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Add privacy field to BiomodelRef and fix versionFlag mapping in webapp
Add privacy (public/private/shared) to BiomodelRef through the full stack: DB query, domain model, REST DTO, OpenAPI spec, and all generated clients. Show privacy badge alongside version badge in the publication editor. Fix webapp to use biomodel.versionFlag instead of misusing biomodel.privacy for the version badge. Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
1 parent 80613a2 commit f13a2d7

15 files changed

Lines changed: 126 additions & 24 deletions

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‎python-restclient/docs/BiomodelRef.md‎

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@@ -9,6 +9,7 @@ Name | Type | Description | Notes
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**owner_name** | **str** | | [optional]
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**owner_key** | **int** | | [optional]
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**version_flag** | **int** | | [optional]
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**privacy** | **int** | | [optional]
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## Example
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‎python-restclient/vcell_client/models/biomodel_ref.py‎

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@@ -36,7 +36,8 @@ class BiomodelRef(BaseModel):
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owner_name: Optional[StrictStr] = Field(default=None, alias="ownerName")
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owner_key: Optional[StrictInt] = Field(default=None, alias="ownerKey")
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version_flag: Optional[StrictInt] = Field(default=None, alias="versionFlag")
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__properties: ClassVar[List[str]] = ["bmKey", "name", "ownerName", "ownerKey", "versionFlag"]
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privacy: Optional[StrictInt] = None
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__properties: ClassVar[List[str]] = ["bmKey", "name", "ownerName", "ownerKey", "versionFlag", "privacy"]
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model_config = {
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"populate_by_name": True,
@@ -95,7 +96,8 @@ def from_dict(cls, obj: Dict) -> Self:
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"name": obj.get("name"),
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"ownerName": obj.get("ownerName"),
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"ownerKey": obj.get("ownerKey"),
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"versionFlag": obj.get("versionFlag")
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"versionFlag": obj.get("versionFlag"),
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"privacy": obj.get("privacy")
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})
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return _obj
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‎tools/openapi.yaml‎

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@@ -2329,6 +2329,9 @@ components:
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versionFlag:
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format: int32
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type: integer
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privacy:
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format: int32
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type: integer
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CompositeCurve:
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required:
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- type

‎vcell-api/src/main/java/org/vcell/rest/server/PublicationServerResource.java‎

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Original file line numberDiff line numberDiff line change
@@ -199,7 +199,7 @@ private Object convertToReferenceRep(String str,Class classType) throws Exceptio
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if(classType.equals(BioModelReferenceRep.class)) {
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BioModelReferenceRep[] biomodelReferenceReps = new BioModelReferenceRep[modelKeys.length];
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for (int i = 0; i < modelKeys.length; i++) {
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biomodelReferenceReps[i] = new BioModelReferenceRep(new KeyValue(modelKeys[i]), null, null,null);
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biomodelReferenceReps[i] = new BioModelReferenceRep(new KeyValue(modelKeys[i]), null, null, null, null);
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}
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return biomodelReferenceReps;
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}else if(classType.equals(MathModelReferenceRep.class)) {

‎vcell-rest/src/main/java/org/vcell/restq/models/BiomodelRef.java‎

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Original file line numberDiff line numberDiff line change
@@ -9,15 +9,17 @@ public record BiomodelRef(
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String name,
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String ownerName,
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Long ownerKey,
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Integer versionFlag) {
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Integer versionFlag,
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Integer privacy) {
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public static BiomodelRef fromBioModelReferenceRep(BioModelReferenceRep bioModelReferenceRep) {
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return new BiomodelRef(
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Long.parseLong(bioModelReferenceRep.getBmKey().toString()),
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bioModelReferenceRep.getName(),
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bioModelReferenceRep.getOwner().getName(),
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Long.parseLong(bioModelReferenceRep.getOwner().getID().toString()),
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bioModelReferenceRep.getVersionFlag().intValue()
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bioModelReferenceRep.getVersionFlag().intValue(),
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bioModelReferenceRep.getPrivacy()
2123
);
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}
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@@ -26,7 +28,8 @@ public BioModelReferenceRep toBioModelReferenceRep() {
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bmKey!=null ? new KeyValue(Long.toString(bmKey)) : null,
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name,
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new User(ownerName, new KeyValue(Long.toString(ownerKey))),
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versionFlag!=null ? versionFlag.longValue() : null
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versionFlag!=null ? versionFlag.longValue() : null,
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privacy
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);
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}
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}

‎vcell-rest/src/test/java/org/vcell/restq/TestEndpointUtils.java‎

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@@ -136,6 +136,7 @@ public static BiomodelRef biomodelRefFromBioModel(org.vcell.restclient.model.Bio
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ref.setOwnerName(biomodel.getOwnerName());
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ref.setOwnerKey(biomodel.getOwnerKey() != null ? Long.parseLong(biomodel.getOwnerKey()) : -1);
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ref.setVersionFlag(biomodel.getVersionFlag());
139+
ref.setPrivacy(biomodel.getPrivacy());
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return ref;
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}
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‎vcell-restclient/api/openapi.yaml‎

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Original file line numberDiff line numberDiff line change
@@ -2638,6 +2638,7 @@ components:
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ownerName: ownerName
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name: name
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versionFlag: 7
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privacy: 9
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ownerKey: 2
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properties:
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bmKey:
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versionFlag:
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format: int32
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type: integer
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privacy:
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format: int32
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type: integer
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type: object
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CompositeCurve:
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allOf:
@@ -3790,9 +3794,9 @@ components:
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example:
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ownerName: ownerName
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name: name
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versionFlag: 2
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mmKey: 9
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ownerKey: 3
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versionFlag: 4
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mmKey: 3
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ownerKey: 2
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properties:
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mmKey:
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format: int64
@@ -4024,25 +4028,27 @@ components:
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ownerName: ownerName
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name: name
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versionFlag: 7
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privacy: 9
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ownerKey: 2
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- bmKey: 5
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ownerName: ownerName
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name: name
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versionFlag: 7
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privacy: 9
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ownerKey: 2
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pubmedid: pubmedid
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url: url
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mathmodelRefs:
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- ownerName: ownerName
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name: name
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versionFlag: 2
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mmKey: 9
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ownerKey: 3
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versionFlag: 4
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mmKey: 3
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ownerKey: 2
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- ownerName: ownerName
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name: name
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versionFlag: 2
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mmKey: 9
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ownerKey: 3
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versionFlag: 4
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mmKey: 3
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ownerKey: 2
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pubKey: 0
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authors:
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- authors

‎vcell-restclient/docs/BiomodelRef.md‎

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@@ -12,6 +12,7 @@
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|**ownerName** | **String** | | [optional] |
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|**ownerKey** | **Long** | | [optional] |
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|**versionFlag** | **Integer** | | [optional] |
15+
|**privacy** | **Integer** | | [optional] |
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‎vcell-restclient/src/main/java/org/vcell/restclient/model/BiomodelRef.java‎

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Original file line numberDiff line numberDiff line change
@@ -36,7 +36,8 @@
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BiomodelRef.JSON_PROPERTY_NAME,
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BiomodelRef.JSON_PROPERTY_OWNER_NAME,
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BiomodelRef.JSON_PROPERTY_OWNER_KEY,
39-
BiomodelRef.JSON_PROPERTY_VERSION_FLAG
39+
BiomodelRef.JSON_PROPERTY_VERSION_FLAG,
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BiomodelRef.JSON_PROPERTY_PRIVACY
4041
})
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@javax.annotation.Generated(value = "org.openapitools.codegen.languages.JavaClientCodegen")
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public class BiomodelRef {
@@ -55,6 +56,9 @@ public class BiomodelRef {
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public static final String JSON_PROPERTY_VERSION_FLAG = "versionFlag";
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private Integer versionFlag;
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59+
public static final String JSON_PROPERTY_PRIVACY = "privacy";
60+
private Integer privacy;
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public BiomodelRef() {
5963
}
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@@ -183,6 +187,31 @@ public void setVersionFlag(Integer versionFlag) {
183187
}
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185189

190+
public BiomodelRef privacy(Integer privacy) {
191+
this.privacy = privacy;
192+
return this;
193+
}
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195+
/**
196+
* Get privacy
197+
* @return privacy
198+
**/
199+
@javax.annotation.Nullable
200+
@JsonProperty(JSON_PROPERTY_PRIVACY)
201+
@JsonInclude(value = JsonInclude.Include.USE_DEFAULTS)
202+
203+
public Integer getPrivacy() {
204+
return privacy;
205+
}
206+
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208+
@JsonProperty(JSON_PROPERTY_PRIVACY)
209+
@JsonInclude(value = JsonInclude.Include.USE_DEFAULTS)
210+
public void setPrivacy(Integer privacy) {
211+
this.privacy = privacy;
212+
}
213+
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186215
/**
187216
* Return true if this BiomodelRef object is equal to o.
188217
*/
@@ -199,12 +228,13 @@ public boolean equals(Object o) {
199228
Objects.equals(this.name, biomodelRef.name) &&
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Objects.equals(this.ownerName, biomodelRef.ownerName) &&
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Objects.equals(this.ownerKey, biomodelRef.ownerKey) &&
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Objects.equals(this.versionFlag, biomodelRef.versionFlag);
231+
Objects.equals(this.versionFlag, biomodelRef.versionFlag) &&
232+
Objects.equals(this.privacy, biomodelRef.privacy);
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}
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205235
@Override
206236
public int hashCode() {
207-
return Objects.hash(bmKey, name, ownerName, ownerKey, versionFlag);
237+
return Objects.hash(bmKey, name, ownerName, ownerKey, versionFlag, privacy);
208238
}
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210240
@Override
@@ -216,6 +246,7 @@ public String toString() {
216246
sb.append(" ownerName: ").append(toIndentedString(ownerName)).append("\n");
217247
sb.append(" ownerKey: ").append(toIndentedString(ownerKey)).append("\n");
218248
sb.append(" versionFlag: ").append(toIndentedString(versionFlag)).append("\n");
249+
sb.append(" privacy: ").append(toIndentedString(privacy)).append("\n");
219250
sb.append("}");
220251
return sb.toString();
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}
@@ -288,6 +319,11 @@ public String toUrlQueryString(String prefix) {
288319
joiner.add(String.format("%sversionFlag%s=%s", prefix, suffix, URLEncoder.encode(String.valueOf(getVersionFlag()), StandardCharsets.UTF_8).replaceAll("\\+", "%20")));
289320
}
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322+
// add `privacy` to the URL query string
323+
if (getPrivacy() != null) {
324+
joiner.add(String.format("%sprivacy%s=%s", prefix, suffix, URLEncoder.encode(String.valueOf(getPrivacy()), StandardCharsets.UTF_8).replaceAll("\\+", "%20")));
325+
}
326+
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return joiner.toString();
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}
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}

‎vcell-server/src/main/java/cbit/vcell/modeldb/BioModelReferenceRep.java‎

Lines changed: 8 additions & 2 deletions
Original file line numberDiff line numberDiff line change
@@ -8,13 +8,15 @@ public class BioModelReferenceRep {
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private final String name;
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private final User owner;
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private final Long versionFlag;
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public BioModelReferenceRep(KeyValue bmKey, String name, User owner,Long versionFlag) {
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private final Integer privacy;
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13+
public BioModelReferenceRep(KeyValue bmKey, String name, User owner, Long versionFlag, Integer privacy) {
1314
super();
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this.bmKey = bmKey;
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this.name = name;
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this.owner = owner;
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this.versionFlag = versionFlag;
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this.privacy = privacy;
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}
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2022
public KeyValue getBmKey() {
@@ -32,4 +34,8 @@ public User getOwner() {
3234
public Long getVersionFlag() {
3335
return versionFlag;
3436
}
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38+
public Integer getPrivacy() {
39+
return privacy;
40+
}
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}

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