Source code

001/*-
002 * #%L
003 * HAPI FHIR JPA Server
004 * %%
005 * Copyright (C) 2014 - 2024 Smile CDR, Inc.
006 * %%
007 * Licensed under the Apache License, Version 2.0 (the "License");
008 * you may not use this file except in compliance with the License.
009 * You may obtain a copy of the License at
010 *
011 *      http://www.apache.org/licenses/LICENSE-2.0
012 *
013 * Unless required by applicable law or agreed to in writing, software
014 * distributed under the License is distributed on an "AS IS" BASIS,
015 * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
016 * See the License for the specific language governing permissions and
017 * limitations under the License.
018 * #L%
019 */
020package ca.uhn.fhir.jpa.term;
021
022import ca.uhn.fhir.context.FhirContext;
023import ca.uhn.fhir.context.FhirVersionEnum;
024import ca.uhn.fhir.i18n.Msg;
025import ca.uhn.fhir.interceptor.model.RequestPartitionId;
026import ca.uhn.fhir.jpa.api.config.JpaStorageSettings;
027import ca.uhn.fhir.jpa.api.svc.IIdHelperService;
028import ca.uhn.fhir.jpa.dao.BaseHapiFhirDao;
029import ca.uhn.fhir.jpa.dao.data.IResourceTableDao;
030import ca.uhn.fhir.jpa.dao.data.ITermCodeSystemDao;
031import ca.uhn.fhir.jpa.dao.data.ITermCodeSystemVersionDao;
032import ca.uhn.fhir.jpa.dao.data.ITermConceptDao;
033import ca.uhn.fhir.jpa.dao.data.ITermConceptDesignationDao;
034import ca.uhn.fhir.jpa.dao.data.ITermConceptParentChildLinkDao;
035import ca.uhn.fhir.jpa.dao.data.ITermConceptPropertyDao;
036import ca.uhn.fhir.jpa.entity.TermCodeSystem;
037import ca.uhn.fhir.jpa.entity.TermCodeSystemVersion;
038import ca.uhn.fhir.jpa.entity.TermConcept;
039import ca.uhn.fhir.jpa.entity.TermConceptDesignation;
040import ca.uhn.fhir.jpa.entity.TermConceptParentChildLink;
041import ca.uhn.fhir.jpa.entity.TermConceptProperty;
042import ca.uhn.fhir.jpa.model.dao.JpaPid;
043import ca.uhn.fhir.jpa.model.entity.ResourceTable;
044import ca.uhn.fhir.jpa.term.api.ITermCodeSystemStorageSvc;
045import ca.uhn.fhir.jpa.term.api.ITermDeferredStorageSvc;
046import ca.uhn.fhir.jpa.term.api.ITermReadSvc;
047import ca.uhn.fhir.jpa.term.api.ITermVersionAdapterSvc;
048import ca.uhn.fhir.jpa.term.custom.CustomTerminologySet;
049import ca.uhn.fhir.rest.api.Constants;
050import ca.uhn.fhir.rest.api.server.RequestDetails;
051import ca.uhn.fhir.rest.api.server.storage.IResourcePersistentId;
052import ca.uhn.fhir.rest.server.exceptions.InvalidRequestException;
053import ca.uhn.fhir.rest.server.exceptions.PreconditionFailedException;
054import ca.uhn.fhir.rest.server.exceptions.UnprocessableEntityException;
055import ca.uhn.fhir.util.ObjectUtil;
056import ca.uhn.fhir.util.UrlUtil;
057import ca.uhn.fhir.util.ValidateUtil;
058import jakarta.annotation.Nonnull;
059import jakarta.persistence.EntityManager;
060import jakarta.persistence.PersistenceContext;
061import jakarta.persistence.PersistenceContextType;
062import org.apache.commons.lang3.Validate;
063import org.hl7.fhir.instance.model.api.IIdType;
064import org.hl7.fhir.r4.model.CodeSystem;
065import org.hl7.fhir.r4.model.ConceptMap;
066import org.hl7.fhir.r4.model.ValueSet;
067import org.slf4j.Logger;
068import org.slf4j.LoggerFactory;
069import org.springframework.beans.factory.annotation.Autowired;
070import org.springframework.transaction.annotation.Propagation;
071import org.springframework.transaction.annotation.Transactional;
072import org.springframework.transaction.support.TransactionSynchronizationManager;
073
074import java.util.ArrayList;
075import java.util.Arrays;
076import java.util.Collection;
077import java.util.Collections;
078import java.util.HashMap;
079import java.util.HashSet;
080import java.util.IdentityHashMap;
081import java.util.List;
082import java.util.Map;
083import java.util.Objects;
084import java.util.Optional;
085import java.util.Set;
086import java.util.UUID;
087import java.util.concurrent.atomic.AtomicInteger;
088import java.util.stream.Collectors;
089
090import static ca.uhn.fhir.jpa.api.dao.IDao.RESOURCE_PID_KEY;
091import static org.apache.commons.lang3.StringUtils.isBlank;
092import static org.apache.commons.lang3.StringUtils.isNotBlank;
093import static org.hl7.fhir.common.hapi.validation.support.ValidationConstants.LOINC_LOW;
094
095public class TermCodeSystemStorageSvcImpl implements ITermCodeSystemStorageSvc {
096        private static final Logger ourLog = LoggerFactory.getLogger(TermCodeSystemStorageSvcImpl.class);
097        private static final Object PLACEHOLDER_OBJECT = new Object();
098
099        @PersistenceContext(type = PersistenceContextType.TRANSACTION)
100        protected EntityManager myEntityManager;
101
102        @Autowired
103        protected ITermCodeSystemDao myCodeSystemDao;
104
105        @Autowired
106        protected ITermCodeSystemVersionDao myCodeSystemVersionDao;
107
108        @Autowired
109        protected ITermConceptDao myConceptDao;
110
111        @Autowired
112        protected ITermConceptPropertyDao myConceptPropertyDao;
113
114        @Autowired
115        protected ITermConceptDesignationDao myConceptDesignationDao;
116
117        @Autowired
118        protected IIdHelperService<JpaPid> myIdHelperService;
119
120        @Autowired
121        private ITermConceptParentChildLinkDao myConceptParentChildLinkDao;
122
123        @Autowired
124        private ITermVersionAdapterSvc myTerminologyVersionAdapterSvc;
125
126        @Autowired
127        private ITermDeferredStorageSvc myDeferredStorageSvc;
128
129        @Autowired
130        private FhirContext myContext;
131
132        @Autowired
133        private ITermReadSvc myTerminologySvc;
134
135        @Autowired
136        private JpaStorageSettings myStorageSettings;
137
138        @Autowired
139        private IResourceTableDao myResourceTableDao;
140
141        @Autowired
142        private TermConceptDaoSvc myTermConceptDaoSvc;
143
144        @Transactional
145        @Override
146        public UploadStatistics applyDeltaCodeSystemsAdd(String theSystem, CustomTerminologySet theAdditions) {
147                ValidateUtil.isNotBlankOrThrowInvalidRequest(theSystem, "No system provided");
148                validateDstu3OrNewer();
149                theAdditions.validateNoCycleOrThrowInvalidRequest();
150
151                TermCodeSystem cs = myCodeSystemDao.findByCodeSystemUri(theSystem);
152                if (cs == null) {
153                        CodeSystem codeSystemResource = new CodeSystem();
154                        codeSystemResource.setUrl(theSystem);
155                        codeSystemResource.setContent(CodeSystem.CodeSystemContentMode.NOTPRESENT);
156                        if (isBlank(codeSystemResource.getIdElement().getIdPart()) && theSystem.contains(LOINC_LOW)) {
157                                codeSystemResource.setId(LOINC_LOW);
158                        }
159                        myTerminologyVersionAdapterSvc.createOrUpdateCodeSystem(codeSystemResource);
160
161                        cs = myCodeSystemDao.findByCodeSystemUri(theSystem);
162                }
163
164                TermCodeSystemVersion csv = cs.getCurrentVersion();
165                Validate.notNull(csv);
166
167                CodeSystem codeSystem = myTerminologySvc.fetchCanonicalCodeSystemFromCompleteContext(theSystem);
168                if (codeSystem.getContent() != CodeSystem.CodeSystemContentMode.NOTPRESENT) {
169                        throw new InvalidRequestException(
170                                        Msg.code(844) + "CodeSystem with url[" + Constants.codeSystemWithDefaultDescription(theSystem)
171                                                        + "] can not apply a delta - wrong content mode: " + codeSystem.getContent());
172                }
173
174                Validate.notNull(cs);
175                Validate.notNull(cs.getPid());
176
177                IIdType codeSystemId = cs.getResource().getIdDt();
178
179                UploadStatistics retVal = new UploadStatistics(codeSystemId);
180                HashMap<String, TermConcept> codeToConcept = new HashMap<>();
181
182                // Add root concepts
183                for (TermConcept nextRootConcept : theAdditions.getRootConcepts()) {
184                        List<String> parentCodes = Collections.emptyList();
185                        addConceptInHierarchy(csv, parentCodes, nextRootConcept, retVal, codeToConcept, 0);
186                }
187
188                return retVal;
189        }
190
191        @Transactional
192        @Override
193        public UploadStatistics applyDeltaCodeSystemsRemove(String theSystem, CustomTerminologySet theValue) {
194                ValidateUtil.isNotBlankOrThrowInvalidRequest(theSystem, "No system provided");
195                validateDstu3OrNewer();
196
197                TermCodeSystem cs = myCodeSystemDao.findByCodeSystemUri(theSystem);
198                if (cs == null) {
199                        throw new InvalidRequestException(Msg.code(845) + "Unknown code system: " + theSystem);
200                }
201                IIdType target = cs.getResource().getIdDt();
202
203                AtomicInteger removeCounter = new AtomicInteger(0);
204
205                // We need to delete all termconcepts, and their children. This stream flattens the TermConcepts and their
206                // children into a single set of TermConcept objects retrieved from the DB. Note that we have to do this because
207                // deleteById() in JPA doesnt appear to actually commit or flush a transaction until way later, and we end up
208                // iterating multiple times over the same elements, which screws up our counter.
209
210                // Grab the actual entities
211                List<TermConcept> collect = theValue.getRootConcepts().stream()
212                                .map(val -> myTerminologySvc.findCode(theSystem, val.getCode()))
213                                .filter(Optional::isPresent)
214                                .map(Optional::get)
215                                .collect(Collectors.toList());
216
217                // Iterate over the actual entities and fill out their children
218                Set<TermConcept> allFoundTermConcepts = collect.stream()
219                                .flatMap(concept -> flattenChildren(concept).stream())
220                                .map(suppliedTermConcept -> myTerminologySvc.findCode(theSystem, suppliedTermConcept.getCode()))
221                                .filter(Optional::isPresent)
222                                .map(Optional::get)
223                                .collect(Collectors.toSet());
224
225                // Delete everything about these codes.
226                for (TermConcept code : allFoundTermConcepts) {
227                        deleteEverythingRelatedToConcept(code, removeCounter);
228                }
229
230                return new UploadStatistics(removeCounter.get(), target);
231        }
232
233        private void deleteEverythingRelatedToConcept(TermConcept theConcept, AtomicInteger theRemoveCounter) {
234
235                for (TermConceptParentChildLink nextParent : theConcept.getParents()) {
236                        nextParent.getParent().getChildren().remove(nextParent);
237                        myConceptParentChildLinkDao.deleteById(nextParent.getId());
238                }
239                for (TermConceptParentChildLink nextChild : theConcept.getChildren()) {
240                        nextChild.getChild().getParents().remove(nextChild);
241                        myConceptParentChildLinkDao.deleteById(nextChild.getId());
242                }
243
244                for (TermConceptDesignation next : theConcept.getDesignations()) {
245                        myConceptDesignationDao.deleteById(next.getPid());
246                }
247                theConcept.getDesignations().clear();
248                for (TermConceptProperty next : theConcept.getProperties()) {
249                        myConceptPropertyDao.deleteById(next.getPid());
250                }
251                theConcept.getProperties().clear();
252
253                ourLog.info("Deleting concept {} - Code {}", theConcept.getId(), theConcept.getCode());
254
255                myConceptDao.deleteById(theConcept.getId());
256                //              myEntityManager.remove(theConcept);
257
258                theRemoveCounter.incrementAndGet();
259        }
260
261        private List<TermConcept> flattenChildren(TermConcept theTermConcept) {
262                if (theTermConcept.getChildren().isEmpty()) {
263                        return Arrays.asList(theTermConcept);
264                }
265
266                // Recursively flatten children
267                List<TermConcept> childTermConcepts = theTermConcept.getChildren().stream()
268                                .map(TermConceptParentChildLink::getChild)
269                                .flatMap(childConcept -> flattenChildren(childConcept).stream())
270                                .collect(Collectors.toList());
271
272                // Add itself before its list of children
273                childTermConcepts.add(0, theTermConcept);
274                return childTermConcepts;
275        }
276
277        /**
278         * Returns the number of saved concepts
279         */
280        @Override
281        public int saveConcept(TermConcept theConcept) {
282                return myTermConceptDaoSvc.saveConcept(theConcept);
283        }
284
285        @Override
286        @Transactional(propagation = Propagation.MANDATORY)
287        public void storeNewCodeSystemVersionIfNeeded(
288                        CodeSystem theCodeSystem, ResourceTable theResourceEntity, RequestDetails theRequestDetails) {
289                if (theCodeSystem != null && isNotBlank(theCodeSystem.getUrl())) {
290                        String codeSystemUrl = theCodeSystem.getUrl();
291                        if (theCodeSystem.getContent() == CodeSystem.CodeSystemContentMode.COMPLETE
292                                        || theCodeSystem.getContent() == null
293                                        || theCodeSystem.getContent() == CodeSystem.CodeSystemContentMode.NOTPRESENT) {
294                                ourLog.info(
295                                                "CodeSystem {} has a status of {}, going to store concepts in terminology tables",
296                                                theResourceEntity.getIdDt().getValue(),
297                                                theCodeSystem.getContentElement().getValueAsString());
298
299                                detectDuplicatesInCodeSystem(theCodeSystem);
300
301                                Long pid = (Long) theCodeSystem.getUserData(RESOURCE_PID_KEY);
302                                assert pid != null;
303                                JpaPid codeSystemResourcePid = JpaPid.fromId(pid);
304
305                                /*
306                                 * If this is a not-present codesystem and codesystem version already exists, we don't want to
307                                 * overwrite the existing version since that will wipe out the existing concepts. We do create
308                                 * or update the TermCodeSystem table though, since that allows the DB to reject changes that would
309                                 * result in duplicate CodeSystem.url values.
310                                 */
311                                if (theCodeSystem.getContent() == CodeSystem.CodeSystemContentMode.NOTPRESENT) {
312                                        TermCodeSystem termCodeSystem = myCodeSystemDao.findByCodeSystemUri(theCodeSystem.getUrl());
313                                        if (termCodeSystem != null) {
314                                                TermCodeSystemVersion codeSystemVersion =
315                                                                getExistingTermCodeSystemVersion(termCodeSystem.getPid(), theCodeSystem.getVersion());
316                                                if (codeSystemVersion != null) {
317                                                        TermCodeSystem myCodeSystemEntity = getOrCreateDistinctTermCodeSystem(
318                                                                        codeSystemResourcePid,
319                                                                        theCodeSystem.getUrl(),
320                                                                        theCodeSystem.getUrl(),
321                                                                        theCodeSystem.getVersion(),
322                                                                        theResourceEntity);
323                                                        return;
324                                                }
325                                        }
326                                }
327
328                                TermCodeSystemVersion persCs = new TermCodeSystemVersion();
329
330                                populateCodeSystemVersionProperties(persCs, theCodeSystem, theResourceEntity);
331
332                                persCs.getConcepts().addAll(TermReadSvcImpl.toPersistedConcepts(theCodeSystem.getConcept(), persCs));
333                                ourLog.debug("Code system has {} concepts", persCs.getConcepts().size());
334                                storeNewCodeSystemVersion(
335                                                codeSystemResourcePid,
336                                                codeSystemUrl,
337                                                theCodeSystem.getName(),
338                                                theCodeSystem.getVersion(),
339                                                persCs,
340                                                theResourceEntity,
341                                                theRequestDetails);
342                        }
343                }
344        }
345
346        private static void detectDuplicatesInCodeSystem(CodeSystem theCodeSystem) {
347                detectDuplicatesInCodeSystem(theCodeSystem.getConcept(), new HashSet<>());
348        }
349
350        private static void detectDuplicatesInCodeSystem(
351                        List<CodeSystem.ConceptDefinitionComponent> theCodeList, Set<String> theFoundCodesBuffer) {
352                for (var next : theCodeList) {
353                        if (isNotBlank(next.getCode())) {
354                                if (!theFoundCodesBuffer.add(next.getCode())) {
355                                        /*
356                                         * Note: We could possibly modify this behaviour to be forgiving, and just
357                                         * ignore duplicates. The only issue is that concepts can have properties,
358                                         * designations, etc. and it could be dangerous to just pick one and ignore the
359                                         * other. So the safer thing seems to be to just throw an error.
360                                         */
361                                        throw new PreconditionFailedException(Msg.code(2528) + "Duplicate concept detected in CodeSystem: "
362                                                        + UrlUtil.sanitizeUrlPart(next.getCode()));
363                                }
364                        }
365                        // Test child concepts within the parent concept
366                        detectDuplicatesInCodeSystem(next.getConcept(), theFoundCodesBuffer);
367                }
368        }
369
370        @Override
371        @Transactional
372        public IIdType storeNewCodeSystemVersion(
373                        CodeSystem theCodeSystemResource,
374                        TermCodeSystemVersion theCodeSystemVersion,
375                        RequestDetails theRequest,
376                        List<ValueSet> theValueSets,
377                        List<ConceptMap> theConceptMaps) {
378                assert TransactionSynchronizationManager.isActualTransactionActive();
379
380                Validate.notBlank(theCodeSystemResource.getUrl(), "theCodeSystemResource must have a URL");
381
382                // Note that this creates the TermCodeSystem and TermCodeSystemVersion entities if needed
383                IIdType csId = myTerminologyVersionAdapterSvc.createOrUpdateCodeSystem(theCodeSystemResource, theRequest);
384
385                JpaPid codeSystemResourcePid = myIdHelperService.resolveResourcePersistentIds(
386                                RequestPartitionId.allPartitions(), csId.getResourceType(), csId.getIdPart());
387                ResourceTable resource = myResourceTableDao.getOne(codeSystemResourcePid.getId());
388
389                ourLog.info("CodeSystem resource has ID: {}", csId.getValue());
390
391                populateCodeSystemVersionProperties(theCodeSystemVersion, theCodeSystemResource, resource);
392
393                storeNewCodeSystemVersion(
394                                codeSystemResourcePid,
395                                theCodeSystemResource.getUrl(),
396                                theCodeSystemResource.getName(),
397                                theCodeSystemResource.getVersion(),
398                                theCodeSystemVersion,
399                                resource,
400                                theRequest);
401
402                myDeferredStorageSvc.addConceptMapsToStorageQueue(theConceptMaps);
403                myDeferredStorageSvc.addValueSetsToStorageQueue(theValueSets);
404
405                return csId;
406        }
407
408        @Override
409        @Transactional
410        public void storeNewCodeSystemVersion(
411                        IResourcePersistentId theCodeSystemResourcePid,
412                        String theSystemUri,
413                        String theSystemName,
414                        String theCodeSystemVersionId,
415                        TermCodeSystemVersion theCodeSystemVersion,
416                        ResourceTable theCodeSystemResourceTable,
417                        RequestDetails theRequestDetails) {
418                assert TransactionSynchronizationManager.isActualTransactionActive();
419
420                ourLog.debug("Storing code system");
421
422                TermCodeSystemVersion codeSystemToStore = theCodeSystemVersion;
423                ValidateUtil.isTrueOrThrowInvalidRequest(codeSystemToStore.getResource() != null, "No resource supplied");
424                ValidateUtil.isNotBlankOrThrowInvalidRequest(theSystemUri, "No system URI supplied");
425
426                TermCodeSystem codeSystem = getOrCreateDistinctTermCodeSystem(
427                                theCodeSystemResourcePid,
428                                theSystemUri,
429                                theSystemName,
430                                theCodeSystemVersionId,
431                                theCodeSystemResourceTable);
432
433                List<TermCodeSystemVersion> existing =
434                                myCodeSystemVersionDao.findByCodeSystemResourcePid(((JpaPid) theCodeSystemResourcePid).getId());
435                for (TermCodeSystemVersion next : existing) {
436                        if (Objects.equals(next.getCodeSystemVersionId(), theCodeSystemVersionId)
437                                        && myConceptDao.countByCodeSystemVersion(next.getPid()) == 0) {
438
439                                /*
440                                 * If we already have a CodeSystemVersion that matches the version we're storing, we
441                                 * can reuse it.
442                                 */
443                                next.setCodeSystemDisplayName(theSystemName);
444                                codeSystemToStore = next;
445
446                        } else {
447
448                                /*
449                                 * If we already have a TermCodeSystemVersion that corresponds to the FHIR Resource ID we're
450                                 * adding a version to, we will mark it for deletion. For any one resource there can only
451                                 * be one TermCodeSystemVersion entity in the DB. Multiple versions of a codesystem uses
452                                 * multiple CodeSystem resources with CodeSystem.version set differently (as opposed to
453                                 * multiple versions of the same CodeSystem, where CodeSystem.meta.versionId is different)
454                                 */
455                                next.setCodeSystemVersionId("DELETED_" + UUID.randomUUID().toString());
456                                myCodeSystemVersionDao.saveAndFlush(next);
457                                myDeferredStorageSvc.deleteCodeSystemVersion(next);
458                        }
459                }
460
461                /*
462                 * Do the upload
463                 */
464
465                codeSystemToStore.setCodeSystem(codeSystem);
466                codeSystemToStore.setCodeSystemDisplayName(theSystemName);
467                codeSystemToStore.setCodeSystemVersionId(theCodeSystemVersionId);
468
469                ourLog.debug("Validating all codes in CodeSystem for storage (this can take some time for large sets)");
470
471                // Validate the code system
472                ArrayList<String> conceptsStack = new ArrayList<>();
473                IdentityHashMap<TermConcept, Object> allConcepts = new IdentityHashMap<>();
474                int totalCodeCount = 0;
475                Collection<TermConcept> conceptsToSave = theCodeSystemVersion.getConcepts();
476                for (TermConcept next : conceptsToSave) {
477                        totalCodeCount += validateConceptForStorage(next, codeSystemToStore, conceptsStack, allConcepts);
478                }
479
480                ourLog.debug("Saving version containing {} concepts", totalCodeCount);
481                if (codeSystemToStore.getPid() == null) {
482                        codeSystemToStore = myCodeSystemVersionDao.saveAndFlush(codeSystemToStore);
483                }
484
485                boolean isMakeVersionCurrent = ITermCodeSystemStorageSvc.isMakeVersionCurrent(theRequestDetails);
486                if (isMakeVersionCurrent) {
487                        codeSystem.setCurrentVersion(codeSystemToStore);
488                        if (codeSystem.getPid() == null) {
489                                codeSystem = myCodeSystemDao.saveAndFlush(codeSystem);
490                        }
491                }
492
493                ourLog.debug("Setting CodeSystemVersion[{}] on {} concepts...", codeSystem.getPid(), totalCodeCount);
494                for (TermConcept next : conceptsToSave) {
495                        populateVersion(next, codeSystemToStore);
496                }
497
498                ourLog.debug("Saving {} concepts...", totalCodeCount);
499                IdentityHashMap<TermConcept, Object> conceptsStack2 = new IdentityHashMap<>();
500                for (TermConcept next : conceptsToSave) {
501                        persistChildren(next, codeSystemToStore, conceptsStack2, totalCodeCount);
502                }
503
504                ourLog.debug("Done saving concepts, flushing to database");
505                if (!myDeferredStorageSvc.isStorageQueueEmpty(true)) {
506                        ourLog.info("Note that some concept saving has been deferred");
507                }
508        }
509
510        private TermCodeSystemVersion getExistingTermCodeSystemVersion(
511                        Long theCodeSystemVersionPid, String theCodeSystemVersion) {
512                TermCodeSystemVersion existing;
513                if (theCodeSystemVersion == null) {
514                        existing = myCodeSystemVersionDao.findByCodeSystemPidVersionIsNull(theCodeSystemVersionPid);
515                } else {
516                        existing =
517                                        myCodeSystemVersionDao.findByCodeSystemPidAndVersion(theCodeSystemVersionPid, theCodeSystemVersion);
518                }
519
520                return existing;
521        }
522
523        private void validateDstu3OrNewer() {
524                Validate.isTrue(
525                                myContext.getVersion().getVersion().isEqualOrNewerThan(FhirVersionEnum.DSTU3),
526                                "Terminology operations only supported in DSTU3+ mode");
527        }
528
529        private void addConceptInHierarchy(
530                        TermCodeSystemVersion theCsv,
531                        Collection<String> theParentCodes,
532                        TermConcept theConceptToAdd,
533                        UploadStatistics theStatisticsTracker,
534                        Map<String, TermConcept> theCodeToConcept,
535                        int theSequence) {
536                TermConcept conceptToAdd = theConceptToAdd;
537                List<TermConceptParentChildLink> childrenToAdd = theConceptToAdd.getChildren();
538
539                String nextCodeToAdd = conceptToAdd.getCode();
540                String parentDescription = "(root concept)";
541
542                ourLog.info(
543                                "Saving concept {} with parent {}", theStatisticsTracker.getUpdatedConceptCount(), parentDescription);
544
545                Optional<TermConcept> existingCodeOpt = myConceptDao.findByCodeSystemAndCode(theCsv.getPid(), nextCodeToAdd);
546                List<TermConceptParentChildLink> existingParentLinks;
547                if (existingCodeOpt.isPresent()) {
548                        TermConcept existingCode = existingCodeOpt.get();
549                        existingCode.setIndexStatus(null);
550                        existingCode.setDisplay(conceptToAdd.getDisplay());
551                        conceptToAdd = existingCode;
552                        existingParentLinks = conceptToAdd.getParents();
553                } else {
554                        existingParentLinks = Collections.emptyList();
555                }
556
557                Set<TermConcept> parentConceptsWeShouldLinkTo = new HashSet<>();
558                for (String nextParentCode : theParentCodes) {
559
560                        // Don't add parent links that already exist for the code
561                        if (existingParentLinks.stream()
562                                        .anyMatch(t -> t.getParent().getCode().equals(nextParentCode))) {
563                                continue;
564                        }
565
566                        TermConcept nextParentOpt = theCodeToConcept.get(nextParentCode);
567                        if (nextParentOpt == null) {
568                                nextParentOpt = myConceptDao
569                                                .findByCodeSystemAndCode(theCsv.getPid(), nextParentCode)
570                                                .orElse(null);
571                        }
572                        if (nextParentOpt == null) {
573                                throw new InvalidRequestException(Msg.code(846) + "Unable to add code \"" + nextCodeToAdd
574                                                + "\" to unknown parent: " + nextParentCode);
575                        }
576                        parentConceptsWeShouldLinkTo.add(nextParentOpt);
577                }
578
579                if (conceptToAdd.getSequence() == null) {
580                        conceptToAdd.setSequence(theSequence);
581                }
582
583                // Null out the hierarchy PIDs for this concept always. We do this because we're going to
584                // force a reindex, and it'll be regenerated then
585                conceptToAdd.setParentPids(null);
586                conceptToAdd.setCodeSystemVersion(theCsv);
587
588                if (conceptToAdd.getProperties() != null)
589                        conceptToAdd.getProperties().forEach(termConceptProperty -> {
590                                termConceptProperty.setConcept(theConceptToAdd);
591                                termConceptProperty.setCodeSystemVersion(theCsv);
592                        });
593                if (theStatisticsTracker.getUpdatedConceptCount() <= myStorageSettings.getDeferIndexingForCodesystemsOfSize()) {
594                        saveConcept(conceptToAdd);
595                        Long nextConceptPid = conceptToAdd.getId();
596                        Validate.notNull(nextConceptPid);
597                } else {
598                        myDeferredStorageSvc.addConceptToStorageQueue(conceptToAdd);
599                }
600
601                theCodeToConcept.put(conceptToAdd.getCode(), conceptToAdd);
602
603                theStatisticsTracker.incrementUpdatedConceptCount();
604
605                // Add link to new child to the parent
606                for (TermConcept nextParentConcept : parentConceptsWeShouldLinkTo) {
607                        TermConceptParentChildLink parentLink = new TermConceptParentChildLink();
608                        parentLink.setParent(nextParentConcept);
609                        parentLink.setChild(conceptToAdd);
610                        parentLink.setCodeSystem(theCsv);
611                        parentLink.setRelationshipType(TermConceptParentChildLink.RelationshipTypeEnum.ISA);
612                        nextParentConcept.getChildren().add(parentLink);
613                        conceptToAdd.getParents().add(parentLink);
614                        ourLog.info(
615                                        "Saving parent/child link - Parent[{}] Child[{}]",
616                                        parentLink.getParent().getCode(),
617                                        parentLink.getChild().getCode());
618
619                        if (theStatisticsTracker.getUpdatedConceptCount()
620                                        <= myStorageSettings.getDeferIndexingForCodesystemsOfSize()) {
621                                myConceptParentChildLinkDao.save(parentLink);
622                        } else {
623                                myDeferredStorageSvc.addConceptLinkToStorageQueue(parentLink);
624                        }
625                }
626
627                ourLog.trace("About to save parent-child links");
628
629                // Save children recursively
630                int childIndex = 0;
631                for (TermConceptParentChildLink nextChildConceptLink : new ArrayList<>(childrenToAdd)) {
632
633                        TermConcept nextChild = nextChildConceptLink.getChild();
634
635                        for (int i = 0; i < nextChild.getParents().size(); i++) {
636                                if (nextChild.getParents().get(i).getId() == null) {
637                                        String parentCode =
638                                                        nextChild.getParents().get(i).getParent().getCode();
639                                        TermConcept parentConcept = theCodeToConcept.get(parentCode);
640                                        if (parentConcept == null) {
641                                                parentConcept = myConceptDao
642                                                                .findByCodeSystemAndCode(theCsv.getPid(), parentCode)
643                                                                .orElse(null);
644                                        }
645                                        if (parentConcept == null) {
646                                                throw new IllegalArgumentException(Msg.code(847) + "Unknown parent code: " + parentCode);
647                                        }
648
649                                        nextChild.getParents().get(i).setParent(parentConcept);
650                                }
651                        }
652
653                        Collection<String> parentCodes = nextChild.getParents().stream()
654                                        .map(t -> t.getParent().getCode())
655                                        .collect(Collectors.toList());
656                        addConceptInHierarchy(theCsv, parentCodes, nextChild, theStatisticsTracker, theCodeToConcept, childIndex);
657
658                        childIndex++;
659                }
660        }
661
662        private void persistChildren(
663                        TermConcept theConcept,
664                        TermCodeSystemVersion theCodeSystem,
665                        IdentityHashMap<TermConcept, Object> theConceptsStack,
666                        int theTotalConcepts) {
667                if (theConceptsStack.put(theConcept, PLACEHOLDER_OBJECT) != null) {
668                        return;
669                }
670
671                if ((theConceptsStack.size() + 1) % 10000 == 0) {
672                        float pct = (float) theConceptsStack.size() / (float) theTotalConcepts;
673                        ourLog.info(
674                                        "Have processed {}/{} concepts ({}%)",
675                                        theConceptsStack.size(), theTotalConcepts, (int) (pct * 100.0f));
676                }
677
678                theConcept.setCodeSystemVersion(theCodeSystem);
679                theConcept.setIndexStatus(BaseHapiFhirDao.INDEX_STATUS_INDEXED);
680
681                if (theConceptsStack.size() <= myStorageSettings.getDeferIndexingForCodesystemsOfSize()) {
682                        saveConcept(theConcept);
683                } else {
684                        myDeferredStorageSvc.addConceptToStorageQueue(theConcept);
685                }
686
687                for (TermConceptParentChildLink next : theConcept.getChildren()) {
688                        persistChildren(next.getChild(), theCodeSystem, theConceptsStack, theTotalConcepts);
689                }
690
691                for (TermConceptParentChildLink next : theConcept.getChildren()) {
692                        if (theConceptsStack.size() <= myStorageSettings.getDeferIndexingForCodesystemsOfSize()) {
693                                saveConceptLink(next);
694                        } else {
695                                myDeferredStorageSvc.addConceptLinkToStorageQueue(next);
696                        }
697                }
698        }
699
700        private void populateVersion(TermConcept theNext, TermCodeSystemVersion theCodeSystemVersion) {
701                theNext.setCodeSystemVersion(theCodeSystemVersion);
702                for (TermConceptParentChildLink next : theNext.getChildren()) {
703                        populateVersion(next.getChild(), theCodeSystemVersion);
704                }
705                theNext.getProperties().forEach(t -> t.setCodeSystemVersion(theCodeSystemVersion));
706                theNext.getDesignations().forEach(t -> t.setCodeSystemVersion(theCodeSystemVersion));
707        }
708
709        private void saveConceptLink(TermConceptParentChildLink next) {
710                if (next.getId() == null) {
711                        myConceptParentChildLinkDao.save(next);
712                }
713        }
714
715        @Nonnull
716        private TermCodeSystem getOrCreateDistinctTermCodeSystem(
717                        IResourcePersistentId theCodeSystemResourcePid,
718                        String theSystemUri,
719                        String theSystemName,
720                        String theSystemVersionId,
721                        ResourceTable theCodeSystemResourceTable) {
722                TermCodeSystem codeSystem = myCodeSystemDao.findByCodeSystemUri(theSystemUri);
723                if (codeSystem == null) {
724                        codeSystem = myCodeSystemDao.findByResourcePid(((JpaPid) theCodeSystemResourcePid).getId());
725                        if (codeSystem == null) {
726                                codeSystem = new TermCodeSystem();
727                        }
728                } else {
729                        checkForCodeSystemVersionDuplicate(
730                                        codeSystem, theSystemUri, theSystemVersionId, theCodeSystemResourceTable);
731                }
732
733                codeSystem.setResource(theCodeSystemResourceTable);
734                codeSystem.setCodeSystemUri(theSystemUri);
735                codeSystem.setName(theSystemName);
736                codeSystem = myCodeSystemDao.save(codeSystem);
737                return codeSystem;
738        }
739
740        private void checkForCodeSystemVersionDuplicate(
741                        TermCodeSystem theCodeSystem,
742                        String theSystemUri,
743                        String theSystemVersionId,
744                        ResourceTable theCodeSystemResourceTable) {
745                TermCodeSystemVersion codeSystemVersionEntity;
746                String msg = null;
747                if (theSystemVersionId == null) {
748                        // Check if a non-versioned TermCodeSystemVersion entity already exists for this TermCodeSystem.
749                        codeSystemVersionEntity = myCodeSystemVersionDao.findByCodeSystemPidVersionIsNull(theCodeSystem.getPid());
750                        if (codeSystemVersionEntity != null) {
751                                msg = myContext
752                                                .getLocalizer()
753                                                .getMessage(
754                                                                TermReadSvcImpl.class,
755                                                                "cannotCreateDuplicateCodeSystemUrl",
756                                                                theSystemUri,
757                                                                codeSystemVersionEntity
758                                                                                .getResource()
759                                                                                .getIdDt()
760                                                                                .toUnqualifiedVersionless()
761                                                                                .getValue());
762                        }
763                } else {
764                        // Check if a TermCodeSystemVersion entity already exists for this TermCodeSystem and version.
765                        codeSystemVersionEntity =
766                                        myCodeSystemVersionDao.findByCodeSystemPidAndVersion(theCodeSystem.getPid(), theSystemVersionId);
767                        if (codeSystemVersionEntity != null) {
768                                msg = myContext
769                                                .getLocalizer()
770                                                .getMessage(
771                                                                TermReadSvcImpl.class,
772                                                                "cannotCreateDuplicateCodeSystemUrlAndVersion",
773                                                                theSystemUri,
774                                                                theSystemVersionId,
775                                                                codeSystemVersionEntity
776                                                                                .getResource()
777                                                                                .getIdDt()
778                                                                                .toUnqualifiedVersionless()
779                                                                                .getValue());
780                        }
781                }
782                // Throw exception if the TermCodeSystemVersion is being duplicated.
783                if (codeSystemVersionEntity != null) {
784                        if (!ObjectUtil.equals(codeSystemVersionEntity.getResource().getId(), theCodeSystemResourceTable.getId())) {
785                                throw new UnprocessableEntityException(Msg.code(848) + msg);
786                        }
787                }
788        }
789
790        private void populateCodeSystemVersionProperties(
791                        TermCodeSystemVersion theCodeSystemVersion,
792                        CodeSystem theCodeSystemResource,
793                        ResourceTable theResourceTable) {
794                theCodeSystemVersion.setResource(theResourceTable);
795                theCodeSystemVersion.setCodeSystemDisplayName(theCodeSystemResource.getName());
796                theCodeSystemVersion.setCodeSystemVersionId(theCodeSystemResource.getVersion());
797        }
798
799        private int validateConceptForStorage(
800                        TermConcept theConcept,
801                        TermCodeSystemVersion theCodeSystemVersion,
802                        ArrayList<String> theConceptsStack,
803                        IdentityHashMap<TermConcept, Object> theAllConcepts) {
804                ValidateUtil.isTrueOrThrowInvalidRequest(
805                                theConcept.getCodeSystemVersion() != null, "CodeSystemVersion is null");
806                ValidateUtil.isNotBlankOrThrowInvalidRequest(
807                                theConcept.getCode(), "CodeSystem contains a code with no code value");
808
809                theConcept.setCodeSystemVersion(theCodeSystemVersion);
810                if (theConceptsStack.contains(theConcept.getCode())) {
811                        throw new InvalidRequestException(
812                                        Msg.code(849) + "CodeSystem contains circular reference around code " + theConcept.getCode());
813                }
814                theConceptsStack.add(theConcept.getCode());
815
816                int retVal = 0;
817                if (theAllConcepts.put(theConcept, theAllConcepts) == null) {
818                        if (theAllConcepts.size() % 1000 == 0) {
819                                ourLog.info("Have validated {} concepts", theAllConcepts.size());
820                        }
821                        retVal = 1;
822                }
823
824                for (TermConceptParentChildLink next : theConcept.getChildren()) {
825                        next.setCodeSystem(theCodeSystemVersion);
826                        retVal +=
827                                        validateConceptForStorage(next.getChild(), theCodeSystemVersion, theConceptsStack, theAllConcepts);
828                }
829
830                theConceptsStack.remove(theConceptsStack.size() - 1);
831
832                return retVal;
833        }
834}