GNU bug report logs - #29365
openmolar looking in /usr/share/openmolar

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Message #5 received at submit <at> debbugs.gnu.org (full text, mbox):

From: Quiliro Ordonez Baca <quiliro <at> riseup.net>
To: bug-guix <at> gnu.org
Subject: openmolar looking in /usr/share/openmolar
Date: Mon, 20 Nov 2017 12:33:29 -0500

When starting OpenMolar for the first time, it has an error when it
creates the application database: 

ERROR - error creating database tables
Traceback (most recent call last):
  File "/gnu/store/smx5rayf45ylqn59czjkvx2hcrl95p5x-openmolar-1.0.15-gd81f9e5/lib/python3.5/site-packages/openmolar/create_db.py", line 145, in create_tables
    f = open(fp, "r")
FileNotFoundError: [Errno 2] No existe el fichero o el directorio: '/usr/share/openmolar/resources/schema.sql'

when it should look for the following file:
/gnu/store/smx5rayf45ylqn59czjkvx2hcrl95p5x-openmolar-1.0.15-gd81f9e5/share/openmolar/resources/schema.sql

The flaw in the definition is in:
/gnu/store/smx5rayf45ylqn59czjkvx2hcrl95p5x-openmolar-1.0.15-gd81f9e5/lib/python3.5/site-packages/openmolar/settings/localsettings.py:    SHARE_DIR = os.path.join("/usr", "share", "openmolar")

I do not know haw to fix it. Please instruct how to do it.

Message #10 received at 29365 <at> debbugs.gnu.org (full text, mbox):

From: Chris Marusich <cmmarusich <at> gmail.com>
To: Quiliro Ordonez Baca <quiliro <at> riseup.net>
Cc: 29365 <at> debbugs.gnu.org
Subject: Re: bug#29365: openmolar looking in /usr/share/openmolar
Date: Wed, 22 Nov 2017 01:35:59 -0800

[Message part 1 (text/plain, inline)]

Quiliro Ordonez Baca <quiliro <at> riseup.net> writes:

> When starting OpenMolar for the first time, it has an error when it
> creates the application database: 
>
> ERROR - error creating database tables
> Traceback (most recent call last):
>   File "/gnu/store/smx5rayf45ylqn59czjkvx2hcrl95p5x-openmolar-1.0.15-gd81f9e5/lib/python3.5/site-packages/openmolar/create_db.py", line 145, in create_tables
>     f = open(fp, "r")
> FileNotFoundError: [Errno 2] No existe el fichero o el directorio: '/usr/share/openmolar/resources/schema.sql'
>
> when it should look for the following file:
> /gnu/store/smx5rayf45ylqn59czjkvx2hcrl95p5x-openmolar-1.0.15-gd81f9e5/share/openmolar/resources/schema.sql
>
> The flaw in the definition is in:
> /gnu/store/smx5rayf45ylqn59czjkvx2hcrl95p5x-openmolar-1.0.15-gd81f9e5/lib/python3.5/site-packages/openmolar/settings/localsettings.py:    SHARE_DIR = os.path.join("/usr", "share", "openmolar")
>
> I do not know haw to fix it. Please instruct how to do it.

Based on your assessment, it looks like the problem is that the
application hard-codes the "/usr" directory path.

One solution for this problem is to replace that line of code in the
source with the correct path.  You can do this in the package definition
by using the substitute* macro provided by the (guix build utils)
module.  In fact, it looks like the current package definition for
openmolar already attempts to do this.  Run "guix edit openmolar" to
view the current package definition.

Perhaps you could modify the package definition to also replace the path
in localsettings.py?  You might also want to look around in the source
for other paths that need to be fixed (a command such as "grep -r /usr"
might be helpful).

For information on how to use substitute*, please refer to
guix/build/utils.scm in the Guix source tree.  For general information
on hacking on Guix, check the section titled "Contributing" in the
manual (e.g., run info '(guix) Contributing' in a terminal).

-- 
Chris

[signature.asc (application/pgp-signature, inline)]

Message #13 received at 29365 <at> debbugs.gnu.org (full text, mbox):

From: Adonay Felipe Nogueira <adfeno <at> hyperbola.info>
To: 29365 <at> debbugs.gnu.org
Subject: Re: bug#29365: openmolar looking in /usr/share/openmolar
Date: Wed, 22 Nov 2017 15:13:32 -0200

Adding to what Chris Marusich described:

'substitute* works somewhat in the following way:

--8<---------------cut here---------------start------------->8---
(substitute FILE-string-or-FILE-list-of-strings
   ((EREGEX-string SYMBOLS-to-put-both-entire-match-and-captures-or-NOTHING)
    REPLACEMENT-string))
--8<---------------cut here---------------end--------------->8---

For example:

--8<---------------cut here---------------start------------->8---
(substitute "file1.txt"
   (("a")
    "b")
   ;; ... would replace every "a" with "b".
   (("1([[:digit:]]*)([^[:digit:]])" full capture1 capture2)
    (string-append full
                   " 2"
                   capture1
                   capture2)))
   ;; ... would replace "1234A" and "1A" with "1234A 2234A" and "1A 2A",
   ;; respectively.

(substitute '("file2.txt"
              "file3.txt"
              "file4.txt")
   (("a\\*\n") ; matches literal asterisk (*) followed by a new
               ; line/line feed.
    "b")
   ;; ... from "a*[newline]" to "b".
   (("(1)[^[:digit:]]*" _ interesting-one) ; use "_" capture to not save
                                           ; the whole match.
    (string-append interesting-one
                   " 1")))
   ;; ... from "1A" or from "1ABC" to "1 1" ("A" and "ABC" parts are
   ;; discarded).
--8<---------------cut here---------------end--------------->8---

Notice that the regular expression that GNU Guile uses is the extended
one (Extended Regular Expression). See the info page for Guile for more
details (type `info guile' in the terminal, and go to the section
"Regular Expressions", inside that section notice that there is one
talking about backslash escapes, this one is also important for reasons
that you'll see in the next paragrah).

Notice that in Guile backslashes in strings also have special meaning,
so one has to take into account string+regex special meaning when doing
backslash escapes. In the examples given, the replacement for
"file2.txt" onwards shows us how to deal with this.

I hope this helps! ;)

2017-11-22T01:35:59-0800 Chris Marusich wrote:
>
> Based on your assessment, it looks like the problem is that the
> application hard-codes the "/usr" directory path.
>
> One solution for this problem is to replace that line of code in the
> source with the correct path.  You can do this in the package definition
> by using the substitute* macro provided by the (guix build utils)
> module.  In fact, it looks like the current package definition for
> openmolar already attempts to do this.  Run "guix edit openmolar" to
> view the current package definition.
>
> Perhaps you could modify the package definition to also replace the path
> in localsettings.py?  You might also want to look around in the source
> for other paths that need to be fixed (a command such as "grep -r /usr"
> might be helpful).
>
> For information on how to use substitute*, please refer to
> guix/build/utils.scm in the Guix source tree.  For general information
> on hacking on Guix, check the section titled "Contributing" in the
> manual (e.g., run info '(guix) Contributing' in a terminal).

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Message #16 received at 29365 <at> debbugs.gnu.org (full text, mbox):

From: Quiliro Ordonez Baca <quiliro <at> riseup.net>
To: Chris Marusich <cmmarusich <at> gmail.com>
Cc: 29365 <at> debbugs.gnu.org
Subject: Re: bug#29365: openmolar looking in /usr/share/openmolar
Date: Wed, 20 Dec 2017 15:11:32 -0500

Chris Marusich <cmmarusich <at> gmail.com> writes:

> Quiliro Ordonez Baca <quiliro <at> riseup.net> writes:
>
>> When starting OpenMolar for the first time, it has an error when it
>> creates the application database: 
>>
>> ERROR - error creating database tables
>> Traceback (most recent call last):
>>   File "/gnu/store/smx5rayf45ylqn59czjkvx2hcrl95p5x-openmolar-1.0.15-gd81f9e5/lib/python3.5/site-packages/openmolar/create_db.py", line 145, in create_tables
>>     f = open(fp, "r")
>> FileNotFoundError: [Errno 2] No existe el fichero o el directorio: '/usr/share/openmolar/resources/schema.sql'
>>
>> when it should look for the following file:
>> /gnu/store/smx5rayf45ylqn59czjkvx2hcrl95p5x-openmolar-1.0.15-gd81f9e5/share/openmolar/resources/schema.sql
>>
>> The flaw in the definition is in:
>> /gnu/store/smx5rayf45ylqn59czjkvx2hcrl95p5x-openmolar-1.0.15-gd81f9e5/lib/python3.5/site-packages/openmolar/settings/localsettings.py:    SHARE_DIR = os.path.join("/usr", "share", "openmolar")
>>
>> I do not know haw to fix it. Please instruct how to do it.
>
> Based on your assessment, it looks like the problem is that the
> application hard-codes the "/usr" directory path.

Yes.

> One solution for this problem is to replace that line of code in the
> source with the correct path.  You can do this in the package definition
> by using the substitute* macro provided by the (guix build utils)
> module.  In fact, it looks like the current package definition for
> openmolar already attempts to do this.  Run "guix edit openmolar" to
> view the current package definition.

Exactly. It already attempts to do that in:

   (arguments
    `(#:use-setuptools? #f
      #:phases
      (modify-phases %standard-phases
        (add-after 'unpack 'patch-/usr
          (lambda* (#:key outputs #:allow-other-keys)
            (substitute* "setup.py"
              (("/usr") (assoc-ref outputs "out")))
            #t)))))

> Perhaps you could modify the package definition to also replace the path
> in localsettings.py?  You might also want to look around in the source
> for other paths that need to be fixed (a command such as "grep -r /usr"
> might be helpful).

$ grep -R /usr
lib/python3.5/site-packages/openmolar/dbtools/records_in_use.py:#! /usr/bin/env p
lib/python3.5/site-packages/openmolar/settings/localsettings.py:    SHARE_DIR = os.path.join("/usr", "share", "openmolar")
Coincidencia en el fichero binario lib/python3.5/site-packages/openmolar/settings/__pycache__/localsettings.cpython-35.pyc

openmolar has three dependencies:
python-pyqt+sqcintilla
python-mysqlclient
qscintilla

But only python-pyqt+sqcintilla files have /usr on them (besides openmolar's). Perhaps the
problem is that package definition. But I cannot figure how to do it yet.

> For information on how to use substitute*, please refer to
> guix/build/utils.scm in the Guix source tree.  For general information
> on hacking on Guix, check the section titled "Contributing" in the
> manual (e.g., run info '(guix) Contributing' in a terminal).

I find that it is needed to download the source. But I do not have a
connection to the web. I have to travel 1 hour every time I need to
connect. Is there any way i can use Emacs to have all necesary files for
hacking on Guix?

Message #21 received at 29365-done <at> debbugs.gnu.org (full text, mbox):

From: Ludovic Courtès <ludo <at> gnu.org>
To: Marco Rimoldi <rimarko <at> libero.it>
Cc: 68720-done <at> debbugs.gnu.org, 29365-done <at> debbugs.gnu.org
Subject: Re: [bug#68720] [PATCH] gnu: openmolar-1: Update to release
 1.1.6-g81838c8 and partial runtime fix.
Date: Sat, 10 Feb 2024 22:56:03 +0100

Hi,

Marco Rimoldi <rimarko <at> libero.it> skribis:

> This commit fixes https://issues.guix.gnu.org/29365.

Alright, applied!

> The package now fails to start with this error message:
>
> File "/gnu/store/zzys4bqllx3a3gramwj2pyyigfb4z75b-openmolar-1.1.6-g81838c85/lib/python3.10/site-packages/openmolar/qt4gui/customwidgets/toothProps.py", line 827, in shapes
>     self.mesial.setPoints(
> TypeError: 'float' object cannot be interpreted as an integer
>
> I will submit a new issue if the patch is accepted.

That’d be great.

Thanks!

Ludo’.

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