Merge pull request #46 from waterflow80/fix-issue-45

Fixed the digits verification for seqCol arrays to be digested - ingestion endpoint

src/main/java/uk/ac/ebi/eva/evaseqcol/controller/admin/AdminController.java

@@ -64,6 +64,7 @@ public ResponseEntity<?> fetchAndInsertSeqColByAssemblyAccession(
             return new ResponseEntity<>(e.getMessage(), HttpStatus.BAD_REQUEST);
         }
         catch (IOException e) {
+            e.printStackTrace();
             return new ResponseEntity<>(e.getMessage(), HttpStatus.INTERNAL_SERVER_ERROR);
         } catch (DuplicateSeqColException e) {
             return new ResponseEntity<>(e.getMessage(), HttpStatus.CONFLICT);

src/main/java/uk/ac/ebi/eva/evaseqcol/datasource/NCBIAssemblySequenceDataSource.java

@@ -71,6 +71,7 @@ public Optional<AssemblySequenceEntity> getAssemblySequencesByAccession(String a
                 Files.deleteIfExists(downloadFilePath.get());
                 Files.deleteIfExists(compressedFilePath.get()); // Deleting the fasta file
             } catch (IOException e) {
+                //e.printStackTrace(); // We might want to uncomment this when debugging
                 logger.warn("Error while trying to disconnect - ncbiBrowser (assembly: " + accession + ")");
             }
         }

src/main/java/uk/ac/ebi/eva/evaseqcol/datasource/NCBISeqColDataSource.java

@@ -64,6 +64,7 @@ public Optional<Map<String, List<SeqColExtendedDataEntity>>> getAllPossibleSeqCo
             logger.error("Could not fetch Sequences FASTA file from NCBI for assembly accession: " + accession);
             return Optional.empty();
         }
+        logger.info("Assembly report and FASTA file have been fetched and parsed successfully");
         seqColResultData.put(
                 "sameValueAttributes",
                 SeqColExtendedDataEntity.constructSameValueExtendedSeqColData(assemblyEntity.get(), sequenceEntity.get()));

src/main/java/uk/ac/ebi/eva/evaseqcol/dus/PassiveAnonymousFTPClient.java

@@ -81,6 +81,7 @@ public boolean downloadFTPFile(String ftpFilePath, Path downloadFilePath, long f
         super.setFileTransferMode(FTP.BINARY_FILE_TYPE);
         Files.deleteIfExists(downloadFilePath);
 
+        logger.info("Downloading file " + ftpFilePath + " in progress...");
         boolean success = super.retrieveFile(ftpFilePath, new FileOutputStream(downloadFilePath.toFile()));
 
         if (success && Files.exists(downloadFilePath) && Files.isReadable(downloadFilePath)) {

src/main/java/uk/ac/ebi/eva/evaseqcol/service/SeqColService.java

@@ -367,13 +367,20 @@ private boolean onlyDigits(String str) {
         return m.matches();
     }
 
+    /**
+     * Check whether the given list contains only digits (in a form of strings)*/
+    private boolean onlyDigitsStringList(List<String> list) {
+        return list.isEmpty() || list.stream()
+                                     .allMatch(this::onlyDigits);
+    }
+
     /**
      * Return a normalized string representation of the given seqColL2Attribute
      * Note: This is the same method as the toString of the JSONExtData class*/
     private String convertSeqColLevelTwoAttributeValuesToString(List<String> seqColL2Attribute) {
         StringBuilder objectStr = new StringBuilder();
         objectStr.append("[");
-        if (onlyDigits(seqColL2Attribute.get(0).toString())) { // Lengths array, No quotes "...". Eg: [1111, 222, 333]
+        if (onlyDigitsStringList(seqColL2Attribute)) { // Lengths array, No quotes "...". Eg: [1111, 222, 333]
             for (int i=0; i<seqColL2Attribute.size()-1; i++) {
                 objectStr.append(seqColL2Attribute.get(i));
                 objectStr.append(",");

src/main/java/uk/ac/ebi/eva/evaseqcol/utils/JSONExtData.java

@@ -27,11 +27,18 @@ private boolean onlyDigits(String str) {
         return m.matches();
     }
 
+    /**
+     * Check whether the given list contains only digits (in a form of strings)*/
+    private boolean onlyDigitsStringList(List<String> list) {
+        return list.isEmpty() || list.stream()
+                .allMatch(this::onlyDigits);
+    }
+
     @Override
     public String toString() {
         StringBuilder objectStr = new StringBuilder();
         objectStr.append("[");
-        if (onlyDigits(object.get(0).toString())) { // Lengths array, No quotes "...". Eg: [1111, 222, 333]
+        if (onlyDigitsStringList(object)) { // Lengths array, No quotes "...". Eg: [1111, 222, 333]
             for (int i=0; i<object.size()-1; i++) {
                objectStr.append(object.get(i));
                objectStr.append(",");

src/test/java/uk/ac/ebi/eva/evaseqcol/refget/DigestCalculatorTest.java

@@ -24,6 +24,7 @@ class DigestCalculatorTest {
     private final String ARRAY_TEST = "[248956422, 242193529, 198295559]";
     private final String ARRAY_DIGEST = "5K4odB173rjao1Cnbk5BnvLt9V7aPAa2";
 
+    private final String sequences_array = "[\"MD5-sqdfsdodshijfsd354768\",\"MD5-fjroptkgqsdfsd5f7sdlp\",\"MD5-sdpohgnjkisqdj,fiokjz\"]";
 
     @BeforeEach
     void setUp() {
@@ -37,7 +38,9 @@ void setUp() {
     void getDigest() throws IOException {
         String res1 = digestCalculator.getSha512Digest(levelOneEntity.toString());
         String res2 = digestCalculator.getSha512Digest(ARRAY_TEST);
+        String res3 = digestCalculator.getSha512Digest(sequences_array);
         assertEquals(DIGEST, res1);
         assertEquals(ARRAY_DIGEST, res2);
+        assertEquals("J8ovDQ2uLIxaOIQvDEQeGf4d5Yp5QJV-", res3);
     }
 }