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upload_all.py
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import argparse
import subprocess
import os, sys
import re
import logging
from utils.colorLogging import ColorizingStreamHandler
parser = argparse.ArgumentParser()
parser.add_argument('-db', '--database', default='tdb', help="database to upload to")
parser.add_argument('--subtypes', nargs='+', type = str, help ="flu subtypes to include, options are: h3n2, h1n1pdm, vic, yam")
parser.add_argument('--sources', nargs='+', type = str, help ="data sources to include, options are: elife, nimr, cdc")
parser.add_argument('--nimr_path', default='data/nimr/', help="directory containing NIMR titers")
parser.add_argument('--cdc_path', default='data/cdc/', help="directory containing CDC titers")
parser.add_argument('--elife_path', default='data/elife/', help="directory containing eLife titers")
parser.add_argument("--debug", action="store_const", dest="loglevel", const=logging.DEBUG, help="Enable debugging logging")
def upload_nimr(database, nimr_path, subtype):
'''
Makes calls to tdb/upload.py for every file in an NIMR titer directory (default data/nimr/).
All files in the directory should be tabular titer tables in CSV format for only one subtype
of virus (H3N2, H1N1pdm, etc.).
'''
path = nimr_path + subtype + "/"
print "Uploading NIMR data for subtype", subtype, "contained in directory", path + "."
for fname in os.listdir(path):
if fname[0] != '.':
fpath = path + fname
fstem = fname[:-4]
print "Uploading " + fname
command = "python tdb/nimr_upload.py -db " + database + " --subtype " + subtype + " --ftype tables --path " + path + " --fstem " + fstem
print "Running with: " + command
subprocess.call(command, shell=True)
print "Done with", fname + "."
print "Done uploading NIMR documents."
def upload_cdc(database, cdc_path):
'''
Makes calls to tdb/upload.py for every flat file in an CDC titer directory (default data/cdc/).
All files in the directory should be flat titer files in TSV format.
There are multiple subtypes within a file.
'''
path = cdc_path
print "Uploading CDC data contained in directory", path + "."
for fname in os.listdir(path):
if fname[0] != '.':
fpath = path + fname
fstem = fname[:-4]
print "Uploading " + fname
command = "python tdb/cdc_upload.py -db cdc_tdb --path " + path + " --fstem " + fstem
print "Running with: " + command
subprocess.call(command, shell=True)
print "Done with", fname + "."
print "Done uploading CDC documents."
def upload_elife(database, elife_path, subtype):
'''
Makes calls to tdb/upload.py for every flat file in an eLife titer directory (default data/elife/).
All files in the directory should be flat titer files in TSV format for only one subtype
of virus (H3N2, H1N1pdm, etc.).
'''
path = elife_path + subtype + "/"
print "Uploading eLife data for subtype", subtype, "contained in directory", path + "."
for fname in os.listdir(path):
if fname[0] != '.':
fpath = path + fname
fstem = fname[:-4]
print "Uploading " + fname
command = "python tdb/elife_upload.py -db " + database + " --subtype " + subtype + " --path " + path + " --fstem " + fstem
print "Running with: " + command
subprocess.call(command, shell=True)
print "Done with", fname + "."
print "Done uploading stored eLife documents."
def upload_vidrl(database, subtypes):
with open('data/vidrl_fail_log.txt', 'w') as o:
base_path = '../../fludata/VIDRL-Melbourne-WHO-CC/raw-data/'
dir_paths = []
subtype_to_paths = {
"h3n2": ["A/H3N2/HI", "A/H3N2/FRA"],
"h1n1pdm": ["A/H1N1pdm/HI"],
"vic": ["B/Victoria/HI"],
"yam": ["B/Yamagata/HI"]
}
for subtype in subtypes:
for dir_path in subtype_to_paths[subtype]:
complete_path = '{}{}/'.format(base_path, dir_path)
assay_type = "hi"
m = re.search(r'fra', complete_path, re.IGNORECASE)
if m is not None:
assay_type = "fra"
for fname in os.listdir(complete_path):
fstem = fname.split('.')[0]
if ' ' in fstem:
fstem = re.escape(fstem)
print "Uploading " + fname
command = "python tdb/vidrl_upload.py -db {} -v flu --subtype {} --assay_type {} --path {} --fstem {} --ftype vidrl".format(database, subtype, assay_type, complete_path, fstem)
print "Running with: " + command
try:
subprocess.call(command, shell=True)
except:
logger.critical("Couldn't upload {}, please try again.".format(fname))
print "Done with", fname + "."
def upload_niid(database, subtypes):
with open('data/niid_fail_log.txt', 'w') as o:
base_path = '/Users/bpotter/fludata/NIID-Tokyo-WHO-CC/raw-data/'
dir_paths = []
subtype_to_paths = {
"h3n2": ["A/H3N2/HI/2015", "A/H3N2/MNT/2016", "A/H3N2/MNT/2017", "A/H3N2/FRA/2018", "A/H3N2/FRA/2017"],
"h1n1pdm": ["A/H1N1pdm/2015", "A/H1N1pdm/2016", "A/H1N1pdm/2017", "A/H1N1pdm/2018"],
"vic": ["B/Victoria/HI/2017", "B/Victoria/HI/2018"],
"yam": ["B/Yamagata/HI/2017", "B/Yamagata/HI/2018"]
}
for subtype in subtypes:
for dir_path in subtype_to_paths[subtype]:
complete_path = '{}{}/'.format(base_path, dir_path)
assay_type = "hi"
m = re.search(r'(fra|MNT)', complete_path, re.IGNORECASE)
if m is not None:
assay_type = "fra"
for fname in os.listdir(complete_path):
fstem = fname.split('.')[0]
fstem = fstem.replace('(','\\(').replace(')','\\)')
if ' ' in fstem:
fstem = re.escape(fstem)
print "Uploading " + fname
command = "python tdb/niid_upload.py -db {} -v flu --subtype {} --assay_type {} --path {} --fstem {} --ftype niid".format(database, subtype, assay_type, complete_path, fstem)
print "Running with: " + command
try:
subprocess.call(command, shell=True)
except:
o.writeline("Couldn't upload {}, please try again.".format(infile))
print "Done with", fname + "."
if __name__=="__main__":
params = parser.parse_args()
## L O G G I N G
# https://docs.python.org/2/howto/logging-cookbook.html#multiple-handlers-and-formatters
# root_logger = logging.getLogger('')
# root_logger.setLevel(args.loglevel if params.loglevel else logging.INFO)
# root_logger.addHandler(ColorizingStreamHandler())
# logger = logging.getLogger(__name__)
print "Beginning construction of", params.database + "."
if params.subtypes is None:
params.subtypes = ['h3n2', 'h1n1pdm', 'vic', 'yam']
if params.sources is None:
params.sources = ['elife', 'nimr', 'cdc', 'vidrl']
for source in params.sources:
if source == "cdc":
upload_cdc(params.database, params.cdc_path)
if source == "elife":
for subtype in params.subtypes:
if subtype != 'h1n1pdm':
upload_elife(params.database, params.elife_path, subtype)
if source == "nimr":
for subtype in params.subtypes:
upload_nimr(params.database, params.nimr_path, subtype)
if source == "vidrl":
upload_vidrl(params.database, params.subtypes)
if source == "niid":
upload_niid(params.database, params.subtypes)
print "Done with all uploads."