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:
173
            xpath.get(root, '/_ignore/inLabel="'+in_label_ref[0]+'"', True)
174
            if out_is_db:
175
                # TODO: Move this to the mappings as some kind of metadata
176
                col_defaults['datasource_id'] = db_xml.put(out_db,
177
                    xpath.path2xml('party/organizationname="'+in_label_ref[0]
178
                        +'"'), row_ins_ct_ref)
179
    
180
    def prep_root():
181
        root.clear()
182
        update_in_label()
183
    prep_root()
184
    
185
    def process_input(root, row_ready, map_path):
186
        '''Inputs datasource to XML tree, mapping if needed'''
187
        # Load map header
188
        in_is_xpaths = True
189
        out_is_xpaths = True
190
        out_label = None
191
        if map_path != None:
192
            metadata = []
193
            mappings = []
194
            stream = open(map_path, 'rb')
195
            reader = csv.reader(stream)
196
            in_label, out_label = reader.next()[:2]
197
            
198
            def split_col_name(name):
199
                label, sep, root = name.partition(':')
200
                label, sep2, prefixes_str = label.partition('[')
201
                prefixes_str = strings.remove_suffix(']', prefixes_str)
202
                prefixes = strings.split(',', prefixes_str)
203
                return label, sep != '', root, prefixes
204
                    # extract datasrc from "datasrc[data_format]"
205
            
206
            in_label, in_root, prefixes = maps.col_info(in_label)
207
            in_is_xpaths = in_root != None
208
            in_label_ref[0] = in_label
209
            update_in_label()
210
            out_label, out_root = maps.col_info(out_label)[:2]
211
            out_is_xpaths = out_root != None
212
            if out_is_xpaths: has_types = out_root.find('/*s/') >= 0
213
                # outer elements are types
214
            
215
            for row in reader:
216
                in_, out = row[:2]
217
                if out != '': mappings.append([in_, out_root+out])
218
            
219
            stream.close()
220
            
221
            root.ownerDocument.documentElement.tagName = out_label
222
        in_is_xml = in_is_xpaths and not in_is_db
223
        out_is_xml_ref[0] = out_is_xpaths and not out_is_db
224
        
225
        def process_rows(process_row, rows, rows_start=0):
226
            '''Processes input rows      
227
            @param process_row(in_row, i)
228
            @rows_start The (0-based) row # of the first row in rows. Set this
229
                only if the pre-start rows have already been skipped.
230
            '''
231
            rows = iter(rows)
232
            
233
            if end != None: row_nums = xrange(rows_start, end)
234
            else: row_nums = itertools.count(rows_start)
235
            i = -1
236
            for i in row_nums:
237
                try: row = rows.next()
238
                except StopIteration:
239
                    i -= 1 # last row # didn't count
240
                    break # no more rows
241
                if i < start: continue # not at start row yet
242
                
243
                # Row # is interally 0-based, but 1-based to the user
244
                log('Processing input row #'+str(i+1), level=1.1)
245
                process_row(row, i)
246
                row_ready(i, row)
247
            row_ct = i-start+1
248
            return row_ct
249
        
250
        def map_rows(get_value, rows, **kw_args):
251
            '''Maps input rows
252
            @param get_value(in_, row):str
253
            '''
254
            # Prevent collisions if multiple inputs mapping to same output
255
            outputs_idxs = dict()
256
            for i, mapping in enumerate(mappings):
257
                in_, out = mapping
258
                default = util.NamedTuple(count=1, first=i)
259
                idxs = outputs_idxs.setdefault(out, default)
260
                if idxs is not default: # key existed, so there was a collision
261
                    if idxs.count == 1: # first key does not yet have /_alt/#
262
                        mappings[idxs.first][1] += '/_alt/0'
263
                    mappings[i][1] += '/_alt/'+str(idxs.count)
264
                    idxs.count += 1
265
            
266
            id_node = None
267
            if out_is_db:
268
                for i, mapping in enumerate(mappings):
269
                    in_, out = mapping
270
                    # All put_obj()s should return the same id_node
271
                    nodes, id_node = xpath.put_obj(root, out, '-1', has_types,
272
                        '$'+str(in_)) # 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
                sys.stdout.write('Put template:\n'+str(root))
277
                sys.stdout.flush()
278
            
279
            def process_row(row, i):
280
                row_id = str(i)
281
                if id_node != None: xml_dom.set_value(id_node, row_id)
282
                for in_, out in mappings:
283
                    log_debug('Getting '+str(in_))
284
                    value = metadata_value(in_)
285
                    if value == None: value = cleanup(get_value(in_, row))
286
                    log_debug('Putting '+repr(value)+' to '+str(out))
287
                    if out_is_db: # out is list of XML nodes
288
                        for node in out: xml_dom.set_value(node, value)
289
                    elif value != None: # out is XPath
290
                        xpath.put_obj(root, out, row_id, has_types, value)
291
            return process_rows(process_row, rows, **kw_args)
292
        
293
        def map_table(col_names, rows, **kw_args):
294
            col_names_ct = len(col_names)
295
            col_idxs = util.list_flip(col_names)
296
            
297
            # Resolve prefixes
298
            mappings_orig = mappings[:] # save a copy
299
            mappings[:] = [] # empty existing elements
300
            for in_, out in mappings_orig:
301
                if metadata_value(in_) == None:
302
                    try: cols = get_with_prefix(col_idxs, prefixes, in_)
303
                    except KeyError: pass
304
                    else: mappings[len(mappings):] = [[db_xml.ColRef(*col), out]
305
                        for col in cols] # can't use += because that uses =
306
            
307
            def get_value(in_, row): return row.list[in_.idx]
308
            def wrap_row(row):
309
                return util.ListDict(util.list_as_length(row, col_names_ct),
310
                    col_names, col_idxs) # handle CSV rows of different lengths
311
            
312
            return map_rows(get_value, util.WrapIter(wrap_row, rows), **kw_args)
313
        
314
        if in_is_db:
315
            def on_error(e): ex_tracker.track(e)
316
            
317
            if by_col: in_db = out_db
318
            else: in_db = connect_db(in_db_config)
319
            
320
            # Get table and schema name
321
            schema = in_schema # modified, so can't have same name as outer var
322
            table = in_table # modified, so can't have same name as outer var
323
            if table == None:
324
                assert in_is_xpaths
325
                schema, sep, table = in_root.partition('.')
326
                if sep == '': # only the table name was specified
327
                    table = schema
328
                    schema = None
329
            table = sql_gen.Table(table, schema)
330
            
331
            # Fetch rows
332
            if by_col: limit = 0 # only fetch column names
333
            else: limit = n
334
            cur = sql.select(in_db, table, limit=limit, start=start,
335
                cacheable=False)
336
            col_names = list(sql.col_names(cur))
337
            
338
            if by_col:
339
                map_table(col_names, []) # just create the template
340
                
341
                if start == 0 and n == None: # doing full re-import
342
                    log('Clearing errors table')
343
                    sql.truncate(in_db, sql_io.errors_table(in_db, table))
344
                
345
                # Strip XML functions not in the DB
346
                xml_func.process(root, is_rel_func=is_rel_func)
347
                if debug: log_debug('Putting stripped:\n'+str(root))
348
                    # only calc if debug
349
                
350
                # Import rows
351
                in_row_ct_ref = [0]
352
                db_xml.put_table(in_db, root.firstChild, table, in_row_ct_ref,
353
                    row_ins_ct_ref, n, start, on_error, col_defaults)
354
                row_ct = in_row_ct_ref[0]
355
            else:
356
                # Use normal by-row method
357
                row_ct = map_table(col_names, sql.rows(cur), rows_start=start)
358
                    # rows_start: pre-start rows have been skipped
359
                
360
                in_db.db.close()
361
        elif in_is_xml:
362
            stdin = streams.LineCountStream(sys.stdin)
363
            def on_error(e):
364
                exc.add_msg(e, term.emph('input line #:')+' '
365
                    +str(stdin.line_num))
366
                ex_tracker.track(e)
367
            
368
            def get_rows(doc2rows):
369
                return iters.flatten(itertools.imap(doc2rows,
370
                    xml_parse.docs_iter(stdin, on_error)))
371
            
372
            if map_path == None:
373
                def doc2rows(in_xml_root):
374
                    iter_ = xml_dom.NodeElemIter(in_xml_root)
375
                    util.skip(iter_, xml_dom.is_text) # skip metadata
376
                    return iter_
377
                
378
                row_ct = process_rows(lambda row, i: root.appendChild(row),
379
                    get_rows(doc2rows))
380
            else:
381
                def doc2rows(in_xml_root):
382
                    rows = xpath.get(in_xml_root, in_root, limit=end)
383
                    if rows == []: warnings.warn(UserWarning('Map warning: '
384
                        'Root "'+in_root+'" not found in input'))
385
                    return rows
386
                
387
                def get_value(in_, row):
388
                    in_ = './{'+(','.join(strings.with_prefixes(
389
                        ['']+prefixes, in_)))+'}' # also with no prefix
390
                    nodes = xpath.get(row, in_, allow_rooted=False)
391
                    if nodes != []: return xml_dom.value(nodes[0])
392
                    else: return None
393
                
394
                row_ct = map_rows(get_value, get_rows(doc2rows))
395
        else: # input is CSV
396
            map_ = dict(mappings)
397
            reader, col_names = csvs.reader_and_header(sys.stdin)
398
            row_ct = map_table(col_names, reader)
399
        
400
        return row_ct
401
    
402
    def process_inputs(root, row_ready):
403
        row_ct = 0
404
        for map_path in map_paths:
405
            row_ct += process_input(root, row_ready, map_path)
406
        return row_ct
407
    
408
    pool.share_vars(locals())
409
    if out_is_db:
410
        try:
411
            if redo: sql.empty_db(out_db)
412
            pool.share_vars(locals())
413
            
414
            def row_ready(row_num, input_row):
415
                row_str_ = [None]
416
                def row_str():
417
                    if row_str_[0] == None:
418
                        # Row # is interally 0-based, but 1-based to the user
419
                        row_str_[0] = (term.emph('row #:')+' '+str(row_num+1)
420
                            +'\n'+term.emph('input row:')+'\n'+str(input_row))
421
                        if verbose_errors: row_str_[0] += ('\n'
422
                            +term.emph('output row:')+'\n'+str(root))
423
                    return row_str_[0]
424
                
425
                if debug: log_debug(row_str()) # only calc if debug
426
                
427
                def on_error(e):
428
                    exc.add_msg(e, row_str())
429
                    ex_tracker.track(e, row_num, detail=verbose_errors)
430
                pool.share_vars(locals())
431
                
432
                row_root = root.cloneNode(True) # deep copy so don't modify root
433
                xml_func.process(row_root, on_error, is_rel_func, out_db)
434
                if not xml_dom.is_empty(row_root):
435
                    assert xml_dom.has_one_child(row_root)
436
                    try:
437
                        sql.with_savepoint(out_db,
438
                            lambda: db_xml.put(out_db, row_root.firstChild,
439
                                row_ins_ct_ref, on_error, col_defaults))
440
                    except sql.DatabaseErrors, e: on_error(e)
441
            
442
            row_ct = process_inputs(root, row_ready)
443
            sys.stdout.write('Inserted '+str(row_ins_ct_ref[0])+
444
                ' new rows into database\n')
445
            sys.stdout.flush()
446
            
447
            # Consume asynchronous tasks
448
            pool.main_loop()
449
        finally: out_db.close()
450
    else:
451
        def on_error(e): ex_tracker.track(e)
452
        def row_ready(row_num, input_row): pass
453
        row_ct = process_inputs(root, row_ready)
454
        xml_func.process(root, on_error)
455
        if out_is_xml_ref[0]:
456
            doc.writexml(sys.stdout, **xml_dom.prettyxml_config)
457
        else: # output is CSV
458
            raise NotImplementedError('CSV output not supported yet')
459
    
460
    # Consume any asynchronous tasks not already consumed above
461
    pool.main_loop()
462
    
463
    profiler.stop(row_ct)
464
    if not by_col: ex_tracker.add_iters(row_ct) # only if errors are done by row
465
    log('Processed '+str(row_ct)+' input rows')
466
    log(profiler.msg())
467
    log(ex_tracker.msg())
468
    ex_tracker.exit()
469

    
470
def main():
471
    try: main_()
472
    except Parser.SyntaxError, e: raise SystemExit(str(e))
473

    
474
if __name__ == '__main__':
475
    profile_to = opts.get_env_var('profile_to', None)
476
    if profile_to != None:
477
        import cProfile
478
        sys.stderr.write('Profiling to '+profile_to+'\n')
479
        cProfile.run(main.func_code, profile_to)
480
    else: main()
(26-26/52)