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The IO bundle for Geneweaver.
/*-
*
* 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;
import java.util.Objects;
import java.util.concurrent.TimeUnit;
// TODO: Auto-generated Javadoc
/**
* The Class Configuration.
*/
public class Configuration {
/**
* Set to true to zip each partition.
*/
private volatile ZipType zipType = ZipType.valueOf(System.getenv().getOrDefault("PARTITION_ZIP", "GZ"));
/**
* The number of lines in each partition.
*/
private volatile int partitionLines = Integer.parseInt(System.getenv().getOrDefault("PARTITION_LINES", "10000"));
/**
* Length of timeout when shutting down notification pool.
*/
private volatile long timeout=Integer.parseInt(System.getenv().getOrDefault("PARTITION_TIMEOUT", "30"));
/**
* Number of background runs which may be running the visitors (which upload files).
*/
private volatile int permits = Integer.parseInt(System.getenv().getOrDefault("SIMULTANEOUS_UPLOAD_PERMITS", "10"));
/**
* Timeout unit.
*/
private volatile TimeUnit unit=TimeUnit.SECONDS;
/**
* Gets the default.
*
* @return the default
*/
public static Configuration getDefault() {
return new Configuration();
}
/**
* Gets the timeout.
*
* @return the timeout
*/
public long getTimeout() {
return timeout;
}
/**
* Sets the timeout.
*
* @param timeout the timeout to set
* @return the configuration
*/
public Configuration setTimeout(long timeout) {
this.timeout = timeout;
return this;
}
/**
* Gets the unit.
*
* @return the unit
*/
public TimeUnit getUnit() {
return unit;
}
/**
* Sets the unit.
*
* @param unit the unit to set
* @return the configuration
*/
public Configuration setUnit(TimeUnit unit) {
this.unit = unit;
return this;
}
/**
* Hash code.
*
* @return the int
*/
@Override
public int hashCode() {
return Objects.hash(partitionLines, timeout, unit, zipType);
}
/**
* Equals.
*
* @param obj the obj
* @return true, if successful
*/
@Override
public boolean equals(Object obj) {
if (this == obj)
return true;
if (!(obj instanceof Configuration))
return false;
Configuration other = (Configuration) obj;
return partitionLines == other.partitionLines && timeout == other.timeout && unit == other.unit
&& zipType == other.zipType;
}
/**
* Gets the partition lines.
*
* @return the partition lines
*/
public int getPartitionLines() {
return partitionLines;
}
/**
* Sets the partition lines.
*
* @param partitionLines the partition lines
* @return the configuration
*/
public Configuration setPartitionLines(int partitionLines) {
this.partitionLines = partitionLines;
return this;
}
/**
* The Enum FileType.
*/
public enum FileType {
/** The gene. */
/*
* Genes, Transcripts and the others.
* Smallish file.
*/
GENE,
/**
* Variant files.
*/
VARIANT,
/**
* If the file type is not known.
* File type will be analysed by file extension if it
* is not known.
*/
UNKNOWN
}
/**
* The Enum ZipType.
*/
public enum ZipType {
/** The none. */
NONE("text/plain"),
/** The zip. */
ZIP("application/zip"),
/** The gz. */
GZ("application/gzip");
/** The ctype. */
private String ctype;
/**
* Instantiates a new zip type.
*
* @param ctype the ctype
*/
ZipType(String ctype) {
this.ctype = ctype;
}
/**
* Gets the content type.
*
* @return the content type
*/
public String getContentType() {
return ctype;
}
}
/**
* Gets the zip type.
*
* @return the zipType
*/
public ZipType getZipType() {
return zipType;
}
/**
* Sets the zip type.
*
* @param zipType the zipType to set
* @return the configuration
*/
public Configuration setZipType(ZipType zipType) {
this.zipType = zipType;
return this;
}
/**
* Gets the permits.
*
* @return the permits
*/
public int getPermits() {
return permits;
}
/**
* Sets the permits.
*
* @param permits the permits to set
*/
public void setPermits(int permits) {
this.permits = permits;
}
}