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Allow parsing in skipped row for C engine #12900

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1 change: 1 addition & 0 deletions doc/source/whatsnew/v0.18.1.txt
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Original file line number Diff line number Diff line change
Expand Up @@ -295,6 +295,7 @@ Bug Fixes



- Bug in ``read_csv`` with the C engine when specifying ``skiprows`` with newlines in quoted items (:issue:`10911`, `12775`)



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83 changes: 83 additions & 0 deletions pandas/io/tests/test_parsers.py
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Expand Up @@ -2867,6 +2867,89 @@ def test_read_only_header_no_rows(self):
df = self.read_csv(StringIO('a,b,c'), index_col=False)
tm.assert_frame_equal(df, expected)

def test_skiprow_with_newline(self):
# see gh-12775 and gh-10911
data = """id,text,num_lines
1,"line 11
line 12",2
2,"line 21
line 22",2
3,"line 31",1"""
expected = [[2, 'line 21\nline 22', 2],
[3, 'line 31', 1]]
expected = DataFrame(expected, columns=[
'id', 'text', 'num_lines'])
df = self.read_csv(StringIO(data), skiprows=[1])
tm.assert_frame_equal(df, expected)

data = ('a,b,c\n~a\n b~,~e\n d~,'
'~f\n f~\n1,2,~12\n 13\n 14~')
expected = [['a\n b', 'e\n d', 'f\n f']]
expected = DataFrame(expected, columns=[
'a', 'b', 'c'])
df = self.read_csv(StringIO(data),
quotechar="~",
skiprows=[2])
tm.assert_frame_equal(df, expected)

data = ('Text,url\n~example\n '
'sentence\n one~,url1\n~'
'example\n sentence\n two~,url2\n~'
'example\n sentence\n three~,url3')
expected = [['example\n sentence\n two', 'url2']]
expected = DataFrame(expected, columns=[
'Text', 'url'])
df = self.read_csv(StringIO(data),
quotechar="~",
skiprows=[1, 3])
tm.assert_frame_equal(df, expected)

def test_skiprow_with_quote(self):
data = """id,text,num_lines
1,"line '11' line 12",2
2,"line '21' line 22",2
3,"line '31' line 32",1"""
expected = [[2, "line '21' line 22", 2],
[3, "line '31' line 32", 1]]
expected = DataFrame(expected, columns=[
'id', 'text', 'num_lines'])
df = self.read_csv(StringIO(data), skiprows=[1])
tm.assert_frame_equal(df, expected)

def test_skiprow_with_newline_and_quote(self):
data = """id,text,num_lines
1,"line \n'11' line 12",2
2,"line \n'21' line 22",2
3,"line \n'31' line 32",1"""
expected = [[2, "line \n'21' line 22", 2],
[3, "line \n'31' line 32", 1]]
expected = DataFrame(expected, columns=[
'id', 'text', 'num_lines'])
df = self.read_csv(StringIO(data), skiprows=[1])
tm.assert_frame_equal(df, expected)

data = """id,text,num_lines
1,"line '11\n' line 12",2
2,"line '21\n' line 22",2
3,"line '31\n' line 32",1"""
expected = [[2, "line '21\n' line 22", 2],
[3, "line '31\n' line 32", 1]]
expected = DataFrame(expected, columns=[
'id', 'text', 'num_lines'])
df = self.read_csv(StringIO(data), skiprows=[1])
tm.assert_frame_equal(df, expected)

data = """id,text,num_lines
1,"line '11\n' \r\tline 12",2
2,"line '21\n' \r\tline 22",2
3,"line '31\n' \r\tline 32",1"""
expected = [[2, "line '21\n' \r\tline 22", 2],
[3, "line '31\n' \r\tline 32", 1]]
expected = DataFrame(expected, columns=[
'id', 'text', 'num_lines'])
df = self.read_csv(StringIO(data), skiprows=[1])
tm.assert_frame_equal(df, expected)


class CompressionTests(object):
def test_zip(self):
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61 changes: 41 additions & 20 deletions pandas/src/parser/tokenizer.c
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Expand Up @@ -478,7 +478,10 @@ static int end_line(parser_t *self) {
}
}

if (self->state == SKIP_LINE) {
if (self->state == SKIP_LINE || \
self->state == QUOTE_IN_SKIP_LINE || \
self->state == QUOTE_IN_QUOTE_IN_SKIP_LINE
) {
TRACE(("end_line: Skipping row %d\n", self->file_lines));
// increment file line count
self->file_lines++;
Expand All @@ -491,8 +494,6 @@ static int end_line(parser_t *self) {
return 0;
}

/* printf("Line: %d, Fields: %d, Ex-fields: %d\n", self->lines, fields, ex_fields); */

if (!(self->lines <= self->header_end + 1)
&& (self->expected_fields < 0 && fields > ex_fields)
&& !(self->usecols)) {
Expand All @@ -505,8 +506,7 @@ static int end_line(parser_t *self) {
// reset field count
self->line_fields[self->lines] = 0;

// file_lines is now the _actual_ file line number (starting at 1)

// file_lines is now the actual file line number (starting at 1)
if (self->error_bad_lines) {
self->error_msg = (char*) malloc(100);
sprintf(self->error_msg, "Expected %d fields in line %d, saw %d\n",
Expand All @@ -526,33 +526,26 @@ static int end_line(parser_t *self) {
free(msg);
}
}
}
else {
/* missing trailing delimiters */
} else {
// missing trailing delimiters
if ((self->lines >= self->header_end + 1) && fields < ex_fields) {

/* Might overrun the buffer when closing fields */
// might overrun the buffer when closing fields
if (make_stream_space(self, ex_fields - fields) < 0) {
self->error_msg = "out of memory";
return -1;
}

while (fields < ex_fields){
end_field(self);
/* printf("Prior word: %s\n", self->words[self->words_len - 2]); */
fields++;
}
}

// increment both line counts
self->file_lines++;

self->lines++;

/* coliter_t it; */
/* coliter_setup(&it, self, 5, self->lines - 1); */
/* printf("word at column 5: %s\n", COLITER_NEXT(it)); */

// good line, set new start point
if (self->lines >= self->lines_cap) {
TRACE(("end_line: ERROR!!! self->lines(%zu) >= self->lines_cap(%zu)\n", self->lines, self->lines_cap)) \
Expand All @@ -574,8 +567,6 @@ static int end_line(parser_t *self) {
return 0;
}



int parser_add_skiprow(parser_t *self, int64_t row) {
khiter_t k;
kh_int64_t *set;
Expand Down Expand Up @@ -763,6 +754,31 @@ int tokenize_bytes(parser_t *self, size_t line_limit)
} else if (IS_CARRIAGE(c)) {
self->file_lines++;
self->state = EAT_CRNL_NOP;
} else if (IS_QUOTE(c)) {
self->state = QUOTE_IN_SKIP_LINE;
}
break;

case QUOTE_IN_SKIP_LINE:
if (IS_QUOTE(c)) {
if (self->doublequote) {
self->state = QUOTE_IN_QUOTE_IN_SKIP_LINE;
} else {
self->state = SKIP_LINE;
}
}
break;

case QUOTE_IN_QUOTE_IN_SKIP_LINE:
if (IS_QUOTE(c)) {
self->state = QUOTE_IN_SKIP_LINE;
} else if (IS_TERMINATOR(c)) {
END_LINE();
} else if (IS_CARRIAGE(c)) {
self->file_lines++;
self->state = EAT_CRNL_NOP;
} else {
self->state = SKIP_LINE;
}
break;

Expand Down Expand Up @@ -815,9 +831,14 @@ int tokenize_bytes(parser_t *self, size_t line_limit)
case START_RECORD:
// start of record
if (skip_this_line(self, self->file_lines)) {
self->state = SKIP_LINE;
if (IS_TERMINATOR(c)) {
END_LINE();
if (IS_QUOTE(c)) {
self->state = QUOTE_IN_SKIP_LINE;
} else {
self->state = SKIP_LINE;

if (IS_TERMINATOR(c)) {
END_LINE();
}
}
break;
} else if (IS_TERMINATOR(c)) {
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2 changes: 2 additions & 0 deletions pandas/src/parser/tokenizer.h
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Expand Up @@ -124,6 +124,8 @@ typedef enum {
EAT_LINE_COMMENT,
WHITESPACE_LINE,
SKIP_LINE,
QUOTE_IN_SKIP_LINE,
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at some point maybe document what these states actually mean a bit more (I know its mostly self-explanatory, but for future readers)

QUOTE_IN_QUOTE_IN_SKIP_LINE,
FINISHED
} ParserState;

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