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 List<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, List<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 List<ClinicalVariantSummaryStats> getStats() {
+        return stats;
+    }
+
+    public ClinicalVariant setStats(List<ClinicalVariantSummaryStats> stats) {
+        this.stats = stats;
+        return this;
+    }
+
     public Status getStatus() {
         return status;
     }

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

@@ -0,0 +1,79 @@
+/*
+ * <!--
+ *   ~ 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.LinkedHashMap;
+import java.util.Map;
+
+public class ClinicalAnalysisStats {
+
+    private Map<String, Long> disorders;
+    private Map<String, Long> probandPhenotypes;
+    private Map<String, Long> probandDisorders;
+
+    public ClinicalAnalysisStats() {
+        this.disorders = new LinkedHashMap<>();
+        this.probandPhenotypes = new LinkedHashMap<>();
+        this.probandDisorders = new LinkedHashMap<>();
+    }
+
+    public ClinicalAnalysisStats(Map<String, Long> disorders, Map<String, Long> probandPhenotypes, Map<String, Long> probandDisorders) {
+        this.disorders = disorders;
+        this.probandPhenotypes = probandPhenotypes;
+        this.probandDisorders = probandDisorders;
+    }
+
+    @Override
+    public String toString() {
+        final StringBuilder sb = new StringBuilder("ClinicalAnalysisStats{");
+        sb.append("disorders=").append(disorders);
+        sb.append(", probandPhenotypes=").append(probandPhenotypes);
+        sb.append(", probandDisorders=").append(probandDisorders);
+        sb.append('}');
+        return sb.toString();
+    }
+
+    public Map<String, Long> getDisorders() {
+        return disorders;
+    }
+
+    public ClinicalAnalysisStats setDisorders(Map<String, Long> disorders) {
+        this.disorders = disorders;
+        return this;
+    }
+
+    public Map<String, Long> getProbandPhenotypes() {
+        return probandPhenotypes;
+    }
+
+    public ClinicalAnalysisStats setProbandPhenotypes(Map<String, Long> probandPhenotypes) {
+        this.probandPhenotypes = probandPhenotypes;
+        return this;
+    }
+
+    public Map<String, Long> getProbandDisorders() {
+        return probandDisorders;
+    }
+
+    public ClinicalAnalysisStats setProbandDisorders(Map<String, Long> probandDisorders) {
+        this.probandDisorders = probandDisorders;
+        return this;
+    }
+}

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

@@ -0,0 +1,160 @@
+/*
+ * <!--
+ *   ~ 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.LinkedHashMap;
+import java.util.Map;
+
+public class ClinicalVariantEvidenceStats {
+
+    private Map<String, Long> transcripts;
+    private Map<String, Long> genes;
+    private Map<String, Long> soTerms;
+    private Map<String, Long> mois;
+    private Map<String, Long> panels;
+    private Map<String, Long> reviewTiers;
+    private Map<String, Long> reviewAcmgs;
+    private Map<String, Long> reviewClinicalSignificances;
+    private Map<String, Long> acmgs;
+
+    public ClinicalVariantEvidenceStats() {
+        this.transcripts = new LinkedHashMap<>();
+        this.genes = new LinkedHashMap<>();
+        this.soTerms = new LinkedHashMap<>();
+        this.mois = new LinkedHashMap<>();
+        this.panels = new LinkedHashMap<>();
+        this.reviewTiers = new LinkedHashMap<>();
+        this.reviewAcmgs = new LinkedHashMap<>();
+        this.reviewClinicalSignificances = new LinkedHashMap<>();
+        this.acmgs = new LinkedHashMap<>();
+    }
+
+    public ClinicalVariantEvidenceStats(Map<String, Long> transcripts, Map<String, Long> genes, Map<String, Long> soTerms,
+                                        Map<String, Long> mois, Map<String, Long> panels, Map<String, Long> reviewTiers,
+                                        Map<String, Long> reviewAcmgs, Map<String, Long> reviewClinicalSignificances,
+                                        Map<String, Long> acmgs) {
+        this.transcripts = transcripts;
+        this.genes = genes;
+        this.soTerms = soTerms;
+        this.mois = mois;
+        this.panels = panels;
+        this.reviewTiers = reviewTiers;
+        this.reviewAcmgs = reviewAcmgs;
+        this.reviewClinicalSignificances = reviewClinicalSignificances;
+        this.acmgs = acmgs;
+    }
+
+    @Override
+    public String toString() {
+        final StringBuilder sb = new StringBuilder("ClinicalVariantEvidenceStats{");
+        sb.append("transcripts=").append(transcripts);
+        sb.append(", genes=").append(genes);
+        sb.append(", soTerms=").append(soTerms);
+        sb.append(", mois=").append(mois);
+        sb.append(", panels=").append(panels);
+        sb.append(", reviewTiers=").append(reviewTiers);
+        sb.append(", reviewAcmgs=").append(reviewAcmgs);
+        sb.append(", reviewClinicalSignificances=").append(reviewClinicalSignificances);
+        sb.append(", acmgs=").append(acmgs);
+        sb.append('}');
+        return sb.toString();
+    }
+
+    public Map<String, Long> getTranscripts() {
+        return transcripts;
+    }
+
+    public ClinicalVariantEvidenceStats setTranscripts(Map<String, Long> transcripts) {
+        this.transcripts = transcripts;
+        return this;
+    }
+
+    public Map<String, Long> getGenes() {
+        return genes;
+    }
+
+    public ClinicalVariantEvidenceStats setGenes(Map<String, Long> genes) {
+        this.genes = genes;
+        return this;
+    }
+
+    public Map<String, Long> getSoTerms() {
+        return soTerms;
+    }
+
+    public ClinicalVariantEvidenceStats setSoTerms(Map<String, Long> soTerms) {
+        this.soTerms = soTerms;
+        return this;
+    }
+
+    public Map<String, Long> getMois() {
+        return mois;
+    }
+
+    public ClinicalVariantEvidenceStats setMois(Map<String, Long> mois) {
+        this.mois = mois;
+        return this;
+    }
+
+    public Map<String, Long> getPanels() {
+        return panels;
+    }
+
+    public ClinicalVariantEvidenceStats setPanels(Map<String, Long> panels) {
+        this.panels = panels;
+        return this;
+    }
+
+    public Map<String, Long> getReviewTiers() {
+        return reviewTiers;
+    }
+
+    public ClinicalVariantEvidenceStats setReviewTiers(Map<String, Long> reviewTiers) {
+        this.reviewTiers = reviewTiers;
+        return this;
+    }
+
+    public Map<String, Long> getReviewAcmgs() {
+        return reviewAcmgs;
+    }
+
+    public ClinicalVariantEvidenceStats setReviewAcmgs(Map<String, Long> reviewAcmgs) {
+        this.reviewAcmgs = reviewAcmgs;
+        return this;
+    }
+
+    public Map<String, Long> getReviewClinicalSignificances() {
+        return reviewClinicalSignificances;
+    }
+
+    public ClinicalVariantEvidenceStats setReviewClinicalSignificances(Map<String, Long> reviewClinicalSignificances) {
+        this.reviewClinicalSignificances = reviewClinicalSignificances;
+        return this;
+    }
+
+    public Map<String, Long> getAcmgs() {
+        return acmgs;
+    }
+
+    public ClinicalVariantEvidenceStats setAcmgs(Map<String, Long> acmgs) {
+        this.acmgs = acmgs;
+        return this;
+    }
+}

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

@@ -0,0 +1,66 @@
+/*
+ * <!--
+ *   ~ 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.LinkedHashMap;
+import java.util.Map;
+
+public class ClinicalVariantStats {
+
+    private Map<String, Long> status;
+    private Map<String, Long> confidences;
+
+    public ClinicalVariantStats() {
+        this.status = new LinkedHashMap<>();
+        this.confidences = new LinkedHashMap<>();
+    }
+
+    public ClinicalVariantStats(Map<String, Long> status, Map<String, Long> confidences) {
+        this.status = status;
+        this.confidences = confidences;
+    }
+
+    @Override
+    public String toString() {
+        final StringBuilder sb = new StringBuilder("ClinicalVariantStats{");
+        sb.append("status=").append(status);
+        sb.append(", confidences=").append(confidences);
+        sb.append('}');
+        return sb.toString();
+    }
+
+    public Map<String, Long> getStatus() {
+        return status;
+    }
+
+    public ClinicalVariantStats setStatus(Map<String, Long> status) {
+        this.status = status;
+        return this;
+    }
+
+    public Map<String, Long> getConfidences() {
+        return confidences;
+    }
+
+    public ClinicalVariantStats setConfidences(Map<String, Long> confidences) {
+        this.confidences = confidences;
+        return this;
+    }
+}