GSoC 2019: Patient Search Criteria Module

.travis.yml

@@ -1,11 +1,15 @@
 language: java
 jdk:
- - oraclejdk8
+ - openjdk8
 addons: 
   firefox: "43.0"
+cache:
+  directories:
+  - .autoconf
+  - $HOME/.m2    
 install:
   - export DISPLAY=:99.0
   - sh -e /etc/init.d/xvfb start
   - tar -xjf /tmp/firefox-43.0.tar.bz2 --directory /tmp
   - export PATH="/tmp/firefox:$PATH"
-script: mvn clean install
+script: mvn clean install -q

api-2.2/src/main/java/org/openmrs/module/coreapps/htmlformentry/EncounterDiagnosesElement.java

@@ -70,6 +70,8 @@ public class EncounterDiagnosesElement implements HtmlGeneratorElement, FormSubm
     private String diagnosisConceptSources;
 
     private String preferredCodingSource;
+
+    private String diagnosisConceptClasses;
 
     private EmrApiProperties emrApiProperties;
 
@@ -141,9 +143,12 @@ public String generateHtml(FormEntryContext context) {
                 Map<String, Object> fragmentConfig = new HashMap<String, Object>();
                 fragmentConfig.put("formFieldName", "encounterDiagnoses");
                 fragmentConfig.put("existingDiagnoses", existingDiagnoses);
-                fragmentConfig.put("diagnosisSets", validateAndFormat(diagnosisSets));
+                // Parse '0' to config attribute if specified such that null value can be used during the search in 'DiagnosesFragmentController' class  
+                fragmentConfig.put("diagnosisSets", "0".equals(diagnosisSets) ? "0" : validateAndFormat(diagnosisSets));
+
                 fragmentConfig.put("preferredCodingSource", preferredCodingSource);
                 fragmentConfig.put("diagnosisConceptSources", StringUtils.deleteWhitespace(diagnosisConceptSources));
+                fragmentConfig.put("diagnosisConceptClasses", StringUtils.deleteWhitespace(diagnosisConceptClasses));
 
                 // add the prior diagnoses if requested
                 if (FormEntryContext.Mode.ENTER == context.getMode() && dispositionTypeForPriorDiagnoses != null) {
@@ -181,8 +186,8 @@ public String generateHtml(FormEntryContext context) {
      * @throws IllegalArgumentException if one or more sets cannot be fetched from the database.
      */
     private String validateAndFormat(String diagnosisSetIds) {
-        if ("".equals(diagnosisSetIds)) {
-            return diagnosisSetIds;
+        if (diagnosisSetIds == null) {
+            return null;
         }
         List<Concept> concepts = new ArrayList<Concept>();
         for (StringTokenizer st = new StringTokenizer(diagnosisSetIds, ","); st.hasMoreTokens();) {
@@ -430,6 +435,14 @@ public void setPreferredCodingSource(String preferredCodingSource) {
     public String getPreferredCodingSource() {
         return preferredCodingSource;
     }
+
+    public void setDiagnosisConceptClasses(String diagnosisConceptClasses) {
+        this.diagnosisConceptClasses = diagnosisConceptClasses;
+    }
+
+    public String getDiagnosisConceptClasses() {
+        return diagnosisConceptClasses;
+    }
 
     public void setUiUtils(UiUtils uiUtils) {
         this.uiUtils = uiUtils;

api-pre2.2/src/main/java/org/openmrs/module/coreapps/htmlformentry/EncounterDiagnosesElement.java

@@ -75,6 +75,8 @@ public class EncounterDiagnosesElement implements HtmlGeneratorElement, FormSubm
     private String diagnosisSets;
 
     private String diagnosisConceptSources;
+
+    private String diagnosisConceptClasses;
 
     private AdtService adtService;
 
@@ -120,9 +122,12 @@ public String generateHtml(FormEntryContext context) {
                 Map<String, Object> fragmentConfig = new HashMap<String, Object>();
                 fragmentConfig.put("formFieldName", "encounterDiagnoses");
                 fragmentConfig.put("existingDiagnoses", existingDiagnoses);
-                fragmentConfig.put("diagnosisSets", validateAndFormat(diagnosisSets));
+                // Parse '0' to config attribute if specified such that null value can be used during the search in 'DiagnosesFragmentController' class
+                fragmentConfig.put("diagnosisSets", "0".equals(diagnosisSets) ? "0" : validateAndFormat(diagnosisSets));
+
                 fragmentConfig.put("preferredCodingSource", preferredCodingSource);
                 fragmentConfig.put("diagnosisConceptSources", StringUtils.deleteWhitespace(diagnosisConceptSources));
+                fragmentConfig.put("diagnosisConceptClasses", StringUtils.deleteWhitespace(diagnosisConceptClasses));
 
                 // add the prior diagnoses if requested
                 if (FormEntryContext.Mode.ENTER == context.getMode() && dispositionTypeForPriorDiagnoses != null) {
@@ -160,8 +165,8 @@ public String generateHtml(FormEntryContext context) {
      * @throws IllegalArgumentException if one or more sets cannot be fetched from the database.
      */
     private String validateAndFormat(String diagnosisSetIds) {
-        if (StringUtils.isEmpty(diagnosisSetIds)) {
-            return "";
+        if (diagnosisSetIds == null) {
+            return null;
         }
         List<Concept> concepts = new ArrayList<Concept>();
         for (StringTokenizer st = new StringTokenizer(diagnosisSetIds, ","); st.hasMoreTokens();) {
@@ -379,6 +384,14 @@ public void setPreferredCodingSource(String preferredCodingSource) {
     public String getPreferredCodingSource() {
         return preferredCodingSource;
     }
+
+    public void setDiagnosisConceptClasses(String diagnosisConceptClasses) {
+        this.diagnosisConceptClasses = diagnosisConceptClasses;
+    }
+
+    public String getDiagnosisConceptClasses() {
+        return diagnosisConceptClasses;
+    }
 
     public void setUiUtils(UiUtils uiUtils) {
         this.uiUtils = uiUtils;

api/src/main/java/org/openmrs/module/coreapps/htmlformentry/EncounterDiagnosesByObsElement.java

@@ -75,6 +75,8 @@ public class EncounterDiagnosesByObsElement implements HtmlGeneratorElement, For
     private String diagnosisConceptSources;
 
     private String preferredCodingSource;
+
+    private String diagnosisConceptClasses;
 
     private AdtService adtService;
 
@@ -120,9 +122,12 @@ public String generateHtml(FormEntryContext context) {
                 Map<String, Object> fragmentConfig = new HashMap<String, Object>();
                 fragmentConfig.put("formFieldName", "encounterDiagnoses");
                 fragmentConfig.put("existingDiagnoses", existingDiagnoses);
-                fragmentConfig.put("diagnosisSets", validateAndFormat(diagnosisSets));
+                // Parse '0' to config attribute if specified such that null value can be used during the search in 'DiagnosesFragmentController' class
+                fragmentConfig.put("diagnosisSets", "0".equals(diagnosisSets) ? "0" : validateAndFormat(diagnosisSets));
+
                 fragmentConfig.put("preferredCodingSource", preferredCodingSource);
                 fragmentConfig.put("diagnosisConceptSources", StringUtils.deleteWhitespace(diagnosisConceptSources));
+                fragmentConfig.put("diagnosisConceptClasses", StringUtils.deleteWhitespace(diagnosisConceptClasses));
 
                 // add the prior diagnoses if requested
                 if (FormEntryContext.Mode.ENTER == context.getMode() && dispositionTypeForPriorDiagnoses != null) {
@@ -160,8 +165,8 @@ public String generateHtml(FormEntryContext context) {
      * @throws IllegalArgumentException if one or more sets cannot be fetched from the database.
      */
     private String validateAndFormat(String diagnosisSetIds) {
-        if ("".equals(diagnosisSetIds)) {
-            return diagnosisSetIds;
+        if (diagnosisSetIds == null) {
+            return null;
         }
         List<Concept> concepts = new ArrayList<Concept>();
         for (StringTokenizer st = new StringTokenizer(diagnosisSetIds, ","); st.hasMoreTokens();) {
@@ -379,6 +384,14 @@ public void setPreferredCodingSource(String preferredCodingSource) {
     public String getPreferredCodingSource() {
         return preferredCodingSource;
     }
+
+    public void setDiagnosisConceptClasses(String diagnosisConceptClasses) {
+        this.diagnosisConceptClasses = diagnosisConceptClasses;
+    }
+
+    public String getDiagnosisConceptClasses() {
+        return diagnosisConceptClasses;
+    }
 
     public void setUiUtils(UiUtils uiUtils) {
         this.uiUtils = uiUtils;

api/src/main/java/org/openmrs/module/coreapps/htmlformentry/EncounterDiagnosesByObsTagHandler.java

@@ -76,8 +76,9 @@ protected String getSubstitution(FormEntrySession session, FormSubmissionControl
         element.setEmrApiProperties(emrApiProperties);
         element.setConceptService(conceptService);
         element.setAdtService(adtService);
-        element.setDiagnosisSets(attributes.get("diagnosisSets") != null ? attributes.get("diagnosisSets") : "");
-        element.setDiagnosisConceptSources(attributes.get("diagnosisConceptSources") != null ? attributes.get("diagnosisConceptSources") : "");
+        element.setDiagnosisSets(attributes.get("diagnosisSets"));
+        element.setDiagnosisConceptClasses(attributes.get("diagnosisConceptClasses"));
+        element.setDiagnosisConceptSources(attributes.get("diagnosisConceptSources"));
         element.setPreferredCodingSource(attributes.get("preferredCodingSource") != null ? attributes.get("preferredCodingSource"): CoreAppsConstants.DEFAULT_CODING_SOURCE);
 
         /**

api/src/main/java/org/openmrs/module/coreapps/htmlformentry/EncounterDiagnosesTagHandler.java

@@ -78,8 +78,9 @@ protected String getSubstitution(FormEntrySession session, FormSubmissionControl
         element.setEmrApiProperties(emrApiProperties);
         element.setConceptService(conceptService);
         element.setAdtService(adtService);
-        element.setDiagnosisSets(attributes.get("diagnosisSets") != null ? attributes.get("diagnosisSets") : "");
-        element.setDiagnosisConceptSources(attributes.get("diagnosisConceptSources") != null ? attributes.get("diagnosisConceptSources") : "");
+        element.setDiagnosisSets(attributes.get("diagnosisSets"));
+        element.setDiagnosisConceptClasses(attributes.get("diagnosisConceptClasses"));
+        element.setDiagnosisConceptSources(attributes.get("diagnosisConceptSources"));
         element.setPreferredCodingSource(attributes.get("preferredCodingSource") != null ? attributes.get("preferredCodingSource"): CoreAppsConstants.DEFAULT_CODING_SOURCE);
 
         /**

omod/pom.xml

@@ -18,6 +18,13 @@
         <gem.path>${basedir}/.rubygems</gem.path>
     </properties>
 
+    <repositories>
+		<repository>
+		    <id>jitpack.io</id>
+		    <url>https://jitpack.io</url>
+		</repository>
+	</repositories>
+
     <dependencies>
 
 		<!-- 
@@ -255,6 +262,20 @@
             <scope>provided</scope>
         </dependency>
 
+        <!-- Patient search criteria module -->
+        <dependency>
+		    <groupId>com.github.Reyano132.openmrs-module-patientsearchcriteria</groupId>
+		    <artifactId>patientsearch-api</artifactId>
+		    <version>v1.0.0</version>
+		    <scope>provided</scope>
+		</dependency>
+        <dependency>
+		    <groupId>com.github.Reyano132.openmrs-module-patientsearchcriteria</groupId>
+		    <artifactId>patientsearch-omod</artifactId>
+		    <version>v1.0.0</version>
+		    <scope>provided</scope>
+		</dependency>
+
 	</dependencies>
 
 	<build>

omod/src/main/java/org/openmrs/module/coreapps/fragment/controller/DiagnosesFragmentController.java

@@ -15,10 +15,12 @@
 package org.openmrs.module.coreapps.fragment.controller;
 
 import org.apache.commons.beanutils.PropertyUtils;
+import org.apache.commons.collections.CollectionUtils;
 import org.apache.commons.lang.StringUtils;
 import org.codehaus.jackson.JsonNode;
 import org.codehaus.jackson.map.ObjectMapper;
 import org.openmrs.Concept;
+import org.openmrs.ConceptClass;
 import org.openmrs.ConceptName;
 import org.openmrs.ConceptSearchResult;
 import org.openmrs.ConceptSource;
@@ -50,49 +52,92 @@
  */
 public class DiagnosesFragmentController {
 
+    private final static String USE_NULL_VALUE = "0";
+
+    /**
+     * Searches for diagnoses with names matching query in the specified 1) diagnosisSets, 2) diagnosisConceptSources and/or diagnosisConceptClasses
+     * If diagnosisSets or diagnosisConceptSources attributes are missing, default values specided by emrApiProperties are used. 
+     * If '0' is specified for any of diagnosisSets or diagnosisConceptSources attributes, null is used for their corresponding values in the search.
+     * 
+     * @param context
+     * @param ui
+     * @param emrApiProperties
+     * @param emrConceptService
+     * @param conceptService
+     * @param query
+     * @param diagnosisSetUuids
+     * @param diagnosisConceptSources
+     * @param diagnosisConceptClasses
+     * @param start
+     * @param size
+     * @return diagnoses search results
+     * @throws Exception
+     */
     public List<SimpleObject> search(UiSessionContext context,
                                      UiUtils ui,
                                      @SpringBean("emrApiProperties") EmrApiProperties emrApiProperties,
                                      @SpringBean("emrConceptService") EmrConceptService emrConceptService,
                                      @SpringBean("conceptService") ConceptService conceptService,
                                      @RequestParam("term") String query,
-                                     @RequestParam(value = "diagnosisSets", defaultValue = "") String diagnosisSetUuids,
-                                     @RequestParam(value = "diagnosisConceptSources", defaultValue = "") String diagnosisConceptSources,
+                                     @RequestParam(value = "diagnosisSets", required = false) String diagnosisSetUuids,
+                                     @RequestParam(value = "diagnosisConceptSources", required = false) String diagnosisConceptSources,
+                                     @RequestParam(value = "diagnosisConceptClasses", required = false) String diagnosisConceptClasses,
                                      @RequestParam(value = "start", defaultValue = "0") Integer start,
                                      @RequestParam(value = "size", defaultValue = "50") Integer size) throws Exception {
 
+        List<ConceptClass> conceptClasses = new ArrayList<ConceptClass>();
+        if (StringUtils.isNotEmpty(diagnosisConceptClasses)) {
+            String [] conceptClassNames = diagnosisConceptClasses.split(",");
+            for (String className : conceptClassNames) {
+                ConceptClass conceptClass = conceptService.getConceptClassByName(className);
+                if (conceptClass != null) {
+                    conceptClasses.add(conceptClass);
+                }                
+            }
+        }
+        else {
+            conceptClasses = null;            
+        }
+
         Collection<Concept> diagnosisSets = new ArrayList<Concept>();
         if (StringUtils.isNotEmpty(diagnosisSetUuids)) {
-            String [] setUuids = diagnosisSetUuids.split(",");
-            for (String setUuid : setUuids) {
-                Concept conceptSet = conceptService.getConceptByUuid(setUuid);
-                if (conceptSet != null) {
-                    diagnosisSets.add(conceptSet);
-                }                
+            if (USE_NULL_VALUE.equals(diagnosisSetUuids) ) {
+                diagnosisSets = null;
+            } else {
+                String [] setUuids = diagnosisSetUuids.split(",");
+                for (String setUuid : setUuids) {
+                    Concept conceptSet = conceptService.getConceptByUuid(setUuid);
+                    if (conceptSet != null) {
+                        diagnosisSets.add(conceptSet);
+                    }                
+                }
             }
         }
-        else{
+        else {
             diagnosisSets = emrApiProperties.getDiagnosisSets();
         }
-
+                       
         List<ConceptSource> sources = new ArrayList<ConceptSource>();
-
         if (StringUtils.isNotEmpty(diagnosisConceptSources)) {
-            String [] sourceNames = diagnosisConceptSources.split(",");
-            for (String sourceName : sourceNames) {
-                ConceptSource source = conceptService.getConceptSourceByName(sourceName);
-                if (source != null) {
-                    sources.add(source);
-                }                
+            if (USE_NULL_VALUE.equals(diagnosisConceptSources) ) {
+                sources = null;
+            } else {
+                String [] sourceNames = diagnosisConceptSources.split(",");
+                for (String sourceName : sourceNames) {
+                    ConceptSource source = conceptService.getConceptSourceByName(sourceName);
+                    if (source != null) {
+                        sources.add(source);
+                    }                
+                }
             }
         }
-        else{
+        else {
             sources = emrApiProperties.getConceptSourcesForDiagnosisSearch();
         }
 
         Locale locale = context.getLocale();
 
-        List<ConceptSearchResult> hits = emrConceptService.conceptSearch(query, locale, null, diagnosisSets, sources, null);
+        List<ConceptSearchResult> hits = emrConceptService.conceptSearch(query, locale, conceptClasses, diagnosisSets, sources, null);
         List<SimpleObject> ret = new ArrayList<SimpleObject>();
         for (ConceptSearchResult hit : hits) {
             ret.add(simplify(hit, ui, locale));
@@ -110,7 +155,7 @@ public List<SimpleObject> searchNonCoded(UiSessionContext context,
                                      @RequestParam(value = "start", defaultValue = "0") Integer start,
                                      @RequestParam(value = "size", defaultValue = "50") Integer size) throws Exception {
 
-        return search(context, ui, emrApiProperties, emrConceptService, conceptService, query, null, null, start, size);
+        return search(context, ui, emrApiProperties, emrConceptService, conceptService, query, null, null, null, start, size);
     }
 
     public FragmentActionResult codeDiagnosis(UiUtils ui,

omod/src/main/webapp/fragments/conditionlist/conditions.gsp

@@ -34,13 +34,28 @@
     <div class="info-body">
         <ul ng-repeat="conditionHistory in conditionHistoryList">
             <li class="conditionStatus" ng-init="condition = conditionHistory.conditions[0]"
-                ng-show="condition.status === 'ACTIVE'">
+                ng-show="condition.status === 'ACTIVE' && condition.voided==false">
                 <span ng-style="strikeThrough(condition.voided)">{{condition.concept.name}}</span>
                 <i class="icon-remove delete-action" title="${ui.message("coreapps.delete")}"
-                   ng-click="removeCondition(condition)" ng-if="condition.voided===false && '${hasModifyConditionsPrivilege}'"></i>
+                   ng-click="conditionConfirmation(condition)" ng-if="condition.voided===false && '${hasModifyConditionsPrivilege}'"></i>
                 <i class="icon-undo delete-action" title="${ui.message("conditionui.undo")}"
                    ng-click="undoCondition(condition)" ng-if="condition.voided===true && '${hasModifyConditionsPrivilege}'"></i>
             </li>
         </ul>
     </div>
+
+    <div id="remove-condition-dialog" class="dialog" style="display: none; position: absolute; left: 35%; top:30%;">
+    <div class="dialog-header">
+        <h3>${ ui.message("coreapps.conditionui.removeCondition") }</h3>
+    </div>
+    <div class="dialog-content">
+        <ul>
+            <li class="info">
+                <span id="removeConditionMessage">${ ui.message("coreapps.conditionui.removeCondition.message","")}</span>
+            </li>
+        </ul>       
+            <button class="confirm right" type="submit" ng-click="removeCondition()">${ ui.message("general.yes") }</button>
+            <button class="cancel" ng-click="cancelDeletion()">${ ui.message("general.no") }</button>
+    </div>
+</div>
 </div>