def csv_generator(study_id, number_of_new_patients):
si = StreamingBytesIO()
filewriter = writer(si)
filewriter.writerow(['Patient ID', "Registration password"])
study_object_id = Study.objects.filter(pk=study_id).values_list('object_id', flat=True).get()
for _ in xrange(number_of_new_patients):
patient_id, password = Participant.create_with_password(study_id=study_id)
# Creates an empty file on s3 indicating that this user exists
s3_upload(patient_id, "", study_object_id)
create_client_key_pair(patient_id, study_object_id)
filewriter.writerow([patient_id, password])
yield si.getvalue()
si.empty()
def participant_credential_generator(study_id, number_of_new_patients, desired_filename):
si = StreamingBytesIO()
filewriter = writer(si)
filewriter.writerow(['Patient ID', "Registration password"])
study_object_id = Study.objects.filter(pk=study_id).values_list('object_id', flat=True).get()
study_name = Study.objects.filter(pk=study_id).values_list('name', flat=True).get()
for _ in xrange(number_of_new_patients):
patient_id, password = Participant.create_with_password(study_id=study_id)
# Creates an empty file on s3 indicating that this user exists
s3_upload(construct_s3_raw_data_path(study_object_id, patient_id), "", study_object_id, raw_path=True)
filewriter.writerow([patient_id, password])
yield si.getvalue()
si.empty()
def zip_generator_for_pipeline(files_list):
pool = ThreadPool(3)
zip_output = StreamingBytesIO()
zip_input = ZipFile(zip_output, mode="w", compression=ZIP_STORED, allowZip64=True)
try:
# chunks_and_content is a list of tuples, of the chunk and the content of the file.
# chunksize (which is a keyword argument of imap, not to be confused with Beiwe Chunks)
# is the size of the batches that are handed to the pool. We always want to add the next
# file to retrieve to the pool asap, so we want a chunk size of 1.
# (In the documentation there are comments about the timeout, it is irrelevant under this construction.)
chunks_and_content = pool.imap_unordered(batch_retrieve_pipeline_s3, files_list, chunksize=1)
for pipeline_upload, file_contents in chunks_and_content:
# file_name = determine_file_name(chunk)
zip_input.writestr("data/" + pipeline_upload.file_name, file_contents)
# These can be large, and we don't want them sticking around in memory as we wait for the yield
del file_contents, pipeline_upload
yield zip_output.getvalue() # yield the (compressed) file information
zip_output.empty()
# close, then yield all remaining data in the zip.
zip_input.close()
yield zip_output.getvalue()
except DummyError:
# The try-except-finally block is here to guarantee the Threadpool is closed and terminated.
# we don't handle any errors, we just re-raise any error that shows up.
# (with statement does not work.)
raise
finally:
# We rely on the finally block to ensure that the threadpool will be closed and terminated,
# and also to print an error to the log if we need to.
pool.close()
pool.terminate()
def zip_generator(files_list, construct_registry=False):
""" Pulls in data from S3 in a multithreaded network operation, constructs a zip file of that
data. This is a generator, advantage is it starts returning data (file by file, but wrapped
in zip compression) almost immediately. """
processed_files = set()
duplicate_files = set()
pool = ThreadPool(3)
# 3 Threads has been heuristically determined to be a good value, it does not cause the server
# to be overloaded, and provides more-or-less the maximum data download speed. This was tested
# on an m4.large instance (dual core, 8GB of ram).
file_registry = {}
zip_output = StreamingBytesIO()
zip_input = ZipFile(zip_output, mode="w", compression=ZIP_STORED, allowZip64=True)
try:
# chunks_and_content is a list of tuples, of the chunk and the content of the file.
# chunksize (which is a keyword argument of imap, not to be confused with Beiwe Chunks)
# is the size of the batches that are handed to the pool. We always want to add the next
# file to retrieve to the pool asap, so we want a chunk size of 1.
# (In the documentation there are comments about the timeout, it is irrelevant under this construction.)
chunks_and_content = pool.imap_unordered(batch_retrieve_s3, files_list, chunksize=1)
total_size = 0
for chunk, file_contents in chunks_and_content:
if construct_registry:
file_registry[chunk['chunk_path']] = chunk["chunk_hash"]
file_name = determine_file_name(chunk)
if file_name in processed_files:
duplicate_files.add((file_name, chunk['chunk_path']))
continue
processed_files.add(file_name)
zip_input.writestr(file_name, file_contents)
# These can be large, and we don't want them sticking around in memory as we wait for the yield
del file_contents, chunk
x = zip_output.getvalue()
total_size += len(x)
# print "%s: %sK, %sM" % (random_id, total_size / 1024, total_size / 1024 / 1024)
yield x # yield the (compressed) file information
del x
zip_output.empty()
if construct_registry:
zip_input.writestr("registry", json.dumps(file_registry))
yield zip_output.getvalue()
zip_output.empty()
# close, then yield all remaining data in the zip.
zip_input.close()
yield zip_output.getvalue()
except DummyError:
# The try-except-finally block is here to guarantee the Threadpool is closed and terminated.
# we don't handle any errors, we just re-raise any error that shows up.
# (with statement does not work.)
raise
finally:
# We rely on the finally block to ensure that the threadpool will be closed and terminated,
# and also to print an error to the log if we need to.
pool.close()
pool.terminate()
