Merge pull request medizininformatik-initiative#272 from medizininfor…

…matik-initiative/release/v5.0.0-alpha.1 Release v5.0.0 alpha.1
geloro94 · Apr 3, 2024 · d96691a · d96691a
2 parents 7487cbc + 21d9d3a
commit d96691a
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diff --git a/.github/integration-test/docker-compose.yml b/.github/integration-test/docker-compose.yml
@@ -90,7 +90,7 @@ services:
       - "blaze-data:/app/data"
 
   flare:
-    image: ghcr.io/medizininformatik-initiative/flare:2.0.0-rc2
+    image: ghcr.io/medizininformatik-initiative/flare:2.1.1
     ports:
       - "8092:8080"
     environment:

diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
@@ -15,27 +15,27 @@ jobs:
   tests:
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
 
       - name: Set up JDK 17
-        uses: actions/setup-java@v3
+        uses: actions/setup-java@v4
         with:
           distribution: 'temurin'
           java-version: 17
 
       - name: Cache Local Maven Repo
-        uses: actions/cache@v3
+        uses: actions/cache@v4
         with:
           path: ~/.m2/repository
           key: tests-maven-${{ hashFiles('pom.xml') }}
 
-      - uses: s4u/maven-settings-action@v2.8.0
+      - uses: s4u/maven-settings-action@v3.0.0
         with:
           servers: |
             [{"id": "mii", "username": "${{ github.actor }}", "password": "${{ secrets.GITHUB_TOKEN }}"}]
 
       - name: Initialize CodeQL
-        uses: github/codeql-action/init@v2
+        uses: github/codeql-action/init@v3
         with:
           languages: java
           queries: security-and-quality
@@ -44,53 +44,55 @@ jobs:
         run: mvn -Pdownload-ontology -B verify
 
       - name: Upload coverage to Codecov
-        uses: codecov/codecov-action@v3
+        uses: codecov/codecov-action@v4
+        env:
+          CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}
         with:
           fail_ci_if_error: true
 
       - name: Perform CodeQL Analysis
-        uses: github/codeql-action/analyze@v2
+        uses: github/codeql-action/analyze@v3
 
       - name: Upload Feasibility Backend Jar
-        uses: actions/upload-artifact@v3
+        uses: actions/upload-artifact@v4
         with:
           name: backend-jar
           path: target/feasibilityBackend.jar
 
       - name: Set up Docker Buildx
-        uses: docker/setup-buildx-action@v2
+        uses: docker/setup-buildx-action@v3
 
       - name: Build and Export to Docker
-        uses: docker/build-push-action@v4
+        uses: docker/build-push-action@v5
         with:
           context: .
           tags: backend:latest
           outputs: type=docker,dest=/tmp/feasibilityBackend.tar
 
       - name: Upload Feasibility Backend Image
-        uses: actions/upload-artifact@v3
+        uses: actions/upload-artifact@v4
         with:
           name: backend-image
           path: /tmp/feasibilityBackend.tar
 
   security-scan:
     runs-on: ubuntu-latest
     steps:
-    - uses: actions/checkout@v3
+    - uses: actions/checkout@v4
 
     - name: Set up JDK 17
-      uses: actions/setup-java@v3
+      uses: actions/setup-java@v4
       with:
         distribution: 'zulu'
         java-version: 17
 
     - name: Cache Local Maven Repo
-      uses: actions/cache@v3
+      uses: actions/cache@v4
       with:
         path: ~/.m2/repository
         key: security-scan-maven-${{ hashFiles('pom.xml') }}
 
-    - uses: s4u/maven-settings-action@v2.8.0
+    - uses: s4u/maven-settings-action@v3.0.0
       with:
         servers: |
           [{"id": "mii", "username": "${{ github.actor }}", "password": "${{ secrets.GITHUB_TOKEN }}"}]
@@ -99,7 +101,7 @@ jobs:
       run: mvn -Pdownload-ontology -B -DskipTests package
 
     - name: Build and push Docker image
-      uses: docker/build-push-action@v4
+      uses: docker/build-push-action@v5
       with:
         context: .
         tags: security-scan-build:latest
@@ -115,7 +117,7 @@ jobs:
         timeout: '15m0s'
 
     - name: Upload Trivy Scan Results to GitHub Security Tab
-      uses: github/codeql-action/upload-sarif@v2
+      uses: github/codeql-action/upload-sarif@v3
       with:
         sarif_file: trivy-results.sarif
 
@@ -125,10 +127,10 @@ jobs:
 
     steps:
       - name: Check out Git repository
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
 
       - name: Download Feasibility Backend Image
-        uses: actions/download-artifact@v3
+        uses: actions/download-artifact@v4
         with:
           name: backend-image
           path: /tmp
@@ -181,21 +183,21 @@ jobs:
       - security-scan
     runs-on: ubuntu-latest
     steps:
-    - uses: actions/checkout@v3
+    - uses: actions/checkout@v4
 
     - name: Set up JDK 17
-      uses: actions/setup-java@v3
+      uses: actions/setup-java@v4
       with:
         distribution: 'temurin'
         java-version: 17
 
     - name: Cache Local Maven Repo
-      uses: actions/cache@v3
+      uses: actions/cache@v4
       with:
         path: ~/.m2/repository
         key: release-maven-${{ hashFiles('pom.xml') }}
 
-    - uses: s4u/maven-settings-action@v2.8.0
+    - uses: s4u/maven-settings-action@v3.0.0
       with:
         servers: |
           [{"id": "mii", "username": "${{ github.actor }}", "password": "${{ secrets.GITHUB_TOKEN }}"}]
@@ -220,10 +222,10 @@ jobs:
       uses: docker/setup-qemu-action@v1
 
     - name: Set up Docker Buildx
-      uses: docker/setup-buildx-action@v1
+      uses: docker/setup-buildx-action@v3
 
     - name: Build and push Docker image
-      uses: docker/build-push-action@v4
+      uses: docker/build-push-action@v5
       with:
         context: .
         platforms: linux/amd64,linux/arm64

diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -4,6 +4,20 @@ 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/),
 
+## [5.0.0-alpha.1] - 2024-04-03
+
+### Added
+- Added an endpoint to validate uploaded structured queries. ([#258](https://github.com/medizininformatik-initiative/feasibility-backend/issues/258))
+### Changed
+- Validation for structured queries has been reworked. ([#260](https://github.com/medizininformatik-initiative/feasibility-backend/issues/260)), ([#266](https://github.com/medizininformatik-initiative/feasibility-backend/issues/266))
+### Deprecated
+### Removed
+### Fixed
+### Security
+- Updated spring boot to 3.2.4 ([#262](https://github.com/medizininformatik-initiative/feasibility-backend/issues/262))
+
+The full changelog can be found [here](https://github.com/medizininformatik-initiative/feasibility-backend/milestone/9?closed=1).
+
 ## [4.3.0] - 2024-02-02
 
 ### Added

diff --git a/pom.xml b/pom.xml
@@ -5,13 +5,13 @@
   <parent>
     <groupId>org.springframework.boot</groupId>
     <artifactId>spring-boot-starter-parent</artifactId>
-    <version>3.2.2</version>
+    <version>3.2.4</version>
     <relativePath /> <!-- lookup parent from repository -->
   </parent>
 
   <groupId>de.medizininformatik-initiative</groupId>
   <artifactId>FeasibilityGuiBackend</artifactId>
-  <version>4.3.0</version>
+  <version>5.0.0-alpha.1</version>
 
   <name>FeasibilityGuiBackend</name>
   <description>Backend of the Feasibility GUI</description>
@@ -236,7 +236,15 @@
     <dependency>
       <groupId>org.testcontainers</groupId>
       <artifactId>testcontainers</artifactId>
-      <version>1.17.6</version>
+      <version>1.19.7</version>
+      <scope>test</scope>
+    </dependency>
+
+    <!-- Remove when testcontainers uses a version > 1.24 -->
+    <dependency>
+      <groupId>org.apache.commons</groupId>
+      <artifactId>commons-compress</artifactId>
+      <version>1.26.1</version>
       <scope>test</scope>
     </dependency>
 

diff --git a/src/main/java/de/numcodex/feasibility_gui_backend/common/api/Criterion.java b/src/main/java/de/numcodex/feasibility_gui_backend/common/api/Criterion.java
@@ -6,6 +6,7 @@
 import de.numcodex.feasibility_gui_backend.query.api.AttributeFilter;
 import de.numcodex.feasibility_gui_backend.query.api.TimeRestriction;
 import de.numcodex.feasibility_gui_backend.query.api.ValueFilter;
+import de.numcodex.feasibility_gui_backend.query.api.status.ValidationIssue;
 import lombok.Builder;
 
 import java.util.List;
@@ -17,7 +18,17 @@ public record Criterion (
     @JsonProperty("termCodes") List<TermCode> termCodes,
     @JsonProperty("attributeFilters") List<AttributeFilter> attributeFilters,
     @JsonProperty("valueFilter") ValueFilter valueFilter,
-    @JsonProperty("timeRestriction") TimeRestriction timeRestriction
+    @JsonProperty("timeRestriction") TimeRestriction timeRestriction,
+    @JsonProperty("issues") List<ValidationIssue> validationIssues
 ) {
-
+  public static Criterion createImmutableCriterion(MutableCriterion mutableCriterion) {
+    return Criterion.builder()
+        .termCodes(mutableCriterion.termCodes)
+        .context(mutableCriterion.context)
+        .attributeFilters(mutableCriterion.attributeFilters)
+        .valueFilter(mutableCriterion.valueFilter)
+        .timeRestriction(mutableCriterion.timeRestriction)
+        .validationIssues(mutableCriterion.validationIssues)
+        .build();
+  }
 }
diff --git a/src/main/java/de/numcodex/feasibility_gui_backend/common/api/MutableCriterion.java b/src/main/java/de/numcodex/feasibility_gui_backend/common/api/MutableCriterion.java
@@ -0,0 +1,36 @@
+package de.numcodex.feasibility_gui_backend.common.api;
+
+import com.fasterxml.jackson.annotation.JsonInclude;
+import com.fasterxml.jackson.annotation.JsonInclude.Include;
+import com.fasterxml.jackson.annotation.JsonProperty;
+import de.numcodex.feasibility_gui_backend.query.api.AttributeFilter;
+import de.numcodex.feasibility_gui_backend.query.api.TimeRestriction;
+import de.numcodex.feasibility_gui_backend.query.api.ValueFilter;
+import de.numcodex.feasibility_gui_backend.query.api.status.ValidationIssue;
+import lombok.Builder;
+import lombok.Data;
+
+import java.util.List;
+
+@JsonInclude(Include.NON_NULL)
+@Builder
+@Data
+public class MutableCriterion {
+    @JsonProperty("context") TermCode context;
+    @JsonProperty("termCodes") List<TermCode> termCodes;
+    @JsonProperty("attributeFilters") List<AttributeFilter> attributeFilters;
+    @JsonProperty("valueFilter") ValueFilter valueFilter;
+    @JsonProperty("timeRestriction") TimeRestriction timeRestriction;
+    @JsonProperty("issues") List<ValidationIssue> validationIssues;
+
+    public static MutableCriterion createMutableCriterion (Criterion criterion) {
+      return MutableCriterion.builder()
+          .termCodes(criterion.termCodes())
+          .context(criterion.context())
+          .attributeFilters(criterion.attributeFilters())
+          .valueFilter(criterion.valueFilter())
+          .timeRestriction(criterion.timeRestriction())
+          .validationIssues(criterion.validationIssues())
+          .build();
+    }
+}
diff --git a/src/main/java/de/numcodex/feasibility_gui_backend/query/QueryHandlerService.java b/src/main/java/de/numcodex/feasibility_gui_backend/query/QueryHandlerService.java
@@ -14,6 +14,7 @@
 import de.numcodex.feasibility_gui_backend.query.result.ResultService;
 import de.numcodex.feasibility_gui_backend.query.templates.QueryTemplateException;
 import de.numcodex.feasibility_gui_backend.query.templates.QueryTemplateHandler;
+import de.numcodex.feasibility_gui_backend.terminology.validation.StructuredQueryValidation;
 import lombok.NonNull;
 import lombok.RequiredArgsConstructor;
 import org.springframework.dao.DataIntegrityViolationException;
@@ -58,6 +59,9 @@ public enum ResultDetail {
     @NonNull
     private final SavedQueryRepository savedQueryRepository;
 
+    @NonNull
+    private final StructuredQueryValidation structuredQueryValidation;
+
     @NonNull
     private ObjectMapper jsonUtil;
 
@@ -235,28 +239,61 @@ public String getAuthorId(Long queryId) throws QueryNotFoundException {
         return queryRepository.getAuthor(queryId).orElseThrow(QueryNotFoundException::new);
     }
 
-    public List<QueryListEntry> convertQueriesToQueryListEntries(List<de.numcodex.feasibility_gui_backend.query.persistence.Query> queryList) {
-        var ret = new ArrayList<QueryListEntry>();
+    public QueryListEntry convertQueryToQueryListEntry(de.numcodex.feasibility_gui_backend.query.persistence.Query query,
+                                                       boolean skipValidation) {
+        boolean isValid = true;
+        if (!skipValidation) {
+            try {
+                var sq = jsonUtil.readValue(query.getQueryContent().getQueryContent(), StructuredQuery.class);
+                isValid = structuredQueryValidation.isValid(sq);
+            } catch (JsonProcessingException e) {
+                isValid = false;
+            }
+        }
 
-        queryList.forEach(q -> {
-            if (q.getSavedQuery() != null) {
-                ret.add(
-                        QueryListEntry.builder()
-                                .id(q.getId())
-                                .label(q.getSavedQuery().getLabel())
-                                .comment(q.getSavedQuery().getComment())
-                                .totalNumberOfPatients(q.getSavedQuery().getResultSize())
-                                .createdAt(q.getCreatedAt())
-                                .build());
+        if (query.getSavedQuery() != null) {
+            if (skipValidation) {
+                return
+                    QueryListEntry.builder()
+                        .id(query.getId())
+                        .label(query.getSavedQuery().getLabel())
+                        .comment(query.getSavedQuery().getComment())
+                        .totalNumberOfPatients(query.getSavedQuery().getResultSize())
+                        .createdAt(query.getCreatedAt())
+                        .build();
             } else {
-                ret.add(
-                        QueryListEntry.builder()
-                                .id(q.getId())
-                                .createdAt(q.getCreatedAt())
-                                .build());
+                return
+                    QueryListEntry.builder()
+                        .id(query.getId())
+                        .label(query.getSavedQuery().getLabel())
+                        .comment(query.getSavedQuery().getComment())
+                        .totalNumberOfPatients(query.getSavedQuery().getResultSize())
+                        .createdAt(query.getCreatedAt())
+                        .isValid(isValid)
+                        .build();
             }
-        });
+        } else {
+            if (skipValidation) {
+                return
+                    QueryListEntry.builder()
+                        .id(query.getId())
+                        .createdAt(query.getCreatedAt())
+                        .build();
+            } else {
+                return
+                    QueryListEntry.builder()
+                        .id(query.getId())
+                        .createdAt(query.getCreatedAt())
+                        .isValid(isValid)
+                        .build();
+            }
+        }
+    }
 
+    public List<QueryListEntry> convertQueriesToQueryListEntries(List<de.numcodex.feasibility_gui_backend.query.persistence.Query> queryList,
+                                                                 boolean skipValidation) {
+        var ret = new ArrayList<QueryListEntry>();
+        queryList.forEach(q -> ret.add(convertQueryToQueryListEntry(q, skipValidation)));
         return ret;
     }