MarsReceiptException (RuntimeException)

elixir-europe · Nov 12, 2024 · 2d72fcb · 2d72fcb
1 parent f3e7f59
commit 2d72fcb
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Showing 9 changed files with 112 additions and 62 deletions.
diff --git a/.../com/elixir/biohackaton/ISAToSRA/biosamples/controller/BioSampleSubmissionController.java b/.../com/elixir/biohackaton/ISAToSRA/biosamples/controller/BioSampleSubmissionController.java
@@ -4,21 +4,27 @@
 import static org.springframework.http.MediaType.APPLICATION_JSON_VALUE;
 import static org.springframework.http.MediaType.APPLICATION_XML_VALUE;
 
+import java.util.List;
+
+import org.springframework.beans.factory.annotation.Autowired;
+import org.springframework.web.bind.annotation.CrossOrigin;
+import org.springframework.web.bind.annotation.PostMapping;
+import org.springframework.web.bind.annotation.RequestBody;
+import org.springframework.web.bind.annotation.RequestParam;
+import org.springframework.web.bind.annotation.RestController;
+
 import com.elixir.biohackaton.ISAToSRA.biosamples.model.BiosampleAccessionsMap;
 import com.elixir.biohackaton.ISAToSRA.biosamples.service.BioSamplesSubmitter;
 import com.elixir.biohackaton.ISAToSRA.biosamples.service.MarsReceiptService;
-import com.elixir.biohackaton.ISAToSRA.receipt.isamodel.*;
-import com.elixir.biohackaton.ISAToSRA.receipt.marsmodel.MarsReceipt;
+import com.elixir.biohackaton.ISAToSRA.receipt.MarsReceiptException;
+import com.elixir.biohackaton.ISAToSRA.receipt.isamodel.IsaJson;
+import com.elixir.biohackaton.ISAToSRA.receipt.isamodel.Study;
 import com.fasterxml.jackson.annotation.JsonInclude;
 import com.fasterxml.jackson.databind.ObjectMapper;
+
 import io.swagger.v3.oas.annotations.responses.ApiResponse;
 import io.swagger.v3.oas.annotations.responses.ApiResponses;
-
-import java.util.List;
-
 import lombok.extern.slf4j.Slf4j;
-import org.springframework.beans.factory.annotation.Autowired;
-import org.springframework.web.bind.annotation.*;
 
 @Slf4j
 @RestController
@@ -42,33 +48,40 @@ public class BioSampleSubmissionController {
     consumes = { APPLICATION_JSON_VALUE, APPLICATION_XML_VALUE })
   public String performSubmissionToBioSamplesAndEna(
       @RequestBody final String submissionPayload,
-      @RequestParam(value = "webinjwt") String webinJwt)
-      throws Exception {
-    String webinToken;
-    if (webinJwt != null) {
-      webinToken = webinJwt;
-    } else {
-      throw new RuntimeException("Webin Authentication Token is not provided");
-    }
+      @RequestParam(value = "webinjwt") String webinJwt) {
+    try {
+      String webinToken;
+      if (webinJwt != null) {
+        webinToken = webinJwt;
+      } else {
+        throw new RuntimeException("Webin Authentication Token is not provided");
+      }
 
-    objectMapper.setSerializationInclusion(JsonInclude.Include.NON_NULL);
+      objectMapper.setSerializationInclusion(JsonInclude.Include.NON_NULL);
 
-    final IsaJson isaJson = this.objectMapper.readValue(submissionPayload, IsaJson.class);
-    final List<Study> studies = getStudies(isaJson);
+      final IsaJson isaJson = this.objectMapper.readValue(submissionPayload, IsaJson.class);
+      final List<Study> studies = getStudies(isaJson);
 
-    final BiosampleAccessionsMap accessionsMap = this.bioSamplesSubmitter.createBioSamples(studies, webinToken);
-    final MarsReceipt marsReceipt = marsReceiptService.convertReceiptToMars(accessionsMap, isaJson);
+      final BiosampleAccessionsMap accessionsMap = this.bioSamplesSubmitter.createBioSamples(studies, webinToken);
+      marsReceiptService.convertReceiptToMars(accessionsMap, isaJson);
 
-    return marsReceiptService.convertMarsReceiptToJson(marsReceipt);
+      return marsReceiptService.convertMarsReceiptToJson();
+    } catch (final MarsReceiptException e) {
+      log.error("Mars receipt excption", e);
+      marsReceiptService.setMarsReceiptErrors(e.getReceiptErrorMessage());
+      return marsReceiptService.convertMarsReceiptToJson();
+    } catch (final Exception e) {
+      log.error("Internal server error", e);
+      marsReceiptService.setMarsReceiptErrors(e.getMessage());
+      return marsReceiptService.convertMarsReceiptToJson();
+    }
   }
 
   public List<Study> getStudies(final IsaJson isaJson) {
     try {
       return isaJson.getInvestigation().getStudies();
     } catch (final Exception e) {
-      log.info("Failed to parse ISA JSON and get studies", e);
+      throw new MarsReceiptException("Failed to parse ISA JSON and get studies", e);
     }
-
-    return null;
   }
 }
diff --git a/...src/main/java/com/elixir/biohackaton/ISAToSRA/biosamples/service/BioSamplesSubmitter.java b/...src/main/java/com/elixir/biohackaton/ISAToSRA/biosamples/service/BioSamplesSubmitter.java
@@ -5,6 +5,7 @@
 import com.elixir.biohackaton.ISAToSRA.biosamples.model.BiosampleAccessionsMap;
 import com.elixir.biohackaton.ISAToSRA.biosamples.model.Relationship;
 import com.elixir.biohackaton.ISAToSRA.biosamples.model.BioSample;
+import com.elixir.biohackaton.ISAToSRA.receipt.MarsReceiptException;
 import com.elixir.biohackaton.ISAToSRA.receipt.ReceiptAccessionsMap;
 import com.elixir.biohackaton.ISAToSRA.receipt.isamodel.*;
 
@@ -80,7 +81,7 @@ public BiosampleAccessionsMap createBioSamples(final List<Study> studies, final
             });
       }
     } catch (final Exception e) {
-      throw new RuntimeException("Failed to parse ISA Json and create samples in BioSamples", e);
+      throw new MarsReceiptException("Failed to parse ISA Json and create samples in BioSamples", e);
     }
 
     return typeToBioSamplesAccessionMap;
@@ -122,7 +123,7 @@ private BioSample createAndUpdateChildSampleWithRelationship(
         return null;
       }
     } catch (final Exception e) {
-      throw new RuntimeException("Failed to handle child samples", e);
+      throw new MarsReceiptException("Failed to handle child samples", e);
     }
   }
 
@@ -165,7 +166,7 @@ private BioSample createSourceBioSample(final List<Study> studies, final String
                     sourceCharacteristics.add(biosampleAccessionCharacteristic);
                     source.setCharacteristics(sourceCharacteristics);
                   } else {
-                    throw new RuntimeException("Failed to store source sample to BioSamples");
+                    throw new MarsReceiptException("Failed to store source sample to BioSamples");
                   }
                 }));
 
@@ -205,7 +206,7 @@ private BioSample updateSampleWithRelationshipsToBioSamples(
           });
       return biosamplesResponse.getBody().getContent();
     } catch (final Exception ex) {
-      throw new RuntimeException("Failed to add relationships to child samples", ex);
+      throw new MarsReceiptException("Failed to add relationships to child samples", ex);
     }
   }
 
@@ -227,7 +228,7 @@ private EntityModel<BioSample> createSampleInBioSamples(
 
       return biosamplesResponse.getBody();
     } catch (final Exception ex) {
-      throw new RuntimeException("Failed to create samples in BioSamples", ex);
+      throw new MarsReceiptException("Failed to create samples in BioSamples", ex);
     }
   }
 

diff --git a/.../src/main/java/com/elixir/biohackaton/ISAToSRA/biosamples/service/MarsReceiptService.java b/.../src/main/java/com/elixir/biohackaton/ISAToSRA/biosamples/service/MarsReceiptService.java
@@ -1,17 +1,22 @@
 /** Elixir BioHackathon 2022 */
 package com.elixir.biohackaton.ISAToSRA.biosamples.service;
 
+import javax.servlet.http.HttpServletRequest;
+import javax.servlet.http.HttpServletResponse;
+
+import org.springframework.stereotype.Service;
+import org.springframework.web.servlet.HandlerInterceptor;
+
 import com.elixir.biohackaton.ISAToSRA.biosamples.model.BiosampleAccessionsMap;
 import com.elixir.biohackaton.ISAToSRA.receipt.MarsReceiptProvider;
-import com.elixir.biohackaton.ISAToSRA.receipt.isamodel.*;
-import com.elixir.biohackaton.ISAToSRA.receipt.marsmodel.*;
+import com.elixir.biohackaton.ISAToSRA.receipt.isamodel.IsaJson;
+import com.elixir.biohackaton.ISAToSRA.receipt.marsmodel.MarsErrorType;
 import com.fasterxml.jackson.annotation.JsonInclude;
 import com.fasterxml.jackson.databind.ObjectMapper;
 import com.fasterxml.jackson.databind.SerializationFeature;
-import org.springframework.stereotype.Service;
 
 @Service
-public class MarsReceiptService extends MarsReceiptProvider {
+public class MarsReceiptService extends MarsReceiptProvider implements HandlerInterceptor {
   private final ObjectMapper jsonMapper = new ObjectMapper();
 
   private void setupJsonMapper() {
@@ -21,29 +26,42 @@ private void setupJsonMapper() {
   }
 
   public MarsReceiptService() {
+    super("biosamples"); // TODO decide whether to use instead
+    // https://registry.identifiers.org/registry/biosample
     setupJsonMapper();
   }
 
-  public String convertMarsReceiptToJson(final MarsReceipt marsReceipt) {
+  // Reset MARS receipt per request
+  @Override
+  public boolean preHandle(HttpServletRequest request, HttpServletResponse response, Object handler)
+      throws Exception {
+    resetMarsReceipt();
+    return HandlerInterceptor.super.preHandle(request, response, handler);
+  }
+
+  public String convertMarsReceiptToJson() {
     try {
-      return jsonMapper.writeValueAsString(marsReceipt);
+      return jsonMapper.writeValueAsString(getMarsReceipt());
     } catch (Exception ex) {
-      throw new RuntimeException("receipt", ex);
+      throw new RuntimeException("Receipt", ex);
     }
   }
 
+  public void setMarsReceiptErrors(String... errors) {
+    super.setMarsReceiptErrors(MarsErrorType.INTERNAL_SERVER_ERROR, errors);
+  }
+
   /**
    * Converting BioSample receipt to Mars data format
    *
    * @see
    *      https://github.com/elixir-europe/MARS/blob/refactor/repository-services/repository-api.md#response
-   * @param biosampleAccessionsMap {@link BiosampleAccessionsMap} Receipt from Biosample
-   * @param isaJson {@link IsaJson} Requested ISA-Json
-   * @return {@link MarsReceipt} Mars response data
+   * @param biosampleAccessionsMap {@link BiosampleAccessionsMap} Receipt from
+   *                               Biosample
+   * @param isaJson                {@link IsaJson} Requested ISA-Json
    */
-  public MarsReceipt convertReceiptToMars(final BiosampleAccessionsMap biosampleAccessionsMap, final IsaJson isaJson) {
-    return buildMarsReceipt(
-        "biosamples", // https://registry.identifiers.org/registry/biosample
+  public void convertReceiptToMars(final BiosampleAccessionsMap biosampleAccessionsMap, final IsaJson isaJson) {
+    buildMarsReceipt(
         biosampleAccessionsMap.studyAccessionsMap,
         biosampleAccessionsMap.sampleAccessionsMap,
         biosampleAccessionsMap.sourceAccessionsMap,

diff --git a/...in/java/com/elixir/biohackaton/ISAToSRA/controller/WebinIsaToXmlSubmissionController.java b/...in/java/com/elixir/biohackaton/ISAToSRA/controller/WebinIsaToXmlSubmissionController.java
@@ -4,6 +4,7 @@
 import static org.springframework.http.MediaType.APPLICATION_JSON_VALUE;
 import static org.springframework.http.MediaType.APPLICATION_XML_VALUE;
 
+import com.elixir.biohackaton.ISAToSRA.receipt.MarsReceiptException;
 import com.elixir.biohackaton.ISAToSRA.receipt.isamodel.*;
 import com.elixir.biohackaton.ISAToSRA.sra.model.Receipt;
 import com.elixir.biohackaton.ISAToSRA.sra.service.MarsReceiptService;
@@ -69,11 +70,11 @@ public String performSubmissionToEna(
       @RequestParam(value = "webinPassword") String webinPassword) {
     try {
       if (webinUserName == null || webinUserName.isEmpty()) {
-        throw new Exception("Webin Authentication username is not provided");
+        throw new MarsReceiptException("Webin Authentication username is not provided");
       }
 
       if (webinPassword == null || webinPassword.isEmpty()) {
-        throw new Exception("Webin Authentication password is not provided");
+        throw new MarsReceiptException("Webin Authentication password is not provided");
       }
 
       final IsaJson isaJson = this.objectMapper.readValue(submissionPayload, IsaJson.class);
@@ -111,7 +112,11 @@ public String performSubmissionToEna(
 
       return marsReceiptService.convertMarsReceiptToJson();
 
-    } catch (Exception e) {
+    } catch (final MarsReceiptException e) {
+      log.error("Mars receipt excption", e);
+      marsReceiptService.setMarsReceiptErrors(e.getReceiptErrorMessage());
+      return marsReceiptService.convertMarsReceiptToJson();
+    } catch (final Exception e) {
       log.error("Internal server error", e);
       marsReceiptService.setMarsReceiptErrors(e.getMessage());
       return marsReceiptService.convertMarsReceiptToJson();
@@ -122,23 +127,19 @@ public List<Study> getStudies(final IsaJson isaJson) {
     try {
       return isaJson.getInvestigation().getStudies();
     } catch (final Exception e) {
-      log.info("Failed to parse ISA JSON and get studies", e);
+      throw new MarsReceiptException("Failed to parse ISA JSON and get studies", e);
     }
-
-    return null;
   }
 
   public Investigation getInvestigation(final IsaJson isaJson) {
     try {
       return isaJson.getInvestigation();
     } catch (final Exception e) {
-      log.info("Failed to parse ISA JSON and get studies", e);
+      throw new MarsReceiptException("Failed to parse ISA JSON and get studies", e);
     }
-
-    return null;
   }
 
-  public Map<String, String> getBiosamples(List<Study> studies) {
+  public Map<String, String> getBiosamples(List<Study> studies) throws Exception {
     HashMap<String, String> biosamples = new HashMap<>();
     for (Study study : studies) {
       for (Source source : study.materials.sources) {
@@ -162,13 +163,11 @@ private String getCharacteresticAnnotation(List<Characteristic> characteristics)
             .collect(Collectors.toList());
 
     if (filteredCharacteristics.isEmpty()) {
-      log.error("No accession found in the characteristics");
-      throw new RuntimeException("No accession found in the characteristics");
+      throw new MarsReceiptException("No accession found in the characteristics");
     }
 
     if (filteredCharacteristics.size() > 1) {
-      log.error("More than one accession found in the characteristics");
-      throw new RuntimeException("Too many accessions found in the characteristics");
+      throw new MarsReceiptException("Too many accessions found in the characteristics");
     }
     return filteredCharacteristics.get(0).value.annotationValue;
   }

diff --git a/...son-ena/src/main/java/com/elixir/biohackaton/ISAToSRA/sra/service/MarsReceiptService.java b/...son-ena/src/main/java/com/elixir/biohackaton/ISAToSRA/sra/service/MarsReceiptService.java
@@ -48,7 +48,7 @@ public String convertMarsReceiptToJson() {
     try {
       return jsonMapper.writeValueAsString(getMarsReceipt());
     } catch (Exception ex) {
-      throw new RuntimeException("receipt", ex);
+      throw new RuntimeException("Receipt", ex);
     }
   }
 

diff --git a/...-ena/src/main/java/com/elixir/biohackaton/ISAToSRA/sra/service/SRAAnalysisXmlCreator.java b/...-ena/src/main/java/com/elixir/biohackaton/ISAToSRA/sra/service/SRAAnalysisXmlCreator.java
@@ -1,6 +1,7 @@
 /** Elixir BioHackathon 2022 */
 package com.elixir.biohackaton.ISAToSRA.sra.service;
 
+import com.elixir.biohackaton.ISAToSRA.receipt.MarsReceiptException;
 import com.elixir.biohackaton.ISAToSRA.receipt.isamodel.*;
 import java.util.List;
 import java.util.Objects;
@@ -75,7 +76,7 @@ private void convertDataFileToFileElement(DataFile dataFile, Element filesElemen
             });
 
     if (Objects.isNull(checksum.get()) || Objects.isNull(checksumType.get())) {
-      log.error("Checksum and checksum type not found");
+      throw new MarsReceiptException("Checksum and checksum type not found");
     } else {
       Element fileElement = filesElement.addElement("FILE");
       fileElement.addAttribute("filename", filename);

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
@@ -1,6 +1,7 @@
 /** Elixir BioHackathon 2022 */
 package com.elixir.biohackaton.ISAToSRA.sra.service;
 
+import com.elixir.biohackaton.ISAToSRA.receipt.MarsReceiptException;
 import com.elixir.biohackaton.ISAToSRA.receipt.isamodel.*;
 import java.util.HashMap;
 import java.util.List;
@@ -32,10 +33,9 @@ public Map<String, String> createENAExperimentSetElement(
           typeToBioSamplesAccessionMap,
           randomSubmissionIdentifier);
     } catch (final Exception e) {
-      log.info("Failed to parse experiments from ISA Json file and create ENA Experiments");
+      throw new MarsReceiptException(
+          "Failed to parse experiments from ISA Json file and create ENA Experiments", e);
     }
-
-    return null;
   }
 
   private String populateProcessSequenceToParameterValuesMapAndGetExecutesProtocolId(

diff --git a/...n-ena/src/main/java/com/elixir/biohackaton/ISAToSRA/sra/service/WebinStudyXmlCreator.java b/...n-ena/src/main/java/com/elixir/biohackaton/ISAToSRA/sra/service/WebinStudyXmlCreator.java
@@ -1,6 +1,7 @@
 /** Elixir BioHackathon 2022 */
 package com.elixir.biohackaton.ISAToSRA.sra.service;
 
+import com.elixir.biohackaton.ISAToSRA.receipt.MarsReceiptException;
 import com.elixir.biohackaton.ISAToSRA.receipt.isamodel.*;
 import java.util.List;
 import lombok.extern.slf4j.Slf4j;
@@ -48,7 +49,7 @@ public void createENAStudySetElement(
                     });
           });
     } catch (final Exception e) {
-      log.info("Failed to parse ISA JSON and create ENA study");
+      throw new MarsReceiptException("Failed to parse ISA JSON and create ENA study");
     }
   }
 }
diff --git a/...s/receipt/src/main/java/com/elixir/biohackaton/ISAToSRA/receipt/MarsReceiptException.java b/...s/receipt/src/main/java/com/elixir/biohackaton/ISAToSRA/receipt/MarsReceiptException.java
@@ -0,0 +1,17 @@
+package com.elixir.biohackaton.ISAToSRA.receipt;
+
+import lombok.Getter;
+
+public class MarsReceiptException extends RuntimeException {
+    @Getter
+    private final String receiptErrorMessage;
+
+    public MarsReceiptException(final String receiptErrorMessage) {
+        this.receiptErrorMessage = receiptErrorMessage;
+    }
+
+    public MarsReceiptException(final String receiptErrorMessage, final Exception exception) {
+        this.addSuppressed(exception);
+        this.receiptErrorMessage = receiptErrorMessage;
+    }
+}