Multiple tags in single cell #188 (virusseq#89)

* Code changes to accept multiple tags in a single cell in the Tsv - ticket #188 * Code changes to accept multiple tags in a single cell in the Tsv - ticket #188 * Refactored code to make the delimiter configurable. - ticket #188 * Refactored code to make the delimiter configurable. - ticket #188 * Incorporated review comments 1 & 3 on git - ticket #188 * Incorporated review comments on git - ticket #188 * Incorporated review comments on git - ticket #188 * Incorporated review comments on git - ticket #188 * Incorporated review comments on git, rectified errors. - ticket #188 Co-authored-by: UmmulkiramR <[email protected]>
african-pathogen-archive · Aug 17, 2022 · 9ed8b79 · 9ed8b79
1 parent 739891e
commit 9ed8b79
Show file tree

Hide file tree

Showing 7 changed files with 49 additions and 10 deletions.
diff --git a/src/main/java/org/cancogenvirusseq/muse/components/PayloadFileMapper.java b/src/main/java/org/cancogenvirusseq/muse/components/PayloadFileMapper.java
@@ -8,10 +8,8 @@
 import com.fasterxml.jackson.databind.ObjectMapper;
 import com.fasterxml.jackson.databind.node.JsonNodeFactory;
 import com.fasterxml.jackson.databind.node.ObjectNode;
-import java.util.ArrayList;
-import java.util.HashMap;
-import java.util.List;
-import java.util.Map;
+
+import java.util.*;
 import java.util.concurrent.ConcurrentHashMap;
 import java.util.function.BiFunction;
 import java.util.function.BinaryOperator;
@@ -30,14 +28,31 @@
 import org.cancogenvirusseq.muse.model.SubmissionBundle;
 import org.cancogenvirusseq.muse.model.SubmissionFile;
 import org.cancogenvirusseq.muse.model.UploadRequest;
+import org.cancogenvirusseq.muse.utils.StringUtils;
 import org.springframework.beans.factory.annotation.Autowired;
+import org.springframework.beans.factory.annotation.Value;
+import org.springframework.security.access.method.P;
 import org.springframework.stereotype.Component;
 
 @Slf4j
 @Component
 public class PayloadFileMapper {
   private final String payloadJsonTemplate;
 
+  private static String multiTagDelimiter;
+  private static List<String> columnKeys;
+
+
+  @Value("${tsv.columnKeys:''}")
+  public void setColumnKeys(List<String> keys) {
+    columnKeys = keys;
+  }
+
+  @Value("${tsv.multiTagDelimiter}")
+  public void setMultiTagDelimiter(String delimiter) {
+    multiTagDelimiter = delimiter;
+  }
+
   @Autowired
   public PayloadFileMapper(MuseAppConfig config) {
     this.payloadJsonTemplate = config.getPayloadJsonTemplate();
@@ -153,7 +168,11 @@ private static ObjectNode convertRecordToPayload(
           } else if (value.toString().trim().equals("")) {
             // empty string map to null value
             return "null";
-          } else {
+          } else if((!Objects.isNull(columnKeys) && columnKeys.contains(key)) && (value.toString().split(multiTagDelimiter).length>0)) {
+            //for multiple tags in single cell
+            return StringUtils.stringToArrayOfStrings(value.toString(), multiTagDelimiter);
+          }
+          else {
             // for string append double quotes and escape any existing double quotes
             return format("\"%s\"", value.toString().replace("\"", "\\\""));
           }
@@ -167,6 +186,8 @@ private static ObjectNode convertRecordToPayload(
     return new ObjectMapper().readValue(templatedStr, ObjectNode.class);
   }
 
+
+
   private static JsonNode createFilesObject(SubmissionFile submissionFile, String fileName) {
     val filesArray = JsonNodeFactory.instance.arrayNode(1);
     val fileObj = JsonNodeFactory.instance.objectNode();

diff --git a/src/main/java/org/cancogenvirusseq/muse/model/tsv_parser/TsvFieldSchema.java b/src/main/java/org/cancogenvirusseq/muse/model/tsv_parser/TsvFieldSchema.java
@@ -14,6 +14,7 @@ public class TsvFieldSchema {
 
   public enum ValueType {
     string,
-    number
+    number,
+    array
   }
 }
diff --git a/src/main/java/org/cancogenvirusseq/muse/service/SongScoreService.java b/src/main/java/org/cancogenvirusseq/muse/service/SongScoreService.java
@@ -57,6 +57,7 @@ private Disposable createSubmitUploadDisposable() {
   }
 
   public Mono<Upload> submitAndUploadToSongScore(UploadEvent uploadEvent) {
+    log.debug("UploadEvent:payload for song - {}", uploadEvent.getPayload());
     return ariaClient
         .submitPayload(uploadEvent.getStudyId(), uploadEvent.getPayload())
         .flatMap(

diff --git a/src/main/java/org/cancogenvirusseq/muse/utils/StringUtils.java b/src/main/java/org/cancogenvirusseq/muse/utils/StringUtils.java
@@ -3,6 +3,8 @@
 import java.util.regex.Pattern;
 import lombok.experimental.UtilityClass;
 
+import static java.lang.String.format;
+
 @UtilityClass
 public class StringUtils {
   private static final Pattern INTEGER_PATTERN = Pattern.compile("^-?\\d+$");
@@ -15,4 +17,13 @@ public static Boolean isDouble(String s) {
   public static Boolean isInteger(String s) {
     return INTEGER_PATTERN.matcher(s).matches();
   }
+
+  public static String stringToArrayOfStrings(String value, String delimiter){
+    StringBuilder sb = new StringBuilder();
+    for (String n : value.toString().split(delimiter)) {
+      if (sb.length() > 0) sb.append(',');
+      sb.append(format("\"%s\"", n.toString().replace("\"", "\\\"")));
+    }
+    return sb.toString();
+  }
 }
diff --git a/src/main/resources/application.yaml b/src/main/resources/application.yaml
@@ -50,3 +50,8 @@ management:
   endpoint:
     health:
       show-details: NEVER
+
+tsv:
+  multiTagDelimiter: ";"
+  columnKeys: anatomical part,purpose of sequencing
+
diff --git a/src/main/resources/payload-template b/src/main/resources/payload-template
@@ -33,7 +33,7 @@
         "purpose_of_sampling": ${purpose of sampling},
         "purpose_of_sampling_details": ${purpose of sampling details},
         "anatomical_material": ${anatomical material},
-        "anatomical_part": ${anatomical part},
+        "anatomical_part": [${anatomical part}],
         "body_product": ${body product},
         "environmental_material": ${environmental material},
         "environmental_site": ${environmental site},
@@ -50,7 +50,7 @@
         "host_gender": ${host gender}
       },
       "experiment": {
-        "purpose_of_sequencing": ${purpose of sequencing},
+        "purpose_of_sequencing": [${purpose of sequencing}],
         "purpose_of_sequencing_details": ${purpose of sequencing details},
         "sequencing_instrument": ${sequencing instrument},
         "sequencing_protocol": ${sequencing protocol}

diff --git a/src/main/resources/tsv-schema.json b/src/main/resources/tsv-schema.json
@@ -13,7 +13,7 @@
   { "name": "purpose of sampling", "valueType": "string" },
   { "name": "purpose of sampling details", "valueType": "string" },
   { "name": "anatomical material", "valueType": "string" },
-  { "name": "anatomical part", "valueType": "string" },
+  { "name": "anatomical part", "valueType": "array" },
   { "name": "body product", "valueType": "string" },
   { "name": "environmental material", "valueType": "string" },
   { "name": "environmental site", "valueType": "string" },
@@ -26,7 +26,7 @@
   { "name": "host age unit", "valueType": "string" },
   { "name": "host age bin", "valueType": "string" },
   { "name": "host gender", "valueType": "string" },
-  { "name": "purpose of sequencing", "valueType": "string" },
+  { "name": "purpose of sequencing", "valueType": "array" },
   { "name": "purpose of sequencing details", "valueType": "string" },
   { "name": "sequencing instrument", "valueType": "string" },
   { "name": "sequencing protocol", "valueType": "string" },
-Original file line number
+Diff line change
@@ Expand Up / @@ -14,6 +14,7 @@ public class TsvFieldSchema { @@
       public enum ValueType {
         string,
-        number
+        number,
+        array
       }
     }