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Raw ss #60

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Raw ss #60

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b56613b
file flow for raw ss
jdhayhurst Feb 9, 2021
ecb2253
file flow for raw ss
jdhayhurst Feb 9, 2021
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2 changes: 1 addition & 1 deletion ftpSummaryStatsScript/create_ftp_structure.py
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Original file line number Diff line number Diff line change
Expand Up @@ -22,7 +22,7 @@


def get_gcst_range(gcst):
number_part = int(gcst.split("GCST")[1])
number_part = int(gcst.split("GCST")[1]) - 1
floor = int(np.fix(number_part / range_size) * range_size) + 1
upper = floor + (range_size -1)
range_str = "GCST{f}-GCST{u}".format(f=str(floor).zfill(6), u=str(upper).zfill(6))
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26 changes: 21 additions & 5 deletions ftpSummaryStatsScript/depo_ftp_to_staging.py
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Original file line number Diff line number Diff line change
Expand Up @@ -23,17 +23,20 @@
# in case of latency for writing the file.

MOD_THRESHOLD_SEC = 3600
#MOD_THRESHOLD_SEC = 36 # DEV ONLY
#MOD_THRESHOLD_SEC = 3 # DEV ONLY
RANGE_SIZE = 1000
RAW_SS_SUFFIX = ".rawSS"
RAW_SS_SUFFIX_REGEX = "\.rawSS$"


def get_dirs_to_sync(source_dir):
dirs = glob.glob(os.path.join(source_dir, 'GCST*'))
logger.debug(dirs)
dirs_older_than_1hr = [d for d in dirs if (time.time() - os.path.getmtime(d)) > MOD_THRESHOLD_SEC]
return dirs_older_than_1hr

def get_gcst_range(gcst):
number_part = int(gcst.split("GCST")[1])
number_part = int(gcst.split("GCST")[1]) - 1
floor = int(np.fix(number_part / RANGE_SIZE) * RANGE_SIZE) + 1
upper = floor + (RANGE_SIZE -1)
range_str = "GCST{f}-GCST{u}".format(f=str(floor).zfill(6), u=str(upper).zfill(6))
Expand All @@ -47,6 +50,15 @@ def move_dir(source, dest):
logger.debug("Moving {} --> {}".format(source, dest))
shutil.move(source, dest)

def rename_file(old, new):
logger.info("Renaming {} --> {}".format(old, new))
os.rename(old, new)

def remove_raw_ss_suffix(directory):
raw_ss_files = glob.glob(os.path.join(directory, '*' + RAW_SS_SUFFIX))
for raw_ss in raw_ss_files:
without_raw_ss_suffix = re.sub(RAW_SS_SUFFIX_REGEX, '', raw_ss)
rename_file(raw_ss, without_raw_ss_suffix)

def sync_files(source_dir, staging_dir, harmonise_dir):
dirs_to_sync = get_dirs_to_sync(source_dir)
Expand All @@ -60,10 +72,14 @@ def sync_files(source_dir, staging_dir, harmonise_dir):
logger.debug(gcst)
gcst_range = get_gcst_range(gcst)
gcst_range_dir = os.path.join(staging_dir, gcst_range)
dest = gcst_range_dir + "/"
gcst_range_dir = gcst_range_dir + "/"
make_dir(gcst_range_dir)
logger.info("Sync {} --> {}".format(study, dest))
subprocess.call(['rsync', '-prvh','--chmod=Du=rwx,Dg=rwx,Do=rx,Fu=rw,Fg=rw,Fo=r', study, dest])
logger.info("Sync {} --> {}".format(study, gcst_range_dir))
# sync to staging
subprocess.call(['rsync', '-prvh','--chmod=Du=rwx,Dg=rwx,Do=rx,Fu=rw,Fg=rw,Fo=r', study, gcst_range_dir])
dest = os.path.join(gcst_range_dir, gcst)
remove_raw_ss_suffix(dest)
# move to harmonisation
move_dir(study, harmonise_dir + "/")


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2 changes: 1 addition & 1 deletion harmonisationUtils/sumstats_file_utils.py
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Original file line number Diff line number Diff line change
Expand Up @@ -35,7 +35,7 @@ def _list_study_dirs(parent, pattern):


def get_gcst_range(gcst):
number_part = int(gcst.split("GCST")[1])
number_part = int(gcst.split("GCST")[1]) - 1
floor = int(np.fix(number_part / range_size) * range_size) + 1
upper = floor + (range_size -1)
range_str = "GCST{f}-GCST{u}".format(f=str(floor).zfill(6), u=str(upper).zfill(6))
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