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scripps_ingest_single_wnam_raw.py
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#!/usr/local/bin/python
#==========================================================================
# Ingest a given scripps dataset into the corresponding databases.
# To be invoked by the overall scripps_ingest.py using subprocess,
# destination data directory and temporary working directory are defined in
# properties.
#
# input: path to the original scripps tar file;
# output: corresponding overall sqlite db file with all data ingested;
# as well as duplicate-filled sqlite db file for individual stations
#
# usage:
# scripps_ingest_single_wnam_raw.py /path/to/download/scripps_data.tar
#
# output:
# /path/to/rdahmm/scripps_data.sqlite
# /path/to/rdahmm/stationID.sqlite
#
# This is a clone of scripps_ingest_single_raw.py with minor updates to handle
# format discrepencies of WNAM_Raw_TrendeNeuTimeSeries_* tar files:
# - use gunzip (vs. unzip) to unpack data
# - reference position lat/lon parsing differently
# - reference position height missing
# - data units in m instead of mm
# - date is only available as decimal year with 2 other columns missing
#
#
# We will only handle stations in the WNAMsites file, and skip others.
#===========================================================================
import os, sys, string, re
import sqlite3 as db
from datetime import date
from datetime import timedelta
from properties import properties
from wnamsites import wnamsites
def decimal_year_to_date(dyear):
year = int(dyear)
rem = dyear - year
base = date(year, 1, 1)
nbase = base.replace(year=base.year + 1)
days = int((nbase - base).days * rem)
ts = date.fromordinal(date(year,1,1).toordinal()+days)
return ts
numargv = len(sys.argv)
if numargv == 1:
sys.exit("usage: scripps_ingest_single_wnam_raw.py /path/to/scripps_data.tar")
elif numargv == 2:
[scripps_path, tarfile] = os.path.split(sys.argv[1])
scripps_path += "/"
else:
sys.exit("Invalid number of parameters!")
station_list = wnamsites()
#rdahmm_path = "/home/yuma/RDAHMM/Data/"
#temp_path = "/home/yuma/RDAHMM/TEMP/"
data_path = properties('data_path')
temp_path = properties('temp_path')
#datadir = data_path + tarfile[:tarfile.rfind("_")] + "/"
datadir = data_path + tarfile[:-13] + "/"
#dbfile = datadir + tarfile[:-4] + ".sqlite"
# get rid of timestamp from db file name
dbfile = datadir + tarfile[:-13] + ".sqlite"
workdir = temp_path + tarfile[:-13] + "/"
#workdir = temp_path + tarfile[:tarfile.rfind("_")] + "/"
#print datadir, dbfile
if not os.path.exists(datadir):
cmd = "mkdir -p " + datadir
os.system(cmd)
if not os.path.exists(workdir):
cmd = "mkdir -p " + workdir
os.system(cmd)
#if the same db file exists, drop it
if os.path.isfile(dbfile):
print "deleting old database " + dbfile
os.remove(dbfile)
# creating/connecting the database
conn = db.connect(dbfile)
# creating a Cursor
cur = conn.cursor()
# creating tables
sql ="""CREATE TABLE GPSTimeSeries (
StationID CHAR(4),
North Num,
East Num,
Up Num,
Nsig Num,
Esig Num,
Usig Num,
Timestamp TEXT,
UNIQUE (StationID, Timestamp))"""
cur.execute(sql)
sql ="""CREATE TABLE ReferencePositions (
StationID CHAR(4),
Latitude Num,
Longitude Num,
Height Num,
UNIQUE (StationID))"""
cur.execute(sql)
conn.commit()
# clear working directory
cmd = "rm -f " + workdir + "*"
os.system(cmd)
print "Processing ", tarfile, "..."
# unpack data
cmd = "tar xvf " + scripps_path + tarfile + " -C " + workdir
os.system(cmd)
dirlist = os.listdir(workdir)
dirlist.sort()
for datafile in dirlist:
if datafile[-2:] == ".Z":
if os.stat(workdir+datafile).st_size == 0: # When .Z file is empty
continue
os.chdir(workdir)
cmd = "gunzip " + workdir + datafile
os.system(cmd)
datafile = datafile[:-2]
stationID = datafile[:4]
#if not stationID in station_list:
# continue
station_dbfile = datadir + stationID + ".sqlite"
if os.path.isfile(station_dbfile):
print "deleting old station database " + station_dbfile
os.remove(station_dbfile)
station_conn = db.connect(station_dbfile)
station_cur = station_conn.cursor()
station_sql ="""CREATE TABLE StationGPSTimeSeries (
North Num,
East Num,
Up Num,
Nsig Num,
Esig Num,
Usig Num,
Timestamp TEXT,
Interploated INT Default 0,
UNIQUE(Timestamp))"""
station_cur.execute(station_sql)
station_conn.commit()
with open(workdir + datafile, 'r') as f:
data = f.readlines()
last_line = ""
for line in data:
if "#" in line:
if "Latitude" in line:
lat = float(line.split(":")[-1])
if "Longitude" in line:
long = float(line.split(":")[-1])
if "Note" in line: # last line of comments
height = -9999 # height not available in the data source
sql = "INSERT INTO ReferencePositions (StationID, Latitude, Longitude, Height) "
sql += " VALUES ('%s', '%s', '%s', '%s')" % (stationID, lat, long, height)
cur.execute(sql)
#if not "#" in line:
else:
record = string.split(line)
if len(record) < 7: # When missing white spaces between columns
tmpstr = ' '.join(record[1:])
record[1:7] = re.findall(r"[+-]?\d+\.\d\d", tmpstr)
timestamp = decimal_year_to_date(float(record[0]))
[north, east, up, nsig, esig, usig] = [float(x)*1000 for x in record[1:7]]
sql = "INSERT INTO GPSTimeSeries (StationID, North, East, Up, Nsig, Esig, Usig, Timestamp) "
sql += " VALUES ('%s', '%s', '%s', '%s', '%s', '%s', '%s', '%s')" % (stationID, north, east, up, nsig, esig, usig, timestamp)
cur.execute(sql)
if last_line == "":
last_line = line
else:
last_record = string.split(last_line)
if len(last_record) < 7:
tmpstr = ' '.join(last_record[1:])
last_record[1:7] = re.findall(r"[+-]?\d+\.\d\d", tmpstr)
last_timestamp = decimal_year_to_date(float(last_record[0]))
[lnorth, least, lup, lnsig, lesig, lusig] = [float(x)*1000 for x in last_record[1:7]]
# if missing days from last to current, fill with last
for i in range(1, (timestamp - last_timestamp).days):
ts = last_timestamp + timedelta(days=i)
interploated = 1
station_sql = "INSERT INTO StationGPSTimeSeries (North, East, Up, Nsig, Esig, Usig, Timestamp, Interploated) "
station_sql += " VALUES ('%s', '%s', '%s', '%s', '%s', '%s', '%s', '%s')" % (lnorth, least, lup, lnsig, lesig, lusig, ts, interploated)
station_cur.execute(station_sql)
last_line = line
station_sql = "INSERT INTO StationGPSTimeSeries (North, East, Up, Nsig, Esig, Usig, Timestamp) "
station_sql += " VALUES ('%s', '%s', '%s', '%s', '%s', '%s', '%s')" % (north, east, up, nsig, esig, usig, timestamp)
station_cur.execute(station_sql)
station_conn.commit()
conn.commit()
f.closed
station_cur.close()
station_conn.close()
#insert duplicates for missing days in the station database
# create index
sql = "CREATE INDEX idx_StationID ON GPSTimeSeries(StationID)"
cur.execute(sql)
sql = "CREATE INDEX idx_Timestamp ON GPSTimeSeries(Timestamp)"
cur.execute(sql)
sql = "CREATE INDEX idx_RefStationID ON ReferencePositions(StationID)"
cur.execute(sql)
conn.commit()
cur.close()
conn.close()
# clear working directory
#cmd = "rm -f " + workdir + "*"
#os.system(cmd)