Introduce support for InterSystems IRIS (#2416)

Author: bdeboe

pom.xml

@@ -30,7 +30,7 @@
 
     <circe.version>1.12.0</circe.version>
     <jersey.version>2.14</jersey.version>
-    <SqlRender.version>1.16.1</SqlRender.version>
+    <SqlRender.version>1.19.1</SqlRender.version>
     <hive-jdbc.version>3.1.2</hive-jdbc.version>
     <pac4j.version>4.0.0</pac4j.version>
     <jackson.version>2.12.7</jackson.version>
@@ -200,7 +200,7 @@
     <server.ssl.key-password></server.ssl.key-password>
     <server.servlet.context-path>/WebAPI</server.servlet.context-path>
 
-    <arachne.version>1.17.3</arachne.version>
+    <arachne.version>1.17.4</arachne.version>
     <jersey-media-multipart.version>2.25.1</jersey-media-multipart.version>
     <execution.invalidation.period>600000</execution.invalidation.period>
     <execution.invalidation.maxage.hours>12</execution.invalidation.maxage.hours>
@@ -1859,6 +1859,20 @@
         </dependency>
       </dependencies>
     </profile>
+    <profile>
+      <id>webapi-iris</id>
+      <properties>
+        <iris.enabled>true</iris.enabled>
+        <iris.driver.version>3.10.2</iris.driver.version>
+      </properties>
+      <dependencies>
+        <dependency>
+          <groupId>com.intersystems</groupId>
+          <artifactId>intersystems-jdbc</artifactId>
+          <version>${iris.driver.version}</version>
+        </dependency>
+      </dependencies>
+    </profile>
     <profile>
       <id>webapi-gis</id>
       <properties>

src/main/extras/iris/README.md

@@ -0,0 +1,46 @@
+# Using WebAPI with InterSystems IRIS support
+
+## Building WebAPI
+
+To build WebAPI with InterSystems IRIS support, you can simply use the `webapi-iris` profile
+when building WebAPI with Maven:
+
+```Shell
+mvn -Pwebapi-postgresql,webapi-iris clean package
+```
+
+or on Windows PowerShell:
+```Shell
+mvn "-Pwebapi-postgresql,webapi-iris" clean package
+```
+
+This will automatically download and package a recent version of the InterSystems IRIS JDBC
+driver from Maven Central.
+
+Alternatively, the JDBC driver for InterSystems IRIS can be found in the `dev/java/lib/1.8/`
+subfolder of your IRIS installation, or as a download from InterSystems Cloud Services portal.
+
+
+## Sample configuration
+
+When configuring Atlas / WebAPI to access CDM on IRIS over a secure connection, your source 
+registration looks like this:
+```SQL
+INSERT INTO webapi.source (source_id, source_name, source_key, source_connection, source_dialect, username, password)
+  VALUES (<#>, 'OHDSI IRIS Database', 'IRIS', 'jdbc:IRIS://<hostname>.elb.us-west-2.amazonaws.com:443/USER/:::true', 
+  'iris', '<username>','<password>');
+```
+
+For a non-encrypted, local connection, this may look like:
+```SQL
+INSERT INTO webapi.source (source_id, source_name, source_key, source_connection, source_dialect, username, password)
+  VALUES (<#>, 'OHDSI IRIS Database', 'IRIS', 'jdbc:IRIS://localhost:1972/USER/', 'iris', '_SYSTEM_','SYS');
+```
+
+
+## References
+
+For more information on how to connect to InterSystems IRIS or InterSystems IRIS Cloud SQL, please see:
+* [Connecting your applications to Cloud SQL](https://docs.intersystems.com/components/csp/docbook/DocBook.UI.Page.cls?KEY=GDRIVE_cloudsql)
+* [Troubleshooting connection issues](https://docs.intersystems.com/services/csp/docbook/DocBook.UI.Page.cls?KEY=ACTS)
+* [InterSystems fork for OHDSI Broadsea](https://github.com/isc-krakshith/InterSystems-Broadsea/)

src/main/java/org/ohdsi/webapi/DataAccessConfig.java

@@ -82,7 +82,7 @@ public DataSource primaryDataSource() {
         //note autocommit defaults vary across vendors. use provided @Autowired TransactionTemplate
 
         String[] supportedDrivers;
-        supportedDrivers = new String[]{"org.postgresql.Driver", "com.microsoft.sqlserver.jdbc.SQLServerDriver", "oracle.jdbc.driver.OracleDriver", "com.amazon.redshift.jdbc.Driver", "com.cloudera.impala.jdbc.Driver", "net.starschema.clouddb.jdbc.BQDriver", "org.netezza.Driver", "com.simba.googlebigquery.jdbc42.Driver", "org.apache.hive.jdbc.HiveDriver", "com.simba.spark.jdbc.Driver", "net.snowflake.client.jdbc.SnowflakeDriver", "com.databricks.client.jdbc.Driver"};
+        supportedDrivers = new String[]{"org.postgresql.Driver", "com.microsoft.sqlserver.jdbc.SQLServerDriver", "oracle.jdbc.driver.OracleDriver", "com.amazon.redshift.jdbc.Driver", "com.cloudera.impala.jdbc.Driver", "net.starschema.clouddb.jdbc.BQDriver", "org.netezza.Driver", "com.simba.googlebigquery.jdbc42.Driver", "org.apache.hive.jdbc.HiveDriver", "com.simba.spark.jdbc.Driver", "net.snowflake.client.jdbc.SnowflakeDriver", "com.databricks.client.jdbc.Driver", "com.intersystems.jdbc.IRISDriver"};
         for (String driverName : supportedDrivers) {
             try {
                 Class.forName(driverName);

src/main/java/org/ohdsi/webapi/util/CancelableJdbcTemplate.java

@@ -156,6 +156,8 @@ private boolean supportsBatchUpdates(Connection connection) throws SQLException
 
     // NOTE:
     // com.cloudera.impala.hivecommon.dataengine.HiveJDBCDataEngine.prepareBatch throws NOT_IMPLEMENTED exception
-    return JdbcUtils.supportsBatchUpdates(connection) && !connection.getMetaData().getURL().startsWith("jdbc:impala");
+    return JdbcUtils.supportsBatchUpdates(connection) 
+              && !connection.getMetaData().getURL().startsWith("jdbc:impala")
+              && !connection.getMetaData().getURL().startsWith("jdbc:IRIS");
   }
 }

src/main/resources/i18n/messages_en.json

@@ -2678,7 +2678,8 @@
           "sqlserver": "SQL server",
           "synapse": "Azure Synapse",
           "snowflake": "Snowflake",
-          "spark": "Apache Spark"
+          "spark": "Apache Spark",
+          "iris": "InterSystems IRIS"
         },
         "title": "Source dialect"
       },

src/main/resources/i18n/messages_ko.json

@@ -2620,7 +2620,8 @@
           "sqlserver": "SQL server",
           "synapse": "Azure Synapse",
           "snowflake": "Snowflake",
-          "spark": "Apache Spark"
+          "spark": "Apache Spark",
+          "iris": "InterSystems IRIS"
         },
         "title": "소스 dialect"
       },

src/main/resources/i18n/messages_ru.json

@@ -2534,7 +2534,8 @@
           "hive": "Hive LLAP",
           "synapse": "Azure Synapse",
           "snowflake": "Snowflake",
-          "spark": "Apache Spark"
+          "spark": "Apache Spark",
+          "iris": "InterSystems IRIS"
         }
       },
       "connectionString": {

src/main/resources/i18n/messages_zh.json

@@ -2620,7 +2620,8 @@
           "sqlserver": "SQL服务器",
           "synapse": "Azure Synapse",
           "snowflake": "Snowflake",
-          "spark": "Apache Spark"
+          "spark": "Apache Spark",
+          "iris": "InterSystems IRIS"
         },
         "title": "源语言"
       },

src/test/java/org/ohdsi/webapi/util/DataSourceDTOParserTest.java

@@ -29,6 +29,7 @@ public class DataSourceDTOParserTest {
     public static final String ORACLE_WO_PWD_CONN_STR = "jdbc:oracle:thin:@myhost:1521:orcl";
     public static final String ORACLE_WITH_PWD_CONN_STR = "jdbc:oracle:thin:scott/tiger@myhost:1521:orcl";
     public static final String HIVE_CONN_STR = "jdbc:hive2://sandbox-hdp.hortonworks.com:2181/synpuf_531_orc;serviceDiscoveryMode=zooKeeper;zooKeeperNamespace=hiveserver2";
+    public static final String IRIS_CONN_STR = "jdbc:IRIS://localhost:1972/USER";
 
     @Test
     public void parseDTO() {
@@ -110,6 +111,12 @@ public void parseDTO() {
         assertThat(dto.getConnectionString(), is(HIVE_CONN_STR));
         assertThat(dto.getUsername(), is(nullValue()));
         assertThat(dto.getPassword(), is(nullValue()));
+
+        dto = DataSourceDTOParser.parseDTO(getIRISSource());
+        assertThat(dto.getType(), is(DBMSType.IRIS));
+        assertThat(dto.getConnectionString(), is(IRIS_CONN_STR));
+        assertThat(dto.getUsername(), is(nullValue()));
+        assertThat(dto.getPassword(), is(nullValue()));
     }
 
     private Source getPostgreSQLPasswordSource() {
@@ -204,4 +211,11 @@ private Source getHiveSource() {
         source.setSourceConnection(HIVE_CONN_STR);
         return source;
     }
+
+    private Source getIRISSource() {
+        Source source = new Source();
+        source.setSourceDialect("iris");
+        source.setSourceConnection(IRIS_CONN_STR);
+        return source;
+    }
 }