Merge branch 'develop' into TASK-5278

opencb · Feb 16, 2024 · 93856d3 · 93856d3
2 parents 7425629 + 0ec0cbb
commit 93856d3
Show file tree

Hide file tree

Showing 15 changed files with 209 additions and 53 deletions.
diff --git a/biodata-external/pom.xml b/biodata-external/pom.xml
@@ -6,7 +6,7 @@
     <parent>
         <artifactId>biodata</artifactId>
         <groupId>org.opencb.biodata</groupId>
-        <version>2.13.0-SNAPSHOT</version>
+        <version>3.0.0-SNAPSHOT</version>
         <relativePath>../pom.xml</relativePath>
     </parent>
 

diff --git a/biodata-formats/pom.xml b/biodata-formats/pom.xml
@@ -22,7 +22,7 @@
     <parent>
         <groupId>org.opencb.biodata</groupId>
         <artifactId>biodata</artifactId>
-        <version>2.13.0-SNAPSHOT</version>
+        <version>3.0.0-SNAPSHOT</version>
         <relativePath>../pom.xml</relativePath>
     </parent>
 
@@ -88,11 +88,11 @@
             <groupId>org.apache.avro</groupId>
             <artifactId>avro</artifactId>
         </dependency>
-        <dependency>
+<!--        <dependency>
             <groupId>org.codehaus.jackson</groupId>
             <artifactId>jackson-mapper-asl</artifactId>
             <scope>test</scope>
-        </dependency>
+        </dependency>-->
         <dependency>
             <groupId>junit</groupId>
             <artifactId>junit</artifactId>

diff --git a/...s/src/test/java/org/opencb/biodata/formats/variant/annotation/io/VepFormatWriterTest.java b/...s/src/test/java/org/opencb/biodata/formats/variant/annotation/io/VepFormatWriterTest.java
@@ -19,7 +19,7 @@
 
 package org.opencb.biodata.formats.variant.annotation.io;
 
-import org.codehaus.jackson.map.ObjectMapper;
+import com.fasterxml.jackson.databind.ObjectMapper;
 import org.junit.Test;
 import org.opencb.biodata.models.variant.Variant;
 import org.opencb.biodata.models.variant.avro.VariantAvro;

diff --git a/biodata-models/pom.xml b/biodata-models/pom.xml
@@ -22,7 +22,7 @@
     <parent>
         <groupId>org.opencb.biodata</groupId>
         <artifactId>biodata</artifactId>
-        <version>2.13.0-SNAPSHOT</version>
+        <version>3.0.0-SNAPSHOT</version>
         <relativePath>../pom.xml</relativePath>
     </parent>
 
@@ -74,10 +74,10 @@
             <groupId>com.fasterxml.jackson.core</groupId>
             <artifactId>jackson-databind</artifactId>
         </dependency>
-        <dependency>
+<!--        <dependency>
             <groupId>org.codehaus.jackson</groupId>
             <artifactId>jackson-mapper-asl</artifactId>
-        </dependency>
+        </dependency>-->
         <dependency>
             <groupId>junit</groupId>
             <artifactId>junit</artifactId>

diff --git a/biodata-models/src/main/java/org/opencb/biodata/models/alignment/RegionCoverage.java b/biodata-models/src/main/java/org/opencb/biodata/models/alignment/RegionCoverage.java
@@ -1,7 +1,7 @@
 package org.opencb.biodata.models.alignment;
 
-import org.codehaus.jackson.map.ObjectMapper;
-import org.codehaus.jackson.map.ObjectWriter;
+import com.fasterxml.jackson.databind.ObjectMapper;
+import com.fasterxml.jackson.databind.ObjectWriter;
 import org.opencb.biodata.models.core.Region;
 
 import java.io.IOException;

diff --git a/biodata-models/src/main/java/org/opencb/biodata/models/clinical/ClinicalAnalyst.java b/biodata-models/src/main/java/org/opencb/biodata/models/clinical/ClinicalAnalyst.java
@@ -1,8 +1,11 @@
 package org.opencb.biodata.models.clinical;
 
+import com.fasterxml.jackson.annotation.JsonIgnore;
 import org.opencb.biodata.models.constants.FieldConstants;
 import org.opencb.commons.annotations.DataField;
 
+import java.util.Map;
+
 public class ClinicalAnalyst {
 
     @DataField(id = "id", indexed = true,
@@ -17,23 +20,31 @@ public class ClinicalAnalyst {
             description = FieldConstants.CLINICAL_ANALYST_EMAIL_DESCRIPTION)
     private String email;
 
-    @DataField(id = "assignedBy", indexed = true,
-            description = FieldConstants.CLINICAL_ANALYST_ASSIGNED_BY_DESCRIPTION)
+    @DataField(id = "role", indexed = true,
+            description = FieldConstants.CLINICAL_ANALYST_ROLE_DESCRIPTION)
+    private String role;
+
+    @DataField(id = "attributes", indexed = true,
+            description = FieldConstants.CLINICAL_ANALYST_ATTRIBUTES_DESCRIPTION)
+    private Map<String, Object> attributes;
+
+    @Deprecated
+    @DataField(id = "assignedBy")
     private String assignedBy;
 
-    @DataField(id = "date", indexed = true,
-            description = FieldConstants.CLINICAL_ANALYST_DATE_DESCRIPTION)
+    @Deprecated
+    @DataField(id = "date")
     private String date;
 
     public ClinicalAnalyst() {
     }
 
-    public ClinicalAnalyst(String id, String name, String email, String assignedBy, String date) {
+    public ClinicalAnalyst(String id, String name, String email, String role, Map<String, Object> attributes) {
         this.id = id;
         this.name = name;
         this.email = email;
-        this.assignedBy = assignedBy;
-        this.date = date;
+        this.role = role;
+        this.attributes = attributes;
     }
 
     @Override
@@ -42,8 +53,8 @@ public String toString() {
         sb.append("id='").append(id).append('\'');
         sb.append(", name='").append(name).append('\'');
         sb.append(", email='").append(email).append('\'');
-        sb.append(", assignedBy='").append(assignedBy).append('\'');
-        sb.append(", date='").append(date).append('\'');
+        sb.append(", role='").append(role).append('\'');
+        sb.append(", attributes=").append(attributes);
         sb.append('}');
         return sb.toString();
     }
@@ -75,21 +86,43 @@ public ClinicalAnalyst setEmail(String email) {
         return this;
     }
 
+    public String getRole() {
+        return role;
+    }
+
+    public ClinicalAnalyst setRole(String role) {
+        this.role = role;
+        return this;
+    }
+
+    public Map<String, Object> getAttributes() {
+        return attributes;
+    }
+
+    public ClinicalAnalyst setAttributes(Map<String, Object> attributes) {
+        this.attributes = attributes;
+        return this;
+    }
+
+    @JsonIgnore
+    @Deprecated
     public String getAssignedBy() {
         return assignedBy;
     }
 
+    @Deprecated
     public ClinicalAnalyst setAssignedBy(String assignedBy) {
-        this.assignedBy = assignedBy;
         return this;
     }
 
+    @JsonIgnore
+    @Deprecated
     public String getDate() {
         return date;
     }
 
+    @Deprecated
     public ClinicalAnalyst setDate(String date) {
-        this.date = date;
         return this;
     }
 }
diff --git a/...dels/src/main/java/org/opencb/biodata/models/clinical/interpretation/ClinicalVariant.java b/...dels/src/main/java/org/opencb/biodata/models/clinical/interpretation/ClinicalVariant.java
@@ -34,6 +34,8 @@ public class ClinicalVariant extends Variant {
     private List<ClinicalVariantEvidence> evidences;
     private List<ClinicalComment> comments;
     private Map<String, Object> filters;
+    private String recommendation;
+    private List<MiniPubmed> references;
     private ClinicalDiscussion discussion;
     private ClinicalVariantConfidence confidence;
     private List<String> tags;
@@ -76,6 +78,7 @@ 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, ClinicalDiscussion discussion,
                            ClinicalVariantConfidence confidence, Status status, List<String> tags,
@@ -92,19 +95,27 @@ 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, 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;
+    }
+
     @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);
-        sb.append('}');
-        return sb.toString();
+        return super.toString();
     }
 
     public List<ClinicalVariantEvidence> getEvidences() {
@@ -134,6 +145,24 @@ public ClinicalVariant setFilters(Map<String, Object> filters) {
         return this;
     }
 
+    public String getRecommendation() {
+        return recommendation;
+    }
+
+    public ClinicalVariant setRecommendation(String recommendation) {
+        this.recommendation = recommendation;
+        return this;
+    }
+
+    public List<MiniPubmed> getReferences() {
+        return references;
+    }
+
+    public ClinicalVariant setReferences(List<MiniPubmed> references) {
+        this.references = references;
+        return this;
+    }
+
     public ClinicalDiscussion getDiscussion() {
         return discussion;
     }

diff --git a/...ta-models/src/main/java/org/opencb/biodata/models/clinical/interpretation/MiniPubmed.java b/...ta-models/src/main/java/org/opencb/biodata/models/clinical/interpretation/MiniPubmed.java
@@ -0,0 +1,90 @@
+package org.opencb.biodata.models.clinical.interpretation;
+
+public class MiniPubmed {
+
+    private String id;
+    private String name;
+    private String journal;
+    private String summary;
+    private String date;
+    private String url;
+
+    public MiniPubmed() {
+    }
+
+    public MiniPubmed(String id, String name, String summary, String date, String url, String journal) {
+        this.id = id;
+        this.name = name;
+        this.summary = summary;
+        this.date = date;
+        this.url = url;
+        this.journal = journal;
+    }
+
+    @Override
+    public String toString() {
+        final StringBuilder sb = new StringBuilder("MiniPubmed{");
+        sb.append("id='").append(id).append('\'');
+        sb.append(", name='").append(name).append('\'');
+        sb.append(", summary='").append(summary).append('\'');
+        sb.append(", date=").append(date);
+        sb.append(", url='").append(url).append('\'');
+        sb.append(", journal='").append(journal).append('\'');
+        sb.append('}');
+        return sb.toString();
+    }
+
+    public String getId() {
+        return id;
+    }
+
+    public MiniPubmed setId(String id) {
+        this.id = id;
+        return this;
+    }
+
+    public String getName() {
+        return name;
+    }
+
+    public MiniPubmed setName(String name) {
+        this.name = name;
+        return this;
+    }
+
+    public String getSummary() {
+        return summary;
+    }
+
+    public MiniPubmed setSummary(String summary) {
+        this.summary = summary;
+        return this;
+    }
+
+    public String getDate() {
+        return date;
+    }
+
+    public MiniPubmed setDate(String date) {
+        this.date = date;
+        return this;
+    }
+
+    public String getUrl() {
+        return url;
+    }
+
+    public MiniPubmed setUrl(String url) {
+        this.url = url;
+        return this;
+    }
+
+    public String getJournal() {
+        return journal;
+    }
+
+    public MiniPubmed setJournal(String journal) {
+        this.journal = journal;
+        return this;
+    }
+}
diff --git a/biodata-models/src/main/java/org/opencb/biodata/models/clinical/pedigree/Pedigree.java b/biodata-models/src/main/java/org/opencb/biodata/models/clinical/pedigree/Pedigree.java
@@ -19,7 +19,7 @@
 
 package org.opencb.biodata.models.clinical.pedigree;
 
-import org.codehaus.jackson.map.ObjectMapper;
+import com.fasterxml.jackson.databind.ObjectMapper;
 import org.opencb.biodata.models.clinical.Disorder;
 import org.opencb.biodata.models.clinical.Phenotype;
 

diff --git a/biodata-models/src/main/java/org/opencb/biodata/models/constants/FieldConstants.java b/biodata-models/src/main/java/org/opencb/biodata/models/constants/FieldConstants.java
@@ -65,8 +65,8 @@ public class FieldConstants {
     public static final String RELATEDNESS_REPORT_SCORES_DESCRIPTION = "Relatedness scores for pair of samples";
     public static final String RELATEDNESS_REPORT_FILES_DESCRIPTION = "List of files of Relatedness Report";
 
-    public static final String CLINICAL_ANALYST_DATE_DESCRIPTION = "Date of the clinical analyst";
-    public static final String CLINICAL_ANALYST_ASSIGNED_BY_DESCRIPTION = "Assigned by field";
+    public static final String CLINICAL_ANALYST_ROLE_DESCRIPTION = "Analyst role";
+    public static final String CLINICAL_ANALYST_ATTRIBUTES_DESCRIPTION = "Analyst attributes";
 
     public static final String CLINICAL_ANALYST_EMAIL_DESCRIPTION = "Email of the analyst";
     public static final String AUDIT_AUTHOR_DESCRIPTION = "Audit author";

diff --git a/biodata-tools/pom.xml b/biodata-tools/pom.xml
@@ -22,7 +22,7 @@
     <parent>
         <groupId>org.opencb.biodata</groupId>
         <artifactId>biodata</artifactId>
-        <version>2.13.0-SNAPSHOT</version>
+        <version>3.0.0-SNAPSHOT</version>
         <relativePath>../pom.xml</relativePath>
     </parent>
 
@@ -90,10 +90,10 @@
             <groupId>org.apache.commons</groupId>
             <artifactId>commons-collections4</artifactId>
         </dependency>
-        <dependency>
+<!--        <dependency>
             <groupId>org.codehaus.jackson</groupId>
             <artifactId>jackson-mapper-asl</artifactId>
-        </dependency>
+        </dependency>-->
         <dependency>
             <groupId>com.google.guava</groupId>
             <artifactId>guava</artifactId>