Refine bulk load tests with data preparation (#16998)

Signed-off-by: yanliang567 <yanliang.qiao@zilliz.com>
This commit is contained in:
yanliang567 2022-05-16 09:55:55 +08:00 committed by GitHub
parent aefff31ba8
commit ab9b091bb1
No known key found for this signature in database
GPG Key ID: 4AEE18F83AFDEB23
3 changed files with 885 additions and 616 deletions

View File

@ -1,15 +1,14 @@
import time
import os
from minio import Minio
from minio.error import S3Error
import numpy as np
import random
from sklearn import preprocessing
from common.common_func import gen_unique_str
from minio_comm import copy_files_to_minio
minio = "10.96.1.23:9000" # TODO update hardcode
bucket_name = "yanliang-bulk-load" # TODO update hardcode
# TODO: remove hardcode with input configurations
minio = "minio_address:port" # minio service and port
bucket_name = "milvus-bulk-load" # bucket name of milvus is using
data_source = "/tmp/bulk_load_data"
@ -17,17 +16,34 @@ BINARY = "binary"
FLOAT = "float"
class DataField:
pk_field = "uid"
vec_field = "vectors"
int_field = "int_scalar"
string_field = "string_scalar"
bool_field = "bool_scalar"
float_field = "float_scalar"
class DataErrorType:
one_entity_wrong_dim = "one_entity_wrong_dim"
str_on_int_pk = "str_on_int_pk"
int_on_float_scalar = "int_on_float_scalar"
float_on_int_pk = "float_on_int_pk"
typo_on_bool = "typo_on_bool"
def gen_file_prefix(row_based=True, auto_id=True, prefix=""):
if row_based:
if auto_id:
return f"{prefix}row_auto"
return f"{prefix}_row_auto"
else:
return f"{prefix}row_cust"
return f"{prefix}_row_cust"
else:
if auto_id:
return f"{prefix}col_auto"
return f"{prefix}_col_auto"
else:
return f"{prefix}col_cust"
return f"{prefix}_col_cust"
def entity_suffix(rows):
@ -54,7 +70,15 @@ def gen_binary_vectors(nb, dim):
return vectors
def gen_row_based_json_file(row_file, str_pk, multi_scalars, float_vect, rows, dim, autoid):
def gen_row_based_json_file(row_file, str_pk, data_fields, float_vect,
rows, dim, start_uid=0, err_type="", **kwargs):
if err_type == DataErrorType.str_on_int_pk:
str_pk = True
if err_type == DataErrorType.one_entity_wrong_dim:
wrong_dim = dim + 8 # add 8 to compatible with binary vectors
wrong_row = kwargs.get("wrong_position", start_uid)
with open(row_file, "w") as f:
f.write("{")
f.write("\n")
@ -64,28 +88,44 @@ def gen_row_based_json_file(row_file, str_pk, multi_scalars, float_vect, rows, d
if i > 0:
f.write(",")
f.write("\n")
# pk fields
if not autoid:
if str_pk:
f.write('{"uid":"' + str(gen_unique_str()) + '",')
else:
f.write('{"uid":' + str(i) + ',')
else:
f.write('{')
# scalar fields
if multi_scalars:
f.write('"int_scalar":' + str(random.randint(-999999, 9999999)) + ',')
f.write('"float_scalar":' + str(random.random()) + ',')
f.write('"string_scalar":"' + str(gen_unique_str()) + '",')
f.write('"bool_scalar":' + str(random.choice(["true", "false"])) + ',')
# vector field
if float_vect:
vectors = gen_float_vectors(1, dim)
else:
vectors = gen_binary_vectors(1, (dim//8))
f.write('"vectors":' + ",".join(str(x) for x in vectors) + "}")
f.write('{')
for j in range(len(data_fields)):
data_field = data_fields[j]
if data_field == DataField.pk_field:
if str_pk:
f.write('"uid":"' + str(gen_unique_str()) + '"')
else:
if err_type == DataErrorType.float_on_int_pk:
f.write('"uid":' + str(i + start_uid + random.random()) + '')
else:
f.write('"uid":' + str(i + start_uid) + '')
if data_field == DataField.int_field:
f.write('"int_scalar":' + str(random.randint(-999999, 9999999)) + '')
if data_field == DataField.float_field:
if err_type == DataErrorType.int_on_float_scalar:
f.write('"float_scalar":' + str(random.randint(-999999, 9999999)) + '')
else:
f.write('"float_scalar":' + str(random.random()) + '')
if data_field == DataField.string_field:
f.write('"string_scalar":"' + str(gen_unique_str()) + '"')
if data_field == DataField.bool_field:
if err_type == DataErrorType.typo_on_bool:
f.write('"bool_scalar":' + str(random.choice(["True", "False", "TRUE", "FALSE", "0", "1"])) + '')
else:
f.write('"bool_scalar":' + str(random.choice(["true", "false"])) + '')
if data_field == DataField.vec_field:
# vector field
if err_type == DataErrorType.one_entity_wrong_dim and i == wrong_row:
vectors = gen_float_vectors(1, wrong_dim) if float_vect else gen_binary_vectors(1, (wrong_dim // 8))
else:
vectors = gen_float_vectors(1, dim) if float_vect else gen_binary_vectors(1, (dim//8))
f.write('"vectors":' + ",".join(str(x) for x in vectors) + '')
# not write common for the last field
if j != len(data_fields) - 1:
f.write(',')
f.write('}')
f.write("\n")
f.write("]")
f.write("\n")
@ -93,217 +133,305 @@ def gen_row_based_json_file(row_file, str_pk, multi_scalars, float_vect, rows, d
f.write("\n")
def gen_column_base_json_file(col_file, str_pk, float_vect, multi_scalars, rows, dim, autoid):
def gen_column_base_json_file(col_file, str_pk, data_fields, float_vect,
rows, dim, start_uid=0, err_type="", **kwargs):
if err_type == DataErrorType.str_on_int_pk:
str_pk = True
with open(col_file, "w") as f:
f.write("{")
f.write("\n")
# pk columns
if not autoid:
if str_pk == "str_pk":
f.write('"uid":["' + ',"'.join(str(gen_unique_str()) + '"' for i in range(rows)) + '],')
f.write("\n")
else:
f.write('"uid":[' + ",".join(str(i) for i in range(rows)) + "],")
f.write("\n")
# scalar columns
if multi_scalars:
f.write('"int_scalar":[' + ",".join(str(random.randint(-999999, 9999999)) for i in range(rows)) + "],")
f.write("\n")
f.write('"float_scalar":[' + ",".join(str(random.random()) for i in range(rows)) + "],")
f.write("\n")
f.write('"string_scalar":["' + ',"'.join(str(gen_unique_str()) + '"' for i in range(rows)) + '],')
f.write("\n")
f.write('"bool_scalar":[' + ",".join(str(random.choice(["true", "false"])) for i in range(rows)) + "],")
f.write("\n")
# vector columns
if float_vect:
vectors = gen_float_vectors(rows, dim)
f.write('"vectors":[' + ",".join(str(x) for x in vectors) + "]")
f.write("\n")
else:
vectors = gen_binary_vectors(rows, (dim//8))
f.write('"vectors":[' + ",".join(str(x) for x in vectors) + "]")
f.write("\n")
if rows > 0:
# data columns
for j in range(len(data_fields)):
data_field = data_fields[j]
if data_field == DataField.pk_field:
if str_pk:
f.write('"uid":["' + ',"'.join(str(gen_unique_str()) + '"' for i in range(rows)) + ']')
f.write("\n")
else:
if err_type == DataErrorType.float_on_int_pk:
f.write('"uid":[' + ",".join(
str(i + random.random()) for i in range(start_uid, start_uid + rows)) + "]")
else:
f.write('"uid":[' + ",".join(str(i) for i in range(start_uid, start_uid + rows)) + "]")
f.write("\n")
if data_field == DataField.int_field:
f.write('"int_scalar":[' + ",".join(str(
random.randint(-999999, 9999999)) for i in range(rows)) + "]")
f.write("\n")
if data_field == DataField.float_field:
if err_type == DataErrorType.int_on_float_scalar:
f.write('"float_scalar":[' + ",".join(
str(random.randint(-999999, 9999999)) for i in range(rows)) + "]")
else:
f.write('"float_scalar":[' + ",".join(
str(random.random()) for i in range(rows)) + "]")
f.write("\n")
if data_field == DataField.string_field:
f.write('"string_scalar":["' + ',"'.join(str(
gen_unique_str()) + '"' for i in range(rows)) + ']')
f.write("\n")
if data_field == DataField.bool_field:
if err_type == DataErrorType.typo_on_bool:
f.write('"bool_scalar":[' + ",".join(
str(random.choice(["True", "False", "TRUE", "FALSE", "1", "0"])) for i in range(rows)) + "]")
else:
f.write('"bool_scalar":[' + ",".join(
str(random.choice(["true", "false"])) for i in range(rows)) + "]")
f.write("\n")
if data_field == DataField.vec_field:
# vector columns
if err_type == DataErrorType.one_entity_wrong_dim:
wrong_dim = dim + 8 # add 8 to compatible with binary vectors
wrong_row = kwargs.get("wrong_position", 0)
if wrong_row <= 0:
vectors1 = []
else:
vectors1 = gen_float_vectors(wrong_row, dim) if float_vect else gen_binary_vectors(wrong_row, (dim//8))
if wrong_row >= rows -1:
vectors2 = []
else:
vectors2 = gen_float_vectors(rows-wrong_row-1, dim) if float_vect else gen_binary_vectors(rows-wrong_row-1, (dim//8))
vectors_wrong_dim = gen_float_vectors(1, wrong_dim) if float_vect else gen_binary_vectors(1, (wrong_dim//8))
vectors = vectors1 + vectors_wrong_dim + vectors2
else:
vectors = gen_float_vectors(rows, dim) if float_vect else gen_binary_vectors(rows, (dim//8))
f.write('"vectors":[' + ",".join(str(x) for x in vectors) + "]")
f.write("\n")
if j != len(data_fields) - 1:
f.write(",")
f.write("}")
f.write("\n")
def gen_vectors_in_numpy_file(dir, vector_type, rows, dim, num):
# vector columns
if vector_type == FLOAT:
vectors = gen_float_vectors(rows, dim)
def gen_vectors_in_numpy_file(dir, float_vector, rows, dim, force=False):
file_name = f"{DataField.vec_field}.npy"
file = f'{dir}/{file_name}'
if not os.path.exists(file) or force:
# vector columns
vectors = []
if rows > 0:
if float_vector:
vectors = gen_float_vectors(rows, dim)
else:
vectors = gen_binary_vectors(rows, (dim // 8))
arr = np.array(vectors)
np.save(file, arr)
return file_name
def gen_int_or_float_in_numpy_file(dir, data_field, rows, start=0, force=False):
file_name = f"{data_field}.npy"
file = f"{dir}/{file_name}"
if not os.path.exists(file) or force:
# non vector columns
data = []
if rows > 0:
if data_field == DataField.float_field:
data = [random.random() for _ in range(rows)]
elif data_field == DataField.pk_field:
data = [i for i in range(start, start + rows)]
elif data_field == DataField.int_field:
data = [random.randint(-999999, 9999999) for _ in range(rows)]
arr = np.array(data)
np.save(file, arr)
return file_name
def gen_file_name(row_based, rows, dim, auto_id, str_pk,
float_vector, data_fields, file_num, file_type, err_type):
row_suffix = entity_suffix(rows)
field_suffix = ""
if len(data_fields) > 3:
field_suffix = "multi_scalars_"
else:
vectors = gen_binary_vectors(rows, (dim // 8))
for data_field in data_fields:
if data_field != DataField.vec_field:
field_suffix += f"{data_field}_"
suffix = entity_suffix(rows)
# print(vectors)
arr = np.array(vectors)
path = f"{dir}/{dim}d_{suffix}_{num}"
if not os.path.isdir(path):
os.mkdir(path)
file = f'{path}/vectors_{dim}d_{suffix}.npy'
np.save(file, arr)
vt = ""
if DataField.vec_field in data_fields:
vt = "float_vectors_" if float_vector else "binary_vectors_"
def gen_scalars_in_numpy_file(dir, vector_type, rows, dim, num, start):
# scalar columns
if vector_type == FLOAT:
data = [random.random() for i in range(rows)]
elif vector_type == "int":
data = [i for i in range(start, start + rows)]
suffix = entity_suffix(rows)
path = f"{dir}/{dim}d_{suffix}_{num}"
arr = np.array(data)
file = f'{path}/uid.npy'
np.save(file, arr)
def gen_json_file_name(row_based, rows, dim, auto_id, str_pk, float_vector, multi_scalars, file_num):
suffix = entity_suffix(rows)
scalars = "only"
if multi_scalars:
scalars = "multi_scalars"
vt = FLOAT
if not float_vector:
vt = BINARY
pk = ""
if str_pk:
pk = "str_pk_"
prefix = gen_file_prefix(row_based=row_based, auto_id=auto_id)
return f"{prefix}_{pk}{vt}_vectors_{scalars}_{dim}d_{suffix}_{file_num}.json"
prefix = gen_file_prefix(row_based=row_based, auto_id=auto_id, prefix=err_type)
file_name = f"{prefix}_{pk}{vt}{field_suffix}{dim}d_{row_suffix}_{file_num}{file_type}"
return file_name
def gen_json_files(row_based, rows, dim, auto_id, str_pk, float_vector, multi_scalars, file_nums, force=False):
"""
row_based: Boolean
generate row based json file if True
generate column base json file if False
rows: entities of data
dim: dim of vector data
auto_id: Boolean
generate primary key data if False, else not
str_pk: Boolean
generate string as primary key if True, else generate INT64 as pk
float_vector: Boolean
generate float vectors if True, else binary vectors
multi_scalars: Boolean
only generate vector data (and pk data depended on auto_switches) if False
besides vector data, generate INT, STRING, BOOLEAN, etc scalar data if True
file_nums: file numbers that to be generated
"""
def gen_subfolder(root, dim, rows, file_num):
suffix = entity_suffix(rows)
subfolder = f"{dim}d_{suffix}_{file_num}"
path = f"{root}/{subfolder}"
if not os.path.isdir(path):
os.mkdir(path)
return subfolder
def gen_json_files(row_based, rows, dim, auto_id, str_pk,
float_vector, data_fields, file_nums, multi_folder,
file_type, err_type, force, **kwargs):
# gen json files
files = []
start_uid = 0
# make sure pk field exists when not auto_id
if not auto_id and DataField.pk_field not in data_fields:
data_fields.append(DataField.pk_field)
for i in range(file_nums):
file_name = gen_json_file_name(row_based=row_based, rows=rows,dim=dim,
auto_id=auto_id,str_pk=str_pk,float_vector=float_vector,
multi_scalars=multi_scalars, file_num=i)
file_name = gen_file_name(row_based=row_based, rows=rows, dim=dim,
auto_id=auto_id, str_pk=str_pk, float_vector=float_vector,
data_fields=data_fields, file_num=i, file_type=file_type, err_type=err_type)
file = f"{data_source}/{file_name}"
if multi_folder:
subfolder = gen_subfolder(root=data_source, dim=dim, rows=rows, file_num=i)
file = f"{data_source}/{subfolder}/{file_name}"
if not os.path.exists(file) or force:
if row_based:
gen_row_based_json_file(row_file=file, str_pk=str_pk,
float_vect=float_vector, multi_scalars=multi_scalars,
rows=rows, dim=dim, autoid=auto_id)
gen_row_based_json_file(row_file=file, str_pk=str_pk, float_vect=float_vector,
data_fields=data_fields, rows=rows, dim=dim,
start_uid=start_uid, err_type=err_type, **kwargs)
else:
gen_column_base_json_file(col_file=file, str_pk=str_pk,
float_vect=float_vector, multi_scalars=multi_scalars,
rows=rows, dim=dim, autoid=auto_id)
def gen_npy_files():
# # gen numpy files
# uid = 0
# for i in range(file_nums):
# gen_vectors_in_numpy_file(data_dir, FLOAT, rows=rows_list[0], dim=dim_list[0], num=i)
# gen_scalars_in_numpy_file(data_dir, "int", rows=rows_list[0], dim=dim_list[0], num=i, start=uid)
# uid += rows_list[0]
pass
gen_column_base_json_file(col_file=file, str_pk=str_pk, float_vect=float_vector,
data_fields=data_fields, rows=rows, dim=dim,
start_uid=start_uid, err_type=err_type, **kwargs)
start_uid += rows
if multi_folder:
files.append(f"{subfolder}/{file_name}")
else:
files.append(file_name)
return files
def copy_files_to_bucket(client, r_source, bucket_name, force=False):
# check 'xxx' bucket exist.
found = client.bucket_exists(bucket_name)
if not found:
print(f"Bucket {bucket_name} not found, create it.")
client.make_bucket(bucket_name)
# copy files from root source folder
os.chdir(r_source)
onlyfiles = [f for f in os.listdir(r_source) if
os.path.isfile(os.path.join(r_source, f))]
for file in onlyfiles:
if not file.startswith("."):
found = False
try:
result = client.stat_object(bucket_name, file)
found = True
except S3Error as exc:
pass
if force:
res = client.fput_object(bucket_name, file, f"{r_source}/{file}")
print(res.object_name)
elif not found:
res = client.fput_object(bucket_name, file, f"{r_source}/{file}")
print(res.object_name)
# copy subfolders
sub_folders = [f.name for f in os.scandir(r_source) if f.is_dir()]
for sub_folder in sub_folders:
if sub_folder not in ["backup", "tested"]:
source = f"{r_source}/{sub_folder}"
os.chdir(source)
onlyfiles = [f for f in os.listdir(source) if
os.path.isfile(os.path.join(source, f))]
for file in onlyfiles:
if not file.startswith("."):
found = False
try:
result = client.stat_object(bucket_name, f"{sub_folder}/{file}")
found = True
except S3Error as exc:
pass
if force:
res = client.fput_object(bucket_name, f"{sub_folder}/{file}", f"{source}/{file}")
print(res.object_name)
elif not found:
res = client.fput_object(bucket_name, f"{sub_folder}/{file}", f"{source}/{file}")
print(res.object_name)
def copy_files_to_minio(host, bucket_name, access_key="minioadmin", secret_key="minioadmin", secure=False):
client = Minio(
host,
access_key=access_key,
secret_key=secret_key,
secure=secure,
)
try:
# TODO: not copy all the files, just copy the new generated files
copy_files_to_bucket(client, r_source=data_source, bucket_name=bucket_name, force=False)
except S3Error as exc:
print("error occurred.", exc)
def parpar_bulk_load_data(json_file, row_based, rows, dim, auto_id, str_pk, float_vector, multi_scalars, file_nums, force=False):
if json_file:
gen_json_files(row_based=row_based, rows=rows, dim=dim,
auto_id=auto_id, str_pk=str_pk, float_vector=float_vector,
multi_scalars=multi_scalars, file_nums=file_nums, force=force)
copy_files_to_minio(host=minio, bucket_name=bucket_name)
def gen_npy_files(float_vector, rows, dim, data_fields, file_nums=1, force=False):
# gen numpy files
files = []
start_uid = 0
if file_nums == 1:
# gen the numpy file without subfolders if only one set of files
for data_field in data_fields:
if data_field == DataField.vec_field:
file_name = gen_vectors_in_numpy_file(dir=data_source, float_vector=float_vector,
rows=rows, dim=dim, force=force)
else:
file_name = gen_int_or_float_in_numpy_file(dir=data_source, data_field=data_field,
rows=rows, force=force)
files.append(file_name)
else:
# TODO: for npy files
# gen_npy_files()
# copy()
pass
for i in range(file_nums):
subfolder = gen_subfolder(root=data_source, dim=dim, rows=rows, file_num=i)
dir = f"{data_source}/{subfolder}"
for data_field in data_fields:
if data_field == DataField.vec_field:
file_name = gen_vectors_in_numpy_file(dir=dir, float_vector=float_vector, rows=rows, dim=dim, force=force)
else:
file_name = gen_int_or_float_in_numpy_file(dir=dir, data_field=data_field, rows=rows, start=start_uid, force=force)
files.append(f"{subfolder}/{file_name}")
start_uid += rows
return files
# if __name__ == '__main__':
# gen_json_files(row_based=True, rows=10,
# dim=4, auto_id=False, str_pk=False,
# float_vector=True, multi_scalars=False, file_nums=2)
#
# copy_files_to_minio(host=minio, bucket_name=bucket_name)
def prepare_bulk_load_json_files(row_based=True, rows=100, dim=128,
auto_id=True, str_pk=False, float_vector=True,
data_fields=[], file_nums=1, multi_folder=False,
file_type=".json", err_type="", force=False, **kwargs):
"""
Generate files based on the params in json format and copy them to minio
:param row_based: indicate the file(s) to be generated is row based or not
:type row_based: boolean
:param rows: the number entities to be generated in the file(s)
:type rows: int
:param dim: dim of vector data
:type dim: int
:param auto_id: generate primary key data or not
:type auto_id: boolean
:param str_pk: generate string or int as primary key
:type str_pk: boolean
:param: float_vector: generate float vectors or binary vectors
:type float_vector: boolean
:param: data_fields: data fields to be generated in the file(s):
It supports one or all of [pk, vectors, int, float, string, boolean]
Note: it automatically adds pk field if auto_id=False
:type data_fields: list
:param file_nums: file numbers to be generated
:type file_nums: int
:param multi_folder: generate the files in bucket root folder or new subfolders
:type multi_folder: boolean
:param file_type: specify the file suffix to be generate
:type file_type: str
:param err_type: inject some errors in the file(s).
All errors should be predefined in DataErrorType
:type err_type: str
:param force: re-generate the file(s) regardless existing or not
:type force: boolean
:param **kwargs
* *wrong_position* (``int``) --
indicate the error entity in the file if DataErrorType.one_entity_wrong_dim
:return list
file names list
"""
files = gen_json_files(row_based=row_based, rows=rows, dim=dim,
auto_id=auto_id, str_pk=str_pk, float_vector=float_vector,
data_fields=data_fields, file_nums=file_nums, multi_folder=multi_folder,
file_type=file_type, err_type=err_type, force=force, **kwargs)
copy_files_to_minio(host=minio, r_source=data_source, files=files, bucket_name=bucket_name, force=force)
return files
def prepare_bulk_load_numpy_files(rows, dim, data_fields=[DataField.vec_field],
float_vector=True, file_nums=1, force=False):
"""
Generate column based files based on params in numpy format and copy them to the minio
Note: each field in data_fields would be generated one numpy file.
:param rows: the number entities to be generated in the file(s)
:type rows: int
:param dim: dim of vector data
:type dim: int
:param: float_vector: generate float vectors or binary vectors
:type float_vector: boolean
:param: data_fields: data fields to be generated in the file(s):
it support one or all of [int_pk, vectors, int, float]
Note: it does not automatically adds pk field
:type data_fields: list
:param file_nums: file numbers to be generated
The file(s) would be geneated in data_source folder if file_nums = 1
The file(s) would be generated in different subfolers if file_nums > 1
:type file_nums: int
:param force: re-generate the file(s) regardless existing or not
:type force: boolean
Return: List
File name list or file name with subfolder list
"""
files = gen_npy_files(rows=rows, dim=dim, float_vector=float_vector,
data_fields=data_fields,
file_nums=file_nums, force=force)
copy_files_to_minio(host=minio, r_source=data_source, files=files, bucket_name=bucket_name, force=force)
return files

View File

@ -0,0 +1,43 @@
import os
from minio import Minio
from minio.error import S3Error
from utils.util_log import test_log as log
def copy_files_to_bucket(client, r_source, target_files, bucket_name, force=False):
# check the bucket exist
found = client.bucket_exists(bucket_name)
if not found:
log.error(f"Bucket {bucket_name} not found.")
return
# copy target files from root source folder
os.chdir(r_source)
for target_file in target_files:
found = False
try:
result = client.stat_object(bucket_name, target_file)
found = True
except S3Error as exc:
pass
if force or not found:
res = client.fput_object(bucket_name, target_file, f"{r_source}/{target_file}")
log.info(f"copied {res.object_name} to minio")
else:
log.info(f"skip copy {res.object_name} to minio")
def copy_files_to_minio(host, r_source, files, bucket_name, access_key="minioadmin", secret_key="minioadmin",
secure=False, force=False):
client = Minio(
host,
access_key=access_key,
secret_key=secret_key,
secure=secure,
)
try:
copy_files_to_bucket(client, r_source=r_source, target_files=files, bucket_name=bucket_name, force=force)
except S3Error as exc:
log.error("fail to copy files to minio", exc)

File diff suppressed because it is too large Load Diff