1 |
1388
|
aaronmk
|
# CSV I/O
|
2 |
|
|
|
3 |
|
|
import csv
|
4 |
5431
|
aaronmk
|
import _csv
|
5 |
1388
|
aaronmk
|
import StringIO
|
6 |
|
|
|
7 |
14594
|
aaronmk
|
import dicts
|
8 |
8069
|
aaronmk
|
import exc
|
9 |
14592
|
aaronmk
|
import lists
|
10 |
5593
|
aaronmk
|
import streams
|
11 |
1623
|
aaronmk
|
import strings
|
12 |
1444
|
aaronmk
|
import util
|
13 |
|
|
|
14 |
5426
|
aaronmk
|
delims = ',;\t|`'
|
15 |
5439
|
aaronmk
|
tab_padded_delims = ['\t|\t']
|
16 |
1623
|
aaronmk
|
tsv_delim = '\t'
|
17 |
|
|
escape = '\\'
|
18 |
1442
|
aaronmk
|
|
19 |
1623
|
aaronmk
|
ending_placeholder = r'\n'
|
20 |
|
|
|
21 |
5437
|
aaronmk
|
def is_tsv(dialect): return dialect.delimiter.startswith(tsv_delim)
|
22 |
1623
|
aaronmk
|
|
23 |
1621
|
aaronmk
|
def sniff(line):
|
24 |
|
|
'''Automatically detects the dialect'''
|
25 |
5435
|
aaronmk
|
line, ending = strings.extract_line_ending(line)
|
26 |
9961
|
aaronmk
|
try: dialect = csv.Sniffer().sniff(line, delims)
|
27 |
|
|
except _csv.Error, e:
|
28 |
|
|
if exc.e_msg(e) == 'Could not determine delimiter': dialect = csv.excel
|
29 |
|
|
else: raise
|
30 |
5435
|
aaronmk
|
|
31 |
5439
|
aaronmk
|
if is_tsv(dialect):
|
32 |
8070
|
aaronmk
|
dialect.quoting = csv.QUOTE_NONE
|
33 |
5439
|
aaronmk
|
# Check multi-char delims using \t
|
34 |
|
|
delim = strings.find_any(line, tab_padded_delims)
|
35 |
|
|
if delim:
|
36 |
|
|
dialect.delimiter = delim
|
37 |
|
|
line_suffix = delim.rstrip('\t')
|
38 |
|
|
if line.endswith(line_suffix): ending = line_suffix+ending
|
39 |
1621
|
aaronmk
|
else: dialect.doublequote = True # Sniffer doesn't turn this on by default
|
40 |
5435
|
aaronmk
|
dialect.lineterminator = ending
|
41 |
|
|
|
42 |
1621
|
aaronmk
|
return dialect
|
43 |
|
|
|
44 |
8202
|
aaronmk
|
def has_unbalanced_quotes(str_): return str_.count('"') % 2 == 1 # odd # of "
|
45 |
|
|
|
46 |
|
|
def has_multiline_column(str_): return has_unbalanced_quotes(str_)
|
47 |
|
|
|
48 |
1923
|
aaronmk
|
def stream_info(stream, parse_header=False):
|
49 |
6589
|
aaronmk
|
'''Automatically detects the dialect based on the header line.
|
50 |
|
|
Uses the Excel dialect if the CSV file is empty.
|
51 |
1923
|
aaronmk
|
@return NamedTuple {header_line, header, dialect}'''
|
52 |
1444
|
aaronmk
|
info = util.NamedTuple()
|
53 |
|
|
info.header_line = stream.readline()
|
54 |
8202
|
aaronmk
|
if has_multiline_column(info.header_line): # 1st line not full header
|
55 |
|
|
# assume it's a header-only csv with multiline columns
|
56 |
|
|
info.header_line += ''.join(stream.readlines()) # use entire file
|
57 |
1923
|
aaronmk
|
info.header = None
|
58 |
|
|
if info.header_line != '':
|
59 |
|
|
info.dialect = sniff(info.header_line)
|
60 |
6589
|
aaronmk
|
else: info.dialect = csv.excel # line of '' indicates EOF = empty stream
|
61 |
|
|
|
62 |
|
|
if parse_header:
|
63 |
|
|
try: info.header = reader_class(info.dialect)(
|
64 |
|
|
StringIO.StringIO(info.header_line), info.dialect).next()
|
65 |
|
|
except StopIteration: info.header = []
|
66 |
|
|
|
67 |
1444
|
aaronmk
|
return info
|
68 |
|
|
|
69 |
5170
|
aaronmk
|
tsv_encode_map = strings.json_encode_map[:]
|
70 |
|
|
tsv_encode_map.append(('\t', r'\t'))
|
71 |
|
|
tsv_decode_map = strings.flip_map(tsv_encode_map)
|
72 |
5146
|
aaronmk
|
|
73 |
1623
|
aaronmk
|
class TsvReader:
|
74 |
|
|
'''Unlike csv.reader, for TSVs, interprets \ as escaping a line ending but
|
75 |
5145
|
aaronmk
|
ignores it before everything else (e.g. \N for NULL).
|
76 |
5170
|
aaronmk
|
Also expands tsv_encode_map escapes.
|
77 |
5145
|
aaronmk
|
'''
|
78 |
1623
|
aaronmk
|
def __init__(self, stream, dialect):
|
79 |
|
|
assert is_tsv(dialect)
|
80 |
|
|
self.stream = stream
|
81 |
|
|
self.dialect = dialect
|
82 |
|
|
|
83 |
|
|
def __iter__(self): return self
|
84 |
|
|
|
85 |
|
|
def next(self):
|
86 |
|
|
record = ''
|
87 |
|
|
ending = None
|
88 |
|
|
while True:
|
89 |
|
|
line = self.stream.readline()
|
90 |
|
|
if line == '': raise StopIteration
|
91 |
|
|
|
92 |
5438
|
aaronmk
|
line = strings.remove_suffix(self.dialect.lineterminator, line)
|
93 |
5433
|
aaronmk
|
contents = strings.remove_suffix(escape, line)
|
94 |
1623
|
aaronmk
|
record += contents
|
95 |
5433
|
aaronmk
|
if len(contents) == len(line): break # no line continuation
|
96 |
1623
|
aaronmk
|
record += ending_placeholder
|
97 |
3055
|
aaronmk
|
|
98 |
|
|
# Prevent "new-line character seen in unquoted field" errors
|
99 |
|
|
record = record.replace('\r', ending_placeholder)
|
100 |
|
|
|
101 |
7211
|
aaronmk
|
# Split line
|
102 |
8071
|
aaronmk
|
if record == '': row = [] # csv.reader would interpret as EOF
|
103 |
|
|
elif len(self.dialect.delimiter) > 1: # multi-char delims
|
104 |
7211
|
aaronmk
|
row = record.split(self.dialect.delimiter)
|
105 |
|
|
else: row = csv.reader(StringIO.StringIO(record), self.dialect).next()
|
106 |
|
|
|
107 |
5170
|
aaronmk
|
return [strings.replace_all(tsv_decode_map, v) for v in row]
|
108 |
1623
|
aaronmk
|
|
109 |
|
|
def reader_class(dialect):
|
110 |
|
|
if is_tsv(dialect): return TsvReader
|
111 |
|
|
else: return csv.reader
|
112 |
|
|
|
113 |
|
|
def make_reader(stream, dialect): return reader_class(dialect)(stream, dialect)
|
114 |
|
|
|
115 |
1388
|
aaronmk
|
def reader_and_header(stream):
|
116 |
|
|
'''Automatically detects the dialect based on the header line
|
117 |
|
|
@return tuple (reader, header)'''
|
118 |
1923
|
aaronmk
|
info = stream_info(stream, parse_header=True)
|
119 |
1958
|
aaronmk
|
return (make_reader(stream, info.dialect), info.header)
|
120 |
1446
|
aaronmk
|
|
121 |
14577
|
aaronmk
|
def header(stream):
|
122 |
|
|
'''fetches just the header line of a stream'''
|
123 |
|
|
reader, header = reader_and_header(stream)
|
124 |
|
|
return header
|
125 |
|
|
|
126 |
1446
|
aaronmk
|
##### csv modifications
|
127 |
|
|
|
128 |
|
|
# Note that these methods only work on *instances* of Dialect classes
|
129 |
|
|
csv.Dialect.__eq__ = lambda self, other: self.__dict__ == other.__dict__
|
130 |
|
|
csv.Dialect.__ne__ = lambda self, other: not (self == other)
|
131 |
2114
|
aaronmk
|
|
132 |
5430
|
aaronmk
|
__Dialect__validate_orig = csv.Dialect._validate
|
133 |
|
|
def __Dialect__validate(self):
|
134 |
|
|
try: __Dialect__validate_orig(self)
|
135 |
|
|
except _csv.Error, e:
|
136 |
|
|
if str(e) == '"delimiter" must be an 1-character string': pass # OK
|
137 |
|
|
else: raise
|
138 |
|
|
csv.Dialect._validate = __Dialect__validate
|
139 |
|
|
|
140 |
2114
|
aaronmk
|
##### Row filters
|
141 |
|
|
|
142 |
|
|
class Filter:
|
143 |
|
|
'''Wraps a reader, filtering each row'''
|
144 |
|
|
def __init__(self, filter_, reader):
|
145 |
|
|
self.reader = reader
|
146 |
|
|
self.filter = filter_
|
147 |
|
|
|
148 |
|
|
def __iter__(self): return self
|
149 |
|
|
|
150 |
|
|
def next(self): return self.filter(self.reader.next())
|
151 |
5574
|
aaronmk
|
|
152 |
|
|
def close(self): pass # support using as a stream
|
153 |
2114
|
aaronmk
|
|
154 |
|
|
std_nulls = [r'\N']
|
155 |
|
|
empty_nulls = [''] + std_nulls
|
156 |
|
|
|
157 |
|
|
class NullFilter(Filter):
|
158 |
|
|
'''Translates special string values to None'''
|
159 |
|
|
def __init__(self, reader, nulls=std_nulls):
|
160 |
|
|
map_ = dict.fromkeys(nulls, None)
|
161 |
|
|
def filter_(row): return [map_.get(v, v) for v in row]
|
162 |
|
|
Filter.__init__(self, filter_, reader)
|
163 |
|
|
|
164 |
|
|
class StripFilter(Filter):
|
165 |
|
|
'''Strips whitespace'''
|
166 |
|
|
def __init__(self, reader):
|
167 |
|
|
def filter_(row): return [v.strip() for v in row]
|
168 |
|
|
Filter.__init__(self, filter_, reader)
|
169 |
5570
|
aaronmk
|
|
170 |
|
|
class ColCtFilter(Filter):
|
171 |
|
|
'''Gives all rows the same # columns'''
|
172 |
|
|
def __init__(self, reader, cols_ct):
|
173 |
|
|
def filter_(row): return util.list_as_length(row, cols_ct)
|
174 |
|
|
Filter.__init__(self, filter_, reader)
|
175 |
5571
|
aaronmk
|
|
176 |
|
|
##### Translators
|
177 |
|
|
|
178 |
5586
|
aaronmk
|
class StreamFilter(Filter):
|
179 |
|
|
'''Wraps a reader in a way that's usable to a filter stream that does not
|
180 |
|
|
require lines to be strings. Reports EOF as '' instead of StopIteration.'''
|
181 |
|
|
def __init__(self, reader):
|
182 |
|
|
Filter.__init__(self, None, reader)
|
183 |
|
|
|
184 |
|
|
def readline(self):
|
185 |
|
|
try: return self.reader.next()
|
186 |
|
|
except StopIteration: return '' # EOF
|
187 |
|
|
|
188 |
14586
|
aaronmk
|
class ProgressInputFilter(streams.ProgressInputStream): # is also a reader
|
189 |
|
|
# ProgressInputStream extends StreamIter, so this can be used as a reader
|
190 |
|
|
'''wraps a reader, reporting the # rows read every n rows and after the last
|
191 |
|
|
row is read
|
192 |
|
|
@param log the output stream for progress messages
|
193 |
|
|
'''
|
194 |
|
|
def __init__(self, reader, log, msg='Read %d row(s)', n=100):
|
195 |
|
|
streams.ProgressInputStream.__init__(self, StreamFilter(reader), log,
|
196 |
|
|
msg, n)
|
197 |
|
|
|
198 |
5735
|
aaronmk
|
class ColInsertFilter(Filter):
|
199 |
7290
|
aaronmk
|
'''Adds column(s) to each row
|
200 |
9509
|
aaronmk
|
@param mk_value(row, row_num) | literal_value
|
201 |
5735
|
aaronmk
|
'''
|
202 |
14592
|
aaronmk
|
def __init__(self, reader, mk_value, index=0, n=1, col_names=None):
|
203 |
|
|
line_num_skip = 0
|
204 |
|
|
if col_names != None:
|
205 |
|
|
col_names = lists.mk_seq(col_names)
|
206 |
|
|
n = len(col_names)
|
207 |
|
|
line_num_skip = 1
|
208 |
|
|
|
209 |
9509
|
aaronmk
|
if not callable(mk_value):
|
210 |
|
|
value = mk_value
|
211 |
|
|
def mk_value(row, row_num): return value
|
212 |
|
|
|
213 |
5735
|
aaronmk
|
def filter_(row):
|
214 |
|
|
row = list(row) # make sure it's mutable; don't modify input!
|
215 |
14592
|
aaronmk
|
|
216 |
|
|
if self.is_header and col_names != None:
|
217 |
|
|
values = col_names
|
218 |
|
|
self.is_header = False
|
219 |
|
|
else: values = n*[mk_value(row, self.reader.line_num-line_num_skip)]
|
220 |
|
|
|
221 |
|
|
for i in xrange(len(values)): row.insert(index+i, values[i])
|
222 |
5735
|
aaronmk
|
return row
|
223 |
|
|
Filter.__init__(self, filter_,
|
224 |
|
|
streams.LineCountInputStream(StreamFilter(reader)))
|
225 |
14592
|
aaronmk
|
self.is_header = True
|
226 |
5735
|
aaronmk
|
|
227 |
5736
|
aaronmk
|
class RowNumFilter(ColInsertFilter):
|
228 |
5593
|
aaronmk
|
'''Adds a row # column at the beginning of each row'''
|
229 |
14593
|
aaronmk
|
def __init__(self, reader, col_name=None):
|
230 |
5736
|
aaronmk
|
def mk_value(row, row_num): return row_num
|
231 |
14593
|
aaronmk
|
ColInsertFilter.__init__(self, reader, mk_value, col_names=col_name)
|
232 |
5593
|
aaronmk
|
|
233 |
14591
|
aaronmk
|
class InputRewriter(StreamFilter): # is also a stream
|
234 |
5571
|
aaronmk
|
'''Wraps a reader, writing each row back to CSV'''
|
235 |
|
|
def __init__(self, reader, dialect=csv.excel):
|
236 |
5587
|
aaronmk
|
StreamFilter.__init__(self, reader)
|
237 |
|
|
|
238 |
5571
|
aaronmk
|
self.dialect = dialect
|
239 |
|
|
|
240 |
|
|
def readline(self):
|
241 |
8069
|
aaronmk
|
try:
|
242 |
14590
|
aaronmk
|
row = StreamFilter.readline(self) # translate EOF
|
243 |
8069
|
aaronmk
|
if row == '': return row # EOF
|
244 |
|
|
|
245 |
|
|
line_stream = StringIO.StringIO()
|
246 |
|
|
csv.writer(line_stream, self.dialect).writerow(row)
|
247 |
|
|
return line_stream.getvalue()
|
248 |
|
|
except Exception, e:
|
249 |
|
|
exc.print_ex(e)
|
250 |
|
|
raise
|
251 |
5571
|
aaronmk
|
|
252 |
|
|
def read(self, n): return self.readline() # forward all reads to readline()
|
253 |
14594
|
aaronmk
|
|
254 |
|
|
def row_dict_to_list(dict_, col_order=[]):
|
255 |
|
|
'''translates a CSV dict-based row to a list-based one
|
256 |
|
|
@param dict_ {'col': 'value', __}
|
257 |
|
|
@return (header, row) = (['col', __], ['value', __])
|
258 |
|
|
'''
|
259 |
|
|
dict_ = dict_.copy() # don't modify input!
|
260 |
|
|
pairs = []
|
261 |
|
|
for col in col_order: pairs.append((col, dict_.pop(col))) # ordered cols 1st
|
262 |
|
|
pairs += sorted(dict_.items()) # then remaining cols in alphabetical order
|
263 |
|
|
return (dicts.pair_keys(pairs), dicts.pair_values(pairs))
|
264 |
14595
|
aaronmk
|
|
265 |
|
|
class JsonReader(Filter):
|
266 |
|
|
'''reads parsed JSON data as row tuples
|
267 |
|
|
@param json_data [{'col': 'value', __}, __]
|
268 |
|
|
'''
|
269 |
|
|
def __init__(self, json_data, col_order=[]):
|
270 |
|
|
self.header = None
|
271 |
|
|
|
272 |
|
|
def filter_(row_dict):
|
273 |
|
|
header, row = row_dict_to_list(row_dict, col_order)
|
274 |
|
|
|
275 |
|
|
if self.header == None: # 1st JSON row: header
|
276 |
|
|
self.header = header
|
277 |
|
|
self.next_row = row
|
278 |
|
|
row = header
|
279 |
|
|
elif self.next_row != None: # 1st JSON row: data
|
280 |
|
|
row = self.next_row
|
281 |
|
|
self.next_row = None
|
282 |
|
|
else: # remaining JSON rows
|
283 |
|
|
assert header == self.header # all rows must have same cols
|
284 |
|
|
|
285 |
|
|
return row
|
286 |
|
|
Filter.__init__(self, filter_, iter(json_data))
|
287 |
|
|
self.next_row = None
|