Release Candidate 4.0.0

Makefile

@@ -83,6 +83,11 @@ _ping_song_server:
 		'http://localhost:8080/isAlive'
 	@echo ""
 
+_ping_song_db:
+	@echo $(YELLOW)$(INFO_HEADER) "Pinging song-db on localhost:8432" $(END)
+	@$(RETRY_CMD) $(DOCKER_COMPOSE_EXE) exec song-db psql -U postgres song -c 'select 1' 
+	@echo ""
+
 
 _setup-object-storage: 
 	@echo $(YELLOW)$(INFO_HEADER) "Setting up bucket oicr.icgc.test and heliograph" $(END)
@@ -170,6 +175,26 @@ clean-output-dirs:
 # Clean everything. Kills all services, maven cleans and removes generated files/directories
 clean: clean-docker clean-mvn clean-log-dirs clean-output-dirs
 
+#############################################################
+#  Flyway and Database Related targets
+#############################################################
+
+refresh-db:
+	@echo $(YELLOW)$(INFO_HEADER) "Refreshing song-db" $(END)
+	@$(DOCKER_COMPOSE_CMD) kill song-db song-server
+	@$(DOCKER_COMPOSE_CMD) rm -f song-db
+	@$(DOCKER_COMPOSE_CMD) up -d song-db
+
+migrate: clean-mvn package refresh-db _ping_song_db
+	@$(MVN_CMD) -X -pl song-server flyway:migrate \
+		-Dflyway.user=postgres \
+		-Dflyway.password=password \
+		-Dflyway.url=jdbc:postgresql://localhost:8432/song?stringtype=unspecified \
+		-Dflyway.locations=classpath:db/migration
+
+login-db:
+	@$(DOCKER_COMPOSE_CMD) exec song-db psql -U postgres song
+
 #############################################################
 #  Building targets
 #############################################################

README.md

@@ -173,8 +173,8 @@ docker run --rm \
   -e 'CLIENT_PROGRAM_NAME=sing' \
   -e 'CLIENT_DEBUG=true' \
   -e 'CLIENT_ACCESS_TOKEN=myAccessToken' \
-  overture/song-client:latest 
-  bin/sing config
+  overture/song-client:latest \
+  sing config
 ```
 
 ### Notes

docker-compose.yml

@@ -96,6 +96,8 @@ services:
       POSTGRES_DB: song
       POSTGRES_USER: postgres
       POSTGRES_PASSWORD: password
+    ports:
+      - "8432:5432"
     volumes:
       - "./docker/song-db-init:/docker-entrypoint-initdb.d"
   aws-cli:

docker/song-example-data/exampleVariantCall.json

@@ -1,35 +1,36 @@
 {
-  "study" : "ABC123",
+  "studyId" : "ABC123",
   "analysisType" : {
-    "name" : "variantCall",
-    "version" : 1
+    "name" : "variantCall"
   },
   "experiment": {
     "variantCallingTool": "silver bullet",
-    "matchedNormalSampleSubmitterId": "sample x24-11a",
+    "matchedNormalSampleSubmitterId": "sample-x24-11a",
     "randomField14" : "we can define any EXPERIMENT field. For example, randomField14",
     "randomField15" : "as a second example, we can define another random EXPERIMENT field called randomField15",
     "info" : {
         "randomField16" : "alternatively, put some extra EXPERIMENT fields here"
     }
   },
-  "sample": [
+  "samples": [
     {
-      "sampleSubmitterId": "internal_sample_98024759826836",
+      "submitterSampleId": "internal_sample_98024759826836",
       "sampleType": "Total RNA",
+      "matchedNormalSubmitterSampleId": "sample-x24-11a",
       "specimen": {
-        "specimenSubmitterId": "internal_specimen_9b73gk8s02dk",
-        "specimenClass": "Tumour",
-        "specimenType": "Primary tumour - other",
+        "submitterSpecimenId": "internal_specimen_9b73gk8s02dk",
+        "specimenType": "Primary tumour",
+        "specimenTissueSource": "Solid tissue",
+        "tumourNormalDesignation": "Tumour",
         "randomField1" : "we can define any SPECIMEN field. For example, randomField1",
         "randomField2" : "as a second example, we can define another random SPECIMEN field called randomField2",
         "info" : {
             "randomField3" : "alternatively, put some extra SPECIMEN fields here"
         }
       },
       "donor": {
-        "donorSubmitterId": "internal_donor_123456789-00",
-        "donorGender": "female",
+        "submitterDonorId": "internal_donor_123456789-00",
+        "gender": "Female",
         "randomField4" : "we can define any DONOR field. For example, randomField4",
         "randomField5" : "as a second example, we can define another random DONOR field called randomField5",
         "info" : {
@@ -43,8 +44,9 @@
       }
     }
   ],
-  "file": [
+  "files": [
     {
+	  "dataType": "Variant Calling Data",
       "fileName": "example.vcf.gz",
       "fileSize": 52,
       "fileMd5sum": "9a793e90d0d1e11301ea8da996446e59",
@@ -57,6 +59,7 @@
       }
     },
     {
+	  "dataType": "Variant Calling Index",
       "fileName": "example.vcf.gz.idx",
       "fileSize": 25,
       "fileMd5sum": "c03274816eb4907a92b8e5632cd6eb81",

pom.xml

@@ -21,7 +21,7 @@
     <groupId>bio.overture</groupId>
     <artifactId>song</artifactId>
     <packaging>pom</packaging>
-    <version>3.1.1</version>
+    <version>4.0.0</version>
     <modules>
         <module>song-core</module>
         <module>song-java-sdk</module>
@@ -41,14 +41,6 @@
             <id>jitpack.io</id>
             <url>https://jitpack.io</url>
         </repository>
-        <repository>
-            <id>dcc-releases</id>
-            <url>https://artifacts.oicr.on.ca/artifactory/dcc-release</url>
-        </repository>
-        <repository>
-            <id>dcc-snapshot</id>
-            <url>https://artifacts.oicr.on.ca/artifactory/dcc-snapshot</url>
-        </repository>
         <repository>
             <id>Atlassian 3rd Party</id>
             <url>https://maven.atlassian.com/3rdparty/</url>
@@ -243,9 +235,8 @@
                 <version>${java-assist.version}</version>
             </dependency>
             <dependency>
-                <groupId>javax.xml.bind</groupId>
-                <artifactId>jaxb-api</artifactId>
-                <version>${jaxb.version}</version>
+                <groupId>org.glassfish.jaxb</groupId>
+                <artifactId>jaxb-runtime</artifactId>
             </dependency>
 
             <dependency>
@@ -254,18 +245,6 @@
                 <version>${javax.interceptor-api.version}</version>
             </dependency>
 
-            <!--ICGC Libs-->
-            <dependency>
-                <groupId>org.icgc.dcc</groupId>
-                <artifactId>dcc-common-core</artifactId>
-                <version>${dcc-common.version}</version>
-            </dependency>
-            <dependency>
-                <groupId>org.icgc.dcc</groupId>
-                <artifactId>dcc-id-client</artifactId>
-                <version>${dcc-id.version}</version>
-            </dependency>
-
             <!--Json Schema-->
             <dependency>
                 <groupId>com.networknt</groupId>
@@ -474,7 +453,6 @@
         <!--<spring-data-commons.version>1.12.11.RELEASE</spring-data-commons.version>-->
         <spring-framework.version>5.1.9.RELEASE</spring-framework.version>
         <spring-cloud.version>Greenwich.SR3</spring-cloud.version>
-        <dcc-common.version>4.3.8</dcc-common.version>
         <postgresql.version>42.2.2</postgresql.version>
         <junit.version>4.12</junit.version>
         <slf4j.version>1.7.25</slf4j.version>
@@ -486,7 +464,6 @@
         <java-uuid-generator.version>3.1.5</java-uuid-generator.version>
         <wiremock.version>2.14.0</wiremock.version>
         <springfox.version>2.9.0</springfox.version>
-        <dcc-id.version>5.2.0</dcc-id.version>
         <spring-security-oauth2.version>2.1.0.RELEASE</spring-security-oauth2.version>
         <hibernate-native-json.version>0.4</hibernate-native-json.version>
 

song-client/pom.xml

@@ -18,7 +18,7 @@
 	<parent>
 		<artifactId>song</artifactId>
 		<groupId>bio.overture</groupId>
-		<version>3.1.1</version>
+		<version>4.0.0</version>
 	</parent>
 	<modelVersion>4.0.0</modelVersion>
 
@@ -35,12 +35,12 @@
 		<dependency>
 			<groupId>bio.overture</groupId>
 			<artifactId>song-java-sdk</artifactId>
-			<version>3.1.1</version>
+			<version>4.0.0</version>
 		</dependency>
 		<dependency>
 			<groupId>bio.overture</groupId>
 			<artifactId>song-core</artifactId>
-			<version>3.1.1</version>
+			<version>4.0.0</version>
 		</dependency>
 
 		<!-- CLI -->

song-client/src/main/java/bio/overture/song/client/Main.java

@@ -1,8 +1,8 @@
 package bio.overture.song.client;
 
 import static bio.overture.song.client.cli.ClientMain.createClientMain;
+import static bio.overture.song.core.utils.Booleans.convertToBoolean;
 import static bio.overture.song.core.utils.JsonDocUtils.getInputStreamClasspath;
-import static java.lang.Boolean.parseBoolean;
 import static java.nio.file.Files.exists;
 import static java.nio.file.Files.newInputStream;
 import static java.util.Objects.isNull;
@@ -62,6 +62,6 @@ private static String getString(String value, String envVar) {
 
   private static boolean getBoolean(boolean value, String envVar) {
     val envValue = System.getenv(envVar);
-    return isNull(envValue) ? value : parseBoolean(envValue);
+    return isNull(envValue) ? value : convertToBoolean(envValue);
   }
 }

song-client/src/main/java/bio/overture/song/client/util/EnumConverter.java

@@ -1,6 +1,6 @@
 package bio.overture.song.client.util;
 
-import static bio.overture.song.core.utils.Joiners.COMMA;
+import static bio.overture.song.core.utils.Separators.COMMA;
 import static java.lang.String.format;
 
 import com.beust.jcommander.IStringConverter;

song-client/src/test/java/bio/overture/song/client/HappyPathClientMainTest.java

@@ -270,7 +270,7 @@ public void testAnalysisSearch() {
             .analysisId(DUMMY_ANALYSIS_ID)
             .analysisState(UNPUBLISHED)
             .analysisType(ANALYSIS_TYPE_ID1)
-            .study(DUMMY_STUDY_ID)
+            .studyId(DUMMY_STUDY_ID)
             .build();
     when(songApi.getAnalysis(DUMMY_STUDY_ID, DUMMY_ANALYSIS_ID)).thenReturn(expectedAnalysis);
     assertOutputJson(objectToTree(expectedAnalysis), "search", "-a", DUMMY_ANALYSIS_ID);
@@ -289,7 +289,7 @@ public void testIdSearch() {
                 .analysisId(DUMMY_ANALYSIS_ID)
                 .analysisState(UNPUBLISHED)
                 .analysisType(ANALYSIS_TYPE_ID1)
-                .study(DUMMY_STUDY_ID)
+                .studyId(DUMMY_STUDY_ID)
                 .build());
 
     when(songApi.idSearch(DUMMY_STUDY_ID, expectedSample.getSampleId(), null, null, null))

song-core/pom.xml

@@ -19,7 +19,7 @@
 	<parent>
 		<artifactId>song</artifactId>
 		<groupId>bio.overture</groupId>
-		<version>3.1.1</version>
+		<version>4.0.0</version>
 	</parent>
 	<modelVersion>4.0.0</modelVersion>
 

song-core/src/main/java/bio/overture/song/core/exceptions/BooleanConversionException.java

@@ -0,0 +1,29 @@
+package bio.overture.song.core.exceptions;
+
+import static java.lang.String.format;
+
+public class BooleanConversionException extends RuntimeException {
+
+  public BooleanConversionException() {}
+
+  public BooleanConversionException(String formattedMessage, Object... args) {
+    super(format(formattedMessage, args));
+  }
+
+  public BooleanConversionException(Throwable cause, String formattedMessage, Object... args) {
+    super(format(formattedMessage, args), cause);
+  }
+
+  public BooleanConversionException(Throwable cause) {
+    super(cause);
+  }
+
+  public BooleanConversionException(
+      Throwable cause,
+      boolean enableSuppression,
+      boolean writableStackTrace,
+      String formattedMessage,
+      Object... args) {
+    super(format(formattedMessage, args), cause, enableSuppression, writableStackTrace);
+  }
+}

song-core/src/main/java/bio/overture/song/core/exceptions/ServerErrors.java

@@ -111,9 +111,11 @@ public enum ServerErrors implements ServerError {
   REST_CLIENT_UNEXPECTED_RESPONSE(BAD_GATEWAY),
   ID_SERVICE_ERROR(BAD_GATEWAY),
   MALFORMED_JSON_SCHEMA(BAD_REQUEST),
+  STORAGE_SERVICE_ERROR(BAD_GATEWAY),
   STORAGE_OBJECT_NOT_FOUND(
       NOT_FOUND), // Used STORAGE instead of SCORE to not tie it to a specific implementation
-  UNKNOWN_ERROR(INTERNAL_SERVER_ERROR);
+  UNKNOWN_ERROR(INTERNAL_SERVER_ERROR),
+  ILLEGAL_ANALYSIS_TYPE_NAME(BAD_REQUEST);
 
   private static final String ERROR_ID_SEPARATOR = ".";
   private static final String ENUM_NAME_SEPARATOR = "_";

song-core/src/main/java/bio/overture/song/core/model/Analysis.java

@@ -18,9 +18,9 @@
 public class Analysis extends DynamicData {
 
   private String analysisId;
-  private String study;
+  private String studyId;
   private AnalysisStates analysisState;
   private AnalysisTypeId analysisType;
-  private List<CompositeSample> sample;
-  private List<FileDTO> file;
+  private List<CompositeSample> samples;
+  private List<FileDTO> files;
 }

song-core/src/main/java/bio/overture/song/core/model/Donor.java

@@ -17,6 +17,6 @@ public class Donor extends Metadata {
 
   private String donorId;
   private String studyId;
-  private String donorSubmitterId;
-  private String donorGender;
+  private String submitterDonorId;
+  private String gender;
 }

song-core/src/main/java/bio/overture/song/core/model/ExportedPayload.java

@@ -17,21 +17,22 @@
 
 package bio.overture.song.core.model;
 
-import com.fasterxml.jackson.annotation.JsonInclude;
 import com.fasterxml.jackson.annotation.JsonPropertyOrder;
 import com.fasterxml.jackson.databind.JsonNode;
 import java.util.List;
-import lombok.NonNull;
-import lombok.Value;
+import lombok.Data;
+import lombok.val;
 
-@Value
+@Data
 @JsonPropertyOrder({"studyId", "payloads"})
-@JsonInclude(JsonInclude.Include.NON_NULL)
 public class ExportedPayload {
-  @NonNull private String studyId;
-  @NonNull private List<JsonNode> payloads;
+  private String studyId;
+  private List<JsonNode> payloads;
 
   public static ExportedPayload createExportedPayload(String studyId, List<JsonNode> payloads) {
-    return new ExportedPayload(studyId, payloads);
+    val p = new ExportedPayload();
+    p.setStudyId(studyId);
+    p.setPayloads(payloads);
+    return p;
   }
 }

song-core/src/main/java/bio/overture/song/core/model/File.java

@@ -28,4 +28,6 @@ public interface File extends FileMetadata, FileContent {
   String getFileName();
 
   String getFileType();
+
+  String getDataType();
 }

song-core/src/main/java/bio/overture/song/core/model/FileDTO.java

@@ -19,4 +19,5 @@ public class FileDTO extends Metadata implements File {
   private String fileMd5sum;
   private Long fileSize;
   private String fileAccess;
+  private String dataType;
 }

song-core/src/main/java/bio/overture/song/core/model/Metadata.java

@@ -39,7 +39,7 @@
 @AllArgsConstructor
 @EqualsAndHashCode
 @ToString
-@JsonInclude(JsonInclude.Include.NON_ABSENT)
+@JsonInclude(JsonInclude.Include.NON_EMPTY)
 public class Metadata {
 
   private final Map<String, Object> info = new TreeMap<>();
@@ -59,6 +59,7 @@ public void setInfo(String info) {
   }
 
   @JsonGetter
+  @JsonInclude(JsonInclude.Include.NON_EMPTY)
   public JsonNode getInfo() {
     return JsonUtils.toJsonNode(info);
   }