From 18e0f6f9773a620fd7a4acf7df2d3de7a5967dcc Mon Sep 17 00:00:00 2001
From: Julie Sullivan <julie.sullivan@gmail.com>
Date: Tue, 10 Mar 2020 16:22:58 +0000
Subject: [PATCH] add interfaces for common manager methods #528

---
 .../cellbase/lib/managers/AggregationApi.java | 34 +++++++++++++
 .../cellbase/lib/managers/FeatureApi.java     | 50 +++++++++++++++++++
 2 files changed, 84 insertions(+)
 create mode 100644 cellbase-lib/src/main/java/org/opencb/cellbase/lib/managers/AggregationApi.java
 create mode 100644 cellbase-lib/src/main/java/org/opencb/cellbase/lib/managers/FeatureApi.java

diff --git a/cellbase-lib/src/main/java/org/opencb/cellbase/lib/managers/AggregationApi.java b/cellbase-lib/src/main/java/org/opencb/cellbase/lib/managers/AggregationApi.java
new file mode 100644
index 0000000000..70c63159e9
--- /dev/null
+++ b/cellbase-lib/src/main/java/org/opencb/cellbase/lib/managers/AggregationApi.java
@@ -0,0 +1,34 @@
+/*
+ * Copyright 2015-2020 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.cellbase.lib.managers;
+
+import org.opencb.cellbase.core.api.queries.AbstractQuery;
+import org.opencb.cellbase.core.result.CellBaseDataResult;
+
+public interface AggregationApi<Q extends AbstractQuery, T> extends FeatureApi {
+
+    default CellBaseDataResult<T> groupBy(Q query) {
+        query.setCount(Boolean.FALSE);
+        return getDBAdaptor().groupBy(query);
+    }
+
+    default CellBaseDataResult<T> aggregationStats(Q query) {
+        query.setCount(Boolean.TRUE);
+        return getDBAdaptor().groupBy(query);
+    }
+
+}
diff --git a/cellbase-lib/src/main/java/org/opencb/cellbase/lib/managers/FeatureApi.java b/cellbase-lib/src/main/java/org/opencb/cellbase/lib/managers/FeatureApi.java
new file mode 100644
index 0000000000..6af8d793b5
--- /dev/null
+++ b/cellbase-lib/src/main/java/org/opencb/cellbase/lib/managers/FeatureApi.java
@@ -0,0 +1,50 @@
+/*
+ * Copyright 2015-2020 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.cellbase.lib.managers;
+
+import org.opencb.cellbase.core.api.core.CellBaseCoreDBAdaptor;
+import org.opencb.cellbase.core.api.queries.AbstractQuery;
+import org.opencb.cellbase.core.api.queries.QueryException;
+import org.opencb.cellbase.core.result.CellBaseDataResult;
+
+import java.util.Iterator;
+import java.util.List;
+
+public interface FeatureApi<Q extends AbstractQuery, T> {
+
+    CellBaseCoreDBAdaptor getDBAdaptor();
+
+    default CellBaseDataResult<T> search(Q query) throws QueryException, IllegalAccessException {
+        query.setDefaults();
+        query.validate();
+        return getDBAdaptor().query(query);
+    }
+
+    default List<CellBaseDataResult<T>> info(List<Q> geneQueries) {
+        List<CellBaseDataResult<T>> geneQueryResults = getDBAdaptor().query(geneQueries);
+        return geneQueryResults;
+    }
+
+    default CellBaseDataResult<String> distinct(Q query) {
+        query.setCount(Boolean.FALSE);
+        return getDBAdaptor().distinct(query);
+    }
+
+    default Iterator<T> iterator(Q query) {
+        return getDBAdaptor().iterator(query);
+    }
+}