[PATCH] Fix ob-clojure handling source block variable's value is a org-mode table or list

[PATCH] Fix ob-clojure handling source block variable's value is a org-mode table or list

[Christopher M. Miles]

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I bellowing example:

#+begin_src org
,#+NAME: ob-clojure-table-test
| a | b | c |
|---+---+---|
| 1 | 2 | 3 |

,#+NAME: ob-clojure-table-test-2
| a | b | c |
|---+---+---|
| 1 | 2 | 3 |

,#+begin_src clojure :var kk=ob-clojure-table-test :var kk2=ob-clojure-table-test-2 :results output
(println kk2)
(println kk)
,#+end_src

#+end_src

Without this patch, it will report error "class java.lang.ClassCastException" from CIDER.

This patch added if condition to handle this table, list type data.


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From 948e8c1ff2c9ba1d9c0fe26f9bdaa096bef80a9d Mon Sep 17 00:00:00 2001
From: stardiviner <numbchild@gmail.com>
Date: Sat, 9 Apr 2022 21:14:22 +0800
Subject: [PATCH] ob-clojure.el: Fix header argument :var binding passed table
 or list data

* lisp/ob-clojure.el (org-babel-expand-body:clojure): Add if condition
to handle source block :var passed org-mode table or list data for
clojure let-binding to avoid java.lang.ClassCastException.
---
 lisp/ob-clojure.el | 25 ++++++++++++++++++-------
 1 file changed, 18 insertions(+), 7 deletions(-)

diff --git a/lisp/ob-clojure.el b/lisp/ob-clojure.el
index 5a44b6487..e6614b2d9 100644
--- a/lisp/ob-clojure.el
+++ b/lisp/ob-clojure.el
@@ -101,13 +101,24 @@
 		 (and (cdr (assq :ns params)) (format "(ns %s)\n" ns))
 		 ;; Variables binding.
 		 (if (null vars) (org-trim body)
-		   (format "(let [%s]\n%s)"
-			   (mapconcat
-			    (lambda (var)
-			      (format "%S %S" (car var) (cdr var)))
-			    vars
-			    "\n      ")
-			   body))))))
+                   ;; variable's value is a list from org-mode passed table or list.
+		   (if (listp (cdr (car vars)))
+                       (format "(let [%s]\n%s)"
+                               (mapconcat
+                                (lambda (var)
+                                  (format "%S '%S" (car var) (cadr var)))
+                                vars
+                                "\n      ")
+                               body)
+                     ;; else, the header argument variable's value is not a list.
+                     (format "(let [%s]\n%s)"
+                             (mapconcat
+                              (lambda (var)
+                                (format "%S %S" (car var) (cdr var)))
+                              vars
+                              "\n      ")
+                             body)
+                     ))))))
     (if (or (member "code" result-params)
 	    (member "pp" result-params))
 	(format "(clojure.pprint/pprint (do %s))" body)
-- 
2.35.1


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From 948e8c1ff2c9ba1d9c0fe26f9bdaa096bef80a9d Mon Sep 17 00:00:00 2001
From: stardiviner <numbchild@gmail.com>
Date: Sat, 9 Apr 2022 21:14:22 +0800
Subject: [PATCH] ob-clojure.el: Fix header argument :var binding passed table
 or list data

* lisp/ob-clojure.el (org-babel-expand-body:clojure): Add if condition
to handle source block :var passed org-mode table or list data for
clojure let-binding to avoid java.lang.ClassCastException.
---
 lisp/ob-clojure.el | 25 ++++++++++++++++++-------
 1 file changed, 18 insertions(+), 7 deletions(-)

diff --git a/lisp/ob-clojure.el b/lisp/ob-clojure.el
index 5a44b6487..e6614b2d9 100644
--- a/lisp/ob-clojure.el
+++ b/lisp/ob-clojure.el
@@ -101,13 +101,24 @@
 		 (and (cdr (assq :ns params)) (format "(ns %s)\n" ns))
 		 ;; Variables binding.
 		 (if (null vars) (org-trim body)
-		   (format "(let [%s]\n%s)"
-			   (mapconcat
-			    (lambda (var)
-			      (format "%S %S" (car var) (cdr var)))
-			    vars
-			    "\n      ")
-			   body))))))
+                   ;; variable's value is a list from org-mode passed table or list.
+		   (if (listp (cdr (car vars)))
+                       (format "(let [%s]\n%s)"
+                               (mapconcat
+                                (lambda (var)
+                                  (format "%S '%S" (car var) (cadr var)))
+                                vars
+                                "\n      ")
+                               body)
+                     ;; else, the header argument variable's value is not a list.
+                     (format "(let [%s]\n%s)"
+                             (mapconcat
+                              (lambda (var)
+                                (format "%S %S" (car var) (cdr var)))
+                              vars
+                              "\n      ")
+                             body)
+                     ))))))
     (if (or (member "code" result-params)
 	    (member "pp" result-params))
 	(format "(clojure.pprint/pprint (do %s))" body)
-- 
2.35.1


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Re: [PATCH] Fix ob-clojure handling source block variable's value is a org-mode table or list

[Ihor Radchenko]

"Christopher M. Miles" <numbchild@gmail.com> writes:

> I bellowing example:
>
> #+begin_src org
> ,#+NAME: ob-clojure-table-test
> | a | b | c |
> |---+---+---|
> | 1 | 2 | 3 |
>
> ,#+NAME: ob-clojure-table-test-2
> | a | b | c |
> |---+---+---|
> | 1 | 2 | 3 |
>
> ,#+begin_src clojure :var kk=ob-clojure-table-test :var kk2=ob-clojure-table-test-2 :results output
> (println kk2)
> (println kk)
> ,#+end_src
>
> #+end_src
>
> Without this patch, it will report error "class java.lang.ClassCastException" from CIDER.

Bastien, could you please take a look? I was unable to setup clojure dev
environment on my machine for testing. So, I am not able to confirm if
the issue exists.

>  		 ;; Variables binding.
>  		 (if (null vars) (org-trim body)
> -		   (format "(let [%s]\n%s)"
> -			   (mapconcat
> -			    (lambda (var)
> -			      (format "%S %S" (car var) (cdr var)))
> -			    vars
> -			    "\n      ")
> -			   body))))))
> +                   ;; variable's value is a list from org-mode passed table or list.
> +		   (if (listp (cdr (car vars)))

This test is fishy. It only tests for the first variable assignment.
What if you have multiple vars some being tables and some not?

-- 
Ihor Radchenko // yantar92,
Org mode contributor,
Learn more about Org mode at <https://orgmode.org/>.
Support Org development at <https://liberapay.com/org-mode>,
or support my work at <https://liberapay.com/yantar92>

Re: [PATCH] Fix ob-clojure handling source block variable's value is a org-mode table or list

[Daniel Kraus]

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Hi!

Ihor Radchenko <yantar92@posteo.net> writes:

> "Christopher M. Miles" <numbchild@gmail.com> writes:
>> Without this patch, it will report error "class java.lang.ClassCastException" from CIDER.
>
> Bastien, could you please take a look? I was unable to setup clojure dev
> environment on my machine for testing. So, I am not able to confirm if
> the issue exists.

Just in case you want to play around with Clojure, installing babashka
(https://github.com/babashka/babashka) is a single binary and very simple to install.

>>  		 ;; Variables binding.
>>  		 (if (null vars) (org-trim body)
>> -		   (format "(let [%s]\n%s)"
>> -			   (mapconcat
>> -			    (lambda (var)
>> -			      (format "%S %S" (car var) (cdr var)))
>> -			    vars
>> -			    "\n      ")
>> -			   body))))))
>> +                   ;; variable's value is a list from org-mode passed table or list.
>> +		   (if (listp (cdr (car vars)))
>
> This test is fishy. It only tests for the first variable assignment.
> What if you have multiple vars some being tables and some not?

I looked at `ob-lisp.el` and simply always quoting seems to be working.
See attached patch and here's my test (based from Chrisophers example):

--cut--

#+NAME: ob-clojure-table-test
| a | b | c |
|---+---+---|
| 1 | 2 | 3 |

#+NAME: ob-clojure-table-test-2
| a | b | c |
|---+---+---|
| 1 | 2 | 3 |
| 4 | 5 | 6 |

#+begin_src clojure :var v1=42 :var v2="foobar" :var v3=ob-clojure-table-test :var v4=ob-clojure-table-test-2 :results output
(prn (+ v1 5))
(prn v2)
(prn v3)
(prn v4)
#+end_src

#+RESULTS:
: 47
: "foobar"
: ((1 2 3))
: ((1 2 3) (4 5 6))

--cut--

Cheers,
  Daniel

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From 1a2fa382e7a5925d4b85d90f1fe4ac7c012f81a4 Mon Sep 17 00:00:00 2001
From: Daniel Kraus <daniel@kraus.my>
Date: Thu, 27 Oct 2022 16:04:02 +0200
Subject: [PATCH] lisp/ob-clojure.el: Fix header argument :var binding

* lisp/ob-clojure.el (org-babel-expand-body:clojure): Always quote
the variables passed from org-mode in clojure let binding.
When a variable is a table or list, it's value is is "(..data..)"
and without quotes, clojure would try to execute the first
value as a function.
---
 lisp/ob-clojure.el | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/lisp/ob-clojure.el b/lisp/ob-clojure.el
index 0649469b3..c76a3f013 100644
--- a/lisp/ob-clojure.el
+++ b/lisp/ob-clojure.el
@@ -132,7 +132,7 @@ or set the `:backend' header argument"))))
 		   (format "(let [%s]\n%s)"
 			   (mapconcat
 			    (lambda (var)
-			      (format "%S %S" (car var) (cdr var)))
+			      (format "%S '%S" (car var) (cdr var)))
 			    vars
 			    "\n      ")
 			   body))))))
-- 
2.38.1

Re: [PATCH] Fix ob-clojure handling source block variable's value is a org-mode table or list

[Ihor Radchenko]

Daniel Kraus <daniel@kraus.my> writes:

> Just in case you want to play around with Clojure, installing babashka
> (https://github.com/babashka/babashka) is a single binary and very simple to install.

Thanks!

> Subject: [PATCH] lisp/ob-clojure.el: Fix header argument :var binding
>
> * lisp/ob-clojure.el (org-babel-expand-body:clojure): Always quote
> the variables passed from org-mode in clojure let binding.
> When a variable is a table or list, it's value is is "(..data..)"

*is is

Otherwise, feel free to push.

-- 
Ihor Radchenko // yantar92,
Org mode contributor,
Learn more about Org mode at <https://orgmode.org/>.
Support Org development at <https://liberapay.com/org-mode>,
or support my work at <https://liberapay.com/yantar92>

Re: [PATCH] Fix ob-clojure handling source block variable's value is a org-mode table or list

[Bastien Guerry]

Hi Daniel,

Daniel Kraus <daniel@kraus.my> writes:

> Just in case you want to play around with Clojure, installing
> babashka (https://github.com/babashka/babashka) is a single binary
> and very simple to install.

For now `org-babel-clojure-backend' is nil.

I suggest to set it to babashka by default: babashka is stable and
well established now, it is by far the most efficient way to run
Clojure code.  Also, it is particularily suitable for Babel use.

What do you think?

-- 
 Bastien

Re: [PATCH] Fix ob-clojure handling source block variable's value is a org-mode table or list

[Daniel Kraus]

Hi!

Bastien Guerry <bzg@gnu.org> writes:
> For now `org-babel-clojure-backend' is nil.
>
> I suggest to set it to babashka by default: babashka is stable and
> well established now, it is by far the most efficient way to run
> Clojure code.  Also, it is particularily suitable for Babel use.
>
> What do you think?

Sounds good.
I would set it to (and (executable-find "bb") 'babashka) so it's still nil
when babashka is installed?

Or we could even test more available backends like

(cond
 ((executable-find "bb") 'babashka)
 ((executable-find "nbb") 'nbb)
 ((featurep 'cider) 'cider)
 ((featurep 'inf-clojure) 'inf-clojure)
 ((featurep 'slime) 'slime))

Or is that too much "magic" in that on some systems the default is bb
and in others it's cider etc?

Cheers,
  Daniel

Re: [PATCH] Fix ob-clojure handling source block variable's value is a org-mode table or list

[Bastien]

Hi Daniel,

Daniel Kraus <daniel@kraus.my> writes:

> I would set it to (and (executable-find "bb") 'babashka) so it's still nil
> when babashka is installed?

(You mean "not installed", right?)

> Or we could even test more available backends like
>
> (cond
>  ((executable-find "bb") 'babashka)
>  ((executable-find "nbb") 'nbb)
>  ((featurep 'cider) 'cider)
>  ((featurep 'inf-clojure) 'inf-clojure)
>  ((featurep 'slime) 'slime))
>
> Or is that too much "magic" in that on some systems the default is bb
> and in others it's cider etc?

I think this is acceptable magic: perhaps we should first check what
is done in other Babel languages and align with their level of magic
for guessing the correct executable -- but I suspect Clojure is a bit
special here, in that it has a lot of different options.

Thanks for taking care of this,

-- 
 Bastien

Re: [PATCH] Fix ob-clojure handling source block variable's value is a org-mode table or list

[Daniel Kraus]

Bastien <bzg@gnu.org> writes:

> Daniel Kraus <daniel@kraus.my> writes:
>> I would set it to (and (executable-find "bb") 'babashka) so it's still nil
>> when babashka is installed?
> (You mean "not installed", right?)

Of course.

>> Or we could even test more available backends like
>>
>> (cond
>>  ((executable-find "bb") 'babashka)
>>  ((executable-find "nbb") 'nbb)
>>  ((featurep 'cider) 'cider)
>>  ((featurep 'inf-clojure) 'inf-clojure)
>>  ((featurep 'slime) 'slime))
>>
>> Or is that too much "magic" in that on some systems the default is bb
>> and in others it's cider etc?
>
> I think this is acceptable magic: perhaps we should first check what
> is done in other Babel languages and align with their level of magic
> for guessing the correct executable -- but I suspect Clojure is a bit
> special here, in that it has a lot of different options.

I looked around a bit but couldn't find another babel package with a
similar problems, i.e. that some backends are completely different
and not just changing the name of the executable.

I think I'll go with the big `cond` above to auto-detect what's
installed. That's probably the best out-of-the-box experience.

Cheers,
  Daniel

Re: [PATCH] Fix ob-clojure handling source block variable's value is a org-mode table or list

[Bastien]

Daniel Kraus <daniel@kraus.my> writes:

> I think I'll go with the big `cond` above to auto-detect what's
> installed. That's probably the best out-of-the-box experience.

Indeed, thank you!

-- 
 Bastien

Re: [PATCH] Fix ob-clojure handling source block variable's value is a org-mode table or list

[Christopher M. Miles]

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Ping Bastien Guerry.

"Christopher M. Miles" <numbchild@gmail.com> writes:

> [[PGP Signed Part:Undecided]]
>
> I bellowing example:
>
> #+begin_src org
> ,#+NAME: ob-clojure-table-test
> | a | b | c |
> |---+---+---|
> | 1 | 2 | 3 |
>
> ,#+NAME: ob-clojure-table-test-2
> | a | b | c |
> |---+---+---|
> | 1 | 2 | 3 |
>
> ,#+begin_src clojure :var kk=ob-clojure-table-test :var kk2=ob-clojure-table-test-2 :results output
> (println kk2)
> (println kk)
> ,#+end_src
>
> #+end_src
>
> Without this patch, it will report error "class java.lang.ClassCastException" from CIDER.
>
> This patch added if condition to handle this table, list type data.
>
> From 948e8c1ff2c9ba1d9c0fe26f9bdaa096bef80a9d Mon Sep 17 00:00:00 2001
> From: stardiviner <numbchild@gmail.com>
> Date: Sat, 9 Apr 2022 21:14:22 +0800
> Subject: [PATCH] ob-clojure.el: Fix header argument :var binding passed table
>  or list data
>
> * lisp/ob-clojure.el (org-babel-expand-body:clojure): Add if condition
> to handle source block :var passed org-mode table or list data for
> clojure let-binding to avoid java.lang.ClassCastException.
> ---
>  lisp/ob-clojure.el | 25 ++++++++++++++++++-------
>  1 file changed, 18 insertions(+), 7 deletions(-)
>
> diff --git a/lisp/ob-clojure.el b/lisp/ob-clojure.el
> index 5a44b6487..e6614b2d9 100644
> --- a/lisp/ob-clojure.el
> +++ b/lisp/ob-clojure.el
> @@ -101,13 +101,24 @@
>  		 (and (cdr (assq :ns params)) (format "(ns %s)\n" ns))
>  		 ;; Variables binding.
>  		 (if (null vars) (org-trim body)
> -		   (format "(let [%s]\n%s)"
> -			   (mapconcat
> -			    (lambda (var)
> -			      (format "%S %S" (car var) (cdr var)))
> -			    vars
> -			    "\n      ")
> -			   body))))))
> +                   ;; variable's value is a list from org-mode passed table or list.
> +		   (if (listp (cdr (car vars)))
> +                       (format "(let [%s]\n%s)"
> +                               (mapconcat
> +                                (lambda (var)
> +                                  (format "%S '%S" (car var) (cadr var)))
> +                                vars
> +                                "\n      ")
> +                               body)
> +                     ;; else, the header argument variable's value is not a list.
> +                     (format "(let [%s]\n%s)"
> +                             (mapconcat
> +                              (lambda (var)
> +                                (format "%S %S" (car var) (cdr var)))
> +                              vars
> +                              "\n      ")
> +                             body)
> +                     ))))))
>      (if (or (member "code" result-params)
>  	    (member "pp" result-params))
>  	(format "(clojure.pprint/pprint (do %s))" body)
> -- 
> 2.35.1
>
> [5. text/x-patch; 0001-ob-clojure.el-Fix-header-argument-var-binding-passed.patch]...


-- 

[ stardiviner ]
I try to make every word tell the meaning that I want to express without misunderstanding.

Blog: https://stardiviner.github.io/
IRC(libera.chat, freenode): stardiviner, Matrix: stardiviner
GPG: F09F650D7D674819892591401B5DF1C95AE89AC3

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Re: [PATCH] Fix ob-clojure handling source block variable's value is a org-mode table or list

[Christopher M. Miles]

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Any review comments about this patch?

"Christopher M. Miles" <numbchild@gmail.com> writes:

> [[PGP Signed Part:Undecided]]
>
> I bellowing example:
>
> #+begin_src org
> ,#+NAME: ob-clojure-table-test
> | a | b | c |
> |---+---+---|
> | 1 | 2 | 3 |
>
> ,#+NAME: ob-clojure-table-test-2
> | a | b | c |
> |---+---+---|
> | 1 | 2 | 3 |
>
> ,#+begin_src clojure :var kk=ob-clojure-table-test :var kk2=ob-clojure-table-test-2 :results output
> (println kk2)
> (println kk)
> ,#+end_src
>
> #+end_src
>
> Without this patch, it will report error "class java.lang.ClassCastException" from CIDER.
>
> This patch added if condition to handle this table, list type data.
>
> From 948e8c1ff2c9ba1d9c0fe26f9bdaa096bef80a9d Mon Sep 17 00:00:00 2001
> From: stardiviner <numbchild@gmail.com>
> Date: Sat, 9 Apr 2022 21:14:22 +0800
> Subject: [PATCH] ob-clojure.el: Fix header argument :var binding passed table
>  or list data
>
> * lisp/ob-clojure.el (org-babel-expand-body:clojure): Add if condition
> to handle source block :var passed org-mode table or list data for
> clojure let-binding to avoid java.lang.ClassCastException.
> ---
>  lisp/ob-clojure.el | 25 ++++++++++++++++++-------
>  1 file changed, 18 insertions(+), 7 deletions(-)
>
> diff --git a/lisp/ob-clojure.el b/lisp/ob-clojure.el
> index 5a44b6487..e6614b2d9 100644
> --- a/lisp/ob-clojure.el
> +++ b/lisp/ob-clojure.el
> @@ -101,13 +101,24 @@
>  		 (and (cdr (assq :ns params)) (format "(ns %s)\n" ns))
>  		 ;; Variables binding.
>  		 (if (null vars) (org-trim body)
> -		   (format "(let [%s]\n%s)"
> -			   (mapconcat
> -			    (lambda (var)
> -			      (format "%S %S" (car var) (cdr var)))
> -			    vars
> -			    "\n      ")
> -			   body))))))
> +                   ;; variable's value is a list from org-mode passed table or list.
> +		   (if (listp (cdr (car vars)))
> +                       (format "(let [%s]\n%s)"
> +                               (mapconcat
> +                                (lambda (var)
> +                                  (format "%S '%S" (car var) (cadr var)))
> +                                vars
> +                                "\n      ")
> +                               body)
> +                     ;; else, the header argument variable's value is not a list.
> +                     (format "(let [%s]\n%s)"
> +                             (mapconcat
> +                              (lambda (var)
> +                                (format "%S %S" (car var) (cdr var)))
> +                              vars
> +                              "\n      ")
> +                             body)
> +                     ))))))
>      (if (or (member "code" result-params)
>  	    (member "pp" result-params))
>  	(format "(clojure.pprint/pprint (do %s))" body)
> -- 
> 2.35.1
>
> [5. text/x-patch; 0001-ob-clojure.el-Fix-header-argument-var-binding-passed.patch]...


-- 

[ stardiviner ]
I try to make every word tell the meaning that I want to express without misunderstanding.

Blog: https://stardiviner.github.io/
IRC(libera.chat, freenode): stardiviner, Matrix: stardiviner
GPG: F09F650D7D674819892591401B5DF1C95AE89AC3

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Re: [PATCH] Fix ob-clojure handling source block variable's value is a org-mode table or list

[Ihor Radchenko]

"Christopher M. Miles" <numbchild@gmail.com> writes:

> Any review comments about this patch?

I have sent the following comment shortly after your followup:

"Christopher M. Miles" <numbchild@gmail.com> writes:

> +                   ;; variable's value is a list from org-mode passed table or list.
> +		   (if (listp (cdr (car vars)))
> ...
> +                       (format "(let [%s]\n%s)"
> +                               (mapconcat
> +                                (lambda (var)
> +                                  (format "%S '%S" (car var) (cdr var)))
> +                                vars
> +                                "\n      ")

Do I miss something, or you only test the first variable assignment here?
What if there are multiple assignments (:var a=X,b=Y)?

-- 
Ihor Radchenko // yantar92,
Org mode contributor,
Learn more about Org mode at <https://orgmode.org/>.
Support Org development at <https://liberapay.com/org-mode>,
or support my work at <https://liberapay.com/yantar92>

Re: [PATCH] Fix ob-clojure handling source block variable's value is a org-mode table or list

[Daniel Kraus]

Hi

Ihor Radchenko <yantar92@posteo.net> writes:
> "Christopher M. Miles" <numbchild@gmail.com> writes:
>> Any review comments about this patch?
> I have sent the following comment shortly after your followup:

I even made another post after that, suggesting that the if condition
is not even needed. Simply always quoting seems to work and is also the
way it's done in `ob-lisp.el`.
See https://list.orgmode.org/orgmode/874jvp9wsg.fsf@kraus.my/

This simple patch is also already installed. Can you test if that works for you?

And in case you missed it, I made another reply for you bug report
about inline comments.
Check https://list.orgmode.org/orgmode/878rl1a1e0.fsf@kraus.my/

Thanks,
  Daniel