-
Notifications
You must be signed in to change notification settings - Fork 143
Commit
This commit does not belong to any branch on this repository, and may belong to a fork outside of the repository.
Consolidate diagnosis service implementations
- Loading branch information
Showing
9 changed files
with
301 additions
and
258 deletions.
There are no files selected for viewing
35 changes: 35 additions & 0 deletions
35
api/src/main/java/org/openmrs/module/emrapi/diagnosis/CoreDiagnosisService.java
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,35 @@ | ||
| package org.openmrs.module.emrapi.diagnosis; | ||
|
|
||
| import org.openmrs.Encounter; | ||
| import org.openmrs.Obs; | ||
| import org.openmrs.Patient; | ||
| import org.openmrs.api.context.Context; | ||
|
|
||
| import java.util.Date; | ||
| import java.util.List; | ||
|
|
||
| /** | ||
| * class implementing the DiagnosisService while delegating calls to the core module | ||
| * */ | ||
| public class CoreDiagnosisService { | ||
|
|
||
| public List<Diagnosis> getDiagnoses(Patient patient, Date fromDate) { | ||
| return DiagnosisUtils.convert(Context.getDiagnosisService().getDiagnoses(patient, fromDate)); | ||
| } | ||
|
|
||
| public List<Diagnosis> getUniqueDiagnoses(Patient patient, Date fromDate){ | ||
| return DiagnosisUtils.convert(Context.getDiagnosisService().getUniqueDiagnoses(patient, fromDate)); | ||
| } | ||
|
|
||
| public List<Diagnosis> getPrimaryDiagnoses(Encounter encounter){ | ||
| return DiagnosisUtils.convert(Context.getDiagnosisService().getPrimaryDiagnoses(encounter)); | ||
| } | ||
|
|
||
| public boolean hasDiagnosis(Encounter encounter, Diagnosis diagnosis){ | ||
| return true; | ||
| } | ||
|
|
||
| public List<Obs> codeNonCodedDiagnosis(Obs nonCodedObs, List<Diagnosis> diagnoses){ | ||
| return null; | ||
| } | ||
| } |
222 changes: 54 additions & 168 deletions
222
api/src/main/java/org/openmrs/module/emrapi/diagnosis/DiagnosisServiceImpl.java
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,200 +1,86 @@ | ||
| package org.openmrs.module.emrapi.diagnosis; | ||
|
|
||
| import org.apache.commons.logging.Log; | ||
| import org.apache.commons.logging.LogFactory; | ||
| import org.openmrs.Concept; | ||
| import org.openmrs.Encounter; | ||
| import org.openmrs.Obs; | ||
| import org.openmrs.Patient; | ||
| import org.openmrs.Person; | ||
| import org.openmrs.api.EncounterService; | ||
| import org.openmrs.api.ObsService; | ||
| import org.openmrs.api.AdministrationService; | ||
| import org.openmrs.api.impl.BaseOpenmrsService; | ||
| import org.openmrs.module.emrapi.EmrApiProperties; | ||
| import org.openmrs.module.emrapi.EmrApiConstants; | ||
|
|
||
| import java.util.ArrayList; | ||
| import java.util.Arrays; | ||
| import java.util.Collection; | ||
| import java.util.Date; | ||
| import java.util.HashSet; | ||
| import java.util.Iterator; | ||
| import java.util.List; | ||
| import java.util.Set; | ||
|
|
||
| /** | ||
| * @deprecated as of 1.25.0, replaced by {@link DiagnosisServiceImpl} in the openmrs core platform 2.2.0 | ||
| */ | ||
| @Deprecated | ||
| * class implementing the DiagnosisService while delegating calls to the core module | ||
| * */ | ||
| public class DiagnosisServiceImpl extends BaseOpenmrsService implements DiagnosisService { | ||
|
|
||
| private static final Log log = LogFactory.getLog(DiagnosisService.class); | ||
| private CoreDiagnosisService coreDiagnosisService; | ||
|
|
||
| private EmrApiProperties emrApiProperties; | ||
| private ObsGroupDiagnosisService obsGroupDiagnosisService; | ||
|
|
||
| private ObsService obsService; | ||
| private AdministrationService adminService; | ||
|
|
||
| private EncounterService encounterService; | ||
| public void setCoreDiagnosisService(CoreDiagnosisService coreDiagnosisService) { | ||
| this.coreDiagnosisService = coreDiagnosisService; | ||
| } | ||
|
|
||
| public void setObsGroupDiagnosisService(ObsGroupDiagnosisService obsGroupDiagnosisService) { | ||
| this.obsGroupDiagnosisService = obsGroupDiagnosisService; | ||
| } | ||
|
|
||
| public void setEmrApiProperties(EmrApiProperties emrApiProperties) { | ||
| this.emrApiProperties = emrApiProperties; | ||
| public void setAdminService(AdministrationService adminService) { | ||
| this.adminService = adminService; | ||
| } | ||
|
|
||
| public void setObsService(ObsService obsService) { | ||
| this.obsService = obsService; | ||
| protected boolean useDiagnosesAsObs() { | ||
| return adminService.getGlobalProperty(EmrApiConstants.GP_USE_LEGACY_DIAGNOSIS_SERVICE, "false").equalsIgnoreCase("true"); | ||
| } | ||
|
|
||
| public void setEncounterService(EncounterService encounterService) { | ||
| this.encounterService = encounterService; | ||
| } | ||
|
|
||
| @Override | ||
| public List<Obs> codeNonCodedDiagnosis(Obs nonCodedObs, List<Diagnosis> diagnoses) { | ||
|
|
||
| List<Obs> newDiagnoses = null; | ||
| if ( (nonCodedObs != null) && (diagnoses != null && diagnoses.size() > 0) ){ | ||
| newDiagnoses = new ArrayList<Obs>(); | ||
|
|
||
| Obs obsGroup = nonCodedObs.getObsGroup(); | ||
| if ( obsGroup != null ){ | ||
| Set<Obs> groupMembers = obsGroup.getGroupMembers(); | ||
| if( (groupMembers!=null) && (groupMembers.size() > 0) ){ | ||
| for (Obs groupMember : groupMembers) { | ||
| obsService.voidObs(groupMember, "code a diagnosis"); | ||
| } | ||
| } | ||
| obsGroup = obsService.voidObs(obsGroup, "code a diagnosis"); | ||
| } | ||
|
|
||
| Encounter encounter = nonCodedObs.getEncounter(); | ||
| List<Diagnosis> primaryDiagnoses = getPrimaryDiagnoses(encounter); | ||
| boolean havePrimary =false; | ||
| if (primaryDiagnoses !=null && primaryDiagnoses.size() > 0 ){ | ||
| // the encounter already has a primary diagnosis | ||
| havePrimary = true; | ||
| } | ||
| DiagnosisMetadata diagnosisMetadata = emrApiProperties.getDiagnosisMetadata(); | ||
| for(Diagnosis diagnosis : diagnoses){ | ||
| if (hasDiagnosis(encounter, diagnosis)){ | ||
| // if this encounter already has this diagnosis skip it | ||
| continue; | ||
| } | ||
| if (havePrimary) { | ||
| diagnosis.setOrder(Diagnosis.Order.SECONDARY); | ||
| } | ||
| Obs obs = diagnosisMetadata.buildDiagnosisObsGroup(diagnosis); | ||
| if (obs != null) { | ||
| newDiagnoses.add(obs); | ||
| encounter.addObs(obs); | ||
| } | ||
|
|
||
| } | ||
| encounterService.saveEncounter(encounter); | ||
| } | ||
| return newDiagnoses; | ||
| } | ||
|
|
||
| @Override | ||
| public List<Diagnosis> getPrimaryDiagnoses(Encounter encounter) { | ||
| List<Diagnosis> diagnoses = null; | ||
| if (encounter != null && !encounter.isVoided()){ | ||
| DiagnosisMetadata diagnosisMetadata = emrApiProperties.getDiagnosisMetadata(); | ||
| diagnoses = new ArrayList<Diagnosis>(); | ||
| for (Obs obs : encounter.getObsAtTopLevel(false) ){ | ||
| if (diagnosisMetadata.isDiagnosis(obs)) { | ||
| try { | ||
| Diagnosis diagnosis = diagnosisMetadata.toDiagnosis(obs); | ||
| if (Diagnosis.Order.PRIMARY == diagnosis.getOrder()) { | ||
| diagnoses.add(diagnosis); | ||
| } | ||
| } catch (Exception ex){ | ||
| log.warn("malformed diagnosis obs group with obsId " + obs.getObsId(), ex); | ||
| } | ||
| } | ||
| } | ||
| } | ||
| return diagnoses; | ||
|
|
||
| } | ||
|
|
||
| @Override | ||
| public boolean hasDiagnosis(Encounter encounter, Diagnosis diagnosis) { | ||
| boolean hasDiagnosis = false; | ||
| if (encounter != null && !encounter.isVoided()){ | ||
| DiagnosisMetadata diagnosisMetadata = emrApiProperties.getDiagnosisMetadata(); | ||
| for (Obs obs : encounter.getObsAtTopLevel(false) ){ | ||
| if (diagnosisMetadata.isDiagnosis(obs)) { | ||
| try { | ||
| Diagnosis existing = diagnosisMetadata.toDiagnosis(obs); | ||
| CodedOrFreeTextAnswer answer = existing.getDiagnosis(); | ||
| if (answer != null && answer.equals(diagnosis.getDiagnosis())){ | ||
| hasDiagnosis = true; | ||
| break; | ||
| } | ||
| } catch (Exception ex){ | ||
| log.warn("malformed diagnosis obs group with obsId " + obs.getObsId(), ex); | ||
| } | ||
| } | ||
| } | ||
| } | ||
| return hasDiagnosis; | ||
|
|
||
| } | ||
|
|
||
| @Override | ||
| public List<Diagnosis> getDiagnoses(Patient patient, Date fromDate) { | ||
| List<Diagnosis> diagnoses = new ArrayList<Diagnosis>(); | ||
|
|
||
| DiagnosisMetadata diagnosisMetadata = emrApiProperties.getDiagnosisMetadata(); | ||
|
|
||
| List<Obs> observations = obsService.getObservations(Arrays.asList((Person) patient), null, Arrays.asList(diagnosisMetadata.getDiagnosisSetConcept()), | ||
| null, null, null, Arrays.asList("obsDatetime"), | ||
| null, null, fromDate, null, false); | ||
|
|
||
| for (Obs obs : observations) { | ||
| Diagnosis diagnosis; | ||
| try { | ||
| diagnosis = diagnosisMetadata.toDiagnosis(obs); | ||
| } | ||
| catch (Exception ex) { | ||
| log.warn("Error trying to interpret " + obs + " as a diagnosis"); | ||
| if (log.isDebugEnabled()) { | ||
| log.debug("Detailed error", ex); | ||
| } | ||
| continue; | ||
| } | ||
|
|
||
| Collection<Concept> nonDiagnosisConcepts = emrApiProperties.getSuppressedDiagnosisConcepts(); | ||
| Collection<Concept> nonDiagnosisConceptSets = emrApiProperties.getNonDiagnosisConceptSets(); | ||
|
|
||
| Set<Concept> filter = new HashSet<Concept>(); | ||
| filter.addAll(nonDiagnosisConcepts); | ||
| for (Concept conceptSet : nonDiagnosisConceptSets) { | ||
| filter.addAll(conceptSet.getSetMembers()); | ||
| } | ||
|
|
||
| if (!filter.contains(diagnosis.getDiagnosis().getCodedAnswer())) { | ||
| diagnoses.add(diagnosis); | ||
| } | ||
| if (useDiagnosesAsObs()) { | ||
| return obsGroupDiagnosisService.getDiagnoses(patient, fromDate); | ||
| } | ||
| else { | ||
| return coreDiagnosisService.getDiagnoses(patient, fromDate); | ||
| } | ||
|
|
||
| return diagnoses; | ||
| } | ||
|
|
||
| @Override | ||
| public List<Diagnosis> getUniqueDiagnoses(Patient patient, Date fromDate) { | ||
| List<Diagnosis> diagnoses = getDiagnoses(patient, fromDate); | ||
| public List<Diagnosis> getUniqueDiagnoses(Patient patient, Date fromDate) { | ||
| if (useDiagnosesAsObs()) { | ||
| return obsGroupDiagnosisService.getUniqueDiagnoses(patient, fromDate); | ||
| } | ||
| else { | ||
| return coreDiagnosisService.getUniqueDiagnoses(patient, fromDate); | ||
| } | ||
|
|
||
| Set<CodedOrFreeTextAnswer> answers = new HashSet<CodedOrFreeTextAnswer>(); | ||
| } | ||
|
|
||
| Iterator<Diagnosis> it = diagnoses.iterator(); | ||
| while(it.hasNext()) { | ||
| Diagnosis diagnosis = it.next(); | ||
| public List<Diagnosis> getPrimaryDiagnoses(Encounter encounter) { | ||
| if (useDiagnosesAsObs()) { | ||
| return obsGroupDiagnosisService.getPrimaryDiagnoses(encounter); | ||
| } | ||
| else { | ||
| return coreDiagnosisService.getPrimaryDiagnoses(encounter); | ||
| } | ||
| } | ||
|
|
||
| if (!answers.add(diagnosis.getDiagnosis())) { | ||
| it.remove(); | ||
| } | ||
| public boolean hasDiagnosis(Encounter encounter, Diagnosis diagnosis) { | ||
| if (useDiagnosesAsObs()) { | ||
| return obsGroupDiagnosisService.hasDiagnosis(encounter, diagnosis); | ||
| } | ||
| else { | ||
| return coreDiagnosisService.hasDiagnosis(encounter, diagnosis); | ||
| } | ||
| } | ||
|
|
||
| return diagnoses; | ||
| public List<Obs> codeNonCodedDiagnosis(Obs nonCodedObs, List<Diagnosis> diagnoses) { | ||
| if (useDiagnosesAsObs()) { | ||
| return obsGroupDiagnosisService.codeNonCodedDiagnosis(nonCodedObs, diagnoses); | ||
| } | ||
| else { | ||
| return coreDiagnosisService.codeNonCodedDiagnosis(nonCodedObs, diagnoses); | ||
| } | ||
| } | ||
|
|
||
| } |
71 changes: 0 additions & 71 deletions
71
api/src/main/java/org/openmrs/module/emrapi/diagnosis/DiagnosisServiceImpl2_2.java
This file was deleted.
Oops, something went wrong.
Oops, something went wrong.