Module Gnumed.gnumed

#!/usr/bin/env python3

""".\\" ========================================================
.\\" SPDX-License-Identifier: GPL-2.0-or-later
.\\" ========================================================

.TH GNUmed 1 "%s" "Manual for GNUmed"

.SH NAME
.B GNUmed
- an electronic medical record software for GP offices

Use at your own risk. You have been warned.

.SH SYNOPSIS
.B gnumed
.RB [--quiet|debug]
.RB [--slave]
.RB [--text-domain=TEXTDOMAIN]
.RB [--log-file=FILE]
.RB [--conf-file=FILE]
.RB [--profile=FILE]
.RB [--lang-gettext=LANGUAGE]
.RB [--tool=TOOL]
.RB [--override-schema-check]
.RB [--skip-update-check]
.RB [--local-import]
.RB [--special=SPECIAL]
.RB [--help]
.RB [--version]
.RB [-V]
.RB [-h|?]


.SH DESCRIPTION
.B GNUmed
is a solution for keeping safe and medically sound electronic
records on a patient's health. It primarily focuses on GP
offices. It is released under the GPL.

GNUmed is written in Python with wxPython/wxWindows. Data is
stored in a PostgreSQL database. Multiple clients can work
with the same database at the same time.

.SH OPTIONS
.PP
.TP
.B \--quiet
Be extra quiet and show only _real_ errors in the log.
.TP
.B \--debug
Pre-set the [debug mode] checkbox in the login dialog
which controls increased verbosity in the log file.

Useful for, well, debugging :-)  Slower, too.
.TP
.B \--slave
Pre-set the [enable remote control] checkbox in the login
dialog to enable the XML-RPC remote control feature.
.TP
.B \--hipaa
Enable HIPAA features with user workflow impact.

Those features which do not affect the workflow of the user
are permanently enabled.
.TP
.B \--log-file=FILE
Use this to change the name of the log file. At startup
GNUmed will tell you the name of the log file in use.
.TP
.B \--conf-file=FILE
Use configuration file FILE instead of searching for it in standard locations.
.TP
.B \--profile=FILE
Activate profiling and write profile data to file FILE.
.TP
.B \--lang-gettext=LANGUAGE
Explicitly set the language to use in gettext translation. The very
same effect can be achieved by setting the environment variable $LANG
from a launcher script.
.TP
.B \--text-domain=TEXTDOMAIN
Set this to change the name of the language file to be loaded.
Note, this does not change the directory the file is searched in,
only the name of the file where messages are loaded from. The
standard textdomain is, of course, "gnumed.mo". You need only
specify the base name of the file without the .mo extension.
.TP
.B \--tool=TOOL
Run the named TOOL instead of a GUI.

Currently implemented tools:

        check_enc_epi_xref: Cross-check that foreign keys values in any given row of any table carrying both of fk_episode and fk_encounter do point to episodes and encounters, respectively, of the very same patient.

        export_pat_emr_structure: Export the EMR structure (issues and episodes) of a patient into a text file.

        check_mimetypes_in_archive: Show mimetypes and related information of all document parts in the archive.

        read_all_rows_of_table: Check readability of all rows of a given table.

        fingerprint_db: Create a fingerprint of a GNUmed database.

        generate_man_page: Generate man page.

        get_object_passphrases: Retrieve encrypted passphrases for a file previously encrypted by and exported from GNUmed.
.TP
.B \--override-schema-check
Continue loading the client even if the database schema
version and the client software version cannot be verified
to be compatible.
.TP
.B \--skip-update-check
Skip checking for client updates. This is useful during
development or when the update check URL is unavailable.
.TP
.B \--local-import
At startup adjust the PYTHONPATH such that the GNUmed client is
run from a local copy of the source tree (say an unpacked tarball
or a GIT repo) rather than from a proper system-wide installation.
.TP
.B \--special=SPECIAL
Used for debugging.
.TP
.B \--version, -V
Show version information about the GNUmed client and the
database it needs.
.TP
.B \--help, -h, or -?
Show this help.


.SH CONFIGURATION
.PP
.TP
.B Client startup and shutdown (OS level)

A shell script /usr/bin/gnumed is used to startup the client.
It checks whether the systemwide configuration file

        /etc/gnumed/gnumed-client.conf

exists. It then executes the following scripts (in that
order) if found:

        /etc/gnumed/gnumed-startup-local.sh

        ~/.config/gnumed/scripts/gnumed-startup-local.sh

When the client terminates it will execute the following
scripts in order if they exist:

        /etc/gnumed/gnumed-shutdown-local.sh

        ~/.config/gnumed/scripts/gnumed-shutdown-local.sh

.PP
.TP
.B wxPython client startup

The gnumed.py script checks for INI style configuration files
and fails if it does not find any. The files are searched for
in the following order and extend/overwrite each others
options:

        in the current working directory (cwd)

                ./gumed.conf

        in the systemwide configuration directory

                /etc/gnumed/gnumed-client.conf

        in the home directory

                ~/.config/gnumed/gnumed.conf

        in a local git tree or unpacked tarball

                .../gnumed/client/gnumed.conf

        explicitly given by CLI option

                --conf-file=<CONF FILE>

.PP
.TP
.B client/system runtime interaction

GNUmed uses scripts and configuration files to customize system interaction at runtime:

.B gm-print_doc(.bat)

Called to print documents if other methods fail. Check the GNUmed debug log for the API.

.B gm-mail_doc(.bat)

Called to e-mail documents if other methods fail. Check the GNUmed debug log for the API.

.B gm-fax_doc(.bat)

Called to fax documents if other methods fail. Check the GNUmed debug log for the API.

.B gm-burn_doc(.bat)

Called to burn a directory onto CD/DVD if other methods fail. Check the GNUmed debug log for the API.

.B gm-unicode2clipboard

Called to help the user enter non-native characters if other methods fail. Check the GNUmed debug log for the API.

.B ~/.config/gnumed/gnumed-xsanerc.conf

(requires XSane > v0.992)

When GNUmed invokes XSane for scanning it passes along this file (via =--xsane-rc=). This way a custom XSane configuration can be used with GNUmed. If the file doesn't exist it will be created from ~/.sane/xsane/xsanerc on the first call to XSane.

When you configure XSane after calling it from GNUmed your changes will be stored in the GNUmed-specific XSane configuration file and will not affect your usual XSane settings.

.B mime_type2file_extension.conf

(searched for in ~/.config/gnumed/ and /etc/gnumed/, in that order)

GNUmed will use these files to map mime types to file extensions if need be.

The file must contain a group [extensions] under which there can be one option per mime type specifying the extension to use on files of said type. Set the value to the raw extension only, omitting the ".", like so:

.nf
[extensions]
image/x-bmp = bmp


.SH EXIT STATUS
.TP
 > 0: some error occurred while the GUI client was run
.TP
   0: normal termination of the client
.TP
 < 0: some error occurred while trying to run a console tool
.TP
  -1: an unknown console tool was requested
.TP
< -1: an error occurred while a console tool was run
.TP
-999: hard abort of the client


.SH ENVIRONMENT
.TP
.B LANG, LC_MESSAGES, etc.
See gettext(1) for how the various locale related environment variables work.


.SH OTHER FILES AND DIRECTORIES
.PP
.TP
.B ~/.local/gnumed/gnumed.log
The default log file.
.TP
.B gnumed-client.tmpfiles.d.conf
Integration with systemd-tmpfiles(8).
.TP
.B gnumed-completion.bash
Integration with BASH completions.


.SH SEE ALSO
.PP
.TP
.B https://www.gnumed.[de|org]
Online documenation.
.TP
.B https://savannah.gnu.org/projects/gnumed
Mailing list home
.TP
.B https://github.org/ncqgm/gnumed
Source code repository (Git)
.TP
.B /usr/share/doc/gnumed/
Local documentation
.TP
.B man -k gm-*
List man pages on gm-* commands.
.TP
.B gettext(1)


.SH BUGS

A lot of functionality is still missing. To make up for
that, there's bugs here and there for you to report :-)

Use at your own risk. You have been warned. Take proper backups !
"""

#==========================================================
# SPDX-License-Identifier: GPL-2.0-or-later
__author__ = "H. Herb <hherb@gnumed.net>, K. Hilbert <Karsten.Hilbert@gmx.net>, I. Haywood <i.haywood@ugrad.unimelb.edu.au>"
__license__ = "GPL v2 or later (details at https://www.gnu.org)"


# standard library
import sys
import os
import platform
import tempfile
import faulthandler
import random
import logging
import datetime
import signal
import os.path
import shutil
import stat
import re as regex


# do not run as module
if __name__ != "__main__":
        print("GNUmed startup: This is not intended to be imported as a module !")
        print("-----------------------------------------------------------------")
#       sys.exit(1)


# do not run as root
if os.name in ['posix'] and os.geteuid() == 0:
        print("""
GNUmed startup: GNUmed should not be run as root.
-------------------------------------------------

Running GNUmed as <root> can potentially put all
your medical data at risk. It is strongly advised
against. Please run GNUmed as a non-root user.
""")
        sys.exit(1)

#----------------------------------------------------------
#current_client_version = '1.8.0rc3'
#current_client_branch = '1.8'
current_client_version = 'head'
current_client_branch = 'master'

_log = None
_pre_log_buffer = []
_cfg = None
_old_sig_term = None
_known_short_options = 'h?V'
_known_long_options = [
        'debug',
        'slave',
        'skip-update-check',
        'profile=',
        'text-domain=',
        'log-file=',
        'conf-file=',
        'lang-gettext=',
        'override-schema-check',
        'local-import',
        'help',
        'version',
        'hipaa',
        'wxp=',
        'tool=',
        'special=',
        'tui'
]

_known_tools = [
        'check_enc_epi_xref',
        'export_pat_emr_structure',
        'check_mimetypes_in_archive',
        'read_all_rows_of_table',
        'fingerprint_db',
        'generate_man_page',
        'get_object_passphrases'
]


import_error_sermon = """
GNUmed startup: Cannot load GNUmed Python modules !
---------------------------------------------------
CRITICAL ERROR: Program halted.

Please make sure you have:

 1) the required third-party Python modules installed
 2) the GNUmed Python modules linked or installed into site-packages/
    (if you do not run from a CVS tree the installer should have taken care of that)
 3) your PYTHONPATH environment variable set up correctly

<sys.path> is currently set to:

 %s

If you are running from a copy of the CVS tree make sure you
did run gnumed/check-prerequisites.sh with good results.

If you still encounter errors after checking the above
requirements please ask on the mailing list.
"""


missing_cli_config_file = """
GNUmed startup: Missing configuration file.
-------------------------------------------

You explicitly specified a configuration file
on the command line:

        --conf-file=%s

The file does not exist, however.
"""


no_config_files = """
GNUmed startup: Missing configuration files.
--------------------------------------------

None of the below candidate configuration
files could be found:

 %s

Cannot run GNUmed without any of them.
"""

#==========================================================
# convenience functions
#----------------------------------------------------------
def _symlink_windows(source, link_name):
        import ctypes
        csl = ctypes.windll.kernel32.CreateSymbolicLinkW
        csl.argtypes = (ctypes.c_wchar_p, ctypes.c_wchar_p, ctypes.c_uint32)
        csl.restype = ctypes.c_ubyte
        if os.path.isdir(source):
                flags = 1
        else:
                flags = 0
        ret_code = csl(link_name, source.replace('/', '\\'), flags)
        if ret_code == 0:
                raise ctypes.WinError()
        return ret_code

#==========================================================
# startup helpers
#----------------------------------------------------------
def setup_fault_handler(target=None):
        if target is None:
                faulthandler.enable()
                _pre_log_buffer.append('<faulthandler> enabled, target = [console]: %s' % faulthandler)
                return
        _pre_log_buffer.append('<faulthandler> enabled, target = [%s]: %s' % (target, faulthandler))
        faulthandler.enable(file = target)

#==========================================================
def setup_console_encoding():
        print_lines = []
        try:
                sys.stdout.reconfigure(errors = 'surrogateescape')
                sys.stderr.reconfigure(errors = 'surrogateescape')
                _pre_log_buffer.append('stdout/stderr reconfigured to use <surrogateescape> for encoding errors')
                return
        except AttributeError:
                line = 'cannot reconfigure sys.stdout/stderr to use <errors="surrogateescape"> (needs Python 3.7+)'
                _pre_log_buffer.append(line)
                print_lines.append(line)
        try:
                _pre_log_buffer.append('sys.stdout/stderr default to "${PYTHONIOENCODING}=%s"' % os.environ['PYTHONIOENCODING'])
                return
        except KeyError:
                lines = [
                        '${PYTHONIOENCODING} is not set up, use <PYTHONIOENCODING=utf-8:surrogateescape> in the shell (for Python < 3.7)',
                        'console encoding errors may occur'
                ]
                for line in lines:
                        print_lines.append(line)
                        _pre_log_buffer.append(line)
                for line in print_lines:
                        print('GNUmed startup:', line)

#==========================================================
def setup_python_path():

        if not '--local-import' in sys.argv:
                _pre_log_buffer.append('running against systemwide install')
                return

        local_python_import_dir = os.path.dirname (
                os.path.abspath(os.path.join(sys.argv[0], '..'))
        )
        print("Running from local source tree (%s) ..." % local_python_import_dir)
        _pre_log_buffer.append("running from local source tree: %s" % local_python_import_dir)

        # does the path exist at all, physically ?
        # (*broken* links are reported as False)
        link_name = os.path.join(local_python_import_dir, 'Gnumed')
        if os.path.exists(link_name):
                _pre_log_buffer.append('local module import dir symlink exists: %s' % link_name)
        else:
                real_dir = os.path.join(local_python_import_dir, 'client')
                print('Creating local module import symlink ...')
                print(' real dir:', real_dir)
                print('     link:', link_name)
                try:
                        os.symlink(real_dir, link_name)
                except AttributeError:
                        _pre_log_buffer.append('Windows does not have os.symlink(), resorting to ctypes')
                        result = _symlink_windows(real_dir, link_name)
                        _pre_log_buffer.append('ctypes.windll.kernel32.CreateSymbolicLinkW() exit code: %s', result)
                _pre_log_buffer.append('created local module import dir symlink: link [%s] => dir [%s]' % (link_name, real_dir))

        sys.path.insert(0, local_python_import_dir)
        _pre_log_buffer.append('sys.path with local module import base dir prepended: %s' % sys.path)

#==========================================================
def setup_local_repo_path():

        local_repo_path = os.path.expanduser(os.path.join (
                '~',
                '.local',
                'gnumed',
                'local_code',
                str(current_client_branch)
        ))
        local_wxGladeWidgets_path = os.path.join(local_repo_path, 'Gnumed', 'wxGladeWidgets')

        if not os.path.exists(local_wxGladeWidgets_path):
                _log.debug('[%s] not found', local_wxGladeWidgets_path)
                _log.info('local wxGlade widgets repository not available')
                return

        _log.info('local wxGlade widgets repository found:')
        _log.info(local_wxGladeWidgets_path)

        if not os.access(local_wxGladeWidgets_path, os.R_OK):
                _log.error('invalid repo: no read access')
                return

        all_entries = os.listdir(os.path.join(local_repo_path, 'Gnumed'))
        _log.debug('repo base contains: %s', all_entries)
        all_entries.remove('wxGladeWidgets')
        try:
                all_entries.remove('__init__.py')
        except ValueError:
                _log.error('invalid repo: lacking __init__.py')
                return
        try:
                all_entries.remove('__init__.pyc')
        except ValueError:
                pass

        if len(all_entries) > 0:
                _log.error('insecure repo: additional files or directories found')
                return

        # repo must be 0700 (rwx------)
        stat_val = os.stat(local_wxGladeWidgets_path)
        _log.debug('repo stat(): %s', stat_val)
        perms = stat.S_IMODE(stat_val.st_mode)
        _log.debug('repo permissions: %s (octal: %s)', perms, oct(perms))
        if perms != 448:                                # octal 0700
                if os.name in ['nt']:
                        _log.warning('this platform does not support os.stat() permission checking')
                else:
                        _log.error('insecure repo: permissions not 0600')
                        return

        print("Activating local wxGlade widgets repository (%s) ..." % local_wxGladeWidgets_path)
        sys.path.insert(0, local_repo_path)
        _log.debug('sys.path with repo:')
        _log.debug(sys.path)

#==========================================================
def setup_logging():
        try:
                from Gnumed.pycommon import gmLog2 as _gmLog2
        except ImportError:
                print(import_error_sermon % '\n '.join(sys.path))
                sys.exit(1)

        setup_fault_handler(target = _gmLog2._logfile)
        global gmLog2
        gmLog2 = _gmLog2
        global _log
        _log = logging.getLogger('gm.launcher')

#==========================================================
def __log_module_sys():
        _log.info('module <sys> info:')
        attrs2skip = ['__doc__', 'copyright', '__name__', '__spec__']
        for attr_name in dir(sys):
                if attr_name in attrs2skip:
                        continue
                if attr_name.startswith('set'):
                        continue
                attr = getattr(sys, attr_name)
                if not attr_name.startswith('get'):
                        _log.info('%s: %s', attr_name.rjust(30), attr)
                        continue
                if callable(attr):
                        try:
                                _log.info('%s: %s', attr_name.rjust(30), attr())
                        except Exception:
                                _log.exception('%s: <cannot log>', attr_name.rjust(30))
                        continue

#----------------------------------------------------------
def __log_module_platform():
        _log.info('module <platform> info:')
        attrs2skip = ['__doc__', '__copyright__', '__name__', '__spec__', '__cached__', '__builtins__']
        for attr_name in dir(platform):
                if attr_name in attrs2skip:
                        continue
                if attr_name.startswith('set'):
                        continue
                attr = getattr(platform, attr_name)
                if callable(attr):
                        if attr_name.startswith('_'):
                                _log.info('%s: %s', attr_name.rjust(30), attr)
                                continue
                        try:
                                _log.info('%s: %s', attr_name.rjust(30), attr())
                        except Exception:
                                _log.exception('%s: <cannot log>', attr_name.rjust(30))
                        continue
                _log.info('%s: %s', attr_name.rjust(30), attr)
                continue

#----------------------------------------------------------
def __log_module_os():
        _log.info('module <os> info:')
        for n in os.confstr_names:
                _log.info('%s: %s', ('confstr[%s]' % n).rjust(40), os.confstr(n))
        for n in os.sysconf_names:
                try:
                        _log.info('%s: %s', ('sysconf[%s]' % n).rjust(40), os.sysconf(n))
                except Exception:
                        _log.exception('%s: <invalid> ??', ('sysconf[%s]' % n).rjust(30))
        os_attrs = ['name', 'ctermid', 'getcwd', 'get_exec_path', 'getegid', 'geteuid', 'getgid', 'getgroups', 'getlogin', 'getpgrp', 'getpid', 'getppid', 'getresuid', 'getresgid', 'getuid', 'supports_bytes_environ', 'uname', 'get_terminal_size', 'pathconf_names', 'times', 'cpu_count', 'curdir', 'pardir', 'sep', 'altsep', 'extsep', 'pathsep', 'defpath', 'linesep', 'devnull']
        for attr_name in os_attrs:
                attr = getattr(os, attr_name)
                if callable(attr):
                        try:
                                _log.info('%s: %s', attr_name.rjust(40), attr())
                        except Exception as exc:
                                _log.error('%s: a callable, but call failed (%s)', attr_name.rjust(40), exc)
                        continue
                _log.info('%s: %s', attr_name.rjust(40), attr)
        _log.info('process environment:')
        for key, val in os.environ.items():
                _log.info(' %s: %s' % (('${%s}' % key).rjust(40), val))

#----------------------------------------------------------
def __log_module_sysconfig():
        import sysconfig
        _log.info('module <sysconfig> info:')
        _log.info(' platform [%s] -- python version [%s]', sysconfig.get_platform(), sysconfig.get_python_version())
        _log.info(' sysconfig.get_paths():')
        paths = sysconfig.get_paths()
        for path in paths:
                _log.info('%s: %s', path.rjust(40), paths[path])
        _log.info(' sysconfig.get_config_vars():')
        conf_vars = sysconfig.get_config_vars()
        for var in conf_vars:
                _log.info('%s: %s', var.rjust(45), conf_vars[var])

#----------------------------------------------------------
def log_startup_info():
        global _pre_log_buffer
        if len(_pre_log_buffer) > 0:
                _log.info('early startup log buffer:')
        for line in _pre_log_buffer:
                _log.info(' ' + line)
        del _pre_log_buffer
        _log.info('GNUmed client version [%s] on branch [%s]', current_client_version, current_client_branch)
        _log.info('Platform: %s', platform.uname())
        _log.info(('Python %s on %s (%s)' % (sys.version, sys.platform, os.name)).replace('\n', '<\\n>'))
        try:
                import lsb_release
                _log.info('lsb_release: %s', lsb_release.get_distro_information())
        except ImportError:
                pass
        __log_module_sys()
        __log_module_platform()
        __log_module_os()
        __log_module_sysconfig()
        #for f in [ mod.__spec__ for mod in sys.modules.values() ]:
        #       print(f.origin)

#==========================================================
def setup_console_exception_handler():
        from Gnumed.pycommon.gmTools import handle_uncaught_exception_console

        sys.excepthook = handle_uncaught_exception_console

#==========================================================
def setup_cli():
        from Gnumed.pycommon import gmCfgINI

        global _cfg
        _cfg = gmCfgINI.gmCfgData()
        _cfg.add_cli (
                short_options = _known_short_options,
                long_options = _known_long_options
        )

        val = _cfg.get(option = '--debug', source_order = [('cli', 'return')])
        if val is None:
                val = False
        _cfg.set_option (
                option = 'debug',
                value = val
        )

        val = _cfg.get(option = '--slave', source_order = [('cli', 'return')])
        if val is None:
                val = False
        _cfg.set_option (
                option = 'slave',
                value = val
        )

        val = _cfg.get(option = '--skip-update-check', source_order = [('cli', 'return')])
        if val is None:
                val = False
        _cfg.set_option (
                option = 'skip-update-check',
                value = val
        )

        val = _cfg.get(option = '--hipaa', source_order = [('cli', 'return')])
        if val is None:
                val = False
        _cfg.set_option (
                option = 'hipaa',
                value = val
        )

        val = _cfg.get(option = '--local-import', source_order = [('cli', 'return')])
        if val is None:
                val = False
        _cfg.set_option (
                option = 'local-import',
                value = val
        )

        value = _cfg.get(option = '--special', source_order = [('cli', 'return')])
        if value:
                value = value.split(',')
                print('GNUmed startup: --special:', value)
        else:
                value = []
        _cfg.set_option(option = 'special', value = value)

        _cfg.set_option (
                option = 'client_version',
                value = current_client_version
        )

        _cfg.set_option (
                option = 'client_branch',
                value = current_client_branch
        )

#==========================================================
def handle_sig_term(signum, frame):
        _log.critical('SIGTERM (SIG%s) received, shutting down ...' % signum)
        gmLog2.flush()
        print('GNUmed: SIGTERM (SIG%s) received, shutting down ...' % signum)
        if frame is not None:
                print('%s::%s@%s' % (frame.f_code.co_filename, frame.f_code.co_name, frame.f_lineno))

        # FIXME: need to do something useful here

        if _old_sig_term in [None, signal.SIG_IGN]:
                sys.exit(1)
        else:
                _old_sig_term(signum, frame)

#----------------------------------------------------------
def setup_signal_handlers():
        global _old_sig_term
        old_sig_term = signal.signal(signal.SIGTERM, handle_sig_term)

#==========================================================
def setup_locale():
        gmI18N.activate_locale()
        td = _cfg.get(option = '--text-domain', source_order = [('cli', 'return')])
        l =  _cfg.get(option = '--lang-gettext', source_order = [('cli', 'return')])
        gmI18N.install_domain(domain = td, language = l, prefer_local_catalog = _cfg.get(option = 'local-import'))

#==========================================================
def generate_man_page(fname=None):
        if fname is None:
                handle, fname = tempfile.mkstemp(text = True, suffix = '.1')
        man_page_file = open(fname, mode = 'wt', encoding = 'utf8')
        man_page_file.write(__doc__ % datetime.date.today().strftime('%x'))
        man_page_file.close()
        return fname

#----------------------------------------------------------
def handle_help_request():
        src = [('cli', 'return')]

        help_requested = (
                _cfg.get(option = '--help', source_order = src) or
                _cfg.get(option = '-h', source_order = src) or
                _cfg.get(option = '-?', source_order = src)
        )

        if help_requested:
                input('\nHit <ENTER> to display commandline help\n')
                if platform.system() == 'Windows':
                        for line in __doc__.split('\n'):
                                print(regex.sub('^\.\w+\s*', '', line, count = 1))
                        sys.exit(0)

                man_page_fname = generate_man_page()
                os.system('man %s' % man_page_fname)
                sys.exit(0)

#==========================================================
def handle_version_request():
        gmTools._client_version = current_client_version

        src = [('cli', 'return')]

        version_requested = (
                _cfg.get(option = '--version', source_order = src) or
                _cfg.get(option = '-V', source_order = src)
        )

        if version_requested:

                from Gnumed.pycommon.gmPG2 import map_client_branch2required_db_version, known_schema_hashes

                print('GNUmed version information')
                print('--------------------------')
                print('client     : %s on branch [%s]' % (current_client_version, current_client_branch))
                print('database   : %s' % map_client_branch2required_db_version[current_client_branch])
                print('schema hash: %s' % known_schema_hashes[map_client_branch2required_db_version[current_client_branch]])
                sys.exit(0)

#==========================================================
def __migrate_old_user_gnumed_conf():
        _old_conf = os.path.join(gmTools.gmPaths().home_dir, '.gnumed', 'gnumed.conf')
        _new_conf = os.path.join(gmTools.gmPaths().user_config_dir, 'gnumed.conf')
        try:
                open(_old_conf, 'r').close()
                print('obsolete: %s' % _old_conf)
                _old_conf_obsolete = _old_conf + '.is_obsolete'
                _obsolete = open(_old_conf_obsolete, mode = 'wt')
                _obsolete.write('obsolete as of version [1.9], use [%s]' % _new_conf)
                _obsolete.close()
        except Exception:
                _log.exception('no [%s], not migrating', _old_conf)
                # ensure there's a user-level config file, even if empty
                open(_new_conf, mode = 'a+t')
                return

        try:
                open(_new_conf, mode = 'x').close()
        except FileExistsError:
                _log.info('[%s] exists, not migrating', _new_conf)
                return

        except Exception:
                _log.exception('error opening [%s]', _new_conf)
                return

        print('migrating: %s -> %s' %(_old_conf, _new_conf))
        shutil.copy2(_old_conf, _new_conf)

#----------------------------------------------------------
def setup_paths_and_files():
        """Create needed paths in user home directory."""

        paths = gmTools.gmPaths(app_name = 'gnumed')    # wxPython not available yet
        print("Temp dir:", paths.tmp_dir)
        # user work dir
        readme = """GNUmed Electronic Medical Record

        %s/

This directory should only ever contain files which the
user will come into direct contact with while using the
application (say, by selecting a file from the file system,
such as when importing files as document parts). You can
create subdirectories here as you see fit for the purpose.

This directory will also serve as the default directory when
GNUmed asks the user to select a directory for storing a
file.

Any files which are NOT intended for direct user interaction
but must be configured to live at a known location (say,
inter-application data exchange files) should be put under
the directory:

        %s/
""" % (paths.user_work_dir, paths.user_appdata_dir)
        gmTools.mkdir(paths.user_work_dir)
        gmTools.create_directory_description_file(directory = paths.user_work_dir, readme = readme)
        gmTools.remove_file(os.path.join(paths.user_work_dir, '00_README'))
        # user app data dir
        gmTools.mkdir(paths.user_appdata_dir)
        readme = """This directory should be used for files not intended for user
interaction at the file system level (file selection dialogs,
file browsers) such as inter-application data exchange files
which need to live at a known location."""
        gmTools.create_directory_description_file(directory = paths.user_appdata_dir, readme = readme)
        # error logs dir
        err_dir = os.path.expanduser(os.path.join(paths.user_appdata_dir, 'error_logs'))
        gmTools.mkdir(err_dir)
        readme = 'Whenever an unhandled exception is detected a copy of the log file is placed here.\n\nThis directory is subject to systemd-tmpfiles cleaning.'
        gmTools.create_directory_description_file(directory = err_dir, readme = readme)
        # mark dir as old
        old_dot_gmd_dir = os.path.expanduser(os.path.join(paths.home_dir, '.gnumed'))
        readme = '[%s]: This directory is not used by GNUmed anymore.' % old_dot_gmd_dir
        gmTools.create_directory_description_file(directory = old_dot_gmd_dir, readme = readme)

        __migrate_old_user_gnumed_conf()
        # symlink log file into temporary directory for easier debugging (everything in one place)
        logfile_link = os.path.join(paths.tmp_dir, 'zzz-gnumed.log')
        gmTools.mklink (gmLog2._logfile.name, logfile_link, overwrite = False)

#==========================================================
def setup_date_time():
        gmDateTime.init()

#==========================================================
def setup_cfg():
        """Detect and setup access to GNUmed config file.

        Parts of this will have limited value due to
        wxPython not yet being available.
        """
        enc = gmI18N.get_encoding()
        paths = gmTools.gmPaths(app_name = 'gnumed')

        candidates = [
                # the current working dir
                ['workbase', os.path.join(paths.working_dir, 'gnumed.conf')],
                # /etc/gnumed/
                ['system', os.path.join(paths.system_config_dir, 'gnumed-client.conf')],
                # ~/.config/gnumed/
                ['user', os.path.join(paths.user_config_dir, 'gnumed.conf')],
                # CVS/tgz tree .../gnumed/client/ (IOW a local installation)
                ['local', os.path.join(paths.local_base_dir, 'gnumed.conf')]
        ]
        # --conf-file=
        explicit_fname = _cfg.get(option = '--conf-file', source_order = [('cli', 'return')])
        if explicit_fname is None:
                candidates.append(['explicit', None])
        else:
                candidates.append(['explicit', explicit_fname])

        for candidate in candidates:
                _cfg.add_file_source (
                        source = candidate[0],
                        file = candidate[1],
                        encoding = enc
                )

        # --conf-file given but does not actually exist ?
        if explicit_fname is not None:
                if _cfg.source_files['explicit'] is None:
                        _log.error('--conf-file argument does not exist')
                        print(missing_cli_config_file % explicit_fname)
                        sys.exit(1)

        # any config file found at all ?
        found_any_file = False
        for f in _cfg.source_files.values():
                if f is not None:
                        found_any_file = True
                        break
        if not found_any_file:
                _log.error('no config file found at all')
                print(no_config_files % '\n '.join(candidates))
                sys.exit(1)

        # mime type handling sources
        fname = 'mime_type2file_extension.conf'
        user_mime = os.path.join(paths.user_config_dir, fname)
        _old_user_mime = os.path.join(paths.home_dir, '.gnumed', fname)
        try:
                open(_old_user_mime, 'r')
                print('obsolete: [%s]' % _old_user_mime)
                _log.error('obsolete: [%s], use [%s]', _old_user_mime, user_mime)
        except FileNotFoundError:
                pass
        except Exception:
                _log.exception('error checking for [%s]', _old_user_mime)
        _cfg.add_file_source (
                source = 'user-mime',
                file = user_mime,
                encoding = enc
        )
        _cfg.add_file_source (
                source = 'system-mime',
                file = os.path.join(paths.system_config_dir, fname),
                encoding = enc
        )

#==========================================================
def setup_backend_environment():

        db_version = gmPG2.map_client_branch2required_db_version[current_client_branch]
        _log.info('client expects database version [%s]', db_version)
        _cfg.set_option (
                option = 'database_version',
                value = db_version
        )

#       # set up database connection timezone
#       timezone = _cfg.get (
#               group = 'backend',
#               option = 'client timezone',
#               source_order = [
#                       ('explicit', 'return'),
#                       ('workbase', 'return'),
#                       ('local', 'return'),
#                       ('user', 'return'),
#                       ('system', 'return')
#               ]
#       )
#       if timezone is not None:
#               gmPG2.set_default_client_timezone(timezone)

#==========================================================
#----------------------------------------------------------
def run_ui():
        """Startup a user interface."""
        gmHooks.run_hook_script(hook = 'startup-before-GUI')
        _use_tui = _cfg.get(option = '--tui', source_order = [('cli', 'return')])
        if _use_tui:
                return run_tui()

        run_gui()
        gmHooks.run_hook_script(hook = 'shutdown-post-GUI')
        return 0

#==========================================================
def run_tui():
        try:
                #import urwid
                pass
        except ModuleNotFoundError:
                _log.exception('cannot import <urwid>')
                return 1

        from Gnumed.urwid import gmTuiMain
        gmTuiMain.main()
        return 0

#==========================================================
def run_gui():
        """Startup wxPython GUI."""
        from Gnumed.wxpython import gmGuiMain
        profile_file = _cfg.get(option = '--profile', source_order = [('cli', 'return')])
        if profile_file is None:
                gmGuiMain.main()
        else:
                _log.info('writing profiling data into %s', profile_file)
                import profile
                profile.run('gmGuiMain.main()', profile_file)

        return 0

#==========================================================
def run_tool():
        """Run a console tool.

        Exit codes as per man page:
                   0: normal termination of the client
                 < 0: some error occurred while trying to run a console tool
                          -1: an unknown console tool was requested
                        < -1: an error occurred while a console tool was run
                -999: hard abort of the client

        One of these needs to be returned from this function (and,
        by extension from the tool having been run, if any).
        """
        tool = _cfg.get(option = '--tool', source_order = [('cli', 'return')])
        if tool is None:
                # not running a tool
                return None

        if tool not in _known_tools:
                _log.error('unknown tool requested: %s', tool)
                print('GNUmed startup: Unknown tool [%s] requested.' % tool)
                print('GNUmed startup: Known tools: %s' % _known_tools)
                return -1

        print('')
        print('==============================================')
        print('Running tool: %s' % tool)
        print('----------------------------------------------')
        print('')

        if tool == 'generate_man_page':
                man_page_fname = generate_man_page(fname = os.path.abspath(os.path.join('.', 'gnumed.1')))
                print('MAN page saved as:', man_page_fname)
                return 0

        login, creds = gmPG2.request_login_params()
        gmConnectionPool._VERBOSE_PG_LOG = _cfg.get(option = 'debug')
        pool = gmConnectionPool.gmConnectionPool()
        pool.credentials = creds
        print('')

        if tool == 'read_all_rows_of_table':
                result = gmPG2.read_all_rows_of_table()
                if result in [None, True]:
                        print('Success.')
                        return 0
                print('Failed. Check the log for details.')
                return -2

        if tool == 'get_object_passphrases':
                return __run_get_object_passphrases_tool()

        if tool == 'check_mimetypes_in_archive':
                from Gnumed.business import gmDocuments
                return gmDocuments.check_mimetypes_in_archive()

        if tool == 'check_enc_epi_xref':
                from Gnumed.business import gmEMRStructItems
                return gmEMRStructItems.check_fk_encounter_fk_episode_x_ref()

        if tool == 'fingerprint_db':
                return gmPG2.run_fingerprint_tool()

        if tool == 'export_pat_emr_structure':
                return __run_emr_export_tool()

        # tool export_patient_as (vcf, gdt, ...)
        #if tool == 'export_pat_demographics':

        # should not happen (because checked against _known_tools)
        return -1

#==========================================================
def __run_get_object_passphrases_tool():
        from Gnumed.business import gmExportArea
        fnames = gmExportArea.save_file_passphrases_into_files()
        print('')
        if not fnames:
                print('No passphrases found.')
                return 0

        print('Encrypted passphrases stored in:')
        for fname in fnames:
                print(' ', fname)
        return 0

#==========================================================
def __run_emr_export_tool():
        # setup praxis
        from Gnumed.business import gmPraxis
        gmPraxis.gmCurrentPraxisBranch(branch = gmPraxis.get_praxis_branches()[0])
        # setup exporters
        from Gnumed.business import gmEMRStructItems
        from Gnumed.exporters import gmTimelineExporter
        from Gnumed.exporters import gmPatientExporter
        # get patient
        from Gnumed.business import gmPersonSearch
        pat = gmPersonSearch.ask_for_patient()
        while pat:
                print('patient:', pat.description_gender)
                # as EMR structure
                fname = os.path.expanduser('~/gnumed/gm-emr_structure-%s.txt' % pat.subdir_name)
                print('EMR structure:', gmEMRStructItems.export_emr_structure(patient = pat, filename = fname))
                # as timeline
                fname = os.path.expanduser('~/gnumed/gm-emr-%s.timeline' % pat.subdir_name)
                try:
                        print('EMR timeline:', gmTimelineExporter.create_timeline_file (
                                patient = pat,
                                filename = fname,
                                include_documents = True,
                                include_vaccinations = True,
                                include_encounters = True
                        ))
                finally:
                        pass
                # as journal by encounter
                exporter = gmPatientExporter.cEMRJournalExporter()
                fname = os.path.expanduser('~/gnumed/gm-emr-journal_by_encounter-%s.txt' % pat.subdir_name)
                print('EMR journal (by encounter):', exporter.save_to_file_by_encounter(patient = pat, filename = fname))
                # as journal by mod time
                fname = os.path.expanduser('~/gnumed/gm-emr-journal_by_mod_time-%s.txt' % pat.subdir_name)
                print('EMR journal (by mod time):', exporter.save_to_file_by_mod_time(patient = pat, filename = fname))
                # as statistical summary
                fname = os.path.expanduser('~/gnumed/gm-emr-statistics-%s.txt' % pat.subdir_name)
                output_file = open(fname, mode = 'wt', encoding = 'utf8', errors = 'replace')
                emr = pat.emr
                output_file.write(emr.format_statistics())
                output_file.close()
                print('EMR statistics:', fname)
                # as text file
                exporter = gmPatientExporter.cEmrExport(patient = pat)
                fname = os.path.expanduser('~/gnumed/gm-emr-text_export-%s.txt' % pat.subdir_name)
                output_file = open(fname, mode = 'wt', encoding = 'utf8', errors = 'replace')
                exporter.set_output_file(output_file)
                exporter.dump_constraints()
                exporter.dump_demographic_record(True)
                exporter.dump_clinical_record()
                exporter.dump_med_docs()
                output_file.close()
                print('EMR text file:', fname)
                # another patient ?
                pat = gmPersonSearch.ask_for_patient()
        return 0

#==========================================================
# shutdown helpers
#----------------------------------------------------------
def shutdown_backend():
        gmPG2.shutdown()

#==========================================================
def shutdown_logging():

#       if _cfg.get(option = u'debug'):
#               import types

#               def get_refcounts():
#                       refcount = {}
#                       # collect all classes
#                       for module in sys.modules.values():
#                               for sym in dir(module):
#                                       obj = getattr(module, sym)
#                                       if type(obj) is types.ClassType:
#                                               refcount[obj] = sys.getrefcount(obj)
#                       # sort by refcount
#                       pairs = map(lambda x: (x[1],x[0]), refcount.items())
#                       pairs.sort()
#                       pairs.reverse()
#                       return pairs

#               rcfile = open('./gm-refcount.lst', 'wt', encoding = 'utf8')
#               for refcount, class_ in get_refcounts():
#                       if not class_.__name__.startswith('wx'):
#                               rcfile.write(u'%10d %s\n' % (refcount, class_.__name__))
#               rcfile.close()

        # do not choke on Windows
        logging.raiseExceptions = False

#==========================================================
def shutdown_tmp_dir():

        tmp_dir = gmTools.gmPaths().tmp_dir

        if _cfg.get(option = 'debug'):
                _log.debug('not removing tmp dir (--debug mode): %s', tmp_dir)
                return

        _log.warning('removing tmp dir: %s', tmp_dir)
        shutil.rmtree(tmp_dir, True)

#==========================================================
# main - launch the GNUmed wxPython GUI client
#----------------------------------------------------------
if __name__ == "__main__":

        random.seed()

        # setup
        setup_fault_handler(target = None)
        setup_console_encoding()
        setup_python_path()
        setup_logging()
        log_startup_info()
        setup_console_exception_handler()
        setup_cli()
        setup_signal_handlers()
        setup_local_repo_path()

        from Gnumed.pycommon import gmI18N
        from Gnumed.pycommon import gmTools
        from Gnumed.pycommon import gmDateTime

        setup_locale()
        handle_help_request()
        handle_version_request()
        setup_paths_and_files()
        setup_date_time()
        setup_cfg()

        from Gnumed.pycommon import gmPG2
        from Gnumed.pycommon import gmConnectionPool
        setup_backend_environment()

        # main
        exit_code = run_tool()
        if exit_code is None:
                from Gnumed.pycommon import gmHooks
                exit_code = run_ui()

        # shutdown
        shutdown_backend()
        shutdown_tmp_dir()
        _log.info('Normally shutting down as main module.')
        shutdown_logging()

        sys.exit(exit_code)

#==========================================================