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 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 parallel
21
import Parser
22
import profiling
23
import sql
24
import streams
25
import strings
26
import term
27
import util
28
import xpath
29
import xml_dom
30
import xml_func
31
import xml_parse
32

    
33
def get_with_prefix(map_, prefixes, key):
34
    '''Gets all entries for the given key with any of the given prefixes'''
35
    values = []
36
    for key_ in strings.with_prefixes(['']+prefixes, key): # also with no prefix
37
        try: value = map_[key_]
38
        except KeyError, e: continue # keep going
39
        values.append(value)
40
    
41
    if values != []: return values
42
    else: raise e # re-raise last KeyError
43

    
44
def metadata_value(name): return None # this feature has been removed
45

    
46
def cleanup(val):
47
    if val == None: return val
48
    return util.none_if(strings.cleanup(strings.ustr(val)), u'', u'\\N')
49

    
50
def main_():
51
    env_names = []
52
    def usage_err():
53
        raise SystemExit('Usage: '+opts.env_usage(env_names, True)+' '
54
            +sys.argv[0]+' [map_path...] [<input] [>output]\n'
55
            'Note: Row #s start with 1')
56
    
57
    ## Get config from env vars
58
    
59
    # Modes
60
    test = opts.env_flag('test', False, env_names)
61
    commit = opts.env_flag('commit', False, env_names) and not test
62
        # never commit in test mode
63
    redo = opts.env_flag('redo', test, env_names) and not commit
64
        # never redo in commit mode (manually run `make empty_db` instead)
65
    
66
    # Ranges
67
    start = util.cast(int, opts.get_env_var('start', 1, env_names)) # 1-based
68
    # Make start interally 0-based.
69
    # It's 1-based to the user to match up with the staging table row #s.
70
    start -= 1
71
    if test: n_default = 1
72
    else: n_default = None
73
    n = util.cast(int, util.none_if(opts.get_env_var('n', n_default, env_names),
74
        u''))
75
    end = n
76
    if end != None: end += start
77
    
78
    # Debugging
79
    debug = opts.env_flag('debug', False, env_names)
80
    sql.run_raw_query.debug = debug
81
    verbose = debug or opts.env_flag('verbose', not test, env_names)
82
    opts.get_env_var('profile_to', None, env_names) # add to env_names
83
    
84
    # DB
85
    def get_db_config(prefix):
86
        return opts.get_env_vars(sql.db_config_names, prefix, env_names)
87
    in_db_config = get_db_config('in')
88
    out_db_config = get_db_config('out')
89
    in_is_db = 'engine' in in_db_config
90
    out_is_db = 'engine' in out_db_config
91
    in_schema = opts.get_env_var('in_schema', None, env_names)
92
    in_table = opts.get_env_var('in_table', None, env_names)
93
    
94
    # Optimization
95
    by_col = in_db_config == out_db_config and opts.env_flag('by_col', False,
96
        env_names) # by-column optimization only applies if mapping to same DB
97
    if test: cpus_default = 0
98
    else: cpus_default = None
99
    cpus = util.cast(int, util.none_if(opts.get_env_var('cpus', cpus_default,
100
        env_names), u''))
101
    
102
    ##
103
    
104
    # Logging
105
    def log(msg, on=verbose):
106
        if on: sys.stderr.write(msg+'\n')
107
    if debug: log_debug = lambda msg: log(msg, debug)
108
    else: log_debug = sql.log_debug_none
109
    
110
    # Parse args
111
    map_paths = sys.argv[1:]
112
    if map_paths == []:
113
        if in_is_db or not out_is_db: usage_err()
114
        else: map_paths = [None]
115
    
116
    def connect_db(db_config):
117
        log('Connecting to '+sql.db_config_str(db_config))
118
        return sql.connect(db_config, log_debug=log_debug)
119
    
120
    if end != None: end_str = str(end-1) # end is one past the last #
121
    else: end_str = 'end'
122
    log('Processing input rows '+str(start)+'-'+end_str)
123
    
124
    ex_tracker = exc.ExPercentTracker(iter_text='row')
125
    profiler = profiling.ItersProfiler(start_now=True, iter_text='row')
126
    
127
    # Parallel processing
128
    pool = parallel.MultiProducerPool(cpus)
129
    log('Using '+str(pool.process_ct)+' parallel CPUs')
130
    
131
    doc = xml_dom.create_doc()
132
    root = doc.documentElement
133
    out_is_xml_ref = [False]
134
    in_label_ref = [None]
135
    def update_in_label():
136
        if in_label_ref[0] != None:
137
            xpath.get(root, '/_ignore/inLabel="'+in_label_ref[0]+'"', True)
138
    def prep_root():
139
        root.clear()
140
        update_in_label()
141
    prep_root()
142
    
143
    # Define before the out_is_db section because it's used by by_col
144
    row_ins_ct_ref = [0]
145
    
146
    def process_input(root, row_ready, map_path):
147
        '''Inputs datasource to XML tree, mapping if needed'''
148
        # Load map header
149
        in_is_xpaths = True
150
        out_is_xpaths = True
151
        out_label = None
152
        if map_path != None:
153
            metadata = []
154
            mappings = []
155
            stream = open(map_path, 'rb')
156
            reader = csv.reader(stream)
157
            in_label, out_label = reader.next()[:2]
158
            
159
            def split_col_name(name):
160
                label, sep, root = name.partition(':')
161
                label, sep2, prefixes_str = label.partition('[')
162
                prefixes_str = strings.remove_suffix(']', prefixes_str)
163
                prefixes = strings.split(',', prefixes_str)
164
                return label, sep != '', root, prefixes
165
                    # extract datasrc from "datasrc[data_format]"
166
            
167
            in_label, in_root, prefixes = maps.col_info(in_label)
168
            in_is_xpaths = in_root != None
169
            in_label_ref[0] = in_label
170
            update_in_label()
171
            out_label, out_root = maps.col_info(out_label)[:2]
172
            out_is_xpaths = out_root != None
173
            if out_is_xpaths: has_types = out_root.find('/*s/') >= 0
174
                # outer elements are types
175
            
176
            for row in reader:
177
                in_, out = row[:2]
178
                if out != '':
179
                    if out_is_xpaths: out = xpath.parse(out_root+out)
180
                    mappings.append((in_, out))
181
            
182
            stream.close()
183
            
184
            root.ownerDocument.documentElement.tagName = out_label
185
        in_is_xml = in_is_xpaths and not in_is_db
186
        out_is_xml_ref[0] = out_is_xpaths and not out_is_db
187
        
188
        def process_rows(process_row, rows, rows_start=0):
189
            '''Processes input rows      
190
            @param process_row(in_row, i)
191
            @rows_start The (0-based) row # of the first row in rows. Set this
192
                only if the pre-start rows have already been skipped.
193
            '''
194
            rows = iter(rows)
195
            
196
            if end != None: row_nums = xrange(rows_start, end)
197
            else: row_nums = itertools.count(rows_start)
198
            for i in row_nums:
199
                try: row = rows.next()
200
                except StopIteration: break # no more rows
201
                if i < start: continue # not at start row yet
202
                
203
                process_row(row, i)
204
                row_ready(i, row)
205
            row_ct = i-start
206
            return row_ct
207
        
208
        def map_rows(get_value, rows, **kw_args):
209
            '''Maps input rows
210
            @param get_value(in_, row):str
211
            '''
212
            def process_row(row, i):
213
                row_id = str(i)
214
                for in_, out in mappings:
215
                    value = metadata_value(in_)
216
                    if value == None:
217
                        log_debug('Getting '+str(in_))
218
                        value = cleanup(get_value(in_, row))
219
                    if out_is_db or value != None:
220
                        log_debug('Putting '+str(out))
221
                        xpath.put_obj(root, out, row_id, has_types, value)
222
            return process_rows(process_row, rows, **kw_args)
223
        
224
        def map_table(col_names, rows, **kw_args):
225
            col_names_ct = len(col_names)
226
            col_idxs = util.list_flip(col_names)
227
            
228
            mappings_orig = mappings[:] # save a copy
229
            mappings[:] = [] # empty existing elements
230
            for in_, out in mappings_orig:
231
                if metadata_value(in_) == None:
232
                    try: names = get_with_prefix(col_idxs, prefixes, in_)
233
                    except KeyError: pass
234
                    else: mappings.append((names, out))
235
            
236
            def get_value(in_, row):
237
                return util.coalesce(*util.list_subset(row.list, in_))
238
            def wrap_row(row):
239
                return util.ListDict(util.list_as_length(row, col_names_ct),
240
                    col_names, col_idxs) # handle CSV rows of different lengths
241
            
242
            return map_rows(get_value, util.WrapIter(wrap_row, rows), **kw_args)
243
        
244
        stdin = streams.LineCountStream(sys.stdin)
245
        def on_error(e):
246
            exc.add_msg(e, term.emph('input line #:')+' '+str(stdin.line_num))
247
            ex_tracker.track(e)
248
        
249
        if in_is_db:
250
            in_db = connect_db(in_db_config)
251
            
252
            # Get table and schema name
253
            schema = in_schema # modified, so can't have same name as outer var
254
            table = in_table # modified, so can't have same name as outer var
255
            if table == None:
256
                assert in_is_xpaths
257
                schema, sep, table = in_root.partition('.')
258
                if sep == '': # only the table name was specified
259
                    table = schema
260
                    schema = None
261
            table_is_esc = False
262
            if schema != None:
263
                table = sql.qual_name(in_db, schema, table)
264
                table_is_esc = True
265
            
266
            # Fetch rows
267
            if by_col: limit = 0 # only fetch column names
268
            else: limit = n
269
            cur = sql.select(in_db, table, limit=limit, start=start,
270
                table_is_esc=table_is_esc)
271
            col_names = list(sql.col_names(cur))
272
            
273
            if by_col:
274
                row_ready = lambda row_num, input_row: None# disable row_ready()
275
                row = ['$'+v for v in col_names] # values are the column names
276
                map_table(col_names, [row]) # map just the sample row
277
                xml_func.strip(root)
278
                db_xml.put_table(in_db, root.firstChild, table, commit,
279
                    row_ins_ct_ref, table_is_esc)
280
            else:
281
                # Use normal by-row method
282
                row_ct = map_table(col_names, sql.rows(cur), rows_start=start)
283
                    # rows_start: pre-start rows have been skipped
284
            
285
            in_db.db.close()
286
        elif in_is_xml:
287
            def get_rows(doc2rows):
288
                return iters.flatten(itertools.imap(doc2rows,
289
                    xml_parse.docs_iter(stdin, on_error)))
290
            
291
            if map_path == None:
292
                def doc2rows(in_xml_root):
293
                    iter_ = xml_dom.NodeElemIter(in_xml_root)
294
                    util.skip(iter_, xml_dom.is_text) # skip metadata
295
                    return iter_
296
                
297
                row_ct = process_rows(lambda row, i: root.appendChild(row),
298
                    get_rows(doc2rows))
299
            else:
300
                def doc2rows(in_xml_root):
301
                    rows = xpath.get(in_xml_root, in_root, limit=end)
302
                    if rows == []: raise SystemExit('Map error: Root "'
303
                        +in_root+'" not found in input')
304
                    return rows
305
                
306
                def get_value(in_, row):
307
                    in_ = './{'+(','.join(strings.with_prefixes(
308
                        ['']+prefixes, in_)))+'}' # also with no prefix
309
                    nodes = xpath.get(row, in_, allow_rooted=False)
310
                    if nodes != []: return xml_dom.value(nodes[0])
311
                    else: return None
312
                
313
                row_ct = map_rows(get_value, get_rows(doc2rows))
314
        else: # input is CSV
315
            map_ = dict(mappings)
316
            reader, col_names = csvs.reader_and_header(sys.stdin)
317
            row_ct = map_table(col_names, reader)
318
        
319
        return row_ct
320
    
321
    def process_inputs(root, row_ready):
322
        row_ct = 0
323
        for map_path in map_paths:
324
            row_ct += process_input(root, row_ready, map_path)
325
        return row_ct
326
    
327
    pool.share_vars(locals())
328
    if out_is_db:
329
        import db_xml
330
        
331
        out_db = connect_db(out_db_config)
332
        try:
333
            if redo: sql.empty_db(out_db)
334
            pool.share_vars(locals())
335
            
336
            def row_ready(row_num, input_row):
337
                def on_error(e):
338
                    exc.add_msg(e, term.emph('row #:')+' '+str(row_num+1))
339
                        # row # is interally 0-based, but 1-based to the user
340
                    exc.add_msg(e, term.emph('input row:')+'\n'+str(input_row))
341
                    exc.add_msg(e, term.emph('output row:')+'\n'+str(root))
342
                    ex_tracker.track(e, row_num)
343
                pool.share_vars(locals())
344
                
345
                xml_func.process(root, on_error)
346
                if not xml_dom.is_empty(root):
347
                    assert xml_dom.has_one_child(root)
348
                    try:
349
                        sql.with_savepoint(out_db,
350
                            lambda: db_xml.put(out_db, root.firstChild,
351
                                row_ins_ct_ref, on_error))
352
                        if commit: out_db.db.commit()
353
                    except sql.DatabaseErrors, e: on_error(e)
354
                prep_root()
355
            
356
            row_ct = process_inputs(root, row_ready)
357
            sys.stdout.write('Inserted '+str(row_ins_ct_ref[0])+
358
                ' new rows into database\n')
359
            
360
            # Consume asynchronous tasks
361
            pool.main_loop()
362
        finally:
363
            out_db.db.rollback()
364
            out_db.db.close()
365
    else:
366
        def on_error(e): ex_tracker.track(e)
367
        def row_ready(row_num, input_row): pass
368
        row_ct = process_inputs(root, row_ready)
369
        xml_func.process(root, on_error)
370
        if out_is_xml_ref[0]:
371
            doc.writexml(sys.stdout, **xml_dom.prettyxml_config)
372
        else: # output is CSV
373
            raise NotImplementedError('CSV output not supported yet')
374
    
375
    # Consume any asynchronous tasks not already consumed above
376
    pool.main_loop()
377
    
378
    profiler.stop(row_ct)
379
    ex_tracker.add_iters(row_ct)
380
    if verbose:
381
        sys.stderr.write('Processed '+str(row_ct)+' input rows\n')
382
        sys.stderr.write(profiler.msg()+'\n')
383
        sys.stderr.write(ex_tracker.msg()+'\n')
384
    ex_tracker.exit()
385

    
386
def main():
387
    try: main_()
388
    except Parser.SyntaxError, e: raise SystemExit(str(e))
389

    
390
if __name__ == '__main__':
391
    profile_to = opts.get_env_var('profile_to', None)
392
    if profile_to != None:
393
        import cProfile
394
        sys.stderr.write('Profiling to '+profile_to+'\n')
395
        cProfile.run(main.func_code, profile_to)
396
    else: main()
(25-25/47)