TASK-5610 Create the CVDB endpoint analysis/clinical/cvdb/variant/summary and overwrite analysis/clinical/variant

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

@@ -21,6 +21,7 @@
 
 import org.opencb.biodata.models.clinical.ClinicalComment;
 import org.opencb.biodata.models.clinical.ClinicalDiscussion;
+import org.opencb.biodata.models.clinical.interpretation.stats.ClinicalVariantSummaryStats;
 import org.opencb.biodata.models.variant.Variant;
 import org.opencb.biodata.models.variant.avro.VariantAvro;
 
@@ -40,6 +41,8 @@ public class ClinicalVariant extends Variant {
     private ClinicalVariantConfidence confidence;
     private List<String> tags;
 
+    private ClinicalVariantSummaryStats stats;
+
     private Status status;
 
     // TODO maybe this parameter should be in Variant
@@ -95,6 +98,7 @@ public ClinicalVariant(VariantAvro avro, List<ClinicalVariantEvidence> evidences
         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,
@@ -113,6 +117,26 @@ public ClinicalVariant(VariantAvro avro, List<ClinicalVariantEvidence> evidences
         this.attributes = attributes;
     }
 
+    public ClinicalVariant(VariantAvro avro, List<ClinicalVariantEvidence> evidences, List<ClinicalComment> comments,
+                           Map<String, Object> filters, String recommendation, List<MiniPubmed> references,
+                           ClinicalDiscussion discussion, ClinicalVariantConfidence confidence, ClinicalVariantSummaryStats stats,
+                           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.stats = stats;
+        this.status = status;
+        this.tags = tags;
+        this.confidence = confidence;
+        this.attributes = attributes;
+    }
+
+
     @Override
     public String toString() {
         return super.toString();
@@ -181,6 +205,15 @@ public ClinicalVariant setConfidence(ClinicalVariantConfidence confidence) {
         return this;
     }
 
+    public ClinicalVariantSummaryStats getStats() {
+        return stats;
+    }
+
+    public ClinicalVariant setStats(ClinicalVariantSummaryStats stats) {
+        this.stats = stats;
+        return this;
+    }
+
     public Status getStatus() {
         return status;
     }

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

@@ -0,0 +1,134 @@
+/*
+ * <!--
+ *   ~ 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.interpretation.stats;
+
+import java.util.HashMap;
+import java.util.Map;
+
+public class ClinicalVariantSummaryStats {
+
+    private int numCases;
+    private Map<String, Integer> variantStatusCounts;
+    private Map<String, Integer> variantConfidenceCounts;
+    private int numPrimaryInterpretations;
+    private int numSecondaryInterpretations;
+    private InterpretationSummaryStats interpretationSummaryStats;
+    private Map<String, Integer> clinicalAnalysisDisorderCounts;
+
+    public ClinicalVariantSummaryStats() {
+        this.numCases = 0;
+        this.variantStatusCounts = new HashMap<>();
+        this.variantConfidenceCounts = new HashMap<>();
+        this.numPrimaryInterpretations = 0;
+        this.numSecondaryInterpretations = 0;
+        this.interpretationSummaryStats = new InterpretationSummaryStats();
+        this.clinicalAnalysisDisorderCounts = new HashMap<>();
+    }
+
+    public ClinicalVariantSummaryStats(int numCases, Map<String, Integer> variantStatusCounts, Map<String, Integer> variantConfidenceCounts,
+                                       int numPrimaryInterpretations, int numSecondaryInterpretations,
+                                       InterpretationSummaryStats interpretationSummaryStats,
+                                       Map<String, Integer> clinicalAnalysisDisorderCounts) {
+        this.numCases = numCases;
+        this.variantStatusCounts = variantStatusCounts;
+        this.variantConfidenceCounts = variantConfidenceCounts;
+        this.numPrimaryInterpretations = numPrimaryInterpretations;
+        this.numSecondaryInterpretations = numSecondaryInterpretations;
+        this.interpretationSummaryStats = interpretationSummaryStats;
+        this.clinicalAnalysisDisorderCounts = clinicalAnalysisDisorderCounts;
+    }
+
+    @Override
+    public String toString() {
+        final StringBuilder sb = new StringBuilder("ClinicalVariantSummaryStats{");
+        sb.append("numCases=").append(numCases);
+        sb.append(", variantStatusCounts=").append(variantStatusCounts);
+        sb.append(", variantConfidenceCounts=").append(variantConfidenceCounts);
+        sb.append(", numPrimaryInterpretations=").append(numPrimaryInterpretations);
+        sb.append(", numSecondaryInterpretations=").append(numSecondaryInterpretations);
+        sb.append(", interpretationSummaryStats=").append(interpretationSummaryStats);
+        sb.append(", clinicalAnalysisDisorderCounts=").append(clinicalAnalysisDisorderCounts);
+        sb.append('}');
+        return sb.toString();
+    }
+
+    public int getNumCases() {
+        return numCases;
+    }
+
+    public ClinicalVariantSummaryStats setNumCases(int numCases) {
+        this.numCases = numCases;
+        return this;
+    }
+
+    public Map<String, Integer> getVariantStatusCounts() {
+        return variantStatusCounts;
+    }
+
+    public ClinicalVariantSummaryStats setVariantStatusCounts(Map<String, Integer> variantStatusCounts) {
+        this.variantStatusCounts = variantStatusCounts;
+        return this;
+    }
+
+    public Map<String, Integer> getVariantConfidenceCounts() {
+        return variantConfidenceCounts;
+    }
+
+    public ClinicalVariantSummaryStats setVariantConfidenceCounts(Map<String, Integer> variantConfidenceCounts) {
+        this.variantConfidenceCounts = variantConfidenceCounts;
+        return this;
+    }
+
+    public int getNumPrimaryInterpretations() {
+        return numPrimaryInterpretations;
+    }
+
+    public ClinicalVariantSummaryStats setNumPrimaryInterpretations(int numPrimaryInterpretations) {
+        this.numPrimaryInterpretations = numPrimaryInterpretations;
+        return this;
+    }
+
+    public int getNumSecondaryInterpretations() {
+        return numSecondaryInterpretations;
+    }
+
+    public ClinicalVariantSummaryStats setNumSecondaryInterpretations(int numSecondaryInterpretations) {
+        this.numSecondaryInterpretations = numSecondaryInterpretations;
+        return this;
+    }
+
+    public InterpretationSummaryStats getInterpretationSummaryStats() {
+        return interpretationSummaryStats;
+    }
+
+    public ClinicalVariantSummaryStats setInterpretationSummaryStats(InterpretationSummaryStats interpretationSummaryStats) {
+        this.interpretationSummaryStats = interpretationSummaryStats;
+        return this;
+    }
+
+    public Map<String, Integer> getClinicalAnalysisDisorderCounts() {
+        return clinicalAnalysisDisorderCounts;
+    }
+
+    public ClinicalVariantSummaryStats setClinicalAnalysisDisorderCounts(Map<String, Integer> clinicalAnalysisDisorderCounts) {
+        this.clinicalAnalysisDisorderCounts = clinicalAnalysisDisorderCounts;
+        return this;
+    }
+}

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

@@ -0,0 +1,148 @@
+/*
+ * <!--
+ *   ~ 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.interpretation.stats;
+
+import java.util.HashMap;
+import java.util.Map;
+
+public class InterpretationSummaryStats {
+
+    private Map<String, Integer> evidenceTranscriptCounts;
+    private Map<String, Integer> evidenceGeneNameCounts;
+    private Map<String, Integer> evidenceModeOfInheritanceCounts;
+    private Map<String, Integer> evidencePanelCounts;
+    private Map<String, Integer> evidenceReviewTierCounts;
+    private Map<String, Integer> evidenceReviewAcmgCounts;
+    private Map<String, Integer> evidenceReviewClinicalSignificanceCounts;
+    private Map<String, Integer> evidenceClassificationAcmgCounts;
+
+    public InterpretationSummaryStats() {
+        this.evidenceTranscriptCounts = new HashMap<>();
+        this.evidenceGeneNameCounts = new HashMap<>();
+        this.evidenceModeOfInheritanceCounts = new HashMap<>();
+        this.evidencePanelCounts = new HashMap<>();
+        this.evidenceReviewTierCounts = new HashMap<>();
+        this.evidenceReviewAcmgCounts = new HashMap<>();
+        this.evidenceReviewClinicalSignificanceCounts = new HashMap<>();
+        this.evidenceClassificationAcmgCounts = new HashMap<>();
+    }
+
+    public InterpretationSummaryStats(Map<String, Integer> evidenceTranscriptCounts, Map<String, Integer> evidenceGeneNameCounts,
+                                      Map<String, Integer> evidenceModeOfInheritanceCounts, Map<String, Integer> evidencePanelCounts,
+                                      Map<String, Integer> evidenceReviewTierCounts, Map<String, Integer> evidenceReviewAcmgCounts,
+                                      Map<String, Integer> evidenceReviewClinicalSignificanceCounts,
+                                      Map<String, Integer> evidenceClassificationAcmgCounts) {
+        this.evidenceTranscriptCounts = evidenceTranscriptCounts;
+        this.evidenceGeneNameCounts = evidenceGeneNameCounts;
+        this.evidenceModeOfInheritanceCounts = evidenceModeOfInheritanceCounts;
+        this.evidencePanelCounts = evidencePanelCounts;
+        this.evidenceReviewTierCounts = evidenceReviewTierCounts;
+        this.evidenceReviewAcmgCounts = evidenceReviewAcmgCounts;
+        this.evidenceReviewClinicalSignificanceCounts = evidenceReviewClinicalSignificanceCounts;
+        this.evidenceClassificationAcmgCounts = evidenceClassificationAcmgCounts;
+    }
+
+    @Override
+    public String toString() {
+        final StringBuilder sb = new StringBuilder("InterpretationSummaryStats{");
+        sb.append("evidenceTranscriptCounts=").append(evidenceTranscriptCounts);
+        sb.append(", evidenceGeneNameCounts=").append(evidenceGeneNameCounts);
+        sb.append(", evidenceModeOfInheritanceCounts=").append(evidenceModeOfInheritanceCounts);
+        sb.append(", evidencePanelCounts=").append(evidencePanelCounts);
+        sb.append(", evidenceReviewTierCounts=").append(evidenceReviewTierCounts);
+        sb.append(", evidenceReviewAcmgCounts=").append(evidenceReviewAcmgCounts);
+        sb.append(", evidenceReviewClinicalSignificanceCounts=").append(evidenceReviewClinicalSignificanceCounts);
+        sb.append(", evidenceClassificationAcmgCounts=").append(evidenceClassificationAcmgCounts);
+        sb.append('}');
+        return sb.toString();
+    }
+
+    public Map<String, Integer> getEvidenceTranscriptCounts() {
+        return evidenceTranscriptCounts;
+    }
+
+    public InterpretationSummaryStats setEvidenceTranscriptCounts(Map<String, Integer> evidenceTranscriptCounts) {
+        this.evidenceTranscriptCounts = evidenceTranscriptCounts;
+        return this;
+    }
+
+    public Map<String, Integer> getEvidenceGeneNameCounts() {
+        return evidenceGeneNameCounts;
+    }
+
+    public InterpretationSummaryStats setEvidenceGeneNameCounts(Map<String, Integer> evidenceGeneNameCounts) {
+        this.evidenceGeneNameCounts = evidenceGeneNameCounts;
+        return this;
+    }
+
+    public Map<String, Integer> getEvidenceModeOfInheritanceCounts() {
+        return evidenceModeOfInheritanceCounts;
+    }
+
+    public InterpretationSummaryStats setEvidenceModeOfInheritanceCounts(Map<String, Integer> evidenceModeOfInheritanceCounts) {
+        this.evidenceModeOfInheritanceCounts = evidenceModeOfInheritanceCounts;
+        return this;
+    }
+
+    public Map<String, Integer> getEvidencePanelCounts() {
+        return evidencePanelCounts;
+    }
+
+    public InterpretationSummaryStats setEvidencePanelCounts(Map<String, Integer> evidencePanelCounts) {
+        this.evidencePanelCounts = evidencePanelCounts;
+        return this;
+    }
+
+    public Map<String, Integer> getEvidenceReviewTierCounts() {
+        return evidenceReviewTierCounts;
+    }
+
+    public InterpretationSummaryStats setEvidenceReviewTierCounts(Map<String, Integer> evidenceReviewTierCounts) {
+        this.evidenceReviewTierCounts = evidenceReviewTierCounts;
+        return this;
+    }
+
+    public Map<String, Integer> getEvidenceReviewAcmgCounts() {
+        return evidenceReviewAcmgCounts;
+    }
+
+    public InterpretationSummaryStats setEvidenceReviewAcmgCounts(Map<String, Integer> evidenceReviewAcmgCounts) {
+        this.evidenceReviewAcmgCounts = evidenceReviewAcmgCounts;
+        return this;
+    }
+
+    public Map<String, Integer> getEvidenceReviewClinicalSignificanceCounts() {
+        return evidenceReviewClinicalSignificanceCounts;
+    }
+
+    public InterpretationSummaryStats setEvidenceReviewClinicalSignificanceCounts(Map<String, Integer> evidenceReviewClinicalSignificanceCounts) {
+        this.evidenceReviewClinicalSignificanceCounts = evidenceReviewClinicalSignificanceCounts;
+        return this;
+    }
+
+    public Map<String, Integer> getEvidenceClassificationAcmgCounts() {
+        return evidenceClassificationAcmgCounts;
+    }
+
+    public InterpretationSummaryStats setEvidenceClassificationAcmgCounts(Map<String, Integer> evidenceClassificationAcmgCounts) {
+        this.evidenceClassificationAcmgCounts = evidenceClassificationAcmgCounts;
+        return this;
+    }
+}