Setup in debian 13 (trixie): bugs + fixes

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Hello, from Debian Trixie!

I ran into some hickups trying to setup gnumed-client and gnumed-sever (gm-bootstrap).
Debugged, and now GNUmed is up and running, healthy and new! Here below my findings + fixes.



*/CLIENT/*

Two dependencies are not automatically installed with gnumed-client, and thus are missing
when trying to run the client.

     - python3-standard-mailcap
     - python3-packaging

Just a simple...

     sudo apt install python3-packaging python3-standard-mailcap

... and the client runs, no problem!

Explanation that I could gather: Mailcap was part of the Standard Python Lib, but now it was
removed, so it needs "manual" installation. Now as for the packaging lib, I don't know why
it was not automatically installed by apt.

I know this is probably something that should be fixed by the debian team maybe? But just
out of curiosity, how does one go about adding these packages to the dependencies list so
that apt installs them automatically? Do we get a say in it, so that if for example we add
these to the prerequisites in gituhub and then the debian team pulls the changes from there?
Always wanted to know the workings behind package management...



*/DATABASE SETUP/*

This was trickier! Debugged with help of LLMs. I had two types of errors:

1- some syntax (?) changes in postresql 17 (used by debian trixie), so that the bootstrapper
has to be updated;
2- some permission troubles with gm-dbo not being able to grant roles.


*1- Syntax (?) error:*

See file attached for the tail of the log after the error (bootstrap_error_1.txt). Ran some
tests, did some tinkering.

Had to modify /var/lib/gnumed/server/bootstrap/bootstrap_gm_db_system.py to fix.

Changing line 420 to 425...

     curs = self.conn.cursor()
     curs.execute(u"select setting from pg_settings where name = 'lc_ctype'")
     data = curs.fetchall()
     lc_ctype = data[0][0]
     _log.info(u'template database LC_CTYPE is [%s]', lc_ctype)
     lc_ctype = lc_ctype.lower()

... for this...

     curs = self.conn.cursor()
     # PG17+: lc_ctype/lc_collate are per-database attrs, not GUCs
     curs.execute(
         u"SELECT datcollate, datctype "
         u"FROM pg_database "
         u"WHERE datname = current_database()"
     )
     row = curs.fetchone()
     if not row:
         _log.error(u"Could not read datcollate/datctype for template DB")
         return None
     lc_collate, lc_ctype = row
     _log.info(u'template database LC_COLLATE is [%s]', lc_collate)
     _log.info(u'template database LC_CTYPE   is [%s]', lc_ctype)
     lc_ctype = lc_ctype.lower()

... fixed the bug, and the bootstrapper was able to continue (until the next error detailed below).

Explanation (textually from the LLM, I'm still a newbie to sql databases): In PostgreSQL 17,
lc_collate and lc_ctype were removed from pg_settings because they are no longer GUCs. They
are per-database attributes stored in pg_database, not cluster-wide runtime parameters. So
the query SELECT setting FROM pg_settings WHERE name='lc_ctype' returns zero rows, data
becomes an empty list [], and we get an IndexError which aborts the bootstrap.


*2- gm-dbo permission troubles:*

Attached parts of log for these errors (bootstrap_error_2.txt).

I first granted just the role for the first error...

     jessie@deb-vivobook:~$ sudo -u postgres psql -d postgres -X -v ON_ERROR_STOP=1 -c \
     'GRANT "gm-logins"  TO "gm-dbo" WITH ADMIN OPTION;'
     [sudo] password for jessie:
     GRANT ROLE
     jessie@deb-vivobook:~$ sudo -u postgres psql -d postgres -X -v ON_ERROR_STOP=1 -c \
     'GRANT "gm-public"  TO "gm-dbo" WITH ADMIN OPTION;'
     NOTICE:  role "gm-dbo" has already been granted membership in role "gm-public" by role "postgres"
     GRANT ROLE
     jessie@deb-vivobook:~$ sudo -u postgres psql -d postgres -X -v ON_ERROR_STOP=1 -c \
     'GRANT "gnumed_v16" TO "gm-dbo" WITH ADMIN OPTION;'
     GRANT ROLE
     jessie@deb-vivobook:~$ sudo -u postgres psql -d postgres -X -c \
     'ALTER ROLE "gm-dbo" CREATEROLE CREATEDB;'
     ALTER ROLE

... but then since the next error was also about gm-dbo not having admin options,
I listed all roles...

     jessie@deb-vivobook:~$ sudo -u postgres psql -d postgres -X -c \
     "SELECT rolname FROM pg_roles WHERE rolname LIKE 'gm-%' ORDER BY 1;"
            rolname
     ---------------------
      gm-dbo
      gm-doctors
      gm-logins
      gm-public
      gm-staff
      gm-staff_medical
      gm-staff_office
      gm-trainees_medical
      gm-trainees_office
     (9 rows)

... then gave admin to gm-dbo to every role...

     jessie@deb-vivobook:~$ sudo -u postgres psql -d postgres -X -v ON_ERROR_STOP=1 -c \
     'GRANT "gm-doctors" TO "gm-dbo" WITH ADMIN OPTION;'
     GRANT ROLE

     jessie@deb-vivobook:~$ sudo -u postgres psql -d postgres -X -v ON_ERROR_STOP=1 -c \
     'GRANT "gm-logins" TO "gm-dbo" WITH ADMIN OPTION;'
     NOTICE:  role "gm-dbo" has already been granted membership in role "gm-logins" by role "postgres"
     GRANT ROLE

     jessie@deb-vivobook:~$ sudo -u postgres psql -d postgres -X -v ON_ERROR_STOP=1 -c \
     'GRANT "gm-public" TO "gm-dbo" WITH ADMIN OPTION;'
     NOTICE:  role "gm-dbo" has already been granted membership in role "gm-public" by role "postgres"
     GRANT ROLE

     jessie@deb-vivobook:~$ sudo -u postgres psql -d postgres -X -v ON_ERROR_STOP=1 -c \
     'GRANT "gm-staff" TO "gm-dbo" WITH ADMIN OPTION;'
     NOTICE:  role "gm-dbo" has already been granted membership in role "gm-staff" by role "postgres"
     GRANT ROLE

     jessie@deb-vivobook:~$ sudo -u postgres psql -d postgres -X -v ON_ERROR_STOP=1 -c \
     'GRANT "gm-staff_medical" TO "gm-dbo" WITH ADMIN OPTION;'
     GRANT ROLE

     jessie@deb-vivobook:~$ sudo -u postgres psql -d postgres -X -v ON_ERROR_STOP=1 -c 'GRANT "gm-staff_office" TO "gm-dbo" WITH ADMIN OPTION;'
     GRANT ROLE

     jessie@deb-vivobook:~$ sudo -u postgres psql -d postgres -X -v ON_ERROR_STOP=1 -c 'GRANT "gm-trainees_medical" TO "gm-dbo" WITH ADMIN OPTION;'
     GRANT ROLE

     jessie@deb-vivobook:~$ sudo -u postgres psql -d postgres -X -v ON_ERROR_STOP=1 -c 'GRANT "gm-trainees_office" TO "gm-dbo" WITH ADMIN OPTION;'
     GRANT ROLE

... surely there's a way to make this with a single query but I wanted to see what resulted for each operation (and didn't know how to make this more efficient :).


Then checked that gm-dbo was granted all roles successfully...

     jessie@deb-vivobook:~$ sudo -u postgres psql -d postgres -X -c \
     "SELECT r.rolname AS member, m.rolname AS role, am.admin_option
      FROM pg_auth_members am
      JOIN pg_roles r ON r.oid = am.member
      JOIN pg_roles m ON m.oid = am.roleid
      WHERE r.rolname='gm-dbo'
        AND (m.rolname LIKE 'gm-%' OR m.rolname='gnumed_v16')
      ORDER BY role;"

      member |        role         | admin_option
     --------+---------------------+--------------
      gm-dbo | gm-doctors          | t
      gm-dbo | gm-logins           | t
      gm-dbo | gm-public           | t
      gm-dbo | gm-staff            | t
      gm-dbo | gm-staff_medical    | t
      gm-dbo | gm-staff_office     | t
      gm-dbo | gm-trainees_medical | t
      gm-dbo | gm-trainees_office  | t
      gm-dbo | gnumed_v16          | t
     (9 rows)

... restarted postresql...

     sudo systemctl restart postgresql

... and ran again the bootstrap, now successfully!


The rest of the setup went smoothly and the client runs great (as far as I've tested it).

María

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    <pre>Hello, from Debian Trixie!

I ran into some hickups trying to setup gnumed-client and gnumed-sever (gm-bootstrap).
Debugged, and now GNUmed is up and running, healthy and new! Here below my findings + fixes.



<b><i>CLIENT</i></b>

Two dependencies are not automatically installed with gnumed-client, and thus are missing
when trying to run the client.

    - python3-standard-mailcap
    - python3-packaging

Just a simple...

    sudo apt install python3-packaging python3-standard-mailcap

... and the client runs, no problem!

Explanation that I could gather: Mailcap was part of the Standard Python Lib, but now it was
removed, so it needs "manual" installation. Now as for the packaging lib, I don't know why 
it was not automatically installed by apt.

I know this is probably something that should be fixed by the debian team maybe? But just 
out of curiosity, how does one go about adding these packages to the dependencies list so 
that apt installs them automatically? Do we get a say in it, so that if for example we add 
these to the prerequisites in gituhub and then the debian team pulls the changes from there? 
Always wanted to know the workings behind package management...



<b><i>DATABASE SETUP</i></b>

This was trickier! Debugged with help of LLMs. I had two types of errors:

1- some syntax (?) changes in postresql 17 (used by debian trixie), so that the bootstrapper 
has to be updated;
2- some permission troubles with gm-dbo not being able to grant roles.


<b>1- Syntax (?) error:</b>

See file attached for the tail of the log after the error (bootstrap_error_1.txt). Ran some 
tests, did some tinkering.

Had to modify /var/lib/gnumed/server/bootstrap/bootstrap_gm_db_system.py to fix. 

Changing line 420 to 425...

    curs = self.conn.cursor()
    curs.execute(u"select setting from pg_settings where name = 'lc_ctype'")
    data = curs.fetchall()
    lc_ctype = data[0][0]
    _log.info(u'template database LC_CTYPE is [%s]', lc_ctype)
    lc_ctype = lc_ctype.lower()

... for this...

    curs = self.conn.cursor()
    # PG17+: lc_ctype/lc_collate are per-database attrs, not GUCs
    curs.execute(
        u"SELECT datcollate, datctype "
        u"FROM pg_database "
        u"WHERE datname = current_database()"
    )
    row = curs.fetchone()
    if not row:
        _log.error(u"Could not read datcollate/datctype for template DB")
        return None
    lc_collate, lc_ctype = row
    _log.info(u'template database LC_COLLATE is [%s]', lc_collate)
    _log.info(u'template database LC_CTYPE   is [%s]', lc_ctype)
    lc_ctype = lc_ctype.lower()

... fixed the bug, and the bootstrapper was able to continue (until the next error detailed below).

Explanation (textually from the LLM, I'm still a newbie to sql databases): In PostgreSQL 17, 
lc_collate and lc_ctype were removed from pg_settings because they are no longer GUCs. They 
are per-database attributes stored in pg_database, not cluster-wide runtime parameters. So 
the query SELECT setting FROM pg_settings WHERE name='lc_ctype' returns zero rows, data 
becomes an empty list [], and we get an IndexError which aborts the bootstrap.


<b>2- gm-dbo permission troubles:</b>

Attached parts of log for these errors (bootstrap_error_2.txt).

I first granted just the role for the first error...

    jessie@deb-vivobook:~$ sudo -u postgres psql -d postgres -X -v ON_ERROR_STOP=1 -c \
    'GRANT "gm-logins"  TO "gm-dbo" WITH ADMIN OPTION;'
    [sudo] password for jessie: 
    GRANT ROLE
    jessie@deb-vivobook:~$ sudo -u postgres psql -d postgres -X -v ON_ERROR_STOP=1 -c \
    'GRANT "gm-public"  TO "gm-dbo" WITH ADMIN OPTION;'
    NOTICE:  role "gm-dbo" has already been granted membership in role "gm-public" by role "postgres"
    GRANT ROLE
    jessie@deb-vivobook:~$ sudo -u postgres psql -d postgres -X -v ON_ERROR_STOP=1 -c \
    'GRANT "gnumed_v16" TO "gm-dbo" WITH ADMIN OPTION;'
    GRANT ROLE
    jessie@deb-vivobook:~$ sudo -u postgres psql -d postgres -X -c \
    'ALTER ROLE "gm-dbo" CREATEROLE CREATEDB;'
    ALTER ROLE

... but then since the next error was also about gm-dbo not having admin options, 
I listed all roles...

    jessie@deb-vivobook:~$ sudo -u postgres psql -d postgres -X -c \
    "SELECT rolname FROM pg_roles WHERE rolname LIKE 'gm-%' ORDER BY 1;"
           rolname       
    ---------------------
     gm-dbo
     gm-doctors
     gm-logins
     gm-public
     gm-staff
     gm-staff_medical
     gm-staff_office
     gm-trainees_medical
     gm-trainees_office
    (9 rows)

... then gave admin to gm-dbo to every role...

    jessie@deb-vivobook:~$ sudo -u postgres psql -d postgres -X -v ON_ERROR_STOP=1 -c \
    'GRANT "gm-doctors" TO "gm-dbo" WITH ADMIN OPTION;'
    GRANT ROLE

    jessie@deb-vivobook:~$ sudo -u postgres psql -d postgres -X -v ON_ERROR_STOP=1 -c \
    'GRANT "gm-logins" TO "gm-dbo" WITH ADMIN OPTION;'
    NOTICE:  role "gm-dbo" has already been granted membership in role "gm-logins" by role "postgres"
    GRANT ROLE

    jessie@deb-vivobook:~$ sudo -u postgres psql -d postgres -X -v ON_ERROR_STOP=1 -c \
    'GRANT "gm-public" TO "gm-dbo" WITH ADMIN OPTION;'
    NOTICE:  role "gm-dbo" has already been granted membership in role "gm-public" by role "postgres"
    GRANT ROLE

    jessie@deb-vivobook:~$ sudo -u postgres psql -d postgres -X -v ON_ERROR_STOP=1 -c \
    'GRANT "gm-staff" TO "gm-dbo" WITH ADMIN OPTION;'
    NOTICE:  role "gm-dbo" has already been granted membership in role "gm-staff" by role "postgres"
    GRANT ROLE

    jessie@deb-vivobook:~$ sudo -u postgres psql -d postgres -X -v ON_ERROR_STOP=1 -c \
    'GRANT "gm-staff_medical" TO "gm-dbo" WITH ADMIN OPTION;'
    GRANT ROLE

    jessie@deb-vivobook:~$ sudo -u postgres psql -d postgres -X -v ON_ERROR_STOP=1 -c 'GRANT "gm-staff_office" TO "gm-dbo" WITH ADMIN OPTION;'
    GRANT ROLE

    jessie@deb-vivobook:~$ sudo -u postgres psql -d postgres -X -v ON_ERROR_STOP=1 -c 'GRANT "gm-trainees_medical" TO "gm-dbo" WITH ADMIN OPTION;'
    GRANT ROLE

    jessie@deb-vivobook:~$ sudo -u postgres psql -d postgres -X -v ON_ERROR_STOP=1 -c 'GRANT "gm-trainees_office" TO "gm-dbo" WITH ADMIN OPTION;'
    GRANT ROLE

... surely there's a way to make this with a single query but I wanted to see what resulted for each operation (and didn't know how to make this more efficient :).


Then checked that gm-dbo was granted all roles successfully...

    jessie@deb-vivobook:~$ sudo -u postgres psql -d postgres -X -c \
    "SELECT r.rolname AS member, m.rolname AS role, am.admin_option
     FROM pg_auth_members am
     JOIN pg_roles r ON r.oid = am.member
     JOIN pg_roles m ON m.oid = am.roleid
     WHERE r.rolname='gm-dbo'
       AND (m.rolname LIKE 'gm-%' OR m.rolname='gnumed_v16')
     ORDER BY role;"

     member |        role         | admin_option 
    --------+---------------------+--------------
     gm-dbo | gm-doctors          | t
     gm-dbo | gm-logins           | t
     gm-dbo | gm-public           | t
     gm-dbo | gm-staff            | t
     gm-dbo | gm-staff_medical    | t
     gm-dbo | gm-staff_office     | t
     gm-dbo | gm-trainees_medical | t
     gm-dbo | gm-trainees_office  | t
     gm-dbo | gnumed_v16          | t
    (9 rows)

... restarted postresql...

    sudo systemctl restart postgresql

... and ran again the bootstrap, now successfully!


The rest of the setup went smoothly and the client runs great (as far as I've tested it).

María
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