Add GLORYS BGC

ext/NumericalEarthCopernicusMarineExt.jl

@@ -30,7 +30,7 @@ function Downloads.download(meta::GLORYSMetadatum;
 
     toolbox = CopernicusMarine.copernicusmarine
 
-    variable_name = GLORYS.GLORYS_dataset_variable_names[meta.name]
+    variable_name = GLORYS.dataset_variable_name(meta)
     variables = CopernicusMarine.pylist([variable_name])
 
     dataset_id = GLORYS.copernicusmarine_dataset_id(meta.dataset)

src/DataWrangling/ECCO/ECCO.jl

@@ -254,11 +254,12 @@ function DataWrangling.metadata_filename(dataset::Union{ECCO2Daily, ECCO2Monthly
 end
 
 # Convenience functions
+
 DataWrangling.dataset_variable_name(data::Metadata{<:ECCO2Daily})   = ECCO2_dataset_variable_names[data.name]
 DataWrangling.dataset_variable_name(data::Metadata{<:ECCO2Monthly}) = ECCO2_dataset_variable_names[data.name]
 DataWrangling.dataset_variable_name(data::Metadata{<:ECCO4Monthly}) = ECCO4_dataset_variable_names[data.name]
-DataWrangling.dataset_location(::ECCODataset, name) = ECCO_location[name]
-
+DataWrangling.dataset_location(::ECCODataset, name) = name in keys(ECCO_location) ? ECCO_location[name] : (Center, Center, Center)
+  
 DataWrangling.is_three_dimensional(data::ECCOMetadata) =
     data.name == :temperature ||
     data.name == :salinity ||

src/DataWrangling/ECCO/ECCO_darwin.jl

@@ -79,7 +79,7 @@ function DataWrangling.conversion_units(metadatum::Metadatum{<:Union{ECCO2Darwin
     elseif dataset_variable_name(metadatum) != "THETA"
         return MicromolePerLiter()
     else
-        return nothing
+        return MolePerLiter()
     end
 end
 

src/DataWrangling/GLORYS/GLORYS.jl

@@ -154,5 +154,7 @@ function z_interfaces(metadata::GLORYSMetadata)
     return zf
 end
 
+include("GLORYS_bgc.jl")
+
 end # module GLORYS
 

src/DataWrangling/GLORYS/GLORYS_bgc.jl

@@ -0,0 +1,69 @@
+struct GLORYSBGCDaily <: GLORYSDataset end
+struct GLORYSBGCMonthly <: GLORYSDataset end
+
+dataset_name(::GLORYSBGCDaily) = "GLORYSBGCDaily"
+dataset_name(::GLORYSBGCMonthly) = "GLORYSBGCMonthly"
+
+const GLORYSBGC = Union{GLORYSBGCDaily, GLORYSBGCMonthly}
+
+const GLORYSBGCMetadatum = 
+    Union{Metadatum{<:GLORYSBGCDaily}, Metadatum{<:GLORYSBGCMonthly}}
+
+Base.size(::GLORYSBGC, variable) = (1140, 680, 75)
+Base.size(::GLORYSBGCMetadatum) = (1140, 680, 75, 1)
+
+all_dates(::GLORYSBGCDaily, var) = range(DateTime("1993-01-01"), stop=DateTime("2026-03-31"), step=Day(1))
+all_dates(::GLORYSBGCMonthly, var) = range(DateTime("1993-01-01"), stop=DateTime("2026-03-31"), step=Month(1))
+
+copernicusmarine_dataset_id(::GLORYSBGCDaily) = "cmems_mod_glo_bgc_my_0.25deg_P1D-m"
+copernicusmarine_dataset_id(::GLORYSBGCMonthly) = "cmems_mod_glo_bgc_my_0.25deg_P1M-m"
+
+available_variables(::GLORYSBGCDaily) = 
+    Dict(:chlorophyll => "chl",
+         :nitrate => "no3",
+         :primary_production => "nppv",
+         :oxygen => "o2",
+         :phosphate => "po4",
+         :silicate => "si")
+
+available_variables(::GLORYSBGCMonthly) = 
+    Dict(:chlorophyll => "chl",
+         :iron => "fe",
+         :nitrate => "no3",
+         :primary_production => "nppv",
+         :oxygen => "o2",
+         :pH => "ph",
+         :phytoplankton => "phyc",
+         :phosphate => "po4",
+         :silicate => "si",
+         :pCO₂ => "spco2")
+
+dataset_variable_name(metadata::GLORYSBGCMetadatum) = available_variables(metadata.dataset)[metadata.name]
+
+function metadata_prefix(dataset::GLORYSBGC, name, date, region)
+    var =  available_variables(dataset)[name]
+    ds = dataset_name(dataset)
+    start_date = start_date_str(date)
+    end_date = end_date_str(date)
+    suffix = region_suffix(region)
+    return string(var, "_",
+                  ds, "_",
+                  start_date, "_",
+                  end_date, suffix) |> colon2dash
+end
+
+is_three_dimensional(metadata::GLORYSBGCMetadatum) = metadata.name != :pCO₂
+
+function z_interfaces(metadata::GLORYSBGCMetadatum)
+    metadata.name == :pCO₂ && return (-1.0, 0.0)
+    paths = metadata_path(metadata)
+    path = paths isa AbstractVector ? first(paths) : paths
+    ds = Dataset(path)
+    zc = - reverse(ds["depth"][:])
+    close(ds)
+    dz = zc[2] - zc[1]
+    zf = (zc[1:end-1] .+ zc[2:end]) / 2
+    push!(zf, 0)
+    pushfirst!(zf, zf[1] - dz)
+    return zf
+end

src/DataWrangling/restoring.jl

@@ -192,7 +192,8 @@ function DatasetRestoring(metadata::Metadata,
                           time_indices_in_memory = default_time_indices_in_memory(metadata),
                           time_indexing = Cyclical(),
                           inpainting = NearestNeighborInpainting(Inf),
-                          cache_inpainted_data = true)
+                          cache_inpainted_data = true,
+						  field_name = oceananigans_fieldnames[metadata.name])
 
     Downloads.download(metadata)
 
@@ -205,10 +206,6 @@ function DatasetRestoring(metadata::Metadata,
     arch = architecture(fts)
     mask = on_architecture(arch, mask)
 
-    # Grab the correct Oceananigans field to restore
-    variable_name = metadata.name
-    field_name = oceananigans_fieldnames[variable_name]
-
     # If we pass the grid we do not need to interpolate
     # so we can save parameter space by setting the native grid to nothing
     on_native_grid = arch_or_grid isa AbstractArchitecture