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comparison cdblib.py @ 14:8ae67e9fb6ff

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Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug]
author miller-lab
date Fri, 28 Sep 2012 11:35:56 -0400
parents 2c498d40ecde
children
comparison
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13:fdb4240fb565 14:8ae67e9fb6ff
1 #!/usr/bin/env python
2
3 '''
4 Manipulate DJB's Constant Databases. These are 2 level disk-based hash tables
5 that efficiently handle many keys, while remaining space-efficient.
6
7 http://cr.yp.to/cdb.html
8
9 When generated databases are only used with Python code, consider using hash()
10 rather than djb_hash() for a tidy speedup.
11 '''
12
13 from _struct import Struct
14 from itertools import chain
15
16
17 def py_djb_hash(s):
18 '''Return the value of DJB's hash function for the given 8-bit string.'''
19 h = 5381
20 for c in s:
21 h = (((h << 5) + h) ^ ord(c)) & 0xffffffff
22 return h
23
24 try:
25 from _cdblib import djb_hash
26 except ImportError:
27 djb_hash = py_djb_hash
28
29 read_2_le4 = Struct('<LL').unpack
30 write_2_le4 = Struct('<LL').pack
31
32
33 class Reader(object):
34 '''A dictionary-like object for reading a Constant Database accessed
35 through a string or string-like sequence, such as mmap.mmap().'''
36
37 def __init__(self, data, hashfn=djb_hash):
38 '''Create an instance reading from a sequence and using hashfn to hash
39 keys.'''
40 if len(data) < 2048:
41 raise IOError('CDB too small')
42
43 self.data = data
44 self.hashfn = hashfn
45
46 self.index = [read_2_le4(data[i:i+8]) for i in xrange(0, 2048, 8)]
47 self.table_start = min(p[0] for p in self.index)
48 # Assume load load factor is 0.5 like official CDB.
49 self.length = sum(p[1] >> 1 for p in self.index)
50
51 def iteritems(self):
52 '''Like dict.iteritems(). Items are returned in insertion order.'''
53 pos = 2048
54 while pos < self.table_start:
55 klen, dlen = read_2_le4(self.data[pos:pos+8])
56 pos += 8
57
58 key = self.data[pos:pos+klen]
59 pos += klen
60
61 data = self.data[pos:pos+dlen]
62 pos += dlen
63
64 yield key, data
65
66 def items(self):
67 '''Like dict.items().'''
68 return list(self.iteritems())
69
70 def iterkeys(self):
71 '''Like dict.iterkeys().'''
72 return (p[0] for p in self.iteritems())
73 __iter__ = iterkeys
74
75 def itervalues(self):
76 '''Like dict.itervalues().'''
77 return (p[1] for p in self.iteritems())
78
79 def keys(self):
80 '''Like dict.keys().'''
81 return [p[0] for p in self.iteritems()]
82
83 def values(self):
84 '''Like dict.values().'''
85 return [p[1] for p in self.iteritems()]
86
87 def __getitem__(self, key):
88 '''Like dict.__getitem__().'''
89 value = self.get(key)
90 if value is None:
91 raise KeyError(key)
92 return value
93
94 def has_key(self, key):
95 '''Return True if key exists in the database.'''
96 return self.get(key) is not None
97 __contains__ = has_key
98
99 def __len__(self):
100 '''Return the number of records in the database.'''
101 return self.length
102
103 def gets(self, key):
104 '''Yield values for key in insertion order.'''
105 # Truncate to 32 bits and remove sign.
106 h = self.hashfn(key) & 0xffffffff
107 start, nslots = self.index[h & 0xff]
108
109 if nslots:
110 end = start + (nslots << 3)
111 slot_off = start + (((h >> 8) % nslots) << 3)
112
113 for pos in chain(xrange(slot_off, end, 8),
114 xrange(start, slot_off, 8)):
115 rec_h, rec_pos = read_2_le4(self.data[pos:pos+8])
116
117 if not rec_h:
118 break
119 elif rec_h == h:
120 klen, dlen = read_2_le4(self.data[rec_pos:rec_pos+8])
121 rec_pos += 8
122
123 if self.data[rec_pos:rec_pos+klen] == key:
124 rec_pos += klen
125 yield self.data[rec_pos:rec_pos+dlen]
126
127 def get(self, key, default=None):
128 '''Get the first value for key, returning default if missing.'''
129 # Avoid exception catch when handling default case; much faster.
130 return chain(self.gets(key), (default,)).next()
131
132 def getint(self, key, default=None, base=0):
133 '''Get the first value for key converted it to an int, returning
134 default if missing.'''
135 value = self.get(key, default)
136 if value is not default:
137 return int(value, base)
138 return value
139
140 def getints(self, key, base=0):
141 '''Yield values for key in insertion order after converting to int.'''
142 return (int(v, base) for v in self.gets(key))
143
144 def getstring(self, key, default=None, encoding='utf-8'):
145 '''Get the first value for key decoded as unicode, returning default if
146 not found.'''
147 value = self.get(key, default)
148 if value is not default:
149 return value.decode(encoding)
150 return value
151
152 def getstrings(self, key, encoding='utf-8'):
153 '''Yield values for key in insertion order after decoding as
154 unicode.'''
155 return (v.decode(encoding) for v in self.gets(key))
156
157
158 class Writer(object):
159 '''Object for building new Constant Databases, and writing them to a
160 seekable file-like object.'''
161
162 def __init__(self, fp, hashfn=djb_hash):
163 '''Create an instance writing to a file-like object, using hashfn to
164 hash keys.'''
165 self.fp = fp
166 self.hashfn = hashfn
167
168 fp.write('\x00' * 2048)
169 self._unordered = [[] for i in xrange(256)]
170
171 def put(self, key, value=''):
172 '''Write a string key/value pair to the output file.'''
173 assert type(key) is str and type(value) is str
174
175 pos = self.fp.tell()
176 self.fp.write(write_2_le4(len(key), len(value)))
177 self.fp.write(key)
178 self.fp.write(value)
179
180 h = self.hashfn(key) & 0xffffffff
181 self._unordered[h & 0xff].append((h, pos))
182
183 def puts(self, key, values):
184 '''Write more than one value for the same key to the output file.
185 Equivalent to calling put() in a loop.'''
186 for value in values:
187 self.put(key, value)
188
189 def putint(self, key, value):
190 '''Write an integer as a base-10 string associated with the given key
191 to the output file.'''
192 self.put(key, str(value))
193
194 def putints(self, key, values):
195 '''Write zero or more integers for the same key to the output file.
196 Equivalent to calling putint() in a loop.'''
197 self.puts(key, (str(value) for value in values))
198
199 def putstring(self, key, value, encoding='utf-8'):
200 '''Write a unicode string associated with the given key to the output
201 file after encoding it as UTF-8 or the given encoding.'''
202 self.put(key, unicode.encode(value, encoding))
203
204 def putstrings(self, key, values, encoding='utf-8'):
205 '''Write zero or more unicode strings to the output file. Equivalent to
206 calling putstring() in a loop.'''
207 self.puts(key, (unicode.encode(value, encoding) for value in values))
208
209 def finalize(self):
210 '''Write the final hash tables to the output file, and write out its
211 index. The output file remains open upon return.'''
212 index = []
213 for tbl in self._unordered:
214 length = len(tbl) << 1
215 ordered = [(0, 0)] * length
216 for pair in tbl:
217 where = (pair[0] >> 8) % length
218 for i in chain(xrange(where, length), xrange(0, where)):
219 if not ordered[i][0]:
220 ordered[i] = pair
221 break
222
223 index.append((self.fp.tell(), length))
224 for pair in ordered:
225 self.fp.write(write_2_le4(*pair))
226
227 self.fp.seek(0)
228 for pair in index:
229 self.fp.write(write_2_le4(*pair))
230 self.fp = None # prevent double finalize()