def create(cls, s, *sources):
composite = add(s, Composite(n_components=0))
for source in sources:
add(
s,
CompositeComponent(input_source=source,
output_source=composite))
composite.n_components += 1
return composite
def injury_notes(old_name, new_name):
injury_id = next(
old.execute('''select id from injury where name like ?''',
[old_name]))[0]
topic = s.query(DiaryTopic).filter(DiaryTopic.name == new_name).one()
notes = s.query(StatisticName).filter(
StatisticName.name == 'Notes',
StatisticName.constraint == topic.id).one()
for row in old.execute(
'''select date, notes from injury_diary where injury_id = ?''',
[injury_id]):
if row['notes']:
# print(row['notes'], len(row['notes']))
tj = add(s,
DiaryTopicJournal(time=to_time(row['date']), topic=topic))
add(
s,
StatisticJournalText(statistic_name=notes,
source=tj,
value=row['notes']))
def test_set(self):
with NamedTemporaryFile() as f:
args, sys, db = bootstrap_file(f, m(V), '5')
bootstrap_file(f, m(V), '5', mm(DEV), configurator=default)
with db.session_context() as s:
source = add(s, Source())
n = s.query(count(Timestamp.id)).scalar()
self.assertEqual(n, 0)
Timestamp.set(s, TestTimestamp, source=source)
n = s.query(count(Timestamp.id)).scalar()
self.assertEqual(n, 1)
t = s.query(Timestamp).filter(
Timestamp.owner == TestTimestamp).one()
self.assertAlmostEqual(t.time.timestamp(),
dt.datetime.now().timestamp(), 1)
def test_set(self):
user = random_test_user()
bootstrap_db(user, m(V), '5')
config = bootstrap_db(user, m(V), '5', mm(DEV), configurator=default)
with config.db.session_context() as s:
source = add(s, Source())
n = s.query(count(Timestamp.id)).scalar()
self.assertEqual(n, 0)
Timestamp.set(s, TestTimestamp, source=source)
n = s.query(count(Timestamp.id)).scalar()
self.assertEqual(n, 1)
t = s.query(Timestamp).filter(
Timestamp.owner == TestTimestamp).one()
self.assertAlmostEqual(t.time.timestamp(),
dt.datetime.now().timestamp(), 1)
def find_and_add_sector_journals(s, sector_group, ajournal, sector_id=None):
sql = text('''
with srid as (select s.id as sector_id,
st_setsrid(s.route, sg.srid) as sector,
st_transform(aj.route_et::geometry, sg.srid) as route_et,
st_transform(aj.route_d::geometry, sg.srid) as route_d,
st_setsrid(s.start, sg.srid) as start,
st_setsrid(s.finish, sg.srid) as finish
from sector as s,
activity_journal as aj,
sector_group as sg
where s.sector_group_id = sg.id
and s.id = coalesce(:sector_id, s.id)
and sg.id = :sector_group_id
and aj.id = :activity_journal_id
and st_intersects(st_setsrid(s.hull, sg.srid), st_transform(aj.route_d::geometry, sg.srid))),
start_point as (select r.sector_id,
r.route_et,
(st_dump(st_multi(st_intersection(r.start, st_force2d(r.route_et))))).geom as point
from srid as r),
start_fraction as (select p.sector_id,
st_linelocatepoint(p.route_et, p.point) as fraction
from start_point as p
where st_geometrytype(p.point) = 'ST_Point'), -- small number of cases intersect as lines
finish_point as (select r.sector_id,
r.route_et,
(st_dump(st_multi(st_intersection(r.finish, st_force2d(r.route_et))))).geom as point
from srid as r),
finish_fraction as (select p.sector_id,
st_linelocatepoint(p.route_et, p.point) as fraction
from finish_point as p
where st_geometrytype(p.point) = 'ST_Point'),
shortest as (select distinct -- multiple starts/finishes can lead to duplicates
r.sector_id,
s.fraction as start_fraction,
f.fraction as finish_fraction,
min(f.fraction - s.fraction) over (partition by r.sector_id) as shortest
from srid as r,
start_fraction as s,
finish_fraction as f
where s.fraction < f.fraction
and s.sector_id = f.sector_id
and s.sector_id = r.sector_id
and st_length(st_linesubstring(r.route_d, s.fraction, f.fraction))
between 0.95 * st_length(r.sector) and 1.05 * st_length(r.sector))
select s.sector_id,
s.start_fraction,
s.finish_fraction,
aj.start + interval '1' second * st_m(st_lineinterpolatepoint(r.route_et, s.start_fraction)) as start_time,
aj.start + interval '1' second * st_m(st_lineinterpolatepoint(r.route_et, s.finish_fraction)) as finish_time,
st_m(st_lineinterpolatepoint(r.route_d, s.start_fraction)) as start_distance,
st_m(st_lineinterpolatepoint(r.route_d, s.finish_fraction)) as finish_distance,
st_z(st_lineinterpolatepoint(r.route_et, s.start_fraction)) as start_elevation,
st_z(st_lineinterpolatepoint(r.route_et, s.finish_fraction)) as finish_elevation
from srid as r,
shortest as s,
activity_journal as aj
where aj.id = :activity_journal_id
and r.sector_id = s.sector_id
and s.finish_fraction - s.start_fraction = s.shortest
''')
log.debug(sql)
result = s.connection().execute(sql,
sector_group_id=sector_group.id,
activity_journal_id=ajournal.id,
sector_id=sector_id)
for row in result.fetchall():
data = {name: value for name, value in zip(result.keys(), row)}
log.debug(
f'Adding SectorJournal for activity_journal_id {ajournal.id}, '
f'activity_group {ajournal.activity_group}: {data}')
sjournal = add(
s,
SectorJournal(activity_journal_id=ajournal.id,
activity_group=ajournal.activity_group,
**data))
s.flush()
yield sjournal
def test_sources(self):
with TemporaryDirectory() as f:
args, data = bootstrap_dir(f, m(V), '5', configurator=acooke)
with data.db.session_context() as s:
# add a diary entry
journal = add(s, DiaryTopicJournal(date='2018-09-29'))
cache = journal.cache(s)
diary = s.query(DiaryTopic).filter(DiaryTopic.title == 'Status').one()
fields = diary.fields
self.assertEqual(len(fields), 6, list(enumerate(map(str, fields))))
self.assertEqual(fields[0].statistic_name.name, 'notes')
self.assertEqual(fields[1].statistic_name.name, 'weight', str(fields[1]))
statistics = [cache[field] for field in fields]
for statistic in statistics:
self.assertTrue(statistic.value is None, statistics)
statistics[0].value = 'hello world'
statistics[1].value = 64.5
with data.db.session_context() as s:
# check the diary entry was persisted
journal = DiaryTopicJournal.get_or_add(s, '2018-09-29')
cache = journal.cache(s)
diary = s.query(DiaryTopic).filter(DiaryTopic.title == 'Status').one()
fields = diary.fields
self.assertEqual(len(fields), 6, list(enumerate(map(str, fields))))
self.assertEqual(fields[0].statistic_name.name, 'notes')
self.assertEqual(fields[1].statistic_name.name, 'weight', str(fields[1]))
statistics = [cache[field] for field in fields]
self.assertEqual(statistics[1].value, 64.5)
self.assertEqual(statistics[1].type, StatisticJournalType.FLOAT)
# generate summary stats
SummaryCalculator(data, schedule='m').run()
SummaryCalculator(data, schedule='y').run()
with data.db.session_context() as s:
# check the summary stats
diary = s.query(DiaryTopic).filter(DiaryTopic.title == 'Status').one()
weights = s.query(StatisticJournal).join(StatisticName). \
filter(StatisticName.owner == diary, StatisticName.name == 'weight'). \
order_by(StatisticJournal.time).all()
self.assertEqual(len(weights), 2)
self.assertEqual(weights[1].value, 64.5)
self.assertEqual(len(weights[1].measures), 2, weights[1].measures)
self.assertEqual(weights[1].measures[0].rank, 1)
self.assertEqual(weights[1].measures[0].percentile, 100, weights[1].measures[0].percentile)
n = s.query(count(StatisticJournalFloat.id)).scalar()
self.assertEqual(n, 4, n)
n = s.query(count(StatisticJournalInteger.id)).scalar()
self.assertEqual(n, 6, n)
m_avg = s.query(StatisticJournalFloat).join(StatisticName). \
filter(StatisticName.name == 'avg-month-weight').one()
self.assertEqual(m_avg.value, 64.5)
y_avg = s.query(StatisticJournalFloat).join(StatisticName). \
filter(StatisticName.name == 'avg-year-weight').one()
self.assertEqual(y_avg.value, 64.5)
month = s.query(Interval).filter(Interval.schedule == 'm').first()
self.assertEqual(month.start, to_date('2018-09-01'), month.start)
self.assertEqual(month.finish, to_date('2018-10-01'), month.finish)
with data.db.session_context() as s:
# delete the diary entry
journal = DiaryTopicJournal.get_or_add(s, '2018-09-29')
s.delete(journal)
with data.db.session_context() as s:
# check the delete cascade
self.assertEqual(s.query(count(DiaryTopicJournal.id)).scalar(), 1)
# this should be zero because the Intervals were automatically deleted
# (well, now +1 because there's an original default weight)
for source in s.query(Source).all():
print(source)
for journal in s.query(StatisticJournal).all():
print(journal)
self.assertEqual(s.query(count(Source.id)).scalar(), 37, list(map(str, s.query(Source).all()))) # constants
self.assertEqual(s.query(count(StatisticJournalText.id)).scalar(), 13, s.query(count(StatisticJournalText.id)).scalar())
self.assertEqual(s.query(count(StatisticJournal.id)).scalar(), 22, s.query(count(StatisticJournal.id)).scalar())
fields = dict((field.statistic_name.name, field.statistic_name)
for field in diary.fields)
notes = fields['Notes']
mood = fields['Mood']
hr = fields['Rest HR']
weight = fields['Weight']
sleep = fields['Sleep']
weather = fields['Weather']
meds = fields['Medication']
for row in old.execute(
'''select date, notes, rest_heart_rate, sleep, mood, weather, medication, weight from diary''',
[]):
if row['notes'] or row['mood'] or row['rest_heart_rate'] or row[
'weight'] or row['sleep'] or row['weather']:
tj = add(s, DiaryTopicJournal(time=to_time(row['date']), topic=diary))
if row['notes']:
add(
s,
StatisticJournalText(statistic_name=notes,
source=tj,
value=row['notes']))
if row['mood']:
add(
s,
StatisticJournalInteger(statistic_name=mood,
source=tj,
value=row['mood']))
if row['rest_heart_rate']:
add(
s,
def test_sources(self):
with NamedTemporaryFile() as f:
args, sys, db = bootstrap_file(f, m(V), '5', configurator=acooke)
with db.session_context() as s:
# add a diary entry
journal = add(s, DiaryTopicJournal(date='2018-09-29'))
cache = journal.cache(s)
diary = s.query(DiaryTopic).filter(
DiaryTopic.name == 'Diary').one()
fields = diary.fields
self.assertEqual(len(fields), 9,
list(enumerate(map(str, fields))))
self.assertEqual(fields[0].statistic_name.name, 'Notes')
self.assertEqual(fields[1].statistic_name.name, 'Weight',
str(fields[1]))
statistics = [cache[field] for field in fields]
for statistic in statistics:
self.assertTrue(statistic.value is None, statistics)
statistics[0].value = 'hello world'
statistics[1].value = 64.5
with db.session_context() as s:
# check the diary entry was persisted
journal = DiaryTopicJournal.get_or_add(s, '2018-09-29')
cache = journal.cache(s)
diary = s.query(DiaryTopic).filter(
DiaryTopic.name == 'Diary').one()
fields = diary.fields
self.assertEqual(len(fields), 9,
list(enumerate(map(str, fields))))
self.assertEqual(fields[0].statistic_name.name, 'Notes')
self.assertEqual(fields[1].statistic_name.name, 'Weight',
str(fields[1]))
statistics = [cache[field] for field in fields]
self.assertEqual(statistics[1].value, 64.5)
self.assertEqual(statistics[1].type,
StatisticJournalType.FLOAT)
# generate summary stats
SummaryCalculator(sys, db, schedule='m').run()
SummaryCalculator(sys, db, schedule='y').run()
with db.session_context() as s:
# check the summary stats
diary = s.query(DiaryTopic).filter(
DiaryTopic.name == 'Diary').one()
weight = s.query(StatisticJournal).join(StatisticName). \
filter(StatisticName.owner == diary, StatisticName.name == 'Weight').one()
self.assertEqual(weight.value, 64.5)
self.assertEqual(len(weight.measures), 2, weight.measures)
self.assertEqual(weight.measures[0].rank, 1)
self.assertEqual(weight.measures[0].percentile, 100,
weight.measures[0].percentile)
n = s.query(count(StatisticJournalFloat.id)).scalar()
self.assertEqual(n, 5, n)
n = s.query(count(StatisticJournalInteger.id)).scalar()
self.assertEqual(n, 10, n)
m_avg = s.query(StatisticJournalFloat).join(StatisticName). \
filter(StatisticName.name == 'Avg/Month Weight').one()
self.assertEqual(m_avg.value, 64.5)
y_avg = s.query(StatisticJournalFloat).join(StatisticName). \
filter(StatisticName.name == 'Avg/Year Weight').one()
self.assertEqual(y_avg.value, 64.5)
month = s.query(Interval).filter(
Interval.schedule == 'm').one()
self.assertEqual(month.start, to_date('2018-09-01'),
month.start)
self.assertEqual(month.finish, to_date('2018-10-01'),
month.finish)
with db.session_context() as s:
# delete the diary entry
journal = DiaryTopicJournal.get_or_add(s, '2018-09-29')
s.delete(journal)
run('sqlite3 %s ".dump"' % f.name, shell=True)
with db.session_context() as s:
# check the delete cascade
self.assertEqual(
s.query(count(DiaryTopicJournal.id)).scalar(), 0)
# this should be zero because the Intervals were automatically deleted
for source in s.query(Source).all():
print(source)
for journal in s.query(StatisticJournal).all():
print(journal)
self.assertEqual(
s.query(count(Source.id)).scalar(), 15,
list(map(str,
s.query(Source).all()))) # constants
self.assertEqual(
s.query(count(StatisticJournalText.id)).scalar(), 8,
s.query(count(StatisticJournalText.id)).scalar())
self.assertEqual(
s.query(count(StatisticJournal.id)).scalar(), 8,
s.query(count(StatisticJournal.id)).scalar())