Merge pull request #70 from elixir-europe/mars-receipt-library

Mars receipt library
elixir-europe · Nov 7, 2024 · 6fe7422 · 6fe7422
2 parents ad636ca + 7af8957
commit 6fe7422
Show file tree

Hide file tree

Showing 6 changed files with 24 additions and 21 deletions.
diff --git a/...src/main/java/com/elixir/biohackaton/ISAToSRA/biosamples/service/BioSamplesSubmitter.java b/...src/main/java/com/elixir/biohackaton/ISAToSRA/biosamples/service/BioSamplesSubmitter.java
@@ -94,7 +94,9 @@ private BioSample createAndUpdateChildSampleWithRelationship(
     final BioSample bioSample = new BioSample.Builder(sample.getName() != null ? sample.getName() : "child_sample")
         .withRelease(Instant.now())
         .withAttributes(
-            Collections.singletonList(Attribute.build("organism", parentSampleOrganism)))
+            List.of(Attribute.build("organism", parentSampleOrganism),
+                    Attribute.build("collection date", "not provided"),
+                    Attribute.build("geographic location (country and/or sea)", "not provided")))
         .build();
     try {
       final EntityModel<BioSample> persistedSampleEntity = this.createSampleInBioSamples(bioSample, webinToken);
@@ -147,7 +149,9 @@ private BioSample createSourceBioSample(final List<Study> studies, final String
 
                   final BioSample sourceSample = new BioSample.Builder(source.getName())
                       .withRelease(Instant.now())
-                      .withAttributes(Collections.singleton(organismAttribute.get()))
+                      .withAttributes(List.of(organismAttribute.get(),
+                              Attribute.build("collection date", "not provided"),
+                              Attribute.build("geographic location (country and/or sea)", "not provided")))
                       .build();
                   final EntityModel<BioSample> persistedParentSampleEntity = this.createSampleInBioSamples(sourceSample,
                       webinToken);

diff --git a/...in/java/com/elixir/biohackaton/ISAToSRA/controller/WebinIsaToXmlSubmissionController.java b/...in/java/com/elixir/biohackaton/ISAToSRA/controller/WebinIsaToXmlSubmissionController.java
@@ -88,7 +88,7 @@ public String performSubmissionToEna(
         webinElement, studies, randomSubmissionIdentifier);
 
     final Map<String, String> typeToBioSamplesAccessionMap = getBiosamples(studies);
-    final Map<Integer, String> experimentSequenceMap =
+    final Map<String, String> experimentSequenceMap =
         this.webinExperimentXmlCreator.createENAExperimentSetElement(
             typeToBioSamplesAccessionMap, webinElement, studies, randomSubmissionIdentifier);
 

diff --git a/.../src/main/java/com/elixir/biohackaton/ISAToSRA/sra/service/WebinExperimentXmlCreator.java b/.../src/main/java/com/elixir/biohackaton/ISAToSRA/sra/service/WebinExperimentXmlCreator.java
@@ -5,7 +5,6 @@
 import java.util.HashMap;
 import java.util.List;
 import java.util.Map;
-import java.util.concurrent.atomic.AtomicInteger;
 import java.util.concurrent.atomic.AtomicReference;
 import lombok.extern.slf4j.Slf4j;
 import org.dom4j.Element;
@@ -16,7 +15,7 @@
 public class WebinExperimentXmlCreator {
   public static final String OTHER_MATERIAL_LIBRARY_NAME_DETERMINES_EXPERIMENT = "Library Name";
 
-  public Map<Integer, String> createENAExperimentSetElement(
+  public Map<String, String> createENAExperimentSetElement(
       final Map<String, String> typeToBioSamplesAccessionMap,
       final Element webinElement,
       final List<Study> studies,
@@ -110,15 +109,14 @@ private AtomicReference<Map<String, List<Parameter>>> populateProtocolToParamete
     return protocolToParameterMap;
   }
 
-  private Map<Integer, String> mapExperiments(
+  private Map<String, String> mapExperiments(
       final List<Study> studies,
       final Element root,
       final Map<String, List<Parameter>> protocolToParameterMap,
       final Map<String, String> bioSampleAccessions,
       final String randomSubmissionIdentifier) {
     final Map<String, List<ParameterValue>> protocolToParameterValuesMap = new HashMap<>();
-    final Map<Integer, String> experimentSequence = new HashMap<>();
-    final AtomicInteger sequenceCounter = new AtomicInteger(0);
+    final Map<String, String> experimentSequence = new HashMap<>();
 
     studies.forEach(
         study ->
@@ -133,11 +131,11 @@ private Map<Integer, String> mapExperiments(
                                 otherMaterial -> {
                                   final Element experimentElement = root.addElement("EXPERIMENT");
                                   final String otherMaterialId = otherMaterial.getId();
+                                  final String experimentId =
+                                      otherMaterialId + "-" + randomSubmissionIdentifier;
 
-                                  experimentSequence.put(
-                                      sequenceCounter.incrementAndGet(), otherMaterialId);
-                                  experimentElement.addAttribute(
-                                      "alias", otherMaterialId + "-" + randomSubmissionIdentifier);
+                                  experimentSequence.put(otherMaterialId, experimentId);
+                                  experimentElement.addAttribute("alias", experimentId);
                                   experimentElement
                                       .addElement("TITLE")
                                       .addText(otherMaterial.getName());

diff --git a/...src/main/java/com/elixir/biohackaton/ISAToSRA/sra/service/WebinHttpSubmissionService.java b/...src/main/java/com/elixir/biohackaton/ISAToSRA/sra/service/WebinHttpSubmissionService.java
@@ -16,7 +16,7 @@
 public class WebinHttpSubmissionService {
   final RestTemplate restTemplate = new RestTemplate();
   private static final String webinSubmissionUrl =
-      "https://wwwdev.ebi.ac.uk/ena/dev/submit/webin-v2/submit";
+      "https://wwwdev.ebi.ac.uk/ena/submit/webin-v2/submit";
 
   public String performWebinSubmission(
       final String submissionAccountId, final String webinXml, final String webinPassword) {

diff --git a/...son-ena/src/main/java/com/elixir/biohackaton/ISAToSRA/sra/service/WebinRunXmlCreator.java b/...son-ena/src/main/java/com/elixir/biohackaton/ISAToSRA/sra/service/WebinRunXmlCreator.java
@@ -14,12 +14,13 @@ public class WebinRunXmlCreator {
   public void createENARunSetElement(
       final Element webinElement,
       final List<Study> studies,
-      final Map<Integer, String> experimentSequenceMap,
+      final Map<String, String> experimentSequenceMap,
       final String randomSubmissionIdentifier) {
-    final String lastExperimentId =
-        experimentSequenceMap.get(
-            Collections.max(experimentSequenceMap.entrySet(), Map.Entry.comparingByValue())
-                .getKey());
+    final String lastExperimentKeyInRawFile =
+        Collections.max(experimentSequenceMap.entrySet(), Map.Entry.comparingByKey()).getKey();
+    final String lastExperimentIdGenerated =
+        Collections.max(experimentSequenceMap.entrySet(), Map.Entry.comparingByKey()).getValue();
+
     final Element runSetElement = webinElement.addElement("RUN_SET");
 
     studies.forEach(
@@ -37,7 +38,7 @@ public void createENARunSetElement(
                       runElement.addElement("TITLE").addText(assayId);
                       runElement
                           .addElement("EXPERIMENT_REF")
-                          .addAttribute("refname", lastExperimentId);
+                          .addAttribute("refname", lastExperimentIdGenerated);
 
                       final AtomicReference<Output> dataFileOutput = new AtomicReference<>();
                       assay
@@ -48,7 +49,7 @@ public void createENARunSetElement(
                                       .getInputs()
                                       .forEach(
                                           input -> {
-                                            if (input.getId().equals(lastExperimentId)) {
+                                            if (input.getId().equals(lastExperimentKeyInRawFile)) {
                                               dataFileOutput.set(
                                                   processSequence.getOutputs().get(0));
                                             }

diff --git a/test-data/biosamples-input-isa.json b/test-data/biosamples-input-isa.json
@@ -853,7 +853,7 @@
             "dataFiles": [
               {
                 "@id": "#data/334",
-                "name": "RD file 1b",
+                "name": "ENA_TEST2.R2.fastq.gz",
                 "type": "Raw Data File",
                 "comments": [
                   {