Merge pull request #42 from elixir-europe/keep_sunspot_happy

Keep sunspot happy
elixir-europe · Jul 22, 2024 · 52c02db · 52c02db
2 parents 5d84a54 + bccafa0
commit 52c02db
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diff --git a/.github/workflows/build-biosamples-service.yml b/.github/workflows/build-biosamples-service.yml
@@ -0,0 +1,32 @@
+name: Build and Push Docker image for BioSamples service
+
+on:
+  push:
+    paths:
+        - "repository-services/isajson-biosamples/**"
+  pull_request:
+    paths:
+        - "repository-services/isajson-biosamples/**"
+    branches:
+      - main
+
+jobs:
+  build:
+    runs-on: ubuntu-latest
+
+    steps:
+      - name: Checkout repository
+        uses: actions/checkout@v4
+
+      - name: Set up QEMU
+        uses: docker/setup-qemu-action@v3
+
+      - name: Set up Docker Buildx
+        uses: docker/setup-buildx-action@v3
+
+      - name: Build Docker image
+        uses: docker/build-push-action@v6
+        with:
+          context: repository-services/isajson-biosamples
+          push: false
+          tags: user/app:latest
diff --git a/.github/workflows/build-ena-service.yml b/.github/workflows/build-ena-service.yml
@@ -0,0 +1,32 @@
+name: Build and Push Docker image for ENA service
+
+on:
+  push:
+    paths:
+        - "repository-services/isajson-ena/**"
+  pull_request:
+    paths:
+        - "repository-services/isajson-ena/**"
+    branches:
+      - main
+
+jobs:
+  build:
+    runs-on: ubuntu-latest
+
+    steps:
+      - name: Checkout repository
+        uses: actions/checkout@v4
+
+      - name: Set up QEMU
+        uses: docker/setup-qemu-action@v3
+
+      - name: Set up Docker Buildx
+        uses: docker/setup-buildx-action@v3
+
+      - name: Build Docker image
+        uses: docker/build-push-action@v6
+        with:
+          context: repository-services/isajson-ena
+          push: false
+          tags: user/app:latest
diff --git a/...in/java/com/elixir/biohackaton/ISAToSRA/controller/WebinIsaToXmlSubmissionController.java b/...in/java/com/elixir/biohackaton/ISAToSRA/controller/WebinIsaToXmlSubmissionController.java
@@ -8,9 +8,9 @@
 import com.elixir.biohackaton.ISAToSRA.model.Investigation;
 import com.elixir.biohackaton.ISAToSRA.model.IsaJson;
 import com.elixir.biohackaton.ISAToSRA.model.Study;
-import com.elixir.biohackaton.ISAToSRA.sra.service.*;
 import com.elixir.biohackaton.ISAToSRA.sra.model.MarsReceipt;
 import com.elixir.biohackaton.ISAToSRA.sra.model.Receipt;
+import com.elixir.biohackaton.ISAToSRA.sra.service.*;
 import com.fasterxml.jackson.databind.ObjectMapper;
 import io.swagger.v3.oas.annotations.responses.ApiResponse;
 import io.swagger.v3.oas.annotations.responses.ApiResponses;
@@ -32,42 +32,36 @@
 @Slf4j
 @RestController
 public class WebinIsaToXmlSubmissionController {
-  @Autowired
-  private BioSamplesAccessionsParser bioSamplesAccessionsParser;
+  @Autowired private BioSamplesAccessionsParser bioSamplesAccessionsParser;
 
-  @Autowired
-  private WebinStudyXmlCreator webinStudyXmlCreator;
+  @Autowired private WebinStudyXmlCreator webinStudyXmlCreator;
 
-  @Autowired
-  private WebinExperimentXmlCreator webinExperimentXmlCreator;
+  @Autowired private WebinExperimentXmlCreator webinExperimentXmlCreator;
 
-  @Autowired
-  private WebinProjectXmlCreator webinProjectXmlCreator;
+  @Autowired private WebinProjectXmlCreator webinProjectXmlCreator;
 
-  @Autowired
-  private WebinRunXmlCreator webinRunXmlCreator;
+  @Autowired private WebinRunXmlCreator webinRunXmlCreator;
 
-  @Autowired
-  private WebinHttpSubmissionService webinHttpSubmissionService;
+  @Autowired private WebinHttpSubmissionService webinHttpSubmissionService;
 
-  @Autowired
-  private ObjectMapper objectMapper;
+  @Autowired private ObjectMapper objectMapper;
 
-  @Autowired
-  private ReceiptConversionService receiptConversionService;
+  @Autowired private ReceiptConversionService receiptConversionService;
 
-  @Autowired
-  private ReceiptMarsService receiptMarsService;
+  @Autowired private ReceiptMarsService receiptMarsService;
 
-  @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")
-  })
-  @PostMapping(value = "/submit", consumes = { APPLICATION_JSON_VALUE, APPLICATION_XML_VALUE })
+  @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")
+      })
+  @PostMapping(
+      value = "/submit",
+      consumes = {APPLICATION_JSON_VALUE, APPLICATION_XML_VALUE})
   public String performSubmissionToEna(
       @RequestBody final String submissionPayload,
       @RequestParam(value = "webinUserName") String webinUserName,
@@ -83,8 +77,9 @@ public String performSubmissionToEna(
 
     final IsaJson isaJson = this.objectMapper.readValue(submissionPayload, IsaJson.class);
     final List<Study> studies = getStudies(isaJson);
-    final Map<String, String> typeToBioSamplesAccessionMap = this.bioSamplesAccessionsParser
-        .parseIsaFileAndGetBioSampleAccessions(studies, new HashMap<>());
+    final Map<String, String> typeToBioSamplesAccessionMap =
+        this.bioSamplesAccessionsParser.parseIsaFileAndGetBioSampleAccessions(
+            studies, new HashMap<>());
 
     final Document document = DocumentHelper.createDocument();
     final Element webinElement = startPreparingWebinV2SubmissionXml(document);
@@ -93,8 +88,9 @@ public String performSubmissionToEna(
     this.webinStudyXmlCreator.createENAStudySetElement(
         webinElement, studies, randomSubmissionIdentifier);
 
-    final Map<Integer, String> experimentSequenceMap = this.webinExperimentXmlCreator.createENAExperimentSetElement(
-        typeToBioSamplesAccessionMap, webinElement, studies, randomSubmissionIdentifier);
+    final Map<Integer, String> experimentSequenceMap =
+        this.webinExperimentXmlCreator.createENAExperimentSetElement(
+            typeToBioSamplesAccessionMap, webinElement, studies, randomSubmissionIdentifier);
 
     this.webinRunXmlCreator.createENARunSetElement(
         webinElement, studies, experimentSequenceMap, randomSubmissionIdentifier);
@@ -106,8 +102,9 @@ public String performSubmissionToEna(
 
     writer.write(document);
 
-    final String receiptXml = webinHttpSubmissionService.performWebinSubmission(
-        webinUserName, document.asXML(), webinPassword);
+    final String receiptXml =
+        webinHttpSubmissionService.performWebinSubmission(
+            webinUserName, document.asXML(), webinPassword);
     final Receipt receiptJson = receiptConversionService.readReceiptXml(receiptXml);
     final MarsReceipt marsReceipt = receiptMarsService.convertReceiptToMars(receiptJson, isaJson);
 

diff --git a/...ices/isajson-ena/src/main/java/com/elixir/biohackaton/ISAToSRA/sra/model/MarsReceipt.java b/...ices/isajson-ena/src/main/java/com/elixir/biohackaton/ISAToSRA/sra/model/MarsReceipt.java
@@ -1,3 +1,4 @@
+/** Elixir BioHackathon 2022 */
 package com.elixir.biohackaton.ISAToSRA.sra.model;
 
 import lombok.Builder;
@@ -6,11 +7,11 @@
 @Builder
 @Data
 public class MarsReceipt {
-    private String targetRepository;
+  private String targetRepository;
 
-    private MarsReceiptError[] errors;
+  private MarsReceiptError[] errors;
 
-    private MarsReceiptInfo[] info;
+  private MarsReceiptInfo[] info;
 
-    private MarsReceiptAccession[] accessions;
+  private MarsReceiptAccession[] accessions;
 }
diff --git a/...son-ena/src/main/java/com/elixir/biohackaton/ISAToSRA/sra/model/MarsReceiptAccession.java b/...son-ena/src/main/java/com/elixir/biohackaton/ISAToSRA/sra/model/MarsReceiptAccession.java
@@ -1,3 +1,4 @@
+/** Elixir BioHackathon 2022 */
 package com.elixir.biohackaton.ISAToSRA.sra.model;
 
 import lombok.Builder;
@@ -6,7 +7,7 @@
 @Builder
 @Data
 public class MarsReceiptAccession {
-    private String value;
+  private String value;
 
-    private MarsReceiptPath[] path;
+  private MarsReceiptPath[] path;
 }
diff --git a/...isajson-ena/src/main/java/com/elixir/biohackaton/ISAToSRA/sra/model/MarsReceiptError.java b/...isajson-ena/src/main/java/com/elixir/biohackaton/ISAToSRA/sra/model/MarsReceiptError.java
@@ -1,18 +1,18 @@
+/** Elixir BioHackathon 2022 */
 package com.elixir.biohackaton.ISAToSRA.sra.model;
 
 import com.fasterxml.jackson.annotation.JsonInclude;
 import com.fasterxml.jackson.annotation.JsonInclude.Include;
-
 import lombok.Builder;
 import lombok.Data;
 
 @Builder
 @Data
 public class MarsReceiptError {
-    private MarsReceiptErrorType type;
+  private MarsReceiptErrorType type;
 
-    private String message;
+  private String message;
 
-    @JsonInclude(Include.NON_NULL)
-    private MarsReceiptPath[] path;
+  @JsonInclude(Include.NON_NULL)
+  private MarsReceiptPath[] path;
 }
diff --git a/...son-ena/src/main/java/com/elixir/biohackaton/ISAToSRA/sra/model/MarsReceiptErrorType.java b/...son-ena/src/main/java/com/elixir/biohackaton/ISAToSRA/sra/model/MarsReceiptErrorType.java
@@ -1,6 +1,7 @@
+/** Elixir BioHackathon 2022 */
 package com.elixir.biohackaton.ISAToSRA.sra.model;
 
 public enum MarsReceiptErrorType {
-    INVALID_METADATA,
-    INVALID_DATA;
+  INVALID_METADATA,
+  INVALID_DATA;
 }
diff --git a/.../isajson-ena/src/main/java/com/elixir/biohackaton/ISAToSRA/sra/model/MarsReceiptInfo.java b/.../isajson-ena/src/main/java/com/elixir/biohackaton/ISAToSRA/sra/model/MarsReceiptInfo.java
@@ -1,16 +1,16 @@
+/** Elixir BioHackathon 2022 */
 package com.elixir.biohackaton.ISAToSRA.sra.model;
 
 import com.fasterxml.jackson.annotation.JsonInclude;
 import com.fasterxml.jackson.annotation.JsonInclude.Include;
-
 import lombok.Builder;
 import lombok.Data;
 
 @Builder
 @Data
 public class MarsReceiptInfo {
-    @JsonInclude(Include.NON_NULL)
-    private String name;
+  @JsonInclude(Include.NON_NULL)
+  private String name;
 
-    private String message;
+  private String message;
 }
diff --git a/...ajson-ena/src/main/java/com/elixir/biohackaton/ISAToSRA/sra/model/MarsReceiptMessage.java b/...ajson-ena/src/main/java/com/elixir/biohackaton/ISAToSRA/sra/model/MarsReceiptMessage.java
@@ -1,18 +1,16 @@
+/** Elixir BioHackathon 2022 */
 package com.elixir.biohackaton.ISAToSRA.sra.model;
 
+import java.util.ArrayList;
+import java.util.List;
 import lombok.Builder;
-import lombok.Data;
 import lombok.Builder.Default;
-
-import java.util.List;
-import java.util.ArrayList;
+import lombok.Data;
 
 @Builder
 @Data
 public class MarsReceiptMessage {
-    @Default
-    private List<MarsReceiptError> errors = new ArrayList<>();
+  @Default private List<MarsReceiptError> errors = new ArrayList<>();
 
-    @Default
-    private List<MarsReceiptInfo> info= new ArrayList<>();
+  @Default private List<MarsReceiptInfo> info = new ArrayList<>();
 }
diff --git a/.../isajson-ena/src/main/java/com/elixir/biohackaton/ISAToSRA/sra/model/MarsReceiptPath.java b/.../isajson-ena/src/main/java/com/elixir/biohackaton/ISAToSRA/sra/model/MarsReceiptPath.java
@@ -1,16 +1,16 @@
+/** Elixir BioHackathon 2022 */
 package com.elixir.biohackaton.ISAToSRA.sra.model;
 
 import com.fasterxml.jackson.annotation.JsonInclude;
 import com.fasterxml.jackson.annotation.JsonInclude.Include;
-
 import lombok.Builder;
 import lombok.Data;
 
 @Builder
 @Data
 public class MarsReceiptPath {
-    private String key;
+  private String key;
 
-    @JsonInclude(Include.NON_NULL)
-    private MarsReceiptWhere where;
+  @JsonInclude(Include.NON_NULL)
+  private MarsReceiptWhere where;
 }
diff --git a/...isajson-ena/src/main/java/com/elixir/biohackaton/ISAToSRA/sra/model/MarsReceiptWhere.java b/...isajson-ena/src/main/java/com/elixir/biohackaton/ISAToSRA/sra/model/MarsReceiptWhere.java
@@ -1,3 +1,4 @@
+/** Elixir BioHackathon 2022 */
 package com.elixir.biohackaton.ISAToSRA.sra.model;
 
 import lombok.Builder;
@@ -6,7 +7,7 @@
 @Builder
 @Data
 public class MarsReceiptWhere {
-    private String key;
+  private String key;
 
-    private String value;
+  private String value;
 }