added non RNG parameters for TOML parameters files

api/src/main/java/org/fairdatapipeline/api/Object_component_read.java

@@ -4,8 +4,11 @@
 import java.nio.file.Path;
 import java.util.List;
 import org.fairdatapipeline.distribution.Distribution;
+import org.fairdatapipeline.distribution.ImmutableDistribution;
+import org.fairdatapipeline.estimate.ImmutableEstimate;
 import org.fairdatapipeline.file.CleanableFileChannel;
 import org.fairdatapipeline.parameters.ReadComponent;
+import org.fairdatapipeline.samples.ImmutableSamples;
 
 /**
  * This represents an object_component to read from (or raise issues with) An object_component
@@ -77,7 +80,11 @@ public Number readEstimate() {
     } catch (IOException e) {
       throw (new RuntimeException("readEstimate() -- IOException trying to read from file", e));
     }
-    return data.getEstimate();
+    if (!(data instanceof ImmutableEstimate)) {
+      throw (new RuntimeException(
+          "readEstimate() -- this objComponent (" + this.component_name + ") is not an estimate"));
+    }
+    return ((ImmutableEstimate) data).getEstimate();
   }
 
   /**
@@ -93,7 +100,13 @@ public Distribution readDistribution() {
       throw (new RuntimeException(
           "readDistribution() -- IOException trying to read from file.", e));
     }
-    return data.getDistribution();
+    if (!(data instanceof ImmutableDistribution)) {
+      throw (new RuntimeException(
+          "readDistribution() -- this objComponent ("
+              + this.component_name
+              + ") is not a distribution"));
+    }
+    return ((ImmutableDistribution) data).getDistribution();
   }
 
   /**
@@ -108,7 +121,11 @@ public List<Number> readSamples() {
     } catch (IOException e) {
       throw (new RuntimeException("readSamples() -- IOException trying to read from file.", e));
     }
-    return data.getSamples();
+    if (!(data instanceof ImmutableSamples)) {
+      throw (new RuntimeException(
+          "readSamples() -- this objComponent (" + this.component_name + ") is not a samples"));
+    }
+    return ((ImmutableSamples) data).getSamples();
   }
 
   void register_me_in_registry() {

api/src/main/java/org/fairdatapipeline/distribution/Distribution.java

@@ -18,7 +18,7 @@
 import org.apache.commons.math3.distribution.RealDistribution;
 import org.apache.commons.math3.distribution.UniformRealDistribution;
 import org.apache.commons.math3.random.EmpiricalDistribution;
-import org.fairdatapipeline.parameters.Component;
+import org.fairdatapipeline.parameters.RngComponent;
 import org.immutables.value.Value.Auxiliary;
 import org.immutables.value.Value.Check;
 import org.immutables.value.Value.Immutable;
@@ -33,7 +33,7 @@
  TODO support other distributions:
  https://github.com/ScottishCovidResponse/SCRCIssueTracking/issues/671
 */
-public interface Distribution extends Component {
+public interface Distribution extends RngComponent {
   enum DistributionType {
     gamma(),
     exponential(),

api/src/main/java/org/fairdatapipeline/estimate/Estimate.java

@@ -6,14 +6,14 @@
 import com.fasterxml.jackson.databind.annotation.JsonSerialize;
 import java.util.List;
 import org.fairdatapipeline.distribution.Distribution;
-import org.fairdatapipeline.parameters.Component;
+import org.fairdatapipeline.parameters.RngComponent;
 import org.immutables.value.Value.Immutable;
 
 /** a component to store a plain simple single Number */
 @Immutable
 @JsonDeserialize
 @JsonSerialize
-public interface Estimate extends Component {
+public interface Estimate extends RngComponent {
   /** @return Number - the value that is stored in this component */
   @JsonProperty("value")
   Number internalValue();

api/src/main/java/org/fairdatapipeline/parameters/BoolList.java

@@ -0,0 +1,19 @@
+package org.fairdatapipeline.parameters;
+
+import com.fasterxml.jackson.annotation.JsonIgnore;
+import com.fasterxml.jackson.databind.annotation.JsonDeserialize;
+import com.fasterxml.jackson.databind.annotation.JsonSerialize;
+import java.util.List;
+import org.immutables.value.Value.Immutable;
+
+@Immutable
+@JsonSerialize
+@JsonDeserialize
+public interface BoolList extends Component {
+  List<Boolean> bools();
+
+  @JsonIgnore
+  default List<Boolean> getBools() {
+    return bools();
+  }
+}

api/src/main/java/org/fairdatapipeline/parameters/Component.java

@@ -1,9 +1,3 @@
 package org.fairdatapipeline.parameters;
 
-import org.apache.commons.math3.random.RandomGenerator;
-import org.immutables.value.Value.Auxiliary;
-
-public interface Component extends ReadComponent, WriteComponent {
-  @Auxiliary
-  RandomGenerator rng();
-}
+public interface Component extends ReadComponent, WriteComponent {}

api/src/main/java/org/fairdatapipeline/parameters/ComponentsDeserializer.java

@@ -29,9 +29,16 @@ public ComponentsDeserializer(RandomGenerator rng) {
 
   private static final Map<String, Class<?>> typeMapping =
       Map.of(
-          "point-estimate", ImmutableEstimate.class,
-          "distribution", ImmutableDistribution.class,
-          "samples", ImmutableSamples.class);
+          "point-estimate",
+          ImmutableEstimate.class,
+          "distribution",
+          ImmutableDistribution.class,
+          "samples",
+          ImmutableSamples.class,
+          "bools",
+          ImmutableBoolList.class,
+          "strings",
+          ImmutableStringList.class);
 
   @Override
   public Components deserialize(JsonParser jsonParser, DeserializationContext ctxt)
@@ -42,23 +49,24 @@ public Components deserialize(JsonParser jsonParser, DeserializationContext ctxt
         Streams.stream(rootNode.fields())
             .map(this::deserializeSingleComponent)
             .collect(Collectors.toMap(Entry::getKey, Entry::getValue));
-
     return ImmutableComponents.builder().components(components).build();
   }
 
   private Entry<String, Component> deserializeSingleComponent(Entry<String, JsonNode> entry) {
     String key = entry.getKey();
     ObjectNode componentNode = entry.getValue().deepCopy();
-    componentNode.putPOJO("rng", new Object()); // this is a hack to force rng to populate via
-    // RandomGeneratorDeserializer.class
     String type = componentNode.get("type").asText();
     componentNode.remove("type");
     Class<?> deserializeClass = typeMapping.get(type);
 
     if (deserializeClass == null) {
       throw new IllegalArgumentException(String.format("Unsupported component type %s", type));
     }
-
+    if (RngComponent.class.isAssignableFrom(deserializeClass.getInterfaces()[0])) {
+      componentNode.putPOJO("rng", new Object());
+      // this is a hack to force rng to populate via
+      // RandomGeneratorDeserializer.class
+    }
     ObjectMapper objectMapper = new DataPipelineMapper(rng);
     Component component;
     try {

api/src/main/java/org/fairdatapipeline/parameters/ComponentsSerializer.java

@@ -24,9 +24,16 @@ public ComponentsSerializer(RandomGenerator rng) {
 
   private static final Map<Class<?>, String> typeMapping =
       Map.of(
-          ImmutableEstimate.class, "point-estimate",
-          ImmutableDistribution.class, "distribution",
-          ImmutableSamples.class, "samples");
+          ImmutableEstimate.class,
+          "point-estimate",
+          ImmutableDistribution.class,
+          "distribution",
+          ImmutableSamples.class,
+          "samples",
+          ImmutableStringList.class,
+          "strings",
+          ImmutableBoolList.class,
+          "bools");
 
   @Override
   public void serialize(Components components, JsonGenerator gen, SerializerProvider serializers)

api/src/main/java/org/fairdatapipeline/parameters/ReadComponent.java

@@ -1,12 +1,3 @@
 package org.fairdatapipeline.parameters;
 
-import java.util.List;
-import org.fairdatapipeline.distribution.Distribution;
-
-public interface ReadComponent {
-  Number getEstimate();
-
-  List<Number> getSamples();
-
-  Distribution getDistribution();
-}
+public interface ReadComponent {}

api/src/main/java/org/fairdatapipeline/parameters/RngComponent.java

@@ -0,0 +1,17 @@
+package org.fairdatapipeline.parameters;
+
+import java.util.List;
+import org.apache.commons.math3.random.RandomGenerator;
+import org.fairdatapipeline.distribution.Distribution;
+import org.immutables.value.Value;
+
+public interface RngComponent extends Component {
+  @Value.Auxiliary
+  RandomGenerator rng();
+
+  Number getEstimate();
+
+  List<Number> getSamples();
+
+  Distribution getDistribution();
+}

api/src/main/java/org/fairdatapipeline/parameters/StringList.java

@@ -0,0 +1,19 @@
+package org.fairdatapipeline.parameters;
+
+import com.fasterxml.jackson.annotation.JsonIgnore;
+import com.fasterxml.jackson.databind.annotation.JsonDeserialize;
+import com.fasterxml.jackson.databind.annotation.JsonSerialize;
+import java.util.List;
+import org.immutables.value.Value.Immutable;
+
+@Immutable
+@JsonSerialize
+@JsonDeserialize
+public interface StringList extends Component {
+  List<String> strings();
+
+  @JsonIgnore
+  default List<String> getStrings() {
+    return strings();
+  }
+}

api/src/main/java/org/fairdatapipeline/samples/Samples.java

@@ -6,13 +6,13 @@
 import java.util.List;
 import org.fairdatapipeline.distribution.Distribution;
 import org.fairdatapipeline.distribution.ImmutableDistribution;
-import org.fairdatapipeline.parameters.Component;
+import org.fairdatapipeline.parameters.RngComponent;
 import org.immutables.value.Value.Immutable;
 
 @Immutable
 @JsonSerialize
 @JsonDeserialize
-public interface Samples extends Component {
+public interface Samples extends RngComponent {
   List<Number> samples();
 
   @JsonIgnore

api/src/test/java/org/fairdatapipeline/parameters/BoolListTest.java

@@ -0,0 +1,13 @@
+package org.fairdatapipeline.parameters;
+
+import static org.assertj.core.api.Assertions.assertThat;
+
+import org.junit.jupiter.api.Test;
+
+class BoolListTest {
+  @Test
+  void makeBoolList() {
+    var boollist = ImmutableBoolList.builder().addBools(true, false, true).build();
+    assertThat(boollist.bools()).contains(true, false);
+  }
+}

api/src/test/java/org/fairdatapipeline/parameters/ComponentsDeserializerTest.java

@@ -6,13 +6,10 @@
 
 import com.fasterxml.jackson.core.JsonProcessingException;
 import com.fasterxml.jackson.databind.ObjectMapper;
-import java.util.Map;
 import org.apache.commons.math3.random.RandomGenerator;
 import org.fairdatapipeline.distribution.Distribution.DistributionType;
 import org.fairdatapipeline.distribution.ImmutableDistribution;
-import org.fairdatapipeline.estimate.ImmutableEstimate;
 import org.fairdatapipeline.mapper.DataPipelineMapper;
-import org.fairdatapipeline.samples.ImmutableSamples;
 import org.junit.jupiter.api.*;
 
 @TestInstance(TestInstance.Lifecycle.PER_CLASS)
@@ -25,17 +22,9 @@ class ComponentsDeserializerTest {
           + "    \"shape\": 1,\n"
           + "    \"type\": \"distribution\"\n"
           + "  },\n"
-          + "  \"example-estimate\": {\n"
-          + "    \"type\": \"point-estimate\",\n"
-          + "    \"value\": 1.0\n"
-          + "  },\n"
-          + "  \"example-samples\": {\n"
-          + "    \"samples\": [\n"
-          + "      1,\n"
-          + "      2,\n"
-          + "      3\n"
-          + "    ],\n"
-          + "    \"type\": \"samples\"\n"
+          + "  \"example-strings\": {\n"
+          + "    \"strings\": [\"bram\",\"rosalie\"],\n"
+          + "    \"type\": \"strings\"\n"
           + "  }\n"
           + "}";
 
@@ -53,27 +42,28 @@ public void setUp() {
   void deserialize() throws JsonProcessingException {
     Components actualComponents = objectMapper.readValue(json, Components.class);
 
-    var estimate = ImmutableEstimate.builder().internalValue(1.0).rng(rng).build();
     var distribution =
         ImmutableDistribution.builder()
             .internalType(DistributionType.gamma)
             .internalShape(1)
             .internalScale(2)
             .rng(rng)
             .build();
-    var samples = ImmutableSamples.builder().addSamples(1, 2, 3).rng(rng).build();
-    var expectedComponents =
+    var strings = ImmutableStringList.builder().addStrings("bram", "rosalie").build();
+    Components components =
         ImmutableComponents.builder()
-            .components(
-                Map.of(
-                    "example-estimate",
-                    estimate,
-                    "example-distribution",
-                    distribution,
-                    "example-samples",
-                    samples))
+            .putComponents("example-distribution", distribution)
+            .putComponents("example-strings", strings)
             .build();
+    /* var expectedComponents =
+                    ImmutableComponents.builder()
+                            .components(
+                                    Map.of(
+                                            "example-distribution",
+                                            distribution
+    ))
+                            .build();*/
 
-    assertThat(actualComponents).isEqualTo(expectedComponents);
+    assertThat(actualComponents).isEqualTo(components);
   }
 }

api/src/test/java/org/fairdatapipeline/parameters/ComponentsSerializerTest.java

@@ -11,9 +11,7 @@
 import org.apache.commons.math3.random.RandomGenerator;
 import org.fairdatapipeline.distribution.Distribution.DistributionType;
 import org.fairdatapipeline.distribution.ImmutableDistribution;
-import org.fairdatapipeline.estimate.ImmutableEstimate;
 import org.fairdatapipeline.mapper.DataPipelineMapper;
-import org.fairdatapipeline.samples.ImmutableSamples;
 import org.json.JSONException;
 import org.junit.jupiter.api.*;
 
@@ -27,17 +25,9 @@ class ComponentsSerializerTest {
           + "    \"shape\": 1,\n"
           + "    \"type\": \"distribution\"\n"
           + "  },\n"
-          + "  \"example-estimate\": {\n"
-          + "    \"type\": \"point-estimate\",\n"
-          + "    \"value\": 1.0\n"
-          + "  },\n"
-          + "  \"example-samples\": {\n"
-          + "    \"samples\": [\n"
-          + "      1,\n"
-          + "      2,\n"
-          + "      3\n"
-          + "    ],\n"
-          + "    \"type\": \"samples\"\n"
+          + "  \"example-strings\": {\n"
+          + "    \"strings\": [\"bram\",\"rosalie\"],\n"
+          + "    \"type\": \"strings\"\n"
           + "  }\n"
           + "}";
 
@@ -54,20 +44,18 @@ public void setUp() {
   @Test
   void serialize() throws IOException, JSONException {
     var writer = new StringWriter();
-    var estimate = ImmutableEstimate.builder().internalValue(1.0).rng(rng).build();
     var distribution =
         ImmutableDistribution.builder()
             .internalType(DistributionType.gamma)
             .internalShape(1)
             .internalScale(2)
             .rng(rng)
             .build();
-    var samples = ImmutableSamples.builder().addSamples(1, 2, 3).rng(rng).build();
+    var strings = ImmutableStringList.builder().addStrings("bram", "rosalie").build();
     Components components =
         ImmutableComponents.builder()
-            .putComponents("example-estimate", estimate)
             .putComponents("example-distribution", distribution)
-            .putComponents("example-samples", samples)
+            .putComponents("example-strings", strings)
             .build();
 
     objectMapper.writeValue(writer, components);