Project

General

Profile

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
# Multi-safe (supports an input appearing multiple times).
5
# For outputting an XML file to a PostgreSQL database, use the general format of
6
# http://vegbank.org/vegdocs/xml/vegbank_example_ver1.0.2.xml
7
# Duplicate-column safe (supports multiple columns of the same name, which will
8
# be combined)
9
# Case- and punctuation-insensitive.
10

    
11
import copy
12
import csv
13
import itertools
14
import os.path
15
import warnings
16
import sys
17
import xml.dom.minidom as minidom
18

    
19
sys.path.append(os.path.dirname(__file__)+"/../lib")
20

    
21
import csvs
22
import db_xml
23
import exc
24
import iters
25
import maps
26
import opts
27
import parallelproc
28
import Parser
29
import profiling
30
import sql
31
import sql_gen
32
import sql_io
33
import streams
34
import strings
35
import term
36
import util
37
import xpath
38
import xml_dom
39
import xml_func
40
import xml_parse
41

    
42
collision_suffix = '/_alt/'
43

    
44
def get_with_prefix(map_, prefixes, key):
45
    '''Gets all entries for the given key with any of the given prefixes
46
    @return tuple(found_key, found_value)
47
    '''
48
    values = []
49
    for key_ in strings.with_prefixes(['']+prefixes, key): # also with no prefix
50
        try: value = map_[key_]
51
        except KeyError, e: continue # keep going
52
        values.append((key_, value))
53
    
54
    if values != []: return values
55
    else: raise e # re-raise last KeyError
56

    
57
def metadata_value(name): return None # this feature has been removed
58

    
59
def cleanup(val):
60
    if val == None: return val
61
    return util.none_if(strings.cleanup(strings.ustr(val)), u'', u'\\N')
62

    
63
def main_():
64
    env_names = []
65
    def usage_err():
66
        raise SystemExit('Usage: '+opts.env_usage(env_names, True)+' '
67
            +sys.argv[0]+' [map_path...] [<input] [>output]\n'
68
            'Note: Row #s start with 1')
69
    
70
    ## Get config from env vars
71
    
72
    # Modes
73
    test = opts.env_flag('test', False, env_names)
74
    commit = opts.env_flag('commit', False, env_names) and not test
75
        # never commit in test mode
76
    redo = opts.env_flag('redo', test, env_names) and not commit
77
        # never redo in commit mode (run `make schemas/reinstall` instead)
78
    
79
    # Ranges
80
    start = util.cast(int, opts.get_env_var('start', 1, env_names)) # 1-based
81
    # Make start interally 0-based.
82
    # It's 1-based to the user to match up with the staging table row #s.
83
    start -= 1
84
    if test: n_default = 1
85
    else: n_default = None
86
    n = util.cast(int, util.none_if(opts.get_env_var('n', n_default, env_names),
87
        u''))
88
    end = n
89
    if end != None: end += start
90
    
91
    # Debugging
92
    verbosity = util.cast(float, opts.get_env_var('verbosity', None, env_names))
93
    opts.get_env_var('profile_to', None, env_names) # add to env_names
94
    
95
    # DB
96
    def get_db_config(prefix):
97
        return opts.get_env_vars(sql.db_config_names, prefix, env_names)
98
    in_db_config = get_db_config('in')
99
    out_db_config = get_db_config('out')
100
    in_is_db = 'engine' in in_db_config
101
    out_is_db = 'engine' in out_db_config
102
    in_schema = opts.get_env_var('in_schema', None, env_names)
103
    in_table = opts.get_env_var('in_table', None, env_names)
104
    if in_schema != None:
105
        for config in [in_db_config, out_db_config]:
106
            config['schemas'] += ','+in_schema
107
    
108
    # Optimization
109
    cache_sql = opts.env_flag('cache_sql', True, env_names)
110
    by_col = in_db_config == out_db_config and opts.env_flag('by_col', False,
111
        env_names) # by-column optimization only applies if mapping to same DB
112
    if test: cpus_default = 0
113
    else: cpus_default = 0 # or None to use parallel processing by default
114
    cpus = util.cast(int, util.none_if(opts.get_env_var('cpus', cpus_default,
115
        env_names), u''))
116
    
117
    # Set default verbosity. Must happen after by_col is set.
118
    if verbosity == None:
119
        if test: verbosity = 0.5 # automated tests should not be verbose
120
        elif by_col: verbosity = 3 # show all queries to assist profiling
121
        else: verbosity = 1.1 # just show row progress
122
    
123
    ##
124
    
125
    # Logging
126
    verbose_errors = test and verbosity > 0
127
    debug = verbosity >= 1.5
128
    def log(msg, level=1):
129
        '''Higher level -> more verbose'''
130
        if level <= verbosity:
131
            if verbosity <= 2:
132
                if level == 1.5: msg = '# '+msg # msg is Redmine list item
133
                elif msg.startswith('DB query:'): # remove extra debug info
134
                    first_line, nl, msg = msg.partition('\n')
135
            elif level > 1: msg = '['+str(level)+'] '+msg # include level in msg
136
            
137
            sys.stderr.write(strings.to_raw_str(msg.rstrip('\n')+'\n'))
138
    if debug: log_debug = lambda msg, level=2: log(msg, level)
139
    else: log_debug = sql.log_debug_none
140
    
141
    # Parse args
142
    map_paths = sys.argv[1:]
143
    if map_paths == []:
144
        if in_is_db or not out_is_db: usage_err()
145
        else: map_paths = [None]
146
    
147
    def connect_db(db_config):
148
        log('Connecting to '+sql.db_config_str(db_config))
149
        return sql.connect(db_config, caching=cache_sql, autocommit=commit,
150
            debug_temp=verbosity > 3 and commit, log_debug=log_debug)
151
    
152
    if end != None: end_str = str(end-1) # end is one past the last #
153
    else: end_str = 'end'
154
    log('Processing input rows '+str(start)+'-'+end_str)
155
    
156
    ex_tracker = exc.ExPercentTracker(iter_text='row')
157
    profiler = profiling.ItersProfiler(start_now=True, iter_text='row')
158
    
159
    # Parallel processing
160
    pool = parallelproc.MultiProducerPool(cpus)
161
    log('Using '+str(pool.process_ct)+' parallel CPUs')
162
    
163
    # Set up DB access
164
    row_ins_ct_ref = [0]
165
    if out_is_db:
166
        out_db = connect_db(out_db_config)
167
        def is_rel_func(name):
168
            return (name in db_xml.put_special_funcs
169
                or sql.function_exists(out_db, sql_gen.Function(name)))
170
    
171
    doc = xml_dom.create_doc()
172
    root = doc.documentElement
173
    out_is_xml_ref = [False]
174
    
175
    in_label_ref = [None]
176
    col_defaults = {}
177
    def update_in_label():
178
        if in_label_ref[0] != None and out_is_db:
179
            # TODO: Move this to the mappings as some kind of metadata
180
            col_defaults['datasource_id'] = db_xml.put(out_db, xpath.path2xml(
181
                'party/organizationname="'+in_label_ref[0]+'"'), row_ins_ct_ref)
182
    
183
    def prep_root():
184
        root.clear()
185
        update_in_label()
186
    prep_root()
187
    
188
    def process_input(root, row_ready, map_path):
189
        '''Inputs datasource to XML tree, mapping if needed'''
190
        # Load map header
191
        in_is_xpaths = True
192
        out_is_xpaths = True
193
        out_label = None
194
        if map_path != None:
195
            metadata = []
196
            mappings = []
197
            stream = open(map_path, 'rb')
198
            reader = csv.reader(stream)
199
            in_label, out_label = reader.next()[:2]
200
            
201
            def split_col_name(name):
202
                label, sep, root = name.partition(':')
203
                return label, sep != '', root, []
204
            
205
            in_label, in_root, prefixes = maps.col_info(in_label)
206
            in_is_xpaths = in_root != None
207
            in_label_ref[0] = in_label
208
            update_in_label()
209
            out_label, out_root = maps.col_info(out_label)[:2]
210
            out_is_xpaths = out_root != None
211
            if out_is_xpaths: has_types = out_root.find('/*s/') >= 0
212
                # outer elements are types
213
            
214
            for row in reader:
215
                in_, out = row[:2]
216
                if out != '': mappings.append([in_, out_root+out])
217
            
218
            stream.close()
219
            
220
            root.ownerDocument.documentElement.tagName = out_label
221
        in_is_xml = in_is_xpaths and not in_is_db
222
        out_is_xml_ref[0] = out_is_xpaths and not out_is_db
223
        
224
        def process_rows(process_row, rows, rows_start=0):
225
            '''Processes input rows
226
            @param process_row(in_row, i)
227
            @rows_start The (0-based) row # of the first row in rows. Set this
228
                only if the pre-start rows have already been skipped.
229
            '''
230
            rows = iter(rows)
231
            
232
            if end != None: row_nums = xrange(rows_start, end)
233
            else: row_nums = itertools.count(rows_start)
234
            i = -1
235
            for i in row_nums:
236
                try: row = rows.next()
237
                except StopIteration:
238
                    i -= 1 # last row # didn't count
239
                    break # no more rows
240
                if i < start: continue # not at start row yet
241
                
242
                # Row # is interally 0-based, but 1-based to the user
243
                log('Processing input row #'+str(i+1), level=1.1)
244
                process_row(row, i)
245
                row_ready(i, row)
246
            row_ct = i-start+1
247
            return row_ct
248
        
249
        def map_rows(get_value, rows, **kw_args):
250
            '''Maps input rows
251
            @param get_value(in_, row):str
252
            '''
253
            # Prevent collisions if multiple inputs mapping to same output
254
            outputs_idxs = dict()
255
            for i, mapping in enumerate(mappings):
256
                in_, out = mapping
257
                default = util.NamedTuple(count=1, first=i)
258
                idxs = outputs_idxs.setdefault(out, default)
259
                if idxs is not default: # key existed, so there was a collision
260
                    if idxs.count == 1: # first key does not yet have suffix
261
                        mappings[idxs.first][1] += collision_suffix+'0'
262
                    mappings[i][1] += collision_suffix+str(idxs.count)
263
                    idxs.count += 1
264
            
265
            id_node = None
266
            if out_is_db:
267
                for i, mapping in enumerate(mappings):
268
                    in_, out = mapping
269
                    # All put_obj()s should return the same id_node
270
                    nodes, id_node = xpath.put_obj(root, out, '-1', has_types,
271
                        '$'+strings.ustr(in_))
272
                        # value is placeholder that documents name
273
                    mappings[i] = [in_, nodes]
274
                if id_node == None:
275
                    warnings.warn(UserWarning('Map warning: No mappings'))
276
                xml_func.simplify(root)
277
                sys.stdout.write(strings.to_raw_str('Put template:\n'
278
                    +strings.ustr(root)))
279
                sys.stdout.flush()
280
            
281
            def process_row(row, i):
282
                row_id = str(i)
283
                if id_node != None: xml_dom.set_value(id_node, row_id)
284
                for in_, out in mappings:
285
                    log_debug('Getting '+strings.ustr(in_))
286
                    value = metadata_value(in_)
287
                    if value == None: value = cleanup(get_value(in_, row))
288
                    log_debug('Putting '+strings.urepr(value)+' to '
289
                        +strings.ustr(out))
290
                    if out_is_db: # out is list of XML nodes
291
                        for node in out: xml_dom.set_value(node, value)
292
                    elif value != None: # out is XPath
293
                        xpath.put_obj(root, out, row_id, has_types, value)
294
            return process_rows(process_row, rows, **kw_args)
295
        
296
        def map_table(col_names, rows, **kw_args):
297
            col_names_ct = len(col_names)
298
            col_idxs = util.list_flip(col_names)
299
            col_names_simp = map(maps.simplify, col_names)
300
            col_names_map = dict(zip(col_names_simp, col_names))
301
            prefixes_simp = map(maps.simplify, prefixes)
302
            
303
            # Resolve prefixes
304
            mappings_orig = mappings[:] # save a copy
305
            mappings[:] = [] # empty existing elements
306
            for in_, out in mappings_orig:
307
                if metadata_value(in_) == None:
308
                    try:
309
                        cols = get_with_prefix(col_names_map, prefixes_simp,
310
                            maps.simplify(in_))
311
                    except KeyError: pass
312
                    else:
313
                        cols = [(orig, col_idxs[orig]) for simp, orig in cols]
314
                        mappings[len(mappings):] = [[db_xml.ColRef(*col), out]
315
                            for col in cols] # can't use += because that uses =
316
            
317
            def get_value(in_, row): return row.list[in_.idx]
318
            def wrap_row(row):
319
                return util.ListDict(util.list_as_length(row, col_names_ct),
320
                    col_names, col_idxs) # handle CSV rows of different lengths
321
            
322
            return map_rows(get_value, util.WrapIter(wrap_row, rows), **kw_args)
323
        
324
        if in_is_db:
325
            def on_error(e): ex_tracker.track(e)
326
            
327
            if by_col: in_db = out_db
328
            else: in_db = connect_db(in_db_config)
329
            
330
            # Get table and schema name
331
            schema = in_schema # modified, so can't have same name as outer var
332
            table = in_table # modified, so can't have same name as outer var
333
            if table == None:
334
                assert in_is_xpaths
335
                schema, sep, table = in_root.partition('.')
336
                if sep == '': # only the table name was specified
337
                    table = schema
338
                    schema = None
339
            table = sql_gen.Table(table, schema)
340
            
341
            # Fetch rows
342
            if by_col: limit = 0 # only fetch column names
343
            else: limit = n
344
            cur = sql.select(in_db, table, limit=limit, start=start,
345
                cacheable=False)
346
            col_names = list(sql.col_names(cur))
347
            
348
            if by_col:
349
                map_table(col_names, []) # just create the template
350
                
351
                if start == 0 and n == None: # doing full re-import
352
                    log('Clearing errors table')
353
                    errors_table_ = sql_io.errors_table(in_db, table)
354
                    if errors_table_ != None:
355
                        sql.drop_table(in_db, errors_table_)
356
                
357
                # Strip XML functions not in the DB
358
                xml_func.process(root, is_rel_func=is_rel_func)
359
                if debug: log_debug('Putting stripped:\n'+strings.ustr(root))
360
                    # only calc if debug
361
                
362
                # Import rows
363
                in_row_ct_ref = [0]
364
                db_xml.put_table(in_db, root.firstChild, table, in_row_ct_ref,
365
                    row_ins_ct_ref, n, start, on_error, col_defaults)
366
                row_ct = in_row_ct_ref[0]
367
            else:
368
                # Use normal by-row method
369
                row_ct = map_table(col_names, sql.rows(cur), rows_start=start)
370
                    # rows_start: pre-start rows have been skipped
371
                
372
                in_db.db.close()
373
        elif in_is_xml:
374
            stdin = streams.LineCountStream(sys.stdin)
375
            def on_error(e):
376
                exc.add_msg(e, term.emph('input line #:')+' '
377
                    +str(stdin.line_num))
378
                ex_tracker.track(e)
379
            
380
            def get_rows(doc2rows):
381
                return iters.flatten(itertools.imap(doc2rows,
382
                    xml_parse.docs_iter(stdin, on_error)))
383
            
384
            if map_path == None:
385
                def doc2rows(in_xml_root):
386
                    iter_ = xml_dom.NodeElemIter(in_xml_root)
387
                    util.skip(iter_, xml_dom.is_text) # skip metadata
388
                    return iter_
389
                
390
                row_ct = process_rows(lambda row, i: root.appendChild(row),
391
                    get_rows(doc2rows))
392
            else:
393
                def doc2rows(in_xml_root):
394
                    rows = xpath.get(in_xml_root, in_root, limit=end)
395
                    if rows == []: warnings.warn(UserWarning('Map warning: '
396
                        'Root "'+in_root+'" not found in input'))
397
                    return rows
398
                
399
                def get_value(in_, row):
400
                    in_ = './{'+(','.join(strings.with_prefixes(
401
                        ['']+prefixes, in_)))+'}' # also with no prefix
402
                    nodes = xpath.get(row, in_, allow_rooted=False)
403
                    if nodes != []: return xml_dom.value(nodes[0])
404
                    else: return None
405
                
406
                row_ct = map_rows(get_value, get_rows(doc2rows))
407
        else: # input is CSV
408
            reader, col_names = csvs.reader_and_header(sys.stdin)
409
            row_ct = map_table(col_names, reader)
410
        
411
        return row_ct
412
    
413
    def process_inputs(root, row_ready):
414
        row_ct = 0
415
        for map_path in map_paths:
416
            row_ct += process_input(root, row_ready, map_path)
417
        return row_ct
418
    
419
    pool.share_vars(locals())
420
    if out_is_db:
421
        try:
422
            if redo: sql.empty_db(out_db)
423
            pool.share_vars(locals())
424
            
425
            def row_ready(row_num, input_row):
426
                row_str_ = [None]
427
                def row_str():
428
                    if row_str_[0] == None:
429
                        # Row # is interally 0-based, but 1-based to the user
430
                        row_str_[0] = (term.emph('row #:')+' '+str(row_num+1)
431
                            +'\n'+term.emph('input row:')+'\n'
432
                            +strings.ustr(input_row))
433
                        if verbose_errors: row_str_[0] += ('\n'
434
                            +term.emph('output row:')+'\n'+strings.ustr(root))
435
                    return row_str_[0]
436
                
437
                if debug: log_debug(row_str()) # only calc if debug
438
                
439
                def on_error(e):
440
                    exc.add_msg(e, row_str())
441
                    ex_tracker.track(e, row_num, detail=verbose_errors)
442
                pool.share_vars(locals())
443
                
444
                row_root = root.cloneNode(True) # deep copy so don't modify root
445
                xml_func.process(row_root, on_error, is_rel_func, out_db)
446
                if debug: log_debug('Putting processed:\n'
447
                    +strings.ustr(row_root)) # only calc if debug
448
                if not xml_dom.is_empty(row_root):
449
                    assert xml_dom.has_one_child(row_root)
450
                    try:
451
                        sql.with_savepoint(out_db,
452
                            lambda: db_xml.put(out_db, row_root.firstChild,
453
                                row_ins_ct_ref, on_error, col_defaults))
454
                    except sql.DatabaseErrors, e: on_error(e)
455
            
456
            row_ct = process_inputs(root, row_ready)
457
            sys.stdout.write('Inserted '+str(row_ins_ct_ref[0])+
458
                ' new rows into database\n')
459
            sys.stdout.flush()
460
            
461
            # Consume asynchronous tasks
462
            pool.main_loop()
463
        finally: out_db.close()
464
    else:
465
        def on_error(e): ex_tracker.track(e)
466
        def row_ready(row_num, input_row): pass
467
        row_ct = process_inputs(root, row_ready)
468
        xml_func.process(root, on_error)
469
        if out_is_xml_ref[0]:
470
            doc.writexml(sys.stdout, **xml_dom.prettyxml_config)
471
        else: # output is CSV
472
            raise NotImplementedError('CSV output not supported yet')
473
    
474
    # Consume any asynchronous tasks not already consumed above
475
    pool.main_loop()
476
    
477
    profiler.stop(row_ct)
478
    if not by_col: ex_tracker.add_iters(row_ct) # only if errors are done by row
479
    log('Processed '+str(row_ct)+' input rows')
480
    log(profiler.msg())
481
    log(ex_tracker.msg())
482
    ex_tracker.exit()
483

    
484
def main():
485
    try: main_()
486
    except Parser.SyntaxError, e: raise SystemExit(strings.ustr(e))
487

    
488
if __name__ == '__main__':
489
    profile_to = opts.get_env_var('profile_to', None)
490
    if profile_to != None:
491
        import cProfile
492
        sys.stderr.write('Profiling to '+profile_to+'\n')
493
        cProfile.run(main.func_code, profile_to)
494
    else: main()
(35-35/63)