Merge pull request #2019 from gabriel090/KHP3-6713

Develop a case report for the flagged syndromes

api/src/main/java/org/openmrs/module/kenyaemr/reporting/cohort/definition/dmi/FebrileIllnessCohortDefinition.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.cohort.definition.dmi;
+
+import org.openmrs.module.reporting.cohort.definition.BaseCohortDefinition;
+import org.openmrs.module.reporting.common.Localized;
+import org.openmrs.module.reporting.definition.configuration.ConfigurationPropertyCachingStrategy;
+import org.openmrs.module.reporting.evaluation.caching.Caching;
+
+/**
+ * Febrile illness cohort definition
+ */
+@Caching(strategy = ConfigurationPropertyCachingStrategy.class)
+@Localized("reporting.FebrileIllnessCohortDefinition")
+public class FebrileIllnessCohortDefinition extends BaseCohortDefinition {
+
+}

api/src/main/java/org/openmrs/module/kenyaemr/reporting/cohort/definition/dmi/FebrileRashCohortDefinition.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.cohort.definition.dmi;
+
+import org.openmrs.module.reporting.cohort.definition.BaseCohortDefinition;
+import org.openmrs.module.reporting.common.Localized;
+import org.openmrs.module.reporting.definition.configuration.ConfigurationPropertyCachingStrategy;
+import org.openmrs.module.reporting.evaluation.caching.Caching;
+
+/**
+ * Febrile Rash cohort definition
+ */
+@Caching(strategy = ConfigurationPropertyCachingStrategy.class)
+@Localized("reporting.FebrileRashCohortDefinition")
+public class FebrileRashCohortDefinition extends BaseCohortDefinition {
+
+}

api/src/main/java/org/openmrs/module/kenyaemr/reporting/cohort/definition/dmi/JaundiceCohortDefinition.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.cohort.definition.dmi;
+
+import org.openmrs.module.reporting.cohort.definition.BaseCohortDefinition;
+import org.openmrs.module.reporting.common.Localized;
+import org.openmrs.module.reporting.definition.configuration.ConfigurationPropertyCachingStrategy;
+import org.openmrs.module.reporting.evaluation.caching.Caching;
+
+/**
+ * Jaundice cohort definition
+ */
+@Caching(strategy = ConfigurationPropertyCachingStrategy.class)
+@Localized("reporting.JaundiceCohortDefinition")
+public class JaundiceCohortDefinition extends BaseCohortDefinition {
+
+}

api/src/main/java/org/openmrs/module/kenyaemr/reporting/cohort/definition/dmi/MeningitisCohortDefinition.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.cohort.definition.dmi;
+
+import org.openmrs.module.reporting.cohort.definition.BaseCohortDefinition;
+import org.openmrs.module.reporting.common.Localized;
+import org.openmrs.module.reporting.definition.configuration.ConfigurationPropertyCachingStrategy;
+import org.openmrs.module.reporting.evaluation.caching.Caching;
+
+/**
+ * Meningitis cohort definition
+ */
+@Caching(strategy = ConfigurationPropertyCachingStrategy.class)
+@Localized("reporting.MeningitisCohortDefinition")
+public class MeningitisCohortDefinition extends BaseCohortDefinition {
+
+}

api/src/main/java/org/openmrs/module/kenyaemr/reporting/cohort/definition/dmi/MpoxCohortDefinition.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.cohort.definition.dmi;
+
+import org.openmrs.module.reporting.cohort.definition.BaseCohortDefinition;
+import org.openmrs.module.reporting.common.Localized;
+import org.openmrs.module.reporting.definition.configuration.ConfigurationPropertyCachingStrategy;
+import org.openmrs.module.reporting.evaluation.caching.Caching;
+
+/**
+ * mpox cohort definition
+ */
+@Caching(strategy = ConfigurationPropertyCachingStrategy.class)
+@Localized("reporting.MpoxCohortDefinition")
+public class MpoxCohortDefinition extends BaseCohortDefinition {
+
+}

api/src/main/java/org/openmrs/module/kenyaemr/reporting/cohort/definition/dmi/NeurologicalSyndromeCohortDefinition.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.cohort.definition.dmi;
+
+import org.openmrs.module.reporting.cohort.definition.BaseCohortDefinition;
+import org.openmrs.module.reporting.common.Localized;
+import org.openmrs.module.reporting.definition.configuration.ConfigurationPropertyCachingStrategy;
+import org.openmrs.module.reporting.evaluation.caching.Caching;
+
+/**
+ * Neurological Syndrome cohort definition
+ */
+@Caching(strategy = ConfigurationPropertyCachingStrategy.class)
+@Localized("reporting.NeurologicalSyndromeCohortDefinition")
+public class NeurologicalSyndromeCohortDefinition extends BaseCohortDefinition {
+
+}

api/src/main/java/org/openmrs/module/kenyaemr/reporting/cohort/definition/dmi/WateryDiarrhoeaCohortDefinition.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.cohort.definition.dmi;
+
+import org.openmrs.module.reporting.cohort.definition.BaseCohortDefinition;
+import org.openmrs.module.reporting.common.Localized;
+import org.openmrs.module.reporting.definition.configuration.ConfigurationPropertyCachingStrategy;
+import org.openmrs.module.reporting.evaluation.caching.Caching;
+
+/**
+ * Watery Diarrhoea cohort definition
+ */
+@Caching(strategy = ConfigurationPropertyCachingStrategy.class)
+@Localized("reporting.WateryDiarrhoeaCohortDefinition")
+public class WateryDiarrhoeaCohortDefinition extends BaseCohortDefinition {
+
+}

api/src/main/java/org/openmrs/module/kenyaemr/reporting/cohort/definition/evaluator/dmi/FebrileIllnessCohortDefinitionEvaluator.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.cohort.definition.evaluator.dmi;
+
+import org.apache.commons.logging.Log;
+import org.apache.commons.logging.LogFactory;
+import org.openmrs.Cohort;
+import org.openmrs.annotation.Handler;
+import org.openmrs.module.kenyaemr.reporting.cohort.definition.dmi.FebrileIllnessCohortDefinition;
+import org.openmrs.module.reporting.cohort.EvaluatedCohort;
+import org.openmrs.module.reporting.cohort.definition.CohortDefinition;
+import org.openmrs.module.reporting.cohort.definition.evaluator.CohortDefinitionEvaluator;
+import org.openmrs.module.reporting.evaluation.EvaluationContext;
+import org.openmrs.module.reporting.evaluation.EvaluationException;
+import org.openmrs.module.reporting.evaluation.querybuilder.SqlQueryBuilder;
+import org.openmrs.module.reporting.evaluation.service.EvaluationService;
+import org.springframework.beans.factory.annotation.Autowired;
+
+import java.util.Date;
+import java.util.HashSet;
+import java.util.List;
+
+/**
+ * Evaluator for Febrile Illness Cohort
+ */
+@Handler(supports = { FebrileIllnessCohortDefinition.class })
+public class FebrileIllnessCohortDefinitionEvaluator implements CohortDefinitionEvaluator {
+
+	private final Log log = LogFactory.getLog(this.getClass());
+
+	@Autowired
+	EvaluationService evaluationService;
+
+	@Override
+	public EvaluatedCohort evaluate(CohortDefinition cohortDefinition, EvaluationContext context) throws EvaluationException {
+
+		FebrileIllnessCohortDefinition definition = (FebrileIllnessCohortDefinition) cohortDefinition;
+
+		if (definition == null)
+			return null;
+		Cohort newCohort = new Cohort();
+		String sqlQuery = "select a.patient_id\n" +
+				"        from (select patient_id, c.visit_date,group_concat(c.complaint) as complaint,\n" +
+				"        CASE\n" +
+				"                         WHEN group_concat(concat_ws('|',c.complaint,c.complaint_duration))  LIKE '%140238%' THEN\n" +
+				"                             SUBSTRING_INDEX(SUBSTRING_INDEX(group_concat(concat_ws('|',c.complaint,c.complaint_duration)) , '|', -1), ',', 1)\n" +
+				"                         END AS fever_duration_from_days\n" +
+				"              from kenyaemr_etl.etl_allergy_chronic_illness c\n" +
+				"              where c.complaint = 140238\n" +
+				"              AND c.complaint_duration < 14\n" +
+				"                and date(c.visit_date) between date(:startDate) and date(:endDate)\n" +
+				"              group by patient_id) a\n" +
+				"                 join kenyaemr_etl.etl_patient_demographics d on a.patient_id = d.patient_id\n" +
+				"                 join kenyaemr_etl.etl_patient_triage t\n" +
+				"                      on a.patient_id = t.patient_id and date(t.visit_date) between date(:startDate) and date(:endDate) and\n" +
+				"                         t.temperature > 38.5 and date(a.visit_date) between date(:startDate) and date(:endDate)\n" +
+				"        where FIND_IN_SET(140238, a.complaint) > 0;";
+
+		SqlQueryBuilder builder = new SqlQueryBuilder();
+		builder.append(sqlQuery);
+		Date startDate = (Date) context.getParameterValue("startDate");
+		Date endDate = (Date) context.getParameterValue("endDate");
+		builder.addParameter("startDate", startDate);
+		builder.addParameter("endDate", endDate);
+
+		List<Integer> ptIds = evaluationService.evaluateToList(builder, Integer.class, context);
+		newCohort.setMemberIds(new HashSet<Integer>(ptIds));
+		return new EvaluatedCohort(newCohort, definition, context);
+	}
+}

api/src/main/java/org/openmrs/module/kenyaemr/reporting/cohort/definition/evaluator/dmi/FebrileRashCohortDefinitionEvaluator.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.cohort.definition.evaluator.dmi;
+
+import org.apache.commons.logging.Log;
+import org.apache.commons.logging.LogFactory;
+import org.openmrs.Cohort;
+import org.openmrs.annotation.Handler;
+import org.openmrs.module.kenyaemr.reporting.cohort.definition.dmi.FebrileRashCohortDefinition;
+import org.openmrs.module.reporting.cohort.EvaluatedCohort;
+import org.openmrs.module.reporting.cohort.definition.CohortDefinition;
+import org.openmrs.module.reporting.cohort.definition.evaluator.CohortDefinitionEvaluator;
+import org.openmrs.module.reporting.evaluation.EvaluationContext;
+import org.openmrs.module.reporting.evaluation.EvaluationException;
+import org.openmrs.module.reporting.evaluation.querybuilder.SqlQueryBuilder;
+import org.openmrs.module.reporting.evaluation.service.EvaluationService;
+import org.springframework.beans.factory.annotation.Autowired;
+
+import java.util.Date;
+import java.util.HashSet;
+import java.util.List;
+
+/**
+ * Evaluator for FebrileRash Cohort
+ */
+@Handler(supports = { FebrileRashCohortDefinition.class })
+public class FebrileRashCohortDefinitionEvaluator implements CohortDefinitionEvaluator {
+
+	private final Log log = LogFactory.getLog(this.getClass());
+
+	@Autowired
+	EvaluationService evaluationService;
+
+	@Override
+	public EvaluatedCohort evaluate(CohortDefinition cohortDefinition, EvaluationContext context) throws EvaluationException {
+
+		FebrileRashCohortDefinition definition = (FebrileRashCohortDefinition) cohortDefinition;
+
+		if (definition == null)
+			return null;
+
+		Cohort newCohort = new Cohort();
+		String sqlQuery = "SELECT a.patient_id\n" +
+				"FROM (\n" +
+				"    SELECT\n" +
+				"        patient_id,\n" +
+				"        c.visit_date,\n" +
+				"        GROUP_CONCAT(c.complaint) AS complaint,\n" +
+				"        DATE_SUB(c.visit_date, INTERVAL c.complaint_duration DAY) AS complaint_date,\n" +
+				"        c.complaint_duration\n" +
+				"    FROM\n" +
+				"        kenyaemr_etl.etl_allergy_chronic_illness c\n" +
+				"    WHERE\n" +
+				"        c.complaint IN (140238, 512)\n" +
+				"        AND c.complaint_duration < 14\n" +
+				"        AND DATE(c.visit_date) BETWEEN DATE(:startDate) AND DATE(:endDate)\n" +
+				"    GROUP BY patient_id) a\n" +
+				"WHERE\n" +
+				"    FIND_IN_SET(140238, a.complaint) > 0\n" +
+				"    AND FIND_IN_SET(512, a.complaint) > 0;";
+
+		SqlQueryBuilder builder = new SqlQueryBuilder();
+		builder.append(sqlQuery);
+		Date startDate = (Date) context.getParameterValue("startDate");
+		Date endDate = (Date) context.getParameterValue("endDate");
+		builder.addParameter("startDate", startDate);
+		builder.addParameter("endDate", endDate);
+
+		List<Integer> ptIds = evaluationService.evaluateToList(builder, Integer.class, context);
+		newCohort.setMemberIds(new HashSet<Integer>(ptIds));
+		return new EvaluatedCohort(newCohort, definition, context);
+	}
+}