Merge pull request #52 from elixir-europe/mars-receipt-library

Mars receipt library

.github/workflows/build-biosamples-service.yml

@@ -27,6 +27,7 @@ jobs:
       - name: Build Docker image
         uses: docker/build-push-action@v6
         with:
-          context: repository-services/isajson-biosamples
+          context: repository-services
+          file: repository-services/isajson-biosamples/Dockerfile
           push: false
-          tags: user/app:latest
+          tags: user/app:latest

.github/workflows/build-ena-service.yml

@@ -27,6 +27,7 @@ jobs:
       - name: Build Docker image
         uses: docker/build-push-action@v6
         with:
-          context: repository-services/isajson-ena
+          context: repository-services
+          file: repository-services/isajson-ena/Dockerfile
           push: false
-          tags: user/app:latest
+          tags: user/app:latest

.gitignore

@@ -163,6 +163,18 @@ cython_debug/
 # Test credentials
 test_credentials.json
 
-tmp/
+### IntelliJ IDEA ###
 .gradle/
+.idea
+*.iws
+*.iml
+*.ipr
+out/
+!**/src/main/**/out/
+!**/src/test/**/out/
+
+### VS Code ###
 .vscode/
+
+### tmp ###
+tmp/

repository-services/docker-compose.yml

@@ -1,12 +1,16 @@
 services:
   isa_biosamples:
-      build: isajson-biosamples
+      build:
+        context: .
+        dockerfile: isajson-biosamples/Dockerfile
       ports:
         - "8032:8032"
       restart: unless-stopped
 
   isa_sra:
-      build: isajson-ena
+      build:
+        context: .
+        dockerfile: isajson-ena/Dockerfile
       ports:
         - "8042:8042"
       restart: unless-stopped

repository-services/isajson-biosamples/Dockerfile

@@ -4,16 +4,23 @@ FROM gradle:jdk11 AS builder
 WORKDIR /app
 
 COPY . .
+
+WORKDIR /app/receipt
+RUN ./gradlew build
+RUN ./gradlew publishToMavenLocal
+
+WORKDIR /app/isajson-biosamples
 RUN ./gradlew build -x test -x spotlessApply --info --stacktrace "-Dorg.gradle.jvmargs=--add-exports jdk.compiler/com.sun.tools.javac.api=ALL-UNNAMED --add-exports jdk.compiler/com.sun.tools.javac.file=ALL-UNNAMED --add-exports jdk.compiler/com.sun.tools.javac.parser=ALL-UNNAMED --add-exports jdk.compiler/com.sun.tools.javac.tree=ALL-UNNAMED --add-exports jdk.compiler/com.sun.tools.javac.util=ALL-UNNAMED"
 
 # Use a lightweight base image to run the jar file
 FROM openjdk:11-jre-slim
+WORKDIR /app
 
-ARG JAR_FILE=/app/build/libs/*.jar
+ARG JAR_FILE=/app/isajson-biosamples/build/libs/*.jar
 
 # Copy the JAR file from the builder stage
 COPY --from=builder ${JAR_FILE} app.jar
 
 # Set the entry point for the application
-ENTRYPOINT ["java", "-jar", "/app.jar"]
+ENTRYPOINT ["java", "-jar", "app.jar"]
 

repository-services/isajson-biosamples/build.gradle

@@ -27,6 +27,8 @@ dependencies {
     implementation group: 'org.apache.commons', name: 'commons-collections4', version: '4.1'
     implementation group: 'org.apache.httpcomponents', name: 'httpclient', version: '4.5'
     implementation group: 'dom4j', name: 'dom4j', version: '1.6.1'
+
+    implementation group: 'com.elixir.biohackaton', name: 'mars-receipt', version: '0.0.1'
 
     compileOnly group: 'org.projectlombok', name: 'lombok', version: '1.18.24'
     annotationProcessor 'org.projectlombok:lombok:1.18.24'

repository-services/isajson-biosamples/src/main/java/com/elixir/biohackaton/ISAToSRA/biosamples/controller/BioSampleSubmissionController.java

@@ -4,19 +4,17 @@
 import static org.springframework.http.MediaType.APPLICATION_JSON_VALUE;
 import static org.springframework.http.MediaType.APPLICATION_XML_VALUE;
 
-import com.elixir.biohackaton.ISAToSRA.biosamples.receipt.Receipt;
-import com.elixir.biohackaton.ISAToSRA.biosamples.receipt.Receipt.Accession;
-import com.elixir.biohackaton.ISAToSRA.biosamples.receipt.Receipt;
+import com.elixir.biohackaton.ISAToSRA.biosamples.model.BiosampleAccessionsMap;
 import com.elixir.biohackaton.ISAToSRA.biosamples.service.BioSamplesSubmitter;
-import com.elixir.biohackaton.ISAToSRA.model.IsaJson;
-import com.elixir.biohackaton.ISAToSRA.model.Study;
+import com.elixir.biohackaton.ISAToSRA.biosamples.service.MarsReceiptService;
+import com.elixir.biohackaton.ISAToSRA.receipt.isamodel.*;
+import com.elixir.biohackaton.ISAToSRA.receipt.marsmodel.MarsReceipt;
 import com.fasterxml.jackson.annotation.JsonInclude;
 import com.fasterxml.jackson.databind.ObjectMapper;
 import io.swagger.v3.oas.annotations.responses.ApiResponse;
 import io.swagger.v3.oas.annotations.responses.ApiResponses;
+
 import java.util.List;
-import java.util.Map;
-import java.util.stream.Collectors;
 
 import lombok.extern.slf4j.Slf4j;
 import org.springframework.beans.factory.annotation.Autowired;
@@ -27,45 +25,41 @@
 public class BioSampleSubmissionController {
   @Autowired private BioSamplesSubmitter bioSamplesSubmitter;
   @Autowired private ObjectMapper objectMapper;
+  @Autowired private MarsReceiptService marsReceiptService;
 
   @ApiResponses(
-          value = {
-                  @ApiResponse(responseCode = "200", description = "Ok"),
-                  @ApiResponse(responseCode = "401", description = "Unauthorized"),
-                  @ApiResponse(responseCode = "403", description = "Forbidden"),
-                  @ApiResponse(responseCode = "400", description = "Bad request"),
-                  @ApiResponse(responseCode = "408", description = "Request Timeout"),
-                  @ApiResponse(responseCode = "415", description = "Unsupported media type")
-          })
+    value = {
+      @ApiResponse(responseCode = "200", description = "Ok"),
+      @ApiResponse(responseCode = "401", description = "Unauthorized"),
+      @ApiResponse(responseCode = "403", description = "Forbidden"),
+      @ApiResponse(responseCode = "400", description = "Bad request"),
+      @ApiResponse(responseCode = "408", description = "Request Timeout"),
+      @ApiResponse(responseCode = "415", description = "Unsupported media type")
+  })
   @CrossOrigin(origins = "http://localhost:8000")
   @PostMapping(
-          value = "/submit",
-          consumes = {APPLICATION_JSON_VALUE, APPLICATION_XML_VALUE})
+    value = "/submit",
+    consumes = { APPLICATION_JSON_VALUE, APPLICATION_XML_VALUE })
   public String performSubmissionToBioSamplesAndEna(
-          @RequestBody final String submissionPayload,
-          @RequestParam(value = "webinjwt") String webinJwt)
-          throws Exception {
+      @RequestBody final String submissionPayload,
+      @RequestParam(value = "webinjwt") String webinJwt)
+      throws Exception {
     String webinToken;
-
-    objectMapper.setSerializationInclusion(JsonInclude.Include.NON_NULL);
-
     if (webinJwt != null) {
       webinToken = webinJwt;
     } else {
       throw new RuntimeException("Webin Authentication Token is not provided");
     }
 
+    objectMapper.setSerializationInclusion(JsonInclude.Include.NON_NULL);
+
     final IsaJson isaJson = this.objectMapper.readValue(submissionPayload, IsaJson.class);
     final List<Study> studies = getStudies(isaJson);
 
-    final Map<String, String> accessionsMap = this.bioSamplesSubmitter.createBioSamples(studies, webinToken);
-    final Receipt repositoryData = new Receipt();
-
-    repositoryData.setTargetRepository("biosamples");
-    repositoryData.setAccessions(accessionsMap.values().stream()
-            .map(value -> new Accession(value, null)).collect(Collectors.toList()));
+    final BiosampleAccessionsMap accessionsMap = this.bioSamplesSubmitter.createBioSamples(studies, webinToken);
+    final MarsReceipt marsReceipt = marsReceiptService.convertReceiptToMars(accessionsMap, isaJson);
 
-    return this.objectMapper.writerWithDefaultPrettyPrinter().writeValueAsString(repositoryData);
+    return marsReceiptService.convertMarsReceiptToJson(marsReceipt);
   }
 
   public List<Study> getStudies(final IsaJson isaJson) {

repository-services/isajson-biosamples/src/main/java/com/elixir/biohackaton/ISAToSRA/biosamples/model/Sample.java → repository-services/isajson-biosamples/src/main/java/com/elixir/biohackaton/ISAToSRA/biosamples/model/BioSample.java

@@ -35,7 +35,7 @@
   "submittedDate",
   "submittedVia"
 })
-public class Sample implements Comparable<Sample> {
+public class BioSample implements Comparable<BioSample> {
   protected String accession;
   protected String name;
 
@@ -61,7 +61,7 @@ public class Sample implements Comparable<Sample> {
   protected SortedSet<Publication> publications;
   protected SubmittedViaType submittedVia;
 
-  protected Sample() {}
+  protected BioSample() {}
 
   @JsonProperty("accession")
   public String getAccession() {
@@ -228,10 +228,10 @@ public SubmittedViaType getSubmittedVia() {
   public boolean equals(Object o) {
 
     if (o == this) return true;
-    if (!(o instanceof Sample)) {
+    if (!(o instanceof BioSample)) {
       return false;
     }
-    Sample other = (Sample) o;
+    BioSample other = (BioSample) o;
 
     // dont use update date for comparisons, too volatile. SubmittedVia doesnt contain information
     // for comparison
@@ -251,7 +251,7 @@ public boolean equals(Object o) {
   }
 
   @Override
-  public int compareTo(Sample other) {
+  public int compareTo(BioSample other) {
     if (other == null) {
       return 1;
     }
@@ -413,7 +413,7 @@ public String toString() {
     return sb.toString();
   }
 
-  public static Sample build(
+  public static BioSample build(
       String name,
       String accession,
       String domain,
@@ -447,7 +447,7 @@ public static Sample build(
         null);
   }
 
-  public static Sample build(
+  public static BioSample build(
       String name,
       String accession,
       String domain,
@@ -484,7 +484,7 @@ public static Sample build(
 
   // Used for deserializtion (JSON -> Java)
   @JsonCreator
-  public static Sample build(
+  public static BioSample build(
       @JsonProperty("name") String name,
       @JsonProperty("accession") String accession,
       @JsonProperty("domain") String domain,
@@ -509,7 +509,7 @@ public static Sample build(
       @JsonProperty("publications") Collection<Publication> publications,
       @JsonProperty("submittedVia") SubmittedViaType submittedVia) {
 
-    Sample sample = new Sample();
+    BioSample sample = new BioSample();
 
     if (accession != null) {
       sample.accession = accession.trim();
@@ -890,8 +890,8 @@ public Builder withNoPublications() {
       return this;
     }
 
-    public Sample build() {
-      return Sample.build(
+    public BioSample build() {
+      return BioSample.build(
           name,
           accession,
           domain,
@@ -931,7 +931,7 @@ private ZonedDateTime parseDateTime(String datetimeString) {
      * @param sample the sample to use as reference
      * @return the Builder
      */
-    public static Builder fromSample(Sample sample) {
+    public static Builder fromSample(BioSample sample) {
       return new Builder(sample.getName(), sample.getAccession())
           .withDomain(sample.getDomain())
           .withWebinSubmissionAccountId(sample.getWebinSubmissionAccountId())

repository-services/isajson-biosamples/src/main/java/com/elixir/biohackaton/ISAToSRA/biosamples/model/BiosampleAccessionsMap.java

@@ -0,0 +1,9 @@
+package com.elixir.biohackaton.ISAToSRA.biosamples.model;
+
+import com.elixir.biohackaton.ISAToSRA.receipt.ReceiptAccessionsMap;
+
+public class BiosampleAccessionsMap {
+    public ReceiptAccessionsMap sourceAccessionsMap = new ReceiptAccessionsMap();
+    public ReceiptAccessionsMap studyAccessionsMap = new ReceiptAccessionsMap();
+    public ReceiptAccessionsMap sampleAccessionsMap = new ReceiptAccessionsMap();
+}