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Continued updates to VIDRL serum mapping

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trvrb committed Sep 25, 2019
1 parent 85b8916 commit 6d141b9741ff44c9996c33e40607621ddc0836db
Showing with 39 additions and 8 deletions.
  1. +34 −3 source-data/vidrl_serum_mapping.tsv
  2. +5 −5 tdb/upload_all.py
@@ -10,6 +10,7 @@ ALASKA/232/2015 A/ALASKA/232/2015
ALASKA/5 A/ALASKA/5/2010
Arizona/8/13 B/ARIZONA/08/2013
AUCK/1 A/AUCKLAND/1/2009
CALI07 A/California/07/2009
B/Canterbury/5/2017 B/Canterbury/5/2017
B/HUBEI-WUJIAGANG/158/2009 B/HUBEI-WUJIAGANG/158/2009
B/MASSACHUSETTS/02/2012 B/MASSACHUSETTS/02/2012
@@ -21,8 +22,11 @@ B/WISCONSIN/01/2010 B/WISCONSIN/01/2010
BANG/3333 B/BANGLADESH/3333/2007
BAY/69 A/BAYERN/69/2009
Bris/1 A/BRISBANE/1/2013
Bris01 A/Brisbane/01/2018
Bris02 A/Brisbane/02/2018
BRIS/10 A/BRISBANE/10/2010
Bris/137 A/BRISBANE/137/2015
Bris117 A/Brisbane/117/2018
BRIS/18 B/BRISBANE/18/2013
Bris/181 A/BRISBANE/181/2015
BRIS/2 B/BRISBANE/2/2012
@@ -37,12 +41,14 @@ BRIS/321 A/BRISBANE/321/2016
BRIS/33 B/BRISBANE/33/2008
BRIS/36 B/BRISBANE/36/2012
BRIS/37 A/BRISBANE/37/2017
Bris37 A/Brisbane/37/2017
BRIS/46 B/BRISBANE/46/2015
BRIS/47 A/BRISBANE/47/2015
BRIS/60 B/BRISBANE/60/2008
BRIS/70 A/BRISBANE/70/2011
BRIS/9 B/BRISBANE/9/2008
BRIS/96 A/BRISBANE/96/2012
A/BRISBANE/192 A/Brisbane/192/2017
Bris321 A/Brisbane/321/2016
BRIS46 B/BRISBANE/46/2015
BRIS60 B/BRISBANE/60/2008
@@ -69,10 +75,13 @@ CHRIST16 A/CHRISTCHURCH/16/2010
Christchurch/5 A/CHRISTCHURCH/5/2016
Col B/COLORADO/6/2017
COL6 B/Colorado/6/2017
Darw6 A/Darwin/6/2018
Dar6 A/Darwin/6/2018
DAR/40 B/DARWIN/40/2012
DAR/56 A/DARWIN/56/2013
DAR40 B/DARWIN/40/2012
DAR56 A/DARWIN/56/2013
Dar102 A/Darwin/102/2019
DAR563 A/DARWIN/56/2013
Darwin/40 B/DARWIN/40/2012
DARWIN/56 A/DARWIN/56/2013
@@ -95,19 +104,22 @@ Idaho37 A/Idaho/37/2016
ILLINOIS/9 A/ILLINOIS/9/2007
INDI/1 B/INDIANA/1/2008
Kan14 A/Kansas/14/2017
A/KANSAS/14 A/Kansas/14/2017
MAL/2506 B/MALAYSIA/2506/2004
MAL/412 B/MALAYSIA/412/2012
MASS02 B/MASSACHUSETTS/02/2012
MASSACH/2 B/MASSACHUSETTS/02/2012
MICH A/MICHIGAN/15/2014
Mich/15 A/MICHIGAN/15/2014
MICH15 A/Michigan/15/2014
Mich/45 A/MICHIGAN/45/2015
MICH45 A/MICHIGAN/45/2015
MICHI A/MICHIGAN/15/2014
MICHI45 A/MICHIGAN/45/2015
MICHIGAN/15 A/MICHIGAN/15/2014
MICHIGAN/15/2014 A/MICHIGAN/15/2014
Michigan/45 A/MICHIGAN/45/2015
A/MICHIGAN/45/2015 A/MICHIGAN/45/2015
NCAL/58 A/NEW CALEDONIA/58/2014
New Cal/104 A/NEW CALEDONIA/104/2014
New Cal/104/2014 A/NEW CALEDONIA/104/2014
@@ -118,8 +130,11 @@ NEWC/22 A/NEWCASTLE/22/2014
NEWC/22/2014 A/NEWCASTLE/22/2014
NEWC/30 A/NEWCASTLE/30/2016
NEWC/30/2016 A/NEWCASTLE/30/2016
Newc46 A/Newcastle/46/2019
NEWC/54 A/NEWCASTLE/54/2014
New82 A/Newcastle/82/2018
Newc82 A/Newcastle/82/2018
A/NEWC/82 A/Newcastle/82/2018
Newcal/104 A/NEW CALEDONIA/104/2014
Newcastle/1 A/NEWCASTLE/1/2013
NORWAY/3806 A/NORWAY/3806/2016
@@ -156,12 +171,15 @@ Sing/GP1911 A/SINGAPORE/GP1911/2015
SING/GP1940 A/SINGAPORE/GP1940/2013
Sing/GP2027/2015 A/SINGAPORE/GP2027/2015
Sing/GP2646 A/Singapore/GP2646/2016
Sing/NFIMH A/SINGAPORE/INFIMH-16-0019/2016
Sing/NFIMH A/Singapore/INFIMH-16-0019/2016
A/SING/INFIMH-16-0019 A/Singapore/INFIMH-16-0019/2016
Sing/TT1374 A/SINGAPORE/TT1374/2016
SING16-0019 A/SINGAPORE/INFIMH-16-0019/2016
SINGAPORE/GP2646 A/SINGAPORE/GP2646/2016
SINGAPORE/INFIMH-16-0019 A/SINGAPORE/INFIMH-16-0019/2016
SINGAPORE/TT1374 A/SINGAPORE/TT1374/2016
SINGAPORE/INFIMH-16-0019 A/Singapore/INFIMH-16-0019/2016
SINGINFIMH-16-0019 A/Singapore/INFIMH-16-0019/2016
SINGAPORE/TT1374 A/Singapore/TT1374/2016
SingTT1384 A/Singapore/TT1384/2016
SINGGP1908 A/SINGAPORE/GP1908/2015
Sri Lanka/61 A/SRI LANKA/61/2015
STH A/11 B/SOUTH AUSTRALIA/11/2012
@@ -186,13 +204,20 @@ STH AUST/6 B/SOUTH AUSTRALIA/6/2012
Sth Aust/81 B/SOUTH AUSTRALIA/81/2012
STH AUST/9 A/SOUTH AUSTRALIA/9/2015
SthAust34 A/SouthAustralia/34/2019
Sth Aust34 A/SouthAustralia/34/2019
A/STH AUS/34 A/SouthAustralia/34/2019
SthAus/84 A/South Australia/84/2017
Sth Aus272 A/South Australia/272/2017
Sth Aust 272 A/South Australia/272/2017
STOCK/12 B/STOCKHOLM/12/2011
SWITZ A/SWITZERLAND/9715293/2013
Switz8060 A/Switzerland/8060/2017
Swit8060 A/Switzerland/8060/2017
A/SWITZ/8060 A/Switzerland/8060/2017
Switz/9715293 A/SWITZERLAND/9715293/2013
SYD/10 B/SYDNEY/10/2016
SYD/39 B/SYDNEY/39/2014
A/SYDNEY/22 A/Sydney/22/2018
SYD/508 B/SYDNEY/508/2010
SYD/7 B/SYDNEY/7/2014
SYD/71 A/SYDNEY/71/2014
@@ -211,10 +236,13 @@ Texas/50/2012 A/TEXAS/50/2012
Town/8 B/TOWNSVILE/8/2016
TOWNS8 B/TOWNSVILLE/8/2016
Townsville/8 B/TOWNSVILLE/8/2016
Towns21 A/Townsville/21/2018
A/Townsville/21/2018 A/Townsville/21/2018
VIC/208 A/VICTORIA/208/2009
VIC/361 A/VICTORIA/361/2011
VIC/502 multiple_matches
VIC/503 A/VICTORIA/503/2016
A/VICTORIA/503/2016 A/Victoria/503/2016
Vic/504 multiple_matches
Vic/505 A/VICTORIA/505/2013
VIC/506 A/VICTORIA/506/2013
@@ -229,6 +257,7 @@ VIC503 X-281 A/VICTORIA/503 X-281
VIC653 A/VICTORIA/653/2017
Victoria/265 A/VICTORIA/265/2014
VICTORIA/653 A/VICTORIA/653/2017
A/VICTORIA/653 A/VICTORIA/653/2017
Victoria/673 A/VICTORIA/673/2014
WELL/1 A/WELLINGTON/1/2004
WELL/3 B/WELLINGTON/3/2012
@@ -239,3 +268,5 @@ WIS/1 B/WISCONSIN/1/2010
WISC/1 B/WISCONSIN/1/2010
WISC01 B/WISCONSIN/01/2010
WISC2010 B/WISCONSIN/01/2010
Wisc04 A/Wisconsin/04/2018
Wis04 A/Wisconsin/04/2018
@@ -79,13 +79,13 @@ def upload_elife(database, elife_path, subtype):

def upload_vidrl(database, subtypes):
with open('data/vidrl_fail_log.txt', 'w') as o:
base_path = '../../fludata/VIDRL-Melbourne-WHO-CC/raw-data/'
base_path = '../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"]
"h3n2": ["A/H3N2/HI/2019", "A/H3N2/FRA/2019"],
"h1n1pdm" : ["A/H1N1pdm/HI/2019"],
"vic": ["B/Victoria/HI/2019"],
"yam": ["B/Yamagata/HI/2019"]
}
for subtype in subtypes:
for dir_path in subtype_to_paths[subtype]:

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