Example mode and unit tests for pipeline functions. (#295)

* unit tests for pipeline functions.

* reformat

* Move dispatch on example mode to the config list constructors with additional unit testing

* reformat

* Add _selector methods to dispatch different pipeline number of scenarios

pipeline/src/constructors/constructors.jl

@@ -1,3 +1,4 @@
+include("selector.jl")
 include("make_gi_params.jl")
 include("make_inf_generating_processes.jl")
 include("make_model_priors.jl")

pipeline/src/constructors/make_inference_configs.jl

@@ -20,5 +20,6 @@ function make_inference_configs(pipeline::AbstractEpiAwarePipeline)
         "gi_std" => gi_param_dict["gi_stds"], "log_I0_prior" => priors["log_I0_prior"]) |>
                         dict_list
 
-    return inference_configs
+    selected_inference_configs = _selector(inference_configs, pipeline)
+    return selected_inference_configs
 end

pipeline/src/constructors/make_truth_data_configs.jl

@@ -1,6 +1,5 @@
 """
-Create a dictionary of truth data configurations for `pipeline <: AbstractEpiAwarePipeline`.
-    This is the default method.
+Create a vector of truth data configurations for `pipeline <: AbstractEpiAwarePipeline`.
 
 # Returns
 A vector of dictionaries containing the mean and standard deviation values for
@@ -9,7 +8,9 @@ A vector of dictionaries containing the mean and standard deviation values for
 """
 function make_truth_data_configs(pipeline::AbstractEpiAwarePipeline)
     gi_param_dict = make_gi_params(pipeline)
-    return Dict(
+    gi_param_dict_list = Dict(
         "gi_mean" => gi_param_dict["gi_means"], "gi_std" => gi_param_dict["gi_stds"]) |>
-           dict_list
+                         dict_list
+    selected_truth_data_configs = _selector(gi_param_dict_list, pipeline)
+    return selected_truth_data_configs
 end

pipeline/src/constructors/selector.jl

@@ -0,0 +1,15 @@
+"""
+Internal method for selecting from a list of items based on the pipeline type.
+Default is to return the list as is.
+"""
+function _selector(list, pipeline::AbstractEpiAwarePipeline)
+    return list
+end
+
+"""
+Internal method for selecting from a list of items based on the pipeline type.
+Example/test mode is to return a randomly selected item from the list.
+"""
+function _selector(list, pipeline::EpiAwareExamplePipeline)
+    return [rand(list)]
+end

pipeline/test/constructors/test_constructors.jl

@@ -85,7 +85,8 @@ end
 
 @testset "make_truth_data_configs" begin
     using EpiAwarePipeline
-    pipeline = EpiAwareExamplePipeline()
+    pipeline = RtwithoutRenewalPipeline()
+    example_pipeline = EpiAwareExamplePipeline()
     @testset "make_truth_data_configs should return a dictionary" begin
         config_dicts = make_truth_data_configs(pipeline)
         @test eltype(config_dicts) <: Dict
@@ -96,14 +97,38 @@ end
         @test all(config_dicts .|> config -> haskey(config, "gi_mean"))
         @test all(config_dicts .|> config -> haskey(config, "gi_std"))
     end
+
+    @testset "make_truth_data_configs should return a vector of length 1 for EpiAwareExamplePipeline" begin
+        config_dicts = make_truth_data_configs(example_pipeline)
+        @test length(config_dicts) == 1
+    end
 end
 
 @testset "default inference configurations" begin
     using EpiAwarePipeline
-    pipeline = EpiAwareExamplePipeline()
 
-    inference_configs = make_inference_configs(pipeline)
-    @test eltype(inference_configs) <: Dict
+    pipeline = RtwithoutRenewalPipeline()
+    example_pipeline = EpiAwareExamplePipeline()
+
+    @testset "make_inference_configs should return a vector of dictionaries" begin
+        inference_configs = make_inference_configs(pipeline)
+        @test eltype(inference_configs) <: Dict
+    end
+
+    @testset "make_inference_configs should contain igp, latent_namemodels, observation_model, gi_mean, gi_std, and log_I0_prior keys" begin
+        inference_configs = make_inference_configs(pipeline)
+        @test inference_configs .|> (config -> haskey(config, "igp")) |> all
+        @test inference_configs .|> (config -> haskey(config, "latent_namemodels")) |> all
+        @test inference_configs .|> (config -> haskey(config, "observation_model")) |> all
+        @test inference_configs .|> (config -> haskey(config, "gi_mean")) |> all
+        @test inference_configs .|> (config -> haskey(config, "gi_std")) |> all
+        @test inference_configs .|> (config -> haskey(config, "log_I0_prior")) |> all
+    end
+
+    @testset "make_inference_configs should return a vector of length 1 for EpiAwareExamplePipeline" begin
+        inference_configs = make_inference_configs(example_pipeline)
+        @test length(inference_configs) == 1
+    end
 end
 
 @testset "make_default_params" begin

pipeline/test/pipeline/test_pipelinefunctions.jl

@@ -0,0 +1,32 @@
+@testset "do_truthdata tests" begin
+    using EpiAwarePipeline, Dagger
+    pipeline = EpiAwareExamplePipeline()
+    truthdata_dg_task = do_truthdata(pipeline)
+    truthdata = fetch.(truthdata_dg_task)
+
+    @test length(truthdata) == 1
+    @test all([data["y_t"] isa Vector{Union{Missing, Real}} for data in truthdata])
+end
+
+@testset "do_inference tests" begin
+    using EpiAwarePipeline
+    pipeline = EpiAwareExamplePipeline()
+
+    function make_inference()
+        truthdata = do_truthdata(pipeline)
+        do_inference(truthdata[1:1], pipeline)
+    end
+
+    inference_results_tsk = make_inference()
+    inference_results = fetch.(inference_results_tsk)
+    @test length(inference_results) == 1
+    @test all([result["inference_results"] isa EpiAwareObservables
+               for result in inference_results])
+end
+
+@testset "do_pipeline test: just run" begin
+    using EpiAwarePipeline
+    pipeline = EpiAwareExamplePipeline()
+    res = do_pipeline(pipeline)
+    @test isnothing(res)
+end

pipeline/test/runtests.jl

@@ -3,6 +3,7 @@ quickactivate(@__DIR__(), "EpiAwarePipeline")
 
 # Run tests
 include("pipeline/test_pipelinetypes.jl");
+include("pipeline/test_pipelinefunctions.jl");
 include("constructors/test_constructors.jl");
 include("simulate/test_TruthSimulationConfig.jl");
 include("simulate/test_SimulationConfig.jl");