Package com.ibm.fhir.persistence.jdbc.dao.impl

Class ResourceReferenceDAO

java.lang.Object

com.ibm.fhir.persistence.jdbc.dao.impl.ResourceReferenceDAO

All Implemented Interfaces:

IResourceReferenceDAO, AutoCloseable

Direct Known Subclasses:

Db2ResourceReferenceDAO, DerbyResourceReferenceDAO, PostgresResourceReferenceDAO

public abstract class ResourceReferenceDAO
extends Object
implements IResourceReferenceDAO, AutoCloseable

DAO to handle maintenance of the local and external reference tables which contain the relationships described by "reference" elements in each resource (e.g. Observation.subject). The DAO uses a cache for looking up the ids for various entities. The DAO can create new entries, but these can only be used locally until the transaction commits, at which point they can be consolidated into the shared cache. This has the benefit that we reduce the number of times we need to lock the global cache, because we only update it once per transaction. For improved performance, we also make use of batch statements which are managed as member variables. This is why it's important to close this DAO before the transaction commits, ensuring that any outstanding DML batched but not yet executed is processed. Calling close does not close the provided Connection. That is up to the caller to manage. Close does close any statements which are opened inside the class.

Field Summary

Fields

Modifier and Type	Field	Description
protected static int	BATCH_SIZE

Constructor Summary

Constructors

Constructor	Description
ResourceReferenceDAO(IDatabaseTranslator t, Connection c, String schemaName, ICommonTokenValuesCache cache, INameIdCache<Integer> parameterNameCache)	Public constructor

Method Summary

Modifier and Type	Method	Description
void	addNormalizedValues(String resourceType, Collection<ResourceTokenValueRec> xrefs, Collection<ResourceProfileRec> profileRecs, Collection<ResourceTokenValueRec> tagRecs, Collection<ResourceTokenValueRec> securityRecs)	Add TOKEN_VALUE_MAP records, creating any CODE_SYSTEMS and COMMON_TOKEN_VALUES as necessary
void	close()
abstract void	doCanonicalValuesUpsert(String paramList, Collection<String> sortedURLS)	Insert any missing values into the common_canonical_values table
protected void	doCodeSystemsFetch(Map<String,Integer> idMap, String inList, List<String> sortedSystemNames)	Fetch the code_system_id values for each of the code_system_name values in the sortedSystemNames list.
abstract void	doCodeSystemsUpsert(String paramList, Collection<String> sortedSystemNames)	Insert any missing values into the code_systems table
protected abstract void	doCommonTokenValuesUpsert(String paramList, Collection<CommonTokenValue> sortedTokenValues)	Execute the insert (upsert) into the common_token_values table for the given collection of values.
void	flush()	Execute any statements with pending batch entries
protected ICommonTokenValuesCache	getCache()	Getter for the ICommonTokenValuesCache held by this DAO
protected Connection	getConnection()	Getter for the Connection held by this DAO
protected int	getParameterNameId(String parameterName)	Get the id from the local (tenant-specific) identity cache, or read/create using the database if needed.
ICommonTokenValuesCache	getResourceReferenceCache()	Get the cache used by the DAO
protected String	getSchemaName()	Getter for subclass access to the schemaName
protected IDatabaseTranslator	getTranslator()	Getter for the IDatabaseTranslator held by this DAO
protected void	insertResourceProfiles(String resourceType, Collection<ResourceProfileRec> profiles)
protected void	insertResourceSecurity(String resourceType, Collection<ResourceTokenValueRec> xrefs)	Insert _security parameters to the resource-specific xx_SECURITY table
protected void	insertResourceTags(String resourceType, Collection<ResourceTokenValueRec> xrefs)	Insert the tags referenced by the given collection of token value records
protected void	insertResourceTokenRefs(String resourceType, Collection<ResourceTokenValueRec> xrefs)	Insert the values in the resource-type-specific _resource_token_refs table.
protected void	insertSystemResourceProfiles(String resourceType, Collection<ResourceProfileRec> profiles)	Insert PROFILE parameters
protected void	insertSystemResourceSecurity(String resourceType, Collection<ResourceTokenValueRec> xrefs)	Insert _security parametes to the whole-system LOGICAL_REOURCE_SECURITY table
protected void	insertSystemResourceTags(String resourceType, Collection<ResourceTokenValueRec> xrefs)	Insert _tag parameters to the whole-system LOGICAL_RESOURCE_TAGS table
protected void	insertSystemResourceTokenRefs(String resourceType, Collection<ResourceTokenValueRec> xrefs)	Insert any whole-system parameters to the token_refs table
void	persist(Collection<ResourceTokenValueRec> records, Collection<ResourceProfileRec> profileRecs, Collection<ResourceTokenValueRec> tagRecs, Collection<ResourceTokenValueRec> securityRecs)	Persist the records, which may span multiple resource types
Integer	readCanonicalId(String canonicalValue)	Read the database canonical_id for the given value
CommonTokenValueResult	readCommonTokenValueId(String codeSystem, String tokenValue)	Find the database id for the given token value and system
List<Long>	readCommonTokenValueIdList(String tokenValue)	Fetch the list of matching common_token_value_id records for the given tokenValue.
Set<CommonTokenValueResult>	readCommonTokenValueIds(Collection<CommonTokenValue> tokenValues)	Find database ids for a set of common token values
protected abstract int	readOrAddParameterNameId(String parameterName)	Fetch the id for the given parameter name from the database, creating a new entry if required.
void	upsertCanonicalValues(List<ResourceProfileRec> profileValues)	Add the missing values to the database (and get ids allocated)
void	upsertCodeSystems(List<ResourceTokenValueRec> systems)	Add all the systems we currently don't have in the database.
void	upsertCommonTokenValues(List<ResourceTokenValueRec> values)	Add reference value records for each unique reference name in the given list

Methods inherited from class java.lang.Object

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

Field Detail

BATCH_SIZE

protected static final int BATCH_SIZE

See Also:

Constant Field Values

Constructor Detail

ResourceReferenceDAO

public ResourceReferenceDAO(IDatabaseTranslator t,
                            Connection c,
                            String schemaName,
                            ICommonTokenValuesCache cache,
                            INameIdCache<Integer> parameterNameCache)

Public constructor

Parameters:

c -

Method Detail

getTranslator

protected IDatabaseTranslator getTranslator()

Getter for the IDatabaseTranslator held by this DAO

Returns:

getCache

protected ICommonTokenValuesCache getCache()

Getter for the ICommonTokenValuesCache held by this DAO

Returns:

getConnection

protected Connection getConnection()

Getter for the Connection held by this DAO

Returns:

getSchemaName

protected String getSchemaName()

Getter for subclass access to the schemaName

Returns:

flush

public void flush()
           throws FHIRPersistenceException

Description copied from interface: IResourceReferenceDAO

Execute any statements with pending batch entries

Specified by:

flush in interface IResourceReferenceDAO

Throws:

FHIRPersistenceException

close

public void close()
           throws FHIRPersistenceException

Specified by:

close in interface AutoCloseable

Throws:

FHIRPersistenceException

getResourceReferenceCache

public ICommonTokenValuesCache getResourceReferenceCache()

Description copied from interface: IResourceReferenceDAO

Get the cache used by the DAO

Specified by:

getResourceReferenceCache in interface IResourceReferenceDAO

Returns:

readCommonTokenValueId

public CommonTokenValueResult readCommonTokenValueId(String codeSystem,
                                                     String tokenValue)

Description copied from interface: IResourceReferenceDAO

Find the database id for the given token value and system

Specified by:

readCommonTokenValueId in interface IResourceReferenceDAO

Returns:

the matching id from common_token_values.common_token_value_id or null if not found

readCommonTokenValueIds

public Set<CommonTokenValueResult> readCommonTokenValueIds(Collection<CommonTokenValue> tokenValues)

Description copied from interface: IResourceReferenceDAO

Find database ids for a set of common token values

Specified by:

readCommonTokenValueIds in interface IResourceReferenceDAO

Returns:

a non-null, possibly-empty set of ids from common_token_values.common_token_value_id; CommonTokenValues with no corresponding record will be omitted from the set

readCanonicalId

public Integer readCanonicalId(String canonicalValue)

Description copied from interface: IResourceReferenceDAO

Read the database canonical_id for the given value

Specified by:

readCanonicalId in interface IResourceReferenceDAO

Returns:

addNormalizedValues

public void addNormalizedValues(String resourceType,
                                Collection<ResourceTokenValueRec> xrefs,
                                Collection<ResourceProfileRec> profileRecs,
                                Collection<ResourceTokenValueRec> tagRecs,
                                Collection<ResourceTokenValueRec> securityRecs)
                         throws FHIRPersistenceException

Description copied from interface: IResourceReferenceDAO

Add TOKEN_VALUE_MAP records, creating any CODE_SYSTEMS and COMMON_TOKEN_VALUES as necessary

Specified by:

addNormalizedValues in interface IResourceReferenceDAO

Throws:

FHIRPersistenceException

insertResourceTokenRefs

protected void insertResourceTokenRefs(String resourceType,
                                       Collection<ResourceTokenValueRec> xrefs)

Insert the values in the resource-type-specific _resource_token_refs table. This is a simple batch insert because all the FKs have already been resolved and updated in the ResourceTokenValueRec records

Parameters:

resourceType -

xrefs -

insertSystemResourceTokenRefs

protected void insertSystemResourceTokenRefs(String resourceType,
                                             Collection<ResourceTokenValueRec> xrefs)

Insert any whole-system parameters to the token_refs table

Parameters:

resourceType -

xrefs -

upsertCodeSystems

public void upsertCodeSystems(List<ResourceTokenValueRec> systems)

Add all the systems we currently don't have in the database. If all target databases handled MERGE properly this would be easy, but they don't so we go old-school with a negative outer join instead (which is pretty much what MERGE does behind the scenes anyway).

Parameters:

systems -

doCodeSystemsFetch

protected void doCodeSystemsFetch(Map<String,Integer> idMap,
                                  String inList,
                                  List<String> sortedSystemNames)

Fetch the code_system_id values for each of the code_system_name values in the sortedSystemNames list.

Parameters:

idMap - the code_system_name -> code_system_id map to populate

inList - a list of bind markers for the values in the sortedSystemNames list

sortedSystemNames - the list of code_system_name values to fetch

upsertCanonicalValues

public void upsertCanonicalValues(List<ResourceProfileRec> profileValues)

Add the missing values to the database (and get ids allocated)

Parameters:

profileValues -

insertResourceProfiles

protected void insertResourceProfiles(String resourceType,
                                      Collection<ResourceProfileRec> profiles)

insertSystemResourceProfiles

protected void insertSystemResourceProfiles(String resourceType,
                                            Collection<ResourceProfileRec> profiles)

Insert PROFILE parameters

Parameters:

resourceType -

profiles -

insertResourceTags

protected void insertResourceTags(String resourceType,
                                  Collection<ResourceTokenValueRec> xrefs)

Insert the tags referenced by the given collection of token value records

Parameters:

resourceType -

xrefs -

insertSystemResourceTags

protected void insertSystemResourceTags(String resourceType,
                                        Collection<ResourceTokenValueRec> xrefs)

Insert _tag parameters to the whole-system LOGICAL_RESOURCE_TAGS table

Parameters:

resourceType -

xrefs -

insertResourceSecurity

protected void insertResourceSecurity(String resourceType,
                                      Collection<ResourceTokenValueRec> xrefs)

Insert _security parameters to the resource-specific xx_SECURITY table

Parameters:

resourceType -

xrefs -

insertSystemResourceSecurity

protected void insertSystemResourceSecurity(String resourceType,
                                            Collection<ResourceTokenValueRec> xrefs)

Insert _security parametes to the whole-system LOGICAL_REOURCE_SECURITY table

Parameters:

resourceType -

xrefs -

doCodeSystemsUpsert

public abstract void doCodeSystemsUpsert(String paramList,
                                         Collection<String> sortedSystemNames)

Insert any missing values into the code_systems table

Parameters:

paramList -

systemNames - a sorted collection of system names

doCanonicalValuesUpsert

public abstract void doCanonicalValuesUpsert(String paramList,
                                             Collection<String> sortedURLS)

Insert any missing values into the common_canonical_values table

Parameters:

paramList -

urls -

upsertCommonTokenValues

public void upsertCommonTokenValues(List<ResourceTokenValueRec> values)

Add reference value records for each unique reference name in the given list

Parameters:

values -

doCommonTokenValuesUpsert

protected abstract void doCommonTokenValuesUpsert(String paramList,
                                                  Collection<CommonTokenValue> sortedTokenValues)

Execute the insert (upsert) into the common_token_values table for the given collection of values. Note, this insert from negative outer join requires the database concurrency implementation to be correct. This does not work for Postgres, hence Postgres gets its own implementation of this method

Parameters:

paramList -

tokenValues -

persist

public void persist(Collection<ResourceTokenValueRec> records,
                    Collection<ResourceProfileRec> profileRecs,
                    Collection<ResourceTokenValueRec> tagRecs,
                    Collection<ResourceTokenValueRec> securityRecs)
             throws FHIRPersistenceException

Description copied from interface: IResourceReferenceDAO

Persist the records, which may span multiple resource types

Specified by:

persist in interface IResourceReferenceDAO

Throws:

FHIRPersistenceException

readCommonTokenValueIdList

public List<Long> readCommonTokenValueIdList(String tokenValue)

Description copied from interface: IResourceReferenceDAO

Fetch the list of matching common_token_value_id records for the given tokenValue.

Specified by:

readCommonTokenValueIdList in interface IResourceReferenceDAO

Returns:

getParameterNameId

protected int getParameterNameId(String parameterName)
                          throws FHIRPersistenceDBConnectException,
                                 FHIRPersistenceDataAccessException

Get the id from the local (tenant-specific) identity cache, or read/create using the database if needed.

Parameters:

parameterName -

Returns:

Throws:

FHIRPersistenceDBConnectException

FHIRPersistenceDataAccessException

readOrAddParameterNameId

protected abstract int readOrAddParameterNameId(String parameterName)
                                         throws FHIRPersistenceDBConnectException,
                                                FHIRPersistenceDataAccessException

Fetch the id for the given parameter name from the database, creating a new entry if required.

Parameters:

parameterName -

Returns:

Throws:

FHIRPersistenceDBConnectException

FHIRPersistenceDataAccessException