Merge pull request #38 from elixir-europe/ena-mars-receipt

Ena mars receipt

repository-services/isajson-ena/src/main/java/com/elixir/biohackaton/ISAToSRA/controller/WebinIsaToXmlSubmissionController.java

@@ -9,6 +9,8 @@
 import com.elixir.biohackaton.ISAToSRA.model.IsaJson;
 import com.elixir.biohackaton.ISAToSRA.model.Study;
 import com.elixir.biohackaton.ISAToSRA.sra.service.*;
+import com.elixir.biohackaton.ISAToSRA.sra.model.MarsReceipt;
+import com.elixir.biohackaton.ISAToSRA.sra.model.Receipt;
 import com.fasterxml.jackson.databind.ObjectMapper;
 import io.swagger.v3.oas.annotations.responses.ApiResponse;
 import io.swagger.v3.oas.annotations.responses.ApiResponses;
@@ -30,34 +32,42 @@
 @Slf4j
 @RestController
 public class WebinIsaToXmlSubmissionController {
-  @Autowired private BioSamplesAccessionsParser bioSamplesAccessionsParser;
+  @Autowired
+  private BioSamplesAccessionsParser bioSamplesAccessionsParser;
 
-  @Autowired private WebinStudyXmlCreator webinStudyXmlCreator;
+  @Autowired
+  private WebinStudyXmlCreator webinStudyXmlCreator;
 
-  @Autowired private WebinExperimentXmlCreator webinExperimentXmlCreator;
+  @Autowired
+  private WebinExperimentXmlCreator webinExperimentXmlCreator;
 
-  @Autowired private WebinProjectXmlCreator webinProjectXmlCreator;
+  @Autowired
+  private WebinProjectXmlCreator webinProjectXmlCreator;
 
-  @Autowired private WebinRunXmlCreator webinRunXmlCreator;
+  @Autowired
+  private WebinRunXmlCreator webinRunXmlCreator;
 
-  @Autowired private WebinHttpSubmissionService webinHttpSubmissionService;
+  @Autowired
+  private WebinHttpSubmissionService webinHttpSubmissionService;
 
-  @Autowired private ObjectMapper objectMapper;
+  @Autowired
+  private ObjectMapper objectMapper;
 
-  @Autowired private ReceiptConversionService receiptConversionService;
+  @Autowired
+  private ReceiptConversionService receiptConversionService;
 
-  @ApiResponses(
-      value = {
-        @ApiResponse(responseCode = "200", description = "Ok"),
-        @ApiResponse(responseCode = "401", description = "Unauthorized"),
-        @ApiResponse(responseCode = "403", description = "Forbidden"),
-        @ApiResponse(responseCode = "400", description = "Bad request"),
-        @ApiResponse(responseCode = "408", description = "Request Timeout"),
-        @ApiResponse(responseCode = "415", description = "Unsupported media type")
-      })
-  @PostMapping(
-      value = "/submit",
-      consumes = {APPLICATION_JSON_VALUE, APPLICATION_XML_VALUE})
+  @Autowired
+  private ReceiptMarsService receiptMarsService;
+
+  @ApiResponses(value = {
+      @ApiResponse(responseCode = "200", description = "Ok"),
+      @ApiResponse(responseCode = "401", description = "Unauthorized"),
+      @ApiResponse(responseCode = "403", description = "Forbidden"),
+      @ApiResponse(responseCode = "400", description = "Bad request"),
+      @ApiResponse(responseCode = "408", description = "Request Timeout"),
+      @ApiResponse(responseCode = "415", description = "Unsupported media type")
+  })
+  @PostMapping(value = "/submit", consumes = { APPLICATION_JSON_VALUE, APPLICATION_XML_VALUE })
   public String performSubmissionToEna(
       @RequestBody final String submissionPayload,
       @RequestParam(value = "webinUserName") String webinUserName,
@@ -73,9 +83,8 @@ public String performSubmissionToEna(
 
     final IsaJson isaJson = this.objectMapper.readValue(submissionPayload, IsaJson.class);
     final List<Study> studies = getStudies(isaJson);
-    final Map<String, String> typeToBioSamplesAccessionMap =
-        this.bioSamplesAccessionsParser.parseIsaFileAndGetBioSampleAccessions(
-            studies, new HashMap<>());
+    final Map<String, String> typeToBioSamplesAccessionMap = this.bioSamplesAccessionsParser
+        .parseIsaFileAndGetBioSampleAccessions(studies, new HashMap<>());
 
     final Document document = DocumentHelper.createDocument();
     final Element webinElement = startPreparingWebinV2SubmissionXml(document);
@@ -84,9 +93,8 @@ public String performSubmissionToEna(
     this.webinStudyXmlCreator.createENAStudySetElement(
         webinElement, studies, randomSubmissionIdentifier);
 
-    final Map<Integer, String> experimentSequenceMap =
-        this.webinExperimentXmlCreator.createENAExperimentSetElement(
-            typeToBioSamplesAccessionMap, webinElement, studies, randomSubmissionIdentifier);
+    final Map<Integer, String> experimentSequenceMap = this.webinExperimentXmlCreator.createENAExperimentSetElement(
+        typeToBioSamplesAccessionMap, webinElement, studies, randomSubmissionIdentifier);
 
     this.webinRunXmlCreator.createENARunSetElement(
         webinElement, studies, experimentSequenceMap, randomSubmissionIdentifier);
@@ -98,11 +106,12 @@ public String performSubmissionToEna(
 
     writer.write(document);
 
-    final String receiptXml =
-        webinHttpSubmissionService.performWebinSubmission(
-            webinUserName, document.asXML(), webinPassword);
+    final String receiptXml = webinHttpSubmissionService.performWebinSubmission(
+        webinUserName, document.asXML(), webinPassword);
+    final Receipt receiptJson = receiptConversionService.readReceiptXml(receiptXml);
+    final MarsReceipt marsReceipt = receiptMarsService.convertReceiptToMars(receiptJson, isaJson);
 
-    return receiptConversionService.convertReceiptXmlToJson(receiptXml);
+    return receiptMarsService.convertMarsReceiptToJson(marsReceipt);
   }
 
   public List<Study> getStudies(final IsaJson isaJson) {

repository-services/isajson-ena/src/main/java/com/elixir/biohackaton/ISAToSRA/sra/model/MarsReceipt.java

@@ -0,0 +1,16 @@
+package com.elixir.biohackaton.ISAToSRA.sra.model;
+
+import lombok.Builder;
+import lombok.Data;
+
+@Builder
+@Data
+public class MarsReceipt {
+    private String targetRepository;
+
+    private MarsReceiptError[] errors;
+
+    private MarsReceiptInfo[] info;
+
+    private MarsReceiptAccession[] accessions;
+}

repository-services/isajson-ena/src/main/java/com/elixir/biohackaton/ISAToSRA/sra/model/MarsReceiptAccession.java

@@ -0,0 +1,12 @@
+package com.elixir.biohackaton.ISAToSRA.sra.model;
+
+import lombok.Builder;
+import lombok.Data;
+
+@Builder
+@Data
+public class MarsReceiptAccession {
+    private String value;
+
+    private MarsReceiptPath[] path;
+}

repository-services/isajson-ena/src/main/java/com/elixir/biohackaton/ISAToSRA/sra/model/MarsReceiptError.java

@@ -0,0 +1,18 @@
+package com.elixir.biohackaton.ISAToSRA.sra.model;
+
+import com.fasterxml.jackson.annotation.JsonInclude;
+import com.fasterxml.jackson.annotation.JsonInclude.Include;
+
+import lombok.Builder;
+import lombok.Data;
+
+@Builder
+@Data
+public class MarsReceiptError {
+    private MarsReceiptErrorType type;
+
+    private String message;
+
+    @JsonInclude(Include.NON_NULL)
+    private MarsReceiptPath[] path;
+}

repository-services/isajson-ena/src/main/java/com/elixir/biohackaton/ISAToSRA/sra/model/MarsReceiptErrorType.java

@@ -0,0 +1,6 @@
+package com.elixir.biohackaton.ISAToSRA.sra.model;
+
+public enum MarsReceiptErrorType {
+    INVALID_METADATA,
+    INVALID_DATA;
+}

repository-services/isajson-ena/src/main/java/com/elixir/biohackaton/ISAToSRA/sra/model/MarsReceiptInfo.java

@@ -0,0 +1,16 @@
+package com.elixir.biohackaton.ISAToSRA.sra.model;
+
+import com.fasterxml.jackson.annotation.JsonInclude;
+import com.fasterxml.jackson.annotation.JsonInclude.Include;
+
+import lombok.Builder;
+import lombok.Data;
+
+@Builder
+@Data
+public class MarsReceiptInfo {
+    @JsonInclude(Include.NON_NULL)
+    private String name;
+
+    private String message;
+}

repository-services/isajson-ena/src/main/java/com/elixir/biohackaton/ISAToSRA/sra/model/MarsReceiptMessage.java

@@ -0,0 +1,18 @@
+package com.elixir.biohackaton.ISAToSRA.sra.model;
+
+import lombok.Builder;
+import lombok.Data;
+import lombok.Builder.Default;
+
+import java.util.List;
+import java.util.ArrayList;
+
+@Builder
+@Data
+public class MarsReceiptMessage {
+    @Default
+    private List<MarsReceiptError> errors = new ArrayList<>();
+
+    @Default
+    private List<MarsReceiptInfo> info= new ArrayList<>();
+}

repository-services/isajson-ena/src/main/java/com/elixir/biohackaton/ISAToSRA/sra/model/MarsReceiptPath.java

@@ -0,0 +1,16 @@
+package com.elixir.biohackaton.ISAToSRA.sra.model;
+
+import com.fasterxml.jackson.annotation.JsonInclude;
+import com.fasterxml.jackson.annotation.JsonInclude.Include;
+
+import lombok.Builder;
+import lombok.Data;
+
+@Builder
+@Data
+public class MarsReceiptPath {
+    private String key;
+
+    @JsonInclude(Include.NON_NULL)
+    private MarsReceiptWhere where;
+}

repository-services/isajson-ena/src/main/java/com/elixir/biohackaton/ISAToSRA/sra/model/MarsReceiptWhere.java

@@ -0,0 +1,12 @@
+package com.elixir.biohackaton.ISAToSRA.sra.model;
+
+import lombok.Builder;
+import lombok.Data;
+
+@Builder
+@Data
+public class MarsReceiptWhere {
+    private String key;
+
+    private String value;
+}