Merge pull request #232 from medizininformatik-initiative/release/v4.1.0

Release/v4.1.0

CHANGELOG.md

@@ -4,6 +4,32 @@ All notable changes to this project will be documented in this file.
 
 The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/),
 
+## [UNRELEASED] - yyyy-mm-dd
+
+### Added
+### Changed
+### Deprecated
+### Removed
+### Fixed
+### Security
+
+The full changelog can be found [here](https://todo).
+
+## [4.1.0] - 2023-11-09
+
+### Added
+- Make order of main categories configurable ([#219](https://github.com/medizininformatik-initiative/feasibility-backend/issues/219))
+- Save and load query results for saved queries ([#199](https://github.com/medizininformatik-initiative/feasibility-backend/issues/199))
+- Support CRUD for query templates ([#214](https://github.com/medizininformatik-initiative/feasibility-backend/issues/214))
+
+### Fixed
+- Fix code scanning alert - parser confusion leads to OOM ([#221](https://github.com/medizininformatik-initiative/feasibility-backend/issues/221))
+- Fix code scanning alert - Missing Override annotation ([#223](https://github.com/medizininformatik-initiative/feasibility-backend/issues/223))
+- Fix code scanning alert - Unread local variable ([#222](https://github.com/medizininformatik-initiative/feasibility-backend/issues/222))
+
+### Security
+- Update Spring Boot to 3.1.5 ([#227](https://github.com/medizininformatik-initiative/feasibility-backend/issues/227))
+
 ## [4.0.0] - 2023-10-06
 
 ### Added

docker-compose.yml

@@ -35,6 +35,7 @@ services:
       API_BASE_URL: ${CODEX_FEASIBILITY_BACKEND_API_BASE_URL:-}
       QUERY_VALIDATION_ENABLED: ${CODEX_FEASIBILITY_BACKEND_QUERY_VALIDATION_ENABLED:-true}
       QUERYRESULT_EXPIRY_MINUTES: ${CODEX_FEASIBILITY_BACKEND_QUERYRESULT_EXPIRY_MINUTES:-5}
+      MAX_SAVED_QUERIES_PER_USER: ${CODEX_FEASIBILITY_BACKEND_MAX_SAVED_QUERIES_PER_USER:-10}
       # ---- Direct
       BROKER_CLIENT_DIRECT_USE_CQL: ${CODEX_FEASIBILITY_BACKEND_BROKER_CLIENT_DIRECT_USE_CQL:-false}
       BROKER_CLIENT_OBFUSCATE_RESULT_COUNT: ${CODEX_FEASIBILITY_BACKEND_BROKER_CLIENT_OBFUSCATE_RESULT_COUNT:-false}

pom.xml

@@ -5,13 +5,13 @@
   <parent>
     <groupId>org.springframework.boot</groupId>
     <artifactId>spring-boot-starter-parent</artifactId>
-    <version>3.1.3</version>
+    <version>3.1.5</version>
     <relativePath /> <!-- lookup parent from repository -->
   </parent>
 
   <groupId>de.medizininformatik-initiative</groupId>
   <artifactId>FeasibilityGuiBackend</artifactId>
-  <version>4.0.0</version>
+  <version>4.1.0</version>
 
   <name>FeasibilityGuiBackend</name>
   <description>Backend of the Feasibility GUI</description>
@@ -26,7 +26,7 @@
     <java.version>17</java.version>
     <mockwebserver.version>4.10.0</mockwebserver.version>
     <okhttp3.version>4.10.0</okhttp3.version>
-    <ontology-tag>v2.1.13-RC</ontology-tag>
+    <ontology-tag>v2.1.24</ontology-tag>
   </properties>
 
   <dependencies>
@@ -124,7 +124,7 @@
     <dependency>
       <groupId>org.json</groupId>
       <artifactId>json</artifactId>
-      <version>20230227</version>
+      <version>20231013</version>
     </dependency>
 
     <dependency>
@@ -198,7 +198,7 @@
     <dependency>
       <groupId>de.medizininformatik-initiative</groupId>
       <artifactId>sq2cql</artifactId>
-      <version>0.2.0-alpha.1</version>
+      <version>0.2.0</version>
     </dependency>
 
     <dependency>

src/main/java/de/numcodex/feasibility_gui_backend/query/QueryHandlerService.java

@@ -21,10 +21,11 @@
 import org.springframework.transaction.annotation.Transactional;
 import reactor.core.publisher.Mono;
 
+import java.sql.Timestamp;
+import java.time.Instant;
 import java.util.ArrayList;
 import java.util.List;
 import java.util.Optional;
-import java.util.UUID;
 
 @Service
 @RequiredArgsConstructor
@@ -126,6 +127,17 @@ public Long saveQuery(Long queryId, String userId, SavedQuery savedQueryApi) {
         return savedQueryRepository.save(savedQuery).getId();
     }
 
+    public void updateSavedQuery(Long queryId, SavedQuery savedQuery) throws QueryNotFoundException {
+        Optional<de.numcodex.feasibility_gui_backend.query.persistence.SavedQuery> savedQueryOptional = savedQueryRepository.findByQueryId(queryId);
+        if (savedQueryOptional.isEmpty()) {
+            throw new QueryNotFoundException();
+        }
+        var oldSavedQuery = savedQueryOptional.get();
+        oldSavedQuery.setLabel(savedQuery.label());
+        oldSavedQuery.setComment(savedQuery.comment());
+        savedQueryRepository.save(oldSavedQuery);
+    }
+
     public de.numcodex.feasibility_gui_backend.query.persistence.QueryTemplate getQueryTemplate(
             Long queryId, String authorId) throws QueryTemplateException {
         de.numcodex.feasibility_gui_backend.query.persistence.QueryTemplate queryTemplate = queryTemplateRepository.findById(
@@ -141,6 +153,36 @@ public List<de.numcodex.feasibility_gui_backend.query.persistence.QueryTemplate>
         return queryTemplateRepository.findByAuthor(authorId);
     }
 
+    public void updateQueryTemplate(Long queryTemplateId, QueryTemplate queryTemplate, String authorId) throws QueryTemplateException {
+        var templates = getQueryTemplatesForAuthor(authorId);
+        Optional<de.numcodex.feasibility_gui_backend.query.persistence.QueryTemplate> templateToUpdate = templates.stream().
+                filter(t -> t.getId().equals(queryTemplateId)).
+                findFirst();
+
+        if (templateToUpdate.isPresent()) {
+            var template = templateToUpdate.get();
+            template.setLabel(queryTemplate.label());
+            template.setComment(queryTemplate.comment());
+            template.setLastModified(Timestamp.from(Instant.now()));
+            queryTemplateRepository.save(template);
+        } else {
+            throw new QueryTemplateException("not found");
+        }
+    }
+
+    public void deleteQueryTemplate(Long queryTemplateId, String authorId) throws QueryTemplateException {
+        var templates = getQueryTemplatesForAuthor(authorId);
+        Optional<de.numcodex.feasibility_gui_backend.query.persistence.QueryTemplate> templateToDelete = templates.stream().
+                filter(t -> t.getId().equals(queryTemplateId)).
+                findFirst();
+
+        if (templateToDelete.isPresent()) {
+            queryTemplateRepository.delete(templateToDelete.get());
+        } else {
+            throw new QueryTemplateException("not found");
+        }
+    }
+
     public QueryTemplate convertTemplatePersistenceToApi(
             de.numcodex.feasibility_gui_backend.query.persistence.QueryTemplate in)
             throws JsonProcessingException {
@@ -172,6 +214,7 @@ private de.numcodex.feasibility_gui_backend.query.persistence.SavedQuery convert
         out.setQuery(queryRepository.getReferenceById(queryId));
         out.setComment(in.comment());
         out.setLabel(in.label());
+        out.setResultSize(in.totalNumberOfPatients());
         return out;
     }
 
@@ -201,6 +244,8 @@ public List<QueryListEntry> convertQueriesToQueryListEntries(List<de.numcodex.fe
                         QueryListEntry.builder()
                                 .id(q.getId())
                                 .label(q.getSavedQuery().getLabel())
+                                .comment(q.getSavedQuery().getComment())
+                                .totalNumberOfPatients(q.getSavedQuery().getResultSize())
                                 .createdAt(q.getCreatedAt())
                                 .build());
             } else {
@@ -220,6 +265,24 @@ public Long getAmountOfQueriesByUserAndInterval(String userId, int minutes) {
     }
 
     public Long getRetryAfterTime(String userId, int offset, long interval) {
-        return 60 * interval - queryRepository.getAgeOfNToLastQueryInSeconds(userId, offset) + 1;
+        try {
+            return 60 * interval - queryRepository.getAgeOfNToLastQueryInSeconds(userId, offset) + 1;
+        } catch (NullPointerException e) {
+            return 0L;
+        }
+    }
+
+    public Long getAmountOfSavedQueriesByUser(String userId) {
+        var queries = queryRepository.findSavedQueriesByAuthor(userId);
+        return queries.map(queryList -> (long) queryList.size()).orElse(0L);
+    }
+
+    public void deleteSavedQuery(Long queryId) throws QueryNotFoundException {
+        var savedQueryOptional = savedQueryRepository.findByQueryId(queryId);
+        if (savedQueryOptional.isPresent()) {
+            savedQueryRepository.deleteById(savedQueryOptional.get().getId());
+        } else {
+            throw new QueryNotFoundException();
+        }
     }
 }

src/main/java/de/numcodex/feasibility_gui_backend/query/api/QueryListEntry.java

@@ -12,7 +12,9 @@
 public record QueryListEntry(
     @JsonProperty long id,
     @JsonProperty String label,
-    @JsonProperty Timestamp createdAt
+    @JsonProperty String comment,
+    @JsonProperty Timestamp createdAt,
+    @JsonProperty Long totalNumberOfPatients
 )  {
 
 }

src/main/java/de/numcodex/feasibility_gui_backend/query/api/SavedQuery.java

@@ -9,7 +9,8 @@
 @Builder
 public record SavedQuery(
     @JsonProperty String label,
-    @JsonProperty String comment
+    @JsonProperty String comment,
+    @JsonProperty Long totalNumberOfPatients
 ) {
 
 }

src/main/java/de/numcodex/feasibility_gui_backend/query/api/status/FeasibilityIssue.java

@@ -12,7 +12,8 @@ public enum FeasibilityIssue {
     QUOTA_EXCEEDED(10002, "Too many requests - quota reached", IssueType.BUSY, Severity.ERROR),
     POLLING_LIMIT_EXCEEDED(10003, "Too many requests - polling limit exceeded", IssueType.BUSY, Severity.ERROR),
     PRIVACY_RESTRICTION_RESULT_SIZE(10004, "Total number of results below threshold", IssueType.BUSY, Severity.ERROR),
-    PRIVACY_RESTRICTION_RESULT_SITES(10005, "Too few responding sites", IssueType.BUSY, Severity.ERROR);
+    PRIVACY_RESTRICTION_RESULT_SITES(10005, "Too few responding sites", IssueType.BUSY, Severity.ERROR),
+    SAVED_QUERY_STORAGE_FULL(10006, "Saved query limit reached. Please delete old saved queries before trying to create new ones.", IssueType.FORBIDDEN, Severity.ERROR);
 
     private static final FeasibilityIssue[] VALUES;
 

src/main/java/de/numcodex/feasibility_gui_backend/query/api/status/SavedQuerySlots.java

@@ -0,0 +1,14 @@
+package de.numcodex.feasibility_gui_backend.query.api.status;
+
+import com.fasterxml.jackson.annotation.JsonInclude;
+import com.fasterxml.jackson.annotation.JsonProperty;
+import lombok.Builder;
+
+@JsonInclude()
+@Builder
+public record SavedQuerySlots(
+        @JsonProperty("used") long used,
+        @JsonProperty("total") long total
+)
+{
+}

src/main/java/de/numcodex/feasibility_gui_backend/query/broker/direct/DirectBrokerClient.java

@@ -78,6 +78,7 @@ public List<String> getResultSiteIds(String brokerQueryId) throws QueryNotFoundE
     return findQuery(brokerQueryId).hasResult() ? Collections.singletonList(SITE_ID_LOCAL) : Collections.emptyList();
   }
 
+  @Override
   public String getSiteName(String siteId) throws SiteNotFoundException {
     if (SITE_ID_LOCAL.equals(siteId)) {
       return SITE_NAME_LOCAL;

src/main/java/de/numcodex/feasibility_gui_backend/query/persistence/Query.java

@@ -27,7 +27,7 @@ public class Query {
     @Column(name = "created_by", updatable = false)
     private String createdBy;
 
-    @ManyToOne(fetch = FetchType.LAZY)
+    @ManyToOne(fetch = FetchType.LAZY, cascade = CascadeType.ALL)
     @JoinColumn(referencedColumnName = "id", name = "query_content_id")
     private QueryContent queryContent;
 

src/main/java/de/numcodex/feasibility_gui_backend/query/persistence/SavedQuery.java

@@ -23,12 +23,12 @@ public class SavedQuery {
   @OneToOne(fetch = FetchType.LAZY)
   private Query query;
 
-  @Column(name = "deleted")
-  private Timestamp deleted;
-
   @Column(name = "label", nullable = false)
   private String label;
 
   @Column(name = "comment")
   private String comment;
+
+  @Column(name = "result_size")
+  private Long resultSize;
 }

src/main/java/de/numcodex/feasibility_gui_backend/query/translation/QueryTranslatorSpringConfig.java

@@ -103,6 +103,7 @@ Translator createCqlTranslator(@Qualifier("translation") ObjectMapper jsonUtil)
                     "frailtyscore"),
                 entry("http://terminology.hl7.org/CodeSystem/consentcategorycodes", "consentcategory"),
                 entry("urn:oid:2.16.840.1.113883.3.1937.777.24.5.3", "consent"),
+                entry("http://hl7.org/fhir/sid/icd-o-3", "icdo3"),
                 entry("http://hl7.org/fhir/consent-provision-type", "provisiontype"))));
     }