Bugfix: error if invalid Parameter name in .yaml file (#24)

* Bugfix: error if invalid Parameter name in .yaml file

* add test for invalid Parameter

* better error message printing

Project.toml

@@ -1,7 +1,7 @@
 name = "PALEOboxes"
 uuid = "804b410e-d900-4b2a-9ecd-f5a06d4c1fd4"
 authors = ["Stuart Daines <[email protected]>"]
-version = "0.18.4"
+version = "0.18.5"
 
 [deps]
 BenchmarkTools = "6e4b80f9-dd63-53aa-95a3-0cdb28fa8baf"

src/Reaction.jl

@@ -361,7 +361,7 @@ function create_reaction_from_config(
 
     # set parameters
     allpars = get_parameters(newreaction)
-    conf_parameters = get(conf_reaction, "parameters", Dict{Any,Any}())
+    conf_parameters = copy(get(conf_reaction, "parameters", Dict{Any,Any}()))
     for par in allpars
         rawvalue = par.v
         par_modified = false
@@ -370,7 +370,7 @@ function create_reaction_from_config(
             par_modified = true
         end
         if !isnothing(conf_parameters) && haskey(conf_parameters, par.name) # empty 'parameters:' will return nothing
-            rawvalue = conf_parameters[par.name]
+            rawvalue = pop!(conf_parameters, par.name)
             par_modified = true
         end
         par_modstr = ("[Default]     ", "[config.yaml] ")[1+par_modified]
@@ -384,7 +384,16 @@ function create_reaction_from_config(
             setvalue!(par, value)
         end
     end    
-
+
+    if !isempty(conf_parameters)
+        io = IOBuffer()
+        write(io, "reaction $(fullname(newreaction)) has no Parameter(s):\n")
+        for (k, v) in conf_parameters
+            write(io, "    $k:    $v\n")
+        end
+        error(String(take!(io)))
+    end
+
     # Read Variable configuration
     # These are applied later by _configure_variables! after Variables are created
     newreaction.base._conf_variable_links = get(conf_reaction, "variable_links", nothing)

test/configbase.yaml

@@ -60,3 +60,24 @@ model_with_loop:
         oceanfloor:
             reactions:
 
+
+# two reactions that depend on each other - sort_reactions! should fail
+model_with_invalid_parameter:
+    domains:
+        ocean:
+
+            reactions:
+                julia_paleo_mock:
+                    class: ReactionPaleoMock
+                    parameters:
+                        par1:          0.15          # double parameter
+                        misspelt_par:  something      # no Parameter with this name
+                    variable_links:
+                        phy*:      mock_phy*
+
+        oceansurface:
+            reactions:
+
+        oceanfloor:
+            reactions:
+

test/runbasetests.jl

@@ -4,7 +4,7 @@ using BenchmarkTools
 
 include("ReactionPaleoMockModule.jl")
 
-@testset "PB.jl base" begin
+@testset "PALEOboxes base" begin
     model = PB.create_model_from_config("configbase.yaml", "model1")
 
     PB.show_methods_setup(model)
@@ -90,8 +90,14 @@ include("ReactionPaleoMockModule.jl")
 end
 
 
-@testset "PB.jl loop" begin
+@testset "PALEOboxes base loop" begin
 
     @test_throws ErrorException("The input graph contains at least one loop.") PB.create_model_from_config("configbase.yaml", "model_with_loop")
 
 end
+
+@testset "PALEOboxes base invalid parameter name" begin
+
+    @test_throws ErrorException("reaction ocean.julia_paleo_mock has no Parameter(s):\n    misspelt_par:    something\n") PB.create_model_from_config("configbase.yaml", "model_with_invalid_parameter")
+
+end