Unverified Commit 6d571e2e authored by Kaiwen Liu's avatar Kaiwen Liu Committed by GitHub
Browse files

Merge pull request #7 from opendatalab/dev

Dev
parents a3358878 37c335ae
...@@ -8,7 +8,6 @@ pdfminer.six==20231228 ...@@ -8,7 +8,6 @@ pdfminer.six==20231228
pydantic>=2.7.2,<2.8.0 pydantic>=2.7.2,<2.8.0
PyMuPDF>=1.24.9 PyMuPDF>=1.24.9
scikit-learn>=1.0.2 scikit-learn>=1.0.2
wordninja>=2.0.0
torch>=2.2.2,<=2.3.1 torch>=2.2.2,<=2.3.1
transformers transformers
# The requirements.txt must ensure that only necessary external dependencies are introduced. If there are new dependencies to add, please contact the project administrator. # The requirements.txt must ensure that only necessary external dependencies are introduced. If there are new dependencies to add, please contact the project administrator.
...@@ -45,6 +45,7 @@ if __name__ == '__main__': ...@@ -45,6 +45,7 @@ if __name__ == '__main__':
"paddlepaddle==2.6.1;platform_system=='Windows' or platform_system=='Darwin'", # windows版本3.0.0b1效率下降,需锁定2.6.1 "paddlepaddle==2.6.1;platform_system=='Windows' or platform_system=='Darwin'", # windows版本3.0.0b1效率下降,需锁定2.6.1
"pypandoc", # 表格解析latex转html "pypandoc", # 表格解析latex转html
"struct-eqtable==0.1.0", # 表格解析 "struct-eqtable==0.1.0", # 表格解析
"doclayout_yolo==0.0.2", # doclayout_yolo
"detectron2" "detectron2"
], ],
}, },
......
{"track_id":"e8824f5a-9fcb-4ee5-b2d4-6bf2c67019dc","path":"s3://sci-hub/enbook-scimag/78800000/libgen.scimag78872000-78872999/10.1017/cbo9780511770425.012.pdf","file_type":"pdf","content_type":"application/pdf","content_length":80078,"title":"German Idealism and the Concept of Punishment || Conclusion","remark":{"file_id":"scihub_78800000/libgen.scimag78872000-78872999.zip_10.1017/cbo9780511770425.012","file_source_type":"paper","original_file_id":"10.1017/cbo9780511770425.012","file_name":"10.1017/cbo9780511770425.012.pdf","author":"Merle, Jean-Christophe"}}
{"track_id":"e8824f5a-9fcb-4ee5-b2d4-6bf2c67019dc","path":"tests/test_data/assets/pdfs/test_02.pdf","file_type":"pdf","content_type":"application/pdf","content_length":80078,"title":"German Idealism and the Concept of Punishment || Conclusion","remark":{"file_id":"scihub_78800000/libgen.scimag78872000-78872999.zip_10.1017/cbo9780511770425.012","file_source_type":"paper","original_file_id":"10.1017/cbo9780511770425.012","file_name":"10.1017/cbo9780511770425.012.pdf","author":"Merle, Jean-Christophe"}}
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)
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'
)
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'
)
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'
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
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
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1147.0,
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"text": "Fig 4 SSCP analysis of FHIT exon 4. T"
},
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"text": "Fig 2Alterations of PCR amplified products of FHIT exon 3,4,5 and"
},
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"text": "microsatellite marker D3S1300、D3S1312.A"
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"text": "Deletion of exon5(arrows);B :"
},
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"text": "Deletion of exon 3 A( arrows);C : Deletion of microsatellite marker D3S1300,"
},
{
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"poly": [
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"text": "D3S1312.T"
},
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"score": 0.96,
"text": "Tumor ; N : Corresponding normal tissue ; L : Corresponding lymph"
},
{
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"poly": [
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],
"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
}
}
]
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