def __init__(self, **kwargs):
Compression.__init__(self)
self.log = _helpers.get_logger(__name__)
self.source_path = kwargs.get('source_path', None)
self.dest_dir = kwargs.get(
'dest_dir', '%s/' % os.path.dirname(self.source_path)
)
self.compressed_path = None
self.remove_source = kwargs.get('remove_source', False)
self.compress_success = None
self.decompress_success = None
self.compressed_path = None
self.decompressed_path = None
# validations
assert self.source_path, '%s missing'
assert isinstance(self.remove_source, bool), \
"remove_source must be True/False"
assert os.path.exists(self.source_path), \
'%s does not exist, skipping compression' % self.source_path
# real paths please
self.source_path = os.path.realpath(self.source_path)
self.dest_dir = os.path.realpath(self.dest_dir)
_helpers.ensure_dir(self.dest_dir)
def __init__(self, **kwargs):
Compression.__init__(self)
self.log = _helpers.get_logger(__name__)
self.source_path = kwargs.get('source_path', None)
self.dest_dir = kwargs.get('dest_dir',
'%s/' % os.path.dirname(self.source_path))
self.compressed_path = None
self.remove_source = kwargs.get('remove_source', False)
self.compress_success = None
self.decompress_success = None
self.compressed_path = None
self.decompressed_path = None
# validations
assert self.source_path, '%s missing'
assert isinstance(self.remove_source, bool), \
"remove_source must be True/False"
assert os.path.exists(self.source_path), \
'%s does not exist, skipping compression' % self.source_path
# real paths please
self.source_path = os.path.realpath(self.source_path)
self.dest_dir = os.path.realpath(self.dest_dir)
_helpers.ensure_dir(self.dest_dir)
def __init__(self, **kwargs):
self.log = _helpers.get_logger(__name__)
Compression.__init__(self)
self.stream = None
self.output_path = kwargs.get('output_path', None)
assert not os.path.exists(self.output_path), \
'%s already exists!' % self.output_path
_helpers.ensure_dir(os.path.dirname(self.output_path))
def __init__(self, **kwargs):
self.log = _helpers.get_logger(__name__)
Compression.__init__(self)
self.stream = None
self.output_path = kwargs.get('output_path', None)
assert not os.path.exists(self.output_path), \
'%s already exists!' % self.output_path
_helpers.ensure_dir(os.path.dirname(self.output_path))
def pytest_configure(config):
if not hasattr(config, 'slaveinput'):
current_day = '{:%Y_%m_%d_%H_%S}'.format(datetime.datetime.now())
ensure_dir('results')
ensure_dir(os.path.join('slaveinput', current_day))
result_dir = os.path.join(os.path.dirname(__file__), 'results', current_day)
ensure_dir(result_dir)
result_dir_test_run = result_dir
ensure_dir(os.path.join(result_dir_test_run, 'screenshots'))
ensure_dir(os.path.join(result_dir_test_run, 'logcat'))
config.screen_shot_dir = os.path.join(result_dir_test_run, 'screenshots')
config.logcat_dir = os.path.join(result_dir_test_run, 'logcat')
def pytest_configure(config):
if not hasattr(config, "slaveinput"):
current_day = (datetime.datetime.now().strftime("%Y_%m_%d_%H_%S"))
ensure_dir("results")
ensure_dir(os.path.join("results", current_day))
result_dir = os.path.join(os.path.dirname(__file__), "results", current_day)
ensure_dir(result_dir)
result_dir_test_run = result_dir
ensure_dir(os.path.join(result_dir_test_run, "screenshots"))
ensure_dir(os.path.join(result_dir_test_run, "logcat"))
config.screen_shot_dir = os.path.join(result_dir_test_run, "screenshots")
config.logcat_dir = os.path.join(result_dir_test_run, "logcat")
def pytest_configure(config):
if not hasattr(config, 'slaveinput'):
current_day = '{:%Y_%m_%d_%H_%S}'.format(datetime.datetime.now())
ensure_dir('results')
ensure_dir(os.path.join('slaveinput', current_day))
result_dir = os.path.join(os.path.dirname(__file__), 'results',
current_day)
ensure_dir(result_dir)
result_dir_test_run = result_dir
ensure_dir(os.path.join(result_dir_test_run, 'screenshots'))
ensure_dir(os.path.join(result_dir_test_run, 'logcat'))
config.screen_shot_dir = os.path.join(result_dir_test_run,
'screenshots')
config.logcat_dir = os.path.join(result_dir_test_run, 'logcat')
def string_to_file(request, input_dict, output_dict, widget):
import helpers
destination = helpers.get_media_root() + '/' + str(
request.user.id) + '/' + str(widget.id) + '.txt'
helpers.ensure_dir(destination)
f = open(destination, 'w')
f.write(str(input_dict['string']))
f.close()
filename = str(request.user.id) + '/' + str(widget.id) + '.txt'
output_dict['filename'] = filename
return render(request, 'visualizations/string_to_file.html', {
'widget': widget,
'input_dict': input_dict,
'output_dict': output_dict
})
def download(self, out_dir=None, prefix=None, build_filter=None):
dld_builds = []
for build in self.builds:
if build_filter and not build.match_filter(build_filter):
log.info("SKIPPING: %s" % build)
continue
if out_dir:
updir_path = out_dir
else:
updir_path = ''
if prefix:
updir_path = os.path.join(updir_path, prefix)
build_path = build.path(prefix=updir_path)
helpers.ensure_dir(build_path)
with helpers.cdir(build_path):
build.download()
dld_builds.append(build)
return dld_builds
def save_data(self):
info = self.eegInlet.info()
desc = info.desc()
chanNum = info.channel_count()
channels = desc.child('channels').first_child()
channelNames = [channels.child_value('label')]
for i in range(1, chanNum):
channels = channels.next_sibling()
channelNames.append(channels.child_value('label'))
startTime = datetime.datetime.fromtimestamp(self.startTime).strftime(Constants.SESSION_FILE_DATETIME_FORMAT)
finishTime = datetime.datetime.fromtimestamp(self.finishTime).strftime(Constants.SESSION_FILE_DATETIME_FORMAT)
# Save EEG Data
fileBase = os.path.join('session_data', self.user, self.mode.name, self.user + '_' + self.mode.name + '_' + startTime + '_' + finishTime)
file = fileBase + '_EEG.csv'
helpers.ensure_dir(file)
with open(file, 'w', newline='') as csvfile:
writer = csv.writer(csvfile, delimiter=',',
quotechar='"', quoting=csv.QUOTE_MINIMAL)
writer.writerow(['timestamp'] + channelNames)
for data in self.eegData:
writer.writerow(data)
print('Saved EEG data to: ' + file)
# Save Marker Data
file = os.path.join('session_data', self.user, self.mode.name, self.user + '_' + self.mode.name + '_' + startTime + '_' + finishTime).replace(':','\ua789')
file = fileBase + '_MRK.csv'
helpers.ensure_dir(file)
with open(file, 'w', newline='') as csvfile:
writer = csv.writer(csvfile, delimiter=',',
quotechar='"', quoting=csv.QUOTE_MINIMAL)
writer.writerow(['timestamp','key marker'])
for data in self.markers:
writer.writerow(data)
print('Saved Marker data to: ' + file)
def saveAssertScreenShot(self, driver, testcaseName):
current_day = (datetime.datetime.now().strftime("%Y_%m_%d_%H_%S"))
ensure_dir("Screenshot")
result_dir = ensure_dir(os.path.join("Screenshot", current_day))
# result_dir = os.path.join(os.path.dirname(__file__), "Screenshot", current_day)
# print(result_dir)
# ensure_dir(result_dir)
result_dir_test_run = result_dir
Execution_screen_shot_dir = os.path.join(result_dir_test_run,
"Assertion")
ensure_dir(Execution_screen_shot_dir)
# print(Execution_screen_shot_dir)
ExeImagePath = os.path.join(Execution_screen_shot_dir,
current_day + '_' + testcaseName + ".png")
driver.save_screenshot(ExeImagePath)
# print(ExeImagePath)
return ExeImagePath
cluster_id = args.cluster_id
host_path = args.host_path
threads = args.threads
verbose = args.verbose
remove_files = args.remove_files
###
log('Building clustering table from amplicon data...')
merged_sorted_output_file = OUTPATH + sample_name + '_SORTED.fna'
merged_output_file = OUTPATH + sample_name + '.fna'
#make directories for processed files
output_subfolders = ['trim/','derep/']
for dirname in output_subfolders:
ensure_dir(OUTPATH + dirname)
demux_files = [f for f in os.listdir(INPATH) if os.path.isfile(os.path.join(INPATH, f))]
log('%s files found...' % len(demux_files))
for i,filename in enumerate(demux_files):
if (i % 100 == 0) :
log('%s files processed...' % i)
#trim
input_full_path = INPATH + filename
sufix = os.path.splitext(filename)[1]
output_filenmae = filename.replace(sufix,'.trim' + sufix)
output_full_path = OUTPATH + 'trim/' + output_filenmae
cmd = ('vsearch '
list_of_clustering_dataframes = args.list_of_clustering_dataframes
OUTPATH = args.outpath
min_pair_count = args.min_shared_occurances
alpha = args.alpha
merge_similar_id = args.merge_similar_id
flag_edges = args.flag_edges
threads = args.threads
verbose = args.verbose
override = args.override
###
ensure_dir(OUTPATH)
frames = []
for clustering_dataframe_file in list_of_clustering_dataframes:
try:
frame = pd.read_csv(clustering_dataframe_file, index_col=0)
frames.append(frame)
except:
log('Unable to load clustering dataframe file -> %s...' % clustering_dataframe_file)
sys.exit()
#construct multi-domain tables
log('Concatenating domain dataframes...')
merged_filtered_clustering_table = pd.concat(frames).reset_index()
DOMAINS = sorted(merged_filtered_clustering_table['domain'].dropna().unique())
