def test_dicom_store_instance_from_gcs(self):
# Store DICOM files to a empty DICOM store from a GCS bucket,
# then check if the store metadata match.
input_dict_store = {}
input_dict_store['project_id'] = self.project
input_dict_store['region'] = REGION
input_dict_store['dataset_id'] = DATA_SET_ID
input_dict_store['dicom_store_id'] = self.temp_dicom_store
expected_output = [True] * NUM_INSTANCE
with self.test_pipeline as p:
gcs_path = DICOM_FILES_PATH + "/io_test_files/*"
results = (p
| fileio.MatchFiles(gcs_path)
| fileio.ReadMatches()
| UploadToDicomStore(input_dict_store, 'fileio')
| beam.Map(lambda x: x['success']))
assert_that(results,
equal_to(expected_output),
label='store first assert')
# Check the metadata using client
result, status_code = DicomApiHttpClient().qido_search(
self.project, REGION, DATA_SET_ID, self.temp_dicom_store,
'instances')
self.assertEqual(status_code, 200)
# List comparison based on different version of python
self.assertCountEqual(result, self.expected_output_all_metadata)
def expand(self, root):
# TODO(robertwb): Handle streaming (with explicit schema).
paths_pcoll = root | beam.Create([self.path])
first = io.filesystems.FileSystems.match(
[self.path], limits=[1])[0].metadata_list[0].path
with io.filesystems.FileSystems.open(first) as handle:
if not self.binary:
handle = TextIOWrapper(handle)
if self.incremental:
sample = next(
self.reader(handle, *self.args,
**dict(self.kwargs, chunksize=100)))
else:
sample = self.reader(handle, *self.args, **self.kwargs)
pcoll = (paths_pcoll
| fileio.MatchFiles(self.path)
| beam.Reshuffle()
| fileio.ReadMatches()
| beam.ParDo(
_ReadFromPandasDoFn(self.reader, self.args, self.kwargs,
self.binary, self.incremental,
self.splitter)))
from apache_beam.dataframe import convert
return convert.to_dataframe(pcoll,
proxy=_prefix_range_index_with(
':', sample[:0]))
def test_dicom_store_instance(self):
# Store DICOM files to a empty DICOM store from a GCS bucket,
# then check if the store metadata match.
input_dict = {}
input_dict['project_id'] = self.project
input_dict['region'] = REGION
input_dict['dataset_id'] = DATA_SET_ID
input_dict['dicom_store_id'] = self.temp_dicom_store
input_dict['search_type'] = "instances"
expected_dict = {}
expected_dict['result'] = self.expected_output_metadata
expected_dict['status'] = 200
expected_dict['input'] = input_dict
expected_dict['success'] = True
with TestPipeline() as p:
gcs_path = DICOM_FILES_PATH + "/*"
results = (p
| fileio.MatchFiles(gcs_path)
| fileio.ReadMatches()
| UploadToDicomStore(input_dict, 'fileio')
| beam.Map(lambda x: x['success']))
assert_that(results, equal_to([True] * NUM_INSTANCE))
with TestPipeline() as p:
results = (p | beam.Create([input_dict]) | DicomSearch())
assert_that(results, equal_to([expected_dict]))
def test_write_to_dynamic_destination(self):
sink_params = [
fileio.TextSink, # pass a type signature
fileio.TextSink() # pass a FileSink object
]
for sink in sink_params:
dir = self._new_tempdir()
with TestPipeline() as p:
_ = (p
| "Create" >> beam.Create(range(100))
| beam.Map(lambda x: str(x))
| fileio.WriteToFiles(
path=dir,
destination=lambda n: "odd" if int(n) % 2 else "even",
sink=sink,
file_naming=fileio.destination_prefix_naming("test")))
with TestPipeline() as p:
result = (
p
| fileio.MatchFiles(FileSystems.join(dir, '*'))
| fileio.ReadMatches()
| beam.Map(lambda f: (
os.path.basename(f.metadata.path).split('-')[0],
sorted(map(int,
f.read_utf8().strip().split('\n'))))))
assert_that(
result,
equal_to([('odd', list(range(1, 100, 2))),
('even', list(range(0, 100, 2)))]))
def ReadImagesFromDisk(pipeline: beam.Pipeline,
base_path: Text) -> beam.pvalue.PCollection:
"""
The Beam PTransform used to load a collection of images and metadata
from a local file system or a remote cloud storage bucket.
Args:
pipeline (beam.Pipeline): Input beam.Pipeline object coming
from a TFX Executor.
base_path (Text): Base directory containing images and labels.
"""
wildcard_qualifier = "*"
# ingest all the files from the base path by supplying the wildcard
file_pattern = os.path.join(base_path, wildcard_qualifier)
allowed_ext = [".jpg", ".json", ".png", ".txt", ".jpeg"]
images, label_file = (
pipeline
| fileio.MatchFiles(file_pattern)
| fileio.ReadMatches()
| beam.Map(read_file_content)
| "FilterOutFiles" >> beam.Filter(lambda x: x[FILE_EXT] in allowed_ext)
| "SplitLabelFile" >> beam.Partition(SplitByFileName, 2))
# label_file is actually a dict
label_dict = beam.pvalue.AsSingleton(label_file)
ready_images = (
images
|
"AddLabelAndMetadata" >> beam.Map(add_label_and_metadata, label_dict))
return ready_images
def expand(self, root):
paths_pcoll = root | beam.Create([self.path])
match = io.filesystems.FileSystems.match([self.path], limits=[1])[0]
if not match.metadata_list:
# TODO(BEAM-12031): This should be allowed for streaming pipelines if
# user provides an explicit schema.
raise FileNotFoundError(f"Found no files that match {self.path!r}")
first_path = match.metadata_list[0].path
with io.filesystems.FileSystems.open(first_path) as handle:
if not self.binary:
handle = TextIOWrapper(handle)
if self.incremental:
sample = next(
self.reader(handle, *self.args,
**dict(self.kwargs, chunksize=100)))
else:
sample = self.reader(handle, *self.args, **self.kwargs)
pcoll = (paths_pcoll
| fileio.MatchFiles(self.path)
| beam.Reshuffle()
| fileio.ReadMatches()
| beam.ParDo(
_ReadFromPandasDoFn(self.reader, self.args, self.kwargs,
self.binary, self.incremental,
self.splitter)))
from apache_beam.dataframe import convert
return convert.to_dataframe(pcoll,
proxy=_prefix_range_index_with(
':', sample[:0]))
def test_write_to_different_file_types_some_spilling(self):
dir = self._new_tempdir()
with TestPipeline() as p:
_ = (
p
| beam.Create(WriteFilesTest.SIMPLE_COLLECTION)
| beam.io.fileio.WriteToFiles(
path=dir,
destination=lambda record: record['foundation'],
sink=lambda dest: (
WriteFilesTest.CsvSink(WriteFilesTest.CSV_HEADERS)
if dest == 'apache' else WriteFilesTest.JsonSink()),
file_naming=fileio.destination_prefix_naming(),
max_writers_per_bundle=1))
with TestPipeline() as p:
cncf_res = (
p
| fileio.MatchFiles(FileSystems.join(dir, 'cncf*'))
| fileio.ReadMatches()
| beam.FlatMap(lambda f: f.read_utf8().strip().split('\n'))
| beam.Map(json.loads))
apache_res = (
p
|
"MatchApache" >> fileio.MatchFiles(FileSystems.join(dir, 'apache*'))
| "ReadApache" >> fileio.ReadMatches()
| "MapApache" >>
beam.FlatMap(lambda rf: csv.reader(_get_file_reader(rf))))
assert_that(
cncf_res,
equal_to([
row for row in self.SIMPLE_COLLECTION
if row['foundation'] == 'cncf'
]),
label='verifyCNCF')
assert_that(
apache_res,
equal_to([[row['project'], row['foundation']]
for row in self.SIMPLE_COLLECTION
if row['foundation'] == 'apache']),
label='verifyApache')
def test_basic_two_files(self):
files = []
tempdir = '%s%s' % (self._new_tempdir(), os.sep)
# Create a couple files to be matched
files.append(self._create_temp_file(dir=tempdir))
files.append(self._create_temp_file(dir=tempdir))
with TestPipeline() as p:
files_pc = p | fileio.MatchFiles(tempdir) | beam.Map(lambda x: x.path)
assert_that(files_pc, equal_to(files))
def run():
p = beam.Pipeline(options=PipelineOptions())
# gcs = GCSFileSystem(PipelineOptions())
# 'gs://dataflow-buffer/parent-unpack/2018/i20180130/PxpFJwJabD-untarI20180130/DESIGN/USD0808610-20180130.ZIP'
# input_pattern = ['gs://dataflow-buffer/parent-unpack/2018/i20180130/PxpFJwJabD-untar*/**/*.ZIP']
input_pattern_1 = 'gs://dataflow-buffer/parent-unpack/2018/i20180130/PxpFJwJabD-untar*/**/*.ZIP'
# result = [m.metadata_list for m in gcs.match(input_pattern)]
(p
| 'Match Files' >> fileio.MatchFiles(input_pattern_1)
| 'Print read file' >> beam.ParDo(ImageExtract()))
p.run().wait_until_finish()
def main(runner):
project_name = 'get-signal-types'
timestamp = datetime.now(pytz.timezone('US/Pacific')).__str__() \
.replace(":", "") \
.replace(" ", "-") \
.replace(".", "")
options = PipelineOptions()
google_cloud_options = options.view_as(GoogleCloudOptions)
google_cloud_options.project = 'vilago-demo'
google_cloud_options.job_name = '%s-%s' % (project_name, timestamp)
if runner == "dataflow":
google_cloud_options.staging_location = 'gs://vilago-dataflow-output/staging/'
google_cloud_options.temp_location = 'gs://vilago-dataflow-output/temp/'
options.view_as(StandardOptions).runner = 'DataflowRunner'
outputdir = 'gs://vilago-dataflow-output/output/%s' % timestamp
inputfiles = 'gs://tuh-eeg-corpus/seizure-v1.5.0/edf/train/*/*/*/*/*.edf'
elif runner == "dataflow-test":
# same as dataflow except on fewer files
google_cloud_options.staging_location = 'gs://vilago-dataflow-output/staging/'
google_cloud_options.temp_location = 'gs://vilago-dataflow-output/temp/'
options.view_as(StandardOptions).runner = 'DataflowRunner'
outputdir = 'gs://vilago-dataflow-output/output/%s' % timestamp
inputfiles = 'gs://tuh-eeg-corpus/seizure-v1.5.0/edf/train/01_tcp_ar/002/*/*/*.edf'
else:
google_cloud_options.staging_location = 'staging/'
google_cloud_options.temp_location = 'temp'
options.view_as(StandardOptions).runner = 'DirectRunner'
outputdir = 'directrunner-output/outputs'
inputfiles = 'gs://tuh-eeg-corpus/seizure-v1.5.0/edf/train/01_tcp_ar/002/00000254/*/*.edf'
print('Starting beam job with runner %s...' %
options.view_as(StandardOptions).runner)
p = beam.Pipeline(options=options)
files = p | 'Match EDF files' >> fileio.MatchFiles(inputfiles)
files = prevent_fusion(files
| 'Extract EDF path' >> beam.Map(lambda x: x.path))
files \
| 'Parse EDF' >> beam.ParDo(GetSignalTypes()) \
| 'Pair with 1' >> beam.ParDo(PairWithOne()) \
| 'Group' >> beam.GroupByKey() \
| 'Sum' >> beam.Map(lambda t: (t[0], sum(t[1]))) \
| 'Format' >> beam.Map(lambda t: '%s, %d' % t) \
| 'Output to folder' >> beam.io.WriteToText(outputdir, file_name_suffix='.txt')
p.run()
print('Beam job finished')
def file_process_pattern_access_metadata():
import apache_beam as beam
from apache_beam.io import fileio
# [START FileProcessPatternAccessMetadataSnip1]
with beam.Pipeline() as p:
readable_files = (p
| fileio.MatchFiles('hdfs://path/to/*.txt')
| fileio.ReadMatches()
| beam.Reshuffle())
files_and_contents = (readable_files
| beam.Map(lambda x: (x.metadata.path,
x.read_utf8())))
def expand(self, root):
# TODO(robertwb): Handle streaming (with explicit schema).
paths_pcoll = root | beam.Create([self.path])
first = io.filesystems.FileSystems.match([self.path],
limits=[1
])[0].metadata_list[0].path
with io.filesystems.FileSystems.open(first) as handle:
df = next(self.reader(handle, *self.args, chunksize=100, **self.kwargs))
pcoll = (
paths_pcoll
| fileio.MatchFiles(self.path)
| fileio.ReadMatches()
| beam.ParDo(_ReadFromPandasDoFn(self.reader, self.args, self.kwargs)))
from apache_beam.dataframe import convert
return convert.to_dataframe(
pcoll, proxy=_prefix_range_index_with(':', df[:0]))
def test_write_to_single_file_batch(self):
dir = self._new_tempdir()
with TestPipeline() as p:
_ = (p
| beam.Create(WriteFilesTest.SIMPLE_COLLECTION)
| "Serialize" >> beam.Map(json.dumps)
| beam.io.fileio.WriteToFiles(path=dir))
with TestPipeline() as p:
result = (p
| fileio.MatchFiles(FileSystems.join(dir, '*'))
| fileio.ReadMatches()
| beam.FlatMap(lambda f: f.read_utf8().strip().split('\n'))
| beam.Map(json.loads))
assert_that(result,
equal_to([row for row in self.SIMPLE_COLLECTION]))
def test_streaming_different_file_types(self):
dir = self._new_tempdir()
input = iter(WriteFilesTest.SIMPLE_COLLECTION)
ts = (TestStream().advance_watermark_to(0).add_elements(
[next(input), next(input)]).advance_watermark_to(10).add_elements(
[next(input),
next(input)]).advance_watermark_to(20).add_elements([
next(input), next(input)
]).advance_watermark_to(30).add_elements([
next(input), next(input)
]).advance_watermark_to(40).advance_watermark_to_infinity())
def no_colon_file_naming(*args):
file_name = fileio.destination_prefix_naming()(*args)
return file_name.replace(':', '_')
with TestPipeline() as p:
_ = (p
| ts
| beam.WindowInto(FixedWindows(10))
| beam.io.fileio.WriteToFiles(
path=dir,
destination=lambda record: record['foundation'],
sink=lambda dest:
(WriteFilesTest.CsvSink(WriteFilesTest.CSV_HEADERS)
if dest == 'apache' else WriteFilesTest.JsonSink()),
file_naming=no_colon_file_naming,
max_writers_per_bundle=0,
))
with TestPipeline() as p:
cncf_files = (p
| fileio.MatchFiles(FileSystems.join(dir, 'cncf*'))
| "CncfFileNames" >> beam.Map(lambda fm: fm.path))
apache_files = (p
| "MatchApache" >> fileio.MatchFiles(
FileSystems.join(dir, 'apache*'))
|
"ApacheFileNames" >> beam.Map(lambda fm: fm.path))
assert_that(
cncf_files,
matches_all([
stringmatches.matches_regexp(
'.*cncf-1970-01-01T00_00_00-1970-01-01T00_00_10--.*'),
stringmatches.matches_regexp(
'.*cncf-1970-01-01T00_00_10-1970-01-01T00_00_20--.*'),
stringmatches.matches_regexp(
'.*cncf-1970-01-01T00_00_20-1970-01-01T00_00_30--.*'),
stringmatches.matches_regexp(
'.*cncf-1970-01-01T00_00_30-1970-01-01T00_00_40--.*')
]),
label='verifyCNCFFiles')
assert_that(
apache_files,
matches_all([
stringmatches.matches_regexp(
'.*apache-1970-01-01T00_00_00-1970-01-01T00_00_10--.*'
),
stringmatches.matches_regexp(
'.*apache-1970-01-01T00_00_10-1970-01-01T00_00_20--.*'
),
stringmatches.matches_regexp(
'.*apache-1970-01-01T00_00_20-1970-01-01T00_00_30--.*'
),
stringmatches.matches_regexp(
'.*apache-1970-01-01T00_00_30-1970-01-01T00_00_40--.*')
]),
label='verifyApacheFiles')
def run(argv=None):
class DataIngestion:
def parse_method(self, string_input):
values = re.split(",", re.sub('\r\n', '', re.sub(u'"', '', string_input)))
row = dict(
zip(('Requisition_Number', 'Opportunity_Title', 'Opportunity_Status', 'Featured', 'Company_Code',
'Company', 'Entity', 'Entity_Desc', 'Source_Job_Code', 'Job_Title', 'FullTime_Or_PartTime',
'Salary_Or_Hourly', 'Recruiter', 'Location_Name', 'Date_Applied', 'Source', 'Step', 'Step_Date',
'Recruiting_Hire_Date', 'Start_Date', 'Candidate', 'Candidate_Email_Address',
'Candidate_Primary_Phone', 'First_Published_Date', 'Average_Days_Between_Publish_Hire_Dates'),
values))
return row
parser = argparse.ArgumentParser()
parser.add_argument(
'--input',
dest='input',
required=False,
help='Input file to read. This can be a local file or '
'a file in a Google Storage Bucket.',
# default='gs://hc_crackerbarrel_ats/Historical'
)
parser.add_argument('--output',
dest='output',
required=False,
help='Output BQ table to write results to.',
default='chs.ats_master')
# Parse arguments from the command line.
known_args, pipeline_args = parser.parse_known_args(argv)
pipeline_args.extend([
'--runner=DataflowRunner',
'--project=hireclix',
'--region=us-east1',
'--staging_location=gs://hc_chs_ats/File_Temp/Source',
'--temp_location=gs://hc_chs_ats/File_Temp/Staging',
'--job_name=chstest1'
])
data_ingestion = DataIngestion()
with beam.Pipeline(options=PipelineOptions(pipeline_args)) as p:
readable_files = (p
| 'Matching .csv files' >> fileio.MatchFiles('gs://hc_chs_ats/File_Temp/Temp_File/*.csv')
| 'Read Matches' >> fileio.ReadMatches()
| 'Rebalance data inputs' >> beam.Reshuffle())
files_and_content = (readable_files
| 'Determine FilePath' >> beam.Map(lambda x: x.metadata.path))
writebq = (files_and_content
| 'Read from a File' >> beam.io.ReadAllFromText(skip_header_lines=1)
| 'String To BigQuery Row' >> beam.Map(lambda s: data_ingestion.parse_method(s))
| 'Write to BigQuery' >> beam.io.Write(
beam.io.WriteToBigQuery(known_args.output,
schema='Requisition_Number:STRING,'
'Opportunity_Title:STRING,'
'Opportunity_Status:STRING,'
'Featured:STRING,'
'Company_Code:STRING,'
'Company:STRING,'
'Entity:STRING,'
'Entity_Desc:STRING,'
'Source_Job_Code:STRING,'
'Job_Title:STRING,'
'FullTime_Or_PartTime:STRING,'
'Salary_Or_Hourly:STRING,'
'Recruiter:STRING,'
'Location_Name:STRING,'
'Date_Applied:DATE,'
'Source:STRING,'
'Step:STRING,'
'Step_Date:DATE,'
'Recruiting_Hire_Date:DATE,'
'Start_Date:DATE,'
'Candidate:STRING,'
'Candidate_Email_Address:STRING,'
'Candidate_Primary_Phone:STRING,'
'First_Published_Date:DATE,'
'Average_Days_Between_Publish_Hire_Dates:STRING',
create_disposition=beam.io.BigQueryDisposition.CREATE_IF_NEEDED,
write_disposition=beam.io.BigQueryDisposition.WRITE_TRUNCATE)))
def run(argv=None):
"""Main entry point; defines and runs the wordcount pipeline."""
parser = argparse.ArgumentParser()
parser.add_argument('--input',
dest='input',
default='gs://dataflow-samples/shakespeare/kinglear.txt',
help='Input file to process.')
parser.add_argument('--output',
dest='output',
required=True,
help='Output file to write results to.')
known_args, pipeline_args = parser.parse_known_args(argv)
# We use the save_main_session option because one or more DoFn's in this
# workflow rely on global context (e.g., a module imported at module level).
pipeline_options = PipelineOptions(pipeline_args)
pipeline_options.view_as(SetupOptions).save_main_session = True
p = beam.Pipeline(options=pipeline_options)
from apache_beam.io import fileio
with beam.Pipeline(options=PipelineOptions()) as p:
output = (p
| "match" >> fileio.MatchFiles(known_args.input)
| "read match" >> fileio.ReadMatches()
| "read_file" >> beam.Map(lambda x: (x.metadata.path,
x.read_utf8()))
| "parse file" >> beam.Map(lambda x: (parse_filename(x[0]),
parse_file(x[1].split('\n'))
))
| "unfold" >> beam.ParDo(MetaAndContent())
# | "debug" >> beam.FlatMap(lambda x: print(x))
)
table_spec = 'brainscode-140622:tf2up.conversions'
table_schema = {'fields': [
{'name': 'date', 'type': 'DATE'},
{'name': 'file_hash', 'type': 'STRING'},
{'name': 'line', 'type': 'INT64'},
{'name': 'position', 'type': 'INT64'},
{'name': 'severity', 'type': 'STRING'},
{'name': 'message', 'type': 'STRING'},
{'name': 'ops', 'type': 'STRING', 'mode': 'REPEATED'}
]}
# two different setups for create_disposition CREATE_IF_NEEDED
# and write_disposition - WRITE_TRUNCATE
output | 'store to BQ' >> beam.io.WriteToBigQuery(
table_spec,
schema=table_schema,
write_disposition=beam.io.BigQueryDisposition.WRITE_APPEND,
create_disposition=beam.io.BigQueryDisposition.CREATE_NEVER,
method="STREAMING_INSERTS"
)
# Write the output using a "Write" transform that has side effects.
# pylint: disable=expression-not-assigned
output | 'write' >> WriteToText(known_args.output)