Project

General

Profile

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