Re: Global variables in Org mode document with source blocks

[John Kitchin]

Given all the different languages involved, I don't think there is a way to use a common variable. 

One way might be to have each block output some kind of string if it fails, and then in the last block you could search for the buffer for that string. Something like this:

* Section 1

#+BEGIN_SRC sh
false || echo "failed"-`date +'%s'`
#+END_SRC

#+RESULTS:
: failed-1621348872


#+BEGIN_SRC python
import time

if not False:
    print(f'failed-{time.time()}')
#+END_SRC

#+RESULTS:
: failed-1621348926.125608


* Final section

#+BEGIN_SRC emacs-lisp
(format "There were %s failed blocks" (count-matches "failed-[0-9]" (point-min) (point-max)))
#+END_SRC

#+RESULTS:
: There were 2 failed blocks

Some alternatives include writing/appending to a file on error, and then counting the number of lines.

Another route is to use a :post header and search for the string there.

#+BEGIN_SRC emacs-lisp
(setq n-failures 0)
#+END_SRC

#+RESULTS:
: 0

#+name: fail-capture
#+BEGIN_SRC emacs-lisp :var data="">(when (string-match "failed-[0-9]" data)
  (incf n-failures)
  (message "captured a failure in %s. n-failures=%s" data n-failures))
#+END_SRC

#+BEGIN_SRC sh :post fail-capture(*this*)
false || echo "failed"-`date +'%s'`
#+END_SRC

#+RESULTS:
: captured a failure in failed-1621349398. n-failures=1


#+BEGIN_SRC python :post fail-capture(*this*)
print('This did not fail')
#+END_SRC

#+RESULTS:
: nil

#+BEGIN_SRC python :post fail-capture(*this*)
print('This failed-9')
#+END_SRC

#+RESULTS:
: captured a failure in This failed-9
: . n-failures=2

All these approaches need you to handle and catch the errors. I think other kinds of errors would stop the export process. e.g. if a block errors out from division by zero or something.

I don't know how easy it would be to check if a src block succeeded or not. If it was easy, you might use the org-babel-after-execute-hook variable to update something when a failure is detected. Some blocks create an *Org-Babel Error Output buffer somewhere, but i don't know if this is 100% reliable across all blocks.

John

-----------------------------------
Professor John Kitchin (he/him/his)
Doherty Hall A207F
Department of Chemical Engineering
Carnegie Mellon University
Pittsburgh, PA 15213
412-268-7803

@johnkitchin
http://kitchingroup.cheme.cmu.edu

On Tue, May 18, 2021 at 9:58 AM Lennart C. Karssen <lennart@karssen.org> wrote:

Dear list,

I am working on a dynamic report in Org mode, where I use source blocks
in various languages to process data. Several blocks produce text or
tables that become part of the PDF on export.

The final chapter should state whether all checks passed, or whether one
or more failed (it is not necessary to know which step failed).

In a single language environment, I would use a variable (called e.g.
nrChecksFailed) that would be incremented for each failing check. In a
single language Org document this could probably be done with a
:session, but given that I mix Awk, Bash, Emacs lisp and R that doesn't
look like the way to go. Do Org documents/source blocks have some
concept of a (global) variable that I can pass to my SRC blocks and
increment inside them?

E.g. after somehow initialising nrChecksFailed = 0, I would like to do:

#+header :var nFailed=nrChecksFailed :var someData=someData
#+begin_src R :results raw
do_some_check_here_on_someData

if (check_results_OK) {
  cat("check A passed\n")
} else {
  cat("check A *failed*\n")
  nFailed <- nFailed + 1
}
#+end_src

So that in my conclusion chapter I can do for example:

#+header: :var nFailed=nrChecksFailed
#+begin_src bash  :results raw
if [[ nFailed -eq 0 ]]; then
  echo "All checks passed
else
 echo "One or more checks *failed!*"
fi
#+end_src


Best regards,

Lennart.

--
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L.C. Karssen
The Netherlands

lennart@karssen.org
http://blog.karssen.org
GPG key ID: A88F554A
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