Gnumed.business.gmDICOM API documentation
Description: GNUmed DICOM handling middleware

# Module `Gnumed.business.gmDICOM`

GNUmed DICOM handling middleware

Expand source code

    # -*- coding: utf-8 -*-

    """GNUmed DICOM handling middleware"""
    #============================================================
    __license__ = "GPL v2 or later"
    __author__ = "K.Hilbert <Karsten.Hilbert@gmx.net>"

    # stdlib
    import io
    import os
    import sys
    import re as regex
    import logging
    import http.client              # exception names used by httplib2
    import socket
    import httplib2
    import json
    import shutil
    import time
    import datetime as pydt
    from urllib.parse import urlencode
    import distutils.version as version

    # GNUmed modules
    if __name__ == '__main__':
            sys.path.insert(0, '../../')
    from Gnumed.pycommon import gmTools
    from Gnumed.pycommon import gmShellAPI
    from Gnumed.pycommon import gmMimeLib
    from Gnumed.pycommon import gmDateTime
    #from Gnumed.pycommon import gmHooks
    #from Gnumed.pycommon import gmDispatcher

    _log = logging.getLogger('gm.dicom')

    _map_gender_gm2dcm = {
            'm': 'M',
            'f': 'F',
            'tm': 'M',
            'tf': 'F',
            'h': 'O'
    }

    #============================================================
    class cOrthancServer:
            # REST API access to Orthanc DICOM servers

    #       def __init__(self):
    #               self.__server_identification = None
    #               self.__user = None
    #               self.__password = None
    #               self.__conn = None
    #               self.__server_url = None

            #--------------------------------------------------------
            def connect(self, host, port, user, password, expected_minimal_version=None, expected_name=None, expected_aet=None):
                    try:
                            int(port)
                    except Exception:
                            _log.error('invalid port [%s]', port)
                            return False
                    if (host is None) or (host.strip() == ''):
                            host = 'localhost'
                    try:
                            self.__server_url = str('http://%s:%s' % (host, port))
                    except Exception:
                            _log.exception('cannot create server url from: host [%s] and port [%s]', host, port)
                            return False
                    self.__user = user
                    self.__password = password
                    _log.info('connecting as [%s] to Orthanc server at [%s]', self.__user, self.__server_url)
                    cache_dir = os.path.join(gmTools.gmPaths().user_tmp_dir, '.orthanc2gm-cache')
                    gmTools.mkdir(cache_dir, 0o700)
                    gmTools.create_directory_description_file(directory = cache_dir, readme = 'this directory caches Orthanc REST data, mainly DICOM files')
                    _log.debug('using cache directory: %s', cache_dir)
                    self.__conn = httplib2.Http(cache = cache_dir)
                    self.__conn.add_credentials(self.__user, self.__password)
                    _log.debug('connected to server: %s', self.server_identification)
                    self.connect_error = ''
                    if self.server_identification is False:
                            self.connect_error += 'retrieving server identification failed'
                            return False
                    if expected_minimal_version is not None:
                            if version.LooseVersion(self.server_identification['Version']) < version.LooseVersion(expected_minimal_version):
                                    _log.error('server too old, needed [%s]', expected_minimal_version)
                                    self.connect_error += 'server too old, needed version [%s]' % expected_minimal_version
                                    return False
                    if expected_name is not None:
                            if self.server_identification['Name'] != expected_name:
                                    _log.error('wrong server name, expected [%s]', expected_name)
                                    self.connect_error += 'wrong server name, expected [%s]' % expected_name
                                    return False
                    if expected_aet is not None:
                            if self.server_identification['DicomAet'] != expected_name:
                                    _log.error('wrong server AET, expected [%s]', expected_aet)
                                    self.connect_error += 'wrong server AET, expected [%s]' % expected_aet
                                    return False
                    return True

            #--------------------------------------------------------
            def _get_server_identification(self):
                    try:
                            return self.__server_identification
                    except AttributeError:
                            pass
                    system_data = self.__run_GET(url = '%s/system' % self.__server_url)
                    if system_data is False:
                            _log.error('unable to get server identification')
                            return False
                    _log.debug('server: %s', system_data)
                    self.__server_identification = system_data

                    self.__initial_orthanc_encoding = self.__run_GET(url = '%s/tools/default-encoding' % self.__server_url)
                    _log.debug('initial Orthanc encoding: %s', self.__initial_orthanc_encoding)

                    # check time skew
                    tolerance = 60 # seconds
                    client_now_as_utc = pydt.datetime.utcnow()
                    start = time.time()
                    orthanc_now_str = self.__run_GET(url = '%s/tools/now' % self.__server_url)              # 20180208T165832
                    end = time.time()
                    query_duration = end - start
                    orthanc_now_unknown_tz = pydt.datetime.strptime(orthanc_now_str, '%Y%m%dT%H%M%S')
                    _log.debug('GNUmed "now" (UTC): %s', client_now_as_utc)
                    _log.debug('Orthanc "now" (UTC): %s', orthanc_now_unknown_tz)
                    _log.debug('wire roundtrip (seconds): %s', query_duration)
                    _log.debug('maximum skew tolerance (seconds): %s', tolerance)
                    if query_duration > tolerance:
                            _log.info('useless to check GNUmed/Orthanc time skew, wire roundtrip (%s) > tolerance (%s)', query_duration, tolerance)
                    else:
                            if orthanc_now_unknown_tz > client_now_as_utc:
                                    real_skew = orthanc_now_unknown_tz - client_now_as_utc
                            else:
                                    real_skew = client_now_as_utc - orthanc_now_unknown_tz
                            _log.info('GNUmed/Orthanc time skew: %s', real_skew)
                            if real_skew > pydt.timedelta(seconds = tolerance):
                                    _log.error('GNUmed/Orthanc time skew > tolerance (may be due to timezone differences on Orthanc < v1.3.2)')

                    return self.__server_identification

            server_identification = property(_get_server_identification, lambda x:x)

            #--------------------------------------------------------
            def _get_as_external_id_issuer(self):
                    # fixed type :: user level instance name :: DICOM AET
                    return 'Orthanc::%(Name)s::%(DicomAet)s' % self.__server_identification

            as_external_id_issuer = property(_get_as_external_id_issuer, lambda x:x)

            #--------------------------------------------------------
            def _get_url_browse_patients(self):
                    if self.__user is None:
                            return self.__server_url
                    return self.__server_url.replace('http://', 'http://%s@' % self.__user)

            url_browse_patients = property(_get_url_browse_patients, lambda x:x)

            #--------------------------------------------------------
            def get_url_browse_patient(self, patient_id):
                    # http://localhost:8042/#patient?uuid=0da01e38-cf792452-65c1e6af-b77faf5a-b637a05b
                    return '%s/#patient?uuid=%s' % (self.url_browse_patients, patient_id)

            #--------------------------------------------------------
            def get_url_browse_study(self, study_id):
                    # http://localhost:8042/#study?uuid=0da01e38-cf792452-65c1e6af-b77faf5a-b637a05b
                    return '%s/#study?uuid=%s' % (self.url_browse_patients, study_id)

            #--------------------------------------------------------
            # download API
            #--------------------------------------------------------
            def get_matching_patients(self, person) -> list:
                    """Fetch matching patients from an Orthanc DICOM server.

                    Matches are searched for via stored "external ID" and
                    via generically generated ID. The external IDs are
                    fetched from the patient store, must be of type
                    "PACS" and must be marked as issued by the
                    instantiated PACS <self.>

                    Args:
                            person: a gmPerson.cPerson instance

                    Returns:
                            A list of Orthanc patient UIDs.
                    """
                    _log.info('searching for Orthanc patients matching %s', person)
                    pacs_ids = person.get_external_ids(id_type = 'PACS', issuer = self.as_external_id_issuer)
                    if len(pacs_ids) > 1:
                            _log.error('GNUmed patient has more than one ID for this PACS: %s', pacs_ids)
                            _log.error('the stored-in-GNUmed PACS ID is expected to be unique _per PACS_')
                            return []

                    pacs_ids2search_by = []
                    pacs_ids2search_by.extend([ pacs_id['value'] for pacs_id in pacs_ids ])
                    pacs_ids2search_by.extend(person.suggest_external_ids(target = 'PACS'))
                    matching_pats = []
                    for pacs_id in pacs_ids2search_by:
                            _log.debug('using PACS ID [%s]', pacs_id)
                            pats = self.get_patients_by_external_id(external_id = pacs_id, fuzzy = False)
                            if len(pats) > 1:
                                    _log.warning('more than one Orthanc patient matches PACS ID: %s', pacs_id)
                            matching_pats.extend(pats)
                    if not matching_pats:
                            _log.debug('no matching patient found in PACS')
                    return matching_pats

            #--------------------------------------------------------
            def get_patients_by_external_id(self, external_id=None, fuzzy=False):
                    """Search for instances by patient ID."""
                    _log.info('external ID >>>%s<<< fuzzy [%s]', external_id, fuzzy)
                    search_term = external_id.strip().strip('*').strip()
                    if fuzzy:
                            search_term = '*%s*' % search_term
                    search_data = {
                            'Level': 'Patient',
                            'CaseSensitive': False,
                            'Expand': True,
                            'Query': {'PatientID': search_term}
                    }
                    matches = self.__run_POST(url = '%s/tools/find' % self.__server_url, data = search_data)
                    # paranoia
                    for match in matches:
                            self.protect_patient(orthanc_id = match['ID'])
                    return matches

            #--------------------------------------------------------
            def get_patients_by_name(self, name_parts=None, gender=None, dob=None, fuzzy=False) -> list:
                    """Search for patients by name.

                    Returns:
                            List of patients matching the search term(s).
                    """
                    _log.info('name parts %s, gender [%s], dob [%s], fuzzy: [%s]', name_parts, gender, dob, fuzzy)
                    if len(name_parts) > 1:
                            return self.get_patients_by_name_parts(name_parts = name_parts, gender = gender, dob = dob, fuzzy = fuzzy)

                    search_term = name_parts[0].strip().strip('*').strip()
                    if search_term == '':
                            _log.debug('search term empty')
                            return []

                    if fuzzy:
                            search_term = '*%s*' % search_term
                    search_data = {
                            'Level': 'Patient',
                            'CaseSensitive': False,
                            'Expand': True,
                            'Query': {'PatientName': search_term}
                    }
                    if gender is not None:
                            gender = _map_gender_gm2dcm[gender.casefold()]
                            if gender is not None:
                                    search_data['Query']['PatientSex'] = gender
                    if dob is not None:
                            search_data['Query']['PatientBirthDate'] = dob.strftime('%Y%m%d')
                    _log.info('server-side C-FIND SCU over REST search, mogrified search data: %s', search_data)
                    matches = self.__run_POST(url = '%s/tools/find' % self.__server_url, data = search_data)
                    return matches

            #--------------------------------------------------------
            def get_patients_by_name_parts(self, name_parts=None, gender=None, dob=None, fuzzy=False):
                    # fuzzy: allow partial/substring matches (but not across name part boundaries ',' or '^')
                    matching_patients = []
                    clean_parts = []
                    for part in name_parts:
                            if part.strip() == '':
                                    continue
                            clean_parts.append(part.casefold().strip())
                    _log.info('client-side patient search, scrubbed search terms: %s', clean_parts)
                    pat_ids = self.__run_GET(url = '%s/patients' % self.__server_url)
                    if pat_ids is False:
                            _log.error('cannot retrieve patients')
                            return []

                    for pat_id in pat_ids:
                            orthanc_pat = self.__run_GET(url = '%s/patients/%s' % (self.__server_url, pat_id))
                            if orthanc_pat is False:
                                    _log.error('cannot retrieve patient')
                                    continue
                            orthanc_name = orthanc_pat['MainDicomTags']['PatientName'].casefold().strip()
                            if not fuzzy:
                                    orthanc_name = orthanc_name.replace(' ', ',').replace('^', ',').split(',')
                            parts_in_orthanc_name = 0
                            for part in clean_parts:
                                    if part in orthanc_name:
                                            parts_in_orthanc_name += 1
                            if parts_in_orthanc_name == len(clean_parts):
                                    _log.debug('name match: "%s" contains all of %s', orthanc_name, clean_parts)
                                    if gender is not None:
                                            gender = _map_gender_gm2dcm[gender.casefold()]
                                            if gender is not None:
                                                    if orthanc_pat['MainDicomTags']['PatientSex'].casefold() != gender:
                                                            _log.debug('gender mismatch: dicom=[%s] gnumed=[%s], skipping', orthanc_pat['MainDicomTags']['PatientSex'], gender)
                                                            continue
                                    if dob is not None:
                                            if orthanc_pat['MainDicomTags']['PatientBirthDate'] != dob.strftime('%Y%m%d'):
                                                    _log.debug('dob mismatch: dicom=[%s] gnumed=[%s], skipping', orthanc_pat['MainDicomTags']['PatientBirthDate'], dob)
                                                    continue
                                    matching_patients.append(orthanc_pat)
                            else:
                                    _log.debug('name mismatch: "%s" does not contain all of %s', orthanc_name, clean_parts)
                    return matching_patients

            #--------------------------------------------------------
            def search_studies_by_patient_name(self, name:str) -> list:
                    """Search for studies with the given patient name snippet.

                    A study (even at the Orthanc DB metadata level) will
                    contain the original patient name (unless manually
                    modified) in contrast to the (artificial Orthanc DB
                    metadata level) patient record. The latter contains
                    the first patient name that had been associated with
                    the given patient ID.

                    Args:
                            name (str): name snippet to search for

                    Returns:
                            The list of matching *studies* (not *patient*).
                    """
                    _log.debug('search term [%s]', name)
                    search_term = name.strip().strip('*').strip()
                    if search_term == '':
                            _log.warning('search term empty')
                            return []

                    search_term = '*%s*' % search_term
                    search_data = {
                            'Level': 'Study',
                            'CaseSensitive': False,
                            'Expand': True,
                            'Query': {'PatientName': search_term}
                    }
                    matches = self.__run_POST(url = '%s/tools/find' % self.__server_url, data = search_data)
                    return matches

            #--------------------------------------------------------
            def search_studies_by_patient_id(self, patient_id:str) -> list:
                    """Search for studies with the given patient ID snippet.

                    This relates to the external world patient ID as
                    stored in DICOM instances, not the Orthanc DB
                    metadata level patient UID.

                    Args:
                            patient_id: patient ID snippet to search for

                    Returns:
                            The list of matching *studies* (not *patient*).
                    """
                    _log.debug('search term >>>%s<<<', patient_id)
                    search_term = patient_id.strip().strip('*').strip()
                    search_term = '*%s*' % search_term
                    search_data = {
                            'Level': 'Study',
                            'CaseSensitive': False,
                            'Expand': True,
                            'Query': {'PatientID': search_term}
                    }
                    matches = self.__run_POST(url = '%s/tools/find' % self.__server_url, data = search_data)
                    return matches

            #--------------------------------------------------------
            def get_studies_list_by_patient_name(self, name_parts=None, gender=None, dob=None, fuzzy=False):
                    return self.get_studies_list_by_orthanc_patient_list (
                            orthanc_patients = self.get_patients_by_name(name_parts = name_parts, gender = gender, dob = dob, fuzzy = fuzzy)
                    )

            #--------------------------------------------------------
            def get_studies_list_by_external_id(self, external_id=None):
                    return self.get_studies_list_by_orthanc_patient_list (
                            orthanc_patients = self.get_patients_by_external_id(external_id = external_id)
                    )

            #--------------------------------------------------------
            def get_study_as_zip(self, study_id=None, filename=None):
                    if filename is None:
                            filename = gmTools.get_unique_filename(prefix = r'DCM-', suffix = r'.zip')
                    _log.info('exporting study [%s] into [%s]', study_id, filename)
                    f = io.open(filename, 'wb')
                    f.write(self.__run_GET(url = '%s/studies/%s/archive' % (self.__server_url, str(study_id)), allow_cached = True))
                    f.close()
                    return filename

            #--------------------------------------------------------
            def get_study_as_zip_with_dicomdir(self, study_id=None, filename=None):
                    if filename is None:
                            filename = gmTools.get_unique_filename(prefix = r'DCM-', suffix = r'.zip')
                    _log.info('exporting study [%s] into [%s]', study_id, filename)
                    f = io.open(filename, 'wb')
                    f.write(self.__run_GET(url = '%s/studies/%s/media' % (self.__server_url, str(study_id)), allow_cached = True))
                    f.close()
                    return filename

            #--------------------------------------------------------
            def get_studies_as_zip(self, study_ids=None, patient_id=None, filename=None):
                    if filename is None:
                            filename = gmTools.get_unique_filename(prefix = r'DCM-', suffix = r'.zip')
                    if study_ids is None:
                            _log.info('exporting all studies of patient [%s] into [%s]', patient_id, filename)
                            f = io.open(filename, 'wb')
                            f.write(self.__run_GET(url = '%s/patients/%s/archive' % (self.__server_url, str(patient_id)), allow_cached = True))
                            f.close()
                            return filename

            #--------------------------------------------------------
            def _manual_get_studies_with_dicomdir(self, study_ids=None, patient_id=None, target_dir=None, filename=None, create_zip=False):

                    if filename is None:
                            filename = gmTools.get_unique_filename(prefix = r'DCM-', suffix = r'.zip', tmp_dir = target_dir)

                    # all studies
                    if study_ids is None:
                            _log.info('exporting all studies of patient [%s] into [%s]', patient_id, filename)
                            f = io.open(filename, 'wb')
                            url = '%s/patients/%s/media' % (self.__server_url, str(patient_id))
                            _log.debug(url)
                            f.write(self.__run_GET(url = url, allow_cached = True))
                            f.close()
                            if create_zip:
                                    return filename
                            if target_dir is None:
                                    target_dir = gmTools.mk_sandbox_dir(prefix = 'dcm-')
                            if not gmTools.unzip_archive(filename, target_dir = target_dir, remove_archive = True):
                                    return False
                            return target_dir

                    # a selection of studies
                    dicomdir_cmd = 'gm-create_dicomdir'             # args: 1) name of DICOMDIR to create 2) base directory where to start recursing for DICOM files
                    found, external_cmd = gmShellAPI.detect_external_binary(dicomdir_cmd)
                    if not found:
                            _log.error('[%s] not found', dicomdir_cmd)
                            return False

                    if create_zip:
                            sandbox_dir = gmTools.mk_sandbox_dir(prefix = 'dcm-')
                            _log.info('exporting studies [%s] into [%s] (sandbox [%s])', study_ids, filename, sandbox_dir)
                    else:
                            sandbox_dir = target_dir
                            _log.info('exporting studies [%s] into [%s]', study_ids, sandbox_dir)
                    _log.debug('sandbox dir: %s', sandbox_dir)
                    idx = 0
                    for study_id in study_ids:
                            study_zip_name = gmTools.get_unique_filename(prefix = 'dcm-', suffix = '.zip')
                            # getting with DICOMDIR returns DICOMDIR compatible subdirs and filenames
                            study_zip_name = self.get_study_as_zip_with_dicomdir(study_id = study_id, filename = study_zip_name)
                            # non-beautiful per-study dir name required by subsequent DICOMDIR generation
                            idx += 1
                            study_unzip_dir = os.path.join(sandbox_dir, 'STUDY%s' % idx)
                            _log.debug('study [%s] -> %s -> %s', study_id, study_zip_name, study_unzip_dir)
                            # need to extract into per-study subdir because get-with-dicomdir
                            # returns identical-across-studies subdirs / filenames
                            if not gmTools.unzip_archive(study_zip_name, target_dir = study_unzip_dir, remove_archive = True):
                                    return False

                    # create DICOMDIR across all studies,
                    # we simply ignore the already existing per-study DICOMDIR files
                    target_dicomdir_name = os.path.join(sandbox_dir, 'DICOMDIR')
                    gmTools.remove_file(target_dicomdir_name, log_error = False)    # better safe than sorry
                    _log.debug('generating [%s]', target_dicomdir_name)
                    cmd = '%(cmd)s %(DICOMDIR)s %(startdir)s' % {
                            'cmd': external_cmd,
                            'DICOMDIR': target_dicomdir_name,
                            'startdir': sandbox_dir
                    }
                    success = gmShellAPI.run_command_in_shell (
                            command = cmd,
                            blocking = True
                    )
                    if not success:
                            _log.error('problem running [gm-create_dicomdir]')
                            return False
                    # paranoia
                    try:
                            io.open(target_dicomdir_name)
                    except Exception:
                            _log.error('[%s] not generated, aborting', target_dicomdir_name)
                            return False

                    # return path to extracted studies
                    if not create_zip:
                            return sandbox_dir

                    # else return ZIP of all studies
                    studies_zip = shutil.make_archive (
                            gmTools.fname_stem_with_path(filename),
                            'zip',
                            root_dir = gmTools.parent_dir(sandbox_dir),
                            base_dir = gmTools.dirname_stem(sandbox_dir),
                            logger = _log
                    )
                    _log.debug('archived all studies with one DICOMDIR into: %s', studies_zip)
                    # studies can be _large_ so attempt to get rid of intermediate files
                    gmTools.rmdir(sandbox_dir)
                    return studies_zip

            #--------------------------------------------------------
            def get_studies_with_dicomdir(self, study_ids=None, patient_id=None, target_dir=None, filename=None, create_zip=False):

                    if filename is None:
                            filename = gmTools.get_unique_filename(prefix = r'DCM-', suffix = r'.zip', tmp_dir = target_dir)

                    # all studies
                    if study_ids is None:
                            if patient_id is None:
                                    raise ValueError('<patient_id> must be defined if <study_ids> is None')
                            _log.info('exporting all studies of patient [%s] into [%s]', patient_id, filename)
                            f = io.open(filename, 'wb')
                            url = '%s/patients/%s/media' % (self.__server_url, str(patient_id))
                            _log.debug(url)
                            f.write(self.__run_GET(url = url, allow_cached = True))
                            f.close()
                            if create_zip:
                                    return filename
                            if target_dir is None:
                                    target_dir = gmTools.mk_sandbox_dir(prefix = 'dcm-')
                            if not gmTools.unzip_archive(filename, target_dir = target_dir, remove_archive = True):
                                    return False
                            return target_dir

                    # selection of studies
                    _log.info('exporting %s studies into [%s]', len(study_ids), filename)
                    _log.debug('studies: %s', study_ids)
                    f = io.open(filename, 'wb')
                    #  You have to make a POST request against URI "/tools/create-media", with a
                    #  JSON body that contains the array of the resources of interest (as Orthanc
                    #  identifiers). Here is a sample command-line:
                    #  curl -X POST http://localhost:8042/tools/create-media -d '["8c4663df-c3e66066-9e20a8fc-dd14d1e5-251d3d84","2cd4848d-02f0005f-812ffef6-a210bbcf-3f01a00a","6eeded74-75005003-c3ae9738-d4a06a4f-6beedeb8","8a622020-c058291c-7693b63f-bc67aa2e-0a02e69c"]' -v > /tmp/a.zip
                    #  (this will not create duplicates but will also not check for single-patient-ness)
                    url = '%s/tools/create-media-extended' % self.__server_url
                    _log.debug(url)
                    try:
                            downloaded = self.__run_POST(url = url, data = study_ids, output_file = f)
                            if not downloaded:
                                    _log.error('this Orthanc version probably does not support "create-media-extended"')
                    except TypeError:
                            f.close()
                            _log.exception('cannot retrieve multiple studies as one archive with DICOMDIR, probably not supported by this Orthanc version')
                            return False
                    # retry with old URL
                    if not downloaded:
                            url = '%s/tools/create-media' % self.__server_url
                            _log.debug('retrying: %s', url)
                            try:
                                    downloaded = self.__run_POST(url = url, data = study_ids, output_file = f)
                                    if not downloaded:
                                            return False
                            except TypeError:
                                    _log.exception('cannot retrieve multiple studies as one archive with DICOMDIR, probably not supported by this Orthanc version')
                                    return False
                            finally:
                                    f.close()
                    if create_zip:
                            return filename
                    if target_dir is None:
                            target_dir = gmTools.mk_sandbox_dir(prefix = 'dcm-')
                            _log.debug('exporting studies into [%s]', target_dir)
                    if not gmTools.unzip_archive(filename, target_dir = target_dir, remove_archive = True):
                            return False
                    return target_dir

            #--------------------------------------------------------
            def get_instance_dicom_tags(self, instance_id, simplified=True):
                    _log.debug('retrieving DICOM tags for instance [%s]', instance_id)
                    if simplified:
                            download_url = '%s/instances/%s/simplified-tags' % (self.__server_url, instance_id)
                    else:
                            download_url = '%s/instances/%s/tags' % (self.__server_url, instance_id)
                    return self.__run_GET(url = download_url, allow_cached = True)

            #--------------------------------------------------------
            def get_instance_preview(self, instance_id, filename=None):
                    if filename is None:
                            filename = gmTools.get_unique_filename(suffix = '.png')
                    _log.debug('exporting preview for instance [%s] into [%s]', instance_id, filename)
                    download_url = '%s/instances/%s/preview' % (self.__server_url, instance_id)
                    f = io.open(filename, 'wb')
                    try:
                            f.write(self.__run_GET(url = download_url, allow_cached = True))
                    except Exception:
                            _log.exception('cannot retrieve instance')
                            filename = None
                    finally:
                            f.close()
                    return filename

            #--------------------------------------------------------
            def get_instance(self, instance_id:str, filename:str=None, allow_cached:bool=True) -> str:
                    if filename is None:
                            filename = gmTools.get_unique_filename(suffix = '.dcm')

                    _log.debug('exporting instance [%s] into [%s]', instance_id, filename)
                    download_url = '%s/instances/%s/attachments/dicom/data' % (self.__server_url, instance_id)
                    f = io.open(filename, 'wb')
                    f.write(self.__run_GET(url = download_url, allow_cached = allow_cached))
                    f.close()
                    return filename

            #--------------------------------------------------------
            # server-side API
            #--------------------------------------------------------
            def get_patient(self, orthanc_id:str):
                    patient_data_url = '%s/patients/%s' % (self.__server_url, str(orthanc_id))
                    patient_data, status = self.__run_GET(patient_data_url, also_return_status = True)
                    if patient_data is False:
                            if status == 404:
                                    _log.debug('no such patient: %s', orthanc_id)
                                    return {}

                            _log.error('cannot retrieve patient data for [%s]', orthanc_id)
                            return False

                    return patient_data

            #--------------------------------------------------------
            def protect_patient(self, orthanc_id:str):
                    url = '%s/patients/%s/protected' % (self.__server_url, str(orthanc_id))
                    if self.__run_GET(url) == 1:
                            _log.debug('patient already protected: %s', orthanc_id)
                            return True
                    _log.warning('patient [%s] not protected against recycling, enabling protection now', orthanc_id)
                    self.__run_PUT(url = url, data = '1')
                    if self.__run_GET(url) == 1:
                            return True
                    _log.error('cannot protect patient [%s] against recycling', orthanc_id)
                    return False

            #--------------------------------------------------------
            def unprotect_patient(self, orthanc_id):
                    url = '%s/patients/%s/protected' % (self.__server_url, str(orthanc_id))
                    if self.__run_GET(url) == 0:
                            return True
                    _log.info('patient [%s] protected against recycling, disabling protection now', orthanc_id)
                    self.__run_PUT(url = url, data = '0')
                    if self.__run_GET(url) == 0:
                            return True
                    _log.error('cannot unprotect patient [%s] against recycling', orthanc_id)
                    return False

            #--------------------------------------------------------
            def patient_is_protected(self, orthanc_id):
                    url = '%s/patients/%s/protected' % (self.__server_url, str(orthanc_id))
                    return (self.__run_GET(url) == 1)

            #--------------------------------------------------------
            def verify_patient_data(self, orthanc_id):
                    _log.info('verifying DICOM data of patient [%s]', orthanc_id)
                    bad_data = []
                    instances_url = '%s/patients/%s/instances' % (self.__server_url, orthanc_id)
                    instances = self.__run_GET(instances_url)
                    for instance in instances:
                            instance_id = instance['ID']
                            attachments_url = '%s/instances/%s/attachments' % (self.__server_url, instance_id)
                            attachments = self.__run_GET(attachments_url, allow_cached = True)
                            for attachment in attachments:
                                    verify_url = '%s/%s/verify-md5' % (attachments_url, attachment)
                                    # False, success = "{}"
                                    #2018-02-08 19:11:27  ERROR     gm.dicom      [-1211701504 MainThread]  (gmDICOM.py::__run_POST() #986): cannot POST: http://localhost:8042/instances/5a8206f4-24619e76-6650d9cd-792cdf25-039e96e6/attachments/dicom-as-json/verify-md5
                                    #2018-02-08 19:11:27  ERROR     gm.dicom      [-1211701504 MainThread]  (gmDICOM.py::__run_POST() #987): response: {'status': '400', 'content-length': '0'}
                                    if self.__run_POST(verify_url) is not False:
                                            continue
                                    _log.error('bad MD5 of DICOM file at url [%s]: patient=%s, attachment_type=%s', verify_url, orthanc_id, attachment)
                                    bad_data.append({'patient': orthanc_id, 'instance': instance_id, 'type': attachment, 'orthanc': '%s [%s]' % (self.server_identification, self.__server_url)})

                    return bad_data

            #--------------------------------------------------------
            def modify_patient_id(self, old_patient_id, new_patient_id):
                    """Modify the patient ID stored in Orthanc.

                    This changes all DICOM files of the patient,
                    identified via (DICOM level) old_patient_id, to
                    contain the new_patient_id. It will update the
                    associated Orthanc metadata DB entries accordingly.
                    """
                    if old_patient_id == new_patient_id:
                            return True

                    modify_data = {
                            'Replace': {
                                    'PatientID': new_patient_id
                                    #,u'0010,0021': praxis.name / "GNUmed vX.X.X"
                                    #,u'0010,1002': series of (old) patient IDs
                            }
                            , 'Force': True
                            # "Keep" doesn't seem to do what it suggests ATM
                            #, u'Keep': True
                    }
                    orth_pat_defs = self.get_patients_by_external_id(external_id = old_patient_id)
                    all_modified = True
                    for orth_pat_def in orth_pat_defs:
                            _log.info('modifying Orthanc patient [%s]: DICOM ID [%s] -> [%s]', orth_pat_def['ID'], old_patient_id, new_patient_id)
                            old_pat_data = self.get_patient(orth_pat_def['ID'])
                            _log.debug('to be modified: %s', old_pat_data)
                            if self.patient_is_protected(orth_pat_def['ID']):
                                    _log.debug('patient protected: %s, unprotecting for modification', orth_pat_def['ID'])
                                    if not self.unprotect_patient(orth_pat_def['ID']):
                                            _log.error('cannot unlock patient [%s], skipping', orth_pat_def['ID'])
                                            all_modified = False
                                            continue
                                    was_protected = True
                            else:
                                    was_protected = False
                            pat_url = '%s/patients/%s' % (self.__server_url, orth_pat_def['ID'])
                            modify_url = '%s/modify' % pat_url
                            result = self.__run_POST(modify_url, data = modify_data)
                            _log.debug('modify result: %s', result)
                            if result is False:
                                    _log.error('cannot modify patient [%s]', orth_pat_def['ID'])
                                    all_modified = False
                                    continue
                            newly_created_orthanc_patient_id = result['ID']
                            _log.info('newly created Orthanc patient ID: %s', newly_created_orthanc_patient_id)
                            mod_pat_data = self.get_patient(newly_created_orthanc_patient_id)
                            _log.debug('modified pat: %s', mod_pat_data)
                            _log.debug('deleting archived patient: %s', self.__run_DELETE(pat_url))
                            if was_protected:
                                    if not self.protect_patient(newly_created_orthanc_patient_id):
                                            _log.error('cannot re-lock (new) patient [%s]', newly_created_orthanc_patient_id)

                    return all_modified

            #--------------------------------------------------------
            # upload API
            #--------------------------------------------------------
            def upload_dicom_file(self, filename:str, check_mime_type:bool=False) -> bool:
                    """Update a DICOM file.

                    Will silently ignore DICOMDIR files (which are application/dicom but
                    Orthanc does not process them).

                    Args:
                            filename: DICOM file to upload
                            check_mime_type: whether to check the file for being application/dicom, and to fail if not

                    Returns:
                            True/False
                    """
                    _log.info('processing: %s', filename)
                    if gmTools.fname_stem(filename) == 'DICOMDIR':
                            _log.debug('ignoring, no use uploading DICOMDIR files to Orthanc')
                            return True

                    if check_mime_type:
                            mimetype = gmMimeLib.guess_mimetype(filename)
                            if mimetype != 'application/dicom':
                                    _log.error('not considered a DICOM (application/dicom) file: %s, not uploading', mimetype)
                                    return False

                    try:
                            f = io.open(filename, 'rb')
                    except Exception:
                            _log.exception('failed to open file')
                            return False

                    dcm_data = f.read()
                    f.close()
                    upload_url = '%s/instances' % self.__server_url
                    uploaded = self.__run_POST(upload_url, data = dcm_data, content_type = 'application/dicom')
                    if uploaded is False:
                            _log.error('upload failed')
                            return False

                    # typically a 404 following the upload of a DICOM file w/o identifiers
                    if uploaded == []:
                            _log.error('upload failed')
                            return False

                    _log.debug(uploaded)
                    # paranoia, as is our custom
                    verified = self.verify_instance (
                            instance_id = uploaded['ID'],
                            filename = filename,
                            attempt_download = True
                    )
                    return verified

            #--------------------------------------------------------
            def verify_instance(self, instance_id:str, filename:str=None, attempt_download:bool=False) -> bool:

                    _BINARY_ATTACHMENTS = ['dicom']

                    _log.debug('verifying instance [%s] against file [%s]', instance_id, filename)
                    is_valid = True

                    attachments_url = '%s/instances/%s/attachments' % (self.__server_url, instance_id)
                    attachments = self.__run_GET(attachments_url, allow_cached = False)
                    if not attachments:
                            _log.error('cannot retrieve instance attachment list')
                            return False

                    for attachment in attachments:
                            md5_orthanc = None
                            # 1) verify MD5 inside Orthanc, if available (checks Orthanc storage corruption)
                            available_fields_url = '%s/instances/%s/attachments/%s' % (self.__server_url, instance_id, attachment)
                            available_fields = self.__run_GET(available_fields_url, allow_cached = False)
                            if 'md5' in available_fields:
                                    md5_url = '%s/md5' % available_fields_url
                                    md5_orthanc = self.__run_GET(md5_url)
                                    verify_url = '%s/%s/verify-md5' % (attachments_url, attachment)
                                    if self.__run_POST(verify_url) is False:
                                            _log.error('MD5 verification failed, instance [%s], attachment=%s, url [%s]', instance_id, attachment, verify_url)
                                            _log.error('potentially Orthanc storage corruption')
                                            is_valid = False
                                    else:
                                            _log.debug('MD5: Orthanc DB <-> Orthanc storage: match')
                            else:
                                    _log.debug('MD5 of instance attachment not available in Orthanc, cannot verify backend storage status')
                            # 2) verify instance attachment can be downloaded
                            md5_downloaded = None
                            if attempt_download:
                                    attachment_filename = gmTools.get_unique_filename()
                                    download_url = '%s/instances/%s/attachments/%s/data' % (self.__server_url, instance_id, attachment)
                                    attachment_data = self.__run_GET(url = download_url, allow_cached = False)
                                    if isinstance(attachment_data, bytes):
                                            attachment_file = io.open(attachment_filename, 'wb')
                                    else:
                                            attachment_file = io.open(attachment_filename, 'wt')
                                            attachment_data = '%s' % attachment_data
                                    attachment_file.write(attachment_data)
                                    del attachment_data
                                    attachment_file.close()
                                    _log.debug('download: Orthanc -> localhost: success')
                                    if attachment not in _BINARY_ATTACHMENTS:
                                            _log.info('attachment of type [%s] not binary, cannot verify MD5 of download or local file against MD5 in Orthanc, skipping', attachment)
                                            continue
                                    md5_downloaded = gmTools.file2md5(attachment_filename)
                            else:
                                    _log.debug('not downloading instance for verification')
                            # 3) verify MD5 of downloaded instance against Orthanc, if possible
                            if md5_downloaded and md5_orthanc:
                                    if md5_downloaded == md5_orthanc:
                                            _log.debug('MD5: Orthanc DB <-> localhost: match')
                                    else:
                                            _log.error('MD5 mismatch: Orthanc DB <-> localhost')
                                            _log.error('download: %s', md5_downloaded)
                                            _log.error('Orthanc : %s', md5_orthanc)
                                            is_valid = False
                            if filename:
                                    md5_local = gmTools.file2md5(filename)
                            else:
                                    _log.debug('local file not available for verification')
                                    md5_local = None
                            # 4) verify MD5 of download against local file
                            if md5_downloaded and md5_local:
                                    if md5_downloaded == md5_local:
                                            _log.debug('MD5: downloaded <-> pre-existing: match')
                                    else:
                                            _log.error('MD5 mismatch: downloaded <-> pre-existing')
                                            _log.error('download: %s', md5_downloaded)
                                            _log.error('locally : %s', md5_local)
                                            is_valid = False
                            # 5) verify MD5 of local file against Orthanc
                            if md5_local and md5_orthanc:
                                    if md5_local == md5_orthanc:
                                            _log.debug('MD5: Orthanc DB <-> pre-existing: match')
                                    else:
                                            _log.error('MD5 mismatch: Orthanc DB <-> pre-existing')
                                            _log.error('locally : %s', md5_local)
                                            _log.error('Orthanc : %s', md5_orthanc)
                                            is_valid = False
                            # 6) consider comparing the raw pixel data or comparing the output of exiftool etc

                    _log.debug('verified: %s', is_valid)
                    return is_valid

            #--------------------------------------------------------
            def upload_dicom_files(self, files=None, check_mime_type=False):
                    uploaded = []
                    not_uploaded = []
                    for filename in files:
                            success = self.upload_dicom_file(filename, check_mime_type = check_mime_type)
                            if success:
                                    uploaded.append(filename)
                                    continue
                            not_uploaded.append(filename)

                    if len(not_uploaded) > 0:
                            _log.error('not all files uploaded')
                    return (uploaded, not_uploaded)

            #--------------------------------------------------------
            def upload_from_directory(self, directory=None, recursive=False, check_mime_type=False, ignore_other_files=True):

                    #--------------------
                    def _on_error(exc):
                            _log.error('DICOM (?) file not accessible: %s', exc.filename)
                            _log.error(exc)
                    #--------------------

                    _log.debug('uploading DICOM files from [%s]', directory)
                    if not recursive:
                            files2try = os.listdir(directory)
                            _log.debug('found %s files', len(files2try))
                            if ignore_other_files:
                                    files2try = [ f for f in files2try if gmMimeLib.guess_mimetype(f) == 'application/dicom' ]
                                    _log.debug('DICOM files therein: %s', len(files2try))
                            return self.upload_dicom_files(files = files2try, check_mime_type = check_mime_type)

                    _log.debug('recursing for DICOM files')
                    uploaded = []
                    not_uploaded = []
                    for curr_root, curr_root_subdirs, curr_root_files in os.walk(directory, onerror = _on_error):
                            _log.debug('recursing into [%s]', curr_root)
                            files2try = [ os.path.join(curr_root, f) for f in curr_root_files ]
                            _log.debug('found %s files', len(files2try))
                            if ignore_other_files:
                                    files2try = [ f for f in files2try if gmMimeLib.guess_mimetype(f) == 'application/dicom' ]
                                    _log.debug('DICOM files therein: %s', len(files2try))
                            up, not_up = self.upload_dicom_files (
                                    files = files2try,
                                    check_mime_type = check_mime_type
                            )
                            uploaded.extend(up)
                            not_uploaded.extend(not_up)

                    return (uploaded, not_uploaded)

            #--------------------------------------------------------
            def upload_by_DICOMDIR(self, DICOMDIR=None):
                    pass

            #--------------------------------------------------------
            # helper functions
            #--------------------------------------------------------
            def get_studies_list_by_orthanc_patient_list(self, orthanc_patients=None):

                    study_keys2hide =  ['ModifiedFrom', 'Type', 'ID', 'ParentPatient', 'Series']
                    series_keys2hide = ['ModifiedFrom', 'Type', 'ID', 'ParentStudy',   'Instances']

                    studies_by_patient = []

                    # loop over patients
                    for pat in orthanc_patients:
                            pat_dict = {
                                    'orthanc_id': pat['ID'],
                                    'name': None,
                                    'external_id': None,
                                    'date_of_birth': None,
                                    'gender': None,
                                    'studies': []
                            }
                            try:
                                    pat_dict['name'] = pat['MainDicomTags']['PatientName'].strip()
                            except KeyError:
                                    pass
                            try:
                                    pat_dict['external_id'] = pat['MainDicomTags']['PatientID'].strip()
                            except KeyError:
                                    pass
                            try:
                                    pat_dict['date_of_birth'] = pat['MainDicomTags']['PatientBirthDate'].strip()
                            except KeyError:
                                    pass
                            try:
                                    pat_dict['gender'] = pat['MainDicomTags']['PatientSex'].strip()
                            except KeyError:
                                    pass
                            for key in pat_dict:
                                    if pat_dict[key] in ['unknown', '(null)', '']:
                                            pat_dict[key] = None
                                    pat_dict[key] = cleanup_dicom_string(pat_dict[key])
                            studies_by_patient.append(pat_dict)

                            # loop over studies of patient
                            orth_studies = self.__run_GET(url = '%s/patients/%s/studies' % (self.__server_url, pat['ID']))
                            if orth_studies is False:
                                    _log.error('cannot retrieve studies')
                                    return []
                            for orth_study in orth_studies:
                                    study_dict = {
                                            'orthanc_id': orth_study['ID'],
                                            'date': None,
                                            'time': None,
                                            'description': None,
                                            'referring_doc': None,
                                            'requesting_doc': None,
                                            'requesting_org': None,
                                            'performing_doc': None,
                                            'operator_name': None,
                                            'radiographer_code': None,
                                            'radiology_org': None,
                                            'radiology_dept': None,
                                            'radiology_org_addr': None,
                                            'station_name': None,
                                            'series': []
                                    }
                                    try:
                                            study_dict['date'] = orth_study['MainDicomTags']['StudyDate'].strip()
                                    except KeyError:
                                            pass
                                    try:
                                            study_dict['time'] = orth_study['MainDicomTags']['StudyTime'].strip()
                                    except KeyError:
                                            pass
                                    try:
                                            study_dict['description'] = orth_study['MainDicomTags']['StudyDescription'].strip()
                                    except KeyError:
                                            pass
                                    try:
                                            study_dict['referring_doc'] = orth_study['MainDicomTags']['ReferringPhysicianName'].strip()
                                    except KeyError:
                                            pass
                                    try:
                                            study_dict['requesting_doc'] = orth_study['MainDicomTags']['RequestingPhysician'].strip()
                                    except KeyError:
                                            pass
                                    try:
                                            study_dict['requesting_org'] = orth_study['MainDicomTags']['RequestingService'].strip()
                                    except KeyError:
                                            pass
                                    try:
                                            study_dict['radiology_org_addr'] = orth_study['MainDicomTags']['InstitutionAddress'].strip()
                                    except KeyError:
                                            pass
                                    try:
                                            study_dict['radiology_org'] = orth_study['MainDicomTags']['InstitutionName'].strip()
                                            if study_dict['radiology_org_addr'] is not None:
                                                    if study_dict['radiology_org'] in study_dict['radiology_org_addr']:
                                                            study_dict['radiology_org'] = None
                                    except KeyError:
                                            pass
                                    try:
                                            study_dict['radiology_dept'] = orth_study['MainDicomTags']['InstitutionalDepartmentName'].strip()
                                            if study_dict['radiology_org'] is not None:
                                                    if study_dict['radiology_dept'] in study_dict['radiology_org']:
                                                            study_dict['radiology_dept'] = None
                                            if study_dict['radiology_org_addr'] is not None:
                                                    if study_dict['radiology_dept'] in study_dict['radiology_org_addr']:
                                                            study_dict['radiology_dept'] = None
                                    except KeyError:
                                            pass
                                    try:
                                            study_dict['station_name'] = orth_study['MainDicomTags']['StationName'].strip()
                                            if study_dict['radiology_org'] is not None:
                                                    if study_dict['station_name'] in study_dict['radiology_org']:
                                                            study_dict['station_name'] = None
                                            if study_dict['radiology_org_addr'] is not None:
                                                    if study_dict['station_name'] in study_dict['radiology_org_addr']:
                                                            study_dict['station_name'] = None
                                            if study_dict['radiology_dept'] is not None:
                                                    if study_dict['station_name'] in study_dict['radiology_dept']:
                                                            study_dict['station_name'] = None
                                    except KeyError:
                                            pass
                                    for key in study_dict:
                                            if study_dict[key] in ['unknown', '(null)', '']:
                                                    study_dict[key] = None
                                            study_dict[key] = cleanup_dicom_string(study_dict[key])
                                    study_dict['all_tags'] = {}
                                    try:
                                            orth_study['PatientMainDicomTags']
                                    except KeyError:
                                            orth_study['PatientMainDicomTags'] = pat['MainDicomTags']
                                    for key in orth_study:
                                            if key == 'MainDicomTags':
                                                    for mkey in orth_study['MainDicomTags']:
                                                            study_dict['all_tags'][mkey] = orth_study['MainDicomTags'][mkey].strip()
                                                    continue
                                            if key == 'PatientMainDicomTags':
                                                    for pkey in orth_study['PatientMainDicomTags']:
                                                            study_dict['all_tags'][pkey] = orth_study['PatientMainDicomTags'][pkey].strip()
                                                    continue
                                            study_dict['all_tags'][key] = orth_study[key]
                                    _log.debug('study: %s', list(study_dict['all_tags']))
                                    for key in study_keys2hide:
                                            try: del study_dict['all_tags'][key]
                                            except KeyError: pass
                                    pat_dict['studies'].append(study_dict)

                                    # loop over series in study
                                    for orth_series_id in orth_study['Series']:
                                            orth_series = self.__run_GET(url = '%s/series/%s' % (self.__server_url, orth_series_id))
                                            ordered_slices = self.__run_GET(url = '%s/series/%s/ordered-slices' % (self.__server_url, orth_series_id))
                                            if ordered_slices is False:
                                                    slices = orth_series['Instances']
                                            else:
                                                    slices = [ s[0] for s in ordered_slices['SlicesShort'] ]
                                            if orth_series is False:
                                                    _log.error('cannot retrieve series')
                                                    return []
                                            series_dict = {
                                                    'orthanc_id': orth_series['ID'],
                                                    'instances': slices,
                                                    'modality': None,
                                                    'date': None,
                                                    'time': None,
                                                    'description': None,
                                                    'body_part': None,
                                                    'protocol': None,
                                                    'performed_procedure_step_description': None,
                                                    'acquisition_device_processing_description': None,
                                                    'operator_name': None,
                                                    'radiographer_code': None,
                                                    'performing_doc': None
                                            }
                                            try:
                                                    series_dict['modality'] = orth_series['MainDicomTags']['Modality'].strip()
                                            except KeyError:
                                                    pass
                                            try:
                                                    series_dict['date'] = orth_series['MainDicomTags']['SeriesDate'].strip()
                                            except KeyError:
                                                    pass
                                            try:
                                                    series_dict['description'] = orth_series['MainDicomTags']['SeriesDescription'].strip()
                                            except KeyError:
                                                    pass
                                            try:
                                                    series_dict['time'] = orth_series['MainDicomTags']['SeriesTime'].strip()
                                            except KeyError:
                                                    pass
                                            try:
                                                    series_dict['body_part'] = orth_series['MainDicomTags']['BodyPartExamined'].strip()
                                            except KeyError:
                                                    pass
                                            try:
                                                    series_dict['protocol'] = orth_series['MainDicomTags']['ProtocolName'].strip()
                                            except KeyError:
                                                    pass
                                            try:
                                                    series_dict['performed_procedure_step_description'] = orth_series['MainDicomTags']['PerformedProcedureStepDescription'].strip()
                                            except KeyError:
                                                    pass
                                            try:
                                                    series_dict['acquisition_device_processing_description'] = orth_series['MainDicomTags']['AcquisitionDeviceProcessingDescription'].strip()
                                            except KeyError:
                                                    pass
                                            try:
                                                    series_dict['operator_name'] = orth_series['MainDicomTags']['OperatorsName'].strip()
                                            except KeyError:
                                                    pass
                                            try:
                                                    series_dict['radiographer_code'] = orth_series['MainDicomTags']['RadiographersCode'].strip()
                                            except KeyError:
                                                    pass
                                            try:
                                                    series_dict['performing_doc'] = orth_series['MainDicomTags']['PerformingPhysicianName'].strip()
                                            except KeyError:
                                                    pass
                                            for key in series_dict:
                                                    if series_dict[key] in ['unknown', '(null)', '']:
                                                            series_dict[key] = None
                                            if series_dict['description'] == series_dict['protocol']:
                                                    _log.debug('<series description> matches <series protocol>, ignoring protocol')
                                                    series_dict['protocol'] = None
                                            if series_dict['performed_procedure_step_description'] in [series_dict['description'], series_dict['protocol']]:
                                                    series_dict['performed_procedure_step_description'] = None
                                            if series_dict['performed_procedure_step_description'] is not None:
                                                    # weed out "numeric" only
                                                    if regex.match ('[.,/\|\-\s\d]+', series_dict['performed_procedure_step_description'], flags = regex.UNICODE):
                                                            series_dict['performed_procedure_step_description'] = None
                                            if series_dict['acquisition_device_processing_description'] in [series_dict['description'], series_dict['protocol']]:
                                                    series_dict['acquisition_device_processing_description'] = None
                                            if series_dict['acquisition_device_processing_description'] is not None:
                                                    # weed out "numeric" only
                                                    if regex.match ('[.,/\|\-\s\d]+', series_dict['acquisition_device_processing_description'], flags = regex.UNICODE):
                                                            series_dict['acquisition_device_processing_description'] = None
                                            if series_dict['date'] == study_dict['date']:
                                                    _log.debug('<series date> matches <study date>, ignoring date')
                                                    series_dict['date'] = None
                                            if series_dict['time'] == study_dict['time']:
                                                    _log.debug('<series time> matches <study time>, ignoring time')
                                                    series_dict['time'] = None
                                            for key in series_dict:
                                                    series_dict[key] = cleanup_dicom_string(series_dict[key])
                                            series_dict['all_tags'] = {}
                                            for key in orth_series:
                                                    if key == 'MainDicomTags':
                                                            for mkey in orth_series['MainDicomTags']:
                                                                    series_dict['all_tags'][mkey] = orth_series['MainDicomTags'][mkey].strip()
                                                            continue
                                                    series_dict['all_tags'][key] = orth_series[key]
                                            _log.debug('series: %s', list(series_dict['all_tags']))
                                            for key in series_keys2hide:
                                                    try: del series_dict['all_tags'][key]
                                                    except KeyError: pass
                                            study_dict['operator_name'] = series_dict['operator_name']                      # will collapse all operators into that of the last series
                                            study_dict['radiographer_code'] = series_dict['radiographer_code']      # will collapse all into that of the last series
                                            study_dict['performing_doc'] = series_dict['performing_doc']            # will collapse all into that of the last series
                                            study_dict['series'].append(series_dict)

                    return studies_by_patient

            #--------------------------------------------------------
            # generic REST helpers
            #--------------------------------------------------------
            def run_GET(self, url=None, data=None, allow_cached=False):
                    url = '%s/%s' % (self.__server_url, url)
                    return self.__run_GET(url = url, data = data, allow_cached = allow_cached)

            #--------------------------------------------------------
            def __run_GET(self, url=None, data=None, allow_cached=False, also_return_status=False):
                    if data is None:
                            data = {}
                    headers = {}
                    if not allow_cached:
                            headers['cache-control'] = 'no-cache'
                    params = ''
                    if data:
                            params = '?' + urlencode(data)
                    url_with_params = url + params
                    #_log.debug('URL with parameters: >>>%s<<<', url_with_params)
                    try:
                            response, content = self.__conn.request(url_with_params, 'GET', headers = headers)
                    except (OverflowError, socket.error, http.client.ResponseNotReady, http.client.InvalidURL, http.client.RemoteDisconnected, httplib2.ServerNotFoundError):
                            # http.client.RemoteDisconnected: observed during GET while Orthanc was shutting down for backup
                            _log.exception('exception in GET')
                            _log.debug(' url: %s', url_with_params)
                            _log.debug(' headers: %s', headers)
                            if also_return_status:
                                    return (False, -1)
                            return False

                    if response.status not in [ 200 ]:
                            _log.error('GET returned non-OK status: %s', response.status)
                            _log.debug(' url: %s', url_with_params)
                            _log.debug(' headers: %s', headers)
                            _log.error(' response: %s', response)
                            _log.debug(' content: %s', content)
                            if also_return_status:
                                    return (False, response.status)
                            return False

                    #_log.debug('response: %s', response)
                    #_log.debug('type(content): %s', type(content))
                    content_type = response['content-type'].strip()
                    if content_type.startswith('text/plain'):
                            # utf8 ?
                            # urldecode ?
                            # latin1 = Orthanc default = tools/default-encoding ?
                            # ascii ?
                            content = content.decode('utf8')
                    elif content_type.startswith('application/json'):
                            try:
                                    content = json.loads(content)
                            except Exception:
                                    _log.exception('failed to json.loads(content) despite application/json indicated, returning content and hoping for the best')
                                    mime_type, charset_def = content_type.split(';')
                                    charset = charset_def.strip().split('=')[1]
                                    #content = content.decode('utf8')
                                    content = content.decode(charset)
                            #_log.debug(content)
                    else:
                            _log.error('content: <%s>, not <text/plain> or <application/json> -- returning raw content', content_type)
                    if also_return_status:
                            return (content, response.status)

                    return content

            #--------------------------------------------------------
            def __run_POST(self, url=None, data=None, content_type=None, output_file=None):
                    body = data
                    headers = {'content-type' : content_type}
                    if isinstance(data, str):
                            if content_type is None:
                                    headers['content-type'] = 'text/plain'
                    elif isinstance(data, bytes):
                            if content_type is None:
                                    headers['content-type'] = 'application/octet-stream'
                    else:
                            body = json.dumps(data)
                            headers['content-type'] = 'application/json'

                    try:
                            try:
                                    response, content = self.__conn.request(url, 'POST', body = body, headers = headers)
                            except BrokenPipeError:
                                    _log.debug('retrying after BrokenPipeError')
                                    response, content = self.__conn.request(url, 'POST', body = body, headers = headers)
                    except (socket.error, http.client.ResponseNotReady, OverflowError):
                            _log.exception('exception in POST')
                            _log.debug(' url: %s', url)
                            _log.debug(' headers: %s', headers)
                            _log.debug(' body: %s', body[:16])
                            return False

                    if response.status == 404:
                            _log.debug('no data, response: %s', response)
                            if output_file is None:
                                    return []
                            return False

                    if response.status not in [ 200, 302 ]:
                            _log.error('POST returned non-OK (not 200,302) status: %s', response.status)
                            _log.debug(' url: %s', url)
                            _log.debug(' headers: %s', headers)
                            _log.debug(' body: %s', body[:16])
                            _log.error(' response: %s', response)
                            _log.debug(' content: %s', content)
                            return False

                    try:
                            content = json.loads(content)
                    except Exception:
                            pass
                    if output_file is None:
                            return content

                    output_file.write(content)
                    return True

            #--------------------------------------------------------
            def __run_PUT(self, url=None, data=None, content_type=None):

                    body = data
                    headers = {'content-type' : content_type}
                    if isinstance(data, str):
                            if content_type is None:
                                    headers['content-type'] = 'text/plain'
                    elif isinstance(data, bytes):
                            if content_type is None:
                                    headers['content-type'] = 'application/octet-stream'
                    else:
                            body = json.dumps(data)
                            headers['content-type'] = 'application/json'

                    try:
                            try:
                                    response, content = self.__conn.request(url, 'PUT', body = body, headers = headers)
                            except BrokenPipeError:
                                    response, content = self.__conn.request(url, 'PUT', body = body, headers = headers)
                    except (socket.error, http.client.ResponseNotReady, OverflowError):
                            _log.exception('exception in PUT')
                            _log.debug(' url: %s', url)
                            _log.debug(' headers: %s', headers)
                            _log.debug(' body: %s', body[:16])
                            return False

                    if response.status == 404:
                            _log.debug('no data, response: %s', response)
                            return []
                    if response.status not in [ 200, 302 ]:
                            _log.error('PUT returned non-OK status: %s', response.status)
                            _log.debug(' url: %s', url)
                            _log.debug(' headers: %s', headers)
                            _log.debug(' body: %s', body[:16])
                            _log.error(' response: %s', response)
                            _log.debug(' content: %s', content)
                            return False

                    if response['content-type'].startswith('text/plain'):
                            # utf8 ?
                            # urldecode ?
                            # latin1 = Orthanc default = tools/default-encoding ?
                            # ascii ?
                            return content.decode('utf8')

                    if response['content-type'].startswith('application/json'):
                            try:
                                    return json.loads(content)
                            except Exception:
                                    return content

                    return content

            #--------------------------------------------------------
            def __run_DELETE(self, url=None):
                    try:
                            response, content = self.__conn.request(url, 'DELETE')
                    except (http.client.ResponseNotReady, socket.error, OverflowError):
                            _log.exception('exception in DELETE')
                            _log.debug(' url: %s', url)
                            return False

                    if response.status not in [ 200 ]:
                            _log.error('DELETE returned non-OK status: %s', response.status)
                            _log.debug(' url: %s', url)
                            _log.error(' response: %s', response)
                            _log.debug(' content: %s', content)
                            return False

                    if response['content-type'].startswith('text/plain'):
                            # utf8 ?
                            # urldecode ?
                            # latin1 = Orthanc default = tools/default-encoding ?
                            # ascii ?
                            return content.decode('utf8')

                    if response['content-type'].startswith('application/json'):
                            try:
                                    return json.loads(content)
                            except Exception:
                                    return content

                    return content

            #--------------------------------------------------------
            def _get_server_url(self):
                    return self.__server_url

            server_url = property(_get_server_url)

    #------------------------------------------------------------
    def cleanup_dicom_string(dicom_str):
            if not isinstance(dicom_str, str):
                    return dicom_str
            dicom_str = regex.sub('\^+', ' ', dicom_str.strip('^'))
            #dicom_str = dicom_str.replace('\r\n', ' [CR] ')
            return dicom_str

    #---------------------------------------------------------------------------
    def dicomize_file(filename, title=None, person=None, dcm_name=None, verbose=False, dcm_template_file=None, dcm_transfer_series=True):
            assert (filename is not None), '<filename> must not be None'
            assert (not ((person is None) and (dcm_template_file is None))), '<person> or <dcm_template_file> must not be None'

            # already DCM ?
            if gmMimeLib.guess_mimetype(filename) == 'application/dicom':
                    _log.error('already a DICOM file: %s', filename)
                    if dcm_name is None:
                            return filename
                    return shutil.copy2(filename, dcm_name)

            dcm_fname = dicomize_pdf (
                    pdf_name = filename,
                    title = title,
                    person = person,
                    dcm_name = dcm_name,
                    verbose = verbose,
                    dcm_template_file = dcm_template_file,
                    dcm_transfer_series = dcm_transfer_series
            )
            if dcm_fname is not None:
                    return dcm_fname

            _log.debug('does not seem to be a PDF: %s', filename)
            converted_fname = gmMimeLib.convert_file(filename = filename, target_mime = 'image/jpeg')
            if converted_fname is None:
                    _log.error('cannot convert to JPG: %s', filename)
                    return None

            dcm_name = dicomize_jpg (
                    jpg_name = converted_fname,
                    title = title,
                    person = person,
                    dcm_name = dcm_name,
                    verbose = verbose,
                    dcm_template_file = dcm_template_file,
                    dcm_transfer_series = dcm_transfer_series
            )
            return dcm_name

    #---------------------------------------------------------------------------
    def dicomize_pdf(pdf_name=None, title=None, person=None, dcm_name=None, verbose=False, dcm_template_file=None, dcm_transfer_series=True):
            assert (pdf_name is not None), '<pdf_name> must not be None'
            assert (not ((person is None) and (dcm_template_file is None))), '<person> or <dcm_template_file> must not be None'

            if dcm_name is None:
                    dcm_name = gmTools.get_unique_filename(suffix = '.dcm')
            _log.debug('%s -> %s', pdf_name, dcm_name)
            if title is None:
                    title = pdf_name
            now = gmDateTime.pydt_now_here()
            cmd_line = [
                    'pdf2dcm',
                    '--title', title,
                    '--key', '0008,0020=%s' % now.strftime('%Y%m%d'),                       # StudyDate
                    '--key', '0008,0021=%s' % now.strftime('%Y%m%d'),                       # SeriesDate
                    '--key', '0008,0023=%s' % now.strftime('%Y%m%d'),                       # ContentDate
                    '--key', '0008,0030=%s' % now.strftime('%H%M%s.0'),                     # StudyTime
                    '--key', '0008,0031=%s' % now.strftime('%H%M%s.0'),                     # SeriesTime
                    '--key', '0008,0033=%s' % now.strftime('%H%M%s.0')                      # ContentTime
            ]
            if dcm_template_file is None:
                    name = person.active_name
                    cmd_line.append('--patient-id')
                    cmd_line.append(person.suggest_external_id(target = 'PACS'))
                    cmd_line.append('--patient-name')
                    cmd_line.append(('%s^%s' % (name['lastnames'], name['firstnames'])).replace(' ', '^'))
                    if person['dob'] is not None:
                            cmd_line.append('--patient-birthdate')
                            cmd_line.append(person.get_formatted_dob(format = '%Y%m%d', honor_estimation = False))
                    if person['gender'] is not None:
                            cmd_line.append('--patient-sex')
                            cmd_line.append(_map_gender_gm2dcm[person['gender']])
            else:
                    _log.debug('DCM template file: %s', dcm_template_file)
                    if dcm_transfer_series:
                            cmd_line.append('--series-from')
                    else:
                            cmd_line.append('--study-from')
                    cmd_line.append(dcm_template_file)
            if verbose:
                    cmd_line.append('--log-level')
                    cmd_line.append('trace')
            cmd_line.append(pdf_name)
            cmd_line.append(dcm_name)
            success, exit_code, stdout = gmShellAPI.run_process(cmd_line = cmd_line, encoding = 'utf8', verbose = verbose)
            if success:
                    return dcm_name

            return None

    #---------------------------------------------------------------------------
    def dicomize_jpg(jpg_name=None, title=None, person=None, dcm_name=None, verbose=False, dcm_template_file=None, dcm_transfer_series=True):
            assert (jpg_name is not None), '<jpg_name> must not be None'
            assert (not ((person is None) and (dcm_template_file is None))), 'both <person> and <dcm_template_file> are None, but one is needed'

            if dcm_name is None:
                    dcm_name = gmTools.get_unique_filename(suffix = '.dcm')
            _log.debug('%s -> %s', jpg_name, dcm_name)
            now = gmDateTime.pydt_now_here()
            cmd_line = [
                    'img2dcm',
                    '--keep-appn',                                                                                  # carry over EXIF data
                    '--insist-on-jfif',                                                                             # process valid JFIF only
                    '--key', '0008,0021=%s' % now.strftime('%Y%m%d'),               # SeriesDate
                    '--key', '0008,0031=%s' % now.strftime('%H%M%s.0'),             # SeriesTime
                    '--key', '0008,0023=%s' % now.strftime('%Y%m%d'),               # ContentDate
                    '--key', '0008,0033=%s' % now.strftime('%H%M%s.0')              # ContentTime
            ]
            if title is not None:
                    # SeriesDescription
                    if title is not None:
                            cmd_line.append('--key')
                            cmd_line.append('0008,103E=%s' % title)
            if dcm_template_file is None:
                    # StudyDescription
                    if title is not None:
                            cmd_line.append('--key')
                            cmd_line.append('0008,1030=%s' % title)
                    # StudyDate
                    cmd_line.append('--key')
                    cmd_line.append('0008,0020=%s' % now.strftime('%Y%m%d'))
                    # StudyTime
                    cmd_line.append('--key')
                    cmd_line.append('0008,0030=%s' % now.strftime('%H%M%s.0'))
                    # PatientName
                    name = person.active_name
                    cmd_line.append('--key')
                    cmd_line.append('0010,0010=%s' % ('%s^%s' % (
                            name['lastnames'],
                            name['firstnames'])
                    ).replace(' ', '^'))
                    # PatientID
                    cmd_line.append('--key')
                    cmd_line.append('0010,0020=%s' % person.suggest_external_id(target = 'PACS'))
                    # DOB
                    cmd_line.append('--key')
                    cmd_line.append('0010,0030=%s' % person.get_formatted_dob(format = '%Y%m%d', honor_estimation = False))
                    # gender
                    if person['gender'] is not None:
                            cmd_line.append('--key')
                            cmd_line.append('0010,0040=%s' % _map_gender_gm2dcm[person['gender']])
            else:
                    _log.debug('DCM template file: %s', dcm_template_file)
                    if dcm_transfer_series:
                            cmd_line.append('--series-from')
                    else:
                            cmd_line.append('--study-from')
                    cmd_line.append(dcm_template_file)
            if verbose:
                    cmd_line.append('--log-level')
                    cmd_line.append('trace')
            cmd_line.append(jpg_name)
            cmd_line.append(dcm_name)
            success, exit_code, stdout = gmShellAPI.run_process(cmd_line = cmd_line, encoding = 'utf8', verbose = verbose)
            if success:
                    return dcm_name

            return None

    #============================================================
    # main
    #------------------------------------------------------------
    if __name__ == "__main__":

            if len(sys.argv) == 1:
                    sys.exit()

            if sys.argv[1] != 'test':
                    sys.exit()

            from Gnumed.pycommon import gmLog2

            #--------------------------------------------------------
            def orthanc_console(host, port):
                    print('Please enter patient name parts, separated by SPACE.')
                    while True:
                            entered_name = gmTools.prompted_input(prompt = "\nEnter person search term or leave blank to exit")
                            if entered_name in ['exit', 'quit', 'bye', None]:
                                    print("user cancelled patient search")
                                    break

                            pats = orthanc.get_patients_by_external_id(external_id = entered_name)
                            if len(pats) > 0:
                                    print('Patients found:')
                                    for pat in pats:
                                            print(' -> ', pat)
                                    continue

                            pats = orthanc.get_patients_by_name(name_parts = entered_name.split(), fuzzy = True, search_level = 'Study')
                            print('Patients found:')
                            for pat in pats:
                                    print(' -> ', pat)
                                    print('  verifying ...')
                                    bad_data = orthanc.verify_patient_data(pat['ID'])
                                    print('  bad data:')
                                    for bad in bad_data:
                                            print('  -> ', bad)
                                    continue

                            continue

                            pats = orthanc.get_studies_list_by_patient_name(name_parts = entered_name.split(), fuzzy = True)
                            print('Patients found from studies list:')
                            for pat in pats:
                                    print(' -> ', pat['name'])
                                    for study in pat['studies']:
                                            print(' ', gmTools.format_dict_like(study, relevant_keys = ['orthanc_id', 'date', 'time'], template = 'study [%%(orthanc_id)s] at %%(date)s %%(time)s contains %s series' % len(study['series'])))
    #                                       for series in study['series']:
    #                                               print (
    #                                                       u'  ',
    #                                                       gmTools.format_dict_like (
    #                                                               series,
    #                                                               relevant_keys = ['orthanc_id', 'date', 'time', 'modality', 'instances', 'body_part', 'protocol', 'description', 'station'],
    #                                                               template = u'series [%(orthanc_id)s] at %(date)s %(time)s: "%(description)s" %(modality)s@%(station)s (%(protocol)s) of body part "%(body_part)s" holds images:\n%(instances)s'
    #                                                       )
    #                                               )
    #                                       print(orthanc.get_studies_with_dicomdir(study_ids = [study['orthanc_id']], filename = 'study_%s.zip' % study['orthanc_id'], create_zip = True))
                                    #print(orthanc.get_study_as_zip(study_id = study['orthanc_id'], filename = 'study_%s.zip' % study['orthanc_id']))
                                    #print(orthanc.get_studies_as_zip_with_dicomdir(study_ids = [ s['orthanc_id'] for s in pat['studies'] ], filename = 'studies_of_%s.zip' % pat['orthanc_id']))
                                    print('--------')

            #--------------------------------------------------------
            def run_console():
                    orthanc_console(host, port)

            #--------------------------------------------------------
            def test_modify_patient_id():
                    print('Please enter patient name parts, separated by SPACE.')
                    entered_name = gmTools.prompted_input(prompt = "\nEnter person search term or leave blank to exit")
                    if entered_name in ['exit', 'quit', 'bye', None]:
                            print("user cancelled patient search")
                            return

                    pats = orthanc.get_patients_by_name(name_parts = entered_name.split(), fuzzy = True)
                    if len(pats) == 0:
                            print('no patient found')
                            return

                    pat = pats[0]
                    print('test patient:')
                    print(pat)
                    old_id = pat['MainDicomTags']['PatientID']
                    new_id = old_id + '-1'
                    print('setting [%s] to [%s]:' % (old_id, new_id), orthanc.modify_patient_id(old_id, new_id))

            #--------------------------------------------------------
            def test_upload_file():
                    orthanc.upload_dicom_file(filename = sys.argv[4], check_mime_type = True)

            #--------------------------------------------------------
            def test_upload_files():
                    #orthanc.upload_dicom_file(sys.argv[2])
                    orthanc.upload_from_directory(directory = sys.argv[4], recursive = True, check_mime_type = False, ignore_other_files = True)

            #--------------------------------------------------------
            def test_get_instance_preview():
                    print(orthanc.get_instance_preview('f4f07d22-0d8265ef-112ea4e9-dc140e13-350c06d1'))
                    print(orthanc.get_instance('f4f07d22-0d8265ef-112ea4e9-dc140e13-350c06d1'))

            #--------------------------------------------------------
            def test_get_instance_tags():
                    instance_id = 'f4f07d22-0d8265ef-112ea4e9-dc140e13-350c06d1'
                    for key, value in orthanc.get_instance_dicom_tags(instance_id, simplified = False).items():
                            print(key, ':', value)
                    print()
                    #print(orthanc.get_instance_dicom_tags(instance_id, simplified = True))

            #--------------------------------------------------------
            def test_pdf2dcm():
                    #print(pdf2dcm(filename = filename, patient_id = 'ID::abcABC', dob = '19900101'))
                    from Gnumed.business import gmPerson
                    pers = gmPerson.cPerson(12)
                    try:
                            print(dicomize_pdf(pdf_name = sys.argv[2], person = pers, dcm_name = None, verbose = True, dcm_template_file = sys.argv[3]))#, title = 'test'))
                    except IndexError:
                            print(dicomize_pdf(pdf_name = sys.argv[2], person = pers, dcm_name = None, verbose = True))#, title = 'test'))

            #--------------------------------------------------------
            def test_img2dcm():
                    #print(pdf2dcm(filename = filename, patient_id = 'ID::abcABC', dob = '19900101'))
                    from Gnumed.business import gmPerson
                    pers = gmPerson.cPerson(12)
                    try:
                            print(dicomize_jpg(jpg_name = sys.argv[2], person = pers, dcm_name = sys.argv[2]+'.dcm', verbose = True, dcm_template_file = sys.argv[3]))#, title = 'test'))
                    except IndexError:
                            print(dicomize_jpg(jpg_name = sys.argv[2], person = pers, dcm_name = sys.argv[2]+'.dcm', verbose = True))#, title = 'test'))

            #--------------------------------------------------------
            def test_file2dcm():
                    from Gnumed.business import gmPersonSearch
                    person = gmPersonSearch.ask_for_patient()
                    if person is None:
                            return
                    print(person)
                    try:
                            print(dicomize_file(filename = sys.argv[2], person = person, dcm_name = sys.argv[2]+'.dcm', verbose = True, dcm_template_file = sys.argv[3], title = sys.argv[4]))
                    except IndexError:
                            pass
                    try:
                            print(dicomize_file(filename = sys.argv[2], person = person, dcm_name = sys.argv[2]+'.dcm', verbose = True, title = sys.argv[3]))
                    except IndexError:
                            print(dicomize_file(filename = sys.argv[2], person = person, dcm_name = sys.argv[2]+'.dcm', verbose = True))

            #--------------------------------------------------------
            def test_patient():
                    print(orthanc.get_patient('89729867-a08815a6-37c59f5a-f1f6ea57-6c1e17cb'))
                    input()
                    print(orthanc.get_patient('1cff9d34-96047a5a-afb97dd0-33a84dc7-a710ef8f'))
                    return

                    #'/patients/89729867-a08815a6-37c59f5a-f1f6ea57-6c1e17cb'
                    orthanc_id = '89729867-a08815a6-37c59f5a-f1f6ea57-6c1e17cb'
                    instances_url = 'patients/%s/instances' % orthanc_id
                    print(instances_url)
                    new_patient_id = 'xxx'
                    instances = orthanc.run_GET(instances_url)
                    for instance in instances:
                            instance_id = instance['ID']
                            tags = orthanc.get_instance_dicom_tags(instance_id, simplified = False)
                            if tags['0010,0030']['Value'] != '19810416':
                                    continue
                            orthanc.modify_patient_id_of_instance(instance_id, new_patient_id)
                            #print(tags['0010,0030']['PatientID'])
                            #print(tags['0010,0030']['PatientName'])
                            #continue
                            for key, value in tags.items():
                                    print(key, ':', value)
    #                       instance_id = instance['ID']
    #                       attachments_url = '%s/instances/%s/attachments' % (self.__server_url, instance_id)
    #                       attachments = self.__run_GET(attachments_url, allow_cached = True)
    #                       for attachment in attachments:
    #                               verify_url = '%s/%s/verify-md5' % (attachments_url, attachment)
    #                               # False, success = "{}"
    #                               #2018-02-08 19:11:27  ERROR     gm.dicom      [-1211701504 MainThread]  (gmDICOM.py::__run_POST() #986): cannot POST: http://localhost:8042/instances/5a8206f4-24619e76-6650d9cd-792cdf25-039e96e6/attachments/dicom-as-json/verify-md5
    #                               #2018-02-08 19:11:27  ERROR     gm.dicom      [-1211701504 MainThread]  (gmDICOM.py::__run_POST() #987): response: {'status': '400', 'content-length': '0'}
    #                               if self.__run_POST(verify_url) is not False:
    #                                       continue
    #                               _log.error('bad MD5 of DICOM file at url [%s]: patient=%s, attachment_type=%s', verify_url, orthanc_id, attachment)
    #                               bad_data.append({'patient': orthanc_id, 'instance': instance_id, 'type': attachment, 'orthanc': '%s [%s]' % (self.server_identification, self.__server_url)})

            #--------------------------------------------------------
            def test_verify_instance():
                    # u'Path': u'/instances/1440110e-9cd02a98-0b1c0452-087d35db-3fd5eb05'
                    #instance_id = '1440110e-9cd02a98-0b1c0452-087d35db-3fd5eb05'
                    #instance_id = '5a8206f4-24619e76-6650d9cd-792cdf25-039e96e6'
                    instance_id = '7e99fa76-3699ab68-7fd9d2de-c621b331-b4fe7394'
                    print('verifying [%s]' % instance_id)
                    result = orthanc.verify_instance (
                            instance_id = instance_id
    #                       , filename = None
                            , attempt_download = True
                    )
                    print(result)

            #--------------------------------------------------------
            def _connect():
                    global host
                    try:
                            host = sys.argv[2]
                    except IndexError:
                            host = None
                    global port
                    try:
                            port = sys.argv[3]
                    except IndexError:
                            port = '8042'

                    global orthanc
                    orthanc = cOrthancServer()
                    if not orthanc.connect(host, port, user = None, password = None):               #, expected_aet = 'another AET'
                            print('error connecting to server:', orthanc.connect_error)
                            sys.exit(-1)
                    print('Connected to Orthanc server "%s" (AET [%s] - version [%s] - DB [%s])' % (
                            orthanc.server_identification['Name'],
                            orthanc.server_identification['DicomAet'],
                            orthanc.server_identification['Version'],
                            orthanc.server_identification['DatabaseVersion']
                    ))
                    print('')

            #--------------------------------------------------------
            #test_pdf2dcm()
            #test_img2dcm()
            #test_file2dcm()
            #sys.exit

            _connect()
            #run_console()
            #test_verify_instance()
            #test_modify_patient_id()
            test_upload_files()
            #test_upload_file()
            #test_get_instance_preview()
            #test_get_instance_tags()
            #test_patient()

## Functions

`def cleanup_dicom_string(dicom_str)`
  Expand source code

      def cleanup_dicom_string(dicom_str):
              if not isinstance(dicom_str, str):
                      return dicom_str
              dicom_str = regex.sub('\^+', ' ', dicom_str.strip('^'))
              #dicom_str = dicom_str.replace('\r\n', ' [CR] ')
              return dicom_str

`def dicomize_file(filename, title=None, person=None, dcm_name=None, verbose=False, dcm_template_file=None, dcm_transfer_series=True)`
  Expand source code

      def dicomize_file(filename, title=None, person=None, dcm_name=None, verbose=False, dcm_template_file=None, dcm_transfer_series=True):
              assert (filename is not None), '<filename> must not be None'
              assert (not ((person is None) and (dcm_template_file is None))), '<person> or <dcm_template_file> must not be None'

              # already DCM ?
              if gmMimeLib.guess_mimetype(filename) == 'application/dicom':
                      _log.error('already a DICOM file: %s', filename)
                      if dcm_name is None:
                              return filename
                      return shutil.copy2(filename, dcm_name)

              dcm_fname = dicomize_pdf (
                      pdf_name = filename,
                      title = title,
                      person = person,
                      dcm_name = dcm_name,
                      verbose = verbose,
                      dcm_template_file = dcm_template_file,
                      dcm_transfer_series = dcm_transfer_series
              )
              if dcm_fname is not None:
                      return dcm_fname

              _log.debug('does not seem to be a PDF: %s', filename)
              converted_fname = gmMimeLib.convert_file(filename = filename, target_mime = 'image/jpeg')
              if converted_fname is None:
                      _log.error('cannot convert to JPG: %s', filename)
                      return None

              dcm_name = dicomize_jpg (
                      jpg_name = converted_fname,
                      title = title,
                      person = person,
                      dcm_name = dcm_name,
                      verbose = verbose,
                      dcm_template_file = dcm_template_file,
                      dcm_transfer_series = dcm_transfer_series
              )
              return dcm_name

`def dicomize_jpg(jpg_name=None, title=None, person=None, dcm_name=None, verbose=False, dcm_template_file=None, dcm_transfer_series=True)`
  Expand source code

      def dicomize_jpg(jpg_name=None, title=None, person=None, dcm_name=None, verbose=False, dcm_template_file=None, dcm_transfer_series=True):
              assert (jpg_name is not None), '<jpg_name> must not be None'
              assert (not ((person is None) and (dcm_template_file is None))), 'both <person> and <dcm_template_file> are None, but one is needed'

              if dcm_name is None:
                      dcm_name = gmTools.get_unique_filename(suffix = '.dcm')
              _log.debug('%s -> %s', jpg_name, dcm_name)
              now = gmDateTime.pydt_now_here()
              cmd_line = [
                      'img2dcm',
                      '--keep-appn',                                                                                  # carry over EXIF data
                      '--insist-on-jfif',                                                                             # process valid JFIF only
                      '--key', '0008,0021=%s' % now.strftime('%Y%m%d'),               # SeriesDate
                      '--key', '0008,0031=%s' % now.strftime('%H%M%s.0'),             # SeriesTime
                      '--key', '0008,0023=%s' % now.strftime('%Y%m%d'),               # ContentDate
                      '--key', '0008,0033=%s' % now.strftime('%H%M%s.0')              # ContentTime
              ]
              if title is not None:
                      # SeriesDescription
                      if title is not None:
                              cmd_line.append('--key')
                              cmd_line.append('0008,103E=%s' % title)
              if dcm_template_file is None:
                      # StudyDescription
                      if title is not None:
                              cmd_line.append('--key')
                              cmd_line.append('0008,1030=%s' % title)
                      # StudyDate
                      cmd_line.append('--key')
                      cmd_line.append('0008,0020=%s' % now.strftime('%Y%m%d'))
                      # StudyTime
                      cmd_line.append('--key')
                      cmd_line.append('0008,0030=%s' % now.strftime('%H%M%s.0'))
                      # PatientName
                      name = person.active_name
                      cmd_line.append('--key')
                      cmd_line.append('0010,0010=%s' % ('%s^%s' % (
                              name['lastnames'],
                              name['firstnames'])
                      ).replace(' ', '^'))
                      # PatientID
                      cmd_line.append('--key')
                      cmd_line.append('0010,0020=%s' % person.suggest_external_id(target = 'PACS'))
                      # DOB
                      cmd_line.append('--key')
                      cmd_line.append('0010,0030=%s' % person.get_formatted_dob(format = '%Y%m%d', honor_estimation = False))
                      # gender
                      if person['gender'] is not None:
                              cmd_line.append('--key')
                              cmd_line.append('0010,0040=%s' % _map_gender_gm2dcm[person['gender']])
              else:
                      _log.debug('DCM template file: %s', dcm_template_file)
                      if dcm_transfer_series:
                              cmd_line.append('--series-from')
                      else:
                              cmd_line.append('--study-from')
                      cmd_line.append(dcm_template_file)
              if verbose:
                      cmd_line.append('--log-level')
                      cmd_line.append('trace')
              cmd_line.append(jpg_name)
              cmd_line.append(dcm_name)
              success, exit_code, stdout = gmShellAPI.run_process(cmd_line = cmd_line, encoding = 'utf8', verbose = verbose)
              if success:
                      return dcm_name

              return None

`def dicomize_pdf(pdf_name=None, title=None, person=None, dcm_name=None, verbose=False, dcm_template_file=None, dcm_transfer_series=True)`
  Expand source code

      def dicomize_pdf(pdf_name=None, title=None, person=None, dcm_name=None, verbose=False, dcm_template_file=None, dcm_transfer_series=True):
              assert (pdf_name is not None), '<pdf_name> must not be None'
              assert (not ((person is None) and (dcm_template_file is None))), '<person> or <dcm_template_file> must not be None'

              if dcm_name is None:
                      dcm_name = gmTools.get_unique_filename(suffix = '.dcm')
              _log.debug('%s -> %s', pdf_name, dcm_name)
              if title is None:
                      title = pdf_name
              now = gmDateTime.pydt_now_here()
              cmd_line = [
                      'pdf2dcm',
                      '--title', title,
                      '--key', '0008,0020=%s' % now.strftime('%Y%m%d'),                       # StudyDate
                      '--key', '0008,0021=%s' % now.strftime('%Y%m%d'),                       # SeriesDate
                      '--key', '0008,0023=%s' % now.strftime('%Y%m%d'),                       # ContentDate
                      '--key', '0008,0030=%s' % now.strftime('%H%M%s.0'),                     # StudyTime
                      '--key', '0008,0031=%s' % now.strftime('%H%M%s.0'),                     # SeriesTime
                      '--key', '0008,0033=%s' % now.strftime('%H%M%s.0')                      # ContentTime
              ]
              if dcm_template_file is None:
                      name = person.active_name
                      cmd_line.append('--patient-id')
                      cmd_line.append(person.suggest_external_id(target = 'PACS'))
                      cmd_line.append('--patient-name')
                      cmd_line.append(('%s^%s' % (name['lastnames'], name['firstnames'])).replace(' ', '^'))
                      if person['dob'] is not None:
                              cmd_line.append('--patient-birthdate')
                              cmd_line.append(person.get_formatted_dob(format = '%Y%m%d', honor_estimation = False))
                      if person['gender'] is not None:
                              cmd_line.append('--patient-sex')
                              cmd_line.append(_map_gender_gm2dcm[person['gender']])
              else:
                      _log.debug('DCM template file: %s', dcm_template_file)
                      if dcm_transfer_series:
                              cmd_line.append('--series-from')
                      else:
                              cmd_line.append('--study-from')
                      cmd_line.append(dcm_template_file)
              if verbose:
                      cmd_line.append('--log-level')
                      cmd_line.append('trace')
              cmd_line.append(pdf_name)
              cmd_line.append(dcm_name)
              success, exit_code, stdout = gmShellAPI.run_process(cmd_line = cmd_line, encoding = 'utf8', verbose = verbose)
              if success:
                      return dcm_name

              return None

## Classes

`class cOrthancServer`
  Expand source code

      class cOrthancServer:
              # REST API access to Orthanc DICOM servers

      #       def __init__(self):
      #               self.__server_identification = None
      #               self.__user = None
      #               self.__password = None
      #               self.__conn = None
      #               self.__server_url = None

              #--------------------------------------------------------
              def connect(self, host, port, user, password, expected_minimal_version=None, expected_name=None, expected_aet=None):
                      try:
                              int(port)
                      except Exception:
                              _log.error('invalid port [%s]', port)
                              return False
                      if (host is None) or (host.strip() == ''):
                              host = 'localhost'
                      try:
                              self.__server_url = str('http://%s:%s' % (host, port))
                      except Exception:
                              _log.exception('cannot create server url from: host [%s] and port [%s]', host, port)
                              return False
                      self.__user = user
                      self.__password = password
                      _log.info('connecting as [%s] to Orthanc server at [%s]', self.__user, self.__server_url)
                      cache_dir = os.path.join(gmTools.gmPaths().user_tmp_dir, '.orthanc2gm-cache')
                      gmTools.mkdir(cache_dir, 0o700)
                      gmTools.create_directory_description_file(directory = cache_dir, readme = 'this directory caches Orthanc REST data, mainly DICOM files')
                      _log.debug('using cache directory: %s', cache_dir)
                      self.__conn = httplib2.Http(cache = cache_dir)
                      self.__conn.add_credentials(self.__user, self.__password)
                      _log.debug('connected to server: %s', self.server_identification)
                      self.connect_error = ''
                      if self.server_identification is False:
                              self.connect_error += 'retrieving server identification failed'
                              return False
                      if expected_minimal_version is not None:
                              if version.LooseVersion(self.server_identification['Version']) < version.LooseVersion(expected_minimal_version):
                                      _log.error('server too old, needed [%s]', expected_minimal_version)
                                      self.connect_error += 'server too old, needed version [%s]' % expected_minimal_version
                                      return False
                      if expected_name is not None:
                              if self.server_identification['Name'] != expected_name:
                                      _log.error('wrong server name, expected [%s]', expected_name)
                                      self.connect_error += 'wrong server name, expected [%s]' % expected_name
                                      return False
                      if expected_aet is not None:
                              if self.server_identification['DicomAet'] != expected_name:
                                      _log.error('wrong server AET, expected [%s]', expected_aet)
                                      self.connect_error += 'wrong server AET, expected [%s]' % expected_aet
                                      return False
                      return True

              #--------------------------------------------------------
              def _get_server_identification(self):
                      try:
                              return self.__server_identification
                      except AttributeError:
                              pass
                      system_data = self.__run_GET(url = '%s/system' % self.__server_url)
                      if system_data is False:
                              _log.error('unable to get server identification')
                              return False
                      _log.debug('server: %s', system_data)
                      self.__server_identification = system_data

                      self.__initial_orthanc_encoding = self.__run_GET(url = '%s/tools/default-encoding' % self.__server_url)
                      _log.debug('initial Orthanc encoding: %s', self.__initial_orthanc_encoding)

                      # check time skew
                      tolerance = 60 # seconds
                      client_now_as_utc = pydt.datetime.utcnow()
                      start = time.time()
                      orthanc_now_str = self.__run_GET(url = '%s/tools/now' % self.__server_url)              # 20180208T165832
                      end = time.time()
                      query_duration = end - start
                      orthanc_now_unknown_tz = pydt.datetime.strptime(orthanc_now_str, '%Y%m%dT%H%M%S')
                      _log.debug('GNUmed "now" (UTC): %s', client_now_as_utc)
                      _log.debug('Orthanc "now" (UTC): %s', orthanc_now_unknown_tz)
                      _log.debug('wire roundtrip (seconds): %s', query_duration)
                      _log.debug('maximum skew tolerance (seconds): %s', tolerance)
                      if query_duration > tolerance:
                              _log.info('useless to check GNUmed/Orthanc time skew, wire roundtrip (%s) > tolerance (%s)', query_duration, tolerance)
                      else:
                              if orthanc_now_unknown_tz > client_now_as_utc:
                                      real_skew = orthanc_now_unknown_tz - client_now_as_utc
                              else:
                                      real_skew = client_now_as_utc - orthanc_now_unknown_tz
                              _log.info('GNUmed/Orthanc time skew: %s', real_skew)
                              if real_skew > pydt.timedelta(seconds = tolerance):
                                      _log.error('GNUmed/Orthanc time skew > tolerance (may be due to timezone differences on Orthanc < v1.3.2)')

                      return self.__server_identification

              server_identification = property(_get_server_identification, lambda x:x)

              #--------------------------------------------------------
              def _get_as_external_id_issuer(self):
                      # fixed type :: user level instance name :: DICOM AET
                      return 'Orthanc::%(Name)s::%(DicomAet)s' % self.__server_identification

              as_external_id_issuer = property(_get_as_external_id_issuer, lambda x:x)

              #--------------------------------------------------------
              def _get_url_browse_patients(self):
                      if self.__user is None:
                              return self.__server_url
                      return self.__server_url.replace('http://', 'http://%s@' % self.__user)

              url_browse_patients = property(_get_url_browse_patients, lambda x:x)

              #--------------------------------------------------------
              def get_url_browse_patient(self, patient_id):
                      # http://localhost:8042/#patient?uuid=0da01e38-cf792452-65c1e6af-b77faf5a-b637a05b
                      return '%s/#patient?uuid=%s' % (self.url_browse_patients, patient_id)

              #--------------------------------------------------------
              def get_url_browse_study(self, study_id):
                      # http://localhost:8042/#study?uuid=0da01e38-cf792452-65c1e6af-b77faf5a-b637a05b
                      return '%s/#study?uuid=%s' % (self.url_browse_patients, study_id)

              #--------------------------------------------------------
              # download API
              #--------------------------------------------------------
              def get_matching_patients(self, person) -> list:
                      """Fetch matching patients from an Orthanc DICOM server.

                      Matches are searched for via stored "external ID" and
                      via generically generated ID. The external IDs are
                      fetched from the patient store, must be of type
                      "PACS" and must be marked as issued by the
                      instantiated PACS <self.>

                      Args:
                              person: a gmPerson.cPerson instance

                      Returns:
                              A list of Orthanc patient UIDs.
                      """
                      _log.info('searching for Orthanc patients matching %s', person)
                      pacs_ids = person.get_external_ids(id_type = 'PACS', issuer = self.as_external_id_issuer)
                      if len(pacs_ids) > 1:
                              _log.error('GNUmed patient has more than one ID for this PACS: %s', pacs_ids)
                              _log.error('the stored-in-GNUmed PACS ID is expected to be unique _per PACS_')
                              return []

                      pacs_ids2search_by = []
                      pacs_ids2search_by.extend([ pacs_id['value'] for pacs_id in pacs_ids ])
                      pacs_ids2search_by.extend(person.suggest_external_ids(target = 'PACS'))
                      matching_pats = []
                      for pacs_id in pacs_ids2search_by:
                              _log.debug('using PACS ID [%s]', pacs_id)
                              pats = self.get_patients_by_external_id(external_id = pacs_id, fuzzy = False)
                              if len(pats) > 1:
                                      _log.warning('more than one Orthanc patient matches PACS ID: %s', pacs_id)
                              matching_pats.extend(pats)
                      if not matching_pats:
                              _log.debug('no matching patient found in PACS')
                      return matching_pats

              #--------------------------------------------------------
              def get_patients_by_external_id(self, external_id=None, fuzzy=False):
                      """Search for instances by patient ID."""
                      _log.info('external ID >>>%s<<< fuzzy [%s]', external_id, fuzzy)
                      search_term = external_id.strip().strip('*').strip()
                      if fuzzy:
                              search_term = '*%s*' % search_term
                      search_data = {
                              'Level': 'Patient',
                              'CaseSensitive': False,
                              'Expand': True,
                              'Query': {'PatientID': search_term}
                      }
                      matches = self.__run_POST(url = '%s/tools/find' % self.__server_url, data = search_data)
                      # paranoia
                      for match in matches:
                              self.protect_patient(orthanc_id = match['ID'])
                      return matches

              #--------------------------------------------------------
              def get_patients_by_name(self, name_parts=None, gender=None, dob=None, fuzzy=False) -> list:
                      """Search for patients by name.

                      Returns:
                              List of patients matching the search term(s).
                      """
                      _log.info('name parts %s, gender [%s], dob [%s], fuzzy: [%s]', name_parts, gender, dob, fuzzy)
                      if len(name_parts) > 1:
                              return self.get_patients_by_name_parts(name_parts = name_parts, gender = gender, dob = dob, fuzzy = fuzzy)

                      search_term = name_parts[0].strip().strip('*').strip()
                      if search_term == '':
                              _log.debug('search term empty')
                              return []

                      if fuzzy:
                              search_term = '*%s*' % search_term
                      search_data = {
                              'Level': 'Patient',
                              'CaseSensitive': False,
                              'Expand': True,
                              'Query': {'PatientName': search_term}
                      }
                      if gender is not None:
                              gender = _map_gender_gm2dcm[gender.casefold()]
                              if gender is not None:
                                      search_data['Query']['PatientSex'] = gender
                      if dob is not None:
                              search_data['Query']['PatientBirthDate'] = dob.strftime('%Y%m%d')
                      _log.info('server-side C-FIND SCU over REST search, mogrified search data: %s', search_data)
                      matches = self.__run_POST(url = '%s/tools/find' % self.__server_url, data = search_data)
                      return matches

              #--------------------------------------------------------
              def get_patients_by_name_parts(self, name_parts=None, gender=None, dob=None, fuzzy=False):
                      # fuzzy: allow partial/substring matches (but not across name part boundaries ',' or '^')
                      matching_patients = []
                      clean_parts = []
                      for part in name_parts:
                              if part.strip() == '':
                                      continue
                              clean_parts.append(part.casefold().strip())
                      _log.info('client-side patient search, scrubbed search terms: %s', clean_parts)
                      pat_ids = self.__run_GET(url = '%s/patients' % self.__server_url)
                      if pat_ids is False:
                              _log.error('cannot retrieve patients')
                              return []

                      for pat_id in pat_ids:
                              orthanc_pat = self.__run_GET(url = '%s/patients/%s' % (self.__server_url, pat_id))
                              if orthanc_pat is False:
                                      _log.error('cannot retrieve patient')
                                      continue
                              orthanc_name = orthanc_pat['MainDicomTags']['PatientName'].casefold().strip()
                              if not fuzzy:
                                      orthanc_name = orthanc_name.replace(' ', ',').replace('^', ',').split(',')
                              parts_in_orthanc_name = 0
                              for part in clean_parts:
                                      if part in orthanc_name:
                                              parts_in_orthanc_name += 1
                              if parts_in_orthanc_name == len(clean_parts):
                                      _log.debug('name match: "%s" contains all of %s', orthanc_name, clean_parts)
                                      if gender is not None:
                                              gender = _map_gender_gm2dcm[gender.casefold()]
                                              if gender is not None:
                                                      if orthanc_pat['MainDicomTags']['PatientSex'].casefold() != gender:
                                                              _log.debug('gender mismatch: dicom=[%s] gnumed=[%s], skipping', orthanc_pat['MainDicomTags']['PatientSex'], gender)
                                                              continue
                                      if dob is not None:
                                              if orthanc_pat['MainDicomTags']['PatientBirthDate'] != dob.strftime('%Y%m%d'):
                                                      _log.debug('dob mismatch: dicom=[%s] gnumed=[%s], skipping', orthanc_pat['MainDicomTags']['PatientBirthDate'], dob)
                                                      continue
                                      matching_patients.append(orthanc_pat)
                              else:
                                      _log.debug('name mismatch: "%s" does not contain all of %s', orthanc_name, clean_parts)
                      return matching_patients

              #--------------------------------------------------------
              def search_studies_by_patient_name(self, name:str) -> list:
                      """Search for studies with the given patient name snippet.

                      A study (even at the Orthanc DB metadata level) will
                      contain the original patient name (unless manually
                      modified) in contrast to the (artificial Orthanc DB
                      metadata level) patient record. The latter contains
                      the first patient name that had been associated with
                      the given patient ID.

                      Args:
                              name (str): name snippet to search for

                      Returns:
                              The list of matching *studies* (not *patient*).
                      """
                      _log.debug('search term [%s]', name)
                      search_term = name.strip().strip('*').strip()
                      if search_term == '':
                              _log.warning('search term empty')
                              return []

                      search_term = '*%s*' % search_term
                      search_data = {
                              'Level': 'Study',
                              'CaseSensitive': False,
                              'Expand': True,
                              'Query': {'PatientName': search_term}
                      }
                      matches = self.__run_POST(url = '%s/tools/find' % self.__server_url, data = search_data)
                      return matches

              #--------------------------------------------------------
              def search_studies_by_patient_id(self, patient_id:str) -> list:
                      """Search for studies with the given patient ID snippet.

                      This relates to the external world patient ID as
                      stored in DICOM instances, not the Orthanc DB
                      metadata level patient UID.

                      Args:
                              patient_id: patient ID snippet to search for

                      Returns:
                              The list of matching *studies* (not *patient*).
                      """
                      _log.debug('search term >>>%s<<<', patient_id)
                      search_term = patient_id.strip().strip('*').strip()
                      search_term = '*%s*' % search_term
                      search_data = {
                              'Level': 'Study',
                              'CaseSensitive': False,
                              'Expand': True,
                              'Query': {'PatientID': search_term}
                      }
                      matches = self.__run_POST(url = '%s/tools/find' % self.__server_url, data = search_data)
                      return matches

              #--------------------------------------------------------
              def get_studies_list_by_patient_name(self, name_parts=None, gender=None, dob=None, fuzzy=False):
                      return self.get_studies_list_by_orthanc_patient_list (
                              orthanc_patients = self.get_patients_by_name(name_parts = name_parts, gender = gender, dob = dob, fuzzy = fuzzy)
                      )

              #--------------------------------------------------------
              def get_studies_list_by_external_id(self, external_id=None):
                      return self.get_studies_list_by_orthanc_patient_list (
                              orthanc_patients = self.get_patients_by_external_id(external_id = external_id)
                      )

              #--------------------------------------------------------
              def get_study_as_zip(self, study_id=None, filename=None):
                      if filename is None:
                              filename = gmTools.get_unique_filename(prefix = r'DCM-', suffix = r'.zip')
                      _log.info('exporting study [%s] into [%s]', study_id, filename)
                      f = io.open(filename, 'wb')
                      f.write(self.__run_GET(url = '%s/studies/%s/archive' % (self.__server_url, str(study_id)), allow_cached = True))
                      f.close()
                      return filename

              #--------------------------------------------------------
              def get_study_as_zip_with_dicomdir(self, study_id=None, filename=None):
                      if filename is None:
                              filename = gmTools.get_unique_filename(prefix = r'DCM-', suffix = r'.zip')
                      _log.info('exporting study [%s] into [%s]', study_id, filename)
                      f = io.open(filename, 'wb')
                      f.write(self.__run_GET(url = '%s/studies/%s/media' % (self.__server_url, str(study_id)), allow_cached = True))
                      f.close()
                      return filename

              #--------------------------------------------------------
              def get_studies_as_zip(self, study_ids=None, patient_id=None, filename=None):
                      if filename is None:
                              filename = gmTools.get_unique_filename(prefix = r'DCM-', suffix = r'.zip')
                      if study_ids is None:
                              _log.info('exporting all studies of patient [%s] into [%s]', patient_id, filename)
                              f = io.open(filename, 'wb')
                              f.write(self.__run_GET(url = '%s/patients/%s/archive' % (self.__server_url, str(patient_id)), allow_cached = True))
                              f.close()
                              return filename

              #--------------------------------------------------------
              def _manual_get_studies_with_dicomdir(self, study_ids=None, patient_id=None, target_dir=None, filename=None, create_zip=False):

                      if filename is None:
                              filename = gmTools.get_unique_filename(prefix = r'DCM-', suffix = r'.zip', tmp_dir = target_dir)

                      # all studies
                      if study_ids is None:
                              _log.info('exporting all studies of patient [%s] into [%s]', patient_id, filename)
                              f = io.open(filename, 'wb')
                              url = '%s/patients/%s/media' % (self.__server_url, str(patient_id))
                              _log.debug(url)
                              f.write(self.__run_GET(url = url, allow_cached = True))
                              f.close()
                              if create_zip:
                                      return filename
                              if target_dir is None:
                                      target_dir = gmTools.mk_sandbox_dir(prefix = 'dcm-')
                              if not gmTools.unzip_archive(filename, target_dir = target_dir, remove_archive = True):
                                      return False
                              return target_dir

                      # a selection of studies
                      dicomdir_cmd = 'gm-create_dicomdir'             # args: 1) name of DICOMDIR to create 2) base directory where to start recursing for DICOM files
                      found, external_cmd = gmShellAPI.detect_external_binary(dicomdir_cmd)
                      if not found:
                              _log.error('[%s] not found', dicomdir_cmd)
                              return False

                      if create_zip:
                              sandbox_dir = gmTools.mk_sandbox_dir(prefix = 'dcm-')
                              _log.info('exporting studies [%s] into [%s] (sandbox [%s])', study_ids, filename, sandbox_dir)
                      else:
                              sandbox_dir = target_dir
                              _log.info('exporting studies [%s] into [%s]', study_ids, sandbox_dir)
                      _log.debug('sandbox dir: %s', sandbox_dir)
                      idx = 0
                      for study_id in study_ids:
                              study_zip_name = gmTools.get_unique_filename(prefix = 'dcm-', suffix = '.zip')
                              # getting with DICOMDIR returns DICOMDIR compatible subdirs and filenames
                              study_zip_name = self.get_study_as_zip_with_dicomdir(study_id = study_id, filename = study_zip_name)
                              # non-beautiful per-study dir name required by subsequent DICOMDIR generation
                              idx += 1
                              study_unzip_dir = os.path.join(sandbox_dir, 'STUDY%s' % idx)
                              _log.debug('study [%s] -> %s -> %s', study_id, study_zip_name, study_unzip_dir)
                              # need to extract into per-study subdir because get-with-dicomdir
                              # returns identical-across-studies subdirs / filenames
                              if not gmTools.unzip_archive(study_zip_name, target_dir = study_unzip_dir, remove_archive = True):
                                      return False

                      # create DICOMDIR across all studies,
                      # we simply ignore the already existing per-study DICOMDIR files
                      target_dicomdir_name = os.path.join(sandbox_dir, 'DICOMDIR')
                      gmTools.remove_file(target_dicomdir_name, log_error = False)    # better safe than sorry
                      _log.debug('generating [%s]', target_dicomdir_name)
                      cmd = '%(cmd)s %(DICOMDIR)s %(startdir)s' % {
                              'cmd': external_cmd,
                              'DICOMDIR': target_dicomdir_name,
                              'startdir': sandbox_dir
                      }
                      success = gmShellAPI.run_command_in_shell (
                              command = cmd,
                              blocking = True
                      )
                      if not success:
                              _log.error('problem running [gm-create_dicomdir]')
                              return False
                      # paranoia
                      try:
                              io.open(target_dicomdir_name)
                      except Exception:
                              _log.error('[%s] not generated, aborting', target_dicomdir_name)
                              return False

                      # return path to extracted studies
                      if not create_zip:
                              return sandbox_dir

                      # else return ZIP of all studies
                      studies_zip = shutil.make_archive (
                              gmTools.fname_stem_with_path(filename),
                              'zip',
                              root_dir = gmTools.parent_dir(sandbox_dir),
                              base_dir = gmTools.dirname_stem(sandbox_dir),
                              logger = _log
                      )
                      _log.debug('archived all studies with one DICOMDIR into: %s', studies_zip)
                      # studies can be _large_ so attempt to get rid of intermediate files
                      gmTools.rmdir(sandbox_dir)
                      return studies_zip

              #--------------------------------------------------------
              def get_studies_with_dicomdir(self, study_ids=None, patient_id=None, target_dir=None, filename=None, create_zip=False):

                      if filename is None:
                              filename = gmTools.get_unique_filename(prefix = r'DCM-', suffix = r'.zip', tmp_dir = target_dir)

                      # all studies
                      if study_ids is None:
                              if patient_id is None:
                                      raise ValueError('<patient_id> must be defined if <study_ids> is None')
                              _log.info('exporting all studies of patient [%s] into [%s]', patient_id, filename)
                              f = io.open(filename, 'wb')
                              url = '%s/patients/%s/media' % (self.__server_url, str(patient_id))
                              _log.debug(url)
                              f.write(self.__run_GET(url = url, allow_cached = True))
                              f.close()
                              if create_zip:
                                      return filename
                              if target_dir is None:
                                      target_dir = gmTools.mk_sandbox_dir(prefix = 'dcm-')
                              if not gmTools.unzip_archive(filename, target_dir = target_dir, remove_archive = True):
                                      return False
                              return target_dir

                      # selection of studies
                      _log.info('exporting %s studies into [%s]', len(study_ids), filename)
                      _log.debug('studies: %s', study_ids)
                      f = io.open(filename, 'wb')
                      #  You have to make a POST request against URI "/tools/create-media", with a
                      #  JSON body that contains the array of the resources of interest (as Orthanc
                      #  identifiers). Here is a sample command-line:
                      #  curl -X POST http://localhost:8042/tools/create-media -d '["8c4663df-c3e66066-9e20a8fc-dd14d1e5-251d3d84","2cd4848d-02f0005f-812ffef6-a210bbcf-3f01a00a","6eeded74-75005003-c3ae9738-d4a06a4f-6beedeb8","8a622020-c058291c-7693b63f-bc67aa2e-0a02e69c"]' -v > /tmp/a.zip
                      #  (this will not create duplicates but will also not check for single-patient-ness)
                      url = '%s/tools/create-media-extended' % self.__server_url
                      _log.debug(url)
                      try:
                              downloaded = self.__run_POST(url = url, data = study_ids, output_file = f)
                              if not downloaded:
                                      _log.error('this Orthanc version probably does not support "create-media-extended"')
                      except TypeError:
                              f.close()
                              _log.exception('cannot retrieve multiple studies as one archive with DICOMDIR, probably not supported by this Orthanc version')
                              return False
                      # retry with old URL
                      if not downloaded:
                              url = '%s/tools/create-media' % self.__server_url
                              _log.debug('retrying: %s', url)
                              try:
                                      downloaded = self.__run_POST(url = url, data = study_ids, output_file = f)
                                      if not downloaded:
                                              return False
                              except TypeError:
                                      _log.exception('cannot retrieve multiple studies as one archive with DICOMDIR, probably not supported by this Orthanc version')
                                      return False
                              finally:
                                      f.close()
                      if create_zip:
                              return filename
                      if target_dir is None:
                              target_dir = gmTools.mk_sandbox_dir(prefix = 'dcm-')
                              _log.debug('exporting studies into [%s]', target_dir)
                      if not gmTools.unzip_archive(filename, target_dir = target_dir, remove_archive = True):
                              return False
                      return target_dir

              #--------------------------------------------------------
              def get_instance_dicom_tags(self, instance_id, simplified=True):
                      _log.debug('retrieving DICOM tags for instance [%s]', instance_id)
                      if simplified:
                              download_url = '%s/instances/%s/simplified-tags' % (self.__server_url, instance_id)
                      else:
                              download_url = '%s/instances/%s/tags' % (self.__server_url, instance_id)
                      return self.__run_GET(url = download_url, allow_cached = True)

              #--------------------------------------------------------
              def get_instance_preview(self, instance_id, filename=None):
                      if filename is None:
                              filename = gmTools.get_unique_filename(suffix = '.png')
                      _log.debug('exporting preview for instance [%s] into [%s]', instance_id, filename)
                      download_url = '%s/instances/%s/preview' % (self.__server_url, instance_id)
                      f = io.open(filename, 'wb')
                      try:
                              f.write(self.__run_GET(url = download_url, allow_cached = True))
                      except Exception:
                              _log.exception('cannot retrieve instance')
                              filename = None
                      finally:
                              f.close()
                      return filename

              #--------------------------------------------------------
              def get_instance(self, instance_id:str, filename:str=None, allow_cached:bool=True) -> str:
                      if filename is None:
                              filename = gmTools.get_unique_filename(suffix = '.dcm')

                      _log.debug('exporting instance [%s] into [%s]', instance_id, filename)
                      download_url = '%s/instances/%s/attachments/dicom/data' % (self.__server_url, instance_id)
                      f = io.open(filename, 'wb')
                      f.write(self.__run_GET(url = download_url, allow_cached = allow_cached))
                      f.close()
                      return filename

              #--------------------------------------------------------
              # server-side API
              #--------------------------------------------------------
              def get_patient(self, orthanc_id:str):
                      patient_data_url = '%s/patients/%s' % (self.__server_url, str(orthanc_id))
                      patient_data, status = self.__run_GET(patient_data_url, also_return_status = True)
                      if patient_data is False:
                              if status == 404:
                                      _log.debug('no such patient: %s', orthanc_id)
                                      return {}

                              _log.error('cannot retrieve patient data for [%s]', orthanc_id)
                              return False

                      return patient_data

              #--------------------------------------------------------
              def protect_patient(self, orthanc_id:str):
                      url = '%s/patients/%s/protected' % (self.__server_url, str(orthanc_id))
                      if self.__run_GET(url) == 1:
                              _log.debug('patient already protected: %s', orthanc_id)
                              return True
                      _log.warning('patient [%s] not protected against recycling, enabling protection now', orthanc_id)
                      self.__run_PUT(url = url, data = '1')
                      if self.__run_GET(url) == 1:
                              return True
                      _log.error('cannot protect patient [%s] against recycling', orthanc_id)
                      return False

              #--------------------------------------------------------
              def unprotect_patient(self, orthanc_id):
                      url = '%s/patients/%s/protected' % (self.__server_url, str(orthanc_id))
                      if self.__run_GET(url) == 0:
                              return True
                      _log.info('patient [%s] protected against recycling, disabling protection now', orthanc_id)
                      self.__run_PUT(url = url, data = '0')
                      if self.__run_GET(url) == 0:
                              return True
                      _log.error('cannot unprotect patient [%s] against recycling', orthanc_id)
                      return False

              #--------------------------------------------------------
              def patient_is_protected(self, orthanc_id):
                      url = '%s/patients/%s/protected' % (self.__server_url, str(orthanc_id))
                      return (self.__run_GET(url) == 1)

              #--------------------------------------------------------
              def verify_patient_data(self, orthanc_id):
                      _log.info('verifying DICOM data of patient [%s]', orthanc_id)
                      bad_data = []
                      instances_url = '%s/patients/%s/instances' % (self.__server_url, orthanc_id)
                      instances = self.__run_GET(instances_url)
                      for instance in instances:
                              instance_id = instance['ID']
                              attachments_url = '%s/instances/%s/attachments' % (self.__server_url, instance_id)
                              attachments = self.__run_GET(attachments_url, allow_cached = True)
                              for attachment in attachments:
                                      verify_url = '%s/%s/verify-md5' % (attachments_url, attachment)
                                      # False, success = "{}"
                                      #2018-02-08 19:11:27  ERROR     gm.dicom      [-1211701504 MainThread]  (gmDICOM.py::__run_POST() #986): cannot POST: http://localhost:8042/instances/5a8206f4-24619e76-6650d9cd-792cdf25-039e96e6/attachments/dicom-as-json/verify-md5
                                      #2018-02-08 19:11:27  ERROR     gm.dicom      [-1211701504 MainThread]  (gmDICOM.py::__run_POST() #987): response: {'status': '400', 'content-length': '0'}
                                      if self.__run_POST(verify_url) is not False:
                                              continue
                                      _log.error('bad MD5 of DICOM file at url [%s]: patient=%s, attachment_type=%s', verify_url, orthanc_id, attachment)
                                      bad_data.append({'patient': orthanc_id, 'instance': instance_id, 'type': attachment, 'orthanc': '%s [%s]' % (self.server_identification, self.__server_url)})

                      return bad_data

              #--------------------------------------------------------
              def modify_patient_id(self, old_patient_id, new_patient_id):
                      """Modify the patient ID stored in Orthanc.

                      This changes all DICOM files of the patient,
                      identified via (DICOM level) old_patient_id, to
                      contain the new_patient_id. It will update the
                      associated Orthanc metadata DB entries accordingly.
                      """
                      if old_patient_id == new_patient_id:
                              return True

                      modify_data = {
                              'Replace': {
                                      'PatientID': new_patient_id
                                      #,u'0010,0021': praxis.name / "GNUmed vX.X.X"
                                      #,u'0010,1002': series of (old) patient IDs
                              }
                              , 'Force': True
                              # "Keep" doesn't seem to do what it suggests ATM
                              #, u'Keep': True
                      }
                      orth_pat_defs = self.get_patients_by_external_id(external_id = old_patient_id)
                      all_modified = True
                      for orth_pat_def in orth_pat_defs:
                              _log.info('modifying Orthanc patient [%s]: DICOM ID [%s] -> [%s]', orth_pat_def['ID'], old_patient_id, new_patient_id)
                              old_pat_data = self.get_patient(orth_pat_def['ID'])
                              _log.debug('to be modified: %s', old_pat_data)
                              if self.patient_is_protected(orth_pat_def['ID']):
                                      _log.debug('patient protected: %s, unprotecting for modification', orth_pat_def['ID'])
                                      if not self.unprotect_patient(orth_pat_def['ID']):
                                              _log.error('cannot unlock patient [%s], skipping', orth_pat_def['ID'])
                                              all_modified = False
                                              continue
                                      was_protected = True
                              else:
                                      was_protected = False
                              pat_url = '%s/patients/%s' % (self.__server_url, orth_pat_def['ID'])
                              modify_url = '%s/modify' % pat_url
                              result = self.__run_POST(modify_url, data = modify_data)
                              _log.debug('modify result: %s', result)
                              if result is False:
                                      _log.error('cannot modify patient [%s]', orth_pat_def['ID'])
                                      all_modified = False
                                      continue
                              newly_created_orthanc_patient_id = result['ID']
                              _log.info('newly created Orthanc patient ID: %s', newly_created_orthanc_patient_id)
                              mod_pat_data = self.get_patient(newly_created_orthanc_patient_id)
                              _log.debug('modified pat: %s', mod_pat_data)
                              _log.debug('deleting archived patient: %s', self.__run_DELETE(pat_url))
                              if was_protected:
                                      if not self.protect_patient(newly_created_orthanc_patient_id):
                                              _log.error('cannot re-lock (new) patient [%s]', newly_created_orthanc_patient_id)

                      return all_modified

              #--------------------------------------------------------
              # upload API
              #--------------------------------------------------------
              def upload_dicom_file(self, filename:str, check_mime_type:bool=False) -> bool:
                      """Update a DICOM file.

                      Will silently ignore DICOMDIR files (which are application/dicom but
                      Orthanc does not process them).

                      Args:
                              filename: DICOM file to upload
                              check_mime_type: whether to check the file for being application/dicom, and to fail if not

                      Returns:
                              True/False
                      """
                      _log.info('processing: %s', filename)
                      if gmTools.fname_stem(filename) == 'DICOMDIR':
                              _log.debug('ignoring, no use uploading DICOMDIR files to Orthanc')
                              return True

                      if check_mime_type:
                              mimetype = gmMimeLib.guess_mimetype(filename)
                              if mimetype != 'application/dicom':
                                      _log.error('not considered a DICOM (application/dicom) file: %s, not uploading', mimetype)
                                      return False

                      try:
                              f = io.open(filename, 'rb')
                      except Exception:
                              _log.exception('failed to open file')
                              return False

                      dcm_data = f.read()
                      f.close()
                      upload_url = '%s/instances' % self.__server_url
                      uploaded = self.__run_POST(upload_url, data = dcm_data, content_type = 'application/dicom')
                      if uploaded is False:
                              _log.error('upload failed')
                              return False

                      # typically a 404 following the upload of a DICOM file w/o identifiers
                      if uploaded == []:
                              _log.error('upload failed')
                              return False

                      _log.debug(uploaded)
                      # paranoia, as is our custom
                      verified = self.verify_instance (
                              instance_id = uploaded['ID'],
                              filename = filename,
                              attempt_download = True
                      )
                      return verified

              #--------------------------------------------------------
              def verify_instance(self, instance_id:str, filename:str=None, attempt_download:bool=False) -> bool:

                      _BINARY_ATTACHMENTS = ['dicom']

                      _log.debug('verifying instance [%s] against file [%s]', instance_id, filename)
                      is_valid = True

                      attachments_url = '%s/instances/%s/attachments' % (self.__server_url, instance_id)
                      attachments = self.__run_GET(attachments_url, allow_cached = False)
                      if not attachments:
                              _log.error('cannot retrieve instance attachment list')
                              return False

                      for attachment in attachments:
                              md5_orthanc = None
                              # 1) verify MD5 inside Orthanc, if available (checks Orthanc storage corruption)
                              available_fields_url = '%s/instances/%s/attachments/%s' % (self.__server_url, instance_id, attachment)
                              available_fields = self.__run_GET(available_fields_url, allow_cached = False)
                              if 'md5' in available_fields:
                                      md5_url = '%s/md5' % available_fields_url
                                      md5_orthanc = self.__run_GET(md5_url)
                                      verify_url = '%s/%s/verify-md5' % (attachments_url, attachment)
                                      if self.__run_POST(verify_url) is False:
                                              _log.error('MD5 verification failed, instance [%s], attachment=%s, url [%s]', instance_id, attachment, verify_url)
                                              _log.error('potentially Orthanc storage corruption')
                                              is_valid = False
                                      else:
                                              _log.debug('MD5: Orthanc DB <-> Orthanc storage: match')
                              else:
                                      _log.debug('MD5 of instance attachment not available in Orthanc, cannot verify backend storage status')
                              # 2) verify instance attachment can be downloaded
                              md5_downloaded = None
                              if attempt_download:
                                      attachment_filename = gmTools.get_unique_filename()
                                      download_url = '%s/instances/%s/attachments/%s/data' % (self.__server_url, instance_id, attachment)
                                      attachment_data = self.__run_GET(url = download_url, allow_cached = False)
                                      if isinstance(attachment_data, bytes):
                                              attachment_file = io.open(attachment_filename, 'wb')
                                      else:
                                              attachment_file = io.open(attachment_filename, 'wt')
                                              attachment_data = '%s' % attachment_data
                                      attachment_file.write(attachment_data)
                                      del attachment_data
                                      attachment_file.close()
                                      _log.debug('download: Orthanc -> localhost: success')
                                      if attachment not in _BINARY_ATTACHMENTS:
                                              _log.info('attachment of type [%s] not binary, cannot verify MD5 of download or local file against MD5 in Orthanc, skipping', attachment)
                                              continue
                                      md5_downloaded = gmTools.file2md5(attachment_filename)
                              else:
                                      _log.debug('not downloading instance for verification')
                              # 3) verify MD5 of downloaded instance against Orthanc, if possible
                              if md5_downloaded and md5_orthanc:
                                      if md5_downloaded == md5_orthanc:
                                              _log.debug('MD5: Orthanc DB <-> localhost: match')
                                      else:
                                              _log.error('MD5 mismatch: Orthanc DB <-> localhost')
                                              _log.error('download: %s', md5_downloaded)
                                              _log.error('Orthanc : %s', md5_orthanc)
                                              is_valid = False
                              if filename:
                                      md5_local = gmTools.file2md5(filename)
                              else:
                                      _log.debug('local file not available for verification')
                                      md5_local = None
                              # 4) verify MD5 of download against local file
                              if md5_downloaded and md5_local:
                                      if md5_downloaded == md5_local:
                                              _log.debug('MD5: downloaded <-> pre-existing: match')
                                      else:
                                              _log.error('MD5 mismatch: downloaded <-> pre-existing')
                                              _log.error('download: %s', md5_downloaded)
                                              _log.error('locally : %s', md5_local)
                                              is_valid = False
                              # 5) verify MD5 of local file against Orthanc
                              if md5_local and md5_orthanc:
                                      if md5_local == md5_orthanc:
                                              _log.debug('MD5: Orthanc DB <-> pre-existing: match')
                                      else:
                                              _log.error('MD5 mismatch: Orthanc DB <-> pre-existing')
                                              _log.error('locally : %s', md5_local)
                                              _log.error('Orthanc : %s', md5_orthanc)
                                              is_valid = False
                              # 6) consider comparing the raw pixel data or comparing the output of exiftool etc

                      _log.debug('verified: %s', is_valid)
                      return is_valid

              #--------------------------------------------------------
              def upload_dicom_files(self, files=None, check_mime_type=False):
                      uploaded = []
                      not_uploaded = []
                      for filename in files:
                              success = self.upload_dicom_file(filename, check_mime_type = check_mime_type)
                              if success:
                                      uploaded.append(filename)
                                      continue
                              not_uploaded.append(filename)

                      if len(not_uploaded) > 0:
                              _log.error('not all files uploaded')
                      return (uploaded, not_uploaded)

              #--------------------------------------------------------
              def upload_from_directory(self, directory=None, recursive=False, check_mime_type=False, ignore_other_files=True):

                      #--------------------
                      def _on_error(exc):
                              _log.error('DICOM (?) file not accessible: %s', exc.filename)
                              _log.error(exc)
                      #--------------------

                      _log.debug('uploading DICOM files from [%s]', directory)
                      if not recursive:
                              files2try = os.listdir(directory)
                              _log.debug('found %s files', len(files2try))
                              if ignore_other_files:
                                      files2try = [ f for f in files2try if gmMimeLib.guess_mimetype(f) == 'application/dicom' ]
                                      _log.debug('DICOM files therein: %s', len(files2try))
                              return self.upload_dicom_files(files = files2try, check_mime_type = check_mime_type)

                      _log.debug('recursing for DICOM files')
                      uploaded = []
                      not_uploaded = []
                      for curr_root, curr_root_subdirs, curr_root_files in os.walk(directory, onerror = _on_error):
                              _log.debug('recursing into [%s]', curr_root)
                              files2try = [ os.path.join(curr_root, f) for f in curr_root_files ]
                              _log.debug('found %s files', len(files2try))
                              if ignore_other_files:
                                      files2try = [ f for f in files2try if gmMimeLib.guess_mimetype(f) == 'application/dicom' ]
                                      _log.debug('DICOM files therein: %s', len(files2try))
                              up, not_up = self.upload_dicom_files (
                                      files = files2try,
                                      check_mime_type = check_mime_type
                              )
                              uploaded.extend(up)
                              not_uploaded.extend(not_up)

                      return (uploaded, not_uploaded)

              #--------------------------------------------------------
              def upload_by_DICOMDIR(self, DICOMDIR=None):
                      pass

              #--------------------------------------------------------
              # helper functions
              #--------------------------------------------------------
              def get_studies_list_by_orthanc_patient_list(self, orthanc_patients=None):

                      study_keys2hide =  ['ModifiedFrom', 'Type', 'ID', 'ParentPatient', 'Series']
                      series_keys2hide = ['ModifiedFrom', 'Type', 'ID', 'ParentStudy',   'Instances']

                      studies_by_patient = []

                      # loop over patients
                      for pat in orthanc_patients:
                              pat_dict = {
                                      'orthanc_id': pat['ID'],
                                      'name': None,
                                      'external_id': None,
                                      'date_of_birth': None,
                                      'gender': None,
                                      'studies': []
                              }
                              try:
                                      pat_dict['name'] = pat['MainDicomTags']['PatientName'].strip()
                              except KeyError:
                                      pass
                              try:
                                      pat_dict['external_id'] = pat['MainDicomTags']['PatientID'].strip()
                              except KeyError:
                                      pass
                              try:
                                      pat_dict['date_of_birth'] = pat['MainDicomTags']['PatientBirthDate'].strip()
                              except KeyError:
                                      pass
                              try:
                                      pat_dict['gender'] = pat['MainDicomTags']['PatientSex'].strip()
                              except KeyError:
                                      pass
                              for key in pat_dict:
                                      if pat_dict[key] in ['unknown', '(null)', '']:
                                              pat_dict[key] = None
                                      pat_dict[key] = cleanup_dicom_string(pat_dict[key])
                              studies_by_patient.append(pat_dict)

                              # loop over studies of patient
                              orth_studies = self.__run_GET(url = '%s/patients/%s/studies' % (self.__server_url, pat['ID']))
                              if orth_studies is False:
                                      _log.error('cannot retrieve studies')
                                      return []
                              for orth_study in orth_studies:
                                      study_dict = {
                                              'orthanc_id': orth_study['ID'],
                                              'date': None,
                                              'time': None,
                                              'description': None,
                                              'referring_doc': None,
                                              'requesting_doc': None,
                                              'requesting_org': None,
                                              'performing_doc': None,
                                              'operator_name': None,
                                              'radiographer_code': None,
                                              'radiology_org': None,
                                              'radiology_dept': None,
                                              'radiology_org_addr': None,
                                              'station_name': None,
                                              'series': []
                                      }
                                      try:
                                              study_dict['date'] = orth_study['MainDicomTags']['StudyDate'].strip()
                                      except KeyError:
                                              pass
                                      try:
                                              study_dict['time'] = orth_study['MainDicomTags']['StudyTime'].strip()
                                      except KeyError:
                                              pass
                                      try:
                                              study_dict['description'] = orth_study['MainDicomTags']['StudyDescription'].strip()
                                      except KeyError:
                                              pass
                                      try:
                                              study_dict['referring_doc'] = orth_study['MainDicomTags']['ReferringPhysicianName'].strip()
                                      except KeyError:
                                              pass
                                      try:
                                              study_dict['requesting_doc'] = orth_study['MainDicomTags']['RequestingPhysician'].strip()
                                      except KeyError:
                                              pass
                                      try:
                                              study_dict['requesting_org'] = orth_study['MainDicomTags']['RequestingService'].strip()
                                      except KeyError:
                                              pass
                                      try:
                                              study_dict['radiology_org_addr'] = orth_study['MainDicomTags']['InstitutionAddress'].strip()
                                      except KeyError:
                                              pass
                                      try:
                                              study_dict['radiology_org'] = orth_study['MainDicomTags']['InstitutionName'].strip()
                                              if study_dict['radiology_org_addr'] is not None:
                                                      if study_dict['radiology_org'] in study_dict['radiology_org_addr']:
                                                              study_dict['radiology_org'] = None
                                      except KeyError:
                                              pass
                                      try:
                                              study_dict['radiology_dept'] = orth_study['MainDicomTags']['InstitutionalDepartmentName'].strip()
                                              if study_dict['radiology_org'] is not None:
                                                      if study_dict['radiology_dept'] in study_dict['radiology_org']:
                                                              study_dict['radiology_dept'] = None
                                              if study_dict['radiology_org_addr'] is not None:
                                                      if study_dict['radiology_dept'] in study_dict['radiology_org_addr']:
                                                              study_dict['radiology_dept'] = None
                                      except KeyError:
                                              pass
                                      try:
                                              study_dict['station_name'] = orth_study['MainDicomTags']['StationName'].strip()
                                              if study_dict['radiology_org'] is not None:
                                                      if study_dict['station_name'] in study_dict['radiology_org']:
                                                              study_dict['station_name'] = None
                                              if study_dict['radiology_org_addr'] is not None:
                                                      if study_dict['station_name'] in study_dict['radiology_org_addr']:
                                                              study_dict['station_name'] = None
                                              if study_dict['radiology_dept'] is not None:
                                                      if study_dict['station_name'] in study_dict['radiology_dept']:
                                                              study_dict['station_name'] = None
                                      except KeyError:
                                              pass
                                      for key in study_dict:
                                              if study_dict[key] in ['unknown', '(null)', '']:
                                                      study_dict[key] = None
                                              study_dict[key] = cleanup_dicom_string(study_dict[key])
                                      study_dict['all_tags'] = {}
                                      try:
                                              orth_study['PatientMainDicomTags']
                                      except KeyError:
                                              orth_study['PatientMainDicomTags'] = pat['MainDicomTags']
                                      for key in orth_study:
                                              if key == 'MainDicomTags':
                                                      for mkey in orth_study['MainDicomTags']:
                                                              study_dict['all_tags'][mkey] = orth_study['MainDicomTags'][mkey].strip()
                                                      continue
                                              if key == 'PatientMainDicomTags':
                                                      for pkey in orth_study['PatientMainDicomTags']:
                                                              study_dict['all_tags'][pkey] = orth_study['PatientMainDicomTags'][pkey].strip()
                                                      continue
                                              study_dict['all_tags'][key] = orth_study[key]
                                      _log.debug('study: %s', list(study_dict['all_tags']))
                                      for key in study_keys2hide:
                                              try: del study_dict['all_tags'][key]
                                              except KeyError: pass
                                      pat_dict['studies'].append(study_dict)

                                      # loop over series in study
                                      for orth_series_id in orth_study['Series']:
                                              orth_series = self.__run_GET(url = '%s/series/%s' % (self.__server_url, orth_series_id))
                                              ordered_slices = self.__run_GET(url = '%s/series/%s/ordered-slices' % (self.__server_url, orth_series_id))
                                              if ordered_slices is False:
                                                      slices = orth_series['Instances']
                                              else:
                                                      slices = [ s[0] for s in ordered_slices['SlicesShort'] ]
                                              if orth_series is False:
                                                      _log.error('cannot retrieve series')
                                                      return []
                                              series_dict = {
                                                      'orthanc_id': orth_series['ID'],
                                                      'instances': slices,
                                                      'modality': None,
                                                      'date': None,
                                                      'time': None,
                                                      'description': None,
                                                      'body_part': None,
                                                      'protocol': None,
                                                      'performed_procedure_step_description': None,
                                                      'acquisition_device_processing_description': None,
                                                      'operator_name': None,
                                                      'radiographer_code': None,
                                                      'performing_doc': None
                                              }
                                              try:
                                                      series_dict['modality'] = orth_series['MainDicomTags']['Modality'].strip()
                                              except KeyError:
                                                      pass
                                              try:
                                                      series_dict['date'] = orth_series['MainDicomTags']['SeriesDate'].strip()
                                              except KeyError:
                                                      pass
                                              try:
                                                      series_dict['description'] = orth_series['MainDicomTags']['SeriesDescription'].strip()
                                              except KeyError:
                                                      pass
                                              try:
                                                      series_dict['time'] = orth_series['MainDicomTags']['SeriesTime'].strip()
                                              except KeyError:
                                                      pass
                                              try:
                                                      series_dict['body_part'] = orth_series['MainDicomTags']['BodyPartExamined'].strip()
                                              except KeyError:
                                                      pass
                                              try:
                                                      series_dict['protocol'] = orth_series['MainDicomTags']['ProtocolName'].strip()
                                              except KeyError:
                                                      pass
                                              try:
                                                      series_dict['performed_procedure_step_description'] = orth_series['MainDicomTags']['PerformedProcedureStepDescription'].strip()
                                              except KeyError:
                                                      pass
                                              try:
                                                      series_dict['acquisition_device_processing_description'] = orth_series['MainDicomTags']['AcquisitionDeviceProcessingDescription'].strip()
                                              except KeyError:
                                                      pass
                                              try:
                                                      series_dict['operator_name'] = orth_series['MainDicomTags']['OperatorsName'].strip()
                                              except KeyError:
                                                      pass
                                              try:
                                                      series_dict['radiographer_code'] = orth_series['MainDicomTags']['RadiographersCode'].strip()
                                              except KeyError:
                                                      pass
                                              try:
                                                      series_dict['performing_doc'] = orth_series['MainDicomTags']['PerformingPhysicianName'].strip()
                                              except KeyError:
                                                      pass
                                              for key in series_dict:
                                                      if series_dict[key] in ['unknown', '(null)', '']:
                                                              series_dict[key] = None
                                              if series_dict['description'] == series_dict['protocol']:
                                                      _log.debug('<series description> matches <series protocol>, ignoring protocol')
                                                      series_dict['protocol'] = None
                                              if series_dict['performed_procedure_step_description'] in [series_dict['description'], series_dict['protocol']]:
                                                      series_dict['performed_procedure_step_description'] = None
                                              if series_dict['performed_procedure_step_description'] is not None:
                                                      # weed out "numeric" only
                                                      if regex.match ('[.,/\|\-\s\d]+', series_dict['performed_procedure_step_description'], flags = regex.UNICODE):
                                                              series_dict['performed_procedure_step_description'] = None
                                              if series_dict['acquisition_device_processing_description'] in [series_dict['description'], series_dict['protocol']]:
                                                      series_dict['acquisition_device_processing_description'] = None
                                              if series_dict['acquisition_device_processing_description'] is not None:
                                                      # weed out "numeric" only
                                                      if regex.match ('[.,/\|\-\s\d]+', series_dict['acquisition_device_processing_description'], flags = regex.UNICODE):
                                                              series_dict['acquisition_device_processing_description'] = None
                                              if series_dict['date'] == study_dict['date']:
                                                      _log.debug('<series date> matches <study date>, ignoring date')
                                                      series_dict['date'] = None
                                              if series_dict['time'] == study_dict['time']:
                                                      _log.debug('<series time> matches <study time>, ignoring time')
                                                      series_dict['time'] = None
                                              for key in series_dict:
                                                      series_dict[key] = cleanup_dicom_string(series_dict[key])
                                              series_dict['all_tags'] = {}
                                              for key in orth_series:
                                                      if key == 'MainDicomTags':
                                                              for mkey in orth_series['MainDicomTags']:
                                                                      series_dict['all_tags'][mkey] = orth_series['MainDicomTags'][mkey].strip()
                                                              continue
                                                      series_dict['all_tags'][key] = orth_series[key]
                                              _log.debug('series: %s', list(series_dict['all_tags']))
                                              for key in series_keys2hide:
                                                      try: del series_dict['all_tags'][key]
                                                      except KeyError: pass
                                              study_dict['operator_name'] = series_dict['operator_name']                      # will collapse all operators into that of the last series
                                              study_dict['radiographer_code'] = series_dict['radiographer_code']      # will collapse all into that of the last series
                                              study_dict['performing_doc'] = series_dict['performing_doc']            # will collapse all into that of the last series
                                              study_dict['series'].append(series_dict)

                      return studies_by_patient

              #--------------------------------------------------------
              # generic REST helpers
              #--------------------------------------------------------
              def run_GET(self, url=None, data=None, allow_cached=False):
                      url = '%s/%s' % (self.__server_url, url)
                      return self.__run_GET(url = url, data = data, allow_cached = allow_cached)

              #--------------------------------------------------------
              def __run_GET(self, url=None, data=None, allow_cached=False, also_return_status=False):
                      if data is None:
                              data = {}
                      headers = {}
                      if not allow_cached:
                              headers['cache-control'] = 'no-cache'
                      params = ''
                      if data:
                              params = '?' + urlencode(data)
                      url_with_params = url + params
                      #_log.debug('URL with parameters: >>>%s<<<', url_with_params)
                      try:
                              response, content = self.__conn.request(url_with_params, 'GET', headers = headers)
                      except (OverflowError, socket.error, http.client.ResponseNotReady, http.client.InvalidURL, http.client.RemoteDisconnected, httplib2.ServerNotFoundError):
                              # http.client.RemoteDisconnected: observed during GET while Orthanc was shutting down for backup
                              _log.exception('exception in GET')
                              _log.debug(' url: %s', url_with_params)
                              _log.debug(' headers: %s', headers)
                              if also_return_status:
                                      return (False, -1)
                              return False

                      if response.status not in [ 200 ]:
                              _log.error('GET returned non-OK status: %s', response.status)
                              _log.debug(' url: %s', url_with_params)
                              _log.debug(' headers: %s', headers)
                              _log.error(' response: %s', response)
                              _log.debug(' content: %s', content)
                              if also_return_status:
                                      return (False, response.status)
                              return False

                      #_log.debug('response: %s', response)
                      #_log.debug('type(content): %s', type(content))
                      content_type = response['content-type'].strip()
                      if content_type.startswith('text/plain'):
                              # utf8 ?
                              # urldecode ?
                              # latin1 = Orthanc default = tools/default-encoding ?
                              # ascii ?
                              content = content.decode('utf8')
                      elif content_type.startswith('application/json'):
                              try:
                                      content = json.loads(content)
                              except Exception:
                                      _log.exception('failed to json.loads(content) despite application/json indicated, returning content and hoping for the best')
                                      mime_type, charset_def = content_type.split(';')
                                      charset = charset_def.strip().split('=')[1]
                                      #content = content.decode('utf8')
                                      content = content.decode(charset)
                              #_log.debug(content)
                      else:
                              _log.error('content: <%s>, not <text/plain> or <application/json> -- returning raw content', content_type)
                      if also_return_status:
                              return (content, response.status)

                      return content

              #--------------------------------------------------------
              def __run_POST(self, url=None, data=None, content_type=None, output_file=None):
                      body = data
                      headers = {'content-type' : content_type}
                      if isinstance(data, str):
                              if content_type is None:
                                      headers['content-type'] = 'text/plain'
                      elif isinstance(data, bytes):
                              if content_type is None:
                                      headers['content-type'] = 'application/octet-stream'
                      else:
                              body = json.dumps(data)
                              headers['content-type'] = 'application/json'

                      try:
                              try:
                                      response, content = self.__conn.request(url, 'POST', body = body, headers = headers)
                              except BrokenPipeError:
                                      _log.debug('retrying after BrokenPipeError')
                                      response, content = self.__conn.request(url, 'POST', body = body, headers = headers)
                      except (socket.error, http.client.ResponseNotReady, OverflowError):
                              _log.exception('exception in POST')
                              _log.debug(' url: %s', url)
                              _log.debug(' headers: %s', headers)
                              _log.debug(' body: %s', body[:16])
                              return False

                      if response.status == 404:
                              _log.debug('no data, response: %s', response)
                              if output_file is None:
                                      return []
                              return False

                      if response.status not in [ 200, 302 ]:
                              _log.error('POST returned non-OK (not 200,302) status: %s', response.status)
                              _log.debug(' url: %s', url)
                              _log.debug(' headers: %s', headers)
                              _log.debug(' body: %s', body[:16])
                              _log.error(' response: %s', response)
                              _log.debug(' content: %s', content)
                              return False

                      try:
                              content = json.loads(content)
                      except Exception:
                              pass
                      if output_file is None:
                              return content

                      output_file.write(content)
                      return True

              #--------------------------------------------------------
              def __run_PUT(self, url=None, data=None, content_type=None):

                      body = data
                      headers = {'content-type' : content_type}
                      if isinstance(data, str):
                              if content_type is None:
                                      headers['content-type'] = 'text/plain'
                      elif isinstance(data, bytes):
                              if content_type is None:
                                      headers['content-type'] = 'application/octet-stream'
                      else:
                              body = json.dumps(data)
                              headers['content-type'] = 'application/json'

                      try:
                              try:
                                      response, content = self.__conn.request(url, 'PUT', body = body, headers = headers)
                              except BrokenPipeError:
                                      response, content = self.__conn.request(url, 'PUT', body = body, headers = headers)
                      except (socket.error, http.client.ResponseNotReady, OverflowError):
                              _log.exception('exception in PUT')
                              _log.debug(' url: %s', url)
                              _log.debug(' headers: %s', headers)
                              _log.debug(' body: %s', body[:16])
                              return False

                      if response.status == 404:
                              _log.debug('no data, response: %s', response)
                              return []
                      if response.status not in [ 200, 302 ]:
                              _log.error('PUT returned non-OK status: %s', response.status)
                              _log.debug(' url: %s', url)
                              _log.debug(' headers: %s', headers)
                              _log.debug(' body: %s', body[:16])
                              _log.error(' response: %s', response)
                              _log.debug(' content: %s', content)
                              return False

                      if response['content-type'].startswith('text/plain'):
                              # utf8 ?
                              # urldecode ?
                              # latin1 = Orthanc default = tools/default-encoding ?
                              # ascii ?
                              return content.decode('utf8')

                      if response['content-type'].startswith('application/json'):
                              try:
                                      return json.loads(content)
                              except Exception:
                                      return content

                      return content

              #--------------------------------------------------------
              def __run_DELETE(self, url=None):
                      try:
                              response, content = self.__conn.request(url, 'DELETE')
                      except (http.client.ResponseNotReady, socket.error, OverflowError):
                              _log.exception('exception in DELETE')
                              _log.debug(' url: %s', url)
                              return False

                      if response.status not in [ 200 ]:
                              _log.error('DELETE returned non-OK status: %s', response.status)
                              _log.debug(' url: %s', url)
                              _log.error(' response: %s', response)
                              _log.debug(' content: %s', content)
                              return False

                      if response['content-type'].startswith('text/plain'):
                              # utf8 ?
                              # urldecode ?
                              # latin1 = Orthanc default = tools/default-encoding ?
                              # ascii ?
                              return content.decode('utf8')

                      if response['content-type'].startswith('application/json'):
                              try:
                                      return json.loads(content)
                              except Exception:
                                      return content

                      return content

              #--------------------------------------------------------
              def _get_server_url(self):
                      return self.__server_url

              server_url = property(_get_server_url)

  ### Instance variables

  `var as_external_id_issuer`
    Expand source code

        def _get_as_external_id_issuer(self):
                # fixed type :: user level instance name :: DICOM AET
                return 'Orthanc::%(Name)s::%(DicomAet)s' % self.__server_identification

  `var server_identification`
    Expand source code

        def _get_server_identification(self):
                try:
                        return self.__server_identification
                except AttributeError:
                        pass
                system_data = self.__run_GET(url = '%s/system' % self.__server_url)
                if system_data is False:
                        _log.error('unable to get server identification')
                        return False
                _log.debug('server: %s', system_data)
                self.__server_identification = system_data

                self.__initial_orthanc_encoding = self.__run_GET(url = '%s/tools/default-encoding' % self.__server_url)
                _log.debug('initial Orthanc encoding: %s', self.__initial_orthanc_encoding)

                # check time skew
                tolerance = 60 # seconds
                client_now_as_utc = pydt.datetime.utcnow()
                start = time.time()
                orthanc_now_str = self.__run_GET(url = '%s/tools/now' % self.__server_url)              # 20180208T165832
                end = time.time()
                query_duration = end - start
                orthanc_now_unknown_tz = pydt.datetime.strptime(orthanc_now_str, '%Y%m%dT%H%M%S')
                _log.debug('GNUmed "now" (UTC): %s', client_now_as_utc)
                _log.debug('Orthanc "now" (UTC): %s', orthanc_now_unknown_tz)
                _log.debug('wire roundtrip (seconds): %s', query_duration)
                _log.debug('maximum skew tolerance (seconds): %s', tolerance)
                if query_duration > tolerance:
                        _log.info('useless to check GNUmed/Orthanc time skew, wire roundtrip (%s) > tolerance (%s)', query_duration, tolerance)
                else:
                        if orthanc_now_unknown_tz > client_now_as_utc:
                                real_skew = orthanc_now_unknown_tz - client_now_as_utc
                        else:
                                real_skew = client_now_as_utc - orthanc_now_unknown_tz
                        _log.info('GNUmed/Orthanc time skew: %s', real_skew)
                        if real_skew > pydt.timedelta(seconds = tolerance):
                                _log.error('GNUmed/Orthanc time skew > tolerance (may be due to timezone differences on Orthanc < v1.3.2)')

                return self.__server_identification

  `var server_url`
    Expand source code

        def _get_server_url(self):
                return self.__server_url

  `var url_browse_patients`
    Expand source code

        def _get_url_browse_patients(self):
                if self.__user is None:
                        return self.__server_url
                return self.__server_url.replace('http://', 'http://%s@' % self.__user)

  ### Methods

  `def connect(self, host, port, user, password, expected_minimal_version=None, expected_name=None, expected_aet=None)`
    Expand source code

        def connect(self, host, port, user, password, expected_minimal_version=None, expected_name=None, expected_aet=None):
                try:
                        int(port)
                except Exception:
                        _log.error('invalid port [%s]', port)
                        return False
                if (host is None) or (host.strip() == ''):
                        host = 'localhost'
                try:
                        self.__server_url = str('http://%s:%s' % (host, port))
                except Exception:
                        _log.exception('cannot create server url from: host [%s] and port [%s]', host, port)
                        return False
                self.__user = user
                self.__password = password
                _log.info('connecting as [%s] to Orthanc server at [%s]', self.__user, self.__server_url)
                cache_dir = os.path.join(gmTools.gmPaths().user_tmp_dir, '.orthanc2gm-cache')
                gmTools.mkdir(cache_dir, 0o700)
                gmTools.create_directory_description_file(directory = cache_dir, readme = 'this directory caches Orthanc REST data, mainly DICOM files')
                _log.debug('using cache directory: %s', cache_dir)
                self.__conn = httplib2.Http(cache = cache_dir)
                self.__conn.add_credentials(self.__user, self.__password)
                _log.debug('connected to server: %s', self.server_identification)
                self.connect_error = ''
                if self.server_identification is False:
                        self.connect_error += 'retrieving server identification failed'
                        return False
                if expected_minimal_version is not None:
                        if version.LooseVersion(self.server_identification['Version']) < version.LooseVersion(expected_minimal_version):
                                _log.error('server too old, needed [%s]', expected_minimal_version)
                                self.connect_error += 'server too old, needed version [%s]' % expected_minimal_version
                                return False
                if expected_name is not None:
                        if self.server_identification['Name'] != expected_name:
                                _log.error('wrong server name, expected [%s]', expected_name)
                                self.connect_error += 'wrong server name, expected [%s]' % expected_name
                                return False
                if expected_aet is not None:
                        if self.server_identification['DicomAet'] != expected_name:
                                _log.error('wrong server AET, expected [%s]', expected_aet)
                                self.connect_error += 'wrong server AET, expected [%s]' % expected_aet
                                return False
                return True

  `def get_instance(self, instance_id: str, filename: str = None, allow_cached: bool = True) ‑> str`
    Expand source code

        def get_instance(self, instance_id:str, filename:str=None, allow_cached:bool=True) -> str:
                if filename is None:
                        filename = gmTools.get_unique_filename(suffix = '.dcm')

                _log.debug('exporting instance [%s] into [%s]', instance_id, filename)
                download_url = '%s/instances/%s/attachments/dicom/data' % (self.__server_url, instance_id)
                f = io.open(filename, 'wb')
                f.write(self.__run_GET(url = download_url, allow_cached = allow_cached))
                f.close()
                return filename

  `def get_instance_dicom_tags(self, instance_id, simplified=True)`
    Expand source code

        def get_instance_dicom_tags(self, instance_id, simplified=True):
                _log.debug('retrieving DICOM tags for instance [%s]', instance_id)
                if simplified:
                        download_url = '%s/instances/%s/simplified-tags' % (self.__server_url, instance_id)
                else:
                        download_url = '%s/instances/%s/tags' % (self.__server_url, instance_id)
                return self.__run_GET(url = download_url, allow_cached = True)

  `def get_instance_preview(self, instance_id, filename=None)`
    Expand source code

        def get_instance_preview(self, instance_id, filename=None):
                if filename is None:
                        filename = gmTools.get_unique_filename(suffix = '.png')
                _log.debug('exporting preview for instance [%s] into [%s]', instance_id, filename)
                download_url = '%s/instances/%s/preview' % (self.__server_url, instance_id)
                f = io.open(filename, 'wb')
                try:
                        f.write(self.__run_GET(url = download_url, allow_cached = True))
                except Exception:
                        _log.exception('cannot retrieve instance')
                        filename = None
                finally:
                        f.close()
                return filename

  `def get_matching_patients(self, person) ‑> list`

    Fetch matching patients from an Orthanc DICOM server.

    Matches are searched for via stored "external ID" and via generically generated ID. The external IDs are fetched from the patient store, must be of type "PACS" and must be marked as issued by the instantiated PACS

    ## Args

    `person`
      a gmPerson.cPerson instance

    ## Returns

    A list of Orthanc patient UIDs.

    Expand source code

        def get_matching_patients(self, person) -> list:
                """Fetch matching patients from an Orthanc DICOM server.

                Matches are searched for via stored "external ID" and
                via generically generated ID. The external IDs are
                fetched from the patient store, must be of type
                "PACS" and must be marked as issued by the
                instantiated PACS <self.>

                Args:
                        person: a gmPerson.cPerson instance

                Returns:
                        A list of Orthanc patient UIDs.
                """
                _log.info('searching for Orthanc patients matching %s', person)
                pacs_ids = person.get_external_ids(id_type = 'PACS', issuer = self.as_external_id_issuer)
                if len(pacs_ids) > 1:
                        _log.error('GNUmed patient has more than one ID for this PACS: %s', pacs_ids)
                        _log.error('the stored-in-GNUmed PACS ID is expected to be unique _per PACS_')
                        return []

                pacs_ids2search_by = []
                pacs_ids2search_by.extend([ pacs_id['value'] for pacs_id in pacs_ids ])
                pacs_ids2search_by.extend(person.suggest_external_ids(target = 'PACS'))
                matching_pats = []
                for pacs_id in pacs_ids2search_by:
                        _log.debug('using PACS ID [%s]', pacs_id)
                        pats = self.get_patients_by_external_id(external_id = pacs_id, fuzzy = False)
                        if len(pats) > 1:
                                _log.warning('more than one Orthanc patient matches PACS ID: %s', pacs_id)
                        matching_pats.extend(pats)
                if not matching_pats:
                        _log.debug('no matching patient found in PACS')
                return matching_pats

  `def get_patient(self, orthanc_id: str)`
    Expand source code

        def get_patient(self, orthanc_id:str):
                patient_data_url = '%s/patients/%s' % (self.__server_url, str(orthanc_id))
                patient_data, status = self.__run_GET(patient_data_url, also_return_status = True)
                if patient_data is False:
                        if status == 404:
                                _log.debug('no such patient: %s', orthanc_id)
                                return {}

                        _log.error('cannot retrieve patient data for [%s]', orthanc_id)
                        return False

                return patient_data

  `def get_patients_by_external_id(self, external_id=None, fuzzy=False)`

    Search for instances by patient ID.

    Expand source code

        def get_patients_by_external_id(self, external_id=None, fuzzy=False):
                """Search for instances by patient ID."""
                _log.info('external ID >>>%s<<< fuzzy [%s]', external_id, fuzzy)
                search_term = external_id.strip().strip('*').strip()
                if fuzzy:
                        search_term = '*%s*' % search_term
                search_data = {
                        'Level': 'Patient',
                        'CaseSensitive': False,
                        'Expand': True,
                        'Query': {'PatientID': search_term}
                }
                matches = self.__run_POST(url = '%s/tools/find' % self.__server_url, data = search_data)
                # paranoia
                for match in matches:
                        self.protect_patient(orthanc_id = match['ID'])
                return matches

  `def get_patients_by_name(self, name_parts=None, gender=None, dob=None, fuzzy=False) ‑> list`

    Search for patients by name.

    ## Returns

    List of patients matching the search term(s).

    Expand source code

        def get_patients_by_name(self, name_parts=None, gender=None, dob=None, fuzzy=False) -> list:
                """Search for patients by name.

                Returns:
                        List of patients matching the search term(s).
                """
                _log.info('name parts %s, gender [%s], dob [%s], fuzzy: [%s]', name_parts, gender, dob, fuzzy)
                if len(name_parts) > 1:
                        return self.get_patients_by_name_parts(name_parts = name_parts, gender = gender, dob = dob, fuzzy = fuzzy)

                search_term = name_parts[0].strip().strip('*').strip()
                if search_term == '':
                        _log.debug('search term empty')
                        return []

                if fuzzy:
                        search_term = '*%s*' % search_term
                search_data = {
                        'Level': 'Patient',
                        'CaseSensitive': False,
                        'Expand': True,
                        'Query': {'PatientName': search_term}
                }
                if gender is not None:
                        gender = _map_gender_gm2dcm[gender.casefold()]
                        if gender is not None:
                                search_data['Query']['PatientSex'] = gender
                if dob is not None:
                        search_data['Query']['PatientBirthDate'] = dob.strftime('%Y%m%d')
                _log.info('server-side C-FIND SCU over REST search, mogrified search data: %s', search_data)
                matches = self.__run_POST(url = '%s/tools/find' % self.__server_url, data = search_data)
                return matches

  `def get_patients_by_name_parts(self, name_parts=None, gender=None, dob=None, fuzzy=False)`
    Expand source code

        def get_patients_by_name_parts(self, name_parts=None, gender=None, dob=None, fuzzy=False):
                # fuzzy: allow partial/substring matches (but not across name part boundaries ',' or '^')
                matching_patients = []
                clean_parts = []
                for part in name_parts:
                        if part.strip() == '':
                                continue
                        clean_parts.append(part.casefold().strip())
                _log.info('client-side patient search, scrubbed search terms: %s', clean_parts)
                pat_ids = self.__run_GET(url = '%s/patients' % self.__server_url)
                if pat_ids is False:
                        _log.error('cannot retrieve patients')
                        return []

                for pat_id in pat_ids:
                        orthanc_pat = self.__run_GET(url = '%s/patients/%s' % (self.__server_url, pat_id))
                        if orthanc_pat is False:
                                _log.error('cannot retrieve patient')
                                continue
                        orthanc_name = orthanc_pat['MainDicomTags']['PatientName'].casefold().strip()
                        if not fuzzy:
                                orthanc_name = orthanc_name.replace(' ', ',').replace('^', ',').split(',')
                        parts_in_orthanc_name = 0
                        for part in clean_parts:
                                if part in orthanc_name:
                                        parts_in_orthanc_name += 1
                        if parts_in_orthanc_name == len(clean_parts):
                                _log.debug('name match: "%s" contains all of %s', orthanc_name, clean_parts)
                                if gender is not None:
                                        gender = _map_gender_gm2dcm[gender.casefold()]
                                        if gender is not None:
                                                if orthanc_pat['MainDicomTags']['PatientSex'].casefold() != gender:
                                                        _log.debug('gender mismatch: dicom=[%s] gnumed=[%s], skipping', orthanc_pat['MainDicomTags']['PatientSex'], gender)
                                                        continue
                                if dob is not None:
                                        if orthanc_pat['MainDicomTags']['PatientBirthDate'] != dob.strftime('%Y%m%d'):
                                                _log.debug('dob mismatch: dicom=[%s] gnumed=[%s], skipping', orthanc_pat['MainDicomTags']['PatientBirthDate'], dob)
                                                continue
                                matching_patients.append(orthanc_pat)
                        else:
                                _log.debug('name mismatch: "%s" does not contain all of %s', orthanc_name, clean_parts)
                return matching_patients

  `def get_studies_as_zip(self, study_ids=None, patient_id=None, filename=None)`
    Expand source code

        def get_studies_as_zip(self, study_ids=None, patient_id=None, filename=None):
                if filename is None:
                        filename = gmTools.get_unique_filename(prefix = r'DCM-', suffix = r'.zip')
                if study_ids is None:
                        _log.info('exporting all studies of patient [%s] into [%s]', patient_id, filename)
                        f = io.open(filename, 'wb')
                        f.write(self.__run_GET(url = '%s/patients/%s/archive' % (self.__server_url, str(patient_id)), allow_cached = True))
                        f.close()
                        return filename

  `def get_studies_list_by_external_id(self, external_id=None)`
    Expand source code

        def get_studies_list_by_external_id(self, external_id=None):
                return self.get_studies_list_by_orthanc_patient_list (
                        orthanc_patients = self.get_patients_by_external_id(external_id = external_id)
                )

  `def get_studies_list_by_orthanc_patient_list(self, orthanc_patients=None)`
    Expand source code

        def get_studies_list_by_orthanc_patient_list(self, orthanc_patients=None):

                study_keys2hide =  ['ModifiedFrom', 'Type', 'ID', 'ParentPatient', 'Series']
                series_keys2hide = ['ModifiedFrom', 'Type', 'ID', 'ParentStudy',   'Instances']

                studies_by_patient = []

                # loop over patients
                for pat in orthanc_patients:
                        pat_dict = {
                                'orthanc_id': pat['ID'],
                                'name': None,
                                'external_id': None,
                                'date_of_birth': None,
                                'gender': None,
                                'studies': []
                        }
                        try:
                                pat_dict['name'] = pat['MainDicomTags']['PatientName'].strip()
                        except KeyError:
                                pass
                        try:
                                pat_dict['external_id'] = pat['MainDicomTags']['PatientID'].strip()
                        except KeyError:
                                pass
                        try:
                                pat_dict['date_of_birth'] = pat['MainDicomTags']['PatientBirthDate'].strip()
                        except KeyError:
                                pass
                        try:
                                pat_dict['gender'] = pat['MainDicomTags']['PatientSex'].strip()
                        except KeyError:
                                pass
                        for key in pat_dict:
                                if pat_dict[key] in ['unknown', '(null)', '']:
                                        pat_dict[key] = None
                                pat_dict[key] = cleanup_dicom_string(pat_dict[key])
                        studies_by_patient.append(pat_dict)

                        # loop over studies of patient
                        orth_studies = self.__run_GET(url = '%s/patients/%s/studies' % (self.__server_url, pat['ID']))
                        if orth_studies is False:
                                _log.error('cannot retrieve studies')
                                return []
                        for orth_study in orth_studies:
                                study_dict = {
                                        'orthanc_id': orth_study['ID'],
                                        'date': None,
                                        'time': None,
                                        'description': None,
                                        'referring_doc': None,
                                        'requesting_doc': None,
                                        'requesting_org': None,
                                        'performing_doc': None,
                                        'operator_name': None,
                                        'radiographer_code': None,
                                        'radiology_org': None,
                                        'radiology_dept': None,
                                        'radiology_org_addr': None,
                                        'station_name': None,
                                        'series': []
                                }
                                try:
                                        study_dict['date'] = orth_study['MainDicomTags']['StudyDate'].strip()
                                except KeyError:
                                        pass
                                try:
                                        study_dict['time'] = orth_study['MainDicomTags']['StudyTime'].strip()
                                except KeyError:
                                        pass
                                try:
                                        study_dict['description'] = orth_study['MainDicomTags']['StudyDescription'].strip()
                                except KeyError:
                                        pass
                                try:
                                        study_dict['referring_doc'] = orth_study['MainDicomTags']['ReferringPhysicianName'].strip()
                                except KeyError:
                                        pass
                                try:
                                        study_dict['requesting_doc'] = orth_study['MainDicomTags']['RequestingPhysician'].strip()
                                except KeyError:
                                        pass
                                try:
                                        study_dict['requesting_org'] = orth_study['MainDicomTags']['RequestingService'].strip()
                                except KeyError:
                                        pass
                                try:
                                        study_dict['radiology_org_addr'] = orth_study['MainDicomTags']['InstitutionAddress'].strip()
                                except KeyError:
                                        pass
                                try:
                                        study_dict['radiology_org'] = orth_study['MainDicomTags']['InstitutionName'].strip()
                                        if study_dict['radiology_org_addr'] is not None:
                                                if study_dict['radiology_org'] in study_dict['radiology_org_addr']:
                                                        study_dict['radiology_org'] = None
                                except KeyError:
                                        pass
                                try:
                                        study_dict['radiology_dept'] = orth_study['MainDicomTags']['InstitutionalDepartmentName'].strip()
                                        if study_dict['radiology_org'] is not None:
                                                if study_dict['radiology_dept'] in study_dict['radiology_org']:
                                                        study_dict['radiology_dept'] = None
                                        if study_dict['radiology_org_addr'] is not None:
                                                if study_dict['radiology_dept'] in study_dict['radiology_org_addr']:
                                                        study_dict['radiology_dept'] = None
                                except KeyError:
                                        pass
                                try:
                                        study_dict['station_name'] = orth_study['MainDicomTags']['StationName'].strip()
                                        if study_dict['radiology_org'] is not None:
                                                if study_dict['station_name'] in study_dict['radiology_org']:
                                                        study_dict['station_name'] = None
                                        if study_dict['radiology_org_addr'] is not None:
                                                if study_dict['station_name'] in study_dict['radiology_org_addr']:
                                                        study_dict['station_name'] = None
                                        if study_dict['radiology_dept'] is not None:
                                                if study_dict['station_name'] in study_dict['radiology_dept']:
                                                        study_dict['station_name'] = None
                                except KeyError:
                                        pass
                                for key in study_dict:
                                        if study_dict[key] in ['unknown', '(null)', '']:
                                                study_dict[key] = None
                                        study_dict[key] = cleanup_dicom_string(study_dict[key])
                                study_dict['all_tags'] = {}
                                try:
                                        orth_study['PatientMainDicomTags']
                                except KeyError:
                                        orth_study['PatientMainDicomTags'] = pat['MainDicomTags']
                                for key in orth_study:
                                        if key == 'MainDicomTags':
                                                for mkey in orth_study['MainDicomTags']:
                                                        study_dict['all_tags'][mkey] = orth_study['MainDicomTags'][mkey].strip()
                                                continue
                                        if key == 'PatientMainDicomTags':
                                                for pkey in orth_study['PatientMainDicomTags']:
                                                        study_dict['all_tags'][pkey] = orth_study['PatientMainDicomTags'][pkey].strip()
                                                continue
                                        study_dict['all_tags'][key] = orth_study[key]
                                _log.debug('study: %s', list(study_dict['all_tags']))
                                for key in study_keys2hide:
                                        try: del study_dict['all_tags'][key]
                                        except KeyError: pass
                                pat_dict['studies'].append(study_dict)

                                # loop over series in study
                                for orth_series_id in orth_study['Series']:
                                        orth_series = self.__run_GET(url = '%s/series/%s' % (self.__server_url, orth_series_id))
                                        ordered_slices = self.__run_GET(url = '%s/series/%s/ordered-slices' % (self.__server_url, orth_series_id))
                                        if ordered_slices is False:
                                                slices = orth_series['Instances']
                                        else:
                                                slices = [ s[0] for s in ordered_slices['SlicesShort'] ]
                                        if orth_series is False:
                                                _log.error('cannot retrieve series')
                                                return []
                                        series_dict = {
                                                'orthanc_id': orth_series['ID'],
                                                'instances': slices,
                                                'modality': None,
                                                'date': None,
                                                'time': None,
                                                'description': None,
                                                'body_part': None,
                                                'protocol': None,
                                                'performed_procedure_step_description': None,
                                                'acquisition_device_processing_description': None,
                                                'operator_name': None,
                                                'radiographer_code': None,
                                                'performing_doc': None
                                        }
                                        try:
                                                series_dict['modality'] = orth_series['MainDicomTags']['Modality'].strip()
                                        except KeyError:
                                                pass
                                        try:
                                                series_dict['date'] = orth_series['MainDicomTags']['SeriesDate'].strip()
                                        except KeyError:
                                                pass
                                        try:
                                                series_dict['description'] = orth_series['MainDicomTags']['SeriesDescription'].strip()
                                        except KeyError:
                                                pass
                                        try:
                                                series_dict['time'] = orth_series['MainDicomTags']['SeriesTime'].strip()
                                        except KeyError:
                                                pass
                                        try:
                                                series_dict['body_part'] = orth_series['MainDicomTags']['BodyPartExamined'].strip()
                                        except KeyError:
                                                pass
                                        try:
                                                series_dict['protocol'] = orth_series['MainDicomTags']['ProtocolName'].strip()
                                        except KeyError:
                                                pass
                                        try:
                                                series_dict['performed_procedure_step_description'] = orth_series['MainDicomTags']['PerformedProcedureStepDescription'].strip()
                                        except KeyError:
                                                pass
                                        try:
                                                series_dict['acquisition_device_processing_description'] = orth_series['MainDicomTags']['AcquisitionDeviceProcessingDescription'].strip()
                                        except KeyError:
                                                pass
                                        try:
                                                series_dict['operator_name'] = orth_series['MainDicomTags']['OperatorsName'].strip()
                                        except KeyError:
                                                pass
                                        try:
                                                series_dict['radiographer_code'] = orth_series['MainDicomTags']['RadiographersCode'].strip()
                                        except KeyError:
                                                pass
                                        try:
                                                series_dict['performing_doc'] = orth_series['MainDicomTags']['PerformingPhysicianName'].strip()
                                        except KeyError:
                                                pass
                                        for key in series_dict:
                                                if series_dict[key] in ['unknown', '(null)', '']:
                                                        series_dict[key] = None
                                        if series_dict['description'] == series_dict['protocol']:
                                                _log.debug('<series description> matches <series protocol>, ignoring protocol')
                                                series_dict['protocol'] = None
                                        if series_dict['performed_procedure_step_description'] in [series_dict['description'], series_dict['protocol']]:
                                                series_dict['performed_procedure_step_description'] = None
                                        if series_dict['performed_procedure_step_description'] is not None:
                                                # weed out "numeric" only
                                                if regex.match ('[.,/\|\-\s\d]+', series_dict['performed_procedure_step_description'], flags = regex.UNICODE):
                                                        series_dict['performed_procedure_step_description'] = None
                                        if series_dict['acquisition_device_processing_description'] in [series_dict['description'], series_dict['protocol']]:
                                                series_dict['acquisition_device_processing_description'] = None
                                        if series_dict['acquisition_device_processing_description'] is not None:
                                                # weed out "numeric" only
                                                if regex.match ('[.,/\|\-\s\d]+', series_dict['acquisition_device_processing_description'], flags = regex.UNICODE):
                                                        series_dict['acquisition_device_processing_description'] = None
                                        if series_dict['date'] == study_dict['date']:
                                                _log.debug('<series date> matches <study date>, ignoring date')
                                                series_dict['date'] = None
                                        if series_dict['time'] == study_dict['time']:
                                                _log.debug('<series time> matches <study time>, ignoring time')
                                                series_dict['time'] = None
                                        for key in series_dict:
                                                series_dict[key] = cleanup_dicom_string(series_dict[key])
                                        series_dict['all_tags'] = {}
                                        for key in orth_series:
                                                if key == 'MainDicomTags':
                                                        for mkey in orth_series['MainDicomTags']:
                                                                series_dict['all_tags'][mkey] = orth_series['MainDicomTags'][mkey].strip()
                                                        continue
                                                series_dict['all_tags'][key] = orth_series[key]
                                        _log.debug('series: %s', list(series_dict['all_tags']))
                                        for key in series_keys2hide:
                                                try: del series_dict['all_tags'][key]
                                                except KeyError: pass
                                        study_dict['operator_name'] = series_dict['operator_name']                      # will collapse all operators into that of the last series
                                        study_dict['radiographer_code'] = series_dict['radiographer_code']      # will collapse all into that of the last series
                                        study_dict['performing_doc'] = series_dict['performing_doc']            # will collapse all into that of the last series
                                        study_dict['series'].append(series_dict)

                return studies_by_patient

  `def get_studies_list_by_patient_name(self, name_parts=None, gender=None, dob=None, fuzzy=False)`
    Expand source code

        def get_studies_list_by_patient_name(self, name_parts=None, gender=None, dob=None, fuzzy=False):
                return self.get_studies_list_by_orthanc_patient_list (
                        orthanc_patients = self.get_patients_by_name(name_parts = name_parts, gender = gender, dob = dob, fuzzy = fuzzy)
                )

  `def get_studies_with_dicomdir(self, study_ids=None, patient_id=None, target_dir=None, filename=None, create_zip=False)`
    Expand source code

        def get_studies_with_dicomdir(self, study_ids=None, patient_id=None, target_dir=None, filename=None, create_zip=False):

                if filename is None:
                        filename = gmTools.get_unique_filename(prefix = r'DCM-', suffix = r'.zip', tmp_dir = target_dir)

                # all studies
                if study_ids is None:
                        if patient_id is None:
                                raise ValueError('<patient_id> must be defined if <study_ids> is None')
                        _log.info('exporting all studies of patient [%s] into [%s]', patient_id, filename)
                        f = io.open(filename, 'wb')
                        url = '%s/patients/%s/media' % (self.__server_url, str(patient_id))
                        _log.debug(url)
                        f.write(self.__run_GET(url = url, allow_cached = True))
                        f.close()
                        if create_zip:
                                return filename
                        if target_dir is None:
                                target_dir = gmTools.mk_sandbox_dir(prefix = 'dcm-')
                        if not gmTools.unzip_archive(filename, target_dir = target_dir, remove_archive = True):
                                return False
                        return target_dir

                # selection of studies
                _log.info('exporting %s studies into [%s]', len(study_ids), filename)
                _log.debug('studies: %s', study_ids)
                f = io.open(filename, 'wb')
                #  You have to make a POST request against URI "/tools/create-media", with a
                #  JSON body that contains the array of the resources of interest (as Orthanc
                #  identifiers). Here is a sample command-line:
                #  curl -X POST http://localhost:8042/tools/create-media -d '["8c4663df-c3e66066-9e20a8fc-dd14d1e5-251d3d84","2cd4848d-02f0005f-812ffef6-a210bbcf-3f01a00a","6eeded74-75005003-c3ae9738-d4a06a4f-6beedeb8","8a622020-c058291c-7693b63f-bc67aa2e-0a02e69c"]' -v > /tmp/a.zip
                #  (this will not create duplicates but will also not check for single-patient-ness)
                url = '%s/tools/create-media-extended' % self.__server_url
                _log.debug(url)
                try:
                        downloaded = self.__run_POST(url = url, data = study_ids, output_file = f)
                        if not downloaded:
                                _log.error('this Orthanc version probably does not support "create-media-extended"')
                except TypeError:
                        f.close()
                        _log.exception('cannot retrieve multiple studies as one archive with DICOMDIR, probably not supported by this Orthanc version')
                        return False
                # retry with old URL
                if not downloaded:
                        url = '%s/tools/create-media' % self.__server_url
                        _log.debug('retrying: %s', url)
                        try:
                                downloaded = self.__run_POST(url = url, data = study_ids, output_file = f)
                                if not downloaded:
                                        return False
                        except TypeError:
                                _log.exception('cannot retrieve multiple studies as one archive with DICOMDIR, probably not supported by this Orthanc version')
                                return False
                        finally:
                                f.close()
                if create_zip:
                        return filename
                if target_dir is None:
                        target_dir = gmTools.mk_sandbox_dir(prefix = 'dcm-')
                        _log.debug('exporting studies into [%s]', target_dir)
                if not gmTools.unzip_archive(filename, target_dir = target_dir, remove_archive = True):
                        return False
                return target_dir

  `def get_study_as_zip(self, study_id=None, filename=None)`
    Expand source code

        def get_study_as_zip(self, study_id=None, filename=None):
                if filename is None:
                        filename = gmTools.get_unique_filename(prefix = r'DCM-', suffix = r'.zip')
                _log.info('exporting study [%s] into [%s]', study_id, filename)
                f = io.open(filename, 'wb')
                f.write(self.__run_GET(url = '%s/studies/%s/archive' % (self.__server_url, str(study_id)), allow_cached = True))
                f.close()
                return filename

  `def get_study_as_zip_with_dicomdir(self, study_id=None, filename=None)`
    Expand source code

        def get_study_as_zip_with_dicomdir(self, study_id=None, filename=None):
                if filename is None:
                        filename = gmTools.get_unique_filename(prefix = r'DCM-', suffix = r'.zip')
                _log.info('exporting study [%s] into [%s]', study_id, filename)
                f = io.open(filename, 'wb')
                f.write(self.__run_GET(url = '%s/studies/%s/media' % (self.__server_url, str(study_id)), allow_cached = True))
                f.close()
                return filename

  `def get_url_browse_patient(self, patient_id)`
    Expand source code

        def get_url_browse_patient(self, patient_id):
                # http://localhost:8042/#patient?uuid=0da01e38-cf792452-65c1e6af-b77faf5a-b637a05b
                return '%s/#patient?uuid=%s' % (self.url_browse_patients, patient_id)

  `def get_url_browse_study(self, study_id)`
    Expand source code

        def get_url_browse_study(self, study_id):
                # http://localhost:8042/#study?uuid=0da01e38-cf792452-65c1e6af-b77faf5a-b637a05b
                return '%s/#study?uuid=%s' % (self.url_browse_patients, study_id)

  `def modify_patient_id(self, old_patient_id, new_patient_id)`

    Modify the patient ID stored in Orthanc.

    This changes all DICOM files of the patient, identified via (DICOM level) old_patient_id, to contain the new_patient_id. It will update the associated Orthanc metadata DB entries accordingly.

    Expand source code

        def modify_patient_id(self, old_patient_id, new_patient_id):
                """Modify the patient ID stored in Orthanc.

                This changes all DICOM files of the patient,
                identified via (DICOM level) old_patient_id, to
                contain the new_patient_id. It will update the
                associated Orthanc metadata DB entries accordingly.
                """
                if old_patient_id == new_patient_id:
                        return True

                modify_data = {
                        'Replace': {
                                'PatientID': new_patient_id
                                #,u'0010,0021': praxis.name / "GNUmed vX.X.X"
                                #,u'0010,1002': series of (old) patient IDs
                        }
                        , 'Force': True
                        # "Keep" doesn't seem to do what it suggests ATM
                        #, u'Keep': True
                }
                orth_pat_defs = self.get_patients_by_external_id(external_id = old_patient_id)
                all_modified = True
                for orth_pat_def in orth_pat_defs:
                        _log.info('modifying Orthanc patient [%s]: DICOM ID [%s] -> [%s]', orth_pat_def['ID'], old_patient_id, new_patient_id)
                        old_pat_data = self.get_patient(orth_pat_def['ID'])
                        _log.debug('to be modified: %s', old_pat_data)
                        if self.patient_is_protected(orth_pat_def['ID']):
                                _log.debug('patient protected: %s, unprotecting for modification', orth_pat_def['ID'])
                                if not self.unprotect_patient(orth_pat_def['ID']):
                                        _log.error('cannot unlock patient [%s], skipping', orth_pat_def['ID'])
                                        all_modified = False
                                        continue
                                was_protected = True
                        else:
                                was_protected = False
                        pat_url = '%s/patients/%s' % (self.__server_url, orth_pat_def['ID'])
                        modify_url = '%s/modify' % pat_url
                        result = self.__run_POST(modify_url, data = modify_data)
                        _log.debug('modify result: %s', result)
                        if result is False:
                                _log.error('cannot modify patient [%s]', orth_pat_def['ID'])
                                all_modified = False
                                continue
                        newly_created_orthanc_patient_id = result['ID']
                        _log.info('newly created Orthanc patient ID: %s', newly_created_orthanc_patient_id)
                        mod_pat_data = self.get_patient(newly_created_orthanc_patient_id)
                        _log.debug('modified pat: %s', mod_pat_data)
                        _log.debug('deleting archived patient: %s', self.__run_DELETE(pat_url))
                        if was_protected:
                                if not self.protect_patient(newly_created_orthanc_patient_id):
                                        _log.error('cannot re-lock (new) patient [%s]', newly_created_orthanc_patient_id)

                return all_modified

  `def patient_is_protected(self, orthanc_id)`
    Expand source code

        def patient_is_protected(self, orthanc_id):
                url = '%s/patients/%s/protected' % (self.__server_url, str(orthanc_id))
                return (self.__run_GET(url) == 1)

  `def protect_patient(self, orthanc_id: str)`
    Expand source code

        def protect_patient(self, orthanc_id:str):
                url = '%s/patients/%s/protected' % (self.__server_url, str(orthanc_id))
                if self.__run_GET(url) == 1:
                        _log.debug('patient already protected: %s', orthanc_id)
                        return True
                _log.warning('patient [%s] not protected against recycling, enabling protection now', orthanc_id)
                self.__run_PUT(url = url, data = '1')
                if self.__run_GET(url) == 1:
                        return True
                _log.error('cannot protect patient [%s] against recycling', orthanc_id)
                return False

  `def run_GET(self, url=None, data=None, allow_cached=False)`
    Expand source code

        def run_GET(self, url=None, data=None, allow_cached=False):
                url = '%s/%s' % (self.__server_url, url)
                return self.__run_GET(url = url, data = data, allow_cached = allow_cached)

  `def search_studies_by_patient_id(self, patient_id: str) ‑> list`

    Search for studies with the given patient ID snippet.

    This relates to the external world patient ID as stored in DICOM instances, not the Orthanc DB metadata level patient UID.

    ## Args

    `patient_id`
      patient ID snippet to search for

    ## Returns

    The list of matching studies (not patient).

    Expand source code

        def search_studies_by_patient_id(self, patient_id:str) -> list:
                """Search for studies with the given patient ID snippet.

                This relates to the external world patient ID as
                stored in DICOM instances, not the Orthanc DB
                metadata level patient UID.

                Args:
                        patient_id: patient ID snippet to search for

                Returns:
                        The list of matching *studies* (not *patient*).
                """
                _log.debug('search term >>>%s<<<', patient_id)
                search_term = patient_id.strip().strip('*').strip()
                search_term = '*%s*' % search_term
                search_data = {
                        'Level': 'Study',
                        'CaseSensitive': False,
                        'Expand': True,
                        'Query': {'PatientID': search_term}
                }
                matches = self.__run_POST(url = '%s/tools/find' % self.__server_url, data = search_data)
                return matches

  `def search_studies_by_patient_name(self, name: str) ‑> list`

    Search for studies with the given patient name snippet.

    A study (even at the Orthanc DB metadata level) will contain the original patient name (unless manually modified) in contrast to the (artificial Orthanc DB metadata level) patient record. The latter contains the first patient name that had been associated with the given patient ID.

    ## Args

    `name` :`str`
      name snippet to search for

    ## Returns

    The list of matching studies (not patient).

    Expand source code

        def search_studies_by_patient_name(self, name:str) -> list:
                """Search for studies with the given patient name snippet.

                A study (even at the Orthanc DB metadata level) will
                contain the original patient name (unless manually
                modified) in contrast to the (artificial Orthanc DB
                metadata level) patient record. The latter contains
                the first patient name that had been associated with
                the given patient ID.

                Args:
                        name (str): name snippet to search for

                Returns:
                        The list of matching *studies* (not *patient*).
                """
                _log.debug('search term [%s]', name)
                search_term = name.strip().strip('*').strip()
                if search_term == '':
                        _log.warning('search term empty')
                        return []

                search_term = '*%s*' % search_term
                search_data = {
                        'Level': 'Study',
                        'CaseSensitive': False,
                        'Expand': True,
                        'Query': {'PatientName': search_term}
                }
                matches = self.__run_POST(url = '%s/tools/find' % self.__server_url, data = search_data)
                return matches

  `def unprotect_patient(self, orthanc_id)`
    Expand source code

        def unprotect_patient(self, orthanc_id):
                url = '%s/patients/%s/protected' % (self.__server_url, str(orthanc_id))
                if self.__run_GET(url) == 0:
                        return True
                _log.info('patient [%s] protected against recycling, disabling protection now', orthanc_id)
                self.__run_PUT(url = url, data = '0')
                if self.__run_GET(url) == 0:
                        return True
                _log.error('cannot unprotect patient [%s] against recycling', orthanc_id)
                return False

  `def upload_by_DICOMDIR(self, DICOMDIR=None)`
    Expand source code

        def upload_by_DICOMDIR(self, DICOMDIR=None):
                pass

  `def upload_dicom_file(self, filename: str, check_mime_type: bool = False) ‑> bool`

    Update a DICOM file.

    Will silently ignore DICOMDIR files (which are application/dicom but Orthanc does not process them).

    ## Args

    `filename`
      DICOM file to upload
    `check_mime_type`
      whether to check the file for being application/dicom, and to fail if not

    ## Returns

    True/False

    Expand source code

        def upload_dicom_file(self, filename:str, check_mime_type:bool=False) -> bool:
                """Update a DICOM file.

                Will silently ignore DICOMDIR files (which are application/dicom but
                Orthanc does not process them).

                Args:
                        filename: DICOM file to upload
                        check_mime_type: whether to check the file for being application/dicom, and to fail if not

                Returns:
                        True/False
                """
                _log.info('processing: %s', filename)
                if gmTools.fname_stem(filename) == 'DICOMDIR':
                        _log.debug('ignoring, no use uploading DICOMDIR files to Orthanc')
                        return True

                if check_mime_type:
                        mimetype = gmMimeLib.guess_mimetype(filename)
                        if mimetype != 'application/dicom':
                                _log.error('not considered a DICOM (application/dicom) file: %s, not uploading', mimetype)
                                return False

                try:
                        f = io.open(filename, 'rb')
                except Exception:
                        _log.exception('failed to open file')
                        return False

                dcm_data = f.read()
                f.close()
                upload_url = '%s/instances' % self.__server_url
                uploaded = self.__run_POST(upload_url, data = dcm_data, content_type = 'application/dicom')
                if uploaded is False:
                        _log.error('upload failed')
                        return False

                # typically a 404 following the upload of a DICOM file w/o identifiers
                if uploaded == []:
                        _log.error('upload failed')
                        return False

                _log.debug(uploaded)
                # paranoia, as is our custom
                verified = self.verify_instance (
                        instance_id = uploaded['ID'],
                        filename = filename,
                        attempt_download = True
                )
                return verified

  `def upload_dicom_files(self, files=None, check_mime_type=False)`
    Expand source code

        def upload_dicom_files(self, files=None, check_mime_type=False):
                uploaded = []
                not_uploaded = []
                for filename in files:
                        success = self.upload_dicom_file(filename, check_mime_type = check_mime_type)
                        if success:
                                uploaded.append(filename)
                                continue
                        not_uploaded.append(filename)

                if len(not_uploaded) > 0:
                        _log.error('not all files uploaded')
                return (uploaded, not_uploaded)

  `def upload_from_directory(self, directory=None, recursive=False, check_mime_type=False, ignore_other_files=True)`
    Expand source code

        def upload_from_directory(self, directory=None, recursive=False, check_mime_type=False, ignore_other_files=True):

                #--------------------
                def _on_error(exc):
                        _log.error('DICOM (?) file not accessible: %s', exc.filename)
                        _log.error(exc)
                #--------------------

                _log.debug('uploading DICOM files from [%s]', directory)
                if not recursive:
                        files2try = os.listdir(directory)
                        _log.debug('found %s files', len(files2try))
                        if ignore_other_files:
                                files2try = [ f for f in files2try if gmMimeLib.guess_mimetype(f) == 'application/dicom' ]
                                _log.debug('DICOM files therein: %s', len(files2try))
                        return self.upload_dicom_files(files = files2try, check_mime_type = check_mime_type)

                _log.debug('recursing for DICOM files')
                uploaded = []
                not_uploaded = []
                for curr_root, curr_root_subdirs, curr_root_files in os.walk(directory, onerror = _on_error):
                        _log.debug('recursing into [%s]', curr_root)
                        files2try = [ os.path.join(curr_root, f) for f in curr_root_files ]
                        _log.debug('found %s files', len(files2try))
                        if ignore_other_files:
                                files2try = [ f for f in files2try if gmMimeLib.guess_mimetype(f) == 'application/dicom' ]
                                _log.debug('DICOM files therein: %s', len(files2try))
                        up, not_up = self.upload_dicom_files (
                                files = files2try,
                                check_mime_type = check_mime_type
                        )
                        uploaded.extend(up)
                        not_uploaded.extend(not_up)

                return (uploaded, not_uploaded)

  `def verify_instance(self, instance_id: str, filename: str = None, attempt_download: bool = False) ‑> bool`
    Expand source code

        def verify_instance(self, instance_id:str, filename:str=None, attempt_download:bool=False) -> bool:

                _BINARY_ATTACHMENTS = ['dicom']

                _log.debug('verifying instance [%s] against file [%s]', instance_id, filename)
                is_valid = True

                attachments_url = '%s/instances/%s/attachments' % (self.__server_url, instance_id)
                attachments = self.__run_GET(attachments_url, allow_cached = False)
                if not attachments:
                        _log.error('cannot retrieve instance attachment list')
                        return False

                for attachment in attachments:
                        md5_orthanc = None
                        # 1) verify MD5 inside Orthanc, if available (checks Orthanc storage corruption)
                        available_fields_url = '%s/instances/%s/attachments/%s' % (self.__server_url, instance_id, attachment)
                        available_fields = self.__run_GET(available_fields_url, allow_cached = False)
                        if 'md5' in available_fields:
                                md5_url = '%s/md5' % available_fields_url
                                md5_orthanc = self.__run_GET(md5_url)
                                verify_url = '%s/%s/verify-md5' % (attachments_url, attachment)
                                if self.__run_POST(verify_url) is False:
                                        _log.error('MD5 verification failed, instance [%s], attachment=%s, url [%s]', instance_id, attachment, verify_url)
                                        _log.error('potentially Orthanc storage corruption')
                                        is_valid = False
                                else:
                                        _log.debug('MD5: Orthanc DB <-> Orthanc storage: match')
                        else:
                                _log.debug('MD5 of instance attachment not available in Orthanc, cannot verify backend storage status')
                        # 2) verify instance attachment can be downloaded
                        md5_downloaded = None
                        if attempt_download:
                                attachment_filename = gmTools.get_unique_filename()
                                download_url = '%s/instances/%s/attachments/%s/data' % (self.__server_url, instance_id, attachment)
                                attachment_data = self.__run_GET(url = download_url, allow_cached = False)
                                if isinstance(attachment_data, bytes):
                                        attachment_file = io.open(attachment_filename, 'wb')
                                else:
                                        attachment_file = io.open(attachment_filename, 'wt')
                                        attachment_data = '%s' % attachment_data
                                attachment_file.write(attachment_data)
                                del attachment_data
                                attachment_file.close()
                                _log.debug('download: Orthanc -> localhost: success')
                                if attachment not in _BINARY_ATTACHMENTS:
                                        _log.info('attachment of type [%s] not binary, cannot verify MD5 of download or local file against MD5 in Orthanc, skipping', attachment)
                                        continue
                                md5_downloaded = gmTools.file2md5(attachment_filename)
                        else:
                                _log.debug('not downloading instance for verification')
                        # 3) verify MD5 of downloaded instance against Orthanc, if possible
                        if md5_downloaded and md5_orthanc:
                                if md5_downloaded == md5_orthanc:
                                        _log.debug('MD5: Orthanc DB <-> localhost: match')
                                else:
                                        _log.error('MD5 mismatch: Orthanc DB <-> localhost')
                                        _log.error('download: %s', md5_downloaded)
                                        _log.error('Orthanc : %s', md5_orthanc)
                                        is_valid = False
                        if filename:
                                md5_local = gmTools.file2md5(filename)
                        else:
                                _log.debug('local file not available for verification')
                                md5_local = None
                        # 4) verify MD5 of download against local file
                        if md5_downloaded and md5_local:
                                if md5_downloaded == md5_local:
                                        _log.debug('MD5: downloaded <-> pre-existing: match')
                                else:
                                        _log.error('MD5 mismatch: downloaded <-> pre-existing')
                                        _log.error('download: %s', md5_downloaded)
                                        _log.error('locally : %s', md5_local)
                                        is_valid = False
                        # 5) verify MD5 of local file against Orthanc
                        if md5_local and md5_orthanc:
                                if md5_local == md5_orthanc:
                                        _log.debug('MD5: Orthanc DB <-> pre-existing: match')
                                else:
                                        _log.error('MD5 mismatch: Orthanc DB <-> pre-existing')
                                        _log.error('locally : %s', md5_local)
                                        _log.error('Orthanc : %s', md5_orthanc)
                                        is_valid = False
                        # 6) consider comparing the raw pixel data or comparing the output of exiftool etc

                _log.debug('verified: %s', is_valid)
                return is_valid

  `def verify_patient_data(self, orthanc_id)`
    Expand source code

        def verify_patient_data(self, orthanc_id):
                _log.info('verifying DICOM data of patient [%s]', orthanc_id)
                bad_data = []
                instances_url = '%s/patients/%s/instances' % (self.__server_url, orthanc_id)
                instances = self.__run_GET(instances_url)
                for instance in instances:
                        instance_id = instance['ID']
                        attachments_url = '%s/instances/%s/attachments' % (self.__server_url, instance_id)
                        attachments = self.__run_GET(attachments_url, allow_cached = True)
                        for attachment in attachments:
                                verify_url = '%s/%s/verify-md5' % (attachments_url, attachment)
                                # False, success = "{}"
                                #2018-02-08 19:11:27  ERROR     gm.dicom      [-1211701504 MainThread]  (gmDICOM.py::__run_POST() #986): cannot POST: http://localhost:8042/instances/5a8206f4-24619e76-6650d9cd-792cdf25-039e96e6/attachments/dicom-as-json/verify-md5
                                #2018-02-08 19:11:27  ERROR     gm.dicom      [-1211701504 MainThread]  (gmDICOM.py::__run_POST() #987): response: {'status': '400', 'content-length': '0'}
                                if self.__run_POST(verify_url) is not False:
                                        continue
                                _log.error('bad MD5 of DICOM file at url [%s]: patient=%s, attachment_type=%s', verify_url, orthanc_id, attachment)
                                bad_data.append({'patient': orthanc_id, 'instance': instance_id, 'type': attachment, 'orthanc': '%s [%s]' % (self.server_identification, self.__server_url)})

                return bad_data