core: create the data model QualityControlStatus and include it in fa…

…mily, individual and sample internals, #TASK-6772, #TASK-6766
opencb · Sep 4, 2024 · 45eea16 · 45eea16
1 parent 536cca9
commit 45eea16
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Showing 4 changed files with 124 additions and 10 deletions.
diff --git a/opencga-core/src/main/java/org/opencb/opencga/core/models/common/QualityControlStatus.java b/opencga-core/src/main/java/org/opencb/opencga/core/models/common/QualityControlStatus.java
@@ -0,0 +1,70 @@
+/*
+ * Copyright 2015-2020 OpenCB
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ *     http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+
+package org.opencb.opencga.core.models.common;
+
+import org.opencb.opencga.core.common.TimeUtils;
+
+public class QualityControlStatus extends Internal {
+
+    public QualityControlStatus() {
+    }
+
+    public QualityControlStatus(InternalStatus status, String registrationDate, String modificationDate) {
+        super(status, registrationDate, modificationDate);
+    }
+
+    public static QualityControlStatus init() {
+        return new QualityControlStatus(null, TimeUtils.getTime(), TimeUtils.getTime());
+    }
+
+    @Override
+    public String toString() {
+        final StringBuilder sb = new StringBuilder("QualityControlStatus{");
+        sb.append("status=").append(status);
+        sb.append(", registrationDate='").append(registrationDate).append('\'');
+        sb.append(", modificationDate='").append(lastModified).append('\'');
+        sb.append('}');
+        return sb.toString();
+    }
+
+    public InternalStatus getStatus() {
+        return status;
+    }
+
+    public QualityControlStatus setStatus(InternalStatus status) {
+        this.status = status;
+        return this;
+    }
+
+    public String getRegistrationDate() {
+        return registrationDate;
+    }
+
+    public QualityControlStatus setRegistrationDate(String registrationDate) {
+        this.registrationDate = registrationDate;
+        return this;
+    }
+
+    public String getLastModified() {
+        return lastModified;
+    }
+
+    public QualityControlStatus setLastModified(String lastModified) {
+        this.lastModified = lastModified;
+        return this;
+    }
+}
diff --git a/opencga-core/src/main/java/org/opencb/opencga/core/models/family/FamilyInternal.java b/opencga-core/src/main/java/org/opencb/opencga/core/models/family/FamilyInternal.java
@@ -18,21 +18,26 @@
 
 import org.opencb.opencga.core.common.TimeUtils;
 import org.opencb.opencga.core.models.common.Internal;
+import org.opencb.opencga.core.models.common.QualityControlStatus;
 
 public class FamilyInternal extends Internal {
 
     private FamilyStatus status;
+    private QualityControlStatus qualityControlStatus;
 
     public FamilyInternal() {
     }
 
-    public FamilyInternal(String registrationDate, String modificationDate, FamilyStatus status) {
+    public FamilyInternal(String registrationDate, String modificationDate, FamilyStatus status,
+                          QualityControlStatus qualityControlStatus) {
         super(null, registrationDate, modificationDate);
         this.status = status;
+        this.qualityControlStatus = qualityControlStatus;
     }
 
     public static FamilyInternal init() {
-        return new FamilyInternal(TimeUtils.getTime(), TimeUtils.getTime(), new FamilyStatus());
+        String time = TimeUtils.getTime();
+        return new FamilyInternal(time, time, new FamilyStatus(), QualityControlStatus.init());
     }
 
     @Override
@@ -71,4 +76,13 @@ public FamilyInternal setLastModified(String lastModified) {
         this.lastModified = lastModified;
         return this;
     }
+
+    public QualityControlStatus getQualityControlStatus() {
+        return qualityControlStatus;
+    }
+
+    public FamilyInternal setQualityControlStatus(QualityControlStatus qualityControlStatus) {
+        this.qualityControlStatus = qualityControlStatus;
+        return this;
+    }
 }
diff --git a/opencga-core/src/main/java/org/opencb/opencga/core/models/individual/IndividualInternal.java b/opencga-core/src/main/java/org/opencb/opencga/core/models/individual/IndividualInternal.java
@@ -19,26 +19,33 @@
 import org.opencb.opencga.core.common.TimeUtils;
 import org.opencb.opencga.core.models.common.Internal;
 import org.opencb.opencga.core.models.common.InternalStatus;
+import org.opencb.opencga.core.models.common.QualityControlStatus;
 
 public class IndividualInternal extends Internal {
 
+    private QualityControlStatus qualityControlStatus;
+
     public IndividualInternal() {
     }
 
-    public IndividualInternal(InternalStatus status, String registrationDate, String modificationDate) {
+    public IndividualInternal(InternalStatus status, String registrationDate, String modificationDate,
+                              QualityControlStatus qualityControlStatus) {
         super(status, registrationDate, modificationDate);
+        this.qualityControlStatus = qualityControlStatus;
     }
 
     public static IndividualInternal init() {
-        return new IndividualInternal(new InternalStatus(InternalStatus.READY), TimeUtils.getTime(), TimeUtils.getTime());
+        String time = TimeUtils.getTime();
+        return new IndividualInternal(new InternalStatus(InternalStatus.READY), time, time, QualityControlStatus.init());
     }
 
     @Override
     public String toString() {
         final StringBuilder sb = new StringBuilder("IndividualInternal{");
         sb.append("status=").append(status);
         sb.append(", registrationDate='").append(registrationDate).append('\'');
-        sb.append(", modificationDate='").append(lastModified).append('\'');
+        sb.append(", lastModified='").append(lastModified).append('\'');
+        sb.append(", qualityControlStatus=").append(qualityControlStatus);
         sb.append('}');
         return sb.toString();
     }
@@ -70,4 +77,12 @@ public IndividualInternal setLastModified(String lastModified) {
         return this;
     }
 
+    public QualityControlStatus getQualityControlStatus() {
+        return qualityControlStatus;
+    }
+
+    public IndividualInternal setQualityControlStatus(QualityControlStatus qualityControlStatus) {
+        this.qualityControlStatus = qualityControlStatus;
+        return this;
+    }
 }
diff --git a/opencga-core/src/main/java/org/opencb/opencga/core/models/sample/SampleInternal.java b/opencga-core/src/main/java/org/opencb/opencga/core/models/sample/SampleInternal.java
@@ -21,6 +21,7 @@
 import org.opencb.opencga.core.common.TimeUtils;
 import org.opencb.opencga.core.models.common.Internal;
 import org.opencb.opencga.core.models.common.InternalStatus;
+import org.opencb.opencga.core.models.common.QualityControlStatus;
 import org.opencb.opencga.core.models.common.RgaIndex;
 
 import java.util.Objects;
@@ -35,20 +36,23 @@ public class SampleInternal extends Internal {
             description = FieldConstants.SAMPLE_INTERNAL_RGA_DESCRIPTION)
     private RgaIndex rga;
     private SampleInternalVariant variant;
+    private QualityControlStatus qualityControlStatus;
 
     public SampleInternal() {
     }
 
     public SampleInternal(String registrationDate, String modificationDate, InternalStatus status, RgaIndex rga,
-                          SampleInternalVariant variant) {
+                          SampleInternalVariant variant, QualityControlStatus qualityControlStatus) {
         super(status, registrationDate, modificationDate);
         this.rga = rga;
         this.variant = variant;
+        this.qualityControlStatus = qualityControlStatus;
     }
 
     public static SampleInternal init() {
-        return new SampleInternal(TimeUtils.getTime(), TimeUtils.getTime(), new InternalStatus(InternalStatus.READY), RgaIndex.init(),
-                SampleInternalVariant.init());
+        String time = TimeUtils.getTime();
+        return new SampleInternal(time, time, new InternalStatus(InternalStatus.READY), RgaIndex.init(), SampleInternalVariant.init(),
+                QualityControlStatus.init());
     }
 
     @Override
@@ -59,6 +63,7 @@ public String toString() {
         sb.append(", lastModified='").append(lastModified).append('\'');
         sb.append(", rga=").append(rga);
         sb.append(", variant=").append(variant);
+        sb.append(", qualityControlStatus=").append(qualityControlStatus);
         sb.append('}');
         return sb.toString();
     }
@@ -108,6 +113,15 @@ public SampleInternal setLastModified(String lastModified) {
         return this;
     }
 
+    public QualityControlStatus getQualityControlStatus() {
+        return qualityControlStatus;
+    }
+
+    public SampleInternal setQualityControlStatus(QualityControlStatus qualityControlStatus) {
+        this.qualityControlStatus = qualityControlStatus;
+        return this;
+    }
+
     @Override
     public boolean equals(Object o) {
         if (this == o) {
@@ -117,11 +131,12 @@ public boolean equals(Object o) {
             return false;
         }
         SampleInternal that = (SampleInternal) o;
-        return Objects.equals(rga, that.rga) && Objects.equals(variant, that.variant);
+        return Objects.equals(rga, that.rga) && Objects.equals(variant, that.variant)
+                && Objects.equals(qualityControlStatus, that.qualityControlStatus);
     }
 
     @Override
     public int hashCode() {
-        return Objects.hash(rga, variant);
+        return Objects.hash(rga, variant, qualityControlStatus);
     }
 }