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rapidsai / cudf

cuDF - GPU DataFrame Library
https://docs.rapids.ai/api/cudf/stable/
Apache License 2.0
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[BUG] csv reader - empty fields treated as null even with `na_filter=False` #6682

Closed galipremsagar closed 3 years ago

galipremsagar commented 4 years ago

Describe the bug We have a parameter called na_filter which will decide whether there should be any nulls in the dataframe or not while reading a csv file content. This parameter seems to be non-functioning.

Steps/Code to reproduce bug

In[193]: import cudf
In[194]: import pandas as pd
In[195]: import io
In[196]: df = pd.DataFrame({'a':['fdsdf',None,'sdffds','','asdf']})
In[197]: df
Out[197]: 
        a
0   fdsdf
1    None
2  sdffds
3        
4    asdf
In[198]: df['a'].isnull()
Out[198]: 
0    False
1     True
2    False
3    False
4    False
Name: a, dtype: bool
In[199]: csv_buf = df.to_csv()
In[200]: pdf = pd.read_csv(io.StringIO(csv_buf), na_filter=False)
In[201]: gdf = cudf.read_csv(io.StringIO(csv_buf), na_filter=False)
In[202]: pdf
Out[202]: 
   Unnamed: 0       a
0           0   fdsdf
1           1        
2           2  sdffds
3           3        
4           4    asdf
In[203]: pdf['a'][1]
Out[203]: ''
In[204]: pdf['a'].isnull()
Out[204]: 
0    False
1    False
2    False
3    False
4    False
Name: a, dtype: bool
In[205]: gdf
Out[205]: 
   Unnamed: 0       a
0           0   fdsdf
1           1    <NA>
2           2  sdffds
3           3    <NA>
4           4    asdf
In[206]: gdf['a'][1]
In[207]: gdf['a'].isnull()
Out[207]: 
0    False
1     True
2    False
3     True
4    False
Name: a, dtype: bool

Expected behavior When na_filter is False we shouldn't actually be having any nulls in the dataframe and rest of the empty values would be read as empty strings pandas does.

Environment overview (please complete the following information)

Environment details Please run and paste the output of the cudf/print_env.sh script here, to gather any other relevant environment details

Click here to see environment details

     **git***
     commit 5cf7106c1a86d49ae345eff31868343a894c864a (HEAD -> branch-0.17, upstream/branch-0.17)
     Author: David <45795991+davidwendt@users.noreply.github.com>
     Date:   Wed Nov 4 09:33:31 2020 -0500

     Add cudf::test::dictionary_column_wrapper class (#6635)
     **git submodules***

     ***OS Information***
     DISTRIB_ID=Ubuntu
     DISTRIB_RELEASE=20.04
     DISTRIB_CODENAME=focal
     DISTRIB_DESCRIPTION="Ubuntu 20.04.1 LTS"
     NAME="Ubuntu"
     VERSION="20.04.1 LTS (Focal Fossa)"
     ID=ubuntu
     ID_LIKE=debian
     PRETTY_NAME="Ubuntu 20.04.1 LTS"
     VERSION_ID="20.04"
     HOME_URL="https://www.ubuntu.com/"
     SUPPORT_URL="https://help.ubuntu.com/"
     BUG_REPORT_URL="https://bugs.launchpad.net/ubuntu/"
     PRIVACY_POLICY_URL="https://www.ubuntu.com/legal/terms-and-policies/privacy-policy"
     VERSION_CODENAME=focal
     UBUNTU_CODENAME=focal
     Linux pgali-HP-Z8-G4-Workstation 5.4.0-52-generic #57-Ubuntu SMP Thu Oct 15 10:57:00 UTC 2020 x86_64 x86_64 x86_64 GNU/Linux

     ***GPU Information***
     Wed Nov  4 12:21:45 2020
     +-----------------------------------------------------------------------------+
     | NVIDIA-SMI 450.80.02    Driver Version: 450.80.02    CUDA Version: 11.0     |
     |-------------------------------+----------------------+----------------------+
     | GPU  Name        Persistence-M| Bus-Id        Disp.A | Volatile Uncorr. ECC |
     | Fan  Temp  Perf  Pwr:Usage/Cap|         Memory-Usage | GPU-Util  Compute M. |
     |                               |                      |               MIG M. |
     |===============================+======================+======================|
     |   0  Quadro RTX 8000     Off  | 00000000:22:00.0 Off |                  Off |
     | 33%   29C    P8     5W / 260W |   1072MiB / 48601MiB |      0%      Default |
     |                               |                      |                  N/A |
     +-------------------------------+----------------------+----------------------+
     |   1  Quadro RTX 8000     Off  | 00000000:2D:00.0  On |                  Off |
     | 33%   32C    P8    21W / 260W |    446MiB / 48592MiB |     10%      Default |
     |                               |                      |                  N/A |
     +-------------------------------+----------------------+----------------------+

     +-----------------------------------------------------------------------------+
     | Processes:                                                                  |
     |  GPU   GI   CI        PID   Type   Process name                  GPU Memory |
     |        ID   ID                                                   Usage      |
     |=============================================================================|
     |    0   N/A  N/A       969      G   /usr/lib/xorg/Xorg                  4MiB |
     |    0   N/A  N/A      1827      G   /usr/lib/xorg/Xorg                  4MiB |
     |    0   N/A  N/A      6875      C   python                            529MiB |
     |    0   N/A  N/A      7480      C   .../envs/cudf_dev/bin/python      529MiB |
     |    1   N/A  N/A       969      G   /usr/lib/xorg/Xorg                 39MiB |
     |    1   N/A  N/A      1827      G   /usr/lib/xorg/Xorg                187MiB |
     |    1   N/A  N/A      1952      G   /usr/bin/gnome-shell              203MiB |
     |    1   N/A  N/A      7325      G   /usr/lib/firefox/firefox            3MiB |
     +-----------------------------------------------------------------------------+

     ***CPU***
     Architecture:                    x86_64
     CPU op-mode(s):                  32-bit, 64-bit
     Byte Order:                      Little Endian
     Address sizes:                   46 bits physical, 48 bits virtual
     CPU(s):                          12
     On-line CPU(s) list:             0-11
     Thread(s) per core:              2
     Core(s) per socket:              6
     Socket(s):                       1
     NUMA node(s):                    1
     Vendor ID:                       GenuineIntel
     CPU family:                      6
     Model:                           85
     Model name:                      Intel(R) Xeon(R) Gold 6128 CPU @ 3.40GHz
     Stepping:                        4
     CPU MHz:                         1201.341
     CPU max MHz:                     3700.0000
     CPU min MHz:                     1200.0000
     BogoMIPS:                        6800.00
     Virtualization:                  VT-x
     L1d cache:                       192 KiB
     L1i cache:                       192 KiB
     L2 cache:                        6 MiB
     L3 cache:                        19.3 MiB
     NUMA node0 CPU(s):               0-11
     Vulnerability Itlb multihit:     KVM: Vulnerable
     Vulnerability L1tf:              Mitigation; PTE Inversion
     Vulnerability Mds:               Mitigation; Clear CPU buffers; SMT vulnerable
     Vulnerability Meltdown:          Mitigation; PTI
     Vulnerability Spec store bypass: Mitigation; Speculative Store Bypass disabled via prctl and seccomp
     Vulnerability Spectre v1:        Mitigation; usercopy/swapgs barriers and __user pointer sanitization
     Vulnerability Spectre v2:        Mitigation; Full generic retpoline, IBPB conditional, IBRS_FW, STIBP conditional, RSB filling
     Vulnerability Srbds:             Not affected
     Vulnerability Tsx async abort:   Mitigation; Clear CPU buffers; SMT vulnerable
     Flags:                           fpu vme de pse tsc msr pae mce cx8 apic sep mtrr pge mca cmov pat pse36 clflush dts acpi mmx fxsr sse sse2 ss ht tm pbe syscall nx pdpe1gb rdtscp lm constant_tsc art arch_perfmon pebs bts rep_good nopl xtopology nonstop_tsc cpuid aperfmperf pni pclmulqdq dtes64 monitor ds_cpl vmx smx est tm2 ssse3 sdbg fma cx16 xtpr pdcm pcid dca sse4_1 sse4_2 x2apic movbe popcnt tsc_deadline_timer aes xsave avx f16c rdrand lahf_lm abm 3dnowprefetch cpuid_fault epb cat_l3 cdp_l3 invpcid_single pti intel_ppin ssbd mba ibrs ibpb stibp tpr_shadow vnmi flexpriority ept vpid ept_ad fsgsbase tsc_adjust bmi1 hle avx2 smep bmi2 erms invpcid rtm cqm mpx rdt_a avx512f avx512dq rdseed adx smap clflushopt clwb intel_pt avx512cd avx512bw avx512vl xsaveopt xsavec xgetbv1 xsaves cqm_llc cqm_occup_llc cqm_mbm_total cqm_mbm_local dtherm ida arat pln pts hwp hwp_act_window hwp_epp hwp_pkg_req pku ospke md_clear flush_l1d

     ***CMake***
     /home/pgali/anaconda3/envs/cudf_dev/bin/cmake
     cmake version 3.18.2

     CMake suite maintained and supported by Kitware (kitware.com/cmake).

     ***g++***
     /usr/bin/g++
     g++ (Ubuntu 9.3.0-17ubuntu1~20.04) 9.3.0
     Copyright (C) 2019 Free Software Foundation, Inc.
     This is free software; see the source for copying conditions.  There is NO
     warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.

     ***nvcc***
     /usr/local/cuda/bin/nvcc
     nvcc: NVIDIA (R) Cuda compiler driver
     Copyright (c) 2005-2020 NVIDIA Corporation
     Built on Wed_Jul_22_19:09:09_PDT_2020
     Cuda compilation tools, release 11.0, V11.0.221
     Build cuda_11.0_bu.TC445_37.28845127_0

     ***Python***
     /home/pgali/anaconda3/envs/cudf_dev/bin/python
     Python 3.7.8

     ***Environment Variables***
     PATH                            : /home/pgali/anaconda3/envs/cudf_dev/bin:/home/pgali/anaconda3/condabin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games:/snap/bin:/usr/local/cuda/bin
     LD_LIBRARY_PATH                 : :/usr/local/cuda/lib64:/usr/local/cuda/extras/CUPTI/lib64
     NUMBAPRO_NVVM                   :
     NUMBAPRO_LIBDEVICE              :
     CONDA_PREFIX                    : /home/pgali/anaconda3/envs/cudf_dev
     PYTHON_PATH                     :

     ***conda packages***
     /home/pgali/anaconda3/condabin/conda
     # packages in environment at /home/pgali/anaconda3/envs/cudf_dev:
     #
     # Name                    Version                   Build  Channel
     _libgcc_mutex             0.1                 conda_forge    conda-forge
     _openmp_mutex             4.5                       1_gnu    conda-forge
     abseil-cpp                20200225.2           he1b5a44_2    conda-forge
     alabaster                 0.7.12                     py_0    conda-forge
     apipkg                    1.5                      pypi_0    pypi
     appdirs                   1.4.3                      py_1    conda-forge
     argon2-cffi               20.1.0           py37h8f50634_2    conda-forge
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     arrow-cpp-proc            1.0.1                      cuda    conda-forge
     async_generator           1.10                       py_0    conda-forge
     attrs                     20.2.0             pyh9f0ad1d_0    conda-forge
     aws-c-common              0.4.59               he1b5a44_0    conda-forge
     aws-c-event-stream        0.1.6                h84e28f3_5    conda-forge
     aws-checksums             0.1.9                he252421_2    conda-forge
     aws-sdk-cpp               1.8.63               h9b98462_0    conda-forge
     babel                     2.8.0                      py_0    conda-forge
     backcall                  0.2.0              pyh9f0ad1d_0    conda-forge
     backports                 1.0                        py_2    conda-forge
     backports.functools_lru_cache 1.6.1                      py_0    conda-forge
     black                     19.10b0                    py_4    conda-forge
     bleach                    3.2.1              pyh9f0ad1d_0    conda-forge
     bokeh                     2.2.2            py37hc8dfbb8_0    conda-forge
     boost-cpp                 1.74.0               h9359b55_0    conda-forge
     brotli                    1.0.9                he1b5a44_2    conda-forge
     brotlipy                  0.7.0           py37hb5d75c8_1001    conda-forge
     bzip2                     1.0.8                h516909a_3    conda-forge
     c-ares                    1.16.1               h516909a_3    conda-forge
     ca-certificates           2020.6.20            hecda079_0    conda-forge
     certifi                   2020.6.20        py37he5f6b98_2    conda-forge
     cffi                      1.14.3           py37h00ebd2e_1    conda-forge
     cfgv                      3.2.0                      py_0    conda-forge
     chardet                   3.0.4           py37he5f6b98_1008    conda-forge
     clang                     8.0.1                hc9558a2_2    conda-forge
     clang-tools               8.0.1                hc9558a2_2    conda-forge
     clangxx                   8.0.1                         2    conda-forge
     click                     7.1.2              pyh9f0ad1d_0    conda-forge
     cloudpickle               1.6.0                      py_0    conda-forge
     cmake                     3.18.2               h3f3948e_0    conda-forge
     cmake_setuptools          0.1.3                      py_0    rapidsai
     commonmark                0.9.1                      py_0    conda-forge
     cryptography              3.1.1            py37hff6837a_1    conda-forge
     cudatoolkit               11.0.221             h6bb024c_0    nvidia
     cudf                      0.17.0a0+170.g308af3c71f.dirty          pypi_0    pypi
     cudnn                     8.0.0                cuda11.0_0    nvidia
     cupy                      7.8.0            py37h0ce7dbb_0    rapidsai
     cython                    0.29.21          py37hb892b2f_1    conda-forge
     cytoolz                   0.11.0           py37h8f50634_1    conda-forge
     dask                      2.30.0+16.gfbe51746          pypi_0    pypi
     dask-cudf                 0.17.0a0+111.gb2ee7809a8.dirty          pypi_0    pypi
     decorator                 4.4.2                      py_0    conda-forge
     defusedxml                0.6.0                      py_0    conda-forge
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     distributed               2.30.0+7.gdcb46d07          pypi_0    pypi
     dlpack                    0.3                  he1b5a44_1    conda-forge
     docutils                  0.16             py37he5f6b98_2    conda-forge
     double-conversion         3.1.5                he1b5a44_2    conda-forge
     editdistance              0.5.3            py37h3340039_2    conda-forge
     entrypoints               0.3             py37hc8dfbb8_1002    conda-forge
     execnet                   1.7.1                    pypi_0    pypi
     expat                     2.2.9                he1b5a44_2    conda-forge
     fastavro                  1.0.0.post1      py37h8f50634_1    conda-forge
     fastrlock                 0.5              py37h3340039_1    conda-forge
     filelock                  3.0.12             pyh9f0ad1d_0    conda-forge
     flake8                    3.8.3                      py_1    conda-forge
     flatbuffers               1.12.0               he1b5a44_0    conda-forge
     freetype                  2.10.3               he06d7ca_0    conda-forge
     fsspec                    0.8.4                      py_0    conda-forge
     future                    0.18.2           py37hc8dfbb8_2    conda-forge
     gflags                    2.2.2             he1b5a44_1004    conda-forge
     glog                      0.4.0                h49b9bf7_3    conda-forge
     gmp                       6.2.0                he1b5a44_3    conda-forge
     grpc-cpp                  1.32.0               h7997a97_1    conda-forge
     heapdict                  1.0.1                      py_0    conda-forge
     hypothesis                5.37.3                     py_0    conda-forge
     icu                       67.1                 he1b5a44_0    conda-forge
     identify                  1.5.6              pyh9f0ad1d_0    conda-forge
     idna                      2.10               pyh9f0ad1d_0    conda-forge
     imagesize                 1.2.0                      py_0    conda-forge
     importlib-metadata        2.0.0                      py_1    conda-forge
     importlib_metadata        2.0.0                         1    conda-forge
     iniconfig                 1.1.0              pyh9f0ad1d_0    conda-forge
     ipykernel                 5.3.4            py37hc6149b9_1    conda-forge
     ipython                   7.18.1           py37hc6149b9_1    conda-forge
     ipython_genutils          0.2.0                      py_1    conda-forge
     isort                     5.0.7            py37hc8dfbb8_0    conda-forge
     jedi                      0.17.2           py37hc8dfbb8_1    conda-forge
     jinja2                    2.11.2             pyh9f0ad1d_0    conda-forge
     jpeg                      9d                   h516909a_0    conda-forge
     jsonschema                3.2.0                      py_2    conda-forge
     jupyter_client            6.1.7                      py_0    conda-forge
     jupyter_core              4.6.3            py37hc8dfbb8_2    conda-forge
     jupyterlab_pygments       0.1.2              pyh9f0ad1d_0    conda-forge
     krb5                      1.17.1               hfafb76e_3    conda-forge
     lcms2                     2.11                 hbd6801e_0    conda-forge
     ld_impl_linux-64          2.35                 h769bd43_9    conda-forge
     libblas                   3.8.0               17_openblas    conda-forge
     libcblas                  3.8.0               17_openblas    conda-forge
     libcurl                   7.71.1               hcdd3856_8    conda-forge
     libedit                   3.1.20191231         he28a2e2_2    conda-forge
     libev                     4.33                 h516909a_1    conda-forge
     libevent                  2.1.10               hcdb4288_3    conda-forge
     libffi                    3.2.1             he1b5a44_1007    conda-forge
     libgcc-ng                 9.3.0               h5dbcf3e_17    conda-forge
     libgfortran-ng            9.3.0               he4bcb1c_17    conda-forge
     libgfortran5              9.3.0               he4bcb1c_17    conda-forge
     libgomp                   9.3.0               h5dbcf3e_17    conda-forge
     liblapack                 3.8.0               17_openblas    conda-forge
     libllvm10                 10.0.1               he513fc3_3    conda-forge
     libllvm8                  8.0.1                hc9558a2_0    conda-forge
     libnghttp2                1.41.0               h8cfc5f6_2    conda-forge
     libopenblas               0.3.10          pthreads_h4812303_5    conda-forge
     libpng                    1.6.37               hed695b0_2    conda-forge
     libprotobuf               3.13.0.1             h8b12597_0    conda-forge
     librmm                    0.17.0a201018   cuda11.0_g8cdd176_21    rapidsai-nightly
     libsodium                 1.0.18               h516909a_1    conda-forge
     libssh2                   1.9.0                hab1572f_5    conda-forge
     libstdcxx-ng              9.3.0               h2ae2ef3_17    conda-forge
     libthrift                 0.13.0               h5aa387f_6    conda-forge
     libtiff                   4.1.0                hc7e4089_6    conda-forge
     libutf8proc               2.5.0                h516909a_2    conda-forge
     libuv                     1.40.0               hd18ef5c_0    conda-forge
     libwebp-base              1.1.0                h516909a_3    conda-forge
     llvmlite                  0.34.0           py37h5202443_2    conda-forge
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     lz4-c                     1.9.2                he1b5a44_3    conda-forge
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     packaging                 20.4               pyh9f0ad1d_0    conda-forge
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     py                        1.9.0              pyh9f0ad1d_0    conda-forge
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     python                    3.7.8           h6f2ec95_1_cpython    conda-forge
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     python_abi                3.7                     1_cp37m    conda-forge
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     re2                       2020.10.01           he1b5a44_0    conda-forge
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     recommonmark              0.6.0                      py_0    conda-forge
     regex                     2020.10.15       py37h8f50634_0    conda-forge
     requests                  2.24.0             pyh9f0ad1d_0    conda-forge
     rhash                     1.3.6             h516909a_1001    conda-forge
     rmm                       0.17.0a201017   cuda_11.0_py37_g8cdd176_21    rapidsai-nightly
     send2trash                1.5.0                      py_0    conda-forge
     setuptools                49.6.0           py37he5f6b98_2    conda-forge
     six                       1.15.0             pyh9f0ad1d_0    conda-forge
     snappy                    1.1.8                he1b5a44_3    conda-forge
     snowballstemmer           2.0.0                      py_0    conda-forge
     sortedcontainers          2.2.2              pyh9f0ad1d_0    conda-forge
     spdlog                    1.7.0                hc9558a2_2    conda-forge
     sphinx                    3.2.1                      py_0    conda-forge
     sphinx-copybutton         0.3.0              pyh9f0ad1d_0    conda-forge
     sphinx-markdown-tables    0.0.14             pyh9f0ad1d_1    conda-forge
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     sphinxcontrib-applehelp   1.0.2                      py_0    conda-forge
     sphinxcontrib-devhelp     1.0.2                      py_0    conda-forge
     sphinxcontrib-htmlhelp    1.0.3                      py_0    conda-forge
     sphinxcontrib-jsmath      1.0.1                      py_0    conda-forge
     sphinxcontrib-qthelp      1.0.3                      py_0    conda-forge
     sphinxcontrib-serializinghtml 1.1.4                      py_0    conda-forge
     sphinxcontrib-websupport  1.2.4              pyh9f0ad1d_0    conda-forge
     sqlite                    3.33.0               h4cf870e_1    conda-forge
     streamz                   0.6.0                    pypi_0    pypi
     tblib                     1.6.0                      py_0    conda-forge
     terminado                 0.9.1            py37hc8dfbb8_1    conda-forge
     testpath                  0.4.4                      py_0    conda-forge
     tk                        8.6.10               hed695b0_1    conda-forge
     toml                      0.10.1             pyh9f0ad1d_0    conda-forge
     toolz                     0.11.1                     py_0    conda-forge
     tornado                   6.0.4            py37h8f50634_2    conda-forge
     traitlets                 5.0.5                      py_0    conda-forge
     typed-ast                 1.4.1            py37h516909a_0    conda-forge
     typing_extensions         3.7.4.3                    py_0    conda-forge
     urllib3                   1.25.10                    py_0    conda-forge
     virtualenv                20.0.35          py37hc8dfbb8_0    conda-forge
     wcwidth                   0.2.5              pyh9f0ad1d_2    conda-forge
     webencodings              0.5.1                      py_1    conda-forge
     wheel                     0.35.1             pyh9f0ad1d_0    conda-forge
     xz                        5.2.5                h516909a_1    conda-forge
     yaml                      0.2.5                h516909a_0    conda-forge
     zeromq                    4.3.3                he1b5a44_2    conda-forge
     zict                      2.0.0                      py_0    conda-forge
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     zlib                      1.2.11            h516909a_1010    conda-forge
     zstd                      1.4.5                h6597ccf_2    conda-forge

Additional context Surfaced while running fuzz tests: #6001

vuule commented 4 years ago

na_filter is partially functional - it disables the na_values from being detected as null/NaN. Looks like what is missing is the change in logic to treat empty fields as null. Good catch. There may be more that can be done with this parameter, like creating non-nullable output columns.