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Change Assert() into Warning for db.user/db.password/... #26

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Change Assert() into Warning for db.user/db.password/... #26

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138 changes: 106 additions & 32 deletions src/main/java/org/mskcc/cbio/portal/dao/JdbcDataSource.java
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Original file line number Diff line number Diff line change
@@ -1,61 +1,135 @@
package org.mskcc.cbio.portal.dao;

import java.util.ArrayList;
import java.util.List;
import org.apache.commons.dbcp2.BasicDataSource;
import org.mskcc.cbio.portal.util.DatabaseProperties;
import org.apache.commons.lang3.StringUtils;
import org.springframework.util.Assert;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;

/**
* Data source that self-initializes based on cBioPortal configuration.
*/
public class JdbcDataSource extends BasicDataSource {

private static final Logger LOG = LoggerFactory.getLogger(JdbcDataSource.class);

class RequiredPropertyInfo {
private String key; // the key string in the .properties file
private String value; // the value for the key set in the properties file
private String label; // the common descriptive label for the property for the error message

public RequiredPropertyInfo(String key, String value, String label) {
this.key = key;
this.value = value;
this.label = label;
}

public String getKey() {
return key;
}

public String getValue() {
return value;
}

public String getLabel() {
return label;
}
}

public JdbcDataSource () {
DatabaseProperties dbProperties = DatabaseProperties.getInstance();

String userName = dbProperties.getSpringDbUser();
logUsedDeprecatedProperties(dbProperties);
// extract required property values
String username = dbProperties.getSpringDbUser();
String password = dbProperties.getSpringDbPassword();
String mysqlDriverClassName = dbProperties.getSpringDbDriverClassName();
String enablePooling = (!StringUtils.isBlank(dbProperties.getDbEnablePooling())) ? dbProperties.getDbEnablePooling(): "false";
String connectionURL = dbProperties.getSpringConnectionURL();

Assert.isTrue(
!defined(dbProperties.getDbHost()) && !defined(dbProperties.getDbUser()) && !defined(dbProperties.getDbPassword()) && !defined(dbProperties.getDbName()) && !defined(dbProperties.getConnectionURL()) && !defined(dbProperties.getDbDriverClassName()) && !defined(dbProperties.getDbUseSSL()),
"\n----------------------------------------------------------------------------------------------------------------" +
"-- Connection error:\n" +
"-- You try to connect to the database using the deprecated 'db.host', 'db.portal_db_name' and 'db.use_ssl' or 'db.connection_string' and. 'db.driver' properties.\n" +
"-- Please remove these properties and use the 'spring.datasource.url' property instead. See https://docs.cbioportal.org/deployment/customization/application.properties-reference/\n" +
"-- for assistance on building a valid connection string.\n" +
"----------------------------------------------------------------------------------------------------------------\n"
);

Assert.hasText(userName, errorMessage("username", "spring.datasource.username"));
Assert.hasText(password, errorMessage("password", "spring.datasource.password"));
Assert.hasText(mysqlDriverClassName, errorMessage("driver class name", "spring.datasource.driver-class-name"));

this.setUrl(connectionURL);

String mysqlDriverClassName = dbProperties.getSpringDbDriverClassName();
// extract optional property values
String enablePooling = dbProperties.getDbEnablePooling();
if (stringIsNullOrBlank(enablePooling)) {
enablePooling = "false"; // default
}
// validate required property values are provided
ArrayList<RequiredPropertyInfo> requiredPropertyInfoList = new ArrayList<>();
requiredPropertyInfoList.add(new RequiredPropertyInfo("spring.datasource.username", username, "username"));
requiredPropertyInfoList.add(new RequiredPropertyInfo("spring.datasource.password", password, "password"));
requiredPropertyInfoList.add(new RequiredPropertyInfo("spring.datasource.url", connectionURL, "connectionURL"));
requiredPropertyInfoList.add(new RequiredPropertyInfo("spring.datasource.driver-class-name", mysqlDriverClassName, "driver class name"));
validateRequiredProperties(requiredPropertyInfoList);
// Set up poolable data source
this.setDriverClassName(mysqlDriverClassName);
this.setUsername(userName);
this.setUsername(username);
this.setPassword(password);
this.setUrl(connectionURL);
this.setDriverClassName(mysqlDriverClassName);
// Disable this to avoid caching statements
this.setPoolPreparedStatements(Boolean.valueOf(enablePooling));
// these are the values cbioportal has been using in their production
// context.xml files when using jndi
// these values are from the production cbioportal application context for a jndi data source
this.setMaxTotal(500);
this.setMaxIdle(30);
this.setMaxWaitMillis(10000);
this.setMinEvictableIdleTimeMillis(30000);
this.setTestOnBorrow(true);
this.setValidationQuery("SELECT 1");
}

private String errorMessage(String displayName, String propertyName) {
return String.format("No %s provided for database connection. Please set '%s' in application.properties.", displayName, propertyName);

private void logUsedDeprecatedProperties(DatabaseProperties dbProperties) {
if (defined(dbProperties.getDbHost()) ||
defined(dbProperties.getDbUser()) ||
defined(dbProperties.getDbPassword()) ||
defined(dbProperties.getDbName()) ||
defined(dbProperties.getConnectionURL()) ||
defined(dbProperties.getDbDriverClassName()) ||
defined(dbProperties.getDbUseSSL())) {
LOG.warn("\n" +
"----------------------------------------------------------------------------------------------------------------\n" +
"-- Connection warning:\n" +
"-- You seem to be attempting to connect to the database by setting some of these deprecated properties:\n" +
"--- db.host\n" +
"--- db.user\n" +
"--- db.password\n" +
"--- db.portal_db_name\n" +
"--- db.connection_string\n" +
"--- db.driver\n" +
"-- Please remove those properties and set these properties instead:\n" +
"--- spring.datasource.username\n" +
"--- spring.datasource.password\n" +
"--- spring.datasource.url\n" +
"--- spring.datasource.driver-class-name\n" +
"-- For examples and assistance on setting these properties see:\n" +
"-- https://github.com/cBioPortal/cbioportal/blob/master/src/main/resources/application.properties.EXAMPLE\n" +
"-- https://docs.cbioportal.org/deployment/customization/application.properties-reference/\n" +
"----------------------------------------------------------------------------------------------------------------\n");
}
}

private void validateRequiredProperties(List<RequiredPropertyInfo> requiredPropertyInfoList) {
boolean requiredPropertyIsMissing = false;
for (RequiredPropertyInfo requiredPropertyInfo : requiredPropertyInfoList) {
if (stringIsNullOrBlank(requiredPropertyInfo.getValue())) {
LOG.error(errorMessage(requiredPropertyInfo));
requiredPropertyIsMissing = true;
}
}
if (requiredPropertyIsMissing) {
// Throw exception. Because this occurs during the bean wiring step, this will cause the context creation to fail and the application to exit.
throw new RuntimeException("Datasource cannot be configured because required properties are missing values. See log for details.");
}
}

private String errorMessage(RequiredPropertyInfo requiredPropertyInfo) {
return String.format(
"No %s provided for database connection. Please provide a value for '%s' in application.properties or as a jvm command line system property.",
requiredPropertyInfo.getLabel(),
requiredPropertyInfo.getKey());
}

private boolean defined(String property) {
return property != null && !property.isEmpty();
return !stringIsNullOrBlank(property);
}

private boolean stringIsNullOrBlank(String s) {
return s == null || s.trim().isEmpty();
}
}
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