Update e2e test

Signed-off-by: Ben Sherman <[email protected]>

Author: bentsherman

modules/nextflow/src/main/groovy/nextflow/config/ConfigBuilder.groovy

@@ -461,7 +461,7 @@ class ConfigBuilder {
      * @param file The source config file/snippet
      * @return
      */
-    protected validate(ConfigObject config, file, String parent=null, List stack = new ArrayList()) {
+    protected void validate(ConfigObject config, file, String parent=null, List stack = new ArrayList()) {
         for( String key : new ArrayList<>(config.keySet()) ) {
             final value = config.get(key)
             if( value instanceof ConfigObject ) {

modules/nextflow/src/main/groovy/nextflow/config/parser/v1/ConfigParserV1.groovy

@@ -110,6 +110,8 @@ class ConfigParserV1 implements ConfigParser {
 
     private Grengine grengine
 
+    private Map<String,Object> declaredParams
+
     @Override
     ConfigParser setProfiles(List<String> profiles) {
         final blockName = 'profiles'
@@ -129,7 +131,7 @@ class ConfigParserV1 implements ConfigParser {
 
     @Override
     Map<String,Object> getDeclaredParams() {
-        [:]
+        declaredParams
     }
 
     private Grengine getGrengine() {
@@ -469,6 +471,11 @@ class ConfigParserV1 implements ConfigParser {
         script.binding = binding
         script.run()
         config.merge(overrides)
+        declaredParams = config.params as Map ?: [:]
+
+        // prevent error thrown by ConfigBuilder::validate()
+        if( !config.params )
+            config.remove('params')
 
         return config
     }

modules/nextflow/src/main/groovy/nextflow/config/parser/v2/ConfigParserV2.groovy

@@ -140,6 +140,7 @@ class ConfigParserV2 implements ConfigParser {
         script.run()
 
         final target = script.getTarget()
+        // prevent error thrown by ConfigBuilder::validate()
         if( !target.params )
             target.remove('params')
         declaredProfiles = script.getDeclaredProfiles()

modules/nextflow/src/test/groovy/nextflow/config/parser/v1/ConfigParserV1Test.groovy

@@ -399,7 +399,7 @@ class ConfigParserV1Test extends Specification {
 
     }
 
-    def 'should return the set of visited block names' () {
+    def 'should return the set of declared profiles' () {
 
         given:
         def text = '''
@@ -426,6 +426,35 @@ class ConfigParserV1Test extends Specification {
         slurper.getDeclaredProfiles() == ['alpha','beta'] as Set
     }
 
+    def 'should return the map of declared params' () {
+
+        given:
+        def text = '''
+        params {
+            a = 1
+            b = 2
+        }
+
+        profiles {
+            alpha {
+                params.a = 3
+            }
+        }
+        '''
+
+        when:
+        def slurper = new ConfigParserV1().setProfiles(['standard'])
+        slurper.parse(text)
+        then:
+        slurper.getDeclaredParams() == [a: 1, b: 2]
+
+        when:
+        slurper = new ConfigParserV1().setProfiles(['alpha'])
+        slurper.parse(text)
+        then:
+        slurper.getDeclaredParams() == [a: 3, b: 2]
+    }
+
     def 'should disable includeConfig parsing' () {
         given:
         def text = '''

modules/nextflow/src/test/groovy/nextflow/config/parser/v2/ConfigParserV2Test.groovy

@@ -374,7 +374,7 @@ class ConfigParserV2Test extends Specification {
 
     }
 
-    def 'should return the set of parsed profiles' () {
+    def 'should return the set of declared profiles' () {
 
         given:
         def text = '''
@@ -401,6 +401,35 @@ class ConfigParserV2Test extends Specification {
         slurper.getDeclaredProfiles() == ['alpha','beta'] as Set
     }
 
+    def 'should return the map of declared params' () {
+
+        given:
+        def text = '''
+        params {
+            a = 1
+            b = 2
+        }
+
+        profiles {
+            alpha {
+                params.a = 3
+            }
+        }
+        '''
+
+        when:
+        def slurper = new ConfigParserV2().setParams([c: 4])
+        slurper.parse(text)
+        then:
+        slurper.getDeclaredParams() == [a: 1, b: 2]
+
+        when:
+        slurper = new ConfigParserV2().setParams([c: 4]).setProfiles(['alpha'])
+        slurper.parse(text)
+        then:
+        slurper.getDeclaredParams() == [a: 3, b: 2]
+    }
+
     def 'should ignore config includes when specified' () {
         given:
         def text = '''

tests/checks/params-dsl.nf/.checks

@@ -1,15 +1,22 @@
 
 echo "Test successful run"
-$NXF_RUN --input ./data | tee stdout
+$NXF_RUN --input ./data &> stdout
+
+[[ $(grep -c 'params.input = [./data]' stdout) == 1 ]] || false
+[[ $(grep -c 'params.save_intermeds = false' stdout) == 1 ]] || false
 
-echo
 echo "Test missing required param"
-$NXF_RUN | tee stdout
+$NXF_RUN &> stdout
+
+[[ $(grep -c 'Parameter `input` is required' stdout) == 1 ]] || false
 
-echo
 echo "Test overwrite script param from config profile"
-$NXF_RUN -c ../../params-dsl.config -profile test | tee stdout
+$NXF_RUN -c ../../params-dsl.config -profile test &> stdout
+
+[[ $(grep -c 'params.input = [alpha, beta, delta]' stdout) == 1 ]] || false
+[[ $(grep -c 'params.save_intermeds = true' stdout) == 1 ]] || false
 
-echo
 echo "Test invalid param"
-$NXF_RUN --inputs ./data | tee stdout
+$NXF_RUN --inputs ./data &> stdout
+
+[[ $(grep -c 'Parameter `inputs` was specified' stdout) == 1 ]] || false

tests/params-dsl.config

@@ -4,5 +4,6 @@ params.outdir = 'results'
 profiles {
     test {
         params.input = 'alpha,beta,delta'
+        params.save_intermeds = true
     }
 }