Source code

001/*
002 * #%L
003 * HAPI FHIR JPA Server
004 * %%
005 * Copyright (C) 2014 - 2023 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.entity;
021
022import ca.uhn.fhir.context.support.IValidationSupport;
023import ca.uhn.fhir.i18n.Msg;
024import ca.uhn.fhir.jpa.entity.TermConceptParentChildLink.RelationshipTypeEnum;
025import ca.uhn.fhir.jpa.search.DeferConceptIndexingRoutingBinder;
026import ca.uhn.fhir.util.ValidateUtil;
027import org.apache.commons.lang3.Validate;
028import org.apache.commons.lang3.builder.EqualsBuilder;
029import org.apache.commons.lang3.builder.HashCodeBuilder;
030import org.apache.commons.lang3.builder.ToStringBuilder;
031import org.apache.commons.lang3.builder.ToStringStyle;
032import org.hibernate.search.engine.backend.types.Projectable;
033import org.hibernate.search.engine.backend.types.Searchable;
034import org.hibernate.search.mapper.pojo.bridge.mapping.annotation.PropertyBinderRef;
035import org.hibernate.search.mapper.pojo.bridge.mapping.annotation.RoutingBinderRef;
036import org.hibernate.search.mapper.pojo.mapping.definition.annotation.FullTextField;
037import org.hibernate.search.mapper.pojo.mapping.definition.annotation.GenericField;
038import org.hibernate.search.mapper.pojo.mapping.definition.annotation.Indexed;
039import org.hibernate.search.mapper.pojo.mapping.definition.annotation.PropertyBinding;
040import org.hl7.fhir.r4.model.Coding;
041
042import java.io.Serializable;
043import java.util.ArrayList;
044import java.util.Collection;
045import java.util.Date;
046import java.util.HashSet;
047import java.util.List;
048import java.util.Set;
049import java.util.stream.Collectors;
050import javax.annotation.Nonnull;
051import javax.persistence.Column;
052import javax.persistence.Entity;
053import javax.persistence.FetchType;
054import javax.persistence.ForeignKey;
055import javax.persistence.GeneratedValue;
056import javax.persistence.GenerationType;
057import javax.persistence.Id;
058import javax.persistence.Index;
059import javax.persistence.JoinColumn;
060import javax.persistence.Lob;
061import javax.persistence.ManyToOne;
062import javax.persistence.OneToMany;
063import javax.persistence.PrePersist;
064import javax.persistence.PreUpdate;
065import javax.persistence.SequenceGenerator;
066import javax.persistence.Table;
067import javax.persistence.Temporal;
068import javax.persistence.TemporalType;
069import javax.persistence.UniqueConstraint;
070
071import static org.apache.commons.lang3.StringUtils.left;
072import static org.apache.commons.lang3.StringUtils.length;
073
074@Entity
075@Indexed(routingBinder = @RoutingBinderRef(type = DeferConceptIndexingRoutingBinder.class))
076@Table(
077                name = "TRM_CONCEPT",
078                uniqueConstraints = {
079                        @UniqueConstraint(
080                                        name = "IDX_CONCEPT_CS_CODE",
081                                        columnNames = {"CODESYSTEM_PID", "CODEVAL"})
082                },
083                indexes = {
084                        @Index(name = "IDX_CONCEPT_INDEXSTATUS", columnList = "INDEX_STATUS"),
085                        @Index(name = "IDX_CONCEPT_UPDATED", columnList = "CONCEPT_UPDATED")
086                })
087public class TermConcept implements Serializable {
088        public static final int MAX_CODE_LENGTH = 500;
089        public static final int MAX_DESC_LENGTH = 400;
090        public static final int MAX_DISP_LENGTH = 500;
091        private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(TermConcept.class);
092        private static final long serialVersionUID = 1L;
093
094        @OneToMany(
095                        fetch = FetchType.LAZY,
096                        mappedBy = "myParent",
097                        cascade = {})
098        private List<TermConceptParentChildLink> myChildren;
099
100        @Column(name = "CODEVAL", nullable = false, length = MAX_CODE_LENGTH)
101        @FullTextField(
102                        name = "myCode",
103                        searchable = Searchable.YES,
104                        projectable = Projectable.YES,
105                        analyzer = "exactAnalyzer")
106        private String myCode;
107
108        @Temporal(TemporalType.TIMESTAMP)
109        @Column(name = "CONCEPT_UPDATED", nullable = true)
110        private Date myUpdated;
111
112        @ManyToOne(fetch = FetchType.LAZY)
113        @JoinColumn(
114                        name = "CODESYSTEM_PID",
115                        referencedColumnName = "PID",
116                        foreignKey = @ForeignKey(name = "FK_CONCEPT_PID_CS_PID"))
117        private TermCodeSystemVersion myCodeSystem;
118
119        @Column(name = "CODESYSTEM_PID", insertable = false, updatable = false)
120        @GenericField(name = "myCodeSystemVersionPid")
121        private long myCodeSystemVersionPid;
122
123        @Column(name = "DISPLAY", nullable = true, length = MAX_DESC_LENGTH)
124        @FullTextField(
125                        name = "myDisplay",
126                        searchable = Searchable.YES,
127                        projectable = Projectable.YES,
128                        analyzer = "standardAnalyzer")
129        @FullTextField(
130                        name = "myDisplayEdgeNGram",
131                        searchable = Searchable.YES,
132                        projectable = Projectable.NO,
133                        analyzer = "autocompleteEdgeAnalyzer")
134        @FullTextField(
135                        name = "myDisplayWordEdgeNGram",
136                        searchable = Searchable.YES,
137                        projectable = Projectable.NO,
138                        analyzer = "autocompleteWordEdgeAnalyzer")
139        @FullTextField(
140                        name = "myDisplayNGram",
141                        searchable = Searchable.YES,
142                        projectable = Projectable.NO,
143                        analyzer = "autocompleteNGramAnalyzer")
144        @FullTextField(
145                        name = "myDisplayPhonetic",
146                        searchable = Searchable.YES,
147                        projectable = Projectable.NO,
148                        analyzer = "autocompletePhoneticAnalyzer")
149        private String myDisplay;
150
151        @OneToMany(mappedBy = "myConcept", orphanRemoval = false, fetch = FetchType.LAZY)
152        @PropertyBinding(binder = @PropertyBinderRef(type = TermConceptPropertyBinder.class))
153        private Collection<TermConceptProperty> myProperties;
154
155        @OneToMany(mappedBy = "myConcept", orphanRemoval = false, fetch = FetchType.LAZY)
156        private Collection<TermConceptDesignation> myDesignations;
157
158        @Id
159        @SequenceGenerator(name = "SEQ_CONCEPT_PID", sequenceName = "SEQ_CONCEPT_PID")
160        @GeneratedValue(strategy = GenerationType.AUTO, generator = "SEQ_CONCEPT_PID")
161        @Column(name = "PID")
162        @GenericField
163        private Long myId;
164
165        @Column(name = "INDEX_STATUS", nullable = true)
166        private Long myIndexStatus;
167
168        @Lob
169        @Column(name = "PARENT_PIDS", nullable = true)
170        @FullTextField(
171                        name = "myParentPids",
172                        searchable = Searchable.YES,
173                        projectable = Projectable.YES,
174                        analyzer = "conceptParentPidsAnalyzer")
175        private String myParentPids;
176
177        @OneToMany(
178                        cascade = {},
179                        fetch = FetchType.LAZY,
180                        mappedBy = "myChild")
181        private List<TermConceptParentChildLink> myParents;
182
183        @Column(name = "CODE_SEQUENCE", nullable = true)
184        private Integer mySequence;
185
186        public TermConcept() {
187                super();
188        }
189
190        public TermConcept(TermCodeSystemVersion theCs, String theCode) {
191                setCodeSystemVersion(theCs);
192                setCode(theCode);
193        }
194
195        public TermConcept addChild(RelationshipTypeEnum theRelationshipType) {
196                TermConcept child = new TermConcept();
197                child.setCodeSystemVersion(myCodeSystem);
198                addChild(child, theRelationshipType);
199                return child;
200        }
201
202        public TermConceptParentChildLink addChild(TermConcept theChild, RelationshipTypeEnum theRelationshipType) {
203                Validate.notNull(theRelationshipType, "theRelationshipType must not be null");
204                TermConceptParentChildLink link = new TermConceptParentChildLink();
205                link.setParent(this);
206                link.setChild(theChild);
207                link.setRelationshipType(theRelationshipType);
208                getChildren().add(link);
209
210                theChild.getParents().add(link);
211                return link;
212        }
213
214        public void addChildren(List<TermConcept> theChildren, RelationshipTypeEnum theRelationshipType) {
215                for (TermConcept next : theChildren) {
216                        addChild(next, theRelationshipType);
217                }
218        }
219
220        public TermConceptDesignation addDesignation() {
221                TermConceptDesignation designation = new TermConceptDesignation();
222                designation.setConcept(this);
223                designation.setCodeSystemVersion(myCodeSystem);
224                getDesignations().add(designation);
225                return designation;
226        }
227
228        private TermConceptProperty addProperty(
229                        @Nonnull TermConceptPropertyTypeEnum thePropertyType,
230                        @Nonnull String thePropertyName,
231                        @Nonnull String thePropertyValue) {
232                Validate.notBlank(thePropertyName);
233
234                TermConceptProperty property = new TermConceptProperty();
235                property.setConcept(this);
236                property.setCodeSystemVersion(myCodeSystem);
237                property.setType(thePropertyType);
238                property.setKey(thePropertyName);
239                property.setValue(thePropertyValue);
240                if (!getProperties().contains(property)) {
241                        getProperties().add(property);
242                }
243
244                return property;
245        }
246
247        public TermConceptProperty addPropertyCoding(
248                        @Nonnull String thePropertyName,
249                        @Nonnull String thePropertyCodeSystem,
250                        @Nonnull String thePropertyCode,
251                        String theDisplayName) {
252                return addProperty(TermConceptPropertyTypeEnum.CODING, thePropertyName, thePropertyCode)
253                                .setCodeSystem(thePropertyCodeSystem)
254                                .setDisplay(theDisplayName);
255        }
256
257        public TermConceptProperty addPropertyString(@Nonnull String thePropertyName, @Nonnull String thePropertyValue) {
258                return addProperty(TermConceptPropertyTypeEnum.STRING, thePropertyName, thePropertyValue);
259        }
260
261        @Override
262        public boolean equals(Object theObj) {
263                if (!(theObj instanceof TermConcept)) {
264                        return false;
265                }
266                if (theObj == this) {
267                        return true;
268                }
269
270                TermConcept obj = (TermConcept) theObj;
271
272                EqualsBuilder b = new EqualsBuilder();
273                b.append(myCodeSystem, obj.myCodeSystem);
274                b.append(myCode, obj.myCode);
275                return b.isEquals();
276        }
277
278        public List<TermConceptParentChildLink> getChildren() {
279                if (myChildren == null) {
280                        myChildren = new ArrayList<>();
281                }
282                return myChildren;
283        }
284
285        public String getCode() {
286                return myCode;
287        }
288
289        public TermConcept setCode(@Nonnull String theCode) {
290                ValidateUtil.isNotBlankOrThrowIllegalArgument(theCode, "theCode must not be null or empty");
291                ValidateUtil.isNotTooLongOrThrowIllegalArgument(
292                                theCode, MAX_CODE_LENGTH, "Code exceeds maximum length (" + MAX_CODE_LENGTH + "): " + length(theCode));
293                myCode = theCode;
294                return this;
295        }
296
297        public TermCodeSystemVersion getCodeSystemVersion() {
298                return myCodeSystem;
299        }
300
301        public TermConcept setCodeSystemVersion(TermCodeSystemVersion theCodeSystemVersion) {
302                myCodeSystem = theCodeSystemVersion;
303                if (theCodeSystemVersion != null && theCodeSystemVersion.getPid() != null) {
304                        myCodeSystemVersionPid = theCodeSystemVersion.getPid();
305                }
306                return this;
307        }
308
309        public List<Coding> getCodingProperties(String thePropertyName) {
310                List<Coding> retVal = new ArrayList<>();
311                for (TermConceptProperty next : getProperties()) {
312                        if (thePropertyName.equals(next.getKey())) {
313                                if (next.getType() == TermConceptPropertyTypeEnum.CODING) {
314                                        Coding coding = new Coding();
315                                        coding.setSystem(next.getCodeSystem());
316                                        coding.setCode(next.getValue());
317                                        coding.setDisplay(next.getDisplay());
318                                        retVal.add(coding);
319                                }
320                        }
321                }
322                return retVal;
323        }
324
325        public Collection<TermConceptDesignation> getDesignations() {
326                if (myDesignations == null) {
327                        myDesignations = new ArrayList<>();
328                }
329                return myDesignations;
330        }
331
332        public String getDisplay() {
333                return myDisplay;
334        }
335
336        public TermConcept setDisplay(String theDisplay) {
337                myDisplay = left(theDisplay, MAX_DESC_LENGTH);
338                return this;
339        }
340
341        public Long getId() {
342                return myId;
343        }
344
345        public TermConcept setId(Long theId) {
346                myId = theId;
347                return this;
348        }
349
350        public Long getIndexStatus() {
351                return myIndexStatus;
352        }
353
354        public TermConcept setIndexStatus(Long theIndexStatus) {
355                myIndexStatus = theIndexStatus;
356                return this;
357        }
358
359        public String getParentPidsAsString() {
360                return myParentPids;
361        }
362
363        public List<TermConceptParentChildLink> getParents() {
364                if (myParents == null) {
365                        myParents = new ArrayList<>();
366                }
367                return myParents;
368        }
369
370        public Collection<TermConceptProperty> getProperties() {
371                if (myProperties == null) {
372                        myProperties = new ArrayList<>();
373                }
374                return myProperties;
375        }
376
377        public Integer getSequence() {
378                return mySequence;
379        }
380
381        public TermConcept setSequence(Integer theSequence) {
382                mySequence = theSequence;
383                return this;
384        }
385
386        public List<String> getStringProperties(String thePropertyName) {
387                List<String> retVal = new ArrayList<>();
388                for (TermConceptProperty next : getProperties()) {
389                        if (thePropertyName.equals(next.getKey())) {
390                                if (next.getType() == TermConceptPropertyTypeEnum.STRING) {
391                                        retVal.add(next.getValue());
392                                }
393                        }
394                }
395                return retVal;
396        }
397
398        public String getStringProperty(String thePropertyName) {
399                List<String> properties = getStringProperties(thePropertyName);
400                if (properties.size() > 0) {
401                        return properties.get(0);
402                }
403                return null;
404        }
405
406        public Date getUpdated() {
407                return myUpdated;
408        }
409
410        public TermConcept setUpdated(Date theUpdated) {
411                myUpdated = theUpdated;
412                return this;
413        }
414
415        @Override
416        public int hashCode() {
417                HashCodeBuilder b = new HashCodeBuilder();
418                b.append(myCodeSystem);
419                b.append(myCode);
420                return b.toHashCode();
421        }
422
423        private void parentPids(TermConcept theNextConcept, Set<Long> theParentPids) {
424                for (TermConceptParentChildLink nextParentLink : theNextConcept.getParents()) {
425                        TermConcept parent = nextParentLink.getParent();
426                        if (parent != null) {
427                                Long parentConceptId = parent.getId();
428                                Validate.notNull(parentConceptId);
429                                if (theParentPids.add(parentConceptId)) {
430                                        parentPids(parent, theParentPids);
431                                }
432                        }
433                }
434        }
435
436        @SuppressWarnings("unused")
437        @PreUpdate
438        @PrePersist
439        public void prePersist() {
440                if (myParentPids == null) {
441                        Set<Long> parentPids = new HashSet<>();
442                        TermConcept entity = this;
443                        parentPids(entity, parentPids);
444                        entity.setParentPids(parentPids);
445
446                        ourLog.trace("Code {}/{} has parents {}", entity.getId(), entity.getCode(), entity.getParentPidsAsString());
447                }
448        }
449
450        private void setParentPids(Set<Long> theParentPids) {
451                StringBuilder b = new StringBuilder();
452                for (Long next : theParentPids) {
453                        if (b.length() > 0) {
454                                b.append(' ');
455                        }
456                        b.append(next);
457                }
458
459                if (b.length() == 0) {
460                        b.append("NONE");
461                }
462
463                setParentPids(b.toString());
464        }
465
466        public TermConcept setParentPids(String theParentPids) {
467                myParentPids = theParentPids;
468                return this;
469        }
470
471        @Override
472        public String toString() {
473                ToStringBuilder b = new ToStringBuilder(this, ToStringStyle.SHORT_PREFIX_STYLE);
474                b.append("pid", myId);
475                b.append("csvPid", myCodeSystemVersionPid);
476                b.append("code", myCode);
477                b.append("display", myDisplay);
478                if (mySequence != null) {
479                        b.append("sequence", mySequence);
480                }
481                return b.build();
482        }
483
484        public List<IValidationSupport.BaseConceptProperty> toValidationProperties() {
485                List<IValidationSupport.BaseConceptProperty> retVal = new ArrayList<>();
486                for (TermConceptProperty next : getProperties()) {
487                        switch (next.getType()) {
488                                case STRING:
489                                        retVal.add(new IValidationSupport.StringConceptProperty(next.getKey(), next.getValue()));
490                                        break;
491                                case CODING:
492                                        retVal.add(new IValidationSupport.CodingConceptProperty(
493                                                        next.getKey(), next.getCodeSystem(), next.getValue(), next.getDisplay()));
494                                        break;
495                                default:
496                                        throw new IllegalStateException(Msg.code(830) + "Don't know how to handle " + next.getType());
497                        }
498                }
499                return retVal;
500        }
501
502        /**
503         * Returns a view of {@link #getChildren()} but containing the actual child codes
504         */
505        public List<TermConcept> getChildCodes() {
506                return getChildren().stream().map(TermConceptParentChildLink::getChild).collect(Collectors.toList());
507        }
508}