def augment(data, newdata, metadata, task, writer, columns=None):
"""
Augments original data based on the task.
:param data: the data to be augmented, as binary file object.
:param newdata: the path to the CSV file to augment with.
:param metadata: the metadata of the data to be augmented.
:param task: the augmentation task.
:param writer: Writer on which to save the files.
:param columns: a list of column indices from newdata that will be added to data
well with data.
"""
if 'id' not in task:
raise AugmentationError(
"Dataset id for the augmentation task not provided")
# TODO: add support for combining multiple columns before an augmentation
# e.g.: [['street number', 'street', 'city']] and [['address']]
# currently, Datamart does not support such cases
# this means that spatial joins (with GPS) are not supported for now
# Perform augmentation
start = time.perf_counter()
if task['augmentation']['type'] == 'join':
output_metadata = join(
data,
newdata,
metadata,
task['metadata'],
writer,
task['augmentation']['left_columns'],
task['augmentation']['right_columns'],
columns=columns,
agg_functions=task['augmentation'].get('agg_functions'),
temporal_resolution=task['augmentation'].get(
'temporal_resolution'),
)
elif task['augmentation']['type'] == 'union':
output_metadata = union(
data,
newdata,
metadata,
task['metadata'],
writer,
task['augmentation']['left_columns'],
task['augmentation']['right_columns'],
)
else:
raise AugmentationError("Augmentation task not provided")
logger.info("Total augmentation: %.4fs", time.perf_counter() - start)
# Write out the metadata
writer.set_metadata(uuid.uuid4().hex, output_metadata)
return writer.finish()
def test_spatial_temporal(self):
"""Join on both space and time columns"""
with setup_augmentation('spatiotemporal_aug.csv',
'spatiotemporal.csv') as (
orig_data,
aug_data,
orig_meta,
aug_meta,
result,
writer,
):
output_metadata = join(
orig_data,
aug_data,
orig_meta,
aug_meta,
writer,
[[1, 2], [0]],
[[1, 2], [0]],
agg_functions={
'color': ['first', 'count'],
},
)
with open(result) as table:
self.assertCsvEqualNoOrder(
table.read(),
'date,latitude,longitude,first color,count color',
[
'2006-06-20T06:00:00,43.237,6.072,green,2',
'2006-06-20T06:00:00,43.238,6.072,red,1',
'2006-06-20T06:00:00,43.237,6.073,orange,2',
'2006-06-20T06:00:00,43.238,6.073,red,6',
'2006-06-20T07:00:00,43.237,6.072,orange,1',
'2006-06-20T07:00:00,43.238,6.072,,0',
'2006-06-20T07:00:00,43.237,6.073,yellow,4',
'2006-06-20T07:00:00,43.238,6.073,blue,4',
'2006-06-20T08:00:00,43.237,6.072,green,2',
'2006-06-20T08:00:00,43.238,6.072,green,2',
'2006-06-20T08:00:00,43.237,6.073,red,6',
'2006-06-20T08:00:00,43.238,6.073,green,2',
],
)
self.assertJson(
output_metadata,
{
'size':
544,
'columns': [
{
'name': 'date',
'structural_type': 'http://schema.org/Text',
'semantic_types': ['http://schema.org/DateTime'],
'num_distinct_values': 3,
},
{
'name': 'latitude',
'structural_type': 'http://schema.org/Float',
'semantic_types': ['http://schema.org/latitude'],
'unclean_values_ratio': 0.0,
'mean': lambda n: round(n, 3) == 43.238,
'stddev': lambda n: round(n, 5) == 0.00050,
'coverage': check_ranges(43.234, 43.241),
},
{
'name': 'longitude',
'structural_type': 'http://schema.org/Float',
'semantic_types': ['http://schema.org/longitude'],
'unclean_values_ratio': 0.0,
'mean': lambda n: round(n, 3) == 6.073,
'stddev': lambda n: round(n, 5) == 0.00050,
'coverage': check_ranges(6.069, 6.11),
},
{
'name': 'first color',
'structural_type': 'http://schema.org/Text',
'semantic_types': ['http://schema.org/Enumeration'],
},
{
'name': 'count color',
'structural_type': 'http://schema.org/Integer',
'semantic_types': [],
},
],
'qualities': [
{
'qualName': 'augmentation_info',
'qualValueType': 'dict',
'qualValue': {
'new_columns': ['first color', 'count color'],
'removed_columns': [],
'nb_rows_before': 12,
'nb_rows_after': 12,
'augmentation_type': 'join',
},
},
],
},
)
def test_temporal_hourly_days_join(self):
"""Join daily data with hourly (= aggregate down to daily)"""
with setup_augmentation('hourly_aug_days.csv', 'hourly.csv') as (
orig_data,
aug_data,
orig_meta,
aug_meta,
result,
writer,
):
output_metadata = join(
orig_data,
aug_data,
orig_meta,
aug_meta,
writer,
[[0]],
[[0]],
)
with open(result) as table:
self.assertCsvEqualNoOrder(
table.read(),
'orig_date,color,rain',
[
'2019-06-12,pink,no',
'2019-06-13,grey,no',
],
)
self.assertJson(
output_metadata,
{
'size':
62,
'columns': [
{
'name': 'orig_date',
'structural_type': 'http://schema.org/Text',
'semantic_types': ['http://schema.org/DateTime'],
'num_distinct_values': 2,
},
{
'name': 'color',
'structural_type': 'http://schema.org/Text',
'semantic_types': [],
'num_distinct_values': 2,
},
{
'name':
'rain',
'structural_type':
'http://schema.org/Text',
'semantic_types': [
'http://schema.org/Boolean',
'http://schema.org/Enumeration',
],
},
],
'qualities': [
{
'qualName': 'augmentation_info',
'qualValueType': 'dict',
'qualValue': {
'new_columns': ['rain'],
'removed_columns': [],
'nb_rows_before': 2,
'nb_rows_after': 2,
'augmentation_type': 'join',
},
},
],
},
)
def test_temporal_daily_hours_join(self):
"""Join hourly data with daily (= repeat for each hour)"""
with setup_augmentation('daily_aug_hours.csv', 'daily.csv') as (
orig_data,
aug_data,
orig_meta,
aug_meta,
result,
writer,
):
output_metadata = join(
orig_data,
aug_data,
orig_meta,
aug_meta,
writer,
[[0]],
[[0]],
)
with open(result) as table:
self.assertCsvEqualNoOrder(
table.read(),
'orig_date,n_people,rain',
[
'2019-04-25T21:00:00Z,3,yes',
'2019-04-26T01:00:00Z,5,no',
'2019-04-26T05:00:00Z,6,no',
'2019-04-26T09:00:00Z,7,no',
'2019-04-26T13:00:00Z,6,no',
'2019-04-26T17:00:00Z,8,no',
'2019-04-26T21:00:00Z,7,no',
'2019-04-27T01:00:00Z,0,yes',
'2019-04-27T05:00:00Z,1,yes',
'2019-04-27T09:00:00Z,0,yes',
'2019-04-27T13:00:00Z,3,yes',
'2019-04-27T17:00:00Z,0,yes',
'2019-04-27T13:00:00Z,0,yes',
],
)
self.assertJson(
output_metadata,
{
'size':
383,
'columns': [
{
'name': 'orig_date',
'structural_type': 'http://schema.org/Text',
'semantic_types': ['http://schema.org/DateTime'],
'num_distinct_values': 12,
},
{
'name': 'n_people',
'structural_type': 'http://schema.org/Integer',
'semantic_types': [],
'unclean_values_ratio': 0.0,
'num_distinct_values': 7,
'mean': lambda n: round(n, 3) == 3.538,
'stddev': lambda n: round(n, 3) == 2.977,
'coverage': check_ranges(0, 8),
},
{
'name':
'rain',
'structural_type':
'http://schema.org/Text',
'semantic_types': [
'http://schema.org/Boolean',
'http://schema.org/Enumeration',
],
},
],
'qualities': [
{
'qualName': 'augmentation_info',
'qualValueType': 'dict',
'qualValue': {
'new_columns': ['rain'],
'removed_columns': [],
'nb_rows_before': 13,
'nb_rows_after': 13,
'augmentation_type': 'join',
},
},
],
},
)
def test_temporal_daily_join(self):
"""Join between temporal keys (daily, daily)"""
with setup_augmentation('daily_aug.csv', 'daily.csv') as (
orig_data,
aug_data,
orig_meta,
aug_meta,
result,
writer,
):
output_metadata = join(
orig_data,
aug_data,
orig_meta,
aug_meta,
writer,
[[0]],
[[0]],
)
with open(result) as table:
self.assertCsvEqualNoOrder(
table.read(),
'orig_date,n_people,rain',
[
'2019-04-28,3,yes',
'2019-04-29,5,yes',
'2019-04-30,0,yes',
'2019-05-01,1,no',
'2019-05-02,3,no',
'2019-05-03,2,yes',
],
)
self.assertJson(
output_metadata,
{
'size':
131,
'columns': [
{
'name': 'orig_date',
'structural_type': 'http://schema.org/Text',
'semantic_types': ['http://schema.org/DateTime'],
'num_distinct_values': 6,
},
{
'name': 'n_people',
'structural_type': 'http://schema.org/Integer',
'semantic_types': [],
'unclean_values_ratio': 0.0,
'num_distinct_values': 5,
'mean': lambda n: round(n, 3) == 2.333,
'stddev': lambda n: round(n, 3) == 1.599,
'coverage': check_ranges(0, 5),
},
{
'name':
'rain',
'structural_type':
'http://schema.org/Text',
'semantic_types': [
'http://schema.org/Boolean',
'http://schema.org/Enumeration',
],
},
],
'qualities': [
{
'qualName': 'augmentation_info',
'qualValueType': 'dict',
'qualValue': {
'new_columns': ['rain'],
'removed_columns': [],
'nb_rows_before': 6,
'nb_rows_after': 6,
'augmentation_type': 'join',
},
},
],
},
)
def test_temporal_hourly_join(self):
"""Join between temporal keys (hourly, hourly)"""
with setup_augmentation('hourly_aug.csv', 'hourly.csv') as (
orig_data,
aug_data,
orig_meta,
aug_meta,
result,
writer,
):
output_metadata = join(
orig_data,
aug_data,
orig_meta,
aug_meta,
writer,
[[0]],
[[0]],
)
with open(result) as table:
self.assertCsvEqualNoOrder(
table.read(),
'orig_date,color,rain',
[
'2019-06-13T01:00:00,yellow,no',
'2019-06-13T02:00:00,yellow,no',
'2019-06-13T03:00:00,brown,no',
'2019-06-13T04:00:00,brown,yes',
'2019-06-13T05:00:00,yellow,no',
],
)
self.assertJson(
output_metadata,
{
'size':
176,
'columns': [
{
'name': 'orig_date',
'structural_type': 'http://schema.org/Text',
'semantic_types': ['http://schema.org/DateTime'],
'num_distinct_values': 5,
},
{
'name': 'color',
'structural_type': 'http://schema.org/Text',
'semantic_types': [],
'num_distinct_values': 2,
},
{
'name':
'rain',
'structural_type':
'http://schema.org/Text',
'semantic_types': [
'http://schema.org/Boolean',
'http://schema.org/Enumeration',
],
},
],
'qualities': [
{
'qualName': 'augmentation_info',
'qualValueType': 'dict',
'qualValue': {
'new_columns': ['rain'],
'removed_columns': [],
'nb_rows_before': 5,
'nb_rows_after': 5,
'augmentation_type': 'join',
},
},
],
},
)
def test_geo_join(self):
"""Join with lat,long keys"""
with setup_augmentation('geo_aug.csv', 'geo.csv') as (
orig_data,
aug_data,
orig_meta,
aug_meta,
result,
writer,
):
output_metadata = join(
orig_data,
aug_data,
orig_meta,
aug_meta,
writer,
[[0, 1]],
[[1, 2]],
)
with open(result) as table:
table_lines = table.read().splitlines(False)
# Truncate fields to work around rounding errors
# FIXME: Deal with rounding errors
table_lines = [
','.join(e[:8] if e[0] < 'a' or e[0] > 'z' else e
for e in line.split(',')) for line in table_lines
]
self.assertCsvEqualNoOrder(
'\n'.join(table_lines[0:6]),
'lat,long,id,letter,id_r,mean height,sum height,max height,min height',
[
'40.73119,-74.0026,place100,a,' +
'place08,41.41971,248.5182,69.64734,5.034845',
'40.72887,-73.9993,place101,b,' +
'place01,43.43270,608.0579,67.62636,17.53429',
'40.73717,-73.9998,place102,c,' +
'place06,49.46972,98.93944,50.59427,48.34517',
'40.72910,-73.9966,place103,d,' +
'place22,53.20234,159.6070,79.72296,32.52235',
'40.73019,-74.0042,place104,e,' +
'place02,39.79917,238.7950,51.92994,25.11753'
],
)
self.assertJson(
output_metadata,
{
'size':
1014,
'columns': [
{
'name': 'lat',
'structural_type': 'http://schema.org/Float',
'semantic_types': ['http://schema.org/latitude'],
'unclean_values_ratio': 0.0,
'mean': lambda n: round(n, 3) == 40.731,
'stddev': lambda n: round(n, 4) == 0.0029,
'coverage': check_ranges(40.68, 40.78),
},
{
'name': 'long',
'structural_type': 'http://schema.org/Float',
'semantic_types': ['http://schema.org/longitude'],
'unclean_values_ratio': 0.0,
'mean': lambda n: round(n, 3) == -73.999,
'stddev': lambda n: round(n, 5) == 0.00375,
'coverage': check_ranges(-74.05, -73.95),
},
{
'name': 'id',
'structural_type': 'http://schema.org/Text',
'semantic_types': [],
'num_distinct_values': 10,
},
{
'name': 'letter',
'structural_type': 'http://schema.org/Text',
'semantic_types': [],
'num_distinct_values': 10,
},
{
'name': 'id_r',
'structural_type': 'http://schema.org/Text',
'semantic_types': [],
},
{
'name': 'mean height',
'structural_type': 'http://schema.org/Float',
'semantic_types': [],
},
{
'name': 'sum height',
'structural_type': 'http://schema.org/Float',
'semantic_types': [],
},
{
'name': 'max height',
'structural_type': 'http://schema.org/Float',
'semantic_types': [],
},
{
'name': 'min height',
'structural_type': 'http://schema.org/Float',
'semantic_types': [],
},
],
'qualities': [
{
'qualName': 'augmentation_info',
'qualValueType': 'dict',
'qualValue': {
'new_columns': [
'id_r',
'mean height',
'sum height',
'max height',
'min height',
],
'removed_columns': [],
'nb_rows_before':
10,
'nb_rows_after':
10,
'augmentation_type':
'join',
},
},
],
},
)
def test_basic_join(self):
"""Simple join between integer keys"""
with setup_augmentation('basic_aug.csv', 'basic.csv') as (
orig_data,
aug_data,
orig_meta,
aug_meta,
result,
writer,
):
output_metadata = join(
orig_data,
aug_data,
orig_meta,
aug_meta,
writer,
[[0]],
[[2]],
)
with open(result) as table:
self.assertCsvEqualNoOrder(
table.read(),
'number,desk_faces,name,color,what',
[
'5,west,james,green,False',
'4,south,john,blue,False',
'7,west,michael,blue,True',
'6,east,robert,blue,False',
'11,,christopher,green,True',
],
)
self.assertJson(
output_metadata,
{
'size':
166,
'columns': [
{
'name': 'number',
'structural_type': 'http://schema.org/Integer',
'semantic_types': [],
'unclean_values_ratio': 0.0,
'num_distinct_values': 5,
'mean': 6.6,
'stddev': lambda n: round(n, 3) == 2.417,
'coverage': check_ranges(4.0, 11.0),
},
{
'name': 'desk_faces',
'structural_type': 'http://schema.org/Text',
'semantic_types': [],
'missing_values_ratio': 0.2,
'num_distinct_values': 3,
},
{
'name': 'name',
'structural_type': 'http://schema.org/Text',
'semantic_types': [],
},
{
'name': 'color',
'structural_type': 'http://schema.org/Text',
'semantic_types': ['http://schema.org/Enumeration'],
},
{
'name':
'what',
'structural_type':
'http://schema.org/Text',
'semantic_types': [
'http://schema.org/Boolean',
'http://schema.org/Enumeration',
],
},
],
'qualities': [
{
'qualName': 'augmentation_info',
'qualValueType': 'dict',
'qualValue': {
'new_columns': ['name', 'color', 'what'],
'removed_columns': [],
'nb_rows_before': 5,
'nb_rows_after': 5,
'augmentation_type': 'join',
},
},
],
},
)
def test_agg_join_specific_functions(self):
"""Join between integer keys, with specified aggregation functions"""
with setup_augmentation('agg_aug.csv', 'agg.csv') as (
orig_data,
aug_data,
orig_meta,
aug_meta,
result,
writer,
):
output_metadata = join(
orig_data,
aug_data,
orig_meta,
aug_meta,
writer,
[[0]],
[[0]],
agg_functions={
'work': 'count',
'salary': ['first', 'sum', 'max'],
},
)
with open(result) as table:
self.assertCsvEqualNoOrder(
table.read(),
'id,location,count work,first salary,sum salary,max salary',
[
'30,south korea,2,200.0,300.0,200.0',
'40,brazil,1,,,',
'70,usa,2,,600.0,600.0',
'80,canada,1,200.0,200.0,200.0',
'100,france,2,300.0,500.0,300.0',
],
)
self.assertJson(
output_metadata,
{
'size':
197,
'columns': [
{
'name': 'id',
'structural_type': 'http://schema.org/Integer',
'semantic_types': ['http://schema.org/identifier'],
'unclean_values_ratio': 0.0,
'num_distinct_values': 5,
'mean': 64.0,
'stddev': lambda n: round(n, 3) == 25.768,
'coverage': check_ranges(30, 100),
},
{
'name': 'location',
'structural_type': 'http://schema.org/Text',
'semantic_types': [],
'num_distinct_values': 5,
},
{
'name': 'count work',
'structural_type': 'http://schema.org/Integer',
'semantic_types': [],
},
{
'name': 'first salary',
'structural_type': 'http://schema.org/Integer',
'semantic_types': [],
},
{
'name': 'sum salary',
'structural_type': 'http://schema.org/Float',
'semantic_types': [],
},
{
'name': 'max salary',
'structural_type': 'http://schema.org/Integer',
'semantic_types': [],
},
],
'qualities': [
{
'qualName': 'augmentation_info',
'qualValue': {
'new_columns': [
'count work',
'first salary',
'sum salary',
'max salary',
],
'removed_columns': [],
'nb_rows_before':
5,
'nb_rows_after':
5,
'augmentation_type':
'join',
},
'qualValueType': 'dict',
},
],
},
)
def test_temporal_hourly_join(self):
with setup_augmentation('hourly_aug.csv', 'hourly.csv') as (
orig_data, aug_data, orig_meta, aug_meta, result, writer,
):
output_metadata = join(
orig_data,
aug_data,
orig_meta,
aug_meta,
writer,
[[0]],
[[0]],
)
with open(result) as table:
self.assertCsvEqualNoOrder(
table.read(),
'orig_date,color,rain',
[
'2019-06-13T01:00:00,blue,no',
'2019-06-13T02:00:00,blue,no',
'2019-06-13T03:00:00,green,no',
'2019-06-13T04:00:00,green,yes',
'2019-06-13T05:00:00,blue,no',
],
)
self.assertJson(
output_metadata,
{
'size': 170,
'columns': [
{
'name': 'orig_date',
'structural_type': 'http://schema.org/Text',
'semantic_types': ['http://schema.org/DateTime'],
'num_distinct_values': 5,
'mean': 1560394777.6,
'stddev': lambda n: round(n, 3) == 5104.874,
'coverage': check_ranges(1560387584.0, 1560402048.0),
'temporal_resolution': 'hour',
},
{
'name': 'color',
'structural_type': 'http://schema.org/Text',
'semantic_types': [],
'num_distinct_values': 2,
},
{
'name': 'rain',
'structural_type': 'http://schema.org/Text',
'semantic_types': [
'http://schema.org/Boolean',
'http://schema.org/Enumeration',
],
},
],
'qualities': [
{
'qualName': 'augmentation_info',
'qualValueType': 'dict',
'qualValue': {
'new_columns': ['rain'],
'removed_columns': [],
'nb_rows_before': 5,
'nb_rows_after': 5,
'augmentation_type': 'join',
},
},
],
},
)
def test_geo_join(self):
with setup_augmentation('geo_aug.csv', 'geo.csv') as (
orig_data, aug_data, orig_meta, aug_meta, result, writer,
):
output_metadata = join(
orig_data,
aug_data,
orig_meta,
aug_meta,
writer,
[[0, 1]],
[[1, 2]],
)
with open(result) as table:
table_lines = table.read().splitlines(False)
# Truncate fields to work around rounding errors
# FIXME: Deal with rounding errors
table_lines = [
','.join(
e[:8] if e[0] < 'a' or e[0] > 'z' else e
for e in line.split(',')
)
for line in table_lines
]
self.assertCsvEqualNoOrder(
'\n'.join(table_lines[0:6]),
'lat,long,id,letter,id_r,mean height,sum height,max height,min height',
[
'40.73279,-73.9985,place100,a,'
+ 'place00,50.24088,351.6862,85.77256,27.97864',
'40.72970,-73.9978,place101,b,'
+ 'place01,42.57717,425.7717,67.62636,17.53429',
'40.73266,-73.9975,place102,c,'
+ 'place06,50.03064,250.1532,79.72296,23.72270',
'40.73117,-74.0018,place103,d,'
+ 'place08,49.40183,395.2146,84.19146,5.034845',
'40.69427,-73.9898,place104,e,'
+ 'place59,47.73903,286.4341,93.16298,11.71055',
],
)
self.assertJson(
output_metadata,
{
'size': 998,
'columns': [
{
'name': 'lat',
'structural_type': 'http://schema.org/Float',
'semantic_types': ['http://schema.org/latitude'],
'unclean_values_ratio': 0.0,
'mean': lambda n: round(n, 3) == 40.709,
'stddev': lambda n: round(n, 3) == 0.019,
},
{
'name': 'long',
'structural_type': 'http://schema.org/Float',
'semantic_types': ['http://schema.org/longitude'],
'unclean_values_ratio': 0.0,
'mean': lambda n: round(n, 3) == -73.993,
'stddev': lambda n: round(n, 5) == 0.00528,
},
{
'name': 'id',
'structural_type': 'http://schema.org/Text',
'semantic_types': [],
'num_distinct_values': 10,
},
{
'name': 'letter',
'structural_type': 'http://schema.org/Text',
'semantic_types': [],
'num_distinct_values': 10,
},
{
'name': 'id_r',
'structural_type': 'http://schema.org/Text',
'semantic_types': [],
},
{
'name': 'mean height',
'structural_type': 'http://schema.org/Float',
'semantic_types': [],
},
{
'name': 'sum height',
'structural_type': 'http://schema.org/Float',
'semantic_types': [],
},
{
'name': 'max height',
'structural_type': 'http://schema.org/Float',
'semantic_types': [],
},
{
'name': 'min height',
'structural_type': 'http://schema.org/Float',
'semantic_types': [],
},
],
'qualities': [
{
'qualName': 'augmentation_info',
'qualValueType': 'dict',
'qualValue': {
'new_columns': [
'id_r', 'mean height',
'sum height', 'max height', 'min height',
],
'removed_columns': [],
'nb_rows_before': 10,
'nb_rows_after': 10,
'augmentation_type': 'join',
},
},
],
},
)