openmolar looking in /usr/share/openmolar

OpenSubmitted by Quiliro Ordonez Baca.
Details
4 participants
  • Adonay Felipe Nogueira
  • Chris Marusich
  • Ludovic Courtès
  • Quiliro Ordonez Baca
Owner
unassigned
Severity
normal
Q
Q
Quiliro Ordonez Baca wrote on 20 Nov 2017 18:33
(address . bug-guix@gnu.org)
878tf0x3bq.fsf@riseup.net
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.
L
L
Ludovic Courtès wrote on 21 Nov 2017 14:38
control message for bug #29365
(address . control@debbugs.gnu.org)
87wp2jlpkk.fsf@gnu.org
tags 29365 easy
C
C
Chris Marusich wrote on 22 Nov 2017 10:35
Re: bug#29365: openmolar looking in /usr/share/openmolar
(name . Quiliro Ordonez Baca)(address . quiliro@riseup.net)(address . 29365@debbugs.gnu.org)
87tvxmfyf4.fsf@gmail.com
Quiliro Ordonez Baca <quiliro@riseup.net> writes:

Toggle quote (17 lines)
> 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
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A
A
Adonay Felipe Nogueira wrote on 22 Nov 2017 18:13
(address . 29365@debbugs.gnu.org)
871skq2q4j.fsf@hyperbola.info
Adding to what Chris Marusich described:

'substitute* works somewhat in the following way:

Toggle snippet (5 lines)
(substitute FILE-string-or-FILE-list-of-strings
((EREGEX-string SYMBOLS-to-put-both-entire-match-and-captures-or-NOTHING)
REPLACEMENT-string))

For example:

Toggle snippet (27 lines)
(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).

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:
Toggle quote (21 lines)
>
> 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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Q
Q
Quiliro Ordonez Baca wrote on 20 Dec 2017 21:11
(name . Chris Marusich)(address . cmmarusich@gmail.com)(address . 29365@debbugs.gnu.org)
87po79rwgb.fsf@portkomputilo.i-did-not-set--mail-host-address--so-tickle-me
Chris Marusich <cmmarusich@gmail.com> writes:

Toggle quote (22 lines)
> Quiliro Ordonez Baca <quiliro@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.

Toggle quote (7 lines)
> 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)))))

Toggle quote (5 lines)
> 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.

Toggle quote (5 lines)
> 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?
?