TASK-2017

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

@@ -35,6 +35,7 @@ public class ClinicalVariant extends Variant {
     private List<ClinicalComment> comments;
     private Map<String, Object> filters;
     private ClinicalDiscussion discussion;
+    private ClinicalVariantConfidence confidence;
     private List<String> tags;
 
     private Status status;
@@ -56,10 +57,11 @@ public ClinicalVariant() {
     }
 
     public ClinicalVariant(VariantAvro avro) {
-        this(avro, new ArrayList<>(), new ArrayList<>(), new HashMap<>(), new ClinicalDiscussion(), Status.NOT_REVIEWED,
-                new ArrayList<>(), new HashMap<>());
+        this(avro, new ArrayList<>(), new ArrayList<>(), new HashMap<>(), new ClinicalDiscussion(), null,
+                Status.NOT_REVIEWED, new ArrayList<>(), new HashMap<>());
     }
 
+    @Deprecated
     public ClinicalVariant(VariantAvro avro, List<ClinicalVariantEvidence> evidences, List<ClinicalComment> comments,
                            Map<String, Object> filters, ClinicalDiscussion discussion, Status status, List<String> tags,
                            Map<String, Object> attributes) {
@@ -74,13 +76,30 @@ public ClinicalVariant(VariantAvro avro, List<ClinicalVariantEvidence> evidences
         this.attributes = attributes;
     }
 
+    public ClinicalVariant(VariantAvro avro, List<ClinicalVariantEvidence> evidences, List<ClinicalComment> comments,
+                           Map<String, Object> filters, ClinicalDiscussion discussion,
+                           ClinicalVariantConfidence confidence, Status status, List<String> tags,
+                           Map<String, Object> attributes) {
+        super(avro);
+
+        this.evidences = evidences;
+        this.comments = comments;
+        this.filters = filters;
+        this.discussion = discussion;
+        this.status = status;
+        this.tags = tags;
+        this.confidence = confidence;
+        this.attributes = attributes;
+    }
+
     @Override
     public String toString() {
         final StringBuilder sb = new StringBuilder("ClinicalVariant{");
         sb.append("evidences=").append(evidences);
         sb.append(", comments=").append(comments);
         sb.append(", filters=").append(filters);
         sb.append(", discussion=").append(discussion);
+        sb.append(", confidence=").append(confidence);
         sb.append(", tags=").append(tags);
         sb.append(", status=").append(status);
         sb.append(", attributes=").append(attributes);
@@ -124,6 +143,15 @@ public ClinicalVariant setDiscussion(ClinicalDiscussion discussion) {
         return this;
     }
 
+    public ClinicalVariantConfidence getConfidence() {
+        return confidence;
+    }
+
+    public ClinicalVariant setConfidence(ClinicalVariantConfidence confidence) {
+        this.confidence = confidence;
+        return this;
+    }
+
     public Status getStatus() {
         return status;
     }

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

@@ -0,0 +1,68 @@
+package org.opencb.biodata.models.clinical.interpretation;
+
+import org.opencb.biodata.models.constants.FieldConstants;
+import org.opencb.commons.annotations.DataField;
+
+public class ClinicalVariantConfidence {
+
+    @DataField(id = "value", description = FieldConstants.CLINICAL_CONFIDENCE_VALUE_DESCRIPTION)
+    private Confidence value;
+
+    @DataField(id = "author", description = FieldConstants.CLINICAL_CONFIDENCE_AUTHOR_DESCRIPTION)
+    private String author;
+
+    @DataField(id = "date", description = FieldConstants.CLINICAL_CONFIDENCE_DATE_DESCRIPTION)
+    private String date;
+
+    public enum Confidence {
+        HIGH,
+        MEDIUM,
+        LOW
+    }
+
+    public ClinicalVariantConfidence() {
+    }
+
+    public ClinicalVariantConfidence(Confidence value, String author, String date) {
+        this.value = value;
+        this.author = author;
+        this.date = date;
+    }
+
+    @Override
+    public String toString() {
+        final StringBuilder sb = new StringBuilder("ClinicalVariantConfidence{");
+        sb.append("value=").append(value);
+        sb.append(", author='").append(author).append('\'');
+        sb.append(", date='").append(date).append('\'');
+        sb.append('}');
+        return sb.toString();
+    }
+
+    public Confidence getValue() {
+        return value;
+    }
+
+    public ClinicalVariantConfidence setValue(Confidence value) {
+        this.value = value;
+        return this;
+    }
+
+    public String getAuthor() {
+        return author;
+    }
+
+    public ClinicalVariantConfidence setAuthor(String author) {
+        this.author = author;
+        return this;
+    }
+
+    public String getDate() {
+        return date;
+    }
+
+    public ClinicalVariantConfidence setDate(String date) {
+        this.date = date;
+        return this;
+    }
+}

biodata-models/src/main/java/org/opencb/biodata/models/constants/FieldConstants.java

@@ -38,6 +38,9 @@ public class FieldConstants {
     public static final String CLINICAL_COMMENT_TAGS_DESCRIPTION = "List of tags for the clinical comment";
     public static final String CLINICAL_COMMENT_DATE_DESCRIPTION = "Date of the clinical comment";
     public static final String RELATEDNESS_REPORT_METHOD_DESCRIPTION = "Method of the relatedness report";
+    public static final String CLINICAL_CONFIDENCE_AUTHOR_DESCRIPTION = "Clinical confidence author";
+    public static final String CLINICAL_CONFIDENCE_DATE_DESCRIPTION = "Date of the clinical confidence";
+    public static final String CLINICAL_CONFIDENCE_VALUE_DESCRIPTION = "Date of the clinical confidence";
 
     public static final String RELATEDNESS_REPORT_MAF_DESCRIPTION = "Minor allele frequency to filter variants, e.g.: 1kg_phase3:CEU>0.35, cohort:ALL>0.05";
     public static final String RELATEDNESS_REPORT_SCORES_DESCRIPTION = "Relatedness scores for pair of samples";

biodata-tools/src/main/java/org/opencb/biodata/tools/clinical/ClinicalVariantCreator.java

@@ -130,7 +130,7 @@ public List<ClinicalVariant> createSecondaryFindings(List<Variant> variants) {
             // If we have clinical variant evidences, then we have to create the clinical variant
             if (CollectionUtils.isNotEmpty(clinicalVariantEvidences)) {
                 ClinicalVariant clinicalVariant = new ClinicalVariant(variant.getImpl(), Collections.emptyList(), Collections.emptyList(),
-                        Collections.emptyMap(), new ClinicalDiscussion(), ClinicalVariant.Status.NOT_REVIEWED,
+                        Collections.emptyMap(), new ClinicalDiscussion(), null, ClinicalVariant.Status.NOT_REVIEWED,
                         Collections.emptyList(), Collections.emptyMap());
                 clinicalVariant.setEvidences(clinicalVariantEvidences);
 

biodata-tools/src/main/java/org/opencb/biodata/tools/clinical/DefaultClinicalVariantCreator.java

@@ -127,7 +127,7 @@ public List<ClinicalVariant> create(List<Variant> variants) {
             // Create a clinical variant only if we have evidences
             if (CollectionUtils.isNotEmpty(clinicalVariantEvidences)) {
                 ClinicalVariant clinicalVariant = new ClinicalVariant(variant.getImpl(), Collections.emptyList(), Collections.emptyList(),
-                        Collections.emptyMap(), new ClinicalDiscussion(), ClinicalVariant.Status.NOT_REVIEWED,
+                        Collections.emptyMap(), new ClinicalDiscussion(), null, ClinicalVariant.Status.NOT_REVIEWED,
                         Collections.emptyList(), Collections.emptyMap());
                 clinicalVariant.setEvidences(clinicalVariantEvidences);
 

biodata-tools/src/main/java/org/opencb/biodata/tools/clinical/TeamClinicalVariantCreator.java

@@ -125,7 +125,7 @@ public List<ClinicalVariant> create(List<Variant> variants) throws Interpretatio
             // If we have clinical variant evidences, then we have to create the clinical variant
             if (CollectionUtils.isNotEmpty(clinicalVariantEvidences)) {
                 ClinicalVariant clinicalVariant = new ClinicalVariant(variant.getImpl(), Collections.emptyList(), Collections.emptyList(),
-                        Collections.emptyMap(), new ClinicalDiscussion(), ClinicalVariant.Status.NOT_REVIEWED,
+                        Collections.emptyMap(), new ClinicalDiscussion(), null, ClinicalVariant.Status.NOT_REVIEWED,
                         Collections.emptyList(), Collections.emptyMap());
                 clinicalVariant.setEvidences(clinicalVariantEvidences);
 

biodata-tools/src/main/java/org/opencb/biodata/tools/clinical/TieringClinicalVariantCreator.java

@@ -271,7 +271,7 @@ public List<ClinicalVariant> create(List<Variant> variants, Map<String, List<Mod
             if (CollectionUtils.isNotEmpty(clinicalVariantEvidences)) {
                 logger.debug(variant.toStringSimple() + ": reported, num. evidences: " + clinicalVariantEvidences.size());
                 ClinicalVariant clinicalVariant = new ClinicalVariant(variant.getImpl(), Collections.emptyList(), Collections.emptyList(),
-                        Collections.emptyMap(), new ClinicalDiscussion(), ClinicalVariant.Status.NOT_REVIEWED,
+                        Collections.emptyMap(), new ClinicalDiscussion(), null, ClinicalVariant.Status.NOT_REVIEWED,
                         Collections.emptyList(), Collections.emptyMap());
                 clinicalVariant.setEvidences(clinicalVariantEvidences);