Refactored ID mapping to use databricks jdbc template instead (#1571) (#1576)

* Refactored ID mapping to use databricks jdbc template instead (#1571)

Signed-off-by: Angelica Ochoa <15623749+ao508@users.noreply.github.com>

* Remove references to user 'laptop' (#1577)

Signed-off-by: Angelica Ochoa <15623749+ao508@users.noreply.github.com>

* Updated databricks view name (#1578)

Signed-off-by: Angelica Ochoa <15623749+ao508@users.noreply.github.com>

* Renamed mat views (#1579)

Signed-off-by: Angelica Ochoa <15623749+ao508@users.noreply.github.com>

---------

Signed-off-by: Angelica Ochoa <15623749+ao508@users.noreply.github.com>

Author: ao508

README.md

@@ -18,8 +18,8 @@ All properties are required with the exception of some NATS connection-specific
 ### Locally
 
 **Requirements:**
-- maven 3.6.1
-- java 8
+- maven 3.8.8
+- java 21
 
 Add `application.properties` to the local application resources: `src/main/resources`
 
@@ -32,7 +32,7 @@ mvn clean install
 Run with
 
 ```
-java -jar server/target/smile_server.jar
+java --add-opens=java.base/java.nio=org.apache.arrow.memory.core,ALL-UNNAMED -jar server/target/smile_server.jar
 ```
 
 ### With Docker
@@ -57,14 +57,14 @@ If the Docker image is built with the properties baked in then simply run with:
 
 ```
 docker run --name smile-server <repo>/<tag>:<version> \
-	-jar /smile-server/smile_server.jar
+	--add-opens=java.base/java.nio=org.apache.arrow.memory.core,ALL-UNNAMED -jar /smile-server/smile_server.jar
 ```
 
 Otherwise use a bind mount to make the local files available to the Docker image and add  `--spring.config.location` to the java arg
 
 ```
 docker run --mount type=bind,source=<local path to properties files>,target=/smile-server/src/main/resources \
 	--name smile-server <repo>/<tag>:<version> \
-	-jar /smile-server/smile_server.jar \
+	--add-opens=java.base/java.nio=org.apache.arrow.memory.core,ALL-UNNAMED -jar /smile-server/smile_server.jar \
 	--spring.config.location=/cmo-metadb/src/main/resources/application.properties
 ```

model/src/main/java/org/mskcc/smile/model/internal/CrdbMappingModel.java

@@ -0,0 +1,68 @@
+package org.mskcc.smile.model.internal;
+
+/**
+ *
+ * @author ochoaa
+ */
+public class PatientIdTriplet {
+    private String mrn;
+    private String cmoPatientId;
+    private String dmpPatientId;
+
+    public PatientIdTriplet() {}
+
+    /**
+     * PatientIdTriplet constructor.
+     * @param mrn
+     * @param cmoPatientId
+     * @param dmpPatientId
+     */
+    public PatientIdTriplet(String mrn, String cmoPatientId, String dmpPatientId) {
+        this.mrn = mrn;
+        this.cmoPatientId = cmoPatientId;
+        this.dmpPatientId = dmpPatientId;
+    }
+
+    /**
+     * @return the mrn
+     */
+    public String getMrn() {
+        return mrn;
+    }
+
+    /**
+     * @param mrn the mrn to set
+     */
+    public void setMrn(String mrn) {
+        this.mrn = mrn;
+    }
+
+    /**
+     * @return the cmoPatientId
+     */
+    public String getCmoPatientId() {
+        return cmoPatientId;
+    }
+
+    /**
+     * @param cmoPatientId the cmoPatientId to set
+     */
+    public void setCmoPatientId(String cmoPatientId) {
+        this.cmoPatientId = cmoPatientId;
+    }
+
+    /**
+     * @return the dmpPatientId
+     */
+    public String getDmpPatientId() {
+        return dmpPatientId;
+    }
+
+    /**
+     * @param dmpPatientId the dmpPatientId to set
+     */
+    public void setDmpPatientId(String dmpPatientId) {
+        this.dmpPatientId = dmpPatientId;
+    }
+
+}

model/src/main/java/org/mskcc/smile/model/internal/PatientIdTriplet.java

@@ -0,0 +1,22 @@
+package org.mskcc.smile.model.internal;
+
+import java.sql.ResultSet;
+import java.sql.SQLException;
+import org.springframework.jdbc.core.RowMapper;
+
+/**
+ *
+ * @author ochoaa
+ */
+public class PatientIdTripletMapper implements RowMapper<PatientIdTriplet> {
+
+    @Override
+    public PatientIdTriplet mapRow(ResultSet rs, int rowNum) throws SQLException {
+        PatientIdTriplet patient = new PatientIdTriplet();
+        patient.setMrn(rs.getString("MRN"));
+        patient.setCmoPatientId(rs.getString("CMO_PATIENT_ID"));
+        patient.setDmpPatientId(rs.getString("DMP_PATIENT_ID"));
+        return patient;
+    }
+
+}

model/src/main/java/org/mskcc/smile/model/internal/PatientIdTripletMapper.java

@@ -16,11 +16,11 @@
       <artifactId>model</artifactId>
       <version>${project.version}</version>
     </dependency>
-    <!-- oracle jdbc driver -->
+    <!-- https://mvnrepository.com/artifact/com.databricks/databricks-jdbc -->
     <dependency>
-      <groupId>com.oracle.database.jdbc</groupId>
-      <artifactId>ojdbc8</artifactId>
-      <version>21.1.0.0</version>
+      <groupId>com.databricks</groupId>
+      <artifactId>databricks-jdbc</artifactId>
+      <version>2.7.3</version>
     </dependency>
   </dependencies>
 </project>

persistence/pom.xml

@@ -0,0 +1,30 @@
+package org.mskcc.smile.persistence.jdbc;
+
+import com.databricks.client.jdbc.Driver;
+import org.springframework.beans.factory.annotation.Value;
+import org.springframework.context.annotation.Bean;
+import org.springframework.context.annotation.Configuration;
+import org.springframework.jdbc.core.JdbcTemplate;
+import org.springframework.jdbc.datasource.SimpleDriverDataSource;
+
+/**
+ *
+ * @author ochoaa
+ */
+@Configuration
+public class DatabricksJdbcConfig {
+    @Value("${databricks.url}")
+    private String databricksUrl;
+
+    /**
+     * Returns the databricks JdbcTemplate.
+     * @return JdbcTemplate
+     */
+    @Bean
+    public JdbcTemplate databricksJdbcTemplate() {
+        SimpleDriverDataSource dataSource = new SimpleDriverDataSource();
+        dataSource.setDriver(new Driver());
+        dataSource.setUrl(databricksUrl);
+        return new JdbcTemplate(dataSource);
+    }
+}

persistence/src/main/java/org/mskcc/smile/persistence/jdbc/DatabricksJdbcConfig.java

@@ -0,0 +1,45 @@
+package org.mskcc.smile.persistence.jdbc;
+
+import java.sql.PreparedStatement;
+import java.sql.SQLException;
+import java.util.List;
+import org.mskcc.smile.model.internal.PatientIdTriplet;
+import org.mskcc.smile.model.internal.PatientIdTripletMapper;
+import org.springframework.beans.factory.annotation.Autowired;
+import org.springframework.jdbc.core.JdbcTemplate;
+import org.springframework.jdbc.core.PreparedStatementSetter;
+import org.springframework.stereotype.Repository;
+
+/**
+ *
+ * @author ochoaa
+ */
+@Repository
+public class DatabricksRepository {
+    @Autowired
+    private JdbcTemplate jdbcTemplate;
+
+    /**
+     * Returns an instance of PatientIdTriplet given an input.
+     * @param inputId
+     * @return PatientIdTriplet
+     */
+    public PatientIdTriplet findPatientIdTripletByInputId(String inputId) {
+        String sqlQuery = "SELECT MRN, CMO_PATIENT_ID, DMP_PATIENT_ID "
+                + "FROM cdsi_eng_phi.id_mapping.mrn_cmo_dmp_patient_fullouter "
+                + "WHERE ? IN (MRN, CMO_PATIENT_ID, DMP_PATIENT_ID)";
+
+        List<PatientIdTriplet> patientIds = jdbcTemplate.query(
+                sqlQuery,
+                new PreparedStatementSetter() {
+                    @Override
+                    public void setValues(PreparedStatement ps) throws SQLException {
+                        ps.setString(1, inputId);
+                    }
+                },
+                new PatientIdTripletMapper()
+        );
+        return patientIds.isEmpty() ? null : patientIds.get(0);
+    }
+
+}

persistence/src/main/java/org/mskcc/smile/persistence/jdbc/DatabricksRepository.java

@@ -8,7 +8,7 @@
 
 /**
  *
- * @author laptop
+ * @author ochoaa
  */
 @Configuration
 @EnableNeo4jRepositories(basePackages = "org.mskcc.smile.persistence.neo4j")