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[REVIEW] Fix N/A detection for empty fields in CSV reader #6922

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merged 15 commits into from
Dec 9, 2020

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vuule
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@vuule vuule commented Dec 5, 2020

Fixes #6682, #6680

Currently, empty fields are treated as N/A regardless on parsing options. However, the desired behavior is to handle empty fields the same way as fields with special values (apply default_na_values, na_filter logic).
This PR irons out the behavior so it matches Pandas in this regard.

  • Tries now support matching empty strings.
  • The list of special NA values is now generated more robustly, so it has correct elements in any parameter combination.
  • Empty string is added to the list of special NA values.
  • Empty string string ("/"/"") is added to NA value list if empty string ("") is included (mirrors Pandas behavior).
  • Added tests for previously failing parameter combinations.
  • Reworked some of the tests to check against Pandas results instead of assumed desired behavior.

@vuule vuule added bug Something isn't working libcudf Affects libcudf (C++/CUDA) code. cuIO cuIO issue labels Dec 5, 2020
@vuule vuule self-assigned this Dec 5, 2020
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Please update the changelog in order to start CI tests.

View the gpuCI docs here.

@vuule vuule added the non-breaking Non-breaking change label Dec 5, 2020
@vuule vuule changed the title [WIP] Fix N/A detection for empty fields in CSV reader [REVIEW] Fix N/A detection for empty fields in CSV reader Dec 5, 2020
@vuule vuule marked this pull request as ready for review December 5, 2020 00:34
@vuule vuule requested review from a team as code owners December 5, 2020 00:34
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LGTM

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codecov bot commented Dec 7, 2020

Codecov Report

Merging #6922 (cfa64bb) into branch-0.18 (598a14d) will increase coverage by 1.96%.
The diff coverage is n/a.

Impacted file tree graph

@@               Coverage Diff               @@
##           branch-0.18    #6922      +/-   ##
===============================================
+ Coverage        81.53%   83.50%   +1.96%     
===============================================
  Files               96       96              
  Lines            15876    18290    +2414     
===============================================
+ Hits             12945    15273    +2328     
- Misses            2931     3017      +86     
Impacted Files Coverage Δ
python/cudf/cudf/io/csv.py 93.75% <ø> (-0.25%) ⬇️
python/cudf/cudf/io/feather.py 100.00% <0.00%> (ø)
python/cudf/cudf/comm/serialize.py 0.00% <0.00%> (ø)
python/cudf/cudf/_fuzz_testing/io.py 0.00% <0.00%> (ø)
python/dask_cudf/dask_cudf/_version.py 0.00% <0.00%> (ø)
python/dask_cudf/dask_cudf/io/tests/test_csv.py 100.00% <0.00%> (ø)
python/dask_cudf/dask_cudf/io/tests/test_orc.py 100.00% <0.00%> (ø)
python/dask_cudf/dask_cudf/io/tests/test_json.py 100.00% <0.00%> (ø)
...ython/dask_cudf/dask_cudf/io/tests/test_parquet.py 100.00% <0.00%> (ø)
python/cudf/cudf/utils/applyutils.py 98.74% <0.00%> (+0.02%) ⬆️
... and 37 more

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vuule commented Dec 8, 2020

rerun tests

@@ -224,7 +224,7 @@ __global__ void __launch_bounds__(csvparse_block_dim)
long tempPos = pos - 1;
long field_len = pos - start;

if (field_len <= 0 || serialized_trie_contains(opts.trie_na, raw_csv + start, field_len)) {
if (field_len < 0 || serialized_trie_contains(opts.trie_na, raw_csv + start, field_len)) {
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I guess field_len < 0 is because we're using inclusive offsets (i.e, [0, 0] includes index 0)... Do we have a bug open for changing inclusive offsets -> exclusive offsets throughout cuio?

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Might want to add a comment to this so it's not thought to be a mistake. Or use <= -1 ?

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@vuule vuule Dec 9, 2020

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Took another look and it seems like field_len can never be negative. Since long field_len = pos - start;, and pos is initialized to start and can only advance.
I left the condition as a sanity check, but it actually makes no sense in the context. Will remove the condition, thanks!

@@ -89,6 +89,8 @@ inline thrust::host_vector<SerialTrieNode> createSerializedTrie(
// Serialize the tree trie
std::deque<IndexedTrieNode> to_visit;
thrust::host_vector<SerialTrieNode> nodes;
// suport for matching empty input
nodes.push_back(SerialTrieNode(trie_terminating_character, tree_trie.is_end_of_word));
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Does this mean all tries match empty input? Difficult to follow the logic how this coordinates with the code below.

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Not always. Here we create a node that will have is_end_of_word = true if the root node of the tree_trie is also end of a word (empty word, since it's the root). Hence, passing tree_trie.is_end_of_word as the second parameter.
I'll expand the comment above to make this clearer. 👍

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pytests lgtm

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[BUG] csv reader - empty fields treated as null even with na_filter=False
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