Re: [PATCH] -for review- Tangling with variable transfer of variables

[Rainer M Krug <Rainer@krugs.de>]

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"Charles C. Berry" <ccberry@ucsd.edu> writes:

V> On Fri, 20 Jun 2014, Rainer M Krug wrote:
>
>> Attached please find =the reworked patch.
>>
>> 1) uses local() and closes connection
>> 2) does not leave a variable cal;led file behind
>>
>
> Seems to work on a few test cases.
>
> I'd move the strings to defconsts.
>
> Putting a newline before each `%S' will outdent the first line of 
> :var value when it is echoed in the session log so it will be easier to 
> view.
>
> ===
>
> With Eric's input on this:
>
> Would you also change this at the end of org-babel-R-assign-elisp:
>
>                          res})" name file header row-names max))))
> -    (format "%s <- %s" name (org-babel-R-quote-tsv-field value))))
> +    (format "%s <- %S" name
> +	    (if (stringp value) value (prin1-to-string value)))))
>
> ??
>
> I think this is innocuous for plain strings with no internal quotes, but 
> allows almost anything to be passed to R as a string.
>
> So
>  	:var x=[1 2 3 "4" 5]
>
> will be passed to R as x <- "[1 2 3 \"4\" 5]"
>
> instead of x <- "[1 2 3 "4" 5] which throws an error.
>
> And this just works:
>
> #+NAME: latex-capt
> #+BEGIN_SRC latex
>    \begin{math}
>      y = X\beta,
>      \mbox{where } \beta = %beta%
>    \end{math}
> #+END_SRC
>
> #+BEGIN_SRC R :var ytxt=latex-capt :results raw :wrap latex
> beta <- 1.234
> sub("%beta%",beta,ytxt)
> #+END_SRC

OK - attached please find two patches:

0001-lisp-ob-R.el-Fix-tangling-with-tables.patch
0002-Make-transfer-of-values-from-R-type-aware.patch

The first one fixes tangling with tables including discussed
suggestions, the second one moves the definition of the R code into
defconst and introduces type awareness for the transfer of *values*, but
not tables. I reworked your suggestion and now integer are transferred
to R as integers (L) and float as double.
This already worked for tables.

Could you please check the second patch? In my checks everything worked
as expected.

Cheers,

Rainer

>
>
> HTH,
>
> Chuck

-- 
Rainer M. Krug, PhD (Conservation Ecology, SUN), MSc (Conservation Biology, UCT), Dipl. Phys. (Germany)

Centre of Excellence for Invasion Biology
Stellenbosch University
South Africa

Tel :       +33 - (0)9 53 10 27 44
Cell:       +33 - (0)6 85 62 59 98
Fax :       +33 - (0)9 58 10 27 44

Fax (D):    +49 - (0)3 21 21 25 22 44

email:      Rainer@krugs.de

Skype:      RMkrug

PGP: 0x0F52F982

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From 38c029b38c85d9f9d35d0867b332eebc3daf1aca Mon Sep 17 00:00:00 2001
From: "Rainer M. Krug" <R.M.Krug@gmail.com>
Date: Fri, 20 Jun 2014 22:19:59 +0200
Subject: [PATCH 1/2] lisp/ob-R.el: Fix tangling with tables

* lisp/ob-R.el (org-babel-R-assign-elisp): Fix variable transfer of
tables by using text connections in R instead of files.  Variable
transfer of tables does not depend on files anymore, i.e. works also
when tangling.
---
 lisp/ob-R.el | 52 ++++++++++++++++++++++++++++++++--------------------
 1 file changed, 32 insertions(+), 20 deletions(-)

diff --git a/lisp/ob-R.el b/lisp/ob-R.el
index a3ae1ec..c77a103 100644
--- a/lisp/ob-R.el
+++ b/lisp/ob-R.el
@@ -190,32 +190,44 @@ This function is called by `org-babel-execute-src-block'."
   (if (listp value)
       (let* ((lengths (mapcar 'length (org-remove-if-not 'sequencep value)))
 	     (max (if lengths (apply 'max lengths) 0))
-	     (min (if lengths (apply 'min lengths) 0))
-	     (transition-file (org-babel-temp-file "R-import-")))
+	     (min (if lengths (apply 'min lengths) 0)))
         ;; Ensure VALUE has an orgtbl structure (depth of at least 2).
         (unless (listp (car value)) (setq value (list value)))
-        (with-temp-file transition-file
-          (insert
-	   (orgtbl-to-tsv value '(:fmt org-babel-R-quote-tsv-field))
-	   "\n"))
-	(let ((file (org-babel-process-file-name transition-file 'noquote))
+	(let ((file (orgtbl-to-tsv value '(:fmt org-babel-R-quote-tsv-field)))
 	      (header (if (or (eq (nth 1 value) 'hline) colnames-p)
 			  "TRUE" "FALSE"))
 	      (row-names (if rownames-p "1" "NULL")))
 	  (if (= max min)
-	      (format "%s <- read.table(\"%s\",
-                      header=%s,
-                      row.names=%s,
-                      sep=\"\\t\",
-                      as.is=TRUE)" name file header row-names)
-	    (format "%s <- read.table(\"%s\",
-                   header=%s,
-                   row.names=%s,
-                   sep=\"\\t\",
-                   as.is=TRUE,
-                   fill=TRUE,
-                   col.names = paste(\"V\", seq_len(%d), sep =\"\"))"
-		    name file header row-names max))))
+	      (format "%s <- local({
+                        con <- textConnection(
+                          %S
+                        )
+                        res <- read.table(
+                          con,
+                          header    = %s,
+                          row.names = %s,
+                          sep       = \"\\t\",
+                          as.is     = TRUE
+                        )
+                        close(con)
+                        res
+                        })" name file header row-names)
+	    (format "%s <- local({
+                       con <- textConnection(
+                         %S
+                       )
+                       res <- read.table(
+                         con,
+                         header    = %s,
+                         row.names = %s,
+                         sep       = \"\\t\",
+                         as.is     = TRUE,
+                         fill      = TRUE,
+                         col.names = paste(\"V\", seq_len(%d), sep =\"\")
+                       )
+                       close(con)
+                       res
+                       })" name file header row-names max))))
     (format "%s <- %s" name (org-babel-R-quote-tsv-field value))))
 
 (defvar ess-ask-for-ess-directory) ; dynamically scoped
-- 
2.0.0


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From e62a75e7227027c406d23fa9f8ac594db2ce81d6 Mon Sep 17 00:00:00 2001
From: "Rainer M. Krug" <R.M.Krug@gmail.com>
Date: Mon, 23 Jun 2014 12:11:59 +0200
Subject: [PATCH 2/2] Make transfer of values from R type aware

* lisp/ob-R.el (org-babel-R-assign-elisp): Added different cases for
transfer of integer, float, string and other variables to R so that
now integer values are transferred as integers (L) and stored in R as
such.  This change is backward compatible as integer values are
numerical values in R.
Moved definition of R functions for transfer of tables into defconst
ob-R-transfer-variable-table-with-header and
ob-R-transfer-variable-table-without-header.
---
 lisp/ob-R.el | 78 ++++++++++++++++++++++++++++++++++++------------------------
 1 file changed, 47 insertions(+), 31 deletions(-)

diff --git a/lisp/ob-R.el b/lisp/ob-R.el
index c77a103..92c1dbc 100644
--- a/lisp/ob-R.el
+++ b/lisp/ob-R.el
@@ -93,6 +93,44 @@ this variable.")
     (when (and session (string-match "^\\*\\(.+?\\)\\*$" session))
       (save-match-data (org-babel-R-initiate-session session nil)))))
 
+(defconst ob-R-transfer-variable-table-with-header
+  "%s <- local({
+     con <- textConnection(
+       %S
+     )
+     res <- read.table(
+       con,
+       header    = %s,
+       row.names = %s,
+       sep       = \"\\t\",
+       as.is     = TRUE
+     )
+     close(con)
+     res
+   })"
+  "R code used to transfer a table defined as a variable from org to R. 
+This function is used when the table contains a header.")
+
+(defconst ob-R-transfer-variable-table-without-header
+  "%s <- local({
+     con <- textConnection(
+       %S
+     )
+     res <- read.table(
+       con,
+       header    = %s,
+       row.names = %s,
+       sep       = \"\\t\",
+       as.is     = TRUE,
+       fill      = TRUE,
+       col.names = paste(\"V\", seq_len(%d), sep =\"\")
+     )
+     close(con)
+     res
+   })"
+  "R code used to transfer a table defined as a variable from org to R. 
+This function is used when the table does not contain a header.")
+
 (defun org-babel-expand-body:R (body params &optional graphics-file)
   "Expand BODY according to PARAMS, return the expanded body."
   (mapconcat 'identity
@@ -198,37 +236,15 @@ This function is called by `org-babel-execute-src-block'."
 			  "TRUE" "FALSE"))
 	      (row-names (if rownames-p "1" "NULL")))
 	  (if (= max min)
-	      (format "%s <- local({
-                        con <- textConnection(
-                          %S
-                        )
-                        res <- read.table(
-                          con,
-                          header    = %s,
-                          row.names = %s,
-                          sep       = \"\\t\",
-                          as.is     = TRUE
-                        )
-                        close(con)
-                        res
-                        })" name file header row-names)
-	    (format "%s <- local({
-                       con <- textConnection(
-                         %S
-                       )
-                       res <- read.table(
-                         con,
-                         header    = %s,
-                         row.names = %s,
-                         sep       = \"\\t\",
-                         as.is     = TRUE,
-                         fill      = TRUE,
-                         col.names = paste(\"V\", seq_len(%d), sep =\"\")
-                       )
-                       close(con)
-                       res
-                       })" name file header row-names max))))
-    (format "%s <- %s" name (org-babel-R-quote-tsv-field value))))
+	      (format ob-R-transfer-variable-table-with-header
+		      name file header row-names)
+	    (format ob-R-transfer-variable-table-without-header
+		    name file header row-names max))))
+    (if (integerp value) (format "%s <- %s" name (concat (number-to-string value) "L"))
+      (if (floatp value) (format "%s <- %s" name value)
+	(if (stringp value) (format "%s <- %S" name value) 
+	  (format "%s <- %S" name (prin1-to-string value)))))))
+
 
 (defvar ess-ask-for-ess-directory) ; dynamically scoped
 (defun org-babel-R-initiate-session (session params)
-- 
2.0.0


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