Add mjr endpoint (#70)

* Add mjr endpoint * serialize json * code review * Trivy * Sonar coverage
DiSSCo · Nov 14, 2023 · e9ac31f · e9ac31f
1 parent 74acdf8
commit e9ac31f
Show file tree

Hide file tree

Showing 14 changed files with 554 additions and 37 deletions.
diff --git a/.github/workflows/.trivyignore b/.github/workflows/.trivyignore
@@ -1,15 +1,4 @@
-# Date: June 16, 2023
-# Issue: snappy-java high issue, https://www.cvedetails.com/cve/CVE-2023-34453/
-# Solution: Spring needs to update its version of kafka
-# CVE-2023-34455
-
-# Date: August 24, 2023
-# Issue: snappy-java used by kafka, which is used by spring-kafka
-# Solution: Spring needs to update its version of kafka
-# CVE-2023-34453
-# CVE-2023-34454
-
-# Date: August 25
-# Manually set kafka version to 3.5.1. This version addresses the above CVEs
-# Should remove this property once spring-kafka updates
-
+# Date: November 14, 2023
+# Issue: openssl: Incorrect cipher key and IV length processing https://avd.aquasec.com/nvd/cve-2023-5363
+# Solution: Docker image needs an update
+CVE-2023-5363
diff --git a/pom.xml b/pom.xml
@@ -6,7 +6,7 @@
   <parent>
     <groupId>org.springframework.boot</groupId>
     <artifactId>spring-boot-starter-parent</artifactId>
-    <version>3.1.4</version>
+    <version>3.1.5</version>
     <relativePath/> <!-- lookup parent from repository -->
   </parent>
   <groupId>eu.dissco</groupId>

diff --git a/src/main/java/eu/dissco/backend/controller/MasJobRecordController.java b/src/main/java/eu/dissco/backend/controller/MasJobRecordController.java
@@ -0,0 +1,56 @@
+package eu.dissco.backend.controller;
+
+import com.fasterxml.jackson.databind.ObjectMapper;
+import eu.dissco.backend.domain.AnnotationState;
+import eu.dissco.backend.domain.jsonapi.JsonApiListResponseWrapper;
+import eu.dissco.backend.domain.jsonapi.JsonApiWrapper;
+import eu.dissco.backend.exceptions.NotFoundException;
+import eu.dissco.backend.properties.ApplicationProperties;
+import eu.dissco.backend.service.MasJobRecordService;
+import jakarta.servlet.http.HttpServletRequest;
+import java.util.UUID;
+import lombok.extern.slf4j.Slf4j;
+import org.springframework.http.MediaType;
+import org.springframework.http.ResponseEntity;
+import org.springframework.web.bind.annotation.GetMapping;
+import org.springframework.web.bind.annotation.PathVariable;
+import org.springframework.web.bind.annotation.RequestMapping;
+import org.springframework.web.bind.annotation.RequestParam;
+import org.springframework.web.bind.annotation.RestController;
+import org.springframework.web.bind.annotation.RestControllerAdvice;
+
+@Slf4j
+@RestControllerAdvice
+@RestController
+@RequestMapping("api/v1/mjr")
+public class MasJobRecordController extends BaseController {
+
+  private final MasJobRecordService service;
+
+  public MasJobRecordController(ObjectMapper mapper,
+      ApplicationProperties applicationProperties, MasJobRecordService service) {
+    super(mapper, applicationProperties);
+    this.service = service;
+  }
+
+  @GetMapping(value = "/{jobId}", produces = MediaType.APPLICATION_JSON_VALUE)
+  public ResponseEntity<JsonApiWrapper> getMasJobRecord(
+      @PathVariable("jobId") UUID jobId, HttpServletRequest request) throws NotFoundException {
+    return ResponseEntity.ok().body(service.getMasJobRecordById(jobId, getPath(request)));
+  }
+
+  @GetMapping(value = "/creator/"
+      + "{creatorId}", produces = MediaType.APPLICATION_JSON_VALUE)
+  public ResponseEntity<JsonApiListResponseWrapper> getMasJobRecordsForCreator(
+      @PathVariable("creatorId") String creatorId,
+      @RequestParam(defaultValue = DEFAULT_PAGE_NUM) int pageNumber,
+      @RequestParam(defaultValue = DEFAULT_PAGE_SIZE) int pageSize,
+      @RequestParam(required = false) AnnotationState state,
+      HttpServletRequest request) {
+    return ResponseEntity.ok().body(
+        service.getMasJobRecordsByCreator(creatorId, getPath(request), pageNumber, pageSize,
+            state));
+
+  }
+
+}
diff --git a/src/main/java/eu/dissco/backend/domain/AnnotationState.java b/src/main/java/eu/dissco/backend/domain/AnnotationState.java
@@ -5,12 +5,30 @@
 @Getter
 public enum AnnotationState {
   SCHEDULED("scheduled"),
-  FAILED("failed");
+  FAILED("failed"),
+  COMPLETED("completed");
 
   private final String state;
 
-  AnnotationState(String s){
+  AnnotationState(String s) {
     this.state = s;
   }
 
+  public static AnnotationState fromString(String s) {
+    switch (s.toLowerCase()) {
+      case "scheduled" -> {
+        return SCHEDULED;
+      }
+      case "failed" -> {
+        return FAILED;
+      }
+      case "completed" -> {
+        return COMPLETED;
+      }
+      default ->
+          throw new IllegalStateException("Unable to construct AnnotationState from state " + s);
+    }
+
+  }
+
 }
diff --git a/src/main/java/eu/dissco/backend/domain/MasJobRecordFull.java b/src/main/java/eu/dissco/backend/domain/MasJobRecordFull.java
@@ -0,0 +1,17 @@
+package eu.dissco.backend.domain;
+
+import com.fasterxml.jackson.databind.JsonNode;
+import java.time.Instant;
+import java.util.UUID;
+
+public record MasJobRecordFull(
+    AnnotationState state,
+    String creatorId,
+    String targetId,
+    UUID jobId,
+    Instant timeStarted,
+    Instant timeCompleted,
+    JsonNode annotations
+) {
+
+}
diff --git a/src/main/java/eu/dissco/backend/repository/MasJobRecordRepository.java b/src/main/java/eu/dissco/backend/repository/MasJobRecordRepository.java
@@ -1,15 +1,23 @@
 package eu.dissco.backend.repository;
 
 import static eu.dissco.backend.database.jooq.Tables.MAS_JOB_RECORD;
+import static eu.dissco.backend.repository.RepositoryUtils.getOffset;
 
+import com.fasterxml.jackson.core.JsonProcessingException;
+import com.fasterxml.jackson.databind.JsonNode;
+import com.fasterxml.jackson.databind.ObjectMapper;
 import eu.dissco.backend.domain.AnnotationState;
 import eu.dissco.backend.domain.MasJobRecord;
+import eu.dissco.backend.domain.MasJobRecordFull;
+import eu.dissco.backend.exceptions.DisscoJsonBMappingException;
 import java.time.Instant;
 import java.util.List;
 import java.util.Map;
+import java.util.Optional;
 import java.util.UUID;
 import lombok.RequiredArgsConstructor;
 import org.jooq.DSLContext;
+import org.jooq.Record;
 import org.jooq.Record4;
 import org.springframework.stereotype.Repository;
 
@@ -18,31 +26,80 @@
 public class MasJobRecordRepository {
 
   private final DSLContext context;
+  private final ObjectMapper mapper;
 
-  public Map<String, UUID> createNewMasJobRecord(List<MasJobRecord> masJobRecord){
+  public Optional<MasJobRecordFull> getMasJobRecordById(UUID masJobRecordId) {
+    return context.select(MAS_JOB_RECORD.asterisk())
+        .from(MAS_JOB_RECORD)
+        .where(MAS_JOB_RECORD.JOB_ID.eq(masJobRecordId))
+        .fetchOptional(this::recordToMasJobRecord);
+  }
+
+  public List<MasJobRecordFull> getMasJobRecordsByCreator(String creatorId, int pageNum, int pageSize){
+    var offset = getOffset(pageNum, pageSize);
+    return context.select(MAS_JOB_RECORD.asterisk())
+        .from(MAS_JOB_RECORD)
+        .where(MAS_JOB_RECORD.CREATOR_ID.eq(creatorId))
+        .limit(pageSize)
+        .offset(offset)
+        .fetch(this::recordToMasJobRecord);
+  }
+
+  public List<MasJobRecordFull> getMasJobRecordsByCreatorAndStatus(String creatorId, String state, int pageNum, int pageSize){
+    var offset = getOffset(pageNum, pageSize);
+    return context.select(MAS_JOB_RECORD.asterisk())
+        .from(MAS_JOB_RECORD)
+        .where(MAS_JOB_RECORD.CREATOR_ID.eq(creatorId))
+        .and(MAS_JOB_RECORD.STATE.eq(state))
+        .limit(pageSize)
+        .offset(offset)
+        .fetch(this::recordToMasJobRecord);
+  }
+
+
+  public Map<String, UUID> createNewMasJobRecord(List<MasJobRecord> masJobRecord) {
     var records = masJobRecord.stream().map(this::mjrToRecord).toList();
 
-    return context.insertInto(MAS_JOB_RECORD, MAS_JOB_RECORD.STATE, MAS_JOB_RECORD.CREATOR_ID, MAS_JOB_RECORD.TARGET_ID, MAS_JOB_RECORD.TIME_STARTED)
+    return context.insertInto(MAS_JOB_RECORD, MAS_JOB_RECORD.STATE, MAS_JOB_RECORD.CREATOR_ID,
+            MAS_JOB_RECORD.TARGET_ID, MAS_JOB_RECORD.TIME_STARTED)
         .valuesOfRecords(records)
         .returning(MAS_JOB_RECORD.CREATOR_ID, MAS_JOB_RECORD.JOB_ID)
         .fetchMap(MAS_JOB_RECORD.CREATOR_ID, MAS_JOB_RECORD.JOB_ID);
   }
 
-  public void markMasJobRecordsAsFailed(List<UUID> ids){
+  public void markMasJobRecordsAsFailed(List<UUID> ids) {
     context.update(MAS_JOB_RECORD)
         .set(MAS_JOB_RECORD.STATE, AnnotationState.FAILED.getState())
         .set(MAS_JOB_RECORD.TIME_COMPLETED, Instant.now())
         .where(MAS_JOB_RECORD.JOB_ID.in(ids))
         .execute();
   }
 
-  private Record4<String, String, String, Instant> mjrToRecord(MasJobRecord masJobRecord){
-    var dbRecord = context.newRecord(MAS_JOB_RECORD.STATE, MAS_JOB_RECORD.CREATOR_ID, MAS_JOB_RECORD.TARGET_ID, MAS_JOB_RECORD.TIME_STARTED);
+  private Record4<String, String, String, Instant> mjrToRecord(MasJobRecord masJobRecord) {
+    var dbRecord = context.newRecord(MAS_JOB_RECORD.STATE, MAS_JOB_RECORD.CREATOR_ID,
+        MAS_JOB_RECORD.TARGET_ID, MAS_JOB_RECORD.TIME_STARTED);
     dbRecord.set(MAS_JOB_RECORD.STATE, masJobRecord.state().getState());
     dbRecord.set(MAS_JOB_RECORD.CREATOR_ID, masJobRecord.creatorId());
     dbRecord.set(MAS_JOB_RECORD.TARGET_ID, masJobRecord.targetId());
     dbRecord.set(MAS_JOB_RECORD.TIME_STARTED, Instant.now());
     return dbRecord;
   }
 
+  private MasJobRecordFull recordToMasJobRecord(Record dbRecord) {
+    try {
+      return new MasJobRecordFull(
+          AnnotationState.fromString(dbRecord.get(MAS_JOB_RECORD.STATE)),
+          dbRecord.get(MAS_JOB_RECORD.CREATOR_ID),
+          dbRecord.get(MAS_JOB_RECORD.TARGET_ID),
+          dbRecord.get(MAS_JOB_RECORD.JOB_ID),
+          dbRecord.get(MAS_JOB_RECORD.TIME_STARTED),
+          dbRecord.get(MAS_JOB_RECORD.TIME_COMPLETED),
+          mapper.readValue(dbRecord.get(MAS_JOB_RECORD.ANNOTATIONS).data(), JsonNode.class)
+      );
+    } catch (JsonProcessingException e) {
+      throw new DisscoJsonBMappingException("Unable to parse annotations from MAS job record", e);
+    }
+
+  }
+
 }
diff --git a/src/main/java/eu/dissco/backend/service/AnnotationService.java b/src/main/java/eu/dissco/backend/service/AnnotationService.java
@@ -24,13 +24,11 @@
 import eu.dissco.backend.repository.MongoRepository;
 import java.io.IOException;
 import java.time.Instant;
-import java.time.format.DateTimeFormatter;
 import java.util.ArrayList;
 import java.util.List;
 import lombok.RequiredArgsConstructor;
 import lombok.extern.slf4j.Slf4j;
 import org.apache.commons.lang3.tuple.Pair;
-import org.apache.kafka.common.protocol.types.Field.Str;
 import org.springframework.stereotype.Service;
 
 @Slf4j
@@ -47,7 +45,6 @@ public class AnnotationService {
   private final MongoRepository mongoRepository;
   private final UserService userService;
   private final ObjectMapper mapper;
-  private final DateTimeFormatter formatter;
 
   public JsonApiWrapper getAnnotation(String id, String path) {
     var annotation = repository.getAnnotation(id);

diff --git a/src/main/java/eu/dissco/backend/service/MasJobRecordService.java b/src/main/java/eu/dissco/backend/service/MasJobRecordService.java
@@ -1,13 +1,23 @@
 package eu.dissco.backend.service;
 
+import com.fasterxml.jackson.databind.ObjectMapper;
 import eu.dissco.backend.domain.AnnotationState;
 import eu.dissco.backend.domain.MachineAnnotationServiceRecord;
 import eu.dissco.backend.domain.MasJobRecord;
+import eu.dissco.backend.domain.MasJobRecordFull;
+import eu.dissco.backend.domain.jsonapi.JsonApiData;
+import eu.dissco.backend.domain.jsonapi.JsonApiLinks;
+import eu.dissco.backend.domain.jsonapi.JsonApiLinksFull;
+import eu.dissco.backend.domain.jsonapi.JsonApiListResponseWrapper;
+import eu.dissco.backend.domain.jsonapi.JsonApiWrapper;
+import eu.dissco.backend.exceptions.NotFoundException;
 import eu.dissco.backend.repository.MasJobRecordRepository;
+
 import java.util.List;
 import java.util.Map;
 import java.util.Set;
 import java.util.UUID;
+
 import lombok.RequiredArgsConstructor;
 import org.springframework.stereotype.Service;
 
@@ -16,15 +26,55 @@
 public class MasJobRecordService {
 
   private final MasJobRecordRepository masJobRecordRepository;
+  private final ObjectMapper mapper;
+
+  public JsonApiWrapper getMasJobRecordById(UUID masJobRecordId, String path)
+      throws NotFoundException {
+    var masJobRecordOptional = masJobRecordRepository.getMasJobRecordById(masJobRecordId);
+    if (masJobRecordOptional.isEmpty()) {
+      throw new NotFoundException(
+          "Unable to find MAS Job Record for job " + masJobRecordId.toString());
+    }
+    var masJobRecord = masJobRecordOptional.get();
+    var dataNode = new JsonApiData(masJobRecordId.toString(), "masJobRecord",
+        mapper.valueToTree(masJobRecord));
+    return new JsonApiWrapper(dataNode, new JsonApiLinks(path));
+  }
+
+  public JsonApiListResponseWrapper getMasJobRecordsByCreator(String creatorId, String path,
+      int pageNum, int pageSize, AnnotationState state) {
+    int pageSizeToCheckNext = pageSize + 1;
+    List<MasJobRecordFull> masJobRecordsPlusOne;
+    if (state == null) {
+      masJobRecordsPlusOne = masJobRecordRepository.getMasJobRecordsByCreator(creatorId, pageNum,
+          pageSizeToCheckNext);
+    } else {
+      masJobRecordsPlusOne = masJobRecordRepository.getMasJobRecordsByCreatorAndStatus(creatorId,
+          state.getState(), pageNum, pageSizeToCheckNext);
+    }
+    boolean hasNext = masJobRecordsPlusOne.size() > pageSize;
+    var masJobRecords = hasNext ? masJobRecordsPlusOne.subList(0, pageSize) : masJobRecordsPlusOne;
+    List<JsonApiData> dataList = masJobRecords.stream().map(
+            mjr -> new JsonApiData(mjr.jobId().toString(), "masJobRecord", mapper.valueToTree(mjr)))
+        .toList();
+    JsonApiLinksFull linksNode;
+    if (masJobRecords.isEmpty()) {
+      linksNode = new JsonApiLinksFull(path);
+    } else {
+      linksNode = new JsonApiLinksFull(pageSize, pageNum, hasNext, path);
+    }
+    return new JsonApiListResponseWrapper(dataList, linksNode);
+  }
 
-  public Map<String, UUID> createMasJobRecord(Set<MachineAnnotationServiceRecord> masRecords, String targetId) {
+  public Map<String, UUID> createMasJobRecord(Set<MachineAnnotationServiceRecord> masRecords,
+      String targetId) {
     var masJobRecordList = masRecords.stream()
         .map(masRecord -> new MasJobRecord(AnnotationState.SCHEDULED, masRecord.id(), targetId))
         .toList();
     return masJobRecordRepository.createNewMasJobRecord(masJobRecordList);
   }
 
-  public void markMasJobRecordAsFailed(List<UUID> failedJobIds){
+  public void markMasJobRecordAsFailed(List<UUID> failedJobIds) {
     masJobRecordRepository.markMasJobRecordsAsFailed(failedJobIds);
   }