diff --git a/pipeline_resources/EastAfrica/configs/advisory_builder/config_EastAfrica_variety_names_tidy.json b/pipeline_resources/EastAfrica/configs/advisory_builder/config_EastAfrica_variety_names_tidy.json
deleted file mode 100644
index 5c8e130ee08fdf1b4cdc077803f1c56b8ba5f455..0000000000000000000000000000000000000000
--- a/pipeline_resources/EastAfrica/configs/advisory_builder/config_EastAfrica_variety_names_tidy.json
+++ /dev/null
@@ -1,1048 +0,0 @@
-{
- "16THSRRSN #6126":
- [
- "16THSRRSN#6126"
- ],
- "15th stemrust":
- [
- "15th stemrust"
- ],
- "AAAFC CANADA#162":
- [
- "AAAFC CANADA#162"
- ],
- "Adaptation trial plot #11":
- [
- "Adaptation trial plot#11"
- ],
- "Abay":
- [
- "Abay"
- ],
- "Alidoro":
- [
- "Alidoro",
- "Alido"
- ],
- "Amibara 2":
- [
- "Amibara_2",
- "Amibara2"
- ],
- "Balcha":
- [
- "Balcha"
- ],
- "Biftu":
- [
- "Biftu"
- ],
- "Boru":
- [
- "Boru"
- ],
- "Bulala":
- [
- "Bulala",
- "Bullala"
- ],
- "Candidate varity VVT":
- [
- "Candidate varity VVT"
- ],
- "CD 21 #16815":
- [
- "CD 21 # 16815"
- ],
- "CD 21 #16296":
- [
- "CD 21 #16296"
- ],
- "CD 22 #761 - ELTSR":
- [
- "CD22#761 -ELTSR"
- ],
- "Daka":
- [
- "Daka",
- "Deka",
- "DAKA",
- "Daka "
- ],
- "Dambal":
- [
- "Dambal",
- "Dambel",
- "Danbal"
- ],
- "Damphe":
- [
- "Damphe",
- "Danfe",
- "Denfe"
- ],
- "Danda'a":
- [
- "Danda'a",
- "Danda'a ",
- "Danda",
- "danda'",
- "danda'a",
- "Danda,a",
- "Dandaha",
- "Dandea",
- "Dend",
- "Denda",
- "Denda'a",
- "denda, a",
- "Dendaa",
- "Dende' a",
- "Dende'a",
- "Dendea",
- "Dendy",
- "Debdea",
- "Denidea",
- "Danada'a",
- "Dandaya",
- "Dehnadea",
- "Danadaha",
- "Deamda",
- "Denda'a ",
- "Danda’",
- "Dendáa",
- "Dandaa",
- "Damda'a",
- "Damdaha"
- ],
- "Db1899":
- [
- "Db1899"
- ],
- "Deneba":
- [
- "Deneba"
- ],
- "Dersolgn":
- [
- "Dersolgn"
- ],
- "Digalu":
- [
- "Digalu",
- "Digelu",
- "Degelu"
- ],
- "Duma":
- [
- "Duma",
- "Duma ",
- " Duma"
- ],
- "Durum CD21 ELTSR #1382":
- [
- "Durum CD21 ELTSR#1382"
- ],
- "Dursa":
- [
- "Dursa",
- "Dursaa"
- ],
- "Eagle 10":
- [
- "Eagle 10"
- ],
- "Eldo Baraka":
- [
- "Eldo Baraka"
- ],
- "ELITE BW #6":
- [
- "ELITE BW#6"
- ],
- "ELITE BW #13":
- [
- "ELITEBW 13",
- "ELITEBW 13"
- ],
- "ELITE BW #14":
- [
- "ELITEBW 14",
- "ELITEBW 14"
- ],
- "ELITE BW #21":
- [
- "ELITEBW-KENYA#21"
- ],
- "Enikoy":
- [
- "Enikoy",
- "Enkoy"
- ],
- "EPCBW #122":
- [
- "EPCBW#122",
- "EPCBW #122",
- "EPCBW #122"
- ],
- "EPCBW #207":
- [
- "EPCBW#207",
- "EPCBW #207",
- "EPCBW #207"
- ],
- "EPCBW #320":
- [
- "EPCBW#320",
- "EPCBW #320",
- "EPCBW #320"
- ],
- "EPCBW #1002":
- [
- "EPCBW#1002",
- "EPCBW #1002",
- "EPCBW #1002"
- ],
- "EPCHPLUS # KEN#58":
- [
- "EPCHPLUS # KEN#58"
- ],
- "EPCHPLUS #154":
- [
- "EPCHPLUS#154"
- ],
- "EPCHPLUS- KEN#120":
- [
- "EPCHPLUS- KEN#120"
- ],
- "EPCHPZN #11" :
- [
- "EPCHPZN#11"
- ],
- "Et 13":
- [
- "Et 13",
- "ET13",
- "Et13",
- "Ey13"
- ],
- "ETHIOPIA #238":
- [
- "ETHIOPIA #238"
- ],
- "F2BW #14" :
- [
- "F2BW#14"
- ],
- "F2BW #57" :
- [
- "F2BW#57"
- ],
- "F2HPZN #156":
- [
- "F2HPZN # 156"
- ],
- "F2HPZN #38" :
- [
- "F2HPZN#38"
- ],
- "F2HPLUS-KEN #111":
- [
- "F2HPLUS-KEN #111"
- ],
- "F3BW #9" :
- [
- "F3BW#9"
- ],
- "F3BW #360":
- [
- "F3BW #360"
- ],
- "F3HPLUS- KEN #59":
- [
- "F3HPLUS- KEN #59"
- ],
- "F3HPZN #59" :
- [
- "F3HPZN#59"
- ],
- "F4 HPLUS KEN":
- [
- "F4 HPLUS KEN"
- ],
- "F5RG #357" :
- [
- "F5RG#357"
- ],
- "F5 RG BW (A) #73":
- [
- "F5 RG BW (A)#73"
- ],
- "F5RG (A) #336":
- [
- "F5RG (A)#336"
- ],
- "F5RG (A) #757":
- [
- "F5RG (A)#757"
- ],
- "F5RG (B) #1026":
- [
- "F5RG (B) #1026"
- ],
- "F5RGBW #181 (A)":
- [
- "F5RGBW#181 (A)"
- ],
- "Farasi":
- [
- "Farasi",
- "KS. Farasi"
- ],
- "Farlly":
- [
- "Farlly"
- ],
- "Fentale-2":
- [
- "Fentale-2",
- "Fentale_2"
- ],
- "Galane":
- [
- "Galane",
- "Gelan",
- "Galan",
- "Gelana"
- ],
- "Ganda":
- [
- "Ganda"
- ],
- "Gembo":
- [
- "Gembo"
- ],
- "Genotypes":
- [
- "Genotypes"
- ],
- "Grace":
- [
- "Grace"
- ],
- "Hachalu":
- [
- "Hachalu"
- ],
- "Harato":
- [
- "Harato"
- ],
- "Hawi":
- [
- "Hawi"
- ],
- "HB13":
- [
- "HB13"
- ],
- "Hidassie":
- [
- "Hidassie",
- "Hidassie ",
- "Hidasse",
- "Hidase",
- "Hidasie",
- "hidassie",
- "Hiddasie",
- "Hisasie",
- "Hisasse",
- "Hiddase",
- "Hidassee"
- ],
- "Hoggana":
- [
- "Hoggana"
- ],
- "HR1685":
- [
- "HR1685"
- ],
- "Huluka":
- [
- "Huluka",
- "Huluqa",
- "Hulaka",
- "Hulka",
- "Hululka",
- "Buluka",
- "Huluka "
- ],
- "Hydero":
- [
- "Hydero"
- ],
- "Hyrax":
- [
- "Hyrax"
- ],
- "Improved":
- [
- "Improved"
- ],
- "Iran#66":
- [
- "Iran#66"
- ],
- "Israel":
- [
- "Israel"
- ],
- "Juhudi":
- [
- "Juhudi"
- ],
- "K. Hyrax":
- [
- "K. Hyrax",
- "K .Hyrax",
- "k. Hyrax",
- "K. hyrax",
- "K Hyrax",
- "k hyrax",
- "K hyrax",
- "k Hyrax"
- ],
- "K. Jacana":
- [
- "Jacana",
- "JACANA",
- "Jalane",
- "K jacana",
- "K.Jacana",
- "Kenya Jacana"
- ],
- "K. Kasuku":
- [
- "Kenya Kasuku",
- "Kenya Kasuku ",
- "Kasuku",
- "KASUKU",
- "Kasuku",
- " Kasuku",
- "K.kasuku",
- "K. kasuku",
- "K .kasuku",
- "K.Kasuku",
- "K. Kasuku",
- "K .Kasuku"
- ],
- "K. Korongo":
- [
- "K. Korongo",
- "K. Korongo ",
- "Korongo",
- "Korongo ",
- "K . Korongo",
- "K. KORONGO",
- "K.Korongo",
- "K Korongo",
- "K Korongo ",
- "Kenya Korongo",
- "Kenya Korongo ",
- "K .Korongo",
- "K.korongo"
- ],
- "KS. Chui":
- [
- "Chui",
- "KS. Chui",
- "KS Chui",
- "KS.CHUI",
- "KS.Chui",
- "KS. Chui",
- "Ks. Chui",
- "Ks.Chui",
- "Ks.Chui ",
- "Ks chui"
- ],
- "KS. Farasi":
- [
- "KS Farasi",
- "KS. Farasi"
- ],
- "KS. Kanga":
- [
- "Kanga",
- " Kanga",
- "KS. Kanga",
- "Ks. Kanga"
- ],
- "KS. Ndume":
- [
- "Ndume",
- "Ks. Ndume",
- "KS. Ndume",
- "Ks. Ndume ",
- "KS. Ndume ",
- "Ks.Ndume",
- "KS.Ndume",
- "Ndume "
- ],
- "KS. Mwamba":
- [
- "KS Mwamba ",
- "KS.MWAMBA",
- "Ks.Mwamba",
- "Mwamba"
- ],
- "K624A":
- [
- "K624A",
- "K62 4A"
- ],
- "K924A":
- [
- "K924A"
- ],
- "Kakaba":
- [
- "Kakab",
- "Kakaba",
- "Kakaba ",
- "Kekeaba",
- "Kekeb",
- "KEKEBA",
- "Kekeba",
- "kekeba",
- "kakaba",
- "Kekebw",
- "Kekekeba",
- "Kebeka"
- ],
- "Kebaba":
- [
- "Kebaba",
- "Kebab"
- ],
- "Kenya Impala":
- [
- "Kenya Impala"
- ],
- "Kenya Pweza":
- [
- "Kenya Pweza"
- ],
- "Kenya Turaco":
- [
- "Kenya Turaco",
- "Kenya Turaco "
- ],
- "Kenya wren":
- [
- "Kenya wren"
- ],
- "Kingbird":
- [
- "Kingbird",
- "King Bird",
- "King bird",
- "Kingbirds",
- "Kimgbard",
- "Kinbird",
- "Kingbard",
- "Kingbird ",
- "King be",
- "King bir",
- "KingBird",
- "Kigbird",
- "Kingbord",
- "Kinberd",
- "Kingberd",
- "kingbird"
- ],
- "Kubsa":
- [
- "Kubsa",
- "kubsa",
- "Kubssa",
- "Kubsa ",
- "Kubsa (1685)",
- "Kibsa"
- ],
- "Kwale":
- [
- "Kwale",
- "Kwale "
- ],
- "Lemu":
- [
- "Lemu",
- "Limu"
- ],
- "Liben":
- [
- "Liben"
- ],
- "Local":
- [
- "Local",
- "Local ",
- "From local market(Unknown)",
- "Emer wheat local",
- "local"
- ],
- "Mandoyu":
- [
- "Mandoyu",
- "Mandoyo"
- ],
- "Mangudo":
- [
- "Mangudo",
- "mangudo",
- "Mangudo "
- ],
- "Mekale 02":
- [
- "Mekale 02",
- "Mekale 02 "
- ],
- "Miju":
- [
- "Miju"
- ],
- "Mixed":
- [
- "Mixed",
- "Digalu mixture with Hidasie",
- "Kingbird (mixed)",
- "mixed",
- "Mixed variety",
- "Mixed hidase and danda'a",
- "Hidassie with danda'a",
- "Kingbird, wane ogolchoo",
- "israel+Et 13",
- "Mixed (Njoro II, Uknown)",
- "Mixed crop (Njoro II & Korongo )",
- "Mixed crop (Njoro II & Korongo)",
- "Mixed crop ( Kwale& unknown )",
- "Mixed crop (Korongo & KS. Chui)",
- "Mixed crop (Korongo & KS.CHUI )",
- "Mixed crop (KS.CHUI &Eagle 10)",
- "Mixed crop (Kwale & unknown )",
- "Mixed crop (Kwale& Njoro II )",
- "Mixed crop (Njoro II & KS.CHUI )",
- "Mixed crop (Njoro II & unknown )",
- "Mixed crop (Njoro II& Korongo )",
- "Mixed(Njoro II & Mwamba)",
- "Mixed crop (Korongo &Njoro II )",
- "Mixed crop (Ndume & Farasi)",
- "Mixed crop (Njoro II & Mwamba )",
- "Mixed crop (Njoro II & Farasi)",
- "Mixed: Danda'a and Kakaba",
- "Mixed varieties",
- "Wane mixture",
- "Dembel and Denda",
- "Mixed ",
- "Mixed (Korongo and old varieties )",
- "Mixed (kasuku, Korongo )",
- "Mixed (korongo, kasuku, old varieties)",
- "Mixed crop ( Korongo & barley )",
- "Mixed crop (Chui & Korongo )",
- "Mixed crop (K . Korongo &Uknown )",
- "Mixed crop (Korongo & Uknown)",
- "Mixed crop( Njoro II, Korongo, old varieties )",
- "Mixed crop(KingBird, Korongo )",
- "Korongo & Njoro 2",
- "Korongo& Eagle 10 (mixed )",
- "Mixed (K. Korongo/barely)",
- "Mixed (Robin, Korongo)",
- "Mixed( Njoro 2 & Korongo)",
- "Njoro 2 & Korongo",
- "Korongo, Robin, Kwale",
- "Mixed (Njoro II, Korongo )",
- "Mixed (Korongo, ks chui)",
- "Mixed (Njoro II, Korongo )",
- "Mixed (Njoro II, Korongo)",
- "Tallo diff#44,tallo diff#24,yr diff#4",
- "Differentials",
- "Kubsa + daka",
- "Mixed (Korongo&Uknown)",
- "Mixed varieties ( Korongo and KS Chui)",
- "King bird ,limu and sofmer",
- "Mixed crop (K.kasuku &K.Korongo. )",
- "Mixed crop (K.korongo & Duma)",
- "Mixed crop (K.korongo & duma)",
- "Mixed crop (K.korongo & K. kasuku)",
- "Mixed crop (K.korongo & K. kasuku. )",
- "Mixed crop (K.korongo & Kasuku )",
- "Mixed crop (K.korongo & uknown variety)",
- "Mixed crop (K.Korongo & unknown )",
- "Mixed crop (K.Korongo & unknown variety )",
- "Mixed crop (K.korongo & unknown)",
- "Mixed crop (K.Korongo &unknown )",
- "Mixed crop (kwale &unknown )",
- "Mixed crop (Njoro 2 & unknown )",
- "Mixed crop (Njoroll & Korongo )",
- "Mixed variety (K.Korongo and Kwale)",
- "Uknown mixed crop",
- "Mixed crop,k.Korongo & ks chui",
- "Mixed njoroll &k.korongo",
- "Mixed variety ks chui & korongo",
- "Mixed variety njoro ll & unknown",
- "Uknown mixed varieties"
- ],
- "Mulifa":
- [
- "Mulifa"
- ],
- "Mwera":
- [
- "Mwera"
- ],
- "Njoro BW II":
- [
- "NJORO BW II",
- "Njoro BW II",
- "NJORO BW II ",
- "Njoro 2",
- "Njoro BW Il",
- "Njoro BWIl",
- "NJORO BWIl ",
- "NjoroBWII",
- "NjoroBWII ",
- "Njoro II",
- "Njoro II ",
- "Njoro Il",
- "Njoro Il ",
- "Njoro ll",
- "Njoro2",
- "Njoro ll",
- "Njoro ll",
- "Njoroll",
- "Njoro ll ",
- "Njoroll "
- ],
- "Oat":
- [
- "Oat"
- ],
- "Oborra":
- [
- "Oborra"
- ],
- "Ogolcho":
- [
- "Ogolcho",
- "Ogolcho ",
- "ogolcho",
- "Ogolccho",
- "Ogelcho",
- "Oglcho",
- "Ogocho",
- "Ogoocho",
- "Ogol cho",
- "Ogolchi",
- "OGOLCHO",
- "Ogolicho",
- "OGOLOCHO",
- "Ogilcho",
- "Ogolch",
- "Ogolucho",
- "Ogolcha"
- ],
- "One":
- [
- "One"
- ],
- "Otuba":
- [
- "Otuba",
- "Utuba"
- ],
- "Paven 76":
- [
- "Paven 76",
- "Paven76",
- "Pavo-76",
- "Pavon",
- "Pavan",
- "Pavon_76",
- "Pavon 76",
- "Pavon-76",
- "pavan",
- "Pavin"
- ],
- "PCBW #560":
- [
- "PCBW# 560"
- ],
- "PCBW #1387" :
- [
- "PCBW#1387"
- ],
- "PCBW #1877":
- [
- "PCBW#1877"
- ],
- "PCBW #4175" :
- [
- "PCBW#4175"
- ],
- "PCBW #4556" :
- [
- "PCBW#4556"
- ],
- "PCBWSR #2431":
- [
- "PCBWSR#2431"
- ],
- "PCBWSR #3421":
- [
- "PCBWSR#3421"
- ],
- "PCBWSR #4409":
- [
- "PCBWSR4409"
- ],
- "PCHZNSR #585" :
- [
- "PCHZNSR #585"
- ],
- "PCHPLUSSR #198":
- [
- "PCHPLUSSR#198"
- ],
- "Robin":
- [
- "Robin",
- "Robin "
- ],
- "Senate":
- [
- "Sanate",
- "Senate",
- "Sanate ",
- "Senata "
- ],
- "Shaki":
- [
- "Shaki",
- "shaki"
- ],
- "Shorima":
- [
- "SHORIMA",
- "Shorima",
- "Shorima ",
- "Shorimo",
- "Shoroma",
- "Shorina"
- ],
- "Sifa":
- [
- "Sifa"
- ],
- "Simba":
- [
- "Simba",
- "Sinba"
- ],
- "Sofumer":
- [
- "Sofumer"
- ],
- "SR DIFFERENTIAL #27":
- [
- "SR DIFFERENTIAL # 27",
- "Sr differentials #27"
-
- ],
- "SR DIFFERENTIAL #51":
- [
- "SR DIFFERENTIAL # 51",
- "SR Differential#51"
- ],
- "SR DIFFERENTIAL #33":
- [
- "Sr differential #33"
- ],
- "SR DIFFERENTIAL #20":
- [
- "SR Differentials#20"
- ],
- "Sydney Australia #83":
- [
- "Sydney Australia #83"
- ],
- "Tate":
- [
- "Tate"
- ],
- "Triticale":
- [
- "Triticale",
- "Triticale ",
- "Tritical"
- ],
- "Tsehay":
- [
- "Tsehay"
- ],
- "Unknown":
- [
- "Unknown",
- "Uknown",
- "Uknown ",
- "unknown",
- "Unknown ",
- "Unkoown",
- "Unkown",
- "unkown",
- "Unkwon",
- "Unkwown",
- "Unkwown ",
- "Unknown (observation nursery)",
- "unknow",
- "Kenya Hawk?",
- "I known",
- "UnKnown",
- "unknown ",
- "Unkwon ",
- "Inknown",
- "Known",
- "Ubknown",
- "Ujknown",
- "Ukown",
- "UNKNOWN",
- "Unknown (Duma?)",
- "Unkowb",
- "Unlnown",
- "Uninown",
- "Unko",
- "Variety",
- "Uknown old Kenyan variety",
- "Uknown variety",
- "Uknown awnless variety",
- "Uknown variety",
- "Unknown variety",
- "Unknown variety"
- ],
- "USDA #105":
- [
- "USDA#105"
- ],
- "USDA #112":
- [
- "USDA#112"
- ],
- "USDA #547":
- [
- "USDA#547"
- ],
- "USDA #747":
- [
- "USDA#747"
- ],
- "USDA #823":
- [
- "USDA#823"
- ],
- "USDA #994":
- [
- "USDA#994",
- "USDA #994"
- ],
- "USDA #1061":
- [
- "USDA#1061",
- "USDA #1061"
- ],
- "USDA #1135":
- [
- "USDA#1135",
- "USDA #1135"
- ],
- "USDA #1458":
- [
- "USDA#1458",
- "USDA #1458"
- ],
- "USDA #1588":
- [
- "USDA#1588",
- "USDA #1588"
- ],
- "USDA #1612":
- [
- "USDA #1612"
- ],
- "USDA #1762":
- [
- "USDA#1762"
- ],
- "Wane":
- [
- "Wane",
- "Wanie",
- "wane"
- ],
- "YR DIFFERENTIAL #1":
- [
- "YR DIFFERENTIAL#1",
- "YR DIFFERENTIAL #1",
- "Yr Differentials #1"
- ],
- "YR DIFFERENTIAL #4":
- [
- "YR DIFFERENTIAL#4",
- "YR DIFFERENTIAL #4",
- "Yr differential #4"
- ],
- "YR DIFFERENTIAL #8":
- [
- "YR DIFFERENTIAL#8",
- "YR DIFFERENTIAL #8"
- ],
- "YR DIFFERENTIAL #10":
- [
- "YR DIFFERENTIAL#10",
- "YR DIFFERENTIAL #10"
- ],
- "YR DIFFERENTIAL #15":
- [
- "YR DIFFERENTIAL#15",
- "YR DIFFERENTIAL #15"
- ],
- "YR DIFFERENTIAL #24":
- [
- "YR DIFFERENTIAL#24",
- "YR DIFFERENTIAL #24"
- ],
- "YR DIFFERENTIAL #27":
- [
- "YR DIFFERENTIAL#27",
- "YR DIFFERENTIAL #27"
- ],
- "YR DIFFERENTIAL #38":
- [
- "YR DIFFERENTIAL#38",
- "YR DIFFERENTIAL #38",
- "Yr Differential 38"
- ],
- "YR DIFFERENTIAL #40":
- [
- "YR DIFFERENTIAL#40",
- "YR DIFFERENTIAL #40",
- "Yr DIFF 40"
- ],
- "YR27/6*AOC":
- [
- "YR27/6*AOC"
- ],
- "YR8/6*AOC":
- [
- "YR8/6*AOC"
- ]
-}
diff --git a/pipeline_resources/EastAfrica/configs/coordinator/README.txt b/pipeline_resources/EastAfrica/configs/coordinator/README.txt
deleted file mode 100644
index b97176485969b5bbde7d4efa7d839eddd327da15..0000000000000000000000000000000000000000
--- a/pipeline_resources/EastAfrica/configs/coordinator/README.txt
+++ /dev/null
@@ -1,3 +0,0 @@
-make a copy of the template file, You can add a files to set system-specific variables (or sensitive passwords)
-
-the template sys config files will be needed for both forecast and analysis runs,
\ No newline at end of file
diff --git a/pipeline_resources/EastAfrica/configs/coordinator/an/depo_config_EastAfrica_an_live.json b/pipeline_resources/EastAfrica/configs/coordinator/an/depo_config_EastAfrica_an_live.json
deleted file mode 100644
index 4cdfee13e4f8c80784c6b516e2beb2b454aeecd3..0000000000000000000000000000000000000000
--- a/pipeline_resources/EastAfrica/configs/coordinator/an/depo_config_EastAfrica_an_live.json
+++ /dev/null
@@ -1,35 +0,0 @@
-{
- "ServerPathTemplate": "${MetoFTP}/metofficeupload/upload/Ethiopia/fromMO/daily_name/",
- "InputFileTemplate" : "WR_NAME_Ethiopia_${StartString}_an",
- "DataFileTemplate" : "deposition_srcs_allregions_${StartString}.nc",
- "TimeExpectedAvailable" : "1500",
- "ProcessPreJob" : "process_pre_job_server_download",
- "ProcessInJob" : "process_in_job_dep",
- "ProcessEWSPlotting" : "process_EWS_plotting_dep",
- "EWS-Plotting" : {
- "SysConfig": "${ConfigsPath}/coordinator/an/sys_config_EastAfrica_an_live.json",
- "NameExtractionConfig": "${ConfigsPath}/plotting///name_extraction/NAME_EXTRACTION_CONFIG.json",
- "RunConfig": "${ConfigsPath}/plotting///deposition/RUN_CONFIG_DEPO.json",
- "RunConfigNorm": "${ConfigsPath}/plotting///deposition/RUN_CONFIG_DEPO_NORMALIZED.json",
- "EastAfrica" : {
- "ChartConfig": "${ConfigsPath}/plotting///chart/CHART_CONFIG_EAST_AFRICA_PINE.json",
- "Normalize" : "False"
- },
- "Ethiopia" : {
- "ChartConfig": "${ConfigsPath}/plotting///chart/CHART_CONFIG_ETHIOPIA_PINE.json",
- "Normalize" : "False"
- },
- "Kenya" : {
- "ChartConfig": "${ConfigsPath}/plotting/chart/CHART_CONFIG_KENYA_PINE.json",
- "Normalize": "False"
- },
- "Zambia": {
- "ChartConfig": "${ConfigsPath}/plotting/chart/CHART_CONFIG_ZAMBIA_PINE.json",
- "Normalize": "False"
- },
- "Tanzania": {
- "ChartConfig": "${ConfigsPath}/plotting/chart/CHART_CONFIG_TANZANIA_EPI.json",
- "Normalize": "False"
- }
- }
-}
diff --git a/pipeline_resources/EastAfrica/configs/coordinator/an/env_suit_config_EastAfrica_an_live.json b/pipeline_resources/EastAfrica/configs/coordinator/an/env_suit_config_EastAfrica_an_live.json
deleted file mode 100644
index a1991b53a23b407b8d6dc7db78b7f2ad97ccf63e..0000000000000000000000000000000000000000
--- a/pipeline_resources/EastAfrica/configs/coordinator/an/env_suit_config_EastAfrica_an_live.json
+++ /dev/null
@@ -1,100 +0,0 @@
-{
- "ServerPathTemplate" : "${MetoFTP}/metofficeupload/upload/Ethiopia/fromMO/daily_name/",
- "InputFileTemplate" : "WR_EnvSuit_Met_Ethiopia_${StartString}_an",
- "ProcessPreJob" : "process_pre_job_server_download",
- "ProcessInJob" : "process_in_job_env2_0",
- "ProcessEWSPlotting" : "process_EWS_plotting_env2_0",
- "CONFIGS_PATH": "${ConfigsPath}",
- "ASSETS_PATH": "${AssetsPath}",
- "WORK_PATH" : "${WorkspacePath}",
- "INPUT_PATH" : "${WorkspacePath}",
- "OUTPUT_PATH" : "${WorkspacePath}",
- "SYS_CONFIG" : "${ConfigsPath}/met_extractor/SYS_CONFIG_PINE.json",
- "FIELD_NAME_CONSTANTS" : "${ConfigsPath}/met_extractor/FIELD_NAME_CONSTANTS.csv",
- "RUN_TYPE" : "operational",
- "EXTRACTION_DAYS": 7,
- "FORECAST_DAYS": 6,
- "STRAINS": ["LeafRust","StemRust","StripeRust","LeafRust_TempOnly","StemRust_TempOnly","StripeRust_TempOnly"],
- "PARAMS": {
- "LeafRust": {
- "suitability_modules": ["semibool_dewperiod"],
- "past_steps": 0,
- "future_steps": 2,
- "thresholds": {
- "temperature": [2,15,20,30],
- "precipitation": 0,
- "relative_humidity": 90
- }
- },
- "StemRust": {
- "suitability_modules": ["semibool_dewperiod"],
- "past_steps": 0,
- "future_steps": 2,
- "thresholds": {
- "temperature": [2,15,24,30],
- "precipitation": 0,
- "relative_humidity": 90
- }
- },
- "StripeRust": {
- "suitability_modules": ["v1_dewperiod"],
- "past_steps": 0,
- "future_steps": 7,
- "thresholds": {
- "temperature": [2.37,19.8],
- "precipitation": 0,
- "relative_humidity": 90
- }
- },
- "LeafRust_TempOnly": {
- "suitability_modules": ["semibool_dewperiod"],
- "past_steps": 0,
- "future_steps": 2,
- "thresholds": {
- "temperature": [2,15,20,30],
- "precipitation": -1,
- "relative_humidity": 90
- }
- },
- "StemRust_TempOnly": {
- "suitability_modules": ["semibool_dewperiod"],
- "past_steps": 0,
- "future_steps": 2,
- "thresholds": {
- "temperature": [2,15,24,30],
- "precipitation": -1,
- "relative_humidity": 90
- }
- },
- "StripeRust_TempOnly": {
- "suitability_modules": ["v1_dewperiod"],
- "past_steps": 0,
- "future_steps": 7,
- "thresholds": {
- "temperature": [2.37,19.8],
- "precipitation": -1,
- "relative_humidity": 90
- }
- }
- },
- "EWS-Plotting" : {
- "SysConfig" : "${ConfigsPath}/coordinator/an/sys_config_EastAfrica_an_live.json",
- "RunConfig" : "${ConfigsPath}/plotting/env_suit/RUN_CONFIG_ENV.json",
- "EastAfrica" : {
- "ChartConfig" : "${ConfigsPath}/plotting/chart/CHART_CONFIG_EAST_AFRICA_PINE.json",
- "FilterForCountry" : "False"
- },
- "Ethiopia" : {
- "ChartConfig" : "${ConfigsPath}/plotting/chart/CHART_CONFIG_ETHIOPIA_PINE.json",
- "FilterForCountry" : "True"
- },
- "Kenya" : {
- "ChartConfig" : "${ConfigsPath}/plotting/chart/CHART_CONFIG_KENYA_PINE.json",
- "FilterForCountry" : "True"
- },
- "Zambia" : {
- "ChartConfig" : "${ConfigsPath}/plotting/chart/CHART_CONFIG_ZAMBIA_PINE.json",
- "FilterForCountry" : "True"
- }
- }
-}
diff --git a/pipeline_resources/EastAfrica/configs/coordinator/an/template_sys_config_EastAfrica_an_live.json b/pipeline_resources/EastAfrica/configs/coordinator/an/template_sys_config_EastAfrica_an_live.json
deleted file mode 100644
index 7b23fb97cf08a9b21d62df4f7fd49d4497599667..0000000000000000000000000000000000000000
--- a/pipeline_resources/EastAfrica/configs/coordinator/an/template_sys_config_EastAfrica_an_live.json
+++ /dev/null
@@ -1,14 +0,0 @@
-{
- "RegionName" : "EastAfrica",
- "SubRegionNames" : ["EastAfrica","Ethiopia","Kenya","Zambia","Tanzania"],
- "StartTime" : "?",
- "StartString" : "?",
- "ProjectRoot" : "<path to project root>",
- "MetoFTP" : "<path to MetoFTP>",
- "WorkspacePathout" : "${ProjectRoot}/regions/EastAfrica/workspace_analysis/",
- "WorkspacePath" : "${ProjectRoot}/regions/EastAfrica/workspace_analysis/",
- "ConfigsPath" : "${ProjectRoot}/code/coordinator/pipeline_resources/EastAfrica/configs",
- "AssetsPath" : "${ProjectRoot}/regions/EastAfrica/resources/assets",
- "LoggingConfigPath" : "${ProjectRoot}/code/coordinator/pipeline_resources/Eastconfigs/coordinator/log_config.json",
- "PLACES_SHAPE_FILE": "${ProjectRoot}/regions/EastAfrica/resources/assets/plotting/gis_data/common/places_shape/east_africa_places.shp"
-}
diff --git a/pipeline_resources/EastAfrica/configs/coordinator/fc/advisory_config_EastAfrica_fc_live.json b/pipeline_resources/EastAfrica/configs/coordinator/fc/advisory_config_EastAfrica_fc_live.json
deleted file mode 100644
index 9d1adc75d5bf5650c9af5327d5b833035a29f44b..0000000000000000000000000000000000000000
--- a/pipeline_resources/EastAfrica/configs/coordinator/fc/advisory_config_EastAfrica_fc_live.json
+++ /dev/null
@@ -1,122 +0,0 @@
-{
- "ProcessPreJob" : "query_past_successes",
- "ProcessInJob" : "process_in_job_advisory",
- "ProcessEWSPlotting" : "do_nothing",
- "seasonStartString" : "20240131",
- "SurveyPathTemplate" : "${WorkspacePath}/SURVEYDATA_${dateString}/Groups/surveys_PROD.csv",
- "DependentComponents" : [
- "Deposition",
- "Environment"
- ],
- "Environment" : {
- "SuccessFileTemplate" : "${WorkspacePath}/ENVIRONMENT_2.0_${StartString}/STATUS_SUCCESS",
- "DataPathTemplate" : "${WorkspacePath}/ENVIRONMENT_2.0_${dateString}/plotting/${SubRegionNameLower}/input_nc/",
- "PlotPathTemplate" : "${WorkspacePath}/ENVIRONMENT_2.0_${dateString}/plotting/${SubRegionNameLower}/images/Weekly/",
- "PlotFilenameTemplates" : {
- "stripe" : "${envPlotPath}/suitability_${SubRegionNameLower}_stripe_rust_total_${dateString}0000_${EnvEndString}0000_map.png",
- "stem" : "${envPlotPath}/suitability_${SubRegionNameLower}_stem_rust_total_${dateString}0000_${EnvEndString}0000_map.png",
- "leaf" : "${envPlotPath}/suitability_${SubRegionNameLower}_leaf_rust_total_${dateString}0000_${EnvEndString}0000_map.png"
- },
- "Aggregation" : {
- "raster_path_template" : "${envDataPath}/suitability_${SubRegionNameLower}_${disease_name_snakecase}_total.nc",
- "raster_name_template" : "RIE_${disease_name_camelcase}_%",
- "shape_fn_entry" : "ShapeFilenameToAggregate",
- "shape_coln" : "ADM2_EN",
- "show_columns" : ["ADM0_EN","ADM1_EN"],
- "separate_rows_for_coln":"ADM0_EN",
- "func" : "mean",
- "multiply_by" : 100,
- "float_format" : ".0f",
- "display_format" : ".0f",
- "save_path_template" : "${jobPath}/images/suitability_${SubRegionNameLower}_${disease_name_snakecase}_mean_per_zone",
- "max_entries" : 20
- }
- },
- "Deposition" : {
- "SuccessFileTemplate" : "${WorkspacePath}/DEPOSITION_${StartString}/STATUS_SUCCESS",
- "DataPathTemplate" : "${WorkspacePath}/DEPOSITION_${dateString}/plotting/${SubRegionNameLower}/input_nc/",
- "PlotPathTemplate" : "${WorkspacePath}/DEPOSITION_${dateString}/plotting/${SubRegionNameLower}/images/Weekly/",
- "PlotFilenameTemplates" : {
- "stripe": "${depPlotPath}/deposition_${SubRegionNameLower}_stripe_rust_total_${dateString}0300_${weekAheadString}0000_map.png",
- "stem": "${depPlotPath}/deposition_${SubRegionNameLower}_stem_rust_total_${dateString}0300_${weekAheadString}0000_map.png",
- "leaf": "${depPlotPath}/deposition_${SubRegionNameLower}_leaf_rust_total_${dateString}0300_${weekAheadString}0000_map.png"
- },
- "Aggregation" : {
- "raster_path_template" : "${depDataPath}/deposition_${SubRegionNameLower}_${disease_name_snakecase}_total.nc",
- "raster_name_template" : "spores_per_m2_per_week_${disease_name_camelcase}",
- "shape_fn_entry" : "ShapeFilenameToAggregate",
- "shape_coln" : "ADM2_EN",
- "show_columns" : ["ADM0_EN","ADM1_EN"],
- "separate_rows_for_coln":"ADM0_EN",
- "func" : "mean",
- "multiply_by" : 1,
- "float_format" : ".1e",
- "display_format" : ".0f",
- "save_path_template" : "${jobPath}/images/deposition_${SubRegionNameLower}_${disease_name_snakecase}_mean_per_zone",
- "max_entries" : 20
- }
- },
- "Epidemiology" : {
- "SuccessFileTemplate" : "${WorkspacePath}/EPI_${StartString}/STATUS_SUCCESS",
- "DataPathTemplate" : "${WorkspacePath}/EPI_${dateString}/plotting/input_csvs/",
- "PlotPathTemplate" : "${WorkspacePath}/EPI_${dateString}/plotting/images/",
- "PlotFilenameTemplates" : {
- "stem": "${epiPlotPath}/infection_${SubRegionNameLower}_stem_seasonincforecast_*0300_*0000_map.png"
- },
- "Aggregation" : {
- "raster_path_template" : "${depDataPath}/${SubRegionNameLower}_${disease_name_snakecase}_masked.csv",
- "raster_name_template" : "predicted_infected_area_${disease_name_camelcase}",
- "shape_fn_entry" : "ShapeFilenameToAggregate",
- "shape_coln" : "ADM2_EN",
- "show_columns" : ["ADM0_EN","ADM1_EN"],
- "separate_rows_for_coln":"ADM0_EN",
- "func" : "mean",
- "multiply_by" : 1,
- "float_format" : ".1e",
- "display_format" : ".0f",
- "save_path_template" : "${jobPath}/images/infection_${SubRegionNameLower}_${disease_name_snakecase}_mean_per_zone",
- "max_entries" : 20
- }
- },
- "Surveys" : {
- "variety_names_tidy_fn" : "${ConfigsPath}/advisory_builder/config_EastAfrica_variety_names_tidy.json",
- "CountryColumnName" : "surveyor_infromation-country",
- "EastAfrica": {
- "CountryList" : ["Ethiopia", "Kenya", "Tanzania", "Uganda", "Zambia"],
- "ShapeFilenameAdmin1" : "${AssetsPath}/advisory_builder/gis/eastafrica/eth_adm1_2021_ken_adm1_2019.shp",
- "ShapeFilenameAdmin2" : "${AssetsPath}/advisory_builder/gis/eastafrica/eth_adm2_2021_ken_adm1_2019_zmb_adm2_2020.shp",
- "ShapeFilenameToAggregate" : "${AssetsPath}/advisory_builder/gis/eastafrica/eth_adm2_2021_ken_adm1_2019_zmb_adm2_2020.shp",
- "Extent" : [21.5, 47, -18.5, 15],
- "LabelZoom" : 5
- },
- "Ethiopia": {
- "ShapeFilenameAdmin1" : "${AssetsPath}/advisory_builder/gis/ethiopia/eth_admbnda_adm1_csa_bofedb_2021.shp",
- "ShapeFilenameAdmin2" : "${AssetsPath}/advisory_builder/gis/ethiopia/eth_admbnda_adm2_csa_bofedb_2021.shp",
- "ShapeFilenameToAggregate" : "${AssetsPath}/advisory_builder/gis/ethiopia/eth_admbnda_adm2_csa_bofedb_2021.shp",
- "Extent" : [32.8, 47, 3.2, 15],
- "LabelZoom" : 7
- },
- "Kenya": {
- "ShapeFilenameAdmin1" : "${AssetsPath}/advisory_builder/gis/kenya/ken_admbnda_adm1_iebc_20191031_adm2_named.shp",
- "ShapeFilenameAdmin2" : "${AssetsPath}/advisory_builder/gis/kenya/ken_admbnda_adm2_iebc_20191031.shp",
- "ShapeFilenameToAggregate" : "${AssetsPath}/advisory_builder/gis/kenya/ken_admbnda_adm1_iebc_20191031_adm2_named.shp",
- "Extent" : [33.8, 42, -5, 5.5],
- "LabelZoom" : 7
- },
- "Zambia": {
- "ShapeFilenameAdmin1" : "${AssetsPath}/advisory_builder/gis/zambia/zmb_admbnda_adm1_dmmu_20201124.shp",
- "ShapeFilenameAdmin2" : "${AssetsPath}/advisory_builder/gis/zambia/zmb_admbnda_adm2_dmmu_20201124.shp",
- "ShapeFilenameToAggregate" : "${AssetsPath}/advisory_builder/gis/zambia/zmb_admbnda_adm2_dmmu_20201124.shp",
- "Extent" : [21.5, 34, -18.5, -8],
- "LabelZoom" : 7
- },
- "Tanzania": {
- "ShapeFilenameAdmin1" : "${AssetsPath}/plotting/gis_data/tanzania/tanzania_admin_shape/admin1/tza_admbnda_adm1_20181019.shp",
- "ShapeFilenameAdmin2" : "${AssetsPath}/plotting/gis_data/tanzania/tanzania_admin_shape/admin2/tza_admbnda_adm2_20181019.shp",
- "ShapeFilenameToAggregate" : "${AssetsPath}/plotting/gis_data/tanzania/tanzania_admin_shape/admin2/tza_admbnda_adm2_20181019.shp",
- "Extent" : [28.93, 41.98, -0.29, -12.37],
- "LabelZoom" : 7
- }
- },
- "logos" : "${AssetsPath}/advisory_builder/logos_EastAfrica_plotting.png"
-}
diff --git a/pipeline_resources/EastAfrica/configs/coordinator/fc/depo_config_EastAfrica_fc_live.json b/pipeline_resources/EastAfrica/configs/coordinator/fc/depo_config_EastAfrica_fc_live.json
deleted file mode 100644
index 6acea59eaf9ad21f09ec6a554b12150e40b68530..0000000000000000000000000000000000000000
--- a/pipeline_resources/EastAfrica/configs/coordinator/fc/depo_config_EastAfrica_fc_live.json
+++ /dev/null
@@ -1,35 +0,0 @@
-{
- "ServerPathTemplate": "${MetoFTP}/metofficeupload/upload/Ethiopia/fromMO/daily_name/",
- "InputFileTemplate": "WR_NAME_Ethiopia_${StartString}_fc",
- "DataFileTemplate": "deposition_srcs_allregions_${StartString}.nc",
- "TimeExpectedAvailable": "1000",
- "ProcessPreJob": "process_pre_job_server_download",
- "ProcessInJob": "process_in_job_dep",
- "ProcessEWSPlotting": "process_EWS_plotting_dep",
- "EWS-Plotting": {
- "SysConfig": "${ConfigsPath}/coordinator/fc/sys_config_EastAfrica_fc_live.json",
- "NameExtractionConfig": "${ConfigsPath}/plotting/name_extraction/NAME_EXTRACTION_CONFIG.json",
- "RunConfig": "${ConfigsPath}/plotting/deposition/RUN_CONFIG_DEPO.json",
- "RunConfigNorm": "${ConfigsPath}/plotting/deposition/RUN_CONFIG_DEPO_NORMALIZED.json",
- "EastAfrica": {
- "ChartConfig": "${ConfigsPath}/plotting/chart/CHART_CONFIG_EAST_AFRICA_PINE.json",
- "Normalize": "False"
- },
- "Ethiopia": {
- "ChartConfig": "${ConfigsPath}/plotting/chart/CHART_CONFIG_ETHIOPIA_PINE.json",
- "Normalize": "False"
- },
- "Kenya": {
- "ChartConfig": "${ConfigsPath}/plotting/chart/CHART_CONFIG_KENYA_PINE.json",
- "Normalize": "False"
- },
- "Zambia": {
- "ChartConfig": "${ConfigsPath}/plotting/chart/CHART_CONFIG_ZAMBIA_PINE.json",
- "Normalize": "False"
- },
- "Tanzania": {
- "ChartConfig": "${ConfigsPath}/plotting/chart/CHART_CONFIG_TANZANIA_EPI.json",
- "Normalize": "False"
- }
- }
-}
diff --git a/pipeline_resources/EastAfrica/configs/coordinator/fc/env_suit_config_EastAfrica_fc_live.json b/pipeline_resources/EastAfrica/configs/coordinator/fc/env_suit_config_EastAfrica_fc_live.json
deleted file mode 100644
index 2901e12bdf822e94b25692f6adb43fdb73fd2294..0000000000000000000000000000000000000000
--- a/pipeline_resources/EastAfrica/configs/coordinator/fc/env_suit_config_EastAfrica_fc_live.json
+++ /dev/null
@@ -1,104 +0,0 @@
-{
- "ServerPathTemplate" : "${MetoFTP}/metofficeupload/upload/Ethiopia/fromMO/daily_name/",
- "InputFileTemplate" : "WR_EnvSuit_Met_Ethiopia_${StartString}_fc",
- "ProcessPreJob" : "process_pre_job_server_download",
- "ProcessInJob" : "process_in_job_env2_0",
- "ProcessEWSPlotting" : "process_EWS_plotting_env2_0",
- "CONFIGS_PATH": "${ConfigsPath}",
- "ASSETS_PATH": "${AssetsPath}",
- "WORK_PATH" : "${WorkspacePath}",
- "INPUT_PATH" : "${WorkspacePath}",
- "OUTPUT_PATH" : "${WorkspacePath}",
- "SYS_CONFIG" : "${ConfigsPath}/met_extractor/SYS_CONFIG_PINE.json",
- "FIELD_NAME_CONSTANTS" : "${ConfigsPath}/met_extractor/FIELD_NAME_CONSTANTS.csv",
- "RUN_TYPE" : "operational",
- "EXTRACTION_DAYS": 7,
- "FORECAST_DAYS": 6,
- "STRAINS": ["LeafRust","StemRust","StripeRust","LeafRust_TempOnly","StemRust_TempOnly","StripeRust_TempOnly"],
- "PARAMS": {
- "LeafRust": {
- "suitability_modules": ["semibool_dewperiod"],
- "past_steps": 0,
- "future_steps": 2,
- "thresholds": {
- "temperature": [2,15,20,30],
- "precipitation": 0,
- "relative_humidity": 90
- }
- },
- "StemRust": {
- "suitability_modules": ["semibool_dewperiod"],
- "past_steps": 0,
- "future_steps": 2,
- "thresholds": {
- "temperature": [2,15,24,30],
- "precipitation": 0,
- "relative_humidity": 90
- }
- },
- "StripeRust": {
- "suitability_modules": ["v1_dewperiod"],
- "past_steps": 0,
- "future_steps": 7,
- "thresholds": {
- "temperature": [2.37,19.8],
- "precipitation": 0,
- "relative_humidity": 90
- }
- },
- "LeafRust_TempOnly": {
- "suitability_modules": ["semibool_dewperiod"],
- "past_steps": 0,
- "future_steps": 2,
- "thresholds": {
- "temperature": [2,15,20,30],
- "precipitation": -1,
- "relative_humidity": 90
- }
- },
- "StemRust_TempOnly": {
- "suitability_modules": ["semibool_dewperiod"],
- "past_steps": 0,
- "future_steps": 2,
- "thresholds": {
- "temperature": [2,15,24,30],
- "precipitation": -1,
- "relative_humidity": 90
- }
- },
- "StripeRust_TempOnly": {
- "suitability_modules": ["v1_dewperiod"],
- "past_steps": 0,
- "future_steps": 7,
- "thresholds": {
- "temperature": [2.37,19.8],
- "precipitation": -1,
- "relative_humidity": 90
- }
- }
- },
- "EWS-Plotting" : {
- "SysConfig" : "${ConfigsPath}/coordinator/fc/sys_config_EastAfrica_fc_live.json",
- "RunConfig" : "${ConfigsPath}/plotting/env_suit/RUN_CONFIG_ENV.json",
- "EastAfrica" : {
- "ChartConfig" : "${ConfigsPath}/plotting/chart/CHART_CONFIG_EAST_AFRICA_PINE.json",
- "FilterForCountry" : "False"
- },
- "Ethiopia" : {
- "ChartConfig" : "${ConfigsPath}/plotting/chart/CHART_CONFIG_ETHIOPIA_PINE.json",
- "FilterForCountry" : "True"
- },
- "Kenya" : {
- "ChartConfig" : "${ConfigsPath}/plotting/chart/CHART_CONFIG_KENYA_PINE.json",
- "FilterForCountry" : "True"
- },
- "Zambia" : {
- "ChartConfig" : "${ConfigsPath}/plotting/chart/CHART_CONFIG_ZAMBIA_PINE.json",
- "FilterForCountry" : "True"
- },
- "Tanzania" : {
- "ChartConfig" : "${ConfigsPath}/plotting/chart/CHART_CONFIG_TANZANIA_EPI.json",
- "FilterForCountry" : "True"
- }
- }
-}
diff --git a/pipeline_resources/EastAfrica/configs/coordinator/fc/epi_config_EastAfrica_fc_live.json b/pipeline_resources/EastAfrica/configs/coordinator/fc/epi_config_EastAfrica_fc_live.json
deleted file mode 100644
index 537285090320d9d626b880a0de5a4a2dff1087fa..0000000000000000000000000000000000000000
--- a/pipeline_resources/EastAfrica/configs/coordinator/fc/epi_config_EastAfrica_fc_live.json
+++ /dev/null
@@ -1,94 +0,0 @@
-{
- "DiseaseNames" : ["StemRust"],
- "CalculationSpanDays" : ["20230715",5],
- "continue" : true,
- "TimeStep_hours": "3",
- "ProcessPreJob" : "process_pre_job_epi",
- "ProcessInJob" : "process_in_job_epi",
- "ProcessEWSPlotting" : "process_EWS_plotting_epi",
- "Host" : {
- "MaxFieldsPerCell" : "1",
- "TargetRaster" : "${AssetsPath}/epimodel/wheat_area_frac_MapSPAM2010_EastAfrica.tif",
- "HostRasters" : {
- "201001010000" : "${AssetsPath}/epimodel/wheat_area_frac_MapSPAM2010_EastAfrica.tif",
- "202309200000" : "${AssetsPath}/epimodel/wheat_area_frac_MapSPAM2010_EastAfrica_20230901.tif",
- "202309260000" : "${AssetsPath}/epimodel/wheat_area_frac_MapSPAM2010_EastAfrica.tif"
- },
- "FileNamePrepared" : "?"
- },
- "Deposition" : {
- "VariableNames" : ["P_GRAMINIS_DEPOSITION"],
- "PathTemplate" : "${WorkspacePath}/DEPOSITION_${DateString}/WR_NAME_Ethiopia_${DateString}_fc/",
- "SuccessFileTemplate" : "${WorkspacePath}DEPOSITION_${StartString}/STATUS_SUCCESS",
- "FileListerFunction" : "list_onefile_operational",
- "FileNameTemplate" : "deposition_srcs_allregions_${DateString}.nc",
- "FileNamePrepared" : "?"
- },
- "Environment" : {
- "PathTemplate" : "${WorkspacePath}/ENVIRONMENT_2.0_${DateString}/processed/${RegionName}/${DiseaseName}/",
- "SuccessFileTemplate" : "${WorkspacePath}/ENVIRONMENT_2.0_${StartString}/STATUS_SUCCESS",
- "FileListerFunction" : "list_onefile_operational",
- "FileNameTemplate" : "RIE_value.nc",
- "FileNamePrepared" : "?"
- },
-"Env" : {
- "SuccessFileTemplate" : "${WorkspacePath}/EPI_${YesterdayString}/STATUS_SUCCESS",
- "PathTemplate" : "${WorkspacePath}/EPI_${YesterdayString}/${RegionName}/${DiseaseName}/",
- "FileNameTemplate" : "infections_config_EastAfrica_fc_live_Epidemiology_*_env_progression.csv",
- "FileListerFunction" : "list_onefile_historical",
- "FileLoaderFunction" : "load_and_restructure_epi_file",
- "FileNamePrepared" : "?"
- },
- "ps" : {
- "SuccessFileTemplate" : "${WorkspacePath}/EPI_${YesterdayString}/STATUS_SUCCESS",
- "PathTemplate" : "${WorkspacePath}/EPI_${YesterdayString}/${RegionName}/${DiseaseName}/",
- "FileNameTemplate" : "infections_config_EastAfrica_fc_live_Epidemiology_*_psbeta0.004gamma0.00025alpha1.0_progression.csv",
- "FileListerFunction" : "list_onefile_historical",
- "FileLoaderFunction" : "load_and_restructure_epi_file",
- "FileNamePrepared" : "?"
- },
- "Epi" : [
- {
- "model" : "Env",
- "modelArguments" : {},
- "infectionRasterFileName" : "?",
- "description": "env. suitability",
- "rescale_output_by_host_raster": false,
- "analysis" : {
- "vmin" : 0.0e+0,
- "vmax" : 1.5e+1,
- "subplot_position" : [0,0],
- "cmapString" : "CMRmap_r",
- "bounds" : [32.5,48.0,3.3,15.0],
- "UTMprojection" : 37
- }
- },{
- "model" : "ps",
- "modelArguments": {
- "beta": 4.0e-3,
- "gamma": 2.5e-4,
- "alpha": 1.0,
- "infection": "previous"
- },
- "infectionRasterFileName" : "?",
- "description": "SE[beta*log10(alpha*D)+gamma*P]",
- "rescale_output_by_host_raster": true,
- "analysis" : {
- "vmin" : 0.0e+0,
- "vmax" : 1,
- "subplot_position" : [0,1],
- "cmapString" : "CMRmap_r",
- "bounds": [32.5,48.0,3.3,15.0],
- "UTMprojection" : 37
- }
- }
- ],
- "EWS-Plotting" : {
- "SysConfig" : "${ConfigsPath}/coordinator/fc/sys_config_EastAfrica_fc_live.json",
- "RunConfig_seasonsofar" : "${ConfigsPath}/plotting/epi/RUN_CONFIG_EPI.json",
- "RunConfig_seasonplusforecast" : "${ConfigsPath}/plotting/epi/RUN_CONFIG_EPI.json",
- "ChartConfig" : "${ConfigsPath}/plotting/chart/CHART_CONFIG_ETHIOPIA_EPI_PINE.json",
- "PlottingRegionName" : "Ethiopia",
- "EpiCase" : "ps"
- }
-}
diff --git a/pipeline_resources/EastAfrica/configs/coordinator/fc/met_resample_config_EastAfrica_fc_live.json b/pipeline_resources/EastAfrica/configs/coordinator/fc/met_resample_config_EastAfrica_fc_live.json
deleted file mode 100644
index 0a91379f9621bdeb654d36c7d3fdcd5535af94a9..0000000000000000000000000000000000000000
--- a/pipeline_resources/EastAfrica/configs/coordinator/fc/met_resample_config_EastAfrica_fc_live.json
+++ /dev/null
@@ -1,7 +0,0 @@
-{
- "RunConfig" : "${ConfigsPath}/met_resample/run_config_MetResample.json",
- "Environment" : {
- "SuccessFileTemplate" : "${WorkspacePath}/ENVIRONMENT_2.0_${StartString}/STATUS_SUCCESS"
- },
- "CalculationSpanDays" : [0,5]
-}
\ No newline at end of file
diff --git a/pipeline_resources/EastAfrica/configs/coordinator/fc/survey_config_EastAfrica_fc_live.json b/pipeline_resources/EastAfrica/configs/coordinator/fc/survey_config_EastAfrica_fc_live.json
deleted file mode 100644
index aad5a586dee9a7b7dce21729dc2eae9795bb0530..0000000000000000000000000000000000000000
--- a/pipeline_resources/EastAfrica/configs/coordinator/fc/survey_config_EastAfrica_fc_live.json
+++ /dev/null
@@ -1,78 +0,0 @@
-{
- "ProcessPreJob": "process_pre_job_survey",
- "ProcessInJob": "process_in_job_survey",
- "ProcessEWSPlotting": "process_EWS_plotting_survey",
- "AcceptableDowntimeDays": 70,
- "SeasonStartString": "20230815",
- "ServerCredentialsFile": "${ConfigsPath}/coordinator/Cred-WRT.json",
- "Groups": {
- "PROD": {
- "Origin": [
- "CSV_01",
- "CSV_02",
- "ODK_01",
- "ODK_02",
- "CSV-CAM"
- ]
- },
- "WRT-Publ": {
- "Origin": [
- "CSV_01",
- "CSV_02",
- "ODK_01",
- "ODK_02"
- ],
- "PublishedLevel": [
- "Publ"
- ]
- },
- "Trial-sites": {
- "Origin": [
- "CSV_01",
- "CSV_02",
- "ODK_01",
- "ODK_02",
- "CSV-CAM"
- ],
- "site_information-survey_site": [
- "Trial"
- ]
- }
- },
- "GroupBy": [
- "Origin",
- "PublishedLevel",
- "site_information-survey_site"
- ],
- "GroupsToIgnore": [
- "ODK-server",
- "kobo-server",
- "newODK",
- "newODK2",
- "CSV-CAM",
- "CSV_01",
- "CSV_02",
- "ODK_01",
- "ODK_02",
- "Unpubl",
- "Publ",
- "Raw",
- "Farmer",
- "farmer_field",
- "Seed_production",
- "Weed",
- "Road",
- "Trial",
- "VCU",
- "Sentinel",
- "Other"
- ],
- "ODKDatabasePathTemplate": "${WorkspacePathout}/ODK_DB/",
- "SurveyFormat": "ODK",
- "SurveyorNameCol": "surveyor_infromation-surveyor_name",
- "SourcesRegionName": "EastAfrica",
- "SourcesConfigs": {
- "WRT-Publ": "${ConfigsPath}/source_gen/config_EastAfrica_mapspam2017.json"
- },
- "SourcesConfigDefault": "${ConfigsPath}/source_gen/config_EastAfrica_mapspam2017.json"
-}
\ No newline at end of file
diff --git a/pipeline_resources/EastAfrica/configs/coordinator/fc/template_sys_config_EastAfrica_fc_live.json b/pipeline_resources/EastAfrica/configs/coordinator/fc/template_sys_config_EastAfrica_fc_live.json
deleted file mode 100644
index 4074af61139d4bf0107d920382d83ef2cd5f821a..0000000000000000000000000000000000000000
--- a/pipeline_resources/EastAfrica/configs/coordinator/fc/template_sys_config_EastAfrica_fc_live.json
+++ /dev/null
@@ -1,14 +0,0 @@
-{
- "RegionName" : "EastAfrica",
- "SubRegionNames" : ["EastAfrica","Ethiopia","Kenya","Zambia","Tanzania"],
- "StartTime" : "?",
- "StartString" : "?",
- "ProjectRoot" : "<path to project root>",
- "MetoFTP" : "<path to MetoFTP>",
- "WorkspacePathout" : "${ProjectRoot}/regions/EastAfrica/workspace_analysis/",
- "WorkspacePath" : "${ProjectRoot}/regions/EastAfrica/workspace_analysis/",
- "ConfigsPath" : "${ProjectRoot}/code/coordinator/pipeline_resources/EastAfrica/configs",
- "AssetsPath" : "${ProjectRoot}/regions/EastAfrica/resources/assets",
- "LoggingConfigPath" : "${ProjectRoot}/code/coordinator/pipeline_resources/EastAfrica/configs/coordinator/log_config.json",
- "PLACES_SHAPE_FILE": "${ProjectRoot}/regions/EastAfrica/resources/assets/plotting/gis_data/common/places_shape/east_africa_places.shp"
-}
diff --git a/pipeline_resources/EastAfrica/configs/coordinator/log_config.json b/pipeline_resources/EastAfrica/configs/coordinator/log_config.json
deleted file mode 100644
index fb6c3a1b737294a37d789de6d142bfc599d67988..0000000000000000000000000000000000000000
--- a/pipeline_resources/EastAfrica/configs/coordinator/log_config.json
+++ /dev/null
@@ -1,68 +0,0 @@
-{
- "version": 1,
- "disable_existing_loggers": false,
- "formatters": {
- "simple": {
- "format": "%(name)s : %(levelname)s - %(message)s"
- },
- "detailed": {
- "format": "For command:\n{arg_string}\n\n%(levelname)s in %(name)s encountered at %(asctime)s:\n\n%(message)s\n\nResolve this error and restart processing.",
- "datefmt": "%Y-%m-%d %H:%M:%S"
- }
- },
- "filters": {
- "mask_passwords": {
- "()": "NOT_SET"
- }
- },
- "handlers": {
- "handler_job": {
- "class": "logging.FileHandler",
- "formatter": "simple",
- "level": "DEBUG",
- "filters": [
- "mask_passwords"
- ],
- "filename": ""
- },
- "handler_stderr": {
- "class": "logging.StreamHandler",
- "formatter": "simple",
- "level": "DEBUG",
- "filters": [
- "mask_passwords"
- ]
- },
- "handler_buffered_email": {
- "class": "BufferingSMTPHandler.BufferingSMTPHandler",
- "level": "ERROR",
- "server": "NOT_SET",
- "credentials": "NOT_SET",
- "fromaddr": "NOT_SET",
- "toaddrs": "NOT_SET",
- "subject": "ERROR in EWS Processor",
- "formatter": "detailed",
- "filters": [
- "mask_passwords"
- ],
- "capacity": 100
- }
- },
- "loggers": {
- "__main__": {
- "level": "INFO",
- "handlers": ["handler_job","handler_buffered_email","handler_stderr"],
- "propagate": false
- },
- "EpiModel": {
- "level": "INFO",
- "handlers": ["handler_job","handler_buffered_email","handler_stderr"],
- "propagate": false
- },
- "ews": {
- "level": "INFO",
- "handlers": ["handler_job","handler_buffered_email","handler_stderr"],
- "propagate": false
- }
- }
-}
\ No newline at end of file
diff --git a/pipeline_resources/EastAfrica/configs/coordinator/template_Cred-WRT.json b/pipeline_resources/EastAfrica/configs/coordinator/template_Cred-WRT.json
deleted file mode 100644
index 576b0b073047604ff8aa69162264f5b64f4a1711..0000000000000000000000000000000000000000
--- a/pipeline_resources/EastAfrica/configs/coordinator/template_Cred-WRT.json
+++ /dev/null
@@ -1,14 +0,0 @@
-{
- "forms" : [
- {
- "type" : "WRT",
- "url" : "https://web15.agro.au.dk/",
- "user" : "",
- "pass" : "",
- "countryID" : "ET;KE;TZ;UG;ZM",
- "publishedLevel" : "Publ;Unpubl",
- "form_id" : "WRT",
- "form_name" : "WRT"
- }
- ]
-}
diff --git a/pipeline_resources/EastAfrica/configs/met_extractor/FIELD_NAME_CONSTANTS.csv b/pipeline_resources/EastAfrica/configs/met_extractor/FIELD_NAME_CONSTANTS.csv
deleted file mode 100644
index 27982bad32ac58c84c50d2fc286f8c96b5ef5e2d..0000000000000000000000000000000000000000
--- a/pipeline_resources/EastAfrica/configs/met_extractor/FIELD_NAME_CONSTANTS.csv
+++ /dev/null
@@ -1,18 +0,0 @@
-ERA5,WIND,ERA5-Land-hourly-10m_u_component_of_wind,wind
-ERA5,WIND2,ERA5-Land-hourly-10m_v_component_of_wind,wind2
-ERA5,DEWPOINT,ERA5-Land-hourly-2m_dewpoint_temperature,dewpoint
-ERA5,TEMP,ERA5-Land-hourly-2m_temperature,temperature
-ERA5,RAD,ERA5-Land-hourly-surface_net_solar_radiation,radiation
-ERA5,PRESSURE,ERA5-Land-hourly-surface_pressure,pressure
-ERA5,PRECIP,ERA5-Land-hourly-total_precipitation,precipitation
-MET_OFFICE,TEMP,air_temperature-none,temperature
-MET_OFFICE,HUMIDITY,specific_humidity-level0,humidity
-MET_OFFICE,SURFACE_AIR_PRESSURE,surface_air_pressure-none,air_pressure
-MET_OFFICE,CONVECTIVE_RAINFALL,convective_rainfall_flux-none,convective_rainfall
-MET_OFFICE,STRATIFORM_RAINFALL,stratiform_rainfall_flux-none,stratiform_rainfall
-NAME,PRECIPITATION_RATE,_PRECIPITATION_RATE_(MM_HR),PRECIPITATION_RATE
-NAME,SOIL_MOISTURE,_SOIL_MOISTURE,SOIL_MOISTURE
-NAME,TOPOGRAPHY,_TOPOGRAPHY,TOPOGRAPHY
-NAME,RELATIVE_HUMIDITY,_RELATIVE_HUMIDITY_(%),RELATIVE_HUMIDITY
-NAME,TEMP,_TEMPERATURE_(C),TEMP
-NAME,SURFACE_AIR_PRESSURE,_PRESSURE_(PA),PRESSURE_PA
diff --git a/pipeline_resources/EastAfrica/configs/met_extractor/SYS_CONFIG_PINE.json b/pipeline_resources/EastAfrica/configs/met_extractor/SYS_CONFIG_PINE.json
deleted file mode 100644
index eb8f495e964a498bf8bea315716538168dd38b87..0000000000000000000000000000000000000000
--- a/pipeline_resources/EastAfrica/configs/met_extractor/SYS_CONFIG_PINE.json
+++ /dev/null
@@ -1,3 +0,0 @@
-{
- "FIELD_NAME_CONSTANTS_PATH": "../data/resources/common/field_name_constants.csv"
-}
diff --git a/pipeline_resources/EastAfrica/configs/met_extractor/template_operational_config.json b/pipeline_resources/EastAfrica/configs/met_extractor/template_operational_config.json
deleted file mode 100644
index e6f6e049f6fe9ac9a74b914f5cd0091681a7741b..0000000000000000000000000000000000000000
--- a/pipeline_resources/EastAfrica/configs/met_extractor/template_operational_config.json
+++ /dev/null
@@ -1,52 +0,0 @@
-{
- "MET_DATA_TYPE": "NAME",
- "DATA_TYPES": [
- "TEMP",
- "PRECIPITATION_RATE",
- "RELATIVE_HUMIDITY"
- ],
- "POST_PROCESSING": {
- "PROCESSORS": [
- {
- "PROCESSOR_NAME": "RIE",
- "OUT_FILE_NAME": "RIE",
- "CLASSPATH": "ews.environmental_suitability.ewses_vectorised_timepoint_processor",
- "CLASSNAME": "EnvSuitColTimePointProcessor",
- "DEPENDS": [],
- "TIMEPOINTS_FILE_PATH": "#",
- "FUTURE_FIELDS": [
- {
- "PROCESSOR_NAME": "TEMP",
- "DURATION": 7,
- "ENABLED": "TRUE"
- },
- {
- "PROCESSOR_NAME": "PRECIPITATION_RATE",
- "DURATION": 7,
- "ENABLED": "TRUE"
- },
- {
- "PROCESSOR_NAME": "RELATIVE_HUMIDITY",
- "DURATION": 7,
- "ENABLED": "TRUE"
- }
- ],
- "PARAMS": {
- "suitability_modules": ["#"],
- "thresholds": {
- "temperature": [2,30],
- "precipitation": 0,
- "relative_humidity": 90
- }
- }
- }
- ]
- },
- "TIMEPOINTS_FILE_PATH": "#",
- "OUTPUT_DIR": "#",
- "SPATIAL_POINTS_FILE_PATH": "#",
- "FIELD_NAME_CONSTANTS_PATH": "#",
- "NCDF_DIR_PATH": "#",
- "RECURSIVE_SEARCH": "FALSE",
- "WRITE_EXTRACTION_CSVS": "FALSE"
-}
diff --git a/pipeline_resources/EastAfrica/configs/met_resample/run_config_MetResample.json b/pipeline_resources/EastAfrica/configs/met_resample/run_config_MetResample.json
deleted file mode 100644
index 2810dc7c4b0d3a8ec355fb3c8815300829438e74..0000000000000000000000000000000000000000
--- a/pipeline_resources/EastAfrica/configs/met_resample/run_config_MetResample.json
+++ /dev/null
@@ -1,91 +0,0 @@
-{
- "Host" : {
- "Bounds" : [21.50,-18.54,36.00,-7.81]
- },
- "components" : [
- "soil_moisture",
- "RH",
- "precip",
- "temperature",
- "cloud_cover",
- "u_wind",
- "v_wind"
- ],
- "RH" : {
- "VariableName" : "_RELATIVE_HUMIDITY_(%)",
- "is_met" : true,
- "resampling" : "interpolate",
- "FileListerFunction" : "list_files_historical_daily",
- "FileLoaderFunction" : "load_NAME_met_file",
- "PathTemplate" : "${WorkspacePath}/../workspace_analysis/ENVIRONMENT_2.0_${DateString}/NAME_Met_as_netcdf/",
- "PathTemplateAlternative" : "${WorkspacePath}/ENVIRONMENT_2.0_${DateString}/NAME_Met_as_netcdf/",
- "FileNameTemplate" : "_RELATIVE_HUMIDITY_(%)_${DateString}.nc",
- "FileNamePrepared" : "${jobPath}/data_resampled/data_input_RH_%.csv"
- },
- "precip" : {
- "VariableName" : "_PRECIPITATION_RATE_(MM/HR)",
- "is_met" : true,
- "resampling" : "backfill",
- "FileListerFunction" : "list_files_historical_daily",
- "FileLoaderFunction" : "load_NAME_met_file",
- "PathTemplate" : "${WorkspacePath}/../workspace_analysis/ENVIRONMENT_2.0_${DateString}/NAME_Met_as_netcdf/",
- "PathTemplateAlternative" : "${WorkspacePath}/ENVIRONMENT_2.0_${DateString}/NAME_Met_as_netcdf/",
- "FileNameTemplate" : "_PRECIPITATION_RATE_(MM_HR)_${DateString}.nc",
- "FileNamePrepared" : "${jobPath}/data_resampled/data_input_precip_mmhr.csv"
- },
- "temperature" : {
- "VariableName" : "_TEMPERATURE_(C)",
- "is_met" : true,
- "resampling" : "interpolate",
- "FileListerFunction" : "list_files_historical_daily",
- "FileLoaderFunction" : "load_NAME_met_file",
- "PathTemplate" : "${WorkspacePath}/../workspace_analysis/ENVIRONMENT_2.0_${DateString}/NAME_Met_as_netcdf/",
- "PathTemplateAlternative" : "${WorkspacePath}/ENVIRONMENT_2.0_${DateString}/NAME_Met_as_netcdf/",
- "FileNameTemplate" : "_TEMPERATURE_(C)_${DateString}.nc",
- "FileNamePrepared" : "${jobPath}/data_resampled/data_input_temperature_C.csv"
- },
- "cloud_cover" : {
- "VariableName" : "_CLOUD_AMOUNT_(OKTAS)",
- "is_met" : true,
- "resampling" : "backfill",
- "FileListerFunction" : "list_files_historical_daily",
- "FileLoaderFunction" : "load_NAME_met_file",
- "PathTemplate" : "${WorkspacePath}/../workspace_analysis/ENVIRONMENT_2.0_${DateString}/NAME_Met_as_netcdf/",
- "PathTemplateAlternative" : "${WorkspacePath}/ENVIRONMENT_2.0_${DateString}/NAME_Met_as_netcdf/",
- "FileNameTemplate" : "_CLOUD_AMOUNT_(OKTAS)_${DateString}.nc",
- "FileNamePrepared" : "${jobPath}/data_resampled/data_input_cloud_cover_oktas.csv"
- },
- "u_wind" : {
- "VariableName" : "_MEAN_FLOW_U",
- "is_met" : true,
- "resampling" : "interpolate",
- "FileListerFunction" : "list_files_historical_daily",
- "FileLoaderFunction" : "load_NAME_met_file",
- "PathTemplate" : "${WorkspacePath}/../workspace_analysis/ENVIRONMENT_2.0_${DateString}/NAME_Met_as_netcdf/",
- "PathTemplateAlternative" : "${WorkspacePath}/ENVIRONMENT_2.0_${DateString}/NAME_Met_as_netcdf/",
- "FileNameTemplate" : "_MEAN_FLOW_U_${DateString}.nc",
- "FileNamePrepared" : "${jobPath}/data_resampled/data_input_u_wind_ms.csv"
- },
- "v_wind" : {
- "VariableName" : "_MEAN_FLOW_V",
- "is_met" : true,
- "resampling" : "interpolate",
- "FileListerFunction" : "list_files_historical_daily",
- "FileLoaderFunction" : "load_NAME_met_file",
- "PathTemplate" : "${WorkspacePath}/../workspace_analysis/ENVIRONMENT_2.0_${DateString}/NAME_Met_as_netcdf/",
- "PathTemplateAlternative" : "${WorkspacePath}/ENVIRONMENT_2.0_${DateString}/NAME_Met_as_netcdf/",
- "FileNameTemplate" : "_MEAN_FLOW_V_${DateString}.nc",
- "FileNamePrepared" : "${jobPath}/data_resampled/data_input_v_wind_ms.csv"
- },
- "soil_moisture" : {
- "VariableName" : "_SOIL_MOISTURE",
- "is_met" : true,
- "resampling" : "interpolate",
- "FileListerFunction" : "list_files_historical_daily",
- "FileLoaderFunction" : "load_NAME_met_file",
- "PathTemplate" : "${WorkspacePath}/../workspace_analysis/ENVIRONMENT_2.0_${DateString}/NAME_Met_as_netcdf/",
- "PathTemplateAlternative" : "${WorkspacePath}/ENVIRONMENT_2.0_${DateString}/NAME_Met_as_netcdf/",
- "FileNameTemplate" : "_SOIL_MOISTURE_${DateString}.nc",
- "FileNamePrepared" : "${jobPath}/data_resampled/data_input_soil_moisture_kgm2.csv"
- }
-}
diff --git a/pipeline_resources/EastAfrica/configs/plotting/chart/CHART_CONFIG_EAST_AFRICA_PINE.json b/pipeline_resources/EastAfrica/configs/plotting/chart/CHART_CONFIG_EAST_AFRICA_PINE.json
deleted file mode 100644
index fde9f2a0309045347ba4920611b9983d26c5cc5a..0000000000000000000000000000000000000000
--- a/pipeline_resources/EastAfrica/configs/plotting/chart/CHART_CONFIG_EAST_AFRICA_PINE.json
+++ /dev/null
@@ -1,18 +0,0 @@
-{
- "IMAGE_WIDTH": 1550,
- "IMAGE_HEIGHT": 2500,
- "COUNTRY_EXTENTS": [20, 60, -19, 36],
- "MAP_TILE": "${ProjectRoot}/regions/EastAfrica/resources/assets/plotting/gis_data/east_africa/east_africa_map_tile.tif",
- "SCALEBAR_LAT": "2",
- "SCALEBAR_TEXT": "200km",
- "RASTER_ALPHA": 0.7,
- "LEGEND_ALPHA": 0.4,
- "TITLE_FONT_SIZE": 25,
- "COUNTRY_LANDPOINTS_FILE": "${ProjectRoot}/regions/EastAfrica/resources/assets/plotting/gis_data/east_africa/east_africa_points.csv",
- "COUNTRY_LOGO_FILE": "${ProjectRoot}/regions/EastAfrica/resources/assets/plotting/images/logos_EastAfrica_plotting.png",
- "COUNTRY_STRING": "eastafrica",
- "PLACES_TO_PLOT": ["CAPITAL","LARGE"],
- "PLACES_TO_RIGHT_ALIGN": ["Beirut", "Tel Aviv-Yafo"],
- "PLACES_TO_EXCLUDE": ["Jerusalem"],
- "PLACES_X_LIMIT": 0.95
-}
diff --git a/pipeline_resources/EastAfrica/configs/plotting/chart/CHART_CONFIG_ETHIOPIA_EPI_PINE.json b/pipeline_resources/EastAfrica/configs/plotting/chart/CHART_CONFIG_ETHIOPIA_EPI_PINE.json
deleted file mode 100644
index 529b72b9086978566785adfd65777d07da2bfa0f..0000000000000000000000000000000000000000
--- a/pipeline_resources/EastAfrica/configs/plotting/chart/CHART_CONFIG_ETHIOPIA_EPI_PINE.json
+++ /dev/null
@@ -1,19 +0,0 @@
-{
- "IMAGE_WIDTH": 1700,
- "IMAGE_HEIGHT": 1275,
- "COUNTRY_ADMIN_2_SHAPE_FILE": "${ProjectRoot}/regions/EastAfrica/resources/assets/plotting/gis_data/ethiopia/admin_shape/eth_admbnda_adm2_csa_bofedb_2021.shp",
- "COUNTRY_ADMIN_1_SHAPE_FILE": "${ProjectRoot}/regions/EastAfrica/resources/assets/plotting/gis_data/ethiopia/admin_shape/eth_admbnda_adm1_csa_bofedb_2021.shp",
- "COUNTRY_SHAPE_FILE": "${ProjectRoot}/regions/EastAfrica/resources/assets/plotting/gis_data/ethiopia/admin_shape/eth_admbnda_adm0_csa_bofedb_itos_2021.shp",
- "COUNTRY_EXTENTS": [31.99, 53.02, 3.19, 14.85],
- "MAP_TILE": "${ProjectRoot}/regions/EastAfrica/resources/assets/plotting/gis_data/ethiopia/ethiopia_map_tile.tif",
- "SCALEBAR_LAT": "3.7",
- "SCALEBAR_TEXT": "400km",
- "LEGEND_ALPHA": 0,
- "TITLE_FONT_SIZE": 30,
- "COUNTRY_LANDPOINTS_FILE": "${ProjectRoot}/regions/EastAfrica/resources/assets/plotting/gis_data/ethiopia/ethiopia_points_epi.csv",
- "COUNTRY_LOGO_FILE": "${ProjectRoot}/regions/EastAfrica/resources/assets/plotting/images/logos_EastAfrica_plotting.png",
- "COUNTRY_STRING": "ethiopia",
- "PLACES_TO_PLOT": ["CAPITAL","LARGE","MEDIUM"],
- "PLACES_TO_EXCLUDE": ["Bandarbeyla","Al Hudaydah"],
- "PLACES_X_LIMIT": 1
-}
diff --git a/pipeline_resources/EastAfrica/configs/plotting/chart/CHART_CONFIG_ETHIOPIA_PINE.json b/pipeline_resources/EastAfrica/configs/plotting/chart/CHART_CONFIG_ETHIOPIA_PINE.json
deleted file mode 100644
index 63991dd88a0179cc24e360b6201a9405b8ff685e..0000000000000000000000000000000000000000
--- a/pipeline_resources/EastAfrica/configs/plotting/chart/CHART_CONFIG_ETHIOPIA_PINE.json
+++ /dev/null
@@ -1,19 +0,0 @@
-{
- "IMAGE_WIDTH": 1700,
- "IMAGE_HEIGHT": 1275,
- "COUNTRY_ADMIN_2_SHAPE_FILE": "${ProjectRoot}/regions/EastAfrica/resources/assets/plotting/gis_data/ethiopia/admin_shape/eth_admbnda_adm2_csa_bofedb_2021.shp",
- "COUNTRY_ADMIN_1_SHAPE_FILE": "${ProjectRoot}/regions/EastAfrica/resources/assets/plotting/gis_data/ethiopia/admin_shape/eth_admbnda_adm1_csa_bofedb_2021.shp",
- "COUNTRY_SHAPE_FILE": "${ProjectRoot}/regions/EastAfrica/resources/assets/plotting/gis_data/ethiopia/admin_shape/eth_admbnda_adm0_csa_bofedb_itos_2021.shp",
- "COUNTRY_EXTENTS": [31.99, 53.02, 3.19, 14.85],
- "MAP_TILE": "${ProjectRoot}/regions/EastAfrica/resources/assets/plotting/gis_data/ethiopia/ethiopia_map_tile.tif",
- "SCALEBAR_LAT": "3.7",
- "SCALEBAR_TEXT": "400km",
- "LEGEND_ALPHA": 0,
- "TITLE_FONT_SIZE": 30,
- "COUNTRY_LANDPOINTS_FILE": "${ProjectRoot}/regions/EastAfrica/resources/assets/plotting/gis_data/ethiopia/ethiopia_points.csv",
- "COUNTRY_LOGO_FILE": "${ProjectRoot}/regions/EastAfrica/resources/assets/plotting/images/logos_EastAfrica_plotting.png",
- "COUNTRY_STRING": "ethiopia",
- "PLACES_TO_PLOT": ["CAPITAL","LARGE","MEDIUM"],
- "PLACES_TO_EXCLUDE": ["Bandarbeyla","Al Hudaydah"],
- "PLACES_X_LIMIT": 1
-}
diff --git a/pipeline_resources/EastAfrica/configs/plotting/chart/CHART_CONFIG_KENYA_PINE.json b/pipeline_resources/EastAfrica/configs/plotting/chart/CHART_CONFIG_KENYA_PINE.json
deleted file mode 100644
index 1dbbf46d2cd76f1fae40084d367a5c36420f8ee3..0000000000000000000000000000000000000000
--- a/pipeline_resources/EastAfrica/configs/plotting/chart/CHART_CONFIG_KENYA_PINE.json
+++ /dev/null
@@ -1,19 +0,0 @@
-{
- "IMAGE_WIDTH": 1700,
- "IMAGE_HEIGHT": 1500,
- "COUNTRY_ADMIN_2_SHAPE_FILE": "${ProjectRoot}/regions/EastAfrica/resources/assets/plotting/gis_data/kenya/kenya_admin_shape/admin2/ken_admbnda_adm2_iebc_20191031.shp",
- "COUNTRY_ADMIN_1_SHAPE_FILE": "${ProjectRoot}/regions/EastAfrica/resources/assets/plotting/gis_data/kenya/kenya_admin_shape/admin1/ken_admbnda_adm1_iebc_20191031.shp",
- "COUNTRY_SHAPE_FILE": "${ProjectRoot}/regions/EastAfrica/resources/assets/plotting/gis_data/kenya/kenya_shape/ken_admbnda_adm0_iebc_20191031.shp",
- "COUNTRY_EXTENTS": [30, 45.5, -5.5, 5.5],
- "MAP_TILE": "${ProjectRoot}/regions/EastAfrica/resources/assets/plotting/gis_data/kenya/kenya_map_tile.tif",
- "SCALEBAR_LAT": "2",
- "SCALEBAR_TEXT": "200km",
- "RASTER_ALPHA": 0.7,
- "LEGEND_ALPHA": 0.4,
- "TITLE_FONT_SIZE": 30,
- "COUNTRY_LANDPOINTS_FILE": "${ProjectRoot}/regions/EastAfrica/resources/assets/plotting/gis_data/kenya/kenya_points.csv",
- "COUNTRY_LOGO_FILE": "${ProjectRoot}/regions/EastAfrica/resources/assets/plotting/images/logos_EastAfrica_plotting.png",
- "COUNTRY_STRING": "kenya",
- "PLACES_TO_PLOT": ["CAPITAL","LARGE", "MEDIUM"],
- "PLACES_X_LIMIT": 0.99
-}
diff --git a/pipeline_resources/EastAfrica/configs/plotting/chart/CHART_CONFIG_TANZANIA_EPI.json b/pipeline_resources/EastAfrica/configs/plotting/chart/CHART_CONFIG_TANZANIA_EPI.json
deleted file mode 100644
index 9633a9291fc72a53b9f4b0664712eef1ff7fe150..0000000000000000000000000000000000000000
--- a/pipeline_resources/EastAfrica/configs/plotting/chart/CHART_CONFIG_TANZANIA_EPI.json
+++ /dev/null
@@ -1,19 +0,0 @@
-{
- "IMAGE_WIDTH": 1700,
- "IMAGE_HEIGHT": 1875,
- "COUNTRY_ADMIN_2_SHAPE_FILE": "${ProjectRoot}/regions/EastAfrica/resources/assets/plotting/gis_data/tanzania/tanzania_admin_shape/admin2/tza_admbnda_adm2_20181019.shp",
- "COUNTRY_ADMIN_1_SHAPE_FILE": "${ProjectRoot}/regions/EastAfrica/resources/assets/plotting/gis_data/tanzania/tanzania_admin_shape/admin1/tza_admbnda_adm1_20181019.shp",
- "COUNTRY_SHAPE_FILE": "${ProjectRoot}/regions/EastAfrica/resources/assets/plotting/gis_data/tanzania/tanzania_shape/tza_admbnda_adm0_20181019.shp",
- "COUNTRY_EXTENTS": [28.93, 41.98, -0.29, -12.37],
- "MAP_TILE": "${ProjectRoot}/regions/EastAfrica/resources/assets/plotting/gis_data/east_africa/east_africa_map_tile.tif",
- "SCALEBAR_LAT": "4.5",
- "SCALEBAR_TEXT": "400km",
- "LEGEND_ALPHA": 0,
- "TITLE_FONT_SIZE": 30,
- "COUNTRY_LANDPOINTS_FILE": "${ProjectRoot}/regions/EastAfrica/resources/assets/plotting/gis_data/tanzania/tanzania_points.csv",
- "COUNTRY_LOGO_FILE": "${ProjectRoot}/regions/EastAfrica/resources/assets/plotting/images/logos_EastAfrica_plotting.png",
- "COUNTRY_STRING": "tanzania",
- "PLACES_TO_PLOT": ["CAPITAL","LARGE","MEDIUM"],
- "PLACES_TO_EXCLUDE": [],
- "PLACES_X_LIMIT": 1
-}
diff --git a/pipeline_resources/EastAfrica/configs/plotting/chart/CHART_CONFIG_ZAMBIA_PINE.json b/pipeline_resources/EastAfrica/configs/plotting/chart/CHART_CONFIG_ZAMBIA_PINE.json
deleted file mode 100644
index 4644a3f75eb0431e184ea5c99acbc1efe4b8d40f..0000000000000000000000000000000000000000
--- a/pipeline_resources/EastAfrica/configs/plotting/chart/CHART_CONFIG_ZAMBIA_PINE.json
+++ /dev/null
@@ -1,18 +0,0 @@
-{
- "IMAGE_WIDTH": 1700,
- "IMAGE_HEIGHT": 1500,
- "COUNTRY_ADMIN_2_SHAPE_FILE": "${ProjectRoot}/regions/EastAfrica/resources/assets/plotting/gis_data/zambia/zambia_admin_shape/zmb_admbnda_adm2_dmmu_20201124.shp",
- "COUNTRY_ADMIN_1_SHAPE_FILE": "${ProjectRoot}/regions/EastAfrica/resources/assets/plotting/gis_data/zambia/zambia_shape/zmb_admbnda_adm0_dmmu_20201124.shp",
- "COUNTRY_SHAPE_FILE": "${ProjectRoot}/regions/EastAfrica/resources/assets/plotting/gis_data/zambia/zambia_shape/zmb_admbnda_adm0_dmmu_20201124.shp",
- "COUNTRY_EXTENTS": [21.50, 36.00, -18.54, -7.81],
- "MAP_TILE": "${ProjectRoot}/regions/EastAfrica/resources/assets/plotting/gis_data/zambia/zambia_map_tile.tif",
- "SCALEBAR_LAT": "3.7",
- "SCALEBAR_TEXT": "400km",
- "LEGEND_ALPHA": 0,
- "TITLE_FONT_SIZE": 30,
- "COUNTRY_LANDPOINTS_FILE": "${ProjectRoot}/regions/EastAfrica/resources/assets/plotting/gis_data/zambia/zambia_points.csv",
- "COUNTRY_LOGO_FILE": "${ProjectRoot}/regions/EastAfrica/resources/assets/plotting/images/logos_EastAfrica_plotting.png",
- "COUNTRY_STRING": "zambia",
- "PLACES_TO_PLOT": ["CAPITAL","LARGE","MEDIUM"],
- "PLACES_X_LIMIT": 1
-}
diff --git a/pipeline_resources/EastAfrica/configs/plotting/deposition/RUN_CONFIG_DEPO.json b/pipeline_resources/EastAfrica/configs/plotting/deposition/RUN_CONFIG_DEPO.json
deleted file mode 100644
index ebb312fc9b38c465705d6aefc21e66ac28464c10..0000000000000000000000000000000000000000
--- a/pipeline_resources/EastAfrica/configs/plotting/deposition/RUN_CONFIG_DEPO.json
+++ /dev/null
@@ -1,20 +0,0 @@
-{
- "IMAGE_WIDTH": 1700,
- "IMAGE_HEIGHT": 1075,
- "WHEAT_SOURCE_INPUT_DIR_NAME": "OVERRIDDEN",
- "WHEAT_SOURCE_DISEASE_NAME": "OVERRIDDEN",
- "OUTPUT_DIR": "OVERRIDDEN",
- "ISSUE_DATE": "OVERRIDDEN",
- "CBAR_VALUES": [0, 1, 100, 1000, 10000, 100000, 1000000],
- "CBAR_LABELS": ["", "1", "100", "1000", "$10^{4}$", "$10^{5}$", "$10^{6}$"],
- "CBAR_COLORS": ["none", "#e6e680","#e6bf19","#e68000","#993380","#4c26bf"],
- "MAP_TITLE": "OVERRIDDEN",
- "RUN_PREFIX": "OVERRIDDEN",
- "LEGEND_TITLE": "Fraction of\ndeposited spores",
- "PLOT_SHAPES": "false",
- "PLOT_TIFS": "true",
- "PLOT_IMAGES": "true",
- "PLOT_DAILY_IMAGES": "false",
- "PLOT_HOURLY_IMAGES": "false",
- "OVERWRITE_MODE": "false"
-}
diff --git a/pipeline_resources/EastAfrica/configs/plotting/deposition/RUN_CONFIG_DEPO_NORMALIZED.json b/pipeline_resources/EastAfrica/configs/plotting/deposition/RUN_CONFIG_DEPO_NORMALIZED.json
deleted file mode 100644
index c6459766868976b7a3955f3611be04570ce06b32..0000000000000000000000000000000000000000
--- a/pipeline_resources/EastAfrica/configs/plotting/deposition/RUN_CONFIG_DEPO_NORMALIZED.json
+++ /dev/null
@@ -1,21 +0,0 @@
-{
- "IMAGE_WIDTH": 1700,
- "IMAGE_HEIGHT": 1075,
- "WHEAT_SOURCE_INPUT_DIR_NAME": "OVERRIDDEN",
- "WHEAT_SOURCE_DISEASE_NAME": "OVERRIDDEN",
- "OUTPUT_DIR": "OVERRIDDEN",
- "ISSUE_DATE": "OVERRIDDEN",
- "CBAR_VALUES": [0, 0.95, 0.99, 1, 1.1],
- "CBAR_LABEL_LOCATIONS": [0.47, 0.97, 0.995, 1.05],
- "CBAR_LABELS": ["0","0.95", "0.99", "1"],
- "CBAR_COLORS": ["darkgrey", "#993380","#e68000","#e6bf19"],
- "MAP_TITLE": "OVERRIDDEN",
- "RUN_PREFIX": "OVERRIDDEN",
- "LEGEND_TITLE": "Fraction of\ndeposited spores",
- "PLOT_SHAPES": "false",
- "PLOT_TIFS": "true",
- "PLOT_IMAGES": "true",
- "PLOT_DAILY_IMAGES": "false",
- "PLOT_HOURLY_IMAGES": "false",
- "OVERWRITE_MODE": "false"
-}
diff --git a/pipeline_resources/EastAfrica/configs/plotting/env_suit/RUN_CONFIG_ENV.json b/pipeline_resources/EastAfrica/configs/plotting/env_suit/RUN_CONFIG_ENV.json
deleted file mode 100644
index e3b72b4e1d2e7520af1e478fff6d3dff9618d255..0000000000000000000000000000000000000000
--- a/pipeline_resources/EastAfrica/configs/plotting/env_suit/RUN_CONFIG_ENV.json
+++ /dev/null
@@ -1,18 +0,0 @@
-{
- "INPUT_CSV": "OVERRIDDEN",
- "OUTPUT_DIR": "OVERRIDDEN",
- "ISSUE_DATE": "OVERRIDDEN",
- "CBAR_VALUES": [0, 0.01, 0.2, 0.4, 0.6, 0.8, 0.99, 1.0],
- "CBAR_LABELS": ["0", "1", "20", "40", "60", "80", "99","100"],
- "CBAR_COLORS": ["#818181", "#FFFFCC", "#7FCDBB", "#2C7FB8", "#253494", "#4B0082", "#000000"],
- "MAP_TITLE": "OVERRIDDEN",
- "RUN_PREFIX": "OVERRIDDEN",
- "LEGEND_TITLE": "relative infection\nefficiency %",
- "PLOT_SHAPES": "false",
- "PLOT_TIFS": "true",
- "PLOT_IMAGES": "true",
- "PLOT_DAILY_IMAGES": "false",
- "PLOT_HOURLY_IMAGES": "false",
- "FILTER_FOR_COUNTRY": "true",
- "OVERWRITE_MODE": "true"
-}
diff --git a/pipeline_resources/EastAfrica/configs/plotting/epi/RUN_CONFIG_EPI.json b/pipeline_resources/EastAfrica/configs/plotting/epi/RUN_CONFIG_EPI.json
deleted file mode 100644
index a1ad1a365d298f1e610819ac14c0ae2cd3e76c53..0000000000000000000000000000000000000000
--- a/pipeline_resources/EastAfrica/configs/plotting/epi/RUN_CONFIG_EPI.json
+++ /dev/null
@@ -1,20 +0,0 @@
-{
- "IMAGE_WIDTH": 1700,
- "IMAGE_HEIGHT": 1075,
- "WHEAT_SOURCE_INPUT_DIR_NAME": "OVERRIDDEN",
- "WHEAT_SOURCE_DISEASE_NAME": "OVERRIDDEN",
- "INPUT_CSV": "OVERRIDDEN",
- "OUTPUT_DIR": "OVERRIDDEN",
- "ISSUE_DATE": "OVERRIDDEN",
- "CBAR_VALUES": [0,0.200,0.255,0.565,1e+20],
- "CBAR_LABEL_LOCATIONS": [0.1, 0.2275, 0.410, 5.0e+19,1.0e+20],
- "CBAR_LABELS": ["negligible","very low","low","medium/\nhigh",""],
- "CBAR_COLORS": ["#ccece6", "#fecc5c","#fd8d3c","#e31a1c"],
- "MAP_TITLE": "OVERRIDDEN",
- "RUN_PREFIX": "OVERRIDDEN",
- "LEGEND_TITLE": "Predicted in-field\nincidence level",
- "PLOT_DAILY_IMAGES": "true",
- "PLOT_HOURLY_IMAGES": "false",
- "FILTER_FOR_COUNTRY": "true",
- "OVERWRITE_MODE": "true"
-}
diff --git a/pipeline_resources/EastAfrica/configs/plotting/epi/RUN_CONFIG_EPI_seasonaccum.json b/pipeline_resources/EastAfrica/configs/plotting/epi/RUN_CONFIG_EPI_seasonaccum.json
deleted file mode 100644
index 9d936462b0cd4e2ddb720b065bb6d6e060e653ce..0000000000000000000000000000000000000000
--- a/pipeline_resources/EastAfrica/configs/plotting/epi/RUN_CONFIG_EPI_seasonaccum.json
+++ /dev/null
@@ -1,19 +0,0 @@
-{
- "IMAGE_WIDTH": 1700,
- "IMAGE_HEIGHT": 1075,
- "WHEAT_SOURCE_INPUT_DIR_NAME": "OVERRIDDEN",
- "WHEAT_SOURCE_DISEASE_NAME": "OVERRIDDEN",
- "INPUT_CSV": "OVERRIDDEN",
- "OUTPUT_DIR": "OVERRIDDEN",
- "ISSUE_DATE": "OVERRIDDEN",
- "CBAR_VALUES": [0,0.001,0.005,0.01,0.05,0.1,0.5,1e+20],
- "CBAR_LABELS": ["0","0.001","0.005","0.01","0.05","0.1","0.5",""],
- "CBAR_COLORS": ["darkgrey", "#e6e680","#e6bf19","#e68000","#993380","#4c26bf","#000000"],
- "MAP_TITLE": "OVERRIDDEN",
- "RUN_PREFIX": "OVERRIDDEN",
- "LEGEND_TITLE": "Increase in\ninfected fraction",
- "PLOT_DAILY_IMAGES": "true",
- "PLOT_HOURLY_IMAGES": "false",
- "FILTER_FOR_COUNTRY": "true",
- "OVERWRITE_MODE": "true"
-}
diff --git a/pipeline_resources/EastAfrica/configs/plotting/epi/RUN_CONFIG_EPI_weekahead.json b/pipeline_resources/EastAfrica/configs/plotting/epi/RUN_CONFIG_EPI_weekahead.json
deleted file mode 100644
index 9d936462b0cd4e2ddb720b065bb6d6e060e653ce..0000000000000000000000000000000000000000
--- a/pipeline_resources/EastAfrica/configs/plotting/epi/RUN_CONFIG_EPI_weekahead.json
+++ /dev/null
@@ -1,19 +0,0 @@
-{
- "IMAGE_WIDTH": 1700,
- "IMAGE_HEIGHT": 1075,
- "WHEAT_SOURCE_INPUT_DIR_NAME": "OVERRIDDEN",
- "WHEAT_SOURCE_DISEASE_NAME": "OVERRIDDEN",
- "INPUT_CSV": "OVERRIDDEN",
- "OUTPUT_DIR": "OVERRIDDEN",
- "ISSUE_DATE": "OVERRIDDEN",
- "CBAR_VALUES": [0,0.001,0.005,0.01,0.05,0.1,0.5,1e+20],
- "CBAR_LABELS": ["0","0.001","0.005","0.01","0.05","0.1","0.5",""],
- "CBAR_COLORS": ["darkgrey", "#e6e680","#e6bf19","#e68000","#993380","#4c26bf","#000000"],
- "MAP_TITLE": "OVERRIDDEN",
- "RUN_PREFIX": "OVERRIDDEN",
- "LEGEND_TITLE": "Increase in\ninfected fraction",
- "PLOT_DAILY_IMAGES": "true",
- "PLOT_HOURLY_IMAGES": "false",
- "FILTER_FOR_COUNTRY": "true",
- "OVERWRITE_MODE": "true"
-}
diff --git a/pipeline_resources/EastAfrica/configs/plotting/name_extraction/NAME_EXTRACTION_CONFIG.json b/pipeline_resources/EastAfrica/configs/plotting/name_extraction/NAME_EXTRACTION_CONFIG.json
deleted file mode 100644
index 646807c060e7e651f5ff42b05125bc1c92b7433f..0000000000000000000000000000000000000000
--- a/pipeline_resources/EastAfrica/configs/plotting/name_extraction/NAME_EXTRACTION_CONFIG.json
+++ /dev/null
@@ -1,8 +0,0 @@
-{
- "NAME_FILE_WILDCARD": "OVERRIDDEN",
- "OUTPUT_DIR": "OVERRIDDEN",
- "NORMALIZE": "true",
- "ISSUE_DATE": "OVERRIDDEN",
- "EXTRACTION_FILE_OUTPUT_PREFIX": "OVERRIDDEN",
- "OVERWRITE_MODE": "false"
-}
diff --git a/pipeline_resources/EastAfrica/configs/source_gen/config_EastAfrica_mapspam2017.json b/pipeline_resources/EastAfrica/configs/source_gen/config_EastAfrica_mapspam2017.json
deleted file mode 100644
index 1b9643d101c156df4604aa2b69e110fbeca73f71..0000000000000000000000000000000000000000
--- a/pipeline_resources/EastAfrica/configs/source_gen/config_EastAfrica_mapspam2017.json
+++ /dev/null
@@ -1,13 +0,0 @@
-{
- "config_name" : "EastAfrica",
- "wheat_source_name" : "MAPSPAM2017",
- "wheat_file" : "NA",
- "wheat_rasters_bydate" : {
- "20170101" : "${AssetsPath}/source_gen/spam2017V1r1_SSA_gr_H_WHEA_A_clipEastAfrica.tif"
- },
- "cluster_poly_file" : "${AssetsPath}/source_gen/UMG_Mk11_grid_EastAfrica_withregions.shp",
- "id_col" : "cluster_id",
- "region_file" : "${AssetsPath}/source_gen/UMG_Mk11_grid_EastAfrica_withregions.shp",
- "region_id_col" : "REGION_ID",
- "wheat_stages_file" : "${AssetsPath}/source_gen/approx_growth_timing_cleaned.csv"
-}
diff --git a/pipeline_resources/SouthAsia/configs/advisory_builder/config_SouthAsia_variety_names_tidy.json b/pipeline_resources/SouthAsia/configs/advisory_builder/config_SouthAsia_variety_names_tidy.json
deleted file mode 100644
index 388521b1c8bfc0d2ee0896f91b46daa71c9c0308..0000000000000000000000000000000000000000
--- a/pipeline_resources/SouthAsia/configs/advisory_builder/config_SouthAsia_variety_names_tidy.json
+++ /dev/null
@@ -1,1235 +0,0 @@
-{
- "Abdul Sattar":
- [
- "Abdul Sattar"
- ],
- "Abdul Sattar 02":
- [
- "Abdul Sattar 02",
- "Abdul Sattar _02",
- "Abdul Sattar_02",
- "Abdul sattar_02"
- ],
- "Achyut" :
- [
- "Achyut"
- ],
- "Aditya" :
- [
- "Aditya",
- "Aaditya"
- ],
- "Akbar-19" :
- [
- "Akbar-19",
- "Akbar-2019",
- "Akbar 19",
- "Akbar19",
- "Akbar",
- "AKBAR 19 ",
- "AKBAR 19",
- "Akber",
- "Akber 19",
- "Akbar 19,",
- "Akbar.19",
- "Akber19",
- "Akber_19"
- ],
- "Anaj-17":
- [
- "Anaj",
- "Anaj 17",
- "Anaj-17",
- "Anaj17"
-
- ],
- "Annapurna-1":
- [
- "Annapurna",
- "Annapurna -1",
- "Annapurna 1",
- "Annapurna-1"
- ],
- "Bajosokha":
- [
- "Bajo Sokha (check)",
- "Bajo Sokha kaa",
- "Bajoka 1"
- ],
- "Banganga" :
- [
- "Banganga",
- "Bandganga",
- "Banaganga",
- "Badganga"
- ],
- "BARI Gom 17" :
- [
- "BARI Gom 17",
- "Bari gom 17",
- "Barigom 17",
- "Barigom17",
- "Bari gom17"
- ],
- "BARI Gom 20" :
- [
- "BARI Gom 20"
- ],
- "BARI Gom 21 (Shatabdi)" :
- [
- "Satapdi",
- "Shatabdi",
- "Shotabdi",
- "Sotabthe",
- "Sotabthi"
- ],
- "BARI Gom 24" :
- [
- "BARI Gom 24",
- "Prodip",
- "prodip",
- "BARI Gm 24",
- "Bari gom24",
- "BARI gom 24"
- ],
- "BARI Gom 25" :
- [
- "BARI Gom 25",
- "Bari gom 25",
- "BARI gom 25",
- "BARI Gom25",
- "BARI Gom25"
- ],
- "BARI Gom 26" :
- [
- "26",
- "Bari 26",
- "BAR Gom 26",
- "Bari gam 26",
- "BARI Gom 26",
- "BARI Gom 26",
- "BARI GOM 26",
- "BARI Gom 26",
- "BARI gom 26",
- "BARI Gom26",
- "Bari Gom 26",
- "Bari gom 26",
- "BSRI Gom 26",
- "Bari gom 36",
- "Bari hgom 26",
- "Bari Gom26",
- "BARI Gpm26",
- "BAR Gon26",
- "BARI Gom. 26",
- "BARI 26",
- "Bari Gam 26",
- "Bari gom26",
- "Bhari Gam 26",
- "বারি ২৬"
- ],
- "BARI Gom 27" :
- [
- "BARI GOM 27",
- "BARI Gom 27",
- "Bari gom 27",
- "BARI gom 27",
- "BARI Gom27",
- "27",
- "BARI 27",
- "BARI GOM27",
- "BARIGOM27"
- ],
- "BARI Gom 28" :
- [
- "Bari Gam 28",
- "Bari gam 28",
- "BARI GOM 28",
- "BARI GOM 28",
- "BARI Gom 28",
- "Bari Gom 28",
- "Bari gom 28",
- "BARI gom 28",
- "Bari gom 28",
- "Barigom 28",
- "BARI Gom28",
- "BARI Gom 28",
- "Bari 28",
- "BATI Gom 28",
- "28",
- "BARI Gog 28",
- "Bari Gom28",
- "BARI Gom. 28",
- "BARI Gom.28",
- "BSRI Gom28",
- "BARI Gomo 28",
- "BARI Gom 28",
- "RABI Gom 28",
- "RARI 28",
- "BARi Gom 28",
- "BARI Gom 28.",
- "BARI GOM28",
- "BARI gom28",
- "BARIGom 28",
- "Barigom28"
- ],
- "BARI Gom 29" :
- [
- "BARI Gom 29",
- "Bari Gom 29",
- "Bari GOM 29",
- "Bari gom 29",
- "BARI GOM 29",
- "BARI gom 29",
- "RARI Gom 29"
- ],
- "BARI Gom 30" :
- [
- "30",
- "BAR Gom 30",
- "BARI GOM 30",
- "BARI Gom 30",
- "BARI Gom 30",
- "Bari gam 30",
- "BARI GOM 30",
- "BARI Gom 30",
- "BARI gom 30",
- "Bari Gom 30",
- "Bari gom 30",
- "BARI Gom30",
- "BARI GOM 30",
- "Barigom30",
- "Barigom 30",
- "BARO Gom 30",
- "BARI Gom 3p",
- "BARI GOM, 30",
- "BARI GOM, 30",
- "NARI Gom 30",
- "BARI Gom 30",
- "Bari gam30",
- "BARI GOM30",
- "BARI GON 30",
- "BARI Gon 30",
- "BARI Hom 30",
- "BAGI Gom 30",
- "BAIR GOM 30",
- "BSRI Gom30",
- "BAri Gom30",
- "BARI gom30",
- "BRI Gom30",
- "VARI Gom30",
- "BARI 30",
- "Bari 30",
- "BARi GOM 30",
- "Bari gom30",
- "BARI Mom 30",
- "BARIGom 30",
- "BARRI Gom 30",
- "Brri gom 30",
- "BARIGom30",
- "VARI Gom 30",
- "Bari Gam 30",
- "Bari GOM 30",
- "BARIG 30",
- "BARIGOM 30",
- "BARRI Gum30",
- "Bari Gom30",
- "Bhari Gam 30",
- "BAARIGom 30",
- "BARRI Ggom 30",
- "BRRI Gom 30"
- ],
- "BARI Gom 31" :
- [
- "BARI Gom31",
- "Barigom,31",
- "Barigom31"
- ],
- "BARI Gom 32" :
- [
- "32",
- "Baarigom 32",
- "BARI GOM 32",
- "BARI GOM 32",
- "BARI Gom 32",
- "Bari gom 32",
- "Barigom 32",
- "Barigom32",
- "BARI Tom 32",
- "BARI gom 32",
- "Bari Gom 32",
- "BARI Gom32",
- "BARI Gom. 32",
- "BARI GOM, 32",
- "BARI Gom 32",
- "BARI GOM32",
- "BARI Gom 32.",
- "Bari gom 32.",
- "BARI gom32",
- "BARIG Gom 32",
- "BARIGom 32",
- "BARRI Gom 32",
- "BARI Gom -32",
- "BARI Gam 32",
- "BARI Gom -32",
- "BARI Gom- 32",
- "Bari Gom32",
- "BARRI Gum 32",
- "BARRI Gum32",
- "BARIGom32",
- "বারি গম ৩২",
- "৩২",
- "BRRI Gom 32",
- "BRRRI gom 32",
- "BRRRI Gom32"
- ],
- "BARI Gom 33" :
- [
- "33",
- "ba 33",
- "Bari 33",
- "Bar 33",
- "BARI GoM 33",
- "BARI Gom 33",
- "Bari gam 33",
- "BARI GOM 33",
- "BARI GOM 33",
- "BARI Gom 33",
- "BARI Gom 33",
- "BARI gom 33",
- "Bari Gom 33",
- "Bari gom 33",
- "BARI GOM33",
- "BARI Gom33",
- "BARI Gon 33",
- "Barigom,33",
- "Barigom 33",
- "BARI Gom,33",
- "BARI Gom-33",
- "VARI Gom 33",
- "BARI Gom 33",
- "BARI Gom-33",
- "VARI Gom 33",
- "Barigom33",
- "BARI Gom al33",
- "Barigom \n33",
- "BARI GoM 33",
- "BARI GOM 33",
- "BARI Gog 33",
- "BARI Gomp33",
- "Bari Bari 33",
- "BARI Gom. 33",
- "BARI Gomv33",
- "BARIVGom 33",
- "BARi Gom 33",
- "BBARI Gom33",
- "BARON Gom33",
- "Bank Gom 33",
- "Bafj Gom 33",
- "BARIGom 33",
- "BARIGom33",
- "BARIgom33",
- "BARIHom 33",
- "BARI 33",
- "BARI Fom 33",
- "BARI Gom -33",
- "BARI Gom 33.",
- "BaRI Gom 33.",
- "Bari gom 33.",
- "BARI GOM. 33",
- "BARI GOM.33",
- "BARI gom33",
- "Bari Gom33",
- "Bari gom33",
- "BARI Gum 33",
- "BARI Gum-33",
- "BARRI GOM 33",
- "BARRI Gom 33",
- "Barri gom 33",
- "BARRI Gum 33",
- "BARRI gum 33",
- "BRRI GOM 33",
- "Brri Gom 33",
- "BARRI Gum33",
- "BARU Gom 33",
- "BATIGom 33",
- "BARI Gam 33",
- "BARIGOM 33",
- "Bari Gom-33",
- "BARI GOm33",
- "BARI33",
- "BRRI Gom 33",
- "BRRI Gon 33",
- "Bsri gom 33",
- "বারি গম ৩৩",
- "BARl Gom 33",
- "BSRIGom 33"
- ],
- "BARI Gom 34":
- [
- "BARI Gom 34",
- "BARI GOM 34"
- ],
- "BARI GOM Sonali" :
- [
- "BARI GOM Sonali",
- "BARI Gom sonali",
- "BARI Gom Sonali"
- ],
- "Bhakhar star":
- [
- "Bhakhar star",
- "Bhakkar star",
- "Bhkar Star"
- ],
- "Bhaskar (Indian)":
- [
- "Bhaskar (Indian)"
- ],
- "Bheriganga":
- [
- "Bheriganga"
- ],
- "Bhirkuti" :
- [
- "Bhirkuti",
- "Bhrikuti"
- ],
- "BL 4341" :
- [
- "BL 4341",
- "BL4341!",
- "BL4341"
-
- ],
- "BL 4669" :
- [
- "BL 4669",
- "BL 4669(pipeline variety)"
- ],
- "BL 4682" :
- [
- "BL 4682"
- ],
- "Bumthang Ka Drukchu":
- [
- "Bumthang ka Drukchu",
- "Bumthang ka drukchu",
- "Bumthangka drukchu",
- "Bumthang Ka Drukchu"
- ],
- "BWMRI Gom 1" :
- [
- "BWMRI 1",
- "BWMRI Gom 1",
- "WMRI Gom 1",
- "WMRI Gom -1",
- "WMRI 1",
- "WMRI,Gom 1",
- "BWMRI GOM 1",
- "BWMRI Gom1",
- "BWMRI-1",
- "wmri 1",
- "WMRI Gom 1",
- "WMRIGom 1"
- ],
- "BWMRI Gom 2" :
- [
- "WMRI Gom 2",
- "BWMRI Gom 2",
- "BWMRI Gom2",
- "BWMRI Gom-2",
- "BWMRI 2",
- "WMRI Gom 2",
- "BWMRI GOM 2",
- "WMRIGom 2"
- ],
- "BWMRI Gom 3" :
- [
- "BWMRI Gom 3",
- "BARI BWMRI 3",
- "BMRI 3",
- "BWMRI3",
- "WMRI Gom 3",
- "WMRI-3",
- "BWMRI 3",
- "WMRI 3"
- ],
- "CIMMYT line 1":
- [
- "CIMMYT line 1",
- "CIMMYT Line 1",
- "CIMMYT LINE 1"
- ],
- "CIMMYT line 2":
- [
- "CIMMYT line 2",
- "CIMMYT Line 2",
- "CIMMYT LINE 2"
- ],
- "CIMMYT line 3":
- [
- "CIMMYT line 3",
- "CIMMYT Line 3",
- "CIMMYT LINE 3"
- ],
- "CIMMYT line 4":
- [
- "CIMMYT line 4",
- "CIMMYT Line 4",
- "CIMMYT LINE 4"
- ],
- "CIMMYT line 5":
- [
- "CIMMYT line 5",
- "CIMMYT Line 5",
- "CIMMYT LINE 5"
- ],
- "CIMMYT line 6":
- [
- "CIMMYT line 6",
- "CIMMYT Line 6",
- "CIMMYT LINE 6"
- ],
- "CIMMYT line 7":
- [
- "CIMMYT line 7",
- "CIMMYT Line 7",
- "CIMMYT LINE 7"
- ],
- "CIMMYT line 8":
- [
- "CIMMYT line 8",
- "CIMMYT Line 8",
- "CIMMYT LINE 8"
- ],
- "CIMMYT line 9":
- [
- "CIMMYT line 9",
- "CIMMYT Line 9",
- "CIMMYT LINE 9"
- ],
- "CIMMYT line 10":
- [
- "CIMMYT line 10",
- "CIMMYT Line 10",
- "CIMMYT LINE 10"
- ],
- "CIMMYT line 11":
- [
- "CIMMYT line 11",
- "CIMMYT Line 11",
- "CIMMYT LINE 11"
- ],
- "CIMMYT line 12":
- [
- "CIMMYT line 12",
- "CIMMYT Line 12",
- "CIMMYT LINE 12"
- ],
- "CIMMYT line 13":
- [
- "CIMMYT line 13",
- "CIMMYT Line 13",
- "CIMMYT LINE 13"
- ],
- "CIMMYT line 14":
- [
- "CIMMYT line 14",
- "CIMMYT Line 14",
- "CIMMYT LINE 14"
- ],
- "CIMMYT line 15":
- [
- "CIMMYT line 15",
- "CIMMYT Line 15",
- "CIMMYT LINE 15"
- ],
- "CIMMYT line 16":
- [
- "CIMMYT line 16",
- "CIMMYT Line 16",
- "CIMMYT LINE 16"
- ],
- "CIMMYT line 17":
- [
- "CIMMYT line 17",
- "CIMMYT Line 17",
- "CIMMYT LINE 17"
- ],
- "CIMMYT line 18":
- [
- "CIMMYT line 18",
- "CIMMYT Line 18",
- "CIMMYT LINE 18"
- ],
- "CIMMYT line 19":
- [
- "CIMMYT line 19",
- "CIMMYT Line 19",
- "CIMMYT LINE 19"
- ],
- "CIMMYT line 20":
- [
- "CIMMYT line 20",
- "CIMMYT Line 20",
- "CIMMYT LINE 20"
- ],
- "CIMMYT line 21":
- [
- "CIMMYT line 21",
- "CIMMYT Line 21",
- "CIMMYT LINE 21"
- ],
- "CIMMYT line 22":
- [
- "CIMMYT line 22",
- "CIMMYT Line 22",
- "CIMMYT LINE 22"
- ],
- "CIMMYT line 23":
- [
- "CIMMYT line 23",
- "CIMMYT Line 23",
- "CIMMYT LINE 23"
- ],
- "CIMMYT line 24":
- [
- "CIMMYT line 24",
- "CIMMYT Line 24",
- "CIMMYT LINE 24"
- ],
- "CIMMYT line 25":
- [
- "CIMMYT line 25",
- "CIMMYT Line 25",
- "CIMMYT LINE 25"
- ],
- "Danphe" :
- [
- "Danphe"
- ],
- "Dhaulagiri":
- [
- "DHAULAGIRI",
- "Dauligiri",
- "Dhaulagiri",
- "Dhauligiri"
- ],
- "Dilkash-20":
- [
- "Dilkash-20",
- "Dilkash 20",
- "DILKASH-20",
- "SILKASH 20",
- "Dilkash20",
- "Dilkkash 20"
- ],
- "Dilkash-21":
- [
- "Dilkash-21",
- "DILKASH-21",
- "DILKASH 21",
- "Dilkash 21"
- ],
- "Durum wheat":
- [
- "Dura. Wheat",
- "Duram",
- "Durum",
- "Durum wheat line imported from Indian market"
- ],
- "Faisalabad-08" :
- [
- "Faisalabad-08",
- "Faisalabad-2008",
- "Faisalabad 2008",
- "Faisalabad2008",
- "Fsd 08",
- "Fsd08",
- "Fsd_08",
- "Fsd-08",
- "Faisalabad 08",
- "Faisalabad _08",
- "Faisalabad_08"
- ],
- "Fakhar e Bhakar":
- [
- "Fakhar e Bhakar",
- "Fakhar e Bhakkar",
- "Fakhra bkhar",
- "Fakhrabkhar",
- "Falhrabhakhar",
- "Fakhar Bakhar"
- ],
- "Gaffar":
- [
- "Gaffar"
- ],
- "Galaxy 13":
- [
- "Galaxy 13",
- "Galaxy 13 ",
- "Galaxy-13",
- "Galaxy-13 ",
- "GALAXY-13",
- "GALAXY-13 ",
- "Galaxy",
- "Galaxy_13"
- ],
- "Gautam" :
- [
- "GAUTAM",
- "Gautam",
- "Gautum",
- "Gautan",
- "Guatam"
- ],
- "Gulzar":
- [
- "Gulzar"
- ],
- "Guma Sokha":
- [
- "Guma Sokha",
- "Guma sokha (check)",
- "Guma sokha ka",
- "Guma sokha- kaap",
- "Guma sokha-kaa",
- "Gumasokha",
- "Gumasokha kaa"
- ],
- "HD 2204":
- [
- "HD 2204"
- ],
- "HD 2967" :
- [
- "HD 2967",
- "HD2967"
- ],
- "HD 3086" :
- [
- "HD 3086"
- ],
- "Himganga":
- [
- "HIMGANGA"
- ],
- "Imdad-05":
- [
- "Imdad_05"
- ],
- "Indian (China 3)" :
- [
- "Indian ( china 3)",
- "IIndian(china 3)",
- "Indian( china 3)",
- "Indian(china 3)",
- "Indian (china 3)",
- "China 3",
- "Indian China 3"
- ],
- "Indian (China 4)" :
- [
- "Indian ( china 4)",
- "Indian(china 4)",
- "Indian (china 4)",
- "IIndian (china 4)",
- "Indian( china 4)",
- "Indian (china4)",
- "indian(china 4)",
- "Chaina 4",
- "Indian ( china 4)"
- ],
- "Jaga kaa":
- [
- "Jaga kaa"
- ],
- "Kanchan" :
- [
- "Kanchan",
- "Kanchon",
- "KANCHAN",
- "KANCHON",
- "kanchon"
- ],
- "Kanti" :
- [
- "Kanti"
- ],
- "Khumal Shakti" :
- [
- "Khumal Shakti"
- ],
- "Kundan":
- [
- "Kundan"
- ],
- "Lok-1" :
- [
- "Lok-1"
- ],
- "Munal" :
- [
- "Munal"
- ],
- "Mudule" :
- [
- "Mudule",
- "Mudule-1"
- ],
- "NAL-52":
- [
- "NAL -52",
- "NAL-52",
- "NAL52"
- ],
- "Nawab-21":
- [
- "Nawab 21",
- "Nawab8_21"
- ],
- "NL 1179":
- [
- "NL 1179",
- "NL 1179, pipeline variety for mid hill, yellow rust resistant, disseminated by NWRP, Bhairahawa from last season in Pyuthan"
- ],
- "NL 1446" :
- [
- "NL1446",
- "NL 1446"
- ],
- "NL 1488":
- [
- "NL 1488"
- ],
- "NL 1612" :
- [
- "NL1612"
- ],
- "NL 1616" :
- [
- "NL 1616"
- ],
- "NL 1716":
- [
- "NL 1716",
- "NL1716"
- ],
- "NL 1835":
- [
- "NL 1835",
- "NL1835"
- ],
- "NL 971" :
- [
- "NL 971",
- "NL-971",
- "NL971"
- ],
- "Nepal 297" :
- [
- "Nepal 297",
- "NL297",
- "NL 297"
- ],
- "NWDSN 03":
- [
- "NWDSN 03"
- ],
- "NWDSN 148":
- [
- "NWDSN 148"
- ],
- "NWDSN 21":
- [
- "NWDSN 21"
- ],
- "NWDSN 79":
- [
- "NWDSN 79"
- ],
- "NWDSN 806":
- [
- "NWDSN 806"
- ],
- "NWDSN 172":
- [
- "NWDSN172"
- ],
- "NWDSN 588":
- [
- "NWDSN588"
- ],
- "Pasang lhamu" :
- [
- "Pasang lhamu"
- ],
- "PBW343" :
- [
- "PBW343"
- ],
- "Punjab 11" :
- [
- "Punjab 11",
- "Punjab11",
- "Punjab11 ",
- "PUNJAB 11"
- ],
- "RR 21" :
- [
- "RR 21",
- "RR-21",
- "RR21"
- ],
- "Sadiq-21":
- [
- "Sadiq 21",
- "Sadiq21"
- ],
- "Saher-06":
- [
- "Saher",
- "Seher 06"
- ],
- "Sehet-06":
- [
- "Sehet06"
- ],
- "Siddhartha":
- [
- "Siddhartha"
- ],
- "Sonalika" :
- [
- "Sonalika"
- ],
- "Subhani-21":
- [
- "Subhani 21",
- "Subhani 21 ",
- "Subhani-21",
- "Subhani-21 ",
- "SUBHANI-21",
- "SUBHANI-21 ",
- "Subahani21",
- "Subahani21 ",
- "Subhani"
- ],
- "Suruma" :
- [
- "Surma",
- "Suruma"
- ],
- "Sworgadwari" :
- [
- "Sorgadwari",
- "Sworgadwari",
- "Sworgdwari",
- "swogadwari",
- "Sorghadwari",
- "Swargadwari"
- ],
- "SW-2" :
- [
- "SW-2"
- ],
- "Ujalla-16":
- [
- "Ujala",
- "Ujalla 16",
- "Ujjala 16"
- ],
- "Vaskar" :
- [
- "Vaskar"
- ],
- "Vijay" :
- [
- "Vijay",
- "Vijaya",
- "VIJAYA",
- "Bijaya",
- "Bijay"
- ],
- "Vinayak":
- [
- "Vinayak"
- ],
- "Wattan" :
- [
- "Wattan",
- "Wattan (unapproved)",
- "Wattan (Unapproved)",
- "Wattan (unapproved)",
- "Wattan",
- "Watan"
- ],
- "WK 1204" :
- [
- "WK 1204",
- "WK1204",
- "Wk1204",
- "WK 1204 ",
- "Wk 1204",
- "we 1204"
- ],
- "WK 1481" :
- [
- "WK1481"
- ],
- "WK 2748 (Bheri-Ganga)" :
- [
- "Bheri-Ganga (WK 2748)"
- ],
- "WK 2891" :
- [
- "WK2891",
- "WK 2891"
- ],
- "WK 3152":
- [
- "WK3152"
- ],
- "WK 3413" :
- [
- "WK3413",
- "WK 3413"
- ],
- "WK 3639" :
- [
- "WK3639",
- "WK 3639"
- ],
- "WK 3927":
- [
- "WK3927"
- ],
- "ZINC Gahun 1" :
- [
- "ZINC 1",
- "ZINC Gagun 1",
- "Zinc Gahun 1",
- "Zinc gahu 1"
- ],
- "ZINC Gahun 2" :
- [
- "Zinc Gahun 2"
- ],
- "Zincole-16":
- [
- "Zincol 16",
- "Zincole 16"
- ],
- "Local" :
- [
- "local",
- "LOCAL",
- "RR-21 and Mix",
- "Local",
- "Local awnless",
- "Local landraces",
- "Local landraces(awnless)",
- "Local mudule",
- "Loc al",
- "Agra local",
- "Annapurna (Local)",
- "Local variety",
- "local mulure",
- "local murule",
- "own less local",
- "Loca",
- "Local bread wheat",
- "Local(janath)"
- ],
- "Mixed" :
- [
- "HD2967 and HD3086",
- "Mixed",
- "mixed",
- "Mix",
- "Mixture",
- "N/A (Mix)",
- "Agralocal+Morocco",
- "Different",
- "Different test entries",
- "Lerma Rojo (mixed)",
- "AARI 11,fsd _08",
- "Akbar 19, Fakhar e Bakkhar, Faisalabad 08, Anaj 17",
- "Akbar19, Anaj 17",
- "Akbar19, Fakhar e Bakkhar",
- "Akbar19, Fakhar e Bakkhar, Faisalabad 08",
- "Anaj and Akbar--19",
- "Anaj and Akbar-21",
- "Anaj and fsd",
- "Dilkash,akbar_19",
- "Fakhar e Bakkhar, Faisalabad 08",
- "Fakhr-e-Bhakkar",
- "Fsd and anaj 17",
- "Fsd-08 and akbar-19",
- "Fsd-08,Dilkash",
- "Fsd08, Anaj,Akbar",
- "Fsd08, galaxy 13",
- "Punjab 11 and galaxy_13",
- "Seher, Fsd 08",
- "Unknown (Mixture)",
- "MIX",
- "Akbar 19, Dilkash",
- "Akbar 19, Dilkash 20, Anaj17",
- "Akbar 19, Dilkash 21, Fakhare Bhakar",
- "Akbar 19, Fsd 08",
- "Different Fsd 08, Akbar19, Dilkash21",
- "Dilkash, Arooj, Akbar",
- "Dilkash, Arooj, Nishan",
- "Dilkash, Faisalabad-2008",
- "Wl-711, Shafaq-06, Morocco",
- "531, NRN 67",
- "600, WVD16",
- "Abdul Sat tar+ TD_1",
- "Akbar 19, Bhakar star",
- "Akbar 19, Dilkas20, Anaj 17",
- "Akbar 19, Dilkash 20, Bhakar star",
- "Akbar 19, Faisalabad 08",
- "Akbar 19, Nawab 21",
- "Akbar with",
- "Akbar, Arooj",
- "Akber-19, Fakhre Bhakker, Dilkash and Mixtureof dofferent varities",
- "Akber_19+Abdul Sattar_02",
- "Anaj17, Akbar 19",
- "Arooj, Akbar, Dilkash",
- "BARI Gom 33 and",
- "Anaj' Akbar",
- "As_02+Akbet_19",
- "Bhakar e Bhakar, Bhakar star, Akbar 19",
- "Bhakhar star + Abdul sattar",
- "Borlauge 16+ Markez+ NARC Supet",
- "Different advance and candidate lines",
- "Different but samples were collected from MOROCCO",
- "Different enteries under disease sceerning Nurseries (Akbar19)",
- "Dilkas 20 Akbar 19",
- "Dilkash 20, Akbar 19",
- "Dilkash 20, Nawab 21, Bhakar star",
- "Dilkash and Arooj",
- "Dilkash and Fakhr e Bhajker",
- "Dilkash, Arooj and Akber19",
- "Dilksh21, Akbar 19, Faisalabad 08,",
- "Faisalabad 08 and unknown variety",
- "Fakhar e Bhakkar, Akbar, Unknown",
- "Fakhr e Bhakkar' Akbar, Ujala",
- "Galaxy 13, Akbar 19, Dilkash20",
- "Galaxy 13,_Akbar 19",
- "Galaxy' Faisalabad' Akbar",
- "Nawab 21, Akbar 19, Dilkash 20,",
- "Nawab 21, Akbar 19, Fakhar e Bhakar",
- "Seher 06, Faisalabad 08",
- "TF_1+Abdul Sattar_02",
- "Trap nurseries and historical lines",
- "Trial+ Susceptible check",
- "Unknown, Mixture",
- "Mixed",
- "Mixture. Unknown",
- "Mixtutr",
- "Morrocco + others",
- "Trap nirseries",
- "Trap nurseries",
- "Trials",
- "Different genotypes",
- "Ujala, Akbar",
- "Akber-19, Arooj, Dilkash, Subhani, Nishan, Fakhr e Bhakkar, Ghazi 19. Wafaq22. and Shahenshah",
- "Akber19 and Dilkash",
- "Akber19, As-2002, Dilkash and Nawab-21",
- "Akber19. Dilkash. Subhani. Arooj . Fakhr e Bhakkar and Nawab 21",
- "Akber_19+ Imdad_05+benazir_13",
- "Akber_19. Dikash . Bakhar star",
- "Arooj-21 and advance line",
- "Bhakker Star. Nawab. Dilkash",
- "Bhakhar and mixture",
- "Dilkash. Akber 19. Nawab and Arooj",
- "Faisalabad 08 and mixtures of different varities",
- "Faisalabad 2008, Fakhre Bhakkar and Dilkash",
- "mixture",
- "Mixturr",
- "Shahenshah, Akber,19, and Nawab21"
- ],
- "Unknown" :
- [
- "Unknown",
- "Unknown (Mix)",
- "UNKNOWN",
- "unknown",
- "UNKNOWN (Old variety)",
- "Unknown (Local)",
- "Unknown mixture",
- "Unkown",
- "unkwown",
- "Unkwon",
- "Un know",
- "Unkbown",
- "Barigom",
- "Bari gom",
- "BARI Gom",
- "BARI gom",
- "Barigom ",
- "BARRI Gom",
- "BARI GOM",
- "Bari gam 2",
- "BARI Gom 3",
- "BARI Gom 34",
- "Bari gom 34",
- "BARI Gom34",
- "Barigom 34",
- "BARI GOM 134",
- "BARI Gom 35",
- "BARI Gom 3e",
- "Bari gom 36",
- "Bari gam 39",
- "BARI GOM 39",
- "BARI GOM 39",
- "BARI Gom 39",
- "BARI Gom 60",
- "BARI Gom50",
- "Fsd",
- "c",
- "e",
- "f",
- "g",
- "Y",
- "G",
- "r",
- "v",
- "2430",
- "66",
- "35",
- "40",
- "50",
- "Advance material",
- "Na",
- "NS",
- "??",
- "???? ??",
- "Annon",
- "Dilkash",
- "na",
- "WMRI Gom 29",
- "Bari Gom",
- "BARI GOM E",
- "Bb",
- "BWAVTH19",
- "Dilash",
- "Dilkas",
- "Un known",
- "Un non",
- "un non",
- "Unknown",
- "Unkonwn",
- "UNKWON",
- "Unnon",
- "Dilkush",
- "Dilkusj",
- "Dilquash",
- "H",
- "TD_1",
- "???? ?? ??",
- "Unknown (Local awnless)"
- ]
-}
diff --git a/pipeline_resources/SouthAsia/configs/coordinator/README.txt b/pipeline_resources/SouthAsia/configs/coordinator/README.txt
deleted file mode 100644
index b97176485969b5bbde7d4efa7d839eddd327da15..0000000000000000000000000000000000000000
--- a/pipeline_resources/SouthAsia/configs/coordinator/README.txt
+++ /dev/null
@@ -1,3 +0,0 @@
-make a copy of the template file, You can add a files to set system-specific variables (or sensitive passwords)
-
-the template sys config files will be needed for both forecast and analysis runs,
\ No newline at end of file
diff --git a/pipeline_resources/SouthAsia/configs/coordinator/an/depo_config_SouthAsia_an_live.json b/pipeline_resources/SouthAsia/configs/coordinator/an/depo_config_SouthAsia_an_live.json
deleted file mode 100755
index 21362d0190c0f4861e7b35e8782e00005d4dba4c..0000000000000000000000000000000000000000
--- a/pipeline_resources/SouthAsia/configs/coordinator/an/depo_config_SouthAsia_an_live.json
+++ /dev/null
@@ -1,35 +0,0 @@
-{
- "ServerPathTemplate" : "${MetoFTP}/metofficeupload/upload/SouthAsia/fromMO/daily_name/",
- "InputFileTemplate" : "WR_NAME_SouthAsia_${StartString}_an",
- "DataFileTemplate" : "deposition_srcs_allregions_${StartString}.nc",
- "TimeExpectedAvailable" : "1500",
- "ProcessPreJob" : "process_pre_job_server_download",
- "ProcessInJob" : "process_in_job_dep",
- "ProcessEWSPlotting" : "process_EWS_plotting_dep",
- "EWS-Plotting" : {
- "SysConfig": "${ConfigsPath}/coordinator/an/sys_config_SouthAsia_an_live.json",
- "NameExtractionConfig": "${ConfigsPath}/plotting///name_extraction/NAME_EXTRACTION_CONFIG.json",
- "RunConfig": "${ConfigsPath}/plotting///deposition/RUN_CONFIG_DEPO.json",
- "RunConfigNorm": "${ConfigsPath}/plotting///deposition/RUN_CONFIG_DEPO_NORMALIZED.json",
- "SouthAsia" : {
- "ChartConfig": "${ConfigsPath}/plotting///chart/CHART_CONFIG_ASIA_PINE.json",
- "Normalize" : "False"
- },
- "Bangladesh" : {
- "ChartConfig" : "${ConfigsPath}/plotting/chart/CHART_CONFIG_BANGLADESH_PINE.json",
- "Normalize" : "False"
- },
- "Nepal" : {
- "ChartConfig" : "${ConfigsPath}/plotting/chart/CHART_CONFIG_NEPAL_PINE.json",
- "Normalize" : "False"
- },
- "Pakistan" : {
- "ChartConfig" : "${ConfigsPath}/plotting/chart/CHART_CONFIG_PAKISTAN_PINE.json",
- "Normalize" : "False"
- },
- "Bhutan" : {
- "ChartConfig" : "${ConfigsPath}/plotting/chart/CHART_CONFIG_BHUTAN_PINE.json",
- "Normalize" : "False"
- }
- }
-}
diff --git a/pipeline_resources/SouthAsia/configs/coordinator/an/env_suit_config_SouthAsia_an_live.json b/pipeline_resources/SouthAsia/configs/coordinator/an/env_suit_config_SouthAsia_an_live.json
deleted file mode 100755
index 5783cce5c609010ed182040c5e17bfc4a3af1a76..0000000000000000000000000000000000000000
--- a/pipeline_resources/SouthAsia/configs/coordinator/an/env_suit_config_SouthAsia_an_live.json
+++ /dev/null
@@ -1,104 +0,0 @@
-{
- "ServerPathTemplate" : "${MetoFTP}/metofficeupload/upload/SouthAsia/fromMO/daily_name/",
- "InputFileTemplate" : "WR_EnvSuit_Met_SouthAsia_${StartString}_an",
- "ProcessPreJob" : "process_pre_job_server_download",
- "ProcessInJob" : "process_in_job_env2_0",
- "ProcessEWSPlotting" : "process_EWS_plotting_env2_0",
- "CONFIGS_PATH": "${ConfigsPath}",
- "ASSETS_PATH": "${AssetsPath}",
- "WORK_PATH" : "${WorkspacePath}",
- "INPUT_PATH" : "${WorkspacePath}",
- "OUTPUT_PATH" : "${WorkspacePath}",
- "SYS_CONFIG" : "${ConfigsPath}/met_extractor/SYS_CONFIG_PINE.json",
- "FIELD_NAME_CONSTANTS" : "${ConfigsPath}/met_extractor/FIELD_NAME_CONSTANTS.csv",
- "RUN_TYPE" : "operational",
- "EXTRACTION_DAYS": 7,
- "FORECAST_DAYS": 6,
- "STRAINS": ["LeafRust","StemRust","StripeRust","LeafRust_TempOnly","StemRust_TempOnly","StripeRust_TempOnly"],
- "PARAMS": {
- "LeafRust": {
- "suitability_modules": ["semibool_dewperiod"],
- "past_steps": 0,
- "future_steps": 2,
- "thresholds": {
- "temperature": [2,15,20,30],
- "precipitation": 0,
- "relative_humidity": 90
- }
- },
- "StemRust": {
- "suitability_modules": ["semibool_dewperiod"],
- "past_steps": 0,
- "future_steps": 2,
- "thresholds": {
- "temperature": [2,15,24,30],
- "precipitation": 0,
- "relative_humidity": 90
- }
- },
- "StripeRust": {
- "suitability_modules": ["v1_dewperiod"],
- "past_steps": 0,
- "future_steps": 7,
- "thresholds": {
- "temperature": [2.37,19.8],
- "precipitation": 0,
- "relative_humidity": 90
- }
- },
- "LeafRust_TempOnly": {
- "suitability_modules": ["semibool_dewperiod"],
- "past_steps": 0,
- "future_steps": 2,
- "thresholds": {
- "temperature": [2,15,20,30],
- "precipitation": -1,
- "relative_humidity": 90
- }
- },
- "StemRust_TempOnly": {
- "suitability_modules": ["semibool_dewperiod"],
- "past_steps": 0,
- "future_steps": 2,
- "thresholds": {
- "temperature": [2,15,24,30],
- "precipitation": -1,
- "relative_humidity": 90
- }
- },
- "StripeRust_TempOnly": {
- "suitability_modules": ["v1_dewperiod"],
- "past_steps": 0,
- "future_steps": 7,
- "thresholds": {
- "temperature": [2.37,19.8],
- "precipitation": -1,
- "relative_humidity": 90
- }
- }
- },
- "EWS-Plotting" : {
- "SysConfig" : "${ConfigsPath}/coordinator/an/sys_config_SouthAsia_an_live.json",
- "RunConfig" : "${ConfigsPath}/plotting/env_suit/RUN_CONFIG_ENV.json",
- "SouthAsia" : {
- "ChartConfig" : "${ConfigsPath}/plotting/chart/CHART_CONFIG_ASIA_PINE.json",
- "FilterForCountry" : "False"
- },
- "Bangladesh" : {
- "ChartConfig" : "${ConfigsPath}/plotting/chart/CHART_CONFIG_BANGLADESH_PINE.json",
- "FilterForCountry" : "True"
- },
- "Nepal" : {
- "ChartConfig" : "${ConfigsPath}/plotting/chart/CHART_CONFIG_NEPAL_PINE.json",
- "FilterForCountry" : "True"
- },
- "Pakistan" : {
- "ChartConfig" : "${ConfigsPath}/plotting/chart/CHART_CONFIG_PAKISTAN_PINE.json",
- "FilterForCountry" : "False"
- },
- "Bhutan" : {
- "ChartConfig" : "${ConfigsPath}/plotting/chart/CHART_CONFIG_BHUTAN_PINE.json",
- "FilterForCountry" : "True"
- }
- }
-}
diff --git a/pipeline_resources/SouthAsia/configs/coordinator/an/template_sys_config_SouthAsia_an_live.json b/pipeline_resources/SouthAsia/configs/coordinator/an/template_sys_config_SouthAsia_an_live.json
deleted file mode 100755
index e145c4c60651faf4d729f0d9c44e94b5bd468879..0000000000000000000000000000000000000000
--- a/pipeline_resources/SouthAsia/configs/coordinator/an/template_sys_config_SouthAsia_an_live.json
+++ /dev/null
@@ -1,14 +0,0 @@
-{
- "RegionName" : "SouthAsia",
- "SubRegionNames" : ["SouthAsia","Nepal","Bangladesh","Pakistan","Bhutan"],
- "StartTime" : "?",
- "StartString" : "?",
- "ProjectRoot" : "<path to project root>",
- "MetoFTP" : "<path to MetoFTP>",
- "WorkspacePathout" : "${ProjectRoot}/regions/SouthAsia/workspace_analysis/",
- "WorkspacePath" : "${ProjectRoot}/regions/SouthAsia/workspace_analysis/",
- "ConfigsPath" : "/home/lb584/git/ews-coordinator/pipeline_resources/SouthAsia/configs",
- "AssetsPath" : "${ProjectRoot}/regions/SouthAsia/resources/assets",
- "LoggingConfigPath" : "${ProjectRoot}/code/coordinator/pipeline_resources/SouthAsia/configs/coordinator/log_config.json",
- "PLACES_SHAPE_FILE": "${ProjectRoot}/regions/SouthAsia/resources/assets/plotting/gis_data/common/places_shape/asia_places.shp"
-}
diff --git a/pipeline_resources/SouthAsia/configs/coordinator/fc/advisory_config_SouthAsia_fc_live.json b/pipeline_resources/SouthAsia/configs/coordinator/fc/advisory_config_SouthAsia_fc_live.json
deleted file mode 100755
index a6d39c4fee282ba9018a0a1b028e99ce9430e24a..0000000000000000000000000000000000000000
--- a/pipeline_resources/SouthAsia/configs/coordinator/fc/advisory_config_SouthAsia_fc_live.json
+++ /dev/null
@@ -1,100 +0,0 @@
-{
- "ProcessPreJob" : "query_past_successes",
- "ProcessInJob" : "process_in_job_advisory",
- "ProcessEWSPlotting" : "do_nothing",
- "seasonStartString" : "20231201",
- "SurveyPathTemplate" : "${WorkspacePath}/SURVEYDATA_${dateString}/Groups/surveys_PROD.csv",
- "DependentComponents" : [
- "Deposition",
- "Environment"
- ],
- "Environment" : {
- "SuccessFileTemplate" : "${WorkspacePath}/ENVIRONMENT_2.0_${StartString}/STATUS_SUCCESS",
- "DataPathTemplate" : "${WorkspacePath}/ENVIRONMENT_2.0_${dateString}/plotting/${SubRegionNameLower}/input_nc/",
- "PlotPathTemplate" : "${WorkspacePath}/ENVIRONMENT_2.0_${dateString}/plotting/${SubRegionNameLower}/images/Weekly/",
- "PlotFilenameTemplates" : {
- "stripe" : "${envPlotPath}/suitability_${SubRegionNameLower}_stripe_rust_total_${dateString}0000_${EnvEndString}0000_map.png",
- "stem" : "${envPlotPath}/suitability_${SubRegionNameLower}_stem_rust_total_${dateString}0000_${EnvEndString}0000_map.png",
- "leaf" : "${envPlotPath}/suitability_${SubRegionNameLower}_leaf_rust_total_${dateString}0000_${EnvEndString}0000_map.png"
- },
- "Aggregation" : {
- "raster_path_template" : "${envDataPath}/suitability_${SubRegionNameLower}_${disease_name_snakecase}_total.nc",
- "raster_name_template" : "RIE_${disease_name_camelcase}_%",
- "shape_fn_entry" : "ShapeFilenameToAggregate",
- "shape_coln" : "admin2Name",
- "show_columns" : ["admin0Name","admin1Name"],
- "separate_rows_for_coln":"admin0Name",
- "func" : "mean",
- "multiply_by" : 100,
- "float_format" : ".0f",
- "display_format" : ".0f",
- "save_path_template" : "${jobPath}/images/suitability_${SubRegionNameLower}_${disease_name_snakecase}_mean_per_zone",
- "max_entries" : 20
- }
- },
- "Deposition" : {
- "SuccessFileTemplate" : "${WorkspacePath}/DEPOSITION_${StartString}/STATUS_SUCCESS",
- "DataPathTemplate" : "${WorkspacePath}/DEPOSITION_${dateString}/plotting/${SubRegionNameLower}/input_nc/",
- "PlotPathTemplate" : "${WorkspacePath}/DEPOSITION_${dateString}/plotting/${SubRegionNameLower}/images/Weekly/",
- "PlotFilenameTemplates" : {
- "stripe": "${depPlotPath}/deposition_${SubRegionNameLower}_stripe_rust_total_${dateString}0300_${weekAheadString}0000_map.png",
- "stem": "${depPlotPath}/deposition_${SubRegionNameLower}_stem_rust_total_${dateString}0300_${weekAheadString}0000_map.png",
- "leaf": "${depPlotPath}/deposition_${SubRegionNameLower}_leaf_rust_total_${dateString}0300_${weekAheadString}0000_map.png"
- },
- "Aggregation" : {
- "raster_path_template" : "${depDataPath}/deposition_${SubRegionNameLower}_${disease_name_snakecase}_total.nc",
- "raster_name_template" : "spores_per_m2_per_week_${disease_name_camelcase}",
- "shape_fn_entry" : "ShapeFilenameToAggregate",
- "shape_coln" : "admin2Name",
- "show_columns" : ["admin0Name","admin1Name"],
- "separate_rows_for_coln":"admin0Name",
- "func" : "mean",
- "multiply_by" : 1,
- "float_format" : ".1e",
- "display_format" : ".0f",
- "save_path_template" : "${jobPath}/images/deposition_${SubRegionNameLower}_${disease_name_snakecase}_mean_per_zone",
- "max_entries" : 20
- }
- },
- "Surveys" : {
- "variety_names_tidy_fn" : "${ConfigsPath}/advisory_builder/config_SouthAsia_variety_names_tidy.json",
- "CountryColumnName" : "surveyor_infromation-country",
- "SouthAsia" : {
- "CountryList" : ["Afghanistan", "Bangladesh", "Bhutan", "India", "Nepal", "Pakistan"],
- "ShapeFilenameAdmin0" : "${AssetsPath}/advisory_builder/BanNepBhu_nogaps_admin0.shp",
- "ShapeFilenameToAggregate" : "${AssetsPath}/advisory_builder/Bangladesh_Bhutan_India_Nepal_Pakistan_admin2_tidynames.shp",
- "Extent" : [60, 93, 10, 37],
- "LabelZoom" : 5
- },
- "Nepal" : {
- "ShapeFilenameAdmin1" : "${AssetsPath}/advisory_builder/Nepal_admin1_withwheat_2017-19.shp",
- "ShapeFilenameAdmin2" : "${AssetsPath}/advisory_builder/Nepal_admin2.shp",
- "ShapeFilenameToAggregate" : "${AssetsPath}/advisory_builder/Nepal_admin2.shp",
- "Extent" : [80, 88.2, 26, 30.5],
- "LabelZoom" : 7
- },
- "Bangladesh" : {
- "ShapeFilenameAdmin1" : "${AssetsPath}/advisory_builder/Bangladesh_admin1.shp",
- "ShapeFilenameAdmin2" : "${AssetsPath}/advisory_builder/Bangladesh_admin2.shp",
- "ShapeFilenameToAggregate" : "${AssetsPath}/advisory_builder/Bangladesh_admin2.shp",
- "Extent" : [88, 93, 20.5, 27],
- "LabelZoom" : 7
- },
- "Pakistan" : {
- "ShapeFilenameAdmin0" : "",
- "ShapeFilenameAdmin1" : "",
- "ShapeFilenameAdmin2" : "",
- "ShapeFilenameToAggregate" : "${AssetsPath}/advisory_builder/Pakistan_admin2_renamed.shp",
- "Extent" : [60.5, 78, 23.5, 37],
- "LabelZoom" : 7
- },
- "Bhutan" : {
- "ShapeFilenameAdmin1" : "${AssetsPath}/advisory_builder/btn_admbnda_adm1_bnlc_20201026.shp",
- "ShapeFilenameAdmin2" : "${AssetsPath}/advisory_builder/btn_admbnda_adm2_bnlc_20201026_renamed.shp",
- "ShapeFilenameToAggregate" : "${AssetsPath}/advisory_builder/btn_admbnda_adm2_bnlc_20201026_renamed.shp",
- "Extent" : [88.5, 92.5, 26.5, 28.5],
- "LabelZoom" : 7
- }
- },
- "logos" : "${AssetsPath}/advisory_builder/logos_SouthAsia_plotting.png"
-}
diff --git a/pipeline_resources/SouthAsia/configs/coordinator/fc/depo_config_SouthAsia_fc_live.json b/pipeline_resources/SouthAsia/configs/coordinator/fc/depo_config_SouthAsia_fc_live.json
deleted file mode 100755
index 68480d1bbb59dc1c54bfa715a939e950803f20b4..0000000000000000000000000000000000000000
--- a/pipeline_resources/SouthAsia/configs/coordinator/fc/depo_config_SouthAsia_fc_live.json
+++ /dev/null
@@ -1,35 +0,0 @@
-{
- "ServerPathTemplate" : "${MetoFTP}/metofficeupload/upload/SouthAsia/fromMO/daily_name/",
- "InputFileTemplate" : "WR_NAME_SouthAsia_${StartString}_fc",
- "DataFileTemplate" : "deposition_srcs_allregions_${StartString}.nc",
- "TimeExpectedAvailable" : "1000",
- "ProcessPreJob" : "process_pre_job_server_download",
- "ProcessInJob" : "process_in_job_dep",
- "ProcessEWSPlotting" : "process_EWS_plotting_dep",
- "EWS-Plotting" : {
- "SysConfig" : "${ConfigsPath}/coordinator/fc/sys_config_SouthAsia_fc_live.json",
- "NameExtractionConfig" : "${ConfigsPath}/plotting/name_extraction/NAME_EXTRACTION_CONFIG.json",
- "RunConfig" : "${ConfigsPath}/plotting/deposition/RUN_CONFIG_DEPO.json",
- "RunConfigNorm" : "${ConfigsPath}/plotting/deposition/RUN_CONFIG_DEPO_NORMALIZED.json",
- "SouthAsia" : {
- "ChartConfig" : "${ConfigsPath}/plotting/chart/CHART_CONFIG_ASIA_PINE.json",
- "Normalize" : "False"
- },
- "Bangladesh" : {
- "ChartConfig" : "${ConfigsPath}/plotting/chart/CHART_CONFIG_BANGLADESH_PINE.json",
- "Normalize" : "False"
- },
- "Nepal" : {
- "ChartConfig" : "${ConfigsPath}/plotting/chart/CHART_CONFIG_NEPAL_PINE.json",
- "Normalize" : "False"
- },
- "Pakistan" : {
- "ChartConfig" : "${ConfigsPath}/plotting/chart/CHART_CONFIG_PAKISTAN_PINE.json",
- "Normalize" : "False"
- },
- "Bhutan" : {
- "ChartConfig" : "${ConfigsPath}/plotting/chart/CHART_CONFIG_BHUTAN_PINE.json",
- "Normalize" : "False"
- }
- }
-}
diff --git a/pipeline_resources/SouthAsia/configs/coordinator/fc/env_suit_config_SouthAsia_fc_live.json b/pipeline_resources/SouthAsia/configs/coordinator/fc/env_suit_config_SouthAsia_fc_live.json
deleted file mode 100755
index 52e507770dd97153934c1b42b6f5e404035caeea..0000000000000000000000000000000000000000
--- a/pipeline_resources/SouthAsia/configs/coordinator/fc/env_suit_config_SouthAsia_fc_live.json
+++ /dev/null
@@ -1,104 +0,0 @@
-{
- "ServerPathTemplate" : "${MetoFTP}/metofficeupload/upload/SouthAsia/fromMO/daily_name/",
- "InputFileTemplate" : "WR_EnvSuit_Met_SouthAsia_${StartString}_fc",
- "ProcessPreJob" : "process_pre_job_server_download",
- "ProcessInJob" : "process_in_job_env2_0",
- "ProcessEWSPlotting" : "process_EWS_plotting_env2_0",
- "CONFIGS_PATH": "${ConfigsPath}",
- "ASSETS_PATH": "${AssetsPath}",
- "WORK_PATH" : "${WorkspacePath}",
- "INPUT_PATH" : "${WorkspacePath}",
- "OUTPUT_PATH" : "${WorkspacePath}",
- "SYS_CONFIG" : "${ConfigsPath}/met_extractor/SYS_CONFIG_PINE.json",
- "FIELD_NAME_CONSTANTS" : "${ConfigsPath}/met_extractor/FIELD_NAME_CONSTANTS.csv",
- "RUN_TYPE" : "operational",
- "EXTRACTION_DAYS": 7,
- "FORECAST_DAYS": 6,
- "STRAINS": ["LeafRust","StemRust","StripeRust","LeafRust_TempOnly","StemRust_TempOnly","StripeRust_TempOnly"],
- "PARAMS": {
- "LeafRust": {
- "suitability_modules": ["semibool_dewperiod"],
- "past_steps": 0,
- "future_steps": 2,
- "thresholds": {
- "temperature": [2,15,20,30],
- "precipitation": 0,
- "relative_humidity": 90
- }
- },
- "StemRust": {
- "suitability_modules": ["semibool_dewperiod"],
- "past_steps": 0,
- "future_steps": 2,
- "thresholds": {
- "temperature": [2,15,24,30],
- "precipitation": 0,
- "relative_humidity": 90
- }
- },
- "StripeRust": {
- "suitability_modules": ["v1_dewperiod"],
- "past_steps": 0,
- "future_steps": 7,
- "thresholds": {
- "temperature": [2.37,19.8],
- "precipitation": 0,
- "relative_humidity": 90
- }
- },
- "LeafRust_TempOnly": {
- "suitability_modules": ["semibool_dewperiod"],
- "past_steps": 0,
- "future_steps": 2,
- "thresholds": {
- "temperature": [2,15,20,30],
- "precipitation": -1,
- "relative_humidity": 90
- }
- },
- "StemRust_TempOnly": {
- "suitability_modules": ["semibool_dewperiod"],
- "past_steps": 0,
- "future_steps": 2,
- "thresholds": {
- "temperature": [2,15,24,30],
- "precipitation": -1,
- "relative_humidity": 90
- }
- },
- "StripeRust_TempOnly": {
- "suitability_modules": ["v1_dewperiod"],
- "past_steps": 0,
- "future_steps": 7,
- "thresholds": {
- "temperature": [2.37,19.8],
- "precipitation": -1,
- "relative_humidity": 90
- }
- }
- },
- "EWS-Plotting" : {
- "SysConfig" : "${ConfigsPath}/coordinator/fc/sys_config_SouthAsia_fc_live.json",
- "RunConfig" : "${ConfigsPath}/plotting/env_suit/RUN_CONFIG_ENV.json",
- "SouthAsia" : {
- "ChartConfig" : "${ConfigsPath}/plotting/chart/CHART_CONFIG_ASIA_PINE.json",
- "FilterForCountry" : "False"
- },
- "Bangladesh" : {
- "ChartConfig" : "${ConfigsPath}/plotting/chart/CHART_CONFIG_BANGLADESH_PINE.json",
- "FilterForCountry" : "True"
- },
- "Nepal" : {
- "ChartConfig" : "${ConfigsPath}/plotting/chart/CHART_CONFIG_NEPAL_PINE.json",
- "FilterForCountry" : "True"
- },
- "Pakistan" : {
- "ChartConfig" : "${ConfigsPath}/plotting/chart/CHART_CONFIG_PAKISTAN_PINE.json",
- "FilterForCountry" : "False"
- },
- "Bhutan" : {
- "ChartConfig" : "${ConfigsPath}/plotting/chart/CHART_CONFIG_BHUTAN_PINE.json",
- "FilterForCountry" : "True"
- }
- }
-}
diff --git a/pipeline_resources/SouthAsia/configs/coordinator/fc/survey_config_SouthAsia_fc_live.json b/pipeline_resources/SouthAsia/configs/coordinator/fc/survey_config_SouthAsia_fc_live.json
deleted file mode 100755
index 8f79ce077e3730e7e5df7bfecd1eefabc933b416..0000000000000000000000000000000000000000
--- a/pipeline_resources/SouthAsia/configs/coordinator/fc/survey_config_SouthAsia_fc_live.json
+++ /dev/null
@@ -1,36 +0,0 @@
-{
- "ProcessPreJob" : "process_pre_job_survey",
- "ProcessInJob" : "process_in_job_survey",
- "ProcessEWSPlotting" : "process_EWS_plotting_survey",
- "AcceptableDowntimeDays" : 21,
- "SeasonStartString" : "20231101",
- "ServerCredentialsFile" : "${ConfigsPath}/coordinator/Cred-WRT.json",
- "Groups" : {
- "PROD" : {
- "Origin" : ["CSV_01", "CSV_02", "ODK_01", "ODK_02", "CSV-CAM"],
- "site_information-survey_site" : ["Farmer", "farmer_field", "Seed_production", "Weed", "Road", "VCU", "Sentinel", "Other"]
- },
- "WRT-Publ" : {
- "Origin" : ["CSV_01", "CSV_02", "ODK_01", "ODK_02"],
- "PublishedLevel" : ["Publ"],
- "site_information-survey_site" : ["Farmer", "farmer_field", "Seed_production", "Weed", "Road", "VCU", "Sentinel", "Other"]
- },
- "Trial-sites" : {
- "Origin" : ["CSV_01", "CSV_02", "ODK_01", "ODK_02", "CSV-CAM"],
- "site_information-survey_site" : ["Trial"]
- }
- },
- "GroupBy" : ["Origin", "PublishedLevel", "site_information-survey_site"],
- "GroupsToIgnore" : ["ODK-server", "kobo-server", "newODK", "newODK2",
- "CSV-CAM", "CSV_01", "CSV_02", "ODK_01", "ODK_02",
- "Unpubl", "Publ", "Raw",
- "Farmer", "farmer_field", "Seed_production", "Weed", "Road", "Trial", "VCU", "Sentinel", "Other"],
- "ODKDatabasePathTemplate" : "${WorkspacePathout}/ODK_DB/",
- "SurveyFormat" : "ODK",
- "SurveyorNameCol" : "surveyor_infromation-surveyor_name",
- "SourcesRegionName" : "SouthAsia",
- "SourcesConfigs" : {
- "Trial-sites" : "${ConfigsPath}/source_gen/config_SouthAsia_trialplots.json"
- },
- "SourcesConfigDefault" : "${ConfigsPath}/source_gen/config_SouthAsia_mapspam2005.json"
-}
diff --git a/pipeline_resources/SouthAsia/configs/coordinator/fc/template_sys_config_SouthAsia_fc_live.json b/pipeline_resources/SouthAsia/configs/coordinator/fc/template_sys_config_SouthAsia_fc_live.json
deleted file mode 100755
index ea331962bceae1cda876f9894d92acd18770d852..0000000000000000000000000000000000000000
--- a/pipeline_resources/SouthAsia/configs/coordinator/fc/template_sys_config_SouthAsia_fc_live.json
+++ /dev/null
@@ -1,14 +0,0 @@
-{
- "RegionName" : "SouthAsia",
- "SubRegionNames" : ["SouthAsia","Nepal","Bangladesh","Pakistan","Bhutan"],
- "StartTime" : "?",
- "StartString" : "?",
- "ProjectRoot" : "<path to project root>",
- "MetoFTP" : "<path to MetoFTP>",
- "WorkspacePathout" : "${ProjectRoot}/regions/SouthAsia/workspace/",
- "WorkspacePath" : "${ProjectRoot}/regions/SouthAsia/workspace/",
- "ConfigsPath" : "/home/lb584/git/ews-coordinator/pipeline_resources/SouthAsia/configs",
- "AssetsPath" : "${ProjectRoot}/regions/SouthAsia/resources/assets",
- "LoggingConfigPath" : "${ProjectRoot}/code/coordinator/pipeline_resources/SouthAsia/configs/coordinator/log_config.json",
- "PLACES_SHAPE_FILE": "${ProjectRoot}/regions/SouthAsia/resources/assets/plotting/gis_data/common/places_shape/asia_places.shp"
- }
diff --git a/pipeline_resources/SouthAsia/configs/coordinator/log_config.json b/pipeline_resources/SouthAsia/configs/coordinator/log_config.json
deleted file mode 100644
index fb6c3a1b737294a37d789de6d142bfc599d67988..0000000000000000000000000000000000000000
--- a/pipeline_resources/SouthAsia/configs/coordinator/log_config.json
+++ /dev/null
@@ -1,68 +0,0 @@
-{
- "version": 1,
- "disable_existing_loggers": false,
- "formatters": {
- "simple": {
- "format": "%(name)s : %(levelname)s - %(message)s"
- },
- "detailed": {
- "format": "For command:\n{arg_string}\n\n%(levelname)s in %(name)s encountered at %(asctime)s:\n\n%(message)s\n\nResolve this error and restart processing.",
- "datefmt": "%Y-%m-%d %H:%M:%S"
- }
- },
- "filters": {
- "mask_passwords": {
- "()": "NOT_SET"
- }
- },
- "handlers": {
- "handler_job": {
- "class": "logging.FileHandler",
- "formatter": "simple",
- "level": "DEBUG",
- "filters": [
- "mask_passwords"
- ],
- "filename": ""
- },
- "handler_stderr": {
- "class": "logging.StreamHandler",
- "formatter": "simple",
- "level": "DEBUG",
- "filters": [
- "mask_passwords"
- ]
- },
- "handler_buffered_email": {
- "class": "BufferingSMTPHandler.BufferingSMTPHandler",
- "level": "ERROR",
- "server": "NOT_SET",
- "credentials": "NOT_SET",
- "fromaddr": "NOT_SET",
- "toaddrs": "NOT_SET",
- "subject": "ERROR in EWS Processor",
- "formatter": "detailed",
- "filters": [
- "mask_passwords"
- ],
- "capacity": 100
- }
- },
- "loggers": {
- "__main__": {
- "level": "INFO",
- "handlers": ["handler_job","handler_buffered_email","handler_stderr"],
- "propagate": false
- },
- "EpiModel": {
- "level": "INFO",
- "handlers": ["handler_job","handler_buffered_email","handler_stderr"],
- "propagate": false
- },
- "ews": {
- "level": "INFO",
- "handlers": ["handler_job","handler_buffered_email","handler_stderr"],
- "propagate": false
- }
- }
-}
\ No newline at end of file
diff --git a/pipeline_resources/SouthAsia/configs/coordinator/template_Cred-WRT.json b/pipeline_resources/SouthAsia/configs/coordinator/template_Cred-WRT.json
deleted file mode 100644
index d188d9e9cd8a364bb5be1cce3e1f58e31f4175bd..0000000000000000000000000000000000000000
--- a/pipeline_resources/SouthAsia/configs/coordinator/template_Cred-WRT.json
+++ /dev/null
@@ -1,14 +0,0 @@
-{
- "forms" : [
- {
- "type" : "WRT",
- "url" : "https://web15.agro.au.dk/",
- "user" : "",
- "pass" : "",
- "countryID" : "BD;BT;NP;PK",
- "publishedLevel" : "Publ;Unpubl",
- "form_id" : "WRT",
- "form_name" : "WRT"
- }
- ]
-}
diff --git a/pipeline_resources/SouthAsia/configs/met_extractor/FIELD_NAME_CONSTANTS.csv b/pipeline_resources/SouthAsia/configs/met_extractor/FIELD_NAME_CONSTANTS.csv
deleted file mode 100755
index 27982bad32ac58c84c50d2fc286f8c96b5ef5e2d..0000000000000000000000000000000000000000
--- a/pipeline_resources/SouthAsia/configs/met_extractor/FIELD_NAME_CONSTANTS.csv
+++ /dev/null
@@ -1,18 +0,0 @@
-ERA5,WIND,ERA5-Land-hourly-10m_u_component_of_wind,wind
-ERA5,WIND2,ERA5-Land-hourly-10m_v_component_of_wind,wind2
-ERA5,DEWPOINT,ERA5-Land-hourly-2m_dewpoint_temperature,dewpoint
-ERA5,TEMP,ERA5-Land-hourly-2m_temperature,temperature
-ERA5,RAD,ERA5-Land-hourly-surface_net_solar_radiation,radiation
-ERA5,PRESSURE,ERA5-Land-hourly-surface_pressure,pressure
-ERA5,PRECIP,ERA5-Land-hourly-total_precipitation,precipitation
-MET_OFFICE,TEMP,air_temperature-none,temperature
-MET_OFFICE,HUMIDITY,specific_humidity-level0,humidity
-MET_OFFICE,SURFACE_AIR_PRESSURE,surface_air_pressure-none,air_pressure
-MET_OFFICE,CONVECTIVE_RAINFALL,convective_rainfall_flux-none,convective_rainfall
-MET_OFFICE,STRATIFORM_RAINFALL,stratiform_rainfall_flux-none,stratiform_rainfall
-NAME,PRECIPITATION_RATE,_PRECIPITATION_RATE_(MM_HR),PRECIPITATION_RATE
-NAME,SOIL_MOISTURE,_SOIL_MOISTURE,SOIL_MOISTURE
-NAME,TOPOGRAPHY,_TOPOGRAPHY,TOPOGRAPHY
-NAME,RELATIVE_HUMIDITY,_RELATIVE_HUMIDITY_(%),RELATIVE_HUMIDITY
-NAME,TEMP,_TEMPERATURE_(C),TEMP
-NAME,SURFACE_AIR_PRESSURE,_PRESSURE_(PA),PRESSURE_PA
diff --git a/pipeline_resources/SouthAsia/configs/met_extractor/SYS_CONFIG_PINE.json b/pipeline_resources/SouthAsia/configs/met_extractor/SYS_CONFIG_PINE.json
deleted file mode 100755
index eb8f495e964a498bf8bea315716538168dd38b87..0000000000000000000000000000000000000000
--- a/pipeline_resources/SouthAsia/configs/met_extractor/SYS_CONFIG_PINE.json
+++ /dev/null
@@ -1,3 +0,0 @@
-{
- "FIELD_NAME_CONSTANTS_PATH": "../data/resources/common/field_name_constants.csv"
-}
diff --git a/pipeline_resources/SouthAsia/configs/met_extractor/template_operational_config.json b/pipeline_resources/SouthAsia/configs/met_extractor/template_operational_config.json
deleted file mode 100755
index bceeab7ad9cc062707bcd91ad6a25d4259e58f17..0000000000000000000000000000000000000000
--- a/pipeline_resources/SouthAsia/configs/met_extractor/template_operational_config.json
+++ /dev/null
@@ -1,57 +0,0 @@
-{
- "MET_DATA_TYPE": "NAME",
- "DATA_TYPES": [
- "TEMP",
- "PRECIPITATION_RATE",
- "RELATIVE_HUMIDITY"
- ],
- "METO_PARAMS": {
- "METO_PARTS": [
- "no_part"
- ]
- },
- "POST_PROCESSING": {
- "PROCESSORS": [
- {
- "PROCESSOR_NAME": "RIE",
- "OUT_FILE_NAME": "RIE",
- "CLASSPATH": "ews.environmental_suitability.ewses_vectorised_timepoint_processor",
- "CLASSNAME": "EnvSuitColTimePointProcessor",
- "DEPENDS": [],
- "TIMEPOINTS_FILE_PATH": "#",
- "FUTURE_FIELDS": [
- {
- "PROCESSOR_NAME": "TEMP",
- "DURATION": 7,
- "ENABLED": "TRUE"
- },
- {
- "PROCESSOR_NAME": "PRECIPITATION_RATE",
- "DURATION": 7,
- "ENABLED": "TRUE"
- },
- {
- "PROCESSOR_NAME": "RELATIVE_HUMIDITY",
- "DURATION": 7,
- "ENABLED": "TRUE"
- }
- ],
- "PARAMS": {
- "suitability_modules": ["#"],
- "thresholds": {
- "temperature": [2,30],
- "precipitation": 0,
- "relative_humidity": 90
- }
- }
- }
- ]
- },
- "TIMEPOINTS_FILE_PATH": "#",
- "OUTPUT_DIR": "#",
- "SPATIAL_POINTS_FILE_PATH": "#",
- "FIELD_NAME_CONSTANTS_PATH": "#",
- "NCDF_DIR_PATH": "#",
- "RECURSIVE_SEARCH": "FALSE",
- "WRITE_EXTRACTION_CSVS": "FALSE"
-}
diff --git a/pipeline_resources/SouthAsia/configs/plotting/chart/CHART_CONFIG_ASIA_PINE.json b/pipeline_resources/SouthAsia/configs/plotting/chart/CHART_CONFIG_ASIA_PINE.json
deleted file mode 100755
index 42dd0eef20c16def29f2f63965a89d949fa27dde..0000000000000000000000000000000000000000
--- a/pipeline_resources/SouthAsia/configs/plotting/chart/CHART_CONFIG_ASIA_PINE.json
+++ /dev/null
@@ -1,16 +0,0 @@
-{
- "IMAGE_WIDTH": 1700,
- "IMAGE_HEIGHT": 1285,
- "COUNTRY_EXTENTS": [55,110,7.07,37],
- "MAP_TILE": "${ProjectRoot}/regions/SouthAsia/resources/assets/plotting/gis_data/asia/asia_map_tile_water_7.tif",
- "SCALEBAR_LAT": "2",
- "SCALEBAR_TEXT": "200km",
- "LEGEND_ALPHA": 0.4,
- "TITLE_FONT_SIZE": 30,
- "COUNTRY_LANDPOINTS_FILE": "${ProjectRoot}/regions/SouthAsia/resources/assets/plotting/gis_data/asia/asia_points.csv",
- "COUNTRY_LOGO_FILE": "${ProjectRoot}/regions/SouthAsia/resources/assets/plotting/images/logos_SouthAsia_plotting.png",
- "COUNTRY_STRING": "southasia",
- "PLACES_TO_PLOT": ["CAPITAL","LARGE"],
- "PLACES_TO_EXCLUDE": ["Peshawar", "Delhi", "Amritsar"],
- "PLACES_TO_RIGHT_ALIGN": ["Bangalore", "Karachi","Kozhikode", "Jamshedpur"]
-}
diff --git a/pipeline_resources/SouthAsia/configs/plotting/chart/CHART_CONFIG_BANGLADESH_PINE.json b/pipeline_resources/SouthAsia/configs/plotting/chart/CHART_CONFIG_BANGLADESH_PINE.json
deleted file mode 100755
index 6ba443ae765e1bb6304a09f0dd01d0f69420d632..0000000000000000000000000000000000000000
--- a/pipeline_resources/SouthAsia/configs/plotting/chart/CHART_CONFIG_BANGLADESH_PINE.json
+++ /dev/null
@@ -1,18 +0,0 @@
-{
- "IMAGE_WIDTH": 1700,
- "IMAGE_HEIGHT": 1275,
- "COUNTRY_ADMIN_2_SHAPE_FILE": "${ProjectRoot}/regions/SouthAsia/resources/assets/plotting/gis_data/bangladesh/bangladesh_admin_shape/bgd_level2/Bangladesh_admin2.shp",
- "COUNTRY_ADMIN_1_SHAPE_FILE": "${ProjectRoot}/regions/SouthAsia/resources/assets/plotting/gis_data/bangladesh/bangladesh_admin_shape/bgd_level1/bgd_admbnda_adm1_bbs_20180410.shp",
- "COUNTRY_SHAPE_FILE": "${ProjectRoot}/regions/SouthAsia/resources/assets/plotting/gis_data/bangladesh/bangladesh_shape/Bangladesh_admin0.shp",
- "COUNTRY_EXTENTS": [84.15,96.04,20.42,27.00],
- "MAP_TILE": "${ProjectRoot}/regions/SouthAsia/resources/assets/plotting/gis_data/bangladesh/bangladesh_map_tile.tif",
- "SCALEBAR_LAT": "2",
- "SCALEBAR_TEXT": "200km",
- "LEGEND_ALPHA": 0.4,
- "TITLE_FONT_SIZE": 30,
- "COUNTRY_LANDPOINTS_FILE": "${ProjectRoot}/regions/SouthAsia/resources/assets/plotting/gis_data/bangladesh/bang_points.csv",
- "COUNTRY_LOGO_FILE": "${ProjectRoot}/regions/SouthAsia/resources/assets/plotting/images/logos_SouthAsia_plotting.png",
- "COUNTRY_STRING": "bangladesh",
- "PLACES_TO_PLOT": ["CAPITAL","LARGE","MEDIUM","SMALL"],
- "PLACES_X_LIMIT": 0.98
-}
diff --git a/pipeline_resources/SouthAsia/configs/plotting/chart/CHART_CONFIG_BHUTAN_PINE.json b/pipeline_resources/SouthAsia/configs/plotting/chart/CHART_CONFIG_BHUTAN_PINE.json
deleted file mode 100755
index bc01fc015580cec322d0247f6c8cc15e472cd28d..0000000000000000000000000000000000000000
--- a/pipeline_resources/SouthAsia/configs/plotting/chart/CHART_CONFIG_BHUTAN_PINE.json
+++ /dev/null
@@ -1,20 +0,0 @@
-{
- "IMAGE_WIDTH": 1700,
- "IMAGE_HEIGHT": 1050,
- "COUNTRY_ADMIN_2_SHAPE_FILE": "${ProjectRoot}/regions/SouthAsia/resources/assets/plotting/gis_data/bhutan/bhutan_admin_shape/bhutan_level2/btn_admbnda_adm2_bnlc_20201026.shp",
- "COUNTRY_ADMIN_1_SHAPE_FILE": "${ProjectRoot}/regions/SouthAsia/resources/assets/plotting/gis_data/bhutan/bhutan_admin_shape/bhutan_level1/btn_admbnda_adm1_bnlc_20201026.shp",
- "COUNTRY_SHAPE_FILE": "${ProjectRoot}/regions/SouthAsia/resources/assets/plotting/gis_data/bhutan/bhutan_admin_shape/bhutan_level0/btn_admbnda_adm0_bnlc_20201026.shp",
- "COUNTRY_EXTENTS": [88.50,93.00,26.30,28.40],
- "MAP_TILE": "${ProjectRoot}/regions/SouthAsia/resources/assets/plotting/gis_data/bhutan/asia_map_tile_water_7.tif",
- "SCALEBAR_LAT": "1",
- "SCALEBAR_TEXT": "100km",
- "LEGEND_ALPHA": 0.4,
- "TITLE_FONT_SIZE": 30,
- "COUNTRY_LANDPOINTS_FILE": "${ProjectRoot}/regions/SouthAsia/resources/assets/plotting/gis_data/bhutan/bhutan_points.csv",
- "COUNTRY_LOGO_FILE": "${ProjectRoot}/regions/SouthAsia/resources/assets/plotting/images/logos_SouthAsia_plotting.png",
- "COUNTRY_LOGO_SCALE": 0.6,
- "COUNTRY_STRING": "bhutan",
- "PLACES_TO_PLOT": ["CAPITAL","LARGE","MEDIUM","SMALL"],
- "PLACES_TO_EXCLUDE": ["Lalitpur"],
- "PLACES_X_LIMIT": 0.98
-}
diff --git a/pipeline_resources/SouthAsia/configs/plotting/chart/CHART_CONFIG_NEPAL_PINE.json b/pipeline_resources/SouthAsia/configs/plotting/chart/CHART_CONFIG_NEPAL_PINE.json
deleted file mode 100755
index 2f067285bdd9bf9f2db016d2277fafc50d80f2c3..0000000000000000000000000000000000000000
--- a/pipeline_resources/SouthAsia/configs/plotting/chart/CHART_CONFIG_NEPAL_PINE.json
+++ /dev/null
@@ -1,20 +0,0 @@
-{
- "IMAGE_WIDTH": 1700,
- "IMAGE_HEIGHT": 1075,
- "COUNTRY_ADMIN_2_SHAPE_FILE": "${ProjectRoot}/regions/SouthAsia/resources/assets/plotting/gis_data/nepal/nepal_admin_shape/nepal_level2/npl_admbnda_districts_nd_20190430.shp",
- "COUNTRY_ADMIN_1_SHAPE_FILE": "${ProjectRoot}/regions/SouthAsia/resources/assets/plotting/gis_data/nepal/nepal_admin_shape/nepal_level1/npl_admbnda_adm1_nd_20190430.shp",
- "COUNTRY_SHAPE_FILE": "${ProjectRoot}/regions/SouthAsia/resources/assets/plotting/gis_data/nepal/nepal_shape/Nepal_admin0.shp",
- "COUNTRY_EXTENTS": [77.729,91.0334,25.0629,31.0879],
- "MAP_TILE": "${ProjectRoot}/regions/SouthAsia/resources/assets/plotting/gis_data/nepal/nepal_map_tile.tif",
- "SCALEBAR_LAT": "2",
- "SCALEBAR_TEXT": "200km",
- "LEGEND_ALPHA": 0.4,
- "TITLE_FONT_SIZE": 30,
- "COUNTRY_LANDPOINTS_FILE": "${ProjectRoot}/regions/SouthAsia/resources/assets/plotting/gis_data/nepal/nepal_points.csv",
- "COUNTRY_LOGO_FILE": "${ProjectRoot}/regions/SouthAsia/resources/assets/plotting/images/logos_SouthAsia_plotting.png",
- "COUNTRY_LOGO_SCALE": 0.6,
- "COUNTRY_STRING": "nepal",
- "PLACES_TO_PLOT": ["CAPITAL","LARGE","MEDIUM","SMALL"],
- "PLACES_TO_EXCLUDE": ["Lalitpur"],
- "PLACES_X_LIMIT": 0.98
-}
diff --git a/pipeline_resources/SouthAsia/configs/plotting/chart/CHART_CONFIG_PAKISTAN_PINE.json b/pipeline_resources/SouthAsia/configs/plotting/chart/CHART_CONFIG_PAKISTAN_PINE.json
deleted file mode 100755
index 8edbc600a0e368c0ecf1426fd7927a102b626fd2..0000000000000000000000000000000000000000
--- a/pipeline_resources/SouthAsia/configs/plotting/chart/CHART_CONFIG_PAKISTAN_PINE.json
+++ /dev/null
@@ -1,17 +0,0 @@
-{
- "IMAGE_WIDTH": 1700,
- "IMAGE_HEIGHT": 1400,
- "COUNTRY_EXTENTS": [60.28,82.00,23.00,37.75],
- "MAP_TILE": "${ProjectRoot}/regions/SouthAsia/resources/assets/plotting/gis_data/pakistan/asia_map_tile_water_7.tif",
- "SCALEBAR_LAT": "2",
- "SCALEBAR_TEXT": "200km",
- "LEGEND_ALPHA": 0.4,
- "TITLE_FONT_SIZE": 30,
- "COUNTRY_LANDPOINTS_FILE": "${ProjectRoot}/regions/SouthAsia/resources/assets/plotting/gis_data/pakistan/pakistan_points.csv",
- "COUNTRY_LOGO_FILE": "${ProjectRoot}/regions/SouthAsia/resources/assets/plotting/images/logos_SouthAsia_plotting.png",
- "COUNTRY_LOGO_SCALE": 0.6,
- "COUNTRY_STRING": "pakistan",
- "PLACES_TO_PLOT": ["CAPITAL","LARGE","MEDIUM","SMALL"],
- "PLACES_TO_EXCLUDE": ["Lalitpur"],
- "PLACES_X_LIMIT": 0.98
-}
diff --git a/pipeline_resources/SouthAsia/configs/plotting/deposition/RUN_CONFIG_DEPO.json b/pipeline_resources/SouthAsia/configs/plotting/deposition/RUN_CONFIG_DEPO.json
deleted file mode 100755
index b21391d536183f06d9cd5bdebeb5b674b5f695ec..0000000000000000000000000000000000000000
--- a/pipeline_resources/SouthAsia/configs/plotting/deposition/RUN_CONFIG_DEPO.json
+++ /dev/null
@@ -1,20 +0,0 @@
-{
- "IMAGE_WIDTH": 1700,
- "IMAGE_HEIGHT": 1075,
- "WHEAT_SOURCE_INPUT_DIR_NAME": "OVERRIDDEN",
- "WHEAT_SOURCE_DISEASE_NAME": "OVERRIDDEN",
- "OUTPUT_DIR": "OVERRIDDEN",
- "ISSUE_DATE": "OVERRIDDEN",
- "CBAR_VALUES": [0, 1, 100, 1000, 10000, 100000, 1000000],
- "CBAR_LABELS": ["0", "1", "100", "1000", "$10^{4}$", "$10^{5}$", "$10^{6}$"],
- "CBAR_COLORS": ["darkgrey", "#e6e680","#e6bf19","#e68000","#993380","#4c26bf"],
- "MAP_TITLE": "OVERRIDDEN",
- "RUN_PREFIX": "OVERRIDDEN",
- "LEGEND_TITLE": "Fraction of\ndeposited spores",
- "PLOT_SHAPES": "false",
- "PLOT_TIFS": "true",
- "PLOT_IMAGES": "true",
- "PLOT_DAILY_IMAGES": "false",
- "PLOT_HOURLY_IMAGES": "false",
- "OVERWRITE_MODE": "false"
-}
diff --git a/pipeline_resources/SouthAsia/configs/plotting/deposition/RUN_CONFIG_DEPO_NORMALIZED.json b/pipeline_resources/SouthAsia/configs/plotting/deposition/RUN_CONFIG_DEPO_NORMALIZED.json
deleted file mode 100755
index 291692b15f62771479a0a68c3d195f8eedb492b1..0000000000000000000000000000000000000000
--- a/pipeline_resources/SouthAsia/configs/plotting/deposition/RUN_CONFIG_DEPO_NORMALIZED.json
+++ /dev/null
@@ -1,21 +0,0 @@
-{
- "IMAGE_WIDTH": 1700,
- "IMAGE_HEIGHT": 1075,
- "WHEAT_SOURCE_INPUT_DIR_NAME": "OVERRIDDEN",
- "WHEAT_SOURCE_DISEASE_NAME": "OVERRIDDEN",
- "OUTPUT_DIR": "OVERRIDDEN",
- "ISSUE_DATE": "OVERRIDDEN",
- "CBAR_VALUES": [0, 0.95, 0.99, 1, 1.1],
- "CBAR_LABEL_LOCATIONS": [0.47, 0.97, 0.995, 1.05],
- "CBAR_LABELS": ["0","0.95", "0.99", "1"],
- "CBAR_COLORS": ["darkgrey", "#993380","#e68000","#e6bf19"],
- "MAP_TITLE": "OVERRIDDEN",
- "RUN_PREFIX": "OVERRIDDEN",
- "LEGEND_TITLE": "Fraction of\ndeposited spores",
- "PLOT_SHAPES": "false",
- "PLOT_TIFS": "true",
- "PLOT_IMAGES": "true",
- "PLOT_DAILY_IMAGES": "false",
- "PLOT_HOURLY_IMAGES": "false",
- "OVERWRITE_MODE": "false"
-}
diff --git a/pipeline_resources/SouthAsia/configs/plotting/env_suit/RUN_CONFIG_ENV.json b/pipeline_resources/SouthAsia/configs/plotting/env_suit/RUN_CONFIG_ENV.json
deleted file mode 100755
index fa164e438614809ddd18c94e5363bdedb9b817d5..0000000000000000000000000000000000000000
--- a/pipeline_resources/SouthAsia/configs/plotting/env_suit/RUN_CONFIG_ENV.json
+++ /dev/null
@@ -1,18 +0,0 @@
-{
- "INPUT_CSV": "OVERRIDDEN",
- "OUTPUT_DIR": "OVERRIDDEN",
- "ISSUE_DATE": "OVERRIDDEN",
- "CBAR_VALUES": [0, 0.01, 0.2, 0.4, 0.6, 0.8, 0.99, 1.0],
- "CBAR_LABELS": ["0", "1", "20", "40", "60", "80", "99","100"],
- "CBAR_COLORS": ["#818181", "#FFFFCC", "#7FCDBB", "#2C7FB8", "#253494", "#4B0082", "#000000"],
- "MAP_TITLE": "OVERRIDDEN",
- "RUN_PREFIX": "OVERRIDDEN",
- "LEGEND_TITLE": "relative infection\nefficiency %",
- "PLOT_SHAPES": "false",
- "PLOT_TIFSS": "true",
- "PLOT_IMAGES": "true",
- "PLOT_DAILY_IMAGES": "false",
- "PLOT_HOURLY_IMAGES": "false",
- "FILTER_FOR_COUNTRY": "true",
- "OVERWRITE_MODE": "true"
-}
diff --git a/pipeline_resources/SouthAsia/configs/plotting/epi/RUN_CONFIG_EPI.json b/pipeline_resources/SouthAsia/configs/plotting/epi/RUN_CONFIG_EPI.json
deleted file mode 100755
index fbaaebc4a72463c44755ec2f9b40b12051b6988a..0000000000000000000000000000000000000000
--- a/pipeline_resources/SouthAsia/configs/plotting/epi/RUN_CONFIG_EPI.json
+++ /dev/null
@@ -1,19 +0,0 @@
-{
- "IMAGE_WIDTH": 1700,
- "IMAGE_HEIGHT": 1075,
- "WHEAT_SOURCE_INPUT_DIR_NAME": "OVERRIDDEN",
- "WHEAT_SOURCE_DISEASE_NAME": "OVERRIDDEN",
- "INPUT_CSV": "OVERRIDDEN",
- "OUTPUT_DIR": "OVERRIDDEN",
- "ISSUE_DATE": "OVERRIDDEN",
- "CBAR_VALUES": [0,0.1,0.3,0.5,0.6,0.9,1.0,1e+20],
- "CBAR_LABELS": ["0","0.1","0.3","0.5","0.7","0.9","1.0",""],
- "CBAR_COLORS": ["darkgrey", "#e6e680","#e6bf19","#e68000","#993380","#4c26bf","#000000"],
- "MAP_TITLE": "OVERRIDDEN",
- "RUN_PREFIX": "OVERRIDDEN",
- "LEGEND_TITLE": "Infectious\nspore index",
- "PLOT_DAILY_IMAGES": "true",
- "PLOT_HOURLY_IMAGES": "false",
- "FILTER_FOR_COUNTRY": "true",
- "OVERWRITE_MODE": "true"
-}
diff --git a/pipeline_resources/SouthAsia/configs/plotting/epi/RUN_CONFIG_EPI_seasonaccum.json b/pipeline_resources/SouthAsia/configs/plotting/epi/RUN_CONFIG_EPI_seasonaccum.json
deleted file mode 100755
index 9d936462b0cd4e2ddb720b065bb6d6e060e653ce..0000000000000000000000000000000000000000
--- a/pipeline_resources/SouthAsia/configs/plotting/epi/RUN_CONFIG_EPI_seasonaccum.json
+++ /dev/null
@@ -1,19 +0,0 @@
-{
- "IMAGE_WIDTH": 1700,
- "IMAGE_HEIGHT": 1075,
- "WHEAT_SOURCE_INPUT_DIR_NAME": "OVERRIDDEN",
- "WHEAT_SOURCE_DISEASE_NAME": "OVERRIDDEN",
- "INPUT_CSV": "OVERRIDDEN",
- "OUTPUT_DIR": "OVERRIDDEN",
- "ISSUE_DATE": "OVERRIDDEN",
- "CBAR_VALUES": [0,0.001,0.005,0.01,0.05,0.1,0.5,1e+20],
- "CBAR_LABELS": ["0","0.001","0.005","0.01","0.05","0.1","0.5",""],
- "CBAR_COLORS": ["darkgrey", "#e6e680","#e6bf19","#e68000","#993380","#4c26bf","#000000"],
- "MAP_TITLE": "OVERRIDDEN",
- "RUN_PREFIX": "OVERRIDDEN",
- "LEGEND_TITLE": "Increase in\ninfected fraction",
- "PLOT_DAILY_IMAGES": "true",
- "PLOT_HOURLY_IMAGES": "false",
- "FILTER_FOR_COUNTRY": "true",
- "OVERWRITE_MODE": "true"
-}
diff --git a/pipeline_resources/SouthAsia/configs/plotting/epi/RUN_CONFIG_EPI_weekahead.json b/pipeline_resources/SouthAsia/configs/plotting/epi/RUN_CONFIG_EPI_weekahead.json
deleted file mode 100755
index 9d936462b0cd4e2ddb720b065bb6d6e060e653ce..0000000000000000000000000000000000000000
--- a/pipeline_resources/SouthAsia/configs/plotting/epi/RUN_CONFIG_EPI_weekahead.json
+++ /dev/null
@@ -1,19 +0,0 @@
-{
- "IMAGE_WIDTH": 1700,
- "IMAGE_HEIGHT": 1075,
- "WHEAT_SOURCE_INPUT_DIR_NAME": "OVERRIDDEN",
- "WHEAT_SOURCE_DISEASE_NAME": "OVERRIDDEN",
- "INPUT_CSV": "OVERRIDDEN",
- "OUTPUT_DIR": "OVERRIDDEN",
- "ISSUE_DATE": "OVERRIDDEN",
- "CBAR_VALUES": [0,0.001,0.005,0.01,0.05,0.1,0.5,1e+20],
- "CBAR_LABELS": ["0","0.001","0.005","0.01","0.05","0.1","0.5",""],
- "CBAR_COLORS": ["darkgrey", "#e6e680","#e6bf19","#e68000","#993380","#4c26bf","#000000"],
- "MAP_TITLE": "OVERRIDDEN",
- "RUN_PREFIX": "OVERRIDDEN",
- "LEGEND_TITLE": "Increase in\ninfected fraction",
- "PLOT_DAILY_IMAGES": "true",
- "PLOT_HOURLY_IMAGES": "false",
- "FILTER_FOR_COUNTRY": "true",
- "OVERWRITE_MODE": "true"
-}
diff --git a/pipeline_resources/SouthAsia/configs/plotting/name_extraction/NAME_EXTRACTION_CONFIG.json b/pipeline_resources/SouthAsia/configs/plotting/name_extraction/NAME_EXTRACTION_CONFIG.json
deleted file mode 100755
index 646807c060e7e651f5ff42b05125bc1c92b7433f..0000000000000000000000000000000000000000
--- a/pipeline_resources/SouthAsia/configs/plotting/name_extraction/NAME_EXTRACTION_CONFIG.json
+++ /dev/null
@@ -1,8 +0,0 @@
-{
- "NAME_FILE_WILDCARD": "OVERRIDDEN",
- "OUTPUT_DIR": "OVERRIDDEN",
- "NORMALIZE": "true",
- "ISSUE_DATE": "OVERRIDDEN",
- "EXTRACTION_FILE_OUTPUT_PREFIX": "OVERRIDDEN",
- "OVERWRITE_MODE": "false"
-}
diff --git a/pipeline_resources/SouthAsia/configs/source_gen/config_SouthAsia_mapspam2005.json b/pipeline_resources/SouthAsia/configs/source_gen/config_SouthAsia_mapspam2005.json
deleted file mode 100755
index a7eacba7670d4a83fb7dd5984174f444112c3eb4..0000000000000000000000000000000000000000
--- a/pipeline_resources/SouthAsia/configs/source_gen/config_SouthAsia_mapspam2005.json
+++ /dev/null
@@ -1,13 +0,0 @@
-{
- "config_name" : "SouthAsia",
- "wheat_source_name" : "MAPSPAM2005",
- "wheat_file" : "NA",
- "wheat_rasters_bydate" : {
- "20050101" : "${AssetsPath}/source_gen/SPAM2005V3r2_global_A_TA_WHEA_A_clipSouthAsia.tif"
- },
- "cluster_poly_file" : "${AssetsPath}/source_gen/UMG_Mk11_grid_SouthAsia_withregions.shp",
- "id_col" : "cluster_id",
- "region_file" : "${AssetsPath}/source_gen/UMG_Mk11_grid_SouthAsia_withregions.shp",
- "region_id_col" : "REGION_ID",
- "wheat_stages_file" : "${AssetsPath}/source_gen/approx_growth_timing_cleaned.csv"
-}
diff --git a/pipeline_resources/SouthAsia/configs/source_gen/config_SouthAsia_trialplots.json b/pipeline_resources/SouthAsia/configs/source_gen/config_SouthAsia_trialplots.json
deleted file mode 100755
index 7207d86a39b197f221fc7a31b9999d68d27f270e..0000000000000000000000000000000000000000
--- a/pipeline_resources/SouthAsia/configs/source_gen/config_SouthAsia_trialplots.json
+++ /dev/null
@@ -1,13 +0,0 @@
-{
- "config_name" : "SouthAsia",
- "wheat_source_name" : "trialplots_fix5m2",
- "wheat_file" : "NA",
- "wheat_rasters_bydate" : {},
- "field_area_na_replacement" : 0.0005,
- "survey_area_overwrite" : true,
- "cluster_poly_file" : "${AssetsPath}/source_gen/UMG_Mk11_grid_SouthAsia_withregions.shp",
- "id_col" : "cluster_id",
- "region_file" : "${AssetsPath}/source_gen/UMG_Mk11_grid_SouthAsia_withregions.shp",
- "region_id_col" : "REGION_ID",
- "wheat_stages_file" : "${AssetsPath}/source_gen/approx_growth_timing_cleaned.csv"
-}