Don't save kebab-case aliases in the params map

modules/nextflow/src/main/groovy/nextflow/cli/CmdRun.groovy

@@ -43,6 +43,8 @@ import nextflow.plugin.Plugins
 import nextflow.scm.AssetManager
 import nextflow.script.ScriptFile
 import nextflow.script.ScriptRunner
+import nextflow.secret.SecretsLoader
+import nextflow.util.AliasMap
 import nextflow.util.CustomPoolFactory
 import nextflow.util.Duration
 import nextflow.util.HistoryFile
@@ -619,7 +621,7 @@ class CmdRun extends CmdBase implements HubOptions {
     @Memoized  // <-- avoid parse multiple times the same file and params
     Map parsedParams(Map configVars) {
 
-        final result = [:]
+        final result = new AliasMap()
         final file = getParamsFile()
         if( file ) {
             def path = validateParamsFile(file)
@@ -634,7 +636,7 @@ class CmdRun extends CmdBase implements HubOptions {
         if( !params )
             return result
 
-        for( Map.Entry<String,String> entry : params ) {
+        for( def entry : params ) {
             addParam( result, entry.key, entry.value )
         }
         return result

modules/nextflow/src/main/groovy/nextflow/script/ScriptBinding.groovy

@@ -25,7 +25,6 @@ import groovy.util.logging.Slf4j
 import nextflow.NF
 import nextflow.Session
 import nextflow.exception.AbortOperationException
-import org.apache.commons.lang.StringUtils
 /**
  * Defines the script execution context. By default provided the following variables
  * <li>{@code __$session}: the current execution session
@@ -202,23 +201,17 @@ class ScriptBinding extends WorkflowBinding {
     }
 
     /**
-     * Holds parameter immutable values
+     * Implements immutable params map
      */
     @CompileStatic
     static class ParamsMap implements Map<String,Object> {
 
-        private Set<String> readOnlyNames
-
-        private List<String> realNames
-
         private List<String> scriptAssignment = []
 
         @Delegate
         private Map<String,Object> target
 
         ParamsMap() {
-            readOnlyNames = []
-            realNames = []
             target = new LinkedHashMap<>()
         }
 
@@ -227,23 +220,15 @@ class ScriptBinding extends WorkflowBinding {
             putAll(values)
         }
 
-        private ParamsMap(ParamsMap template, Map overrides) {
-            this(template)
-            allowNames(overrides.keySet())
-            putAll(overrides)
-        }
+        private ParamsMap(ParamsMap values, Map<String,?> overrides) {
+            this(values)
 
-        ParamsMap copyWith(Map overrides) {
-            return new ParamsMap(this, overrides)
+            for( def entry : overrides )
+                put0(entry.key, entry.value, true)
         }
 
-        private ParamsMap allowNames(Set names) {
-            for( String name : names ) {
-                final name2 = name.contains('-') ? hyphenToCamelCase(name) : camelCaseToHyphen(name)
-                readOnlyNames.remove(name)
-                readOnlyNames.remove(name2)
-            }
-            return this
+        ParamsMap copyWith(Map<String,?> overrides) {
+            return new ParamsMap(this, overrides)
         }
 
         @Override
@@ -269,142 +254,26 @@ class ScriptBinding extends WorkflowBinding {
         @Override
         String put(String name, Object value) {
             assert name
-            (name in scriptAssignment
-                    ? log.warn("`params.$name` is defined multiple times -- Assignments following the first are ignored")
-                    : scriptAssignment << name )
+            if( name in scriptAssignment )
+                log.warn("`params.$name` is defined multiple times -- Assignments following the first are ignored")
+            else
+                scriptAssignment << name
             return put0(name,value)
         }
 
-        private String put0(String name, Object value) {
-
-            // keep track of the real name
-            realNames << name
-
-            // normalize the name
-            def name2 = name.contains('-') ? hyphenToCamelCase(name) : camelCaseToHyphen(name)
-
-            final readOnly = name in readOnlyNames || name2 in readOnlyNames
-
-            def result = null
-            if( !readOnly ) {
-                readOnlyNames << name
-                readOnlyNames << name2
-                result = target.put(name, value)
-                target.put(name2, value)
-            }
-
-            return result
+        private String put0(String name, Object value, boolean allowOverride=false) {
+            return allowOverride || !target.containsKey(name)
+                ? target.put(name, value)
+                : null
         }
 
         @Override
-        void putAll(Map other) {
-            for( Entry<String,Object> entry : other.entrySet() ) {
+        void putAll(Map<String,Object> other) {
+            for( def entry : other.entrySet() ) {
                 put0(entry.getKey(), entry.getValue())
             }
         }
 
-        /**
-         * Renders a string containing all name-value pairs as a command line string
-         *
-         * @param opts String formatting options:
-         *   {@code sep}: the key-value pair separator
-         *   {@code quote}: the character to be used to quote the parameter value
-         *   {@code prefix}: the character(s) prepended to the parameter key
-         *
-         * @return A command line formatted string e.g. {@code --foo x --bar y}
-         */
-        String all(Map opts = null) {
-
-            String sep = opts?.sep ?: ' '
-            String quote = opts?.quote ?: ''
-            String prefix = opts?.prefix ?: '--'
-
-            def result = []
-            realNames.each {
-                result << ("$prefix$it$sep${wrap(this.get(it).toString(), quote)}".toString())
-            }
-            return result.join(' ')
-        }
-
-        /**
-         * Wrap a string value with quote characters
-         *
-         * @param str The string with value to be wrapped by quote characters
-         * @param quote The quote character
-         * @return The quoted string
-         */
-        @PackageScope
-        static String wrap( String str, String quote ) {
-            if( !quote && (str.contains(' ') || str.contains('"') || str.contains("'") ))
-                quote = '"'
-
-            if( !quote )
-                return str
-
-            def result = new StringBuilder()
-            result.append(quote)
-            str.each {
-                result.append( it == quote ? '\\'+quote : it )
-            }
-            result.append(quote)
-            return result.toString()
-        }
-
-        /**
-         *  Converts a string containing words separated by a hyphen character to a camelCase string
-         *
-         * @param str The string to be converted
-         * @return
-         */
-        @PackageScope
-        static String hyphenToCamelCase( String str ) {
-
-            if( !str ) { return str }
-
-            def result = new StringBuilder()
-            str.split('-').eachWithIndex{ String entry, int i ->
-                result << (i>0 ? StringUtils.capitalize(entry) : entry )
-            }
-
-            return result.toString()
-        }
-
-        /**
-         * Converts a camel-case string to a string where words are separated by hyphen character
-         *
-         * @param str The string to be converted
-         * @return A string where camel-case words are converted to words separated by hyphen character
-         */
-        @PackageScope
-        static String camelCaseToHyphen( String str ) {
-
-            def lower = 'a'..'z'
-            def upper = 'A'..'Z'
-
-            def result = new StringBuilder()
-            if( !str ) {
-                return str
-            }
-
-            result << str[0]
-            for( int i=1; i<str.size(); i++ ) {
-                if( str[i] in upper && str[i-1] in lower  ) {
-                    result << '-'
-                    if( i+1<str.size() && str[i+1] in lower ) {
-                        result << str[i].toLowerCase()
-                    }
-                    else {
-                        result << str[i]
-                    }
-                }
-                else {
-                    result << str[i]
-                }
-            }
-
-            return result.toString()
-        }
-
     }
 
 }

modules/nextflow/src/test/groovy/nextflow/script/ScriptBindingTest.groovy

@@ -75,65 +75,30 @@ class ScriptBindingTest extends Specification {
 
     }
 
-    def 'should convert hyphen separated string to camel case' () {
-
-        expect:
-        ScriptBinding.ParamsMap.hyphenToCamelCase('a') == 'a'
-        ScriptBinding.ParamsMap.hyphenToCamelCase('A') == 'A'
-        ScriptBinding.ParamsMap.hyphenToCamelCase('a-b-c-') == 'aBC'
-        ScriptBinding.ParamsMap.hyphenToCamelCase('aa-bb-cc') == 'aaBbCc'
-        ScriptBinding.ParamsMap.hyphenToCamelCase('alpha-beta-delta') == 'alphaBetaDelta'
-        ScriptBinding.ParamsMap.hyphenToCamelCase('Alpha-Beta-delta') == 'AlphaBetaDelta'
-
-    }
-
-    def 'should convert camel case string to hyphen separated' () {
-
-        expect:
-        ScriptBinding.ParamsMap.camelCaseToHyphen('alphaBetaDelta') == 'alpha-beta-delta'
-        ScriptBinding.ParamsMap.camelCaseToHyphen('AlphaBetaDelta') == 'Alpha-beta-delta'
-        ScriptBinding.ParamsMap.camelCaseToHyphen('Field1') == 'Field1'
-        ScriptBinding.ParamsMap.camelCaseToHyphen('FieldUno') == 'Field-uno'
-        ScriptBinding.ParamsMap.camelCaseToHyphen('FieldUNO') == 'Field-UNO'
-        ScriptBinding.ParamsMap.camelCaseToHyphen('FieldA') == 'Field-A'
-        ScriptBinding.ParamsMap.camelCaseToHyphen('FieldAB') == 'Field-AB'
-        ScriptBinding.ParamsMap.camelCaseToHyphen('FieldAb') == 'Field-ab'
-
-    }
-
     def 'should put an entry in the params map' () {
 
         when:
         def map = new ScriptBinding.ParamsMap()
         map['alphaBeta'] = 1
         map['alphaBeta'] = 2
-        map['alpha-beta'] = 3
-
         then:
         map['alphaBeta'] == 1
-        map['alpha-beta'] == 1
-
 
         when:
         map = new ScriptBinding.ParamsMap()
-        map['aaa-bbb-ccc'] = 1
         map['aaaBbbCcc'] = 10
         map['AaaBbbCcc'] = 20
-
         then:
-        map['aaaBbbCcc'] == 1
-        map['aaa-bbb-ccc'] == 1
-
+        map['aaaBbbCcc'] == 10
+        map['AaaBbbCcc'] == 20
 
         when:
         map = new ScriptBinding.ParamsMap()
         map['field1'] = 1
         map['field2'] = 2
         map['Field2'] = 3
-
         then:
         map['field1'] == 1
-        map['field-1'] == null
         map['field2']  == 2
         map['Field2']  == 3
 
@@ -151,7 +116,6 @@ class ScriptBindingTest extends Specification {
         then:
         map.alpha == 0
         map.alphaBeta == 0
-        map.'alpha-beta' == 0
         map.delta == 2
         map.gamma == 3
 
@@ -160,68 +124,17 @@ class ScriptBindingTest extends Specification {
         then:
         copy.foo == 1
         copy.alphaBeta == 4
-        copy.'alpha-beta' == 4
         copy.delta == 2
         copy.gamma == 3
         copy.omega == 9
         and:
         // source does not change
         map.alpha == 0
         map.alphaBeta == 0
-        map.'alpha-beta' == 0
         map.delta == 2
         map.gamma == 3
         !map.containsKey('omega')
 
     }
 
-    def 'should wrap a string value with quote character' () {
-
-        expect:
-        ScriptBinding.ParamsMap.wrap('hello',null) == 'hello'
-        ScriptBinding.ParamsMap.wrap('hello','"') == '"hello"'
-        ScriptBinding.ParamsMap.wrap('hello world',null) == '"hello world"'
-        ScriptBinding.ParamsMap.wrap('hello world',"'") == "'hello world'"
-        ScriptBinding.ParamsMap.wrap('hello"world',"'") == "'hello\"world'"
-        ScriptBinding.ParamsMap.wrap('hello"world',null) == '"hello\\"world"'
-
-    }
-
-    def 'should return a command line formatted string'() {
-
-        when:
-        def params = new ScriptBinding.ParamsMap('foo-bar':1)
-        then:
-        params.size() == 2
-        params.fooBar == 1
-        params.'foo-bar' == 1
-        params.all() == '--foo-bar 1'
-
-        expect:
-        new ScriptBinding.ParamsMap(x:1).all() == '--x 1'
-        new ScriptBinding.ParamsMap(x:1, y: 2).all() == '--x 1 --y 2'
-        new ScriptBinding.ParamsMap(x:1, y: 2).all(sep:'=') == '--x=1 --y=2'
-        new ScriptBinding.ParamsMap(x:1, y: 2).all(sep:'=', prefix:'-') == '-x=1 -y=2'
-        new ScriptBinding.ParamsMap(x:1, y: 'hello world').all() == '--x 1 --y "hello world"'
-        new ScriptBinding.ParamsMap(x:1, y: 'hello world').all(quote:"'") == '--x \'1\' --y \'hello world\''
-        new ScriptBinding.ParamsMap(x:1, y: "O'Connors").all(quote:"'") == "--x '1' --y 'O\\'Connors'"
-
-    }
-
-    def 'should get the variable name giving the value'() {
-
-        given:
-        def X=1
-        def Y='hello'
-        def binding = new ScriptBinding([:])
-        binding.setVariable('foo', X)
-        binding.setVariable('bar', Y)
-
-        expect:
-        binding.getVariableName(X) == 'foo'
-        binding.getVariableName(Y) == 'bar'
-        binding.getVariableName(new String(Y)) == null
-        binding.getVariableName(null) == null
-    }
-
 }