Merge pull request #2056 from njorocs/dmi-case-report

Dmi case report

api/src/main/java/org/openmrs/module/kenyaemr/reporting/cohort/definition/dmi/casereport/CaseComplaintsCohortDefinition.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.casereport;
+
+import org.openmrs.Visit;
+import org.openmrs.module.reporting.common.Localized;
+import org.openmrs.module.reporting.definition.configuration.ConfigurationProperty;
+import org.openmrs.module.reporting.definition.configuration.ConfigurationPropertyCachingStrategy;
+import org.openmrs.module.reporting.evaluation.caching.Caching;
+import org.openmrs.module.reporting.query.BaseQuery;
+import org.openmrs.module.reporting.query.visit.definition.VisitQuery;
+
+import java.util.Date;
+
+/**
+ * Surveillance cases cohort definition
+ */
+
+@Caching(strategy = ConfigurationPropertyCachingStrategy.class)
+@Localized("reporting.CaseComplaintsCohortDefinition")
+public class CaseComplaintsCohortDefinition extends BaseQuery<Visit> implements VisitQuery {
+    @ConfigurationProperty
+    private Date asOfDate;
+
+    public CaseComplaintsCohortDefinition() {
+    }
+
+    public Date getAsOfDate() {
+        return asOfDate;
+    }
+
+    public void setAsOfDate(Date asOfDate) {
+        this.asOfDate = asOfDate;
+    }
+
+}

api/src/main/java/org/openmrs/module/kenyaemr/reporting/cohort/definition/dmi/casereport/CaseDiagnosisCohortDefinition.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.casereport;
+
+import org.openmrs.Visit;
+import org.openmrs.module.reporting.common.Localized;
+import org.openmrs.module.reporting.definition.configuration.ConfigurationProperty;
+import org.openmrs.module.reporting.definition.configuration.ConfigurationPropertyCachingStrategy;
+import org.openmrs.module.reporting.evaluation.caching.Caching;
+import org.openmrs.module.reporting.query.BaseQuery;
+import org.openmrs.module.reporting.query.visit.definition.VisitQuery;
+
+import java.util.Date;
+
+/**
+ * Surveillance cases cohort definition
+ */
+
+@Caching(strategy = ConfigurationPropertyCachingStrategy.class)
+@Localized("reporting.CaseDiagnosisCohortDefinition")
+public class CaseDiagnosisCohortDefinition extends BaseQuery<Visit> implements VisitQuery {
+    @ConfigurationProperty
+    private Date asOfDate;
+
+    public CaseDiagnosisCohortDefinition() {
+    }
+
+    public Date getAsOfDate() {
+        return asOfDate;
+    }
+
+    public void setAsOfDate(Date asOfDate) {
+        this.asOfDate = asOfDate;
+    }
+
+}

api/src/main/java/org/openmrs/module/kenyaemr/reporting/cohort/definition/dmi/casereport/CaseLabsCohortDefinition.java

@@ -0,0 +1,43 @@
+/**
+ * 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.casereport;
+
+import org.openmrs.Visit;
+import org.openmrs.module.reporting.common.Localized;
+import org.openmrs.module.reporting.definition.configuration.ConfigurationProperty;
+import org.openmrs.module.reporting.definition.configuration.ConfigurationPropertyCachingStrategy;
+import org.openmrs.module.reporting.evaluation.caching.Caching;
+import org.openmrs.module.reporting.query.BaseQuery;
+import org.openmrs.module.reporting.query.visit.definition.VisitQuery;
+
+import java.util.Date;
+
+/**
+ * Surveillance cases cohort definition
+ */
+
+@Caching(strategy = ConfigurationPropertyCachingStrategy.class)
+@Localized("reporting.CaseLabsCohortDefinition")
+public class CaseLabsCohortDefinition extends BaseQuery<Visit> implements VisitQuery {
+    @ConfigurationProperty
+    private Date asOfDate;
+
+    public CaseLabsCohortDefinition() {
+    }
+
+    public Date getAsOfDate() {
+        return asOfDate;
+    }
+
+    public void setAsOfDate(Date asOfDate) {
+        this.asOfDate = asOfDate;
+    }
+
+}

api/src/main/java/org/openmrs/module/kenyaemr/reporting/cohort/definition/dmi/casereport/CaseVitalsCohortDefinition.java

@@ -0,0 +1,43 @@
+/**
+ * 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.casereport;
+
+import org.openmrs.Visit;
+import org.openmrs.module.reporting.common.Localized;
+import org.openmrs.module.reporting.definition.configuration.ConfigurationProperty;
+import org.openmrs.module.reporting.definition.configuration.ConfigurationPropertyCachingStrategy;
+import org.openmrs.module.reporting.evaluation.caching.Caching;
+import org.openmrs.module.reporting.query.BaseQuery;
+import org.openmrs.module.reporting.query.visit.definition.VisitQuery;
+
+import java.util.Date;
+
+/**
+ * Surveillance cases cohort definition
+ */
+
+@Caching(strategy = ConfigurationPropertyCachingStrategy.class)
+@Localized("reporting.CaseVitalsCohortDefinition")
+public class CaseVitalsCohortDefinition extends BaseQuery<Visit> implements VisitQuery {
+    @ConfigurationProperty
+    private Date asOfDate;
+
+    public CaseVitalsCohortDefinition() {
+    }
+
+    public Date getAsOfDate() {
+        return asOfDate;
+    }
+
+    public void setAsOfDate(Date asOfDate) {
+        this.asOfDate = asOfDate;
+    }
+
+}

api/src/main/java/org/openmrs/module/kenyaemr/reporting/cohort/definition/dmi/casereport/IllCasesCohortDefinition.java

@@ -0,0 +1,43 @@
+/**
+ * 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.casereport;
+
+import org.openmrs.Visit;
+import org.openmrs.module.reporting.common.Localized;
+import org.openmrs.module.reporting.definition.configuration.ConfigurationProperty;
+import org.openmrs.module.reporting.definition.configuration.ConfigurationPropertyCachingStrategy;
+import org.openmrs.module.reporting.evaluation.caching.Caching;
+import org.openmrs.module.reporting.query.BaseQuery;
+import org.openmrs.module.reporting.query.visit.definition.VisitQuery;
+
+import java.util.Date;
+
+/**
+ * Surveillance cases cohort definition
+ */
+
+@Caching(strategy = ConfigurationPropertyCachingStrategy.class)
+@Localized("reporting.IllCasesCohortDefinition")
+public class IllCasesCohortDefinition extends BaseQuery<Visit> implements VisitQuery {
+    @ConfigurationProperty
+    private Date asOfDate;
+
+    public IllCasesCohortDefinition() {
+    }
+
+    public Date getAsOfDate() {
+        return asOfDate;
+    }
+
+    public void setAsOfDate(Date asOfDate) {
+        this.asOfDate = asOfDate;
+    }
+
+}

api/src/main/java/org/openmrs/module/kenyaemr/reporting/cohort/definition/evaluator/dmi/casereport/CaseComplaintsCohortDefinitionEvaluator.java

@@ -0,0 +1,62 @@
+/**
+ * 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.casereport;
+
+import org.apache.commons.logging.Log;
+import org.apache.commons.logging.LogFactory;
+import org.openmrs.annotation.Handler;
+import org.openmrs.module.kenyaemr.reporting.cohort.definition.dmi.casereport.CaseComplaintsCohortDefinition;
+import org.openmrs.module.reporting.common.ObjectUtil;
+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.openmrs.module.reporting.query.visit.VisitQueryResult;
+import org.openmrs.module.reporting.query.visit.definition.VisitQuery;
+import org.openmrs.module.reporting.query.visit.evaluator.VisitQueryEvaluator;
+import org.springframework.beans.factory.annotation.Autowired;
+
+import java.util.Date;
+import java.util.List;
+
+/**
+ * Evaluator for case complaints Cohort
+ */
+@Handler(supports = {CaseComplaintsCohortDefinition.class})
+public class CaseComplaintsCohortDefinitionEvaluator implements VisitQueryEvaluator {
+
+    private final Log log = LogFactory.getLog(this.getClass());
+
+    @Autowired
+    EvaluationService evaluationService;
+
+    @Override
+    public VisitQueryResult evaluate(VisitQuery visitQuery, EvaluationContext context) throws EvaluationException {
+        context = ObjectUtil.nvl(context, new EvaluationContext());
+        VisitQueryResult queryResult = new VisitQueryResult(visitQuery, context);
+
+        String qry = "select i.visit_id\n" +
+                "from kenyaemr_etl.etl_allergy_chronic_illness i\n" +
+                "where i.visit_date between date(:startDate) and date(:endDate)\n" +
+                "  and i.complaint is not null\n" +
+                "group by visit_id;";
+
+        SqlQueryBuilder builder = new SqlQueryBuilder();
+        builder.append(qry);
+        Date startDate = (Date) context.getParameterValue("startDate");
+        Date endDate = (Date) context.getParameterValue("endDate");
+        builder.addParameter("endDate", endDate);
+        builder.addParameter("startDate", startDate);
+
+        List<Integer> results = evaluationService.evaluateToList(builder, Integer.class, context);
+        queryResult.getMemberIds().addAll(results);
+        return queryResult;
+    }
+}

api/src/main/java/org/openmrs/module/kenyaemr/reporting/cohort/definition/evaluator/dmi/casereport/CaseDiagnosisCohortDefinitionEvaluator.java

@@ -0,0 +1,63 @@
+/**
+ * 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.casereport;
+
+import org.apache.commons.logging.Log;
+import org.apache.commons.logging.LogFactory;
+import org.openmrs.annotation.Handler;
+import org.openmrs.module.kenyaemr.reporting.cohort.definition.dmi.casereport.CaseDiagnosisCohortDefinition;
+import org.openmrs.module.reporting.common.ObjectUtil;
+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.openmrs.module.reporting.query.visit.VisitQueryResult;
+import org.openmrs.module.reporting.query.visit.definition.VisitQuery;
+import org.openmrs.module.reporting.query.visit.evaluator.VisitQueryEvaluator;
+import org.springframework.beans.factory.annotation.Autowired;
+
+import java.util.Date;
+import java.util.List;
+
+/**
+ * Evaluator for case complaints Cohort
+ */
+@Handler(supports = {CaseDiagnosisCohortDefinition.class})
+public class CaseDiagnosisCohortDefinitionEvaluator implements VisitQueryEvaluator {
+
+    private final Log log = LogFactory.getLog(this.getClass());
+
+    @Autowired
+    EvaluationService evaluationService;
+
+    @Override
+    public VisitQueryResult evaluate(VisitQuery visitQuery, EvaluationContext context) throws EvaluationException {
+        context = ObjectUtil.nvl(context, new EvaluationContext());
+        VisitQueryResult queryResult = new VisitQueryResult(visitQuery, context);
+
+        String qry = "select e.visit_id\n" +
+                "from kenyaemr_etl.etl_clinical_encounter e\n" +
+                "         inner join openmrs.encounter_diagnosis d\n" +
+                "                    on e.encounter_id = d.encounter_id and d.dx_rank = 2 and d.voided = 0\n" +
+                "where e.visit_date between date(:startDate) and date(:endDate)\n" +
+                "GROUP BY e.visit_id;";
+
+        SqlQueryBuilder builder = new SqlQueryBuilder();
+        builder.append(qry);
+        Date startDate = (Date) context.getParameterValue("startDate");
+        Date endDate = (Date) context.getParameterValue("endDate");
+        builder.addParameter("endDate", endDate);
+        builder.addParameter("startDate", startDate);
+
+        List<Integer> results = evaluationService.evaluateToList(builder, Integer.class, context);
+        queryResult.getMemberIds().addAll(results);
+        return queryResult;
+    }
+}