- Supports multiple extensions per type

Author: Alan Christie

.gitignore

@@ -10,6 +10,6 @@ dist
 work
 .nextflow
 .nextflow.log*
-/tmp
+**/tmp
 **/*.egg-info
 **/.DS_Store

src/groovy/MediaChecker.groovy

@@ -55,16 +55,26 @@ class MediaChecker {
         def opDescriptors = serviceDescriptor.serviceConfig.outputDescriptors
         opDescriptors.each { desc ->
 
-            // Expected extension...
-            // (use the media type to lookup it up)
-            // And construct full path to the expected file...
-            String opExt = mediaTypesLookup.media_type[desc.mediaType]
-            String opName = desc.name + opExt
-            String opPath = path.toString() + File.separator + opName
-            if (!new File(opPath).exists()) {
-                Log.err("The pipeline's 'outputDescriptor'" +
-                        " expected '$opName' but the file wasn't found")
-                retVal = false
+            // There must be a matching media type in our txt/lookup file.
+            def typeExtList = mediaTypesLookup.media_types[desc.mediaType]
+            if (typeExtList == null || typeExtList.size() == 0) {
+                Log.err("Pipeline service descriptor output mediaType" +
+                        " '$desc.mediaType' is not listed in '$mediaTypesFile'")
+            } else {
+                // What are the expected file extensions for this media type?
+                // It's a list of 1 or more entries.
+                typeExtList.each { extension ->
+
+                    String opName = desc.name + extension
+                    Log.info('Media check', opName)
+                    String opPath = path.toString() + File.separator + opName
+                    if (!new File(opPath).exists()) {
+                        Log.err("The pipeline's 'outputDescriptor'" +
+                                " expected '$opName' but the file wasn't found")
+                        retVal = false
+                    }
+
+                }
             }
 
         }

src/groovy/MediaTypes.txt

@@ -4,15 +4,15 @@
 //
 // Read by MediaChecker.groovy
 
-media_type = [
+media_types = [
 
     // Please keep the keys in alphabetical order...
 
-    'application/x-squonk-dataset-molecule+json': '.data.gz',
-    'application/x-squonk-dataset-basic+json': '.data.gz',
+    'application/x-squonk-dataset-molecule+json': ['.data.gz', '.metadata'],
+    'application/x-squonk-dataset-basic+json': ['.data.gz', '.metadata'],
 
-    'image/gif': '.gif',
-    'image/jpeg': '.jpg',
-    'image/png': '.png',
+    'image/gif': ['.gif'],
+    'image/jpeg': ['.jpg'],
+    'image/png': ['.png'],
 
 ]

src/groovy/Tester.groovy

@@ -130,7 +130,7 @@ class Tester {
             filesUsed += 1
 
             Log.separate()
-            Log.info('File', currentTestFilename)
+            Log.info('Test file', currentTestFilename)
             // Collect the files we find...
             if (!observedFiles.contains(currentTestFilename)) {
                 observedFiles.add(currentTestFilename)
@@ -635,8 +635,8 @@ class Tester {
         File testOutputPath = new File(test_pout)
         testOutputPath.mkdir()
 
-        Log.info('Input', test_pin)
-        Log.info('Output', test_pout)
+        Log.info('Input path', test_pin)
+        Log.info('Output path', test_pout)
 
         // Redirect the '-o' option, if there is a '-o' in the command
         def oOption = pipelineCommand =~ /$outputRegex/