Merge branch 'develop' into TASK-4158

opencb · Feb 6, 2024 · 946755f · 946755f
2 parents 3c256ba + 255a2df
commit 946755f
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Showing 9 changed files with 11 additions and 102 deletions.
diff --git a/...main/java/org/opencb/opencga/analysis/variant/metadata/CatalogVariantMetadataFactory.java b/...main/java/org/opencb/opencga/analysis/variant/metadata/CatalogVariantMetadataFactory.java
@@ -164,7 +164,7 @@ private void fillSamples(String studyId, List<org.opencb.biodata.models.metadata
             if (annotationSets != null) {
                 sample.setAnnotations(new LinkedHashMap<>(sample.getAnnotations()));
                 for (AnnotationSet annotationSet : annotationSets) {
-                    String prefix = annotationSets.size() > 1 ? annotationSet.getName() + '.' : "";
+                    String prefix = annotationSets.size() > 1 ? annotationSet.getId() + '.' : "";
                     Map<String, Object> annotations = annotationSet.getAnnotations();
                     for (Map.Entry<String, Object> annotationEntry : annotations.entrySet()) {
                         Object value = annotationEntry.getValue();

diff --git a/...g/src/main/java/org/opencb/opencga/catalog/db/mongodb/converters/AnnotationConverter.java b/...g/src/main/java/org/opencb/opencga/catalog/db/mongodb/converters/AnnotationConverter.java
@@ -177,8 +177,7 @@ public List<AnnotationSet> fromDBToAnnotation(List<Document> annotationList, Doc
                     String variableSetId = variableSetUidIdMap.getString(String.valueOf(variableSetUid));
 
                     if (!annotationSetMap.containsKey(compoundKey)) {
-                        annotationSetMap.put(compoundKey, new AnnotationSet(annSetName, variableSetId, new HashMap<>(),
-                                Collections.emptyMap()));
+                        annotationSetMap.put(compoundKey, new AnnotationSet(annSetName, variableSetId, new HashMap<>()));
                     }
 
                     annotationSetMap.get(compoundKey).getAnnotations().put(annotationDocument.getString(ID), annotationDocument.get(VALUE));
@@ -203,8 +202,7 @@ public List<AnnotationSet> fromDBToAnnotation(List<Document> annotationList, Doc
                     String variableSetId = variableSetUidIdMap.getString(String.valueOf(variableSetUid));
 
                     if (!annotationSetMap.containsKey(compoundKey)) {
-                        annotationSetMap.put(compoundKey, new AnnotationSet(annSetName, variableSetId, new HashMap<>(),
-                                Collections.emptyMap()));
+                        annotationSetMap.put(compoundKey, new AnnotationSet(annSetName, variableSetId, new HashMap<>()));
                     }
 
                     // We provide the map from the annotation set in order to be automatically filled in

diff --git a/opencga-catalog/src/main/java/org/opencb/opencga/catalog/utils/AnnotationUtils.java b/opencga-catalog/src/main/java/org/opencb/opencga/catalog/utils/AnnotationUtils.java
@@ -79,10 +79,6 @@ public static void checkVariable(Variable variable) throws CatalogException {
             throw new CatalogException("Only variables with type \"OBJECT\" can define an internal variableSet");
         }
 
-        if (variable.getType() == Variable.VariableType.TEXT) {
-            variable.setType(Variable.VariableType.STRING);
-        }
-
         //Check default values
         switch (variable.getType()) {
             case BOOLEAN:
@@ -431,7 +427,7 @@ private static void checkAllowedValue(Variable variable, Object value, String me
                         Map objectMap = (Map) object;
                         checkAnnotationSet(new VariableSet(variable.getId(), variable.getId(), false, false, false,
                                         variable.getDescription(), variable.getVariables(), null, 1, null),
-                                new AnnotationSet("", variable.getId(), objectMap, null, 1, null), null, true);
+                                new AnnotationSet("", variable.getId(), objectMap), null, true);
                     }
                 }
                 break;

diff --git a/...atalog/src/main/java/org/opencb/opencga/catalog/utils/CatalogSampleAnnotationsLoader.java b/...atalog/src/main/java/org/opencb/opencga/catalog/utils/CatalogSampleAnnotationsLoader.java
@@ -86,8 +86,7 @@ public DataResult<Sample> loadSampleAnnotations(File pedFile, String variableSet
         for (Individual individual : ped.getIndividuals().values()) {
             Map<String, Object> annotation = getAnnotation(individual, sampleMap, variableSet, ped.getFields());
             try {
-                AnnotationUtils.checkAnnotationSet(variableSet, new AnnotationSet("", variableSet.getId(), annotation, "", 1,
-                        null), null, true);
+                AnnotationUtils.checkAnnotationSet(variableSet, new AnnotationSet("", variableSet.getId(), annotation), null, true);
             } catch (CatalogException e) {
                 String message = "Validation with the variableSet {id: " + variableSetId + "} over ped File = {path: " + pedFile.getPath()
                         + ", name: \"" + pedFile.getName() + "\"} failed";

diff --git a/...talog/src/test/java/org/opencb/opencga/catalog/utils/CatalogAnnotationsValidatorTest.java b/...talog/src/test/java/org/opencb/opencga/catalog/utils/CatalogAnnotationsValidatorTest.java
@@ -201,7 +201,7 @@ public void mergeAnnotationsTest() {
         annotations.put("K", "V");
         annotations.put("K2", "V2");
         annotations.put("K4", false);
-        AnnotationSet annotationSet = new AnnotationSet("", "", annotations, "", 1, Collections.emptyMap());
+        AnnotationSet annotationSet = new AnnotationSet("", "", annotations);
         Map<String, Object> newAnnotations = new ObjectMap()
                 .append("K", "newValue")        //Modify
                 .append("K2", null)             //Delete

diff --git a/...og/src/test/java/org/opencb/opencga/catalog/utils/CatalogSampleAnnotationsLoaderTest.java b/...og/src/test/java/org/opencb/opencga/catalog/utils/CatalogSampleAnnotationsLoaderTest.java
@@ -151,8 +151,7 @@ public void testLoadPedigreeCatalog() throws Exception {
     private void validate(Pedigree pedigree, VariableSet variableSet) throws CatalogException {
         for (Map.Entry<String, Individual> entry : pedigree.getIndividuals().entrySet()) {
             Map<String, Object> annotation = loader.getAnnotation(entry.getValue(), null, variableSet, pedigree.getFields());
-            AnnotationUtils.checkAnnotationSet(variableSet, new AnnotationSet("", variableSet.getId(), annotation, "", 1,
-                    null), null, true);
+            AnnotationUtils.checkAnnotationSet(variableSet, new AnnotationSet("", variableSet.getId(), annotation), null, true);
         }
     }
 }
diff --git a/opencga-core/src/main/java/org/opencb/opencga/core/models/common/AnnotationSet.java b/opencga-core/src/main/java/org/opencb/opencga/core/models/common/AnnotationSet.java
@@ -16,13 +16,10 @@
 
 package org.opencb.opencga.core.models.common;
 
-import org.apache.commons.lang3.StringUtils;
 import org.apache.commons.lang3.builder.EqualsBuilder;
 import org.apache.commons.lang3.builder.HashCodeBuilder;
 import org.opencb.opencga.core.common.JacksonUtils;
-import org.opencb.opencga.core.common.TimeUtils;
 
-import java.util.Collections;
 import java.util.Map;
 
 /**
@@ -31,38 +28,16 @@
 public class AnnotationSet {
 
     private String id;
-    @Deprecated
-    private String name;
     private String variableSetId;
     private Map<String, Object> annotations;
-    @Deprecated
-    private String creationDate;
-    @Deprecated
-    private int release;
-    @Deprecated
-    private Map<String, Object> attributes;
-
 
     public AnnotationSet() {
     }
 
     public AnnotationSet(String id, String variableSetId, Map<String, Object> annotations) {
-        this(id, variableSetId, annotations, TimeUtils.getTime(), 1, Collections.emptyMap());
-    }
-
-    public AnnotationSet(String id, String variableSetId, Map<String, Object> annotations, Map<String, Object> attributes) {
-        this(id, variableSetId, annotations, TimeUtils.getTime(), 1, attributes);
-    }
-
-    public AnnotationSet(String id, String variableSetId, Map<String, Object> annotations, String creationDate, int release,
-                         Map<String, Object> attributes) {
         this.id = id;
-        this.name = id;
         this.variableSetId = variableSetId;
         this.annotations = annotations;
-        this.creationDate = creationDate;
-        this.release = release;
-        this.attributes = attributes;
     }
 
     @Override
@@ -71,9 +46,6 @@ public String toString() {
         sb.append("id='").append(id).append('\'');
         sb.append(", variableSetId=").append(variableSetId);
         sb.append(", annotations=").append(annotations);
-        sb.append(", creationDate='").append(creationDate).append('\'');
-        sb.append(", release=").append(release);
-        sb.append(", attributes=").append(attributes);
         sb.append('}');
         return sb.toString();
     }
@@ -89,15 +61,13 @@ public boolean equals(Object o) {
         }
 
         AnnotationSet that = (AnnotationSet) o;
-        return new EqualsBuilder().append(variableSetId, that.variableSetId).append(release, that.release).append(id, that.id)
-                .append(annotations, that.annotations).append(creationDate, that.creationDate).append(attributes, that.attributes)
+        return new EqualsBuilder().append(variableSetId, that.variableSetId).append(id, that.id).append(annotations, that.annotations)
                 .isEquals();
     }
 
     @Override
     public int hashCode() {
-        return new HashCodeBuilder(17, 37).append(id).append(variableSetId).append(annotations).append(creationDate).append(release)
-                .append(attributes).toHashCode();
+        return new HashCodeBuilder(17, 37).append(id).append(variableSetId).append(annotations).toHashCode();
     }
 
     public String getId() {
@@ -106,17 +76,6 @@ public String getId() {
 
     public AnnotationSet setId(String id) {
         this.id = id;
-        this.name = StringUtils.isEmpty(this.name) ? this.id : this.name;
-        return this;
-    }
-
-    public String getName() {
-        return name;
-    }
-
-    public AnnotationSet setName(String name) {
-        this.name = name;
-        this.id = StringUtils.isEmpty(this.id) ? this.name : this.id;
         return this;
     }
 
@@ -138,33 +97,6 @@ public AnnotationSet setAnnotations(Map<String, Object> annotations) {
         return this;
     }
 
-    public String getCreationDate() {
-        return creationDate;
-    }
-
-    public AnnotationSet setCreationDate(String creationDate) {
-        this.creationDate = creationDate;
-        return this;
-    }
-
-    public int getRelease() {
-        return release;
-    }
-
-    public AnnotationSet setRelease(int release) {
-        this.release = release;
-        return this;
-    }
-
-    public Map<String, Object> getAttributes() {
-        return attributes;
-    }
-
-    public AnnotationSet setAttributes(Map<String, Object> attributes) {
-        this.attributes = attributes;
-        return this;
-    }
-
     public <T> T to(Class<T> tClass) {
         return JacksonUtils.getDefaultObjectMapper().convertValue(this.getAnnotations(), tClass);
     }

diff --git a/opencga-core/src/main/java/org/opencb/opencga/core/models/study/Variable.java b/opencga-core/src/main/java/org/opencb/opencga/core/models/study/Variable.java
@@ -47,11 +47,7 @@ public class Variable {
     private long rank;
     private String dependsOn;
     private String description;
-    /**
-     * Variables for validate internal fields. Only valid if type is OBJECT.
-     **/
-    @Deprecated
-    private Set<Variable> variableSet;
+
     private Set<Variable> variables;
     private Map<String, Object> attributes;
 
@@ -90,8 +86,6 @@ public enum VariableType {
         CATEGORICAL,
         INTEGER,
         DOUBLE,
-        @Deprecated
-        TEXT,
         STRING,
         OBJECT,
         MAP_BOOLEAN,
@@ -229,16 +223,6 @@ public Variable setDescription(String description) {
         return this;
     }
 
-    @Deprecated
-    public Set<Variable> getVariableSet() {
-        return getVariables();
-    }
-
-    @Deprecated
-    public Variable setVariableSet(Set<Variable> variableSet) {
-        return setVariables(variableSet);
-    }
-
     public Set<Variable> getVariables() {
         return variables;
     }

diff --git a/pom.xml b/pom.xml
@@ -154,6 +154,7 @@
          -->
         <sonar.scanner.force-deprecated-java-version>true</sonar.scanner.force-deprecated-java-version>
         <kryo.version>2.23.0</kryo.version>
+
         <lombok.version>1.18.30</lombok.version>
         <maven-war-plugin.version>3.4.0</maven-war-plugin.version>
     </properties>