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A DSL modelled around the UNIX pipe concept, that simplifies writing parallel and scalable pipelines in a portable manner
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/*
* Copyright 2013-2024, Seqera Labs
*
* 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 java.util.regex.Pattern
import groovy.transform.CompileStatic
import nextflow.extension.Bolts
/**
* Validation helper
*
* @author Paolo Di Tommaso
*/
@CompileStatic
class CheckHelper {
/**
* Valid a method named parameters map
*
* @param name The name of the method, only in the error reported message
* @param params The actual parameters map
* @param valid A map providing for each parameter name the valid values
* @throws IllegalArgumentException when the parameter include an unexpected parameter name or value
*/
static void checkParams( String name, Map params, Map valid ) {
if( !params ) return
def allKeys = valid.keySet()
for( String key : params.keySet() ) {
if( !allKeys.contains(key) )
throw new IllegalArgumentException("Unknown argument '${key}' for operator '$name' -- Possible arguments: ${allKeys.join(', ')}")
final value = params.get(key)
final accepted = valid.get(key)
if( accepted instanceof Collection ) {
boolean ok = false
final itr = accepted.iterator()
while( !ok && itr.hasNext() )
ok |= isValid(value, itr.next())
if( !ok )
throw new IllegalArgumentException("Value '${value}' cannot be used in in parameter '${key}' for operator '$name' -- Possible values: ${(accepted as Collection).join(', ')}")
}
else if( !isValid(value, accepted) )
throw new IllegalArgumentException("Value '${value}' cannot be used in in parameter '${key}' for operator '$name' -- Value don't match: ${accepted}")
}
}
/**
* Check if the provide value is included in the specified range
*
* @param value A value to verify
* @param range The range it may be a {@link Class} a {@link Collection} of values, a regexp {@link Pattern} or a specific value
* @return {@code true} is the match is satisfied or {@code false} otherwise
*/
static boolean isValid( value, range ) {
if( range instanceof Class && value != null )
return range.isAssignableFrom(value.class)
if( range instanceof Collection )
return range.contains(value)
if( value != null && range instanceof Pattern )
return range.matcher(value.toString()).matches()
value == range
}
/**
* Verify that all method named parameters are included in the provided list
*
* @param name The method name used in the reported error message
* @param params The list of accepted named parameters
* @param valid The list of accepted parameter names
* @throws IllegalArgumentException a parameter is not included the in valid names list
*/
static void checkParams( String name, Map params, List valid ) {
if( !params ) return
for( String key : params.keySet() ) {
if( !valid.contains(key) ) {
def matches = Bolts.closest(valid,key) ?: valid
def message = "Unknown argument '${key}' for operator '$name'. Did you mean one of these?\n" + matches.collect { " $it"}.join('\n')
throw new IllegalArgumentException(message)
}
}
}
/**
* Verify that all method named parameters are included in the provided list
*
* @param name The method name used in the reported error message
* @param params The list of accepted named parameters
* @param valid The list of accepted parameter names
* @throws IllegalArgumentException a parameter is not included the in valid names list
*/
static void checkParams( String name, Map params, String... valid ) {
checkParams(name, params, Arrays.asList(valid))
}
}