rbbt-util 5.21.78 → 5.21.80

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA1:
-  metadata.gz: 79f060e03080aa195d6e1c4372dd004653ed8801
-  data.tar.gz: 0af2cbb746b785018adbc4b37e377a74f84def35
+  metadata.gz: 6643742cb59acfc08425d4ec6c6796bd300fada7
+  data.tar.gz: 2351b438d3a5f6f270e54643fd82b3d5466f8e69
 SHA512:
-  metadata.gz: 5c791b7f553c8bc32512c7eab3bffc9d94bf072d878f5daf32dd0afc7a2e87b7cfcc290bab5430c99c715e7672856d1007bae8b6501aa71eb7f211b820a36b66
-  data.tar.gz: 4af9194d609ee3537a4add26274448316976a61f8f9064f7f0cadb9f37b8db0784cf3f3b4469ceb9a15324934e92e67e795b4ee07e0834801ba94c82fcb09500
+  metadata.gz: ad3faa128f65be8d20566da34e756ac9c68ae4766450982ba61fdfb5e599e3593427e2c4ca86d03694796d42f74167b1528f2ef6cc23b7368c604baf45af98d6
+  data.tar.gz: ee4da1fc28221199b1418f868aff6324a6c4b9f21aa6293de2b4f3c2160b8613d172f40b9503748084382718eaa5bdf325795632eab79ae75b7f187989586ac1

data/share/Rlib/util.R

@@ -39,22 +39,30 @@ rbbt.job <- function(workflow, task, load=TRUE, flat = FALSE, type = 'tsv', jobn
 
     str = paste(str, code, sep="\n")
 
-    str = paste(str, paste("Workflow.require_workflow '", workflow, "'", sep=""), sep="\n")
+    str = paste(str, paste("wf = Workflow.require_workflow '", workflow, "'", sep=""), sep="\n")
 
     args_list = list(...)
     args_strs = c()
     for (input in names(args_list)){
         value = args_list[[input]]
+        input = sub('input\\.', '', input)
         if (!is.numeric(value)){
-            value = paste("'", value, "'", sep="")
+            if (value == TRUE){
+                value = 'true'
+            }else{
+                if (value == FALSE){
+                    value = 'false'
+                }else{
+                    value = paste("'", value, "'", sep="")
+                }
+            }
         }
         args_strs = c(args_strs, paste(":",input,' => ',value, sep=""))
     }
 
     args_str = paste(args_strs, sep=",")
-    str = paste(str, paste(workflow, '.job(:', task, ", '", jobname, "', ", args_str,').produce.path', sep=""), sep="\n")
-    cat(str)
-    rbbt.ruby(str, load, flat, type)
+    str = paste(str, paste('wf.job(:', task, ", '", jobname, "', ", args_str,').produce.path', sep=""), sep="\n")
+    return(rbbt.ruby(str, load, flat, type));
 }
 
 rbbt.ruby.substitutions <- function(script, substitutions = list(), ...){

data/share/rbbt_commands/workflow/task

@@ -317,9 +317,11 @@ begin
 
     case
     when res.respond_to?(:gets)
-      while block = res.read(2048)
-        out.write block
+      begin
+        Misc.consume_stream(res, false, out)
+      rescue EOFError, IOError
       end
+      res.join if res.respond_to? :join
     when Array === res
       out.puts res * "\n"
     when TSV === res

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: rbbt-util
 version: !ruby/object:Gem::Version
-  version: 5.21.78
+  version: 5.21.80
 platform: ruby
 authors:
 - Miguel Vazquez
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2017-04-18 00:00:00.000000000 Z
+date: 2017-04-28 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: rake