changed the return object/type of the ingestion endpoint into a more …

…standardized one
EBIvariation · Jan 3, 2024 · 468ce6a · 468ce6a
1 parent 9a38601
commit 468ce6a
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Showing 3 changed files with 28 additions and 16 deletions.
diff --git a/src/main/java/uk/ac/ebi/eva/evaseqcol/controller/admin/AdminController.java b/src/main/java/uk/ac/ebi/eva/evaseqcol/controller/admin/AdminController.java
@@ -15,6 +15,7 @@
 import uk.ac.ebi.eva.evaseqcol.exception.AssemblyNotFoundException;
 import uk.ac.ebi.eva.evaseqcol.exception.DuplicateSeqColException;
 import uk.ac.ebi.eva.evaseqcol.exception.IncorrectAccessionException;
+import uk.ac.ebi.eva.evaseqcol.model.IngestionResultEntity;
 import uk.ac.ebi.eva.evaseqcol.service.SeqColService;
 
 import java.io.IOException;
@@ -54,10 +55,8 @@ public ResponseEntity<?> fetchAndInsertSeqColByAssemblyAccession(
             example = "GCA_000146045.2",
             required = true) @PathVariable String asmAccession) {
         try {
-            List<String> level0Digests = seqColService.fetchAndInsertAllSeqColByAssemblyAccession(asmAccession);
-            return new ResponseEntity<>(
-                    "Successfully inserted seqCol object(s) for assembly accession " + asmAccession + "\nSeqCol digests=" + level0Digests
-                    , HttpStatus.OK);
+            IngestionResultEntity ingestionResult = seqColService.fetchAndInsertAllSeqColByAssemblyAccession(asmAccession);
+            return ResponseEntity.ok(ingestionResult);
         } catch (IncorrectAccessionException e) {
             return new ResponseEntity<>(e.getMessage(), HttpStatus.BAD_REQUEST);
         } catch (IllegalArgumentException e) {

diff --git a/src/main/java/uk/ac/ebi/eva/evaseqcol/entities/SeqColExtendedDataEntity.java b/src/main/java/uk/ac/ebi/eva/evaseqcol/entities/SeqColExtendedDataEntity.java
@@ -48,6 +48,7 @@ public class SeqColExtendedDataEntity<T> {
     @Transient
     // This is needed when constructing multiple seqCol objects from the datasource to
     // identify the naming convention used for the sequences.
+    // Note: This will probably be required by the namesAttributeList and might be null for the others
     private SeqColEntity.NamingConvention namingConvention;
 
     public enum AttributeType {

diff --git a/src/main/java/uk/ac/ebi/eva/evaseqcol/service/SeqColService.java b/src/main/java/uk/ac/ebi/eva/evaseqcol/service/SeqColService.java
@@ -17,6 +17,8 @@
 import uk.ac.ebi.eva.evaseqcol.exception.DuplicateSeqColException;
 import uk.ac.ebi.eva.evaseqcol.exception.SeqColNotFoundException;
 import uk.ac.ebi.eva.evaseqcol.exception.UnableToLoadServiceInfoException;
+import uk.ac.ebi.eva.evaseqcol.model.IngestionResultEntity;
+import uk.ac.ebi.eva.evaseqcol.model.InsertedSeqColEntity;
 import uk.ac.ebi.eva.evaseqcol.utils.JSONExtData;
 import uk.ac.ebi.eva.evaseqcol.utils.JSONIntegerListExtData;
 import uk.ac.ebi.eva.evaseqcol.utils.JSONStringListExtData;
@@ -154,14 +156,16 @@ public void removeAllSeqCol() {
      * NOTE: All possible seqCol objects means with all possible/provided naming conventions that could be found in the
      * assembly report.
      * Return the list of level 0 digests of the inserted seqcol objects*/
-    public List<String> fetchAndInsertAllSeqColByAssemblyAccession(
+    public IngestionResultEntity fetchAndInsertAllSeqColByAssemblyAccession(
             String assemblyAccession) throws IOException, DuplicateSeqColException {
-        List<String> insertedSeqColDigests = new ArrayList<>();
+        IngestionResultEntity ingestionResultEntity = new IngestionResultEntity();
+        ingestionResultEntity.setAssemblyAccession(assemblyAccession);
         Optional<Map<String, Object>> seqColDataMap = ncbiSeqColDataSource
                 .getAllPossibleSeqColExtendedData(assemblyAccession);
         if (!seqColDataMap.isPresent()) {
             logger.warn("No seqCol data corresponding to assemblyAccession " + assemblyAccession + " could be found on NCBI datasource");
-            return insertedSeqColDigests;
+            ingestionResultEntity.setErrorMessage("No seqCol data corresponding to assemblyAccession " + assemblyAccession + " could be found on NCBI datasource");
+            return ingestionResultEntity;
         }
 
         // Retrieving the Map's data
@@ -198,17 +202,25 @@ public List<String> fetchAndInsertAllSeqColByAssemblyAccession(
                     seqColStringListExtDataEntities, seqColIntegerListExtDataEntities, extendedNamesEntity.getNamingConvention()
                     );
 
-            Optional<String> seqColDigest = insertSeqColL1AndL2( // TODO: Check for possible self invocation problem
-                    levelOneEntity, seqColStringListExtDataEntities, seqColIntegerListExtDataEntities);
-            if (seqColDigest.isPresent()) {
-                logger.info(
-                        "Successfully inserted seqCol for assembly Accession " + assemblyAccession + " with naming convention " + extendedNamesEntity.getNamingConvention());
-                insertedSeqColDigests.add(seqColDigest.get());
-            } else {
-                logger.warn("Could not insert seqCol for assembly Accession " + assemblyAccession + " with naming convention " + extendedNamesEntity.getNamingConvention());
+            try {
+                Optional<String> seqColDigest = insertSeqColL1AndL2( // TODO: Check for possible self invocation problem
+                                                                     levelOneEntity, seqColStringListExtDataEntities, seqColIntegerListExtDataEntities);
+                if (seqColDigest.isPresent()) {
+                    logger.info(
+                            "Successfully inserted seqCol for assembly Accession " + assemblyAccession + " with naming convention " + extendedNamesEntity.getNamingConvention());
+                    InsertedSeqColEntity insertedSeqCol = new InsertedSeqColEntity(seqColDigest.get(), extendedNamesEntity.getNamingConvention().toString());
+                    ingestionResultEntity.addInsertedSeqCol(insertedSeqCol);
+                    ingestionResultEntity.incrementNumberOfInsertedSeqCols();
+                } else {
+                    logger.warn("Could not insert seqCol for assembly Accession " + assemblyAccession + " with naming convention " + extendedNamesEntity.getNamingConvention());
+                }
+            } catch (DuplicateSeqColException e) {
+                logger.info("Seqcol for " + assemblyAccession + " and naming convention " + extendedNamesEntity.getNamingConvention() +
+                " already exists. Skipping.");
+                continue;
             }
         }
-        return insertedSeqColDigests;
+        return ingestionResultEntity;
     }
 
     /**