Merge branch 'main' into refactor-backend-configuration

README.md

@@ -1,6 +1,6 @@
-# OFN Record Manager
+# Record Manager
 
-Manager of records based on OFN (https://data.gov.cz/ofn/).
+Record Manager is an application for generic form-based collection of data. This repository contains the backend of the application.
 
 ## Required Technologies
 
@@ -9,14 +9,21 @@ Manager of records based on OFN (https://data.gov.cz/ofn/).
 
 ## System Architecture
 
-The system can be split into two parts. __Main application__ provides management of users, organizations and their records. The system manages multiple types of records which are generated dynamically by __Form service__ defined in https://github.com/opendata-mvcr/sgov-forms .  
+The system can be split into two parts. __Main application__ provides management of users, organizations and their records. The system manages multiple types of records which are generated dynamically by __Form service__.  
 
-## Documentation
+## Configuration
 
-Build configuration and deployment is described in [Setup Guide](doc/setup.md).
-Development is described in [Development notes](doc/development.md).
+### Further Record Manager Configuration
+
+The following table lists the names of environment variables that can be
+passed to Record Manager backend either directly in `docker-compose.yml`, in
+an [env_file](https://docs.docker.com/compose/compose-file/compose-file-v3/#env_file), or via command line.
 
------
+| Variable                                           | Explanation                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                |
+|:---------------------------------------------------|:-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|
+| ```RECORDS_ALLOWEDREJECTREASON```                  | Allow user to enter reason when rejecting records. Default value: `false.`                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                |
 
-Tento repozitář je udržován v rámci projektu OPZ č. CZ.03.4.74/0.0/0.0/15_025/0004172.
-![Evropská unie - Evropský sociální fond - Operační program Zaměstnanost](https://data.gov.cz/images/ozp_logo_cz.jpg)
+## Documentation
+
+Build configuration and deployment are described in [Setup Guide](doc/setup.md).
+Development is described in [Development notes](doc/development.md).

src/main/java/cz/cvut/kbss/study/dto/PatientRecordDto.java

@@ -41,6 +41,10 @@ public class PatientRecordDto extends AbstractEntity implements HasOwlKey {
     @OWLObjectProperty(iri = Vocabulary.s_p_has_phase)
     private RecordPhase phase;
 
+    @OWLDataProperty(iri = Vocabulary.s_p_reject_reason)
+    private String rejectReason;
+
+
     @Override
     public String getKey() {
         return key;
@@ -115,6 +119,14 @@ public void setPhase(RecordPhase phase) {
         this.phase = phase;
     }
 
+    public String getRejectReason() {
+        return rejectReason;
+    }
+
+    public void setRejectReason(String rejectReason) {
+        this.rejectReason = rejectReason;
+    }
+
     @Override
     public String toString() {
         return "PatientRecordDto{" +

src/main/java/cz/cvut/kbss/study/model/PatientRecord.java

@@ -59,6 +59,9 @@ public class PatientRecord implements Serializable, HasOwlKey, HasUri {
     @OWLObjectProperty(iri = Vocabulary.s_p_has_phase, cascade = {CascadeType.MERGE}, fetch = FetchType.EAGER)
     private RecordPhase phase;
 
+   @OWLDataProperty(iri = Vocabulary.s_p_reject_reason)
+    private String rejectReason;
+
     @Override
     public URI getUri() {
         return uri;
@@ -146,6 +149,15 @@ public RecordPhase getPhase() {
         return phase;
     }
 
+    public String getRejectReason() {
+        return rejectReason;
+    }
+
+    public void setRejectReason(String rejectReason) {
+        this.rejectReason = rejectReason;
+    }
+
+
     public void setPhase(RecordPhase phase) {
         this.phase = phase;
     }

src/main/java/cz/cvut/kbss/study/rest/PatientRecordController.java

@@ -354,4 +354,9 @@ public void removeRecord(@PathVariable("key") String key) {
             LOG.trace("Patient record {} successfully removed.", toRemove);
         }
     }
+
+    @GetMapping(value = "/allowedRejectReason", produces = MediaType.APPLICATION_JSON_VALUE)
+    public boolean getAllowedRejectReason(){
+        return configReader.getConfig(ConfigParam.RECORDS_ALLOWED_REJECT_REASON).equals("true");
+    }
 }

src/main/java/cz/cvut/kbss/study/service/ExcelRecordConverter.java

@@ -1,5 +1,6 @@
 package cz.cvut.kbss.study.service;
 
+ import cz.cvut.kbss.study.model.RecordPhase;
 import cz.cvut.kbss.study.model.export.ExportRecord;
 import cz.cvut.kbss.study.model.export.Path;
 import cz.cvut.kbss.study.model.export.RawRecord;
@@ -63,6 +64,11 @@ private List<ExportRecord> findExportRecordsData(List<RawRecord> rawRecords){
         codeListValuesDao.findItems(uris).forEach(i -> translatorMap.put(i.getUri(), i.getName()));
         codeListValuesDao.findAircraft().forEach(i -> translatorMap.put(i.getUri(), i.getName()));
         codeListValuesDao.findInstitutions().forEach(i -> translatorMap.put(i.getUri(), i.getName()));
+        rawRecords.stream().map(r -> r.getPhase()).filter(p -> p != null)
+                .forEach(pUri ->
+                        Optional.of(RecordPhase.fromIri(pUri.toString()))
+                                .ifPresent(pStr -> translatorMap.put(pUri, pStr.name()))
+                );
 
         Map<URI, List<String>> pathMap = new HashMap<>();
         paths.forEach(p -> pathMap.put(p.getUri(), Arrays.asList(
@@ -78,6 +84,7 @@ private List<ExportRecord> findExportRecordsData(List<RawRecord> rawRecords){
         for(RawRecord r : rawRecords){
             ExportRecord er = new ExportRecord();
             exportRecords.add(er);
+            er.setPhase(translatorMap.get(r.getPhase()));
             er.setPath(pathMap.get(r.getAc_comp()));
             er.setInstitution(translatorMap.get(r.getInstitution()));
             er.setAircraftType(translatorMap.get(r.getAircraftType()));
@@ -118,7 +125,7 @@ private void addDataToExcel(XSSFWorkbook workbook, List<ExportRecord> data) thro
         for(ExportRecord rec : data) {
             XSSFRow r = s.createRow(rowIndex++);
             r.createCell(0).setCellValue(rowIndex);
-//            r.createCell(1).setCellValue(rowIndex);
+            r.createCell(1).setCellValue(rec.getPhase());
             r.createCell(2).setCellValue(rec.getCreated());
 //            r.createCell(3).setCellValue(rec.ed);
             r.createCell(4).setCellValue(rec.getLastModified());

src/main/java/cz/cvut/kbss/study/service/repository/RepositoryPatientRecordService.java

@@ -73,6 +73,9 @@ protected void prePersist(PatientRecord instance) {
 
     @Override
     protected void preUpdate(PatientRecord instance) {
+        if(instance.getPhase() != RecordPhase.rejected) {
+            instance.setRejectReason(null);
+        }
         instance.setLastModifiedBy(securityUtils.getCurrentUser());
         instance.setLastModified(new Date());
         recordDao.requireUniqueNonEmptyLocalName(instance);

src/main/java/cz/cvut/kbss/study/util/ConfigParam.java

@@ -41,7 +41,9 @@ public enum ConfigParam {
 
     OIDC_ROLE_CLAIM("security.oidc.roleClaim"),
 
-    CORS_ALLOWED_ORIGINS("security.cors.allowedOrigins");
+    CORS_ALLOWED_ORIGINS("security.cors.allowedOrigins"),
+
+    RECORDS_ALLOWED_REJECT_REASON("records.allowedRejectReason");
 
     private final String name;
 

src/main/resources/config.properties

@@ -61,4 +61,6 @@ security.provider=internal
 security.oidc.roleClaim=realm_access.roles
 
 # Configures allowed origins for CORS (e.g. http://localhost:3000). Use a comma to separate multiple values
-security.cors.allowedOrigins=
+security.cors.allowedOrigins=
+
+records.allowedRejectReason=true

src/main/resources/model.ttl

@@ -132,6 +132,9 @@ rm:token rdf:type owl:DatatypeProperty .
 <http://xmlns.com/foaf/0.1/mbox> rdf:type owl:DatatypeProperty .
 
 
+###  http://onto.fel.cvut.cz/ontologies/record-manager/reject-reason
+rm:reject-reason rdf:type owl:DatatypeProperty .
+
 #################################################################
 #    Classes
 #################################################################

src/test/java/cz/cvut/kbss/study/rest/PatientRecordControllerTest.java

@@ -15,8 +15,10 @@
 import cz.cvut.kbss.study.persistence.dao.util.RecordSort;
 import cz.cvut.kbss.study.rest.event.PaginatedResultRetrievedEvent;
 import cz.cvut.kbss.study.rest.util.RestUtils;
+import cz.cvut.kbss.study.service.ConfigReader;
 import cz.cvut.kbss.study.service.PatientRecordService;
 import cz.cvut.kbss.study.service.UserService;
+import cz.cvut.kbss.study.util.ConfigParam;
 import cz.cvut.kbss.study.util.Constants;
 import cz.cvut.kbss.study.util.IdentificationUtils;
 import org.junit.jupiter.api.BeforeEach;
@@ -65,6 +67,9 @@ public class PatientRecordControllerTest extends BaseControllerTestRunner {
     @Mock
     private ApplicationEventPublisher eventPublisherMock;
 
+    @Mock
+    private ConfigReader configReaderMock;
+
     @Mock
     private UserService userService;
 
@@ -487,4 +492,30 @@ void exportRecordsPublishesPagingEvent() throws Exception {
         final PaginatedResultRetrievedEvent event = captor.getValue();
         assertEquals(page, event.getPage());
     }
+
+    @Test
+    void getAllowedRejectReasonTrue() throws Exception {
+        String expectedValue = "true";
+        when(configReaderMock.getConfig(ConfigParam.RECORDS_ALLOWED_REJECT_REASON)).thenReturn(expectedValue);
+          final MvcResult result = mockMvc.perform(get("/records/allowedRejectReason").param("institution", user.getInstitution().toString())).andReturn();
+
+        final String body = objectMapper.readValue(result.getResponse().getContentAsString(),
+                new TypeReference<>() {
+                });
+        assertEquals(result.getResponse().getStatus(), HttpStatus.OK.value());
+        assertEquals(expectedValue, body);
+    }
+
+    @Test
+    void getAllowedRejectReasonFalse() throws Exception {
+        String expectedValue = "false";
+        when(configReaderMock.getConfig(ConfigParam.RECORDS_ALLOWED_REJECT_REASON)).thenReturn(expectedValue);
+        final MvcResult result = mockMvc.perform(get("/records/allowedRejectReason").param("institution", user.getInstitution().toString())).andReturn();
+
+        final String body = objectMapper.readValue(result.getResponse().getContentAsString(),
+                new TypeReference<>() {
+                });
+        assertEquals(result.getResponse().getStatus(), HttpStatus.OK.value());
+        assertEquals(expectedValue, body);
+    }
 }