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Importer/Run Importer: Also accept params from Environment Variables
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For DB connection and other params, accept params from Environment
Variables and if not set then from config file.
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@danjasuw
danjasuw committed Nov 8, 2021
1 parent 79b0a75 commit 2472a4a
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Showing 5 changed files with 94 additions and 32 deletions.
4 changes: 2 additions & 2 deletions ...a/org/yeastrc/proxl/import_xml_to_db/program_default/ImporterDefaultMainProgramEntry.java
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Expand Up @@ -39,7 +39,7 @@
import org.yeastrc.proxl.import_xml_to_db.dao.ConfigSystemDAO;
import org.yeastrc.proxl.import_xml_to_db.dao.ProxlXMLFileImportTrackingRun_For_ImporterRunner_DAO;
import org.yeastrc.proxl.import_xml_to_db.database_update_with_transaction_services.UpdateTrackingTrackingRunRecordsDBTransaction;
import org.yeastrc.proxl.import_xml_to_db.db.DBConnectionParametersProviderFromPropertiesFile;
import org.yeastrc.proxl.import_xml_to_db.db.DBConnectionParametersProviderFromPropertiesFileEnvironmentVariables;
import org.yeastrc.proxl.import_xml_to_db.db.DBConnectionParametersProviderPropertiesFileContentsErrorException;
import org.yeastrc.proxl.import_xml_to_db.db.DBConnectionParametersProviderPropertiesFileErrorException;
import org.yeastrc.proxl.import_xml_to_db.db.ImportDBConnectionFactory;
Expand Down Expand Up @@ -324,7 +324,7 @@ public ImportResults importerDefaultMainProgramEntryPassingArgsAndProxlXMLObject
Runtime runtime = Runtime.getRuntime();
runtime.addShutdownHook( importProgramShutdownThread );
if ( createDatabaseConnectionFactory ) {
DBConnectionParametersProviderFromPropertiesFile dbConnectionParametersProvider = new DBConnectionParametersProviderFromPropertiesFile();
DBConnectionParametersProviderFromPropertiesFileEnvironmentVariables dbConnectionParametersProvider = new DBConnectionParametersProviderFromPropertiesFileEnvironmentVariables();
if ( dbConfigFile != null ) {
dbConnectionParametersProvider.setConfigFile( dbConfigFile );
}
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63 changes: 48 additions & 15 deletions ...ParametersProviderFromPropertiesFile.java → ...omPropertiesFileEnvironmentVariables.java
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Expand Up @@ -17,7 +17,7 @@
* Default version of IDBConnectionParametersProvider that reads a property file
*
*/
public class DBConnectionParametersProviderFromPropertiesFile implements IDBConnectionParametersProvider {
public class DBConnectionParametersProviderFromPropertiesFileEnvironmentVariables implements IDBConnectionParametersProvider {


private static final String NO_PROPERTIES_FILE_ERROR_MESSAGE = "No DB Connection Properties file found.";
Expand All @@ -33,9 +33,17 @@ public class DBConnectionParametersProviderFromPropertiesFile implements IDBConn
private static final String PROPERTY_NAME__PROXL_DB_NAME = "proxl.db.name";


private static final String ENVIRONMENT_VARIABLE__USERNAME = "PROXL_DB_USER";
private static final String ENVIRONMENT_VARIABLE__PASSWORD = "PROXL_DB_PASSWORD";
private static final String ENVIRONMENT_VARIABLE__DB_HOST = "PROXL_DB_HOST_ADDRESS";
private static final String ENVIRONMENT_VARIABLE__DB_PORT = "PROXL_DB_HOST_PORT";

private static final String ENVIRONMENT_VARIABLE__PROXL_DB_NAME = "PROXL_DB_NAME";


private static final Logger log = LoggerFactory.getLogger( DBConnectionParametersProviderFromPropertiesFile.class );


private static final Logger log = LoggerFactory.getLogger( DBConnectionParametersProviderFromPropertiesFileEnvironmentVariables.class );


private File configFile;
Expand Down Expand Up @@ -186,13 +194,32 @@ public void init()
public void getConfigPropertiesFromPropertiesObj( Properties configProps )
throws DBConnectionParametersProviderPropertiesFileContentsErrorException {

username = configProps.getProperty( PROPERTY_NAME__USERNAME );
password = configProps.getProperty( PROPERTY_NAME__PASSWORD );
dbHost = configProps.getProperty( PROPERTY_NAME__DB_HOST );
dbPort = configProps.getProperty( PROPERTY_NAME__DB_PORT );
username = System.getenv( ENVIRONMENT_VARIABLE__USERNAME );
password = System.getenv( ENVIRONMENT_VARIABLE__PASSWORD );
dbHost = System.getenv( ENVIRONMENT_VARIABLE__DB_HOST );
dbPort = System.getenv( ENVIRONMENT_VARIABLE__DB_PORT );

proxlDbName = System.getenv( ENVIRONMENT_VARIABLE__PROXL_DB_NAME );

// Get from Config file if NOT in Environment Variables

proxlDbName = configProps.getProperty( PROPERTY_NAME__PROXL_DB_NAME );
if ( username == null ) {
username = configProps.getProperty( PROPERTY_NAME__USERNAME );
}
if ( password == null ) {
password = configProps.getProperty( PROPERTY_NAME__PASSWORD );
}
if ( dbHost == null ) {
dbHost = configProps.getProperty( PROPERTY_NAME__DB_HOST );
}
if ( dbPort == null ) {
dbPort = configProps.getProperty( PROPERTY_NAME__DB_PORT );
}
if ( proxlDbName == null ) {
proxlDbName = configProps.getProperty( PROPERTY_NAME__PROXL_DB_NAME );
}


if ( StringUtils.isEmpty( username ) ) {

String msg = "For Database connection parameters file: parameter '" + PROPERTY_NAME__USERNAME + "' is not provided or is empty string.";
Expand All @@ -213,25 +240,31 @@ public void getConfigPropertiesFromPropertiesObj( Properties configProps )
}


if ( log.isInfoEnabled() ) {
// if ( log.isInfoEnabled() ) {

System.out.println( "Database connection parameters:");

if ( StringUtils.isNotEmpty( username ) ) {

System.out.println( PROPERTY_NAME__USERNAME + " has a value" );
System.out.println( "Environment Variable '" + ENVIRONMENT_VARIABLE__DB_HOST
+ "' OR Database connection parameters file: parameter '" + PROPERTY_NAME__USERNAME + "' has a value" );
}
if ( StringUtils.isNotEmpty( password ) ) {

System.out.println( PROPERTY_NAME__PASSWORD + " has a value" );
System.out.println( "Environment Variable '" + ENVIRONMENT_VARIABLE__PASSWORD
+ "' OR Database connection parameters file: parameter '" + PROPERTY_NAME__PASSWORD + "' has a value" );
}
System.out.println( PROPERTY_NAME__DB_HOST + ": " + dbHost );
System.out.println( PROPERTY_NAME__DB_PORT + ": " + dbPort );
System.out.println( "Environment Variable '" + ENVIRONMENT_VARIABLE__DB_HOST
+ "' OR Database connection parameters file: parameter '" + PROPERTY_NAME__DB_HOST + "': " + dbHost );

System.out.println( "Environment Variable '" + ENVIRONMENT_VARIABLE__DB_PORT
+ "' OR Database connection parameters file: parameter '" + PROPERTY_NAME__DB_PORT + "': " + dbPort );

if ( StringUtils.isNotEmpty( proxlDbName ) ) {
System.out.println( "Environment Variable '" + ENVIRONMENT_VARIABLE__PROXL_DB_NAME
+ "' OR Database connection parameters file: parameter '" + PROPERTY_NAME__PROXL_DB_NAME + "': " + proxlDbName );

System.out.println( PROPERTY_NAME__PROXL_DB_NAME + ": " + proxlDbName );
}
}
// }

configured = true;
}
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2 changes: 1 addition & 1 deletion ...shared/src/main/java/org/yeastrc/proxl/import_xml_to_db/db/ImportDBConnectionFactory.java
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Expand Up @@ -148,7 +148,7 @@ private Connection getConnectionInternal( String db, boolean inserterConnection

if ( dbConnectionParametersProvider == null ) {

dbConnectionParametersProvider = new DBConnectionParametersProviderFromPropertiesFile();
dbConnectionParametersProvider = new DBConnectionParametersProviderFromPropertiesFileEnvironmentVariables();

dbConnectionParametersProvider.init();

Expand Down
53 changes: 41 additions & 12 deletions ...org/yeastrc/proxl/import_xml_to_db_runner_pgm/config/ProcessImporterRunnerConfigFile.java
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Expand Up @@ -13,7 +13,7 @@
import org.slf4j.LoggerFactory;
import org.slf4j.Logger;

import org.yeastrc.proxl.import_xml_to_db.db.DBConnectionParametersProviderFromPropertiesFile;
import org.yeastrc.proxl.import_xml_to_db.db.DBConnectionParametersProviderFromPropertiesFileEnvironmentVariables;
import org.yeastrc.proxl.import_xml_to_db_runner_pgm.exceptions.ConfigPropertiesFileErrorException;


Expand All @@ -27,6 +27,11 @@ public class ProcessImporterRunnerConfigFile {
private static final Logger log = LoggerFactory.getLogger( ProcessImporterRunnerConfigFile.class );


private static final String ENVIRONMENT_VARIABLE_NAME__JAVA_EXECUTABLE_PARAMETERS = "PROXL_JAVA_EXECUTE_PARAMS";

private static final String ENVIRONMENT_VARIABLE__PROXL_WEB_APP_BASE_URL = "PROXL_WEB_APP_BASE_URL";


private static final String NO_PROPERTIES_FILE_ERROR_MESSAGE = "No DB Connection Properties file found.";

private static final String CONFIG_FILENAME = "run_importer_config_file.properties";
Expand All @@ -43,7 +48,7 @@ public class ProcessImporterRunnerConfigFile {
public static final String PROPERTY_NAME__IMPORTER_PID_FILE_WITH_PATH = "importer.pid.file.with.path";

private static final String PROPERTY_NAME__PROXL_WEB_APP_BASE_URL = "proxl.web.app.base.url";

private static final String PROPERTY_NAME__COMMAND_RUN_ON_SUCCESSFUL_IMPORT = "command.run.successful.import";
private static final String PROPERTY_NAME__COMMAND_RUN_ON_SUCCESSFUL_IMPORT_SYSOUT_SYSERR_DIR = "command.run.successful.import.sysout.syserr.dir";

Expand All @@ -69,9 +74,18 @@ public static ProcessImporterRunnerConfigFile getInstance() {
* @return
* @throws Exception
*/
public DBConnectionParametersProviderFromPropertiesFile processConfigFile( File configFileFromCommandLine ) throws Exception {
public DBConnectionParametersProviderFromPropertiesFileEnvironmentVariables processConfigFile( File configFileFromCommandLine ) throws Exception {

try {
// First get from Environment Variables

// Do Not set PROPERTY_NAME__PROXL_WEB_APP_BASE_URL to Not send email on import completion
String proxlWebAppBaseURL = System.getenv( ENVIRONMENT_VARIABLE__PROXL_WEB_APP_BASE_URL );

String javaExecutableParametersString = System.getenv( ENVIRONMENT_VARIABLE_NAME__JAVA_EXECUTABLE_PARAMETERS );

// Then where still null get from config file

Properties configProps = null;
InputStream propertiesFileAsStream = null;

Expand Down Expand Up @@ -136,15 +150,24 @@ public DBConnectionParametersProviderFromPropertiesFile processConfigFile( File
String waitTimeForNextCheckForImportToProcess_InSecondsString = configProps.getProperty( PROPERTY_NAME__WAIT_TIME_FOR_NEXT_CHECK_FOR_IMPORT_TO_PROCESS );

String javaExecutableWithPath = configProps.getProperty( PROPERTY_NAME__JAVA_EXECUTABLE_WITH_PATH );
String javaExecutableParametersString = configProps.getProperty( PROPERTY_NAME__JAVA_EXECUTABLE_PARAMETERS );

if ( proxlWebAppBaseURL == null ) {
// Not set in enviroment variable so get from config file
javaExecutableParametersString = configProps.getProperty( PROPERTY_NAME__JAVA_EXECUTABLE_PARAMETERS );
}


String importerJarWithPath = configProps.getProperty( PROPERTY_NAME__IMPORTER_JAR_WITH_PATH );
String importerDbConfigWithPath = configProps.getProperty( PROPERTY_NAME__IMPORTER_DB_CONFIG_WITH_PATH );

String importerPidFileWithPath = configProps.getProperty( PROPERTY_NAME__IMPORTER_PID_FILE_WITH_PATH );

// Do Not set PROPERTY_NAME__PROXL_WEB_APP_BASE_URL to Not send email on import completion
String proxlWebAppBaseURL = configProps.getProperty( PROPERTY_NAME__PROXL_WEB_APP_BASE_URL );

if ( proxlWebAppBaseURL == null ) {
// Not set in enviroment variable so get from config file
proxlWebAppBaseURL = configProps.getProperty( PROPERTY_NAME__PROXL_WEB_APP_BASE_URL );
}

String commandToRunOnSuccessfulImport = configProps.getProperty( PROPERTY_NAME__COMMAND_RUN_ON_SUCCESSFUL_IMPORT );
String commandToRunOnSuccessfulImportSyoutSyserrDir = configProps.getProperty( PROPERTY_NAME__COMMAND_RUN_ON_SUCCESSFUL_IMPORT_SYSOUT_SYSERR_DIR );
Expand Down Expand Up @@ -178,13 +201,13 @@ public DBConnectionParametersProviderFromPropertiesFile processConfigFile( File

// Do Not set PROPERTY_NAME__PROXL_WEB_APP_BASE_URL to Not send email on import completion

String msg = "INFO:: For config file: parameter '" + PROPERTY_NAME__PROXL_WEB_APP_BASE_URL
String msg = "INFO:: Enviroment Variable '" + ENVIRONMENT_VARIABLE__PROXL_WEB_APP_BASE_URL + "' OR config file: parameter '" + PROPERTY_NAME__PROXL_WEB_APP_BASE_URL
+ "' is not provided or is empty string. Not calling server to send email on import completion.";
log.warn( msg );
} else {

String msg = "INFO:: Config file: parameter '" + PROPERTY_NAME__PROXL_WEB_APP_BASE_URL
+ "' is provided so calling server to send email on import completion.";
String msg = "INFO:: Enviroment Variable '" + ENVIRONMENT_VARIABLE__PROXL_WEB_APP_BASE_URL + "' OR Config file: parameter '" + PROPERTY_NAME__PROXL_WEB_APP_BASE_URL
+ "' is provided so calling server to send email on import completion. URL Used: " + proxlWebAppBaseURL;
log.warn( msg );
}

Expand All @@ -207,12 +230,18 @@ public DBConnectionParametersProviderFromPropertiesFile processConfigFile( File
String[] javaExecutableParametersArray = javaExecutableParametersString.split( " " );
List<String> javaExecutableParametersLocal = new ArrayList<>( javaExecutableParametersArray.length );
for ( String javaExecutableParameter : javaExecutableParametersArray ) {
if ( StringUtils.isNotEmpty(javaExecutableParameter) ) {
javaExecutableParametersLocal.add( javaExecutableParameter );
String javaExecutableParameter_Trimmed = javaExecutableParameter.trim();
if ( StringUtils.isNotEmpty(javaExecutableParameter_Trimmed) ) {
javaExecutableParametersLocal.add( javaExecutableParameter_Trimmed );
}
}
if ( ! javaExecutableParametersLocal.isEmpty() ) {
ImporterRunnerConfigData.setJavaExecutableParameters( javaExecutableParametersLocal );

String msg = "INFO:: Enviroment Variable: '" + ENVIRONMENT_VARIABLE_NAME__JAVA_EXECUTABLE_PARAMETERS
+ "' OR Config file: parameter '" + PROPERTY_NAME__JAVA_EXECUTABLE_PARAMETERS
+ "' so these parameters will be passed to java executable. values: " + StringUtils.join( javaExecutableParametersLocal, " " );
log.warn( msg );
}
}

Expand Down Expand Up @@ -258,8 +287,8 @@ public DBConnectionParametersProviderFromPropertiesFile processConfigFile( File
ImporterRunnerConfigData.setConfigured(true);


DBConnectionParametersProviderFromPropertiesFile dbConnectionParametersProviderFromPropertiesFile =
new DBConnectionParametersProviderFromPropertiesFile();
DBConnectionParametersProviderFromPropertiesFileEnvironmentVariables dbConnectionParametersProviderFromPropertiesFile =
new DBConnectionParametersProviderFromPropertiesFileEnvironmentVariables();

dbConnectionParametersProviderFromPropertiesFile.getConfigPropertiesFromPropertiesObj( configProps );

Expand Down
4 changes: 2 additions & 2 deletions ...ain/java/org/yeastrc/proxl/import_xml_to_db_runner_pgm/program/ImporterRunnerProgram.java
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Original file line number Diff line number Diff line change
Expand Up @@ -12,7 +12,7 @@
import org.slf4j.Logger;

import org.yeastrc.proxl.import_xml_to_db.dao.ConfigSystemDAO;
import org.yeastrc.proxl.import_xml_to_db.db.DBConnectionParametersProviderFromPropertiesFile;
import org.yeastrc.proxl.import_xml_to_db.db.DBConnectionParametersProviderFromPropertiesFileEnvironmentVariables;
import org.yeastrc.proxl.import_xml_to_db.db.DBConnectionParametersProviderPropertiesFileErrorException;
import org.yeastrc.proxl.import_xml_to_db.db.ImportDBConnectionFactory;
import org.yeastrc.proxl.import_xml_to_db_runner_pgm.config.ProcessImporterRunnerConfigFile;
Expand Down Expand Up @@ -105,7 +105,7 @@ public static void main(String[] args) throws Exception {
}
}

DBConnectionParametersProviderFromPropertiesFile dbConnectionParametersProvider = null;
DBConnectionParametersProviderFromPropertiesFileEnvironmentVariables dbConnectionParametersProvider = null;
try {
if ( log.isDebugEnabled() ) {
log.debug( "processing config file from command line: " + configFileFromCommandLine.getAbsolutePath() );
Expand Down

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