TASK-7645 - Integrated Clinical Preprocessing, Variant Assessment, and Reporting

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

@@ -35,19 +35,25 @@ public class ClinicalEvidenceReview {
     private List<ClinicalAcmg> acmg;
     private ClinicalProperty.ClinicalSignificance clinicalSignificance;
     private ClinicalDiscussion discussion;
+    private List<String> tags;
+    private double score;
 
     public ClinicalEvidenceReview() {
         this.select = false;
         this.acmg = new ArrayList<>();
+        this.tags = new ArrayList<>();
     }
 
     public ClinicalEvidenceReview(boolean select, String tier, List<ClinicalAcmg> acmg,
-                                  ClinicalSignificance clinicalSignificance, ClinicalDiscussion discussion) {
+                                  ClinicalSignificance clinicalSignificance, ClinicalDiscussion discussion,
+                                  List<String> tags, double score) {
         this.select = select;
         this.tier = tier;
         this.acmg = acmg;
         this.clinicalSignificance = clinicalSignificance;
         this.discussion = discussion;
+        this.tags = tags;
+        this.score = score;
     }
 
     @Override
@@ -58,6 +64,8 @@ public String toString() {
         sb.append(", acmg=").append(acmg);
         sb.append(", clinicalSignificance=").append(clinicalSignificance);
         sb.append(", discussion='").append(discussion).append('\'');
+        sb.append(", tags=").append(tags);
+        sb.append(", score=").append(score);
         sb.append('}');
         return sb.toString();
     }
@@ -106,4 +114,22 @@ public ClinicalEvidenceReview setDiscussion(ClinicalDiscussion discussion) {
         this.discussion = discussion;
         return this;
     }
+
+    public List<String> getTags() {
+        return tags;
+    }
+
+    public ClinicalEvidenceReview setTags(List<String> tags) {
+        this.tags = tags;
+        return this;
+    }
+
+    public double getScore() {
+        return score;
+    }
+
+    public ClinicalEvidenceReview setScore(double score) {
+        this.score = score;
+        return this;
+    }
 }

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

@@ -19,39 +19,45 @@
 
 package org.opencb.biodata.models.clinical.interpretation;
 
+import org.apache.commons.collections4.CollectionUtils;
+import org.apache.commons.collections4.MapUtils;
 import org.opencb.biodata.models.clinical.ClinicalComment;
 import org.opencb.biodata.models.clinical.ClinicalDiscussion;
+import org.opencb.biodata.models.clinical.ClinicalProperty;
 import org.opencb.biodata.models.clinical.interpretation.stats.ClinicalVariantSummaryStats;
 import org.opencb.biodata.models.variant.Variant;
 import org.opencb.biodata.models.variant.avro.VariantAvro;
 
-import java.util.ArrayList;
-import java.util.HashMap;
-import java.util.List;
-import java.util.Map;
+import java.util.*;
 
 public class ClinicalVariant extends Variant {
 
     private List<ClinicalVariantEvidence> evidences;
     private List<ClinicalComment> comments;
-    private Map<String, Object> filters;
+    private ClinicalVariantFilter filter;
+    private List<ClinicalProperty.ModeOfInheritance> modesOfInheritance; // all compatible MoIs
     private String recommendation;
     private List<MiniPubmed> references;
     private ClinicalDiscussion discussion;
     private ClinicalVariantConfidence confidence;
     private List<String> tags;
+    private List<String> images;
 
     private List<ClinicalVariantSummaryStats> stats;
 
     private Status status;
+    private int version;
 
     // TODO maybe this parameter should be in Variant
     private Map<String, Object> attributes;
 
     public enum Status {
         NOT_REVIEWED,
-        REVIEW_REQUESTED,
+        UNDER_CONSIDERATION,
+        CANDIDATE,
         REVIEWED,
+        VALIDATION_REQUESTED,
+        VALIDATED,
         DISCARDED,
         REPORTED,
         ARTIFACT
@@ -62,81 +68,44 @@ public ClinicalVariant() {
     }
 
     public ClinicalVariant(VariantAvro avro) {
-        this(avro, new ArrayList<>(), new ArrayList<>(), new HashMap<>(), new ClinicalDiscussion(), null,
-                Status.NOT_REVIEWED, new ArrayList<>(), new HashMap<>());
+        this(avro, new ArrayList<>(), new ArrayList<>(), new ClinicalVariantFilter(), Collections.emptyList(), "", Collections.emptyList(),
+                new ClinicalDiscussion(), new ClinicalVariantConfidence(), Collections.emptyList(), Status.NOT_REVIEWED,
+                Collections.emptyList(), Collections.emptyList(), 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) {
-        super(avro);
-
-        this.evidences = evidences;
-        this.comments = comments;
-        this.filters = filters;
-        this.discussion = discussion;
-        this.status = status;
-        this.tags = tags;
-        this.attributes = attributes;
-    }
-
-    @Deprecated
-    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;
-    }
-
-    @Deprecated
-    public ClinicalVariant(VariantAvro avro, List<ClinicalVariantEvidence> evidences, List<ClinicalComment> comments,
-                           Map<String, Object> filters, String recommendation, List<MiniPubmed> references,
-                           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.recommendation = recommendation;
-        this.references = references;
-        this.discussion = discussion;
-        this.status = status;
-        this.tags = tags;
-        this.confidence = confidence;
-        this.attributes = attributes;
+                           ClinicalVariantFilter filter, List<ClinicalProperty.ModeOfInheritance> modesOfInheritance, String recommendation,
+                           List<MiniPubmed> references,
+                           ClinicalDiscussion discussion, ClinicalVariantConfidence confidence, List<ClinicalVariantSummaryStats> stats,
+                           Status status, List<String> tags, List<String> images, Map<String, Object> attributes) {
+        this(avro, evidences, comments, filter, modesOfInheritance, recommendation, references, discussion, confidence, stats,
+                status, tags, images, 1, attributes);
     }
 
     public ClinicalVariant(VariantAvro avro, List<ClinicalVariantEvidence> evidences, List<ClinicalComment> comments,
-                           Map<String, Object> filters, String recommendation, List<MiniPubmed> references,
+                           ClinicalVariantFilter filter, List<ClinicalProperty.ModeOfInheritance> modesOfInheritance, String recommendation,
+                           List<MiniPubmed> references,
                            ClinicalDiscussion discussion, ClinicalVariantConfidence confidence, List<ClinicalVariantSummaryStats> stats,
-                           Status status, List<String> tags, Map<String, Object> attributes) {
+                           Status status, List<String> tags, List<String> images, int version, Map<String, Object> attributes) {
         super(avro);
 
         this.evidences = evidences;
         this.comments = comments;
-        this.filters = filters;
+        this.filter = filter;
+        this.modesOfInheritance = modesOfInheritance;
         this.recommendation = recommendation;
         this.references = references;
         this.discussion = discussion;
         this.stats = stats;
         this.status = status;
         this.tags = tags;
+        this.images = images;
         this.confidence = confidence;
+        this.version = version;
         this.attributes = attributes;
     }
 
-
     @Override
     public String toString() {
         return super.toString();
@@ -160,12 +129,21 @@ public ClinicalVariant setComments(List<ClinicalComment> comments) {
         return this;
     }
 
-    public Map<String, Object> getFilters() {
-        return filters;
+    public ClinicalVariantFilter getFilter() {
+        return filter;
+    }
+
+    public ClinicalVariant setFilter(ClinicalVariantFilter filter) {
+        this.filter = filter;
+        return this;
+    }
+
+    public List<ClinicalProperty.ModeOfInheritance> getModesOfInheritance() {
+        return modesOfInheritance;
     }
 
-    public ClinicalVariant setFilters(Map<String, Object> filters) {
-        this.filters = filters;
+    public ClinicalVariant setModesOfInheritance(List<ClinicalProperty.ModeOfInheritance> modesOfInheritance) {
+        this.modesOfInheritance = modesOfInheritance;
         return this;
     }
 
@@ -232,6 +210,24 @@ public ClinicalVariant setTags(List<String> tags) {
         return this;
     }
 
+    public List<String> getImages() {
+        return images;
+    }
+
+    public ClinicalVariant setImages(List<String> images) {
+        this.images = images;
+        return this;
+    }
+
+    public int getVersion() {
+        return version;
+    }
+
+    public ClinicalVariant setVersion(int version) {
+        this.version = version;
+        return this;
+    }
+
     public Map<String, Object> getAttributes() {
         return attributes;
     }

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

@@ -0,0 +1,56 @@
+package org.opencb.biodata.models.clinical.interpretation;
+
+import java.util.Map;
+
+public class ClinicalVariantFilter {
+
+    private Map<String, Object> query;
+    private String opencgaVersion;
+    private String cellbaseVersion;
+
+    public ClinicalVariantFilter() {
+    }
+
+    public ClinicalVariantFilter(Map<String, Object> query, String opencgaVersion, String cellbaseVersion) {
+        this.query = query;
+        this.opencgaVersion = opencgaVersion;
+        this.cellbaseVersion = cellbaseVersion;
+    }
+
+    @Override
+    public String toString() {
+        final StringBuilder sb = new StringBuilder("ClinicalVariantFilter{");
+        sb.append("query=").append(query);
+        sb.append(", opencgaVersion='").append(opencgaVersion).append('\'');
+        sb.append(", cellbaseVersion='").append(cellbaseVersion).append('\'');
+        sb.append('}');
+        return sb.toString();
+    }
+
+    public Map<String, Object> getQuery() {
+        return query;
+    }
+
+    public ClinicalVariantFilter setQuery(Map<String, Object> query) {
+        this.query = query;
+        return this;
+    }
+
+    public String getOpencgaVersion() {
+        return opencgaVersion;
+    }
+
+    public ClinicalVariantFilter setOpencgaVersion(String opencgaVersion) {
+        this.opencgaVersion = opencgaVersion;
+        return this;
+    }
+
+    public String getCellbaseVersion() {
+        return cellbaseVersion;
+    }
+
+    public ClinicalVariantFilter setCellbaseVersion(String cellbaseVersion) {
+        this.cellbaseVersion = cellbaseVersion;
+        return this;
+    }
+}