/*
Copyright 2014 Google Inc. All rights reserved.
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 com.google.cloud.genomics.api.client.commands;
import com.beust.jcommander.Parameter;
import com.beust.jcommander.Parameters;
import com.google.api.services.genomics.Genomics;
import com.google.api.services.genomics.model.Dataset;
import com.google.api.services.genomics.model.SearchCallSetsRequest;
import com.google.cloud.genomics.utils.Paginator;
import com.google.common.collect.Lists;
import java.io.IOException;
@Parameters(commandDescription = "Search over call sets")
public class SearchCallSetsCommand extends SearchCommand {
@Parameter(names = "--variant_set_id",
description = "The Genomics API variant set ID to get call sets for.",
required = true)
public String datasetId;
@Parameter(names = "--name",
description = "Only return call sets for which a substring of the name matches this string.")
public String name;
@Override
public void handleRequest(Genomics genomics) throws IOException {
Dataset dataset = getDataset(genomics, datasetId);
if (dataset == null) {
return;
}
System.out.println("Getting call sets from: " + dataset.getName());
SearchCallSetsRequest request = new SearchCallSetsRequest()
.setVariantSetIds(Lists.newArrayList(datasetId))
.setName(name)
.setPageSize(getMaxResults());
printResults(Paginator.Callsets.create(genomics), request);
}
}