def write_to_bq(self, dataset, gcs_bucket, **attrs):
gcs_files = self.get_attr(attrs, 'filename')
# In this instance, we expect filename to be a string with
# comma-separated CSV filenames.
if ',' not in gcs_files:
raise ValueError('filename passed to write_to_bq is not a '
'comma-separated list of files')
files = gcs_files.split(',')
print("Files that will be written to BQ:", files)
# For each of the files, we load it as a dataframe and add it as a
# table in the BigQuery dataset. We expect that all aggregation and
# standardization of the data has been done by this point.
int_cols = [std_col.COVID_CASES, std_col.COVID_HOSP_Y,
std_col.COVID_HOSP_N, std_col.COVID_HOSP_UNKNOWN,
std_col.COVID_DEATH_Y, std_col.COVID_DEATH_N,
std_col.COVID_DEATH_UNKNOWN]
for f in files:
# Explicitly specify county_fips is a string.
df = gcs_to_bq_util.load_csv_as_dataframe(
gcs_bucket, f, dtype={'county_fips': str})
# All columns are str, except outcome columns.
column_types = {c: 'STRING' for c in df.columns}
for col in int_cols:
if col in column_types:
column_types[col] = 'INT64'
# Clean up column names.
self.clean_frame_column_names(df)
table_name = f.replace('.csv', '') # Table name is file name
gcs_to_bq_util.add_dataframe_to_bq(
df, dataset, table_name, column_types=column_types)
def testAddDataframeToBq_IgnoreColModes(self):
"""Tests that col_modes is ignored when no column_types are provided
to add_dataframe_to_bq."""
test_frame = DataFrame(data=self._test_data[1:],
columns=self._test_data[0],
index=[1, 2])
with patch('ingestion.gcs_to_bq_util.bigquery.Client') as mock_client:
# Set up mock calls
mock_instance = mock_client.return_value
mock_table = Mock()
mock_instance.dataset.return_value = mock_table
mock_table.table.return_value = 'test-project.test-dataset.table'
gcs_to_bq_util.add_dataframe_to_bq(test_frame.copy(deep=True),
"test-dataset",
"table",
col_modes={
'label1': 'REPEATED',
'label2': 'REQUIRED'
})
mock_instance.load_table_from_json.assert_called()
call_args = mock_instance.load_table_from_json.call_args
test_frame['ingestion_ts'] = datetime(
2020, 1, 1,
tzinfo=timezone.utc).strftime("%Y-%m-%d %H:%M:%S.%f %Z")
self.assertEqual(call_args.args[0],
json.loads(test_frame.to_json(orient='records')))
job_config = call_args.kwargs['job_config']
self.assertTrue(job_config.autodetect)
def write_to_bq(self, dataset, gcs_bucket, filename):
"""Writes county adjacencies to BigQuery from the provided GCS bucket
dataset: The BigQuery dataset to write to
table_name: The name of the biquery table to write to
gcs_bucket: The name of the gcs bucket to read the data from
filename: The name of the file in the gcs bucket to read from"""
frame = gcs_to_bq_util.load_csv_as_dataframe(gcs_bucket, filename, dtype={
'fipscounty': 'string',
'fipsneighbor': 'string'
})
frame = frame[['fipscounty', 'fipsneighbor']]
frame = frame.rename(columns={
'fipscounty': 'county_geoid',
'fipsneighbor': 'neighbor_geoids'
})
frame = frame.groupby('county_geoid', as_index=False).agg(list)
column_types = {
'county_geoid': 'STRING',
'neighbor_geoids': 'STRING'
}
col_modes = {'neighbor_geoids': 'REPEATED'}
gcs_to_bq_util.add_dataframe_to_bq(
frame, dataset, self.get_table_name(), column_types=column_types,
col_modes=col_modes)
def write_to_bq(self, dataset, gcs_bucket):
# Get an ACS mapping of Fip Codes to State Names and county codes to county names
self.get_state_fips_mapping()
self.get_county_fips_mapping()
# Pull data from GCS and aggregate in memory
self.get_health_insurance_data_by_sex(use_gcs=True,
gcs_bucket=gcs_bucket)
self.get_health_insurance_data_by_race(use_gcs=True,
gcs_bucket=gcs_bucket)
# Split internal memory into data frames for sex/race by state/county
self.split_data_frames()
# Create BQ columns and write dataframes to BQ
for table_name, df in self.frames.items():
# All breakdown columns are strings
column_types = {c: 'STRING' for c in df.columns}
column_types[WITH_HEALTH_INSURANCE_COL] = 'INT64'
column_types[WITHOUT_HEALTH_INSURANCE_COL] = 'INT64'
column_types[TOTAL_HEALTH_INSURANCE_COL] = 'INT64'
gcs_to_bq_util.add_dataframe_to_bq(df,
dataset,
table_name,
column_types=column_types)
def write_to_bq(self, dataset, gcs_bucket, filename):
"""Writes state names to BigQuery from the provided GCS bucket
dataset: The BigQuery dataset to write to
table_name: The name of the biquery table to write to
gcs_bucket: The name of the gcs bucket to read the data from
filename: The name of the file in the gcs bucket to read from"""
try:
frame = gcs_to_bq_util.load_values_as_dataframe(
gcs_bucket, filename)
frame = frame.rename(columns={
'state': 'state_fips_code',
'NAME': 'state_name'
})
column_types = {
'state_fips_code': 'STRING',
'state_name': 'STRING'
}
gcs_to_bq_util.add_dataframe_to_bq(frame,
dataset,
self.get_table_name(),
column_types=column_types)
except json.JSONDecodeError as err:
logging.error(
'Unable to write to BigQuery due to improperly formatted data: %s',
err)
def write_to_bq_table(self,
dataset: str,
gcs_bucket: str,
filename: str,
table_name: str,
project=None):
"""Writes source data from GCS bucket to BigQuery
dataset: The BigQuery dataset to write to
gcs_bucket: The name of the gcs bucket to read the data from
filename: The name of the file in the gcs bucket to read from
table_name: The name of the BigQuery table to write to"""
chunked_frame = gcs_to_bq_util.load_csv_as_dataframe(gcs_bucket,
filename,
chunksize=1000)
# For the very first chunk, we set the mode to overwrite to clear the
# previous table. For subsequent chunks we append.
overwrite = True
for chunk in chunked_frame:
self.clean_frame_column_names(chunk)
gcs_to_bq_util.add_dataframe_to_bq(chunk,
dataset,
table_name,
project=project,
overwrite=overwrite)
overwrite = False
def write_to_bq(self, dataset, gcs_bucket, **attrs):
gcs_file = self.get_attr(attrs, "filename")
# Download the raw data
df = gcs_to_bq_util.load_csv_as_dataframe(gcs_bucket, gcs_file)
df = self.standardize(df)
# Write to BQ
gcs_to_bq_util.add_dataframe_to_bq(df, dataset, self.get_table_name())
def write_to_bq(self, dataset, gcs_bucket, **attrs):
filename = self.get_attr(attrs, 'filename')
df = gcs_to_bq_util.load_csv_as_dataframe(gcs_bucket,
filename,
parse_dates=['Date'],
thousands=',')
self.clean_frame_column_names(df)
# Massage the data into the standard format.
df.drop(columns=[
'cases_latinx', 'deaths_latinx', 'hosp_latinx', 'tests_latinx'
],
inplace=True)
df = df.melt(id_vars=['date', 'state'])
df[['variable_type',
col_std.RACE_COL]] = df.variable.str.split("_", 1, expand=True)
df.drop('variable', axis=1, inplace=True)
df.rename(columns={'state': 'state_postal_abbreviation'}, inplace=True)
df.replace({col_std.RACE_COL: self.get_standard_columns()},
inplace=True)
df['date'] = df['date'].map(lambda ts: ts.strftime("%Y-%m-%d"))
# Get the metadata table
metadata = self._download_metadata(dataset)
if len(metadata.index) == 0:
raise RuntimeError(
'BigQuery call to {} returned 0 rows'.format(dataset))
# Merge the tables
merged = pd.merge(df,
metadata,
how='left',
on=['state_postal_abbreviation', 'variable_type'])
# Rename combined race categories
self._rename_race_category(merged, 'reports_api', Race.ASIAN, Race.API)
self._rename_race_category(merged, 'reports_ind', Race.AIAN,
Race.INDIGENOUS)
merged.drop(columns=['reports_api', 'reports_ind'], inplace=True)
# Split into separate tables by variable type
for variable_type in ['cases', 'deaths', 'tests', 'hosp']:
result = merged.copy()
result = result.loc[result['variable_type'] == variable_type]
result.rename(columns={'value': variable_type}, inplace=True)
result.drop('variable_type', axis='columns', inplace=True)
# Write to BQ
gcs_to_bq_util.add_dataframe_to_bq(
result, dataset,
self.get_table_name() + '_' + variable_type)
def write_to_bq(self, dataset, gcs_bucket):
"""Writes population data to BigQuery from the provided GCS bucket
dataset: The BigQuery dataset to write to
gcs_bucket: The name of the gcs bucket to read the data from"""
# TODO change this to have it read metadata from GCS bucket
metadata = fetch_acs_metadata(self.base_acs_url)
var_map = parse_acs_metadata(metadata, list(GROUPS.keys()))
race_and_hispanic_frame = gcs_to_bq_util.load_values_as_dataframe(
gcs_bucket, self.get_filename(HISPANIC_BY_RACE_CONCEPT))
race_and_hispanic_frame = update_col_types(race_and_hispanic_frame)
race_and_hispanic_frame = standardize_frame(
race_and_hispanic_frame,
get_vars_for_group(HISPANIC_BY_RACE_CONCEPT, var_map, 2),
[HISPANIC_COL, RACE_COL],
self.county_level,
POPULATION_COL)
total_frame = gcs_to_bq_util.load_values_as_dataframe(
gcs_bucket, self.add_filename_suffix(TOTAL_POP_VARIABLE_ID))
total_frame = update_col_types(total_frame)
total_frame = standardize_frame(
total_frame,
{TOTAL_POP_VARIABLE_ID: ['Total']},
[RACE_OR_HISPANIC_COL],
self.county_level,
POPULATION_COL)
sex_by_age_frames = {}
for concept in SEX_BY_AGE_CONCEPTS_TO_RACE:
sex_by_age_frame = gcs_to_bq_util.load_values_as_dataframe(
gcs_bucket, self.get_filename(concept))
sex_by_age_frame = update_col_types(sex_by_age_frame)
sex_by_age_frames[concept] = sex_by_age_frame
frames = {
self.get_table_name_by_race(): self.get_all_races_frame(
race_and_hispanic_frame, total_frame),
self.get_table_name_by_sex_age_race(): self.get_sex_by_age_and_race(
var_map, sex_by_age_frames)
}
for table_name, df in frames.items():
# All breakdown columns are strings
column_types = {c: 'STRING' for c in df.columns}
column_types[POPULATION_COL] = 'INT64'
gcs_to_bq_util.add_dataframe_to_bq(
df, dataset, table_name, column_types=column_types)
def write_to_bq(self, dataset, bucket):
self.getData(bucket)
# Split internal memory into data frames for sex/race by state/county
self.split_data_frames()
# Create BQ columns and write dataframes to BQ
for table_name, df in self.frames.items():
# All breakdown columns are strings
column_types = {c: "STRING" for c in df.columns}
column_types[ABOVE_POVERTY_COL] = "INT64"
column_types[BELOW_POVERTY_COL] = "INT64"
gcs_to_bq_util.add_dataframe_to_bq(
df, dataset, table_name, column_types=column_types
)
def write_to_bq(self, dataset, bucket):
self.getData(bucket)
# Split internal memory into data frames for sex/race by state/county
self.split_data_frames()
# Create BQ columns and write dataframes to BQ
for table_name, df in self.frames.items():
# All breakdown columns are strings
column_types = {c: "STRING" for c in df.columns}
if RACE_INCLUDES_HISPANIC_COL in df.columns:
column_types[RACE_INCLUDES_HISPANIC_COL] = 'BOOL'
column_types[POPULATION_COL] = "INT64"
gcs_to_bq_util.add_dataframe_to_bq(
df, dataset, table_name, column_types=column_types
)
def write_to_bq(self, dataset, gcs_bucket):
self.getData(gcs_bucket=gcs_bucket)
# Split internal memory into data frames for sex/race by state/county
self.split_data_frames()
# Create BQ columns and write dataframes to BQ
for table_name, df in self.frames.items():
# All breakdown columns are strings
column_types = {c: "STRING" for c in df.columns}
column_types[WITH_HEALTH_INSURANCE_COL] = "INT64"
column_types[WITHOUT_HEALTH_INSURANCE_COL] = "INT64"
column_types[TOTAL_HEALTH_INSURANCE_COL] = "INT64"
gcs_to_bq_util.add_dataframe_to_bq(
df, dataset, table_name, column_types=column_types
)
def write_to_bq(self, dataset, gcs_bucket, filename):
"""Writes primary care access stats to BigQuery from bucket
dataset: The BigQuery dataset to write to
table_name: The name of the biquery table to write to
gcs_bucket: The name of the gcs bucket to read the data from
filename: The prefix of files in the landing bucket to read from"""
client = storage.Client()
bucket = client.get_bucket(gcs_bucket)
data = []
for state_name in constants.STATE_NAMES:
filename = self._FILEPATH.format(filename, state_name)
blob = bucket.blob(filename)
local_path = '/tmp/{}'.format(filename)
blob.download_to_filename(local_path)
frame = read_excel(io=local_path,
sheet_name='Ranked Measure Data',
skiprows=[0, 2])
for _, row in frame.iterrows():
# These fields may not be set for every county.
# If they're not set, we'll use -1 as the numerical value
# Number of physicians in the county
num_physicians = row[108] if not math.isnan(row[108]) else -1
# Primary Care Physicians per 100,000 population
physicians_rate = row[109] if not math.isnan(row[108]) else -1
row = [row[0], row[1], row[2], num_physicians, physicians_rate]
data.append(row)
new_dataframe = DataFrame(data=data,
columns=('county_fips_code', 'state_name',
'county_name',
'num_primary_care_physicians',
'primary_care_physicians_rate'))
column_types = {
'county_fips_code': 'INT64',
'state_name': 'STRING',
'county_name': 'STRING',
'num_primary_care_physicians': 'FLOAT64',
'primary_care_physicians_rate': 'FLOAT64',
}
gcs_to_bq_util.add_dataframe_to_bq(new_dataframe,
dataset,
self.get_table_name(),
column_types=column_types)
def write_to_bq(self, dataset, gcs_bucket, **attrs):
df = gcs_to_bq_util.load_csv_as_dataframe_from_web(BASE_UHC_URL)
for breakdown in [
std_col.RACE_OR_HISPANIC_COL, std_col.AGE_COL, std_col.SEX_COL
]:
breakdown_df = self.generate_breakdown(breakdown, df)
column_types = {c: 'STRING' for c in breakdown_df.columns}
for col in [std_col.COPD_PCT, std_col.DIABETES_PCT]:
column_types[col] = 'FLOAT'
if std_col.RACE_INCLUDES_HISPANIC_COL in breakdown_df.columns:
column_types[std_col.RACE_INCLUDES_HISPANIC_COL] = 'BOOL'
gcs_to_bq_util.add_dataframe_to_bq(breakdown_df,
dataset,
breakdown,
column_types=column_types)
def testAddDataframeToBq_SpecifySchema(self):
"""Tests that the BigQuery schema is properly defined when column_types
are provided to add_dataframe_to_bq."""
test_frame = DataFrame(data=self._test_data[1:],
columns=self._test_data[0],
index=[1, 2])
with patch('ingestion.gcs_to_bq_util.bigquery.Client') as mock_client:
# Set up mock calls
mock_instance = mock_client.return_value
mock_table = Mock()
mock_instance.dataset.return_value = mock_table
mock_table.table.return_value = 'test-project.test-dataset.table'
column_types = {label: 'STRING' for label in test_frame.columns}
col_modes = {'label1': 'REPEATED', 'label2': 'REQUIRED'}
gcs_to_bq_util.add_dataframe_to_bq(test_frame.copy(deep=True),
'test-dataset',
'table',
column_types=column_types,
col_modes=col_modes)
mock_instance.load_table_from_json.assert_called()
call_args = mock_instance.load_table_from_json.call_args
test_frame['ingestion_ts'] = datetime(
2020, 1, 1,
tzinfo=timezone.utc).strftime('%Y-%m-%d %H:%M:%S.%f %Z')
self.assertEqual(call_args.args[0],
json.loads(test_frame.to_json(orient='records')))
job_config = call_args.kwargs['job_config']
self.assertFalse(job_config.autodetect)
expected_cols = ['label1', 'label2', 'label3', 'ingestion_ts']
expected_types = ['STRING', 'STRING', 'STRING', 'TIMESTAMP']
expected_modes = ['REPEATED', 'REQUIRED', 'NULLABLE', 'NULLABLE']
self.assertListEqual([field.name for field in job_config.schema],
expected_cols)
self.assertListEqual(
[field.field_type for field in job_config.schema],
expected_types)
self.assertListEqual([field.mode for field in job_config.schema],
expected_modes)
def write_to_bq(self, dataset, gcs_bucket, filename):
"""Fetches all SAIPE blobs from a GCS bucket and uploads to a single BQ table.
Also does some preprocessing.
dataset: The BigQuery dataset to write to
table_name: The name of the BigQuery table to write to
gcs_bucket: The name of the GCS bucket to pull from
filename: File name prefix used to identify which GCS blobs to fetch"""
client = storage.Client()
saipe_blobs = client.list_blobs(gcs_bucket, prefix=filename)
frames = []
for blob in saipe_blobs:
frame = gcs_to_bq_util.load_values_blob_as_dataframe(blob)
frames.append(frame)
concat = pandas.concat(frames, ignore_index=True)
# The SAIPE API includes the query predicate columns, which are duplicates of their
# ALL_CAPS counterparts. Toss 'em.
concat.drop(columns=['state', 'county', 'time'], inplace=True)
gcs_to_bq_util.add_dataframe_to_bq(concat, dataset,
self.get_table_name())
def write_to_bq(self, dataset, gcs_bucket, **attrs):
filename = self.get_attr(attrs, "filename")
df = gcs_to_bq_util.load_csv_as_dataframe(
gcs_bucket, filename, parse_dates=["Date"], thousands=",")
df = self.standardize(df)
# Get the metadata table
metadata = self._download_metadata(dataset)
if len(metadata.index) == 0:
raise RuntimeError("BigQuery call to {} returned 0 rows".format(dataset))
merged = CovidTrackingProject.merge_with_metadata(df, metadata)
# Split into separate tables by variable type
for variable_type in ["cases", "deaths", "tests", "hosp"]:
result = merged.copy()
result = result.loc[result["variable_type"] == variable_type]
result.rename(columns={"value": variable_type}, inplace=True)
result.drop("variable_type", axis="columns", inplace=True)
# Write to BQ
gcs_to_bq_util.add_dataframe_to_bq(
result, dataset, self.get_table_name() + "_" + variable_type)
def write_to_bq(self, dataset, gcs_bucket, **attrs):
gcs_file = self.get_attr(attrs, 'filename')
# Download the raw data
df = gcs_to_bq_util.load_csv_as_dataframe(gcs_bucket, gcs_file)
self.clean_frame_column_names(df)
# Standardize the data
# The metadata currently only has information for cases and deaths,
# not tests or hospitalizations.
keep_cols = [
'state_postal_abbreviation', 'api_death', 'defines_other_death',
'race_ethnicity_separately_death', 'race_ethnicity_combined_death',
'race_mutually_exclusive_death',
'combined_category_other_than_api_death', 'race_death',
'ethnicity_death', 'api_cases', 'defines_other_cases',
'race_ethnicity_separately_cases', 'race_ethnicity_combined_cases',
'race_mutually_exclusive_cases',
'combined_category_other_than_api_cases', 'race_cases',
'ethnicity_cases'
]
df = df[keep_cols]
df = df.melt(id_vars=['state_postal_abbreviation'])
df[['col_name', 'variable_type']] = df.variable.str.rsplit('_',
1,
expand=True)
df.drop('variable', axis=1, inplace=True)
df = df.pivot(index=['state_postal_abbreviation', 'variable_type'],
columns='col_name',
values='value').reset_index()
df.replace({'variable_type': {'death': 'deaths'}}, inplace=True)
df.rename_axis(None, inplace=True)
df.rename(columns=self._metadata_columns_map(), inplace=True)
# Write to BQ
gcs_to_bq_util.add_dataframe_to_bq(df, dataset, self.get_table_name())
