def get_orbits(self, type):
options = self.options
orbits1 = pySp3.GetSp3Orbits(options['sp3'], self.rinex.date, type, os.path.join(self.rootdir, 'orbits'), True)
orbits2 = pySp3.GetSp3Orbits(options['sp3'], self.rinex.date + 1, type,
os.path.join(self.rootdir, 'orbits'), True)
clocks1 = pyClk.GetClkFile(options['sp3'], self.rinex.date, type, os.path.join(self.rootdir, 'orbits'), True)
clocks2 = pyClk.GetClkFile(options['sp3'], self.rinex.date + 1, type,
os.path.join(self.rootdir, 'orbits'), True)
try:
eop_file = pyEOP.GetEOP(options['sp3'], self.rinex.date, type, self.rootdir)
eop_file = eop_file.eop_filename
except pyEOP.pyEOPException:
# no eop, continue with out one
eop_file = 'dummy.eop'
self.orbits1 = orbits1
self.orbits2 = orbits2
self.clocks1 = clocks1
self.clocks2 = clocks2
self.eop_file = eop_file
# get the type of orbit
self.orbit_type = orbits1.type
def test_node(check_gamit_tables=None, software_sync=()):
# test node: function that makes sure that all required packages and tools are present in the nodes
import traceback
import platform
import os
import sys
def check_tab_file(tabfile, date):
if os.path.isfile(tabfile):
# file exists, check contents
with open(tabfile, 'rt', encoding='utf-8', errors='ignore') as f:
lines = f.readlines()
tabdate = pyDate.Date(mjd=lines[-1].split()[0])
if tabdate < date:
return ' -- %s: Last entry in %s is %s but processing %s' \
% (platform.node(), tabfile, tabdate.yyyyddd(), date.yyyyddd())
return []
else:
return ' -- %s: Could not find file %s' % (platform.node(),
tabfile)
# BEFORE ANYTHING! check the python version
version = sys.version_info
# if version.major > 2 or version.minor < 7 or (version.micro < 12 and version.minor <= 7):
# return ' -- %s: Incorrect Python version: %i.%i.%i. Recommended version >= 2.7.12' \
# % (platform.node(), version.major, version.minor, version.micro)
if version.major < 3:
return ' -- %s: Incorrect Python version: %i.%i.%i. Recommended version >= 3.0.0' \
% (platform.node(), version.major, version.minor, version.micro)
# start importing the modules needed
try:
import shutil
import datetime
import time
import uuid
import traceback
# deps
import numpy
import pg
import dirsync
# app
import pyRinex
import dbConnection
import pyStationInfo
import pyArchiveStruct
import pyPPP
import pyBrdc
import pyOptions
import Utils
import pyOTL
import pySp3
import pyETM
import pyRunWithRetry
import pyDate
except:
return ' -- %s: Problem found while importing modules:\n%s' % (
platform.node(), traceback.format_exc())
try:
if len(software_sync) > 0:
# synchronize directories listed in the src and dst arguments
from dirsync import sync
for source_dest in software_sync:
if isinstance(source_dest, str) and ',' in source_dest:
s = source_dest.split(',')[0].strip()
d = source_dest.split(',')[1].strip()
print(' -- Synchronizing %s -> %s' % (s, d))
updated = sync(s, d, 'sync', purge=True, create=True)
for f in updated:
print(' -- Updated %s' % f)
except:
return ' -- %s: Problem found while synchronizing software:\n%s ' % (
platform.node(), traceback.format_exc())
# continue with a test SQL connection
# make sure that the gnss_data.cfg is present
try:
cnn = dbConnection.Cnn('gnss_data.cfg')
q = cnn.query('SELECT count(*) FROM networks')
if int(pg.version[0]) < 5:
return ' -- %s: Incorrect PyGreSQL version!: %s' % (
platform.node(), pg.version)
except:
return ' -- %s: Problem found while connecting to postgres:\n%s ' % (
platform.node(), traceback.format_exc())
# make sure we can create the production folder
try:
test_dir = os.path.join('production/node_test')
if not os.path.exists(test_dir):
os.makedirs(test_dir)
except:
return ' -- %s: Could not create production folder:\n%s ' % (
platform.node(), traceback.format_exc())
# test
try:
Config = pyOptions.ReadOptions('gnss_data.cfg')
# check that all paths exist and can be reached
if not os.path.exists(Config.archive_path):
return ' -- %s: Could not reach archive path %s' % (
platform.node(), Config.archive_path)
if not os.path.exists(Config.repository):
return ' -- %s: Could not reach repository path %s' % (
platform.node(), Config.repository)
# pick a test date to replace any possible parameters in the config file
date = pyDate.Date(year=2010, doy=1)
except:
return ' -- %s: Problem while reading config file and/or testing archive access:\n%s' \
% (platform.node(), traceback.format_exc())
try:
brdc = pyBrdc.GetBrdcOrbits(Config.brdc_path, date, test_dir)
except:
return ' -- %s: Problem while testing the broadcast ephemeris archive (%s) access:\n%s' \
% (platform.node(), Config.brdc_path, traceback.format_exc())
try:
sp3 = pySp3.GetSp3Orbits(Config.sp3_path, date, Config.sp3types,
test_dir)
except:
return ' -- %s: Problem while testing the sp3 orbits archive (%s) access:\n%s' \
% (platform.node(), Config.sp3_path, traceback.format_exc())
# check that all executables and GAMIT bins are in the path
for prg in ('crz2rnx', 'crx2rnx', 'rnx2crx', 'rnx2crz', 'gfzrnx_lx',
'svdiff', 'svpos', 'tform', 'sh_rx2apr', 'doy', 'sed',
'compress'):
with pyRunWithRetry.command('which ' + prg) as run:
run.run()
if run.stdout == '':
return ' -- %s: Could not find path to %s' % (platform.node(),
prg)
# check grdtab and ppp from the config file
for opt in ('grdtab', 'otlgrid', 'ppp_exe'):
path = Config.options[opt]
if not os.path.isfile(path):
return ' -- %s: Could not find %s in %s' % (platform.node(), opt,
path)
ppp_path = Config.options['ppp_path']
for f in ('gpsppp.stc', 'gpsppp.svb_gps_yrly', 'gpsppp.flt', 'gpsppp.stc',
'gpsppp.met'):
if not os.path.isfile(os.path.join(ppp_path, f)):
return ' -- %s: Could not find %s in %s' % (platform.node(), f,
ppp_path)
for frame in Config.options['frames']:
if not os.path.isfile(frame['atx']):
return ' -- %s: Could not find atx in %s' % (platform.node(),
frame['atx'])
if check_gamit_tables is not None:
# check the gamit tables if not none
date = check_gamit_tables[0]
eop = check_gamit_tables[1]
gg = os.path.expanduser('~/gg')
tables = os.path.expanduser('~/gg/tables')
if not os.path.isdir(gg):
return ' -- %s: Could not GAMIT installation dir (gg)' % (
platform.node())
elif not os.path.isdir(tables):
return ' -- %s: Could not GAMIT tables dir (gg)' % (
platform.node())
# DDG: deprecated -> GAMIT now uses a single nbody file (binary)
# for t_name in ('luntab.' + date.yyyy() + '.J2000',
# 'soltab.' + date.yyyy() + '.J2000',
# 'ut1.' + eop,
# # leapseconds
# # vmf1
# 'pole.' + eop
# ):
# result = check_tab_file(os.path.join(tables, t_name), date)
# if result:
# return result
# fes_cmc consistency
return ' -- %s: Test passed!' % platform.node()
def start(self, dirname, year, doy, dry_run=False):
monitor_open = False
try:
# copy the folder created by GamitSession in the solution_pwd to the remote_pwd (pwd)
try:
if not os.path.exists(os.path.dirname(self.pwd)):
os.makedirs(os.path.dirname(self.pwd))
except OSError:
# racing condition having several processes trying to create the same folder
# if OSError occurs, ignore and continue
pass
# if the local folder exists (due to previous incomplete processing, erase it).
if os.path.exists(self.pwd):
shutil.rmtree(self.pwd)
# ready to copy the shared solution_dir to pwd
shutil.copytree(self.solution_pwd, self.pwd, symlinks=True)
with open(os.path.join(self.pwd, 'monitor.log'), 'a') as monitor:
monitor_open = True
monitor.write(
datetime.datetime.now().strftime('%Y-%m-%d %H:%M:%S') +
' -> %s %i %i executing on %s\n' %
(dirname, year, doy, platform.node()))
monitor.write(
datetime.datetime.now().strftime('%Y-%m-%d %H:%M:%S') +
' -> fetching orbits\n')
try:
Sp3 = pySp3.GetSp3Orbits(self.orbits['sp3_path'],
self.date,
self.orbits['sp3types'],
self.pwd_igs,
True) # type: pySp3.GetSp3Orbits
except pySp3.pySp3Exception:
monitor.write(
datetime.datetime.now().strftime('%Y-%m-%d %H:%M:%S') +
' -> could not find principal orbits, fetching alternative\n'
)
# try alternative orbits
if self.options['sp3altrn']:
Sp3 = pySp3.GetSp3Orbits(
self.orbits['sp3_path'], self.date,
self.orbits['sp3altrn'], self.pwd_igs,
True) # type: pySp3.GetSp3Orbits
else:
raise
if Sp3.type != 'igs':
# rename file
shutil.copyfile(Sp3.file_path,
Sp3.file_path.replace(Sp3.type, 'igs'))
monitor.write(
datetime.datetime.now().strftime('%Y-%m-%d %H:%M:%S') +
' -> fetching broadcast orbits\n')
pyBrdc.GetBrdcOrbits(
self.orbits['brdc_path'],
self.date,
self.pwd_brdc,
no_cleanup=True) # type: pyBrdc.GetBrdcOrbits
for rinex in self.params['rinex']:
monitor.write(
datetime.datetime.now().strftime('%Y-%m-%d %H:%M:%S') +
' -> fetching rinex for %s.%s %s %s\n' %
(rinex['NetworkCode'], rinex['StationCode'],
rinex['StationAlias'], '{:10.6f} {:11.6f}'.format(
rinex['lat'], rinex['lon'])))
try:
with pyRinex.ReadRinex(
rinex['NetworkCode'], rinex['StationCode'],
rinex['source'],
False) as Rinex: # type: pyRinex.ReadRinex
# WARNING! some multiday RINEX were generating conflicts because the RINEX has a name, say,
# tuc12302.10o and the program wants to rename it as tuc12030.10o but because it's a
# multiday file, during __init__ it's already split and renamed as tuc12300.10o and
# additional folders are generated with the information for each file. Therefore, find
# the rinex that corresponds to the date being processed and use that one instead of the
# original file. These files are not allowed by pyArchiveService, but the "start point" of
# the database (i.e. the files already in the folders read by pyScanArchive) has such
# problems.
# figure out if this station has been affected by an earthquake
# if so, window the data
if rinex['jump'] is not None:
monitor.write(
' -> RINEX file has been windowed: ETM detected jump on '
+ rinex['jump'].datetime().strftime(
'%Y-%m-%d %H:%M:%S') + '\n')
if Rinex.multiday:
# find the rinex that corresponds to the session being processed
for Rnx in Rinex.multiday_rnx_list:
if Rnx.date == self.date:
Rnx.rename(rinex['destiny'])
if rinex['jump'] is not None:
self.window_rinex(
Rnx, rinex['jump'])
# before creating local copy, decimate file
Rnx.decimate(30)
Rnx.purge_comments()
Rnx.compress_local_copyto(
self.pwd_rinex)
break
else:
Rinex.rename(rinex['destiny'])
if rinex['jump'] is not None:
self.window_rinex(Rinex, rinex['jump'])
# before creating local copy, decimate file
Rinex.decimate(30)
Rinex.purge_comments()
Rinex.compress_local_copyto(self.pwd_rinex)
except (OSError, IOError):
monitor.write(
datetime.datetime.now().strftime(
'%Y-%m-%d %H:%M:%S') +
' -> An error occurred while trying to copy ' +
rinex['source'] + ' to ' + rinex['destiny'] +
': File skipped.\n')
except (pyRinex.pyRinexException, Exception) as e:
monitor.write(
datetime.datetime.now().strftime(
'%Y-%m-%d %H:%M:%S') +
' -> An error occurred while trying to copy ' +
rinex['source'] + ': ' + str(e) + '\n')
monitor.write(
datetime.datetime.now().strftime('%Y-%m-%d %H:%M:%S') +
' -> executing GAMIT\n')
# create the run script
self.create_replace_links()
self.create_run_script()
self.create_finish_script()
# run the script to replace the links of the tables directory
self.p = subprocess.Popen(
'find ./tables ! -name "otl.grid" -type l -exec ./replace_links.sh {} +',
shell=True,
stdout=subprocess.PIPE,
stderr=subprocess.PIPE,
cwd=self.pwd)
_, _ = self.p.communicate()
# now execute the run script
if not dry_run:
self.p = subprocess.Popen('./run.sh',
shell=False,
stdout=subprocess.PIPE,
stderr=subprocess.PIPE,
cwd=self.pwd)
self.stdout, self.stderr = self.p.communicate()
self.p = subprocess.Popen('./finish.sh',
shell=False,
stdout=subprocess.PIPE,
stderr=subprocess.PIPE,
cwd=self.pwd)
self.stdout, self.stderr = self.p.communicate()
# check for any fatals
self.p = subprocess.Popen('grep -q \'FATAL\' monitor.log',
shell=True,
stdout=subprocess.PIPE,
stderr=subprocess.PIPE,
cwd=self.pwd)
_, _ = self.p.communicate()
if self.p.returncode == 0:
self.success = False
else:
self.success = True
# output statistics to the parent to display
result = self.parse_monitor(self.success)
with open(os.path.join(self.pwd, 'monitor.log'), 'a') as monitor:
monitor.write(
datetime.datetime.now().strftime('%Y-%m-%d %H:%M:%S') +
' -> return to Parallel.GAMIT\n')
# no matter the result of the processing, move folder to final destination
if not dry_run:
self.finish()
return result
except Exception:
msg = traceback.format_exc() + '\nProcessing %s date %s on node %s' \
% (self.params['NetName'], self.date.yyyyddd(), platform.node())
# DDG: do not attempt to write to monitor.log or do any file operations (maybe permission problem)
# problem might occur during copytree or rmtree or some other operation before opening monitor.log
if monitor_open:
with open(os.path.join(self.pwd, 'monitor.log'),
'a') as monitor:
monitor.write(
datetime.datetime.now().strftime('%Y-%m-%d %H:%M:%S') +
' -> ERROR in pyGamitTask.start()\n%s' % msg)
# the solution folder exists because it was created by GamitSession to start the processing.
# erase it to upload the result
if os.path.exists(self.solution_pwd):
shutil.rmtree(self.solution_pwd)
# execute final error step: copy to self.solution_pwd
shutil.copytree(self.pwd, self.solution_pwd, symlinks=True)
# remove the remote pwd
shutil.rmtree(self.pwd)
# output statistics to the parent to display
result = self.parse_monitor(False)
else:
result = {
'session':
'%s %s' % (self.date.yyyyddd(), self.params['DirName']),
'Project':
self.params['NetName'],
'subnet':
self.params['subnet'],
'Year':
self.date.year,
'DOY':
self.date.doy,
'FYear':
self.date.fyear,
'wl':
0,
'nl':
0,
'nrms':
0,
'relaxed_constrains':
'',
'max_overconstrained':
'',
'node':
platform.node(),
'execution_time':
0,
'execution_date':
0,
'missing':
'',
'success':
False,
'fatals': []
}
result['error'] = msg
# return useful information to the main node
return result
