kbss-cvut · blcham · Jun 6, 2024 · Jun 5, 2024 · Jun 6, 2024
diff --git a/pom.xml b/pom.xml
@@ -15,39 +15,13 @@
     <name>OFN Record Manager</name>
     <packaging>jar</packaging>
 
-    <!-- The snapshot repositories are necessary only for JOPA 2.0.0-SNAPSHOT -->
-    <repositories>
-        <repository>
-            <id>central-snapshots</id>
-            <url>https://oss.sonatype.org/content/repositories/snapshots</url>
-            <releases>
-                <enabled>false</enabled>
-            </releases>
-            <snapshots>
-                <enabled>true</enabled>
-            </snapshots>
-        </repository>
-    </repositories>
-    <pluginRepositories>
-        <pluginRepository>
-            <id>central-snapshots</id>
-            <url>https://oss.sonatype.org/content/repositories/snapshots</url>
-            <releases>
-                <enabled>false</enabled>
-            </releases>
-            <snapshots>
-                <enabled>true</enabled>
-            </snapshots>
-        </pluginRepository>
-    </pluginRepositories>
-
     <properties>
         <project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
         <jdk.version>17</jdk.version>
         <maven.compiler.source>${jdk.version}</maven.compiler.source>
         <maven.compiler.target>${jdk.version}</maven.compiler.target>
 
-        <cz.cvut.kbss.jopa.version>2.0.0-SNAPSHOT</cz.cvut.kbss.jopa.version>
+        <cz.cvut.kbss.jopa.version>2.0.0</cz.cvut.kbss.jopa.version>
         <org.mockito.version>4.11.0</org.mockito.version>
         <org.mapstruct.version>1.5.5.Final</org.mapstruct.version>
     </properties>
@@ -101,7 +75,7 @@
         <dependency>
             <groupId>com.github.ledsoft</groupId>
             <artifactId>jopa-spring-transaction</artifactId>
-            <version>0.3.0-SNAPSHOT</version>
+            <version>0.3.0</version>
         </dependency>
 
         <!-- Logging -->

diff --git a/src/main/java/cz/cvut/kbss/study/config/WebAppConfig.java b/src/main/java/cz/cvut/kbss/study/config/WebAppConfig.java
@@ -5,10 +5,8 @@
 import com.fasterxml.jackson.databind.ObjectMapper;
 import com.fasterxml.jackson.databind.SerializationFeature;
 import com.fasterxml.jackson.datatype.jsr310.JavaTimeModule;
-import cz.cvut.kbss.jopa.sessions.UnitOfWorkImpl;
 import cz.cvut.kbss.study.rest.servlet.DiagnosticsContextFilter;
 import cz.cvut.kbss.study.util.Constants;
-import cz.cvut.kbss.study.util.json.ManageableIgnoreMixin;
 import org.springframework.boot.web.servlet.FilterRegistrationBean;
 import org.springframework.context.annotation.Bean;
 import org.springframework.context.annotation.Configuration;
@@ -46,8 +44,6 @@ public static ObjectMapper createJsonObjectMapper() {
         final ObjectMapper objectMapper = new ObjectMapper();
         objectMapper.setSerializationInclusion(JsonInclude.Include.NON_NULL);
         objectMapper.configure(DeserializationFeature.FAIL_ON_UNKNOWN_PROPERTIES, false);
-        // Ignore UoW references injected into entities
-        objectMapper.addMixIn(UnitOfWorkImpl.class, ManageableIgnoreMixin.class);
         // JSR 310 (Java 8 DateTime API)
         objectMapper.registerModule(new JavaTimeModule());
         // Serialize datetime as ISO strings

diff --git a/src/main/java/cz/cvut/kbss/study/persistence/dao/PatientRecordDao.java b/src/main/java/cz/cvut/kbss/study/persistence/dao/PatientRecordDao.java
@@ -240,6 +240,7 @@ private <T> Page<T> findRecords(RecordFilterParams filters, Pageable pageSpec, C
     private void setQueryParameters(TypedQuery<?> query, Map<String, Object> queryParams) {
         query.setParameter("type", typeUri)
              .setParameter("hasPhase", URI.create(Vocabulary.s_p_has_phase))
+            .setParameter("hasFormTemplate", URI.create(Vocabulary.s_p_has_form_template))
              .setParameter("hasInstitution",
                            URI.create(Vocabulary.s_p_was_treated_at))
              .setParameter("hasKey", URI.create(Vocabulary.s_p_key))
@@ -256,6 +257,7 @@ private static String constructWhereClause(RecordFilterParams filters, Map<Strin
                 "?hasInstitution ?institution . " +
                 "?institution ?hasKey ?institutionKey ." +
                 "OPTIONAL { ?r ?hasPhase ?phase . } " +
+                "OPTIONAL { ?r ?hasFormTemplate ?formTemplate . } " +
                 "OPTIONAL { ?r ?hasLastModified ?lastModified . } " +
                 "BIND (COALESCE(?lastModified, ?created) AS ?date) ";
         whereClause += mapParamsToQuery(filters, queryParams);
@@ -280,6 +282,11 @@ private static String mapParamsToQuery(RecordFilterParams filterParams, Map<Stri
             queryParams.put("phases",
                             filterParams.getPhaseIds().stream().map(URI::create).collect(Collectors.toList()));
         }
+        if (!filterParams.getFormTemplateIds().isEmpty()) {
+            filters.add("FILTER (?formTemplate in (?formTemplates))");
+            queryParams.put("formTemplates",
+                filterParams.getFormTemplateIds().stream().map(id -> new LangString(id, Constants.PU_LANGUAGE)).collect(Collectors.toList()));
+        }
         return String.join(" ", filters);
     }
 

diff --git a/src/main/java/cz/cvut/kbss/study/persistence/dao/util/RecordFilterParams.java b/src/main/java/cz/cvut/kbss/study/persistence/dao/util/RecordFilterParams.java
@@ -17,6 +17,8 @@ public class RecordFilterParams {
 
     private LocalDate maxModifiedDate = LocalDate.now();
 
+    private Set<String> formTemplateIds = Collections.emptySet();
+
     private Set<String> phaseIds = Collections.emptySet();
 
     public RecordFilterParams() {
@@ -28,11 +30,12 @@ public RecordFilterParams(String institutionKey) {
 
     // This one mainly is for test data setup
     public RecordFilterParams(String institutionKey, LocalDate minModifiedDate, LocalDate maxModifiedDate,
-                              Set<String> phaseIds) {
+                              Set<String> phaseIds, Set<String> formTemplateIds) {
         this.institutionKey = institutionKey;
         this.minModifiedDate = minModifiedDate;
         this.maxModifiedDate = maxModifiedDate;
         this.phaseIds = phaseIds;
+        this.formTemplateIds = formTemplateIds;
     }
 
     public Optional<String> getInstitutionKey() {
@@ -59,6 +62,14 @@ public void setMaxModifiedDate(LocalDate maxModifiedDate) {
         this.maxModifiedDate = maxModifiedDate;
     }
 
+    public Set<String> getFormTemplateIds() {
+        return formTemplateIds;
+    }
+
+    public void setFormTemplateIds(Set<String> formTemplateIds) {
+        this.formTemplateIds = formTemplateIds;
+    }
+
     public Set<String> getPhaseIds() {
         return phaseIds;
     }
@@ -78,12 +89,13 @@ public boolean equals(Object o) {
         return Objects.equals(institutionKey, that.institutionKey)
                 && Objects.equals(minModifiedDate, that.minModifiedDate)
                 && Objects.equals(maxModifiedDate, that.maxModifiedDate)
+                && Objects.equals(formTemplateIds, that.formTemplateIds)
                 && Objects.equals(phaseIds, that.phaseIds);
     }
 
     @Override
     public int hashCode() {
-        return Objects.hash(institutionKey, minModifiedDate, maxModifiedDate, phaseIds);
+        return Objects.hash(institutionKey, minModifiedDate, maxModifiedDate, formTemplateIds, phaseIds);
     }
 
     @Override
@@ -92,6 +104,7 @@ public String toString() {
                 "institutionKey='" + institutionKey + '\'' +
                 ", minModifiedDate=" + minModifiedDate +
                 ", maxModifiedDate=" + maxModifiedDate +
+                ", formTemplateIds=" + formTemplateIds +
                 ", phaseIds=" + phaseIds +
                 '}';
     }

diff --git a/src/main/java/cz/cvut/kbss/study/rest/util/RecordFilterMapper.java b/src/main/java/cz/cvut/kbss/study/rest/util/RecordFilterMapper.java
@@ -3,6 +3,7 @@
 import cz.cvut.kbss.study.model.RecordPhase;
 import cz.cvut.kbss.study.persistence.dao.util.RecordFilterParams;
 import cz.cvut.kbss.study.rest.exception.BadRequestException;
+import java.util.HashSet;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 import org.springframework.util.LinkedMultiValueMap;
@@ -30,6 +31,8 @@ public class RecordFilterMapper {
 
     private static final String INSTITUTION_KEY_PARAM = "institution";
 
+    private static final String FORM_TEMPLATE_ID_PARAM = "formTemplate";
+
     private static final String PHASE_ID_PARAM = "phase";
 
     /**
@@ -69,6 +72,10 @@ public static RecordFilterParams constructRecordFilter(MultiValueMap<String, Str
         getSingleValue(INSTITUTION_KEY_PARAM, params).ifPresent(result::setInstitutionKey);
         result.setPhaseIds(params.getOrDefault(PHASE_ID_PARAM, Collections.emptyList()).stream()
                                  .map(s -> RecordPhase.fromIriOrName(s).getIri()).collect(Collectors.toSet()));
+
+        result.setFormTemplateIds(
+            new HashSet<>(params.getOrDefault(FORM_TEMPLATE_ID_PARAM, Collections.emptyList()))
+        );
         return result;
     }
 

diff --git a/src/test/java/cz/cvut/kbss/study/persistence/dao/PatientRecordDaoTest.java b/src/test/java/cz/cvut/kbss/study/persistence/dao/PatientRecordDaoTest.java
@@ -277,7 +277,7 @@ void findAllFullReturnsRecordsMatchingSpecifiedDatePeriod() {
         }).toList();
 
         final Page<PatientRecord> result =
-                sut.findAllRecordsFull(new RecordFilterParams(null, minDate, maxDate, Collections.emptySet()),
+                sut.findAllRecordsFull(new RecordFilterParams(null, minDate, maxDate, Collections.emptySet(), Collections.emptySet()),
                                        Pageable.unpaged());
         assertFalse(result.isEmpty());
         assertThat(result.getContent(), containsSameEntities(expected));
@@ -316,7 +316,7 @@ void findAllFullReturnsRecordsMatchingSpecifiedDatePeriodAndInstitution() {
         }).toList();
 
         final Page<PatientRecord> result =
-                sut.findAllRecordsFull(new RecordFilterParams(institution.getKey(), minDate, maxDate, Collections.emptySet()),
+                sut.findAllRecordsFull(new RecordFilterParams(institution.getKey(), minDate, maxDate, Collections.emptySet(), Collections.emptySet()),
                                        Pageable.unpaged());
         assertFalse(result.isEmpty());
         assertThat(result.getContent(), containsSameEntities(expected));
@@ -327,7 +327,7 @@ void findAllFullReturnsRecordsMatchingSpecifiedPhase() {
         final User author = generateAuthorWithInstitution();
         final List<PatientRecord> allRecords = generateRecordsForAuthor(author, 5);
         transactional(() -> allRecords.forEach(r -> {
-            r.setPhase(RecordPhase.values()[Generator.randomInt(RecordPhase.values().length)]);
+            r.setPhase(RecordPhase.values()[Generator.randomInt(0, RecordPhase.values().length)]);
             persistRecordWithIdentification(r);
         }));
         final RecordPhase phase = allRecords.get(Generator.randomIndex(allRecords)).getPhase();
@@ -339,6 +339,28 @@ void findAllFullReturnsRecordsMatchingSpecifiedPhase() {
         result.forEach(res -> assertEquals(phase, res.getPhase()));
     }
 
+    @Test
+    void findAllFullReturnsRecordsMatchingSpecifiedFormTemplate() {
+        String[] formTemplates = new String[]{
+            "http://example.org/form-template-1",
+            "http://example.org/form-template-2"
+        };
+        final User author = generateAuthorWithInstitution();
+        final List<PatientRecord> allRecords = generateRecordsForAuthor(author, 5);
+        transactional(() -> allRecords.forEach(r -> {
+            r.setFormTemplate(formTemplates[Generator.randomInt(0, formTemplates.length)]);
+            persistRecordWithIdentification(r);
+        }));
+        final String formTemplate = allRecords.get(Generator.randomIndex(allRecords)).getFormTemplate();
+        final RecordFilterParams filterParams = new RecordFilterParams();
+        filterParams.setFormTemplateIds(Set.of(formTemplate));
+
+        final Page<PatientRecord> result = sut.findAllRecordsFull(filterParams, Pageable.unpaged());
+        assertFalse(result.isEmpty());
+        result.forEach(res -> assertEquals(formTemplate, res.getFormTemplate()));
+    }
+
+
     @Test
     void findAllFullReturnsRecordsMatchingSpecifiedPage() {
         final User author = generateAuthorWithInstitution();
@@ -408,7 +430,7 @@ void findAllRecordsReturnsPageWithMatchingRecords() {
         final int pageSize = 3;
 
         final Page<PatientRecordDto> result =
-                sut.findAllRecords(new RecordFilterParams(null, minDate, maxDate, Collections.emptySet()),
+                sut.findAllRecords(new RecordFilterParams(null, minDate, maxDate, Collections.emptySet(), Collections.emptySet()),
                                        PageRequest.of(0, pageSize, Sort.Direction.ASC, RecordSort.SORT_DATE_PROPERTY));
         assertEquals(Math.min(pageSize, allMatching.size()), result.getNumberOfElements());
         assertEquals(allMatching.size(), result.getTotalElements());

diff --git a/src/test/java/cz/cvut/kbss/study/rest/PatientRecordControllerTest.java b/src/test/java/cz/cvut/kbss/study/rest/PatientRecordControllerTest.java
@@ -263,7 +263,7 @@ void exportRecordsParsesProvidedDateBoundsAndPassesThemToService() throws Except
         });
         assertThat(result, containsSameEntities(records));
         verify(patientRecordServiceMock).findAllFull(
-                new RecordFilterParams(null, minDate, maxDate, Collections.emptySet()), Pageable.unpaged());
+                new RecordFilterParams(null, minDate, maxDate, Collections.emptySet(), Collections.emptySet()), Pageable.unpaged());
     }
 
     @Test
@@ -298,7 +298,7 @@ void exportRecordsExportsRecordsForProvidedInstitutionForSpecifiedPeriod() throw
         });
         assertThat(result, containsSameEntities(records));
         verify(patientRecordServiceMock).findAllFull(
-                new RecordFilterParams(user.getInstitution().getKey(), minDate, maxDate, Collections.emptySet()),
+                new RecordFilterParams(user.getInstitution().getKey(), minDate, maxDate, Collections.emptySet(), Collections.emptySet()),
                 Pageable.unpaged());
     }
 
@@ -369,7 +369,7 @@ void getRecordsResolvesPagingConfigurationFromRequestParameters() throws Excepti
         });
         assertThat(result, containsSameEntities(records));
         verify(patientRecordServiceMock).findAllFull(
-                new RecordFilterParams(null, minDate, maxDate, Collections.emptySet()),
+                new RecordFilterParams(null, minDate, maxDate, Collections.emptySet(), Collections.emptySet()),
                 PageRequest.of(page, pageSize, Sort.Direction.DESC, RecordSort.SORT_DATE_PROPERTY));
     }
 
@@ -417,7 +417,7 @@ void exportRecordsPublishesPagingEvent() throws Exception {
         });
         assertThat(result, containsSameEntities(records));
         verify(patientRecordServiceMock).findAllFull(
-                new RecordFilterParams(null, minDate, maxDate, Collections.emptySet()), PageRequest.of(0, 50));
+                new RecordFilterParams(null, minDate, maxDate, Collections.emptySet(), Collections.emptySet()), PageRequest.of(0, 50));
         final ArgumentCaptor<PaginatedResultRetrievedEvent> captor =
                 ArgumentCaptor.forClass(PaginatedResultRetrievedEvent.class);
         verify(eventPublisherMock).publishEvent(captor.capture());

diff --git a/src/test/java/cz/cvut/kbss/study/rest/util/RecordFilterMapperTest.java b/src/test/java/cz/cvut/kbss/study/rest/util/RecordFilterMapperTest.java
@@ -30,27 +30,27 @@ static Stream<Arguments> testValues() {
                 Arguments.of(new LinkedMultiValueMap<>(Map.of(
                         "minDate", List.of(LocalDate.now().minusYears(1).toString())
                 )), new RecordFilterParams(null, LocalDate.now().minusYears(1), LocalDate.now(),
-                                           Collections.emptySet())),
+                                           Collections.emptySet(), Collections.emptySet())),
                 Arguments.of(new LinkedMultiValueMap<>(Map.of(
                         "minDate", List.of(LocalDate.now().minusYears(1).toString()),
                         "maxDate", List.of(LocalDate.now().minusDays(1).toString())
                 )), new RecordFilterParams(null, LocalDate.now().minusYears(1), LocalDate.now().minusDays(1),
-                                           Collections.emptySet())),
+                                           Collections.emptySet(), Collections.emptySet())),
                 Arguments.of(new LinkedMultiValueMap<>(Map.of(
                         "institution", List.of("1111111")
-                )), new RecordFilterParams("1111111", LocalDate.EPOCH, LocalDate.now(), Collections.emptySet())),
+                )), new RecordFilterParams("1111111", LocalDate.EPOCH, LocalDate.now(), Collections.emptySet(), Collections.emptySet())),
                 Arguments.of(new LinkedMultiValueMap<>(Map.of(
                         "institution", List.of("1111111"),
                         "phase", List.of(RecordPhase.open.getIri(), RecordPhase.completed.name())
                 )), new RecordFilterParams("1111111", LocalDate.EPOCH, LocalDate.now(),
-                                           Set.of(RecordPhase.open.getIri(), RecordPhase.completed.getIri()))),
+                                           Set.of(RecordPhase.open.getIri(), RecordPhase.completed.getIri()), Collections.emptySet())),
                 Arguments.of(new LinkedMultiValueMap<>(Map.of(
                         "minDate", List.of(LocalDate.now().minusYears(1).toString()),
                         "maxDate", List.of(LocalDate.now().minusDays(1).toString()),
                         "institution", List.of("1111111"),
                         "phase", List.of(RecordPhase.published.name())
                 )), new RecordFilterParams("1111111", LocalDate.now().minusYears(1), LocalDate.now().minusDays(1),
-                                           Set.of(RecordPhase.published.getIri())))
+                                           Set.of(RecordPhase.published.getIri()), Collections.emptySet()))
         );
     }
 }