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 exc
|
17
|
import iters
|
18
|
import maps
|
19
|
import opts
|
20
|
import Parser
|
21
|
import profiling
|
22
|
import sql
|
23
|
import streams
|
24
|
import strings
|
25
|
import term
|
26
|
import util
|
27
|
import xpath
|
28
|
import xml_dom
|
29
|
import xml_func
|
30
|
import xml_parse
|
31
|
|
32
|
def get_with_prefix(map_, prefixes, key):
|
33
|
'''Gets all entries for the given key with any of the given prefixes'''
|
34
|
values = []
|
35
|
for key_ in strings.with_prefixes(['']+prefixes, key): # also with no prefix
|
36
|
try: value = map_[key_]
|
37
|
except KeyError, e: continue # keep going
|
38
|
values.append(value)
|
39
|
|
40
|
if values != []: return values
|
41
|
else: raise e # re-raise last KeyError
|
42
|
|
43
|
def metadata_value(name): return None # this feature has been removed
|
44
|
|
45
|
def cleanup(val):
|
46
|
if val == None: return val
|
47
|
return util.none_if(strings.cleanup(strings.ustr(val)), u'', u'\\N')
|
48
|
|
49
|
def main_():
|
50
|
env_names = []
|
51
|
def usage_err():
|
52
|
raise SystemExit('Usage: '+opts.env_usage(env_names, True)+' '
|
53
|
+sys.argv[0]+' [map_path...] [<input] [>output]')
|
54
|
|
55
|
## Get config from env vars
|
56
|
|
57
|
# Modes
|
58
|
test = opts.env_flag('test', False, env_names)
|
59
|
commit = opts.env_flag('commit', False, env_names) and not test
|
60
|
# never commit in test mode
|
61
|
redo = opts.env_flag('redo', test, env_names) and not commit
|
62
|
# never redo in commit mode (manually run `make empty_db` instead)
|
63
|
|
64
|
# Ranges
|
65
|
start = util.cast(int, opts.get_env_var('start', '0', env_names))
|
66
|
if test: end_default = 1
|
67
|
else: end_default = None
|
68
|
end = util.cast(int, util.none_if(
|
69
|
opts.get_env_var('n', end_default, env_names), u''))
|
70
|
if end != None: end += start
|
71
|
|
72
|
# Optimization
|
73
|
cpus = util.cast(int, opts.get_env_var('cpus', None, env_names))
|
74
|
|
75
|
# Debugging
|
76
|
debug = opts.env_flag('debug', False, env_names)
|
77
|
sql.run_raw_query.debug = debug
|
78
|
verbose = debug or opts.env_flag('verbose', not test, env_names)
|
79
|
opts.get_env_var('profile_to', None, env_names) # add to env_names
|
80
|
|
81
|
# DB
|
82
|
db_config_names = ['engine', 'host', 'user', 'password', 'database']
|
83
|
def get_db_config(prefix):
|
84
|
return opts.get_env_vars(db_config_names, prefix, env_names)
|
85
|
in_db_config = get_db_config('in')
|
86
|
out_db_config = get_db_config('out')
|
87
|
in_is_db = 'engine' in in_db_config
|
88
|
out_is_db = 'engine' in out_db_config
|
89
|
|
90
|
##
|
91
|
|
92
|
# Logging
|
93
|
def log(msg, on=verbose):
|
94
|
if on: sys.stderr.write(msg)
|
95
|
def log_start(action, on=verbose): log(action+'...\n', on)
|
96
|
|
97
|
# Parse args
|
98
|
map_paths = sys.argv[1:]
|
99
|
if map_paths == []:
|
100
|
if in_is_db or not out_is_db: usage_err()
|
101
|
else: map_paths = [None]
|
102
|
|
103
|
def connect_db(db_config):
|
104
|
log_start('Connecting to '+sql.db_config_str(db_config))
|
105
|
return sql.connect(db_config)
|
106
|
|
107
|
if end != None: end_str = str(end-1)
|
108
|
else: end_str = 'end'
|
109
|
log_start('Processing input rows '+str(start)+'-'+end_str)
|
110
|
|
111
|
ex_tracker = exc.ExPercentTracker(iter_text='row')
|
112
|
profiler = profiling.ItersProfiler(start_now=True, iter_text='row')
|
113
|
|
114
|
try: import pp
|
115
|
except ImportError: cpus = 0
|
116
|
if cpus != 0:
|
117
|
if cpus != None: args = [cpus]
|
118
|
else: args = []
|
119
|
job_server = pp.Server(*args)
|
120
|
log_start('Using '+str(job_server.get_ncpus())+' CPUs')
|
121
|
|
122
|
doc = xml_dom.create_doc()
|
123
|
root = doc.documentElement
|
124
|
out_is_xml_ref = [False]
|
125
|
in_label_ref = [None]
|
126
|
def update_in_label():
|
127
|
if in_label_ref[0] != None:
|
128
|
xpath.get(root, '/_ignore/inLabel="'+in_label_ref[0]+'"', True)
|
129
|
def prep_root():
|
130
|
root.clear()
|
131
|
update_in_label()
|
132
|
prep_root()
|
133
|
|
134
|
def process_input(root, row_ready, map_path):
|
135
|
'''Inputs datasource to XML tree, mapping if needed'''
|
136
|
# Load map header
|
137
|
in_is_xpaths = True
|
138
|
out_is_xpaths = True
|
139
|
out_label = None
|
140
|
if map_path != None:
|
141
|
metadata = []
|
142
|
mappings = []
|
143
|
stream = open(map_path, 'rb')
|
144
|
reader = csv.reader(stream)
|
145
|
in_label, out_label = reader.next()[:2]
|
146
|
|
147
|
def split_col_name(name):
|
148
|
label, sep, root = name.partition(':')
|
149
|
label, sep2, prefixes_str = label.partition('[')
|
150
|
prefixes_str = strings.remove_suffix(']', prefixes_str)
|
151
|
prefixes = strings.split(',', prefixes_str)
|
152
|
return label, sep != '', root, prefixes
|
153
|
# extract datasrc from "datasrc[data_format]"
|
154
|
|
155
|
in_label, in_root, prefixes = maps.col_info(in_label)
|
156
|
in_is_xpaths = in_root != None
|
157
|
in_label_ref[0] = in_label
|
158
|
update_in_label()
|
159
|
out_label, out_root = maps.col_info(out_label)[:2]
|
160
|
out_is_xpaths = out_root != None
|
161
|
if out_is_xpaths: has_types = out_root.find('/*s/') >= 0
|
162
|
# outer elements are types
|
163
|
|
164
|
for row in reader:
|
165
|
in_, out = row[:2]
|
166
|
if out != '':
|
167
|
if out_is_xpaths: out = xpath.parse(out_root+out)
|
168
|
mappings.append((in_, out))
|
169
|
|
170
|
stream.close()
|
171
|
|
172
|
root.ownerDocument.documentElement.tagName = out_label
|
173
|
in_is_xml = in_is_xpaths and not in_is_db
|
174
|
out_is_xml_ref[0] = out_is_xpaths and not out_is_db
|
175
|
|
176
|
def process_rows(process_row, rows):
|
177
|
'''Processes input rows
|
178
|
@param process_row(in_row, i)
|
179
|
'''
|
180
|
i = 0
|
181
|
while end == None or i < end:
|
182
|
try: row = rows.next()
|
183
|
except StopIteration: break # no more rows
|
184
|
if i < start: continue # not at start row yet
|
185
|
|
186
|
process_row(row, i)
|
187
|
row_ready(i, row)
|
188
|
i += 1
|
189
|
row_ct = i-start
|
190
|
return row_ct
|
191
|
|
192
|
def map_rows(get_value, rows):
|
193
|
'''Maps input rows
|
194
|
@param get_value(in_, row):str
|
195
|
'''
|
196
|
def process_row(row, i):
|
197
|
row_id = str(i)
|
198
|
for in_, out in mappings:
|
199
|
value = metadata_value(in_)
|
200
|
if value == None:
|
201
|
log_start('Getting '+str(in_), debug)
|
202
|
value = cleanup(get_value(in_, row))
|
203
|
if value != None:
|
204
|
log_start('Putting '+str(out), debug)
|
205
|
xpath.put_obj(root, out, row_id, has_types, value)
|
206
|
return process_rows(process_row, rows)
|
207
|
|
208
|
def map_table(col_names, rows):
|
209
|
col_names_ct = len(col_names)
|
210
|
col_idxs = util.list_flip(col_names)
|
211
|
|
212
|
i = 0
|
213
|
while i < len(mappings): # mappings len changes in loop
|
214
|
in_, out = mappings[i]
|
215
|
if metadata_value(in_) == None:
|
216
|
try: mappings[i] = (
|
217
|
get_with_prefix(col_idxs, prefixes, in_), out)
|
218
|
except KeyError:
|
219
|
del mappings[i]
|
220
|
continue # keep i the same
|
221
|
i += 1
|
222
|
|
223
|
def get_value(in_, row):
|
224
|
return util.coalesce(*util.list_subset(row.list, in_))
|
225
|
def wrap_row(row):
|
226
|
return util.ListDict(util.list_as_length(row, col_names_ct),
|
227
|
col_names, col_idxs) # handle CSV rows of different lengths
|
228
|
|
229
|
return map_rows(get_value, util.WrapIter(wrap_row, rows))
|
230
|
|
231
|
stdin = streams.LineCountStream(sys.stdin)
|
232
|
def on_error(e):
|
233
|
exc.add_msg(e, term.emph('input line #:')+' '+str(stdin.line_num))
|
234
|
ex_tracker.track(e)
|
235
|
|
236
|
if in_is_db:
|
237
|
assert in_is_xpaths
|
238
|
|
239
|
in_db = connect_db(in_db_config)
|
240
|
cur = sql.select(in_db, table=in_root, fields=None, conds=None,
|
241
|
limit=end, start=0)
|
242
|
row_ct = map_table(list(sql.col_names(cur)), sql.rows(cur))
|
243
|
|
244
|
in_db.db.close()
|
245
|
elif in_is_xml:
|
246
|
def get_rows(doc2rows):
|
247
|
return iters.flatten(itertools.imap(doc2rows,
|
248
|
xml_parse.docs_iter(stdin, on_error)))
|
249
|
|
250
|
if map_path == None:
|
251
|
def doc2rows(in_xml_root):
|
252
|
iter_ = xml_dom.NodeElemIter(in_xml_root)
|
253
|
util.skip(iter_, xml_dom.is_text) # skip metadata
|
254
|
return iter_
|
255
|
|
256
|
row_ct = process_rows(lambda row, i: root.appendChild(row),
|
257
|
get_rows(doc2rows))
|
258
|
else:
|
259
|
def doc2rows(in_xml_root):
|
260
|
rows = xpath.get(in_xml_root, in_root, limit=end)
|
261
|
if rows == []: raise SystemExit('Map error: Root "'
|
262
|
+in_root+'" not found in input')
|
263
|
return rows
|
264
|
|
265
|
def get_value(in_, row):
|
266
|
in_ = './{'+(','.join(strings.with_prefixes(
|
267
|
['']+prefixes, in_)))+'}' # also with no prefix
|
268
|
nodes = xpath.get(row, in_, allow_rooted=False)
|
269
|
if nodes != []: return xml_dom.value(nodes[0])
|
270
|
else: return None
|
271
|
|
272
|
row_ct = map_rows(get_value, get_rows(doc2rows))
|
273
|
else: # input is CSV
|
274
|
map_ = dict(mappings)
|
275
|
reader, col_names = csvs.reader_and_header(sys.stdin)
|
276
|
row_ct = map_table(col_names, reader)
|
277
|
|
278
|
return row_ct
|
279
|
|
280
|
def process_inputs(root, row_ready):
|
281
|
row_ct = 0
|
282
|
for map_path in map_paths:
|
283
|
row_ct += process_input(root, row_ready, map_path)
|
284
|
return row_ct
|
285
|
|
286
|
if out_is_db:
|
287
|
import db_xml
|
288
|
|
289
|
out_db = connect_db(out_db_config)
|
290
|
try:
|
291
|
if redo: sql.empty_db(out_db)
|
292
|
row_ins_ct_ref = [0]
|
293
|
|
294
|
def row_ready(row_num, input_row):
|
295
|
def on_error(e):
|
296
|
exc.add_msg(e, term.emph('row #:')+' '+str(row_num))
|
297
|
exc.add_msg(e, term.emph('input row:')+'\n'+str(input_row))
|
298
|
exc.add_msg(e, term.emph('output row:')+'\n'+str(root))
|
299
|
ex_tracker.track(e, row_num)
|
300
|
|
301
|
xml_func.process(root, on_error)
|
302
|
if not xml_dom.is_empty(root):
|
303
|
assert xml_dom.has_one_child(root)
|
304
|
try:
|
305
|
sql.with_savepoint(out_db,
|
306
|
lambda: db_xml.put(out_db, root.firstChild,
|
307
|
row_ins_ct_ref, on_error))
|
308
|
if commit: out_db.db.commit()
|
309
|
except sql.DatabaseErrors, e: on_error(e)
|
310
|
prep_root()
|
311
|
|
312
|
row_ct = process_inputs(root, row_ready)
|
313
|
sys.stdout.write('Inserted '+str(row_ins_ct_ref[0])+
|
314
|
' new rows into database\n')
|
315
|
finally:
|
316
|
out_db.db.rollback()
|
317
|
out_db.db.close()
|
318
|
else:
|
319
|
def on_error(e): ex_tracker.track(e)
|
320
|
def row_ready(row_num, input_row): pass
|
321
|
row_ct = process_inputs(root, row_ready)
|
322
|
xml_func.process(root, on_error)
|
323
|
if out_is_xml_ref[0]:
|
324
|
doc.writexml(sys.stdout, **xml_dom.prettyxml_config)
|
325
|
else: # output is CSV
|
326
|
raise NotImplementedError('CSV output not supported yet')
|
327
|
|
328
|
profiler.stop(row_ct)
|
329
|
ex_tracker.add_iters(row_ct)
|
330
|
if verbose:
|
331
|
sys.stderr.write('Processed '+str(row_ct)+' input rows\n')
|
332
|
sys.stderr.write(profiler.msg()+'\n')
|
333
|
sys.stderr.write(ex_tracker.msg()+'\n')
|
334
|
ex_tracker.exit()
|
335
|
|
336
|
def main():
|
337
|
try: main_()
|
338
|
except Parser.SyntaxError, e: raise SystemExit(str(e))
|
339
|
|
340
|
if __name__ == '__main__':
|
341
|
profile_to = opts.get_env_var('profile_to', None)
|
342
|
if profile_to != None:
|
343
|
import cProfile
|
344
|
sys.stderr.write('Profiling to '+profile_to+'\n')
|
345
|
cProfile.run(main.func_code, profile_to)
|
346
|
else: main()
|