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org.ehrbase.repository.AbstractVersionedObjectRepository Maven / Gradle / Ivy
/*
* Copyright (c) 2024 vitasystems GmbH.
*
* This file is part of project EHRbase
*
* Licensed under the Apache License, Version 2.0 (the "License");
* you may not use this file except in compliance with the License.
* You may obtain a copy of the License at
*
* https://www.apache.org/licenses/LICENSE-2.0
*
* Unless required by applicable law or agreed to in writing, software
* distributed under the License is distributed on an "AS IS" BASIS,
* WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
* See the License for the specific language governing permissions and
* limitations under the License.
*/
package org.ehrbase.repository;
import static org.ehrbase.repository.EhrFolderRepository.NOT_MATCH_LATEST_VERSION;
import com.nedap.archie.rm.archetyped.Locatable;
import com.nedap.archie.rm.changecontrol.OriginalVersion;
import com.nedap.archie.rm.datatypes.CodePhrase;
import com.nedap.archie.rm.datavalues.DvCodedText;
import com.nedap.archie.rm.generic.AuditDetails;
import com.nedap.archie.rm.support.identification.HierObjectId;
import com.nedap.archie.rm.support.identification.ObjectRef;
import com.nedap.archie.rm.support.identification.ObjectVersionId;
import com.nedap.archie.rm.support.identification.UIDBasedId;
import java.time.OffsetDateTime;
import java.util.Arrays;
import java.util.List;
import java.util.Optional;
import java.util.UUID;
import java.util.function.Consumer;
import java.util.function.Function;
import java.util.stream.Stream;
import javax.annotation.Nullable;
import org.ehrbase.api.exception.ObjectNotFoundException;
import org.ehrbase.api.exception.PreconditionFailedException;
import org.ehrbase.api.exception.StateConflictException;
import org.ehrbase.api.service.SystemService;
import org.ehrbase.jooq.pg.enums.ContributionChangeType;
import org.ehrbase.jooq.pg.enums.ContributionDataType;
import org.ehrbase.jooq.pg.util.AdditionalSQLFunctions;
import org.ehrbase.openehr.dbformat.DbToRmFormat;
import org.ehrbase.openehr.dbformat.jooq.prototypes.AbstractRecordPrototype;
import org.ehrbase.openehr.dbformat.jooq.prototypes.AbstractTablePrototype;
import org.ehrbase.openehr.dbformat.jooq.prototypes.ObjectDataHistoryTablePrototype;
import org.ehrbase.openehr.dbformat.jooq.prototypes.ObjectDataTablePrototype;
import org.ehrbase.openehr.dbformat.jooq.prototypes.ObjectVersionHistoryTablePrototype;
import org.ehrbase.openehr.dbformat.jooq.prototypes.ObjectVersionTablePrototype;
import org.ehrbase.service.TimeProvider;
import org.jooq.Condition;
import org.jooq.DSLContext;
import org.jooq.Field;
import org.jooq.InsertQuery;
import org.jooq.JSONB;
import org.jooq.Record;
import org.jooq.Record2;
import org.jooq.Record3;
import org.jooq.Result;
import org.jooq.SelectConditionStep;
import org.jooq.SelectFromStep;
import org.jooq.SelectJoinStep;
import org.jooq.SelectLimitPercentStep;
import org.jooq.SelectOnConditionStep;
import org.jooq.SelectQuery;
import org.jooq.Table;
import org.jooq.TableField;
import org.jooq.UpdatableRecord;
import org.jooq.impl.DSL;
public abstract class AbstractVersionedObjectRepository<
VR extends UpdatableRecord,
DR extends UpdatableRecord,
VH extends UpdatableRecord,
DH extends UpdatableRecord,
O extends Locatable> {
protected static final ObjectVersionTablePrototype VERSION_PROTOTYPE = ObjectVersionTablePrototype.INSTANCE;
protected static final ObjectVersionHistoryTablePrototype VERSION_HISTORY_PROTOTYPE =
ObjectVersionHistoryTablePrototype.INSTANCE;
protected static final ObjectDataTablePrototype DATA_PROTOTYPE = ObjectDataTablePrototype.INSTANCE;
protected static final ObjectDataHistoryTablePrototype DATA_HISTORY_PROTOTYPE =
ObjectDataHistoryTablePrototype.INSTANCE;
private final AuditDetailsTargetType targetType;
protected final class Tables {
private final Table versionHead;
private final Table dataHead;
private final Table versionHistory;
private final Table dataHistory;
private Tables(Table versionHead, Table dataHead, Table versionHistory, Table dataHistory) {
this.versionHead = versionHead;
this.dataHead = dataHead;
this.versionHistory = versionHistory;
this.dataHistory = dataHistory;
}
public Table versionHead() {
return versionHead;
}
public Table dataHead() {
return dataHead;
}
public Table versionHistory() {
return versionHistory;
}
public Table dataHistory() {
return dataHistory;
}
public Table get(boolean version, boolean head) {
if (version) {
if (head) {
return versionHead;
} else {
return versionHistory;
}
} else if (head) {
return dataHead;
} else {
return dataHistory;
}
}
}
protected final Tables tables;
protected final DSLContext context;
protected final ContributionRepository contributionRepository;
protected final SystemService systemService;
protected final TimeProvider timeProvider;
protected AbstractVersionedObjectRepository(
AuditDetailsTargetType targetType,
Table versionHead,
Table dataHead,
Table versionHistory,
Table dataHistory,
DSLContext context,
ContributionRepository contributionRepository,
SystemService systemService,
TimeProvider timeProvider) {
this.targetType = targetType;
this.tables = new Tables(versionHead, dataHead, versionHistory, dataHistory);
this.context = context;
this.contributionRepository = contributionRepository;
this.systemService = systemService;
this.timeProvider = timeProvider;
}
public static ObjectVersionId buildObjectVersionId(
UUID versionedObjectId, int sysVersion, SystemService systemService) {
return new ObjectVersionId(
versionedObjectId.toString(), systemService.getSystemId(), Integer.toString(sysVersion));
}
protected Optional findHead(Condition condition) {
SelectQuery> locatableDataQuery = buildLocatableDataQuery(condition, true);
return toLocatable(locatableDataQuery.fetchOne(), getLocatableClass());
}
public Optional findByVersion(Condition condition, Condition historyCondition, int version) {
SelectQuery> headQuery = buildLocatableDataQuery(condition, true);
headQuery.addConditions(field(VERSION_PROTOTYPE.SYS_VERSION).eq(version));
SelectQuery> historyQuery = buildLocatableDataQuery(historyCondition, false);
historyQuery.addConditions(field(VERSION_HISTORY_PROTOTYPE.SYS_VERSION).eq(version));
Record3 dataRecord =
headQuery.unionAll(historyQuery).fetchOne();
if (dataRecord == null && !isDeleted(condition, historyCondition, version)) {
String typeName = targetType.name();
throw new ObjectNotFoundException(typeName, "No %s with given ID found".formatted(typeName));
}
return toLocatable(dataRecord, getLocatableClass());
}
protected Field field(TableField, T> field) {
if (field.getTable() instanceof AbstractTablePrototype t) {
var targetTable =
switch (t) {
case ObjectVersionTablePrototype __ -> tables.versionHead;
case ObjectVersionHistoryTablePrototype __ -> tables.versionHistory;
case ObjectDataTablePrototype __ -> tables.dataHead;
case ObjectDataHistoryTablePrototype __ -> tables.dataHistory;
};
return targetTable.field(field);
} else {
throw new IllegalArgumentException("Type of table not supported: %s".formatted(field.getTable()));
}
}
protected Optional findRootRecordByVersion(Condition condition, Condition historyCondition, int version) {
var head = tables.versionHead;
var history = tables.versionHistory;
Field[] historyFields = Stream.concat(
Arrays.stream(head.fields()),
Stream.of(VERSION_HISTORY_PROTOTYPE.SYS_PERIOD_UPPER, VERSION_HISTORY_PROTOTYPE.SYS_DELETED))
.map(history::field)
.toArray(Field[]::new);
return versionHeadQueryExtended(context)
.where(condition)
.and(field(VERSION_PROTOTYPE.SYS_VERSION).eq(version))
.unionAll(context.select(historyFields)
.from(history)
.where(historyCondition)
.and(history.field(VERSION_HISTORY_PROTOTYPE.SYS_VERSION)
.eq(version)))
.fetchOptional()
.map(r -> r.into(history));
}
public List findVersionIdsByContribution(UUID ehrId, UUID contributionId) {
return context
.select(field(VERSION_PROTOTYPE.VO_ID), field(VERSION_PROTOTYPE.SYS_VERSION))
.from(tables.versionHead)
.where(contributionCondition(ehrId, contributionId, tables.versionHead))
.unionAll(context.select(
tables.versionHistory.field(VERSION_HISTORY_PROTOTYPE.VO_ID),
tables.versionHistory.field(VERSION_HISTORY_PROTOTYPE.SYS_VERSION))
.from(tables.versionHistory)
.where(contributionCondition(ehrId, contributionId, tables.versionHistory)))
.orderBy(tables.versionHead.field(VERSION_PROTOTYPE.SYS_VERSION).asc())
.stream()
.map(r -> buildObjectVersionId(r.value1(), r.value2(), systemService))
.toList();
}
protected Condition contributionCondition(UUID ehrId, UUID contributionId, Table table) {
return table.field(VERSION_PROTOTYPE.CONTRIBUTION_ID)
.eq(contributionId)
.and(table.field(VERSION_PROTOTYPE.EHR_ID).eq(ehrId));
}
protected boolean isDeleted(Condition condition, Condition historyCondition, Integer version) {
return findRootRecordByVersion(condition, historyCondition, version)
.filter(r -> r.get(field(VERSION_HISTORY_PROTOTYPE.SYS_DELETED)))
.isPresent();
}
protected Optional findLatestHistoryRoot(Condition condition) {
return context.selectFrom(tables.versionHistory)
.where(condition)
.orderBy(field(VERSION_HISTORY_PROTOTYPE.SYS_VERSION).desc())
.limit(1)
.fetchOptional();
}
protected void delete(
UUID ehrId,
Condition condition,
int version,
@Nullable UUID contributionId,
@Nullable UUID auditId,
String notfoundMessage) {
Result versionHeads = findVersionHeadRecords(condition);
if (versionHeads.isEmpty()) {
// not found
throw new ObjectNotFoundException(getLocatableClass().getSimpleName(), notfoundMessage);
}
if (versionHeads.size() > 1) {
throw new IllegalArgumentException("The implementation is limited to deleting one entry");
}
// The record is recycled fot the delete entry in the history
VH versionHead = versionHeads.getFirst();
VH firstRecord = versionHead.into(tables.versionHistory);
if (firstRecord.get(VERSION_HISTORY_PROTOTYPE.SYS_VERSION) != version) {
// concurrent modification
throw new StateConflictException(NOT_MATCH_LATEST_VERSION);
}
copyHeadToHistory(versionHead, createCurrentTime(firstRecord.get(VERSION_HISTORY_PROTOTYPE.SYS_PERIOD_LOWER)));
deleteHead(condition, version, StateConflictException::new);
UUID finalContributionId = Optional.ofNullable(contributionId)
.orElseGet(() -> contributionRepository.createDefault(
ehrId, ContributionDataType.folder, ContributionChangeType.deleted));
UUID finalAuditId = Optional.ofNullable(auditId)
.orElseGet(() -> contributionRepository.createDefaultAudit(ContributionChangeType.deleted, targetType));
firstRecord.set(VERSION_HISTORY_PROTOTYPE.SYS_DELETED, true);
firstRecord.set(VERSION_HISTORY_PROTOTYPE.SYS_VERSION, version + 1);
firstRecord.set(VERSION_HISTORY_PROTOTYPE.AUDIT_ID, finalAuditId);
firstRecord.set(VERSION_HISTORY_PROTOTYPE.CONTRIBUTION_ID, finalContributionId);
firstRecord.changed(true);
firstRecord.insert();
}
protected Optional> getOriginalVersion(
Condition condition, Condition historyCondition, int version) {
Optional root = findRootRecordByVersion(condition, historyCondition, version);
if (root.isEmpty()) {
return Optional.empty();
}
VH versionRecord = root.get();
// create data for output, i.e. fields of the OriginalVersion
ObjectVersionId versionId =
buildObjectVersionId(versionRecord.get(VERSION_HISTORY_PROTOTYPE.VO_ID), version, systemService);
DvCodedText lifecycleState = new DvCodedText(
"complete", new CodePhrase("532")); // TODO: once lifecycle state is supported, get it here dynamically
AuditDetails commitAudit =
contributionRepository.findAuditDetails(versionRecord.get(VERSION_HISTORY_PROTOTYPE.AUDIT_ID));
ObjectRef objectRef = new ObjectRef<>(
new HierObjectId(versionRecord
.get(VERSION_HISTORY_PROTOTYPE.CONTRIBUTION_ID)
.toString()),
"openehr",
"contribution");
ObjectVersionId precedingVersionId = null;
// check if there is a preceding version and set it, if available
if (version > 1) {
// in the current scope version is an int and therefore: preceding = current - 1
precedingVersionId = buildObjectVersionId(
versionRecord.get(VERSION_HISTORY_PROTOTYPE.VO_ID), version - 1, systemService);
}
Optional composition = findByVersion(condition, historyCondition, version);
OriginalVersion originalVersion = new OriginalVersion<>(
versionId,
precedingVersionId,
composition.orElse(null),
lifecycleState,
commitAudit,
objectRef,
null,
null,
null);
return Optional.of(originalVersion);
}
protected abstract Class getLocatableClass();
public static int extractVersion(UIDBasedId compositionUid) {
return Integer.parseInt(
((ObjectVersionId) compositionUid).getVersionTreeId().getValue());
}
public static UUID extractUid(UIDBasedId compositionUid) {
return UUID.fromString(compositionUid.getRoot().getValue());
}
protected void commitHead(
UUID ehrId,
Locatable composition,
@Nullable UUID contributionId,
@Nullable UUID auditId,
ContributionChangeType changeType,
Consumer addVersionFieldsFunction,
Consumer addDataFieldsFunction) {
UUID finalContributionId = Optional.ofNullable(contributionId)
.orElseGet(() ->
contributionRepository.createDefault(ehrId, ContributionDataType.composition, changeType));
UUID finalAuditId = Optional.ofNullable(auditId)
.orElseGet(() -> contributionRepository.createDefaultAudit(changeType, targetType));
VersionDataDbRecord versionData = toRecords(ehrId, composition, finalContributionId, finalAuditId);
// Version
VR versionRecord = versionData.versionRecord().into(tables.versionHead);
addVersionFieldsFunction.accept(versionRecord);
versionRecord.store();
// Data
RepositoryHelper.executeBulkInsert(
context,
versionData
.dataRecords()
.get()
.map(r -> r.into(tables.dataHead))
.map(r -> {
addDataFieldsFunction.accept(r);
return r;
}),
tables.dataHead);
}
protected final VersionDataDbRecord toRecords(
UUID ehrId, Locatable versionDataObject, UUID contributionId, UUID auditId) {
return VersionDataDbRecord.toRecords(
ehrId, versionDataObject, contributionId, auditId, timeProvider.getNow(), context);
}
public void update(
UUID ehrId,
O composition,
Condition condition,
Condition historyCondition,
@Nullable UUID contributionId,
@Nullable UUID auditId,
Consumer addVersionFieldsFunction,
Consumer addDataFieldsFunction,
String notFoundErrorMessage) {
Result versionHeads = findVersionHeadRecords(condition);
int oldVersion;
OffsetDateTime now;
VH delRecord;
if (versionHeads.isEmpty()) {
Optional latestHistoryRoot = findLatestHistoryRoot(historyCondition);
if (latestHistoryRoot.isEmpty()) {
// not found
throw new ObjectNotFoundException(getLocatableClass().getSimpleName(), notFoundErrorMessage);
}
delRecord = latestHistoryRoot
.filter(r -> r.get(VERSION_HISTORY_PROTOTYPE.SYS_DELETED))
.orElseThrow(() -> new PreconditionFailedException(NOT_MATCH_LATEST_VERSION));
oldVersion = delRecord.get(VERSION_HISTORY_PROTOTYPE.SYS_VERSION);
now = createCurrentTime(delRecord.get(VERSION_HISTORY_PROTOTYPE.SYS_PERIOD_LOWER));
} else if (versionHeads.size() > 1) {
throw new IllegalArgumentException("%d versions were returned".formatted(versionHeads.size()));
} else {
delRecord = null;
VH root = versionHeads.getFirst();
oldVersion = root.get(VERSION_HISTORY_PROTOTYPE.SYS_VERSION);
now = createCurrentTime(root.get(VERSION_HISTORY_PROTOTYPE.SYS_PERIOD_LOWER));
}
// versions not consecutive
if (oldVersion + 1 != extractVersion(composition.getUid())) {
throw new PreconditionFailedException(NOT_MATCH_LATEST_VERSION);
}
if (delRecord != null) {
// update delete record period
delRecord.set(VERSION_HISTORY_PROTOTYPE.SYS_PERIOD_UPPER, now);
int updateCount = context.executeUpdate(delRecord);
if (updateCount != 1) {
// concurrent modification
throw new PreconditionFailedException(NOT_MATCH_LATEST_VERSION);
}
} else {
copyHeadToHistory(versionHeads.getFirst(), now);
deleteHead(condition, oldVersion, PreconditionFailedException::new);
}
// commit new version
commitHead(
ehrId,
composition,
contributionId,
auditId,
ContributionChangeType.modification,
addVersionFieldsFunction,
addDataFieldsFunction);
}
protected SelectQuery> buildLocatableDataQuery(Condition condition, boolean head) {
Table versionTable = tables.get(true, head);
Table dataTable = tables.get(false, head);
Field voIdField = versionTable.field(VERSION_PROTOTYPE.VO_ID);
Field sysVersionField = versionTable.field(VERSION_PROTOTYPE.SYS_VERSION);
Field jsonbField = DSL.jsonbObjectAgg(
dataTable.field(DATA_PROTOTYPE.ENTITY_IDX), dataTable.field(DATA_PROTOTYPE.DATA))
.as(DSL.name("data"));
return fromJoinedVersionData(context.select(voIdField, sysVersionField, jsonbField), head)
.where(condition)
.groupBy(voIdField, sysVersionField)
.getQuery();
}
protected , R extends Record> SelectOnConditionStep fromJoinedVersionData(
S select, boolean head) {
Table versionTable = tables.get(true, head);
Table dataTable = tables.get(false, head);
Condition joinCondition =
versionDataJoinCondition(f -> versionTable.field(f).eq(dataTable.field(f)));
if (!head) {
joinCondition = joinCondition.and(versionTable
.field(VERSION_PROTOTYPE.SYS_VERSION)
.eq(dataTable.field(DATA_HISTORY_PROTOTYPE.SYS_VERSION)));
}
return select.from(versionTable).join(dataTable).on(joinCondition);
}
protected abstract List> getVersionDataJoinFields();
private Condition versionDataJoinCondition(Function fieldConditionCreator) {
var versionDataJoinFields = getVersionDataJoinFields();
Condition joinCondition;
if (versionDataJoinFields.size() == 1) {
joinCondition = fieldConditionCreator.apply(versionDataJoinFields.getFirst());
} else {
joinCondition = DSL.and(
versionDataJoinFields.stream().map(fieldConditionCreator).toList());
}
return joinCondition;
}
protected Condition dataRootCondition(Table dataTable) {
return dataTable.field(DATA_PROTOTYPE.NUM).eq(0);
}
protected Optional findVersionByTime(
Condition condition, Condition historyCondition, OffsetDateTime time) {
SelectLimitPercentStep> headQuery = context.select(
field(VERSION_PROTOTYPE.SYS_VERSION), field(VERSION_PROTOTYPE.VO_ID))
.from(tables.versionHead)
.where(field(VERSION_PROTOTYPE.SYS_PERIOD_LOWER).lessOrEqual(time))
.and(condition)
.limit(1);
SelectLimitPercentStep> historyQuery = context.select(
field(VERSION_HISTORY_PROTOTYPE.SYS_VERSION), field(VERSION_HISTORY_PROTOTYPE.VO_ID))
.from(tables.versionHistory)
.where(
field(VERSION_HISTORY_PROTOTYPE.SYS_PERIOD_LOWER).lessOrEqual(time),
field(VERSION_HISTORY_PROTOTYPE.SYS_PERIOD_UPPER)
.greaterThan(time)
.or(field(VERSION_HISTORY_PROTOTYPE.SYS_PERIOD_UPPER)
.isNull()))
.and((historyCondition))
.limit(1);
return headQuery
.unionAll(historyQuery)
.limit(1)
.fetchOptional()
.map(r -> buildObjectVersionId(r.value2(), r.value1(), systemService));
}
/**
*
* @param jsonbRecord {vo_id, sys_version, jsonData}
* @param locatableClass
* @return
* @param
*/
protected Optional toLocatable(
Record3 jsonbRecord, Class locatableClass) {
if (jsonbRecord == null) {
return Optional.empty();
}
final L composition = DbToRmFormat.reconstructRmObject(
locatableClass, jsonbRecord.value3().data());
composition.setUid(buildObjectVersionId(jsonbRecord.value1(), jsonbRecord.value2(), systemService));
return Optional.of(composition);
}
protected void copyHeadToHistory(VH versionRecord, OffsetDateTime now) {
// copy version to history
versionRecord.set(VERSION_HISTORY_PROTOTYPE.SYS_PERIOD_UPPER, now);
versionRecord.set(VERSION_HISTORY_PROTOTYPE.SYS_DELETED, false);
versionRecord.changed(true);
versionRecord.insert();
Field[] headFields = Stream.concat(
Arrays.stream(tables.dataHead.fields()), Stream.of(field(VERSION_PROTOTYPE.SYS_VERSION)))
.toArray(Field[]::new);
Field[] historyFields =
Arrays.stream(headFields).map(tables.dataHistory::field).toArray(Field[]::new);
InsertQuery dataInsert = context.insertQuery(tables.dataHistory);
// copy data directly: select by join fields, add sys_version
Condition joinCondition =
versionDataJoinCondition(f -> tables.dataHead.field(f).eq(DSL.val(versionRecord.get(f))));
SelectConditionStep dataSelect =
fromJoinedVersionData(context.select(headFields), true).where(joinCondition);
dataInsert.setSelect(historyFields, dataSelect);
dataInsert.execute();
}
protected void deleteHead(
Condition versionCondition, int oldVersion, Function exceptionProvider) {
// delete head
int deleteCount = context.deleteFrom(tables.versionHead)
.where(versionCondition.and(field(VERSION_PROTOTYPE.SYS_VERSION).eq(oldVersion)))
.execute();
if (deleteCount == 0) {
// concurrent modification
throw exceptionProvider.apply(NOT_MATCH_LATEST_VERSION);
}
}
/**
* version head + empty history fields:
* SYS_PERIOD_UPPER,
* SYS_DELETED
*
* @param context
* @return
*/
protected SelectJoinStep versionHeadQueryExtended(DSLContext context) {
return context.select(tables.versionHead.fields())
.select(
DSL.inline((Object) null).as(VERSION_HISTORY_PROTOTYPE.SYS_PERIOD_UPPER.getName()),
DSL.inline(false).as(VERSION_HISTORY_PROTOTYPE.SYS_DELETED.getName()))
.from(tables.versionHead);
}
protected Result findVersionHeadRecords(Condition condition) {
return versionHeadQueryExtended(context).where(condition).fetchInto(tables.versionHistory);
}
protected Field jsonDataField(Table table, String... path) {
return AdditionalSQLFunctions.jsonbAttributePathText(table.field(DATA_PROTOTYPE.DATA), path);
}
/**
* Determines the current time.
*
* @param lowerBound For proper version intervals the value is guaranteed to be at least 1 microsecond after lowerBound
* @return
*/
protected OffsetDateTime createCurrentTime(OffsetDateTime lowerBound) {
OffsetDateTime now = timeProvider.getNow();
// sysPeriodUpper must be after sysPeriodLower for proper intervals
if (now.isAfter(lowerBound)) {
return now;
}
// Add one microsecond, so the interval is valid.
// Resolution of postgres timestamps is 1 microsecond
// https://www.postgresql.org/docs/14/datatype-datetime.html#DATATYPE-DATETIME-TABLE
return lowerBound.plusNanos(1_000);
}
}
