def uploadzone_upload():
if not current_user.is_authenticated:
return redirect(url_for('login_page', next=url_for('uploadzone_view')))
fl = request.files.get('file')
if fl and fl.filename:
filename = secure_filename(fl.filename)
p = join(cfg.UPLOAD_ZONE_PATH,
get_formatted_datetime('%d-%m-%Y %H-%M-%S'))
if not Path(p).exists():
create_folder(p)
fl.save(join(p, filename))
session['uploadzone_info'] = 'Uploaded Successfully'
return redirect(url_for('uploadzone_view'))
else:
session['uploadzone_error'] = 'Upload Failed. File not found'
return redirect(url_for('uploadzone_view'))
def __init__(self, parent, name, number=-1, mkdir=True):
self.number = number
self.parent = parent
# set parent directory for subfolder creation
if self.parent:
parent_dir = self.parent.target_directory
else:
parent_dir = OutputDirectory.output_dir
# numbering of directory (if a number is supplied)
if number >= 0:
self.target_directory = os.path.join(parent_dir,
"%s_%04d" % (name, number))
else:
self.target_directory = os.path.join(parent_dir, name)
# create directory if it is non-existent
if mkdir:
tools.create_folder(self.target_directory)
def saveImagesOneByOne(in_path, out_path):
tools.create_folder(out_path)
for filename in tools.getImages(in_path, out_path, ".png"):
print("Saving...", filename)
image = mpimg.imread(in_path + filename)
np.save(out_path + filename[:-4], image)
os.path.join(os.getcwd(), 'data_files', 'data'),
'gap_statistic':
os.path.join(os.getcwd(), 'data_files', 'output', 'gap_statistic'),
'clustering':
os.path.join(os.getcwd(), 'data_files', 'output', 'clustering'),
'clustering_info':
os.path.join(os.getcwd(), 'data_files', 'output', 'clustering', 'info'),
'clustering_figures':
os.path.join(os.getcwd(), 'data_files', 'output', 'clustering', 'figures'),
'correlation_figures':
os.path.join(os.getcwd(), 'data_files', 'output', 'correlations'),
'association_figures':
os.path.join(os.getcwd(), 'data_files', 'output', 'associations'),
}
tools.create_folder(args.paths['gap_statistic'])
tools.create_folder(args.paths['clustering_info'])
tools.create_folder(args.paths['clustering_figures'])
tools.create_folder(args.paths['correlation_figures'])
tools.create_folder(args.paths['association_figures'])
########### ------------------- Assert args are valid ----------------- ###########
assert type(args.name_data) is str
assert type(args.name_compartment) is str
assert type(args.log_transform) is bool
assert type(args.max_testing_k) is int
assert type(args.max_final_k) is int
assert args.max_final_k <= args.max_testing_k
assert type(args.outcomes) is list
assert type(args.covariates) is list
def save_data(self):
# 0.0 set output folder structure
output_path = "output_dir/standalone/examples/cmd_0001"
if os.path.exists(output_path):
self.results_main = "results/"
if not os.path.exists(self.results_main):
tools.create_folder(self.results_main)
# 1.0 save data from output_dir/standalone/examples/cmd_0001
try:
for folder in os.listdir(output_path):
folder_path = os.path.join(output_path, folder)
if not os.path.isdir(folder_path):
continue
for file in os.listdir(folder_path):
# create results sub-directory if it is non-existent
self.results_sub = "results/%s" % folder + self.suffix
if not os.path.exists(self.results_sub):
tools.create_folder(self.results_sub)
file_path = os.path.join(folder_path, file)
# save files with different endings
ext = [".csv", ".pdf", ".txt", "parameter.ini", "std.out"]
# ".m2ts", ".mkv", ".mov", ".mp4", ".mpg", ".mpeg", \
# ".rm", ".swf", ".vob", ".wmv"]
if file.endswith(tuple(ext)):
os.system("cp " + file_path + " " + self.results_sub +
"/.")
except Exception as ex:
print(
"save_data: cannote store any data because (some) output was not created"
)
print('Error: ' + str(ex))
# 1.1 save convergence data from output_dir/standalone/examples/cmd_0001
try:
for file in os.listdir(output_path):
if file.endswith(".pdf"):
try:
if file.index('order') != -1:
order = file[
file.index('order') + 5:
-4] # get string from 'order' + 5 to the end, but remove last 4 character ".pdf"
#new_name = "L2"+self.suffix+"_order%s.pdf" % order # add suffix to name
new_name = self.prefix + file
except:
new_name = "L2" + self.suffix + ".pdf"
os.system("cp output_dir/standalone/examples/cmd_0001/" +
file + " " + self.results_main +
new_name) # move file to upper most path
if file.endswith(".csv"):
try:
if file.index('order') != -1:
order = file[
file.index('order') + 5:
-4] # get string from 'order' + 5 to the end, but remove last 4 character ".pdf"
#new_name = "L2"+self.suffix+"_order%s.csv" % order # add suffix to name
new_name = self.prefix + file
except:
new_name = "L2" + self.suffix + ".csv"
os.system("cp output_dir/standalone/examples/cmd_0001/" +
file + " " + self.results_main +
new_name) # move file to upper most path
except Exception as ex:
print(
"save_data: cannote store convergence data because (some) output was not created"
)
print('Error: ' + str(ex))
# Remove possible calls with binaries
c = CheckBinaryCall(c)
# Add the new command line only if it is unique
if c not in commands:
commands.append(c) # add command line to list
cases.append(gitlab_ci_tools.Case(
c)) # and the case to the list of cases
print(132 * '=')
if not args.dryrun: # do not execute anythin in dryrun mode
#switch to basedir+/output_dir_gitlab_tool
target_directory = os.path.join(basedir, 'output_dir_gitlab_tool')
shutil.rmtree(target_directory, ignore_errors=True)
tools.create_folder(target_directory)
os.chdir(target_directory)
print("Creating output under %s" % target_directory)
else:
print("List of possible cases from gitlab-ci.yml are")
print(" ")
i = 1
nErrors = 0
for case in cases:
# extract the reggie case from the command in the gitlay-ci.yml line by looking for "reggie.py" and "/regressioncheck/checks"
c = case.command[case.command.find("reggie.py") + 9:].strip()
c = c[c.find("/regressioncheck/checks"):].strip()
c = str(basedir + c).strip() # add basedir to reggie-checks folder
case_dir = c.split(" ")[0]
if not os.path.exists(