Experimental CommonDataModel extension

Project.toml

@@ -30,9 +30,16 @@ TestEnv = "1e6cf692-eddd-4d53-88a5-2d735e33781b"
 TimerOutputs = "a759f4b9-e2f1-59dc-863e-4aeb61b1ea8f"
 YAML = "ddb6d928-2868-570f-bddf-ab3f9cf99eb6"
 
+[weakdeps]
+CommonDataModel = "1fbeeb36-5f17-413c-809b-666fb144f157"
+
+[extensions]
+CommonDataModelExt = "CommonDataModel"
+
 [compat]
 Atomix = "0.1, 1.0"
 BenchmarkTools = "1.0"
+CommonDataModel = "0.3.7"
 DataFrames = "1.1"
 DocStringExtensions = "0.8, 0.9"
 Documenter = "1"
@@ -52,12 +59,13 @@ StructArrays = "0.6, 0.7"
 TestEnv = "1.0"
 TimerOutputs = "0.5"
 YAML = "0.4.7"
-julia = "1.6"
+julia = "1.10"
 
 [extras]
+CommonDataModel = "1fbeeb36-5f17-413c-809b-666fb144f157"
 Documenter = "e30172f5-a6a5-5a46-863b-614d45cd2de4"
 Logging = "56ddb016-857b-54e1-b83d-db4d58db5568"
 Test = "8dfed614-e22c-5e08-85e1-65c5234f0b40"
 
 [targets]
-test = ["Documenter", "Logging", "Test"]
+test = ["CommonDataModel", "Documenter", "Logging", "Test"]

ext/CommonDataModelExt/CommonDataModelExt.jl

@@ -0,0 +1,93 @@
+module CommonDataModelExt
+
+import PALEOboxes as PB
+import CommonDataModel as CDM
+
+#####################################
+# Wrapper types
+######################################
+
+struct ModelCDM <: CDM.AbstractDataset
+    model::PB.Model
+    modeldata::Union{Nothing, PB.AbstractModelData}
+end
+
+PB.CDModel(model::PB.Model) = ModelCDM(model, nothing)
+PB.CDModel(modeldata::PB.AbstractModelData) = ModelCDM(modeldata.model, modeldata)
+
+struct DomainCDM <: CDM.AbstractDataset
+    domain::PB.Domain
+    modeldata::Union{Nothing, PB.AbstractModelData}
+end
+
+PB.CDModel(domain::PB.Domain) = DomainCDM(domain, nothing)
+
+
+struct VariableDomainCDM <: CDM.AbstractDataset
+    variabledomain::PB.VariableDomain
+    modeldata::Union{Nothing, PB.AbstractModelData}
+    data
+end
+
+PB.CDModel(variabledomain::PB.VariableDomain) = VariableDomainCDM(variabledomain, nothing, nothing)
+
+######################################
+# Model
+######################################
+
+# iterable with all group names
+CDM.groupnames(m::ModelCDM) = [d.name for d in m.model.domains]
+
+CDM.group(m::ModelCDM, name::AbstractString) = DomainCDM(PB.get_domain(m.model, name; allow_not_found=false), m.modeldata)
+
+###############################################
+# Domain
+################################################
+
+CDM.name(d::DomainCDM) = d.domain.name
+
+# TODO
+# parentdataset(d::DomainCDM)
+
+# returns a list of variable names as strings
+Base.keys(d::DomainCDM) = [v.name for v in PB.get_variables(d.domain)]
+
+function CDM.variable(d::DomainCDM, varname::AbstractString)
+    variabledomain = PB.get_variable(d.domain, varname; allow_not_found=false)
+    if isnothing(d.modeldata)
+        data = nothing
+    else
+        data = PB.get_data(variabledomain, d.modeldata)
+    end
+    return VariableDomainCDM(variabledomain, d.modeldata, data)
+end
+
+CDM.dimnames(d::DomainCDM) = [nd.name for nd in PB.get_dimensions(d.domain)]
+
+CDM.dim(d::DomainCDM, name::AbstractString) = PB.get_dimension(d.domain, name).size
+
+
+###############################################
+# VariableDomain
+################################################
+
+CDM.name(v::VariableDomainCDM) = v.variabledomain.name
+
+CDM.dataset(v::VariableDomainCDM) = DomainCDM(v.variabledomain.domain, v.modeldata)
+
+CDM.dimnames(v::VariableDomainCDM) = [nd.name for nd in PB.get_dimensions(v.variabledomain)]
+
+Base.ndims(v::VariableDomainCDM) = length(CDM.dimnames(v))
+
+Base.size(v::VariableDomainCDM) = (nd.size for nd in PB.get_dimensions(v.variabledomain))
+
+CDM.attribnames(v::VariableDomainCDM) = keys(v.variabledomain.attributes)
+
+CDM.attrib(v::VariableDomainCDM, name::Symbol) = v.variabledomain.attributes[name]
+
+Base.getindex(v::VariableDomainCDM, indices...) = Base.getindex(v.data, indices...)
+
+Base.eltype(v::VariableDomainCDM) = Base.eltype(v.data)
+
+
+end # module

src/Types.jl

@@ -1,6 +1,17 @@
 # TODO there doesn't seem to be an easy way of parameterising ModelData by an Array type ?
 const PaleoArrayType = Array
 
+################################
+# CommonDataModel adaptor
+################################
+
+"""
+    CDModel(x)
+
+Create a CommonDataModel adaptor for PALEO object x
+"""
+function CDModel end
+
 ################################
 # Parameters
 ###############################