def commit_starter_project(self):
pushdir(self.details.starter_project_dir)
run([
"git", "commit", "-m",
F"'Update to Approvals {self.details.new_version}'"
])
popdir()
def install_packages():
"""Get required Ubuntu/Debian packages.
It is OK if they are already installed
"""
for package in ['apache2',
'subversion',
'trac',
'libapache2-svn',
'libapache2-mod-python',
'libapache2-mod-python-doc']:
if package == 'trac':
# Hack to get TRAC 0.11.4 on Ubuntu <9.04
# See http://serverfault.com/questions/11851/attachments-not-showing-up-in-trac
s = 'apt-get remove trac'
run(s)
s = 'easy_install http://svn.edgewall.org/repos/trac/tags/trac-0.11.4'
run(s)
continue
s = 'apt-get -y install %s > %s_install.log' % (package, package)
err = run(s)
if err != 0:
msg = 'Installation of package %s failed. ' % package
msg += 'See log file %s_install.log for details' % package
raise Exception(msg)
def install_ubuntu_packages():
"""Get required Ubuntu packages for riab_server.
It is OK if they are already installed
"""
header('Installing Ubuntu packages')
s = 'apt-get clean'
run(s, verbose=True)
for package in ['python-setuptools']:
s = 'apt-get -y install %s' % package
log_base = '%s_install' % package
try:
run(s,
stdout=log_base + '.out',
stderr=log_base + '.err',
verbose=True)
except:
msg = 'Installation of package %s failed. ' % package
msg += 'See log file %s.out and %s.err for details' % (log_base, log_base)
raise Exception(msg)
def delete_style(self, style_name, verbose=False):
"""docstring for delete_style"""
# TODO: add test
run('curl -u %s:%s -d "purge=true" -X DELETE localhost:8080/geoserver/rest/styles/%s' % (self.geoserver_username,
self.geoserver_userpass,
style_name))
def update_starter_project(self):
STARTER_PATH_OLD_SINGLE_HEADER = F"{self.details.starter_project_dir}/lib/{self.details.old_single_header}"
STARTER_PATH_NEW_SINGLE_HEADER = F"{self.details.starter_project_dir}/lib/{self.details.new_single_header}"
# Make sure starter project folder is clean
pushdir(self.details.starter_project_dir)
# Delete untracked files:
# - does not delete ignored files
# - does not delete untracked files in new, untracked directories
run(["git", "clean", "-f"])
run(["git", "reset", "--hard"])
popdir()
shutil.copyfile(self.details.release_new_single_header,
STARTER_PATH_NEW_SINGLE_HEADER)
# Delete the last release:
if os.path.exists(STARTER_PATH_OLD_SINGLE_HEADER):
os.remove(STARTER_PATH_OLD_SINGLE_HEADER)
# Update the version in the "redirect" header:
replace_text_in_file(
F"{self.details.starter_project_dir}/lib/ApprovalTests.hpp",
self.details.old_version, self.details.new_version)
# Update the version number in the Visual Studio project:
replace_text_in_file(
F"{self.details.starter_project_dir}/visual-studio-2017/StarterProject.vcxproj",
self.details.old_single_header, self.details.new_single_header)
def run(self, filename, filter_set,
asset_path, output_path,
interactive=False, verbose=False):
arguments = [
"-p", asset_path + "\\",
"-o", output_path + "\\",
"-s", filter_set]
if interactive:
arguments.append("-i")
arguments.append(filename)
command = [self.havok_filter_manager] + arguments
if verbose:
utilities.print_line()
print("Starting Havok Filter Manager...")
utilities.print_line(True)
print(' '.join(command))
# It's important that the current directory is set to the output path
# or it won't output to the expected directory
utilities.run(command, False, output_path)
return
def run_nc2prof(windfield_directory, verbose=True):
"""Run nc2prof - extract wind profiles from NCEP data
Requires
- input file
- NCEP wind files
TMP.nc
HGT.nc
UGRD.nc
VGRD.nc
"""
# FIXME: Perhaps include into AIM class (somehow)
Fall3d_dir = get_fall3d_home()
utilities_dir = os.path.join(Fall3d_dir, 'Utilities')
executable = os.path.join(utilities_dir, 'nc2prof', 'nc2prof.exe')
if verbose:
header('Running nc2prof in %s' % windfield_directory)
cmd = 'cd %s; %s ' % (windfield_directory, executable)
logfile = 'run_nc2prof.log'
run(cmd, verbose=verbose, stdout=logfile, stderr='/dev/null')
def set_granum(self, verbose=True):
"""Create grainsize profile
Requires
- input file
"""
grainfilename = self.scenario_name + '.grn'
if grainfilename in os.listdir('.'):
print 'Grainfile found - will not run SetGrn'
s = 'cp %s %s' % (grainfilename, self.grainfile)
run(s)
return
executable = os.path.join(self.utilities_dir,
'SetGrn', 'SetGrn.PUB.exe')
logfile = self.logbasepath + '.SetGrn.log'
if verbose:
header('Setting grain size (SetGrn)')
cmd = '%s %s %s %s' % (executable, logfile,
self.inputfile, self.grainfile)
self.runscript(cmd, 'SetGrn', logfile, lines=4,
verbose=verbose)
def run_nc2prof(windfield_directory, verbose=True):
"""Run nc2prof - extract wind profiles from NCEP data
Requires
- input file
- NCEP wind files
TMP.nc
HGT.nc
UGRD.nc
VGRD.nc
"""
# FIXME: Perhaps include into AIM class (somehow)
Fall3d_dir = get_fall3d_home()
utilities_dir = os.path.join(Fall3d_dir, 'Utilities')
executable = os.path.join(utilities_dir, 'nc2prof', 'nc2prof.exe')
if verbose:
header('Running nc2prof in %s' % windfield_directory)
cmd = 'cd %s; %s ' % (windfield_directory, executable)
logfile = 'run_nc2prof.log'
run(cmd, verbose=verbose, stdout=logfile, stderr='/dev/null')
def set_database(self, verbose=True):
"""Create meteorological database
Requires
- input file
- topography
- wind profile
"""
dbsfilename = self.scenario_name + '.dbs.nc'
if dbsfilename in os.listdir('.'):
print 'DBS file found - will not run SetDbs'
s = 'cp %s %s' % (dbsfilename, self.databasefile)
run(s)
return
executable = os.path.join(self.utilities_dir,
'SetDbs', 'SetDbs.PUB.exe')
logfile = self.logbasepath + '.SetDbs.log'
if verbose:
header('Building meteorological database (SetDbs)')
cmd = '%s '*7 % (executable, logfile,
self.inputfile, self.wind_profile,
self.databasefile,
self.topography, self.meteorological_model)
self.runscript(cmd, 'SetDbs', logfile, lines=5,
verbose=verbose)
def set_granum(self, verbose=True):
"""Create grainsize profile
Requires
- input file
"""
grainfilename = self.scenario_name + '.grn'
if grainfilename in os.listdir('.'):
print 'Grainfile found - will not run SetGrn'
s = 'cp %s %s' % (grainfilename, self.grainfile)
run(s)
return
executable = os.path.join(self.utilities_dir, 'SetGrn',
'SetGrn.PUB.exe')
logfile = self.logbasepath + '.SetGrn.log'
if verbose:
header('Setting grain size (SetGrn)')
cmd = '%s %s %s %s' % (executable, logfile, self.inputfile,
self.grainfile)
self.runscript(cmd, 'SetGrn', logfile, lines=4, verbose=verbose)
def set_database(self, verbose=True):
"""Create meteorological database
Requires
- input file
- topography
- wind profile
"""
dbsfilename = self.scenario_name + '.dbs.nc'
if dbsfilename in os.listdir('.'):
print 'DBS file found - will not run SetDbs'
s = 'cp %s %s' % (dbsfilename, self.databasefile)
run(s)
return
executable = os.path.join(self.utilities_dir, 'SetDbs',
'SetDbs.PUB.exe')
logfile = self.logbasepath + '.SetDbs.log'
if verbose:
header('Building meteorological database (SetDbs)')
cmd = '%s ' * 7 % (executable, logfile, self.inputfile,
self.wind_profile, self.databasefile,
self.topography, self.meteorological_model)
self.runscript(cmd, 'SetDbs', logfile, lines=5, verbose=verbose)
def install_ubuntu_packages():
"""Get required Ubuntu packages for geoserver.
It is OK if they are already installed
"""
header('Installing Ubuntu packages')
s = 'apt-get clean'
run(s, verbose=True)
#s = 'apt-get update'
#run(s, verbose=True)
for package in ['apache2', 'libxml2', 'libxml2-dev', 'libxslt1-dev', 'postgresql', 'postgis']:
s = 'apt-get -y install %s' % package
log_base = '%s_install' % package
try:
run(s,
stdout=log_base + '.out',
stderr=log_base + '.err',
verbose=True)
except:
msg = 'Installation of package %s failed. ' % package
msg += 'See log file %s.out and %s.err for details' % (log_base, log_base)
raise Exception(msg)
def install_ubuntu_packages():
"""Get required Ubuntu packages for geoserver.
It is OK if they are already installed
"""
header('Installing Ubuntu packages')
s = 'apt-get clean'
run(s, verbose=True)
#s = 'apt-get update'
#run(s, verbose=True)
for package in ['build-essential', 'libxaw7-dev']:
# Possibly also 'netcdfg-dev'
s = 'apt-get -y install %s' % package
log_base = '%s_install' % package
try:
run(s,
stdout=log_base + '.out',
stderr=log_base + '.err',
verbose=True)
except:
msg = 'Installation of package %s failed. ' % package
msg += 'See log file %s.out and %s.err for details' % (log_base, log_base)
raise Exception(msg)
def publish_tweet(self):
# Draft the tweet
check_step(
"that you have created a screenshot of the release notes, for the Tweet"
)
tweet_text = F"'https://twitter.com/intent/tweet?text=%23ApprovalTests.cpp+{self.details.new_version}+released%2C+now+with+___%21%0D%0Ahttps%3A%2F%2Fgithub.com%2Fapprovals%2FApprovalTests.cpp%2Freleases%2Ftag%2F{self.details.new_version}+%0D%0Aor+try+the+starter+project%3A+https%3A%2F%2Fgithub.com%2Fapprovals%2FApprovalTests.cpp.StarterProject%0D%0AThanks+%40LlewellynFalco+%40ClareMacraeUK+%21'"
run(["open", tweet_text])
check_step("that the tweet is published")
def publish_starter_project(self):
self.commit_starter_project()
self.push_starter_project()
run([
"open",
"https://github.com/approvals/ApprovalTests.cpp.StarterProject/commits/master"
])
check_step("that the starter project is published")
def restore_output(self, verbose=False):
"""Move files back for post processing
"""
for dir in os.listdir(self.output_dir):
if dir.endswith('h'):
s = 'mv %s/%s/* %s' % (self.output_dir, dir, self.output_dir)
run(s)
def restore_output(self, verbose=False):
"""Move files back for post processing
"""
for dir in os.listdir(self.output_dir):
if dir.endswith('h'):
s = 'mv %s/%s/* %s' % (self.output_dir, dir, self.output_dir)
run(s)
def organise_output(self, verbose=False):
"""Organise output files in directories by time
Output files named e.g.
merapi.grd.18may2010.03:00.depload.grd
are renamed to
merapi.03h.depload.asc
and will all go to a sub directory named 03h
"""
# FIXME: I think it is better to place them in their final locations from the start.
# Move log files away
#logdir = os.path.join(self.output_dir, 'logfiles')
#makedir(logdir)
#for file in os.listdir(self.output_dir):
# _, ext = os.path.splitext(file)
# if ext in ['.log', '.stdout', '.stderr']:
# filename = os.path.join(self.output_dir, file)
# s = 'mv %s %s' % (filename, logdir)
# run(s, verbose=False)
# FIXME: This really needs to use a proper standard for time stamps
dirname = None
last_hour = -1
last_dir = None
for file in os.listdir(self.output_dir):
if file.startswith(self.scenario_name):
fields = file.split('.')
if fields[1][-1] == 'h':
dirname = os.path.join(self.output_dir, fields[1])
filename = os.path.join(self.output_dir, file)
makedir(dirname)
s = 'mv %s %s' % (filename, dirname)
run(s, verbose=verbose)
# Record last hour
hour = int(fields[1][:-1])
if hour > last_hour:
last_hour = hour
last_dir = dirname
# Create shortcut to last dir
if last_dir:
s = 'ln -s %s %s/final_output' % (last_dir, self.output_dir)
try:
run(s, verbose=verbose)
except:
pass
def upload_release_to_github(self):
# Draft the upload to github
release_notes = read_file(self.details.new_release_notes_path)
pyperclip.copy(release_notes)
print('The release notes are on the clipboard')
github_url = F"'https://github.com/approvals/ApprovalTests.cpp/releases/new?tag={self.details.new_version}&title=Single%20Hpp%20File%20-%20{self.details.new_version}'"
run(["open", github_url])
run(["open", self.details.release_dir])
check_step("that the release is published")
def verify_signature(john_home):
# Verify signature
os.chdir(john_home)
print 'Current working dir', os.getcwd()
s = 'pgp -ka openwall-signatures.asc'
run(s, verbose=True)
s = 'pgp %s.tar.gz.sign %s.tar.gz' % (package_name, package_name)
run(s, verbose=True)
def create_useraccount_interactively(username):
if os.path.isfile(password_filename):
cmd = 'htpasswd -m'
else:
cmd = 'htpasswd -cm'
s = cmd + ' %s %s' % (password_filename, username)
run(s)
filenames_updated[password_filename] = 1
def predict(model_file_path, lable_feature_map_file_path, feature_extractors, input_file_path, prediction_file_path, output_file_path):
# build corpus for prediction
liblinear_file_path = input_file_path + ".liblinear"
corpus = Corpus(input_file_path, lable_feature_map_file_path, feature_extractors)
corpus.build(liblinear_file_path, is_for_training = False)
# predict -q -b 1 convert_to_liblinear.test.liblinear model.liblinear predict.predictions.liblinear
run(PREDICT_CMD + " -q -b 1 %s %s %s" % (liblinear_file_path, model_file_path, prediction_file_path))
lable_to_id_map = LabelFeatureMap.load_label_map(lable_feature_map_file_path)
prediction_parser = PredictionParser(lable_to_id_map)
prediction_parser.parse_predictions(prediction_file_path, output_file_path)
def organise_output(self, verbose=False):
"""Organise output files in directories by time
Output files named e.g.
merapi.grd.18may2010.03:00.depload.grd
are renamed to
merapi.03h.depload.asc
and will all go to a sub directory named 03h
"""
# FIXME: I think it is better to place them in their final locations from the start.
# Move log files away
#logdir = os.path.join(self.output_dir, 'logfiles')
#makedir(logdir)
#for file in os.listdir(self.output_dir):
# _, ext = os.path.splitext(file)
# if ext in ['.log', '.stdout', '.stderr']:
# filename = os.path.join(self.output_dir, file)
# s = 'mv %s %s' % (filename, logdir)
# run(s, verbose=False)
# FIXME: This really needs to use a proper standard for time stamps
dirname = None
last_hour = -1
last_dir = None
for file in os.listdir(self.output_dir):
if file.startswith(self.scenario_name):
fields = file.split('.')
if fields[1][-1] == 'h':
dirname = os.path.join(self.output_dir, fields[1])
filename = os.path.join(self.output_dir, file)
makedir(dirname)
s = 'mv %s %s' % (filename, dirname)
run(s, verbose=verbose)
# Record last hour
hour = int(fields[1][:-1])
if hour > last_hour:
last_hour = hour
last_dir = dirname
# Create shortcut to last dir
if last_dir:
s = 'ln -s %s %s/final_output' % (last_dir, self.output_dir)
try:
run(s, verbose=verbose)
except:
pass
def evaluate(model_file_path, lable_feature_map_file_path, feature_extractors,
input_file_path, prediction_output_file_path,
eval_output_file_path):
# build corpus for evaluation
liblinear_file_path = input_file_path + ".liblinear"
corpus = Corpus(input_file_path, lable_feature_map_file_path,
feature_extractors)
corpus.build(liblinear_file_path, is_for_training=False)
run(PREDICT_CMD + " -b 1 %s %s %s > %s" %
(liblinear_file_path, model_file_path, prediction_output_file_path,
eval_output_file_path))
def install_openlayers():
"""Install OpenLayers locally
This will allow web frontend to run without Internet access
"""
ol_dir = '/var/www/openlayers'
cmd = 'svn checkout http://svn.openlayers.org/trunk/openlayers/ %s' % ol_dir
run(cmd, verbose=True)
cmd = 'chown -R www-data:www-data %s' % ol_dir
run(cmd, verbose=True)
def run_startup():
"""Run geoserver startup script
"""
#cmd = '/etc/init.d/geoserver start'
#run(cmd, verbose=True)
geo_home = '/usr/local/%s' % geoserver
cmd = 'export JAVA_HOME=%s; export GEOSERVER_HOME=%s; $GEOSERVER_HOME/bin/startup.sh &' % (java_home,
geo_home)
run(cmd, verbose=True)
print 'Done'
def download():
""" Download ncview
"""
path = os.path.join(url, tarball)
if not os.path.isfile(tarball):
# FIXME: Should also check integrity of tgz file.
cmd = 'wget ' + path
run(cmd, verbose=True)
else:
print 'Using tarball: %s' % tarball
def Xgenerate_contours(self, interval=1, verbose=True):
"""Contour NetCDF grids directly
"""
# FIXME (Ole): This does not work - probably due to the GDAL NetCDF driver ignoring coordinate system
if verbose:
header('Contouring NetCDF thickness grids')
for filename in os.listdir(self.output_dir):
if filename.endswith('.res.nc'):
pathname = os.path.join(self.output_dir, filename)
if verbose: print ' ', pathname
basename, ext = os.path.splitext(pathname)
tiffile = basename + '.tif'
shpfile = basename + '.shp'
kmlfile = basename + '.kml'
prjfile = basename + '.prj'
# Generate GeoTIFF raster
netcdf_subdata = 'NETCDF:"%s":THICKNESS' % pathname
s = 'gdal_translate -of GTiff -b 1 %s %s' % (netcdf_subdata, tiffile) # FIXME: Band is hardwired
run_with_errorcheck(s, tiffile,
verbose=verbose)
# Generate contours as shapefiles
s = '/bin/rm -rf %s' % shpfile # Clear the way
run(s, verbose=False)
s = 'gdal_contour -i %f %s %s' % (interval, tiffile, shpfile)
run_with_errorcheck(s, shpfile,
verbose=verbose)
# Generate KML
if self.WKT_projection:
# Create associated projection file
fid = open(prjfile, 'w')
fid.write(self.WKT_projection)
fid.close()
s = 'ogr2ogr -f KML -t_srs EPSG:4623 -s_srs %s %s %s' % (prjfile, kmlfile, shpfile)
else:
s = 'ogr2ogr -f KML -t_srs EPSG:4623 %s %s' % (kmlfile, shpfile)
run_with_errorcheck(s, kmlfile,
verbose=verbose)
def store_inputdata(self, verbose=False):
"""Create exact copy of input data into output area
The intention is to ensure that all output has an audit trail.
"""
audit_dir = os.path.join(self.output_dir, 'input_data')
makedir(audit_dir)
# Store input files
if os.path.exists(self.params['wind_profile']):
s = 'cp %s %s' % (self.params['wind_profile'], audit_dir)
try:
run(s, verbose=verbose)
except:
pass
#s = 'cp %s %s' % (self.topography_grid, audit_dir)
#run(s, verbose=verbose)
# Copy only if scenario is a file.
scenario_file = self.params['scenario_name'] + '.py'
if os.path.isfile(scenario_file):
s = 'cp %s %s' % (scenario_file, audit_dir)
run(s, verbose=verbose)
else:
if verbose:
print(
'Scenario file "%s" does not exist. '
'Assuming scenario was specified as a dictionary' %
scenario_file)
# Store actual parameters (as Python file)
actual_params_file = os.path.join(audit_dir, 'actual_parameters.py')
#if os.path.isfile(actual_params_file):
# run('chmod +w %s' % actual_params_file, verbose=verbose) # In case it was there already
fid = open(actual_params_file, 'w')
fid.write('"""All actual parameters used in scenario %s\n\n'\
% self.basepath)
fid.write('This file is automatically generated by AIM\n')
fid.write('and in serves a log of all input parameters used in\n')
fid.write('Fall3d/AIM whether supplied or derived.\n')
fid.write('"""\n\n\n')
for param in self.params:
value = self.params[param]
if isinstance(value, basestring):
fid.write('%s = \'%s\'\n' % (param, value))
else:
fid.write('%s = %s\n' % (param, value))
fid.close()
def install_python_packages():
"""Python packages that are not part of Ubuntu
"""
# OWSLIB frozen at r1672 (5 August 2010)
try:
import owslib
except:
cmd = 'cd /tmp; svn co -r 1672 http://svn.gispython.org/svn/gispy/OWSLib/trunk OWSLib'
run(cmd)
cmd = 'cd /tmp/OWSLib; sudo python setup.py install'
run(cmd)
def store_inputdata(self, verbose=False):
"""Create exact copy of input data into output area
The intention is to ensure that all output has an audit trail.
"""
audit_dir = os.path.join(self.output_dir, 'input_data')
makedir(audit_dir)
# Store input files
if os.path.exists(self.params['wind_profile']):
s = 'cp %s %s' % (self.params['wind_profile'], audit_dir)
try:
run(s, verbose=verbose)
except:
pass
#s = 'cp %s %s' % (self.topography_grid, audit_dir)
#run(s, verbose=verbose)
# Copy only if scenario is a file.
scenario_file = self.params['scenario_name'] + '.py'
if os.path.isfile(scenario_file):
s = 'cp %s %s' % (scenario_file, audit_dir)
run(s, verbose=verbose)
else:
if verbose:
print ('Scenario file "%s" does not exist. '
'Assuming scenario was specified as a dictionary'
% scenario_file)
# Store actual parameters (as Python file)
actual_params_file = os.path.join(audit_dir, 'actual_parameters.py')
#if os.path.isfile(actual_params_file):
# run('chmod +w %s' % actual_params_file, verbose=verbose) # In case it was there already
fid = open(actual_params_file, 'w')
fid.write('"""All actual parameters used in scenario %s\n\n'\
% self.basepath)
fid.write('This file is automatically generated by AIM\n')
fid.write('and in serves a log of all input parameters used in\n')
fid.write('Fall3d/AIM whether supplied or derived.\n')
fid.write('"""\n\n\n')
for param in self.params:
value = self.params[param]
if isinstance(value, basestring):
fid.write('%s = \'%s\'\n' % (param, value))
else:
fid.write('%s = %s\n' % (param, value))
fid.close()
def backup(project):
dumppath = join(backup_dir, project)
makedir(dumppath, cd=False)
# Dump SVN repository
projectpath = join(svn_home, project)
dumpfile = join(dumppath, svndumpname)
s = 'svnadmin dump %s > %s 2> %s' % (projectpath, dumpfile, errlog)
err = run(s)
if err != 0:
print 'WARNING: SVN dump did not succeed for project %s. Error message was' % project
run('cat %s' % errlog, verbose=False)
# Dump TRAC system
projectpath = join(trac_home, project)
dumpdir = join(dumppath, tracdumpname)
run('/bin/rm -rf %s' % dumpdir, verbose=False) # Clean up in case there was one already
s = 'trac-admin %s hotcopy %s > %s 2> %s' % (projectpath, dumpdir, logfile, errlog)
err = run(s)
if err != 0:
print 'WARNING: TRAC hotcopy did not succeed for project %s. Error message was' % project
run('cat %s' % errlog, verbose=False)
os.remove(errlog)
os.remove(logfile)
def get_plugins():
"""Get plugins such as REST
"""
path = geoserver_rest_plugin_url
if not os.path.isfile(geoserver_rest_plugin):
# FIXME: Should also check integrity of zip file.
cmd = 'wget ' + path
run(cmd, verbose=True)
# Unpack into geoserver installation
s = 'unzip %s -d /usr/local/%s/webapps/geoserver/WEB-INF/lib' % (geoserver_rest_plugin, geoserver)
run(s, verbose=True)
def install_postgis_from_source(postgis):
makedir(os.path.expanduser('~/Downloads'))
if not os.path.exists('%s.tar.gz' % postgis):
s = 'wget http://postgis.refractions.net/download/%s.tar.gz' % postgis
run(s)
s = 'tar xvfz %s.tar.gz' % postgis; run(s)
os.chdir(postgis)
s = './configure'; run(s)
s = 'make'; run(s)
s = 'make install'; run(s)
def train(model_file_path, lable_feature_map_file_path, feature_extractors, input_file_path):
# build corpus for evaluation
un_compacted_model_file_path = model_file_path + ".tmp"
un_compacted_lable_feature_map_file_path = lable_feature_map_file_path + ".tmp"
liblinear_file_path = input_file_path + ".liblinear"
corpus = Corpus(input_file_path, un_compacted_lable_feature_map_file_path, feature_extractors)
corpus.build(liblinear_file_path, is_for_training = True)
# train model
# train -s 6 -e 0.01 -c 3.0 -p 0.1 -B -1 -W /gpfs/nlu/data/users/xiaoliu/svn/git_root/dragon-mobile-assistant-nlu-switch/training/hertz_nlucore_main_lxh_prediction_annotator_feature_extractor_with_david_model/domain_classifier/cross_validation/fold_0/train_liblinear/convert_to_liblinear.weight.liblinear /gpfs/nlu/data/users/xiaoliu/svn/git_root/dragon-mobile-assistant-nlu-switch/training/hertz_nlucore_main_lxh_prediction_annotator_feature_extractor_with_david_model/domain_classifier/cross_validation/fold_0/train_liblinear/convert_to_liblinear.train.liblinear /gpfs/nlu/data/users/xiaoliu/svn/git_root/dragon-mobile-assistant-nlu-switch/training/hertz_nlucore_main_lxh_prediction_annotator_feature_extractor_with_david_model/domain_classifier/cross_validation/fold_0/train_liblinear/model.liblinear
run(TRAIN_CMD + " -s 6 -e 0.01 -c 3.0 -p 0.1 -B -1 %s %s" % (liblinear_file_path, un_compacted_model_file_path))
# compact model
compact(un_compacted_lable_feature_map_file_path, un_compacted_model_file_path, lable_feature_map_file_path, model_file_path)
os.remove(un_compacted_model_file_path)
os.remove(un_compacted_lable_feature_map_file_path)
def check_conan_repo(self):
repo = Repo(self.details.conan_repo_dir)
assert not repo.bare
# TODO Add descriptions in case of failure
assert (repo.active_branch.name == 'master')
assert (len(repo.index.diff(None)) == 0) # Modified
assert (len(repo.index.diff("HEAD")) == 0) # Staged
run(["open", "https://github.com/conan-io/conan/releases"])
run(["conan", "--version"])
# TODO pip3 install --upgrade conan
check_step("you are running the latest Conan release")
def create_single_header_file(self):
os.chdir("../ApprovalTests")
print(os.getcwd())
run(["java", "-version"])
run([
"java", "-jar", "../build/SingleHpp.v.0.0.2.jar",
self.details.release_new_single_header
])
text = read_file(self.details.release_new_single_header)
text = \
F"""// Approval Tests version {self.details.new_version}
// More information at: https://github.com/approvals/ApprovalTests.cpp
{text}"""
write_file(self.details.release_new_single_header, text)
def Xgenerate_contours(self, interval=1, verbose=True):
"""Contour NetCDF grids directly
"""
# FIXME (Ole): This does not work - probably due to the GDAL NetCDF driver ignoring coordinate system
if verbose:
header('Contouring NetCDF thickness grids')
for filename in os.listdir(self.output_dir):
if filename.endswith('.res.nc'):
pathname = os.path.join(self.output_dir, filename)
if verbose: print ' ', pathname
basename, ext = os.path.splitext(pathname)
tiffile = basename + '.tif'
shpfile = basename + '.shp'
kmlfile = basename + '.kml'
prjfile = basename + '.prj'
# Generate GeoTIFF raster
netcdf_subdata = 'NETCDF:"%s":THICKNESS' % pathname
s = 'gdal_translate -of GTiff -b 1 %s %s' % (
netcdf_subdata, tiffile) # FIXME: Band is hardwired
run_with_errorcheck(s, tiffile, verbose=verbose)
# Generate contours as shapefiles
s = '/bin/rm -rf %s' % shpfile # Clear the way
run(s, verbose=False)
s = 'gdal_contour -i %f %s %s' % (interval, tiffile, shpfile)
run_with_errorcheck(s, shpfile, verbose=verbose)
# Generate KML
if self.WKT_projection:
# Create associated projection file
fid = open(prjfile, 'w')
fid.write(self.WKT_projection)
fid.close()
s = 'ogr2ogr -f KML -t_srs EPSG:4623 -s_srs %s %s %s' % (
prjfile, kmlfile, shpfile)
else:
s = 'ogr2ogr -f KML -t_srs EPSG:4623 %s %s' % (kmlfile,
shpfile)
run_with_errorcheck(s, kmlfile, verbose=verbose)
def test_conan_and_create_pr(self):
# TODO Fix this directory name
pushdir(self.details.conan_data_dir)
# We cannot test the new Conan recipe until the new release has been
# published on github
new_version_without_v = version.get_version_without_v(
self.details.new_version)
run(['conan', 'create', '.', F'{new_version_without_v}@'])
# TODO Commit the changes - with message f'Add approvaltests.cpp {new_version_without_v}'
# TODO Push the changes - NB on the feature branch for the release
popdir()
check_step(
"that you have created a Pull Request for conan-center-index?")
def runscript(self, cmd, name, logfile, lines=5, verbose=False):
"""Run Fall3d script and report
"""
if verbose:
print 'Logfile: %s' % logfile
#print 'Shortcut: %s' % os.path.join(self.symlink, os.path.split(logfile)[-1])
stdout = self.logbasepath + '.%s.stdout' % name
stderr = self.logbasepath + '.%s.stderr' % name
err=run(cmd,
stdout=stdout,
stderr=stderr,
verbose=False)
if verbose:
print 'Logfile ended as follows:'
tail(logfile, lines)
if err:
msg = 'Script %s ended abnormally. Log files are:\n' % cmd
msg += ' %s\n' % logfile
msg += ' %s\n' % stdout
msg += ' %s\n' % stderr
raise Exception(msg)
def install_ubuntu_packages():
"""Get required PostGIS packages.
It is OK if they are already installed
"""
for package in ['postgresql',
'postgresql-server-dev-8.4',
'proj',
'libgeos-dev',
'postgis', # For things like shp2pgsql
#'pgadmin3',
#'libpq-dev',
#'postgresql-contrib',
]:
s = 'apt-get -y install %s > %s_install.log' % (package, package)
run(s)
def get_plugins():
"""Get plugins such as REST
"""
path = geoserver_rest_plugin_url
archive = workdir + '/' + geoserver_rest_plugin
print 'Archive', archive
if not os.path.isfile(archive):
# FIXME: Should also check integrity of zip file.
cmd = 'cd %s; wget %s' % (workdir, path)
run(cmd, verbose=True)
# Unpack into geoserver installation
s = 'unzip %s -d /usr/local/%s/webapps/geoserver/WEB-INF/lib' % (archive,
geoserver)
run(s, verbose=True)
def check_pre_conditions_for_publish(self):
if self.details.push_to_production:
repo = Repo(self.details.main_project_dir)
assert not repo.bare
assert (repo.active_branch.name == 'master')
# From https://stackoverflow.com/questions/31959425/how-to-get-staged-files-using-gitpython
assert len(
repo.index.diff(None)
) == 0, "there are un-committed changes to ApprovalTests.cpp" # Modified
assert len(
repo.index.diff("HEAD")
) == 0, "there are un-committed changes to ApprovalTests.cpp" # Staged
# From https://stackoverflow.com/questions/15849640/how-to-get-count-of-unpublished-commit-with-gitpython
assert len(
list(repo.iter_commits('master@{u}..master'))
) == 0, "there are un-pushed changes in ApprovalTests.cpp"
run([
"open",
"https://github.com/approvals/ApprovalTests.cpp/commits/master"
])
check_step("the builds are passing")
run([
"open",
"https://github.com/approvals/ApprovalTests.cpp/blob/master/build/relnotes_x.y.z.md"
])
run([
"open",
F"https://github.com/approvals/ApprovalTests.cpp/compare/{self.details.old_version}...master"
])
check_step("the release notes are ready")
run(["open", "https://github.com/approvals/ApprovalTests.cpp/issues"])
check_step("any issues resolved in this release are closed")
run([
"open", "https://github.com/approvals/ApprovalTests.cpp/milestones"
])
check_step(
"the milestone (if any) is up to date, including actual version number of release"
)
def run(self, filename):
arguments = []
arguments.append(filename)
utilities.print_line()
print("Starting Havok Filter Manager...")
command = [self.havok_tool_standalone] + arguments
utilities.print_line(True)
print(' '.join(command))
cd = os.path.dirname(filename)
# It's important that the current directory is set to the output path
# or it won't output to the expected directory
utilities.run(command, False, cd)
return
def parseeazy(catalog, n):
from utilities import run
import os
f = open(catalog, 'r').readlines()
sntmp = open('sntmp', 'w')
keys = []
for line in f:
if line[0:2] == '# ':
import re
res2 = re.split('\s+', line[:-1])
print res2
for k in res2[1:]:
keys.append('EAZY_' + k)
break
if line[0] != '#':
break
print keys
tempconf = '/tmp/' + os.environ['USER'] + 'photoz.conf'
conflist = open(tempconf, 'w')
for key in keys:
if key == 'EAZY_id':
conflist.write(
'COL_NAME = SeqNr\nCOL_TTYPE = LONG\nCOL_HTYPE = INT\nCOL_COMM = ""\nCOL_UNIT = ""\nCOL_DEPTH = 1\n#\n'
)
else:
conflist.write(
'COL_NAME = ' + key +
'\nCOL_TTYPE = DOUBLE\nCOL_HTYPE = FLOAT\nCOL_COMM = ""\nCOL_UNIT = ""\nCOL_DEPTH = 1\n#\n'
)
conflist.close()
import os
tempcat = '/tmp/' + os.environ['USER'] + 'zs.cat'
run(
'asctoldac -i ' + catalog + ' -o ' + catalog + '.temp.tab' + ' -c ' +
tempconf + ' -t STDTAB', [tempcat])
command = 'ldacaddkey -i ' + catalog + '.temp.tab -o ' + catalog + '.tab -t STDTAB -k EAZY_NUMBER ' + str(
n) + ' FLOAT "" '
print command
os.system(command)
print catalog + '.tab'
def download_john_source(john_home):
makedir(john_home)
os.chdir(john_home)
print 'Current working dir', os.getcwd()
# Clean out
s = '/bin/rm -rf %s/*' % john_home
run(s, verbose=True)
# Get source and verification
files = ['http://www.openwall.com/john/g/%s.tar.gz' % package_name,
'http://www.openwall.com/john/g/%s.tar.gz.sign' % package_name,
'http://www.openwall.com/signatures/openwall-signatures.asc']
for file in files:
path = os.path.join(john_home, file)
s = 'wget %s' % file
run(s, verbose=True)
def run_hazardmap(model_output_directory, verbose=True):
"""Run HazardMapping.exe
Requires
- input file
- Directory with FALL3D model outputs
"""
# FIXME: Perhaps include into AIM class (somehow)
Fall3d_dir = get_fall3d_home()
utilities_dir = os.path.join(Fall3d_dir, 'Utilities')
executable = os.path.join(utilities_dir, 'HazardMaps', 'HazardMapping.exe')
if verbose:
header('Running hazard mapping in %s' % model_output_directory)
cmd = 'cd %s; %s ' % (model_output_directory, executable)
logfile = 'run_hazardmapping.log'
run(cmd, verbose=verbose, stdout=logfile, stderr='/dev/null')
def run_hazardmap(model_output_directory, verbose=True):
"""Run HazardMapping.exe
Requires
- input file
- Directory with FALL3D model outputs
"""
# FIXME: Perhaps include into AIM class (somehow)
Fall3d_dir = get_fall3d_home()
utilities_dir = os.path.join(Fall3d_dir, 'Utilities')
executable = os.path.join(utilities_dir, 'HazardMaps', 'HazardMapping.exe')
if verbose:
header('Running hazard mapping in %s' % model_output_directory)
cmd = 'cd %s; %s ' % (model_output_directory, executable)
logfile = 'run_hazardmapping.log'
run(cmd, verbose=verbose, stdout=logfile, stderr='/dev/null')
def test_conan_and_create_pr(self):
pushdir(os.path.join(self.details.conan_approvaltests_dir, 'all'))
# We cannot test the new Conan recipe until the new release has been
# published on github
new_version_without_v = version.get_version_without_v(
self.details.new_version)
run(['conan', 'create', '.', F'{new_version_without_v}@'])
check_step(
F"Commit the changes - with message 'Add approvaltests.cpp {new_version_without_v}'"
)
check_step(
'Push the changes - NB on the feature branch for the release')
popdir()
print(
F"Create a pull request, including this in the description: **approvaltests.cpp/{new_version_without_v}**"
)
check_step(
"that you have created a Pull Request for conan-center-index?")
def parsebpz(catalog, n):
'''this adds BPZ_NUMBER on the end, but it's always =0 currently (see /nfs/slac/g/ki/ki18/anja/SUBARU/MACS1226+21/PHOTOMETRY_W-C-RC_aper/all_bpzAPER1CWWSB_capak.list1_0.bpz.tab.txt)'''
import os, re
from utilities import run
f = open(catalog, 'r').readlines()
sntmp = open(os.environ['USER'] + 'sntmp', 'w')
keys = []
for line in f:
if line[0:2] == '# ':
res2 = re.split('\s+', line[:-1])
print res2
keys.append('BPZ_' + res2[2])
if line[0] != '#':
break
tempconf = '/tmp/' + os.environ['USER'] + 'photoz.conf'
conflist = open(tempconf, 'w')
for key in keys:
if key == 'BPZ_ID':
conflist.write(
'COL_NAME = SeqNr\nCOL_TTYPE = LONG\nCOL_HTYPE = INT\nCOL_COMM = ""\nCOL_UNIT = ""\nCOL_DEPTH = 1\n#\n'
)
else:
conflist.write(
'COL_NAME = ' + key +
'\nCOL_TTYPE = DOUBLE\nCOL_HTYPE = FLOAT\nCOL_COMM = ""\nCOL_UNIT = ""\nCOL_DEPTH = 1\n#\n'
)
conflist.close()
tempcat = '/tmp/' + os.environ['USER'] + 'zs.cat'
run(
'asctoldac -i ' + catalog + ' -o ' + catalog + '.temp.tab' + ' -c ' +
tempconf + ' -t STDTAB', [tempcat])
command = 'ldacaddkey -i ' + catalog + '.temp.tab -o ' + catalog + '.tab -t STDTAB -k BPZ_NUMBER ' + str(
n) + ' FLOAT "" '
print ' command=', command
os.system(command)
print catalog + '.tab'
print 'here'
def cutout(infile, color='red'):
import os, utilities
ppid = str(os.getppid())
print ppid + 'a'
#pylab.show()
outfile = raw_input('name of output file?')
color = raw_input('color of regions?')
limits = ['lower_mag', 'upper_mag', 'lower_diff', 'upper_diff']
lim_dict = {}
for lim in limits:
print lim + '?'
b = raw_input()
lim_dict[lim] = b
utilities.run(
'ldacfilter -i ' + infile + ' -t PSSC\
-c "(((SEx_' + mag + '_' + filter + '>' +
str(lim_dict['lower_mag']) + ') AND (SEx_' + mag + '_' + filter + '<' +
str(lim_dict['upper_mag']) + ')) AND (magdiff>' +
str(lim_dict['lower_diff']) + ')) AND (magdiff<' +
str(lim_dict['upper_diff']) + ');"\
-o cutout1.' + ppid, ['cutout1.' + ppid])
utilities.run(
'ldactoasc -b -q -i cutout1.' + ppid + ' -t PSSC\
-k Ra Dec > /tmp/' + outfile, ['/tmp/' + outfile])
utilities.run('mkreg.pl -c -rad 8 -xcol 0 -ycol 1 -wcs -colour ' + color +
' /tmp/' + outfile)
def compile_ncview():
"""Configure and make
"""
cmd = 'cd %s; ./configure' % ncview
run(cmd)
cmd = 'cd %s; make' % ncview
run(cmd)
cmd = 'cd %s; make install' % ncview
run(cmd)
def extract():
"""Extract files from tarball
"""
# Cleanup
#s = '/bin/rm -rf %s' % fall3d_distro
#run(s, verbose=False)
print 'Unpacking tarball'
print
# Unpack FALL3D using tar:
#
# x: Extract
# v: Be verbose
# f: Filename coming up
# z: Uncompress as well
#
err = run('tar xvfz %s > /dev/null' % tarball, verbose=False)
if err != 0:
msg = 'Could not unpack %s' % tarball
raise Exception(msg)