models: update QC data models, #TASK-6722, #TASK-6766

biodata-models/src/main/java/org/opencb/biodata/models/clinical/interpretation/Software.java

@@ -22,6 +22,7 @@
 import org.opencb.biodata.models.constants.FieldConstants;
 import org.opencb.commons.annotations.DataField;
 
+import java.util.HashMap;
 import java.util.Map;
 
 public class Software {
@@ -51,15 +52,7 @@ public class Software {
     private Map<String, String> params;
 
     public Software() {
-    }
-
-    @Deprecated
-    public Software(String name, String version, String commit, String website, Map<String, String> params) {
-        this.name = name;
-        this.version = version;
-        this.commit = commit;
-        this.website = website;
-        this.params = params;
+        this("", "", "", "", "", new HashMap<>());
     }
 
     public Software(String name, String version, String repository, String commit, String website, Map<String, String> params) {

biodata-models/src/main/java/org/opencb/biodata/models/clinical/qc/InferredSex.java

@@ -0,0 +1,145 @@
+/*
+ * <!--
+ *   ~ Copyright 2015-2017 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.biodata.models.clinical.qc;
+
+import org.opencb.biodata.models.clinical.interpretation.Software;
+import org.opencb.biodata.models.common.Image;
+import org.opencb.biodata.models.constants.FieldConstants;
+import org.opencb.commons.annotations.DataField;
+import org.opencb.commons.datastore.core.ObjectMap;
+
+import java.util.ArrayList;
+import java.util.List;
+
+public class InferredSex {
+
+    @DataField(id = "method", description = FieldConstants.INFERRED_SEX_METHOD_DESCRIPTION)
+    private String method;
+
+    @DataField(id = "sampleId", description = FieldConstants.INFERRED_SEX_SAMPLE_DESCRIPTION)
+    private String sampleId;
+
+    @DataField(id = "software", description = FieldConstants.INFERRED_SEX_SOFTWARE_DESCRIPTION)
+    private Software software;
+
+    @DataField(id = "inferredKaryotypicSex", description = FieldConstants.INFERRED_SEX_INFERRED_KARYOTYPIC_SEX_DESCRIPTION)
+    private String inferredKaryotypicSex;
+
+    @DataField(id = "values", description = FieldConstants.INFERRED_SEX_VALUES_DESCRIPTION)
+    private ObjectMap values;
+
+    @DataField(id = "images", description = FieldConstants.INFERRED_SEX_IMAGES_DESCRIPTION)
+    private List<Image> images;
+
+    @DataField(id = "attributes", description = FieldConstants.INFERRED_SEX_ATTRIBUTES_DESCRIPTION)
+    private ObjectMap attributes;
+
+    public InferredSex() {
+        this("","", new Software(), "", new ObjectMap(), new ArrayList<>(), new ObjectMap());
+    }
+
+    public InferredSex(String method, String sampleId, Software software, String inferredKaryotypicSex, ObjectMap values,
+                       List<Image> images, ObjectMap attributes) {
+        this.method = method;
+        this.sampleId = sampleId;
+        this.software = software;
+        this.inferredKaryotypicSex = inferredKaryotypicSex;
+        this.values = values;
+        this.images = images;
+        this.attributes = attributes;
+    }
+
+    @Override
+    public String toString() {
+        final StringBuilder sb = new StringBuilder("InferredSex{");
+        sb.append("method='").append(method).append('\'');
+        sb.append(", sampleId='").append(sampleId).append('\'');
+        sb.append(", software=").append(software);
+        sb.append(", inferredKaryotypicSex='").append(inferredKaryotypicSex).append('\'');
+        sb.append(", values=").append(values);
+        sb.append(", images=").append(images);
+        sb.append(", attributes=").append(attributes);
+        sb.append('}');
+        return sb.toString();
+    }
+
+    public String getMethod() {
+        return method;
+    }
+
+    public InferredSex setMethod(String method) {
+        this.method = method;
+        return this;
+    }
+
+    public String getSampleId() {
+        return sampleId;
+    }
+
+    public InferredSex setSampleId(String sampleId) {
+        this.sampleId = sampleId;
+        return this;
+    }
+
+    public Software getSoftware() {
+        return software;
+    }
+
+    public InferredSex setSoftware(Software software) {
+        this.software = software;
+        return this;
+    }
+
+    public String getInferredKaryotypicSex() {
+        return inferredKaryotypicSex;
+    }
+
+    public InferredSex setInferredKaryotypicSex(String inferredKaryotypicSex) {
+        this.inferredKaryotypicSex = inferredKaryotypicSex;
+        return this;
+    }
+
+    public ObjectMap getValues() {
+        return values;
+    }
+
+    public InferredSex setValues(ObjectMap values) {
+        this.values = values;
+        return this;
+    }
+
+    public List<Image> getImages() {
+        return images;
+    }
+
+    public InferredSex setImages(List<Image> images) {
+        this.images = images;
+        return this;
+    }
+
+    public ObjectMap getAttributes() {
+        return attributes;
+    }
+
+    public InferredSex setAttributes(ObjectMap attributes) {
+        this.attributes = attributes;
+        return this;
+    }
+}

biodata-models/src/main/java/org/opencb/biodata/models/clinical/qc/MendelianErrorReport.java → biodata-models/src/main/java/org/opencb/biodata/models/clinical/qc/MendelianError.java

@@ -19,6 +19,11 @@
 
 package org.opencb.biodata.models.clinical.qc;
 
+import org.opencb.biodata.models.common.Image;
+import org.opencb.biodata.models.constants.FieldConstants;
+import org.opencb.commons.annotations.DataField;
+import org.opencb.commons.datastore.core.ObjectMap;
+
 import java.util.ArrayList;
 import java.util.List;
 import java.util.Map;
@@ -27,13 +32,21 @@
 // M E N D E L I A N     E R R O R S     R E P O R T
 //-------------------------------------------------------------------------
 
-public class MendelianErrorReport {
+public class MendelianError {
 
-    // Number total of errors for that family
+    @DataField(id = "numErrors", description = FieldConstants.MENDELIAN_ERROR_NUM_ERRORS_DESCRIPTION)
     private int numErrors;
 
+    @DataField(id = "sampleAggregation", description = FieldConstants.MENDELIAN_ERROR_SAMPLE_AGGREGATION_DESCRIPTION)
     private List<SampleAggregation> sampleAggregation;
 
+    @DataField(id = "images", description = FieldConstants.MENDELIAN_ERROR_IMAGES_DESCRIPTION)
+    private List<Image> images;
+
+    @DataField(id = "attributes", description = FieldConstants.MENDELIAN_ERROR_ATTRIBUTES_DESCRIPTION)
+    private ObjectMap attributes;
+
+
     //-------------------------------------------------------------------------
     // S A M P L E     A G G R E G A T I O N
     //-------------------------------------------------------------------------
@@ -153,21 +166,33 @@ public ChromosomeAggregation setErrorCodeAggregation(Map<String, Integer> errorC
         }
     }
 
-    public MendelianErrorReport() {
-        this.numErrors = 0;
-        this.sampleAggregation = new ArrayList<>();
+    public MendelianError() {
+        this(0, new ArrayList<>(), new ArrayList<>(), new ObjectMap());
     }
 
-    public MendelianErrorReport(int numErrors, List<SampleAggregation> sampleAggregation) {
+    public MendelianError(int numErrors, List<SampleAggregation> sampleAggregation, List<Image> images, ObjectMap attributes) {
         this.numErrors = numErrors;
         this.sampleAggregation = sampleAggregation;
+        this.images = images;
+        this.attributes = attributes;
+    }
+
+    @Override
+    public String toString() {
+        final StringBuilder sb = new StringBuilder("MendelianError{");
+        sb.append("numErrors=").append(numErrors);
+        sb.append(", sampleAggregation=").append(sampleAggregation);
+        sb.append(", images=").append(images);
+        sb.append(", attributes=").append(attributes);
+        sb.append('}');
+        return sb.toString();
     }
 
     public int getNumErrors() {
         return numErrors;
     }
 
-    public MendelianErrorReport setNumErrors(int numErrors) {
+    public MendelianError setNumErrors(int numErrors) {
         this.numErrors = numErrors;
         return this;
     }
@@ -176,8 +201,26 @@ public List<SampleAggregation> getSampleAggregation() {
         return sampleAggregation;
     }
 
-    public MendelianErrorReport setSampleAggregation(List<SampleAggregation> sampleAggregation) {
+    public MendelianError setSampleAggregation(List<SampleAggregation> sampleAggregation) {
         this.sampleAggregation = sampleAggregation;
         return this;
     }
+
+    public List<Image> getImages() {
+        return images;
+    }
+
+    public MendelianError setImages(List<Image> images) {
+        this.images = images;
+        return this;
+    }
+
+    public ObjectMap getAttributes() {
+        return attributes;
+    }
+
+    public MendelianError setAttributes(ObjectMap attributes) {
+        this.attributes = attributes;
+        return this;
+    }
 }