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[BUG] <NA> should be added to the list of na_values in csv reader #6678

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galipremsagar opened this issue Nov 4, 2020 · 0 comments · Fixed by #6693
Closed

[BUG] <NA> should be added to the list of na_values in csv reader #6678

galipremsagar opened this issue Nov 4, 2020 · 0 comments · Fixed by #6693
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@galipremsagar
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bug Something isn't working cuIO cuIO issue libcudf Affects libcudf (C++/CUDA) code.

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@galipremsagar
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Describe the bug
"<NA>" seems to be a recent new addition to the list of na_values in read_csv: https://pandas.pydata.org/pandas-docs/stable/reference/api/pandas.read_csv.html

It appears to be that we haven't added it to our list of default na_values:

cudf/cpp/include/cudf/io/csv.hpp

Lines 119 to 135 in 5cf7106

// Additional values to recognize as null values
std::vector<std::string> _na_values{"#N/A",
"#N/A N/A",
"#NA",
"-1.#IND",
"-1.#QNAN",
"-NaN",
"-nan",
"1.#IND",
"1.#QNAN",
"N/A",
"NA",
"NULL",
"NaN",
"n/a",
"nan",
"null"};

Steps/Code to reproduce bug

In[98]: import pandas as pd
In[99]: pdf = pd.DataFrame({'a':[0.4334, None, 1, 2]})
In[100]: csv_buf = pdf.to_csv(na_rep="<NA>")
In[101]: csv_buf
Out[101]: ',a\n0,0.4334\n1,<NA>\n2,1.0\n3,2.0\n'
In[102]: import io
In[103]: new_pdf = pd.read_csv(io.StringIO(csv_buf))
In[104]: new_pdf
Out[104]: 
   Unnamed: 0       a
0           0  0.4334
1           1     NaN
2           2  1.0000
3           3  2.0000
In[105]: new_pdf['a']
Out[105]: 
0    0.4334
1       NaN
2    1.0000
3    2.0000
Name: a, dtype: float64
In[106]: import cudf
In[107]: new_gdf = cudf.read_csv(io.StringIO(csv_buf))
In[108]: new_gdf
Out[108]: 
   Unnamed: 0       a
0           0  0.4334
1           1    <NA>
2           2     1.0
3           3     2.0
In[109]: new_gdf['a']
Out[109]: 
0    0.4334
1      <NA>
2       1.0
3       2.0
Name: a, dtype: object
In[110]: new_gdf['a'].isnull()
Out[110]: 
0    False
1    False
2    False
3    False
Name: a, dtype: bool
In[111]: new_pdf['a'].isnull()
Out[111]: 
0    False
1     True
2    False
3    False
Name: a, dtype: bool

Expected behavior
Our csv reader should as-well recognize <NA> as part of default na_values.

Environment overview (please complete the following information)

  • Environment location: [Bare-metal]
  • Method of cuDF install: [from source]

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 <[email protected]>
 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
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 argon2-cffi               20.1.0           py37h8f50634_2    conda-forge
 arrow-cpp                 1.0.1           py37hd1d2865_14_cuda    conda-forge
 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
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 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
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 bokeh                     2.2.2            py37hc8dfbb8_0    conda-forge
 boost-cpp                 1.74.0               h9359b55_0    conda-forge
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 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
 distlib                   0.3.1              pyh9f0ad1d_0    conda-forge
 distributed               2.30.0+7.gdcb46d07          pypi_0    pypi
 dlpack                    0.3                  he1b5a44_1    conda-forge
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 double-conversion         3.1.5                he1b5a44_2    conda-forge
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 entrypoints               0.3             py37hc8dfbb8_1002    conda-forge
 execnet                   1.7.1                    pypi_0    pypi
 expat                     2.2.9                he1b5a44_2    conda-forge
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 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
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 future                    0.18.2           py37hc8dfbb8_2    conda-forge
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 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
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 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
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 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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 python                    3.7.8           h6f2ec95_1_cpython    conda-forge
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 pyzmq                     19.0.2           py37hac76be4_2    conda-forge
 rapidjson                 1.1.0             he1b5a44_1002    conda-forge
 re2                       2020.10.01           he1b5a44_0    conda-forge
 readline                  8.0                  he28a2e2_2    conda-forge
 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
 sphinx_rtd_theme          0.5.0              pyh9f0ad1d_0    conda-forge
 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
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 xz                        5.2.5                h516909a_1    conda-forge
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 zipp                      3.3.1                      py_0    conda-forge
 zlib                      1.2.11            h516909a_1010    conda-forge
 zstd                      1.4.5                h6597ccf_2    conda-forge

Additional context
Surfaced while running fuzz tests: #6001
@galipremsagar galipremsagar added bug Something isn't working Needs Triage Need team to review and classify libcudf Affects libcudf (C++/CUDA) code. cuIO cuIO issue labels Nov 4, 2020
@vuule vuule mentioned this issue Nov 5, 2020
Closed
@galipremsagar galipremsagar removed the Needs Triage Need team to review and classify label Nov 5, 2020
@galipremsagar galipremsagar self-assigned this Nov 5, 2020
@galipremsagar galipremsagar mentioned this issue Nov 6, 2020
Merged
2 tasks
galipremsagar added a commit that referenced this issue Nov 6, 2020
@galipremsagar
Fix issue related to na_values input in read_csv (#6693)
bfb1b88 
Fixes: #6678 , #6677

This PR:

 Adds <NA> to default list of na_values.
 Fixes issue where na_values is a scalar and libcudf only expects list.
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bug Something isn't working cuIO cuIO issue libcudf Affects libcudf (C++/CUDA) code.
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[REVIEW] Fix issue related to na_values input in read_csv galipremsagar/cudf
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