renamed

Dockerfile

@@ -17,7 +17,7 @@ ENV APP_UID 9999
 ENV APP_GID 9999
 
 
-COPY --from=builder /usr/src/app/target/seq-data-*.jar $APP_HOME/seq-data.jar
+COPY --from=builder /usr/src/app/target/muse-*.jar $APP_HOME/muse.jar
 
 RUN addgroup -S -g $APP_GID $APP_USER  \
     && adduser -S -u $APP_UID -G $APP_USER $APP_USER \
@@ -28,5 +28,5 @@ WORKDIR $APP_HOME
 
 USER $APP_UID
 
-CMD ["java", "-ea", "-jar", "/srv/seq-data.jar"]
+CMD ["java", "-ea", "-jar", "/srv/muse.jar"]
 EXPOSE 8080/tcp

Jenkinsfile

@@ -1,13 +1,13 @@
-def dockerRepo = "ghcr.io/cancogen-virus-seq/seq-data"
-def gitHubRepo = "cancogen-virus-seq/seq-data"
+def dockerRepo = "ghcr.io/cancogen-virus-seq/muse"
+def gitHubRepo = "cancogen-virus-seq/muse"
 def chartVersion = "0.1.0"
 def commit = "UNKNOWN"
 def version = "UNKNOWN"
 
 pipeline {
     agent {
         kubernetes {
-            label 'seq-data'
+            label 'muse'
             yaml """
 apiVersion: v1
 kind: Pod
@@ -91,8 +91,8 @@ spec:
 //            steps {
 //                build(job: "/provision/helm", parameters: [
 //                    [$class: 'StringParameterValue', name: 'AP_RDPC_ENV', value: 'dev' ],
-//                    [$class: 'StringParameterValue', name: 'AP_CHART_NAME', value: 'seq-data'],
-//                    [$class: 'StringParameterValue', name: 'AP_RELEASE_NAME', value: 'seq-data'],
+//                    [$class: 'StringParameterValue', name: 'AP_CHART_NAME', value: 'muse'],
+//                    [$class: 'StringParameterValue', name: 'AP_RELEASE_NAME', value: 'muse'],
 //                    [$class: 'StringParameterValue', name: 'AP_HELM_CHART_VERSION', value: "${chartVersion}"],
 //                    [$class: 'StringParameterValue', name: 'AP_ARGS_LINE', value: "--set-string image.tag=${version}-${commit}" ]
 //                ])
@@ -130,8 +130,8 @@ spec:
 //            steps {
 //                build(job: "/provision/helm", parameters: [
 //                    [$class: 'StringParameterValue', name: 'AP_RDPC_ENV', value: 'qa' ],
-//                    [$class: 'StringParameterValue', name: 'AP_CHART_NAME', value: 'seq-data'],
-//                    [$class: 'StringParameterValue', name: 'AP_RELEASE_NAME', value: 'seq-data'],
+//                    [$class: 'StringParameterValue', name: 'AP_CHART_NAME', value: 'muse'],
+//                    [$class: 'StringParameterValue', name: 'AP_RELEASE_NAME', value: 'muse'],
 //                    [$class: 'StringParameterValue', name: 'AP_HELM_CHART_VERSION', value: "${chartVersion}"],
 //                    [$class: 'StringParameterValue', name: 'AP_ARGS_LINE', value: "--set-string image.tag=${version}" ]
 //                ])

pom.xml

@@ -9,9 +9,9 @@
         <relativePath/> <!-- lookup parent from repository -->
     </parent>
     <groupId>org.cancogen-virus-seq</groupId>
-    <artifactId>seq-data</artifactId>
+    <artifactId>muse</artifactId>
     <version>0.0.1-SNAPSHOT</version>
-    <name>seq-data</name>
+    <name>muse</name>
     <description>Service to submit, validate, and download virus-seq data</description>
     <properties>
         <java.version>11</java.version>

src/main/java/org/cancogenvirusseq/seqdata/SeqDataApplication.java → src/main/java/org/cancogenvirusseq/muse/SeqDataApplication.java

@@ -16,7 +16,7 @@
  * ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
  */
 
-package org.cancogenvirusseq.seqdata;
+package org.cancogenvirusseq.muse;
 
 import org.springframework.boot.SpringApplication;
 import org.springframework.boot.autoconfigure.SpringBootApplication;

src/main/java/org/cancogenvirusseq/seqdata/api/ApiController.java → src/main/java/org/cancogenvirusseq/muse/api/ApiController.java

@@ -16,7 +16,7 @@
  * ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
  */
 
-package org.cancogenvirusseq.seqdata.api;
+package org.cancogenvirusseq.muse.api;
 
 import java.nio.ByteBuffer;
 import java.util.Optional;
@@ -26,13 +26,13 @@
 import lombok.RequiredArgsConstructor;
 import lombok.extern.slf4j.Slf4j;
 import lombok.val;
-import org.cancogenvirusseq.seqdata.api.model.DownloadRequest;
-import org.cancogenvirusseq.seqdata.api.model.SubmissionCreateResponse;
-import org.cancogenvirusseq.seqdata.api.model.SubmissionListResponse;
-import org.cancogenvirusseq.seqdata.api.model.UploadListResponse;
-import org.cancogenvirusseq.seqdata.service.DownloadsService;
-import org.cancogenvirusseq.seqdata.service.SubmissionsService;
-import org.cancogenvirusseq.seqdata.service.UploadsService;
+import org.cancogenvirusseq.muse.api.model.DownloadRequest;
+import org.cancogenvirusseq.muse.api.model.SubmissionCreateResponse;
+import org.cancogenvirusseq.muse.api.model.SubmissionListResponse;
+import org.cancogenvirusseq.muse.api.model.UploadListResponse;
+import org.cancogenvirusseq.muse.service.DownloadsService;
+import org.cancogenvirusseq.muse.service.SubmissionsService;
+import org.cancogenvirusseq.muse.service.UploadsService;
 import org.springframework.http.HttpStatus;
 import org.springframework.http.ResponseEntity;
 import org.springframework.http.codec.multipart.FilePart;

src/main/java/org/cancogenvirusseq/seqdata/api/ApiDefinition.java → src/main/java/org/cancogenvirusseq/muse/api/ApiDefinition.java

@@ -16,13 +16,13 @@
  * ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
  */
 
-package org.cancogenvirusseq.seqdata.api;
+package org.cancogenvirusseq.muse.api;
 
 import io.swagger.annotations.*;
 import java.nio.ByteBuffer;
 import java.util.UUID;
 import javax.validation.Valid;
-import org.cancogenvirusseq.seqdata.api.model.*;
+import org.cancogenvirusseq.muse.api.model.*;
 import org.springframework.http.MediaType;
 import org.springframework.http.ResponseEntity;
 import org.springframework.http.codec.multipart.FilePart;

src/main/java/org/cancogenvirusseq/seqdata/api/model/DownloadRequest.java → src/main/java/org/cancogenvirusseq/muse/api/model/DownloadRequest.java

@@ -16,7 +16,7 @@
  * ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
  */
 
-package org.cancogenvirusseq.seqdata.api.model;
+package org.cancogenvirusseq.muse.api.model;
 
 import java.util.List;
 import lombok.AllArgsConstructor;

src/main/java/org/cancogenvirusseq/seqdata/api/model/ErrorResponse.java → src/main/java/org/cancogenvirusseq/muse/api/model/ErrorResponse.java

@@ -16,7 +16,7 @@
  * ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
  */
 
-package org.cancogenvirusseq.seqdata.api.model;
+package org.cancogenvirusseq.muse.api.model;
 
 import io.swagger.annotations.ApiModel;
 import lombok.AllArgsConstructor;

src/main/java/org/cancogenvirusseq/seqdata/api/model/SubmissionCreateResponse.java → src/main/java/org/cancogenvirusseq/muse/api/model/SubmissionCreateResponse.java

@@ -16,7 +16,7 @@
  * ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
  */
 
-package org.cancogenvirusseq.seqdata.api.model;
+package org.cancogenvirusseq.muse.api.model;
 
 import io.swagger.annotations.ApiModel;
 import lombok.AllArgsConstructor;

src/main/java/org/cancogenvirusseq/seqdata/api/model/SubmissionListResponse.java → src/main/java/org/cancogenvirusseq/muse/api/model/SubmissionListResponse.java

@@ -16,15 +16,15 @@
  * ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
  */
 
-package org.cancogenvirusseq.seqdata.api.model;
+package org.cancogenvirusseq.muse.api.model;
 
 import io.swagger.annotations.ApiModel;
 import java.util.List;
 import lombok.AllArgsConstructor;
 import lombok.Builder;
 import lombok.Data;
 import lombok.NonNull;
-import org.cancogenvirusseq.seqdata.model.SubmissionDTO;
+import org.cancogenvirusseq.muse.model.SubmissionDTO;
 
 @Data
 @Builder

src/main/java/org/cancogenvirusseq/seqdata/api/model/UploadListResponse.java → src/main/java/org/cancogenvirusseq/muse/api/model/UploadListResponse.java

@@ -16,15 +16,15 @@
  * ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
  */
 
-package org.cancogenvirusseq.seqdata.api.model;
+package org.cancogenvirusseq.muse.api.model;
 
 import io.swagger.annotations.ApiModel;
 import java.util.List;
 import lombok.AllArgsConstructor;
 import lombok.Builder;
 import lombok.Data;
 import lombok.NonNull;
-import org.cancogenvirusseq.seqdata.model.UploadDTO;
+import org.cancogenvirusseq.muse.model.UploadDTO;
 
 @Data
 @Builder

src/main/java/org/cancogenvirusseq/seqdata/components/FilePayloadMapper.java → src/main/java/org/cancogenvirusseq/muse/components/FilePayloadMapper.java

@@ -1,4 +1,4 @@
-package org.cancogenvirusseq.seqdata.components;
+package org.cancogenvirusseq.muse.components;
 
 import com.fasterxml.jackson.databind.JsonNode;
 import com.fasterxml.jackson.databind.node.JsonNodeFactory;
@@ -8,7 +8,7 @@
 import java.util.function.Function;
 import lombok.RequiredArgsConstructor;
 import lombok.val;
-import org.cancogenvirusseq.seqdata.model.FileMeta;
+import org.cancogenvirusseq.muse.model.FileMeta;
 import reactor.core.publisher.Flux;
 
 @RequiredArgsConstructor

src/main/java/org/cancogenvirusseq/seqdata/components/FileProcessor.java → src/main/java/org/cancogenvirusseq/muse/components/FileProcessor.java

@@ -1,4 +1,4 @@
-package org.cancogenvirusseq.seqdata.components;
+package org.cancogenvirusseq.muse.components;
 
 import com.google.common.hash.HashCode;
 import com.google.common.hash.Hashing;
@@ -10,7 +10,7 @@
 import java.util.concurrent.ConcurrentHashMap;
 import lombok.SneakyThrows;
 import lombok.val;
-import org.cancogenvirusseq.seqdata.model.FileMeta;
+import org.cancogenvirusseq.muse.model.FileMeta;
 
 public class FileProcessor {
   public static final String FASTA_TYPE = "FASTA";

src/main/java/org/cancogenvirusseq/seqdata/components/TsvParser.java → src/main/java/org/cancogenvirusseq/muse/components/TsvParser.java

@@ -1,4 +1,4 @@
-package org.cancogenvirusseq.seqdata.components;
+package org.cancogenvirusseq.muse.components;
 
 import com.fasterxml.jackson.core.JsonProcessingException;
 import com.fasterxml.jackson.databind.ObjectMapper;
@@ -12,7 +12,7 @@
 import lombok.val;
 import org.apache.velocity.VelocityContext;
 import org.apache.velocity.app.Velocity;
-import org.cancogenvirusseq.seqdata.model.TsvParserProperties;
+import org.cancogenvirusseq.muse.model.TsvParserProperties;
 import reactor.core.publisher.Flux;
 
 @Slf4j

src/main/java/org/cancogenvirusseq/seqdata/config/SwaggerConfig.java → src/main/java/org/cancogenvirusseq/muse/config/SwaggerConfig.java

@@ -16,7 +16,7 @@
  * ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
  */
 
-package org.cancogenvirusseq.seqdata.config;
+package org.cancogenvirusseq.muse.config;
 
 import static java.util.Collections.singletonList;
 

src/main/java/org/cancogenvirusseq/seqdata/config/TsvParserConfig.java → src/main/java/org/cancogenvirusseq/muse/config/TsvParserConfig.java

@@ -1,4 +1,4 @@
-package org.cancogenvirusseq.seqdata.config;
+package org.cancogenvirusseq.muse.config;
 
 import com.fasterxml.jackson.core.type.TypeReference;
 import com.fasterxml.jackson.databind.ObjectMapper;
@@ -10,8 +10,8 @@
 import lombok.SneakyThrows;
 import lombok.extern.slf4j.Slf4j;
 import lombok.val;
-import org.cancogenvirusseq.seqdata.model.TsvFieldSchema;
-import org.cancogenvirusseq.seqdata.model.TsvParserProperties;
+import org.cancogenvirusseq.muse.model.TsvFieldSchema;
+import org.cancogenvirusseq.muse.model.TsvParserProperties;
 import org.springframework.context.annotation.Bean;
 import org.springframework.context.annotation.Configuration;
 

src/main/java/org/cancogenvirusseq/seqdata/config/websecurity/AuthDisabledConfig.java → src/main/java/org/cancogenvirusseq/muse/config/websecurity/AuthDisabledConfig.java

@@ -16,7 +16,7 @@
  * ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
  */
 
-package org.cancogenvirusseq.seqdata.config.websecurity;
+package org.cancogenvirusseq.muse.config.websecurity;
 
 import org.springframework.context.annotation.Bean;
 import org.springframework.context.annotation.Profile;

src/main/java/org/cancogenvirusseq/seqdata/config/websecurity/AuthEnabledConfig.java → src/main/java/org/cancogenvirusseq/muse/config/websecurity/AuthEnabledConfig.java

@@ -16,7 +16,7 @@
  * ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
  */
 
-package org.cancogenvirusseq.seqdata.config.websecurity;
+package org.cancogenvirusseq.muse.config.websecurity;
 
 import static java.util.stream.Collectors.toList;
 import static java.util.stream.Collectors.toUnmodifiableList;

src/main/java/org/cancogenvirusseq/seqdata/config/websecurity/AuthProperties.java → src/main/java/org/cancogenvirusseq/muse/config/websecurity/AuthProperties.java

@@ -16,7 +16,7 @@
  * ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
  */
 
-package org.cancogenvirusseq.seqdata.config.websecurity;
+package org.cancogenvirusseq.muse.config.websecurity;
 
 import com.google.common.collect.ImmutableList;
 import java.util.List;

src/main/java/org/cancogenvirusseq/seqdata/model/FileMeta.java → src/main/java/org/cancogenvirusseq/muse/model/FileMeta.java

@@ -1,4 +1,4 @@
-package org.cancogenvirusseq.seqdata.model;
+package org.cancogenvirusseq.muse.model;
 
 import lombok.Builder;
 import lombok.Value;

src/main/java/org/cancogenvirusseq/seqdata/model/SubmissionDTO.java → src/main/java/org/cancogenvirusseq/muse/model/SubmissionDTO.java

@@ -16,7 +16,7 @@
  * ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
  */
 
-package org.cancogenvirusseq.seqdata.model;
+package org.cancogenvirusseq.muse.model;
 
 import java.time.LocalDateTime;
 import java.util.List;

src/main/java/org/cancogenvirusseq/seqdata/model/TsvFieldSchema.java → src/main/java/org/cancogenvirusseq/muse/model/TsvFieldSchema.java

@@ -1,4 +1,4 @@
-package org.cancogenvirusseq.seqdata.model;
+package org.cancogenvirusseq.muse.model;
 
 import lombok.AllArgsConstructor;
 import lombok.Data;

src/main/java/org/cancogenvirusseq/seqdata/model/TsvParserProperties.java → src/main/java/org/cancogenvirusseq/muse/model/TsvParserProperties.java

@@ -1,4 +1,4 @@
-package org.cancogenvirusseq.seqdata.model;
+package org.cancogenvirusseq.muse.model;
 
 import com.google.common.collect.ImmutableList;
 import lombok.Value;

src/main/java/org/cancogenvirusseq/seqdata/model/UploadDTO.java → src/main/java/org/cancogenvirusseq/muse/model/UploadDTO.java

@@ -16,7 +16,7 @@
  * ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
  */
 
-package org.cancogenvirusseq.seqdata.model;
+package org.cancogenvirusseq.muse.model;
 
 import java.util.List;
 import java.util.UUID;

src/main/java/org/cancogenvirusseq/seqdata/model/UploadStatus.java → src/main/java/org/cancogenvirusseq/muse/model/UploadStatus.java

@@ -16,7 +16,7 @@
  * ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
  */
 
-package org.cancogenvirusseq.seqdata.model;
+package org.cancogenvirusseq.muse.model;
 
 import lombok.RequiredArgsConstructor;
 

src/main/java/org/cancogenvirusseq/seqdata/service/DownloadsService.java → src/main/java/org/cancogenvirusseq/muse/service/DownloadsService.java

@@ -16,10 +16,10 @@
  * ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
  */
 
-package org.cancogenvirusseq.seqdata.service;
+package org.cancogenvirusseq.muse.service;
 
 import java.nio.ByteBuffer;
-import org.cancogenvirusseq.seqdata.api.model.DownloadRequest;
+import org.cancogenvirusseq.muse.api.model.DownloadRequest;
 import org.springframework.stereotype.Service;
 import reactor.core.publisher.Flux;
 import reactor.core.publisher.Mono;

src/main/java/org/cancogenvirusseq/seqdata/service/SubmissionsService.java → src/main/java/org/cancogenvirusseq/muse/service/SubmissionsService.java

@@ -16,15 +16,15 @@
  * ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
  */
 
-package org.cancogenvirusseq.seqdata.service;
+package org.cancogenvirusseq.muse.service;
 
 import java.nio.charset.StandardCharsets;
 import java.util.Collections;
 import java.util.stream.Collectors;
 import lombok.extern.slf4j.Slf4j;
 import lombok.val;
-import org.cancogenvirusseq.seqdata.api.model.SubmissionCreateResponse;
-import org.cancogenvirusseq.seqdata.api.model.SubmissionListResponse;
+import org.cancogenvirusseq.muse.api.model.SubmissionCreateResponse;
+import org.cancogenvirusseq.muse.api.model.SubmissionListResponse;
 import org.springframework.core.io.buffer.DataBufferUtils;
 import org.springframework.http.codec.multipart.FilePart;
 import org.springframework.stereotype.Service;

src/main/java/org/cancogenvirusseq/seqdata/service/UploadsService.java → src/main/java/org/cancogenvirusseq/muse/service/UploadsService.java

@@ -16,12 +16,12 @@
  * ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
  */
 
-package org.cancogenvirusseq.seqdata.service;
+package org.cancogenvirusseq.muse.service;
 
 import java.util.Collections;
 import java.util.Optional;
 import java.util.UUID;
-import org.cancogenvirusseq.seqdata.api.model.UploadListResponse;
+import org.cancogenvirusseq.muse.api.model.UploadListResponse;
 import org.springframework.stereotype.Service;
 import reactor.core.publisher.Mono;
 

src/test/java/org/cancogenvirusseq/seqdata/SeqDataApplicationTests.java → src/test/java/org/cancogenvirusseq/muse/SeqDataApplicationTests.java

@@ -16,7 +16,7 @@
  * ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
  */
 
-package org.cancogenvirusseq.seqdata;
+package org.cancogenvirusseq.muse;
 
 import org.junit.jupiter.api.Test;
 import org.springframework.boot.test.context.SpringBootTest;