Merged from staging for next release (#9)

* replace pagetoken by page in variants response * add externalReferences to callsets and hide filters that are not managed on search/callsets * POM update --------- Co-authored-by: Alice Boizet <[email protected]>
GuilhemSempere · Jun 21, 2024 · 128bb59 · 128bb59
1 parent 4414ed8
commit 128bb59
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Showing 4 changed files with 83 additions and 53 deletions.
diff --git a/pom.xml b/pom.xml
@@ -6,7 +6,7 @@
         <java.version>17</java.version>
         <maven.compiler.source>${java.version}</maven.compiler.source>
         <maven.compiler.target>${java.version}</maven.compiler.target>
-	    <project.version>1.0.4-RELEASE</project.version>
+	    <project.version>1.0.5-RELEASE</project.version>
     </properties>
 
     <groupId>fr.cirad</groupId>

diff --git a/src/main/java/org/brapi/v2/model/CallSet.java b/src/main/java/org/brapi/v2/model/CallSet.java
@@ -1,30 +1,29 @@
 package org.brapi.v2.model;
 
+import java.util.Objects;
+import com.fasterxml.jackson.annotation.JsonProperty;
+import io.swagger.v3.oas.annotations.media.Schema;
 import java.util.ArrayList;
 import java.util.HashMap;
 import java.util.List;
 import java.util.Map;
-import java.util.Objects;
-
-import javax.validation.Valid;
-
+import org.threeten.bp.OffsetDateTime;
 import org.springframework.validation.annotation.Validated;
-
-import com.fasterxml.jackson.annotation.JsonProperty;
-
-import io.swagger.annotations.ApiModel;
-import io.swagger.annotations.ApiModelProperty;
+import javax.validation.Valid;
+import javax.validation.constraints.*;
 
 /**
  * A CallSet is a collection of calls that were generated by the same analysis of the same sample.
  */
-@ApiModel(description = "A CallSet is a collection of calls that were generated by the same analysis of the same sample.")
+@Schema(description = "A CallSet is a collection of calls that were generated by the same analysis of the same sample.")
 @Validated
-@javax.annotation.Generated(value = "io.swagger.codegen.v3.generators.java.SpringCodegen", date = "2019-11-19T12:30:12.318Z[GMT]")
+@javax.annotation.Generated(value = "io.swagger.codegen.v3.generators.java.SpringCodegen", date = "2022-09-19T13:16:35.755Z[GMT]")
+
+
 public class CallSet   {
   @JsonProperty("additionalInfo")
   @Valid
-  private Map<String, Object> additionalInfo = null;
+  private Map<String, String> additionalInfo = null;
 
   @JsonProperty("callSetDbId")
   private String callSetDbId = null;
@@ -33,7 +32,10 @@ public class CallSet   {
   private String callSetName = null;
 
   @JsonProperty("created")
-  private String created = null;
+  private OffsetDateTime created = null;
+
+  @JsonProperty("externalReferences")
+  private ExternalReferences externalReferences = null;
 
   @JsonProperty("sampleDbId")
   private String sampleDbId = null;
@@ -42,20 +44,20 @@ public class CallSet   {
   private String studyDbId = null;
 
   @JsonProperty("updated")
-  private String updated = null;
+  private OffsetDateTime updated = null;
 
   @JsonProperty("variantSetDbIds")
   @Valid
   private List<String> variantSetDbIds = null;
 
-  public CallSet additionalInfo(Map<String, Object> additionalInfo) {
+  public CallSet additionalInfo(Map<String, String> additionalInfo) {
     this.additionalInfo = additionalInfo;
     return this;
   }
 
-  public CallSet putAdditionalInfoItem(String key, Object additionalInfoItem) {
+  public CallSet putAdditionalInfoItem(String key, String additionalInfoItem) {
     if (this.additionalInfo == null) {
-      this.additionalInfo = new HashMap<>();
+      this.additionalInfo = new HashMap<String, String>();
     }
     this.additionalInfo.put(key, additionalInfoItem);
     return this;
@@ -64,14 +66,14 @@ public CallSet putAdditionalInfoItem(String key, Object additionalInfoItem) {
   /**
    * Additional arbitrary info
    * @return additionalInfo
-  **/
-  @ApiModelProperty(value = "Additional arbitrary info")
+   **/
+  @Schema(description = "Additional arbitrary info")
 
-    public Map<String, Object> getAdditionalInfo() {
+    public Map<String, String> getAdditionalInfo() {
     return additionalInfo;
   }
 
-  public void setAdditionalInfo(Map<String, Object> additionalInfo) {
+  public void setAdditionalInfo(Map<String, String> additionalInfo) {
     this.additionalInfo = additionalInfo;
   }
 
@@ -81,10 +83,10 @@ public CallSet callSetDbId(String callSetDbId) {
   }
 
   /**
-   * The call set ID.
+   * The ID which uniquely identifies a CallSet within the given database server
    * @return callSetDbId
-  **/
-  @ApiModelProperty(value = "The call set ID.")
+   **/
+  @Schema(example = "eb2bfd3d", description = "The ID which uniquely identifies a CallSet within the given database server")
 
     public String getCallSetDbId() {
     return callSetDbId;
@@ -100,10 +102,10 @@ public CallSet callSetName(String callSetName) {
   }
 
   /**
-   * The call set name.
+   * The human readable name which identifies a germplasm within the given database server
    * @return callSetName
-  **/
-  @ApiModelProperty(value = "The call set name.")
+   **/
+  @Schema(example = "Sample_123_DNA_Run_456", description = "The human readable name which identifies a germplasm within the given database server")
 
     public String getCallSetName() {
     return callSetName;
@@ -113,25 +115,46 @@ public void setCallSetName(String callSetName) {
     this.callSetName = callSetName;
   }
 
-  public CallSet created(String created) {
+  public CallSet created(OffsetDateTime created) {
     this.created = created;
     return this;
   }
 
   /**
-   * The date this call set was created in milliseconds from the epoch.
+   * The date this call set was created
    * @return created
-  **/
-  @ApiModelProperty(value = "The date this call set was created in milliseconds from the epoch.")
+   **/
+  @Schema(description = "The date this call set was created")
 
-    public String getCreated() {
+    @Valid
+    public OffsetDateTime getCreated() {
     return created;
   }
 
-  public void setCreated(String created) {
+  public void setCreated(OffsetDateTime created) {
     this.created = created;
   }
 
+  public CallSet externalReferences(ExternalReferences externalReferences) {
+    this.externalReferences = externalReferences;
+    return this;
+  }
+
+  /**
+   * Get externalReferences
+   * @return externalReferences
+   **/
+  @Schema(description = "")
+
+    @Valid
+    public ExternalReferences getExternalReferences() {
+    return externalReferences;
+  }
+
+  public void setExternalReferences(ExternalReferences externalReferences) {
+    this.externalReferences = externalReferences;
+  }
+
   public CallSet sampleDbId(String sampleDbId) {
     this.sampleDbId = sampleDbId;
     return this;
@@ -140,8 +163,8 @@ public CallSet sampleDbId(String sampleDbId) {
   /**
    * The Biosample entity the call set data was generated from.
    * @return sampleDbId
-  **/
-  @ApiModelProperty(value = "The Biosample entity the call set data was generated from.")
+   **/
+  @Schema(example = "5e50e11d", description = "The Biosample entity the call set data was generated from.")
 
     public String getSampleDbId() {
     return sampleDbId;
@@ -159,8 +182,8 @@ public CallSet studyDbId(String studyDbId) {
   /**
    * The ID which uniquely identifies a study within the given database server
    * @return studyDbId
-  **/
-  @ApiModelProperty(value = "The ID which uniquely identifies a study within the given database server")
+   **/
+  @Schema(example = "708149c1", description = "The ID which uniquely identifies a study within the given database server")
 
     public String getStudyDbId() {
     return studyDbId;
@@ -170,22 +193,23 @@ public void setStudyDbId(String studyDbId) {
     this.studyDbId = studyDbId;
   }
 
-  public CallSet updated(String updated) {
+  public CallSet updated(OffsetDateTime updated) {
     this.updated = updated;
     return this;
   }
 
   /**
-   * The time at which this call set was last updated in milliseconds from the epoch.
+   * The time at which this call set was last updated
    * @return updated
-  **/
-  @ApiModelProperty(value = "The time at which this call set was last updated in milliseconds from the epoch.")
+   **/
+  @Schema(description = "The time at which this call set was last updated")
 
-    public String getUpdated() {
+    @Valid
+    public OffsetDateTime getUpdated() {
     return updated;
   }
 
-  public void setUpdated(String updated) {
+  public void setUpdated(OffsetDateTime updated) {
     this.updated = updated;
   }
 
@@ -203,10 +227,10 @@ public CallSet addVariantSetDbIdsItem(String variantSetDbIdsItem) {
   }
 
   /**
-   * The IDs of the variant sets this call set has calls in.
+   * The IDs of the variantSets this callSet has calls in.
    * @return variantSetDbIds
-  **/
-  @ApiModelProperty(value = "The IDs of the variant sets this call set has calls in.")
+   **/
+  @Schema(example = "[\"cfd3d60f\",\"a4e8bfe9\"]", description = "The IDs of the variantSets this callSet has calls in.")
 
     public List<String> getVariantSetDbIds() {
     return variantSetDbIds;
@@ -230,6 +254,7 @@ public boolean equals(java.lang.Object o) {
         Objects.equals(this.callSetDbId, callSet.callSetDbId) &&
         Objects.equals(this.callSetName, callSet.callSetName) &&
         Objects.equals(this.created, callSet.created) &&
+        Objects.equals(this.externalReferences, callSet.externalReferences) &&
         Objects.equals(this.sampleDbId, callSet.sampleDbId) &&
         Objects.equals(this.studyDbId, callSet.studyDbId) &&
         Objects.equals(this.updated, callSet.updated) &&
@@ -238,7 +263,7 @@ public boolean equals(java.lang.Object o) {
 
   @Override
   public int hashCode() {
-    return Objects.hash(additionalInfo, callSetDbId, callSetName, created, sampleDbId, studyDbId, updated, variantSetDbIds);
+    return Objects.hash(additionalInfo, callSetDbId, callSetName, created, externalReferences, sampleDbId, studyDbId, updated, variantSetDbIds);
   }
 
   @Override
@@ -250,6 +275,7 @@ public String toString() {
     sb.append("    callSetDbId: ").append(toIndentedString(callSetDbId)).append("\n");
     sb.append("    callSetName: ").append(toIndentedString(callSetName)).append("\n");
     sb.append("    created: ").append(toIndentedString(created)).append("\n");
+    sb.append("    externalReferences: ").append(toIndentedString(externalReferences)).append("\n");
     sb.append("    sampleDbId: ").append(toIndentedString(sampleDbId)).append("\n");
     sb.append("    studyDbId: ").append(toIndentedString(studyDbId)).append("\n");
     sb.append("    updated: ").append(toIndentedString(updated)).append("\n");
@@ -268,4 +294,4 @@ private String toIndentedString(java.lang.Object o) {
     }
     return o.toString().replace("\n", "\n    ");
   }
-}
+}
diff --git a/src/main/java/org/brapi/v2/model/CallSetsSearchRequest.java b/src/main/java/org/brapi/v2/model/CallSetsSearchRequest.java
@@ -5,6 +5,8 @@
 import com.fasterxml.jackson.annotation.JsonCreator;
 import io.swagger.annotations.ApiModel;
 import io.swagger.annotations.ApiModelProperty;
+import io.swagger.v3.oas.annotations.Hidden;
+import io.swagger.v3.oas.annotations.media.Schema;
 import java.util.ArrayList;
 import java.util.List;
 import org.springframework.validation.annotation.Validated;
@@ -24,6 +26,7 @@ public class CallSetsSearchRequest   {
 
   @JsonProperty("callSetNames")
   @Valid
+  @Schema(hidden = true)
   private List<String> callSetNames = null;
 
   @JsonProperty("germplasmDbIds")
@@ -32,6 +35,7 @@ public class CallSetsSearchRequest   {
 
   @JsonProperty("germplasmNames")
   @Valid
+  @Schema(hidden = true)
   private List<String> germplasmNames = null;
 
   @JsonProperty("sampleDbIds")

diff --git a/src/main/java/org/brapi/v2/model/VariantListResponse.java b/src/main/java/org/brapi/v2/model/VariantListResponse.java
@@ -23,7 +23,7 @@ public class VariantListResponse   {
   private Context _atContext = null;
 
   @JsonProperty("metadata")
-  private MetadataTokenPagination metadata = null;
+  private Metadata metadata = null;
 
   @JsonProperty("result")
   private VariantListResponseResult result = null;
@@ -48,7 +48,7 @@ public void setAtContext(Context _atContext) {
     this._atContext = _atContext;
   }
 
-  public VariantListResponse metadata(MetadataTokenPagination metadata) {
+  public VariantListResponse metadata(Metadata metadata) {
     this.metadata = metadata;
     return this;
   }
@@ -61,11 +61,11 @@ public VariantListResponse metadata(MetadataTokenPagination metadata) {
       @NotNull
 
     @Valid
-    public MetadataTokenPagination getMetadata() {
+    public Metadata getMetadata() {
     return metadata;
   }
 
-  public void setMetadata(MetadataTokenPagination metadata) {
+  public void setMetadata(Metadata metadata) {
     this.metadata = metadata;
   }