Merge pull request #1869 from patryllus/moh240_706

Initial stubs for MOH 240 and MOH 706 pulling from kenyaemr_etl reporting tables

api/src/main/java/org/openmrs/module/kenyaemr/reporting/MohReportUtils/ReportAddonUtils.java

@@ -63,16 +63,16 @@ public static List<ColumnParameters> getGeneralOutPatientFilters() {
  "state=NEW|age=<5|gender=F", "03");
  ColumnParameters under5FemaleRevisit = new ColumnParameters("over5FemaleRevisit", "below 5 and revisit",
  "state=RVT|age=<5|gender=F", "04");
- ColumnParameters over5MaleNew = new ColumnParameters("over5MaleNew", "above 5 and new", "state=NEW|age=>5|gender=M",
+ ColumnParameters over5MaleNew = new ColumnParameters("over5MaleNew", "above 5 and new", "state=NEW|age=5+|gender=M",
  "05");
  ColumnParameters over5MaleRevisit = new ColumnParameters("over5MaleRevisit", "above 5 and revisit",
- "state=RVT|age=>5|gender=M", "06");
+ "state=RVT|age=5+|gender=M", "06");
  ColumnParameters over5FemaleNew = new ColumnParameters("over5MaleNew", "above 5 and new",
- "state=NEW|age=>5|gender=F", "07");
+ "state=NEW|age=5+|gender=F", "07");
  ColumnParameters over5FemaleRevisit = new ColumnParameters("over5MaleRevisit", "above 5 and revisit",
- "state=RVT|age=>5|gender=F", "08");
- ColumnParameters over60New = new ColumnParameters("over60New", "above 60 and new", "state=NEW|age=>60", "09");
- ColumnParameters over60Revisit = new ColumnParameters("over60Revisit", "above 60 and revisit", "state=RVT|age=>60",
+ "state=RVT|age=5+|gender=F", "08");
+ ColumnParameters over60New = new ColumnParameters("over60New", "above 60 and new", "state=NEW|age=60+", "09");
+ ColumnParameters over60Revisit = new ColumnParameters("over60Revisit", "above 60 and revisit", "state=RVT|age=60+",
  "10");
 
  return Arrays.asList(under5MaleNew, under5MaleRevisit, under5FemaleNew, under5FemaleRevisit, over5MaleNew,

api/src/main/java/org/openmrs/module/kenyaemr/reporting/builder/common/SetupMOH240LabReportBuilder.java

@@ -0,0 +1,117 @@
+/**
+ * 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 https://mozilla.org/MPL/2.0/. OpenMRS is also distributed under
+ * the terms of the Healthcare Disclaimer located at https://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;
+
+@Component
+@Builds({ "kenyaemr.ehrReports.report.240" })
+public class SetupMOH240LabReportBuilder extends AbstractHybridReportBuilder {
+
+ public static final String ENC_DATE_FORMAT = "yyyy/MM/dd";
+
+ @Override
+ protected Mapped<CohortDefinition> buildCohort(HybridReportDescriptor hybridReportDescriptor,
+ PatientDataSetDefinition patientDataSetDefinition) {
+ return null;
+ }
+
+ @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}"));
+
+ return Arrays.asList(ReportUtils.map((DataSetDefinition) dsd, "startDate=${startDate},endDate=${endDate}"));
+ }
+
+ @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));
+ }
+
+ 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);
+
+ PersonAttributeType personAttributeType = Context.getPersonService().getPersonAttributeTypeByUuid(CommonMetadata._PersonAttributeType.TELEPHONE_CONTACT);
+
+ 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);
+
+ 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;
+
+ }
+
+ 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;
+ }
+
+}

api/src/main/java/org/openmrs/module/kenyaemr/reporting/builder/common/SetupMOH706LabReportBuilder.java

@@ -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 https://mozilla.org/MPL/2.0/. OpenMRS is also distributed under
+ * the terms of the Healthcare Disclaimer located at https://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;
+
+import java.util.Arrays;
+import java.util.Date;
+import java.util.List;
+
+import static org.openmrs.module.kenyacore.report.ReportUtils.map;
+
+@Component
+@Builds({ "kenyaemr.ehrReports.706.report" })
+public class SetupMOH706LabReportBuilder extends AbstractReportBuilder {
+
+
+ private final Moh706IndicatorLibrary moh706IndicatorLibrary;
+
+ @Autowired
+ public SetupMOH706LabReportBuilder(Moh706LabCohortLibrary moh706CohortLibrary, Moh706IndicatorLibrary moh706IndicatorLibrary) {
+ this.moh706IndicatorLibrary = moh706IndicatorLibrary;
+ }
+
+ @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));
+ }
+
+ @Override
+ protected List<Mapped<DataSetDefinition>> buildDataSets(ReportDescriptor reportDescriptor,
+ ReportDefinition reportDefinition) {
+ return Arrays.asList(map(getMoh706LabDatasetDefinition(),
+ "startDate=${startDate},endDate=${endDate+23h}"));
+ }
+
+ 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");
+
+ //URINE ANALYSIS
+ cohortDsd.addColumn("UAGL", "1.2 Glucose",
+ ReportUtils.map(moh706IndicatorLibrary.getAllUrineAnalysisGlucoseTestsPositives(), "startDate=${startDate},endDate=${endDate}"), "");
+
+ return cohortDsd;
+ }
+
+}
+

api/src/main/java/org/openmrs/module/kenyaemr/reporting/library/MOH706/Moh706IndicatorLibrary.java

@@ -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 https://mozilla.org/MPL/2.0/. OpenMRS is also distributed under
+ * the terms of the Healthcare Disclaimer located at https://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;
+
+import org.openmrs.module.reporting.indicator.CohortIndicator;
+import org.springframework.stereotype.Component;
+
+import static org.openmrs.module.kenyacore.report.ReportUtils.map;
+import static org.openmrs.module.kenyaemr.reporting.MohReportUtils.ReportingUtils.cohortIndicator;
+
+@Component
+public class Moh706IndicatorLibrary {
+ private final Moh706LabCohortLibrary moh706LabCohortLibrary;
+
+ public Moh706IndicatorLibrary(Moh706LabCohortLibrary moh706LabCohortLibrary) {
+ this.moh706LabCohortLibrary = moh706LabCohortLibrary;
+ }
+
+ public CohortIndicator getAllUrineAnalysisGlucoseTestsPositives() {
+ return cohortIndicator(
+ "All patients who have urinalysis glucose",
+ map(moh706LabCohortLibrary.getAllUrineAnalysisGlucoseTestsPositives(),
+ "startDate=${startDate},endDate=${endDate}"));
+ }
+}

api/src/main/java/org/openmrs/module/kenyaemr/reporting/library/MOH706/Moh706LabCohortLibrary.java

@@ -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 https://mozilla.org/MPL/2.0/. OpenMRS is also distributed under
+ * the terms of the Healthcare Disclaimer located at https://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;
+
+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;
+
+import java.util.Date;
+
+@Component
+public class Moh706LabCohortLibrary {
+
+ 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;
+ }
+}

api/src/main/resources/content/kenyaemr.common.xml

@@ -98,6 +98,8 @@
  <ref bean="kenyaemr.ehrReports.report.moh204A" />
  <ref bean="kenyaemr.ehrReports.report.moh204B" />
  <ref bean="kenyaemr.ehrReports.report.facility.monthly.collection" />
+ <ref bean="kenyaemr.ehrReports.706.report" />
+ <ref bean="kenyaemr.ehrReports.report.240" />
  </set>
  </property>
  </bean>
@@ -981,5 +983,27 @@
  </set></property>
  <property name="template" value="kenyaemr:MOH_717.xls" />
  </bean>
+ <bean id="kenyaemr.ehrReports.706.report" class="org.openmrs.module.kenyacore.report.IndicatorReportDescriptor">
+ <property name="targetUuid" value="cf9f6e96-bfd4-41c0-8dfe-9807707bbf9d" />
+ <property name="name" value="MOH 706" />
+ <property name="description" value="MOH 706 Report" />
+ <property name="apps">
+ <set>
+ <ref bean="kenyaemr.app.reports" />
+ </set></property>
+ <property name="template" value="kenyaemr:MOH706.xls" />
+ </bean>
+ <bean id="kenyaemr.ehrReports.report.240" class="org.openmrs.module.kenyacore.report.HybridReportDescriptor">
+ <property name="targetUuid" value="30ca99ad-97a8-47f8-92fd-da2997a64bfb" />
+ <property name="name" value="Laboratory Register - MOH 240" />
+ <property name="description" value="Laboratory Register - MOH 240 Report" />
+ <property name="apps">
+ <set>
+ <ref bean="kenyaemr.app.reports" />
+ </set>
+ </property>
+ <property name="template" value="kenyaemr:MOH240.xls" />
+ <property name="repeatingSection" value="sheet:3,row:3,dataset:lrr" />
+ </bean>
 
 </beans>