Re: Bug: [patch] Fix org-babel-result-to-file never expanding links when babel is evaluated in indirect buffer [9.3.7 (release_9.3.7-728-g1efc4e @ /home/yantar92/.emacs.d/straight/build/org/)]

[Ihor Radchenko]

> I don't have a real world scenario, just the one I made up below. I used
> that to play around with the function.

I see. FYI: I do change default-directory during src block execution in
my config. The following code makes src blocks execute inside attachment
folder by default:

(define-advice org-babel-execute-src-block (:filter-args (&optional args) 
set-detault-dir-to-org-attach-path)
  "Set working directory to the current entry's attach directory."
  (if (eq major-mode 'org-mode)
      (let* ((directory (file-name-as-directory (org-attach-dir 
'create-if-none)))
             (arg (car args))
             (info (cadr args))
             (params (org-babel-merge-params (nth 2 info) (caddr args)))
             (dir-param (alist-get :dir params)))
        (unless (and dir-param (or (equal (f-full default-directory) (f-full 
dir-param))
                                   (f-absolute-p dir-param)))
          (setf (alist-get :dir params)
                (if dir-param
                    (f-join directory (alist-get :dir params))
                  directory)))
        (list arg info params))
    (list arg info params)))

That's actually how I found the reported bug.

Best,
Ihor

John Herrlin <jherrlin@gmail.com> writes:

> Ihor Radchenko <yantar92@gmail.com> writes:
>
>>> It's intended to change directory and dont clone base buffer values. I
>>> tried to accomplish "If the `default-directory' is different from the
>>> containing file's directory then expand relative links."
>>
>> Not sure if I understand your use-case. Can you explain why you need to
>> achieve such behaviour? There might be an easier way to get what you
>> want.
>
> I don't have a real world scenario, just the one I made up below. I used
> that to play around with the function.
>
> Best regards
> John
>
>>
>> Best,
>> Ihor
>>
>>
>> John Herrlin <jherrlin@gmail.com> writes:
>>
>>> It's intended to change directory and dont clone base buffer values. I
>>> tried to accomplish "If the `default-directory' is different from the
>>> containing file's directory then expand relative links." As I
>>> understands it that's when it inserts a relative link, otherwise it just
>>> `result'. I was looking from the indirect buffers point of view and from
>>> there the relative link is off in this case. But from the base buffers
>>> point of view everything works fine. I guess that it was my use case
>>> that is strange.
>>>
>>> Looks good!
>>>
>>> Best regards
>>> John
>>>
>>>>> In my case the result is a relative link, but if I follow the link I end
>>>>> up in the wrong place.
>>>>
>>>> Do you mean that the generated script.sh ends up in your home dir?
>>>> It is expected since default-directory in your buffer is "~/":
>>>>
>>>>>   (dired "~/")
>>>>>   (make-indirect-buffer "tmp.org" "tmp-indirect")
>>>>
>>>> Note that you called make-indirect-buffer without third argument.
>>>>
>>>> According to manual:
>>>>
>>>>> (make-indirect-buffer BASE-BUFFER NAME &optional CLONE)
>>>>> CLONE nil means the indirect buffer's state is reset to default values.
>>>>
>>>>>     Org first tries to generate the filename from the value of the
>>>>>     ‘file’ header argument and the directory specified using the
>>>>>     ‘output-dir’ header arguments.  If ‘output-dir’ is not specified,
>>>>>     Org assumes it is the current directory.
>>>>
>>>> No surprise you got your file in the default-directory (~/).
>>>>
>>>> If you use (make-indirect-buffer "tmp.org" "tmp-indirect" t) instead,
>>>> the script.sh link will be relative, as expected.
>>>>
>>>> Let me know if I miss something.
>>>>
>>>> Best,
>>>> Ihor
>>>>
>>>>
>>>>> Hey Ihor,
>>>>>
>>>>> Could not get the patch to work.
>>>>>
>>>>> I used this use case.
>>>>>
>>>>> (with-current-buffer
>>>>>   (find-file "/tmp/tmp.org")
>>>>>   (insert "* A\n** b\n** c\n\n   some text")
>>>>>   (dired "~/")
>>>>>   (make-indirect-buffer "tmp.org" "tmp-indirect")
>>>>>   (switch-to-buffer "tmp-indirect")
>>>>>   (goto-char (point-max))
>>>>>   (funcall 'org-mode)
>>>>>   (insert (concat "\n\n| default-directory | " default-directory " |\n"
>>>>>                   "| org-link-file-path-type | " (symbol-name 
>>>>> org-link-file-path-type) " |\n"
>>>>>                   "| (expand-file-name default-directory) | " 
>>>>> (expand-file-name default-directory) " |\n"
>>>>>                   "| (buffer-file-name (buffer-base-buffer)) | " 
>>>>> (buffer-file-name (buffer-base-buffer)) " |\n"))
>>>>>   (org-table-align)
>>>>>   (insert "\n\n#+BEGIN_SRC shell :results file :file script.sh
>>>>>        echo \"#!/bin/bash\"
>>>>>        echo \"echo Hey\"\n#+END_SRC")
>>>>>   (org-babel-execute-src-block))
>>>>>
>>>>> In my case the result is a relative link, but if I follow the link I end
>>>>> up in the wrong place.
>>>>>
>>>>> src_emacs-lisp{emacs-version} {{{results(=26.3=)}}}
>>>>> src_emacs-lisp{org-version} {{{results(=9.3.7=)}}}
>>>>>
>>>>> Best regards
>>>>> John
>>>>>
>>>>>
>>>>> Ihor Radchenko <yantar92@gmail.com> writes:
>>>>>
>>>>>> Remember to cover the basics, that is, what you expected to happen and
>>>>>> what in fact did happen.  You don't know how to make a good report?  See
>>>>>>
>>>>>>      https://orgmode.org/manual/Feedback.html#Feedback
>>>>>>
>>>>>> Your bug report will be posted to the Org mailing list.
>>>>>> ------------------------------------------------------------------------
>>>>>>
>>>>>> I noticed that org-babel-result-to-file never expands file: links in
>>>>>> src block results when ran from indirect buffer and default-directory
>>>>>> is not same with base buffer file's directory. This is against the
>>>>>> docstring stating that
>>>>>>
>>>>>>> If the `default-directory' is different from the containing
>>>>>>> file's directory then expand relative links.
>>>>>>
>>>>>> The misbehavior happens because buffer-file-name variable is always
>>>>>> nil in indirect buffers. We need to call (file-name-directory
>>>>>> (buffer-file-name (buffer-base-buffer))) instead.
>>>>>>
>>>>>> The patch is attached.
>>>>>>
>>>>>> Best,
>>>>>> Ihor
>>>>>>
>>>>>> diff --git a/lisp/ob-core.el b/lisp/ob-core.el
>>>>>> index f86282f0f..d37eef5f9 100644
>>>>>> --- a/lisp/ob-core.el
>>>>>> +++ b/lisp/ob-core.el
>>>>>> @@ -2561,16 +2561,16 @@ If the `default-directory' is different from the 
>>>>>> containing
>>>>>>  file's directory then expand relative links."
>>>>>>    (when (stringp result)
>>>>>>      (let ((same-directory?
>>>>>> -           (and buffer-file-name
>>>>>> +           (and (buffer-file-name (buffer-base-buffer))
>>>>>>                  (not (string= (expand-file-name default-directory)
>>>>>> -                              (expand-file-name
>>>>>> -                               (file-name-directory 
>>>>>> buffer-file-name)))))))
>>>>>> +                            (expand-file-name
>>>>>> +                             (file-name-directory (buffer-file-name 
>>>>>> (buffer-base-buffer)))))))))
>>>>>>        (format "[[file:%s]%s]"
>>>>>> -              (if (and default-directory buffer-file-name 
>>>>>> same-directory?)
>>>>>> +              (if (and default-directory (buffer-file-name 
>>>>>> (buffer-base-buffer)) same-directory?)
>>>>>>                    (if (eq org-link-file-path-type 'adaptive)
>>>>>>                        (file-relative-name
>>>>>>                         (expand-file-name result default-directory)
>>>>>> -                       (file-name-directory (buffer-file-name)))
>>>>>> +                       (file-name-directory (buffer-file-name 
>>>>>> (buffer-base-buffer))))
>>>>>>                      (expand-file-name result default-directory))
>>>>>>                  result)
>>>>>>                (if description (concat "[" description "]") "")))))
>>>>>>
>>>>>> Emacs  : GNU Emacs 28.0.50 (build 4, x86_64-pc-linux-gnu, GTK+ Version 
>>>>>> 3.24.20, cairo version 1.16.0)
>>>>>>  of 2020-07-27
>>>>>> Package: Org mode version 9.3.7 (release_9.3.7-728-g1efc4e @ 
>>>>>> /home/yantar92/.emacs.d/straight/build/org/)

-- 
Ihor Radchenko,
PhD,
Center for Advancing Materials Performance from the Nanoscale (CAMP-nano)
State Key Laboratory for Mechanical Behavior of Materials, Xi'an Jiaotong 
University, Xi'an, China
Email: yantar92@gmail.com, ihor_radchenko@alumni.sutd.edu.sg