Merge pull request #671 from open-AIMS/handle_cluster_ids

Fix erroneous handling of location IDs

src/ADRIA.jl

@@ -103,7 +103,7 @@ export ReefModDomain
 # export dims, ndims
 
 # List out compatible domain datapackages
-const COMPAT_DPKG = ["0.4.0-rc", "0.4.0", "0.5.0-rc", "0.5.0"]
+const COMPAT_DPKG = ["0.5.0-rc", "0.5.0"]
 
 # This adds ~30 seconds to package load times
 if ccall(:jl_generating_output, Cint, ()) == 1

src/Domain.jl

@@ -9,7 +9,7 @@ mutable struct EnvLayer{S<:AbstractString,TF}
     dpkg_path::S
     site_data_fn::S
     const site_id_col::S
-    const unique_site_id_col::S
+    const cluster_id_col::S
     init_coral_cov_fn::S
     connectivity_fn::S
     DHW_fn::S
@@ -31,7 +31,7 @@ function load_domain(path::String)::Domain
 end
 
 function unique_sites(d::Domain)::Vector{String}
-    return d.site_data[:, d.unique_site_id_col]
+    return d.site_data[:, d.cluster_id_col]
 end
 
 """

src/ExtInterface/ADRIA/Domain.jl

@@ -20,7 +20,7 @@ mutable struct ADRIADomain{
     const strong_pred::Vector{Int64}  # strongest predecessor
     site_data::D  # table of site data (depth, carrying capacity, etc)
     const site_id_col::String  # column to use as site ids, also used by the connectivity dataset (indicates order of `conn`)
-    const unique_site_id_col::String  # column of unique site ids
+    const cluster_id_col::String  # column of unique site ids
     init_coral_cover::M  # initial coral cover dataset
     const coral_growth::CoralGrowth  # coral
     const site_ids::Vector{String}  # Site IDs that are represented (i.e., subset of site_data[:, site_id_col], after missing sites are filtered)
@@ -47,7 +47,7 @@ function Domain(
     strongest_predecessor::Vector{Int64},
     site_data::DataFrame,
     site_id_col::String,
-    unique_site_id_col::String,
+    cluster_id_col::String,
     init_coral_cover::NamedDimsArray,
     coral_growth::CoralGrowth,
     site_ids::Vector{String},
@@ -91,7 +91,7 @@ function Domain(
         strongest_predecessor,
         site_data,
         site_id_col,
-        unique_site_id_col,
+        cluster_id_col,
         init_coral_cover,
         coral_growth,
         site_ids,
@@ -105,7 +105,7 @@ function Domain(
 end
 
 """
-    Domain(name::String, rcp::String, timeframe::Vector, site_data_fn::String, site_id_col::String, unique_site_id_col::String, init_coral_fn::String, conn_path::String, dhw_fn::String, wave_fn::String, cyclone_mortality_fn::String)::Domain
+    Domain(name::String, rcp::String, timeframe::Vector, site_data_fn::String, site_id_col::String, cluster_id_col::String, init_coral_fn::String, conn_path::String, dhw_fn::String, wave_fn::String, cyclone_mortality_fn::String)::Domain
 
 Convenience constructor for Domain.
 
@@ -116,7 +116,7 @@ Convenience constructor for Domain.
 - `timeframe` : Time steps represented
 - `site_data_fn` : File name of spatial data used
 - `site_id_col` : Column holding name of reef the site is associated with (non-unique)
-- `unique_site_id_col` : Column holding unique site names/ids
+- `cluster_id_col` : Column holding unique site names/ids
 - `init_coral_fn` : Name of file holding initial coral cover values
 - `conn_path` : Path to directory holding connectivity data
 - `dhw_fn` : Filename of DHW data cube in use
@@ -130,7 +130,7 @@ function Domain(
     timeframe::Vector,
     site_data_fn::String,
     site_id_col::String,
-    unique_site_id_col::String,
+    cluster_id_col::String,
     init_coral_fn::String,
     conn_path::String,
     dhw_fn::String,
@@ -148,16 +148,18 @@ function Domain(
         end
     end
 
-    if unique_site_id_col ∉ names(site_data)
-        @warn "Unique location ID column $(unique_site_id_col) not found. Defaulting to UNIQUE_ID."
-        unique_site_id_col = "UNIQUE_ID"
+    if cluster_id_col ∉ names(site_data)
+        @warn "Cluster ID column $(cluster_id_col) not found. Defaulting to UNIQUE_ID."
+        cluster_id_col = "UNIQUE_ID"
     end
 
+    site_data[!, cluster_id_col] .= string.(Int64.(site_data[:, cluster_id_col]))
+
     env_layer_md::EnvLayer = EnvLayer(
         dpkg_path,
         site_data_fn,
         site_id_col,
-        unique_site_id_col,
+        cluster_id_col,
         init_coral_fn,
         conn_path,
         dhw_fn,
@@ -247,7 +249,7 @@ function Domain(
         conns.strongest_predecessor,
         site_data,
         site_id_col,
-        unique_site_id_col,
+        cluster_id_col,
         coral_cover,
         coral_growth,
         site_conn.site_ids,

src/ExtInterface/ReefMod/Domain.jl

@@ -17,7 +17,7 @@ mutable struct ReefModDomain <: Domain
     const strong_pred
     const site_data
     const site_id_col
-    const unique_site_id_col
+    const cluster_id_col
     init_coral_cover
     const coral_growth::CoralGrowth
     const site_ids
@@ -56,8 +56,8 @@ function load_domain(::Type{ReefModDomain}, fn_path::String, RCP::String)::ReefM
     site_data_path = joinpath(data_files, "region", "reefmod_gbr.gpkg")
     site_data = GDF.read(site_data_path)
     site_id_col = "LOC_NAME_S"
-    unique_site_id_col = "LOC_NAME_S"
-    site_ids = site_data[:, unique_site_id_col]
+    cluster_id_col = "LOC_NAME_S"
+    site_ids = site_data[:, site_id_col]
 
     id_list = CSV.read(
         joinpath(data_files, "id", "id_list_2023_03_30.csv"),
@@ -132,7 +132,7 @@ function load_domain(::Type{ReefModDomain}, fn_path::String, RCP::String)::ReefM
         fn_path,
         site_data_path,
         site_id_col,
-        unique_site_id_col,
+        cluster_id_col,
         "",
         "",
         "",
@@ -158,7 +158,7 @@ function load_domain(::Type{ReefModDomain}, fn_path::String, RCP::String)::ReefM
         strong_pred,
         site_data,
         site_id_col,
-        unique_site_id_col,
+        cluster_id_col,
         init_coral_cover,
         CoralGrowth(nrow(site_data)),
         site_ids,

src/io/ResultSet.jl

@@ -147,7 +147,7 @@ function combine_results(result_sets...)::ResultSet
         envlayer.dpkg_path,
         envlayer.site_data_fn,
         envlayer.site_id_col,
-        envlayer.unique_site_id_col,
+        envlayer.cluster_id_col,
         envlayer.init_coral_cov_fn,
         envlayer.connectivity_fn,
         dirname(envlayer.DHW_fn),
@@ -458,15 +458,15 @@ function Base.show(io::IO, mime::MIME"text/plain", rs::ResultSet)
 
     println("""
     Domain: $(rs.name)
-    
+
     Run with ADRIA $(vers_id) on $(rs.invoke_time)
     Results stored at: $(result_location(rs))
-    
+
     RCP(s) represented: $(rcps)
     Scenarios run: $(scens)
     Number of sites: $(sites)
     Timesteps: $(tf)
-    
+
     Input layers
     ------------""")
 

src/io/result_io.jl

@@ -155,7 +155,7 @@ function scenario_attributes(
         :ADRIA_VERSION => "v" * string(PkgVersion.Version(@__MODULE__)),
         :site_data_file => env_layer.site_data_fn,
         :site_id_col => env_layer.site_id_col,
-        :unique_site_id_col => env_layer.unique_site_id_col,
+        :cluster_id_col => env_layer.cluster_id_col,
         :init_coral_cover_file => env_layer.init_coral_cov_fn,
         :connectivity_file => env_layer.connectivity_fn,
         :DHW_file => env_layer.DHW_fn,
@@ -607,7 +607,7 @@ function load_results(result_loc::String)::ResultSet
 
     # Spatial data
     site_data = GDF.read(joinpath(result_loc, SITE_DATA, input_set.attrs["name"] * ".gpkg"))
-    sort!(site_data, [Symbol(input_set.attrs["unique_site_id_col"])])
+    sort!(site_data, [Symbol(input_set.attrs["site_id_col"])])
 
     # Model specification
     model_spec = CSV.read(
@@ -642,7 +642,7 @@ function load_results(result_loc::String)::ResultSet
         result_loc,
         input_set.attrs["site_data_file"],
         input_set.attrs["site_id_col"],
-        input_set.attrs["unique_site_id_col"],
+        input_set.attrs["cluster_id_col"],
         input_set.attrs["init_coral_cover_file"],
         input_set.attrs["connectivity_file"],
         input_set.attrs["DHW_file"],