Package org.ehrbase.dao.access.jooq

Class EhrAccess

java.lang.Object

org.ehrbase.dao.access.support.DataAccess

org.ehrbase.dao.access.jooq.EhrAccess

All Implemented Interfaces:

I_DomainAccess, I_EhrAccess, I_SimpleCRUD

public class EhrAccess
extends DataAccess
implements I_EhrAccess

Persistence operations on EHR.

Since:

1.0.0

Author:

Christian Chevalley, Jake Smolka, Luis Marco-Ruiz

Nested Class Summary

Nested Classes

Modifier and Type	Class	Description
static class	EhrAccess.PARTY_MODE

Field Summary

Fields

Modifier and Type	Field	Description
static String	COULD_NOT_RETRIEVE_EHR_FOR_ID
static String	COULD_NOT_RETRIEVE_EHR_FOR_PARTY
static String	EXCEPTION
static String	JSONB

Fields inherited from interface org.ehrbase.dao.access.interfaces.I_DomainAccess

DBCP2_POOL, KEY_AUTO_RECONNECT, KEY_CONNECTION_MODE, KEY_DATABASE, KEY_DIALECT, KEY_HOST, KEY_INITIAL_CONNECTIONS, KEY_INTROSPECT_CACHE, KEY_KNOWLEDGE, KEY_LOG_ABANDONNED, KEY_LOGIN, KEY_MAX_ACTIVE, KEY_MAX_CONNECTION, KEY_MAX_IDLE, KEY_PASSWORD, KEY_PORT, KEY_REMOVE_ABANDONNED, KEY_REMOVE_ABANDONNED_TIMEOUT, KEY_SCHEMA, KEY_SET_MAX_PREPARED_STATEMENTS, KEY_SET_POOL_PREPARED_STATEMENTS, KEY_TEST_ON_BORROW, KEY_URL, KEY_WAIT_MS, PG_POOL

Fields inherited from interface org.ehrbase.dao.access.interfaces.I_EhrAccess

TAG_TEMPLATE_ID

Constructor Summary

Constructors

Constructor	Description
EhrAccess(org.jooq.DSLContext context, ServerConfig serverConfig, UUID partyId, UUID systemId, UUID directoryId, UUID accessId, UUID ehrId)

Method Summary

Modifier and Type	Method	Description
void	adminDeleteEhr()	Invoke physical deletion.
UUID	commit()	Deprecated.
UUID	commit(Timestamp transactionTime)	storeComposition a new entry in the DB
UUID	commit(UUID committerId, UUID systemId, String description)
Integer	delete()	Deprecated.
static Map<String,Object>	fetchSubjectIdentifiers(I_DomainAccess domainAccess, UUID ehrId)	retrieve the list of identifiers for a subject owning an Ehr the identifiers are formatted as: "CODE:ISSUER"
UUID	getAccessId()
String	getArchetypeNodeId()
static Map<String,Map<String,String>>	getCompositionList(I_DomainAccess domainAccess, UUID ehrId)	FIXME: check this method.
I_ContributionAccess	getContributionAccess()
DataAccess	getDataAccess()
UUID	getDirectoryId()
EhrRecord	getEhrRecord()
UUID	getId()
com.nedap.archie.rm.datastructures.ItemStructure	getOtherDetails()
UUID	getParty()
com.nedap.archie.rm.ehr.EhrStatus	getStatus()	Gets latest EHR_STATUS, which is attached to this EHR instance after retrieving it.
I_StatusAccess	getStatusAccess()
UUID	getStatusId()
UUID	getSystemId()
static boolean	hasEhr(I_DomainAccess domainAccess, UUID ehrId)	Check for existence of given ID as EHR.
Boolean	isModifiable()
static boolean	isModifiable(I_DomainAccess domainAccess, UUID ehrId)	Check if the EHR identified by the given ID is marked as modifiable.
boolean	isNew()	check if Ehr is newly created (uncommitted)
Boolean	isQueryable()
UUID	reload()	TODO: doc or is this one really not needed anymore? delete if so.
static boolean	removeDirectory(I_DomainAccess domainAccess, UUID ehrId)	Removes the directory row value by setting it to 'NULL'.
I_EhrAccess	retrieve(UUID id)
static I_EhrAccess	retrieveInstance(I_DomainAccess domainAccess, UUID ehrId)	Retrieve the Ehr entry from its ID (incl latest STATUS).
static I_EhrAccess	retrieveInstanceByStatus(I_DomainAccess domainAccess, UUID ehrId, UUID status, Integer version)
static UUID	retrieveInstanceBySubject(I_DomainAccess domainAccess, String subjectId, String issuerSpace)	// TODO: keep! likely to be used by EHR controller retrieve an Ehr for a subject identification with an identifier a subject identification consists of the issuer identification (ex.
static UUID	retrieveInstanceBySubject(I_DomainAccess domainAccess, UUID subjectUuid)	// TODO: keep! likely to be used by EHR controller retrieve an Ehr for a subject UUID a subject identification consists of the issuer identification (ex.
static UUID	retrieveInstanceBySubjectExternalRef(I_DomainAccess domainAccess, String subjectId, String issuerSpace)	// TODO: keep! likely to be used by EHR controller retrieve an Ehr for a subject identification by external reference a subject identification consists of the issuer identification (ex.
void	setAccess(UUID access)	set access id
void	setArchetypeNodeId(String archetypeNodeId)
void	setContributionAccess(I_ContributionAccess contributionAccess)
void	setDirectory(UUID directory)	set directory id
void	setModifiable(Boolean modifiable)
void	setName(com.nedap.archie.rm.datavalues.DvCodedText name)
void	setName(com.nedap.archie.rm.datavalues.DvText name)
void	setOtherDetails(com.nedap.archie.rm.datastructures.ItemStructure otherDetails, String templateId)
void	setParty(UUID partyId)
void	setQueryable(Boolean queryable)
void	setStatus(com.nedap.archie.rm.ehr.EhrStatus status)
void	setStatusAccess(I_StatusAccess statusAccess)
void	setSystem(UUID system)	set system Id
Boolean	update()	Deprecated.
Boolean	update(Boolean force)	Deprecated.
Boolean	update(Timestamp transactionTime)	updateComposition the current entry depending on the implementation, records are updated only if one or more field(s) have been changed
Boolean	update(Timestamp transactionTime, boolean force)	updateComposition the current entry even if the record is not modified intended to be used with temporal tables to ensure that a set of interdependent tables are updated in sync.
Boolean	update(UUID committerId, UUID systemId, UUID contributionId, ContributionDef.ContributionState state, I_ConceptAccess.ContributionChangeType contributionChangeType, String description)	Updates the whole EHR access in the DB, e.g.

Methods inherited from class org.ehrbase.dao.access.support.DataAccess

getConnection, getContext, getDialect, getIntrospectService, getKnowledgeManager, getServerConfig, releaseConnection

Methods inherited from class java.lang.Object

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

Field Detail

JSONB

public static final String JSONB

See Also:

Constant Field Values

EXCEPTION

public static final String EXCEPTION

See Also:

Constant Field Values

COULD_NOT_RETRIEVE_EHR_FOR_ID

public static final String COULD_NOT_RETRIEVE_EHR_FOR_ID

See Also:

Constant Field Values

COULD_NOT_RETRIEVE_EHR_FOR_PARTY

public static final String COULD_NOT_RETRIEVE_EHR_FOR_PARTY

See Also:

Constant Field Values

Constructor Detail

EhrAccess

public EhrAccess(org.jooq.DSLContext context,
                 ServerConfig serverConfig,
                 UUID partyId,
                 UUID systemId,
                 UUID directoryId,
                 UUID accessId,
                 UUID ehrId)

Throws:

InternalServerException - if creating or retrieving system failed

Method Detail

retrieveInstanceBySubject

public static UUID retrieveInstanceBySubject(I_DomainAccess domainAccess,
                                             UUID subjectUuid)

Description copied from interface: I_EhrAccess

// TODO: keep! likely to be used by EHR controller retrieve an Ehr for a subject UUID
a subject identification consists of the issuer identification (ex. NHS) and an identification code

Parameters:

domainAccess - SQL access

subjectUuid - the subject uuid

Returns:

UUID of corresponding Ehr or null

Throws:

IllegalArgumentException - if retrieving failed for given input

retrieveInstanceBySubject

public static UUID retrieveInstanceBySubject(I_DomainAccess domainAccess,
                                             String subjectId,
                                             String issuerSpace)

Description copied from interface: I_EhrAccess

// TODO: keep! likely to be used by EHR controller retrieve an Ehr for a subject identification with an identifier
a subject identification consists of the issuer identification (ex. NHS) and an identification code

Parameters:

domainAccess - SQL access

subjectId - the subject code or number

issuerSpace - the issuer identifier

Returns:

UUID of corresponding Ehr or null

Throws:

IllegalArgumentException - if retrieving failed for given input

retrieveInstanceBySubjectExternalRef

public static UUID retrieveInstanceBySubjectExternalRef(I_DomainAccess domainAccess,
                                                        String subjectId,
                                                        String issuerSpace)

Description copied from interface: I_EhrAccess

// TODO: keep! likely to be used by EHR controller retrieve an Ehr for a subject identification by external reference
a subject identification consists of the issuer identification (ex. NHS) and an identification code

Parameters:

domainAccess - SQL access

subjectId - the subject code or number

issuerSpace - the namespace

Returns:

UUID of corresponding Ehr or null

Throws:

IllegalArgumentException - if retrieving failed for given input

retrieveInstanceByStatus

public static I_EhrAccess retrieveInstanceByStatus(I_DomainAccess domainAccess,
                                                   UUID ehrId,
                                                   UUID status,
                                                   Integer version)

retrieveInstance

public static I_EhrAccess retrieveInstance(I_DomainAccess domainAccess,
                                           UUID ehrId)

Description copied from interface: I_EhrAccess

Retrieve the Ehr entry from its ID (incl latest STATUS).

Parameters:

domainAccess - SQL access

ehrId - the Ehr UUID

Returns:

UUID of corresponding Ehr or null

Throws:

IllegalArgumentException - when either no EHR for ID, or problem with data structure of EHR, or DB inconsistency

fetchSubjectIdentifiers

public static Map<String,Object> fetchSubjectIdentifiers(I_DomainAccess domainAccess,
                                                               UUID ehrId)

Description copied from interface: I_EhrAccess

retrieve the list of identifiers for a subject owning an Ehr
the identifiers are formatted as: "CODE:ISSUER"

Parameters:

domainAccess - SQL access

ehrId - the Ehr Id to search the subject from

Returns:

a list of identifiers

Throws:

IllegalArgumentException - when no EHR found for ID

getCompositionList

public static Map<String,Map<String,String>> getCompositionList(I_DomainAccess domainAccess,
                                                                            UUID ehrId)

FIXME: check this method. appears to be needed later on. problematic: it actually gets a list of entries, not compositions. why only with three attributes? what about the unique key problem below?

Returns:

Throws:

IllegalArgumentException - when no EHR found for ID

removeDirectory

public static boolean removeDirectory(I_DomainAccess domainAccess,
                                      UUID ehrId)

Removes the directory row value by setting it to 'NULL'. Usually his will be used after the deletion of a directories root folder.

Parameters:

domainAccess - - Database access

ehrId - - Target EHR id

Returns:

Setting NULL value succeeded

getDataAccess

public DataAccess getDataAccess()

Specified by:

getDataAccess in interface I_DomainAccess

setAccess

public void setAccess(UUID access)

Description copied from interface: I_EhrAccess

set access id

Specified by:

setAccess in interface I_EhrAccess

Parameters:

access - UUID

setDirectory

public void setDirectory(UUID directory)

Description copied from interface: I_EhrAccess

set directory id

Specified by:

setDirectory in interface I_EhrAccess

Parameters:

directory - UUID

setSystem

public void setSystem(UUID system)

Description copied from interface: I_EhrAccess

set system Id

Specified by:

setSystem in interface I_EhrAccess

Parameters:

system - UUID

setModifiable

public void setModifiable(Boolean modifiable)

Specified by:

setModifiable in interface I_EhrAccess

setArchetypeNodeId

public void setArchetypeNodeId(String archetypeNodeId)

Specified by:

setArchetypeNodeId in interface I_EhrAccess

getArchetypeNodeId

public String getArchetypeNodeId()

Specified by:

getArchetypeNodeId in interface I_EhrAccess

setName

public void setName(com.nedap.archie.rm.datavalues.DvText name)

Specified by:

setName in interface I_EhrAccess

setName

public void setName(com.nedap.archie.rm.datavalues.DvCodedText name)

Specified by:

setName in interface I_EhrAccess

setQueryable

public void setQueryable(Boolean queryable)

Specified by:

setQueryable in interface I_EhrAccess

commit

public UUID commit(Timestamp transactionTime)

Description copied from interface: I_SimpleCRUD

storeComposition a new entry in the DB

Specified by:

commit in interface I_SimpleCRUD

Returns:

the UUID of the newly created record

Throws:

InvalidApiParameterException - when input couldn't be processed, i.e. EHR not stored

commit

@Deprecated
public UUID commit()

Deprecated.

Description copied from interface: I_SimpleCRUD

storeComposition a new entry in the DB, using a default transaction time
only implemented with "root" tables: ehr, contribution and composition!

Specified by:

commit in interface I_SimpleCRUD

Returns:

the UUID of the newly created record

Throws:

InternalServerException - because inherited interface function isn't implemented in this class

commit

public UUID commit(UUID committerId,
                   UUID systemId,
                   String description)

Specified by:

commit in interface I_EhrAccess

Throws:

IllegalArgumentException - when EHR couldn't be stored

update

public Boolean update(Timestamp transactionTime)

updateComposition the current entry
depending on the implementation, records are updated only if one or more field(s) have been changed

Specified by:

update in interface I_SimpleCRUD

Returns:

Throws:

InvalidApiParameterException - when marshalling of EHR_STATUS / OTHER_DETAILS failed

update

public Boolean update(Timestamp transactionTime,
                      boolean force)

updateComposition the current entry even if the record is not modified
intended to be used with temporal tables to ensure that a set of interdependent tables are updated in sync. This approach is used to simplify versions retrieval.

Specified by:

update in interface I_SimpleCRUD

Returns:

Throws:

InvalidApiParameterException - when marshalling of EHR_STATUS / OTHER_DETAILS failed

update

@Deprecated
public Boolean update()

Deprecated.

Description copied from interface: I_SimpleCRUD

updateComposition the current entry using time now as the system transaction time
only implemented at root level object (contribution, composition, ehr). depending on the implementation, records are updated only if one or more field(s) have been changed

Specified by:

update in interface I_SimpleCRUD

Returns:

Throws:

InternalServerException - because inherited interface function isn't implemented in this class

update

@Deprecated
public Boolean update(Boolean force)

Deprecated.

Description copied from interface: I_SimpleCRUD

updateComposition the current entry using time now as the system transaction time
only implemented at root level object (contribution, composition, ehr). depending on the implementation, records are updated only if one or more field(s) have been changed

Specified by:

update in interface I_SimpleCRUD

Returns:

Throws:

InternalServerException - because inherited interface function isn't implemented in this class

update

public Boolean update(UUID committerId,
                      UUID systemId,
                      UUID contributionId,
                      ContributionDef.ContributionState state,
                      I_ConceptAccess.ContributionChangeType contributionChangeType,
                      String description)

Description copied from interface: I_EhrAccess

Updates the whole EHR access in the DB, e.g. to update the status. Embeds contribution and audit handling.

Specified by:

update in interface I_EhrAccess

Parameters:

committerId - ID of committer

systemId - ID of committing system

contributionId - Optional custom contribution ID, can be null

state - State of contribution

contributionChangeType - Change type of contribution

description - Description field

Returns:

True for success

delete

@Deprecated
public Integer delete()

Deprecated.

Description copied from interface: I_SimpleCRUD

delete the Versioned Object associated with the instance implementing this Data Access Interface. Relies on ON DELETE CASCADE

Specified by:

delete in interface I_SimpleCRUD

Returns:

Throws:

InternalServerException - because inherited interface function isn't implemented in this class

reload

public UUID reload()

Description copied from interface: I_EhrAccess

TODO: doc or is this one really not needed anymore? delete if so.

Specified by:

reload in interface I_EhrAccess

Returns:

Throws:

IllegalArgumentException - when instance's EHR ID can't be matched to existing one

retrieve

public I_EhrAccess retrieve(UUID id)

getEhrRecord

public EhrRecord getEhrRecord()

Specified by:

getEhrRecord in interface I_EhrAccess

isNew

public boolean isNew()

Description copied from interface: I_EhrAccess

check if Ehr is newly created (uncommitted)

Specified by:

isNew in interface I_EhrAccess

Returns:

true if new, false otherwise

getParty

public UUID getParty()

Specified by:

getParty in interface I_EhrAccess

setParty

public void setParty(UUID partyId)

Specified by:

setParty in interface I_EhrAccess

getId

public UUID getId()

Specified by:

getId in interface I_EhrAccess

isModifiable

public Boolean isModifiable()

Specified by:

isModifiable in interface I_EhrAccess

isQueryable

public Boolean isQueryable()

Specified by:

isQueryable in interface I_EhrAccess

getSystemId

public UUID getSystemId()

Specified by:

getSystemId in interface I_EhrAccess

getStatusId

public UUID getStatusId()

Specified by:

getStatusId in interface I_EhrAccess

getDirectoryId

public UUID getDirectoryId()

Specified by:

getDirectoryId in interface I_EhrAccess

getAccessId

public UUID getAccessId()

Specified by:

getAccessId in interface I_EhrAccess

setOtherDetails

public void setOtherDetails(com.nedap.archie.rm.datastructures.ItemStructure otherDetails,
                            String templateId)

Specified by:

setOtherDetails in interface I_EhrAccess

getOtherDetails

public com.nedap.archie.rm.datastructures.ItemStructure getOtherDetails()

Specified by:

getOtherDetails in interface I_EhrAccess

getContributionAccess

public I_ContributionAccess getContributionAccess()

setContributionAccess

public void setContributionAccess(I_ContributionAccess contributionAccess)

Specified by:

setContributionAccess in interface I_EhrAccess

getStatusAccess

public I_StatusAccess getStatusAccess()

Specified by:

getStatusAccess in interface I_EhrAccess

setStatusAccess

public void setStatusAccess(I_StatusAccess statusAccess)

Specified by:

setStatusAccess in interface I_EhrAccess

setStatus

public void setStatus(com.nedap.archie.rm.ehr.EhrStatus status)

Specified by:

setStatus in interface I_EhrAccess

getStatus

public com.nedap.archie.rm.ehr.EhrStatus getStatus()

Description copied from interface: I_EhrAccess

Gets latest EHR_STATUS, which is attached to this EHR instance after retrieving it.

Specified by:

getStatus in interface I_EhrAccess

Returns:

Latest EHR_STATUS

adminDeleteEhr

public void adminDeleteEhr()

Description copied from interface: I_EhrAccess

Invoke physical deletion.

Specified by:

adminDeleteEhr in interface I_EhrAccess

hasEhr

public static boolean hasEhr(I_DomainAccess domainAccess,
                             UUID ehrId)

Description copied from interface: I_EhrAccess

Check for existence of given ID as EHR.

Parameters:

domainAccess - Context

ehrId - EHR ID to check

Returns:

true or false

isModifiable

public static boolean isModifiable(I_DomainAccess domainAccess,
                                   UUID ehrId)

Description copied from interface: I_EhrAccess

Check if the EHR identified by the given ID is marked as modifiable. Use this method if you do not need a full I_EhrAccess instance.

Parameters:

domainAccess - Context

ehrId - EHR ID to check

Returns:

true if EHR.ehr_status.isModifiable, false otherwise (missing EHR will also return false)