def _populate_with_data(self):
pat = gmPerson.gmCurrentPatient()
if not pat.connected:
return True
wx.BeginBusyCursor()
try:
self.__tl_file = gmTimelineExporter.create_timeline_file(patient = pat)
self._PNL_timeline.open_timeline(self.__tl_file)
except Exception: # more specifically: TimelineIOError
_log.exception('cannot load EMR from timeline XML')
self._PNL_timeline.clear_timeline()
self.__tl_file = gmTimelineExporter.create_fake_timeline_file(patient = pat)
self._PNL_timeline.open_timeline(self.__tl_file)
return True
finally:
wx.EndBusyCursor()
return True
def _populate_with_data(self):
pat = gmPerson.gmCurrentPatient()
if not pat.connected:
return True
wx.BeginBusyCursor()
try:
self.__tl_file = gmTimelineExporter.create_timeline_file(patient = pat)
self._PNL_timeline.open_timeline(self.__tl_file)
except Exception: # more specifically: TimelineIOError
_log.exception('cannot load EMR from timeline XML')
self._PNL_timeline.clear_timeline()
self.__tl_file = gmTimelineExporter.create_fake_timeline_file(patient = pat)
self._PNL_timeline.open_timeline(self.__tl_file)
return True
finally:
wx.EndBusyCursor()
return True
def run_tool():
tool = _cfg.get(option='--tool', source_order=[('cli', 'return')])
if tool is None:
# not running a tool
return None
if tool not in _known_tools:
_log.error('unknown tool requested: %s', tool)
print('GNUmed startup: Unknown tool [%s] requested.' % tool)
print('GNUmed startup: Known tools: %s' % _known_tools)
return -1
print('')
print('==============================================')
print('Running tool: %s' % tool)
print('----------------------------------------------')
print('')
if tool == 'check_enc_epi_xref':
from Gnumed.business import gmEMRStructItems
return gmEMRStructItems.check_fk_encounter_fk_episode_x_ref()
if tool == 'export_pat_emr_structure':
# setup praxis
from Gnumed.business import gmPraxis
praxis = gmPraxis.gmCurrentPraxisBranch(
branch=gmPraxis.get_praxis_branches()[0])
# get patient
from Gnumed.business import gmPersonSearch
pat = gmPersonSearch.ask_for_patient()
# setup exporters
from Gnumed.business import gmEMRStructItems
from Gnumed.exporters import gmTimelineExporter
from Gnumed.exporters import gmPatientExporter
while pat is not None:
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 = io.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 = io.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
# tool export_patient_as (vcf, gdt, ...)
#if tool == 'export_pat_demographics':
# should not happen (because checked against _known_tools)
return -1
def run_tool():
"""Run a console tool.
Exit codes as per man page:
0: normal termination of the client
< 0: some error occurred while trying to run a console tool
-1: an unknown console tool was requested
< -1: an error occurred while a console tool was run
-999: hard abort of the client
One of these needs to be returned from this function (and,
by extension from the tool having been run, if any).
"""
tool = _cfg.get(option='--tool', source_order=[('cli', 'return')])
if tool is None:
# not running a tool
return None
if tool not in _known_tools:
_log.error('unknown tool requested: %s', tool)
print('GNUmed startup: Unknown tool [%s] requested.' % tool)
print('GNUmed startup: Known tools: %s' % _known_tools)
return -1
print('')
print('==============================================')
print('Running tool: %s' % tool)
print('----------------------------------------------')
print('')
if tool == 'generate_man_page':
man_page_fname = os.path.abspath(os.path.join('.', 'gnumed.1'))
man_page_file = open(man_page_fname, mode='wt', encoding='utf8')
man_page_file.write(__doc__ % datetime.date.today().strftime('%x'))
man_page_file.close()
print('MAN page saved as:', man_page_fname)
return 0
login, creds = gmPG2.request_login_params()
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 == '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':
fname = 'db-fingerprint.txt'
result = gmPG2.get_db_fingerprint(fname=fname, with_dump=True)
if result == fname:
print('Success: %s' % fname)
return 0
print('Failed. Check the log for details.')
return -2
if tool == 'export_pat_emr_structure':
# setup praxis
from Gnumed.business import gmPraxis
praxis = gmPraxis.gmCurrentPraxisBranch(
branch=gmPraxis.get_praxis_branches()[0])
# get patient
from Gnumed.business import gmPersonSearch
pat = gmPersonSearch.ask_for_patient()
# setup exporters
from Gnumed.business import gmEMRStructItems
from Gnumed.exporters import gmTimelineExporter
from Gnumed.exporters import gmPatientExporter
while pat is not None:
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
# tool export_patient_as (vcf, gdt, ...)
#if tool == 'export_pat_demographics':
# should not happen (because checked against _known_tools)
return -1
def run_tool():
tool = _cfg.get(option = '--tool', source_order = [('cli', 'return')])
if tool is None:
# not running a tool
return None
if tool not in _known_tools:
_log.error('unknown tool requested: %s', tool)
print('GNUmed startup: Unknown tool [%s] requested.' % tool)
print('GNUmed startup: Known tools: %s' % _known_tools)
return -1
print('')
print('==============================================')
print('Running tool: %s' % tool)
print('----------------------------------------------')
print('')
if tool == 'check_enc_epi_xref':
from Gnumed.business import gmEMRStructItems
return gmEMRStructItems.check_fk_encounter_fk_episode_x_ref()
if tool == 'export_pat_emr_structure':
# setup praxis
from Gnumed.business import gmPraxis
praxis = gmPraxis.gmCurrentPraxisBranch(branch = gmPraxis.get_praxis_branches()[0])
# get patient
from Gnumed.business import gmPersonSearch
pat = gmPersonSearch.ask_for_patient()
# setup exporters
from Gnumed.business import gmEMRStructItems
from Gnumed.exporters import gmTimelineExporter
from Gnumed.exporters import gmPatientExporter
while pat is not None:
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 = io.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 = io.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
# tool export_patient_as (vcf, gdt, ...)
#if tool == 'export_pat_demographics':
# should not happen (because checked against _known_tools)
return -1