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Unverified Commit 82dd7ac5 authored by Xiaomeng Zhao's avatar Xiaomeng Zhao Committed by GitHub
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Merge pull request #782 from icecraft/feat/data_api 

Feat/data api
parents e36627be c200effc
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tests/test_data/data_reader_writer/test_filebase.py 0 → 100644
View file @ 82dd7ac5
import os
import shutil
from magic_pdf.data.data_reader_writer import (FileBasedDataReader,
FileBasedDataWriter)
def test_filebased_reader_writer():
unitest_dir = '/tmp/magic_pdf/unittest/data/filebased_reader_writer'
sub_dir = os.path.join(unitest_dir, 'sub')
abs_fn = os.path.join(unitest_dir, 'abspath.txt')
os.makedirs(sub_dir, exist_ok=True)
writer = FileBasedDataWriter(sub_dir)
reader = FileBasedDataReader(sub_dir)
writer.write('test.txt', b'hello world')
assert reader.read('test.txt') == b'hello world'
writer.write(abs_fn, b'hello world')
assert reader.read(abs_fn) == b'hello world'
shutil.rmtree(unitest_dir)
tests/test_data/data_reader_writer/test_multi_bucket_s3.py 0 → 100644
View file @ 82dd7ac5
import json
import os
import fitz
import pytest
from magic_pdf.data.data_reader_writer import (MultiBucketS3DataReader,
MultiBucketS3DataWriter)
from magic_pdf.data.schemas import S3Config
@pytest.mark.skipif(
os.getenv('S3_ACCESS_KEY_2', None) is None, reason='need s3 config!'
)
def test_multi_bucket_s3_reader_writer():
"""test multi bucket s3 reader writer must config s3 config in the
environment export S3_BUCKET=xxx export S3_ACCESS_KEY=xxx export
S3_SECRET_KEY=xxx export S3_ENDPOINT=xxx.
export S3_BUCKET_2=xxx export S3_ACCESS_KEY_2=xxx export S3_SECRET_KEY_2=xxx export S3_ENDPOINT_2=xxx
"""
bucket = os.getenv('S3_BUCKET', '')
ak = os.getenv('S3_ACCESS_KEY', '')
sk = os.getenv('S3_SECRET_KEY', '')
endpoint_url = os.getenv('S3_ENDPOINT', '')
bucket_2 = os.getenv('S3_BUCKET_2', '')
ak_2 = os.getenv('S3_ACCESS_KEY_2', '')
sk_2 = os.getenv('S3_SECRET_KEY_2', '')
endpoint_url_2 = os.getenv('S3_ENDPOINT_2', '')
s3configs = [
S3Config(
bucket_name=bucket, access_key=ak, secret_key=sk, endpoint_url=endpoint_url
),
S3Config(
bucket_name=bucket_2,
access_key=ak_2,
secret_key=sk_2,
endpoint_url=endpoint_url_2,
),
]
reader = MultiBucketS3DataReader(default_bucket=bucket, s3_configs=s3configs)
writer = MultiBucketS3DataWriter(default_bucket=bucket, s3_configs=s3configs)
bits = reader.read('meta-index/scihub/v001/scihub/part-66210c190659-000026.jsonl')
assert bits == reader.read(
f's3://{bucket}/meta-index/scihub/v001/scihub/part-66210c190659-000026.jsonl'
)
bits = reader.read(
f's3://{bucket_2}/enbook-scimag/78800000/libgen.scimag78872000-78872999/10.1017/cbo9780511770425.012.pdf'
)
docs = fitz.open('pdf', bits)
assert len(docs) == 10
bits = reader.read(
'meta-index/scihub/v001/scihub/part-66210c190659-000026.jsonl?bytes=566,713'
)
assert bits == reader.read_at(
'meta-index/scihub/v001/scihub/part-66210c190659-000026.jsonl', 566, 713
)
assert len(json.loads(bits)) > 0
writer.write_string(
'unittest/data/data_reader_writer/multi_bucket_s3_data/test01.txt', 'abc'
)
assert 'abc'.encode() == reader.read(
'unittest/data/data_reader_writer/multi_bucket_s3_data/test01.txt'
)
writer.write(
'unittest/data/data_reader_writer/multi_bucket_s3_data/test02.txt',
'123'.encode(),
)
assert '123'.encode() == reader.read(
'unittest/data/data_reader_writer/multi_bucket_s3_data/test02.txt'
)
tests/test_data/data_reader_writer/test_s3.py 0 → 100644
View file @ 82dd7ac5
import json
import os
import pytest
from magic_pdf.data.data_reader_writer import S3DataReader, S3DataWriter
@pytest.mark.skipif(
os.getenv('S3_ACCESS_KEY', None) is None, reason='need s3 config!'
)
def test_multi_bucket_s3_reader_writer():
"""test multi bucket s3 reader writer must config s3 config in the
environment export S3_BUCKET=xxx export S3_ACCESS_KEY=xxx export
S3_SECRET_KEY=xxx export S3_ENDPOINT=xxx."""
bucket = os.getenv('S3_BUCKET', '')
ak = os.getenv('S3_ACCESS_KEY', '')
sk = os.getenv('S3_SECRET_KEY', '')
endpoint_url = os.getenv('S3_ENDPOINT', '')
reader = S3DataReader(bucket=bucket, ak=ak, sk=sk, endpoint_url=endpoint_url)
writer = S3DataWriter(bucket=bucket, ak=ak, sk=sk, endpoint_url=endpoint_url)
bits = reader.read('meta-index/scihub/v001/scihub/part-66210c190659-000026.jsonl')
assert bits == reader.read(
f's3://{bucket}/meta-index/scihub/v001/scihub/part-66210c190659-000026.jsonl'
)
bits = reader.read(
'meta-index/scihub/v001/scihub/part-66210c190659-000026.jsonl?bytes=566,713'
)
assert bits == reader.read_at(
'meta-index/scihub/v001/scihub/part-66210c190659-000026.jsonl', 566, 713
)
assert len(json.loads(bits)) > 0
writer.write_string(
'unittest/data/data_reader_writer/multi_bucket_s3_data/test01.txt', 'abc'
)
assert 'abc'.encode() == reader.read(
'unittest/data/data_reader_writer/multi_bucket_s3_data/test01.txt'
)
writer.write(
f'{bucket}/unittest/data/data_reader_writer/multi_bucket_s3_data/test02.txt',
'123'.encode(),
)
assert '123'.encode() == reader.read(
'unittest/data/data_reader_writer/multi_bucket_s3_data/test02.txt'
)
tests/test_data/io/test_s3.py 0 → 100644
View file @ 82dd7ac5
import json
import os
import pytest
from magic_pdf.data.io.s3 import S3Reader, S3Writer
@pytest.mark.skipif(
os.getenv('S3_ACCESS_KEY', None) is None, reason='s3 config not found'
)
def test_s3_reader():
"""test s3 reader.
must config s3 config in the environment export S3_BUCKET=xxx export S3_ACCESS_KEY=xxx export S3_SECRET_KEY=xxx
export S3_ENDPOINT=xxx
"""
bucket = os.getenv('S3_BUCKET', '')
ak = os.getenv('S3_ACCESS_KEY', '')
sk = os.getenv('S3_SECRET_KEY', '')
endpoint_url = os.getenv('S3_ENDPOINT', '')
reader = S3Reader(bucket=bucket, ak=ak, sk=sk, endpoint_url=endpoint_url)
bits = reader.read(
'meta-index/scihub/v001/scihub/part-66210c190659-000026.jsonl'
)
assert len(bits) > 0
bits = reader.read_at(
'meta-index/scihub/v001/scihub/part-66210c190659-000026.jsonl',
566,
713,
)
assert len(json.loads(bits)) > 0
@pytest.mark.skipif(
os.getenv('S3_ACCESS_KEY', None) is None, reason='s3 config not found'
)
def test_s3_writer():
"""test s3 reader.
must config s3 config in the environment export S3_BUCKET=xxx export S3_ACCESS_KEY=xxx export S3_SECRET_KEY=xxx
export S3_ENDPOINT=xxx
"""
bucket = os.getenv('S3_BUCKET', '')
ak = os.getenv('S3_ACCESS_KEY', '')
sk = os.getenv('S3_SECRET_KEY', '')
endpoint_url = os.getenv('S3_ENDPOINT', '')
writer = S3Writer(bucket=bucket, ak=ak, sk=sk, endpoint_url=endpoint_url)
test_fn = 'unittest/io/test.jsonl'
writer.write(test_fn, '123'.encode())
reader = S3Reader(bucket=bucket, ak=ak, sk=sk, endpoint_url=endpoint_url)
bits = reader.read(test_fn)
assert bits.decode() == '123'
tests/test_data/test_dataset.py 0 → 100644
View file @ 82dd7ac5
from magic_pdf.data.dataset import ImageDataset, PymuDocDataset
def test_pymudataset():
with open('tests/test_data/assets/pdfs/test_01.pdf', 'rb') as f:
bits = f.read()
datasets = PymuDocDataset(bits)
assert len(datasets) > 0
assert datasets.get_page(0).get_page_info().h > 100
def test_imagedataset():
with open('tests/test_data/assets/pngs/test_01.png', 'rb') as f:
bits = f.read()
datasets = ImageDataset(bits)
assert len(datasets) == 1
assert datasets.get_page(0).get_page_info().w > 100
tests/test_data/test_read_api.py 0 → 100644
View file @ 82dd7ac5
import os
import pytest
from magic_pdf.data.data_reader_writer import MultiBucketS3DataReader
from magic_pdf.data.read_api import (read_jsonl, read_local_images,
read_local_pdfs)
from magic_pdf.data.schemas import S3Config
def test_read_local_pdfs():
datasets = read_local_pdfs('tests/test_data/assets/pdfs')
assert len(datasets) == 2
assert len(datasets[0]) > 0
assert len(datasets[1]) > 0
assert datasets[0].get_page(0).get_page_info().w > 0
assert datasets[0].get_page(0).get_page_info().h > 0
def test_read_local_images():
datasets = read_local_images('tests/test_data/assets/pngs', suffixes=['png'])
assert len(datasets) == 2
assert len(datasets[0]) == 1
assert len(datasets[1]) == 1
assert datasets[0].get_page(0).get_page_info().w > 0
assert datasets[0].get_page(0).get_page_info().h > 0
@pytest.mark.skipif(
os.getenv('S3_ACCESS_KEY_2', None) is None, reason='need s3 config!'
)
def test_read_json():
"""test multi bucket s3 reader writer must config s3 config in the
environment export S3_BUCKET=xxx export S3_ACCESS_KEY=xxx export
S3_SECRET_KEY=xxx export S3_ENDPOINT=xxx.
export S3_BUCKET_2=xxx export S3_ACCESS_KEY_2=xxx export S3_SECRET_KEY_2=xxx export S3_ENDPOINT_2=xxx
"""
bucket = os.getenv('S3_BUCKET', '')
ak = os.getenv('S3_ACCESS_KEY', '')
sk = os.getenv('S3_SECRET_KEY', '')
endpoint_url = os.getenv('S3_ENDPOINT', '')
bucket_2 = os.getenv('S3_BUCKET_2', '')
ak_2 = os.getenv('S3_ACCESS_KEY_2', '')
sk_2 = os.getenv('S3_SECRET_KEY_2', '')
endpoint_url_2 = os.getenv('S3_ENDPOINT_2', '')
s3configs = [
S3Config(
bucket_name=bucket, access_key=ak, secret_key=sk, endpoint_url=endpoint_url
),
S3Config(
bucket_name=bucket_2,
access_key=ak_2,
secret_key=sk_2,
endpoint_url=endpoint_url_2,
),
]
reader = MultiBucketS3DataReader(bucket, s3configs)
datasets = read_jsonl(
f's3://{bucket}/meta-index/scihub/v001/scihub/part-66210c190659-000026.jsonl',
reader,
)
assert len(datasets) > 0
assert len(datasets[0]) == 10
datasets = read_jsonl('tests/test_data/assets/jsonl/test_01.jsonl', reader)
assert len(datasets) == 1
assert len(datasets[0]) == 10
datasets = read_jsonl('tests/test_data/assets/jsonl/test_02.jsonl')
assert len(datasets) == 1
assert len(datasets[0]) == 1
tests/test_model/assets/test_01.model.json 0 → 100644
View file @ 82dd7ac5
[
{
"layout_dets": [
{
"category_id": 3,
"poly": [
776.7277221679688,
688.448974609375,
1242.224365234375,
688.448974609375,
1242.224365234375,
1182.0628662109375,
776.7277221679688,
1182.0628662109375
],
"score": 0.999997079372406
},
{
"category_id": 3,
"poly": [
775.9269409179688,
1389.754638671875,
1243.672119140625,
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1859.716064453125,
775.9269409179688,
1859.716064453125
],
"score": 0.9999949932098389
},
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"poly": [
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1939.3634033203125,
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752.11572265625,
2041.1771240234375
],
"score": 0.999975323677063
},
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1803.419189453125
],
"score": 0.999961256980896
},
{
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"poly": [
33.684722900390625,
150.77980041503906,
1238.0679931640625,
150.77980041503906,
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33.684722900390625,
524.98291015625
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"score": 0.9999504089355469
},
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24.685693740844727,
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"score": 0.8580453395843506
},
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189.0360870361328,
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],
"score": 0.3083903193473816
},
{
"category_id": 13,
"poly": [
1190,
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1206,
1980,
1206,
1997,
1190,
1997
],
"score": 0.51,
"latex": ":"
},
{
"category_id": 13,
"poly": [
1219,
1331,
1235,
1331,
1235,
1348,
1219,
1348
],
"score": 0.49,
"latex": ":"
},
{
"category_id": 13,
"poly": [
798,
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813,
2016,
813,
2033,
798,
2033
],
"score": 0.41,
"latex": ":"
},
{
"category_id": 13,
"poly": [
135,
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148,
1991,
148,
2006,
135,
2006
],
"score": 0.39,
"latex": ":"
},
{
"category_id": 13,
"poly": [
400,
1916,
416,
1916,
416,
1933,
400,
1933
],
"score": 0.38,
"latex": ":"
},
{
"category_id": 13,
"poly": [
1148,
1944,
1162,
1944,
1162,
1961,
1148,
1961
],
"score": 0.31,
"latex": ":"
},
{
"category_id": 15,
"poly": [
798.0,
1943.0,
1147.0,
1943.0,
1147.0,
1968.0,
798.0,
1968.0
],
"score": 0.95,
"text": "Fig 4 SSCP analysis of FHIT exon 4. T"
},
{
"category_id": 15,
"poly": [
1163.0,
1943.0,
1425.0,
1943.0,
1425.0,
1968.0,
1163.0,
1968.0
],
"score": 0.96,
"text": "Tumor tissue ; N :Corresponding"
},
{
"category_id": 15,
"poly": [
755.0,
1979.0,
1189.0,
1979.0,
1189.0,
2004.0,
755.0,
2004.0
],
"score": 0.92,
"text": "normal tissue ; M : PBR322/Hae II Marker ; ssDNA"
},
{
"category_id": 15,
"poly": [
1207.0,
1979.0,
1422.0,
1979.0,
1422.0,
2004.0,
1207.0,
2004.0
],
"score": 0.97,
"text": "Single-stranded DNA ; ds-"
},
{
"category_id": 15,
"poly": [
755.0,
2015.0,
797.0,
2015.0,
797.0,
2038.0,
755.0,
2038.0
],
"score": 1.0,
"text": "DNA"
},
{
"category_id": 15,
"poly": [
814.0,
2015.0,
996.0,
2015.0,
996.0,
2038.0,
814.0,
2038.0
],
"score": 0.98,
"text": "Double-stranded DNA"
},
{
"category_id": 15,
"poly": [
71.0,
1880.0,
698.0,
1880.0,
698.0,
1902.0,
71.0,
1902.0
],
"score": 0.96,
"text": "Fig 2Alterations of PCR amplified products of FHIT exon 3,4,5 and"
},
{
"category_id": 15,
"poly": [
28.0,
1916.0,
399.0,
1916.0,
399.0,
1937.0,
28.0,
1937.0
],
"score": 0.98,
"text": "microsatellite marker D3S1300、D3S1312.A"
},
{
"category_id": 15,
"poly": [
417.0,
1916.0,
701.0,
1916.0,
701.0,
1937.0,
417.0,
1937.0
],
"score": 0.9,
"text": "Deletion of exon5(arrows）;B :"
},
{
"category_id": 15,
"poly": [
29.0,
1953.0,
700.0,
1953.0,
700.0,
1974.0,
29.0,
1974.0
],
"score": 0.95,
"text": "Deletion of exon 3 A( arrows）;C : Deletion of microsatellite marker D3S1300,"
},
{
"category_id": 15,
"poly": [
28.0,
1989.0,
134.0,
1989.0,
134.0,
2014.0,
28.0,
2014.0
],
"score": 1.0,
"text": "D3S1312.T"
},
{
"category_id": 15,
"poly": [
149.0,
1989.0,
696.0,
1989.0,
696.0,
2014.0,
149.0,
2014.0
],
"score": 0.96,
"text": "Tumor ; N : Corresponding normal tissue ; L : Corresponding lymph"
},
{
"category_id": 15,
"poly": [
30.0,
2027.0,
634.0,
2027.0,
634.0,
2047.0,
30.0,
2047.0
],
"score": 0.94,
"text": "node tissue;M :DL2000 DNA marker;L1:Lewis ;A :A549;S SPAC-1"
},
{
"category_id": 15,
"poly": [
801.0,
1259.0,
1427.0,
1259.0,
1427.0,
1280.0,
801.0,
1280.0
],
"score": 0.94,
"text": "Fig 3SSCP analysis of FHIT exon 3.The arrow indicateda deletion of"
},
{
"category_id": 15,
"poly": [
757.0,
1294.0,
1424.0,
1294.0,
1424.0,
1318.0,
757.0,
1318.0
],
"score": 0.96,
"text": "exon 3 of 41T. T : Tumor tissue ; N : Corresponding normal tissue ; M PBR322/"
},
{
"category_id": 15,
"poly": [
755.0,
1329.0,
1218.0,
1329.0,
1218.0,
1355.0,
755.0,
1355.0
],
"score": 0.95,
"text": "Hae Il Marker / ssDNA : Single-stranded DNA ; dsDNA"
},
{
"category_id": 15,
"poly": [
1236.0,
1329.0,
1418.0,
1329.0,
1418.0,
1355.0,
1236.0,
1355.0
],
"score": 1.0,
"text": "Double-strandedDNA"
},
{
"category_id": 15,
"poly": [
910.0,
1217.0,
1269.0,
1217.0,
1269.0,
1241.0,
910.0,
1241.0
],
"score": 1.0,
"text": "图3FHIT基因外显子3的SSCP分析"
},
{
"category_id": 15,
"poly": [
909.0,
1904.0,
1269.0,
1904.0,
1269.0,
1927.0,
909.0,
1927.0
],
"score": 1.0,
"text": "图4FHIT基因外显子4的SSCP分析"
},
{
"category_id": 15,
"poly": [
374.0,
563.0,
1077.0,
563.0,
1077.0,
583.0,
374.0,
583.0
],
"score": 0.99,
"text": "图1FHIT基因外显子3、4、5、8和微卫星灶的PCR扩增产物琼脂糖电泳图"
},
{
"category_id": 15,
"poly": [
1351.0,
81.0,
1376.0,
81.0,
1376.0,
102.0,
1351.0,
102.0
],
"score": 1.0,
"text": "13"
},
{
"category_id": 15,
"poly": [
207.0,
600.0,
1245.0,
600.0,
1245.0,
624.0,
207.0,
624.0
],
"score": 0.96,
"text": "Fig 1 Agarose electrophoresis of PCR products of exor( A)3 ,4 ,5 ,8 and three microsatellite markers( B）of FHIT gene"
},
{
"category_id": 15,
"poly": [
309.0,
634.0,
1142.0,
634.0,
1142.0,
662.0,
309.0,
662.0
],
"score": 0.97,
"text": "M1 :DL2000 DNA marker ; M2 PBR322/Hae Il marker ; T :Tumor ; N :Corresponding normal tissue"
},
{
"category_id": 15,
"poly": [
73.0,
1840.0,
651.0,
1840.0,
651.0,
1864.0,
73.0,
1864.0
],
"score": 1.0,
"text": "图2FHIT基因外显子和微卫星灶PCR扩增产物缺失电泳图"
},
{
"category_id": 15,
"poly": [
207.0,
600.0,
1245.0,
600.0,
1245.0,
625.0,
207.0,
625.0
],
"score": 0.96,
"text": "Fig 1 Agarose electrophoresis of PCR products of exor A)3 ,4 ,5 ,8 and three microsatellite markers( B)of FHIT gene"
},
{
"category_id": 15,
"poly": [
309.0,
635.0,
1142.0,
635.0,
1142.0,
661.0,
309.0,
661.0
],
"score": 0.97,
"text": "M1 :DL2000 DNA marker ; M2 PBR322/Hae Il marker ; T Tumor ; N :Corresponding normal tissue"
}
],
"page_info": {
"page_no": 0,
"height": 2080,
"width": 1472
}
}
]
tests/test_model/assets/test_02.model.json 0 → 100644
View file @ 82dd7ac5
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tests/test_model/test_magic_model.py 0 → 100644
View file @ 82dd7ac5
import json
from magic_pdf.data.read_api import read_local_pdfs
from magic_pdf.model.magic_model import MagicModel
def test_magic_model_image_v2():
datasets = read_local_pdfs('tests/test_model/assets/test_01.pdf')
with open('tests/test_model/assets/test_01.model.json') as f:
model_json = json.load(f)
magic_model = MagicModel(model_json, datasets[0])
imgs = magic_model.get_imgs_v2(0)
print(imgs)
tables = magic_model.get_tables_v2(0)
print(tables)
def test_magic_model_table_v2():
datasets = read_local_pdfs('tests/test_model/assets/test_02.pdf')
with open('tests/test_model/assets/test_02.model.json') as f:
model_json = json.load(f)
magic_model = MagicModel(model_json, datasets[0])
tables = magic_model.get_tables_v2(5)
print(tables)
tables = magic_model.get_tables_v2(8)
print(tables)
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