Package dev.dsf.fhir.dao.jdbc

Class PatientDaoJdbc

java.lang.Object

dev.dsf.fhir.dao.jdbc.PatientDaoJdbc

All Implemented Interfaces:

PatientDao, ResourceDao<org.hl7.fhir.r4.model.Patient>, org.springframework.beans.factory.InitializingBean

public class PatientDaoJdbc
extends Object
implements PatientDao

Field Summary

Fields inherited from interface dev.dsf.fhir.dao.ResourceDao

FIRST_VERSION, FIRST_VERSION_STRING

Constructor Summary

Constructors

Constructor	Description
PatientDaoJdbc(DataSource dataSource, DataSource permanentDeleteDataSource, ca.uhn.fhir.context.FhirContext fhirContext)

Method Summary

Modifier and Type	Method	Description
void	afterPropertiesSet()
protected org.hl7.fhir.r4.model.Patient	copy(org.hl7.fhir.r4.model.Patient resource)
final org.hl7.fhir.r4.model.Patient	create(org.hl7.fhir.r4.model.Patient resource)
final SearchQuery<org.hl7.fhir.r4.model.Patient>	createSearchQuery(Identity identity, int page, int count)
SearchQuery<org.hl7.fhir.r4.model.Patient>	createSearchQueryWithoutUserFilter(int page, int count)
org.hl7.fhir.r4.model.Patient	createWithId(org.hl7.fhir.r4.model.Patient resource, UUID uuid)
org.hl7.fhir.r4.model.Patient	createWithTransactionAndId(Connection connection, org.hl7.fhir.r4.model.Patient resource, UUID uuid)
protected final boolean	delete(Connection connection, UUID uuid)
final boolean	delete(UUID uuid)	Returns false if a matching resource was already marked as deleted
void	deletePermanently(UUID uuid)	Permanently delete a resource that was previously marked as deleted.
void	deletePermanentlyWithTransaction(Connection connection, UUID uuid)	Permanently delete a resource that was previously marked as deleted.
boolean	deleteWithTransaction(Connection connection, UUID uuid)	Returns false if a matching resource was already marked as deleted
boolean	existsNotDeleted(String idString, String versionString)
boolean	existsNotDeletedWithTransaction(Connection connection, String idString, String versionString)
protected static <R extends org.hl7.fhir.r4.model.Resource> SearchQueryParameterFactory<R>	factory(String parameterName, Supplier<SearchQueryParameter<R>> supplier)
protected static <R extends org.hl7.fhir.r4.model.Resource> SearchQueryParameterFactory<R>	factory(String parameterName, Supplier<SearchQueryParameter<R>> supplier, List<String> nameModifiers)
protected static <R extends org.hl7.fhir.r4.model.Resource> SearchQueryParameterFactory<R>	factory(String parameterName, Supplier<SearchQueryParameter<R>> supplier, List<String> nameModifiers, Supplier<SearchQueryIncludeParameter<R>> includeSupplier, List<String> includeParameterValues)
protected static SearchQueryRevIncludeParameterFactory	factory(Supplier<SearchQueryRevIncludeParameter> revIncludeSupplier, List<String> revIncludeParameterValues)
protected DataSource	getDataSource()
protected final dev.dsf.fhir.dao.jdbc.AbstractResourceDaoJdbc.LatestVersion	getLatestVersion(UUID uuid, Connection connection)
protected final dev.dsf.fhir.dao.jdbc.AbstractResourceDaoJdbc.LatestVersion	getLatestVersion(org.hl7.fhir.r4.model.Patient resource, Connection connection)
protected final Optional<dev.dsf.fhir.dao.jdbc.AbstractResourceDaoJdbc.LatestVersion>	getLatestVersionIfExists(UUID uuid, Connection connection)
protected dev.dsf.fhir.dao.jdbc.PreparedStatementFactory<org.hl7.fhir.r4.model.Patient>	getPreparedStatementFactory()
protected org.hl7.fhir.r4.model.Patient	getResource(ResultSet result, int index)
protected String	getResourceColumn()
protected String	getResourceIdColumn()
protected String	getResourceTable()
Class<org.hl7.fhir.r4.model.Patient>	getResourceType()
String	getResourceTypeName()
protected void	modifySearchResultResource(org.hl7.fhir.r4.model.Patient resource, Connection connection)	Override this method to modify resources retrieved by search queries before returning to the user.
Connection	newReadWriteTransaction()
final Optional<org.hl7.fhir.r4.model.Patient>	read(UUID uuid)
List<org.hl7.fhir.r4.model.Patient>	readAll()
List<org.hl7.fhir.r4.model.Patient>	readAllWithTransaction(Connection connection)
Optional<org.hl7.fhir.r4.model.Patient>	readIncludingDeleted(UUID uuid)
Optional<org.hl7.fhir.r4.model.Patient>	readIncludingDeletedWithTransaction(Connection connection, UUID uuid)
final Optional<org.hl7.fhir.r4.model.Patient>	readVersion(UUID uuid, long version)
Optional<org.hl7.fhir.r4.model.Patient>	readVersionWithTransaction(Connection connection, UUID uuid, long version)
Optional<org.hl7.fhir.r4.model.Patient>	readWithTransaction(Connection connection, UUID uuid)
final PartialResult<org.hl7.fhir.r4.model.Patient>	search(DbSearchQuery query)
PartialResult<org.hl7.fhir.r4.model.Patient>	searchWithTransaction(Connection connection, DbSearchQuery query)
protected final Long	toLong(String version)
protected final UUID	toUuid(String id)
final org.hl7.fhir.r4.model.Patient	update(org.hl7.fhir.r4.model.Patient resource, Long expectedVersion)	Sets the version of the stored resource to latest version from DB plus 1.
org.hl7.fhir.r4.model.Patient	updateWithTransaction(Connection connection, org.hl7.fhir.r4.model.Patient resource, Long expectedVersion)	Sets the version of the stored resource to latest version from DB plus 1.

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Methods inherited from interface dev.dsf.fhir.dao.ResourceDao

create, createSearchQuery, createSearchQueryWithoutUserFilter, createWithId, createWithTransactionAndId, delete, deletePermanently, deletePermanentlyWithTransaction, deleteWithTransaction, existsNotDeleted, existsNotDeletedWithTransaction, getResourceType, getResourceTypeName, newReadWriteTransaction, read, readAll, readAllWithTransaction, readIncludingDeleted, readIncludingDeletedWithTransaction, readVersion, readVersionWithTransaction, readWithTransaction, search, searchWithTransaction, update, update, updateWithTransaction, updateWithTransaction

Constructor Details

PatientDaoJdbc

public PatientDaoJdbc(DataSource dataSource,
 DataSource permanentDeleteDataSource,
 ca.uhn.fhir.context.FhirContext fhirContext)

Method Details

copy

protected org.hl7.fhir.r4.model.Patient copy(org.hl7.fhir.r4.model.Patient resource)

factory

protected static <R extends org.hl7.fhir.r4.model.Resource>
SearchQueryParameterFactory<R> factory(String parameterName,
 Supplier<SearchQueryParameter<R>> supplier)

factory

protected static SearchQueryRevIncludeParameterFactory factory(Supplier<SearchQueryRevIncludeParameter> revIncludeSupplier,
 List<String> revIncludeParameterValues)

factory

protected static <R extends org.hl7.fhir.r4.model.Resource>
SearchQueryParameterFactory<R> factory(String parameterName,
 Supplier<SearchQueryParameter<R>> supplier,
 List<String> nameModifiers,
 Supplier<SearchQueryIncludeParameter<R>> includeSupplier,
 List<String> includeParameterValues)

factory

protected static <R extends org.hl7.fhir.r4.model.Resource>
SearchQueryParameterFactory<R> factory(String parameterName,
 Supplier<SearchQueryParameter<R>> supplier,
 List<String> nameModifiers)

afterPropertiesSet

public void afterPropertiesSet()
                        throws Exception

Specified by:

afterPropertiesSet in interface org.springframework.beans.factory.InitializingBean

Throws:

Exception

getDataSource

protected DataSource getDataSource()

getResourceTable

protected String getResourceTable()

getResourceIdColumn

protected String getResourceIdColumn()

getResourceColumn

protected String getResourceColumn()

getPreparedStatementFactory

protected dev.dsf.fhir.dao.jdbc.PreparedStatementFactory<org.hl7.fhir.r4.model.Patient> getPreparedStatementFactory()

getResourceTypeName

public String getResourceTypeName()

Specified by:

getResourceTypeName in interface ResourceDao<R extends org.hl7.fhir.r4.model.Resource>

getResourceType

public Class<org.hl7.fhir.r4.model.Patient> getResourceType()

Specified by:

getResourceType in interface ResourceDao<R extends org.hl7.fhir.r4.model.Resource>

newReadWriteTransaction

public Connection newReadWriteTransaction()
                                   throws SQLException

Specified by:

newReadWriteTransaction in interface ResourceDao<R extends org.hl7.fhir.r4.model.Resource>

Throws:

SQLException

create

public final org.hl7.fhir.r4.model.Patient create(org.hl7.fhir.r4.model.Patient resource)
                                           throws SQLException

Specified by:

create in interface ResourceDao<R extends org.hl7.fhir.r4.model.Resource>

Parameters:

resource - not null

Returns:

the stored resource, not the same object as the given resource (defensive copy)

Throws:

SQLException - if database access errors occur

createWithId

public org.hl7.fhir.r4.model.Patient createWithId(org.hl7.fhir.r4.model.Patient resource,
 UUID uuid)
                                           throws SQLException

Specified by:

createWithId in interface ResourceDao<R extends org.hl7.fhir.r4.model.Resource>

Parameters:

resource - not null

uuid - not null

Returns:

the stored resource, not the same object as the given resource (defensive copy)

Throws:

SQLException - if database access errors occur

createWithTransactionAndId

public org.hl7.fhir.r4.model.Patient createWithTransactionAndId(Connection connection,
 org.hl7.fhir.r4.model.Patient resource,
 UUID uuid)
                                                         throws SQLException

Specified by:

createWithTransactionAndId in interface ResourceDao<R extends org.hl7.fhir.r4.model.Resource>

Parameters:

connection - not null, not Connection.isReadOnly()

resource - not null

uuid - not null

Returns:

the stored resource, not the same object as the given resource

Throws:

SQLException - if database access errors occur

getResource

protected org.hl7.fhir.r4.model.Patient getResource(ResultSet result,
 int index)
                                             throws SQLException

Throws:

SQLException

read

public final Optional<org.hl7.fhir.r4.model.Patient> read(UUID uuid)
                                                   throws SQLException,
ResourceDeletedException

Specified by:

read in interface ResourceDao<R extends org.hl7.fhir.r4.model.Resource>

Parameters:

uuid - may be null

Returns:

Optional.empty() if the given uuid is null or no resource could be found for the given uuid

Throws:

SQLException - if database access errors occur

ResourceDeletedException - if a resource with the given uuid could be found, but is marked as delete

readWithTransaction

public Optional<org.hl7.fhir.r4.model.Patient> readWithTransaction(Connection connection,
 UUID uuid)
                                                            throws SQLException,
ResourceDeletedException

Specified by:

readWithTransaction in interface ResourceDao<R extends org.hl7.fhir.r4.model.Resource>

Parameters:

connection - not null

uuid - may be null

Returns:

Optional.empty() if the given uuid is null or no resource could be found for the given uuid

Throws:

SQLException - if database access errors occur

ResourceDeletedException - if a resource with the given uuid could be found, but is marked as delete

readVersion

public final Optional<org.hl7.fhir.r4.model.Patient> readVersion(UUID uuid,
 long version)
                                                          throws SQLException,
ResourceDeletedException

Specified by:

readVersion in interface ResourceDao<R extends org.hl7.fhir.r4.model.Resource>

Parameters:

uuid - may be null

version - may be less then 1

Returns:

Optional.empty() if the given uuid is null, the given version is less then 1 or no resource could be found for the given uuid and version

Throws:

SQLException - if database access errors occur

ResourceDeletedException - if a resource with the given uuid and version could be found, but is the delete history entry

readVersionWithTransaction

public Optional<org.hl7.fhir.r4.model.Patient> readVersionWithTransaction(Connection connection,
 UUID uuid,
 long version)
                                                                   throws SQLException,
ResourceDeletedException

Specified by:

readVersionWithTransaction in interface ResourceDao<R extends org.hl7.fhir.r4.model.Resource>

Parameters:

connection - not null

uuid - may be null

version - may be less then 1

Returns:

Optional.empty() if the given uuid is null, the given version is less then 1 or no resource could be found for the given uuid and version

Throws:

SQLException - if database access errors occur

ResourceDeletedException - if a resource with the given uuid and version could be found, but is the delete history entry

readIncludingDeleted

public Optional<org.hl7.fhir.r4.model.Patient> readIncludingDeleted(UUID uuid)
                                                             throws SQLException

Specified by:

readIncludingDeleted in interface ResourceDao<R extends org.hl7.fhir.r4.model.Resource>

Parameters:

uuid - may be null

Returns:

Optional.empty() if the given uuid is null or no resource could be found for the given uuid

Throws:

SQLException - if database access errors occur

readIncludingDeletedWithTransaction

public Optional<org.hl7.fhir.r4.model.Patient> readIncludingDeletedWithTransaction(Connection connection,
 UUID uuid)
                                                                            throws SQLException

Specified by:

readIncludingDeletedWithTransaction in interface ResourceDao<R extends org.hl7.fhir.r4.model.Resource>

Parameters:

connection - not null

uuid - may be null

Returns:

Optional.empty() if the given uuid is null or no resource could be found for the given uuid

Throws:

SQLException - if database access errors occur

readAll

public List<org.hl7.fhir.r4.model.Patient> readAll()
                                            throws SQLException

Specified by:

readAll in interface ResourceDao<R extends org.hl7.fhir.r4.model.Resource>

Throws:

SQLException

readAllWithTransaction

public List<org.hl7.fhir.r4.model.Patient> readAllWithTransaction(Connection connection)
                                                           throws SQLException

Specified by:

readAllWithTransaction in interface ResourceDao<R extends org.hl7.fhir.r4.model.Resource>

Parameters:

connection - not null

Returns:

List containing matching resources

Throws:

SQLException - if database access errors occur

existsNotDeleted

public boolean existsNotDeleted(String idString,
 String versionString)
                         throws SQLException

Specified by:

existsNotDeleted in interface ResourceDao<R extends org.hl7.fhir.r4.model.Resource>

Parameters:

idString - not null

versionString - may be null

Returns:

if the given id is null false; if the given version is null or blank and a resource with the given id exists and is not marked as deleted true; if the given version is not null and not blank and a resource with the given id and version exists and is not marked as deleted true

Throws:

SQLException - if database access errors occur

See Also:

• String.isBlank()

existsNotDeletedWithTransaction

public boolean existsNotDeletedWithTransaction(Connection connection,
 String idString,
 String versionString)
                                        throws SQLException

Specified by:

existsNotDeletedWithTransaction in interface ResourceDao<R extends org.hl7.fhir.r4.model.Resource>

Parameters:

connection - not null

idString - not null

versionString - may be null

Returns:

if the given id is null false; if the given version is null or blank and a resource with the given id exists and is not marked as deleted true; if the given version is not null and not blank and a resource with the given id and version exists and is not marked as deleted true

Throws:

SQLException - if database access errors occur

See Also:

• String.isBlank()

update

public final org.hl7.fhir.r4.model.Patient update(org.hl7.fhir.r4.model.Patient resource,
 Long expectedVersion)
                                           throws SQLException,
ResourceNotFoundException,
ResourceVersionNoMatchException

Description copied from interface: ResourceDao

Sets the version of the stored resource to latest version from DB plus 1. If the given expectedVersion is not null, checks if the given expectedVersion is the latest version in DB before storing the update. Resurrects all old versions (removes deleted flag) if the latest version in DB is marked as deleted.

Specified by:

update in interface ResourceDao<R extends org.hl7.fhir.r4.model.Resource>

Parameters:

resource - not null

expectedVersion - may be null

Returns:

the stored resource, not the same object as the given resource (defensive copy)

Throws:

SQLException - if database access errors occur

ResourceNotFoundException - if the given resource could not be found

ResourceVersionNoMatchException - if the given expectedVersion is not null and the latest version does not match the given expectedVersion

updateWithTransaction

public org.hl7.fhir.r4.model.Patient updateWithTransaction(Connection connection,
 org.hl7.fhir.r4.model.Patient resource,
 Long expectedVersion)
                                                    throws SQLException,
ResourceNotFoundException,
ResourceVersionNoMatchException

Description copied from interface: ResourceDao

Sets the version of the stored resource to latest version from DB plus 1. If the given expectedVersion is not null, checks if the given expectedVersion is the latest version in DB before storing the update. Resurrects all old versions (removes deleted flag) if the latest version in DB is marked as deleted.

Specified by:

updateWithTransaction in interface ResourceDao<R extends org.hl7.fhir.r4.model.Resource>

Parameters:

connection - not null, not Connection.isReadOnly() and not Connection.getAutoCommit() and Connection.getTransactionIsolation() one of Connection.TRANSACTION_REPEATABLE_READ or Connection.TRANSACTION_SERIALIZABLE

resource - not null

expectedVersion - may be null

Returns:

the stored resource, not the same object as the given resource (defensive copy)

Throws:

SQLException - if database access errors occur

ResourceNotFoundException - if the given resource could not be found

ResourceVersionNoMatchException - if the given expectedVersion is not null and is not the latest version

toUuid

protected final UUID toUuid(String id)

toLong

protected final Long toLong(String version)

getLatestVersion

protected final dev.dsf.fhir.dao.jdbc.AbstractResourceDaoJdbc.LatestVersion getLatestVersion(org.hl7.fhir.r4.model.Patient resource,
 Connection connection)
                                                                                      throws SQLException,
ResourceNotFoundException

Throws:

SQLException

ResourceNotFoundException

getLatestVersion

protected final dev.dsf.fhir.dao.jdbc.AbstractResourceDaoJdbc.LatestVersion getLatestVersion(UUID uuid,
 Connection connection)
                                                                                      throws SQLException,
ResourceNotFoundException

Throws:

SQLException

ResourceNotFoundException

getLatestVersionIfExists

protected final Optional<dev.dsf.fhir.dao.jdbc.AbstractResourceDaoJdbc.LatestVersion> getLatestVersionIfExists(UUID uuid,
 Connection connection)
                                                                                                        throws SQLException,
ResourceNotFoundException

Throws:

SQLException

ResourceNotFoundException

delete

public final boolean delete(UUID uuid)
                     throws SQLException,
ResourceNotFoundException

Description copied from interface: ResourceDao

Returns false if a matching resource was already marked as deleted

Specified by:

delete in interface ResourceDao<R extends org.hl7.fhir.r4.model.Resource>

Parameters:

uuid - may be null

Returns:

true if a resource with the given uuid could be found and marked as deleted, false if a resource with the given uuid was already marked as deleted

Throws:

SQLException - if database access errors occur

ResourceNotFoundException - if the given uuid is null or no resource could be found with the given uuid

deleteWithTransaction

public boolean deleteWithTransaction(Connection connection,
 UUID uuid)
                              throws SQLException,
ResourceNotFoundException

Description copied from interface: ResourceDao

Returns false if a matching resource was already marked as deleted

Specified by:

deleteWithTransaction in interface ResourceDao<R extends org.hl7.fhir.r4.model.Resource>

Parameters:

connection - not null, not Connection.isReadOnly()

uuid - may be null

Returns:

true if a resource with the given uuid could be found and marked as deleted, false if a resource with the given uuid was already marked as deleted

Throws:

SQLException - if database access errors occur

ResourceNotFoundException - if the given uuid is null or no resource could be found with the given uuid

delete

protected final boolean delete(Connection connection,
 UUID uuid)
                        throws SQLException,
ResourceNotFoundException

Throws:

SQLException

ResourceNotFoundException

search

public final PartialResult<org.hl7.fhir.r4.model.Patient> search(DbSearchQuery query)
                                                          throws SQLException

Specified by:

search in interface ResourceDao<R extends org.hl7.fhir.r4.model.Resource>

Parameters:

query - not null

Returns:

PartialResult that matched the search query

Throws:

SQLException - if database access errors occur

searchWithTransaction

public PartialResult<org.hl7.fhir.r4.model.Patient> searchWithTransaction(Connection connection,
 DbSearchQuery query)
                                                                   throws SQLException

Specified by:

searchWithTransaction in interface ResourceDao<R extends org.hl7.fhir.r4.model.Resource>

Parameters:

connection - not null

query - not null

Returns:

PartialResult that matched the search query

Throws:

SQLException - if database access errors occur

modifySearchResultResource

protected void modifySearchResultResource(org.hl7.fhir.r4.model.Patient resource,
 Connection connection)
                                   throws SQLException

Override this method to modify resources retrieved by search queries before returning to the user. This method can be used, if the resource returned by the search is not complete and additional content needs to be retrieved. For example the content of a Binary resource might not be stored in the json column.

Parameters:

resource - not null

connection - not null

Throws:

SQLException - if database access errors occur

createSearchQuery

public final SearchQuery<org.hl7.fhir.r4.model.Patient> createSearchQuery(Identity identity,
 int page,
 int count)

Specified by:

createSearchQuery in interface ResourceDao<R extends org.hl7.fhir.r4.model.Resource>

createSearchQueryWithoutUserFilter

public SearchQuery<org.hl7.fhir.r4.model.Patient> createSearchQueryWithoutUserFilter(int page,
 int count)

Specified by:

createSearchQueryWithoutUserFilter in interface ResourceDao<R extends org.hl7.fhir.r4.model.Resource>

deletePermanently

public void deletePermanently(UUID uuid)
                       throws SQLException,
ResourceNotFoundException,
ResourceNotMarkedDeletedException

Description copied from interface: ResourceDao

Permanently delete a resource that was previously marked as deleted.

Specified by:

deletePermanently in interface ResourceDao<R extends org.hl7.fhir.r4.model.Resource>

Parameters:

uuid - may be null

Throws:

SQLException - if database access errors occur

ResourceNotFoundException - if the given uuid is null or no resource could be found with the given uuid

ResourceNotMarkedDeletedException - if the resource was not marked as deleted

deletePermanentlyWithTransaction

public void deletePermanentlyWithTransaction(Connection connection,
 UUID uuid)
                                      throws SQLException,
ResourceNotFoundException,
ResourceNotMarkedDeletedException

Description copied from interface: ResourceDao

Permanently delete a resource that was previously marked as deleted.

Specified by:

deletePermanentlyWithTransaction in interface ResourceDao<R extends org.hl7.fhir.r4.model.Resource>

Parameters:

connection - not null, not Connection.isReadOnly()

uuid - may be null

Throws:

SQLException - if database access errors occur

ResourceNotFoundException - if the given uuid is null or no resource could be found with the given uuid

ResourceNotMarkedDeletedException - if the resource was not marked as deleted