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Merge branch 'master' into rel_4_2_0

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jamesagnew
2020-02-16 09:27:05 -05:00
parent b108ef73e4 61965fb078
commit c2ee10814d
7 changed files with 268 additions and 640 deletions
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304
src/main/java/ca/uhn/fhir/jpa/starter/FhirServerConfigCommon.java
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@@ -26,174 +26,184 @@ import java.sql.Driver;
@EnableTransactionManagement()
public class FhirServerConfigCommon {
private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(FhirServerConfigCommon.class);
private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(FhirServerConfigCommon.class);
private Boolean enableIndexMissingFields = HapiProperties.getEnableIndexMissingFields();
private Boolean autoCreatePlaceholderReferenceTargets = HapiProperties.getAutoCreatePlaceholderReferenceTargets();
private Boolean enforceReferentialIntegrityOnWrite = HapiProperties.getEnforceReferentialIntegrityOnWrite();
private Boolean enforceReferentialIntegrityOnDelete = HapiProperties.getEnforceReferentialIntegrityOnDelete();
private Boolean allowContainsSearches = HapiProperties.getAllowContainsSearches();
private Boolean allowMultipleDelete = HapiProperties.getAllowMultipleDelete();
private Boolean allowExternalReferences = HapiProperties.getAllowExternalReferences();
private Boolean expungeEnabled = HapiProperties.getExpungeEnabled();
private Boolean allowPlaceholderReferences = HapiProperties.getAllowPlaceholderReferences();
private Boolean subscriptionRestHookEnabled = HapiProperties.getSubscriptionRestHookEnabled();
private Boolean subscriptionEmailEnabled = HapiProperties.getSubscriptionEmailEnabled();
private Boolean allowOverrideDefaultSearchParams = HapiProperties.getAllowOverrideDefaultSearchParams();
private String emailFrom = HapiProperties.getEmailFrom();
private Boolean emailEnabled = HapiProperties.getEmailEnabled();
private String emailHost = HapiProperties.getEmailHost();
private Integer emailPort = HapiProperties.getEmailPort();
private String emailUsername = HapiProperties.getEmailUsername();
private String emailPassword = HapiProperties.getEmailPassword();
@Autowired
private SubscriptionDeliveryHandlerFactory mySubscriptionDeliveryHandlerFactory;
private Boolean enableIndexMissingFields = HapiProperties.getEnableIndexMissingFields();
private Boolean autoCreatePlaceholderReferenceTargets = HapiProperties.getAutoCreatePlaceholderReferenceTargets();
private Boolean enforceReferentialIntegrityOnWrite = HapiProperties.getEnforceReferentialIntegrityOnWrite();
private Boolean enforceReferentialIntegrityOnDelete = HapiProperties.getEnforceReferentialIntegrityOnDelete();
private Boolean allowContainsSearches = HapiProperties.getAllowContainsSearches();
private Boolean allowMultipleDelete = HapiProperties.getAllowMultipleDelete();
private Boolean allowExternalReferences = HapiProperties.getAllowExternalReferences();
private Boolean expungeEnabled = HapiProperties.getExpungeEnabled();
private Boolean allowPlaceholderReferences = HapiProperties.getAllowPlaceholderReferences();
private Boolean subscriptionRestHookEnabled = HapiProperties.getSubscriptionRestHookEnabled();
private Boolean subscriptionEmailEnabled = HapiProperties.getSubscriptionEmailEnabled();
private Boolean allowOverrideDefaultSearchParams = HapiProperties.getAllowOverrideDefaultSearchParams();
private String emailFrom = HapiProperties.getEmailFrom();
private Boolean emailEnabled = HapiProperties.getEmailEnabled();
private String emailHost = HapiProperties.getEmailHost();
private Integer emailPort = HapiProperties.getEmailPort();
private String emailUsername = HapiProperties.getEmailUsername();
private String emailPassword = HapiProperties.getEmailPassword();
private Boolean emailAuth = HapiProperties.getEmailAuth();
private Boolean emailStartTlsEnable = HapiProperties.getEmailStartTlsEnable();
private Boolean emailStartTlsRequired = HapiProperties.getEmailStartTlsRequired();
private Boolean emailQuitWait = HapiProperties.getEmailQuitWait();
public FhirServerConfigCommon() {
ourLog.info("Server configured to " + (this.allowContainsSearches ? "allow" : "deny") + " contains searches");
ourLog.info("Server configured to " + (this.allowMultipleDelete ? "allow" : "deny") + " multiple deletes");
ourLog.info("Server configured to " + (this.allowExternalReferences ? "allow" : "deny") + " external references");
ourLog.info("Server configured to " + (this.expungeEnabled ? "enable" : "disable") + " expunges");
ourLog.info("Server configured to " + (this.allowPlaceholderReferences ? "allow" : "deny") + " placeholder references");
ourLog.info("Server configured to " + (this.allowOverrideDefaultSearchParams ? "allow" : "deny") + " overriding default search params");
@Autowired
private SubscriptionDeliveryHandlerFactory mySubscriptionDeliveryHandlerFactory;
if (this.emailEnabled) {
ourLog.info("Server is configured to enable email with host '" + this.emailHost + "' and port " + this.emailPort.toString());
ourLog.info("Server will use '" + this.emailFrom + "' as the from email address");
public FhirServerConfigCommon() {
ourLog.info("Server configured to " + (this.allowContainsSearches ? "allow" : "deny") + " contains searches");
ourLog.info("Server configured to " + (this.allowMultipleDelete ? "allow" : "deny") + " multiple deletes");
ourLog.info("Server configured to " + (this.allowExternalReferences ? "allow" : "deny") + " external references");
ourLog.info("Server configured to " + (this.expungeEnabled ? "enable" : "disable") + " expunges");
ourLog.info("Server configured to " + (this.allowPlaceholderReferences ? "allow" : "deny") + " placeholder references");
ourLog.info("Server configured to " + (this.allowOverrideDefaultSearchParams ? "allow" : "deny") + " overriding default search params");
if (this.emailUsername != null && this.emailUsername.length() > 0) {
ourLog.info("Server is configured to use username '" + this.emailUsername + "' for email");
}
if (this.emailEnabled) {
ourLog.info("Server is configured to enable email with host '" + this.emailHost + "' and port " + this.emailPort.toString());
ourLog.info("Server will use '" + this.emailFrom + "' as the from email address");
if (this.emailPassword != null && this.emailPassword.length() > 0) {
ourLog.info("Server is configured to use a password for email");
}
}
if (this.emailUsername != null && this.emailUsername.length() > 0) {
ourLog.info("Server is configured to use username '" + this.emailUsername + "' for email");
}
if (this.subscriptionRestHookEnabled) {
ourLog.info("REST-hook subscriptions enabled");
}
if (this.subscriptionEmailEnabled) {
ourLog.info("Email subscriptions enabled");
}
if (this.emailPassword != null && this.emailPassword.length() > 0) {
ourLog.info("Server is configured to use a password for email");
}
}
/**
* Configure FHIR properties around the the JPA server via this bean
*/
@Bean()
public DaoConfig daoConfig() {
DaoConfig retVal = new DaoConfig();
retVal.setIndexMissingFields(this.enableIndexMissingFields ? DaoConfig.IndexEnabledEnum.ENABLED : DaoConfig.IndexEnabledEnum.DISABLED);
retVal.setAutoCreatePlaceholderReferenceTargets(this.autoCreatePlaceholderReferenceTargets);
retVal.setEnforceReferentialIntegrityOnWrite(this.enforceReferentialIntegrityOnWrite);
retVal.setEnforceReferentialIntegrityOnDelete(this.enforceReferentialIntegrityOnDelete);
retVal.setAllowContainsSearches(this.allowContainsSearches);
retVal.setAllowMultipleDelete(this.allowMultipleDelete);
retVal.setAllowExternalReferences(this.allowExternalReferences);
retVal.setExpungeEnabled(this.expungeEnabled);
retVal.setAutoCreatePlaceholderReferenceTargets(this.allowPlaceholderReferences);
retVal.setEmailFromAddress(this.emailFrom);
Integer maxFetchSize = HapiProperties.getMaximumFetchSize();
retVal.setFetchSizeDefaultMaximum(maxFetchSize);
ourLog.info("Server configured to have a maximum fetch size of " + (maxFetchSize == Integer.MAX_VALUE ? "'unlimited'" : maxFetchSize));
Long reuseCachedSearchResultsMillis = HapiProperties.getReuseCachedSearchResultsMillis();
retVal.setReuseCachedSearchResultsForMillis(reuseCachedSearchResultsMillis);
ourLog.info("Server configured to cache search results for {} milliseconds", reuseCachedSearchResultsMillis);
Long retainCachedSearchesMinutes = HapiProperties.getExpireSearchResultsAfterMins();
retVal.setExpireSearchResultsAfterMillis(retainCachedSearchesMinutes * 60 * 1000);
// Subscriptions are enabled by channel type
if (HapiProperties.getSubscriptionRestHookEnabled()) {
ourLog.info("Enabling REST-hook subscriptions");
retVal.addSupportedSubscriptionType(Subscription.SubscriptionChannelType.RESTHOOK);
}
if (HapiProperties.getSubscriptionEmailEnabled()) {
ourLog.info("Enabling email subscriptions");
retVal.addSupportedSubscriptionType(Subscription.SubscriptionChannelType.EMAIL);
}
if (HapiProperties.getSubscriptionWebsocketEnabled()) {
ourLog.info("Enabling websocket subscriptions");
retVal.addSupportedSubscriptionType(Subscription.SubscriptionChannelType.WEBSOCKET);
}
retVal.setFilterParameterEnabled(HapiProperties.getFilterSearchEnabled());
return retVal;
if (this.subscriptionRestHookEnabled) {
ourLog.info("REST-hook subscriptions enabled");
}
@Bean
public ModelConfig modelConfig() {
ModelConfig modelConfig = new ModelConfig();
modelConfig.setAllowContainsSearches(this.allowContainsSearches);
modelConfig.setAllowExternalReferences(this.allowExternalReferences);
modelConfig.setDefaultSearchParamsCanBeOverridden(this.allowOverrideDefaultSearchParams);
modelConfig.setEmailFromAddress(this.emailFrom);
if (this.subscriptionEmailEnabled) {
ourLog.info("Email subscriptions enabled");
}
}
// You can enable these if you want to support Subscriptions from your server
if (this.subscriptionRestHookEnabled) {
modelConfig.addSupportedSubscriptionType(Subscription.SubscriptionChannelType.RESTHOOK);
}
/**
* Configure FHIR properties around the the JPA server via this bean
*/
@Bean()
public DaoConfig daoConfig() {
DaoConfig retVal = new DaoConfig();
if (this.subscriptionEmailEnabled) {
modelConfig.addSupportedSubscriptionType(Subscription.SubscriptionChannelType.EMAIL);
}
retVal.setIndexMissingFields(this.enableIndexMissingFields ? DaoConfig.IndexEnabledEnum.ENABLED : DaoConfig.IndexEnabledEnum.DISABLED);
retVal.setAutoCreatePlaceholderReferenceTargets(this.autoCreatePlaceholderReferenceTargets);
retVal.setEnforceReferentialIntegrityOnWrite(this.enforceReferentialIntegrityOnWrite);
retVal.setEnforceReferentialIntegrityOnDelete(this.enforceReferentialIntegrityOnDelete);
retVal.setAllowContainsSearches(this.allowContainsSearches);
retVal.setAllowMultipleDelete(this.allowMultipleDelete);
retVal.setAllowExternalReferences(this.allowExternalReferences);
retVal.setExpungeEnabled(this.expungeEnabled);
retVal.setAutoCreatePlaceholderReferenceTargets(this.allowPlaceholderReferences);
retVal.setEmailFromAddress(this.emailFrom);
return modelConfig;
Integer maxFetchSize = HapiProperties.getMaximumFetchSize();
retVal.setFetchSizeDefaultMaximum(maxFetchSize);
ourLog.info("Server configured to have a maximum fetch size of " + (maxFetchSize == Integer.MAX_VALUE ? "'unlimited'" : maxFetchSize));
Long reuseCachedSearchResultsMillis = HapiProperties.getReuseCachedSearchResultsMillis();
retVal.setReuseCachedSearchResultsForMillis(reuseCachedSearchResultsMillis);
ourLog.info("Server configured to cache search results for {} milliseconds", reuseCachedSearchResultsMillis);
Long retainCachedSearchesMinutes = HapiProperties.getExpireSearchResultsAfterMins();
retVal.setExpireSearchResultsAfterMillis(retainCachedSearchesMinutes * 60 * 1000);
// Subscriptions are enabled by channel type
if (HapiProperties.getSubscriptionRestHookEnabled()) {
ourLog.info("Enabling REST-hook subscriptions");
retVal.addSupportedSubscriptionType(Subscription.SubscriptionChannelType.RESTHOOK);
}
if (HapiProperties.getSubscriptionEmailEnabled()) {
ourLog.info("Enabling email subscriptions");
retVal.addSupportedSubscriptionType(Subscription.SubscriptionChannelType.EMAIL);
}
if (HapiProperties.getSubscriptionWebsocketEnabled()) {
ourLog.info("Enabling websocket subscriptions");
retVal.addSupportedSubscriptionType(Subscription.SubscriptionChannelType.WEBSOCKET);
}
/**
* The following bean configures the database connection. The 'url' property value of "jdbc:derby:directory:jpaserver_derby_files;create=true" indicates that the server should save resources in a
* directory called "jpaserver_derby_files".
* <p>
* A URL to a remote database could also be placed here, along with login credentials and other properties supported by BasicDataSource.
*/
@Bean(destroyMethod = "close")
public BasicDataSource dataSource() throws ClassNotFoundException, NoSuchMethodException, IllegalAccessException, InvocationTargetException, InstantiationException {
BasicDataSource retVal = new BasicDataSource();
Driver driver = (Driver) Class.forName(HapiProperties.getDataSourceDriver()).getConstructor().newInstance();
retVal.setDriver(driver);
retVal.setUrl(HapiProperties.getDataSourceUrl());
retVal.setUsername(HapiProperties.getDataSourceUsername());
retVal.setPassword(HapiProperties.getDataSourcePassword());
retVal.setMaxTotal(HapiProperties.getDataSourceMaxPoolSize());
return retVal;
retVal.setFilterParameterEnabled(HapiProperties.getFilterSearchEnabled());
return retVal;
}
@Bean
public ModelConfig modelConfig() {
ModelConfig modelConfig = new ModelConfig();
modelConfig.setAllowContainsSearches(this.allowContainsSearches);
modelConfig.setAllowExternalReferences(this.allowExternalReferences);
modelConfig.setDefaultSearchParamsCanBeOverridden(this.allowOverrideDefaultSearchParams);
modelConfig.setEmailFromAddress(this.emailFrom);
// You can enable these if you want to support Subscriptions from your server
if (this.subscriptionRestHookEnabled) {
modelConfig.addSupportedSubscriptionType(Subscription.SubscriptionChannelType.RESTHOOK);
}
@Lazy
@Bean
public IBinaryStorageSvc binaryStorageSvc() {
DatabaseBlobBinaryStorageSvcImpl binaryStorageSvc = new DatabaseBlobBinaryStorageSvcImpl();
if (HapiProperties.getMaxBinarySize() != null) {
binaryStorageSvc.setMaximumBinarySize(HapiProperties.getMaxBinarySize());
}
return binaryStorageSvc;
if (this.subscriptionEmailEnabled) {
modelConfig.addSupportedSubscriptionType(Subscription.SubscriptionChannelType.EMAIL);
}
@Bean()
public IEmailSender emailSender() {
if (this.emailEnabled) {
JavaMailEmailSender retVal = new JavaMailEmailSender();
return modelConfig;
}
retVal.setSmtpServerHostname(this.emailHost);
retVal.setSmtpServerPort(this.emailPort);
retVal.setSmtpServerUsername(this.emailUsername);
retVal.setSmtpServerPassword(this.emailPassword);
/**
* The following bean configures the database connection. The 'url' property value of "jdbc:derby:directory:jpaserver_derby_files;create=true" indicates that the server should save resources in a
* directory called "jpaserver_derby_files".
* <p>
* A URL to a remote database could also be placed here, along with login credentials and other properties supported by BasicDataSource.
*/
@Bean(destroyMethod = "close")
public BasicDataSource dataSource() throws ClassNotFoundException, NoSuchMethodException, IllegalAccessException, InvocationTargetException, InstantiationException {
BasicDataSource retVal = new BasicDataSource();
Driver driver = (Driver) Class.forName(HapiProperties.getDataSourceDriver()).getConstructor().newInstance();
retVal.setDriver(driver);
retVal.setUrl(HapiProperties.getDataSourceUrl());
retVal.setUsername(HapiProperties.getDataSourceUsername());
retVal.setPassword(HapiProperties.getDataSourcePassword());
retVal.setMaxTotal(HapiProperties.getDataSourceMaxPoolSize());
return retVal;
}
Validate.notNull(mySubscriptionDeliveryHandlerFactory, "No subscription delivery handler");
mySubscriptionDeliveryHandlerFactory.setEmailSender(retVal);
@Lazy
@Bean
public IBinaryStorageSvc binaryStorageSvc() {
DatabaseBlobBinaryStorageSvcImpl binaryStorageSvc = new DatabaseBlobBinaryStorageSvcImpl();
return retVal;
}
return null;
if (HapiProperties.getMaxBinarySize() != null) {
binaryStorageSvc.setMaximumBinarySize(HapiProperties.getMaxBinarySize());
}
return binaryStorageSvc;
}
@Bean()
public IEmailSender emailSender() {
if (this.emailEnabled) {
JavaMailEmailSender retVal = new JavaMailEmailSender();
retVal.setSmtpServerHostname(this.emailHost);
retVal.setSmtpServerPort(this.emailPort);
retVal.setSmtpServerUsername(this.emailUsername);
retVal.setSmtpServerPassword(this.emailPassword);
// TODO KHS add these when HAPI 4.2.0 is released
// retVal.setAuth(this.emailAuth);
// retVal.setStartTlsEnable(this.emailStartTlsEnable);
// retVal.setStartTlsRequired(this.emailStartTlsRequired);
// retVal.setQuitWait(this.emailQuitWait);
Validate.notNull(mySubscriptionDeliveryHandlerFactory, "No subscription delivery handler");
mySubscriptionDeliveryHandlerFactory.setEmailSender(retVal);
return retVal;
}
return null;
}
}

50
src/main/java/ca/uhn/fhir/jpa/starter/HapiProperties.java
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@@ -14,11 +14,14 @@ import javax.annotation.Nonnull;
import java.io.FileInputStream;
import java.io.InputStream;
import java.util.Arrays;
import java.util.Locale;
import java.util.Properties;
import java.util.Set;
import java.util.stream.Collectors;
import static org.apache.commons.lang3.StringUtils.*;
import static org.apache.commons.lang3.StringUtils.defaultString;
import static org.apache.commons.lang3.StringUtils.isNotBlank;
import static org.apache.commons.lang3.StringUtils.trim;
public class HapiProperties {
static final String ENABLE_INDEX_MISSING_FIELDS = "enable_index_missing_fields";
@@ -102,7 +105,7 @@ public class HapiProperties {
builder.setRestUrl(getProperty("elasticsearch.rest_url"));
builder.setUsername(getProperty("elasticsearch.username"));
builder.setPassword(getProperty("elasticsearch.password"));
builder.setIndexSchemaManagementStrategy(getPropertyEnum("elasticsearch.schema_management_strateg", IndexSchemaManagementStrategy.class, IndexSchemaManagementStrategy.CREATE));
builder.setIndexSchemaManagementStrategy(getPropertyEnum("elasticsearch.schema_management_strategy", IndexSchemaManagementStrategy.class, IndexSchemaManagementStrategy.CREATE));
builder.setDebugRefreshAfterWrite(getPropertyBoolean("elasticsearch.debug.refresh_after_write", false));
builder.setDebugPrettyPrintJsonLog(getPropertyBoolean("elasticsearch.debug.pretty_print_json_log", false));
builder.apply(retVal);
@@ -160,24 +163,28 @@ public class HapiProperties {
}
private static String getProperty(String propertyName) {
Properties properties = HapiProperties.getProperties();
String env = "HAPI_" + propertyName.toUpperCase(Locale.US);
env = env.replace(".", "_");
env = env.replace("-", "_");
if (properties != null) {
return properties.getProperty(propertyName);
String propertyValue = System.getenv(env);
if (propertyValue != null) {
return propertyValue;
}
return null;
Properties properties = HapiProperties.getProperties();
if (properties != null) {
propertyValue = properties.getProperty(propertyName);
}
return propertyValue;
}
private static String getProperty(String propertyName, String defaultValue) {
Properties properties = HapiProperties.getProperties();
String value = getProperty(propertyName);
if (properties != null) {
String value = properties.getProperty(propertyName);
if (value != null && value.length() > 0) {
return value;
}
if (value != null && value.length() > 0) {
return value;
}
return defaultValue;
@@ -398,6 +405,23 @@ public class HapiProperties {
return HapiProperties.getProperty("email.password");
}
// Defaults from https://javaee.github.io/javamail/docs/api/com/sun/mail/smtp/package-summary.html
public static Boolean getEmailAuth() {
return HapiProperties.getBooleanProperty("email.auth", false);
}
public static Boolean getEmailStartTlsEnable() {
return HapiProperties.getBooleanProperty("email.starttls.enable", false);
}
public static Boolean getEmailStartTlsRequired() {
return HapiProperties.getBooleanProperty("email.starttls.required", false);
}
public static Boolean getEmailQuitWait() {
return HapiProperties.getBooleanProperty("email.quitwait", true);
}
public static Long getReuseCachedSearchResultsMillis() {
String value = HapiProperties.getProperty(REUSE_CACHED_SEARCH_RESULTS_MILLIS, "60000");
return Long.valueOf(value);