Module Gnumed.business.gmDevices

# -*- coding: utf-8 -*-
#======================================================================
# GNUmed Device handling
#
# @copyright: author
#======================================================================
__author__ = "Sebastian Hilbert"
__license__ = 'GPL v2 or later (details at https://www.gnu.org)'


import sys, logging


if __name__ == '__main__':
        sys.path.insert(0, '../../')
        _ = lambda x:x

_log = logging.getLogger('gm.dev')
#======================================================================
# XML cardiac device description parsing
#----------------------------------------------------------------------


# since those methods appear in a top-level generic file (gmDevices.py)
# they need more specific names because things like drivers for
# urinalyzers, ecg, spiro, ... all conceptually belong into gmDevices.py


# Devices holds a list of all cardiac devices in the xml
# each list item holds a device context ( generator and one or more leads )
##Devices = []
# DeviceParts is the device context and holds one or more device parts. Each list item
# is a device part such as lead , generator which in turn can consist of 
# device parts such as mainboard or battery
##DeviceParts = []

def extractDevices(DevicesTree=None):
        Devices = []
        # sort device list, first ICD, then pacemaker, then disconnected devices
        for Device in DevicesTree:
                Devices.append(Device)
        return Devices

def sortDevicesByTypeAndStatus(Devices=None):
        # todo: sort later, for now return like order gotten from XML 
        return Devices

def extractDeviceParts(Device=None,Type=None):
        DeviceParts = []
        for DevicePart in Device:
                if DevicePart.get("type") == Type:
                        DeviceParts.append(DevicePart)
        return DeviceParts

def sortLeadsByPosition(Leads=None):
        #skips sorting for now
        return Leads

def extractActions(DevicePart=None,Type=None):
        Actions = []
        # get a list of all procedures for this DevicePart
        for tag in DevicePart.getchildren():
                if tag.get("type") == Type:
                        Actions.append(tag)
        return Actions

def extractTagData(start_node=None,SearchTag=None):
        #tag = None
        for tag in start_node.getchildren():
                if tag.tag==SearchTag:
                        return tag.text

def extractTagAttribute(start_node=None,SearchTag=None,Attribute=None):
        for tag in start_node.getchildren():
                if tag.tag == SearchTag:
                        return tag.get(Attribute)

def device_status_as_text(tree=None):
        DevicesDisplayed = []

        """ In this area GNUmed will place the status of all cardiac devices and device parts. 
        There can be more than one device at a time\n\n
        It potentially looks like this\n
        ----------------------------------------------------------------------------------------------------------------\n
        Device: SJM Atlas DR (active)     Battery: 2.4V (MOL)      Implanted:  Feb 09 2008\n\n
        RA: Medtronic Sprint fidelis (active, flaky, replacement)             Implanted: Feb 09 2008\n
        Sensing: 2 (1.5) mV    Threshold: 0.7/0.5 (1/0.4) V/ms       Impedance: 800 (900) Ohm\n\n
        RV: Medtronic Sprint fidelis (active, flaky, replacement)             Implanted: Feb 09 2008\n
        Sensing: 7 (15) mV    Threshold: 0.7/0.5 (1/0.4) V/ms       Impedance: 800 (900) Ohm\n\n
        LV: Medtronic Sprint fidelis (active, flaky, Y-connector)             Implanted: Feb 09 2008\n
        Sensing: 7 ( ?) mV    Threshold: 1/1.5 (1/1) V/ms       Impedance: 800 (900) Ohm\n
        ----------------------------------------------------------------------------------------------------------------\n
        Device: Medtronic Relia SR (inactive)     Battery 2.1V (EOL)   Implanted: Jan 23 2000\n\n
        Device: Medtronic Kappa SR (explanted)     Battery 2.1V (EOL)   Explanted: Jan 23 2000 (Jan 23 1995)\n
        -----------------------------------------------------------------------------------------------------------------\n
        RA Lead: Medtronic ? (inactive, capped)             Implanted: Jan 23 2000\n
        RV Lead: Medtronic ? (explanted)                        Explanted: Feb 09 2008
        """
        """
        first search for devices, produce a list, 
        sort in active devices first, ICD befor pacemaker before disconnted devices
        per convention a single generator or lead which is not connected is a self contained device
        there are virtual devices such as 'ICD' or 'pacemaker' which consist of parts such as leads and generator
        there are true devices such as inactive leads or non-explanted generators
        class will be 'lead' instead of type 'lead' for DeviceParts
        """

        DevicesTree = tree.getroot()
        Devices = extractDevices(DevicesTree)
        DevicesSorted = sortDevicesByTypeAndStatus(Devices)
        #print 'Number of devices: %s' %len(Devices)

        for Device in DevicesSorted:
                DevicesDisplayed.append('-------------------------------------------------------------\n')
                # check for class
                DeviceClass=Device.get("class")
                if DeviceClass == 'ICD':
                        # get generator xml node
                        Generator = extractDeviceParts(Device=Device,Type='generator')[0]
                        # get generator vendor, model, devicestate
                        vendor = extractTagData(start_node=Generator,SearchTag='vendor')
                        model = extractTagData(start_node=Generator,SearchTag='model')
                        devicestate = extractTagData(start_node=Generator,SearchTag='devicestate')
                        # get subpart battery
                        battery = extractDeviceParts(Device=Generator,Type='battery')[0]
                        action = extractActions(DevicePart=battery,Type='interrogation')[0]
                        battery_voltage = extractTagData(start_node=action,SearchTag='voltage')
                        battery_voltage_unit = extractTagAttribute(start_node=action,SearchTag='voltage',Attribute='unit')
                        battery_status = extractTagData(start_node=action,SearchTag='status')
                        implantation_date= extractTagData(start_node=Generator,SearchTag='doi')
                        line = _('Device(%s):') %DeviceClass + ' ' + vendor + ' ' + model + ' ' + '('+ devicestate + ')'+'   '+_('Battery:')+' '+battery_voltage+' '+battery_voltage_unit+'('+battery_status+')'+'  '+_('Implanted:')+' '+implantation_date+'\n\n'
                        # append each line to a list, later produce display string by parsing list
                        DevicesDisplayed.append(line)
                        #DevicesDisplayed.append('\n')
                        # now get the leads, RA then RV and last LV if they exist
                        # todo: think about four leads : pace/sense but on another thought they both simply show up as RV leads
                        Leads = extractDeviceParts(Device=Device,Type='lead')
                        LeadsSorted = sortLeadsByPosition(Leads)
                        for Lead in LeadsSorted:
                                leadposition = extractTagData(start_node=Lead,SearchTag='leadposition')
                                leadslot = extractTagData(start_node=Lead,SearchTag='leadslot')
                                vendor = extractTagData(start_node=Lead,SearchTag='manufacturer')
                                model = extractTagData(start_node=Lead,SearchTag='model')
                                devicestate = extractTagData(start_node=Lead,SearchTag='devicestate')
                                comment = extractTagData(start_node=Lead,SearchTag='comment')
                                implantation_date = extractTagData(start_node=Lead,SearchTag='doi')
                                line = '%s-lead in %s-position:' %(leadposition,leadslot) + ' ' + vendor + ' ' + model + ' ' + '(' + devicestate + ',' + comment + ')' + ' ' + 'Implanted:' + ' ' + implantation_date +'\n'
                                DevicesDisplayed.append(line)
                                #now get the newest interrogation
                                action = extractActions(DevicePart=Lead,Type='interrogation')[0]
                                action_date = extractTagData(start_node=action,SearchTag='dop')
                                sensing = extractTagData(start_node=action,SearchTag='sensing')
                                sensingunit = extractTagAttribute(start_node=action,SearchTag='sensing',Attribute='unit')
                                threshold = extractTagData(start_node=action,SearchTag='thresholdvoltage')
                                thresholdunit = extractTagAttribute(start_node=action,SearchTag='thresholdvoltage',Attribute='unit')
                                impedance = extractTagData(start_node=action,SearchTag='impedance')
                                impedanceunit = extractTagAttribute(start_node=action,SearchTag='impedance',Attribute='unit')
                                line = _('last check:')+' '+action_date+' '+_('Sensing:')+' '+sensing+sensingunit+' '+_('Threshold')+' '+threshold+thresholdunit+' '+_('Impedance:')+' '+impedance+' '+impedanceunit+'\n\n' 
                                DevicesDisplayed.append(line)

        return DevicesDisplayed

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

        from lxml import etree

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

        if len(sys.argv) > 1 and sys.argv[1] == 'test':

                #----------------------------------------------------
                def test_parsing_cardio_dev_state():
                        # for now assume that the xml file provide the cardiac device context.
                        # that pretty much means logical connection of leads and generator is provided in the xml
                        print("parsing device status from XML file:", sys.argv[2])
                        xml_device_desc = etree.parse(sys.argv[2])
                        formatted_device_status = device_status_as_text(xml_device_desc)
                        for line in formatted_device_status:
                                print(line)
                #----------------------------------------------------

                test_parsing_cardio_dev_state()