Fix failing tests

Signed-off-by: Ben Sherman <bentshermann@gmail.com>

modules/nextflow/src/main/groovy/nextflow/extension/PublishOp.groovy

@@ -21,7 +21,6 @@ import java.nio.file.Path
 import groovy.transform.CompileStatic
 import groovy.util.logging.Slf4j
 import groovyx.gpars.dataflow.DataflowReadChannel
-import nextflow.Global
 import nextflow.Session
 import nextflow.processor.PublishDir
 import nextflow.util.CsvWriter
@@ -35,6 +34,8 @@ import nextflow.util.CsvWriter
 @CompileStatic
 class PublishOp {
 
+    private Session session
+
     private DataflowReadChannel source
 
     private Map opts
@@ -49,9 +50,8 @@ class PublishOp {
 
     private volatile boolean complete
 
-    private Session getSession() { Global.session as Session }
-
-    PublishOp(DataflowReadChannel source, Map opts) {
+    PublishOp(Session session, DataflowReadChannel source, Map opts) {
+        this.session = session
         this.source = source
         this.opts = opts
         this.path = opts.path as String

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

@@ -198,7 +198,7 @@ abstract class BaseScript extends Script implements ExecutionContext {
         final ret = entryFlow.invoke_a(BaseScriptConsts.EMPTY_ARGS)
         if( !publisher )
             publisher = new OutputDef()
-        publisher.run(session.publishTargets)
+        publisher.run(session)
         session.notifyAfterWorkflowExecution()
         return ret
     }

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

@@ -19,6 +19,7 @@ package nextflow.script
 import groovy.transform.CompileStatic
 import groovy.util.logging.Slf4j
 import groovyx.gpars.dataflow.DataflowWriteChannel
+import nextflow.Session
 /**
  * Models the workflow output definition
  *
@@ -38,7 +39,7 @@ class OutputDef {
         this.closure = null
     }
 
-    void run(Map<DataflowWriteChannel,String> targets) {
+    void run(Session session) {
         final dsl = new OutputDsl()
         if( closure ) {
             final cl = (Closure)closure.clone()
@@ -47,7 +48,7 @@ class OutputDef {
             cl.call()
         }
 
-        dsl.build(targets)
+        dsl.build(session)
     }
 
 }

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

@@ -21,7 +21,6 @@ import java.nio.file.Path
 import groovy.transform.CompileStatic
 import groovy.util.logging.Slf4j
 import groovyx.gpars.dataflow.DataflowWriteChannel
-import nextflow.Global
 import nextflow.Session
 import nextflow.exception.ScriptRuntimeException
 import nextflow.extension.CH
@@ -37,8 +36,6 @@ import nextflow.file.FileHelper
 @CompileStatic
 class OutputDsl {
 
-    private Session session = Global.session as Session
-
     private Map<String,Map> targetConfigs = [:]
 
     private volatile List<PublishOp> ops = []
@@ -56,7 +53,8 @@ class OutputDsl {
         targetConfigs[name] = dsl.getOptions()
     }
 
-    void build(Map<DataflowWriteChannel,String> targets) {
+    void build(Session session) {
+        final targets = session.publishTargets
         final defaults = session.config.navigate('workflow.output', Collections.emptyMap()) as Map
 
         // construct mapping of target name -> source channels
@@ -86,7 +84,7 @@ class OutputDsl {
             final opts = publishOptions(name, defaults, overrides)
 
             if( opts.enabled == null || opts.enabled )
-                ops << new PublishOp(CH.getReadChannel(mixed), opts).apply()
+                ops << new PublishOp(session, CH.getReadChannel(mixed), opts).apply()
         }
     }
 

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

@@ -83,7 +83,10 @@ class BaseScriptTest extends Dsl2Spec {
         given:
         def script = Files.createTempFile('test',null)
         and:
-        def session = Mock(Session)
+        def session = Mock(Session) {
+            getPublishTargets() >> [:]
+            getConfig() >> [:]
+        }
         def binding = new ScriptBinding([:])
         def parser = new ScriptParser(session)
 
@@ -115,7 +118,10 @@ class BaseScriptTest extends Dsl2Spec {
         def module = folder.resolve('module.nf')
         def script = folder.resolve('main.nf')
         and:
-        def session = Mock(Session)
+        def session = Mock(Session) {
+            getPublishTargets() >> [:]
+            getConfig() >> [:]
+        }
         def binding = new ScriptBinding([:])
         def parser = new ScriptParser(session)
 

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

@@ -26,6 +26,7 @@ class OutputDslTest extends Specification {
         def file2 = work2.resolve('file2.txt'); file2.text = 'world'
         and:
         def session = Mock(Session) {
+            getPublishTargets() >> [:]
             getConfig() >> [
                 workflow: [
                     output: [
@@ -47,10 +48,8 @@ class OutputDslTest extends Specification {
         ch2.bind(file2)
         ch2.bind(Channel.STOP)
         and:
-        def targets = [
-            (ch1): 'foo',
-            (ch2): 'bar'
-        ]
+        session.publishTargets.put(ch1, 'foo')
+        session.publishTargets.put(ch2, 'bar')
         def dsl = new OutputDsl()
         and:
         SysEnv.push(NXF_FILE_ROOT: root.toString())
@@ -62,7 +61,7 @@ class OutputDslTest extends Specification {
                 path 'index.csv'
             }
         }
-        dsl.build(targets)
+        dsl.build(session)
 
         def now = System.currentTimeMillis()
         while( !dsl.complete ) {
@@ -74,13 +73,13 @@ class OutputDslTest extends Specification {
         then:
         outputDir.resolve('foo/file1.txt').text == 'Hello'
         outputDir.resolve('barbar/file2.txt').text == 'world'
-        outputDir.resolve('barbar/index.csv').text == """\
+        outputDir.resolve('index.csv').text == """\
             "file2","${outputDir}/barbar/file2.txt"
             """.stripIndent()
         and:
         1 * session.notifyFilePublish(outputDir.resolve('foo/file1.txt'), file1)
         1 * session.notifyFilePublish(outputDir.resolve('barbar/file2.txt'), file2)
-        1 * session.notifyFilePublish(outputDir.resolve('barbar/index.csv'))
+        1 * session.notifyFilePublish(outputDir.resolve('index.csv'))
 
         cleanup:
         SysEnv.pop()

modules/nextflow/src/test/groovy/nextflow/script/params/ParamsDsl2Test.groovy

@@ -110,7 +110,7 @@ class ParamsDsl2Test extends Dsl2Spec {
     def 'should allow unqualified stdin and stdout' () {
 
         given:
-        new Session()
+        def session = new Session()
         and:
         def config = new CompilerConfiguration()
         config.setScriptBaseClass(BaseScript.class.name)
@@ -131,7 +131,7 @@ class ParamsDsl2Test extends Dsl2Spec {
         '''
 
         when:
-        def binding = new ScriptBinding().setSession(Mock(Session))
+        def binding = new ScriptBinding().setSession(session)
         def script = (BaseScript)new GroovyShell(binding,config).parse(SCRIPT); script.run()
         and:
         def process = ScriptMeta.get(script).getProcess('alpha'); process.initialize()
@@ -151,7 +151,7 @@ class ParamsDsl2Test extends Dsl2Spec {
     def 'should allow unqualified tuple stdin and stdout' () {
 
         given:
-        new Session()
+        def session = new Session()
         and:
         def config = new CompilerConfiguration()
         config.setScriptBaseClass(BaseScript.class.name)
@@ -172,7 +172,7 @@ class ParamsDsl2Test extends Dsl2Spec {
         '''
 
         when:
-        def binding = new ScriptBinding().setSession(Mock(Session))
+        def binding = new ScriptBinding().setSession(session)
         def script = (BaseScript)new GroovyShell(binding,config).parse(SCRIPT); script.run()
         and:
         def process = ScriptMeta.get(script).getProcess('beta'); process.initialize()

plugins/nf-amazon/src/test/nextflow/extension/PublishOpS3Test.groovy

@@ -40,9 +40,8 @@ class PublishOpS3Test extends BaseSpec {
             getWorkDir() >> BASE
             getBucketDir() >> BUCKET_DIR
         }
-        Global.session = sess
 
-        def op = new PublishOp(Mock(DataflowReadChannel), [to:'/target'])
+        def op = new PublishOp(sess, Mock(DataflowReadChannel), [to:'/target'])
 
         when:
         def result = op.getTaskDir( BASE.resolve('xx/yyyy/this/and/that.txt') )