Improved study and experiment handling, paired end data handling, multiple experiment handling

repository-services/isajson-biosamples/src/test/java/com/elixir/biohackaton/ISAToSRA/BiosampleReceiptToMarsTest.java

@@ -1,6 +1,7 @@
 /** Elixir BioHackathon 2022 */
 package com.elixir.biohackaton.ISAToSRA;
 
+import com.elixir.biohackaton.ISAToSRA.biosamples.model.BioSample;
 import com.elixir.biohackaton.ISAToSRA.biosamples.model.BiosampleAccessionsMap;
 import com.elixir.biohackaton.ISAToSRA.biosamples.service.BioSamplesSubmitter;
 import com.elixir.biohackaton.ISAToSRA.biosamples.service.MarsReceiptService;
@@ -11,7 +12,9 @@
 import com.fasterxml.jackson.databind.ObjectMapper;
 import java.io.File;
 import java.nio.file.Files;
+import java.util.ArrayList;
 import java.util.List;
+import org.junit.jupiter.api.Assertions;
 import org.junit.jupiter.api.Test;
 import org.springframework.boot.test.context.SpringBootTest;
 
@@ -54,4 +57,157 @@ void convertToMars() {
       System.console().printf("%s", ex);
     }
   }
+
+  @Test
+  void createBioSamplesUsesSampleCollectionProcessParametersForChildSampleAttributes()
+      throws Exception {
+    final String isaJsonFilePath = "../../test-data/biosamples-input-isa.json";
+    final String isaJsonFile = Files.readString(new File(isaJsonFilePath).toPath());
+    final ObjectMapper objectMapper = new ObjectMapper();
+    final IsaJson isaJson = objectMapper.readValue(isaJsonFile, IsaJson.class);
+    final CapturingBioSamplesSubmitter bioSamplesSubmitter = new CapturingBioSamplesSubmitter();
+
+    bioSamplesSubmitter.createBioSamples(isaJson.getInvestigation().getStudies(), "test-token");
+
+    final BioSample leafSample =
+        bioSamplesSubmitter.updatedSamples.stream()
+            .filter(sample -> "leaf 1".equals(sample.getName()))
+            .findFirst()
+            .orElseThrow();
+    final BioSample sourceSample = bioSamplesSubmitter.createdSampleByName("plant 1");
+
+    Assertions.assertTrue(hasAttribute(sourceSample, "genotype", "Col-0"));
+    Assertions.assertTrue(
+        hasAttribute(sourceSample, "growth condition", "16 h light / 8 h dark growth chamber"));
+    Assertions.assertTrue(hasAttribute(sourceSample, "dev_stage", "vegetative rosette stage"));
+    Assertions.assertTrue(hasAttribute(sourceSample, "isolation_source", "whole plant"));
+    Assertions.assertTrue(hasAttribute(leafSample, "organism part", "leaf"));
+    Assertions.assertTrue(
+        hasAttribute(
+            leafSample,
+            "sample description",
+            "young rosette leaf collected for DNA extraction"));
+    Assertions.assertTrue(
+        leafSample.getAttributes().stream()
+            .anyMatch(
+                attribute ->
+                    "isolation_source".equals(attribute.getType())
+                        && "leaf tissue".equals(attribute.getValue())),
+        "Expected child BioSample to include the sample-collection process parameter.");
+    Assertions.assertTrue(hasAttribute(leafSample, "collection method", "sterile scalpel excision"));
+    Assertions.assertTrue(
+        hasAttribute(leafSample, "sample preservation", "flash frozen in liquid nitrogen"));
+  }
+
+  @Test
+  void createBioSamplesKeepsEachChildSampleLinkedToItsOwnSource() throws Exception {
+    final String isaJsonFilePath = "../../test-data/biosamples-input-isa-multi.json";
+    final String isaJsonFile = Files.readString(new File(isaJsonFilePath).toPath());
+    final ObjectMapper objectMapper = new ObjectMapper();
+    final IsaJson isaJson = objectMapper.readValue(isaJsonFile, IsaJson.class);
+    final CapturingBioSamplesSubmitter bioSamplesSubmitter = new CapturingBioSamplesSubmitter();
+
+    bioSamplesSubmitter.createBioSamples(isaJson.getInvestigation().getStudies(), "test-token");
+
+    final BioSample leafSample = bioSamplesSubmitter.updatedSampleByName("leaf 1");
+    final BioSample rootSample = bioSamplesSubmitter.updatedSampleByName("root 1");
+
+    Assertions.assertEquals("SAMEA_TEST_1", derivedFromTarget(leafSample));
+    Assertions.assertEquals("SAMEA_TEST_2", derivedFromTarget(rootSample));
+    Assertions.assertTrue(hasAttribute(rootSample, "collection date", "2022-01-03"));
+    Assertions.assertTrue(hasAttribute(rootSample, "organism part", "root"));
+    Assertions.assertTrue(hasAttribute(rootSample, "isolation_source", "root tissue"));
+    Assertions.assertTrue(hasAttribute(rootSample, "collection method", "washed root excision"));
+    Assertions.assertTrue(
+        hasAttribute(rootSample, "sample preservation", "flash frozen in liquid nitrogen"));
+  }
+
+  @Test
+  void createBioSamplesSupportsMultipleChildSamplesFromTheSameSource() throws Exception {
+    final String isaJsonFilePath = "../../test-data/biosamples-input-isa-multi.json";
+    final String isaJsonFile = Files.readString(new File(isaJsonFilePath).toPath());
+    final ObjectMapper objectMapper = new ObjectMapper();
+    final IsaJson isaJson = objectMapper.readValue(isaJsonFile, IsaJson.class);
+    final Study study = isaJson.getInvestigation().getStudies().get(0);
+
+    study.getMaterials().getSamples().stream()
+        .filter(sample -> "root 1".equals(sample.getName()))
+        .findFirst()
+        .orElseThrow()
+        .getDerivesFrom()
+        .get(0)
+        .setId("#source/330");
+    study.getProcessSequence().stream()
+        .filter(process -> "#process/sample_collection/431".equals(process.getId()))
+        .findFirst()
+        .orElseThrow()
+        .getInputs()
+        .get(0)
+        .setId("#source/330");
+
+    final CapturingBioSamplesSubmitter bioSamplesSubmitter = new CapturingBioSamplesSubmitter();
+    bioSamplesSubmitter.createBioSamples(isaJson.getInvestigation().getStudies(), "test-token");
+
+    final BioSample leafSample = bioSamplesSubmitter.updatedSampleByName("leaf 1");
+    final BioSample rootSample = bioSamplesSubmitter.updatedSampleByName("root 1");
+
+    Assertions.assertEquals("SAMEA_TEST_1", derivedFromTarget(leafSample));
+    Assertions.assertEquals("SAMEA_TEST_1", derivedFromTarget(rootSample));
+    Assertions.assertTrue(hasAttribute(rootSample, "organism part", "root"));
+    Assertions.assertTrue(hasAttribute(rootSample, "collection method", "washed root excision"));
+  }
+
+  private static String derivedFromTarget(final BioSample sample) {
+    return sample.getRelationships().stream()
+        .filter(relationship -> "derived from".equals(relationship.getType()))
+        .findFirst()
+        .orElseThrow()
+        .getTarget();
+  }
+
+  private static boolean hasAttribute(
+      final BioSample sample, final String attributeType, final String attributeValue) {
+    return sample.getAttributes().stream()
+        .anyMatch(
+            attribute ->
+                attributeType.equals(attribute.getType())
+                    && attributeValue.equals(attribute.getValue()));
+  }
+
+  private static class CapturingBioSamplesSubmitter extends BioSamplesSubmitter {
+    private final List<BioSample> createdSamples = new ArrayList<>();
+    private final List<BioSample> updatedSamples = new ArrayList<>();
+    private int accessionSequence = 1;
+
+    @Override
+    protected BioSample createSampleInBioSamples(final BioSample sample, final String webinToken) {
+      final BioSample createdSample =
+          BioSample.Builder.fromSample(sample)
+              .withAccession("SAMEA_TEST_" + accessionSequence++)
+              .build();
+      createdSamples.add(createdSample);
+      return createdSample;
+    }
+
+    @Override
+    protected BioSample updateSampleWithRelationshipsToBioSamples(
+        final BioSample sampleWithRelationship, final String webinToken) {
+      updatedSamples.add(sampleWithRelationship);
+      return sampleWithRelationship;
+    }
+
+    private BioSample updatedSampleByName(final String sampleName) {
+      return updatedSamples.stream()
+          .filter(sample -> sampleName.equals(sample.getName()))
+          .findFirst()
+          .orElseThrow();
+    }
+
+    private BioSample createdSampleByName(final String sampleName) {
+      return createdSamples.stream()
+          .filter(sample -> sampleName.equals(sample.getName()))
+          .findFirst()
+          .orElseThrow();
+    }
+  }
 }

repository-services/isajson-ena/src/main/java/com/elixir/biohackaton/ISAToSRA/controller/WebinIsaToXmlSubmissionController.java

@@ -11,7 +11,6 @@
 import com.elixir.biohackaton.ISAToSRA.sra.service.ReceiptConversionService;
 import com.elixir.biohackaton.ISAToSRA.sra.service.WebinExperimentXmlCreator;
 import com.elixir.biohackaton.ISAToSRA.sra.service.WebinHttpSubmissionService;
-import com.elixir.biohackaton.ISAToSRA.sra.service.WebinProjectXmlCreator;
 import com.elixir.biohackaton.ISAToSRA.sra.service.WebinRunXmlCreator;
 import com.elixir.biohackaton.ISAToSRA.sra.service.WebinStudyXmlCreator;
 import com.fasterxml.jackson.core.type.TypeReference;
@@ -41,14 +40,14 @@
  *
  * <ol>
  *   <li>Parse ISA-JSON payload
- *   <li>Convert ISA-JSON elements to ENA XML (Study, Project, Experiment, Run)
+ *   <li>Convert ISA-JSON elements to ENA XML (Study, Experiment, Run)
  *   <li>Submit XML to ENA Webin API
  *   <li>Convert ENA receipt to MARS receipt format
  *   <li>Return MARS receipt as JSON
  * </ol>
  *
  * <p>The conversion follows a bottom-up approach for Experiments and Runs (starting from DataFiles
- * and working up), while Study and Project use a top-down approach.
+ * and working up), while Study uses a top-down approach.
  */
 @Slf4j
 @RestController
@@ -57,8 +56,6 @@ public class WebinIsaToXmlSubmissionController {
 
   @Autowired private WebinExperimentXmlCreator webinExperimentXmlCreator;
 
-  @Autowired private WebinProjectXmlCreator webinProjectXmlCreator;
-
   @Autowired private WebinRunXmlCreator webinRunXmlCreator;
 
   @Autowired private WebinHttpSubmissionService webinHttpSubmissionService;
@@ -90,7 +87,6 @@ public class WebinIsaToXmlSubmissionController {
    *   <li>Get BioSamples accessions for study samples
    *   <li>Convert Library → ENA EXPERIMENT (bottom-up: DataFile → Library)
    *   <li>Convert DataFile → ENA RUN (bottom-up: DataFile → Experiment reference)
-   *   <li>Convert Investigation → ENA PROJECT (top-down)
    *   <li>Submit XML to ENA Webin API
    *   <li>Convert ENA receipt to MARS receipt format
    * </ol>
@@ -154,27 +150,23 @@ public String performSubmissionToEna(
     this.webinRunXmlCreator.createENARunSetElement(
         webinElement, studies, experimentSequenceMap, randomSubmissionIdentifier);
 
-    // Step 5: Convert Investigation → ENA PROJECT (top-down approach)
-    this.webinProjectXmlCreator.createENAProjectSetElement(
-        webinElement, getInvestigation(isaJson), randomSubmissionIdentifier);
-
     // Debug: Print generated XML to console
     final OutputFormat format = OutputFormat.createPrettyPrint();
     final XMLWriter writer = new XMLWriter(System.out, format);
     writer.write(document);
 
-    // Step 6: Submit XML to ENA Webin API
+    // Step 5: Submit XML to ENA Webin API
     final String receiptXml =
         webinHttpSubmissionService.performWebinSubmission(
             webinUserName, document.asXML(), webinPassword);
 
-    // Step 7: Convert ENA XML receipt to JSON
+    // Step 6: Convert ENA XML receipt to JSON
     final Receipt receiptJson = receiptConversionService.readReceiptXml(receiptXml);
 
-    // Step 8: Convert ENA receipt to MARS receipt format
+    // Step 7: Convert ENA receipt to MARS receipt format
     final MarsReceipt marsReceipt = marsReceiptService.convertReceiptToMars(receiptJson, isaJson);
 
-    // Step 9: Return MARS receipt as JSON
+    // Step 8: Return MARS receipt as JSON
     return marsReceiptService.convertMarsReceiptToJson(marsReceipt);
   }
 
@@ -194,27 +186,11 @@ public List<Study> getStudies(final IsaJson isaJson) {
     return null;
   }
 
-  /**
-   * Extracts Investigation object from ISA-JSON.
-   *
-   * @param isaJson the parsed ISA-JSON object
-   * @return Investigation object, or null if extraction fails
-   */
-  public Investigation getInvestigation(final IsaJson isaJson) {
-    try {
-      return isaJson.getInvestigation();
-    } catch (final Exception e) {
-      log.error("Failed to parse ISA JSON and get investigation", e);
-    }
-
-    return null;
-  }
-
   /**
    * Parses BioSamples accessions from input parameter or extracts from ISA-JSON.
    *
    * <p>If the bioSampleAccessions JSON string is provided, it will be parsed and used. Otherwise,
-   * falls back to extracting from ISA-JSON Study samples first, then sources.
+   * falls back to extracting from ISA-JSON Study samples.
    *
    * <p>Expected format: JSON string with "SOURCE" as key, e.g., {@code {"SOURCE":"SAMEA130793922"}}
    *