def cleanAmberProject(sourceDirectory):
for file in scandir(sourceDirectory):
if path.isdir(file):
cleanAmberProject(file)
else:
if "AmberProblem.txt" in file.name:
os.remove(file)
def creation_directory(directory: str):
"""
This function allows you to factor out the verification
for the creation of the results file
"""
if path.isdir(directory):
pass
else:
mkdir(directory)
def mkdir_p(mypath):
from errno import EEXIST
from os import makedirs,path
try:
makedirs(mypath)
except OSError as exc:
if exc.errno == EEXIST and path.isdir(mypath):
pass
else: raise
def foundLegacyKeyStore(repository):
found = False
#find if any jks file in the project
for file in scandir(repository):
if path.isdir(file):
found = foundLegacyKeyStore(file)
if found:
return found
elif '.jks' in file.name.lower():
return True
return found
def getTranslatorHome ():
# Check that the path to the translator can be found before returning its absolute path
from string import split
from os import environ, path, pathsep
translatorEnvVariable = 'IMPERIAL_TRANSLATOR_HOME'
if not environ.has_key(translatorEnvVariable):
errorMessage = "=" * 80 + \
"\nYou need to set the environment variable '" + translatorEnvVariable + "' to point to the base directory of the translator infrastructure." + \
"\nThis is the path ending with the directory 'OP2_ROSE_Fortran'." + \
"\nFor example, 'export IMPERIAL_TRANSLATOR_HOME=/usr/joe/bloggs/subdir/OP_ROSE_FORTRAN'\n" + "=" * 80
debug.exitMessage(errorMessage)
translatorHome = split(environ.get(translatorEnvVariable), pathsep)[0]
if not path.isdir(translatorHome):
debug.exitMessage("The source-to-source translator path '%s' is not a directory" % (translatorHome))
return translatorHome
def process_wattbike_cfg(**kwargs):
'''
read in a config variables, validate and process
will return the index of the fields in the dat file
minimum args expected are:
valid_config_keys, valid_headers, valid_mavg_units, valid_delim
headers, delim, mavg, mavg_unit, dir_name, datfile_delim, dir_ext
'''
try:
for k in valid_config_keys:
kwargs[k]
except:
raise MissingConfigException(k)
fields = kwargs['header'].split(kwargs['delim'])
# validate that config values are ok
field_indexes=[]
for f in fields:
try:
index = kwargs['valid_headers'].index(f)
field_indexes.append(index)
except ValueError:
raise UnknownHeaderException(f)
if kwargs['mavg'] < 0 or kwargs['mavg'] > 100:
raise MAVGOutOfRangeException(kwargs['mavg'])
if not kwargs['mavg_unit'] in kwargs['valid_mavg_units']:
raise InvalidMAVG_UNITException(kwargs['mavg_unit'])
if not kwargs['delim'] in kwargs['valid_delims']:
raise InvalidDELIMException(kwargs['delim'])
if not kwargs['datfile_delim'] in kwargs['valid_delims']:
raise InvalidDATFILE_DELIMException(kwargs['datfile_delim'])
if not path.isdir(kwargs['dir_name']):
raise InvalidDIR_NAMEException(kwargs['dir_name'])
return(field_indexes)
def findValueOfTheVersionOfDependencyRecurse(versionVar, repository):
#find all files with .properties or .gradle extension
# print("Trying to find out this :"+repository)
#search the key in them
for file in scandir(repository):
# print("in scanDir with :"+file.path)
if path.isdir(file):
# print("Recurse with :"+file.path)
result = findValueOfTheVersionOfDependencyRecurse(
versionVar, file.path)
if result != None:
return result
else:
if ".gradle" in file.name or ".properties" in file.name:
#read the file
fileStream = open(file, "r")
for line in fileStream:
if versionVar in line and "=" in line:
result = line.split("=")[-1].replace("\n", "")
# print("Have found version value of "+versionVar+"="+result)
return result
return None
def parse_stats_from_runs(experiment_name):
"""
Analyses a list of given stats from a group of runs saved under an
"experiment_name" folder. Creates a summary .csv file which can be used by
plotting functions in utilities.save_plot. Saves a file of the format:
run0_gen0 run1_gen0 . . . run(n-1)_gen0
run0_gen1 run1_gen1 . . . run(n-1)_gen1
run0_gen2 run1_gen2 . . . run(n-1)_gen2
. . . . . .
. . . . . .
. . . . . .
run0_gen(n-1) run1_gen(n-1) . . . run(n-1)_gen(n-1)
run0_gen(n) run1_gen(n) . . . run(n-1)_gen(n)
Generated file is compatible with
utilities.save_plot.save_average_plot_across_runs()
:param experiment_name: The name of a collecting folder within the
./results folder which holds multiple runs.
:param graph: A boolean flag for whether or not to save figure.
:return: Nothing.
"""
# Since results files are not kept in source directory, need to escape
# one folder.
file_path = path.join(getcwd(), "..", "results")
# Check for use of experiment manager.
if experiment_name:
file_path = path.join(file_path, experiment_name)
else:
s = "scripts.parse_stats.parse_stats_from_runs\n" \
"Error: experiment name not specified."
raise Exception(s)
# Find list of all runs contained in the specified folder.
runs = [
run for run in listdir(file_path)
if path.isdir(path.join(file_path, run))
]
# Place to store the header for full stats file.
header = ""
# Array to store all stats
full_stats = []
# Get list of all stats to parse. Check stats file of first run from
# runs folder.
ping_file = path.join(file_path, str(runs[0]), "stats.tsv")
# Load in data and get the names of all stats.
stats = list(pd.read_csv(ping_file, sep="\t"))
# Make list of stats we do not wish to parse.
no_parse_list = ["gen", "total_inds", "time_adjust"]
for stat in [
stat for stat in stats
if stat not in no_parse_list and not stat.startswith("Unnamed")
]:
# Iterate over all stats.
print("Parsing", stat)
summary_stats = []
# Iterate over all runs
for run in runs:
# Get file name
file_name = path.join(file_path, str(run), "stats.tsv")
# Load in data
data = pd.read_csv(file_name, sep="\t")
try:
# Try to extract specific stat from the data.
if list(data[stat]):
summary_stats.append(list(data[stat]))
else:
s = "scripts.parse_stats.parse_stats_from_runs\n" \
"Error: stat %s is empty for run %s." % (stat, run)
raise Exception(s)
except KeyError:
# The requested stat doesn't exist.
s = "scripts.parse_stats.parse_stats_from_runs\nError: " \
"stat %s does not exist in run %s." % (stat, run)
raise Exception(s)
try:
# Generate numpy array of all stats
summary_stats = np.array(summary_stats)
# Append Stat to header.
header = header + stat + "_mean,"
summary_stats_mean = np.nanmean(summary_stats, axis=0)
full_stats.append(summary_stats_mean)
# Append Stat to header.
header = header + stat + "_std,"
summary_stats_std = np.nanstd(summary_stats, axis=0)
full_stats.append(summary_stats_std)
summary_stats = np.transpose(summary_stats)
# Save stats as a .csv file.
np.savetxt(path.join(file_path, (stat + ".csv")),
summary_stats,
delimiter=",")
# Graph stat by calling graphing function.
save_average_plot_across_runs(path.join(file_path,
(stat + ".csv")))
except FloatingPointError:
print("scripts.stats_parser.parse_stats_from_runs\n"
"Warning: FloatingPointError encountered while parsing %s "
"stats." % (stat))
# Convert and rotate full stats
full_stats = np.array(full_stats)
full_stats = np.transpose(full_stats)
# Save full stats to csv file.
np.savetxt(path.join(file_path, "full_stats.csv"),
full_stats,
delimiter=",",
header=header[:-1])
"SingleEleCR": "Wen",
"SingleMuCR": "Wmn",
"GammaCR": "gjets"
}
procmap = {
"Data": "data",
"ZJets": "zjets",
"WJets": "wjets",
"DYJets": "zll",
"GJets": "gjets",
"TTJets": "top",
"DiBoson": "diboson",
"QCD": "qcd"
}
signalmap = {"Axial": "axial"}
if not path.isdir("Systematics"): mkdir("Systematics")
def validHisto(hs, total=0, threshold=0.2):
return hs.Integral() > threshold * total
def validShape(up, dn):
return any(up[ibin] != dn[ibin]
for ibin in range(1,
up.GetNbinsX() +
1)) and validHisto(up) and validHisto(dn)
def SaveRegion(region, save):
region = Region(path=region, show=False, autovar=True)
def migrateGradleBuildFile(repository, projectMetaData):
print(RED +
'\n\n\n\nStarting a new Migration\n-------------------------\n')
print(RED + 'Working dir:' + repository)
print(RED + 'ROOT_PYTHON_PATH:' + ROOT_PYTHON_PATH)
#check if it's an Eclipse project
if not path.isdir(repository + '\\src'):
print(RED + "Not an eclipse project, returning")
return
global REPO_NAME
REPO_NAME = repository.split('\\')[-1]
print(RED + 'RepoName is the following:' + REPO_NAME)
#First open the source gradle file
buildGradle = repository + "\\app\\build.gradle"
#Parse it and paste it in a temp file:
#Need to find the file
referentGradleBuildFile = open(buildGradle, "r")
destinationFile = open(buildGradle + '_temp', "w+")
#and update it according to our generic config file
dependenciesBloc = False
signingConfigBloc = False
#the depth when reading dependencies in {}
dependencyDepth = 0
signingConfigDepth = 0
for line in referentGradleBuildFile:
#When reaching signing config, keep source
if (dependenciesBloc):
#managing depth in {} bloc
if '{' in line:
dependencyDepth = dependencyDepth + 1
elif '}' in line:
dependencyDepth = dependencyDepth - 1
if (dependencyDepth == 0):
#add the crashlitics and the junit blocs
dependenciesBloc = False
#Do the stuff: Log those you don't find in ref
pass
if (signingConfigBloc):
#Probably a more general problem, linked with keystore: As to be handled by ProjMetaData
#managing depth in {} bloc
if '{' in line:
signingConfigDepth = signingConfigDepth + 1
elif '}' in line:
signingConfigDepth = signingConfigDepth - 1
if (signingConfigDepth == 0):
signingConfigBloc = False
#you are in signin in, just copy initial element from your ProjectMetaData
# You also have this block later to handle :'(
# buildTypes {
# release {
# signingConfig signingConfigs.release
# minifyEnabled true
# shrinkResources true
# useProguard true
# proguardFiles getDefaultProguardFile('proguard-android.txt'), 'proguard-rules.pro'
# //add tests coverage using Jacoco
# testCoverageEnabled false
# }
# debug {
# // Run code coverage reports by default on debug builds.
# // testCoverageEnabled = true
# signingConfig signingConfigs.debug
# applicationIdSuffix '.debug'
# versionNameSuffix '.debug'
# //add tests coverage using Jacoco
# testCoverageEnabled true
# useProguard false
# }
# }
pass
else:
if 'dependencies' in line:
dependencyDepth = 1
dependenciesBloc = True
elif 'signingConfigs {' in line:
signingConfigDepth = 1
signingConfigBloc = True
#When reaching the dependencies block, use our own line if not already the good format
#List all the unknown library
#else copy line
destinationFile.write(line)
destinationFile.close
referentGradleBuildFile.close
def parse_stats_from_runs(experiment_name):
"""
Analyses a list of given stats from a group of runs saved under an
"experiment_name" folder. Creates a summary .csv file which can be used by
plotting functions in utilities.save_plot. Saves a file of the format:
run0_gen0 run1_gen0 . . . run(n-1)_gen0
run0_gen1 run1_gen1 . . . run(n-1)_gen1
run0_gen2 run1_gen2 . . . run(n-1)_gen2
. . . . . .
. . . . . .
. . . . . .
run0_gen(n-1) run1_gen(n-1) . . . run(n-1)_gen(n-1)
run0_gen(n) run1_gen(n) . . . run(n-1)_gen(n)
Generated file is compatible with
utilities.save_plot.save_average_plot_across_runs()
:param experiment_name: The name of a collecting folder within the
./results folder which holds multiple runs.
:param graph: A boolean flag for whether or not to save figure.
:return: Nothing.
"""
# Since results files are not kept in source directory, need to escape
# one folder.
file_path = path.join(getcwd(), "..", "results")
# Check for use of experiment manager.
if experiment_name:
file_path = path.join(file_path, experiment_name)
else:
s = "scripts.parse_stats.parse_stats_from_runs\n" \
"Error: experiment name not specified."
raise Exception(s)
# Find list of all runs contained in the specified folder.
runs = [run for run in listdir(file_path) if
path.isdir(path.join(file_path, run))]
# Place to store the header for full stats file.
header = ""
# Array to store all stats
full_stats = []
# Get list of all stats to parse. Check stats file of first run from
# runs folder.
ping_file = path.join(file_path, str(runs[0]), "stats.tsv")
# Load in data and get the names of all stats.
stats = list(pd.read_csv(ping_file, sep="\t"))
# Make list of stats we do not wish to parse.
no_parse_list = ["gen", "total_inds", "time_adjust"]
for stat in [stat for stat in stats if stat not in no_parse_list and
not stat.startswith("Unnamed")]:
# Iterate over all stats.
print("Parsing", stat)
summary_stats = []
# Iterate over all runs
for run in runs:
# Get file name
file_name = path.join(file_path, str(run), "stats.tsv")
# Load in data
data = pd.read_csv(file_name, sep="\t")
try:
# Try to extract specific stat from the data.
if list(data[stat]):
summary_stats.append(list(data[stat]))
else:
s = "scripts.parse_stats.parse_stats_from_runs\n" \
"Error: stat %s is empty for run %s." % (stat, run)
raise Exception(s)
except KeyError:
# The requested stat doesn't exist.
s = "scripts.parse_stats.parse_stats_from_runs\nError: " \
"stat %s does not exist in run %s." % (stat, run)
raise Exception(s)
try:
# Generate numpy array of all stats
summary_stats = np.array(summary_stats)
# Append Stat to header.
header = header + stat + "_mean,"
summary_stats_mean = np.nanmean(summary_stats, axis=0)
full_stats.append(summary_stats_mean)
# Append Stat to header.
header = header + stat + "_std,"
summary_stats_std = np.nanstd(summary_stats, axis=0)
full_stats.append(summary_stats_std)
summary_stats = np.transpose(summary_stats)
# Save stats as a .csv file.
np.savetxt(path.join(file_path, (stat + ".csv")), summary_stats,
delimiter=",")
# Graph stat by calling graphing function.
save_average_plot_across_runs(path.join(file_path, (stat +
".csv")))
except FloatingPointError:
print("scripts.stats_parser.parse_stats_from_runs\n"
"Warning: FloatingPointError encountered while parsing %s "
"stats." % (stat))
# Convert and rotate full stats
full_stats = np.array(full_stats)
full_stats = np.transpose(full_stats)
# Save full stats to csv file.
np.savetxt(path.join(file_path, "full_stats.csv"), full_stats,
delimiter=",", header=header[:-1])
def recursiveCargoDoc():
for filename in listdir(specificPath):
if "PARS MANIFESTS" in filename and filename[-4:] == ".pdf" or filename[-4:] == ".PDF":
cargoDoc(specificPath+'\\'+filename)
elif(path.isdir(specificPath+"\\"+filename) and not filename=="Flattened"):
recursiveCargoDoc(specificPath+"\\"+filename)
elif(k.getObject()['/T']=="Consignee"):
consignee=k.getObject()['/V']
elif(k.getObject()['/T']=="Shipper"):
shipper=k.getObject()['/V']
elif(k.getObject()['/T']=="ETA DATE"):
eta=k.getObject()['/V']
elif(k.getObject()['/T']=="undefined"):
portOfLoading=k.getObject()['/V']
elif(k.getObject()['/T']=="Port of Discharge"):
portOfDischarge=k.getObject()['/V']
elif(k.getObject()['/T']=="Description of goods"):
description=k.getObject()['/V']
except KeyError:
True
if __name__ == '__main__':
specificPath = ''
for i in range(len(argv)):
if i!=0:
specificPath+=argv[i]
if i != len(argv) - 1:
specificPath+=" "
# destinationOfFiles = workOrderLocation[:workOrderLocation.rfind('\\')] + "\\"
# print(specificPath)
if path.isdir(specificPath):
recursiveCargoDoc(specificPath)
elif "PARS MANIFESTS" in specificPath and (specificPath[-4:] == ".pdf" or specificPath[-4:] == ".PDF"):
cargoDoc(specificPath)
