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Improve parsing of H5N1 documents

1. Include additional host rules
2. Include additional geo data
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trvrb committed Jan 5, 2019
1 parent 6592e6f commit 08319bafdd62b671d0eca2c307d66f6ef5d2b366
Showing with 121 additions and 91 deletions.
  1. +7 −0 source-data/flu_fix_location_label.tsv
  2. +2 −0 source-data/geo_regions.tsv
  3. +83 −11 source-data/geo_synonyms.tsv
  4. +29 −80 vdb/avian_flu_upload.py
@@ -369,6 +369,9 @@ Ujain Ujjain
Uttrakhand Uttarakhand
Ytml Yavatmal

# Indonesia
Bandungjava Bandung

# Iran
Bandar_Abbas BandarAbbas
Azarbayejan-Sharghi AzarbayejanSharghi
@@ -504,6 +507,9 @@ Mangua Managua
Beithlehem Bethlehem
Qalqilia Qalqilya

# Pakistan
Manshera Mansehra

# PapuaNewGuinea
EAST SEPIK PROVINCE EastSepik
Eastsepikprovince EastSepik
@@ -606,6 +612,7 @@ Ossetia-Alania OssetiaAlania
Rostov-On-Don RostovOnDon
Rostov-on-Don RostovOnDon
Rostovoblast Rostov
Russia_Krasnodar Krasnodar
Salehard Salekhard
SaintPetersburg StPetersburg
Sosnoviy_Bor SosnoviyBor
@@ -1,6 +1,7 @@
country region

algeria africa
benin africa
canary_islands africa
egypt africa
morocco africa
@@ -126,6 +127,7 @@ china china
hong_kong china
macau china
taiwan china
tibet china

bangladesh south_asia
bhutan south_asia
@@ -134,6 +134,9 @@ Wallonia Belgium Wallonia Wallonia
# Belize
Belize Belize Belize Belize

# Benin
Benin Benin Benin Benin

# Bermuda
Bermuda Bermuda Bermuda Bermuda

@@ -145,11 +148,6 @@ Bolivia Bolivia Bolivia Bolivia
Cochabamba Bolivia Cochabamba Cochabamba
LaPaz Bolivia LaPaz LaPaz

# Borneo
Borneo Indonesia Borneo Borneo
Kalimantan Indonesia Borneo Borneo
Sarawak Indonesia Borneo Sarawak

# BosniaHerzegovina
BosniaHerzegovina BosniaHerzegovina BosniaHerzegovina BosniaHerzegovina
Sarajevo BosniaHerzegovina FederationOfBosniaAndHerzegovina Sarajevo
@@ -494,6 +492,7 @@ HunanWuling China Hunan Wuling
HunanYuhua China Hunan Yuhua
InnerMongolia China Neimenggu Neimenggu
Jinlinnanguan China China China
Jiande China Zhejiang sJiande
Jiangan China Hubei Jiangan
Jiangmenguangdong China Guangdong Jiangmen
Jiangsu China Jiangsu Jiangsu
@@ -621,6 +620,7 @@ Zhejiangyiwu China Zhejiang Yiwu
Zhenjiang China Jiangsu Zhenjiang
Zhongshan China Guangdong Zhongshan
Zhejiang China Zhejiang Zhejiang
Zhengzhou China Henan Zhengzhou
Zhoushan China Zhejiang Zhoushan
Zhuhai China Guangdong Zhuhai
Zhongyuan China Henan Zhongyuan
@@ -744,6 +744,7 @@ Ismailia Egypt Ismailia Ismailia
Gharbia Egypt Gharbia Gharbia
Giza Egypt Giza Giza
NorthSinai Egypt NorthSinai NorthSinai
Qalubia Egypt Qalubia Qalubia

# ElSalvador
ElSalvador ElSalvador ElSalvador ElSalvador
@@ -1073,6 +1074,7 @@ Itarsi India MadhyaPradesh Itarsi
Jabalpur India MadhyaPradesh Jabalpur
Jaipurrajasthan India Rajasthan Jaipur
Jodhpur India Rajasthan Jodhpur
Jalgaon India Maharashtra Jalgaon
Jalna India Maharashtra Jalna
JammuKashmir India JammuKashmir JammuKashmir
Jhabua India MadhyaPradesh Jhabua
@@ -1092,7 +1094,9 @@ Mumbai India Maharashtra Mumbai
Nagda India MadhyaPradesh Nagda
Nagpur India Maharashtra Nagpur
Nanded India Maharashtra Nanded
Nandurbar India Maharashtra Nandurbar
Nashik India Maharashtra Nashik
Navapur India Maharashtra Navapur
Odisha India Odisha Odisha
Pachpadra India Rajasthan Pachpadra
Panchgani India Maharashtra Panchgani
@@ -1109,6 +1113,7 @@ Ratnagiri India Maharashtra Ratnagiri
Rewa India MadhyaPradesh Rewa
Rtng India India India
Satna India MadhyaPradesh Satna
Sikkim India Sikkim Sikkim
Shajapur India MadhyaPradesh Shajapur
Srinigar India JammuAndKashmir Srinagar
TamilNaidu India TamilNaidu TamilNaidu
@@ -1124,40 +1129,79 @@ Yavatmal India Maharashtra Yavatmal

# Indonesia
Indonesia Indonesia Indonesia Indonesia
Agam Indonesia Sumatra Agam
Bali Indonesia Bali Bali
BandarLampung Indonesia Sumatra BandarLampung
Bandung Indonesia Java Bandung
Banten Indonesia Banten Banten
Banyumas Indonesia Java Banyumas
Banyuwangi Indonesia Java Banyuwangi
Bengkulu Indonesia Bengkulu Bengkulu
Bogorwestjava Indonesia WestJava Bogor
Bogorwestjava Indonesia Java Bogor
Bojonggenteng Indonesia Java Bojonggenteng
Boyolali Indonesia Java Boyolali
CentralJava Indonesia Java CentralJava
Cicurug Indonesia Java Cicurug
Cileungsi Indonesia Java Cileungsi
DeliDerdang Indonesia Sumatra DeliDerdang
Denpasar Indonesia Bali Denpasar
EastJava Indonesia Java EastJava
EastKalimantan Indonesia Borneo EastKalimantan
Gorontalo Indonesia Sulawesi Gorontalo
GunungKidul Indonesia Java GunungKidul
Indramayu Indonesia Java Indramayu
Jakarta Indonesia Jakarta Jakarta
Jambi Indonesia Sumatra Jambi
Java Indonesia Java Java
Jembrana Indonesia Bali Jembrana
Jombang Indonesia Java Jombang
Kapuas Indonesia Borneo Kapuas
Kediri Indonesia Java Kediri
Klapanunggal Indonesia Java Klapanunggal
Klaten Indonesia Java Klaten
Kuningan Indonesia WestJava Kuningan
Kudus Indonesia Java Kudus
Kuningan Indonesia Java Kuningan
LampungUtara Indonesia Sulawesi LampungUtara
Lamongan Indonesia Java Lamongan
Lampung Indonesia Sumatra Lampung
Leuwiliang Indonesia Java Leuwiliang
Lumajang Indonesia Java Lumajang
Bandungjava Indonesia Java Bandung
Madiun Indonesia Java Madiun
Makassar Indonesia Makassar Makassar
Medan Indonesia Sumatra Medan
MuraoJambi Indonesia Sumatra MuraoJambi
Nagrak Indonesia Java Nagrak
NorthSumatra Indonesia Sumatra NorthSumatra
Palembangsumatra Indonesia Sumatra Palembang
Raas Indonesia EastJava Raas
Pangkalpinang Indonesia BangkaBelitung Pangkalpinang
Parung Indonesia Java Parung
Payakumbuh Indonesia Sumatra Payakumbuh
Pekalongan Indonesia Java Pekalongan
Raas Indonesia Java Raas
Riau Indonesia Sumatra Riau
Semarang Indonesia Java Semarang
Sembawa Indonesia Java Sembawa
SouthSumatra Indonesia Sumatra SouthSumatra
Sumatra Indonesia Sumatra Sumatra
Surabaya Indonesia JawaTimur Surabaya
Serpong Indonesia Banten Serpong
Sidrap Indonesia Sulawesi Sidrap
Sleman Indonesia Java Sleman
Sragen Indonesia Java Sragen
Surakarta Indonesia Jateng Surakarta
Sulawesi Indonesia Sulawesi Sulawesi
Sukoharjo Indonesia Java Sukoharjo
TanahDatar Indonesia Sumatra TanahDatar
Tasikmalaya Indonesia Java Tasikmalaya
Temanggung Indonesia Java Temanggung
WestJava Indonesia Java WestJava
Wonogiri Indonesia Java Wonogiri
Wonosobo Indonesia Java Wonosobo
Yogyakarta Indonesia Java Yogyakarta
Borneo Indonesia Borneo Borneo
Kalimantan Indonesia Borneo Borneo
Sarawak Indonesia Borneo Sarawak
SouthKalimantan Indonesia Borneo SouthKalimantan

# Iran
Iran Iran Iran Iran
@@ -1348,8 +1392,7 @@ SouthKazakhstan Kazakhstan SouthKazakhstan SouthKazakhstan
NorthKazakhstan Kazakhstan NorthKazakhstan NorthKazakhstan
Akmola Kazakhstan Akmola Akmola
Kyzylorda Kazakhstan Kyzylorda Kyzylorda


Pavlodar Kazakhstan Pavlodar Pavlodar

# Kenya
Kenya Kenya Kenya Kenya
@@ -1610,6 +1653,8 @@ Mandalay Myanmar Mandalay Mandalay
Sagaing Myanmar Sagaing Sagaing
Yangon Myanmar Yangon Yangon
Naypyitaw Myanmar Naypyitaw Naypyitaw
Shan Myanmar Shan Shan
Yinmarbin Myanmar Sagaing Yinmarbin

# Nauru
Nauru Nauru Nauru Nauru
@@ -1715,7 +1760,9 @@ Salalah Oman Dhofar Salalah

# Pakistan
Pakistan Pakistan Pakistan Pakistan
Islamabad Pakistan Islamabad Islamabad
Lahore Pakistan Punjab Lahore
Mansehra Pakistan KhyberPakhtunkhwa Mansehra
Muridke Pakistan Punjab Muridke
Karachi Pakistan Sindh Karachi

@@ -1725,6 +1772,7 @@ Palau Palau Palau Palau
# Palestine
Palestine Palestine Palestine Palestine
Bethlehem Palestine Bethlehem Bethlehem
Gaza Palestine Gaza Gaza
Hebron Palestine Hebron Hebron
Jenin Palestine Jenin Jenin
Jericho Palestine Jericho Jericho
@@ -1878,6 +1926,7 @@ Chelyabinsk Russia Chelyabinsk Chelyabinsk
Cherkessk Russia Karachay-Cherkess Cherkessk
Chita Russia ZabaykalskyKrai Chita
Dagestan Russia Dagestan Dagestan
Domodedovo Russia Moscow Domodedovo
Dovolnoe Russia Novosibirsk Dovolnoe
Ekaterinburg Russia SverdlovskOblast Ekaterinburg
GornoAltaysk Russia Altaia GornoAltaysk
@@ -1886,6 +1935,7 @@ Ivanovo Russia Ivanovo Ivanovo
Izhevsk Russia Udmurt Izhevsk
Kaliningrad Russia Kaliningrad Kaliningrad
Kalingrad Russia Kaliningrad Kaliningrad
Kalmykia Russia Kalmykia Kalmykia
Kaluga Russia Kaluga Kaluga
Karasuk Russia Novosibirsk Karasuk
Kazan Russia Tatarstan Kazan
@@ -1899,11 +1949,14 @@ Koltsovo Russia Novosibirsk Koltsovo
Komi Russia Komi Komi
Kostroma Russia Kostroma Kostroma
Krasnodar Russia Krasnodar Krasnodar
Krasnoozerka Russia Khakassia Krasnoozerka
Krasnoozerskoe Russia Khakassia Krasnoozerka
Krasnoyarsk Russia Krasnoyarsk Krasnoyarsk
Kurgan Russia Kurgan Kurgan
Kursk Russia Kursk Kursk
Leningrad Russia Leningrad Leningrad
Lipetsk Russia Lipetsk Lipetsk
Mahachkala Russia Dagestan Mahachkala
Magadan Russia Magadan Magadan
Majkop Russia Adygeya Majkop
MariEl Russia MariEl MariEl
@@ -1924,6 +1977,8 @@ Penza Russia Penza Penza
Perm Russia Perm Perm
Petrozavodsk Russia Karelia Petrozavodsk
Podporozhie Russia Podporozhie Podporozhie
Primorsky Russia Primorsky Primorsky
Reshoty Russia Pskov Reshoty
RostovOnDon Russia Rostov RostovOnDon
Rostov Russia Rostov Rostov
Ryazan Russia Ryazan Ryazan
@@ -1936,13 +1991,15 @@ Saratov Russia Saratov Saratov
Stavropol Russia Stavropol Stavropol
Smolensk Russia Smolensk Smolensk
SosnoviyBor Russia Leningrad SosnoviyBor
Suzdalka Russia Novosibirsk Suzdalka
Surgut Russia KhantyMansia Surgut
Syktyvkar Russia Komi Syktyvkar
Tambov Russia Tambov Tambov
Tatarstan Russia Tatarstan Tatarstan
Tomsk Russia Tomsk Tomsk
Tula Russia Tula Tula
Tver Russia Tver Tver
Tyva Russia Tyva Tyva
Tyumen Russia Tyumen Tyumen
Ufa Russia Bashkortostan Ufa
UlanUde Russia Buryatia UlanUde
@@ -2122,6 +2179,7 @@ Aragon Spain Aragon Aragon
Asturias Spain Asturias Asturias
Baleares Spain BalearicIslands Baleares
Barcelona Spain Catalonia Barcelona
BasqueCountry Spain BasqueCountry BasqueCountry
Burgos Spain CastillaLaMancha Burgos
Canarias Spain CanaryIslands Canarias
Cantabria Spain Cantabria Cantabria
@@ -2232,16 +2290,21 @@ Tajikistan Tajikistan Tajikistan Tajikistan
Tanzania Tanzania Tanzania Tanzania
Tanzaniaunitedrepublicof Tanzania Tanzania Tanzania

# Tibet
Tibet Tibet Tibet Tibet

# Thailand
Thailand Thailand Thailand Thailand
Ayutthaya Thailand Ayutthaya Ayutthaya
Bangkok Thailand Bangkok Bangkok
Chachoengsao Thailand Chachoengsao Chachoengsao
Chaiyaphum Thailand Chaiyaphum Chaiyaphum
Chanthaburi Thailand Chanthaburi Chanthaburi
ChiangMai Thailand ChiangMai ChiangMai
ChiangRai Thailand ChiangRai ChiangRai
Chonburi Thailand Chonburi Chonburi
CuTha Thailand Thailand CuTha
Kalasin Thailand Kalasin Kalasin
Kanchanaburi Thailand Kanchanaburi Kanchanaburi
Kampheangphet Thailand KamphaengPhet KamphaengPhet
Kampheangephet Thailand KamphaengPhet KamphaengPhet
@@ -2253,14 +2316,20 @@ LopBuri Thailand LopBuri LopBuri
Loei Thailand Loei Loei
MaeHongSon Thailand MaeHongSon MaeHongSon
MahaSarakham Thailand MahaSarakham MahaSarakham
Mukdahan Thailand Mukdahan Mukdahan
Nakhonphanom Thailand NakhonPhanom NakhonPhanom
NakhonPathom Thailand NakhonPathom NakhonPathom
NakhonRatachasima Thailand NakhonRatachasima NakhonRatachasima
Nakhonsawan Thailand Nakhonsawan Nakhonsawan
NakhonSiThammarat Thailand NakhonSiThammarat NakhonSiThammarat
Nan Thailand Nan Nan
NongKhai Thailand NongKhai NongKhai
Nonthaburi Thailand Nonthaburi Nonthaburi
PathumThani Thailand PathumThani PathumThani
PhangNga Thailand PhangNga PhangNga
Phetchaburi Thailand Phetchaburi Phetchaburi
Phetchabun Thailand Phetchabun Phetchabun
Phichit Thailand Phichit Phichit
Phitsanulok Thailand Phitsanulok Phitsanulok
PhraNakhonSiAyutthaya Thailand PhraNakhonSiAyutthaya PhraNakhonSiAyutthaya
Phuket Thailand Phuket Phuket
@@ -2281,6 +2350,8 @@ SuratThani Thailand SuratThani SuratThani
Tak Thailand Tak Tak
Trang Thailand Trang Trang
Udorn Thailand NakhonRatachasima NongPhaiLom
Uthaiyhani Thailand Uthaiyhani Uthaiyhani
Uthaithani Thailand Uthaithani Uthaithani
Uttaradit Thailand Uttaradit Uttaradit
Yasothon Thailand Yasothon Yasothon

@@ -2396,6 +2467,7 @@ Odessa Ukraine Odessa Odessa
Poltava Ukraine Poltava Poltava
Rivne Ukraine Rivne Rivne
Ternopil Ukraine Ternopil Ternopil
Sevastopol Ukraine Crimea Sevastopol
Sumy Ukraine Sumy Sumy
Volyn Ukraine Volyn Volyn
Zaporizhia Ukraine Zaporizhia Zaporizhia
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