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Merge pull request #1869 from patryllus/moh240_706
Initial stubs for MOH 240 and MOH 706 pulling from kenyaemr_etl reporting tables
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117 changes: 117 additions & 0 deletions
117
...ava/org/openmrs/module/kenyaemr/reporting/builder/common/SetupMOH240LabReportBuilder.java
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| /** | ||
| * This Source Code Form is subject to the terms of the Mozilla Public License, | ||
| * v. 2.0. If a copy of the MPL was not distributed with this file, You can | ||
| * obtain one at http://mozilla.org/MPL/2.0/. OpenMRS is also distributed under | ||
| * the terms of the Healthcare Disclaimer located at http://openmrs.org/license. | ||
| * | ||
| * Copyright (C) OpenMRS Inc. OpenMRS is a registered trademark and the OpenMRS | ||
| * graphic logo is a trademark of OpenMRS Inc. | ||
| */ | ||
| package org.openmrs.module.kenyaemr.reporting.builder.common; | ||
|
|
||
| import org.openmrs.PatientIdentifierType; | ||
| import org.openmrs.PersonAttributeType; | ||
| import org.openmrs.api.context.Context; | ||
| import org.openmrs.module.kenyacore.report.HybridReportDescriptor; | ||
| import org.openmrs.module.kenyacore.report.ReportDescriptor; | ||
| import org.openmrs.module.kenyacore.report.ReportUtils; | ||
| import org.openmrs.module.kenyacore.report.builder.AbstractHybridReportBuilder; | ||
| import org.openmrs.module.kenyacore.report.builder.Builds; | ||
| import org.openmrs.module.kenyacore.report.data.patient.definition.CalculationDataDefinition; | ||
| import org.openmrs.module.kenyaemr.calculation.library.mchcs.PersonAddressCalculation; | ||
| import org.openmrs.module.kenyaemr.metadata.CommonMetadata; | ||
| import org.openmrs.module.kenyaemr.reporting.calculation.converter.RDQACalculationResultConverter; | ||
| import org.openmrs.module.reporting.cohort.definition.CohortDefinition; | ||
| import org.openmrs.module.reporting.cohort.definition.SqlCohortDefinition; | ||
| import org.openmrs.module.reporting.data.DataDefinition; | ||
| import org.openmrs.module.reporting.data.converter.BirthdateConverter; | ||
| import org.openmrs.module.reporting.data.converter.DataConverter; | ||
| import org.openmrs.module.reporting.data.converter.DateConverter; | ||
| import org.openmrs.module.reporting.data.converter.ObjectFormatter; | ||
| import org.openmrs.module.reporting.data.encounter.definition.EncounterDatetimeDataDefinition; | ||
| import org.openmrs.module.reporting.data.patient.definition.ConvertedPatientDataDefinition; | ||
| import org.openmrs.module.reporting.data.patient.definition.PatientIdentifierDataDefinition; | ||
| import org.openmrs.module.reporting.data.person.definition.*; | ||
| import org.openmrs.module.reporting.dataset.definition.DataSetDefinition; | ||
| import org.openmrs.module.reporting.dataset.definition.PatientDataSetDefinition; | ||
| import org.openmrs.module.reporting.evaluation.parameter.Mapped; | ||
| import org.openmrs.module.reporting.evaluation.parameter.Parameter; | ||
| import org.openmrs.module.reporting.report.definition.ReportDefinition; | ||
| import org.springframework.stereotype.Component; | ||
|
|
||
| import java.util.Arrays; | ||
| import java.util.Date; | ||
| import java.util.List; | ||
|
|
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| @Component | ||
| @Builds({ "kenyaemr.ehrReports.report.240" }) | ||
| public class SetupMOH240LabReportBuilder extends AbstractHybridReportBuilder { | ||
|
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| public static final String ENC_DATE_FORMAT = "yyyy/MM/dd"; | ||
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| @Override | ||
| protected Mapped<CohortDefinition> buildCohort(HybridReportDescriptor hybridReportDescriptor, | ||
| PatientDataSetDefinition patientDataSetDefinition) { | ||
| return null; | ||
| } | ||
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| @Override | ||
| protected List<Mapped<DataSetDefinition>> buildDataSets(ReportDescriptor descriptor, ReportDefinition report) { | ||
| PatientDataSetDefinition dsd = LabRegister(); | ||
| dsd.setName("lrr"); | ||
| dsd.addParameter(new Parameter("startDate", "Start Date", Date.class)); | ||
| dsd.addParameter(new Parameter("endDate", "End Date", Date.class)); | ||
| report.setBaseCohortDefinition(ReportUtils.map(getLabOrderEncounter(), "startDate=${startDate},endDate=${endDate}")); | ||
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| return Arrays.asList(ReportUtils.map((DataSetDefinition) dsd, "startDate=${startDate},endDate=${endDate}")); | ||
| } | ||
|
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| @Override | ||
| protected List<Parameter> getParameters(ReportDescriptor reportDescriptor) { | ||
| return Arrays.asList(new Parameter("startDate", "Start Date", Date.class), new Parameter("endDate", "End Date", | ||
| Date.class), new Parameter("dateBasedReporting", "", String.class)); | ||
| } | ||
|
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| private PatientDataSetDefinition LabRegister() { | ||
| PatientDataSetDefinition dsd = new PatientDataSetDefinition(); | ||
| dsd.setName("lrr"); | ||
| dsd.addParameter(new Parameter("startDate", "Start Date", Date.class)); | ||
| dsd.addParameter(new Parameter("endDate", "End Date", Date.class)); | ||
| dsd.addRowFilter(getLabOrderEncounter(), "startDate=${startDate},endDate=${endDate+23h}"); | ||
| DataConverter nameFormatter = new ObjectFormatter("{familyName}, {givenName}, {middleName}"); | ||
| DataDefinition nameDef = new ConvertedPersonDataDefinition("name", new PreferredNameDataDefinition(), nameFormatter); | ||
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| PersonAttributeType personAttributeType = Context.getPersonService().getPersonAttributeTypeByUuid(CommonMetadata._PersonAttributeType.TELEPHONE_CONTACT); | ||
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| PatientIdentifierType openmrsID = Context.getPatientService().getPatientIdentifierTypeByUuid("dfacd928-0370-4315-99d7-6ec1c9f7ae76"); | ||
| DataConverter identifierFormatter = new ObjectFormatter("{identifier}"); | ||
| DataDefinition identifierDef = new ConvertedPatientDataDefinition("identifier", new PatientIdentifierDataDefinition( | ||
| openmrsID.getName(), openmrsID), identifierFormatter); | ||
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| dsd.addColumn("id", new PersonIdDataDefinition(), ""); | ||
| dsd.addColumn("identifier", identifierDef, ""); | ||
| //dsd.addColumn("Date", new EncounterDatetimeDataDefinition(),"", new DateConverter(ENC_DATE_FORMAT)); | ||
| dsd.addColumn("Name", nameDef, ""); | ||
| dsd.addColumn("Sex", new GenderDataDefinition(), "", null); | ||
| dsd.addColumn("DOB", new BirthdateDataDefinition(), "", new BirthdateConverter("yyyy-MM-dd")); | ||
| dsd.addColumn("age", new AgeDataDefinition(), ""); | ||
| dsd.addColumn("village", new CalculationDataDefinition("Village/Estate/Landmark", new PersonAddressCalculation()), "",new RDQACalculationResultConverter()); | ||
| dsd.addColumn("telephone", new PersonAttributeDataDefinition(personAttributeType), "", | ||
| null); | ||
| return dsd; | ||
|
|
||
| } | ||
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| private CohortDefinition getLabOrderEncounter() { | ||
| SqlCohortDefinition sqlEncounterQuery = new SqlCohortDefinition(); | ||
| sqlEncounterQuery.setName("Get unique lab encounter types"); | ||
| sqlEncounterQuery.addParameter(new Parameter("startDate", "Start Date", Date.class)); | ||
| sqlEncounterQuery.addParameter(new Parameter("endDate", "End Date", Date.class)); | ||
| sqlEncounterQuery | ||
| .setQuery("SELECT d.patient_id FROM kenyaemr_etl.etl_patient_demographics d\n" + | ||
| " INNER JOIN kenyaemr_etl.etl_laboratory_extract x ON x.patient_id = d.patient_id\n" + | ||
| " AND date(x.visit_date) BETWEEN :startDate AND :endDate;"); | ||
| return sqlEncounterQuery; | ||
| } | ||
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|
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| } |
72 changes: 72 additions & 0 deletions
72
...ava/org/openmrs/module/kenyaemr/reporting/builder/common/SetupMOH706LabReportBuilder.java
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,72 @@ | ||
| /** | ||
| * This Source Code Form is subject to the terms of the Mozilla Public License, | ||
| * v. 2.0. If a copy of the MPL was not distributed with this file, You can | ||
| * obtain one at http://mozilla.org/MPL/2.0/. OpenMRS is also distributed under | ||
| * the terms of the Healthcare Disclaimer located at http://openmrs.org/license. | ||
| * | ||
| * Copyright (C) OpenMRS Inc. OpenMRS is a registered trademark and the OpenMRS | ||
| * graphic logo is a trademark of OpenMRS Inc. | ||
| */ | ||
| package org.openmrs.module.kenyaemr.reporting.builder.common; | ||
|
|
||
| import org.openmrs.module.kenyacore.report.ReportDescriptor; | ||
| import org.openmrs.module.kenyacore.report.ReportUtils; | ||
| import org.openmrs.module.kenyacore.report.builder.AbstractReportBuilder; | ||
| import org.openmrs.module.kenyacore.report.builder.Builds; | ||
| import org.openmrs.module.kenyaemr.reporting.library.MOH706.Moh706LabCohortLibrary; | ||
| import org.openmrs.module.kenyaemr.reporting.library.MOH706.Moh706IndicatorLibrary; | ||
| import org.openmrs.module.reporting.dataset.definition.CohortIndicatorDataSetDefinition; | ||
| import org.openmrs.module.reporting.dataset.definition.DataSetDefinition; | ||
| import org.openmrs.module.reporting.evaluation.parameter.Mapped; | ||
| import org.openmrs.module.reporting.evaluation.parameter.Parameter; | ||
| import org.openmrs.module.reporting.report.definition.ReportDefinition; | ||
| import org.springframework.beans.factory.annotation.Autowired; | ||
| import org.springframework.stereotype.Component; | ||
|
|
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| import java.util.Arrays; | ||
| import java.util.Date; | ||
| import java.util.List; | ||
|
|
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| import static org.openmrs.module.kenyacore.report.ReportUtils.map; | ||
|
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| @Component | ||
| @Builds({ "kenyaemr.ehrReports.706.report" }) | ||
| public class SetupMOH706LabReportBuilder extends AbstractReportBuilder { | ||
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| private final Moh706IndicatorLibrary moh706IndicatorLibrary; | ||
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| @Autowired | ||
| public SetupMOH706LabReportBuilder(Moh706LabCohortLibrary moh706CohortLibrary, Moh706IndicatorLibrary moh706IndicatorLibrary) { | ||
| this.moh706IndicatorLibrary = moh706IndicatorLibrary; | ||
| } | ||
|
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| @Override | ||
| protected List<Parameter> getParameters(ReportDescriptor reportDescriptor) { | ||
| return Arrays.asList(new Parameter("startDate", "Start Date", Date.class), new Parameter("endDate", "End Date", | ||
| Date.class), new Parameter("dateBasedReporting", "", String.class)); | ||
| } | ||
|
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| @Override | ||
| protected List<Mapped<DataSetDefinition>> buildDataSets(ReportDescriptor reportDescriptor, | ||
| ReportDefinition reportDefinition) { | ||
| return Arrays.asList(map(getMoh706LabDatasetDefinition(), | ||
| "startDate=${startDate},endDate=${endDate+23h}")); | ||
| } | ||
|
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| private DataSetDefinition getMoh706LabDatasetDefinition() { | ||
| CohortIndicatorDataSetDefinition cohortDsd = new CohortIndicatorDataSetDefinition(); | ||
| cohortDsd.addParameter(new Parameter("startDate", "Start Date", Date.class)); | ||
| cohortDsd.addParameter(new Parameter("endDate", "End Date", Date.class)); | ||
| cohortDsd.setName("MOH706"); | ||
| cohortDsd.setDescription("MOH 706 for the lab"); | ||
|
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| //URINE ANALYSIS | ||
| cohortDsd.addColumn("UAGL", "1.2 Glucose", | ||
| ReportUtils.map(moh706IndicatorLibrary.getAllUrineAnalysisGlucoseTestsPositives(), "startDate=${startDate},endDate=${endDate}"), ""); | ||
|
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| return cohortDsd; | ||
| } | ||
|
|
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| } | ||
|
|
32 changes: 32 additions & 0 deletions
32
...ain/java/org/openmrs/module/kenyaemr/reporting/library/MOH706/Moh706IndicatorLibrary.java
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,32 @@ | ||
| /** | ||
| * This Source Code Form is subject to the terms of the Mozilla Public License, | ||
| * v. 2.0. If a copy of the MPL was not distributed with this file, You can | ||
| * obtain one at http://mozilla.org/MPL/2.0/. OpenMRS is also distributed under | ||
| * the terms of the Healthcare Disclaimer located at http://openmrs.org/license. | ||
| * | ||
| * Copyright (C) OpenMRS Inc. OpenMRS is a registered trademark and the OpenMRS | ||
| * graphic logo is a trademark of OpenMRS Inc. | ||
| */ | ||
| package org.openmrs.module.kenyaemr.reporting.library.MOH706; | ||
|
|
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| import org.openmrs.module.reporting.indicator.CohortIndicator; | ||
| import org.springframework.stereotype.Component; | ||
|
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| import static org.openmrs.module.kenyacore.report.ReportUtils.map; | ||
| import static org.openmrs.module.kenyaemr.reporting.MohReportUtils.ReportingUtils.cohortIndicator; | ||
|
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| @Component | ||
| public class Moh706IndicatorLibrary { | ||
| private final Moh706LabCohortLibrary moh706LabCohortLibrary; | ||
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| public Moh706IndicatorLibrary(Moh706LabCohortLibrary moh706LabCohortLibrary) { | ||
| this.moh706LabCohortLibrary = moh706LabCohortLibrary; | ||
| } | ||
|
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| public CohortIndicator getAllUrineAnalysisGlucoseTestsPositives() { | ||
| return cohortIndicator( | ||
| "All patients who have urinalysis glucose", | ||
| map(moh706LabCohortLibrary.getAllUrineAnalysisGlucoseTestsPositives(), | ||
| "startDate=${startDate},endDate=${endDate}")); | ||
| } | ||
| } |
38 changes: 38 additions & 0 deletions
38
...ain/java/org/openmrs/module/kenyaemr/reporting/library/MOH706/Moh706LabCohortLibrary.java
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,38 @@ | ||
| /** | ||
| * This Source Code Form is subject to the terms of the Mozilla Public License, | ||
| * v. 2.0. If a copy of the MPL was not distributed with this file, You can | ||
| * obtain one at http://mozilla.org/MPL/2.0/. OpenMRS is also distributed under | ||
| * the terms of the Healthcare Disclaimer located at http://openmrs.org/license. | ||
| * | ||
| * Copyright (C) OpenMRS Inc. OpenMRS is a registered trademark and the OpenMRS | ||
| * graphic logo is a trademark of OpenMRS Inc. | ||
| */ | ||
| package org.openmrs.module.kenyaemr.reporting.library.MOH706; | ||
|
|
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| import org.openmrs.module.reporting.cohort.definition.CohortDefinition; | ||
| import org.openmrs.module.reporting.cohort.definition.SqlCohortDefinition; | ||
| import org.openmrs.module.reporting.evaluation.parameter.Parameter; | ||
| import org.springframework.stereotype.Component; | ||
|
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| import java.util.Date; | ||
|
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| @Component | ||
| public class Moh706LabCohortLibrary { | ||
|
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| public CohortDefinition getAllUrineAnalysisGlucoseTestsPositives() { | ||
| SqlCohortDefinition sql = new SqlCohortDefinition(); | ||
| sql.setName("Get urine analysis patients - glucose"); | ||
| sql.addParameter(new Parameter("startDate", "Start Date", Date.class)); | ||
| sql.addParameter(new Parameter("endDate", "End Date", Date.class)); | ||
| sql.setQuery("SELECT d.patient_id FROM kenyaemr_etl.etl_patient_demographics d\n" + | ||
| " INNER JOIN kenyaemr_etl.etl_laboratory_extract x ON x.patient_id = d.patient_id\n" + | ||
| " WHERE x.lab_test = 1305 AND x.test_result = 1302 AND date(x.visit_date) BETWEEN :startDate AND :endDate\n" + | ||
| " UNION\n" + | ||
| " SELECT d.patient_id FROM kenyaemr_etl.etl_patient_demographics d\n" + | ||
| " INNER JOIN kenyaemr_etl.etl_laboratory_extract x ON x.patient_id = d.patient_id\n" + | ||
| " WHERE x.lab_test = 856 AND x.test_result IS NOT NULL AND date(x.visit_date) BETWEEN :startDate AND :endDate;" | ||
|
|
||
| ); | ||
| return sql; | ||
| } | ||
| } |
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