def add_file(self, filename=None, hint=None):
try:
open(filename).close()
except Exception:
_log.exception('cannot open file <%s>', filename)
return None
file_md5 = gmTools.file2md5(filename=filename, return_hex=True)
existing_item = self.md5_exists(md5=file_md5,
include_document_parts=False)
if existing_item is not None:
_log.debug('md5 match (%s): %s already in export area', file_md5,
filename)
return existing_item
path, basename = os.path.split(filename)
item = create_export_item(
description=u'%s: %s (%s/)' %
(gmTools.coalesce(hint, _(u'file'), u'%s'), basename, path),
pk_identity=self.__pk_identity,
filename=filename)
if item.update_data_from_file(filename=filename):
return item
delete_export_item(pk_export_item=item['pk_export_item'])
return None
def add_file(self, filename=None, hint=None):
try:
open(filename).close()
except Exception:
_log.exception('cannot open file <%s>', filename)
return None
file_md5 = gmTools.file2md5(filename = filename, return_hex = True)
existing_item = self.md5_exists(md5 = file_md5, include_document_parts = False)
if existing_item is not None:
_log.debug('md5 match (%s): %s already in export area', file_md5, filename)
return existing_item
path, basename = os.path.split(filename)
item = create_export_item (
description = u'%s: %s (%s/)' % (
gmTools.coalesce(hint, _(u'file'), u'%s'),
basename,
path
),
pk_identity = self.__pk_identity,
filename = filename
)
if item.update_data_from_file(filename = filename):
return item
delete_export_item(pk_export_item = item['pk_export_item'])
return None
def update_data_from_file(self, fname=None, link_obj=None):
# sanity check
if not (os.access(fname, os.R_OK) and os.path.isfile(fname)):
_log.error('[%s] is not a readable file' % fname)
return False
cmd = "UPDATE blobs.doc_obj SET data = %(data)s::BYTEA WHERE pk = %(pk)s RETURNING md5(data) AS md5"
args = {'pk': self.pk_obj}
md5 = gmTools.file2md5(filename = fname, return_hex = True)
if not gmPG2.file2bytea(conn = link_obj, query = cmd, filename = fname, args = args, file_md5 = md5):
return False
# must update XMIN now ...
self.refetch_payload(link_obj = link_obj)
return True
def update_data_from_file(self, fname=None, link_obj=None):
# sanity check
if not (os.access(fname, os.R_OK) and os.path.isfile(fname)):
_log.error('[%s] is not a readable file' % fname)
return False
if not gmPG2.file2bytea (
conn = link_obj,
query = "UPDATE blobs.doc_obj SET data = %(data)s::bytea WHERE pk = %(pk)s RETURNING md5(data) AS md5",
filename = fname,
args = {'pk': self.pk_obj},
file_md5 = gmTools.file2md5(filename = fname, return_hex = True)
):
return False
# must update XMIN now ...
self.refetch_payload(link_obj = link_obj)
return True
def download_data_pack(pack_url, filename=None, md5_url=None):
_log.debug('downloading data pack from: %s', pack_url)
dp_fname = download_file(pack_url, filename = filename, suffix = 'zip')
_log.debug('downloading MD5 from: %s', md5_url)
md5_fname = download_file(md5_url, filename = dp_fname + u'.md5')
md5_file = io.open(md5_fname, mode = 'rt', encoding = 'utf8')
md5_expected = md5_file.readline().strip('\n')
md5_file.close()
_log.debug('expected MD5: %s', md5_expected)
md5_calculated = gmTools.file2md5(dp_fname, return_hex = True)
_log.debug('calculated MD5: %s', md5_calculated)
if md5_calculated != md5_expected:
_log.error('mismatch of expected vs calculated MD5: [%s] vs [%s]', md5_expected, md5_calculated)
return (False, (md5_expected, md5_calculated))
return True, dp_fname
def download_data_pack(pack_url, filename=None, md5_url=None):
_log.debug('downloading data pack from: %s', pack_url)
dp_fname = download_file(pack_url, filename = filename, suffix = 'zip')
_log.debug('downloading MD5 from: %s', md5_url)
md5_fname = download_file(md5_url, filename = dp_fname + '.md5')
md5_file = io.open(md5_fname, mode = 'rt', encoding = 'utf8')
md5_expected = md5_file.readline().strip('\n')
md5_file.close()
_log.debug('expected MD5: %s', md5_expected)
md5_calculated = gmTools.file2md5(dp_fname, return_hex = True)
_log.debug('calculated MD5: %s', md5_calculated)
if md5_calculated != md5_expected:
_log.error('mismatch of expected vs calculated MD5: [%s] vs [%s]', md5_expected, md5_calculated)
return (False, (md5_expected, md5_calculated))
return True, dp_fname
def print_generic_document(parent=None, jobtype:str=None, episode=None):
"""Call LibreOffice Writer with a generated (fake) ODT file.
Once Writer is closed, the ODT is imported if different from its initial content.
Note:
The file passed to LO _must_ reside in a directory the parents of
which are all R-X by the user or else LO will throw up its arms
in despair and fall back to the user's home dir upon saving.
So,
/tmp/user/$UID/some-file.odt
will *not* work (because .../user/... is "drwx--x--x root.root") while
/home/$USER/some/dir/some-file.odt
does.
"""
sandbox = os.path.join(gmTools.gmPaths().user_tmp_dir, 'libreoffice')
gmTools.mkdir(sandbox)
fpath = gmTools.get_unique_filename(suffix = '.txt', tmp_dir = sandbox)
doc_file = open(fpath, mode = 'wt')
doc_file.write(__ODT_FILE_PREAMBLE)
doc_file.write(_('Today: %s') % gmDateTime.pydt_now_here().strftime('%c'))
doc_file.write('\n\n')
prax = gmPraxis.gmCurrentPraxisBranch()
doc_file.write('Praxis:\n')
doc_file.write(prax.format())
doc_file.write('\n')
doc_file.write('Praxis branch:\n')
doc_file.write('\n'.join(prax.org_unit.format (
with_address = True,
with_org = True,
with_comms = True
)))
doc_file.write('\n\n')
pat = gmPerson.gmCurrentPatient(gmPerson.cPatient(12))
if pat.connected:
doc_file.write('Patient:\n')
doc_file.write(pat.get_description_gender())
doc_file.write('\n\n')
for adr in pat.get_addresses():
doc_file.write(adr.format(single_line = False, verbose = True, show_type = True))
doc_file.write('\n\n')
for chan in pat.get_comm_channels():
doc_file.werite(chan.format())
doc_file.write('\n\n')
doc_file.write('Provider:\n')
doc_file.write('\n'.join(gmStaff.gmCurrentProvider().get_staff().format()))
doc_file.write('\n\n-----------------------------------------------------------------------------\n\n')
doc_file.close()
# convert txt -> odt
success, ret_code, stdout = gmShellAPI.run_process (
cmd_line = [
'lowriter',
'--convert-to', 'odt',
'--outdir', os.path.split(fpath)[0],
fpath
],
verbose = True
)
if success:
fpath = gmTools.fname_stem_with_path(fpath) + '.odt'
else:
_log.warning('cannot convert .txt to .odt')
md5_before = gmTools.file2md5(fpath)
gmShellAPI.run_process(cmd_line = ['lowriter', fpath], verbose = True)
md5_after = gmTools.file2md5(fpath)
if md5_before == md5_after:
gmDispatcher.send(signal = 'statustext', msg = _('Document not modified. Discarding.'), beep = False)
return
if not pat.connected:
shutil.move(fpath, gmTools.gmPaths().user_work_dir)
gmDispatcher.send(signal = 'statustext', msg = _('No patient. Moved file into %s') % gmTools.gmPaths().user_work_dir, beep = False)
return
pat.export_area.add_file (
filename = fpath,
hint = _('Generic letter, written at %s') % gmDateTime.pydt_now_here().strftime('%Y %b %d %H:%M')
)
gmDispatcher.send(signal = 'display_widget', name = 'gmExportAreaPlugin')
def edit_visual_progress_note(filename=None,
episode=None,
discard_unmodified=False,
doc_part=None,
health_issue=None):
"""This assumes <filename> contains an image which can be handled by the configured image editor."""
if doc_part is not None:
filename = doc_part.export_to_file()
if filename is None:
gmDispatcher.send(
signal=u'statustext',
msg=_('Cannot export visual progress note to file.'))
return None
dbcfg = gmCfg.cCfgSQL()
cmd = dbcfg.get2(
option=u'external.tools.visual_soap_editor_cmd',
workplace=gmPraxis.gmCurrentPraxisBranch().active_workplace,
bias='user')
if cmd is None:
gmDispatcher.send(
signal=u'statustext',
msg=_('Editor for visual progress note not configured.'),
beep=False)
cmd = configure_visual_progress_note_editor()
if cmd is None:
gmDispatcher.send(
signal=u'statustext',
msg=_('Editor for visual progress note not configured.'),
beep=True)
return None
if u'%(img)s' in cmd:
cmd = cmd % {u'img': filename}
else:
cmd = u'%s %s' % (cmd, filename)
if discard_unmodified:
original_stat = os.stat(filename)
original_md5 = gmTools.file2md5(filename)
success = gmShellAPI.run_command_in_shell(cmd, blocking=True)
if not success:
gmGuiHelpers.gm_show_error(
_('There was a problem with running the editor\n'
'for visual progress notes.\n'
'\n'
' [%s]\n'
'\n') % cmd, _('Editing visual progress note'))
return None
try:
open(filename, 'r').close()
except Exception:
_log.exception('problem accessing visual progress note file [%s]',
filename)
gmGuiHelpers.gm_show_error(
_('There was a problem reading the visual\n'
'progress note from the file:\n'
'\n'
' [%s]\n'
'\n') % filename, _('Saving visual progress note'))
return None
if discard_unmodified:
modified_stat = os.stat(filename)
# same size ?
if original_stat.st_size == modified_stat.st_size:
modified_md5 = gmTools.file2md5(filename)
# same hash ?
if original_md5 == modified_md5:
_log.debug('visual progress note (template) not modified')
# ask user to decide
msg = _(
u'You either created a visual progress note from a template\n'
u'in the database (rather than from a file on disk) or you\n'
u'edited an existing visual progress note.\n'
u'\n'
u'The template/original was not modified at all, however.\n'
u'\n'
u'Do you still want to save the unmodified image as a\n'
u'visual progress note into the EMR of the patient ?\n')
save_unmodified = gmGuiHelpers.gm_show_question(
msg, _('Saving visual progress note'))
if not save_unmodified:
_log.debug('user discarded unmodified note')
return
if doc_part is not None:
_log.debug('updating visual progress note')
doc_part.update_data_from_file(fname=filename)
doc_part.set_reviewed(technically_abnormal=False,
clinically_relevant=True)
return None
if not isinstance(episode, gmEMRStructItems.cEpisode):
if episode is None:
episode = _('visual progress notes')
pat = gmPerson.gmCurrentPatient()
emr = pat.emr
episode = emr.add_episode(episode_name=episode.strip(),
pk_health_issue=health_issue,
is_open=False)
doc = gmDocumentWidgets.save_file_as_new_document(
filename=filename,
document_type=gmDocuments.DOCUMENT_TYPE_VISUAL_PROGRESS_NOTE,
episode=episode,
unlock_patient=False,
pk_org_unit=gmPraxis.gmCurrentPraxisBranch()['pk_org_unit'])
doc.set_reviewed(technically_abnormal=False, clinically_relevant=True)
return doc
def edit_visual_progress_note(filename=None,
episode=None,
discard_unmodified=False,
doc_part=None,
health_issue=None):
"""This assumes <filename> contains an image which can be handled by the configured image editor."""
if doc_part is not None:
filename = doc_part.save_to_file()
if filename is None:
gmDispatcher.send(
signal='statustext',
msg=_('Cannot export visual progress note to file.'))
return None
editor = gmCfgDB.get4user(
option='external.tools.visual_soap_editor_cmd',
workplace=gmPraxis.gmCurrentPraxisBranch().active_workplace)
if editor is None:
_log.error(
'no editor for visual progress notes configured, trying mimetype editor'
)
gmDispatcher.send(
signal='statustext',
msg=_('Editor for visual progress note not configured.'),
beep=False)
mimetype = gmMimeLib.guess_mimetype(filename=filename)
editor = gmMimeLib.get_editor_cmd(mimetype=mimetype, filename=filename)
if editor is None:
_log.error(
'no editor for mimetype <%s> configured, trying mimetype viewer',
mimetype)
success, msg = gmMimeLib.call_viewer_on_file(aFile=filename,
block=True)
if not success:
_log.debug('problem running mimetype <%s> viewer', mimetype)
gmGuiHelpers.gm_show_error(
_('There is no editor for visual progress notes defined.\n'
'Also, there is no editor command defined for the file type\n'
'\n'
' [%s].\n'
'\n'
'Therefor GNUmed attempted to at least *show* this\n'
'visual progress note. That failed as well, however:\n'
'\n'
'%s') % (mimetype, msg),
_('Editing visual progress note'))
editor = configure_visual_progress_note_editor()
if editor is None:
gmDispatcher.send(
signal='statustext',
msg=_(
'Editor for visual progress note not configured.'),
beep=True)
return None
if '%(img)s' in editor:
editor = editor % {'img': filename}
else:
editor = '%s %s' % (editor, filename)
if discard_unmodified:
original_stat = os.stat(filename)
original_md5 = gmTools.file2md5(filename)
success = gmShellAPI.run_command_in_shell(editor, blocking=True)
if not success:
success, msg = gmMimeLib.call_viewer_on_file(aFile=filename,
block=True)
if not success:
_log.debug('problem running mimetype <%s> viewer', mimetype)
gmGuiHelpers.gm_show_error(
_('There was a problem running the editor\n'
'\n'
' [%s] (%s)\n'
'\n'
'on the visual progress note.\n'
'\n'
'Therefor GNUmed attempted to at least *show* it.\n'
'That failed as well, however:\n'
'\n'
'%s') % (editor, mimetype, msg),
_('Editing visual progress note'))
editor = configure_visual_progress_note_editor()
if editor is None:
gmDispatcher.send(
signal='statustext',
msg=_('Editor for visual progress note not configured.'),
beep=True)
return None
try:
open(filename, 'r').close()
except Exception:
_log.exception('problem accessing visual progress note file [%s]',
filename)
gmGuiHelpers.gm_show_error(
_('There was a problem reading the visual\n'
'progress note from the file:\n'
'\n'
' [%s]\n'
'\n') % filename, _('Saving visual progress note'))
return None
if discard_unmodified:
modified_stat = os.stat(filename)
# same size ?
if original_stat.st_size == modified_stat.st_size:
modified_md5 = gmTools.file2md5(filename)
# same hash ?
if original_md5 == modified_md5:
_log.debug('visual progress note (template) not modified')
# ask user to decide
msg = _(
'You either created a visual progress note from a template\n'
'in the database (rather than from a file on disk) or you\n'
'edited an existing visual progress note.\n'
'\n'
'The template/original was not modified at all, however.\n'
'\n'
'Do you still want to save the unmodified image as a\n'
'visual progress note into the EMR of the patient ?\n')
save_unmodified = gmGuiHelpers.gm_show_question(
msg, _('Saving visual progress note'))
if not save_unmodified:
_log.debug('user discarded unmodified note')
return
if doc_part is not None:
_log.debug('updating visual progress note')
doc_part.update_data_from_file(fname=filename)
doc_part.set_reviewed(technically_abnormal=False,
clinically_relevant=True)
return None
if not isinstance(episode, gmEMRStructItems.cEpisode):
if episode is None:
episode = _('visual progress notes')
pat = gmPerson.gmCurrentPatient()
emr = pat.emr
episode = emr.add_episode(episode_name=episode.strip(),
pk_health_issue=health_issue,
is_open=False)
doc = gmDocumentWidgets.save_file_as_new_document(
filename=filename,
document_type=gmDocuments.DOCUMENT_TYPE_VISUAL_PROGRESS_NOTE,
episode=episode,
unlock_patient=False,
pk_org_unit=gmPraxis.gmCurrentPraxisBranch()['pk_org_unit'],
date_generated=gmDateTime.pydt_now_here())
doc.set_reviewed(technically_abnormal=False, clinically_relevant=True)
return doc