add metamanager, checkstyle #528

opencb · Feb 17, 2020 · 39c430b · 39c430b
1 parent cbd7a3a
commit 39c430b
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Showing 29 changed files with 819 additions and 1,098 deletions.
diff --git a/cellbase-app/src/main/java/org/opencb/cellbase/app/cli/main/CellBaseCliOptionsParser.java b/cellbase-app/src/main/java/org/opencb/cellbase/app/cli/main/CellBaseCliOptionsParser.java
@@ -83,9 +83,6 @@ public class QueryCommandOptions {
         @Parameter(names = {"--group-by"}, description = "", required = false, arity = 1)
         public String groupBy;
 
-        @Parameter(names = {"--rank"}, description = "", required = false, arity = 1)
-        public String rank;
-
         @Parameter(names = {"--distinct"}, description = "", required = false, arity = 1)
         public String distinct;
 

diff --git a/...se-app/src/main/java/org/opencb/cellbase/app/cli/main/executors/QueryCommandExecutor.java b/...se-app/src/main/java/org/opencb/cellbase/app/cli/main/executors/QueryCommandExecutor.java
@@ -276,12 +276,6 @@ private void executeFeatureAggregation(FeatureDBAdaptor featureDBAdaptor, Query
             return;
         }
 
-        if (queryCommandOptions.rank != null && !queryCommandOptions.rank.isEmpty()) {
-            CellBaseDataResult rank = featureDBAdaptor.rank(query, queryCommandOptions.rank, queryCommandOptions.limit, true);
-            output.println(objectMapper.writeValueAsString(rank));
-            return;
-        }
-
         if (queryCommandOptions.count) {
             CellBaseDataResult count = featureDBAdaptor.count(query);
             output.println(objectMapper.writeValueAsString(count));

diff --git a/cellbase-core/src/main/java/org/opencb/cellbase/core/api/core/CellBaseDBAdaptor.java b/cellbase-core/src/main/java/org/opencb/cellbase/core/api/core/CellBaseDBAdaptor.java
@@ -53,11 +53,11 @@ default CellBaseDataResult<String> distinct(String field) {
     CellBaseDataResult<String> distinct(Query query, String field);
 
 
-    default CellBaseDataResult stats() {
-        return stats(new Query());
-    }
-
-    CellBaseDataResult stats(Query query);
+//    default CellBaseDataResult stats() {
+//        return stats(new Query());
+//    }
+//
+//    CellBaseDataResult stats(Query query);
 
     /*
      Main methods to query.
@@ -97,7 +97,7 @@ default Iterator nativeIterator() {
 
     Iterator nativeIterator(Query query, QueryOptions options);
 
-    CellBaseDataResult rank(Query query, String field, int numResults, boolean asc);
+//    CellBaseDataResult rank(Query query, String field, int numResults, boolean asc);
 
     CellBaseDataResult groupBy(Query query, String field, QueryOptions options);
 

diff --git a/cellbase-core/src/main/java/org/opencb/cellbase/core/api/core/TranscriptDBAdaptor.java b/cellbase-core/src/main/java/org/opencb/cellbase/core/api/core/TranscriptDBAdaptor.java
@@ -17,10 +17,6 @@
 package org.opencb.cellbase.core.api.core;
 
 import org.opencb.commons.datastore.core.QueryParam;
-import org.opencb.cellbase.core.result.CellBaseDataResult;
-
-import java.util.ArrayList;
-import java.util.List;
 
 import static org.opencb.commons.datastore.core.QueryParam.Type.TEXT_ARRAY;
 
@@ -51,7 +47,6 @@ enum QueryParams implements QueryParam {
         private Type type;
         private String description;
 
-
         @Override
         public String key() {
             return key;
@@ -68,14 +63,14 @@ public Type type() {
         }
     }
 
-    CellBaseDataResult<String> getCdna(String id);
-
-    default List<CellBaseDataResult<String>> getCdna(List<String> idList) {
-        List<CellBaseDataResult<String>> cellBaseDataResults = new ArrayList<>();
-        for (String id : idList) {
-            cellBaseDataResults.add(getCdna(id));
-        }
-        return cellBaseDataResults;
-    }
+//    CellBaseDataResult<String> getCdna(String id);
+//
+//    default List<CellBaseDataResult<String>> getCdna(List<String> idList) {
+//        List<CellBaseDataResult<String>> cellBaseDataResults = new ArrayList<>();
+//        for (String id : idList) {
+//            cellBaseDataResults.add(getCdna(id));
+//        }
+//        return cellBaseDataResults;
+//    }
 
 }
diff --git a/cellbase-lib/src/main/java/org/opencb/cellbase/lib/impl/core/ClinicalMongoDBAdaptor.java b/cellbase-lib/src/main/java/org/opencb/cellbase/lib/impl/core/ClinicalMongoDBAdaptor.java
@@ -58,10 +58,10 @@ public CellBaseDataResult nativeNext(Query query, QueryOptions options) {
         return null;
     }
 
-    @Override
-    public CellBaseDataResult rank(Query query, String field, int numResults, boolean asc) {
-        return null;
-    }
+//    @Override
+//    public CellBaseDataResult rank(Query query, String field, int numResults, boolean asc) {
+//        return null;
+//    }
 
     @Override
     public CellBaseDataResult groupBy(Query query, String field, QueryOptions options) {
@@ -95,10 +95,10 @@ public CellBaseDataResult distinct(Query query, String field) {
         return new CellBaseDataResult<>(mongoDBCollection.distinct(field, bson));
     }
 
-    @Override
-    public CellBaseDataResult stats(Query query) {
-        return null;
-    }
+//    @Override
+//    public CellBaseDataResult stats(Query query) {
+//        return null;
+//    }
 
     @Override
     public CellBaseDataResult<Variant> get(Query query, QueryOptions options) {

diff --git a/cellbase-lib/src/main/java/org/opencb/cellbase/lib/impl/core/ConservationMongoDBAdaptor.java b/cellbase-lib/src/main/java/org/opencb/cellbase/lib/impl/core/ConservationMongoDBAdaptor.java
@@ -64,10 +64,10 @@ public CellBaseDataResult distinct(Query query, String field) {
         return new CellBaseDataResult<>(mongoDBCollection.distinct(field, bson));
     }
 
-    @Override
-    public CellBaseDataResult stats(Query query) {
-        return null;
-    }
+//    @Override
+//    public CellBaseDataResult stats(Query query) {
+//        return null;
+//    }
 
     @Override
     public CellBaseDataResult get(Query query, QueryOptions options) {
@@ -91,10 +91,10 @@ public Iterator nativeIterator(Query query, QueryOptions options) {
         return mongoDBCollection.nativeQuery().find(bson, options);
     }
 
-    @Override
-    public CellBaseDataResult rank(Query query, String field, int numResults, boolean asc) {
-        return null;
-    }
+//    @Override
+//    public CellBaseDataResult rank(Query query, String field, int numResults, boolean asc) {
+//        return null;
+//    }
 
     @Override
     public CellBaseDataResult groupBy(Query query, String field, QueryOptions options) {

diff --git a/cellbase-lib/src/main/java/org/opencb/cellbase/lib/impl/core/GeneMongoDBAdaptor.java b/cellbase-lib/src/main/java/org/opencb/cellbase/lib/impl/core/GeneMongoDBAdaptor.java
@@ -96,10 +96,10 @@ public CellBaseDataResult<String> distinct(Query query, String field) {
         return new CellBaseDataResult<>(mongoDBCollection.distinct(field, bsonDocument));
     }
 
-    @Override
-    public CellBaseDataResult stats(Query query) {
-        return null;
-    }
+//    @Override
+//    public CellBaseDataResult stats(Query query) {
+//        return null;
+//    }
 
     @Override
     public CellBaseDataResult<Gene> get(Query query, QueryOptions inputOptions) {
@@ -164,10 +164,10 @@ public void forEach(Query query, Consumer<? super Object> action, QueryOptions o
         }
     }
 
-    @Override
-    public CellBaseDataResult rank(Query query, String field, int numResults, boolean asc) {
-        return null;
-    }
+//    @Override
+//    public CellBaseDataResult rank(Query query, String field, int numResults, boolean asc) {
+//        return null;
+//    }
 
     @Override
     public CellBaseDataResult groupBy(Query query, String field, QueryOptions options) {

diff --git a/cellbase-lib/src/main/java/org/opencb/cellbase/lib/impl/core/GenomeMongoDBAdaptor.java b/cellbase-lib/src/main/java/org/opencb/cellbase/lib/impl/core/GenomeMongoDBAdaptor.java
@@ -286,10 +286,10 @@ public CellBaseDataResult distinct(Query query, String field) {
         return new CellBaseDataResult<>(mongoDBCollection.distinct(field, bson));
     }
 
-    @Override
-    public CellBaseDataResult stats(Query query) {
-        return null;
-    }
+//    @Override
+//    public CellBaseDataResult stats(Query query) {
+//        return null;
+//    }
 
     @Override
     public CellBaseDataResult get(Query query, QueryOptions options) {
@@ -314,10 +314,10 @@ public Iterator nativeIterator(Query query, QueryOptions options) {
         return mongoDBCollection.nativeQuery().find(bson, options);
     }
 
-    @Override
-    public CellBaseDataResult rank(Query query, String field, int numResults, boolean asc) {
-        return null;
-    }
+//    @Override
+//    public CellBaseDataResult rank(Query query, String field, int numResults, boolean asc) {
+//        return null;
+//    }
 
     @Override
     public CellBaseDataResult groupBy(Query query, String field, QueryOptions options) {

diff --git a/cellbase-lib/src/main/java/org/opencb/cellbase/lib/impl/core/MetaMongoDBAdaptor.java b/cellbase-lib/src/main/java/org/opencb/cellbase/lib/impl/core/MetaMongoDBAdaptor.java
@@ -56,10 +56,10 @@ public CellBaseDataResult distinct(Query query, String field) {
         return null;
     }
 
-    @Override
-    public CellBaseDataResult stats(Query query) {
-        return null;
-    }
+//    @Override
+//    public CellBaseDataResult stats(Query query) {
+//        return null;
+//    }
 
     @Override
     public CellBaseDataResult get(Query query, QueryOptions options) {
@@ -82,10 +82,10 @@ public Iterator nativeIterator(Query query, QueryOptions options) {
         return null;
     }
 
-    @Override
-    public CellBaseDataResult rank(Query query, String field, int numResults, boolean asc) {
-        return null;
-    }
+//    @Override
+//    public CellBaseDataResult rank(Query query, String field, int numResults, boolean asc) {
+//        return null;
+//    }
 
     @Override
     public CellBaseDataResult groupBy(Query query, String field, QueryOptions options) {