def compare_versions(left_version, right_version):
"""
0: left == right
-1: left < right
1: left > right
"""
_log.debug('comparing [%s] with [%s]', left_version, right_version)
if left_version == right_version:
_log.debug('same version')
return 0
if right_version in ['head', 'dev', 'devel']:
_log.debug('development code')
return -1
if left_version in ['head', 'dev', 'devel']:
_log.debug('development code')
return 1
left_parts = left_version.split('.')
right_parts = right_version.split('.')
tmp, left_major = gmTools.input2decimal('%s.%s' %
(left_parts[0], left_parts[1]))
tmp, right_major = gmTools.input2decimal('%s.%s' %
(right_parts[0], right_parts[1]))
if left_major < right_major:
_log.debug('left version [%s] < right version [%s]: major part',
left_version, right_version)
return -1
if left_major > right_major:
_log.debug('left version [%s] > right version [%s]: major part',
left_version, right_version)
return 1
tmp, left_part3 = gmTools.input2decimal(left_parts[2].replace('rc', '0.'))
tmp, right_part3 = gmTools.input2decimal(right_parts[2].replace(
'rc', '0.'))
if left_part3 < right_part3:
_log.debug('left version [%s] < right version [%s]: minor part',
left_version, right_version)
return -1
if left_part3 > right_part3:
_log.debug('left version [%s] > right version [%s]: minor part',
left_version, right_version)
return 1
return 0
def compare_versions(left_version, right_version):
"""
0: left == right
-1: left < right
1: left > right
"""
if left_version == right_version:
_log.debug('same version: [%s] = [%s]', left_version, right_version)
return 0
left_parts = left_version.split('.')
right_parts = right_version.split('.')
tmp, left_major = gmTools.input2decimal(u'%s.%s' %
(left_parts[0], left_parts[1]))
tmp, right_major = gmTools.input2decimal(u'%s.%s' %
(right_parts[0], right_parts[1]))
if left_major < right_major:
_log.debug('left version [%s] < right version [%s]: major part',
left_version, right_version)
return -1
if left_major > right_major:
_log.debug('left version [%s] > right version [%s]: major part',
left_version, right_version)
return 1
tmp, left_part3 = gmTools.input2decimal(left_parts[2].replace('rc', '0.'))
tmp, right_part3 = gmTools.input2decimal(right_parts[2].replace(
'rc', '0.'))
if left_part3 < right_part3:
_log.debug('left version [%s] < right version [%s]: minor part',
left_version, right_version)
return -1
if left_part3 > right_part3:
_log.debug('left version [%s] > right version [%s]: minor part',
left_version, right_version)
return 1
return 0
def compare_versions(left_version, right_version):
"""
0: left == right
-1: left < right
1: left > right
"""
if left_version == right_version:
_log.debug('same version: [%s] = [%s]', left_version, right_version)
return 0
left_parts = left_version.split('.')
right_parts = right_version.split('.')
tmp, left_major = gmTools.input2decimal(u'%s.%s' % (left_parts[0], left_parts[1]))
tmp, right_major = gmTools.input2decimal(u'%s.%s' % (right_parts[0], right_parts[1]))
if left_major < right_major:
_log.debug('left version [%s] < right version [%s]: major part', left_version, right_version)
return -1
if left_major > right_major:
_log.debug('left version [%s] > right version [%s]: major part', left_version, right_version)
return 1
tmp, left_part3 = gmTools.input2decimal(left_parts[2].replace('rc', '0.'))
tmp, right_part3 = gmTools.input2decimal(right_parts[2].replace('rc', '0.'))
if left_part3 < right_part3:
_log.debug('left version [%s] < right version [%s]: minor part', left_version, right_version)
return -1
if left_part3 > right_part3:
_log.debug('left version [%s] > right version [%s]: minor part', left_version, right_version)
return 1
return 0
def __import_single_PID_hl7_file(filename, emr=None):
"""Assumes single-PID/single-MSH HL7 file."""
_log.debug('importing single-PID single-MSH HL7 data from [%s]', filename)
# read the file
MSH_file = io.open(filename, mode = 'rt', encoding = 'utf8')
HL7 = pyhl7.parse(MSH_file.read(1024 * 1024 * 5)) # 5 MB max
MSH_file.close()
# sanity checks
if len(HL7.segments('MSH')) != 1:
_log.error('more than one MSH segment')
return False
if len(HL7.segments('PID')) != 1:
_log.error('more than one PID segment')
return False
# ensure lab is in database
hl7_lab = HL7.extract_field('MSH', field_num = MSH_field__sending_lab)
gm_lab = __find_or_create_lab(hl7_lab)
# ensure test types exist
conn = gmPG2.get_connection(readonly = False)
__ensure_hl7_test_types_exist_in_gnumed(link_obj = conn, hl7_data = HL7, pk_test_org = gm_lab['pk_test_org'])
# find patient
if emr is None:
#PID = HL7.segment('PID')
pats = __PID2dto(HL7 = HL7)
if len(pats) == 0:
conn.rollback()
return False
if len(pats) > 1:
conn.rollback()
return False
emr = pats[0].emr
# import values: loop over segments
when_list = {}
current_result = None
previous_segment = None
had_errors = False
msh_seen = False
pid_seen = False
last_obr = None
obr = {}
for seg_idx in range(len(HL7)):
seg = HL7[seg_idx]
seg_type = seg[0][0]
_log.debug('processing line #%s = segment of type <%s>', seg_idx, seg_type)
if seg_type == u'MSH':
msh_seen = True
if seg_type == u'PID':
if not msh_seen:
conn.rollback()
_log.error('PID segment before MSH segment')
return False
pid_seen = True
if seg_type in [u'MSH', u'PID']:
_log.info('segment already handled')
previous_segment = seg_type
obr = {}
current_result = None
continue
if seg_type in [u'ORC']:
_log.info('currently ignoring %s segments', seg_type)
previous_segment = seg_type
obr = {}
current_result = None
continue
if seg_type == u'OBR':
previous_segment = seg_type
last_obr = seg
current_result = None
obr['abbrev'] = (u'%s' % seg[OBR_field__service_name][0]).strip()
try:
obr['name'] = (u'%s' % seg[OBR_field__service_name][1]).strip()
except IndexError:
obr['name'] = obr['abbrev']
for field_name in [OBR_field__ts_ended, OBR_field__ts_started, OBR_field__ts_specimen_received, OBR_field__ts_requested]:
obr['clin_when'] = seg[field_name][0].strip()
if obr['clin_when'] != u'':
break
continue
if seg_type == u'OBX':
current_result = None
# determine value
val_alpha = seg[OBX_field__value][0].strip()
is_num, val_num = gmTools.input2decimal(initial = val_alpha)
if is_num:
val_alpha = None
else:
val_num = None
val_alpha = val_alpha.replace('\.br\\', u'\n')
# determine test type
unit = seg[OBX_field__unit][0].strip()
if unit == u'':
if is_num:
unit = u'1/1'
else:
unit = None
test_type = __find_or_create_test_type (
loinc = u'%s' % seg[OBX_field__type][0][OBX_component__loinc-1],
name = u'%s' % seg[OBX_field__type][0][OBX_component__name-1],
pk_lab = gm_lab['pk_test_org'],
unit = unit
)
# eventually, episode should be read from lab_request
epi = emr.add_episode (
link_obj = conn,
episode_name = u'administrative',
is_open = False,
allow_dupes = False
)
current_result = emr.add_test_result (
link_obj = conn,
episode = epi['pk_episode'],
type = test_type['pk_test_type'],
intended_reviewer = gmStaff.gmCurrentProvider()['pk_staff'],
val_num = val_num,
val_alpha = val_alpha,
unit = unit
)
# handle range information et al
ref_range = seg[OBX_field__range][0].strip()
if ref_range != u'':
current_result.reference_range = ref_range
flag = seg[OBX_field__abnormal_flag][0].strip()
if flag != u'':
current_result['abnormality_indicator'] = flag
current_result['status'] = seg[OBX_field__status][0].strip()
current_result['val_grouping'] = seg[OBX_field__subid][0].strip()
current_result['source_data'] = u''
if last_obr is not None:
current_result['source_data'] += unicode(last_obr)
current_result['source_data'] += u'\n'
current_result['source_data'] += unicode(seg)
clin_when = seg[OBX_field__timestamp][0].strip()
if clin_when == u'':
_log.warning('no <Observation timestamp> in OBX, trying OBR timestamp')
clin_when = obr['clin_when']
try:
clin_when = __hl7dt2pydt(clin_when)
except ValueError:
_log.exception('clin_when from OBX or OBR not useable, assuming <today>')
if clin_when is not None:
current_result['clin_when'] = clin_when
current_result.save(conn = conn)
when_list[gmDateTime.pydt_strftime(current_result['clin_when'], '%Y %b %d')] = 1
previous_segment = seg_type
continue
if seg_type == u'NTE':
note = seg[NET_field__note][0].strip().replace('\.br\\', u'\n')
if note == u'':
_log.debug('empty NTE segment')
previous_segment = seg_type # maybe not ? (HL7 providers happen to use empty NTE segments to "structure" raw HL7 |-)
continue
# if this is an NTE following an OBR (IOW an order-related
# comment): make this a test result all of its own :-)
if previous_segment == u'OBR':
_log.debug('NTE following OBR: general note, using OBR timestamp [%s]', obr['clin_when'])
current_result = None
name = obr['name']
if name == u'':
name = _('Comment')
# FIXME: please suggest a LOINC for "order comment"
test_type = __find_or_create_test_type(name = name, pk_lab = gm_lab['pk_test_org'], abbrev = obr['abbrev'])
# eventually, episode should be read from lab_request
epi = emr.add_episode (
link_obj = conn,
episode_name = u'administrative',
is_open = False,
allow_dupes = False
)
nte_result = emr.add_test_result (
link_obj = conn,
episode = epi['pk_episode'],
type = test_type['pk_test_type'],
intended_reviewer = gmStaff.gmCurrentProvider()['pk_staff'],
val_alpha = note
)
#nte_result['val_grouping'] = seg[OBX_field__subid][0].strip()
nte_result['source_data'] = unicode(seg)
try:
nte_result['clin_when'] = __hl7dt2pydt(obr['clin_when'])
except ValueError:
_log.exception('no .clin_when from OBR for NTE pseudo-OBX available')
nte_result.save(conn = conn)
continue
if (previous_segment == u'OBX') and (current_result is not None):
current_result['source_data'] += u'\n'
current_result['source_data'] += unicode(seg)
current_result['note_test_org'] = gmTools.coalesce (
current_result['note_test_org'],
note,
u'%%s\n%s' % note
)
current_result.save(conn = conn)
previous_segment = seg_type
continue
_log.error(u'unexpected NTE segment')
had_errors = True
break
_log.error('unknown segment, aborting')
_log.debug('line: %s', seg)
had_errors = True
break
if had_errors:
conn.rollback()
return False
conn.commit()
# record import in chart
try:
no_results = len(HL7.segments('OBX'))
except KeyError:
no_results = u'?'
soap = _(
'Imported HL7 file [%s]:\n'
' lab "%s" (%s@%s), %s results (%s)'
) % (
filename,
hl7_lab,
gm_lab['unit'],
gm_lab['organization'],
no_results,
u' / '.join(when_list.keys())
)
epi = emr.add_episode (
episode_name = u'administrative',
is_open = False,
allow_dupes = False
)
emr.add_clin_narrative (
note = soap,
soap_cat = None,
episode = epi
)
# keep copy of HL7 data in document archive
folder = gmPerson.cPatient(emr.pk_patient).document_folder
hl7_docs = folder.get_documents (
doc_type = u'HL7 data',
episodes = [epi['pk_episode']],
order_by = u'ORDER BY clin_when DESC'
)
if len(hl7_docs) > 0:
# there should only ever be one unless the user manually creates more,
# also, it should always be the latest since "ORDER BY clin_when DESC"
hl7_doc = hl7_docs[0]
else:
hl7_doc = folder.add_document (
document_type = u'HL7 data',
encounter = emr.active_encounter['pk_encounter'],
episode = epi['pk_episode']
)
hl7_doc['comment'] = _('list of imported HL7 data files')
hl7_doc['clin_when'] = gmDateTime.pydt_now_here()
hl7_doc.save()
part = hl7_doc.add_part(file = filename)
part['obj_comment'] = _('Result dates: %s') % u' / '.join(when_list.keys())
part.save()
hl7_doc.set_reviewed(technically_abnormal = False, clinically_relevant = False)
return True
def __import_single_PID_hl7_file(filename, emr=None):
"""Assumes single-PID/single-MSH HL7 file."""
_log.debug('importing single-PID single-MSH HL7 data from [%s]', filename)
# read the file
MSH_file = io.open(filename, mode = 'rt', encoding = 'utf8', newline = '')
HL7 = pyhl7.parse(MSH_file.read(1024 * 1024 * 5)) # 5 MB max
MSH_file.close()
# sanity checks
if len(HL7.segments('MSH')) != 1:
_log.error('more than one MSH segment')
return False
if len(HL7.segments('PID')) != 1:
_log.error('more than one PID segment')
return False
# ensure lab is in database
hl7_lab = HL7.extract_field('MSH', field_num = MSH_field__sending_lab)
gm_lab = __find_or_create_lab(hl7_lab)
# ensure test types exist
conn = gmPG2.get_connection(readonly = False)
__ensure_hl7_test_types_exist_in_gnumed(link_obj = conn, hl7_data = HL7, pk_test_org = gm_lab['pk_test_org'])
# find patient
if emr is None:
#PID = HL7.segment('PID')
pats = __PID2dto(HL7 = HL7)
if len(pats) == 0:
conn.rollback()
return False
if len(pats) > 1:
conn.rollback()
return False
emr = pats[0].emr
# import values: loop over segments
when_list = {}
current_result = None
previous_segment = None
had_errors = False
msh_seen = False
pid_seen = False
last_obr = None
obr = {}
for seg_idx in range(len(HL7)):
seg = HL7[seg_idx]
seg_type = seg[0][0]
_log.debug('processing line #%s = segment of type <%s>', seg_idx, seg_type)
if seg_type == 'MSH':
msh_seen = True
if seg_type == 'PID':
if not msh_seen:
conn.rollback()
_log.error('PID segment before MSH segment')
return False
pid_seen = True
if seg_type in ['MSH', 'PID']:
_log.info('segment already handled')
previous_segment = seg_type
obr = {}
current_result = None
continue
if seg_type in ['ORC']:
_log.info('currently ignoring %s segments', seg_type)
previous_segment = seg_type
obr = {}
current_result = None
continue
if seg_type == 'OBR':
previous_segment = seg_type
last_obr = seg
current_result = None
obr['abbrev'] = ('%s' % seg[OBR_field__service_name][0]).strip()
try:
obr['name'] = ('%s' % seg[OBR_field__service_name][1]).strip()
except IndexError:
obr['name'] = obr['abbrev']
for field_name in [OBR_field__ts_ended, OBR_field__ts_started, OBR_field__ts_specimen_received, OBR_field__ts_requested]:
obr['clin_when'] = seg[field_name][0].strip()
if obr['clin_when'] != '':
break
continue
if seg_type == 'OBX':
current_result = None
# determine value
val_alpha = seg[OBX_field__value][0].strip()
is_num, val_num = gmTools.input2decimal(initial = val_alpha)
if is_num:
val_alpha = None
else:
val_num = None
val_alpha = val_alpha.replace('\.br\\', '\n')
# determine test type
unit = seg[OBX_field__unit][0].strip()
if unit == '':
if is_num:
unit = '1/1'
else:
unit = None
test_type = __find_or_create_test_type (
loinc = '%s' % seg[OBX_field__type][0][OBX_component__loinc-1],
name = '%s' % seg[OBX_field__type][0][OBX_component__name-1],
pk_lab = gm_lab['pk_test_org'],
unit = unit,
link_obj = conn
)
# eventually, episode should be read from lab_request
epi = emr.add_episode (
link_obj = conn,
episode_name = 'administrative',
is_open = False,
allow_dupes = False
)
current_result = emr.add_test_result (
link_obj = conn,
episode = epi['pk_episode'],
type = test_type['pk_test_type'],
intended_reviewer = gmStaff.gmCurrentProvider()['pk_staff'],
val_num = val_num,
val_alpha = val_alpha,
unit = unit
)
# handle range information et al
ref_range = seg[OBX_field__range][0].strip()
if ref_range != '':
current_result.reference_range = ref_range
flag = seg[OBX_field__abnormal_flag][0].strip()
if flag != '':
current_result['abnormality_indicator'] = flag
current_result['status'] = seg[OBX_field__status][0].strip()
current_result['val_grouping'] = seg[OBX_field__subid][0].strip()
current_result['source_data'] = ''
if last_obr is not None:
current_result['source_data'] += str(last_obr)
current_result['source_data'] += '\n'
current_result['source_data'] += str(seg)
clin_when = seg[OBX_field__timestamp][0].strip()
if clin_when == '':
_log.warning('no <Observation timestamp> in OBX, trying OBR timestamp')
clin_when = obr['clin_when']
try:
clin_when = __hl7dt2pydt(clin_when)
except ValueError:
_log.exception('clin_when from OBX or OBR not useable, assuming <today>')
if clin_when is not None:
current_result['clin_when'] = clin_when
current_result.save(conn = conn)
when_list[gmDateTime.pydt_strftime(current_result['clin_when'], '%Y %b %d')] = 1
previous_segment = seg_type
continue
if seg_type == 'NTE':
note = seg[NET_field__note][0].strip().replace('\.br\\', '\n')
if note == '':
_log.debug('empty NTE segment')
previous_segment = seg_type # maybe not ? (HL7 providers happen to use empty NTE segments to "structure" raw HL7 |-)
continue
# if this is an NTE following an OBR (IOW an order-related
# comment): make this a test result all of its own :-)
if previous_segment == 'OBR':
_log.debug('NTE following OBR: general note, using OBR timestamp [%s]', obr['clin_when'])
current_result = None
name = obr['name']
if name == '':
name = _('Comment')
# FIXME: please suggest a LOINC for "order comment"
test_type = __find_or_create_test_type(name = name, pk_lab = gm_lab['pk_test_org'], abbrev = obr['abbrev'], link_obj = conn)
# eventually, episode should be read from lab_request
epi = emr.add_episode (
link_obj = conn,
episode_name = 'administrative',
is_open = False,
allow_dupes = False
)
nte_result = emr.add_test_result (
link_obj = conn,
episode = epi['pk_episode'],
type = test_type['pk_test_type'],
intended_reviewer = gmStaff.gmCurrentProvider()['pk_staff'],
val_alpha = note
)
#nte_result['val_grouping'] = seg[OBX_field__subid][0].strip()
nte_result['source_data'] = str(seg)
try:
nte_result['clin_when'] = __hl7dt2pydt(obr['clin_when'])
except ValueError:
_log.exception('no .clin_when from OBR for NTE pseudo-OBX available')
nte_result.save(conn = conn)
continue
if (previous_segment == 'OBX') and (current_result is not None):
current_result['source_data'] += '\n'
current_result['source_data'] += str(seg)
current_result['note_test_org'] = gmTools.coalesce (
current_result['note_test_org'],
note,
'%%s\n%s' % note
)
current_result.save(conn = conn)
previous_segment = seg_type
continue
_log.error('unexpected NTE segment')
had_errors = True
break
_log.error('unknown segment, aborting')
_log.debug('line: %s', seg)
had_errors = True
break
if had_errors:
conn.rollback()
return False
conn.commit()
# record import in chart
try:
no_results = len(HL7.segments('OBX'))
except KeyError:
no_results = '?'
soap = _(
'Imported HL7 file [%s]:\n'
' lab "%s" (%s@%s), %s results (%s)'
) % (
filename,
hl7_lab,
gm_lab['unit'],
gm_lab['organization'],
no_results,
' / '.join(list(when_list))
)
epi = emr.add_episode (
episode_name = 'administrative',
is_open = False,
allow_dupes = False
)
emr.add_clin_narrative (
note = soap,
soap_cat = None,
episode = epi
)
# keep copy of HL7 data in document archive
folder = gmPerson.cPatient(emr.pk_patient).document_folder
hl7_docs = folder.get_documents (
doc_type = 'HL7 data',
pk_episodes = [epi['pk_episode']],
order_by = 'ORDER BY clin_when DESC'
)
if len(hl7_docs) > 0:
# there should only ever be one unless the user manually creates more,
# also, it should always be the latest since "ORDER BY clin_when DESC"
hl7_doc = hl7_docs[0]
else:
hl7_doc = folder.add_document (
document_type = 'HL7 data',
encounter = emr.active_encounter['pk_encounter'],
episode = epi['pk_episode']
)
hl7_doc['comment'] = _('list of imported HL7 data files')
hl7_doc['pk_org_unit'] = gmPraxis.gmCurrentPraxisBranch()['pk_org_unit']
hl7_doc['clin_when'] = gmDateTime.pydt_now_here()
hl7_doc.save()
part = hl7_doc.add_part(file = filename)
part['obj_comment'] = _('Result dates: %s') % ' / '.join(list(when_list))
part.save()
hl7_doc.set_reviewed(technically_abnormal = False, clinically_relevant = False)
return True
def create_sql(filename):
csv_file = open(filename, mode='rt', encoding='utf-8-sig')
csv_lines = gmTools.unicode_csv_reader(csv_file,
fieldnames=field_names,
delimiter=';',
quotechar='"',
dict=True)
print SQL_start
line_idx = 0
skip_line = False
for line in csv_lines:
line_idx += 1
print "-- line #%s" % line_idx
# normalize field content
for field in field_names:
try:
line[field] = line[field].strip().strip(';,').strip().replace(
"'", "''")
except AttributeError: # trailing fields are a list
pass
# verify required fields
for field in non_empty_fields:
if line[field] == '':
print "-- ignoring line: empty field [%s]" % field
print "--", line
print ""
skip_line = True
break
if skip_line:
skip_line = False
continue
# verify numeric fields
for field in numeric_fields:
if line[field] == '':
continue
success, num_val = gmTools.input2decimal(initial=line[field])
if not success:
print "-- ignoring line: field [%s] not numeric: >>>%s<<<" % (
field, line[field])
print "--", line
print ""
skip_line = True
break
line[field] = num_val
if skip_line:
skip_line = False
continue
# actually create SQL
# loop over strengths
for field in numeric_fields:
if line[field] == '':
continue
line['brand_name'] = ('%%(product)s %%(%s)s (%%(company)s)' %
field) % line
line['strength'] = line[field]
print SQL_stage_drug % line
print SQL_end
def create_sql(filename): csv_file = io.open(filename, mode = 'rt', encoding = u'utf8') csv_lines = gmTools.unicode_csv_reader ( csv_file, fieldnames = field_names, delimiter = ';', quotechar = '"', dict = True ) print SQL_start line_idx = 0 skip_line = False for line in csv_lines: line_idx += 1 print "-- line #%s" % line_idx # normalize field content for field in field_names: try: line[field] = line[field].strip().strip(u';,').strip().replace(u"'", u"''") except AttributeError: # trailing fields are a list pass # verify required fields for field in non_empty_fields: if line[field] == u'': print "-- ignoring line: empty field [%s]" % field print "--", line print "" skip_line = True break if skip_line: skip_line = False continue # verify numeric fields for field in numeric_fields: if line[field] == u'': continue success, num_val = gmTools.input2decimal(initial = line[field]) if not success: print "-- ignoring line: field [%s] not numeric: >>>%s<<<" % (field, line[field]) print "--", line print "" skip_line = True break line[field] = num_val if skip_line: skip_line = False continue # actually create SQL # loop over strengths for field in numeric_fields: if line[field] == u'': continue line['brand_name'] = (u'%%(brand)s %%(%s)s (%%(company)s)' % field) % line line['strength'] = line[field] print SQL_stage_drug % line print SQL_end
