Bug: [Babel] sqlite if: End of file during parsing

Bug: [Babel] sqlite if: End of file during parsing

[Philip Rooke]

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

     http://orgmode.org/manual/Feedback.html#Feedback

Your bug report will be posted to the Org-mode mailing list.
------------------------------------------------------------------------
(Warning, this is the first time I have tried to use org babel and so
there could be user error in the following.  Sorry if that is the
case.)

Starting from emacs -Q evaluate the following code blocks in
succession.  The #+results: blocks below are what I am seeing on my
system.

#+begin_src emacs-lisp :results silent
  (require 'org)
  (require 'org-install)
  (org-babel-do-load-languages
   'org-babel-load-languages
   '((sqlite . t)
     (sh . t)))
#+end_src

The next block will create a small 2k file, ob-bug.db, in the current
directory.  You will probably want to delete later.

#+begin_src sqlite :db ob-bug.db :results silent
  drop table if exists person;
  create table person (f_name text, l_name text);
  insert into person (f_name, l_name) values ('Joe', 'Bloggs');
#+end_src

Check this worked:

#+begin_src sqlite :db ob-bug.db :results output
  select * from person;
#+end_src

#+results:
| Joe | Bloggs |

Formatting the name using the sqlite string concat operator ||
also works as expected:

#+begin_src sqlite :db ob-bug.db :results output
  select f_name || " " || l_name from person;
#+end_src

#+results:
: Joe Bloggs

Add a second line of data:

#+begin_src sqlite :db ob-bug.db :results output silent
  insert into person (f_name, l_name) values ('Fred', 'Smith');
#+end_src

Repeat the last two queries.
#+begin_src sqlite :db ob-bug.db :results output
  select * from person;
#+end_src

#+results:
| Joe  | Bloggs |
| Fred | Smith  |

but...

#+begin_src sqlite :db ob-bug.db :results output
  select f_name || " " || l_name from person;
#+end_src

errors with the unhelpful message "if: End of file during parsing"

Although the query works from a shell:

#+begin_src sh :results output
  sqlite3 ob-bug.db 'select f_name || " " || l_name from person;'
#+end_src

#+results:
: Joe Bloggs
: Fred Smith

Remove the debug database file if you want:

#+begin_src sh :results silent
  rm ob-bug.db
#+end_src

(toggle-debug-on-error) offers no information and so I have tried edebug
stepping through the code.  It seems that the error is happening in the
function org-babel-read at line 2335 when it tries to evaluate
(read "\"Joe").

The query at first ran successfully when there was just one line of
data in the database and stepping through that query shows that the
string being passed through org-babel-read is "Joe Bloggs" rather than
"\"Joe" and therefore follows a different code path at line 2334.

At this point I am stuck.

Phil

Emacs  : GNU Emacs 24.0.92.1 (i386-apple-darwin10.8.0, NS apple-appkit-1038.36)
 of 2012-01-28 on bo
Package: Org-mode version 7.8.03 (release_7.8.03.346.gf9c4)

current state:
==============
(setq
 org-export-preprocess-before-selecting-backend-code-hook '(org-beamer-select-beamer-code)
 org-tab-first-hook '(org-hide-block-toggle-maybe org-src-native-tab-command-maybe org-babel-hide-result-toggle-maybe)
 org-speed-command-hook '(org-speed-command-default-hook org-babel-speed-command-hook)
 org-occur-hook '(org-first-headline-recenter)
 org-metaup-hook '(org-babel-load-in-session-maybe)
 org-export-preprocess-before-normalizing-links-hook '(org-remove-file-link-modifiers)
 org-confirm-shell-link-function 'yes-or-no-p
 org-export-latex-final-hook '(org-beamer-amend-header org-beamer-fix-toc org-beamer-auto-fragile-frames org-beamer-place-default-actions-for-lists)
 org-export-latex-after-initial-vars-hook '(org-beamer-after-initial-vars)
 org-after-todo-state-change-hook '(org-clock-out-if-current)
 org-src-mode-hook '(org-src-babel-configure-edit-buffer org-src-mode-configure-edit-buffer)
 org-agenda-before-write-hook '(org-agenda-add-entry-text)
 org-babel-pre-tangle-hook '(save-buffer)
 org-mode-hook '((lambda nil (org-add-hook (quote change-major-mode-hook) (quote org-show-block-all) (quote append) (quote local)))
                 (lambda nil (org-add-hook (quote change-major-mode-hook) (quote org-babel-show-result-all) (quote append) (quote local)))
                 org-babel-result-hide-spec org-babel-hide-all-hashes)
 org-ctrl-c-ctrl-c-hook '(org-babel-hash-at-point org-babel-execute-safely-maybe)
 org-cycle-hook '(org-cycle-hide-archived-subtrees org-cycle-hide-drawers org-cycle-show-empty-lines org-optimize-window-after-visibility-change)
 org-export-latex-format-toc-function 'org-export-latex-format-toc-default
 org-export-blocks '((src org-babel-exp-src-block nil) (export-comment org-export-blocks-format-comment t) (ditaa org-export-blocks-format-ditaa nil)
                     (dot org-export-blocks-format-dot nil))
 org-export-first-hook '(org-beamer-initialize-open-trackers)
 org-export-interblocks '((src org-babel-exp-non-block-elements))
 org-confirm-elisp-link-function 'yes-or-no-p
 org-metadown-hook '(org-babel-pop-to-session-maybe)
 org-babel-load-languages '((sqlite . t) (sh . t))
 org-clock-out-hook '(org-clock-remove-empty-clock-drawer)
 )

Re: Bug: [Babel] sqlite if: End of file during parsing

[Eric Schulte]

Does the following work with the addition of ":results scalar"?

#+begin_src sqlite :db ob-bug.db :results output scalar
  select f_name || " " || l_name from person;
#+end_src

If so could you send me the contents of the results block?  It appears
that ob-sqlite is choking trying to parse the results into a table.

Thanks,

Philip Rooke <phil@yax.org.uk> 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
>
>      http://orgmode.org/manual/Feedback.html#Feedback
>
> Your bug report will be posted to the Org-mode mailing list.
> ------------------------------------------------------------------------
> (Warning, this is the first time I have tried to use org babel and so
> there could be user error in the following.  Sorry if that is the
> case.)
>
> Starting from emacs -Q evaluate the following code blocks in
> succession.  The #+results: blocks below are what I am seeing on my
> system.
>
> #+begin_src emacs-lisp :results silent
>   (require 'org)
>   (require 'org-install)
>   (org-babel-do-load-languages
>    'org-babel-load-languages
>    '((sqlite . t)
>      (sh . t)))
> #+end_src
>
> The next block will create a small 2k file, ob-bug.db, in the current
> directory.  You will probably want to delete later.
>
> #+begin_src sqlite :db ob-bug.db :results silent
>   drop table if exists person;
>   create table person (f_name text, l_name text);
>   insert into person (f_name, l_name) values ('Joe', 'Bloggs');
> #+end_src
>
> Check this worked:
>
> #+begin_src sqlite :db ob-bug.db :results output
>   select * from person;
> #+end_src
>
> #+results:
> | Joe | Bloggs |
>
> Formatting the name using the sqlite string concat operator ||
> also works as expected:
>
> #+begin_src sqlite :db ob-bug.db :results output
>   select f_name || " " || l_name from person;
> #+end_src
>
> #+results:
> : Joe Bloggs
>
> Add a second line of data:
>
> #+begin_src sqlite :db ob-bug.db :results output silent
>   insert into person (f_name, l_name) values ('Fred', 'Smith');
> #+end_src
>
> Repeat the last two queries.
> #+begin_src sqlite :db ob-bug.db :results output
>   select * from person;
> #+end_src
>
> #+results:
> | Joe  | Bloggs |
> | Fred | Smith  |
>
> but...
>
> #+begin_src sqlite :db ob-bug.db :results output
>   select f_name || " " || l_name from person;
> #+end_src
>
> errors with the unhelpful message "if: End of file during parsing"
>
> Although the query works from a shell:
>
> #+begin_src sh :results output
>   sqlite3 ob-bug.db 'select f_name || " " || l_name from person;'
> #+end_src
>
> #+results:
> : Joe Bloggs
> : Fred Smith
>
> Remove the debug database file if you want:
>
> #+begin_src sh :results silent
>   rm ob-bug.db
> #+end_src
>
> (toggle-debug-on-error) offers no information and so I have tried edebug
> stepping through the code.  It seems that the error is happening in the
> function org-babel-read at line 2335 when it tries to evaluate
> (read "\"Joe").
>
> The query at first ran successfully when there was just one line of
> data in the database and stepping through that query shows that the
> string being passed through org-babel-read is "Joe Bloggs" rather than
> "\"Joe" and therefore follows a different code path at line 2334.
>
> At this point I am stuck.
>
> Phil
>
> Emacs  : GNU Emacs 24.0.92.1 (i386-apple-darwin10.8.0, NS apple-appkit-1038.36)
>  of 2012-01-28 on bo
> Package: Org-mode version 7.8.03 (release_7.8.03.346.gf9c4)
>
> current state:
> ==============
> (setq
>  org-export-preprocess-before-selecting-backend-code-hook '(org-beamer-select-beamer-code)
>  org-tab-first-hook '(org-hide-block-toggle-maybe org-src-native-tab-command-maybe org-babel-hide-result-toggle-maybe)
>  org-speed-command-hook '(org-speed-command-default-hook org-babel-speed-command-hook)
>  org-occur-hook '(org-first-headline-recenter)
>  org-metaup-hook '(org-babel-load-in-session-maybe)
>  org-export-preprocess-before-normalizing-links-hook '(org-remove-file-link-modifiers)
>  org-confirm-shell-link-function 'yes-or-no-p
>  org-export-latex-final-hook '(org-beamer-amend-header org-beamer-fix-toc org-beamer-auto-fragile-frames org-beamer-place-default-actions-for-lists)
>  org-export-latex-after-initial-vars-hook '(org-beamer-after-initial-vars)
>  org-after-todo-state-change-hook '(org-clock-out-if-current)
>  org-src-mode-hook '(org-src-babel-configure-edit-buffer org-src-mode-configure-edit-buffer)
>  org-agenda-before-write-hook '(org-agenda-add-entry-text)
>  org-babel-pre-tangle-hook '(save-buffer)
>  org-mode-hook '((lambda nil (org-add-hook (quote change-major-mode-hook) (quote org-show-block-all) (quote append) (quote local)))
>                  (lambda nil (org-add-hook (quote change-major-mode-hook) (quote org-babel-show-result-all) (quote append) (quote local)))
>                  org-babel-result-hide-spec org-babel-hide-all-hashes)
>  org-ctrl-c-ctrl-c-hook '(org-babel-hash-at-point org-babel-execute-safely-maybe)
>  org-cycle-hook '(org-cycle-hide-archived-subtrees org-cycle-hide-drawers org-cycle-show-empty-lines org-optimize-window-after-visibility-change)
>  org-export-latex-format-toc-function 'org-export-latex-format-toc-default
>  org-export-blocks '((src org-babel-exp-src-block nil) (export-comment org-export-blocks-format-comment t) (ditaa org-export-blocks-format-ditaa nil)
>                      (dot org-export-blocks-format-dot nil))
>  org-export-first-hook '(org-beamer-initialize-open-trackers)
>  org-export-interblocks '((src org-babel-exp-non-block-elements))
>  org-confirm-elisp-link-function 'yes-or-no-p
>  org-metadown-hook '(org-babel-pop-to-session-maybe)
>  org-babel-load-languages '((sqlite . t) (sh . t))
>  org-clock-out-hook '(org-clock-remove-empty-clock-drawer)
>  )
>

-- 
Eric Schulte
http://cs.unm.edu/~eschulte/

Re: Bug: [Babel] sqlite if: End of file during parsing

[Philip Rooke]

Eric Schulte <eric.schulte@gmx.com> writes:

> Does the following work with the addition of ":results scalar"?

Yes, there is no error although the format of the result is different to
the one database line query or the equivalent shell command.  This is
what happens for me:

#+begin_src sqlite :db ob-bug.db :results output scalar
  select f_name || " " || l_name from person;
#+end_src

#+results:
: "Joe Bloggs"
: "Fred Smith"

Phil

Re: Bug: [Babel] sqlite if: End of file during parsing

[Eric Schulte]

Philip Rooke <phil@yax.org.uk> writes:

> Eric Schulte <eric.schulte@gmx.com> writes:
>
>> Does the following work with the addition of ":results scalar"?
>
> Yes, there is no error although the format of the result is different to
> the one database line query or the equivalent shell command.  This is
> what happens for me:
>
> #+begin_src sqlite :db ob-bug.db :results output scalar
>   select f_name || " " || l_name from person;
> #+end_src
>
> #+results:
> : "Joe Bloggs"
> : "Fred Smith"
>

Hi Phil,

Thanks for the detailed reproduction information in your original email,
it made this issue much easier to solve.  I've just pushed up a fix,
please let me know if the problem continues.

Best,

-- 
Eric Schulte
http://cs.unm.edu/~eschulte/

Re: Bug: [Babel] sqlite if: End of file during parsing

[Philip Rooke]

Eric Schulte <eric.schulte@gmx.com> writes:

>
> Thanks for the detailed reproduction information in your original email,
> it made this issue much easier to solve.  I've just pushed up a fix,
> please let me know if the problem continues.

Eric, seems to work perfectly now.

Thank you so much for your help.

Phil