# Module `Gnumed.business.gmDocuments`

This module encapsulates a document stored in a GNUmed database.

Expand source code

    """This module encapsulates a document stored in a GNUmed database."""
    #============================================================
    __author__ = "Karsten Hilbert <Karsten.Hilbert@gmx.net>"
    __license__ = "GPL v2 or later"

    import sys
    import os
    import time
    import logging

    if __name__ == '__main__':
            sys.path.insert(0, '../../')
            _ = lambda x:x
    from Gnumed.pycommon import gmExceptions
    from Gnumed.pycommon import gmBusinessDBObject
    from Gnumed.pycommon import gmPG2
    from Gnumed.pycommon import gmTools
    from Gnumed.pycommon import gmMimeLib
    from Gnumed.pycommon import gmDateTime
    from Gnumed.pycommon import gmWorkerThread

    from Gnumed.business import gmOrganization

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

    MUGSHOT=26
    DOCUMENT_TYPE_VISUAL_PROGRESS_NOTE = 'visual progress note'
    DOCUMENT_TYPE_PRESCRIPTION = 'prescription'

    #============================================================
    class cDocumentFolder:
            """Represents a folder with medical documents for a single patient."""

            def __init__(self, aPKey = None):
                    """Fails if

                    - patient referenced by aPKey does not exist
                    """
                    self.pk_patient = aPKey                 # == identity.pk == primary key
                    if not self._pkey_exists():
                            raise gmExceptions.ConstructorError("No patient with PK [%s] in database." % aPKey)

                    # register backend notification interests
                    # (keep this last so we won't hang on threads when
                    #  failing this constructor for other reasons ...)
    #               if not self._register_interests():
    #                       raise gmExceptions.ConstructorError, "cannot register signal interests"

                    _log.debug('instantiated document folder for patient [%s]' % self.pk_patient)
            #--------------------------------------------------------
            def cleanup(self):
                    pass
            #--------------------------------------------------------
            # internal helper
            #--------------------------------------------------------
            def _pkey_exists(self):
                    """Does this primary key exist ?

                    - true/false/None
                    """
                    # patient in demographic database ?
                    rows, idx = gmPG2.run_ro_queries(queries = [
                            {'cmd': "select exists(select pk from dem.identity where pk = %s)", 'args': [self.pk_patient]}
                    ])
                    if not rows[0][0]:
                            _log.error("patient [%s] not in demographic database" % self.pk_patient)
                            return None
                    return True
            #--------------------------------------------------------
            # API
            #--------------------------------------------------------
            def get_latest_freediams_prescription(self):
                    cmd = """
                            SELECT pk_doc
                            FROM blobs.v_doc_med
                            WHERE
                                    pk_patient = %(pat)s
                                            AND
                                    type = %(typ)s
                                            AND
                                    ext_ref = %(ref)s
                            ORDER BY
                                    clin_when DESC
                            LIMIT 1
                    """
                    args = {
                            'pat': self.pk_patient,
                            'typ': DOCUMENT_TYPE_PRESCRIPTION,
                            'ref': 'FreeDiams'
                    }
                    rows, idx = gmPG2.run_ro_queries(queries = [{'cmd': cmd, 'args': args}])
                    if len(rows) == 0:
                            _log.info('no FreeDiams prescription available for patient [%s]' % self.pk_patient)
                            return None
                    prescription = cDocument(aPK_obj = rows[0][0])
                    return prescription

            #--------------------------------------------------------
            def get_latest_mugshot(self):
                    cmd = "SELECT pk_obj FROM blobs.v_latest_mugshot WHERE pk_patient = %s"
                    rows, idx = gmPG2.run_ro_queries(queries = [{'cmd': cmd, 'args': [self.pk_patient]}])
                    if len(rows) == 0:
                            _log.info('no mugshots available for patient [%s]' % self.pk_patient)
                            return None
                    return cDocumentPart(aPK_obj = rows[0][0])

            latest_mugshot = property(get_latest_mugshot, lambda x:x)

            #--------------------------------------------------------
            def get_mugshot_list(self, latest_only=True):
                    if latest_only:
                            cmd = "select pk_doc, pk_obj from blobs.v_latest_mugshot where pk_patient=%s"
                    else:
                            cmd = """
                                    select
                                            vdm.pk_doc as pk_doc,
                                            dobj.pk as pk_obj
                                    from
                                            blobs.v_doc_med vdm
                                            blobs.doc_obj dobj
                                    where
                                            vdm.pk_type = (select pk from blobs.doc_type where name = 'patient photograph')
                                            and vdm.pk_patient = %s
                                            and dobj.fk_doc = vdm.pk_doc
                            """
                    rows, idx = gmPG2.run_ro_queries(queries = [{'cmd': cmd, 'args': [self.pk_patient]}])
                    return rows

            #--------------------------------------------------------
            def get_doc_list(self, doc_type=None):
                    """return flat list of document IDs"""

                    args = {
                            'ID': self.pk_patient,
                            'TYP': doc_type
                    }

                    cmd = """
                            select vdm.pk_doc
                            from blobs.v_doc_med vdm
                            where
                                    vdm.pk_patient = %%(ID)s
                                    %s
                            order by vdm.clin_when"""

                    if doc_type is None:
                            cmd = cmd % ''
                    else:
                            try:
                                    int(doc_type)
                                    cmd = cmd % 'and vdm.pk_type = %(TYP)s'
                            except (TypeError, ValueError):
                                    cmd = cmd % 'and vdm.pk_type = (select pk from blobs.doc_type where name = %(TYP)s)'

                    rows, idx = gmPG2.run_ro_queries(queries = [{'cmd': cmd, 'args': args}])
                    doc_ids = []
                    for row in rows:
                            doc_ids.append(row[0])
                    return doc_ids

            #--------------------------------------------------------
            def get_visual_progress_notes(self, episodes=None, encounter=None):
                    return self.get_documents (
                            doc_type = DOCUMENT_TYPE_VISUAL_PROGRESS_NOTE,
                            pk_episodes = episodes,
                            encounter = encounter
                    )

            #--------------------------------------------------------
            def get_unsigned_documents(self):
                    args = {'pat': self.pk_patient}
                    cmd = _SQL_get_document_fields % """
                            pk_doc IN (
                                    SELECT DISTINCT ON (b_vo.pk_doc) b_vo.pk_doc
                                    FROM blobs.v_obj4doc_no_data b_vo
                                    WHERE
                                            pk_patient = %(pat)s
                                                    AND
                                            reviewed IS FALSE
                            )
                            ORDER BY clin_when DESC"""
                    rows, idx = gmPG2.run_ro_queries(queries = [{'cmd': cmd, 'args': args}], get_col_idx = True)
                    return [ cDocument(row = {'pk_field': 'pk_doc', 'idx': idx, 'data': r}) for r in rows ]

            #--------------------------------------------------------
            def get_documents(self, doc_type=None, pk_episodes=None, encounter=None, order_by=None, exclude_unsigned=False, pk_types=None):
                    """Return list of documents."""

                    args = {
                            'pat': self.pk_patient,
                            'type': doc_type,
                            'enc': encounter
                    }
                    where_parts = ['pk_patient = %(pat)s']

                    if doc_type is not None:
                            try:
                                    int(doc_type)
                                    where_parts.append('pk_type = %(type)s')
                            except (TypeError, ValueError):
                                    where_parts.append('pk_type = (SELECT pk FROM blobs.doc_type WHERE name = %(type)s)')

                    if pk_types is not None:
                            where_parts.append('pk_type IN %(pk_types)s')
                            args['pk_types'] = tuple(pk_types)

                    if (pk_episodes is not None) and (len(pk_episodes) > 0):
                            where_parts.append('pk_episode IN %(epis)s')
                            args['epis'] = tuple(pk_episodes)

                    if encounter is not None:
                            where_parts.append('pk_encounter = %(enc)s')

                    if exclude_unsigned:
                            where_parts.append('pk_doc IN (SELECT b_vo.pk_doc FROM blobs.v_obj4doc_no_data b_vo WHERE b_vo.pk_patient = %(pat)s AND b_vo.reviewed IS TRUE)')

                    if order_by is None:
                            order_by = 'ORDER BY clin_when'

                    cmd = "%s\n%s" % (_SQL_get_document_fields % ' AND '.join(where_parts), order_by)
                    rows, idx = gmPG2.run_ro_queries(queries = [{'cmd': cmd, 'args': args}], get_col_idx = True)

                    return [ cDocument(row = {'pk_field': 'pk_doc', 'idx': idx, 'data': r}) for r in rows ]

            documents = property(get_documents, lambda x:x)

            #--------------------------------------------------------
            def add_document(self, document_type=None, encounter=None, episode=None, link_obj=None):
                    return create_document(link_obj = link_obj, document_type = document_type, encounter = encounter, episode = episode)

            #--------------------------------------------------------
            def add_prescription(self, encounter=None, episode=None, link_obj=None):
                    return self.add_document (
                            link_obj = link_obj,
                            document_type = create_document_type (
                                    document_type = DOCUMENT_TYPE_PRESCRIPTION
                            )['pk_doc_type'],
                            encounter = encounter,
                            episode = episode
                    )

            #--------------------------------------------------------
            def _get_all_document_org_units(self):
                    cmd = gmOrganization._SQL_get_org_unit % (
                            'pk_org_unit IN (SELECT DISTINCT ON (pk_org_unit) pk_org_unit FROM blobs.v_doc_med WHERE pk_patient = %(pat)s)'
                    )
                    args = {'pat': self.pk_patient}
                    rows, idx = gmPG2.run_ro_queries(queries = [{'cmd': cmd, 'args': args}], get_col_idx = True)
                    return [ gmOrganization.cOrgUnit(row = {'data': r, 'idx': idx, 'pk_field': 'pk_org_unit'}) for r in rows ]

            all_document_org_units = property(_get_all_document_org_units, lambda x:x)

    #============================================================
    _SQL_get_document_part_fields = "select * from blobs.v_obj4doc_no_data where %s"

    class cDocumentPart(gmBusinessDBObject.cBusinessDBObject):
            """Represents one part of a medical document."""

            _cmd_fetch_payload = _SQL_get_document_part_fields % "pk_obj = %s"
            _cmds_store_payload = [
                    """UPDATE blobs.doc_obj SET
                                    seq_idx = %(seq_idx)s,
                                    comment = gm.nullify_empty_string(%(obj_comment)s),
                                    filename = gm.nullify_empty_string(%(filename)s),
                                    fk_intended_reviewer = %(pk_intended_reviewer)s
                            WHERE
                                    pk = %(pk_obj)s
                                            AND
                                    xmin = %(xmin_doc_obj)s
                            RETURNING
                                    xmin AS xmin_doc_obj"""
            ]
            _updatable_fields = [
                    'seq_idx',
                    'obj_comment',
                    'pk_intended_reviewer',
                    'filename'
            ]
            #--------------------------------------------------------
            # retrieve data
            #--------------------------------------------------------
            def save_to_file(self, aChunkSize=0, filename=None, target_mime=None, target_extension=None, ignore_conversion_problems=False, directory=None, adjust_extension=False, conn=None):

                    if filename is None:
                            filename = self.get_useful_filename(make_unique = True, directory = directory)

                    filename = self.__download_to_file(filename = filename)
                    if filename is None:
                            return None

                    if target_mime is None:
                            if filename.endswith('.dat'):
                                    if adjust_extension:
                                            return gmMimeLib.adjust_extension_by_mimetype(filename)
                            return filename

                    if target_extension is None:
                            target_extension = gmMimeLib.guess_ext_by_mimetype(mimetype = target_mime)

                    target_path, name = os.path.split(filename)
                    name, tmp = os.path.splitext(name)
                    target_fname = gmTools.get_unique_filename (
                            prefix = '%s-conv-' % name,
                            suffix = target_extension
                    )
                    _log.debug('attempting conversion: [%s] -> [<%s>:%s]', filename, target_mime, target_fname)
                    converted_fname = gmMimeLib.convert_file (
                            filename = filename,
                            target_mime = target_mime,
                            target_filename = target_fname
                    )
                    if converted_fname is not None:
                            return converted_fname

                    _log.warning('conversion failed')
                    if not ignore_conversion_problems:
                            return None

                    if filename.endswith('.dat'):
                            if adjust_extension:
                                    filename = gmMimeLib.adjust_extension_by_mimetype(filename)
                    _log.warning('programmed to ignore conversion problems, hoping receiver can handle [%s]', filename)
                    return filename

            #--------------------------------------------------------
            def get_reviews(self):
                    cmd = """
    SELECT
            reviewer,
            reviewed_when,
            is_technically_abnormal,
            clinically_relevant,
            is_review_by_responsible_reviewer,
            is_your_review,
            coalesce(comment, '')
    FROM blobs.v_reviewed_doc_objects
    WHERE pk_doc_obj = %s
    ORDER BY
            is_your_review desc,
            is_review_by_responsible_reviewer desc,
            reviewed_when desc
    """
                    rows, idx = gmPG2.run_ro_queries(queries = [{'cmd': cmd, 'args': [self.pk_obj]}])
                    return rows

            #--------------------------------------------------------
            def __get_containing_document(self):
                    return cDocument(aPK_obj = self._payload[self._idx['pk_doc']])

            containing_document = property(__get_containing_document)

            #--------------------------------------------------------
            # store data
            #--------------------------------------------------------
            def update_data_from_file(self, fname=None, link_obj=None):
                    # sanity check
                    if not (os.access(fname, os.R_OK) and os.path.isfile(fname)):
                            _log.error('[%s] is not a readable file' % fname)
                            return False

                    cmd = "UPDATE blobs.doc_obj SET data = %(data)s::BYTEA WHERE pk = %(pk)s RETURNING md5(data) AS md5"
                    args = {'pk': self.pk_obj}
                    md5 = gmTools.file2md5(filename = fname, return_hex = True)
                    if not gmPG2.file2bytea(conn = link_obj, query = cmd, filename = fname, args = args, file_md5 = md5):
                            return False

                    # must update XMIN now ...
                    self.refetch_payload(link_obj = link_obj)
                    return True

            #--------------------------------------------------------
            def set_reviewed(self, technically_abnormal=None, clinically_relevant=None):
                    # row already there ?
                    cmd = """
    select pk
    from blobs.reviewed_doc_objs
    where
            fk_reviewed_row = %s and
            fk_reviewer = (select pk from dem.staff where db_user = current_user)"""
                    rows, idx = gmPG2.run_ro_queries(queries = [{'cmd': cmd, 'args': [self.pk_obj]}])

                    # INSERT needed
                    if len(rows) == 0:
                            cols = [
                                    "fk_reviewer",
                                    "fk_reviewed_row",
                                    "is_technically_abnormal",
                                    "clinically_relevant"
                            ]
                            vals = [
                                    '%(fk_row)s',
                                    '%(abnormal)s',
                                    '%(relevant)s'
                            ]
                            args = {
                                    'fk_row': self.pk_obj,
                                    'abnormal': technically_abnormal,
                                    'relevant': clinically_relevant
                            }
                            cmd = """
    insert into blobs.reviewed_doc_objs (
            %s
    ) values (
            (select pk from dem.staff where db_user=current_user),
            %s
    )""" % (', '.join(cols), ', '.join(vals))

                    # UPDATE needed
                    if len(rows) == 1:
                            pk_review = rows[0][0]
                            args = {
                                    'abnormal': technically_abnormal,
                                    'relevant': clinically_relevant,
                                    'pk_review': pk_review
                            }
                            cmd = """
                                    UPDATE blobs.reviewed_doc_objs SET
                                            is_technically_abnormal = %(abnormal)s,
                                            clinically_relevant = %(relevant)s
                                    WHERE
                                            pk = %(pk_review)s
                            """
                    rows, idx = gmPG2.run_rw_queries(queries = [{'cmd': cmd, 'args': args}])

                    return True

            #--------------------------------------------------------
            def set_as_active_photograph(self):
                    if self._payload[self._idx['type']] != 'patient photograph':
                            return False
                    # set seq_idx to current max + 1
                    cmd = 'SELECT coalesce(max(seq_idx)+1, 1) FROM blobs.doc_obj WHERE fk_doc = %(doc_id)s'
                    rows, idx = gmPG2.run_ro_queries (
                            queries = [{
                                    'cmd': cmd,
                                    'args': {'doc_id': self._payload[self._idx['pk_doc']]}
                            }]
                    )
                    self._payload[self._idx['seq_idx']] = rows[0][0]
                    self._is_modified = True
                    self.save_payload()

            #--------------------------------------------------------
            def reattach(self, pk_doc=None):
                    if pk_doc == self._payload[self._idx['pk_doc']]:
                            return True

                    cmd = """
                            UPDATE blobs.doc_obj SET
                                    fk_doc = %(pk_doc_target)s,
                                    -- coalesce needed for no-parts target docs
                                    seq_idx = (SELECT coalesce(max(seq_idx) + 1, 1) FROM blobs.doc_obj WHERE fk_doc = %(pk_doc_target)s)
                            WHERE
                                    EXISTS(SELECT 1 FROM blobs.doc_med WHERE pk = %(pk_doc_target)s)
                                            AND
                                    pk = %(pk_obj)s
                                            AND
                                    xmin = %(xmin_doc_obj)s
                            RETURNING fk_doc
                    """
                    args = {
                            'pk_doc_target': pk_doc,
                            'pk_obj': self.pk_obj,
                            'xmin_doc_obj': self._payload[self._idx['xmin_doc_obj']]
                    }
                    rows, idx = gmPG2.run_rw_queries(queries = [{'cmd': cmd, 'args': args}], return_data = True, get_col_idx = False)
                    if len(rows) == 0:
                            return False
                    # The following should never hold true because the target
                    # fk_doc is returned from the query and it is checked for
                    # equality before the UPDATE already. Assuming the update
                    # failed to update a row because the target fk_doc did
                    # not exist we would not get *any* rows in return - for
                    # which condition we also already checked
                    if rows[0]['fk_doc'] == self._payload[self._idx['pk_doc']]:
                            return False

                    self.refetch_payload()
                    return True

            #--------------------------------------------------------
            def display_via_mime(self, chunksize=0, block=None):

                    fname = self.save_to_file(aChunkSize = chunksize)
                    if fname is None:
                            return False, ''

                    success, msg = gmMimeLib.call_viewer_on_file(fname, block = block)
                    if not success:
                            return False, msg

                    return True, ''

            #--------------------------------------------------------
            def format_single_line(self):
                    f_ext = ''
                    if self._payload[self._idx['filename']] is not None:
                            f_ext = os.path.splitext(self._payload[self._idx['filename']])[1].strip('.').strip()
                    if f_ext != '':
                            f_ext = ' .' + f_ext.upper()
                    txt = _('part %s, %s%s%s of document %s from %s%s') % (
                            self._payload[self._idx['seq_idx']],
                            gmTools.size2str(self._payload[self._idx['size']]),
                            f_ext,
                            gmTools.coalesce(self._payload[self._idx['obj_comment']], '', ' ("%s")'),
                            self._payload[self._idx['l10n_type']],
                            gmDateTime.pydt_strftime(self._payload[self._idx['date_generated']], '%Y %b %d'),
                            gmTools.coalesce(self._payload[self._idx['doc_comment']], '', ' ("%s")')
                    )
                    return txt

            #--------------------------------------------------------
            def format(self, single_line=False):
                    if single_line:
                            return self.format_single_line()

                    txt = _('%s document part                 [#%s]\n') % (
                            gmTools.bool2str (
                                    boolean = self._payload[self._idx['reviewed']],
                                    true_str = _('Reviewed'),
                                    false_str = _('Unreviewed')
                            ),
                            self._payload[self._idx['pk_obj']]
                    )
                    f_ext = ''
                    if self._payload[self._idx['filename']] is not None:
                            f_ext = os.path.splitext(self._payload[self._idx['filename']])[1].strip('.').strip()
                    if f_ext != '':
                            f_ext = '.' + f_ext.upper() + ' '
                    txt += _(' Part %s: %s %s(%s Bytes)\n') % (
                            self._payload[self._idx['seq_idx']],
                            gmTools.size2str(self._payload[self._idx['size']]),
                            f_ext,
                            self._payload[self._idx['size']]
                    )
                    if self._payload[self._idx['filename']] is not None:
                            path, fname = os.path.split(self._payload[self._idx['filename']])
                            if not path.endswith(os.path.sep):
                                    if path != '':
                                            path += os.path.sep
                            if path != '':
                                    path = ' (%s)' % path
                            txt += _(' Filename: %s%s\n') % (fname, path)
                    if self._payload[self._idx['obj_comment']] is not None:
                            txt += '\n%s\n' % self._payload[self._idx['obj_comment']]
                    return txt

            #--------------------------------------------------------
            def format_metainfo(self, callback=None):
                    """If <callback> is not None it will receive a tuple (status, description, pk_obj)."""
                    if callback is None:
                            return self.__run_metainfo_formatter()

                    gmWorkerThread.execute_in_worker_thread (
                            payload_function = self.__run_metainfo_formatter,
                            completion_callback = callback,
                            worker_name = 'doc_part-metainfo_formatter-'
                    )

            #--------------------------------------------------------
            def get_useful_filename(self, patient=None, make_unique=False, directory=None, include_gnumed_tag=True, date_before_type=False, name_first=True):
                    patient_part = ''
                    if patient is not None:
                            if name_first:
                                    patient_part = '%s-' % patient.subdir_name
                            else:
                                    patient_part = '-%s' % patient.subdir_name

                    # preserve original filename extension if available
                    suffix = '.dat'
                    if self._payload[self._idx['filename']] is not None:
                            tmp, suffix = os.path.splitext (
                                    gmTools.fname_sanitize(self._payload[self._idx['filename']]).lower()
                            )
                            if suffix == '':
                                    suffix = '.dat'

                    if include_gnumed_tag:
                            fname_template = 'gm_doc-part_%s-%%s' % self._payload[self._idx['seq_idx']]
                    else:
                            fname_template = '%%s-part_%s' % self._payload[self._idx['seq_idx']]

                    if date_before_type:
                            date_type_part = '%s-%s' % (
                                    gmDateTime.pydt_strftime(self._payload[self._idx['date_generated']], '%Y-%m-%d', 'utf-8', gmDateTime.acc_days),
                                    self._payload[self._idx['l10n_type']].replace(' ', '_').replace('-', '_'),
                            )
                    else:
                            date_type_part = '%s-%s' % (
                                    self._payload[self._idx['l10n_type']].replace(' ', '_').replace('-', '_'),
                                    gmDateTime.pydt_strftime(self._payload[self._idx['date_generated']], '%Y-%m-%d', 'utf-8', gmDateTime.acc_days)
                            )

                    if name_first:
                            date_type_name_part = patient_part + date_type_part
                    else:
                            date_type_name_part = date_type_part + patient_part

                    fname = fname_template % date_type_name_part

                    if make_unique:
                            fname = gmTools.get_unique_filename (
                                    prefix = '%s-' % gmTools.fname_sanitize(fname),
                                    suffix = suffix,
                                    tmp_dir = directory
                            )
                    else:
                            fname = gmTools.fname_sanitize(os.path.join(gmTools.coalesce(directory, gmTools.gmPaths().tmp_dir), fname + suffix))

                    return fname

            useful_filename = property(get_useful_filename)

            #--------------------------------------------------------
            # internal helpers
            #--------------------------------------------------------
            def __download_to_file(self, filename=None, aChunkSize=0, conn=None):
                    if self._payload[self._idx['size']] == 0:
                            _log.debug('part size 0, nothing to download')
                            return None

                    if filename is None:
                            filename = gmTools.get_unique_filename()
                    success = gmPG2.bytea2file (
                            data_query = {
                                    'cmd': 'SELECT substring(data from %(start)s for %(size)s) FROM blobs.doc_obj WHERE pk=%(pk)s',
                                    'args': {'pk': self.pk_obj}
                            },
                            filename = filename,
                            chunk_size = aChunkSize,
                            data_size = self._payload[self._idx['size']],
                            conn = conn
                    )
                    if not success:
                            return None

                    return filename

            #--------------------------------------------------------
            def __run_metainfo_formatter(self):
                    filename = self.__download_to_file()
                    if filename is None:
                            _log.error('problem downloading part')
                            return (False, _('problem downloading document part'))

                    status, desc = gmMimeLib.describe_file(filename)
                    return (status, desc, self.pk_obj)

    #------------------------------------------------------------
    def delete_document_part(part_pk=None, encounter_pk=None):
            cmd = """
                    SELECT blobs.delete_document_part(%(pk)s, %(enc)s)
                    WHERE NOT EXISTS
                            (SELECT 1 FROM clin.export_item where fk_doc_obj = %(pk)s)
            """
            args = {'pk': part_pk, 'enc': encounter_pk}
            rows, idx = gmPG2.run_rw_queries(queries = [{'cmd': cmd, 'args': args}])
            return

    #============================================================
    _SQL_get_document_fields = "SELECT * FROM blobs.v_doc_med b_vdm WHERE %s"

    class cDocument(gmBusinessDBObject.cBusinessDBObject):
            """Represents one medical document."""

            _cmd_fetch_payload = _SQL_get_document_fields % "pk_doc = %s"
            _cmds_store_payload = [
                    """UPDATE blobs.doc_med SET
                                    fk_type = %(pk_type)s,
                                    fk_episode = %(pk_episode)s,
                                    fk_encounter = %(pk_encounter)s,
                                    fk_org_unit = %(pk_org_unit)s,
                                    unit_is_receiver = %(unit_is_receiver)s,
                                    clin_when = %(clin_when)s,
                                    comment = gm.nullify_empty_string(%(comment)s),
                                    ext_ref = gm.nullify_empty_string(%(ext_ref)s),
                                    fk_hospital_stay = %(pk_hospital_stay)s
                            WHERE
                                    pk = %(pk_doc)s and
                                    xmin = %(xmin_doc_med)s
                            RETURNING
                                    xmin AS xmin_doc_med"""
            ]
            _updatable_fields = [
                    'pk_type',
                    'comment',
                    'clin_when',
                    'ext_ref',
                    'pk_episode',
                    'pk_encounter',                 # mainly useful when moving visual progress notes to their respective encounters
                    'pk_org_unit',
                    'unit_is_receiver',
                    'pk_hospital_stay'
            ]

            #--------------------------------------------------------
            def refetch_payload(self, ignore_changes=False, link_obj=None):
                    try: del self.__has_unreviewed_parts
                    except AttributeError: pass

                    return super(cDocument, self).refetch_payload(ignore_changes = ignore_changes, link_obj = link_obj)

            #--------------------------------------------------------
            def get_descriptions(self, max_lng=250):
                    """Get document descriptions.

                    - will return a list of rows
                    """
                    if max_lng is None:
                            cmd = "SELECT pk, text FROM blobs.doc_desc WHERE fk_doc = %s"
                    else:
                            cmd = "SELECT pk, substring(text from 1 for %s) FROM blobs.doc_desc WHERE fk_doc=%%s" % max_lng
                    rows, idx = gmPG2.run_ro_queries(queries = [{'cmd': cmd, 'args': [self.pk_obj]}])
                    return rows

            #--------------------------------------------------------
            def add_description(self, description=None):
                    cmd = "insert into blobs.doc_desc (fk_doc, text) values (%s, %s)"
                    gmPG2.run_rw_queries(queries = [{'cmd': cmd, 'args': [self.pk_obj, description]}])
                    return True

            #--------------------------------------------------------
            def update_description(self, pk=None, description=None):
                    cmd = "update blobs.doc_desc set text = %(desc)s where fk_doc = %(doc)s and pk = %(pk_desc)s"
                    gmPG2.run_rw_queries(queries = [
                            {'cmd': cmd, 'args': {'doc': self.pk_obj, 'pk_desc': pk, 'desc': description}}
                    ])
                    return True

            #--------------------------------------------------------
            def delete_description(self, pk=None):
                    cmd = "delete from blobs.doc_desc where fk_doc = %(doc)s and pk = %(desc)s"
                    gmPG2.run_rw_queries(queries = [{'cmd': cmd, 'args': {'doc': self.pk_obj, 'desc': pk}}])
                    return True

            #--------------------------------------------------------
            def _get_parts(self):
                    cmd = _SQL_get_document_part_fields % "pk_doc = %s ORDER BY seq_idx"
                    rows, idx = gmPG2.run_ro_queries(queries = [{'cmd': cmd, 'args': [self.pk_obj]}], get_col_idx = True)
                    return [ cDocumentPart(row = {'pk_field': 'pk_obj', 'idx': idx, 'data': r}) for r in rows ]

            parts = property(_get_parts, lambda x:x)

            #--------------------------------------------------------
            def add_part(self, file=None, link_obj=None):
                    """Add a part to the document."""
                    # create dummy part
                    cmd = """
                            INSERT INTO blobs.doc_obj (
                                    fk_doc, data, seq_idx
                            ) VALUES (
                                    %(doc_id)s,
                                    ''::bytea,
                                    (SELECT coalesce(max(seq_idx)+1, 1) FROM blobs.doc_obj WHERE fk_doc = %(doc_id)s)
                            ) RETURNING pk"""
                    rows, idx = gmPG2.run_rw_queries (
                            link_obj = link_obj,
                            queries = [{'cmd': cmd, 'args': {'doc_id': self.pk_obj}}],
                            return_data = True
                    )
                    # init document part instance
                    pk_part = rows[0][0]
                    new_part = cDocumentPart(aPK_obj = pk_part, link_obj = link_obj)
                    if not new_part.update_data_from_file(link_obj = link_obj, fname = file):
                            _log.error('cannot import binary data from [%s] into document part' % file)
                            gmPG2.run_rw_queries (
                                    link_obj = link_obj,
                                    queries = [{'cmd': "DELETE FROM blobs.doc_obj WHERE pk = %s", 'args': [pk_part]}]
                            )
                            return None
                    new_part['filename'] = file
                    new_part.save_payload(conn = link_obj)

                    return new_part

            #--------------------------------------------------------
            def add_parts_from_files(self, files=None, reviewer=None):

                    new_parts = []

                    for filename in files:
                            new_part = self.add_part(file = filename)
                            if new_part is None:
                                    msg = 'cannot instantiate document part object from [%s]' % filename
                                    _log.error(msg)
                                    return (False, msg, filename)
                            new_parts.append(new_part)

                            if reviewer is not None:
                                    new_part['pk_intended_reviewer'] = reviewer                     # None == Null
                                    success, data = new_part.save_payload()
                                    if not success:
                                            msg = 'cannot set reviewer to [%s] on [%s]' % (reviewer, filename)
                                            _log.error(msg)
                                            _log.error(str(data))
                                            return (False, msg, filename)

                    return (True, '', new_parts)

            #--------------------------------------------------------
            def save_parts_to_files(self, export_dir=None, chunksize=0, conn=None):
                    fnames = []
                    for part in self.parts:
                            fname = part.save_to_file(aChunkSize = chunksize, directory = export_dir, conn = conn)
                            if fname is None:
                                    _log.error('cannot export document part [%s]', part)
                                    continue
                            fnames.append(fname)
                    return fnames

            #--------------------------------------------------------
            def _get_has_unreviewed_parts(self):
                    try:
                            return self.__has_unreviewed_parts
                    except AttributeError:
                            pass

                    cmd = "SELECT EXISTS(SELECT 1 FROM blobs.v_obj4doc_no_data WHERE pk_doc = %(pk)s AND reviewed IS FALSE)"
                    args = {'pk': self.pk_obj}
                    rows, idx = gmPG2.run_ro_queries(queries = [{'cmd': cmd, 'args': args}])
                    self.__has_unreviewed_parts = rows[0][0]

                    return self.__has_unreviewed_parts

            has_unreviewed_parts = property(_get_has_unreviewed_parts, lambda x:x)

            #--------------------------------------------------------
            def set_reviewed(self, technically_abnormal=None, clinically_relevant=None):
                    # FIXME: this is probably inefficient
                    for part in self.parts:
                            if not part.set_reviewed(technically_abnormal, clinically_relevant):
                                    return False
                    return True

            #--------------------------------------------------------
            def set_primary_reviewer(self, reviewer=None):
                    for part in self.parts:
                            part['pk_intended_reviewer'] = reviewer
                            success, data = part.save_payload()
                            if not success:
                                    _log.error('cannot set reviewer to [%s]' % reviewer)
                                    _log.error(str(data))
                                    return False
                    return True

            #--------------------------------------------------------
            def format_single_line(self):

                    part_count = len(self._payload[self._idx['seq_idx_list']])
                    if part_count == 0:
                            parts = _('no parts')
                    elif part_count == 1:
                            parts = _('1 part')
                    else:
                            parts = _('%s parts') % part_count

                    detail = ''
                    if self._payload[self._idx['ext_ref']] is not None:
                            detail = self._payload[self._idx['ext_ref']]
                    if self._payload[self._idx['unit']] is not None:
                            template = _('%s of %s')
                            if detail == '':
                                    detail = _('%s of %s') % (
                                            self._payload[self._idx['unit']],
                                            self._payload[self._idx['organization']]
                                    )
                            else:
                                    detail += (' @ ' + template % (
                                            self._payload[self._idx['unit']],
                                            self._payload[self._idx['organization']]
                                    ))
                    if detail != '':
                            detail = ' (%s)' % detail

                    return '%s %s (%s):%s%s' % (
                            gmDateTime.pydt_strftime(self._payload[self._idx['clin_when']], '%Y %b %d', accuracy = gmDateTime.acc_days),
                            self._payload[self._idx['l10n_type']],
                            parts,
                            gmTools.coalesce(self._payload[self._idx['comment']], '', ' "%s"'),
                            detail
                    )

            #--------------------------------------------------------
            def format(self, single_line=False):
                    if single_line:
                            return self.format_single_line()

                    part_count = len(self._payload[self._idx['seq_idx_list']])
                    if part_count == 0:
                            parts = _('no parts')
                    elif part_count == 1:
                            parts = _('1 part')
                    else:
                            parts = _('%s parts') % part_count
                    org = ''
                    if self._payload[self._idx['unit']] is not None:
                            if self._payload[self._idx['unit_is_receiver']]:
                                    org = _(' Receiver: %s @ %s\n') % (
                                            self._payload[self._idx['unit']],
                                            self._payload[self._idx['organization']]
                                    )
                            else:
                                    org = _(' Sender: %s @ %s\n') % (
                                            self._payload[self._idx['unit']],
                                            self._payload[self._idx['organization']]
                                    )
                    stay = ''
                    if self._payload[self._idx['pk_hospital_stay']] is not None:
                            stay = _('Hospital stay') + ': %s\n' % self.hospital_stay.format (
                                    left_margin = 0,
                                    include_procedures = False,
                                    include_docs = False,
                                    include_episode = False
                            )

                    txt = _(
                            '%s (%s)   #%s\n'
                            ' Created: %s\n'
                            ' Episode: %s\n'
                            '%s'
                            '%s'
                            '%s'
                            '%s'
                            '%s'
                    ) % (
                            self._payload[self._idx['l10n_type']],
                            parts,
                            self._payload[self._idx['pk_doc']],
                            gmDateTime.pydt_strftime(self._payload[self._idx['clin_when']], format = '%Y %b %d', accuracy = gmDateTime.acc_days),
                            self._payload[self._idx['episode']],
                            gmTools.coalesce(self._payload[self._idx['health_issue']], '', _(' Health issue: %s\n')),
                            gmTools.coalesce(self._payload[self._idx['ext_ref']], '', _(' External reference: %s\n')),
                            org,
                            stay,
                            gmTools.coalesce(self._payload[self._idx['comment']], '', ' %s')
                    )

                    return txt

            #--------------------------------------------------------
            def _get_hospital_stay(self):
                    if self._payload[self._idx['pk_hospital_stay']] is None:
                            return None
                    from Gnumed.business import gmEMRStructItems
                    return gmEMRStructItems.cHospitalStay(self._payload[self._idx['pk_hospital_stay']])

            hospital_stay = property(_get_hospital_stay, lambda x:x)

            #--------------------------------------------------------
            def _get_org_unit(self):
                    if self._payload[self._idx['pk_org_unit']] is None:
                            return None
                    return gmOrganization.cOrgUnit(self._payload[self._idx['pk_org_unit']])

            org_unit = property(_get_org_unit, lambda x:x)

            #--------------------------------------------------------
            def _get_procedures(self):
                    from Gnumed.business.gmEMRStructItems import get_procedures4document
                    return get_procedures4document(pk_document = self.pk_obj)

            procedures = property(_get_procedures, lambda x:x)

            #--------------------------------------------------------
            def _get_bills(self):
                    from Gnumed.business.gmBilling import get_bills4document
                    return get_bills4document(pk_document = self.pk_obj)

            bills = property(_get_bills, lambda x:x)

    #------------------------------------------------------------
    def create_document(document_type=None, encounter=None, episode=None, link_obj=None):
            """Returns new document instance or raises an exception."""
            try:
                    int(document_type)
                    cmd = """INSERT INTO blobs.doc_med (fk_type, fk_encounter, fk_episode) VALUES (%(type)s, %(enc)s, %(epi)s) RETURNING pk"""
            except ValueError:
                    create_document_type(document_type = document_type)
                    cmd = """
                            INSERT INTO blobs.doc_med (
                                    fk_type,
                                    fk_encounter,
                                    fk_episode
                            ) VALUES (
                                    coalesce (
                                            (SELECT pk from blobs.doc_type bdt where bdt.name = %(type)s),
                                            (SELECT pk from blobs.doc_type bdt where _(bdt.name) = %(type)s)
                                    ),
                                    %(enc)s,
                                    %(epi)s
                            ) RETURNING pk"""
            args = {'type': document_type, 'enc': encounter, 'epi': episode}
            rows, idx = gmPG2.run_rw_queries(link_obj = link_obj, queries = [{'cmd': cmd, 'args': args}], return_data = True)
            doc = cDocument(aPK_obj = rows[0][0], link_obj = link_obj)
            return doc

    #------------------------------------------------------------
    def search_for_documents(patient_id=None, type_id=None, external_reference=None, pk_episode=None, pk_types=None):
            """Searches for documents with the given patient and type ID."""

            if (patient_id is None) and (pk_episode is None):
                    raise ValueError('need patient_id or pk_episode to search for document')

            where_parts = []
            args = {
                    'pat_id': patient_id,
                    'type_id': type_id,
                    'ref': external_reference,
                    'pk_epi': pk_episode
            }

            if patient_id is not None:
                    where_parts.append('pk_patient = %(pat_id)s')

            if type_id is not None:
                    where_parts.append('pk_type = %(type_id)s')

            if external_reference is not None:
                    where_parts.append('ext_ref = %(ref)s')

            if pk_episode is not None:
                    where_parts.append('pk_episode = %(pk_epi)s')

            if pk_types is not None:
                    where_parts.append('pk_type IN %(pk_types)s')
                    args['pk_types'] = tuple(pk_types)

            cmd = _SQL_get_document_fields % ' AND '.join(where_parts)
            rows, idx = gmPG2.run_ro_queries(queries = [{'cmd': cmd, 'args': args}], get_col_idx = True)
            return [ cDocument(row = {'data': r, 'idx': idx, 'pk_field': 'pk_doc'}) for r in rows ]

    #------------------------------------------------------------
    def delete_document(document_id=None, encounter_id=None):
            # cascades to doc_obj and doc_desc but not bill.bill
            cmd = "SELECT blobs.delete_document(%(pk)s, %(enc)s)"
            args = {'pk': document_id, 'enc': encounter_id}
            rows, idx = gmPG2.run_rw_queries(queries = [{'cmd': cmd, 'args': args}], return_data = True)
            if not rows[0][0]:
                    _log.error('cannot delete document [%s]', document_id)
                    return False
            return True

    #------------------------------------------------------------
    def reclassify_documents_by_type(original_type=None, target_type=None):

            _log.debug('reclassifying documents by type')
            _log.debug('original: %s', original_type)
            _log.debug('target: %s', target_type)

            if target_type['pk_doc_type'] == original_type['pk_doc_type']:
                    return True

            cmd = """
    update blobs.doc_med set
            fk_type = %(new_type)s
    where
            fk_type = %(old_type)s
    """
            args = {'new_type': target_type['pk_doc_type'], 'old_type': original_type['pk_doc_type']}

            gmPG2.run_rw_queries(queries = [{'cmd': cmd, 'args': args}])

            return True

    #============================================================
    class cDocumentType(gmBusinessDBObject.cBusinessDBObject):
            """Represents a document type."""
            _cmd_fetch_payload = """select * from blobs.v_doc_type where pk_doc_type=%s"""
            _cmds_store_payload = [
                    """update blobs.doc_type set
                                    name = %(type)s
                            where
                                    pk=%(pk_obj)s and
                                    xmin=%(xmin_doc_type)s""",
                    """select xmin_doc_type from blobs.v_doc_type where pk_doc_type = %(pk_obj)s"""
            ]
            _updatable_fields = ['type']
            #--------------------------------------------------------
            def set_translation(self, translation=None):

                    if translation.strip() == '':
                            return False

                    if translation.strip() == self._payload[self._idx['l10n_type']].strip():
                            return True

                    rows, idx = gmPG2.run_rw_queries (
                            queries = [
                                    {'cmd': 'select i18n.i18n(%s)', 'args': [self._payload[self._idx['type']]]},
                                    {'cmd': 'select i18n.upd_tx((select i18n.get_curr_lang()), %(orig)s, %(tx)s)',
                                     'args': {
                                            'orig': self._payload[self._idx['type']],
                                            'tx': translation
                                            }
                                    }
                            ],
                            return_data = True
                    )
                    if not rows[0][0]:
                            _log.error('cannot set translation to [%s]' % translation)
                            return False

                    return self.refetch_payload()

    #------------------------------------------------------------
    def get_document_types():
            rows, idx = gmPG2.run_ro_queries (
                    queries = [{'cmd': "SELECT * FROM blobs.v_doc_type"}],
                    get_col_idx = True
            )
            doc_types = []
            for row in rows:
                    row_def = {'pk_field': 'pk_doc_type', 'idx': idx, 'data': row}
                    doc_types.append(cDocumentType(row = row_def))
            return doc_types

    #------------------------------------------------------------
    def get_document_type_pk(document_type=None):
            args = {'typ': document_type.strip()}

            cmd = 'SELECT pk FROM blobs.doc_type WHERE name = %(typ)s'
            rows, idx = gmPG2.run_ro_queries(queries = [{'cmd': cmd, 'args': args}], get_col_idx = False)
            if len(rows) == 0:
                    cmd = 'SELECT pk FROM blobs.doc_type WHERE _(name) = %(typ)s'
                    rows, idx = gmPG2.run_ro_queries(queries = [{'cmd': cmd, 'args': args}], get_col_idx = False)

            if len(rows) == 0:
                    return None

            return rows[0]['pk']

    #------------------------------------------------------------
    def map_types2pk(document_types=None):
            args = {'types': tuple(document_types)}
            cmd = 'SELECT pk_doc_type, coalesce(l10n_type, type) as desc FROM blobs.v_doc_type WHERE l10n_type IN %(types)s OR type IN %(types)s'
            rows, idx = gmPG2.run_ro_queries(queries = [{'cmd': cmd, 'args': args}], get_col_idx = False)
            return rows

    #------------------------------------------------------------
    def create_document_type(document_type=None):
            # check for potential dupes:
            cmd = 'SELECT pk FROM blobs.doc_type WHERE name = %s'
            rows, idx = gmPG2.run_ro_queries (
                    queries = [{'cmd': cmd, 'args': [document_type]}]
            )
            if len(rows) == 0:
                    _log.debug('creating document type [%s]', document_type)
                    cmd1 = "INSERT INTO blobs.doc_type (name) VALUES (%s) RETURNING pk"
                    rows, idx = gmPG2.run_rw_queries (
                            queries = [{'cmd': cmd1, 'args': [document_type]}],
                            return_data = True
                    )
            return cDocumentType(aPK_obj = rows[0][0])

    #------------------------------------------------------------
    def delete_document_type(document_type=None):
            if document_type['is_in_use']:
                    return False

            gmPG2.run_rw_queries (
                    queries = [{
                            'cmd': 'delete from blobs.doc_type where pk=%s',
                            'args': [document_type['pk_doc_type']]
                    }]
            )
            return True

    #------------------------------------------------------------
    def get_ext_ref():
            """This needs *considerably* more smarts."""
            dirname = gmTools.get_unique_filename (
                    prefix = '',
                    suffix = time.strftime(".%Y%m%d-%H%M%S", time.localtime())
            )
            # extract name for dir
            path, doc_ID = os.path.split(dirname)
            return doc_ID

    #============================================================
    def check_mimetypes_in_archive():
            mimetypes = {}
            cmd = 'SELECT pk FROM blobs.doc_med'
            doc_pks, idx = gmPG2.run_ro_queries(queries = [{'cmd': cmd}])
            print('Detecting mimetypes in document archive ...')
            doc_idx = 0
            part_count = 0
            for pk_row in doc_pks:
                    doc_idx += 1
                    print('\n#%s - document %s of %s: ' % (pk_row['pk'], doc_idx, len(doc_pks)), end = '')
                    doc = cDocument(aPK_obj = pk_row['pk'])
                    for part in doc.parts:
                            part_count += 1
                            print('#%s:%s bytes, ' % (part['pk_obj'], part['size']), end = '')
                            part_fname = part.save_to_file()
                            mimetype = gmMimeLib.guess_mimetype(part_fname)
                            try:
                                    mimetypes[mimetype]['count'] += 1
                            except KeyError:
                                    mimetypes[mimetype] = {
                                            'count': 1,
                                            'viewer': gmMimeLib.get_viewer_cmd(mimetype),
                                            'editor': gmMimeLib.get_editor_cmd(mimetype),
                                            'extension': gmMimeLib.guess_ext_by_mimetype(mimetype)
                                    }
            print('')
            print('')
            print('Number of documents :', len(doc_pks))
            print('Number of parts     :', part_count)
            print('Number of mime types:', len(mimetypes))
            for mimetype in mimetypes:
                    print('')
                    print('<%s>' % mimetype)
                    print(' Extension:', mimetypes[mimetype]['extension'])
                    print(' Use count:', mimetypes[mimetype]['count'])
                    print('    Viewer:', mimetypes[mimetype]['viewer'])
                    print('    Editor:', mimetypes[mimetype]['editor'])
            return 0

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

            if len(sys.argv) < 2:
                    sys.exit()

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

            #--------------------------------------------------------
            def test_doc_types():

                    print("----------------------")
                    print("listing document types")
                    print("----------------------")

                    for dt in get_document_types():
                            print(dt)

                    print("------------------------------")
                    print("testing document type handling")
                    print("------------------------------")

                    dt = create_document_type(document_type = 'dummy doc type for unit test 1')
                    print("created:", dt)

                    dt['type'] = 'dummy doc type for unit test 2'
                    dt.save_payload()
                    print("changed base name:", dt)

                    dt.set_translation(translation = 'Dummy-Dokumenten-Typ fuer Unit-Test')
                    print("translated:", dt)

                    print("deleted:", delete_document_type(document_type = dt))

                    return
            #--------------------------------------------------------
            def test_adding_doc_part():

                    print("-----------------------")
                    print("testing document import")
                    print("-----------------------")

                    docs = search_for_documents(patient_id=12)
                    doc = docs[0]
                    print("adding to doc:", doc)

                    fname = sys.argv[1]
                    print("adding from file:", fname)
                    part = doc.add_part(file=fname)
                    print("new part:", part)

                    return
            #--------------------------------------------------------
            def test_get_documents():

                    doc_folder = cDocumentFolder(aPKey=12)

                    #photo = doc_folder.get_latest_mugshot()
                    #print type(photo), photo

                    docs = doc_folder.get_documents()
                    for doc in docs:
                            #print type(doc), doc
                            #print doc.parts
                            #print doc.format_single_line()
                            print('--------------------------')
                            print(doc.format(single_line = True))
                            print(doc.format())

            #--------------------------------------------------------
            def test_get_useful_filename():
                    pk = 12
                    from Gnumed.business.gmPerson import cPatient
                    pat = cPatient(pk)
                    doc_folder = cDocumentFolder(aPKey = pk)
                    for doc in doc_folder.documents:
                            for part in doc.parts:
                                    print(part.get_useful_filename (
                                            patient = pat,
                                            make_unique = True,
                                            directory = None,
                                            include_gnumed_tag = False,
                                            date_before_type = True,
                                            name_first = False
                                    ))
            #--------------------------------------------------------
            def test_check_mimetypes_in_archive():
                    check_mimetypes_in_archive()

            #--------------------------------------------------------
            def test_part_metainfo_formatter():

                    #--------------------------------
                    def desc_printer(worker_result):
                            status, desc = worker_result
                            print('printer callback:')
                            print(status)
                            print(desc)
                            print('<hit key> for next')
                            return
                    #--------------------------------

                    pk = 12
    #               from Gnumed.business.gmPerson import cPatient
    #               pat = cPatient(pk)
                    doc_folder = cDocumentFolder(aPKey = pk)
                    for doc in doc_folder.documents:
                            for part in doc.parts:
                                    part.format_metainfo(callback = desc_printer)
                                    input('waiting ...')
    #                               success, desc = part.format_metainfo()
    #                               print(success)
    #                               print(desc)
    #                               input('next')

    #                               print(part.get_useful_filename (
    #                                       patient = pat,
    #                                       make_unique = True,
    #                                       directory = None,
    #                                       include_gnumed_tag = False,
    #                                       date_before_type = True,
    #                                       name_first = False
    #                               ))

            #--------------------------------------------------------
            from Gnumed.pycommon import gmI18N
            gmI18N.activate_locale()
            gmI18N.install_domain()

            #test_doc_types()
            #test_adding_doc_part()
            #test_get_documents()
            #test_get_useful_filename()
            #test_part_metainfo_formatter()
            test_check_mimetypes_in_archive()

    #       print get_ext_ref()

## Functions

`def check_mimetypes_in_archive()`
  Expand source code

      def check_mimetypes_in_archive():
              mimetypes = {}
              cmd = 'SELECT pk FROM blobs.doc_med'
              doc_pks, idx = gmPG2.run_ro_queries(queries = [{'cmd': cmd}])
              print('Detecting mimetypes in document archive ...')
              doc_idx = 0
              part_count = 0
              for pk_row in doc_pks:
                      doc_idx += 1
                      print('\n#%s - document %s of %s: ' % (pk_row['pk'], doc_idx, len(doc_pks)), end = '')
                      doc = cDocument(aPK_obj = pk_row['pk'])
                      for part in doc.parts:
                              part_count += 1
                              print('#%s:%s bytes, ' % (part['pk_obj'], part['size']), end = '')
                              part_fname = part.save_to_file()
                              mimetype = gmMimeLib.guess_mimetype(part_fname)
                              try:
                                      mimetypes[mimetype]['count'] += 1
                              except KeyError:
                                      mimetypes[mimetype] = {
                                              'count': 1,
                                              'viewer': gmMimeLib.get_viewer_cmd(mimetype),
                                              'editor': gmMimeLib.get_editor_cmd(mimetype),
                                              'extension': gmMimeLib.guess_ext_by_mimetype(mimetype)
                                      }
              print('')
              print('')
              print('Number of documents :', len(doc_pks))
              print('Number of parts     :', part_count)
              print('Number of mime types:', len(mimetypes))
              for mimetype in mimetypes:
                      print('')
                      print('<%s>' % mimetype)
                      print(' Extension:', mimetypes[mimetype]['extension'])
                      print(' Use count:', mimetypes[mimetype]['count'])
                      print('    Viewer:', mimetypes[mimetype]['viewer'])
                      print('    Editor:', mimetypes[mimetype]['editor'])
              return 0

`def create_document(document_type=None, encounter=None, episode=None, link_obj=None)`

  Returns new document instance or raises an exception.

  Expand source code

      def create_document(document_type=None, encounter=None, episode=None, link_obj=None):
              """Returns new document instance or raises an exception."""
              try:
                      int(document_type)
                      cmd = """INSERT INTO blobs.doc_med (fk_type, fk_encounter, fk_episode) VALUES (%(type)s, %(enc)s, %(epi)s) RETURNING pk"""
              except ValueError:
                      create_document_type(document_type = document_type)
                      cmd = """
                              INSERT INTO blobs.doc_med (
                                      fk_type,
                                      fk_encounter,
                                      fk_episode
                              ) VALUES (
                                      coalesce (
                                              (SELECT pk from blobs.doc_type bdt where bdt.name = %(type)s),
                                              (SELECT pk from blobs.doc_type bdt where _(bdt.name) = %(type)s)
                                      ),
                                      %(enc)s,
                                      %(epi)s
                              ) RETURNING pk"""
              args = {'type': document_type, 'enc': encounter, 'epi': episode}
              rows, idx = gmPG2.run_rw_queries(link_obj = link_obj, queries = [{'cmd': cmd, 'args': args}], return_data = True)
              doc = cDocument(aPK_obj = rows[0][0], link_obj = link_obj)
              return doc

`def create_document_type(document_type=None)`
  Expand source code

      def create_document_type(document_type=None):
              # check for potential dupes:
              cmd = 'SELECT pk FROM blobs.doc_type WHERE name = %s'
              rows, idx = gmPG2.run_ro_queries (
                      queries = [{'cmd': cmd, 'args': [document_type]}]
              )
              if len(rows) == 0:
                      _log.debug('creating document type [%s]', document_type)
                      cmd1 = "INSERT INTO blobs.doc_type (name) VALUES (%s) RETURNING pk"
                      rows, idx = gmPG2.run_rw_queries (
                              queries = [{'cmd': cmd1, 'args': [document_type]}],
                              return_data = True
                      )
              return cDocumentType(aPK_obj = rows[0][0])

`def delete_document(document_id=None, encounter_id=None)`
  Expand source code

      def delete_document(document_id=None, encounter_id=None):
              # cascades to doc_obj and doc_desc but not bill.bill
              cmd = "SELECT blobs.delete_document(%(pk)s, %(enc)s)"
              args = {'pk': document_id, 'enc': encounter_id}
              rows, idx = gmPG2.run_rw_queries(queries = [{'cmd': cmd, 'args': args}], return_data = True)
              if not rows[0][0]:
                      _log.error('cannot delete document [%s]', document_id)
                      return False
              return True

`def delete_document_part(part_pk=None, encounter_pk=None)`
  Expand source code

      def delete_document_part(part_pk=None, encounter_pk=None):
              cmd = """
                      SELECT blobs.delete_document_part(%(pk)s, %(enc)s)
                      WHERE NOT EXISTS
                              (SELECT 1 FROM clin.export_item where fk_doc_obj = %(pk)s)
              """
              args = {'pk': part_pk, 'enc': encounter_pk}
              rows, idx = gmPG2.run_rw_queries(queries = [{'cmd': cmd, 'args': args}])
              return

`def delete_document_type(document_type=None)`
  Expand source code

      def delete_document_type(document_type=None):
              if document_type['is_in_use']:
                      return False

              gmPG2.run_rw_queries (
                      queries = [{
                              'cmd': 'delete from blobs.doc_type where pk=%s',
                              'args': [document_type['pk_doc_type']]
                      }]
              )
              return True

`def get_document_type_pk(document_type=None)`
  Expand source code

      def get_document_type_pk(document_type=None):
              args = {'typ': document_type.strip()}

              cmd = 'SELECT pk FROM blobs.doc_type WHERE name = %(typ)s'
              rows, idx = gmPG2.run_ro_queries(queries = [{'cmd': cmd, 'args': args}], get_col_idx = False)
              if len(rows) == 0:
                      cmd = 'SELECT pk FROM blobs.doc_type WHERE _(name) = %(typ)s'
                      rows, idx = gmPG2.run_ro_queries(queries = [{'cmd': cmd, 'args': args}], get_col_idx = False)

              if len(rows) == 0:
                      return None

              return rows[0]['pk']

`def get_document_types()`
  Expand source code

      def get_document_types():
              rows, idx = gmPG2.run_ro_queries (
                      queries = [{'cmd': "SELECT * FROM blobs.v_doc_type"}],
                      get_col_idx = True
              )
              doc_types = []
              for row in rows:
                      row_def = {'pk_field': 'pk_doc_type', 'idx': idx, 'data': row}
                      doc_types.append(cDocumentType(row = row_def))
              return doc_types

`def get_ext_ref()`

  This needs considerably more smarts.

  Expand source code

      def get_ext_ref():
              """This needs *considerably* more smarts."""
              dirname = gmTools.get_unique_filename (
                      prefix = '',
                      suffix = time.strftime(".%Y%m%d-%H%M%S", time.localtime())
              )
              # extract name for dir
              path, doc_ID = os.path.split(dirname)
              return doc_ID

`def map_types2pk(document_types=None)`
  Expand source code

      def map_types2pk(document_types=None):
              args = {'types': tuple(document_types)}
              cmd = 'SELECT pk_doc_type, coalesce(l10n_type, type) as desc FROM blobs.v_doc_type WHERE l10n_type IN %(types)s OR type IN %(types)s'
              rows, idx = gmPG2.run_ro_queries(queries = [{'cmd': cmd, 'args': args}], get_col_idx = False)
              return rows

`def reclassify_documents_by_type(original_type=None, target_type=None)`
  Expand source code

      def reclassify_documents_by_type(original_type=None, target_type=None):

              _log.debug('reclassifying documents by type')
              _log.debug('original: %s', original_type)
              _log.debug('target: %s', target_type)

              if target_type['pk_doc_type'] == original_type['pk_doc_type']:
                      return True

              cmd = """
      update blobs.doc_med set
              fk_type = %(new_type)s
      where
              fk_type = %(old_type)s
      """
              args = {'new_type': target_type['pk_doc_type'], 'old_type': original_type['pk_doc_type']}

              gmPG2.run_rw_queries(queries = [{'cmd': cmd, 'args': args}])

              return True

`def search_for_documents(patient_id=None, type_id=None, external_reference=None, pk_episode=None, pk_types=None)`

  Searches for documents with the given patient and type ID.

  Expand source code

      def search_for_documents(patient_id=None, type_id=None, external_reference=None, pk_episode=None, pk_types=None):
              """Searches for documents with the given patient and type ID."""

              if (patient_id is None) and (pk_episode is None):
                      raise ValueError('need patient_id or pk_episode to search for document')

              where_parts = []
              args = {
                      'pat_id': patient_id,
                      'type_id': type_id,
                      'ref': external_reference,
                      'pk_epi': pk_episode
              }

              if patient_id is not None:
                      where_parts.append('pk_patient = %(pat_id)s')

              if type_id is not None:
                      where_parts.append('pk_type = %(type_id)s')

              if external_reference is not None:
                      where_parts.append('ext_ref = %(ref)s')

              if pk_episode is not None:
                      where_parts.append('pk_episode = %(pk_epi)s')

              if pk_types is not None:
                      where_parts.append('pk_type IN %(pk_types)s')
                      args['pk_types'] = tuple(pk_types)

              cmd = _SQL_get_document_fields % ' AND '.join(where_parts)
              rows, idx = gmPG2.run_ro_queries(queries = [{'cmd': cmd, 'args': args}], get_col_idx = True)
              return [ cDocument(row = {'data': r, 'idx': idx, 'pk_field': 'pk_doc'}) for r in rows ]

## Classes

`class cDocument (aPK_obj=None, row: dict = None, link_obj=None)`

  Represents one medical document.

  Init business object.

  Call from child classes like so:

          super().__init__(aPK_obj = aPK_obj, row = row, link_obj = link_obj)

  ## Args

  `aPK_obj`
    retrieve data from backend * a simple value the primary key WHERE condition must be a simple column * a dictionary of values the primary key WHERE condition must be a subselect consuming the dict and producing the single-value primary key
  `row`
    must hold the fields * idx: a dict mapping field names to position * data: the field values in a list (as returned by cursor.fetchone() in the DB-API) * pk_field: the name of the primary key field OR * pk_obj: a dictionary suitable for passed to cursor.execute and holding the primary key values, used for composite PKs

  ## Examples

  row = { 'data': rows[0], 'idx': idx, 'pk_field': 'pk_XXX (the PK column name)', 'pk_obj': {'pk_col1': pk_col1_val, 'pk_col2': pk_col2_val} } rows, idx = gmPG2.run_ro_queries(queries = [{'cmd': cmd, 'args': args}], get_col_idx = True) objects = [ cChildClass(row = {'data': r, 'idx': idx, 'pk_field': 'the PK column name'}) for r in rows ]

  Expand source code

      class cDocument(gmBusinessDBObject.cBusinessDBObject):
              """Represents one medical document."""

              _cmd_fetch_payload = _SQL_get_document_fields % "pk_doc = %s"
              _cmds_store_payload = [
                      """UPDATE blobs.doc_med SET
                                      fk_type = %(pk_type)s,
                                      fk_episode = %(pk_episode)s,
                                      fk_encounter = %(pk_encounter)s,
                                      fk_org_unit = %(pk_org_unit)s,
                                      unit_is_receiver = %(unit_is_receiver)s,
                                      clin_when = %(clin_when)s,
                                      comment = gm.nullify_empty_string(%(comment)s),
                                      ext_ref = gm.nullify_empty_string(%(ext_ref)s),
                                      fk_hospital_stay = %(pk_hospital_stay)s
                              WHERE
                                      pk = %(pk_doc)s and
                                      xmin = %(xmin_doc_med)s
                              RETURNING
                                      xmin AS xmin_doc_med"""
              ]
              _updatable_fields = [
                      'pk_type',
                      'comment',
                      'clin_when',
                      'ext_ref',
                      'pk_episode',
                      'pk_encounter',                 # mainly useful when moving visual progress notes to their respective encounters
                      'pk_org_unit',
                      'unit_is_receiver',
                      'pk_hospital_stay'
              ]

              #--------------------------------------------------------
              def refetch_payload(self, ignore_changes=False, link_obj=None):
                      try: del self.__has_unreviewed_parts
                      except AttributeError: pass

                      return super(cDocument, self).refetch_payload(ignore_changes = ignore_changes, link_obj = link_obj)

              #--------------------------------------------------------
              def get_descriptions(self, max_lng=250):
                      """Get document descriptions.

                      - will return a list of rows
                      """
                      if max_lng is None:
                              cmd = "SELECT pk, text FROM blobs.doc_desc WHERE fk_doc = %s"
                      else:
                              cmd = "SELECT pk, substring(text from 1 for %s) FROM blobs.doc_desc WHERE fk_doc=%%s" % max_lng
                      rows, idx = gmPG2.run_ro_queries(queries = [{'cmd': cmd, 'args': [self.pk_obj]}])
                      return rows

              #--------------------------------------------------------
              def add_description(self, description=None):
                      cmd = "insert into blobs.doc_desc (fk_doc, text) values (%s, %s)"
                      gmPG2.run_rw_queries(queries = [{'cmd': cmd, 'args': [self.pk_obj, description]}])
                      return True

              #--------------------------------------------------------
              def update_description(self, pk=None, description=None):
                      cmd = "update blobs.doc_desc set text = %(desc)s where fk_doc = %(doc)s and pk = %(pk_desc)s"
                      gmPG2.run_rw_queries(queries = [
                              {'cmd': cmd, 'args': {'doc': self.pk_obj, 'pk_desc': pk, 'desc': description}}
                      ])
                      return True

              #--------------------------------------------------------
              def delete_description(self, pk=None):
                      cmd = "delete from blobs.doc_desc where fk_doc = %(doc)s and pk = %(desc)s"
                      gmPG2.run_rw_queries(queries = [{'cmd': cmd, 'args': {'doc': self.pk_obj, 'desc': pk}}])
                      return True

              #--------------------------------------------------------
              def _get_parts(self):
                      cmd = _SQL_get_document_part_fields % "pk_doc = %s ORDER BY seq_idx"
                      rows, idx = gmPG2.run_ro_queries(queries = [{'cmd': cmd, 'args': [self.pk_obj]}], get_col_idx = True)
                      return [ cDocumentPart(row = {'pk_field': 'pk_obj', 'idx': idx, 'data': r}) for r in rows ]

              parts = property(_get_parts, lambda x:x)

              #--------------------------------------------------------
              def add_part(self, file=None, link_obj=None):
                      """Add a part to the document."""
                      # create dummy part
                      cmd = """
                              INSERT INTO blobs.doc_obj (
                                      fk_doc, data, seq_idx
                              ) VALUES (
                                      %(doc_id)s,
                                      ''::bytea,
                                      (SELECT coalesce(max(seq_idx)+1, 1) FROM blobs.doc_obj WHERE fk_doc = %(doc_id)s)
                              ) RETURNING pk"""
                      rows, idx = gmPG2.run_rw_queries (
                              link_obj = link_obj,
                              queries = [{'cmd': cmd, 'args': {'doc_id': self.pk_obj}}],
                              return_data = True
                      )
                      # init document part instance
                      pk_part = rows[0][0]
                      new_part = cDocumentPart(aPK_obj = pk_part, link_obj = link_obj)
                      if not new_part.update_data_from_file(link_obj = link_obj, fname = file):
                              _log.error('cannot import binary data from [%s] into document part' % file)
                              gmPG2.run_rw_queries (
                                      link_obj = link_obj,
                                      queries = [{'cmd': "DELETE FROM blobs.doc_obj WHERE pk = %s", 'args': [pk_part]}]
                              )
                              return None
                      new_part['filename'] = file
                      new_part.save_payload(conn = link_obj)

                      return new_part

              #--------------------------------------------------------
              def add_parts_from_files(self, files=None, reviewer=None):

                      new_parts = []

                      for filename in files:
                              new_part = self.add_part(file = filename)
                              if new_part is None:
                                      msg = 'cannot instantiate document part object from [%s]' % filename
                                      _log.error(msg)
                                      return (False, msg, filename)
                              new_parts.append(new_part)

                              if reviewer is not None:
                                      new_part['pk_intended_reviewer'] = reviewer                     # None == Null
                                      success, data = new_part.save_payload()
                                      if not success:
                                              msg = 'cannot set reviewer to [%s] on [%s]' % (reviewer, filename)
                                              _log.error(msg)
                                              _log.error(str(data))
                                              return (False, msg, filename)

                      return (True, '', new_parts)

              #--------------------------------------------------------
              def save_parts_to_files(self, export_dir=None, chunksize=0, conn=None):
                      fnames = []
                      for part in self.parts:
                              fname = part.save_to_file(aChunkSize = chunksize, directory = export_dir, conn = conn)
                              if fname is None:
                                      _log.error('cannot export document part [%s]', part)
                                      continue
                              fnames.append(fname)
                      return fnames

              #--------------------------------------------------------
              def _get_has_unreviewed_parts(self):
                      try:
                              return self.__has_unreviewed_parts
                      except AttributeError:
                              pass

                      cmd = "SELECT EXISTS(SELECT 1 FROM blobs.v_obj4doc_no_data WHERE pk_doc = %(pk)s AND reviewed IS FALSE)"
                      args = {'pk': self.pk_obj}
                      rows, idx = gmPG2.run_ro_queries(queries = [{'cmd': cmd, 'args': args}])
                      self.__has_unreviewed_parts = rows[0][0]

                      return self.__has_unreviewed_parts

              has_unreviewed_parts = property(_get_has_unreviewed_parts, lambda x:x)

              #--------------------------------------------------------
              def set_reviewed(self, technically_abnormal=None, clinically_relevant=None):
                      # FIXME: this is probably inefficient
                      for part in self.parts:
                              if not part.set_reviewed(technically_abnormal, clinically_relevant):
                                      return False
                      return True

              #--------------------------------------------------------
              def set_primary_reviewer(self, reviewer=None):
                      for part in self.parts:
                              part['pk_intended_reviewer'] = reviewer
                              success, data = part.save_payload()
                              if not success:
                                      _log.error('cannot set reviewer to [%s]' % reviewer)
                                      _log.error(str(data))
                                      return False
                      return True

              #--------------------------------------------------------
              def format_single_line(self):

                      part_count = len(self._payload[self._idx['seq_idx_list']])
                      if part_count == 0:
                              parts = _('no parts')
                      elif part_count == 1:
                              parts = _('1 part')
                      else:
                              parts = _('%s parts') % part_count

                      detail = ''
                      if self._payload[self._idx['ext_ref']] is not None:
                              detail = self._payload[self._idx['ext_ref']]
                      if self._payload[self._idx['unit']] is not None:
                              template = _('%s of %s')
                              if detail == '':
                                      detail = _('%s of %s') % (
                                              self._payload[self._idx['unit']],
                                              self._payload[self._idx['organization']]
                                      )
                              else:
                                      detail += (' @ ' + template % (
                                              self._payload[self._idx['unit']],
                                              self._payload[self._idx['organization']]
                                      ))
                      if detail != '':
                              detail = ' (%s)' % detail

                      return '%s %s (%s):%s%s' % (
                              gmDateTime.pydt_strftime(self._payload[self._idx['clin_when']], '%Y %b %d', accuracy = gmDateTime.acc_days),
                              self._payload[self._idx['l10n_type']],
                              parts,
                              gmTools.coalesce(self._payload[self._idx['comment']], '', ' "%s"'),
                              detail
                      )

              #--------------------------------------------------------
              def format(self, single_line=False):
                      if single_line:
                              return self.format_single_line()

                      part_count = len(self._payload[self._idx['seq_idx_list']])
                      if part_count == 0:
                              parts = _('no parts')
                      elif part_count == 1:
                              parts = _('1 part')
                      else:
                              parts = _('%s parts') % part_count
                      org = ''
                      if self._payload[self._idx['unit']] is not None:
                              if self._payload[self._idx['unit_is_receiver']]:
                                      org = _(' Receiver: %s @ %s\n') % (
                                              self._payload[self._idx['unit']],
                                              self._payload[self._idx['organization']]
                                      )
                              else:
                                      org = _(' Sender: %s @ %s\n') % (
                                              self._payload[self._idx['unit']],
                                              self._payload[self._idx['organization']]
                                      )
                      stay = ''
                      if self._payload[self._idx['pk_hospital_stay']] is not None:
                              stay = _('Hospital stay') + ': %s\n' % self.hospital_stay.format (
                                      left_margin = 0,
                                      include_procedures = False,
                                      include_docs = False,
                                      include_episode = False
                              )

                      txt = _(
                              '%s (%s)   #%s\n'
                              ' Created: %s\n'
                              ' Episode: %s\n'
                              '%s'
                              '%s'
                              '%s'
                              '%s'
                              '%s'
                      ) % (
                              self._payload[self._idx['l10n_type']],
                              parts,
                              self._payload[self._idx['pk_doc']],
                              gmDateTime.pydt_strftime(self._payload[self._idx['clin_when']], format = '%Y %b %d', accuracy = gmDateTime.acc_days),
                              self._payload[self._idx['episode']],
                              gmTools.coalesce(self._payload[self._idx['health_issue']], '', _(' Health issue: %s\n')),
                              gmTools.coalesce(self._payload[self._idx['ext_ref']], '', _(' External reference: %s\n')),
                              org,
                              stay,
                              gmTools.coalesce(self._payload[self._idx['comment']], '', ' %s')
                      )

                      return txt

              #--------------------------------------------------------
              def _get_hospital_stay(self):
                      if self._payload[self._idx['pk_hospital_stay']] is None:
                              return None
                      from Gnumed.business import gmEMRStructItems
                      return gmEMRStructItems.cHospitalStay(self._payload[self._idx['pk_hospital_stay']])

              hospital_stay = property(_get_hospital_stay, lambda x:x)

              #--------------------------------------------------------
              def _get_org_unit(self):
                      if self._payload[self._idx['pk_org_unit']] is None:
                              return None
                      return gmOrganization.cOrgUnit(self._payload[self._idx['pk_org_unit']])

              org_unit = property(_get_org_unit, lambda x:x)

              #--------------------------------------------------------
              def _get_procedures(self):
                      from Gnumed.business.gmEMRStructItems import get_procedures4document
                      return get_procedures4document(pk_document = self.pk_obj)

              procedures = property(_get_procedures, lambda x:x)

              #--------------------------------------------------------
              def _get_bills(self):
                      from Gnumed.business.gmBilling import get_bills4document
                      return get_bills4document(pk_document = self.pk_obj)

              bills = property(_get_bills, lambda x:x)

  ### Ancestors

  - cBusinessDBObject

  ### Instance variables

  `var bills`
    Expand source code

        def _get_bills(self):
                from Gnumed.business.gmBilling import get_bills4document
                return get_bills4document(pk_document = self.pk_obj)

  `var has_unreviewed_parts`
    Expand source code

        def _get_has_unreviewed_parts(self):
                try:
                        return self.__has_unreviewed_parts
                except AttributeError:
                        pass

                cmd = "SELECT EXISTS(SELECT 1 FROM blobs.v_obj4doc_no_data WHERE pk_doc = %(pk)s AND reviewed IS FALSE)"
                args = {'pk': self.pk_obj}
                rows, idx = gmPG2.run_ro_queries(queries = [{'cmd': cmd, 'args': args}])
                self.__has_unreviewed_parts = rows[0][0]

                return self.__has_unreviewed_parts

  `var hospital_stay`
    Expand source code

        def _get_hospital_stay(self):
                if self._payload[self._idx['pk_hospital_stay']] is None:
                        return None
                from Gnumed.business import gmEMRStructItems
                return gmEMRStructItems.cHospitalStay(self._payload[self._idx['pk_hospital_stay']])

  `var org_unit`
    Expand source code

        def _get_org_unit(self):
                if self._payload[self._idx['pk_org_unit']] is None:
                        return None
                return gmOrganization.cOrgUnit(self._payload[self._idx['pk_org_unit']])

  `var parts`
    Expand source code

        def _get_parts(self):
                cmd = _SQL_get_document_part_fields % "pk_doc = %s ORDER BY seq_idx"
                rows, idx = gmPG2.run_ro_queries(queries = [{'cmd': cmd, 'args': [self.pk_obj]}], get_col_idx = True)
                return [ cDocumentPart(row = {'pk_field': 'pk_obj', 'idx': idx, 'data': r}) for r in rows ]

  `var procedures`
    Expand source code

        def _get_procedures(self):
                from Gnumed.business.gmEMRStructItems import get_procedures4document
                return get_procedures4document(pk_document = self.pk_obj)

  ### Methods

  `def add_description(self, description=None)`
    Expand source code

        def add_description(self, description=None):
                cmd = "insert into blobs.doc_desc (fk_doc, text) values (%s, %s)"
                gmPG2.run_rw_queries(queries = [{'cmd': cmd, 'args': [self.pk_obj, description]}])
                return True

  `def add_part(self, file=None, link_obj=None)`

    Add a part to the document.

    Expand source code

        def add_part(self, file=None, link_obj=None):
                """Add a part to the document."""
                # create dummy part
                cmd = """
                        INSERT INTO blobs.doc_obj (
                                fk_doc, data, seq_idx
                        ) VALUES (
                                %(doc_id)s,
                                ''::bytea,
                                (SELECT coalesce(max(seq_idx)+1, 1) FROM blobs.doc_obj WHERE fk_doc = %(doc_id)s)
                        ) RETURNING pk"""
                rows, idx = gmPG2.run_rw_queries (
                        link_obj = link_obj,
                        queries = [{'cmd': cmd, 'args': {'doc_id': self.pk_obj}}],
                        return_data = True
                )
                # init document part instance
                pk_part = rows[0][0]
                new_part = cDocumentPart(aPK_obj = pk_part, link_obj = link_obj)
                if not new_part.update_data_from_file(link_obj = link_obj, fname = file):
                        _log.error('cannot import binary data from [%s] into document part' % file)
                        gmPG2.run_rw_queries (
                                link_obj = link_obj,
                                queries = [{'cmd': "DELETE FROM blobs.doc_obj WHERE pk = %s", 'args': [pk_part]}]
                        )
                        return None
                new_part['filename'] = file
                new_part.save_payload(conn = link_obj)

                return new_part

  `def add_parts_from_files(self, files=None, reviewer=None)`
    Expand source code

        def add_parts_from_files(self, files=None, reviewer=None):

                new_parts = []

                for filename in files:
                        new_part = self.add_part(file = filename)
                        if new_part is None:
                                msg = 'cannot instantiate document part object from [%s]' % filename
                                _log.error(msg)
                                return (False, msg, filename)
                        new_parts.append(new_part)

                        if reviewer is not None:
                                new_part['pk_intended_reviewer'] = reviewer                     # None == Null
                                success, data = new_part.save_payload()
                                if not success:
                                        msg = 'cannot set reviewer to [%s] on [%s]' % (reviewer, filename)
                                        _log.error(msg)
                                        _log.error(str(data))
                                        return (False, msg, filename)

                return (True, '', new_parts)

  `def delete_description(self, pk=None)`
    Expand source code

        def delete_description(self, pk=None):
                cmd = "delete from blobs.doc_desc where fk_doc = %(doc)s and pk = %(desc)s"
                gmPG2.run_rw_queries(queries = [{'cmd': cmd, 'args': {'doc': self.pk_obj, 'desc': pk}}])
                return True

  `def format_single_line(self)`
    Expand source code

        def format_single_line(self):

                part_count = len(self._payload[self._idx['seq_idx_list']])
                if part_count == 0:
                        parts = _('no parts')
                elif part_count == 1:
                        parts = _('1 part')
                else:
                        parts = _('%s parts') % part_count

                detail = ''
                if self._payload[self._idx['ext_ref']] is not None:
                        detail = self._payload[self._idx['ext_ref']]
                if self._payload[self._idx['unit']] is not None:
                        template = _('%s of %s')
                        if detail == '':
                                detail = _('%s of %s') % (
                                        self._payload[self._idx['unit']],
                                        self._payload[self._idx['organization']]
                                )
                        else:
                                detail += (' @ ' + template % (
                                        self._payload[self._idx['unit']],
                                        self._payload[self._idx['organization']]
                                ))
                if detail != '':
                        detail = ' (%s)' % detail

                return '%s %s (%s):%s%s' % (
                        gmDateTime.pydt_strftime(self._payload[self._idx['clin_when']], '%Y %b %d', accuracy = gmDateTime.acc_days),
                        self._payload[self._idx['l10n_type']],
                        parts,
                        gmTools.coalesce(self._payload[self._idx['comment']], '', ' "%s"'),
                        detail
                )

  `def get_descriptions(self, max_lng=250)`

    Get document descriptions.

    - will return a list of rows
    Expand source code

        def get_descriptions(self, max_lng=250):
                """Get document descriptions.

                - will return a list of rows
                """
                if max_lng is None:
                        cmd = "SELECT pk, text FROM blobs.doc_desc WHERE fk_doc = %s"
                else:
                        cmd = "SELECT pk, substring(text from 1 for %s) FROM blobs.doc_desc WHERE fk_doc=%%s" % max_lng
                rows, idx = gmPG2.run_ro_queries(queries = [{'cmd': cmd, 'args': [self.pk_obj]}])
                return rows

  `def save_parts_to_files(self, export_dir=None, chunksize=0, conn=None)`
    Expand source code

        def save_parts_to_files(self, export_dir=None, chunksize=0, conn=None):
                fnames = []
                for part in self.parts:
                        fname = part.save_to_file(aChunkSize = chunksize, directory = export_dir, conn = conn)
                        if fname is None:
                                _log.error('cannot export document part [%s]', part)
                                continue
                        fnames.append(fname)
                return fnames

  `def set_primary_reviewer(self, reviewer=None)`
    Expand source code

        def set_primary_reviewer(self, reviewer=None):
                for part in self.parts:
                        part['pk_intended_reviewer'] = reviewer
                        success, data = part.save_payload()
                        if not success:
                                _log.error('cannot set reviewer to [%s]' % reviewer)
                                _log.error(str(data))
                                return False
                return True

  `def set_reviewed(self, technically_abnormal=None, clinically_relevant=None)`
    Expand source code

        def set_reviewed(self, technically_abnormal=None, clinically_relevant=None):
                # FIXME: this is probably inefficient
                for part in self.parts:
                        if not part.set_reviewed(technically_abnormal, clinically_relevant):
                                return False
                return True

  `def update_description(self, pk=None, description=None)`
    Expand source code

        def update_description(self, pk=None, description=None):
                cmd = "update blobs.doc_desc set text = %(desc)s where fk_doc = %(doc)s and pk = %(pk_desc)s"
                gmPG2.run_rw_queries(queries = [
                        {'cmd': cmd, 'args': {'doc': self.pk_obj, 'pk_desc': pk, 'desc': description}}
                ])
                return True

  ### Inherited members

  - `cBusinessDBObject`:
    - `fields_as_dict`
    - `format`
    - `get_fields`
    - `get_patient`
    - `get_updatable_fields`
    - `is_modified`
    - `patient_pk`
    - `refetch_payload`
    - `same_payload`
    - `save`
    - `save_payload`
    - `staff_id`
`class cDocumentFolder (aPKey=None)`

  Represents a folder with medical documents for a single patient.

  Fails if

  - patient referenced by aPKey does not exist
  Expand source code

      class cDocumentFolder:
              """Represents a folder with medical documents for a single patient."""

              def __init__(self, aPKey = None):
                      """Fails if

                      - patient referenced by aPKey does not exist
                      """
                      self.pk_patient = aPKey                 # == identity.pk == primary key
                      if not self._pkey_exists():
                              raise gmExceptions.ConstructorError("No patient with PK [%s] in database." % aPKey)

                      # register backend notification interests
                      # (keep this last so we won't hang on threads when
                      #  failing this constructor for other reasons ...)
      #               if not self._register_interests():
      #                       raise gmExceptions.ConstructorError, "cannot register signal interests"

                      _log.debug('instantiated document folder for patient [%s]' % self.pk_patient)
              #--------------------------------------------------------
              def cleanup(self):
                      pass
              #--------------------------------------------------------
              # internal helper
              #--------------------------------------------------------
              def _pkey_exists(self):
                      """Does this primary key exist ?

                      - true/false/None
                      """
                      # patient in demographic database ?
                      rows, idx = gmPG2.run_ro_queries(queries = [
                              {'cmd': "select exists(select pk from dem.identity where pk = %s)", 'args': [self.pk_patient]}
                      ])
                      if not rows[0][0]:
                              _log.error("patient [%s] not in demographic database" % self.pk_patient)
                              return None
                      return True
              #--------------------------------------------------------
              # API
              #--------------------------------------------------------
              def get_latest_freediams_prescription(self):
                      cmd = """
                              SELECT pk_doc
                              FROM blobs.v_doc_med
                              WHERE
                                      pk_patient = %(pat)s
                                              AND
                                      type = %(typ)s
                                              AND
                                      ext_ref = %(ref)s
                              ORDER BY
                                      clin_when DESC
                              LIMIT 1
                      """
                      args = {
                              'pat': self.pk_patient,
                              'typ': DOCUMENT_TYPE_PRESCRIPTION,
                              'ref': 'FreeDiams'
                      }
                      rows, idx = gmPG2.run_ro_queries(queries = [{'cmd': cmd, 'args': args}])
                      if len(rows) == 0:
                              _log.info('no FreeDiams prescription available for patient [%s]' % self.pk_patient)
                              return None
                      prescription = cDocument(aPK_obj = rows[0][0])
                      return prescription

              #--------------------------------------------------------
              def get_latest_mugshot(self):
                      cmd = "SELECT pk_obj FROM blobs.v_latest_mugshot WHERE pk_patient = %s"
                      rows, idx = gmPG2.run_ro_queries(queries = [{'cmd': cmd, 'args': [self.pk_patient]}])
                      if len(rows) == 0:
                              _log.info('no mugshots available for patient [%s]' % self.pk_patient)
                              return None
                      return cDocumentPart(aPK_obj = rows[0][0])

              latest_mugshot = property(get_latest_mugshot, lambda x:x)

              #--------------------------------------------------------
              def get_mugshot_list(self, latest_only=True):
                      if latest_only:
                              cmd = "select pk_doc, pk_obj from blobs.v_latest_mugshot where pk_patient=%s"
                      else:
                              cmd = """
                                      select
                                              vdm.pk_doc as pk_doc,
                                              dobj.pk as pk_obj
                                      from
                                              blobs.v_doc_med vdm
                                              blobs.doc_obj dobj
                                      where
                                              vdm.pk_type = (select pk from blobs.doc_type where name = 'patient photograph')
                                              and vdm.pk_patient = %s
                                              and dobj.fk_doc = vdm.pk_doc
                              """
                      rows, idx = gmPG2.run_ro_queries(queries = [{'cmd': cmd, 'args': [self.pk_patient]}])
                      return rows

              #--------------------------------------------------------
              def get_doc_list(self, doc_type=None):
                      """return flat list of document IDs"""

                      args = {
                              'ID': self.pk_patient,
                              'TYP': doc_type
                      }

                      cmd = """
                              select vdm.pk_doc
                              from blobs.v_doc_med vdm
                              where
                                      vdm.pk_patient = %%(ID)s
                                      %s
                              order by vdm.clin_when"""

                      if doc_type is None:
                              cmd = cmd % ''
                      else:
                              try:
                                      int(doc_type)
                                      cmd = cmd % 'and vdm.pk_type = %(TYP)s'
                              except (TypeError, ValueError):
                                      cmd = cmd % 'and vdm.pk_type = (select pk from blobs.doc_type where name = %(TYP)s)'

                      rows, idx = gmPG2.run_ro_queries(queries = [{'cmd': cmd, 'args': args}])
                      doc_ids = []
                      for row in rows:
                              doc_ids.append(row[0])
                      return doc_ids

              #--------------------------------------------------------
              def get_visual_progress_notes(self, episodes=None, encounter=None):
                      return self.get_documents (
                              doc_type = DOCUMENT_TYPE_VISUAL_PROGRESS_NOTE,
                              pk_episodes = episodes,
                              encounter = encounter
                      )

              #--------------------------------------------------------
              def get_unsigned_documents(self):
                      args = {'pat': self.pk_patient}
                      cmd = _SQL_get_document_fields % """
                              pk_doc IN (
                                      SELECT DISTINCT ON (b_vo.pk_doc) b_vo.pk_doc
                                      FROM blobs.v_obj4doc_no_data b_vo
                                      WHERE
                                              pk_patient = %(pat)s
                                                      AND
                                              reviewed IS FALSE
                              )
                              ORDER BY clin_when DESC"""
                      rows, idx = gmPG2.run_ro_queries(queries = [{'cmd': cmd, 'args': args}], get_col_idx = True)
                      return [ cDocument(row = {'pk_field': 'pk_doc', 'idx': idx, 'data': r}) for r in rows ]

              #--------------------------------------------------------
              def get_documents(self, doc_type=None, pk_episodes=None, encounter=None, order_by=None, exclude_unsigned=False, pk_types=None):
                      """Return list of documents."""

                      args = {
                              'pat': self.pk_patient,
                              'type': doc_type,
                              'enc': encounter
                      }
                      where_parts = ['pk_patient = %(pat)s']

                      if doc_type is not None:
                              try:
                                      int(doc_type)
                                      where_parts.append('pk_type = %(type)s')
                              except (TypeError, ValueError):
                                      where_parts.append('pk_type = (SELECT pk FROM blobs.doc_type WHERE name = %(type)s)')

                      if pk_types is not None:
                              where_parts.append('pk_type IN %(pk_types)s')
                              args['pk_types'] = tuple(pk_types)

                      if (pk_episodes is not None) and (len(pk_episodes) > 0):
                              where_parts.append('pk_episode IN %(epis)s')
                              args['epis'] = tuple(pk_episodes)

                      if encounter is not None:
                              where_parts.append('pk_encounter = %(enc)s')

                      if exclude_unsigned:
                              where_parts.append('pk_doc IN (SELECT b_vo.pk_doc FROM blobs.v_obj4doc_no_data b_vo WHERE b_vo.pk_patient = %(pat)s AND b_vo.reviewed IS TRUE)')

                      if order_by is None:
                              order_by = 'ORDER BY clin_when'

                      cmd = "%s\n%s" % (_SQL_get_document_fields % ' AND '.join(where_parts), order_by)
                      rows, idx = gmPG2.run_ro_queries(queries = [{'cmd': cmd, 'args': args}], get_col_idx = True)

                      return [ cDocument(row = {'pk_field': 'pk_doc', 'idx': idx, 'data': r}) for r in rows ]

              documents = property(get_documents, lambda x:x)

              #--------------------------------------------------------
              def add_document(self, document_type=None, encounter=None, episode=None, link_obj=None):
                      return create_document(link_obj = link_obj, document_type = document_type, encounter = encounter, episode = episode)

              #--------------------------------------------------------
              def add_prescription(self, encounter=None, episode=None, link_obj=None):
                      return self.add_document (
                              link_obj = link_obj,
                              document_type = create_document_type (
                                      document_type = DOCUMENT_TYPE_PRESCRIPTION
                              )['pk_doc_type'],
                              encounter = encounter,
                              episode = episode
                      )

              #--------------------------------------------------------
              def _get_all_document_org_units(self):
                      cmd = gmOrganization._SQL_get_org_unit % (
                              'pk_org_unit IN (SELECT DISTINCT ON (pk_org_unit) pk_org_unit FROM blobs.v_doc_med WHERE pk_patient = %(pat)s)'
                      )
                      args = {'pat': self.pk_patient}
                      rows, idx = gmPG2.run_ro_queries(queries = [{'cmd': cmd, 'args': args}], get_col_idx = True)
                      return [ gmOrganization.cOrgUnit(row = {'data': r, 'idx': idx, 'pk_field': 'pk_org_unit'}) for r in rows ]

              all_document_org_units = property(_get_all_document_org_units, lambda x:x)

  ### Instance variables

  `var all_document_org_units`
    Expand source code

        def _get_all_document_org_units(self):
                cmd = gmOrganization._SQL_get_org_unit % (
                        'pk_org_unit IN (SELECT DISTINCT ON (pk_org_unit) pk_org_unit FROM blobs.v_doc_med WHERE pk_patient = %(pat)s)'
                )
                args = {'pat': self.pk_patient}
                rows, idx = gmPG2.run_ro_queries(queries = [{'cmd': cmd, 'args': args}], get_col_idx = True)
                return [ gmOrganization.cOrgUnit(row = {'data': r, 'idx': idx, 'pk_field': 'pk_org_unit'}) for r in rows ]

  `var documents`

    Return list of documents.

    Expand source code

        def get_documents(self, doc_type=None, pk_episodes=None, encounter=None, order_by=None, exclude_unsigned=False, pk_types=None):
                """Return list of documents."""

                args = {
                        'pat': self.pk_patient,
                        'type': doc_type,
                        'enc': encounter
                }
                where_parts = ['pk_patient = %(pat)s']

                if doc_type is not None:
                        try:
                                int(doc_type)
                                where_parts.append('pk_type = %(type)s')
                        except (TypeError, ValueError):
                                where_parts.append('pk_type = (SELECT pk FROM blobs.doc_type WHERE name = %(type)s)')

                if pk_types is not None:
                        where_parts.append('pk_type IN %(pk_types)s')
                        args['pk_types'] = tuple(pk_types)

                if (pk_episodes is not None) and (len(pk_episodes) > 0):
                        where_parts.append('pk_episode IN %(epis)s')
                        args['epis'] = tuple(pk_episodes)

                if encounter is not None:
                        where_parts.append('pk_encounter = %(enc)s')

                if exclude_unsigned:
                        where_parts.append('pk_doc IN (SELECT b_vo.pk_doc FROM blobs.v_obj4doc_no_data b_vo WHERE b_vo.pk_patient = %(pat)s AND b_vo.reviewed IS TRUE)')

                if order_by is None:
                        order_by = 'ORDER BY clin_when'

                cmd = "%s\n%s" % (_SQL_get_document_fields % ' AND '.join(where_parts), order_by)
                rows, idx = gmPG2.run_ro_queries(queries = [{'cmd': cmd, 'args': args}], get_col_idx = True)

                return [ cDocument(row = {'pk_field': 'pk_doc', 'idx': idx, 'data': r}) for r in rows ]

  `var latest_mugshot`
    Expand source code

        def get_latest_mugshot(self):
                cmd = "SELECT pk_obj FROM blobs.v_latest_mugshot WHERE pk_patient = %s"
                rows, idx = gmPG2.run_ro_queries(queries = [{'cmd': cmd, 'args': [self.pk_patient]}])
                if len(rows) == 0:
                        _log.info('no mugshots available for patient [%s]' % self.pk_patient)
                        return None
                return cDocumentPart(aPK_obj = rows[0][0])

  ### Methods

  `def add_document(self, document_type=None, encounter=None, episode=None, link_obj=None)`
    Expand source code

        def add_document(self, document_type=None, encounter=None, episode=None, link_obj=None):
                return create_document(link_obj = link_obj, document_type = document_type, encounter = encounter, episode = episode)

  `def add_prescription(self, encounter=None, episode=None, link_obj=None)`
    Expand source code

        def add_prescription(self, encounter=None, episode=None, link_obj=None):
                return self.add_document (
                        link_obj = link_obj,
                        document_type = create_document_type (
                                document_type = DOCUMENT_TYPE_PRESCRIPTION
                        )['pk_doc_type'],
                        encounter = encounter,
                        episode = episode
                )

  `def cleanup(self)`
    Expand source code

        def cleanup(self):
                pass

  `def get_doc_list(self, doc_type=None)`

    return flat list of document IDs

    Expand source code

        def get_doc_list(self, doc_type=None):
                """return flat list of document IDs"""

                args = {
                        'ID': self.pk_patient,
                        'TYP': doc_type
                }

                cmd = """
                        select vdm.pk_doc
                        from blobs.v_doc_med vdm
                        where
                                vdm.pk_patient = %%(ID)s
                                %s
                        order by vdm.clin_when"""

                if doc_type is None:
                        cmd = cmd % ''
                else:
                        try:
                                int(doc_type)
                                cmd = cmd % 'and vdm.pk_type = %(TYP)s'
                        except (TypeError, ValueError):
                                cmd = cmd % 'and vdm.pk_type = (select pk from blobs.doc_type where name = %(TYP)s)'

                rows, idx = gmPG2.run_ro_queries(queries = [{'cmd': cmd, 'args': args}])
                doc_ids = []
                for row in rows:
                        doc_ids.append(row[0])
                return doc_ids

  `def get_documents(self, doc_type=None, pk_episodes=None, encounter=None, order_by=None, exclude_unsigned=False, pk_types=None)`

    Return list of documents.

    Expand source code

        def get_documents(self, doc_type=None, pk_episodes=None, encounter=None, order_by=None, exclude_unsigned=False, pk_types=None):
                """Return list of documents."""

                args = {
                        'pat': self.pk_patient,
                        'type': doc_type,
                        'enc': encounter
                }
                where_parts = ['pk_patient = %(pat)s']

                if doc_type is not None:
                        try:
                                int(doc_type)
                                where_parts.append('pk_type = %(type)s')
                        except (TypeError, ValueError):
                                where_parts.append('pk_type = (SELECT pk FROM blobs.doc_type WHERE name = %(type)s)')

                if pk_types is not None:
                        where_parts.append('pk_type IN %(pk_types)s')
                        args['pk_types'] = tuple(pk_types)

                if (pk_episodes is not None) and (len(pk_episodes) > 0):
                        where_parts.append('pk_episode IN %(epis)s')
                        args['epis'] = tuple(pk_episodes)

                if encounter is not None:
                        where_parts.append('pk_encounter = %(enc)s')

                if exclude_unsigned:
                        where_parts.append('pk_doc IN (SELECT b_vo.pk_doc FROM blobs.v_obj4doc_no_data b_vo WHERE b_vo.pk_patient = %(pat)s AND b_vo.reviewed IS TRUE)')

                if order_by is None:
                        order_by = 'ORDER BY clin_when'

                cmd = "%s\n%s" % (_SQL_get_document_fields % ' AND '.join(where_parts), order_by)
                rows, idx = gmPG2.run_ro_queries(queries = [{'cmd': cmd, 'args': args}], get_col_idx = True)

                return [ cDocument(row = {'pk_field': 'pk_doc', 'idx': idx, 'data': r}) for r in rows ]

  `def get_latest_freediams_prescription(self)`
    Expand source code

        def get_latest_freediams_prescription(self):
                cmd = """
                        SELECT pk_doc
                        FROM blobs.v_doc_med
                        WHERE
                                pk_patient = %(pat)s
                                        AND
                                type = %(typ)s
                                        AND
                                ext_ref = %(ref)s
                        ORDER BY
                                clin_when DESC
                        LIMIT 1
                """
                args = {
                        'pat': self.pk_patient,
                        'typ': DOCUMENT_TYPE_PRESCRIPTION,
                        'ref': 'FreeDiams'
                }
                rows, idx = gmPG2.run_ro_queries(queries = [{'cmd': cmd, 'args': args}])
                if len(rows) == 0:
                        _log.info('no FreeDiams prescription available for patient [%s]' % self.pk_patient)
                        return None
                prescription = cDocument(aPK_obj = rows[0][0])
                return prescription

  `def get_latest_mugshot(self)`
    Expand source code

        def get_latest_mugshot(self):
                cmd = "SELECT pk_obj FROM blobs.v_latest_mugshot WHERE pk_patient = %s"
                rows, idx = gmPG2.run_ro_queries(queries = [{'cmd': cmd, 'args': [self.pk_patient]}])
                if len(rows) == 0:
                        _log.info('no mugshots available for patient [%s]' % self.pk_patient)
                        return None
                return cDocumentPart(aPK_obj = rows[0][0])

  `def get_mugshot_list(self, latest_only=True)`
    Expand source code

        def get_mugshot_list(self, latest_only=True):
                if latest_only:
                        cmd = "select pk_doc, pk_obj from blobs.v_latest_mugshot where pk_patient=%s"
                else:
                        cmd = """
                                select
                                        vdm.pk_doc as pk_doc,
                                        dobj.pk as pk_obj
                                from
                                        blobs.v_doc_med vdm
                                        blobs.doc_obj dobj
                                where
                                        vdm.pk_type = (select pk from blobs.doc_type where name = 'patient photograph')
                                        and vdm.pk_patient = %s
                                        and dobj.fk_doc = vdm.pk_doc
                        """
                rows, idx = gmPG2.run_ro_queries(queries = [{'cmd': cmd, 'args': [self.pk_patient]}])
                return rows

  `def get_unsigned_documents(self)`
    Expand source code

        def get_unsigned_documents(self):
                args = {'pat': self.pk_patient}
                cmd = _SQL_get_document_fields % """
                        pk_doc IN (
                                SELECT DISTINCT ON (b_vo.pk_doc) b_vo.pk_doc
                                FROM blobs.v_obj4doc_no_data b_vo
                                WHERE
                                        pk_patient = %(pat)s
                                                AND
                                        reviewed IS FALSE
                        )
                        ORDER BY clin_when DESC"""
                rows, idx = gmPG2.run_ro_queries(queries = [{'cmd': cmd, 'args': args}], get_col_idx = True)
                return [ cDocument(row = {'pk_field': 'pk_doc', 'idx': idx, 'data': r}) for r in rows ]

  `def get_visual_progress_notes(self, episodes=None, encounter=None)`
    Expand source code

        def get_visual_progress_notes(self, episodes=None, encounter=None):
                return self.get_documents (
                        doc_type = DOCUMENT_TYPE_VISUAL_PROGRESS_NOTE,
                        pk_episodes = episodes,
                        encounter = encounter
                )

`class cDocumentPart (aPK_obj=None, row: dict = None, link_obj=None)`

  Represents one part of a medical document.

  Init business object.

  Call from child classes like so:

          super().__init__(aPK_obj = aPK_obj, row = row, link_obj = link_obj)

  ## Args

  `aPK_obj`
    retrieve data from backend * a simple value the primary key WHERE condition must be a simple column * a dictionary of values the primary key WHERE condition must be a subselect consuming the dict and producing the single-value primary key
  `row`
    must hold the fields * idx: a dict mapping field names to position * data: the field values in a list (as returned by cursor.fetchone() in the DB-API) * pk_field: the name of the primary key field OR * pk_obj: a dictionary suitable for passed to cursor.execute and holding the primary key values, used for composite PKs

  ## Examples

  row = { 'data': rows[0], 'idx': idx, 'pk_field': 'pk_XXX (the PK column name)', 'pk_obj': {'pk_col1': pk_col1_val, 'pk_col2': pk_col2_val} } rows, idx = gmPG2.run_ro_queries(queries = [{'cmd': cmd, 'args': args}], get_col_idx = True) objects = [ cChildClass(row = {'data': r, 'idx': idx, 'pk_field': 'the PK column name'}) for r in rows ]

  Expand source code

      class cDocumentPart(gmBusinessDBObject.cBusinessDBObject):
              """Represents one part of a medical document."""

              _cmd_fetch_payload = _SQL_get_document_part_fields % "pk_obj = %s"
              _cmds_store_payload = [
                      """UPDATE blobs.doc_obj SET
                                      seq_idx = %(seq_idx)s,
                                      comment = gm.nullify_empty_string(%(obj_comment)s),
                                      filename = gm.nullify_empty_string(%(filename)s),
                                      fk_intended_reviewer = %(pk_intended_reviewer)s
                              WHERE
                                      pk = %(pk_obj)s
                                              AND
                                      xmin = %(xmin_doc_obj)s
                              RETURNING
                                      xmin AS xmin_doc_obj"""
              ]
              _updatable_fields = [
                      'seq_idx',
                      'obj_comment',
                      'pk_intended_reviewer',
                      'filename'
              ]
              #--------------------------------------------------------
              # retrieve data
              #--------------------------------------------------------
              def save_to_file(self, aChunkSize=0, filename=None, target_mime=None, target_extension=None, ignore_conversion_problems=False, directory=None, adjust_extension=False, conn=None):

                      if filename is None:
                              filename = self.get_useful_filename(make_unique = True, directory = directory)

                      filename = self.__download_to_file(filename = filename)
                      if filename is None:
                              return None

                      if target_mime is None:
                              if filename.endswith('.dat'):
                                      if adjust_extension:
                                              return gmMimeLib.adjust_extension_by_mimetype(filename)
                              return filename

                      if target_extension is None:
                              target_extension = gmMimeLib.guess_ext_by_mimetype(mimetype = target_mime)

                      target_path, name = os.path.split(filename)
                      name, tmp = os.path.splitext(name)
                      target_fname = gmTools.get_unique_filename (
                              prefix = '%s-conv-' % name,
                              suffix = target_extension
                      )
                      _log.debug('attempting conversion: [%s] -> [<%s>:%s]', filename, target_mime, target_fname)
                      converted_fname = gmMimeLib.convert_file (
                              filename = filename,
                              target_mime = target_mime,
                              target_filename = target_fname
                      )
                      if converted_fname is not None:
                              return converted_fname

                      _log.warning('conversion failed')
                      if not ignore_conversion_problems:
                              return None

                      if filename.endswith('.dat'):
                              if adjust_extension:
                                      filename = gmMimeLib.adjust_extension_by_mimetype(filename)
                      _log.warning('programmed to ignore conversion problems, hoping receiver can handle [%s]', filename)
                      return filename

              #--------------------------------------------------------
              def get_reviews(self):
                      cmd = """
      SELECT
              reviewer,
              reviewed_when,
              is_technically_abnormal,
              clinically_relevant,
              is_review_by_responsible_reviewer,
              is_your_review,
              coalesce(comment, '')
      FROM blobs.v_reviewed_doc_objects
      WHERE pk_doc_obj = %s
      ORDER BY
              is_your_review desc,
              is_review_by_responsible_reviewer desc,
              reviewed_when desc
      """
                      rows, idx = gmPG2.run_ro_queries(queries = [{'cmd': cmd, 'args': [self.pk_obj]}])
                      return rows

              #--------------------------------------------------------
              def __get_containing_document(self):
                      return cDocument(aPK_obj = self._payload[self._idx['pk_doc']])

              containing_document = property(__get_containing_document)

              #--------------------------------------------------------
              # store data
              #--------------------------------------------------------
              def update_data_from_file(self, fname=None, link_obj=None):
                      # sanity check
                      if not (os.access(fname, os.R_OK) and os.path.isfile(fname)):
                              _log.error('[%s] is not a readable file' % fname)
                              return False

                      cmd = "UPDATE blobs.doc_obj SET data = %(data)s::BYTEA WHERE pk = %(pk)s RETURNING md5(data) AS md5"
                      args = {'pk': self.pk_obj}
                      md5 = gmTools.file2md5(filename = fname, return_hex = True)
                      if not gmPG2.file2bytea(conn = link_obj, query = cmd, filename = fname, args = args, file_md5 = md5):
                              return False

                      # must update XMIN now ...
                      self.refetch_payload(link_obj = link_obj)
                      return True

              #--------------------------------------------------------
              def set_reviewed(self, technically_abnormal=None, clinically_relevant=None):
                      # row already there ?
                      cmd = """
      select pk
      from blobs.reviewed_doc_objs
      where
              fk_reviewed_row = %s and
              fk_reviewer = (select pk from dem.staff where db_user = current_user)"""
                      rows, idx = gmPG2.run_ro_queries(queries = [{'cmd': cmd, 'args': [self.pk_obj]}])

                      # INSERT needed
                      if len(rows) == 0:
                              cols = [
                                      "fk_reviewer",
                                      "fk_reviewed_row",
                                      "is_technically_abnormal",
                                      "clinically_relevant"
                              ]
                              vals = [
                                      '%(fk_row)s',
                                      '%(abnormal)s',
                                      '%(relevant)s'
                              ]
                              args = {
                                      'fk_row': self.pk_obj,
                                      'abnormal': technically_abnormal,
                                      'relevant': clinically_relevant
                              }
                              cmd = """
      insert into blobs.reviewed_doc_objs (
              %s
      ) values (
              (select pk from dem.staff where db_user=current_user),
              %s
      )""" % (', '.join(cols), ', '.join(vals))

                      # UPDATE needed
                      if len(rows) == 1:
                              pk_review = rows[0][0]
                              args = {
                                      'abnormal': technically_abnormal,
                                      'relevant': clinically_relevant,
                                      'pk_review': pk_review
                              }
                              cmd = """
                                      UPDATE blobs.reviewed_doc_objs SET
                                              is_technically_abnormal = %(abnormal)s,
                                              clinically_relevant = %(relevant)s
                                      WHERE
                                              pk = %(pk_review)s
                              """
                      rows, idx = gmPG2.run_rw_queries(queries = [{'cmd': cmd, 'args': args}])

                      return True

              #--------------------------------------------------------
              def set_as_active_photograph(self):
                      if self._payload[self._idx['type']] != 'patient photograph':
                              return False
                      # set seq_idx to current max + 1
                      cmd = 'SELECT coalesce(max(seq_idx)+1, 1) FROM blobs.doc_obj WHERE fk_doc = %(doc_id)s'
                      rows, idx = gmPG2.run_ro_queries (
                              queries = [{
                                      'cmd': cmd,
                                      'args': {'doc_id': self._payload[self._idx['pk_doc']]}
                              }]
                      )
                      self._payload[self._idx['seq_idx']] = rows[0][0]
                      self._is_modified = True
                      self.save_payload()

              #--------------------------------------------------------
              def reattach(self, pk_doc=None):
                      if pk_doc == self._payload[self._idx['pk_doc']]:
                              return True

                      cmd = """
                              UPDATE blobs.doc_obj SET
                                      fk_doc = %(pk_doc_target)s,
                                      -- coalesce needed for no-parts target docs
                                      seq_idx = (SELECT coalesce(max(seq_idx) + 1, 1) FROM blobs.doc_obj WHERE fk_doc = %(pk_doc_target)s)
                              WHERE
                                      EXISTS(SELECT 1 FROM blobs.doc_med WHERE pk = %(pk_doc_target)s)
                                              AND
                                      pk = %(pk_obj)s
                                              AND
                                      xmin = %(xmin_doc_obj)s
                              RETURNING fk_doc
                      """
                      args = {
                              'pk_doc_target': pk_doc,
                              'pk_obj': self.pk_obj,
                              'xmin_doc_obj': self._payload[self._idx['xmin_doc_obj']]
                      }
                      rows, idx = gmPG2.run_rw_queries(queries = [{'cmd': cmd, 'args': args}], return_data = True, get_col_idx = False)
                      if len(rows) == 0:
                              return False
                      # The following should never hold true because the target
                      # fk_doc is returned from the query and it is checked for
                      # equality before the UPDATE already. Assuming the update
                      # failed to update a row because the target fk_doc did
                      # not exist we would not get *any* rows in return - for
                      # which condition we also already checked
                      if rows[0]['fk_doc'] == self._payload[self._idx['pk_doc']]:
                              return False

                      self.refetch_payload()
                      return True

              #--------------------------------------------------------
              def display_via_mime(self, chunksize=0, block=None):

                      fname = self.save_to_file(aChunkSize = chunksize)
                      if fname is None:
                              return False, ''

                      success, msg = gmMimeLib.call_viewer_on_file(fname, block = block)
                      if not success:
                              return False, msg

                      return True, ''

              #--------------------------------------------------------
              def format_single_line(self):
                      f_ext = ''
                      if self._payload[self._idx['filename']] is not None:
                              f_ext = os.path.splitext(self._payload[self._idx['filename']])[1].strip('.').strip()
                      if f_ext != '':
                              f_ext = ' .' + f_ext.upper()
                      txt = _('part %s, %s%s%s of document %s from %s%s') % (
                              self._payload[self._idx['seq_idx']],
                              gmTools.size2str(self._payload[self._idx['size']]),
                              f_ext,
                              gmTools.coalesce(self._payload[self._idx['obj_comment']], '', ' ("%s")'),
                              self._payload[self._idx['l10n_type']],
                              gmDateTime.pydt_strftime(self._payload[self._idx['date_generated']], '%Y %b %d'),
                              gmTools.coalesce(self._payload[self._idx['doc_comment']], '', ' ("%s")')
                      )
                      return txt

              #--------------------------------------------------------
              def format(self, single_line=False):
                      if single_line:
                              return self.format_single_line()

                      txt = _('%s document part                 [#%s]\n') % (
                              gmTools.bool2str (
                                      boolean = self._payload[self._idx['reviewed']],
                                      true_str = _('Reviewed'),
                                      false_str = _('Unreviewed')
                              ),
                              self._payload[self._idx['pk_obj']]
                      )
                      f_ext = ''
                      if self._payload[self._idx['filename']] is not None:
                              f_ext = os.path.splitext(self._payload[self._idx['filename']])[1].strip('.').strip()
                      if f_ext != '':
                              f_ext = '.' + f_ext.upper() + ' '
                      txt += _(' Part %s: %s %s(%s Bytes)\n') % (
                              self._payload[self._idx['seq_idx']],
                              gmTools.size2str(self._payload[self._idx['size']]),
                              f_ext,
                              self._payload[self._idx['size']]
                      )
                      if self._payload[self._idx['filename']] is not None:
                              path, fname = os.path.split(self._payload[self._idx['filename']])
                              if not path.endswith(os.path.sep):
                                      if path != '':
                                              path += os.path.sep
                              if path != '':
                                      path = ' (%s)' % path
                              txt += _(' Filename: %s%s\n') % (fname, path)
                      if self._payload[self._idx['obj_comment']] is not None:
                              txt += '\n%s\n' % self._payload[self._idx['obj_comment']]
                      return txt

              #--------------------------------------------------------
              def format_metainfo(self, callback=None):
                      """If <callback> is not None it will receive a tuple (status, description, pk_obj)."""
                      if callback is None:
                              return self.__run_metainfo_formatter()

                      gmWorkerThread.execute_in_worker_thread (
                              payload_function = self.__run_metainfo_formatter,
                              completion_callback = callback,
                              worker_name = 'doc_part-metainfo_formatter-'
                      )

              #--------------------------------------------------------
              def get_useful_filename(self, patient=None, make_unique=False, directory=None, include_gnumed_tag=True, date_before_type=False, name_first=True):
                      patient_part = ''
                      if patient is not None:
                              if name_first:
                                      patient_part = '%s-' % patient.subdir_name
                              else:
                                      patient_part = '-%s' % patient.subdir_name

                      # preserve original filename extension if available
                      suffix = '.dat'
                      if self._payload[self._idx['filename']] is not None:
                              tmp, suffix = os.path.splitext (
                                      gmTools.fname_sanitize(self._payload[self._idx['filename']]).lower()
                              )
                              if suffix == '':
                                      suffix = '.dat'

                      if include_gnumed_tag:
                              fname_template = 'gm_doc-part_%s-%%s' % self._payload[self._idx['seq_idx']]
                      else:
                              fname_template = '%%s-part_%s' % self._payload[self._idx['seq_idx']]

                      if date_before_type:
                              date_type_part = '%s-%s' % (
                                      gmDateTime.pydt_strftime(self._payload[self._idx['date_generated']], '%Y-%m-%d', 'utf-8', gmDateTime.acc_days),
                                      self._payload[self._idx['l10n_type']].replace(' ', '_').replace('-', '_'),
                              )
                      else:
                              date_type_part = '%s-%s' % (
                                      self._payload[self._idx['l10n_type']].replace(' ', '_').replace('-', '_'),
                                      gmDateTime.pydt_strftime(self._payload[self._idx['date_generated']], '%Y-%m-%d', 'utf-8', gmDateTime.acc_days)
                              )

                      if name_first:
                              date_type_name_part = patient_part + date_type_part
                      else:
                              date_type_name_part = date_type_part + patient_part

                      fname = fname_template % date_type_name_part

                      if make_unique:
                              fname = gmTools.get_unique_filename (
                                      prefix = '%s-' % gmTools.fname_sanitize(fname),
                                      suffix = suffix,
                                      tmp_dir = directory
                              )
                      else:
                              fname = gmTools.fname_sanitize(os.path.join(gmTools.coalesce(directory, gmTools.gmPaths().tmp_dir), fname + suffix))

                      return fname

              useful_filename = property(get_useful_filename)

              #--------------------------------------------------------
              # internal helpers
              #--------------------------------------------------------
              def __download_to_file(self, filename=None, aChunkSize=0, conn=None):
                      if self._payload[self._idx['size']] == 0:
                              _log.debug('part size 0, nothing to download')
                              return None

                      if filename is None:
                              filename = gmTools.get_unique_filename()
                      success = gmPG2.bytea2file (
                              data_query = {
                                      'cmd': 'SELECT substring(data from %(start)s for %(size)s) FROM blobs.doc_obj WHERE pk=%(pk)s',
                                      'args': {'pk': self.pk_obj}
                              },
                              filename = filename,
                              chunk_size = aChunkSize,
                              data_size = self._payload[self._idx['size']],
                              conn = conn
                      )
                      if not success:
                              return None

                      return filename

              #--------------------------------------------------------
              def __run_metainfo_formatter(self):
                      filename = self.__download_to_file()
                      if filename is None:
                              _log.error('problem downloading part')
                              return (False, _('problem downloading document part'))

                      status, desc = gmMimeLib.describe_file(filename)
                      return (status, desc, self.pk_obj)

  ### Ancestors

  - cBusinessDBObject

  ### Instance variables

  `var containing_document`
    Expand source code

        def __get_containing_document(self):
                return cDocument(aPK_obj = self._payload[self._idx['pk_doc']])

  `var useful_filename`
    Expand source code

        def get_useful_filename(self, patient=None, make_unique=False, directory=None, include_gnumed_tag=True, date_before_type=False, name_first=True):
                patient_part = ''
                if patient is not None:
                        if name_first:
                                patient_part = '%s-' % patient.subdir_name
                        else:
                                patient_part = '-%s' % patient.subdir_name

                # preserve original filename extension if available
                suffix = '.dat'
                if self._payload[self._idx['filename']] is not None:
                        tmp, suffix = os.path.splitext (
                                gmTools.fname_sanitize(self._payload[self._idx['filename']]).lower()
                        )
                        if suffix == '':
                                suffix = '.dat'

                if include_gnumed_tag:
                        fname_template = 'gm_doc-part_%s-%%s' % self._payload[self._idx['seq_idx']]
                else:
                        fname_template = '%%s-part_%s' % self._payload[self._idx['seq_idx']]

                if date_before_type:
                        date_type_part = '%s-%s' % (
                                gmDateTime.pydt_strftime(self._payload[self._idx['date_generated']], '%Y-%m-%d', 'utf-8', gmDateTime.acc_days),
                                self._payload[self._idx['l10n_type']].replace(' ', '_').replace('-', '_'),
                        )
                else:
                        date_type_part = '%s-%s' % (
                                self._payload[self._idx['l10n_type']].replace(' ', '_').replace('-', '_'),
                                gmDateTime.pydt_strftime(self._payload[self._idx['date_generated']], '%Y-%m-%d', 'utf-8', gmDateTime.acc_days)
                        )

                if name_first:
                        date_type_name_part = patient_part + date_type_part
                else:
                        date_type_name_part = date_type_part + patient_part

                fname = fname_template % date_type_name_part

                if make_unique:
                        fname = gmTools.get_unique_filename (
                                prefix = '%s-' % gmTools.fname_sanitize(fname),
                                suffix = suffix,
                                tmp_dir = directory
                        )
                else:
                        fname = gmTools.fname_sanitize(os.path.join(gmTools.coalesce(directory, gmTools.gmPaths().tmp_dir), fname + suffix))

                return fname

  ### Methods

  `def display_via_mime(self, chunksize=0, block=None)`
    Expand source code

        def display_via_mime(self, chunksize=0, block=None):

                fname = self.save_to_file(aChunkSize = chunksize)
                if fname is None:
                        return False, ''

                success, msg = gmMimeLib.call_viewer_on_file(fname, block = block)
                if not success:
                        return False, msg

                return True, ''

  `def format_metainfo(self, callback=None)`

    If is not None it will receive a tuple (status, description, pk_obj).

    Expand source code

        def format_metainfo(self, callback=None):
                """If <callback> is not None it will receive a tuple (status, description, pk_obj)."""
                if callback is None:
                        return self.__run_metainfo_formatter()

                gmWorkerThread.execute_in_worker_thread (
                        payload_function = self.__run_metainfo_formatter,
                        completion_callback = callback,
                        worker_name = 'doc_part-metainfo_formatter-'
                )

  `def format_single_line(self)`
    Expand source code

        def format_single_line(self):
                f_ext = ''
                if self._payload[self._idx['filename']] is not None:
                        f_ext = os.path.splitext(self._payload[self._idx['filename']])[1].strip('.').strip()
                if f_ext != '':
                        f_ext = ' .' + f_ext.upper()
                txt = _('part %s, %s%s%s of document %s from %s%s') % (
                        self._payload[self._idx['seq_idx']],
                        gmTools.size2str(self._payload[self._idx['size']]),
                        f_ext,
                        gmTools.coalesce(self._payload[self._idx['obj_comment']], '', ' ("%s")'),
                        self._payload[self._idx['l10n_type']],
                        gmDateTime.pydt_strftime(self._payload[self._idx['date_generated']], '%Y %b %d'),
                        gmTools.coalesce(self._payload[self._idx['doc_comment']], '', ' ("%s")')
                )
                return txt

  `def get_reviews(self)`
    Expand source code

                def get_reviews(self):
                        cmd = """
        SELECT
                reviewer,
                reviewed_when,
                is_technically_abnormal,
                clinically_relevant,
                is_review_by_responsible_reviewer,
                is_your_review,
                coalesce(comment, '')
        FROM blobs.v_reviewed_doc_objects
        WHERE pk_doc_obj = %s
        ORDER BY
                is_your_review desc,
                is_review_by_responsible_reviewer desc,
                reviewed_when desc
        """
                        rows, idx = gmPG2.run_ro_queries(queries = [{'cmd': cmd, 'args': [self.pk_obj]}])
                        return rows

  `def get_useful_filename(self, patient=None, make_unique=False, directory=None, include_gnumed_tag=True, date_before_type=False, name_first=True)`
    Expand source code

        def get_useful_filename(self, patient=None, make_unique=False, directory=None, include_gnumed_tag=True, date_before_type=False, name_first=True):
                patient_part = ''
                if patient is not None:
                        if name_first:
                                patient_part = '%s-' % patient.subdir_name
                        else:
                                patient_part = '-%s' % patient.subdir_name

                # preserve original filename extension if available
                suffix = '.dat'
                if self._payload[self._idx['filename']] is not None:
                        tmp, suffix = os.path.splitext (
                                gmTools.fname_sanitize(self._payload[self._idx['filename']]).lower()
                        )
                        if suffix == '':
                                suffix = '.dat'

                if include_gnumed_tag:
                        fname_template = 'gm_doc-part_%s-%%s' % self._payload[self._idx['seq_idx']]
                else:
                        fname_template = '%%s-part_%s' % self._payload[self._idx['seq_idx']]

                if date_before_type:
                        date_type_part = '%s-%s' % (
                                gmDateTime.pydt_strftime(self._payload[self._idx['date_generated']], '%Y-%m-%d', 'utf-8', gmDateTime.acc_days),
                                self._payload[self._idx['l10n_type']].replace(' ', '_').replace('-', '_'),
                        )
                else:
                        date_type_part = '%s-%s' % (
                                self._payload[self._idx['l10n_type']].replace(' ', '_').replace('-', '_'),
                                gmDateTime.pydt_strftime(self._payload[self._idx['date_generated']], '%Y-%m-%d', 'utf-8', gmDateTime.acc_days)
                        )

                if name_first:
                        date_type_name_part = patient_part + date_type_part
                else:
                        date_type_name_part = date_type_part + patient_part

                fname = fname_template % date_type_name_part

                if make_unique:
                        fname = gmTools.get_unique_filename (
                                prefix = '%s-' % gmTools.fname_sanitize(fname),
                                suffix = suffix,
                                tmp_dir = directory
                        )
                else:
                        fname = gmTools.fname_sanitize(os.path.join(gmTools.coalesce(directory, gmTools.gmPaths().tmp_dir), fname + suffix))

                return fname

  `def reattach(self, pk_doc=None)`
    Expand source code

        def reattach(self, pk_doc=None):
                if pk_doc == self._payload[self._idx['pk_doc']]:
                        return True

                cmd = """
                        UPDATE blobs.doc_obj SET
                                fk_doc = %(pk_doc_target)s,
                                -- coalesce needed for no-parts target docs
                                seq_idx = (SELECT coalesce(max(seq_idx) + 1, 1) FROM blobs.doc_obj WHERE fk_doc = %(pk_doc_target)s)
                        WHERE
                                EXISTS(SELECT 1 FROM blobs.doc_med WHERE pk = %(pk_doc_target)s)
                                        AND
                                pk = %(pk_obj)s
                                        AND
                                xmin = %(xmin_doc_obj)s
                        RETURNING fk_doc
                """
                args = {
                        'pk_doc_target': pk_doc,
                        'pk_obj': self.pk_obj,
                        'xmin_doc_obj': self._payload[self._idx['xmin_doc_obj']]
                }
                rows, idx = gmPG2.run_rw_queries(queries = [{'cmd': cmd, 'args': args}], return_data = True, get_col_idx = False)
                if len(rows) == 0:
                        return False
                # The following should never hold true because the target
                # fk_doc is returned from the query and it is checked for
                # equality before the UPDATE already. Assuming the update
                # failed to update a row because the target fk_doc did
                # not exist we would not get *any* rows in return - for
                # which condition we also already checked
                if rows[0]['fk_doc'] == self._payload[self._idx['pk_doc']]:
                        return False

                self.refetch_payload()
                return True

  `def save_to_file(self, aChunkSize=0, filename=None, target_mime=None, target_extension=None, ignore_conversion_problems=False, directory=None, adjust_extension=False, conn=None)`
    Expand source code

        def save_to_file(self, aChunkSize=0, filename=None, target_mime=None, target_extension=None, ignore_conversion_problems=False, directory=None, adjust_extension=False, conn=None):

                if filename is None:
                        filename = self.get_useful_filename(make_unique = True, directory = directory)

                filename = self.__download_to_file(filename = filename)
                if filename is None:
                        return None

                if target_mime is None:
                        if filename.endswith('.dat'):
                                if adjust_extension:
                                        return gmMimeLib.adjust_extension_by_mimetype(filename)
                        return filename

                if target_extension is None:
                        target_extension = gmMimeLib.guess_ext_by_mimetype(mimetype = target_mime)

                target_path, name = os.path.split(filename)
                name, tmp = os.path.splitext(name)
                target_fname = gmTools.get_unique_filename (
                        prefix = '%s-conv-' % name,
                        suffix = target_extension
                )
                _log.debug('attempting conversion: [%s] -> [<%s>:%s]', filename, target_mime, target_fname)
                converted_fname = gmMimeLib.convert_file (
                        filename = filename,
                        target_mime = target_mime,
                        target_filename = target_fname
                )
                if converted_fname is not None:
                        return converted_fname

                _log.warning('conversion failed')
                if not ignore_conversion_problems:
                        return None

                if filename.endswith('.dat'):
                        if adjust_extension:
                                filename = gmMimeLib.adjust_extension_by_mimetype(filename)
                _log.warning('programmed to ignore conversion problems, hoping receiver can handle [%s]', filename)
                return filename

  `def set_as_active_photograph(self)`
    Expand source code

        def set_as_active_photograph(self):
                if self._payload[self._idx['type']] != 'patient photograph':
                        return False
                # set seq_idx to current max + 1
                cmd = 'SELECT coalesce(max(seq_idx)+1, 1) FROM blobs.doc_obj WHERE fk_doc = %(doc_id)s'
                rows, idx = gmPG2.run_ro_queries (
                        queries = [{
                                'cmd': cmd,
                                'args': {'doc_id': self._payload[self._idx['pk_doc']]}
                        }]
                )
                self._payload[self._idx['seq_idx']] = rows[0][0]
                self._is_modified = True
                self.save_payload()

  `def set_reviewed(self, technically_abnormal=None, clinically_relevant=None)`
    Expand source code

                def set_reviewed(self, technically_abnormal=None, clinically_relevant=None):
                        # row already there ?
                        cmd = """
        select pk
        from blobs.reviewed_doc_objs
        where
                fk_reviewed_row = %s and
                fk_reviewer = (select pk from dem.staff where db_user = current_user)"""
                        rows, idx = gmPG2.run_ro_queries(queries = [{'cmd': cmd, 'args': [self.pk_obj]}])

                        # INSERT needed
                        if len(rows) == 0:
                                cols = [
                                        "fk_reviewer",
                                        "fk_reviewed_row",
                                        "is_technically_abnormal",
                                        "clinically_relevant"
                                ]
                                vals = [
                                        '%(fk_row)s',
                                        '%(abnormal)s',
                                        '%(relevant)s'
                                ]
                                args = {
                                        'fk_row': self.pk_obj,
                                        'abnormal': technically_abnormal,
                                        'relevant': clinically_relevant
                                }
                                cmd = """
        insert into blobs.reviewed_doc_objs (
                %s
        ) values (
                (select pk from dem.staff where db_user=current_user),
                %s
        )""" % (', '.join(cols), ', '.join(vals))

                        # UPDATE needed
                        if len(rows) == 1:
                                pk_review = rows[0][0]
                                args = {
                                        'abnormal': technically_abnormal,
                                        'relevant': clinically_relevant,
                                        'pk_review': pk_review
                                }
                                cmd = """
                                        UPDATE blobs.reviewed_doc_objs SET
                                                is_technically_abnormal = %(abnormal)s,
                                                clinically_relevant = %(relevant)s
                                        WHERE
                                                pk = %(pk_review)s
                                """
                        rows, idx = gmPG2.run_rw_queries(queries = [{'cmd': cmd, 'args': args}])

                        return True

  `def update_data_from_file(self, fname=None, link_obj=None)`
    Expand source code

        def update_data_from_file(self, fname=None, link_obj=None):
                # sanity check
                if not (os.access(fname, os.R_OK) and os.path.isfile(fname)):
                        _log.error('[%s] is not a readable file' % fname)
                        return False

                cmd = "UPDATE blobs.doc_obj SET data = %(data)s::BYTEA WHERE pk = %(pk)s RETURNING md5(data) AS md5"
                args = {'pk': self.pk_obj}
                md5 = gmTools.file2md5(filename = fname, return_hex = True)
                if not gmPG2.file2bytea(conn = link_obj, query = cmd, filename = fname, args = args, file_md5 = md5):
                        return False

                # must update XMIN now ...
                self.refetch_payload(link_obj = link_obj)
                return True

  ### Inherited members

  - `cBusinessDBObject`:
    - `fields_as_dict`
    - `format`
    - `get_fields`
    - `get_patient`
    - `get_updatable_fields`
    - `is_modified`
    - `patient_pk`
    - `refetch_payload`
    - `same_payload`
    - `save`
    - `save_payload`
    - `staff_id`
`class cDocumentType (aPK_obj=None, row: dict = None, link_obj=None)`

  Represents a document type.

  Init business object.

  Call from child classes like so:

          super().__init__(aPK_obj = aPK_obj, row = row, link_obj = link_obj)

  ## Args

  `aPK_obj`
    retrieve data from backend * a simple value the primary key WHERE condition must be a simple column * a dictionary of values the primary key WHERE condition must be a subselect consuming the dict and producing the single-value primary key
  `row`
    must hold the fields * idx: a dict mapping field names to position * data: the field values in a list (as returned by cursor.fetchone() in the DB-API) * pk_field: the name of the primary key field OR * pk_obj: a dictionary suitable for passed to cursor.execute and holding the primary key values, used for composite PKs

  ## Examples

  row = { 'data': rows[0], 'idx': idx, 'pk_field': 'pk_XXX (the PK column name)', 'pk_obj': {'pk_col1': pk_col1_val, 'pk_col2': pk_col2_val} } rows, idx = gmPG2.run_ro_queries(queries = [{'cmd': cmd, 'args': args}], get_col_idx = True) objects = [ cChildClass(row = {'data': r, 'idx': idx, 'pk_field': 'the PK column name'}) for r in rows ]

  Expand source code

      class cDocumentType(gmBusinessDBObject.cBusinessDBObject):
              """Represents a document type."""
              _cmd_fetch_payload = """select * from blobs.v_doc_type where pk_doc_type=%s"""
              _cmds_store_payload = [
                      """update blobs.doc_type set
                                      name = %(type)s
                              where
                                      pk=%(pk_obj)s and
                                      xmin=%(xmin_doc_type)s""",
                      """select xmin_doc_type from blobs.v_doc_type where pk_doc_type = %(pk_obj)s"""
              ]
              _updatable_fields = ['type']
              #--------------------------------------------------------
              def set_translation(self, translation=None):

                      if translation.strip() == '':
                              return False

                      if translation.strip() == self._payload[self._idx['l10n_type']].strip():
                              return True

                      rows, idx = gmPG2.run_rw_queries (
                              queries = [
                                      {'cmd': 'select i18n.i18n(%s)', 'args': [self._payload[self._idx['type']]]},
                                      {'cmd': 'select i18n.upd_tx((select i18n.get_curr_lang()), %(orig)s, %(tx)s)',
                                       'args': {
                                              'orig': self._payload[self._idx['type']],
                                              'tx': translation
                                              }
                                      }
                              ],
                              return_data = True
                      )
                      if not rows[0][0]:
                              _log.error('cannot set translation to [%s]' % translation)
                              return False

                      return self.refetch_payload()

  ### Ancestors

  - cBusinessDBObject

  ### Methods

  `def set_translation(self, translation=None)`
    Expand source code

        def set_translation(self, translation=None):

                if translation.strip() == '':
                        return False

                if translation.strip() == self._payload[self._idx['l10n_type']].strip():
                        return True

                rows, idx = gmPG2.run_rw_queries (
                        queries = [
                                {'cmd': 'select i18n.i18n(%s)', 'args': [self._payload[self._idx['type']]]},
                                {'cmd': 'select i18n.upd_tx((select i18n.get_curr_lang()), %(orig)s, %(tx)s)',
                                 'args': {
                                        'orig': self._payload[self._idx['type']],
                                        'tx': translation
                                        }
                                }
                        ],
                        return_data = True
                )
                if not rows[0][0]:
                        _log.error('cannot set translation to [%s]' % translation)
                        return False

                return self.refetch_payload()

  ### Inherited members

  - `cBusinessDBObject`:
    - `fields_as_dict`
    - `format`
    - `get_fields`
    - `get_patient`
    - `get_updatable_fields`
    - `is_modified`
    - `patient_pk`
    - `refetch_payload`
    - `same_payload`
    - `save`
    - `save_payload`
    - `staff_id`