fix erroneous messages printed about pre-existing files after run fin…

…ished

src/main/groovy/bpipe/Dependencies.groovy

@@ -56,7 +56,7 @@ class Dependencies {
     /**
      * List of output files created in *this run*
      */
-    List<String> outputFilesGenerated = []
+    List<PipelineFile> outputFilesGenerated = []
 
     /**
      * List of files whose timestamps are overridden, so that their real

src/main/groovy/bpipe/Pipeline.groovy

@@ -1621,20 +1621,13 @@ public class Pipeline implements ResourceRequestor {
 
         Dependencies.instance.reset()
         def graph = Dependencies.instance.outputGraph
-        List all = Dependencies.instance.findLeaves(graph)*.values.flatten()*.outputPath
+        List<PipelineFile> leaves = Dependencies.instance.findLeaves(graph)*.values.flatten()*.outputFile
 
         Utils.time("Save output graph") {
             Dependencies.instance.saveOutputGraphCache()
         }
 
-        def runFiles = Dependencies.instance.outputFilesGenerated
-
-        // Sort to put files generated by this run first
-        all = all.sort {runFiles.contains(it) ? 0 : 1 }
-                 // Remove files that don't exist any more
-                 .grep { it && new File(it).exists() }.
-                 // Add 'pre-existing' for files that were not generated by this Bpipe run
-                 collect { runFiles.contains(it) ? it : it + ' (pre-existing)' }
+        List<String> all = formatOutputFiles(leaves)
 
         if(all.size() == 1) {
             log.info "Output is " + all[0]
@@ -1655,6 +1648,29 @@ public class Pipeline implements ResourceRequestor {
         }
         rootContext.outputLog.flush()
     }
+
+    @CompileStatic
+    private List<String> formatOutputFiles(List<PipelineFile> all) {
+
+        final Map<String, PipelineFile> runFiles = Dependencies.theInstance.outputFilesGenerated.collectEntries {
+            [ it.toString(), it]
+        }
+
+        List<String> result = (List<String>)all
+
+            // Sort to put files generated by this run first
+            .sort { runFiles.containsKey(it?.toString()) ? 0 : 1 }
+
+            // Remove files that don't exist any more
+            .grep { PipelineFile pf -> pf && pf.exists() }
+
+            // Add 'pre-existing' for files that were not generated by this Bpipe run
+            .collect {
+                runFiles.containsKey(it.toString()) ? it : (it.toString() + ' (pre-existing)')
+            }
+
+        return result
+    }
 
     /**
      * Convenience function to convert the given string to a file.

tests/print_created_files/cleanup.sh

@@ -0,0 +1 @@
+rm -rf .bpipe test.*.csv test.*.xml 

tests/print_created_files/run.sh

@@ -0,0 +1,22 @@
+source ../testsupport.sh
+
+set -e
+
+bpipe run test2.groovy test.txt   > test.out
+
+grep -q 'Output is test.hello.csv' test.out || err "did not print expected message about output"
+grep -q 'pre-existing' test.out && err "printed output as pre-existing when not"
+
+bpipe run -p worldy=true test2.groovy test.txt > test2.out
+
+grep -q 'Outputs are:' test2.out || err "did not print expected message about output"
+grep -q 'test.world.xml' test2.out || err "did not print expected message about output file"
+grep -q 'xml.*pre-existing' test2.out && err "printed output as pre-existing when not"
+grep -q 'csv.*pre-existing' test2.out || err "did not print CSV outout as pre-existing when it was"
+
+true
+
+
+
+
+

tests/print_created_files/test1.groovy

@@ -0,0 +1,9 @@
+hello = {
+    exec """
+        cp $input.txt $output.xml
+    """
+}
+
+run {
+    hello
+}

tests/print_created_files/test2.groovy

@@ -0,0 +1,20 @@
+hello = {
+    exec """
+        cp $input.txt $output.csv
+    """
+}
+
+world = {
+    var worldy: false
+
+    if(worldy) {
+        exec """
+            cp $input.txt $output.xml
+        """
+    }
+}
+
+run {
+    hello + world
+}
+