add sim state pipeline (#24)

* add sim state pipeline

* update filename

src/main/java/gov/hhs/aspr/ms/gcm/pipeline/pipelines/SimulationStatePipeline.java

@@ -0,0 +1,134 @@
+package gov.hhs.aspr.ms.gcm.pipeline.pipelines;
+
+import java.nio.file.Path;
+import java.time.LocalDate;
+import java.time.format.DateTimeFormatter;
+import java.time.format.DateTimeParseException;
+import java.util.ArrayList;
+import java.util.List;
+
+import gov.hhs.aspr.ms.gcm.pipeline.input.SimulationStatePipelineInput;
+import gov.hhs.aspr.ms.gcm.pipeline.support.GCMPipelineFileHeaders;
+import gov.hhs.aspr.ms.gcm.pipeline.IPipeline;
+import gov.hhs.aspr.ms.gcm.simulation.nucleus.SimulationState;
+import gov.hhs.aspr.ms.gcm.taskit.protobuf.nucleus.NucleusTranslator;
+import gov.hhs.aspr.ms.gcm.taskit.protobuf.nucleus.input.SimulationStateInput;
+import gov.hhs.aspr.ms.gcm.taskit.protobuf.nucleus.translationSpecs.SimulationStateTranslationSpec;
+import gov.hhs.aspr.ms.taskit.core.TranslationController;
+import gov.hhs.aspr.ms.taskit.core.TranslationEngineType;
+import gov.hhs.aspr.ms.taskit.protobuf.ProtobufTranslationEngine;
+import gov.hhs.aspr.ms.util.errors.ContractException;
+import gov.hhs.aspr.ms.util.readers.TextTableReader;
+import gov.hhs.aspr.ms.util.resourcehelper.ResourceError;
+import gov.hhs.aspr.ms.util.resourcehelper.ResourceHelper;
+
+/**
+ * A utility for constructing the SimulationState file from the
+ * simStateSettingsFile
+ */
+public class SimulationStatePipeline implements IPipeline {
+
+    /**
+     * Given a {@link SimulationStatePipelineInput}, an input directory path and an
+     * output directory path, return a {@link SimulationStatePipeline}
+     * 
+     * @throws ContractException
+     *                           <ul>
+     *                           <li>{@link ResourceError#UNKNOWN_FILE} if any of
+     *                           the input paths are not valid</li>
+     *                           <li>{@link ResourceError#FILE_PATH_IS_DIRECTORY} if
+     *                           any of the input paths or output path point to a directory</li>
+     *                           </ul>
+     */
+    public static SimulationStatePipeline from(SimulationStatePipelineInput pipelineInput, Path inputDirectory,
+            Path outputDirectory) {
+        String simStateSettingsFile = inputDirectory.resolve(pipelineInput.getSimulationSettingsFile()).toString();
+        String simStateFile = outputDirectory.resolve(pipelineInput.getSimulationStateFile()).toString();
+
+        Path simStateSettingsPath = ResourceHelper.validateFile(simStateSettingsFile);
+
+        Path simStatePath = ResourceHelper.validateFilePath(simStateFile);
+
+        return new SimulationStatePipeline(simStateSettingsPath, simStatePath);
+    }
+
+    private final Path simStateSettingsFile;
+
+    private final Path simStateFile;
+
+    private SimulationStatePipeline(Path simStateSettingsFile, Path simStateDataFile) {
+        this.simStateSettingsFile = simStateSettingsFile;
+        this.simStateFile = simStateDataFile;
+    }
+
+    /**
+     * Executes the pipeline with the given input files
+     * <p>
+     * writes out the resulting simState file to the path provided
+     */
+    public void execute() {
+        SimulationState.Builder builder = SimulationState.builder();
+
+        System.out.println("SimulationState Pipeline::loading simulation state settings file");
+        loadSimStateSettingsFile(builder);
+
+        System.out.println("SimulationState Pipeline::translating simulation state");
+        // create the translation engine and have it use the nucleus translator and
+        ProtobufTranslationEngine protobufTranslationEngine = ProtobufTranslationEngine.builder()//
+                .addTranslator(NucleusTranslator.getTranslator())//
+                .build();//
+
+        SimulationStateTranslationSpec translationSpec = new SimulationStateTranslationSpec();
+        translationSpec.init(protobufTranslationEngine);
+
+        SimulationStateInput input = translationSpec.convert(builder.build());
+        builder = null;
+
+        System.out.println("SimulationState Pipeline::writing simulation state");
+        // build the translation controller and have it write the SimulationState file
+        TranslationController.builder()
+                .addTranslationEngine(protobufTranslationEngine)//
+                .build()//
+                .writeOutput(input, simStateFile, TranslationEngineType.PROTOBUF);//
+
+        System.out.println("SimulationState Pipeline::done");
+
+    }
+
+    private void loadSimStateSettingsFile(SimulationState.Builder builder) {
+        List<DateTimeFormatter> formatters = new ArrayList<>();
+
+        formatters.add(DateTimeFormatter.ofPattern("M-d-uuuu"));
+        formatters.add(DateTimeFormatter.ofPattern("M/d/uuuu"));
+        formatters.add(DateTimeFormatter.ofPattern("uuuu-M-d"));
+        formatters.add(DateTimeFormatter.ofPattern("uuuu/M/d"));
+
+        TextTableReader.read(",", GCMPipelineFileHeaders.SIM_STATE_SETTINGS, simStateSettingsFile, (values) -> {
+            switch (values[0]) {
+            case "start_time":
+                builder.setStartTime(Double.parseDouble(values[1]));
+                break;
+            case "base_date":
+                LocalDate localDate;
+                RuntimeException runtimeException = null;
+                for (DateTimeFormatter formatter : formatters) {
+                    try {
+                        localDate = LocalDate.parse(values[1], formatter);
+                        builder.setBaseDate(localDate);
+                        runtimeException = null;
+                        break;
+                    } catch (DateTimeParseException e) {
+                        runtimeException = new RuntimeException(e);
+                    }
+                }
+
+                if (runtimeException != null) {
+                    throw runtimeException;
+                }
+
+                break;
+            // plans are not currently supported
+            }
+        });
+    }
+}

src/main/java/gov/hhs/aspr/ms/gcm/pipeline/support/GCMPipelineFileHeaders.java

@@ -0,0 +1,9 @@
+package gov.hhs.aspr.ms.gcm.pipeline.support;
+
+public class GCMPipelineFileHeaders {
+
+    private GCMPipelineFileHeaders() {
+    }
+
+    public static String SIM_STATE_SETTINGS = "property,value";	
+}

src/main/proto/gov/hhs/aspr/ms/gcm/pipeline/pipeline.proto

@@ -0,0 +1,10 @@
+syntax = "proto3";
+package gov.hhs.aspr.ms.gcm.pipeline;
+
+option java_multiple_files = true;
+option java_package = "gov.hhs.aspr.ms.gcm.pipeline.input";
+
+message SimulationStatePipelineInput {
+    string simulationSettingsFile = 1;
+    string simulationStateFile = 2;
+}

src/test/java/gov/hhs/aspr/ms/gcm/pipeline/PipelineTestHelper.java

@@ -0,0 +1,35 @@
+package gov.hhs.aspr.ms.gcm.pipeline;
+
+import gov.hhs.aspr.ms.gcm.taskit.protobuf.nucleus.NucleusTranslator;
+import gov.hhs.aspr.ms.gcm.taskit.protobuf.plugins.groups.GroupsTranslator;
+import gov.hhs.aspr.ms.gcm.taskit.protobuf.plugins.people.PeopleTranslator;
+import gov.hhs.aspr.ms.gcm.taskit.protobuf.plugins.personproperties.PersonPropertiesTranslator;
+import gov.hhs.aspr.ms.gcm.taskit.protobuf.plugins.properties.PropertiesTranslator;
+import gov.hhs.aspr.ms.gcm.taskit.protobuf.plugins.regions.RegionsTranslator;
+import gov.hhs.aspr.ms.gcm.taskit.protobuf.plugins.reports.ReportsTranslator;
+import gov.hhs.aspr.ms.gcm.taskit.protobuf.plugins.stochastics.StochasticsTranslator;
+import gov.hhs.aspr.ms.taskit.protobuf.ProtobufTranslationEngine;
+
+/**
+ * This class is to help test the pipelines
+ */
+public class PipelineTestHelper {
+
+    /*
+     * static method to return a new protobuf translation engine.
+     * 
+     * used in a method due to nature of static access
+     */
+    public static ProtobufTranslationEngine getProtobufTranslationEngine() {
+        return ProtobufTranslationEngine.builder()
+                .addTranslator(PeopleTranslator.getTranslator())
+                .addTranslator(PersonPropertiesTranslator.getTranslator())
+                .addTranslator(GroupsTranslator.getTranslator())
+                .addTranslator(RegionsTranslator.getTranslator())
+                .addTranslator(ReportsTranslator.getTranslator())
+                .addTranslator(StochasticsTranslator.getTranslator())
+                .addTranslator(PropertiesTranslator.getTranslator())
+                .addTranslator(NucleusTranslator.getTranslator())
+                .build();
+    }
+}

src/test/java/gov/hhs/aspr/ms/gcm/pipeline/PipelineTestPaths.java

@@ -0,0 +1,92 @@
+package gov.hhs.aspr.ms.gcm.pipeline;
+
+import java.nio.file.Path;
+
+import gov.hhs.aspr.ms.util.resourcehelper.ResourceHelper;
+
+/**
+ * This is a class that contains all of the paths for all pipeline test output
+ * files and the test resource directory.
+ * 
+ * When adding a new dimension or plugin data, first add the file name in the
+ * respective section, and then add the path in the respective section.
+ */
+public class PipelineTestPaths {
+    // name of expected output directory
+    private static final String EXPECTED_OUTPUT_DIR_NAME = "expectedOutput";
+
+    // name of test output directory
+    private static final String TEST_OUTPUT_DIR_NAME = "testOutput";
+
+    // name of pipelineInput directory
+    private static final String PIPELINE_INPUT_DIR_NAME = "pipelineInput";
+
+    // name of each of the pipeline input files
+    private static final String SIM_STATE_PIPELINE_INPUT_F_NAME = "simulationStatePipeline.json";
+
+    // name of each the plugin data files
+    private static final String POPULATION_P_DATA_F_NAME = "populationPluginData.json";
+    private static final String PEOPLE_P_DATA_F_NAME = "peoplePluginData.json";
+    private static final String PEOPLE_P_DATA_EMPTY_F_NAME = "peoplePluginData_empty.json";
+    private static final String PERSON_PROPS_P_DATA_F_NAME = "personPropertiesPluginData.json";
+    private static final String GROUPS_P_DATA_F_NAME = "groupsPluginData.json";
+    private static final String REGIONS_P_DATA_F_NAME = "regionsPluginData.json";
+    private static final String STOCHASTICS_P_DATA_F_NAME = "stochasticsPluginData.json";
+
+    // name of gcm experiment params and sim state files
+    private static final String EXPERIMENT_PARAMS_F_NAME = "experimentParameterData.json";
+    private static final String SIM_STATE_F_NAME = "simulationState.json";
+
+    // Absolute path to the resource directory used in testing
+    public static final Path RESOURCE_DIR = ResourceHelper.getResourceDir(PipelineTestPaths.class);
+
+    // absolute path to the expected output directory based on the resource dir
+    // above
+    public static final Path EXPECTED_OUTPUT_DIR = getResolvedResourcePath(EXPECTED_OUTPUT_DIR_NAME);
+
+    // absolute path to the test output directory based on the resource dir above
+    public static final Path TEST_OUTPUT_DIR = getResolvedResourcePath(TEST_OUTPUT_DIR_NAME);
+
+    // absolute path to the pipeline input directory based on the resource dir above
+    public static final Path PIPELINE_INPUT_DIR = getResolvedResourcePath(PIPELINE_INPUT_DIR_NAME);
+
+    // absolute paths to each of the pipeline input files
+    public static final Path SIM_STATE_PIPELINE = getResolvedPipelineInputPath(SIM_STATE_PIPELINE_INPUT_F_NAME);
+
+    // absolute paths to each of the expected output plugin data files
+    public static final Path EXPECTED_POPULATION_PLUGIN_DATA = getResolvedOutputPath(POPULATION_P_DATA_F_NAME);
+    public static final Path EXPECTED_PEOPLE_PLUGIN_DATA = getResolvedOutputPath(PEOPLE_P_DATA_F_NAME);
+    public static final Path EXPECTED_PEOPLE_PLUGIN_DATA_EMPTY = getResolvedOutputPath(PEOPLE_P_DATA_EMPTY_F_NAME);
+    public static final Path EXPECTED_PERSON_PROPS_PLUGIN_DATA = getResolvedOutputPath(PERSON_PROPS_P_DATA_F_NAME);
+    public static final Path EXPECTED_GROUPS_PLUGIN_DATA = getResolvedOutputPath(GROUPS_P_DATA_F_NAME);
+    public static final Path EXPECTED_REGIONS_PLUGIN_DATA = getResolvedOutputPath(REGIONS_P_DATA_F_NAME);
+    public static final Path EXPECTED_STOCHASTICS_PLUGIN_DATA = getResolvedOutputPath(STOCHASTICS_P_DATA_F_NAME);
+
+    // absolute paths to the gcm experiment params and sim state files
+    public static final Path EXPECTED_EXPERIMENT_PARAMETER_DATA = getResolvedOutputPath(EXPERIMENT_PARAMS_F_NAME);
+    public static final Path EXPECTED_SIMULATION_STATE = getResolvedOutputPath(SIM_STATE_F_NAME);
+
+    private PipelineTestPaths() {
+    }
+
+    /**
+     * Given a path, return it resolved against the resource directory path
+     */
+    public static Path getResolvedResourcePath(String path) {
+        return RESOURCE_DIR.resolve(path).toAbsolutePath();
+    }
+
+    /**
+     * Given a path, return it resolved against the expected output directory path
+     */
+    public static Path getResolvedOutputPath(String path) {
+        return EXPECTED_OUTPUT_DIR.resolve(path);
+    }
+
+    /**
+     * Given a path, return it resolved against the pipeline input directory path
+     */
+    public static Path getResolvedPipelineInputPath(String path) {
+        return PIPELINE_INPUT_DIR.resolve(path);
+    }
+}

src/test/java/gov/hhs/aspr/ms/gcm/pipeline/pipelines/AT_SimulationStatePipeline.java

@@ -0,0 +1,98 @@
+package gov.hhs.aspr.ms.gcm.pipeline.pipelines;
+
+import static org.junit.jupiter.api.Assertions.assertEquals;
+import static org.junit.jupiter.api.Assertions.assertNotNull;
+import static org.junit.jupiter.api.Assertions.assertThrows;
+import static org.junit.jupiter.api.Assertions.assertTrue;
+
+import java.nio.file.Path;
+import java.time.format.DateTimeParseException;
+
+import org.junit.jupiter.api.Test;
+
+import gov.hhs.aspr.ms.gcm.pipeline.PipelineTestHelper;
+import gov.hhs.aspr.ms.gcm.pipeline.PipelineTestPaths;
+import gov.hhs.aspr.ms.gcm.pipeline.input.SimulationStatePipelineInput;
+import gov.hhs.aspr.ms.gcm.pipeline.testsupport.PipelineTestSupport;
+import gov.hhs.aspr.ms.gcm.simulation.nucleus.SimulationState;
+import gov.hhs.aspr.ms.gcm.taskit.protobuf.nucleus.input.SimulationStateInput;
+import gov.hhs.aspr.ms.util.annotations.UnitTestMethod;
+import gov.hhs.aspr.ms.util.errors.ContractException;
+import gov.hhs.aspr.ms.util.resourcehelper.ResourceError;
+import gov.hhs.aspr.ms.util.resourcehelper.ResourceHelper;
+
+public class AT_SimulationStatePipeline {
+    PipelineTestSupport<SimulationStatePipelineInput> pipelineInputTestSupport = new PipelineTestSupport<>(
+            PipelineTestHelper.getProtobufTranslationEngine(),
+            SimulationStatePipelineInput.getDefaultInstance(), SimulationStatePipelineInput.class,
+            PipelineTestPaths::getResolvedResourcePath, PipelineTestPaths.TEST_OUTPUT_DIR);
+
+    SimulationStatePipelineInput unresolvedPipelineInput = pipelineInputTestSupport
+            .getUnresolvedPipelineInput(PipelineTestPaths.SIM_STATE_PIPELINE.toString());
+
+    SimulationStatePipelineInput resolvedPipelineInput = pipelineInputTestSupport
+            .getResolvedPipelineInput(unresolvedPipelineInput, false, false);
+
+    @Test
+    @UnitTestMethod(target = SimulationStatePipeline.class, name = "from", args = {
+            SimulationStatePipelineInput.class,
+            Path.class, Path.class })
+    public void testFrom() {
+
+        Path inputPath = Path.of("");
+        Path outputPath = Path.of("");
+
+        SimulationStatePipelineInput pipelineInput = resolvedPipelineInput;
+
+        SimulationStatePipeline pipeline = SimulationStatePipeline.from(pipelineInput, inputPath, outputPath);
+
+        assertNotNull(pipeline);
+
+        // preconditions
+        // simStateSettingsFile is invalid
+        ContractException contractException = assertThrows(ContractException.class, () -> {
+            SimulationStatePipeline.from(
+                    pipelineInput.toBuilder().setSimulationSettingsFile("invalidPath").build(),
+                    inputPath, outputPath);
+        });
+
+        assertEquals(ResourceError.UNKNOWN_FILE, contractException.getErrorType());
+    }
+
+    @Test
+    @UnitTestMethod(target = SimulationStatePipeline.class, name = "execute", args = {})
+    public void testExecute() {
+
+        Path resourceDir = PipelineTestPaths.RESOURCE_DIR;
+
+        Path inputPath = Path.of("");
+        Path outputPath = Path.of("");
+
+        SimulationStatePipelineInput pipelineInput = resolvedPipelineInput;
+
+        Path dataFile = resourceDir.resolve(pipelineInput.getSimulationStateFile());
+
+        ResourceHelper.createDirectory(dataFile.getParent());
+        ResourceHelper.createFile(dataFile.getParent(), dataFile.getFileName().toString());
+
+        SimulationStatePipeline pipeline = SimulationStatePipeline.from(pipelineInput, inputPath, outputPath);
+
+        pipeline.execute();
+
+        assertTrue(pipelineInputTestSupport.filesAreSame(SimulationStateInput.class,
+                SimulationState.class, PipelineTestPaths.EXPECTED_SIMULATION_STATE, dataFile));
+
+        // preconditions
+        // base date is invalid
+        SimulationStatePipelineInput badDate = pipelineInput.toBuilder()
+                .setSimulationSettingsFile(pipelineInput.getSimulationSettingsFile()
+                        .replace("simulation_settings.csv", "simulation_settings_bad_date.csv"))
+                .build();
+
+        RuntimeException runtimeException = assertThrows(RuntimeException.class, () -> {
+            SimulationStatePipeline.from(badDate, inputPath, outputPath).execute();
+        });
+
+        assertEquals(DateTimeParseException.class, runtimeException.getCause().getClass());
+    }
+}