Gnumed.gnumed API documentation
Description: .\" ======================================================== .\" SPDX-License-Identifier: GPL-2.0-or-later .\" …

# Module `Gnumed.gnumed`

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

.TH GNUmed 1 "%(today)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 %(options)s

.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 --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:

%(tools)s .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

GNUmed uses scripts and configuration files to customize interaction with the system at startup and runtime.

.PP .TP .B Shell level startup

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 Application level 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 Runtime interaction

These scripts must be found in the PATH for the client to be able to use them. When attempting to run a script the client will store API information into the log file (at DEBUG level).

.B gm-print_doc(.bat)

Called to print documents if other methods fail.

.B gm-mail_doc(.bat)

Called to e-mail documents if other methods fail.

.B gm-fax_doc(.bat)

Called to fax documents if other methods fail.

.B gm-burn_doc(.bat)

Called to burn a directory onto CD/DVD if other methods fail.

.B gm-describe_file

Called to retrieve metadata about a file.

.B gm-convert_file

Called to convert files among formats if other methods fail.

.B gm-create_datamatrix

Called to create a datamatrix.

.B gm-create_dicomdir

Called to generate a DICOMDIR file for a range of DICOM images.

.B gm-unicode2clipboard

Called to help the user enter non-native characters if other methods fail.

.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, like this:

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

.SH EXIT STATUS .TP

> 0: an error occurred while running the GUI client .TP 0: normal termination of the client .TP < 0: an error occurred while trying to run a console tool .TP -1: an unknown console tool was requested .TP < -1: an error occurred while running a known console tool .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. .TP .B ~/gnumed/auto-incoming/ Directory from which files are auto-imported for archival as patient documents. This directory is meant for the user to manually drop files into.

It will also contain a README listing another auto-import directory meant for programmatic dropping of files. Under Linux this path will likely be ~/.local/gnumed/auto-incoming/

.SH SEE ALSO .PP .TP .B https://www.gnumed.de 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 !

Expand source code

    #!/usr/bin/env python3

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

    .TH GNUmed 1 "%(today)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
    %(options)s

    .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 \--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:

    %(tools)s
    .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

    GNUmed uses scripts and configuration files to customize
    interaction with the system at startup and runtime.

    .PP
    .TP
    .B Shell level startup

    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 Application level 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 Runtime interaction

    These scripts must be found in the PATH for the client to be
    able to use them. When attempting to run a script the client
    will store API information into the log file (at DEBUG
    level).

    .B gm-print_doc(.bat)

    Called to print documents if other methods fail.

    .B gm-mail_doc(.bat)

    Called to e-mail documents if other methods fail.

    .B gm-fax_doc(.bat)

    Called to fax documents if other methods fail.

    .B gm-burn_doc(.bat)

    Called to burn a directory onto CD/DVD if other methods fail.

    .B gm-describe_file

    Called to retrieve metadata about a file.

    .B gm-convert_file

    Called to convert files among formats if other methods fail.

    .B gm-create_datamatrix

    Called to create a datamatrix.

    .B gm-create_dicomdir

    Called to generate a DICOMDIR file for a range of DICOM images.

    .B gm-unicode2clipboard

    Called to help the user enter non-native characters if other methods fail.

    .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, like this:

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

    .SH EXIT STATUS
    .TP
     > 0: an error occurred while running the GUI client
    .TP
       0: normal termination of the client
    .TP
     < 0: an error occurred while trying to run a console tool
    .TP
              -1: an unknown console tool was requested
    .TP
            < -1: an error occurred while running a known console tool
    .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.
    .TP
    .B ~/gnumed/auto-incoming/
    Directory from which files are auto-imported for archival as
    patient documents. This directory is meant for the user to
    manually drop files into.

    It will also contain a README listing another auto-import
    directory meant for programmatic dropping of files. Under
    Linux this path will likely be ~/.local/gnumed/auto-incoming/

    .SH SEE ALSO
    .PP
    .TP
    .B https://www.gnumed.de
    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 and '--tool=' not in '#'.join(sys.argv):
            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 = [
            'help',
            'version',
            'debug',
            'slave',
            'skip-update-check',
            'override-schema-check',
            'local-import',
            'hipaa',
            'log-file=',
            'conf-file=',
            'tool=',
            'profile=',
            'text-domain=',
            'lang-gettext=',
            'special=',
            'tui'
    ]

    _known_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.',
            'update_collations': 'Update collations version information in the database.'
    }

    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
            create_symlink_on_windows = ctypes.windll.kernel32.CreateSymbolicLinkW
            create_symlink_on_windows.argtypes = (ctypes.c_wchar_p, ctypes.c_wchar_p, ctypes.c_uint32)
            create_symlink_on_windows.restype = ctypes.c_ubyte
            if os.path.isdir(source):
                    flags = 1
            else:
                    flags = 0
            ret_code = create_symlink_on_windows(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
            gmLog2.print_logfile_name()
            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')
            opts = [ '.RB [-%s]' % o for o in  _known_short_options ]
            for long_opt in _known_long_options:
                    if long_opt.endswith('='):
                            opts.append('.RB [--%s%s]' % (long_opt, long_opt.upper()[:-1]))
                            continue
                    opts.append('.RB [--%s]' % long_opt)
            args = {
                    'today': datetime.date.today().strftime('%x'),
                    'tools': '\t\t\t\n\n'.join([ '%s: %s' % (tool, desc) for tool, desc in _known_tools.items() ]),
                    'options': '\n'.join(opts)
            }
            man_page_file.write(__doc__ % args)
            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)
            # directory for patient specific subdirs for storing data
            pats_dir = os.path.expanduser(os.path.join(paths.user_work_dir, 'patients'))
            gmTools.mkdir(pats_dir)
            readme = '\t[%s]\n\nIn this directory GNUmed will create subdirectories for patient data export.\n\nIt should be cleaned up from time to time.' % pats_dir
            gmTools.create_directory_description_file(directory = pats_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' % list(_known_tools.keys()))
                    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

            if tool == 'update_collations':
                    return gmPG2.run_collations_tool()

            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)

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

## Functions

`def generate_man_page(fname=None)`
  Expand source code

      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')
              opts = [ '.RB [-%s]' % o for o in  _known_short_options ]
              for long_opt in _known_long_options:
                      if long_opt.endswith('='):
                              opts.append('.RB [--%s%s]' % (long_opt, long_opt.upper()[:-1]))
                              continue
                      opts.append('.RB [--%s]' % long_opt)
              args = {
                      'today': datetime.date.today().strftime('%x'),
                      'tools': '\t\t\t\n\n'.join([ '%s: %s' % (tool, desc) for tool, desc in _known_tools.items() ]),
                      'options': '\n'.join(opts)
              }
              man_page_file.write(__doc__ % args)
              man_page_file.close()
              return fname

`def handle_help_request()`
  Expand source code

      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_sig_term(signum, frame)`
  Expand source code

      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 handle_version_request()`
  Expand source code

      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 log_startup_info()`
  Expand source code

      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 run_gui()`

  Startup wxPython GUI.

  Expand source code

      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).

  Expand source code

      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' % list(_known_tools.keys()))
                      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

              if tool == 'update_collations':
                      return gmPG2.run_collations_tool()

              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_tui()`
  Expand source code

      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_ui()`

  Startup a user interface.

  Expand source code

      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 setup_backend_environment()`
  Expand source code

      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
              )

`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.

  Expand source code

      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_cli()`
  Expand source code

      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 setup_console_encoding()`
  Expand source code

      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_console_exception_handler()`
  Expand source code

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

              sys.excepthook = handle_uncaught_exception_console

`def setup_date_time()`
  Expand source code

      def setup_date_time():
              gmDateTime.init()

`def setup_fault_handler(target=None)`
  Expand source code

      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_local_repo_path()`
  Expand source code

      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_locale()`
  Expand source code

      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 setup_logging()`
  Expand source code

      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
              gmLog2.print_logfile_name()
              global _log
              _log = logging.getLogger('gm.launcher')

`def setup_paths_and_files()`

  Create needed paths in user home directory.

  Expand source code

      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)
              # directory for patient specific subdirs for storing data
              pats_dir = os.path.expanduser(os.path.join(paths.user_work_dir, 'patients'))
              gmTools.mkdir(pats_dir)
              readme = '\t[%s]\n\nIn this directory GNUmed will create subdirectories for patient data export.\n\nIt should be cleaned up from time to time.' % pats_dir
              gmTools.create_directory_description_file(directory = pats_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_python_path()`
  Expand source code

      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_signal_handlers()`
  Expand source code

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

`def shutdown_backend()`
  Expand source code

      def shutdown_backend():
              gmPG2.shutdown()

`def shutdown_logging()`
  Expand source code

      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()`
  Expand source code

      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)