Mars receipt, null pointer exception handling

elixir-europe · Nov 12, 2024 · 62597cd · 62597cd
1 parent 72aa346
commit 62597cd
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Showing 5 changed files with 14 additions and 16 deletions.
diff --git a/.../com/elixir/biohackaton/ISAToSRA/biosamples/controller/BioSampleSubmissionController.java b/.../com/elixir/biohackaton/ISAToSRA/biosamples/controller/BioSampleSubmissionController.java
@@ -50,10 +50,7 @@ public String performSubmissionToBioSamplesAndEna(
       @RequestBody final String submissionPayload,
       @RequestParam(value = "webinjwt") String webinJwt) {
     try {
-      String webinToken;
-      if (webinJwt != null) {
-        webinToken = webinJwt;
-      } else {
+      if (webinJwt == null || webinJwt.isEmpty()) {
         throw new RuntimeException("Webin Authentication Token is not provided");
       }
 
@@ -62,7 +59,7 @@ public String performSubmissionToBioSamplesAndEna(
       final IsaJson isaJson = this.objectMapper.readValue(submissionPayload, IsaJson.class);
       final List<Study> studies = getStudies(isaJson);
 
-      final BiosampleAccessionsMap accessionsMap = this.bioSamplesSubmitter.createBioSamples(studies, webinToken);
+      final BiosampleAccessionsMap accessionsMap = this.bioSamplesSubmitter.createBioSamples(studies, webinJwt);
       marsReceiptService.convertReceiptToMars(accessionsMap, isaJson);
 
       return marsReceiptService.convertMarsReceiptToJson();

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
@@ -48,7 +48,7 @@ public String convertMarsReceiptToJson() {
   }
 
   public void setMarsReceiptErrors(String... errors) {
-    super.setMarsReceiptErrors(MarsErrorType.INTERNAL_SERVER_ERROR, errors);
+    super.setMarsReceiptErrors(MarsErrorType.INVALID_METADATA, errors);
   }
 
   /**

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
@@ -53,7 +53,7 @@ public String convertMarsReceiptToJson() {
   }
 
   public void setMarsReceiptErrors(String... errors) {
-    super.setMarsReceiptErrors(MarsErrorType.INTERNAL_SERVER_ERROR, errors);
+    super.setMarsReceiptErrors(MarsErrorType.INVALID_METADATA, errors);
   }
 
   /**

diff --git a/...es/receipt/src/main/java/com/elixir/biohackaton/ISAToSRA/receipt/MarsReceiptProvider.java b/...es/receipt/src/main/java/com/elixir/biohackaton/ISAToSRA/receipt/MarsReceiptProvider.java
@@ -69,8 +69,11 @@ protected void buildMarsReceipt(
       final List<String> info,
       final List<String> errors,
       final IsaJson isaJson) {
-    setMarsReceiptErrors(MarsErrorType.INVALID_METADATA, errors.toArray(String[]::new));
-    setMarsReceiptInfo(info.toArray(String[]::new));
+    final String[] errorArray = Optional.ofNullable(errors).orElse(new ArrayList<>()).toArray(String[]::new);
+    final String[] infoArray = Optional.ofNullable(info).orElse(new ArrayList<>()).toArray(String[]::new);
+
+    setMarsReceiptErrors(MarsErrorType.INVALID_METADATA, errorArray);
+    setMarsReceiptInfo(infoArray);
     setMarsAccessions(
         studiesAccessionsMap,
         samplesAccessionsMap,
@@ -122,7 +125,7 @@ protected void setMarsAccessions(
                 if (studyAccessionMap.accession != null) {
                   marsAccessions.add(getStudyMarsAccession(studyAccessionMap));
                 }
-                if (samplesAccessionsMap != null) {
+                if (samplesAccessionsMap != null && study.materials != null) {
                   Optional.ofNullable(study.materials.samples)
                       .orElse(new ArrayList<>())
                       .forEach(
@@ -134,7 +137,7 @@ protected void setMarsAccessions(
                             }
                           });
                 }
-                if (sourcesAccessionsMap != null) {
+                if (sourcesAccessionsMap != null && study.materials != null) {
                   Optional.ofNullable(study.materials.sources)
                       .orElse(new ArrayList<>())
                       .forEach(
@@ -151,7 +154,7 @@ protected void setMarsAccessions(
                       .orElse(new ArrayList<>())
                       .forEach(
                           assay -> {
-                            if (otherMaterialsAccessionsMap != null) {
+                            if (otherMaterialsAccessionsMap != null && assay.materials != null) {
                               Optional.ofNullable(assay.materials.otherMaterials)
                                   .orElse(new ArrayList<>())
                                   .forEach(
@@ -167,8 +170,7 @@ protected void setMarsAccessions(
                                       });
                             }
                             if (dataFilesAccessionsMap != null) {
-                              Optional.ofNullable(
-                                  assay.dataFiles)
+                              Optional.ofNullable(assay.dataFiles)
                                   .orElse(new ArrayList<>())
                                   .forEach(
                                       dataFile -> {

diff --git a/...eceipt/src/main/java/com/elixir/biohackaton/ISAToSRA/receipt/marsmodel/MarsErrorType.java b/...eceipt/src/main/java/com/elixir/biohackaton/ISAToSRA/receipt/marsmodel/MarsErrorType.java
@@ -2,6 +2,5 @@
 
 public enum MarsErrorType {
   INVALID_METADATA,
-  INVALID_DATA,
-  INTERNAL_SERVER_ERROR;
+  INVALID_DATA;
 }
-Original file line number
+Diff line change
@@ Expand Up / @@ -48,7 +48,7 @@ public String convertMarsReceiptToJson() { @@
       }
       public void setMarsReceiptErrors(String... errors) {
-        super.setMarsReceiptErrors(MarsErrorType.INTERNAL_SERVER_ERROR, errors);
+        super.setMarsReceiptErrors(MarsErrorType.INVALID_METADATA, errors);
       }
       /**
@@ Expand Down @@