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
# 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 copy
8
import csv
9
import itertools
10
import os.path
11
import warnings
12
import sys
13
import xml.dom.minidom as minidom
14

    
15
sys.path.append(os.path.dirname(__file__)+"/../lib")
16

    
17
import csvs
18
import db_xml
19
import exc
20
import iters
21
import maps
22
import opts
23
import parallelproc
24
import Parser
25
import profiling
26
import sql
27
import sql_gen
28
import sql_io
29
import streams
30
import strings
31
import term
32
import util
33
import xpath
34
import xml_dom
35
import xml_func
36
import xml_parse
37

    
38
def get_with_prefix(map_, prefixes, key):
39
    '''Gets all entries for the given key with any of the given prefixes
40
    @return tuple(found_key, found_value)
41
    '''
42
    values = []
43
    for key_ in strings.with_prefixes(['']+prefixes, key): # also with no prefix
44
        try: value = map_[key_]
45
        except KeyError, e: continue # keep going
46
        values.append((key_, value))
47
    
48
    if values != []: return values
49
    else: raise e # re-raise last KeyError
50

    
51
def metadata_value(name): return None # this feature has been removed
52

    
53
def cleanup(val):
54
    if val == None: return val
55
    return util.none_if(strings.cleanup(strings.ustr(val)), u'', u'\\N')
56

    
57
def main_():
58
    env_names = []
59
    def usage_err():
60
        raise SystemExit('Usage: '+opts.env_usage(env_names, True)+' '
61
            +sys.argv[0]+' [map_path...] [<input] [>output]\n'
62
            'Note: Row #s start with 1')
63
    
64
    ## Get config from env vars
65
    
66
    # Modes
67
    test = opts.env_flag('test', False, env_names)
68
    commit = opts.env_flag('commit', False, env_names) and not test
69
        # never commit in test mode
70
    redo = opts.env_flag('redo', test, env_names) and not commit
71
        # never redo in commit mode (run `make schemas/reinstall` instead)
72
    
73
    # Ranges
74
    start = util.cast(int, opts.get_env_var('start', 1, env_names)) # 1-based
75
    # Make start interally 0-based.
76
    # It's 1-based to the user to match up with the staging table row #s.
77
    start -= 1
78
    if test: n_default = 1
79
    else: n_default = None
80
    n = util.cast(int, util.none_if(opts.get_env_var('n', n_default, env_names),
81
        u''))
82
    end = n
83
    if end != None: end += start
84
    
85
    # Debugging
86
    verbosity = util.cast(float, opts.get_env_var('verbosity', None, 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
    if in_schema != None:
99
        for config in [in_db_config, out_db_config]:
100
            config['schemas'] += ','+in_schema
101
    
102
    # Optimization
103
    cache_sql = opts.env_flag('cache_sql', True, env_names)
104
    by_col = in_db_config == out_db_config and opts.env_flag('by_col', False,
105
        env_names) # by-column optimization only applies if mapping to same DB
106
    if test: cpus_default = 0
107
    else: cpus_default = 0 # or None to use parallel processing by default
108
    cpus = util.cast(int, util.none_if(opts.get_env_var('cpus', cpus_default,
109
        env_names), u''))
110
    
111
    # Set default verbosity. Must happen after by_col is set.
112
    if verbosity == None: 
113
        if test: verbosity = 0.5 # automated tests should not be verbose
114
        elif by_col: verbosity = 3 # show all queries to assist profiling
115
        else: verbosity = 1.1 # just show row progress
116
    
117
    ##
118
    
119
    # Logging
120
    verbose_errors = test and verbosity > 0
121
    debug = verbosity >= 1.5
122
    def log(msg, level=1):
123
        '''Higher level -> more verbose'''
124
        if level <= verbosity:
125
            if verbosity <= 2:
126
                if level == 1.5: msg = '# '+msg # msg is Redmine list item
127
                elif msg.startswith('DB query:'): # remove extra debug info
128
                    first_line, nl, msg = msg.partition('\n')
129
            elif level > 1: msg = '['+str(level)+'] '+msg # include level in msg
130
            
131
            sys.stderr.write(strings.to_raw_str(msg.rstrip('\n')+'\n'))
132
    if debug: log_debug = lambda msg, level=2: log(msg, level)
133
    else: log_debug = sql.log_debug_none
134
    
135
    # Parse args
136
    map_paths = sys.argv[1:]
137
    if map_paths == []:
138
        if in_is_db or not out_is_db: usage_err()
139
        else: map_paths = [None]
140
    
141
    def connect_db(db_config):
142
        log('Connecting to '+sql.db_config_str(db_config))
143
        return sql.connect(db_config, caching=cache_sql, autocommit=commit,
144
            debug_temp=verbosity > 3 and commit, log_debug=log_debug)
145
    
146
    if end != None: end_str = str(end-1) # end is one past the last #
147
    else: end_str = 'end'
148
    log('Processing input rows '+str(start)+'-'+end_str)
149
    
150
    ex_tracker = exc.ExPercentTracker(iter_text='row')
151
    profiler = profiling.ItersProfiler(start_now=True, iter_text='row')
152
    
153
    # Parallel processing
154
    pool = parallelproc.MultiProducerPool(cpus)
155
    log('Using '+str(pool.process_ct)+' parallel CPUs')
156
    
157
    # Set up DB access
158
    row_ins_ct_ref = [0]
159
    if out_is_db:
160
        out_db = connect_db(out_db_config)
161
        def is_rel_func(name):
162
            return (name in db_xml.put_special_funcs
163
                or sql.function_exists(out_db, sql_gen.Function(name)))
164
    
165
    doc = xml_dom.create_doc()
166
    root = doc.documentElement
167
    out_is_xml_ref = [False]
168
    
169
    in_label_ref = [None]
170
    col_defaults = {}
171
    def update_in_label():
172
        if in_label_ref[0] != None and out_is_db:
173
            # TODO: Move this to the mappings as some kind of metadata
174
            col_defaults['datasource_id'] = db_xml.put(out_db, xpath.path2xml(
175
                'party/organizationname="'+in_label_ref[0]+'"'), row_ins_ct_ref)
176
    
177
    def prep_root():
178
        root.clear()
179
        update_in_label()
180
    prep_root()
181
    
182
    def process_input(root, row_ready, map_path):
183
        '''Inputs datasource to XML tree, mapping if needed'''
184
        # Load map header
185
        in_is_xpaths = True
186
        out_is_xpaths = True
187
        out_label = None
188
        if map_path != None:
189
            metadata = []
190
            mappings = []
191
            stream = open(map_path, 'rb')
192
            reader = csv.reader(stream)
193
            in_label, out_label = reader.next()[:2]
194
            
195
            def split_col_name(name):
196
                label, sep, root = name.partition(':')
197
                label, sep2, prefixes_str = label.partition('[')
198
                prefixes_str = strings.remove_suffix(']', prefixes_str)
199
                prefixes = strings.split(',', prefixes_str)
200
                return label, sep != '', root, prefixes
201
                    # extract datasrc from "datasrc[data_format]"
202
            
203
            in_label, in_root, prefixes = maps.col_info(in_label)
204
            in_is_xpaths = in_root != None
205
            in_label_ref[0] = in_label
206
            update_in_label()
207
            out_label, out_root = maps.col_info(out_label)[:2]
208
            out_is_xpaths = out_root != None
209
            if out_is_xpaths: has_types = out_root.find('/*s/') >= 0
210
                # outer elements are types
211
            
212
            for row in reader:
213
                in_, out = row[:2]
214
                if out != '': mappings.append([in_, out_root+out])
215
            
216
            stream.close()
217
            
218
            root.ownerDocument.documentElement.tagName = out_label
219
        in_is_xml = in_is_xpaths and not in_is_db
220
        out_is_xml_ref[0] = out_is_xpaths and not out_is_db
221
        
222
        def process_rows(process_row, rows, rows_start=0):
223
            '''Processes input rows      
224
            @param process_row(in_row, i)
225
            @rows_start The (0-based) row # of the first row in rows. Set this
226
                only if the pre-start rows have already been skipped.
227
            '''
228
            rows = iter(rows)
229
            
230
            if end != None: row_nums = xrange(rows_start, end)
231
            else: row_nums = itertools.count(rows_start)
232
            i = -1
233
            for i in row_nums:
234
                try: row = rows.next()
235
                except StopIteration:
236
                    i -= 1 # last row # didn't count
237
                    break # no more rows
238
                if i < start: continue # not at start row yet
239
                
240
                # Row # is interally 0-based, but 1-based to the user
241
                log('Processing input row #'+str(i+1), level=1.1)
242
                process_row(row, i)
243
                row_ready(i, row)
244
            row_ct = i-start+1
245
            return row_ct
246
        
247
        def map_rows(get_value, rows, **kw_args):
248
            '''Maps input rows
249
            @param get_value(in_, row):str
250
            '''
251
            # Prevent collisions if multiple inputs mapping to same output
252
            outputs_idxs = dict()
253
            for i, mapping in enumerate(mappings):
254
                in_, out = mapping
255
                default = util.NamedTuple(count=1, first=i)
256
                idxs = outputs_idxs.setdefault(out, default)
257
                if idxs is not default: # key existed, so there was a collision
258
                    if idxs.count == 1: # first key does not yet have /_alt/#
259
                        mappings[idxs.first][1] += '/_alt/0'
260
                    mappings[i][1] += '/_alt/'+str(idxs.count)
261
                    idxs.count += 1
262
            
263
            id_node = None
264
            if out_is_db:
265
                for i, mapping in enumerate(mappings):
266
                    in_, out = mapping
267
                    # All put_obj()s should return the same id_node
268
                    nodes, id_node = xpath.put_obj(root, out, '-1', has_types,
269
                        '$'+str(in_)) # value is placeholder that documents name
270
                    mappings[i] = [in_, nodes]
271
                if id_node == None:
272
                    warnings.warn(UserWarning('Map warning: No mappings'))                
273
                sys.stdout.write('Put template:\n'+str(root))
274
                sys.stdout.flush()
275
            
276
            def process_row(row, i):
277
                row_id = str(i)
278
                if id_node != None: xml_dom.set_value(id_node, row_id)
279
                for in_, out in mappings:
280
                    log_debug('Getting '+str(in_))
281
                    value = metadata_value(in_)
282
                    if value == None: value = cleanup(get_value(in_, row))
283
                    log_debug('Putting '+repr(value)+' to '+str(out))
284
                    if out_is_db: # out is list of XML nodes
285
                        for node in out: xml_dom.set_value(node, value)
286
                    elif value != None: # out is XPath
287
                        xpath.put_obj(root, out, row_id, has_types, value)
288
            return process_rows(process_row, rows, **kw_args)
289
        
290
        def map_table(col_names, rows, **kw_args):
291
            col_names_ct = len(col_names)
292
            col_idxs = util.list_flip(col_names)
293
            
294
            # Resolve prefixes
295
            mappings_orig = mappings[:] # save a copy
296
            mappings[:] = [] # empty existing elements
297
            for in_, out in mappings_orig:
298
                if metadata_value(in_) == None:
299
                    try: cols = get_with_prefix(col_idxs, prefixes, in_)
300
                    except KeyError: pass
301
                    else: mappings[len(mappings):] = [[db_xml.ColRef(*col), out]
302
                        for col in cols] # can't use += because that uses =
303
            
304
            def get_value(in_, row): return row.list[in_.idx]
305
            def wrap_row(row):
306
                return util.ListDict(util.list_as_length(row, col_names_ct),
307
                    col_names, col_idxs) # handle CSV rows of different lengths
308
            
309
            return map_rows(get_value, util.WrapIter(wrap_row, rows), **kw_args)
310
        
311
        if in_is_db:
312
            def on_error(e): ex_tracker.track(e)
313
            
314
            if by_col: in_db = out_db
315
            else: in_db = connect_db(in_db_config)
316
            
317
            # Get table and schema name
318
            schema = in_schema # modified, so can't have same name as outer var
319
            table = in_table # modified, so can't have same name as outer var
320
            if table == None:
321
                assert in_is_xpaths
322
                schema, sep, table = in_root.partition('.')
323
                if sep == '': # only the table name was specified
324
                    table = schema
325
                    schema = None
326
            table = sql_gen.Table(table, schema)
327
            
328
            # Fetch rows
329
            if by_col: limit = 0 # only fetch column names
330
            else: limit = n
331
            cur = sql.select(in_db, table, limit=limit, start=start,
332
                cacheable=False)
333
            col_names = list(sql.col_names(cur))
334
            
335
            if by_col:
336
                map_table(col_names, []) # just create the template
337
                
338
                if start == 0 and n == None: # doing full re-import
339
                    log('Clearing errors table')
340
                    sql.truncate(in_db, sql_io.errors_table(in_db, table))
341
                
342
                # Strip XML functions not in the DB
343
                xml_func.process(root, is_rel_func=is_rel_func)
344
                if debug: log_debug('Putting stripped:\n'+str(root))
345
                    # only calc if debug
346
                
347
                # Import rows
348
                in_row_ct_ref = [0]
349
                db_xml.put_table(in_db, root.firstChild, table, in_row_ct_ref,
350
                    row_ins_ct_ref, n, start, on_error, col_defaults)
351
                row_ct = in_row_ct_ref[0]
352
            else:
353
                # Use normal by-row method
354
                row_ct = map_table(col_names, sql.rows(cur), rows_start=start)
355
                    # rows_start: pre-start rows have been skipped
356
                
357
                in_db.db.close()
358
        elif in_is_xml:
359
            stdin = streams.LineCountStream(sys.stdin)
360
            def on_error(e):
361
                exc.add_msg(e, term.emph('input line #:')+' '
362
                    +str(stdin.line_num))
363
                ex_tracker.track(e)
364
            
365
            def get_rows(doc2rows):
366
                return iters.flatten(itertools.imap(doc2rows,
367
                    xml_parse.docs_iter(stdin, on_error)))
368
            
369
            if map_path == None:
370
                def doc2rows(in_xml_root):
371
                    iter_ = xml_dom.NodeElemIter(in_xml_root)
372
                    util.skip(iter_, xml_dom.is_text) # skip metadata
373
                    return iter_
374
                
375
                row_ct = process_rows(lambda row, i: root.appendChild(row),
376
                    get_rows(doc2rows))
377
            else:
378
                def doc2rows(in_xml_root):
379
                    rows = xpath.get(in_xml_root, in_root, limit=end)
380
                    if rows == []: warnings.warn(UserWarning('Map warning: '
381
                        'Root "'+in_root+'" not found in input'))
382
                    return rows
383
                
384
                def get_value(in_, row):
385
                    in_ = './{'+(','.join(strings.with_prefixes(
386
                        ['']+prefixes, in_)))+'}' # also with no prefix
387
                    nodes = xpath.get(row, in_, allow_rooted=False)
388
                    if nodes != []: return xml_dom.value(nodes[0])
389
                    else: return None
390
                
391
                row_ct = map_rows(get_value, get_rows(doc2rows))
392
        else: # input is CSV
393
            map_ = dict(mappings)
394
            reader, col_names = csvs.reader_and_header(sys.stdin)
395
            row_ct = map_table(col_names, reader)
396
        
397
        return row_ct
398
    
399
    def process_inputs(root, row_ready):
400
        row_ct = 0
401
        for map_path in map_paths:
402
            row_ct += process_input(root, row_ready, map_path)
403
        return row_ct
404
    
405
    pool.share_vars(locals())
406
    if out_is_db:
407
        try:
408
            if redo: sql.empty_db(out_db)
409
            pool.share_vars(locals())
410
            
411
            def row_ready(row_num, input_row):
412
                row_str_ = [None]
413
                def row_str():
414
                    if row_str_[0] == None:
415
                        # Row # is interally 0-based, but 1-based to the user
416
                        row_str_[0] = (term.emph('row #:')+' '+str(row_num+1)
417
                            +'\n'+term.emph('input row:')+'\n'+str(input_row))
418
                        if verbose_errors: row_str_[0] += ('\n'
419
                            +term.emph('output row:')+'\n'+str(root))
420
                    return row_str_[0]
421
                
422
                if debug: log_debug(row_str()) # only calc if debug
423
                
424
                def on_error(e):
425
                    exc.add_msg(e, row_str())
426
                    ex_tracker.track(e, row_num, detail=verbose_errors)
427
                pool.share_vars(locals())
428
                
429
                row_root = root.cloneNode(True) # deep copy so don't modify root
430
                xml_func.process(row_root, on_error, is_rel_func, out_db)
431
                if debug: log_debug('Putting processed:\n'+str(row_root))
432
                    # only calc if debug
433
                if not xml_dom.is_empty(row_root):
434
                    assert xml_dom.has_one_child(row_root)
435
                    try:
436
                        sql.with_savepoint(out_db,
437
                            lambda: db_xml.put(out_db, row_root.firstChild,
438
                                row_ins_ct_ref, on_error, col_defaults))
439
                    except sql.DatabaseErrors, e: on_error(e)
440
            
441
            row_ct = process_inputs(root, row_ready)
442
            sys.stdout.write('Inserted '+str(row_ins_ct_ref[0])+
443
                ' new rows into database\n')
444
            sys.stdout.flush()
445
            
446
            # Consume asynchronous tasks
447
            pool.main_loop()
448
        finally: out_db.close()
449
    else:
450
        def on_error(e): ex_tracker.track(e)
451
        def row_ready(row_num, input_row): pass
452
        row_ct = process_inputs(root, row_ready)
453
        xml_func.process(root, on_error)
454
        if out_is_xml_ref[0]:
455
            doc.writexml(sys.stdout, **xml_dom.prettyxml_config)
456
        else: # output is CSV
457
            raise NotImplementedError('CSV output not supported yet')
458
    
459
    # Consume any asynchronous tasks not already consumed above
460
    pool.main_loop()
461
    
462
    profiler.stop(row_ct)
463
    if not by_col: ex_tracker.add_iters(row_ct) # only if errors are done by row
464
    log('Processed '+str(row_ct)+' input rows')
465
    log(profiler.msg())
466
    log(ex_tracker.msg())
467
    ex_tracker.exit()
468

    
469
def main():
470
    try: main_()
471
    except Parser.SyntaxError, e: raise SystemExit(str(e))
472

    
473
if __name__ == '__main__':
474
    profile_to = opts.get_env_var('profile_to', None)
475
    if profile_to != None:
476
        import cProfile
477
        sys.stderr.write('Profiling to '+profile_to+'\n')
478
        cProfile.run(main.func_code, profile_to)
479
    else: main()
(26-26/52)