Module Gnumed.exporters.gmTimelineExporter

# -*- coding: utf8 -*-
"""Timeline exporter.

Copyright: authors
"""
#============================================================
__author__ = "Karsten Hilbert <Karsten.Hilbert@gmx.net>"
__license__ = 'GPL v2 or later (details at https://www.gnu.org)'

import sys
import logging
import io
import os


if __name__ == '__main__':
        sys.path.insert(0, '../../')
        from Gnumed.pycommon import gmI18N
from Gnumed.pycommon import gmTools
from Gnumed.pycommon import gmDateTime


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

#============================================================
ERA_NAME_CARE_PERIOD = _('Care Period')

#============================================================

# <icon>base-64 encoded PNG image data</icon>

#============================================================
xml_start = """<?xml version="1.0" encoding="utf-8"?>
<timeline>
        <version>1.20.0</version>
        <timetype>gregoriantime</timetype>
        <!-- ======================================== Eras ======================================== -->
        <eras>
                <era>
                        <name>%s</name>
                        <start>%s</start>
                        <end>%s</end>
                        <color>205,238,241</color>
                        <ends_today>%s</ends_today>
                </era>
                <era>
                        <name>%s</name>
                        <start>%s</start>
                        <end>%s</end>
                        <color>161,210,226</color>
                        <ends_today>%s</ends_today>
                </era>
        </eras>
        <!-- ======================================== Categories ======================================== -->
        <categories>
                <!-- health issues -->
                <category>
                        <name>%s</name>
                        <color>255,0,0</color>
                        <font_color>0,0,0</font_color>
                </category>
                <!-- episodes -->
                <category>
                        <name>%s</name>
                        <color>0,255,0</color>
                        <font_color>0,0,0</font_color>
                </category>
                <!-- encounters -->
                <category>
                        <name>%s</name>
                        <color>30,144,255</color>
                        <font_color>0,0,0</font_color>
                </category>
                <!-- hospital stays -->
                <category>
                        <name>%s</name>
                        <color>255,255,0</color>
                        <font_color>0,0,0</font_color>
                </category>
                <!-- procedures -->
                <category>
                        <name>%s</name>
                        <color>160,32,140</color>
                        <font_color>0,0,0</font_color>
                </category>
                <!-- documents -->
                <category>
                        <name>%s</name>
                        <color>255,165,0</color>
                        <font_color>0,0,0</font_color>
                </category>
                <!-- vaccinations -->
                <category>
                        <name>%s</name>
                        <color>144,238,144</color>
                        <font_color>0,0,0</font_color>
                </category>
                <!-- substance intake -->
                <category>
                        <name>%s</name>
                        <color>165,42,42</color>
                        <font_color>0,0,0</font_color>
                </category>
                <!-- life events -->
                <category>
                        <name>%s</name>
                        <color>30,144,255</color>
                        <font_color>0,0,0</font_color>
                </category>
        </categories>
        <!-- ======================================== Events ======================================== -->
        <events>"""

xml_end = """
        </events>
        <view>
                <displayed_period>
                        <start>%s</start>
                        <end>%s</end>
                </displayed_period>
        <hidden_categories>
        </hidden_categories>
        </view>
</timeline>"""

#============================================================
def format_pydt(pydt, format = '%Y-%m-%d %H:%M:%S'):
        return gmDateTime.pydt_strftime(pydt, format = format, accuracy = gmDateTime.acc_seconds)

#------------------------------------------------------------
# health issues
#------------------------------------------------------------
__xml_issue_template = """
                <event>
                        <start>%(start)s</start>
                        <end>%(end)s</end>
                        <text>%(container_id)s%(label)s</text>
                        <fuzzy>%(fuzzy)s</fuzzy>
                        <locked>True</locked>
                        <ends_today>%(ends2day)s</ends_today>
                        <category>%(category)s</category>
                        <description>%(desc)s</description>
                </event>"""

def __format_health_issue_as_timeline_xml(issue, patient, emr):
        # container IDs are supposed to be numeric
        # 85bd7a14a1e74aab8db072ff8f417afb@H30.rldata.local
        data = {'category': _('Health issues')}
        possible_start = issue.possible_start_date
        safe_start = issue.safe_start_date
        end = issue.clinical_end_date
        ends_today = 'False'
        if end is None:
                # open episode or active
                ends_today = 'True'
                end = now
        # somewhat hacky and not really correct:
        start2use = safe_start
        if safe_start > end:
                if possible_start < end:
                        start2use = possible_start
                else:
                        start2use = end
        data['desc'] = gmTools.xml_escape_string(issue.format (
                patient = patient,
                with_summary = True,
                with_codes = True,
                with_episodes = True,
                with_encounters = False,
                with_medications = False,
                with_hospital_stays = False,
                with_procedures = False,
                with_family_history = False,
                with_documents = False,
                with_tests = False,
                with_vaccinations = False
        ).strip().strip('\n').strip())
        label = gmTools.shorten_words_in_line(text = issue['description'], max_length = 25, min_word_length = 5)
        xml = ''
#       if possible_start < safe_start:
#               data['start'] = format_pydt(possible_start)
#               data['end'] = format_pydt(safe_start)
#               data['ends2day'] = 'False'
#               data['fuzzy'] = 'True'
#               data['container_id'] = ''
#               data['label'] = '?%s?' % gmTools.xml_escape_string(label)
#               xml += __xml_issue_template % data
        data['start'] = format_pydt(start2use)
        data['end'] = format_pydt(end)
        data['ends2day'] = ends_today
        data['fuzzy'] = 'False'
        data['container_id'] = '[%s]' % issue['pk_health_issue']
        data['label'] = gmTools.xml_escape_string(label)
        xml += __xml_issue_template % data
        return xml

#------------------------------------------------------------
# episodes
#------------------------------------------------------------
__xml_episode_template = """
                <event>
                        <start>%(start)s</start>
                        <end>%(end)s</end>
                        <text>%(container_id)s%(label)s</text>
                        <progress>%(progress)s</progress>
                        <fuzzy>False</fuzzy>
                        <locked>True</locked>
                        <ends_today>%(ends2day)s</ends_today>
                        <category>%(category)s</category>
                        <description>%(desc)s</description>
                </event>"""

def __format_episode_as_timeline_xml(episode, patient):
        data = {
                'category': _('Episodes'),
                'start': format_pydt(episode.best_guess_clinical_start_date),
                'container_id': gmTools.coalesce (
                        value2test = episode['pk_health_issue'],
                        return_instead = '',
                        template4value = '(%s)'
                ),
                'label': gmTools.xml_escape_string (
                        gmTools.shorten_words_in_line(text = episode['description'], max_length = 20, min_word_length = 5)
                ),
                'ends2day': gmTools.bool2subst(episode['episode_open'], 'True', 'False'),
                'progress': gmTools.bool2subst(episode['episode_open'], '0', '100'),
                'desc': gmTools.xml_escape_string(episode.format (
                        patient = patient,
                        with_summary = True,
                        with_codes = True,
                        with_encounters = True,
                        with_documents = False,
                        with_hospital_stays = False,
                        with_procedures = False,
                        with_family_history = False,
                        with_tests = False,
                        with_vaccinations = False,
                        with_health_issue = True
                ).strip().strip('\n').strip())
        }
        end = episode.best_guess_clinical_end_date
        if end is None:
                data['end'] = format_pydt(now)
        else:
                data['end'] = format_pydt(end)
        return __xml_episode_template % data

#------------------------------------------------------------
# encounters
#------------------------------------------------------------
__xml_encounter_template = """
                <event>
                        <start>%s</start>
                        <end>%s</end>
                        <text>%s</text>
                        <progress>0</progress>
                        <fuzzy>False</fuzzy>
                        <locked>True</locked>
                        <ends_today>False</ends_today>
                        <category>%s</category>
                        <description>%s</description>
                        <milestone>%s</milestone>
                </event>"""

def __format_encounter_as_timeline_xml(encounter, patient):
        return __xml_encounter_template % (
                format_pydt(encounter['started']),
                format_pydt(encounter['last_affirmed']),
                #u'(%s)' % encounter['pk_episode'],
                gmTools.xml_escape_string(format_pydt(encounter['started'], format = '%b %d')),
                _('Encounters'),                                                                                                # category
                gmTools.xml_escape_string(encounter.format (
                        patient = patient,
                        with_soap = True,
                        with_docs = False,
                        with_tests = False,
                        fancy_header = False,
                        with_vaccinations = False,
                        with_co_encountlet_hints = False,
                        with_rfe_aoe = True,
                        with_family_history = False
                ).strip().strip('\n').strip()),
                'False'
        )

#------------------------------------------------------------
# hospital stays
#------------------------------------------------------------
__xml_hospital_stay_template = """
                <event>
                        <start>%s</start>
                        <end>%s</end>
                        <text>%s</text>
                        <fuzzy>False</fuzzy>
                        <locked>True</locked>
                        <ends_today>False</ends_today>
                        <category>%s</category>
                        <description>%s</description>
                </event>"""

def __format_hospital_stay_as_timeline_xml(stay):
        end = stay['discharge']
        if end is None:
                end = now
        return __xml_hospital_stay_template % (
                format_pydt(stay['admission']),
                format_pydt(end),
                gmTools.xml_escape_string(stay['hospital']),
                _('Hospital stays'),                                                                                            # category
                gmTools.xml_escape_string(stay.format().strip().strip('\n').strip())
        )

#------------------------------------------------------------
# procedures
#------------------------------------------------------------
__xml_procedure_template = """
                <event>
                        <start>%s</start>
                        <end>%s</end>
                        <text>%s</text>
                        <fuzzy>False</fuzzy>
                        <locked>True</locked>
                        <ends_today>False</ends_today>
                        <category>%s</category>
                        <description>%s</description>
                </event>"""

def __format_procedure_as_timeline_xml(proc):
        if proc['is_ongoing']:
                end = now
        else:
                if proc['clin_end'] is None:
                        end = proc['clin_when']
                else:
                        end = proc['clin_end']
        desc = gmTools.shorten_words_in_line(text = proc['performed_procedure'], max_length = 20, min_word_length = 5)
        return __xml_procedure_template % (
                format_pydt(proc['clin_when']),
                format_pydt(end),
                gmTools.xml_escape_string(desc),
                _('Procedures'),
                gmTools.xml_escape_string(proc.format (
                        include_episode = True,
                        include_codes = True
                ).strip().strip('\n').strip())
        )

#------------------------------------------------------------
# documents
#------------------------------------------------------------
__xml_document_template = """
                <event>
                        <start>%s</start>
                        <end>%s</end>
                        <text>%s</text>
                        <fuzzy>False</fuzzy>
                        <locked>True</locked>
                        <ends_today>False</ends_today>
                        <category>%s</category>
                        <description>%s</description>
                </event>"""

def __format_document_as_timeline_xml(doc):
        desc = gmTools.shorten_words_in_line(text = doc['l10n_type'], max_length = 20, min_word_length = 5)
        return __xml_document_template % (
                format_pydt(doc['clin_when']),
                format_pydt(doc['clin_when']),
                gmTools.xml_escape_string(desc),
                _('Documents'),
                gmTools.xml_escape_string(doc.format().strip().strip('\n').strip())
        )

#------------------------------------------------------------
# vaccinations
#------------------------------------------------------------
__xml_vaccination_template = """
                <event>
                        <start>%s</start>
                        <end>%s</end>
                        <text>%s</text>
                        <fuzzy>False</fuzzy>
                        <locked>True</locked>
                        <ends_today>False</ends_today>
                        <category>%s</category>
                        <description>%s</description>
                </event>"""

def __format_vaccination_as_timeline_xml(vacc):
        return __xml_vaccination_template % (
                format_pydt(vacc['date_given']),
                format_pydt(vacc['date_given']),
                gmTools.xml_escape_string(vacc['vaccine']),
                _('Vaccinations'),
                gmTools.xml_escape_string('\n'.join(vacc.format (
                        with_indications = True,
                        with_comment = True,
                        with_reaction = True,
                        date_format = '%Y %b %d'
                )).strip().strip('\n').strip())
        )

#------------------------------------------------------------
# substance intake
#------------------------------------------------------------
__xml_intake_template = """
                <event>
                        <start>%s</start>
                        <end>%s</end>
                        <text>%s</text>
                        <fuzzy>False</fuzzy>
                        <locked>True</locked>
                        <ends_today>False</ends_today>
                        <category>%s</category>
                        <description>%s</description>
                </event>"""

def __format_intake_as_timeline_xml(intake):
        if intake['discontinued'] is None:
                if intake['planned_duration'] is None:
                        if intake['seems_inactive']:
                                end = intake['started']
                        else:
                                end = now
                else:
                        end = intake['started'] + intake['planned_duration']
        else:
                end = intake['discontinued']

        return __xml_intake_template % (
                format_pydt(intake['started']),
                format_pydt(end),
                gmTools.xml_escape_string(intake['substance']),
                _('Substances'),
                gmTools.xml_escape_string(intake.format (
                        single_line = False,
                        show_all_product_components = False
                ).strip().strip('\n').strip())
        )

#------------------------------------------------------------
# main library entry point
#------------------------------------------------------------
def create_timeline_file(patient=None, filename=None, include_documents=False, include_vaccinations=False, include_encounters=False):

        emr = patient.emr
        global now
        now = gmDateTime.pydt_now_here()

        if filename is None:
                timeline_fname = gmTools.get_unique_filename(prefix = 'gm-', suffix = '.timeline')      # .timeline required ...
        else:
                timeline_fname = filename
        _log.debug('exporting EMR as timeline into [%s]', timeline_fname)
        timeline = io.open(timeline_fname, mode = 'wt', encoding = 'utf8', errors = 'xmlcharrefreplace')

        if patient['dob'] is None:
                lifespan_start = format_pydt(now.replace(year = now.year - 100))
        else:
                lifespan_start = format_pydt(patient['dob'])

        if patient['deceased'] is None:
                life_ends2day = 'True'
                lifespan_end = format_pydt(now)
        else:
                life_ends2day = 'False'
                lifespan_end = format_pydt(patient['deceased'])

        earliest_care_date = emr.earliest_care_date
        most_recent_care_date = emr.most_recent_care_date
        if most_recent_care_date is None:
                most_recent_care_date = lifespan_end
                care_ends2day = life_ends2day
        else:
                most_recent_care_date = format_pydt(most_recent_care_date)
                care_ends2day = 'False'

        timeline.write(xml_start % (
                # era: life span of patient
                _('Lifespan'),
                lifespan_start,
                lifespan_end,
                life_ends2day,
                ERA_NAME_CARE_PERIOD,
                format_pydt(earliest_care_date),
                most_recent_care_date,
                care_ends2day,
                # categories
                _('Health issues'),
                _('Episodes'),
                _('Encounters'),
                _('Hospital stays'),
                _('Procedures'),
                _('Documents'),
                _('Vaccinations'),
                _('Substances'),
                _('Life events')
        ))
        # birth
        if patient['dob'] is None:
                start = now.replace(year = now.year - 100)
                timeline.write(__xml_encounter_template % (
                        format_pydt(start),
                        format_pydt(start),
                        '?',
                        _('Life events'),
                        _('Date of birth unknown'),
                        'True'
                ))
        else:
                start = patient['dob']
                timeline.write(__xml_encounter_template % (
                        format_pydt(patient['dob']),
                        format_pydt(patient['dob']),
                        '*',
                        _('Life events'),
                        _('Birth: %s') % patient.get_formatted_dob(format = '%Y %b %d %H:%M', honor_estimation = True),
                        'True'
                ))

        # start of care
        timeline.write(__xml_encounter_template % (
                format_pydt(earliest_care_date),
                format_pydt(earliest_care_date),
                gmTools.u_heavy_greek_cross,
                _('Life events'),
                _('Start of Care: %s\n(the earliest recorded event of care in this praxis)') % format_pydt(earliest_care_date, format = '%Y %b %d'),
                'True'
        ))

        # containers must be defined before their
        # subevents, so put health issues first
        timeline.write('\n              <!-- ========================================\n Health issues\n======================================== -->')
        for issue in emr.health_issues:
                timeline.write(__format_health_issue_as_timeline_xml(issue, patient, emr))

        timeline.write('\n              <!-- ========================================\n Episodes\n======================================== -->')
        for epi in emr.get_episodes(order_by = 'pk_health_issue'):
                timeline.write(__format_episode_as_timeline_xml(epi, patient))

        if include_encounters:
                timeline.write(u'\n<!--\n========================================\n Encounters\n======================================== -->')
                for enc in emr.get_encounters(skip_empty = True):
                        timeline.write(__format_encounter_as_timeline_xml(enc, patient))

        timeline.write('\n<!--\n========================================\n Hospital stays\n======================================== -->')
        for stay in emr.hospital_stays:
                timeline.write(__format_hospital_stay_as_timeline_xml(stay))

        timeline.write('\n<!--\n========================================\n Procedures\n======================================== -->')
        for proc in emr.performed_procedures:
                timeline.write(__format_procedure_as_timeline_xml(proc))

        if include_vaccinations:
                timeline.write(u'\n<!--\n========================================\n Vaccinations\n======================================== -->')
                for vacc in emr.vaccinations:
                        timeline.write(__format_vaccination_as_timeline_xml(vacc))

        timeline.write('\n<!--\n========================================\n Substance intakes\n======================================== -->')
        for intake in emr.get_current_medications(include_inactive = True):
                timeline.write(__format_intake_as_timeline_xml(intake))

        if include_documents:
                timeline.write(u'\n<!--\n========================================\n Documents\n======================================== -->')
                for doc in patient.document_folder.documents:
                        timeline.write(__format_document_as_timeline_xml(doc))

        # allergies ?
        # - unclear where and how to place
        # test results ?
        # - too many events, at most "day sample drawn"

        # death
        if patient['deceased'] is None:
                end = now
        else:
                end = patient['deceased']
                death_ago = gmDateTime.format_apparent_age_medically (
                        age = gmDateTime.calculate_apparent_age(start = end, end = now)
                )
                timeline.write(__xml_encounter_template % (
                        format_pydt(end),
                        format_pydt(end),
                        gmTools.u_dagger,
                        _('Life events'),
                        _('Death: %s\n(%s ago at age %s)') % (
                                format_pydt(end, format = '%Y %b %d %H:%M'),
                                death_ago,
                                patient.get_medical_age()
                        ),
                        'True'
                ))

        # display range
        if end.month == 2:
                if end.day == 29:
                        # leap years aren't consecutive
                        end = end.replace(day = 28)
        target_year = end.year + 1
        end = end.replace(year = target_year)
        timeline.write(xml_end % (
                format_pydt(start),
                format_pydt(end)
        ))

        timeline.close()
        return timeline_fname

#------------------------------------------------------------
__fake_timeline_start = """<?xml version="1.0" encoding="utf-8"?>
<timeline>
        <version>0.20.0</version>
        <categories>
                <!-- life events -->
                <category>
                        <name>%s</name>
                        <color>30,144,255</color>
                        <font_color>0,0,0</font_color>
                </category>
        </categories>
        <events>""" % _('Life events')

__fake_timeline_body_template = """
                <event>
                        <start>%s</start>
                        <end>%s</end>
                        <text>%s</text>
                        <fuzzy>False</fuzzy>
                        <locked>True</locked>
                        <ends_today>False</ends_today>
                        <!-- category></category -->
                        <description>%s
                        </description>
                </event>"""

def create_fake_timeline_file(patient=None, filename=None):
        """Used to create an 'empty' timeline file for display.

        - needed because .clear_timeline() doesn't really work
        """
        global now
        now = gmDateTime.pydt_now_here()

        if filename is None:
                timeline_fname = gmTools.get_unique_filename(prefix = 'gm-', suffix = '.timeline')
        else:
                timeline_fname = filename

        _log.debug('creating dummy timeline in [%s]', timeline_fname)
        timeline = io.open(timeline_fname, mode = 'wt', encoding = 'utf8', errors = 'xmlcharrefreplace')

        timeline.write(__fake_timeline_start)

        # birth
        if patient['dob'] is None:
                start = now.replace(year = now.year - 100)
                timeline.write(__xml_encounter_template % (
                        format_pydt(start),
                        format_pydt(start),
                        _('Birth') + ': ?',
                        _('Life events'),
                        _('Date of birth unknown'),
                        'False'
                ))
        else:
                start = patient['dob']
                timeline.write(__xml_encounter_template % (
                        format_pydt(patient['dob']),
                        format_pydt(patient['dob']),
                        _('Birth') + gmTools.bool2subst(patient['dob_is_estimated'], ' (%s)' % gmTools.u_almost_equal_to, ''),
                        _('Life events'),
                        '',
                        'False'
                ))

        # death
        if patient['deceased'] is None:
                end = now
        else:
                end = patient['deceased']
                timeline.write(__xml_encounter_template % (
                        format_pydt(end),
                        format_pydt(end),
                        #u'',
                        _('Death'),
                        _('Life events'),
                        '',
                        'False'
                ))

        # fake issue
        timeline.write(__fake_timeline_body_template % (
                format_pydt(start),
                format_pydt(end),
                _('Cannot display timeline.'),
                _('Cannot display timeline.')
        ))

        # display range
        if end.month == 2:
                if end.day == 29:
                        # leap years aren't consecutive
                        end = end.replace(day = 28)
        target_year = end.year + 1
        end = end.replace(year = target_year)
        timeline.write(xml_end % (
                format_pydt(start),
                format_pydt(end)
        ))

        timeline.close()
        return timeline_fname

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

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

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

        gmI18N.activate_locale()
        gmI18N.install_domain('gnumed')

        from Gnumed.business import gmPraxis
        praxis = gmPraxis.gmCurrentPraxisBranch(branch = gmPraxis.get_praxis_branches()[0])

        from Gnumed.business import gmPerson
        # 14 / 20 / 138 / 58 / 20 / 5
        pat = gmPerson.gmCurrentPatient(gmPerson.cPatient(aPK_obj = 14))
        fname = '~/gnumed/gm2tl-%s.timeline' % pat.subdir_name

        print (create_timeline_file (
                patient = pat,
                filename = os.path.expanduser(fname),
                include_documents = True,
                include_vaccinations = True,
                include_encounters = True
        ))