feat: add maskFromPaths

Author: heuermh

src/main/groovy/nextflow/validation/config/SummaryConfig.groovy

@@ -39,6 +39,10 @@ class SummaryConfig implements ConfigScope {
     @Description('Mask /s3/bucket/ and s3://bucket/ from path values.')
     final public boolean maskBucketNames
 
+    @ConfigOption
+    @Description('A list of subpaths to mask from path values.')
+    final public List<CharSequence> maskFromPaths
+
     SummaryConfig(Map map, Boolean monochromeLogs) {
         Map config = map ?: Collections.emptyMap()
 
@@ -84,15 +88,33 @@ class SummaryConfig implements ConfigScope {
         }
 
         // maskFusionMount
-        if(config.containsKey("maskFusionMount")) {
-            maskFusionMount = config.maskFusionMount
-            log.debug("Set `maskFusionMount` to ${maskFusionMount}")
+        if(config.containsKey('maskFusionMount')) {
+            if(config.maskFusionMount instanceof Boolean) {
+                maskFusionMount = config.maskFusionMount
+                log.debug("Set `maskFusionMount` to ${maskFusionMount}")
+            } else {
+                log.warn('Incorrect value detected for `validation.summary.maskFusionMount`, a boolean is expected. Defaulting to `false`')
+            }
         }
 
         // maskBucketNames
-        if(config.containsKey("maskBucketNames")) {
-            maskBucketNames = config.maskBucketNames
-            log.debug("Set `maskBucketNames` to ${maskBucketNames}")
+        if(config.containsKey('maskBucketNames')) {
+            if(config.maskBucketNames instanceof Boolean) {
+                maskBucketNames = config.maskBucketNames
+                log.debug("Set `maskBucketNames` to ${maskBucketNames}")
+            } else {
+                log.warn('Incorrect value detected for `validation.summary.maskBucketNames`, a boolean is expected. Defaulting to `false`')
+            }
+        }
+
+        // maskFromPaths
+        if(config.containsKey('maskFromPaths')) {
+            if(config.maskFromPaths instanceof List<CharSequence>) {
+                maskFromPaths = config.maskFromPaths
+                log.debug("Set `maskFromPaths` to ${maskFromPaths}")
+            } else {
+                log.warn('Incorrect value detected for `validation.summary.maskFromPaths`, a list of strings is expected. Defaulting to ``')
+            }
         }
     }
 }

src/main/groovy/nextflow/validation/summary/SummaryCreator.groovy

@@ -50,12 +50,12 @@ class SummaryCreator {
             workflowSummary['container'] = workflow.container
         }
 
-        workflowSummary['launchDir']    = workflow.launchDir
-        workflowSummary['workDir']      = workflow.workDir
-        workflowSummary['projectDir']   = workflow.projectDir
+        workflowSummary['launchDir']    = maybeMask(workflow.launchDir)
+        workflowSummary['workDir']      = maybeMask(workflow.workDir)
+        workflowSummary['projectDir']   = maybeMask(workflow.projectDir)
         workflowSummary['userName']     = workflow.userName
         workflowSummary['profile']      = workflow.profile
-        workflowSummary['configFiles']  = workflow.configFiles ? workflow.configFiles.join(', ') : ''
+        workflowSummary['configFiles']  = maybeMask(workflow.configFiles ? workflow.configFiles.join(', ') : '')
 
         // Get pipeline parameters defined in JSON Schema
         Map paramsSummary = [:]
@@ -121,32 +121,49 @@ class SummaryCreator {
 
                 // We have a default in the schema, and this isn't it
                 if (defaultValue != null && value != defaultValue) {
-                    summary.put(param, maybeMaskFusionMount(maybeMaskBucketNames((value))))
+                    summary.put(param, maybeMask(value))
                 }
                 // No default in the schema, and this isn't empty or false
                 else if (defaultValue == null && value != '' && value != null && value != false && value != 'false') {
-                    summary.put(param, maybeMaskFusionMount(maybeMaskBucketNames((value))))
+                    summary.put(param, maybeMask(value))
                 }
             }
         }
         return summary
     }
 
-    private String maybeMaskFusionMount(String value) {
+    private CharSequence maybeMask(Path value) {
+        return maybeMask(value.toString())
+    }
+
+    private CharSequence maybeMask(CharSequence value) {
+        return maybeMaskFusionMount(maybeMaskBucketNames(maybeMaskFromPaths(value)))
+    }
+
+    private CharSequence maybeMaskFusionMount(CharSequence value) {
         if(config.summary.maskFusionMount) {
             return value.replace('/fusion', '')
         }
         return value
     }
 
     // see https://docs.aws.amazon.com/AmazonS3/latest/userguide/bucketnamingrules.html
-    static final String S3_BUCKET_PATH_PREFIX = '\\/s3\\/[a-z0-9][a-z0-9-]{1,61}[a-z0-9]\\/'
-    static final String S3_BUCKET_URI_PREFIX = 's3:\\/\\/[a-z0-9][a-z0-9-]{1,61}[a-z0-9]\\/'
+    static final CharSequence S3_BUCKET_PATH_PREFIX = '\\/s3\\/[a-z0-9][a-z0-9-]{1,61}[a-z0-9]\\/'
+    static final CharSequence S3_BUCKET_URI_PREFIX = 's3:\\/\\/[a-z0-9][a-z0-9-]{1,61}[a-z0-9]\\/'
 
-    private String maybeMaskBucketNames(String value) {
-        if (config.summary.maskBucketNames) {
-            value.replaceAll(S3_BUCKET_PATH_PREFIX, '')
-            value.replaceAll(S3_BUCKET_URI_PREFIX, '')
+    private CharSequence maybeMaskBucketNames(CharSequence value) {
+        if(config.summary.maskBucketNames) {
+            value = value.replaceAll(S3_BUCKET_PATH_PREFIX, '/[** masked **]/')
+            value = value.replaceAll(S3_BUCKET_URI_PREFIX, '[** masked **]/')
+        }
+        return value
+    }
+
+    private CharSequence maybeMaskFromPaths(CharSequence value) {
+        if(config.summary.maskFromPaths != null && config.summary.maskFromPaths.size() > 0) {
+            for (CharSequence toReplace : config.summary.maskFromPaths) {
+                value = value.replace(toReplace, '[** masked **]')
+            }
         }
         return value
     }