/CTD/cnv/dfr2900*.cnv -k PRES TEMP PSAL DOX2 DENS -i CTD
#
# usage DOS:
# > python file_extractor.py data/CTD/cnv/dfr2900?.cnv -d -i CTD
# > python file_extractor.py data/CTD/cnv/dfr2900?.cnv -k PRES TEMP PSAL DOX2 DENS -i CTD
#
parser = argparse.ArgumentParser(
description='This class read multiple ASCII file, extract physical parameter \
from ROSCOP codification at the given column and fill arrays ',
epilog='J. Grelet IRD US191 - March 2019')
parser.add_argument('-d', '--debug', help='display debug informations',
action='store_true')
parser.add_argument('-c', '--config', help="toml configuration file, (default: %(default)s)",
default='tests/test.toml')
parser.add_argument('-i', '--instrument', nargs='?', choices=['CTD','XBT'],
help='specify the instrument that produce files, eg CTD, XBT, TSG, LADCP')
parser.add_argument('-k', '--keys', nargs='+', default=['PRES', 'TEMP', 'PSAL'],
help='display dictionary for key(s), (default: %(default)s)')
parser.add_argument('fname', nargs='*',
help='cnv file(s) to parse, (default: data/cnv/dfr29*.cnv)')
# display extra logging info
# see: https://stackoverflow.com/questions/14097061/easier-way-to-enable-verbose-logging
# https://docs.python.org/2/howto/argparse.html
args = parser.parse_args()
if args.debug:
logging.basicConfig(
format='%(levelname)s:%(message)s', level=logging.DEBUG)
fe = FileExtractor(args.fname, Roscop('code_roscop.csv'), args.keys)
print("File(s): {}, Config: {}".format(args.fname, args.config))
cfg = toml.load(args.config)
fe.set_regex(cfg, args.instrument)
fe.read_files(cfg, args.instrument)
# print("Indices: {} x {}\nkeys: {}".format(fe.n, fe.m, fe.keys))
# fe.second_pass(cfg, args.instrument, ['TIME', 'LATITUDE', 'LONGITUDE','BATH'])
# # debug
# print(fe['PRES'])
# print(fe['TEMP'])
# print(fe['PSAL'])