Fix several bugs:

- handling relative pipeline interfaces
- handling null metadata attributes

R/constants.R

@@ -1,3 +1,5 @@
 kOldPipelinesSection = "pipelines_dir"
-kRelativeMetadataSections = c("output_dir", kOldPipelinesSection, 
-	"pipeline_interfaces", "results_subdir", "submission_subdir")
+kRelativeToOutputDirMetadataSections = c("results_subdir", "submission_subdir")
+
+kRelativeToConfigSections = c("metadata", "pipeline_config")
+

R/loadConfig.R

@@ -180,7 +180,7 @@ makeMetadataSectionAbsolute = function(config, parent) {
 	for (metadataAttribute in names(config$metadata)) {
 		value = config$metadata[[metadataAttribute]]
 
-		if (metadataAttribute %in% kRelativeMetadataSections) {
+		if (metadataAttribute %in% kRelativeToOutputDirMetadataSections) {
 			if (metadataAttribute == kOldPipelinesSection) {
 				warning(sprintf(
 					"Config contains old pipeline location specification section: '%s'", 
@@ -194,7 +194,7 @@ makeMetadataSectionAbsolute = function(config, parent) {
 		else { value = absViaParent(value) }    # No special handling
 
 		# Check for and warn about nonexistent path before setting value.
-		if (!(file.exists(value) | dir.exists(value))) {
+		if (!(!.isDefined(value) || file.exists(value) || dir.exists(value))) {
 			warning(sprintf("Value for '%s' doesn't exist: '%s'", metadataAttribute, value))
 		}
 		absoluteMetadata[[metadataAttribute]] = value

R/utils.R

@@ -6,6 +6,8 @@
 #
 #' @return	Target itself if already absolute, else target nested within parent.
 .makeAbsPath = function(perhapsRelative, parent) {
+	if (!.isDefined(perhapsRelative)) { return(perhapsRelative)}
+	perhapsRelative = expandPath(perhapsRelative)
 	if (.isAbsolute(perhapsRelative)) {
 		abspath = perhapsRelative
 	} else {
@@ -19,7 +21,9 @@
 	return(abspath)
 }
 
-.isDefined = function(var) { ! (is.na(var) | is.null(var)) }
+# Must test for is.null first, since is.na(NULL) returns a logical(0) which is
+# not a boolean
+.isDefined = function(var) { ! (is.null(var) || is.na(var)) }
 
 # Filesystem utilities