Merge pull request #44 from elixir-europe/biosamples-receipt

BioSamples response as per receipt format
elixir-europe · Sep 16, 2024 · b901090 · b901090
2 parents 259eb9a + bf80c49
commit b901090
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Showing 4 changed files with 119 additions and 17 deletions.
diff --git a/repository-services/README.md b/repository-services/README.md
@@ -10,7 +10,7 @@ Change to the correct directory:
 cd repository-test-services
 ```
 
-Use docker compose to deploy both services simultaniously:
+Use docker compose to deploy both services simultaneously:
 
  ```sh
  docker compose up

diff --git a/.../com/elixir/biohackaton/ISAToSRA/biosamples/controller/BioSampleSubmissionController.java b/.../com/elixir/biohackaton/ISAToSRA/biosamples/controller/BioSampleSubmissionController.java
@@ -4,6 +4,9 @@
 import static org.springframework.http.MediaType.APPLICATION_JSON_VALUE;
 import static org.springframework.http.MediaType.APPLICATION_XML_VALUE;
 
+import com.elixir.biohackaton.ISAToSRA.biosamples.receipt.Receipt;
+import com.elixir.biohackaton.ISAToSRA.biosamples.receipt.Receipt.Accession;
+import com.elixir.biohackaton.ISAToSRA.biosamples.receipt.Receipt;
 import com.elixir.biohackaton.ISAToSRA.biosamples.service.BioSamplesSubmitter;
 import com.elixir.biohackaton.ISAToSRA.model.IsaJson;
 import com.elixir.biohackaton.ISAToSRA.model.Study;
@@ -12,6 +15,9 @@
 import io.swagger.v3.oas.annotations.responses.ApiResponse;
 import io.swagger.v3.oas.annotations.responses.ApiResponses;
 import java.util.List;
+import java.util.Map;
+import java.util.stream.Collectors;
+
 import lombok.extern.slf4j.Slf4j;
 import org.springframework.beans.factory.annotation.Autowired;
 import org.springframework.web.bind.annotation.*;
@@ -23,22 +29,22 @@ public class BioSampleSubmissionController {
   @Autowired private ObjectMapper objectMapper;
 
   @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")
-      })
+          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")
+          })
   @CrossOrigin(origins = "http://localhost:8000")
   @PostMapping(
-      value = "/submit",
-      consumes = {APPLICATION_JSON_VALUE, APPLICATION_XML_VALUE})
+          value = "/submit",
+          consumes = {APPLICATION_JSON_VALUE, APPLICATION_XML_VALUE})
   public String performSubmissionToBioSamplesAndEna(
-      @RequestBody final String submissionPayload,
-      @RequestParam(value = "webinjwt") String webinJwt)
-      throws Exception {
+          @RequestBody final String submissionPayload,
+          @RequestParam(value = "webinjwt") String webinJwt)
+          throws Exception {
     String webinToken;
 
     objectMapper.setSerializationInclusion(JsonInclude.Include.NON_NULL);
@@ -52,9 +58,14 @@ public String performSubmissionToBioSamplesAndEna(
     final IsaJson isaJson = this.objectMapper.readValue(submissionPayload, IsaJson.class);
     final List<Study> studies = getStudies(isaJson);
 
-    this.bioSamplesSubmitter.createBioSamples(studies, webinToken);
+    final Map<String, String> accessionsMap = this.bioSamplesSubmitter.createBioSamples(studies, webinToken);
+    final Receipt repositoryData = new Receipt();
+
+    repositoryData.setTargetRepository("biosamples");
+    repositoryData.setAccessions(accessionsMap.values().stream()
+            .map(value -> new Accession(value, null)).collect(Collectors.toList()));
 
-    return this.objectMapper.writerWithDefaultPrettyPrinter().writeValueAsString(isaJson);
+    return this.objectMapper.writerWithDefaultPrettyPrinter().writeValueAsString(repositoryData);
   }
 
   public List<Study> getStudies(final IsaJson isaJson) {

diff --git a/...-biosamples/src/main/java/com/elixir/biohackaton/ISAToSRA/biosamples/receipt/Receipt.java b/...-biosamples/src/main/java/com/elixir/biohackaton/ISAToSRA/biosamples/receipt/Receipt.java
@@ -0,0 +1,89 @@
+package com.elixir.biohackaton.ISAToSRA.biosamples.receipt;
+
+import lombok.Getter;
+
+import java.util.List;
+
+@Getter
+public class Receipt {
+    private String targetRepository;
+    private List<Accession> accessions;
+    private List<Error> errors;
+    private List<Info> info;
+
+    public void setTargetRepository(String targetRepository) {
+        this.targetRepository = targetRepository;
+    }
+
+    public void setAccessions(List<Accession> accessions) {
+        this.accessions = accessions;
+    }
+
+    public void setErrors(List<Error> errors) {
+        this.errors = errors;
+    }
+
+    public void setInfo(List<Info> info) {
+        this.info = info;
+    }
+
+    @Getter
+    public static class Accession {
+        private String id;
+        private String data;
+
+        public Accession(String id, String data) {
+            this.id = id;
+            this.data = data;
+        }
+
+        public void setId(String id) {
+            this.id = id;
+        }
+
+        public void setData(String data) {
+            this.data = data;
+        }
+    }
+
+    // Error class
+    @Getter
+    static class Error {
+        private String code;
+        private String message;
+
+        public Error(String code, String message) {
+            this.code = code;
+            this.message = message;
+        }
+
+        public void setCode(String code) {
+            this.code = code;
+        }
+
+        public void setMessage(String message) {
+            this.message = message;
+        }
+    }
+
+    // Info class
+    @Getter
+    static class Info {
+        // Define fields, constructor, getters, and setters
+        private String key;
+        private String value;
+
+        public Info(String key, String value) {
+            this.key = key;
+            this.value = value;
+        }
+
+        public void setKey(String key) {
+            this.key = key;
+        }
+
+        public void setValue(String value) {
+            this.value = value;
+        }
+    }
+}
diff --git a/.../src/main/java/com/elixir/biohackaton/ISAToSRA/sra/service/WebinExperimentXmlCreator.java b/.../src/main/java/com/elixir/biohackaton/ISAToSRA/sra/service/WebinExperimentXmlCreator.java
@@ -146,7 +146,9 @@ private Map<Integer, String> mapExperiments(
                                       .addText(otherMaterial.getName());
                                   experimentElement
                                       .addElement("STUDY_REF")
-                                      .addAttribute("refname", study.getTitle() + "-" + randomSubmissionIdentifier);
+                                      .addAttribute(
+                                          "refname",
+                                          study.getTitle() + "-" + randomSubmissionIdentifier);
 
                                   final Element designElement =
                                       experimentElement.addElement("DESIGN");