Merge pull request #75 from apriltuesday/fixes-from-testing

Fixes from testing
elixir-europe · Nov 7, 2024 · d3e7230 · d3e7230
2 parents 6fe7422 + 19c2eed
commit d3e7230
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Showing 3 changed files with 22 additions and 3 deletions.
diff --git a/...in/java/com/elixir/biohackaton/ISAToSRA/controller/WebinIsaToXmlSubmissionController.java b/...in/java/com/elixir/biohackaton/ISAToSRA/controller/WebinIsaToXmlSubmissionController.java
@@ -106,6 +106,8 @@ public String performSubmissionToEna(
         webinHttpSubmissionService.performWebinSubmission(
             webinUserName, document.asXML(), webinPassword);
     final Receipt receiptJson = receiptConversionService.readReceiptXml(receiptXml);
+    System.out.println(receiptXml);
+    System.out.println(receiptJson);
     final MarsReceipt marsReceipt = marsReceiptService.convertReceiptToMars(receiptJson, isaJson);
 
     return marsReceiptService.convertMarsReceiptToJson(marsReceipt);

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
@@ -50,11 +50,12 @@ public String convertMarsReceiptToJson(final MarsReceipt marsReceipt) {
    */
   public MarsReceipt convertReceiptToMars(final Receipt receipt, final IsaJson isaJson) {
     return buildMarsReceipt(
-        "ena.embl", // https://registry.identifiers.org/registry/ena.embl
+        "ena", // TODO decide whether to use instead
+        // https://registry.identifiers.org/registry/ena.embl
         getAliasAccessionPairs(
             Study.Fields.title,
             Optional.ofNullable(receipt.getStudies()).orElse(receipt.getProjects())),
-        getAliasAccessionPairs(Sample.Fields.id, receipt.getSamples()),
+        null,
         null,
         getAliasAccessionPairs(OtherMaterial.Fields.id, receipt.getExperiments()),
         getAliasAccessionPairs(DataFile.Fields.id, receipt.getRuns()),
@@ -63,6 +64,12 @@ public MarsReceipt convertReceiptToMars(final Receipt receipt, final IsaJson isa
         isaJson);
   }
 
+  private static String getPreRandomizedAlias(ReceiptObject receiptObject) {
+    // Convert Arabidopsis thaliana-0.49105604184136276 -> Arabidopsis thaliana
+    String alias = receiptObject.getAlias();
+    return alias.substring(0, alias.lastIndexOf("-"));
+  }
+
   private ReceiptAccessionsMap getAliasAccessionPairs(
       String keyNameInput, final List<ReceiptObject> items) {
     return new ReceiptAccessionsMap() {
@@ -73,7 +80,9 @@ private ReceiptAccessionsMap getAliasAccessionPairs(
                 Optional.ofNullable(items).orElse(new ArrayList<>()).stream()
                     .filter(item -> item != null)
                     .collect(
-                        Collectors.toMap(ReceiptObject::getAlias, ReceiptObject::getAccession)));
+                        Collectors.toMap(
+                            MarsReceiptService::getPreRandomizedAlias,
+                            ReceiptObject::getAccession)));
       }
     };
   }

diff --git a/...s/receipt/src/main/java/com/elixir/biohackaton/ISAToSRA/receipt/ReceiptAccessionsMap.java b/...s/receipt/src/main/java/com/elixir/biohackaton/ISAToSRA/receipt/ReceiptAccessionsMap.java
@@ -19,4 +19,12 @@ public ReceiptAccessionsMap(String keyName, String keyValue) {
             }
         };
     }
+
+    public String toString() {
+        String result = "ReceiptAccessionsMap:" + keyName + "\n";
+        for (String key: accessionMap.keySet()) {
+            result += key + ":" + accessionMap.get(key) + "\n";
+        }
+        return result;
+    }
 }