aggregationModuleCDB/finalAgg.R
In SWS-Methodology/faoswsFisheryStandardization: Package to compute Fishery FBS
## load the library
library(faosws)
library(faoswsUtil)
library(data.table)
#-- Token QA ----
if(CheckDebug()){
library(faoswsModules)
SETTINGS = ReadSettings("sws.yml")
## If you're not on the system, your settings will overwrite any others
R_SWS_SHARE_PATH = SETTINGS[["share"]]
## Define where your certificates are stored
SetClientFiles(SETTINGS[["certdir"]])
## Get session information from SWS. Token must be obtained from web interface
GetTestEnvironment(baseUrl = SETTINGS[["server"]],
token = '27ded447-71ec-413b-bcd4-87669ac20c70')
}
message('CDB aggregation : getting parameters')
sessionKey_CDB = swsContext.datasets[[1]]
sessionCountry0 <- swsContext.datasets[[1]]@dimensions$geographicAreaM49_fi@keys
sessionISSCFC0 <- swsContext.datasets[[1]]@dimensions$measuredItemISSCFC@keys
sessionElement <- swsContext.datasets[[1]]@dimensions$measuredElement@keys
region_level <- swsContext.computationParams$region_level # World, continent, regions
group_level <- swsContext.computationParams$group_level # lev 3, lev 2, lev 1, grandtotal
min_year <- swsContext.computationParams$min_year
max_year <- swsContext.computationParams$max_year
sel_years <- as.character(min_year:max_year)
message('CDB aggregation : loading datatables')
country2cont <- ReadDatatable('fi_commodity_aggregates_geo')
if(region_level %in% c('World', 'All')){
M49 <- GetCodeList("FisheriesCommodities", "commodities_total","geographicAreaM49_fi" )[type == 'country',code]
sessionCountry <- M49
} else if(region_level == 'Continent'){
continents <- unique(country2cont[un_codecountry %in% sessionCountry0]$un_code)
sessionCountry <- country2cont[un_code %in% continents]$un_codecountry
} else if(region_level == 'Region'){
regions <- unique(country2cont[un_codecountry %in% sessionCountry0]$un_codereg)
sessionCountry <- country2cont[un_codereg %in% regions]$un_codecountry
} else if(region_level == 'None'){
sessionCountry <- sessionCountry0
}
isscfc2fao <- ReadDatatable('fi_commodity_aggregates_comm')
if(group_level %in% c('Grandtotal', 'All')){
sessionISSCFC <- GetCodeList("FisheriesCommodities", "commodities_total","measuredItemISSCFC" )[,code]
} else if(group_level == 'Level 1'){
l1 <- unique(isscfc2fao[code %in% sessionISSCFC0]$fao_code)
sessionISSCFC <- isscfc2fao[fao_code %in% l1]$code
} else if(group_level == 'Level 2'){
l2 <- unique(isscfc2fao[code %in% sessionISSCFC0]$fao_codel2)
sessionISSCFC <- isscfc2fao[fao_codel2 %in% l2]$code
} else if(group_level == 'Level 3'){
l3 <- unique(isscfc2fao[code %in% sessionISSCFC0]$fao_codel3)
sessionISSCFC <- isscfc2fao[fao_codel3 %in% l3]$code
} else if(group_level == 'None'){
sessionISSCFC <- sessionISSCFC0
}
sessionCountry <- sessionCountry[sessionCountry != 680 ]
print(sessionCountry)
print(sessionISSCFC)
#-- Pulling data from Commodites dataset") ----
message('CDB aggregation : loading dataset')
commodityDB0 <- data.table()
for(i in 1:length(sessionCountry)){
KeyComm <- DatasetKey(domain = "Fisheries Commodities", dataset = "commodities_total", dimensions = list(
geographicAreaM49_fi = Dimension(name = "geographicAreaM49_fi", keys = sessionCountry[i]),
measuredItemISSCFC = Dimension(name = "measuredItemISSCFC", keys = sessionISSCFC),
measuredElement = Dimension(name = "measuredElement", keys = sessionElement),
timePointYears = Dimension(name = "timePointYears", keys = sel_years)))
commodityDBchunk <- GetData(KeyComm)
commodityDB0 <- rbind(commodityDB0, commodityDBchunk)
print(i)
}
commodityDB <- copy(commodityDB0)
commodityDB$flagObservationStatus <- factor(commodityDB$flagObservationStatus,
levels = c('M', 'O', 'N', '', 'X', 'T', 'E', 'I'),
ordered = TRUE)
#-- Geographical aggregates ----
message('CDB aggregation : geographical aggregation.')
if(region_level == 'World'){
commodityDBW <- copy(commodityDB)
commodityGeo <- commodityDBW[ , c('geo', 'Value',
'flagObservationStatus',
'flagMethod') := list('1', sum(Value, na.rm = TRUE),
max(flagObservationStatus),
'x'),
by = c('measuredItemISSCFC',
'measuredElement',
'timePointYears')]
commodityGeo[ , geographicAreaM49_fi := NULL]
setnames(commodityGeo, 'geo', 'geographicAreaM49_fi')
} else if(region_level == 'Continent'){
commodityDBC <- copy(commodityDB)
commodityGeo <- merge(commodityDBC, country2cont[start_year < max_year & end_year > min_year,
.(un_code, un_codecountry)],
by.x = 'geographicAreaM49_fi', by.y = 'un_codecountry')
commodityGeo <- commodityGeo[ , c('Value', 'flagObservationStatus',
'flagMethod') := list(sum(Value, na.rm = TRUE),
max(flagObservationStatus),
'x'),
by = c('un_code', 'measuredItemISSCFC',
'measuredElement',
'timePointYears')]
commodityGeo[ , geographicAreaM49_fi := NULL]
setnames(commodityGeo, 'un_code', 'geographicAreaM49_fi')
} else if(region_level == 'Region'){
commodityDBR <- copy(commodityDB)
commodityGeo <- merge(commodityDBR, country2cont[start_year < max_year & end_year > min_year,
.(un_codereg, un_codecountry)],
by.x = 'geographicAreaM49_fi', by.y = 'un_codecountry')
commodityGeo <- commodityGeo[ , c('Value', 'flagObservationStatus',
'flagMethod') := list(sum(Value, na.rm = TRUE),
max(flagObservationStatus),
'x'),
by = c('un_codereg', 'measuredItemISSCFC',
'measuredElement',
'timePointYears')]
commodityGeo[ , geographicAreaM49_fi := NULL]
setnames(commodityGeo, 'un_codereg', 'geographicAreaM49_fi')
} else if(region_level == 'All') {
# World
commodityDBW <- copy(commodityDB)
commodityGeo1 <- commodityDBW[ , c('geo', 'Value',
'flagObservationStatus',
'flagMethod') := list('1', sum(Value, na.rm = TRUE),
max(flagObservationStatus),
'x'),
by = c('measuredItemISSCFC',
'measuredElement',
'timePointYears')]
commodityGeo1[ , geographicAreaM49_fi := NULL]
setnames(commodityGeo1, 'geo', 'geographicAreaM49_fi')
# Continent
commodityDBC <- copy(commodityDB)
commodityGeo2 <- merge(commodityDBC, country2cont[start_year < max_year & end_year > min_year,
.(un_code, un_codecountry)],
by.x = 'geographicAreaM49_fi', by.y = 'un_codecountry')
commodityGeo2 <- commodityGeo2[ , c('Value', 'flagObservationStatus',
'flagMethod') := list(sum(Value, na.rm = TRUE),
max(flagObservationStatus),
'x'),
by = c('un_code', 'measuredItemISSCFC',
'measuredElement',
'timePointYears')]
commodityGeo2[ , geographicAreaM49_fi := NULL]
setnames(commodityGeo2, 'un_code', 'geographicAreaM49_fi')
# Region
commodityDBR <- copy(commodityDB)
commodityGeo3 <- merge(commodityDBR, country2cont[start_year < max_year & end_year > min_year,
.(un_codereg, un_codecountry)],
by.x = 'geographicAreaM49_fi', by.y = 'un_codecountry')
commodityGeo3 <- commodityGeo3[ , c('Value', 'flagObservationStatus',
'flagMethod') := list(sum(Value, na.rm = TRUE),
max(flagObservationStatus),
'x'),
by = c('un_codereg', 'measuredItemISSCFC',
'measuredElement',
'timePointYears')]
commodityGeo3[ , geographicAreaM49_fi := NULL]
setnames(commodityGeo3, 'un_codereg', 'geographicAreaM49_fi')
# All
commodityGeo <- rbind(commodityGeo1, commodityGeo2)
commodityGeo <- rbind(commodityGeo, commodityGeo3)
} else if(region_level == 'None'){
commodityGeo <- commodityDB
}
setkey(commodityGeo)
commodityGeo <- unique(commodityGeo)
# if(any(sessionCountry0 != sessionCountry)){
#
# sepGeo <- commodityDB[geographicAreaM49_fi %in% sessionCountry0 ]
# commodityGeo <- rbind(commodityGeo, sepGeo)
#
# }
print(commodityGeo)
#-- Commodities aggregates ----
message('CDB aggregation : commodity aggregation.')
if(group_level == 'Grandtotal'){
commodityGeoG <- copy(commodityGeo)
commodityAgg <- commodityGeoG[ , c('isscfc', 'Value',
'flagObservationStatus',
'flagMethod') := list('FAOCLASSIFICATION',
sum(Value, na.rm = TRUE),
max(flagObservationStatus),
'x'),
by = c('geographicAreaM49_fi',
'measuredElement',
'timePointYears')]
commodityAgg[ , measuredItemISSCFC := NULL]
setnames(commodityAgg, 'isscfc', 'measuredItemISSCFC')
} else if(group_level == 'Level 1'){
commodityGeoL1 <- copy(commodityGeo)
commodityAgg <- merge(commodityGeoL1, isscfc2fao[ , .(fao_code, code)],
by.x = 'measuredItemISSCFC', by.y = 'code')
commodityAgg <- commodityAgg[ , c('Value', 'flagObservationStatus',
'flagMethod') := list(sum(Value, na.rm = TRUE),
max(flagObservationStatus),
'x'),
by = c('geographicAreaM49_fi',
'fao_code',
'measuredElement',
'timePointYears')]
commodityAgg[ , measuredItemISSCFC := NULL]
setnames(commodityAgg, 'fao_code', 'measuredItemISSCFC')
} else if(group_level == 'Level 2'){
commodityGeoL2 <- copy(commodityGeo)
commodityAgg <- merge(commodityGeoL2, isscfc2fao[ , .(fao_codel2, code)],
by.x = 'measuredItemISSCFC', by.y = 'code')
commodityAgg <- commodityAgg[ , c('Value', 'flagObservationStatus',
'flagMethod') := list(sum(Value, na.rm = TRUE),
max(flagObservationStatus),
'x'),
by = c('geographicAreaM49_fi',
'fao_codel2',
'measuredElement',
'timePointYears')]
commodityAgg[ , measuredItemISSCFC := NULL]
setnames(commodityAgg, 'fao_codel2', 'measuredItemISSCFC')
} else if(group_level == 'Level 3'){
commodityGeoL3 <- copy(commodityGeo)
commodityAgg <- merge(commodityGeoL3, isscfc2fao[ , .(fao_codel3, code)],
by.x = 'measuredItemISSCFC', by.y = 'code')
commodityAgg <- commodityAgg[ , c('Value', 'flagObservationStatus',
'flagMethod') := list(sum(Value, na.rm = TRUE),
max(flagObservationStatus),
'x'),
by = c('geographicAreaM49_fi',
'fao_codel3',
'measuredElement',
'timePointYears')]
commodityAgg[ , measuredItemISSCFC := NULL]
setnames(commodityAgg, 'fao_codel3', 'measuredItemISSCFC')
} else if(group_level == 'All') {
# Grandtotal
commodityGeoG <- copy(commodityGeo)
commodityAgg1 <- commodityGeoG[ , c('isscfc', 'Value',
'flagObservationStatus',
'flagMethod') := list('FAOCLASSIFICATION',
sum(Value, na.rm = TRUE),
max(flagObservationStatus),
'x'),
by = c('geographicAreaM49_fi',
'measuredElement',
'timePointYears')]
commodityAgg1[ , measuredItemISSCFC := NULL]
setnames(commodityAgg1, 'isscfc', 'measuredItemISSCFC')
# Level 1
commodityGeoL1 <- copy(commodityGeo)
commodityAgg2 <- merge(commodityGeoL1, isscfc2fao[ , .(fao_code, code)],
by.x = 'measuredItemISSCFC', by.y = 'code')
commodityAgg2 <- commodityAgg2[ , c('Value', 'flagObservationStatus',
'flagMethod') := list(sum(Value, na.rm = TRUE),
max(flagObservationStatus),
'x'),
by = c('geographicAreaM49_fi',
'fao_code',
'measuredElement',
'timePointYears')]
commodityAgg2[ , measuredItemISSCFC := NULL]
setnames(commodityAgg2, 'fao_code', 'measuredItemISSCFC')
# Level 2
commodityGeoL2 <- copy(commodityGeo)
commodityAgg3 <- merge(commodityGeoL2, isscfc2fao[ , .(fao_codel2, code)],
by.x = 'measuredItemISSCFC', by.y = 'code')
commodityAgg3 <- commodityAgg3[ , c('Value', 'flagObservationStatus',
'flagMethod') := list(sum(Value, na.rm = TRUE),
max(flagObservationStatus),
'x'),
by = c('geographicAreaM49_fi',
'fao_codel2',
'measuredElement',
'timePointYears')]
commodityAgg3[ , measuredItemISSCFC := NULL]
setnames(commodityAgg3, 'fao_codel2', 'measuredItemISSCFC')
# Level 3
commodityGeoL3 <- copy(commodityGeo)
commodityAgg4 <- merge(commodityGeoL3, isscfc2fao[ , .(fao_codel3, code)],
by.x = 'measuredItemISSCFC', by.y = 'code')
commodityAgg4 <- commodityAgg4[ , c('Value', 'flagObservationStatus',
'flagMethod') := list(sum(Value, na.rm = TRUE),
max(flagObservationStatus),
'x'),
by = c('geographicAreaM49_fi',
'fao_codel3',
'measuredElement',
'timePointYears')]
commodityAgg4[ , measuredItemISSCFC := NULL]
setnames(commodityAgg4, 'fao_codel3', 'measuredItemISSCFC')
# All
commodityAgg <- rbind(commodityAgg1, commodityAgg2)
commodityAgg <- rbind(commodityAgg, commodityAgg3)
commodityAgg <- rbind(commodityAgg, commodityAgg4)
} else if(group_level == 'None'){
commodityAgg <- commodityGeo
}
setkey(commodityAgg)
commodityAgg <- unique(commodityAgg)
print(commodityAgg)
# if(any(sessionISSCFC0 != sessionISSCFC)){
#
# sepComm <- commodityGeo[measuredItemISSCFC %in% sessionISSCFC0]
#
# commodityAgg <- rbind(commodityAgg, sepComm)
#
# }
message('CDB aggregation : saving data.')
CONFIG <- GetDatasetConfig(sessionKey_CDB@domain, sessionKey_CDB@dataset)
stats <- SaveData(domain = CONFIG$domain,
dataset = CONFIG$dataset,
data = commodityAgg,
waitTimeout = Inf)
##-- send Email with notification of correct execution ----
## Initiate email
from = "sws@fao.org"
to = swsContext.userEmail
subject = "Aggregation plug-in has correctly run"
body = paste("The plug-in has saved the data in your sessions.
Please note these results cannot be saved in the dataset as they are aggregates linked to virtual SWS codes.
Best regards.")
sendmailR::sendmail(from = from, to = to, subject = subject, msg = body)
paste0("Email sent to ", swsContext.userEmail)
msg <- paste0("Aggregation process completed successfully! ",
stats$inserted, " observations written, ",
stats$ignored, " weren't updated, ",
stats$discarded, " had problems.")
SWS-Methodology/faoswsFisheryStandardization documentation built on July 3, 2022, 6:11 p.m.
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## load the library
library(faosws)
library(faoswsUtil)
library(data.table)
#-- Token QA ----
if(CheckDebug()){
library(faoswsModules)
SETTINGS = ReadSettings("sws.yml")
## If you're not on the system, your settings will overwrite any others
R_SWS_SHARE_PATH = SETTINGS[["share"]]
## Define where your certificates are stored
SetClientFiles(SETTINGS[["certdir"]])
## Get session information from SWS. Token must be obtained from web interface
GetTestEnvironment(baseUrl = SETTINGS[["server"]],
token = '27ded447-71ec-413b-bcd4-87669ac20c70')
}
message('CDB aggregation : getting parameters')
sessionKey_CDB = swsContext.datasets[[1]]
sessionCountry0 <- swsContext.datasets[[1]]@dimensions$geographicAreaM49_fi@keys
sessionISSCFC0 <- swsContext.datasets[[1]]@dimensions$measuredItemISSCFC@keys
sessionElement <- swsContext.datasets[[1]]@dimensions$measuredElement@keys
region_level <- swsContext.computationParams$region_level # World, continent, regions
group_level <- swsContext.computationParams$group_level # lev 3, lev 2, lev 1, grandtotal
min_year <- swsContext.computationParams$min_year
max_year <- swsContext.computationParams$max_year
sel_years <- as.character(min_year:max_year)
message('CDB aggregation : loading datatables')
country2cont <- ReadDatatable('fi_commodity_aggregates_geo')
if(region_level %in% c('World', 'All')){
M49 <- GetCodeList("FisheriesCommodities", "commodities_total","geographicAreaM49_fi" )[type == 'country',code]
sessionCountry <- M49
} else if(region_level == 'Continent'){
continents <- unique(country2cont[un_codecountry %in% sessionCountry0]$un_code)
sessionCountry <- country2cont[un_code %in% continents]$un_codecountry
} else if(region_level == 'Region'){
regions <- unique(country2cont[un_codecountry %in% sessionCountry0]$un_codereg)
sessionCountry <- country2cont[un_codereg %in% regions]$un_codecountry
} else if(region_level == 'None'){
sessionCountry <- sessionCountry0
}
isscfc2fao <- ReadDatatable('fi_commodity_aggregates_comm')
if(group_level %in% c('Grandtotal', 'All')){
sessionISSCFC <- GetCodeList("FisheriesCommodities", "commodities_total","measuredItemISSCFC" )[,code]
} else if(group_level == 'Level 1'){
l1 <- unique(isscfc2fao[code %in% sessionISSCFC0]$fao_code)
sessionISSCFC <- isscfc2fao[fao_code %in% l1]$code
} else if(group_level == 'Level 2'){
l2 <- unique(isscfc2fao[code %in% sessionISSCFC0]$fao_codel2)
sessionISSCFC <- isscfc2fao[fao_codel2 %in% l2]$code
} else if(group_level == 'Level 3'){
l3 <- unique(isscfc2fao[code %in% sessionISSCFC0]$fao_codel3)
sessionISSCFC <- isscfc2fao[fao_codel3 %in% l3]$code
} else if(group_level == 'None'){
sessionISSCFC <- sessionISSCFC0
}
sessionCountry <- sessionCountry[sessionCountry != 680 ]
print(sessionCountry)
print(sessionISSCFC)
#-- Pulling data from Commodites dataset") ----
message('CDB aggregation : loading dataset')
commodityDB0 <- data.table()
for(i in 1:length(sessionCountry)){
KeyComm <- DatasetKey(domain = "Fisheries Commodities", dataset = "commodities_total", dimensions = list(
geographicAreaM49_fi = Dimension(name = "geographicAreaM49_fi", keys = sessionCountry[i]),
measuredItemISSCFC = Dimension(name = "measuredItemISSCFC", keys = sessionISSCFC),
measuredElement = Dimension(name = "measuredElement", keys = sessionElement),
timePointYears = Dimension(name = "timePointYears", keys = sel_years)))
commodityDBchunk <- GetData(KeyComm)
commodityDB0 <- rbind(commodityDB0, commodityDBchunk)
print(i)
}
commodityDB <- copy(commodityDB0)
commodityDB$flagObservationStatus <- factor(commodityDB$flagObservationStatus,
levels = c('M', 'O', 'N', '', 'X', 'T', 'E', 'I'),
ordered = TRUE)
#-- Geographical aggregates ----
message('CDB aggregation : geographical aggregation.')
if(region_level == 'World'){
commodityDBW <- copy(commodityDB)
commodityGeo <- commodityDBW[ , c('geo', 'Value',
'flagObservationStatus',
'flagMethod') := list('1', sum(Value, na.rm = TRUE),
max(flagObservationStatus),
'x'),
by = c('measuredItemISSCFC',
'measuredElement',
'timePointYears')]
commodityGeo[ , geographicAreaM49_fi := NULL]
setnames(commodityGeo, 'geo', 'geographicAreaM49_fi')
} else if(region_level == 'Continent'){
commodityDBC <- copy(commodityDB)
commodityGeo <- merge(commodityDBC, country2cont[start_year < max_year & end_year > min_year,
.(un_code, un_codecountry)],
by.x = 'geographicAreaM49_fi', by.y = 'un_codecountry')
commodityGeo <- commodityGeo[ , c('Value', 'flagObservationStatus',
'flagMethod') := list(sum(Value, na.rm = TRUE),
max(flagObservationStatus),
'x'),
by = c('un_code', 'measuredItemISSCFC',
'measuredElement',
'timePointYears')]
commodityGeo[ , geographicAreaM49_fi := NULL]
setnames(commodityGeo, 'un_code', 'geographicAreaM49_fi')
} else if(region_level == 'Region'){
commodityDBR <- copy(commodityDB)
commodityGeo <- merge(commodityDBR, country2cont[start_year < max_year & end_year > min_year,
.(un_codereg, un_codecountry)],
by.x = 'geographicAreaM49_fi', by.y = 'un_codecountry')
commodityGeo <- commodityGeo[ , c('Value', 'flagObservationStatus',
'flagMethod') := list(sum(Value, na.rm = TRUE),
max(flagObservationStatus),
'x'),
by = c('un_codereg', 'measuredItemISSCFC',
'measuredElement',
'timePointYears')]
commodityGeo[ , geographicAreaM49_fi := NULL]
setnames(commodityGeo, 'un_codereg', 'geographicAreaM49_fi')
} else if(region_level == 'All') {
# World
commodityDBW <- copy(commodityDB)
commodityGeo1 <- commodityDBW[ , c('geo', 'Value',
'flagObservationStatus',
'flagMethod') := list('1', sum(Value, na.rm = TRUE),
max(flagObservationStatus),
'x'),
by = c('measuredItemISSCFC',
'measuredElement',
'timePointYears')]
commodityGeo1[ , geographicAreaM49_fi := NULL]
setnames(commodityGeo1, 'geo', 'geographicAreaM49_fi')
# Continent
commodityDBC <- copy(commodityDB)
commodityGeo2 <- merge(commodityDBC, country2cont[start_year < max_year & end_year > min_year,
.(un_code, un_codecountry)],
by.x = 'geographicAreaM49_fi', by.y = 'un_codecountry')
commodityGeo2 <- commodityGeo2[ , c('Value', 'flagObservationStatus',
'flagMethod') := list(sum(Value, na.rm = TRUE),
max(flagObservationStatus),
'x'),
by = c('un_code', 'measuredItemISSCFC',
'measuredElement',
'timePointYears')]
commodityGeo2[ , geographicAreaM49_fi := NULL]
setnames(commodityGeo2, 'un_code', 'geographicAreaM49_fi')
# Region
commodityDBR <- copy(commodityDB)
commodityGeo3 <- merge(commodityDBR, country2cont[start_year < max_year & end_year > min_year,
.(un_codereg, un_codecountry)],
by.x = 'geographicAreaM49_fi', by.y = 'un_codecountry')
commodityGeo3 <- commodityGeo3[ , c('Value', 'flagObservationStatus',
'flagMethod') := list(sum(Value, na.rm = TRUE),
max(flagObservationStatus),
'x'),
by = c('un_codereg', 'measuredItemISSCFC',
'measuredElement',
'timePointYears')]
commodityGeo3[ , geographicAreaM49_fi := NULL]
setnames(commodityGeo3, 'un_codereg', 'geographicAreaM49_fi')
# All
commodityGeo <- rbind(commodityGeo1, commodityGeo2)
commodityGeo <- rbind(commodityGeo, commodityGeo3)
} else if(region_level == 'None'){
commodityGeo <- commodityDB
}
setkey(commodityGeo)
commodityGeo <- unique(commodityGeo)
# if(any(sessionCountry0 != sessionCountry)){
#
# sepGeo <- commodityDB[geographicAreaM49_fi %in% sessionCountry0 ]
# commodityGeo <- rbind(commodityGeo, sepGeo)
#
# }
print(commodityGeo)
#-- Commodities aggregates ----
message('CDB aggregation : commodity aggregation.')
if(group_level == 'Grandtotal'){
commodityGeoG <- copy(commodityGeo)
commodityAgg <- commodityGeoG[ , c('isscfc', 'Value',
'flagObservationStatus',
'flagMethod') := list('FAOCLASSIFICATION',
sum(Value, na.rm = TRUE),
max(flagObservationStatus),
'x'),
by = c('geographicAreaM49_fi',
'measuredElement',
'timePointYears')]
commodityAgg[ , measuredItemISSCFC := NULL]
setnames(commodityAgg, 'isscfc', 'measuredItemISSCFC')
} else if(group_level == 'Level 1'){
commodityGeoL1 <- copy(commodityGeo)
commodityAgg <- merge(commodityGeoL1, isscfc2fao[ , .(fao_code, code)],
by.x = 'measuredItemISSCFC', by.y = 'code')
commodityAgg <- commodityAgg[ , c('Value', 'flagObservationStatus',
'flagMethod') := list(sum(Value, na.rm = TRUE),
max(flagObservationStatus),
'x'),
by = c('geographicAreaM49_fi',
'fao_code',
'measuredElement',
'timePointYears')]
commodityAgg[ , measuredItemISSCFC := NULL]
setnames(commodityAgg, 'fao_code', 'measuredItemISSCFC')
} else if(group_level == 'Level 2'){
commodityGeoL2 <- copy(commodityGeo)
commodityAgg <- merge(commodityGeoL2, isscfc2fao[ , .(fao_codel2, code)],
by.x = 'measuredItemISSCFC', by.y = 'code')
commodityAgg <- commodityAgg[ , c('Value', 'flagObservationStatus',
'flagMethod') := list(sum(Value, na.rm = TRUE),
max(flagObservationStatus),
'x'),
by = c('geographicAreaM49_fi',
'fao_codel2',
'measuredElement',
'timePointYears')]
commodityAgg[ , measuredItemISSCFC := NULL]
setnames(commodityAgg, 'fao_codel2', 'measuredItemISSCFC')
} else if(group_level == 'Level 3'){
commodityGeoL3 <- copy(commodityGeo)
commodityAgg <- merge(commodityGeoL3, isscfc2fao[ , .(fao_codel3, code)],
by.x = 'measuredItemISSCFC', by.y = 'code')
commodityAgg <- commodityAgg[ , c('Value', 'flagObservationStatus',
'flagMethod') := list(sum(Value, na.rm = TRUE),
max(flagObservationStatus),
'x'),
by = c('geographicAreaM49_fi',
'fao_codel3',
'measuredElement',
'timePointYears')]
commodityAgg[ , measuredItemISSCFC := NULL]
setnames(commodityAgg, 'fao_codel3', 'measuredItemISSCFC')
} else if(group_level == 'All') {
# Grandtotal
commodityGeoG <- copy(commodityGeo)
commodityAgg1 <- commodityGeoG[ , c('isscfc', 'Value',
'flagObservationStatus',
'flagMethod') := list('FAOCLASSIFICATION',
sum(Value, na.rm = TRUE),
max(flagObservationStatus),
'x'),
by = c('geographicAreaM49_fi',
'measuredElement',
'timePointYears')]
commodityAgg1[ , measuredItemISSCFC := NULL]
setnames(commodityAgg1, 'isscfc', 'measuredItemISSCFC')
# Level 1
commodityGeoL1 <- copy(commodityGeo)
commodityAgg2 <- merge(commodityGeoL1, isscfc2fao[ , .(fao_code, code)],
by.x = 'measuredItemISSCFC', by.y = 'code')
commodityAgg2 <- commodityAgg2[ , c('Value', 'flagObservationStatus',
'flagMethod') := list(sum(Value, na.rm = TRUE),
max(flagObservationStatus),
'x'),
by = c('geographicAreaM49_fi',
'fao_code',
'measuredElement',
'timePointYears')]
commodityAgg2[ , measuredItemISSCFC := NULL]
setnames(commodityAgg2, 'fao_code', 'measuredItemISSCFC')
# Level 2
commodityGeoL2 <- copy(commodityGeo)
commodityAgg3 <- merge(commodityGeoL2, isscfc2fao[ , .(fao_codel2, code)],
by.x = 'measuredItemISSCFC', by.y = 'code')
commodityAgg3 <- commodityAgg3[ , c('Value', 'flagObservationStatus',
'flagMethod') := list(sum(Value, na.rm = TRUE),
max(flagObservationStatus),
'x'),
by = c('geographicAreaM49_fi',
'fao_codel2',
'measuredElement',
'timePointYears')]
commodityAgg3[ , measuredItemISSCFC := NULL]
setnames(commodityAgg3, 'fao_codel2', 'measuredItemISSCFC')
# Level 3
commodityGeoL3 <- copy(commodityGeo)
commodityAgg4 <- merge(commodityGeoL3, isscfc2fao[ , .(fao_codel3, code)],
by.x = 'measuredItemISSCFC', by.y = 'code')
commodityAgg4 <- commodityAgg4[ , c('Value', 'flagObservationStatus',
'flagMethod') := list(sum(Value, na.rm = TRUE),
max(flagObservationStatus),
'x'),
by = c('geographicAreaM49_fi',
'fao_codel3',
'measuredElement',
'timePointYears')]
commodityAgg4[ , measuredItemISSCFC := NULL]
setnames(commodityAgg4, 'fao_codel3', 'measuredItemISSCFC')
# All
commodityAgg <- rbind(commodityAgg1, commodityAgg2)
commodityAgg <- rbind(commodityAgg, commodityAgg3)
commodityAgg <- rbind(commodityAgg, commodityAgg4)
} else if(group_level == 'None'){
commodityAgg <- commodityGeo
}
setkey(commodityAgg)
commodityAgg <- unique(commodityAgg)
print(commodityAgg)
# if(any(sessionISSCFC0 != sessionISSCFC)){
#
# sepComm <- commodityGeo[measuredItemISSCFC %in% sessionISSCFC0]
#
# commodityAgg <- rbind(commodityAgg, sepComm)
#
# }
message('CDB aggregation : saving data.')
CONFIG <- GetDatasetConfig(sessionKey_CDB@domain, sessionKey_CDB@dataset)
stats <- SaveData(domain = CONFIG$domain,
dataset = CONFIG$dataset,
data = commodityAgg,
waitTimeout = Inf)
##-- send Email with notification of correct execution ----
## Initiate email
from = "sws@fao.org"
to = swsContext.userEmail
subject = "Aggregation plug-in has correctly run"
body = paste("The plug-in has saved the data in your sessions.
Please note these results cannot be saved in the dataset as they are aggregates linked to virtual SWS codes.
Best regards.")
sendmailR::sendmail(from = from, to = to, subject = subject, msg = body)
paste0("Email sent to ", swsContext.userEmail)
msg <- paste0("Aggregation process completed successfully! ",
stats$inserted, " observations written, ",
stats$ignored, " weren't updated, ",
stats$discarded, " had problems.")
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