- in execute(), when cache does already exist, make it clean before e…

…xecuting

the pipeline steps (= preventing inconsistent cache upon crash/forced
interruption)
- bumped version to 1.3.4

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: CytoPipeline
 Title: Automation and visualization of flow cytometry data analysis pipelines
-Version: 1.3.3
+Version: 1.3.4
 Authors@R:
     c(person(given = "Philippe",
              family = "Hauchamps",

NEWS.md

@@ -1,5 +1,10 @@
 # CytoPipeline 1.3
 
+## CytoPipeline 1.3.4
+- in execute(), when cache does already exist, make it clean before executing 
+the pipeline steps (= preventing inconsistent cache upon crash/forced 
+interruption)
+
 ## CytoPipeline 1.3.3
 - added `collectNbOfRetainedEvents()` function
 

R/CytoPipeline-functions.R

@@ -312,6 +312,20 @@ showProcessingSteps <- function(x,
     }
 }
 
+# internal function to remove ill-defined bfc entries ("type" col is NA)
+# which could have been generated when a previous pipeline run 
+# either crashed or was manually forced to stop in the middle of a step
+makeBFCClean <- function(bfc){
+    cacheInfo <- BiocFileCache::bfcinfo(bfc)
+    if (nrow(cacheInfo) > 0) {
+        toRemoveRids <- cacheInfo[is.na(cacheInfo$type),"rid"]
+        if (nrow(toRemoveRids) > 0) {
+            bfc <- BiocFileCache::bfcremove(bfc, toRemoveRids)    
+        }
+    }
+    invisible(bfc)
+}
+
 
 #' @title executing CytoPipeline object
 #' @description this function triggers the execution of the processing queues of
@@ -619,6 +633,10 @@ execute <- function(x,
             bfc <- BiocFileCache::BiocFileCache(localCacheDir, ask = FALSE)
         }
     }
+
+    # for robustness-sake, clean bfc from potentially interrupted previous run 
+    # (crash/manually forced interruption)
+    bfc <- makeBFCClean(bfc)
 
     # checking consistency between to-be-run processing steps and cache
     res <- checkCytoPipelineConsistencyWithCache(x, path = path)