org.geneweaver.io.connector.Connector Maven / Gradle / Ivy
/*-
*
* Copyright 2018, 2020 The Jackson Laboratory Inc.
*
* 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.
*
* @author Matthew Gerring
*/
package org.geneweaver.io.connector;
import java.io.PrintStream;
import java.util.function.Function;
import java.util.stream.Stream;
import org.geneweaver.domain.Entity;
import org.neo4j.ogm.session.Session;
/**
* A function which runs to expand entities as they are being read.
* Examples of doing this:
* 1. Create a relationship between Transcript and Gene.
* 2. Create a VariantEffect back to an existing transcript.
* 3.
*
* @author gerrim
* @param Output of connection e.g. Produces or VariantEffect
* @param Input e.g. Transcript, Gene, Variant
*
* Function>
*/
public interface Connector extends Function> {
/**
* Simply calls 'stream(...)'
*/
default Stream apply(I entity) {
return stream(entity);
}
/**
* Create a stream from the entity. Note that if threads and
* multiple sessions are used the session should not be cached
* between calls of this method, or anything.
* @param entity From which we will create a stream of connections
* @param session The current session, NOTE multiple sessions may be active.
* @return Stream of connections including the original entity.
*/
default Stream stream(I entity) {
return stream(entity, null);
}
/**
* Create a stream from the entity. Note that if threads and
* multiple sessions are used the session should not be cached
* between calls of this method, or anything.
* @param entity From which we will create a stream of connections
* @param session The current session, NOTE multiple sessions may be active.
* @return Stream of connections including the original entity.
*/
default Stream stream(I ent, Session session) {
return stream(ent, session, null);
}
/**
* Create a stream from the entity. Note that if threads and
* multiple sessions are used the session should not be cached
* between calls of this method, or anything.
* @param entity From which we will create a stream of connections
* @param session The current session, NOTE multiple sessions may be active.
* @param log for logging usually set in a -v command line to generate more verbose messages. Null for a normal run.
* @return Stream of connections including the original entity.
*/
abstract Stream stream(I ent, Session session, PrintStream log);
}