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A DSL modelled around the UNIX pipe concept, that simplifies writing parallel and scalable pipelines in a portable manner
/*
* Copyright 2013-2019, Centre for Genomic Regulation (CRG)
*
* 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 nextflow.util
import com.google.common.util.concurrent.RateLimiter
import groovy.transform.CompileStatic
import groovy.transform.EqualsAndHashCode
/**
* Model am execution rate limit measure unit
*
* @author Paolo Di Tommaso
*/
@CompileStatic
@EqualsAndHashCode(includeFields=true,includes='rate')
class RateUnit {
private static String RATE_FORMAT = ~/^(\d+\.?\d*)\s*([a-zA-Z]*)/
private double rate
static RateUnit of(String str) { new RateUnit(str) }
/**
* Create a rate unit by a double value representing the number of events per second
*
* @param rate The rate unit as a double value
*/
RateUnit(double rate) {
assert rate>0, "Rate unit must be greater than zero"
this.rate = rate
}
/**
* Create a rate unit using a string annotation as `10 sec` ie. 10 per second
* or `100 / 5 min` 100 events each 5 minutes
*
* @param str The rate string
*/
RateUnit(String str) {
this.rate = parse(str)
}
/**
* @return The actual rate unit as a double
*/
double getRate() { rate }
/**
* Create a {@link RateLimiter} object for rate unit
*
* @return An instance of {@link RateLimiter}
*/
RateLimiter getRateLimiter() { RateLimiter.create(rate) }
protected double parse(String limit) {
def tokens = limit.tokenize('/')
if( tokens.size() == 2 ) {
/*
* the rate limit is provide num of task over a duration
* - eg. 100 / 5 min
* - ie. max 100 task per 5 minutes
*/
final X = tokens[0].trim()
final Y = tokens[1].trim()
return parse0(X, Y, limit)
}
/*
* the rate limit is provide as a duration
* - eg. 200 min
* - ie. max 200 task per minutes
*/
final matcher = (limit =~ RATE_FORMAT)
if( !matcher.matches() )
throw new IllegalArgumentException("Invalid submit-rate-limit value: $limit -- It must be provide using the following format `num request sec|min|hour` eg. 10 sec ie. max 10 tasks per second")
final num = matcher.group(1) ?: '_'
final unit = matcher.group(2) ?: 'sec'
return parse0(num, "1 $unit", limit)
}
private double parse0(String X, String Y, String limit ) {
if( !X.isInteger() )
throw new IllegalArgumentException("Invalid submit-rate-limit value: $limit -- It must be provide using the following format `num request / duration` eg. 10/1s")
final num = Integer.parseInt(X)
final duration = Y.isInteger() ? Duration.of( Y+'sec' ) : ( Y[0].isInteger() ? Duration.of(Y) : Duration.of('1'+Y) )
long seconds = duration.toSeconds()
if( !seconds )
throw new IllegalArgumentException("Invalid submit-rate-limit value: $limit -- The interval must be at least 1 second")
num / seconds as double
}
String toString() {
String.format("%.2f", rate) + '/sec'
}
}