FLAG-81: Fix the module warning (#93)

api-metadata/src/main/java/org/openmrs/module/patientflags/metadatadeploy/bundle/PatientFlagMetadataBundle.java

@@ -19,6 +19,7 @@
 
 public abstract class PatientFlagMetadataBundle extends AbstractMetadataBundle {
 
+    @SuppressWarnings("unchecked")
     protected void install(TagDescriptor tagDescriptor) {
         Tag tag = new Tag(tagDescriptor.name());
         if (StringUtils.isNotBlank(tagDescriptor.uuid())) {
@@ -48,6 +49,7 @@ protected void install(PriorityDescriptor priorityDescriptor) {
         this.install((OpenmrsObject) priority);
     }
 
+    @SuppressWarnings("unchecked")
     protected void install(FlagDescriptor flagDescriptor) {
         Flag flag = new Flag(flagDescriptor.name(), flagDescriptor.criteria(), flagDescriptor.message());
         if (StringUtils.isNotBlank(flagDescriptor.priority())) {

api/src/main/java/org/openmrs/module/patientflags/db/hibernate/HibernateFlagDAO.java

@@ -101,6 +101,7 @@ public Flag getFlagByName(String name) throws DAOException {
 			criteria.add(Restrictions.eq("name", name));
 		}
 
+		@SuppressWarnings("unchecked")
 		List<Flag> list = criteria.list();
 
 		if (list.size() == 1) {
@@ -185,6 +186,7 @@ public Tag getTag(String name) {
 			criteria.add(Restrictions.eq("name", name));
 		}
 
+		@SuppressWarnings("unchecked")
 		List<Tag> list = criteria.list();
 
 		if (list.size() == 1) {
@@ -269,6 +271,7 @@ public Priority getPriorityByName(String name) throws DAOException {
 			criteria.add(Restrictions.eq("name", name));
 		}
 
+		@SuppressWarnings("unchecked")
 		List<Priority> list = criteria.list();
 
 		if (list.size() == 1) {

api/src/main/java/org/openmrs/module/patientflags/evaluator/CQLFlagEvaluator.java

@@ -14,8 +14,10 @@
 package org.openmrs.module.patientflags.evaluator;
 
 import java.util.ArrayList;
+import java.util.HashSet;
 import java.util.List;
 import java.util.Map;
+import java.util.Set;
 
 import org.apache.commons.lang3.StringUtils;
 import org.openmrs.Cohort;
@@ -30,7 +32,7 @@ public class CQLFlagEvaluator implements FlagEvaluator {
 
 	@Override
 	public Boolean eval(Flag flag, Patient patient, Map<Object, Object> context) {
-		if(patient.isVoided())
+		if(patient.getVoided())
 			throw new APIException("Unable to evaluate CQL flag " + flag.getName() + " against voided patient");
 
 		// create a Cohort that contains just the patient, and then evaluate that Cohort
@@ -65,12 +67,14 @@ public Cohort evalCohort(Flag flag, Cohort cohort, Map<Object, Object> context)
 	}
 
 	private List<Patient> getPatients(Cohort cohort) {
-
+		Set<Integer> memberIds = new HashSet<>();
+		cohort.getMemberships().forEach(member -> memberIds.add(member.getPatientId()));
+
 		PatientService patientService = Context.getPatientService();
 
 		List<Patient> patients = new ArrayList<Patient>();
 		if (cohort != null) {
-			for (Integer patientId : cohort.getMemberIds()) {
+			for (Integer patientId : memberIds) {
 				patients.add(patientService.getPatient(patientId));
 			}
 		}

api/src/main/java/org/openmrs/module/patientflags/evaluator/GroovyFlagEvaluator.java

@@ -32,7 +32,7 @@ public class GroovyFlagEvaluator implements FlagEvaluator {
 	 */
 	public Boolean eval(Flag flag, Patient patient, Map<Object, Object> context) {
 
-		if(patient.isVoided())
+		if(patient.getVoided())
 			throw new APIException("Unable to evaluate Groovy flag " + flag.getName() + " against voided patient");
 
 		// create a Cohort that contains just the patient to test, and then evaluate that Cohort

api/src/main/java/org/openmrs/module/patientflags/evaluator/SQLFlagEvaluator.java

@@ -41,7 +41,7 @@ public class SQLFlagEvaluator implements FlagEvaluator {
 	 */
 	public Boolean eval(Flag flag, Patient patient, Map<Object, Object> context) {
 
-		if(patient.isVoided())
+		if(patient.getVoided())
 			throw new APIException("Unable to evaluate SQL flag " + flag.getName() + " against voided patient");
 
 		String criteria = flag.getCriteria();
@@ -98,7 +98,7 @@ public Cohort evalCohort(Flag flag, Cohort cohort, Map<Object, Object> context)
 			Integer patient_id = (Integer) row.get(0);
 
 			// only add patients that haven't been voided
-			if(!Context.getPatientService().getPatient(patient_id).isVoided())
+			if(!Context.getPatientService().getPatient(patient_id).getVoided())
 				resultCohort.addMember((Integer) row.get(0));
 		}
 
@@ -148,7 +148,7 @@ public String evalMessage(Flag flag, int patientId) {
 		log.info("Replacing values in "+message);
 
 		Patient p = Context.getPatientService().getPatient(patientId);
-		if(p.isVoided())
+		if(p.getVoided())
 			throw new APIException("VOIDED PATIENT");
 
 		String criteria = flag.getCriteria();

api/src/main/java/org/openmrs/module/patientflags/task/PatientFlagTask.java

@@ -15,7 +15,10 @@
 
 import java.util.HashMap;
 import java.util.List;
+import java.util.Set;
+import java.util.stream.Collectors;
 
+import org.openmrs.CohortMembership;
 import org.openmrs.Patient;
 import org.openmrs.api.context.Context;
 import org.openmrs.api.context.Daemon;
@@ -78,7 +81,7 @@ private static void generatePatientFlags(Flag flag, FlagService service) {
 	}
 
 	private static void generatePatientFlagsForFlagAndPatient(Flag flag, FlagService service){
-		if (!flag.getEnabled() || flag.isRetired()) {
+		if (!flag.getEnabled() || flag.getRetired()) {
 			return;
 		}
 
@@ -87,9 +90,15 @@ private static void generatePatientFlagsForFlagAndPatient(Flag flag, FlagService
 		if (cohort == null) {
 			return;
 		}
-
-		java.util.Set<Integer> members =  cohort.getMemberIds();
+
+		Set<Integer> members = cohort.getMemberships()
+				.stream()
+				.map(CohortMembership::getPatientId)
+				.collect(Collectors.toSet());
+
 		for (Integer patientId : members) {
+
+			@SuppressWarnings("unchecked")
 			List<String> flgs = (List<String>)context.get(patientId);
 			if (flgs != null) {
 				for (String flg : flgs) {
@@ -108,6 +117,8 @@ private void generatePatientFlags(Patient patient, FlagService service) {
 		HashMap<Object, Object> context = new HashMap<Object, Object>();
 		List<Flag> flags = service.generateFlagsForPatient(patient, context);
 		for (Flag flag : flags) {
+
+			@SuppressWarnings("unchecked")
 			List<String> flgs = (List<String>)context.get(patient.getPatientId());
 			if (flgs != null) {
 				for (String flg : flgs) {

api/src/test/java/org/openmrs/module/patientflags/FlagTest.java

@@ -13,7 +13,7 @@
  */
 package org.openmrs.module.patientflags;
 
-import junit.framework.Assert;
+import org.junit.Assert;
 
 import org.junit.Before;
 import org.junit.Test;

omod/src/main/java/org/openmrs/module/patientflags/web/FindFlaggedPatientsController.java

@@ -23,6 +23,7 @@
 import javax.servlet.http.HttpServletRequest;
 
 import org.openmrs.Cohort;
+import org.openmrs.CohortMembership;
 import org.openmrs.Patient;
 import org.openmrs.api.context.Context;
 import org.openmrs.module.patientflags.Flag;
@@ -116,7 +117,12 @@ public ModelAndView processSubmit(@ModelAttribute("flag") Flag flag, BindingResu
 		List<Map<String, Object>> fpl = new ArrayList<Map<String, Object>>();
 
 		if(flaggedPatients != null){
-			Set<Integer> idsFp = flaggedPatients.getMemberIds();
+
+			Set<Integer> idsFp = flaggedPatients.getMemberships()
+					.stream()
+					.map(CohortMembership::getPatientId)
+					.collect(Collectors.toSet());
+
 			for (Integer patientId : idsFp) {
 				Map<String, Object> mapFp = new HashMap<String, Object>();
 
@@ -140,31 +146,34 @@ public ModelAndView processSubmit(@ModelAttribute("flag") Flag flag, BindingResu
 
 	@RequestMapping(method = RequestMethod.GET, params = "tags")
 	public ModelAndView processSubmit(@ModelAttribute("filter") Filter filter, BindingResult result, SessionStatus status) {
-		
+
 		if (result.hasErrors()) {
 			return new ModelAndView("/module/patientflags/findFlaggedPatients");
 		}
-		
+
 		FlagService flagService = Context.getService(FlagService.class);
-		
+
 		// get the flags to test on
 		List<Flag> flags = flagService.getFlagsByFilter(filter);
-		
+
 		// returns a map of flagged Patients and the respective flags
-		Cohort flaggedPatients = flagService.getFlaggedPatients(flags, null);
+		Set<Integer> flaggedPatients = flagService.getFlaggedPatients(flags, null).getMemberships()
+				.stream()
+				.map(CohortMembership::getPatientId)
+				.collect(Collectors.toSet());
+
 		Cohort allPatients = new Cohort();
 
 		Context.getPatientService().getAllPatients().forEach( patient ->
 				allPatients.addMember(patient.getPatientId())
 		);
-		
+
 		// create the model map
 		ModelMap model = new ModelMap();
-		model.addAttribute("allPatients", allPatients);
 
-		Set<Integer> flaggedPatientIds = flaggedPatients.getMemberIds();
+		model.addAttribute("allPatients", allPatients);
 
-		List<Map<String, Integer>> flaggedPatientList = flaggedPatientIds.stream()
+		List<Map<String, Integer>> flaggedPatientList = flaggedPatients.stream()
 				.map(patientId -> {
 					Map<String, Integer> mapFlaggerPatient = new HashMap<>();
 					mapFlaggerPatient.put("patientId", patientId);
@@ -177,7 +186,7 @@ public ModelAndView processSubmit(@ModelAttribute("filter") Filter filter, Bindi
 
 		// clears the command object from the session
 		status.setComplete();
-		
+
 		// displays the query results
 		return new ModelAndView("/module/patientflags/findFlaggedPatientsResults", model);
 	}

omod/src/main/java/org/openmrs/module/patientflags/web/FindFlaggedPatientsEmailController.java

@@ -14,6 +14,7 @@
 package org.openmrs.module.patientflags.web;
 
 import org.openmrs.Cohort;
+import org.openmrs.CohortMembership;
 import org.openmrs.Patient;
 import org.openmrs.api.APIException;
 import org.openmrs.api.context.Context;
@@ -29,6 +30,8 @@
 import org.springframework.web.servlet.ModelAndView;
 
 import java.util.List;
+import java.util.Set;
+import java.util.stream.Collectors;
 
 /**
  * Controller that handles retrieving Patients that match a Flag criteria for email output
@@ -58,6 +61,12 @@ public ModelAndView processRequest(@ModelAttribute("flag") Flag flag, BindingRes
 		FlagService flagService = Context.getService(FlagService.class);
 		flag = flagService.getFlag(flag.getFlagId());
 		Cohort flaggedPatients = flagService.getFlaggedPatients(flag, null);
+
+		Set<Integer> patientIds = flaggedPatients.getMemberships()
+				.stream()
+				.map(CohortMembership::getPatientId)
+				.collect(Collectors.toSet());
+
 		Cohort allPatients = new Cohort();
 		List<Patient> patients = Context.getPatientService().getAllPatients();
 		for (Patient i : patients) {
@@ -69,7 +78,7 @@ public ModelAndView processRequest(@ModelAttribute("flag") Flag flag, BindingRes
 		model.addAttribute("flag", flag);
 		model.addAttribute("allPatients", allPatients);
 		if(flaggedPatients != null){
-			model.addAttribute("flaggedPatients", flaggedPatients.getMemberIds());
+			model.addAttribute("flaggedPatients", patientIds);
 		}
 		else{
 			model.addAttribute("flaggedPatients", null);

omod/src/main/java/org/openmrs/module/patientflags/web/rest/resources/PatientFlagResource.java

@@ -85,7 +85,7 @@ public PatientFlag save(PatientFlag delegate) {
 	 */
 	@Override
 	protected void delete(PatientFlag delegate, String reason, RequestContext context) throws ResponseException {
-		if (delegate.isVoided()) {
+		if (delegate.getVoided()) {
 			// DELETE is idempotent, so we return success here
 			return;
 		}
@@ -98,7 +98,7 @@ protected void delete(PatientFlag delegate, String reason, RequestContext contex
 	 */
 	@Override
 	protected PatientFlag undelete(PatientFlag delegate, RequestContext context) throws ResponseException {
-		if (delegate.isVoided()) {
+		if (delegate.getVoided()) {
 			Context.getService(FlagService.class).unvoidPatientFlag(delegate);
 		}
 		return delegate;