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fix #19
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@eblondel
eblondel committed Jun 12, 2023
1 parent 355d63d commit 5849e39
Showing 1 changed file with 14 additions and 14 deletions.
28 changes: 14 additions & 14 deletions tunaatlas_actions/load_dataset.R
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Original file line number Diff line number Diff line change
Expand Up @@ -118,13 +118,13 @@ load_dataset <- function(action,entity, config, options){
df_codelists_input<-df_codelists[which(df_codelists$dimension %in% dimensions),]

# convert columns that are not character to character and ensure that the column "value" is a numeric
cols<-setdiff(colnames(df_to_load),"value")
cols<-setdiff(colnames(df_to_load),"measurement_value")
for (i in 1:length(cols)){
if (typeof(df_to_load[,cols[i]])!="character"){
df_to_load[,cols[i]]<-as.character(df_to_load[,cols[i]])
}
}
df_to_load$value<-as.numeric(df_to_load$value)
df_to_load$measurement_value<-as.numeric(df_to_load$measurement_value)

#### First we deal with all the dimensions that are "real" code lists: area,catchtype,catchunit,effortunit,fishingfleet,gear,schooltype,species,sex,ocean
# Dimensions time and sizeclass are not "real" code lists. They are dealt in a second step
Expand Down Expand Up @@ -227,7 +227,7 @@ load_dataset <- function(action,entity, config, options){
# One by one, retrieve the numeric codes
for (dim in 1:nrow(db_nondf_inputlike_dimensions_parameters)){

if (db_nondf_inputlike_dimensions_parameters$dimension[dim]=="sizeclass"){
if (db_nondf_inputlike_dimensions_parameters$dimension[dim]=="size_class"){
df_to_load$size_min<-as.numeric(df_to_load$size_min)
df_to_load$size_step<-as.numeric(df_to_load$size_step)
}
Expand Down Expand Up @@ -476,16 +476,16 @@ load_dataset <- function(action,entity, config, options){
new_comment <- switch(column_names[i],
"source_authority" = paste0("COMMENT ON COLUMN ",paste0(schema_name_for_view,".",database_view_name,".source_authority")," IS 'Source authority in charge of producing the source statistics collated and harmonized.';"),
"source_authority_label" = paste0("COMMENT ON COLUMN ",paste0(schema_name_for_view,".",database_view_name,".source_authority_label")," IS 'source_authority_label.';"),
"fishingfleet" = paste0("COMMENT ON COLUMN ",paste0(schema_name_for_view,".",database_view_name,".fishingfleet")," IS 'Fishing fleet. A group of fishing vessels authorized to operate in a t-RFMO convention area / area of competence, and whose fishing operations and catches of tuna and tuna-like species are responsibility of, and accounted for by a political entity or sub-entity recognized by the corresponding t-RFMO. To be noted that the actual occurrences of the Fishing fleet concept do not necessarily refer or correspond to a recognized country (e.g.: EUR - European Union, FRAT – French territories), nor to a distinct member / contracting party / cooperating, non-contracting party of a t-RFMO (e.g.: EU,ESP - EU (Spain), TWN – Chinese Taipei / Taiwan province of China – for some t-RFMOs). The proposed list of fishing fleet codes also includes a generic reference that applies to fishing operations and catches from unidentified sources (e.g.: NEI - not elsewhere identified).';"),
"fishingfleet_label" = paste0("COMMENT ON COLUMN ",paste0(schema_name_for_view,".",database_view_name,".fishingfleet_label")," IS 'fishingfleet_label.';"),
"gear" = paste0("COMMENT ON COLUMN ",paste0(schema_name_for_view,".",database_view_name,".gear")," IS 'Fishing gear used. Fishing gear are grouped by categories, in accordance with the International Standard Statitical Classficiation of Fishing Gear (ISSCFG) endorsed by the CWP. The number of gears varies a lot depending on the RFMOs. ICCAT, for instance, has around 60 gears while IATTC has 10 gears. This table is a dimension of the data warehouse: a list of codes which gives the context of the values stored in the fact table.';"),
"gear_label" = paste0("COMMENT ON COLUMN ",paste0(schema_name_for_view,".",database_view_name,".gear_label")," IS 'gear_label.';"),
"fishing_fleet" = paste0("COMMENT ON COLUMN ",paste0(schema_name_for_view,".",database_view_name,".fishing_fleet")," IS 'Fishing fleet. A group of fishing vessels authorized to operate in a t-RFMO convention area / area of competence, and whose fishing operations and catches of tuna and tuna-like species are responsibility of, and accounted for by a political entity or sub-entity recognized by the corresponding t-RFMO. To be noted that the actual occurrences of the Fishing fleet concept do not necessarily refer or correspond to a recognized country (e.g.: EUR - European Union, FRAT – French territories), nor to a distinct member / contracting party / cooperating, non-contracting party of a t-RFMO (e.g.: EU,ESP - EU (Spain), TWN – Chinese Taipei / Taiwan province of China – for some t-RFMOs). The proposed list of fishing fleet codes also includes a generic reference that applies to fishing operations and catches from unidentified sources (e.g.: NEI - not elsewhere identified).';"),
"fishing_fleet_label" = paste0("COMMENT ON COLUMN ",paste0(schema_name_for_view,".",database_view_name,".fishing_fleet_label")," IS 'fishing_fleet_label.';"),
"gear_type" = paste0("COMMENT ON COLUMN ",paste0(schema_name_for_view,".",database_view_name,".gear_type")," IS 'Fishing gear used. Fishing gear are grouped by categories, in accordance with the International Standard Statitical Classficiation of Fishing Gear (ISSCFG) endorsed by the CWP. The number of gears varies a lot depending on the RFMOs. ICCAT, for instance, has around 60 gears while IATTC has 10 gears. This table is a dimension of the data warehouse: a list of codes which gives the context of the values stored in the fact table.';"),
"gear_type_label" = paste0("COMMENT ON COLUMN ",paste0(schema_name_for_view,".",database_view_name,".gear_type_label")," IS 'gear_type_label.';"),
"gear_group" = paste0("COMMENT ON COLUMN ",paste0(schema_name_for_view,".",database_view_name,".gear_group")," IS 'Group of fishing gears.';"),
"gear_group_label" = paste0("COMMENT ON COLUMN ",paste0(schema_name_for_view,".",database_view_name,".gear_group_label")," IS 'gear_group_label.';"),
"species" = paste0("COMMENT ON COLUMN ",paste0(schema_name_for_view,".",database_view_name,".species")," IS 'Species captured. The main tuna species are available in all the RFMOs Depending on the RFMO, some non-target species (e.g. some sharks or turtles) are also reported. This table is a dimension of the data warehouse: a list of codes which gives the context of the values stored in the fact table.';"),
"species_label" = paste0("COMMENT ON COLUMN ",paste0(schema_name_for_view,".",database_view_name,".species_label")," IS 'species_label.';"),
"schooltype" = paste0("COMMENT ON COLUMN ",paste0(schema_name_for_view,".",database_view_name,".schooltype")," IS 'A school is a group of fishes evolving together. The type of school indicates the nature of the school on which the catch has been made: free school, log school, unknown, dolphin.';"),
"schooltype_label" = paste0("COMMENT ON COLUMN ",paste0(schema_name_for_view,".",database_view_name,".schooltype_label")," IS 'Type of school.';"),
"fishing_mode" = paste0("COMMENT ON COLUMN ",paste0(schema_name_for_view,".",database_view_name,".fishing_mode")," IS 'A school is a group of fishes evolving together. The type of school indicates the nature of the school on which the catch has been made: free school, log school, unknown, dolphin.';"),
"schooltype_label" = paste0("COMMENT ON COLUMN ",paste0(schema_name_for_view,".",database_view_name,".fishing_mode_label")," IS 'Type of school.';"),
"time" = paste0("COMMENT ON COLUMN ",paste0(schema_name_for_view,".",database_view_name,".time")," IS 'Dating of the fact. In Sardara, the dating is provided as two columns: time_start gives the first date of availability of the measure (included) and time_end gives the last date of availability of the measure (not included). The data in Sardara are mainly defined over the following time steps: 1) Nominal catch are mostly defined on 1 year resolution. 2) Georeferenced catch-and-effort and catch-at-size are mostly defined on 1 month resolution. This table is a dimension of the data warehouse: a list of codes which gives the context of the values stored in the fact table.';"),
"time_period" = paste0("COMMENT ON COLUMN ",paste0(schema_name_for_view,".",database_view_name,".time_period")," IS 'Interval of time over which the measure is defined.';"),
"time_start" = paste0("COMMENT ON COLUMN ",paste0(schema_name_for_view,".",database_view_name,".time_start")," IS 'Start time of the fact. Starting time - first date of availability of the measure (inclusive).';"),
Expand All @@ -500,11 +500,11 @@ load_dataset <- function(action,entity, config, options){
"the_geom" = paste0("COMMENT ON COLUMN ",paste0(schema_name_for_view,".",database_view_name,".the_geom" )," IS 'Geometry in one of the standard data formats (e.g. GML, WKT).';"),
"longitude" = paste0("COMMENT ON COLUMN ",paste0(schema_name_for_view,".",database_view_name,".longitude" )," IS 'Longitude of the centroid of the pixel or point location (EPSG:4326).';"),
"latitude" = paste0("COMMENT ON COLUMN ",paste0(schema_name_for_view,".",database_view_name,".latitude")," IS 'Latitude of the centroid of the pixel or point location (EPSG:4326).';"),
"catchtype" = paste0("COMMENT ON COLUMN ",paste0(schema_name_for_view,".",database_view_name,".catchtype")," IS 'Fate of the catch, i.e. landed, discarded, unknown. Given the nature of the data, only landing data are currently available in SARDARA, with a very few exceptions of discarded fishes for ICCAT. This table is a dimension of the data warehouse: a list of codes which gives the context of the values stored in the fact table.';"),
"catchtype_label" = paste0("COMMENT ON COLUMN ",paste0(schema_name_for_view,".",database_view_name,".catchtype_label")," IS 'catchtype_label.';"),
"value" = paste0("COMMENT ON COLUMN ",paste0(schema_name_for_view,".",database_view_name,".value" )," IS 'the measure of the fact (variable).';"),
"unit" = paste0("COMMENT ON COLUMN ",paste0(schema_name_for_view,".",database_view_name,".unit")," IS 'unit.';"),
"unit_label" = paste0("COMMENT ON COLUMN ",paste0(schema_name_for_view,".",database_view_name,".unit_label" )," IS 'unit_label.';")
"measurement_type" = paste0("COMMENT ON COLUMN ",paste0(schema_name_for_view,".",database_view_name,".measurement_type")," IS 'Fate of the catch, i.e. landed, discarded, unknown. Given the nature of the data, only landing data are currently available in SARDARA, with a very few exceptions of discarded fishes for ICCAT. This table is a dimension of the data warehouse: a list of codes which gives the context of the values stored in the fact table.';"),
"measurement_type_label" = paste0("COMMENT ON COLUMN ",paste0(schema_name_for_view,".",database_view_name,".measurement_type_label")," IS 'measurement_type_label.';"),
"measurement_value" = paste0("COMMENT ON COLUMN ",paste0(schema_name_for_view,".",database_view_name,".measurement_value" )," IS 'the measure of the fact (variable).';"),
"measurement_unit" = paste0("COMMENT ON COLUMN ",paste0(schema_name_for_view,".",database_view_name,".measurement_unit")," IS 'measurement_unit.';"),
"measurement_unit_label" = paste0("COMMENT ON COLUMN ",paste0(schema_name_for_view,".",database_view_name,".measurement_unit_label" )," IS 'unit_label.';")
# "catchunit" = paste0("COMMENT ON COLUMN ",paste0(schema_name_for_view,".",database_view_name,".catchunit")," IS 'Unit of catch.';"),
# "effortunit" = paste0("COMMENT ON COLUMN ",paste0(schema_name_for_view,".",database_view_name,".effortunit")," IS 'Unit of effort.';"),
# "cmax" = paste0("COMMENT ON COLUMN ",paste0(schema_name_for_view,".",database_view_name,".cmax" )," IS 'cmax';"),
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