1
|
#!/usr/bin/env python
|
2
|
# Maps one datasource to another, using a map spreadsheet if needed
|
3
|
# Exit status is the # of errors in the import, up to the maximum exit status
|
4
|
# For outputting an XML file to a PostgreSQL database, use the general format of
|
5
|
# http://vegbank.org/vegdocs/xml/vegbank_example_ver1.0.2.xml
|
6
|
|
7
|
import csv
|
8
|
import itertools
|
9
|
import os.path
|
10
|
import sys
|
11
|
import xml.dom.minidom as minidom
|
12
|
|
13
|
sys.path.append(os.path.dirname(__file__)+"/../lib")
|
14
|
|
15
|
import csvs
|
16
|
import db_xml
|
17
|
import exc
|
18
|
import iters
|
19
|
import maps
|
20
|
import opts
|
21
|
import parallelproc
|
22
|
import Parser
|
23
|
import profiling
|
24
|
import sql
|
25
|
import sql_gen
|
26
|
import streams
|
27
|
import strings
|
28
|
import term
|
29
|
import util
|
30
|
import xpath
|
31
|
import xml_dom
|
32
|
import xml_func
|
33
|
import xml_parse
|
34
|
|
35
|
def get_with_prefix(map_, prefixes, key):
|
36
|
'''Gets all entries for the given key with any of the given prefixes
|
37
|
@return tuple(found_key, found_value)
|
38
|
'''
|
39
|
values = []
|
40
|
for key_ in strings.with_prefixes(['']+prefixes, key): # also with no prefix
|
41
|
try: value = map_[key_]
|
42
|
except KeyError, e: continue # keep going
|
43
|
values.append((key_, value))
|
44
|
|
45
|
if values != []: return values
|
46
|
else: raise e # re-raise last KeyError
|
47
|
|
48
|
def metadata_value(name): return None # this feature has been removed
|
49
|
|
50
|
def cleanup(val):
|
51
|
if val == None: return val
|
52
|
return util.none_if(strings.cleanup(strings.ustr(val)), u'', u'\\N')
|
53
|
|
54
|
def main_():
|
55
|
env_names = []
|
56
|
def usage_err():
|
57
|
raise SystemExit('Usage: '+opts.env_usage(env_names, True)+' '
|
58
|
+sys.argv[0]+' [map_path...] [<input] [>output]\n'
|
59
|
'Note: Row #s start with 1')
|
60
|
|
61
|
## Get config from env vars
|
62
|
|
63
|
# Modes
|
64
|
test = opts.env_flag('test', False, env_names)
|
65
|
commit = opts.env_flag('commit', False, env_names) and not test
|
66
|
# never commit in test mode
|
67
|
redo = opts.env_flag('redo', test, env_names) and not commit
|
68
|
# never redo in commit mode (manually run `make empty_db` instead)
|
69
|
|
70
|
# Ranges
|
71
|
start = util.cast(int, opts.get_env_var('start', 1, env_names)) # 1-based
|
72
|
# Make start interally 0-based.
|
73
|
# It's 1-based to the user to match up with the staging table row #s.
|
74
|
start -= 1
|
75
|
if test: n_default = 1
|
76
|
else: n_default = None
|
77
|
n = util.cast(int, util.none_if(opts.get_env_var('n', n_default, env_names),
|
78
|
u''))
|
79
|
end = n
|
80
|
if end != None: end += start
|
81
|
|
82
|
# Debugging
|
83
|
if test: default_verbosity = 1
|
84
|
else: default_verbosity = 0
|
85
|
verbosity = util.cast(float, opts.get_env_var('verbose', default_verbosity,
|
86
|
env_names))
|
87
|
opts.get_env_var('profile_to', None, env_names) # add to env_names
|
88
|
|
89
|
# DB
|
90
|
def get_db_config(prefix):
|
91
|
return opts.get_env_vars(sql.db_config_names, prefix, env_names)
|
92
|
in_db_config = get_db_config('in')
|
93
|
out_db_config = get_db_config('out')
|
94
|
in_is_db = 'engine' in in_db_config
|
95
|
out_is_db = 'engine' in out_db_config
|
96
|
in_schema = opts.get_env_var('in_schema', None, env_names)
|
97
|
in_table = opts.get_env_var('in_table', None, env_names)
|
98
|
|
99
|
# Optimization
|
100
|
cache_sql = opts.env_flag('cache_sql', True, env_names)
|
101
|
by_col = in_db_config == out_db_config and opts.env_flag('by_col', False,
|
102
|
env_names) # by-column optimization only applies if mapping to same DB
|
103
|
if test: cpus_default = 0
|
104
|
else: cpus_default = 0 # or None to use parallel processing by default
|
105
|
cpus = util.cast(int, util.none_if(opts.get_env_var('cpus', cpus_default,
|
106
|
env_names), u''))
|
107
|
|
108
|
##
|
109
|
|
110
|
# Logging
|
111
|
verbose_errors = verbosity >= 1
|
112
|
debug = verbosity > 1
|
113
|
def log(msg, level=1):
|
114
|
'''Higher level -> more verbose'''
|
115
|
if level <= verbosity:
|
116
|
if level > 1: msg = '['+str(level)+'] '+msg # include level in msg
|
117
|
sys.stderr.write(msg+'\n')
|
118
|
if debug: log_debug = lambda msg, level=2: log(msg, level)
|
119
|
else: log_debug = sql.log_debug_none
|
120
|
|
121
|
# Parse args
|
122
|
map_paths = sys.argv[1:]
|
123
|
if map_paths == []:
|
124
|
if in_is_db or not out_is_db: usage_err()
|
125
|
else: map_paths = [None]
|
126
|
|
127
|
def connect_db(db_config):
|
128
|
log('Connecting to '+sql.db_config_str(db_config))
|
129
|
return sql.connect(db_config, caching=cache_sql,
|
130
|
autocommit=debug and commit, log_debug=log_debug)
|
131
|
|
132
|
if end != None: end_str = str(end-1) # end is one past the last #
|
133
|
else: end_str = 'end'
|
134
|
log('Processing input rows '+str(start)+'-'+end_str)
|
135
|
|
136
|
ex_tracker = exc.ExPercentTracker(iter_text='row')
|
137
|
profiler = profiling.ItersProfiler(start_now=True, iter_text='row')
|
138
|
|
139
|
# Parallel processing
|
140
|
pool = parallelproc.MultiProducerPool(cpus)
|
141
|
log('Using '+str(pool.process_ct)+' parallel CPUs')
|
142
|
|
143
|
doc = xml_dom.create_doc()
|
144
|
root = doc.documentElement
|
145
|
out_is_xml_ref = [False]
|
146
|
in_label_ref = [None]
|
147
|
def update_in_label():
|
148
|
if in_label_ref[0] != None:
|
149
|
xpath.get(root, '/_ignore/inLabel="'+in_label_ref[0]+'"', True)
|
150
|
def prep_root():
|
151
|
root.clear()
|
152
|
update_in_label()
|
153
|
prep_root()
|
154
|
|
155
|
# Define before the out_is_db section because it's used by by_col
|
156
|
row_ins_ct_ref = [0]
|
157
|
|
158
|
def process_input(root, row_ready, map_path):
|
159
|
'''Inputs datasource to XML tree, mapping if needed'''
|
160
|
# Load map header
|
161
|
in_is_xpaths = True
|
162
|
out_is_xpaths = True
|
163
|
out_label = None
|
164
|
if map_path != None:
|
165
|
metadata = []
|
166
|
mappings = []
|
167
|
stream = open(map_path, 'rb')
|
168
|
reader = csv.reader(stream)
|
169
|
in_label, out_label = reader.next()[:2]
|
170
|
|
171
|
def split_col_name(name):
|
172
|
label, sep, root = name.partition(':')
|
173
|
label, sep2, prefixes_str = label.partition('[')
|
174
|
prefixes_str = strings.remove_suffix(']', prefixes_str)
|
175
|
prefixes = strings.split(',', prefixes_str)
|
176
|
return label, sep != '', root, prefixes
|
177
|
# extract datasrc from "datasrc[data_format]"
|
178
|
|
179
|
in_label, in_root, prefixes = maps.col_info(in_label)
|
180
|
in_is_xpaths = in_root != None
|
181
|
in_label_ref[0] = in_label
|
182
|
update_in_label()
|
183
|
out_label, out_root = maps.col_info(out_label)[:2]
|
184
|
out_is_xpaths = out_root != None
|
185
|
if out_is_xpaths: has_types = out_root.find('/*s/') >= 0
|
186
|
# outer elements are types
|
187
|
|
188
|
for row in reader:
|
189
|
in_, out = row[:2]
|
190
|
if out != '': mappings.append([in_, out_root+out])
|
191
|
|
192
|
stream.close()
|
193
|
|
194
|
root.ownerDocument.documentElement.tagName = out_label
|
195
|
in_is_xml = in_is_xpaths and not in_is_db
|
196
|
out_is_xml_ref[0] = out_is_xpaths and not out_is_db
|
197
|
|
198
|
def process_rows(process_row, rows, rows_start=0):
|
199
|
'''Processes input rows
|
200
|
@param process_row(in_row, i)
|
201
|
@rows_start The (0-based) row # of the first row in rows. Set this
|
202
|
only if the pre-start rows have already been skipped.
|
203
|
'''
|
204
|
rows = iter(rows)
|
205
|
|
206
|
if end != None: row_nums = xrange(rows_start, end)
|
207
|
else: row_nums = itertools.count(rows_start)
|
208
|
i = -1
|
209
|
for i in row_nums:
|
210
|
try: row = rows.next()
|
211
|
except StopIteration:
|
212
|
i -= 1 # last row # didn't count
|
213
|
break # no more rows
|
214
|
if i < start: continue # not at start row yet
|
215
|
|
216
|
process_row(row, i)
|
217
|
row_ready(i, row)
|
218
|
row_ct = i-start+1
|
219
|
return row_ct
|
220
|
|
221
|
def map_rows(get_value, rows, **kw_args):
|
222
|
'''Maps input rows
|
223
|
@param get_value(in_, row):str
|
224
|
'''
|
225
|
# Prevent collisions if multiple inputs mapping to same output
|
226
|
outputs_idxs = dict()
|
227
|
for i, mapping in enumerate(mappings):
|
228
|
in_, out = mapping
|
229
|
default = util.NamedTuple(count=1, first=i)
|
230
|
idxs = outputs_idxs.setdefault(out, default)
|
231
|
if idxs is not default: # key existed, so there was a collision
|
232
|
if idxs.count == 1: # first key does not yet have /_alt/#
|
233
|
mappings[idxs.first][1] += '/_alt/0'
|
234
|
mappings[i][1] += '/_alt/'+str(idxs.count)
|
235
|
idxs.count += 1
|
236
|
|
237
|
id_node = None
|
238
|
if out_is_db:
|
239
|
for i, mapping in enumerate(mappings):
|
240
|
in_, out = mapping
|
241
|
# All put_obj()s should return the same id_node
|
242
|
nodes, id_node = xpath.put_obj(root, out, '-1', has_types,
|
243
|
'$'+str(in_)) # value is placeholder that documents name
|
244
|
mappings[i] = [in_, nodes]
|
245
|
assert id_node != None
|
246
|
|
247
|
if debug: # only calc if debug
|
248
|
log_debug('Put template:\n'+str(root))
|
249
|
|
250
|
def process_row(row, i):
|
251
|
row_id = str(i)
|
252
|
if id_node != None: xml_dom.set_value(id_node, row_id)
|
253
|
for in_, out in mappings:
|
254
|
log_debug('Getting '+str(in_))
|
255
|
value = metadata_value(in_)
|
256
|
if value == None: value = cleanup(get_value(in_, row))
|
257
|
log_debug('Putting '+repr(value)+' to '+str(out))
|
258
|
if out_is_db: # out is list of XML nodes
|
259
|
for node in out: xml_dom.set_value(node, value)
|
260
|
elif value != None: # out is XPath
|
261
|
xpath.put_obj(root, out, row_id, has_types, value)
|
262
|
return process_rows(process_row, rows, **kw_args)
|
263
|
|
264
|
def map_table(col_names, rows, **kw_args):
|
265
|
col_names_ct = len(col_names)
|
266
|
col_idxs = util.list_flip(col_names)
|
267
|
|
268
|
# Resolve prefixes
|
269
|
mappings_orig = mappings[:] # save a copy
|
270
|
mappings[:] = [] # empty existing elements
|
271
|
for in_, out in mappings_orig:
|
272
|
if metadata_value(in_) == None:
|
273
|
try: cols = get_with_prefix(col_idxs, prefixes, in_)
|
274
|
except KeyError: pass
|
275
|
else: mappings[len(mappings):] = [[db_xml.ColRef(*col), out]
|
276
|
for col in cols] # can't use += because that uses =
|
277
|
|
278
|
def get_value(in_, row): return row.list[in_.idx]
|
279
|
def wrap_row(row):
|
280
|
return util.ListDict(util.list_as_length(row, col_names_ct),
|
281
|
col_names, col_idxs) # handle CSV rows of different lengths
|
282
|
|
283
|
return map_rows(get_value, util.WrapIter(wrap_row, rows), **kw_args)
|
284
|
|
285
|
stdin = streams.LineCountStream(sys.stdin)
|
286
|
def on_error(e):
|
287
|
exc.add_msg(e, term.emph('input line #:')+' '+str(stdin.line_num))
|
288
|
ex_tracker.track(e)
|
289
|
|
290
|
if in_is_db:
|
291
|
in_db = connect_db(in_db_config)
|
292
|
|
293
|
# Get table and schema name
|
294
|
schema = in_schema # modified, so can't have same name as outer var
|
295
|
table = in_table # modified, so can't have same name as outer var
|
296
|
if table == None:
|
297
|
assert in_is_xpaths
|
298
|
schema, sep, table = in_root.partition('.')
|
299
|
if sep == '': # only the table name was specified
|
300
|
table = schema
|
301
|
schema = None
|
302
|
table = sql_gen.Table(table, schema)
|
303
|
|
304
|
# Fetch rows
|
305
|
if by_col: limit = 0 # only fetch column names
|
306
|
else: limit = n
|
307
|
cur = sql.select(in_db, table, limit=limit, start=start,
|
308
|
cacheable=False)
|
309
|
col_names = list(sql.col_names(cur))
|
310
|
|
311
|
if by_col:
|
312
|
map_table(col_names, []) # just create the template
|
313
|
xml_func.strip(root, ['_simplifyPath'])
|
314
|
if debug: log_debug('Putting stripped:\n'+str(root))
|
315
|
# only calc if debug
|
316
|
in_row_ct_ref = [0]
|
317
|
db_xml.put_table(in_db, root.firstChild, table, commit,
|
318
|
in_row_ct_ref, row_ins_ct_ref, n, start)
|
319
|
row_ct = in_row_ct_ref[0]
|
320
|
else:
|
321
|
# Use normal by-row method
|
322
|
row_ct = map_table(col_names, sql.rows(cur), rows_start=start)
|
323
|
# rows_start: pre-start rows have been skipped
|
324
|
|
325
|
in_db.db.close()
|
326
|
elif in_is_xml:
|
327
|
def get_rows(doc2rows):
|
328
|
return iters.flatten(itertools.imap(doc2rows,
|
329
|
xml_parse.docs_iter(stdin, on_error)))
|
330
|
|
331
|
if map_path == None:
|
332
|
def doc2rows(in_xml_root):
|
333
|
iter_ = xml_dom.NodeElemIter(in_xml_root)
|
334
|
util.skip(iter_, xml_dom.is_text) # skip metadata
|
335
|
return iter_
|
336
|
|
337
|
row_ct = process_rows(lambda row, i: root.appendChild(row),
|
338
|
get_rows(doc2rows))
|
339
|
else:
|
340
|
def doc2rows(in_xml_root):
|
341
|
rows = xpath.get(in_xml_root, in_root, limit=end)
|
342
|
if rows == []: raise SystemExit('Map error: Root "'
|
343
|
+in_root+'" not found in input')
|
344
|
return rows
|
345
|
|
346
|
def get_value(in_, row):
|
347
|
in_ = './{'+(','.join(strings.with_prefixes(
|
348
|
['']+prefixes, in_)))+'}' # also with no prefix
|
349
|
nodes = xpath.get(row, in_, allow_rooted=False)
|
350
|
if nodes != []: return xml_dom.value(nodes[0])
|
351
|
else: return None
|
352
|
|
353
|
row_ct = map_rows(get_value, get_rows(doc2rows))
|
354
|
else: # input is CSV
|
355
|
map_ = dict(mappings)
|
356
|
reader, col_names = csvs.reader_and_header(sys.stdin)
|
357
|
row_ct = map_table(col_names, reader)
|
358
|
|
359
|
return row_ct
|
360
|
|
361
|
def process_inputs(root, row_ready):
|
362
|
row_ct = 0
|
363
|
for map_path in map_paths:
|
364
|
row_ct += process_input(root, row_ready, map_path)
|
365
|
return row_ct
|
366
|
|
367
|
pool.share_vars(locals())
|
368
|
if out_is_db:
|
369
|
out_db = connect_db(out_db_config)
|
370
|
try:
|
371
|
if redo: sql.empty_db(out_db)
|
372
|
pool.share_vars(locals())
|
373
|
|
374
|
def row_ready(row_num, input_row):
|
375
|
row_str_ = [None]
|
376
|
def row_str():
|
377
|
if row_str_[0] == None:
|
378
|
# Row # is interally 0-based, but 1-based to the user
|
379
|
row_str_[0] = (term.emph('row #:')+' '+str(row_num+1)
|
380
|
+'\n'+term.emph('input row:')+'\n'+str(input_row))
|
381
|
if verbose_errors: row_str_[0] += ('\n'
|
382
|
+term.emph('output row:')+'\n'+str(root))
|
383
|
return row_str_[0]
|
384
|
|
385
|
if debug: log_debug(row_str()) # only calc if debug
|
386
|
|
387
|
def on_error(e):
|
388
|
exc.add_msg(e, row_str())
|
389
|
ex_tracker.track(e, row_num, detail=verbose_errors)
|
390
|
pool.share_vars(locals())
|
391
|
|
392
|
row_root = root.cloneNode(True) # deep copy so don't modify root
|
393
|
xml_func.process(row_root, on_error, out_db)
|
394
|
if not xml_dom.is_empty(row_root):
|
395
|
assert xml_dom.has_one_child(row_root)
|
396
|
try:
|
397
|
sql.with_savepoint(out_db,
|
398
|
lambda: db_xml.put(out_db, row_root.firstChild,
|
399
|
row_ins_ct_ref, on_error))
|
400
|
if commit: out_db.db.commit()
|
401
|
except sql.DatabaseErrors, e: on_error(e)
|
402
|
|
403
|
row_ct = process_inputs(root, row_ready)
|
404
|
sys.stdout.write('Inserted '+str(row_ins_ct_ref[0])+
|
405
|
' new rows into database\n')
|
406
|
|
407
|
# Consume asynchronous tasks
|
408
|
pool.main_loop()
|
409
|
finally:
|
410
|
if out_db.connected():
|
411
|
out_db.db.rollback()
|
412
|
out_db.db.close()
|
413
|
else:
|
414
|
def on_error(e): ex_tracker.track(e)
|
415
|
def row_ready(row_num, input_row): pass
|
416
|
row_ct = process_inputs(root, row_ready)
|
417
|
xml_func.process(root, on_error)
|
418
|
if out_is_xml_ref[0]:
|
419
|
doc.writexml(sys.stdout, **xml_dom.prettyxml_config)
|
420
|
else: # output is CSV
|
421
|
raise NotImplementedError('CSV output not supported yet')
|
422
|
|
423
|
# Consume any asynchronous tasks not already consumed above
|
424
|
pool.main_loop()
|
425
|
|
426
|
profiler.stop(row_ct)
|
427
|
ex_tracker.add_iters(row_ct)
|
428
|
log('Processed '+str(row_ct)+' input rows')
|
429
|
log(profiler.msg())
|
430
|
log(ex_tracker.msg())
|
431
|
ex_tracker.exit()
|
432
|
|
433
|
def main():
|
434
|
try: main_()
|
435
|
except Parser.SyntaxError, e: raise SystemExit(str(e))
|
436
|
|
437
|
if __name__ == '__main__':
|
438
|
profile_to = opts.get_env_var('profile_to', None)
|
439
|
if profile_to != None:
|
440
|
import cProfile
|
441
|
sys.stderr.write('Profiling to '+profile_to+'\n')
|
442
|
cProfile.run(main.func_code, profile_to)
|
443
|
else: main()
|