Merge pull request #285 from overture-stack/feature/song-128-score-mo…

…unt-endpoint Feature/song 128 score mount endpoint
overture-stack · May 28, 2018 · 851a4bc · 851a4bc
2 parents 008d741 + 938c64d
commit 851a4bc
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Showing 23 changed files with 903 additions and 136 deletions.
diff --git a/pom.xml b/pom.xml
@@ -106,6 +106,18 @@
                 <version>${hibernate-native-json.version}</version>
             </dependency>
 
+            <!-- Mapstruct - automated pojo mapping -->
+            <dependency>
+                <groupId>org.mapstruct</groupId>
+                <artifactId>mapstruct-jdk8</artifactId>
+                <version>${mapstruct.version}</version>
+            </dependency>
+            <dependency>
+                <groupId>org.mapstruct</groupId>
+                <artifactId>mapstruct-processor</artifactId>
+                <version>${mapstruct.version}</version>
+            </dependency>
+
             <!-- Hibernate Validator              -->
             <!--Validates annotations at build time-->
             <dependency>
@@ -114,6 +126,11 @@
                 <version>${hibernate-validator.version}</version>
             </dependency>
 
+            <dependency>
+                <groupId>com.github.bohnman</groupId>
+                <artifactId>squiggly-filter-jackson</artifactId>
+                <version>${squiggly-version}</version>
+            </dependency>
             <dependency>
                 <groupId>com.fasterxml.uuid</groupId>
                 <artifactId>java-uuid-generator</artifactId>
@@ -203,6 +220,7 @@
                 <plugin>
                     <groupId>org.apache.maven.plugins</groupId>
                     <artifactId>maven-compiler-plugin</artifactId>
+                    <version>${maven-compiler-plugin.version}</version>
                     <inherited>true</inherited>
                     <configuration>
                         <source>${java.version}</source>
@@ -254,6 +272,7 @@
 
     <properties>
         <!-- Project Related Properties -->
+        <maven-compiler-plugin.version>3.7.0</maven-compiler-plugin.version>
         <project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
         <project.reporting.outputEncoding>UTF-8</project.reporting.outputEncoding>
         <java.version>1.8</java.version>
@@ -284,6 +303,9 @@
         <guava.version>24.1-jre</guava.version>
         <jcommander.version>1.69</jcommander.version>
         <jansi.version>1.16</jansi.version>
+        <squiggly-version>1.3.11</squiggly-version>
+        <mapstruct.version>1.2.0.Final</mapstruct.version>
+
     </properties>
 
 </project>
diff --git a/song-core/src/main/java/org/icgc/dcc/song/core/exceptions/ServerErrors.java b/song-core/src/main/java/org/icgc/dcc/song/core/exceptions/ServerErrors.java
@@ -58,6 +58,7 @@ public enum ServerErrors implements ServerError {
   PAYLOAD_PARSING(UNPROCESSABLE_ENTITY),
   UPLOAD_ID_NOT_FOUND(NOT_FOUND ),
   FILE_NOT_FOUND(NOT_FOUND ),
+  LEGACY_ENTITY_NOT_FOUND(NOT_FOUND ),
   INFO_NOT_FOUND(NOT_FOUND ),
   UPLOAD_ID_NOT_VALIDATED(CONFLICT),
   ANALYSIS_ID_NOT_CREATED(INTERNAL_SERVER_ERROR),
@@ -85,6 +86,9 @@ public enum ServerErrors implements ServerError {
   SEQUENCING_READ_CORRUPTED_DUPLICATE(INTERNAL_SERVER_ERROR),
   DUPLICATE_ANALYSIS_ATTEMPT(CONFLICT),
   STUDY_ALREADY_EXISTS(CONFLICT),
+  ILLEGAL_FILTER_PARAMETER(BAD_REQUEST),
+  ILLEGAL_QUERY_PARAMETER(BAD_REQUEST),
+  UNREGISTERED_TYPE(INTERNAL_SERVER_ERROR),
   UNKNOWN_ERROR(INTERNAL_SERVER_ERROR);
 
   private static final String ERROR_ID_SEPARATOR = ".";

diff --git a/song-core/src/main/java/org/icgc/dcc/song/core/utils/RandomGenerator.java b/song-core/src/main/java/org/icgc/dcc/song/core/utils/RandomGenerator.java
@@ -18,6 +18,7 @@
 package org.icgc.dcc.song.core.utils;
 
 import com.fasterxml.uuid.impl.RandomBasedGenerator;
+import com.google.common.collect.ImmutableList;
 import com.google.common.hash.Hashing;
 import lombok.Getter;
 import lombok.NonNull;
@@ -36,7 +37,9 @@
 import static com.google.common.base.Preconditions.checkArgument;
 import static com.google.common.collect.Lists.newArrayList;
 import static java.lang.Integer.MAX_VALUE;
+import static java.util.Collections.shuffle;
 import static java.util.stream.Collectors.toList;
+import static org.icgc.dcc.common.core.util.stream.Collectors.toImmutableList;
 
 /**
  * Utility for generating random integers, strings and UUIDs using seed values while recording call counts to
@@ -115,19 +118,19 @@ public int generateRandomInt(){
   }
 
   /**
-   * Generate a random integer between the interval [min, max)
-   * @param min inclusive lower bound
-   * @param max exclusive upper bound
+   * Generate a random integer between the interval [inclusiveMin, exlusiveMax)
+   * @param inclusiveMin inclusive lower bound
+   * @param exlusiveMax exclusive upper bound
    */
-  public int generateRandomIntRange(int min, int max){
+  public int generateRandomIntRange(int inclusiveMin, int exlusiveMax){
     log.info("Generating RandomIntRange for RandomGenerator[{}] with seed '{}' and callCount '{}'",
         id, seed, callCount);
-    checkArgument(min<max,"The min(%s) must be LESS THAN max(%s)", min, max);
-    val difference = (long)max - min;
+    checkArgument(inclusiveMin<exlusiveMax,"The inclusiveMin(%s) must be LESS THAN exclusiveMax(%s)", inclusiveMin, exlusiveMax);
+    val difference = (long)exlusiveMax - inclusiveMin;
     checkArgument(difference <= MAX_VALUE,
-        "The difference (%s) between max (%s) and (%s) must not exceed the integer max (%s)",
-        difference, max, min, MAX_VALUE);
-    return generateRandomInt(min, max-min);
+        "The difference (%s) between exclusiveMax (%s) and (%s) must not exceed the integer exclusiveMax (%s)",
+        difference, exlusiveMax, inclusiveMin, MAX_VALUE);
+    return generateRandomInt(inclusiveMin, exlusiveMax-inclusiveMin);
   }
 
   /**
@@ -158,6 +161,42 @@ public <E extends Enum<E>> E randomEnum(Class<E> enumClass){
     return randomElement(enumList);
   }
 
+  /**
+   * Creates a new shuffled list. Assumes the input list is immutable
+   * @param list input List
+   * @return shuffles list
+   */
+  public <T> List<T> shuffleList(List<T> list){
+    log.info("Shuffling list for RandomGenerator[{}] with seed '{}' and callCount '{}'",
+        id, seed, callCount++);
+    val mutableList = newArrayList(list);
+    shuffle(mutableList, random);
+    return ImmutableList.copyOf(mutableList);
+  }
+
+  /**
+   * Creates a random sublist of size {@code size}, from an input list
+   */
+  public <T> List<T> randomSublist(List<T> list, int size){
+    checkArgument(size <= list.size(),
+        "The input sublist size (%s) is greater than the list size (%s)", size, list.size());
+    val shuffledList = shuffleList(IntStream.range(0,list.size()).boxed().collect(toList()));
+    return IntStream.range(0, size)
+        .boxed()
+        .map(shuffledList::get)
+        .map(list::get)
+        .collect(toImmutableList());
+  }
+
+  /**
+   * Take an input list of size {@code inputSize}, and generate a random sublist of size {@code outputSize}
+   * where {@code outputSize} is in the range [1, inputSize )
+   */
+  public <T> List<T> randomSublist(List<T> list){
+    val size = generateRandomIntRange(1,list.size());
+    return randomSublist(list, size);
+  }
+
   /**
    * Select a random element from a list
    * @param list input list to select from

diff --git a/song-core/src/test/java/org/icgc/dcc/song/core/utils/RandomGeneratorTest.java b/song-core/src/test/java/org/icgc/dcc/song/core/utils/RandomGeneratorTest.java
@@ -63,8 +63,6 @@ public void testRandomMd5(){
     assertThat(md5).isEqualTo("953a2fb1afb52dc0ef6a95ec5cac8680");
     val randomGenerator2 = createRandomGenerator("rand1-seed1", 100);
     assertThat(randomGenerator2.generateRandomMD5()).isNotEqualTo(md5);
-
-
   }
 
   @Test
@@ -177,7 +175,7 @@ public void runRandomIntRangeTest(int min, int max){
     assertThat(throwable1)
         .isInstanceOf(IllegalArgumentException.class)
         .hasMessage(
-            format("The min(%s) must be LESS THAN max(%s)", max, min));
+            format("The inclusiveMin(%s) must be LESS THAN exclusiveMax(%s)", max, min));
 
     val throwable2 = catchThrowable( () -> randomGenerator1.generateRandomIntRange(MIN_VALUE, MAX_VALUE));
     assertThat(throwable2)

diff --git a/song-server/pom.xml b/song-server/pom.xml
@@ -76,6 +76,17 @@
             <artifactId>postgresql</artifactId>
         </dependency>
 
+        <dependency>
+            <groupId>org.mapstruct</groupId>
+            <artifactId>mapstruct-jdk8</artifactId>
+            <scope>provided</scope>
+        </dependency>
+        <dependency>
+            <groupId>org.mapstruct</groupId>
+            <artifactId>mapstruct-processor</artifactId>
+            <scope>provided</scope>
+        </dependency>
+
         <!-- Hibernate Json Types -->
         <dependency>
             <groupId>com.marvinformatics.hibernate</groupId>
@@ -110,6 +121,12 @@
             <artifactId>jackson-datatype-jsr310</artifactId>
         </dependency>
 
+        <!-- Squiggly - Dynamic JSON Views -->
+        <dependency>
+            <groupId>com.github.bohnman</groupId>
+            <artifactId>squiggly-filter-jackson</artifactId>
+        </dependency>
+
         <!-- spring-kafka -->
         <dependency>
             <groupId>org.springframework.kafka</groupId>
@@ -120,6 +137,7 @@
         <dependency>
             <groupId>org.projectlombok</groupId>
             <artifactId>lombok</artifactId>
+            <scope>provided</scope>
         </dependency>
         <dependency>
             <groupId>org.icgc.dcc</groupId>
@@ -193,6 +211,7 @@
                     <!--</execution>-->
                 <!--</executions>-->
             <!--</plugin>-->
+
             <plugin>
                 <groupId>org.springframework.boot</groupId>
                 <artifactId>spring-boot-maven-plugin</artifactId>

diff --git a/song-server/src/main/java/org/icgc/dcc/song/server/config/ConverterConfig.java b/song-server/src/main/java/org/icgc/dcc/song/server/config/ConverterConfig.java
@@ -0,0 +1,16 @@
+package org.icgc.dcc.song.server.config;
+
+import org.icgc.dcc.song.server.converter.LegacyEntityConverter;
+import org.mapstruct.factory.Mappers;
+import org.springframework.context.annotation.Bean;
+import org.springframework.context.annotation.Configuration;
+
+@Configuration
+public class ConverterConfig {
+
+  @Bean
+  public LegacyEntityConverter legacyEntityConverter(){
+    return Mappers.getMapper(LegacyEntityConverter.class);
+  }
+
+}
diff --git a/song-server/src/main/java/org/icgc/dcc/song/server/config/ValidationConfig.java b/song-server/src/main/java/org/icgc/dcc/song/server/config/ValidationConfig.java
@@ -24,6 +24,10 @@
 import lombok.val;
 import org.icgc.dcc.song.core.utils.JsonDocUtils;
 import org.icgc.dcc.song.core.utils.JsonSchemaUtils;
+import org.icgc.dcc.song.server.model.legacy.LegacyEntity;
+import org.icgc.dcc.song.server.model.entity.IdView;
+import org.icgc.dcc.song.server.repository.search.IdSearchRequest;
+import org.icgc.dcc.song.server.utils.ParameterChecker;
 import org.icgc.dcc.song.server.validation.SchemaValidator;
 import org.springframework.beans.factory.annotation.Value;
 import org.springframework.context.annotation.Bean;
@@ -33,6 +37,8 @@
 import java.util.HashMap;
 import java.util.Map;
 
+import static org.icgc.dcc.song.server.utils.ParameterChecker.createParameterChecker;
+
 @Slf4j
 @Configuration
 @Data
@@ -49,6 +55,16 @@ public SchemaValidator schemaValidator() {
     return new SchemaValidator();
   }
 
+  @Bean
+  public ParameterChecker parameterChecker(){
+    return createParameterChecker(
+        LegacyEntity.class,
+        IdSearchRequest.class,
+        IdView.class,
+        IdView.IdViewProjection.class
+    );
+  }
+
   @Bean
   @Profile("async-test")
   public Long validationDelayMs(){

diff --git a/song-server/src/main/java/org/icgc/dcc/song/server/controller/LegacyEntityController.java b/song-server/src/main/java/org/icgc/dcc/song/server/controller/LegacyEntityController.java
@@ -17,15 +17,20 @@
 
 package org.icgc.dcc.song.server.controller;
 
+import com.fasterxml.jackson.databind.JsonNode;
 import io.swagger.annotations.Api;
 import io.swagger.annotations.ApiOperation;
 import lombok.RequiredArgsConstructor;
-import org.icgc.dcc.song.server.model.LegacyEntity;
+import org.icgc.dcc.song.server.model.legacy.Legacy;
+import org.icgc.dcc.song.server.model.legacy.LegacyDto;
 import org.icgc.dcc.song.server.service.LegacyEntityService;
 import org.springframework.beans.factory.annotation.Autowired;
-import org.springframework.data.domain.Page;
+import org.springframework.data.domain.Pageable;
+import org.springframework.data.web.PageableDefault;
 import org.springframework.http.ResponseEntity;
+import org.springframework.util.MultiValueMap;
 import org.springframework.web.bind.annotation.GetMapping;
+import org.springframework.web.bind.annotation.ModelAttribute;
 import org.springframework.web.bind.annotation.PathVariable;
 import org.springframework.web.bind.annotation.RequestMapping;
 import org.springframework.web.bind.annotation.RequestParam;
@@ -49,18 +54,18 @@ public class LegacyEntityController {
   @ApiOperation(value = "ReadLegacyEntity", notes = "Read entity data for a legacy entity id")
   @GetMapping(value = "/{id}")
   @ResponseBody
-  public ResponseEntity<LegacyEntity> read(@PathVariable("id") String id) {
+  public ResponseEntity<Legacy> read(@PathVariable("id") String id) {
     return ok(legacyEntityService.getEntity(id));
   }
 
-  @ApiOperation(value = "ReadLegacyEntitiesByGnosId", notes = "Page through LegacyEntity data for a gnosId")
-  @GetMapping
+  @ApiOperation(value = "FindLegacyEntities", notes = "Page through LegacyEntity data")
   @ResponseBody
-  public ResponseEntity<Page<LegacyEntity>> readGnosId(
-      @RequestParam(value = "gnosId") String gnosId,
-      @RequestParam(value = "size", required = false, defaultValue = "2000") int size,
-      @RequestParam(value = "page", required = false, defaultValue = "0") int page ) {
-    return ok(legacyEntityService.getEntitiesByGnosId(gnosId,size,page));
+  @GetMapping
+  public ResponseEntity<JsonNode> find(
+      @RequestParam MultiValueMap<String, String> params,
+      @ModelAttribute LegacyDto probe,
+      @PageableDefault(sort = "id") Pageable pageable) {
+    return ok(legacyEntityService.find(params, probe, pageable));
   }
 
 }
diff --git a/song-server/src/main/java/org/icgc/dcc/song/server/converter/LegacyEntityConverter.java b/song-server/src/main/java/org/icgc/dcc/song/server/converter/LegacyEntityConverter.java
@@ -0,0 +1,14 @@
+package org.icgc.dcc.song.server.converter;
+
+import org.icgc.dcc.song.server.model.legacy.Legacy;
+import org.icgc.dcc.song.server.model.legacy.LegacyDto;
+import org.icgc.dcc.song.server.model.legacy.LegacyEntity;
+import org.mapstruct.Mapper;
+
+@Mapper
+public interface LegacyEntityConverter {
+
+    LegacyDto convertToLegacyDto(Legacy legacy);
+    LegacyEntity convertToLegacyEntity(Legacy legacy);
+
+}
diff --git a/song-server/src/main/java/org/icgc/dcc/song/server/model/enums/AnalysisStates.java b/song-server/src/main/java/org/icgc/dcc/song/server/model/enums/AnalysisStates.java
@@ -17,6 +17,10 @@
 
 package org.icgc.dcc.song.server.model.enums;
 
+import lombok.NonNull;
+import org.icgc.dcc.common.core.util.stream.Streams;
+
+import static java.lang.String.format;
 import static java.util.Arrays.stream;
 
 public enum AnalysisStates {
@@ -28,6 +32,14 @@ public String toString(){
     return this.name();
   }
 
+  public static AnalysisStates resolveAnalysisState(@NonNull String analysisState) {
+    return Streams.stream(values())
+        .filter(x -> x.toString().equals(analysisState))
+        .findFirst()
+        .orElseThrow(
+            () -> new IllegalStateException(format("The analysis state '%s' cannot be resolved", analysisState)));
+  }
+
   public static String[] toStringArray(){
     return stream(values())
         .map(Enum::name)

diff --git a/song-server/src/main/java/org/icgc/dcc/song/server/model/legacy/Legacy.java b/song-server/src/main/java/org/icgc/dcc/song/server/model/legacy/Legacy.java
@@ -0,0 +1,24 @@
+package org.icgc.dcc.song.server.model.legacy;
+
+public interface Legacy {
+
+  String getId();
+
+  String getGnosId();
+
+  String getFileName();
+
+  String getProjectCode();
+
+  String getAccess();
+
+  void setId(String id);
+
+  void setGnosId(String gnosId);
+
+  void setFileName(String fileName);
+
+  void setProjectCode(String projectCode);
+
+  void setAccess(String access);
+}