Add sqlite data stores for migration

pace-datastore/pace-sqlite-datastore/pom.xml

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+<?xml version="1.0" encoding="UTF-8"?>
+<project xmlns="http://maven.apache.org/POM/4.0.0"
+  xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
+  xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd">
+  <modelVersion>4.0.0</modelVersion>
+  <parent>
+    <groupId>io.github.ci-cmg</groupId>
+    <artifactId>pace-datastore</artifactId>
+    <version>0.1.0-SNAPSHOT</version>
+  </parent>
+
+  <artifactId>pace-sqlite-datastore</artifactId>
+
+  <properties>
+    <maven.compiler.source>17</maven.compiler.source>
+    <maven.compiler.target>17</maven.compiler.target>
+    <project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
+  </properties>
+
+  <dependencies>
+    <dependency>
+      <groupId>io.github.ci-cmg</groupId>
+      <artifactId>pace-common-datastore</artifactId>
+    </dependency>
+    <dependency>
+      <groupId>org.xerial</groupId>
+      <artifactId>sqlite-jdbc</artifactId>
+      <version>3.45.3.0</version>
+    </dependency>
+
+    <dependency>
+      <groupId>org.junit.jupiter</groupId>
+      <artifactId>junit-jupiter-api</artifactId>
+      <version>5.10.1</version>
+      <scope>test</scope>
+    </dependency>
+    <dependency>
+      <groupId>commons-io</groupId>
+      <artifactId>commons-io</artifactId>
+      <version>2.16.0</version>
+      <scope>test</scope>
+    </dependency>
+    <dependency>
+      <groupId>org.mockito</groupId>
+      <artifactId>mockito-core</artifactId>
+      <version>5.11.0</version>
+      <scope>test</scope>
+    </dependency>
+  </dependencies>
+
+  <profiles>
+    <profile>
+      <id>coverage</id>
+      <build>
+        <plugins>
+          <plugin>
+            <groupId>org.jacoco</groupId>
+            <artifactId>jacoco-maven-plugin</artifactId>
+            <configuration>
+              <rules>
+                <rule>
+                  <element>BUNDLE</element>
+                  <limits>
+                    <limit>
+                      <counter>LINE</counter>
+                      <value>COVEREDRATIO</value>
+                      <minimum>0.90</minimum>
+                    </limit>
+                    <limit>
+                      <counter>BRANCH</counter>
+                      <value>COVEREDRATIO</value>
+                      <minimum>0.90</minimum>
+                    </limit>
+                  </limits>
+                </rule>
+              </rules>
+            </configuration>
+          </plugin>
+          <plugin>
+            <groupId>org.apache.maven.plugins</groupId>
+            <artifactId>maven-surefire-plugin</artifactId>
+          </plugin>
+        </plugins>
+      </build>
+    </profile>
+  </profiles>
+
+</project>

pace-datastore/pace-sqlite-datastore/src/main/java/edu/colorado/cires/pace/datastore/sqlite/DetectionTypeSQLiteDatastore.java

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+package edu.colorado.cires.pace.datastore.sqlite;
+
+import edu.colorado.cires.pace.data.object.DetectionType;
+import java.nio.file.Path;
+import java.sql.ResultSet;
+import java.sql.SQLException;
+import java.util.ArrayList;
+import java.util.List;
+import java.util.stream.Stream;
+
+public class DetectionTypeSQLiteDatastore extends SQLiteDatastore<DetectionType> {
+
+  protected DetectionTypeSQLiteDatastore(Path sqliteFile) {
+    super(sqliteFile, "DETECTION_TYPES");
+  }
+
+  @Override
+  protected Stream<DetectionType> resultSetToStream(ResultSet resultSet) throws SQLException {
+    List<DetectionType> detectionTypes = new ArrayList<>(0);
+
+    while (resultSet.next()) {
+      detectionTypes.add(DetectionType.builder()
+              .source(resultSet.getString("SOURCE"))
+              .scienceName(resultSet.getString("SCIENCE_NAME"))
+          .build());
+    }
+
+    return detectionTypes.stream();
+  }
+}

pace-datastore/pace-sqlite-datastore/src/main/java/edu/colorado/cires/pace/datastore/sqlite/FileTypeSQLiteDatastore.java

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+package edu.colorado.cires.pace.datastore.sqlite;
+
+import edu.colorado.cires.pace.data.object.FileType;
+import java.nio.file.Path;
+import java.sql.ResultSet;
+import java.sql.SQLException;
+import java.util.ArrayList;
+import java.util.List;
+import java.util.stream.Stream;
+
+public class FileTypeSQLiteDatastore extends SQLiteDatastore<FileType> {
+
+  protected FileTypeSQLiteDatastore(Path sqliteFile) {
+    super(sqliteFile, "FILE_TYPES");
+  }
+
+  @Override
+  protected Stream<FileType> resultSetToStream(ResultSet resultSet) throws SQLException {
+    List<FileType> fileTypes = new ArrayList<>(0);
+
+    while (resultSet.next()) {
+      fileTypes.add(FileType.builder()
+              .type(resultSet.getString("TYPE"))
+          .build());
+    }
+
+    return fileTypes.stream();
+  }
+}

pace-datastore/pace-sqlite-datastore/src/main/java/edu/colorado/cires/pace/datastore/sqlite/InstrumentSQLiteDatastore.java

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+package edu.colorado.cires.pace.datastore.sqlite;
+
+import edu.colorado.cires.pace.data.object.FileType;
+import edu.colorado.cires.pace.data.object.Instrument;
+import edu.colorado.cires.pace.datastore.Datastore;
+import edu.colorado.cires.pace.datastore.DatastoreException;
+import java.nio.file.Path;
+import java.sql.ResultSet;
+import java.sql.SQLException;
+import java.util.ArrayList;
+import java.util.Arrays;
+import java.util.List;
+import java.util.stream.Stream;
+
+public class InstrumentSQLiteDatastore extends SQLiteDatastore<Instrument> {
+
+  private final Datastore<FileType> fileTypeDatastore;
+
+  protected InstrumentSQLiteDatastore(Path sqliteFile, Datastore<FileType> fileTypeDatastore) {
+    super(sqliteFile, "INSTRUMENTS");
+    this.fileTypeDatastore = fileTypeDatastore;
+  }
+
+  @Override
+  protected Stream<Instrument> resultSetToStream(ResultSet resultSet) throws SQLException {
+    List<Instrument> instruments = new ArrayList<>(0);
+
+    while (resultSet.next()) {
+      instruments.add(Instrument.builder()
+              .name(resultSet.getString("Name"))
+              .fileTypes(Arrays.stream(resultSet.getString("FILE_TYPES").split(","))
+                  .map(ft -> {
+                    try {
+                      return fileTypeDatastore.findByUniqueField(ft).orElseThrow(
+                          () -> new DatastoreException(String.format(
+                              "file type %s not found", ft 
+                          ), null)
+                      );
+                    } catch (DatastoreException e) {
+                      throw new RuntimeException(e);
+                    }
+                  })
+                  .toList())
+          .build());
+    }
+
+    return instruments.stream();
+  }
+}

pace-datastore/pace-sqlite-datastore/src/main/java/edu/colorado/cires/pace/datastore/sqlite/OrganizationsSQLiteDatastore.java

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+package edu.colorado.cires.pace.datastore.sqlite;
+
+import edu.colorado.cires.pace.data.object.Organization;
+import java.nio.file.Path;
+import java.sql.ResultSet;
+import java.sql.SQLException;
+import java.util.ArrayList;
+import java.util.List;
+import java.util.UUID;
+import java.util.stream.Stream;
+
+public class OrganizationsSQLiteDatastore extends SQLiteDatastore<Organization> {
+
+  protected OrganizationsSQLiteDatastore(Path sqliteFile) {
+    super(sqliteFile, "ORGANIZATIONS");
+  }
+
+  @Override
+  protected Stream<Organization> resultSetToStream(ResultSet resultSet) throws SQLException {
+    List<Organization> organizations = new ArrayList<>(0);
+
+    while (resultSet.next()) {
+      organizations.add(Organization.builder()
+              .name(resultSet.getString("NAME"))
+              .street(resultSet.getString("STREET"))
+              .city(resultSet.getString("CITY"))
+              .state(resultSet.getString("STATE"))
+              .zip(resultSet.getString("ZIP"))
+              .country(resultSet.getString("COUNTRY"))
+              .email(resultSet.getString("EMAIL"))
+              .phone(resultSet.getString("PHONE"))
+              .uuid(UUID.fromString(resultSet.getString("UUID")))
+          .build());
+    }
+
+    return organizations.stream();
+  }
+}

pace-datastore/pace-sqlite-datastore/src/main/java/edu/colorado/cires/pace/datastore/sqlite/PersonSQLiteDatastore.java

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+package edu.colorado.cires.pace.datastore.sqlite;
+
+import edu.colorado.cires.pace.data.object.Person;
+import java.nio.file.Path;
+import java.sql.ResultSet;
+import java.sql.SQLException;
+import java.util.ArrayList;
+import java.util.List;
+import java.util.UUID;
+import java.util.stream.Stream;
+
+public class PersonSQLiteDatastore extends SQLiteDatastore<Person> {
+
+  protected PersonSQLiteDatastore(Path sqliteFile) {
+    super(sqliteFile, "PEOPLE");
+  }
+
+  @Override
+  protected Stream<Person> resultSetToStream(ResultSet resultSet) throws SQLException {
+    List<Person> people = new ArrayList<>(0);
+
+    while (resultSet.next()) {
+      people.add(Person.builder()
+              .name(resultSet.getString("NAME"))
+              .street(resultSet.getString("STREET"))
+              .city(resultSet.getString("CITY"))
+              .state(resultSet.getString("STATE"))
+              .zip(resultSet.getString("ZIP"))
+              .country(resultSet.getString("COUNTRY"))
+              .email(resultSet.getString("EMAIL"))
+              .phone(resultSet.getString("PHONE"))
+              .uuid(UUID.fromString(resultSet.getString("UUID")))
+              .orcid(resultSet.getString("ORCID"))
+              .organization(resultSet.getString("ORGANIZATION"))
+              .position(resultSet.getString("POSITION"))
+          .build());
+    }
+
+    return people.stream();
+  }
+}

pace-datastore/pace-sqlite-datastore/src/main/java/edu/colorado/cires/pace/datastore/sqlite/PlatformSQLiteDatastore.java

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+package edu.colorado.cires.pace.datastore.sqlite;
+
+import edu.colorado.cires.pace.data.object.Platform;
+import java.nio.file.Path;
+import java.sql.ResultSet;
+import java.sql.SQLException;
+import java.util.ArrayList;
+import java.util.List;
+import java.util.stream.Stream;
+
+public class PlatformSQLiteDatastore extends SQLiteDatastore<Platform> {
+
+  protected PlatformSQLiteDatastore(Path sqliteFile) {
+    super(sqliteFile, "PLATFORMS");
+  }
+
+  @Override
+  protected Stream<Platform> resultSetToStream(ResultSet resultSet) throws SQLException {
+    List<Platform> platforms = new ArrayList<>(0);
+
+    while (resultSet.next()) {
+      platforms.add(Platform.builder()
+              .name(resultSet.getString("NAME"))
+          .build());
+    }
+
+    return platforms.stream();
+  }
+}

pace-datastore/pace-sqlite-datastore/src/main/java/edu/colorado/cires/pace/datastore/sqlite/ProjectSQLiteDatastore.java

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+package edu.colorado.cires.pace.datastore.sqlite;
+
+import edu.colorado.cires.pace.data.object.Project;
+import java.nio.file.Path;
+import java.sql.ResultSet;
+import java.sql.SQLException;
+import java.util.ArrayList;
+import java.util.List;
+import java.util.stream.Stream;
+
+public class ProjectSQLiteDatastore extends SQLiteDatastore<Project> {
+
+  protected ProjectSQLiteDatastore(Path sqliteFile) {
+    super(sqliteFile, "PROJECTS");
+  }
+
+  @Override
+  protected Stream<Project> resultSetToStream(ResultSet resultSet) throws SQLException {
+    List<Project> projects = new ArrayList<>(0);
+
+    while (resultSet.next()) {
+      projects.add(Project.builder()
+              .name(resultSet.getString("NAME"))
+          .build());
+    }
+
+    return projects.stream();
+  }
+}