Project

General

Profile

1 53 aaronmk
#!/usr/bin/env python
2
# Maps one datasource to another, using a map spreadsheet if needed
3 986 aaronmk
# Exit status is the # of errors in the import, up to the maximum exit status
4 53 aaronmk
# 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 1014 aaronmk
import csv
8 1714 aaronmk
import itertools
9 53 aaronmk
import os.path
10
import sys
11 299 aaronmk
import xml.dom.minidom as minidom
12 53 aaronmk
13 266 aaronmk
sys.path.append(os.path.dirname(__file__)+"/../lib")
14 53 aaronmk
15 1389 aaronmk
import csvs
16 344 aaronmk
import exc
17 1714 aaronmk
import iters
18 1705 aaronmk
import maps
19 64 aaronmk
import opts
20 1859 aaronmk
import parallel
21 281 aaronmk
import Parser
22 982 aaronmk
import profiling
23 131 aaronmk
import sql
24 1758 aaronmk
import streams
25 715 aaronmk
import strings
26 828 aaronmk
import term
27 310 aaronmk
import util
28 1014 aaronmk
import xpath
29 133 aaronmk
import xml_dom
30 86 aaronmk
import xml_func
31 1713 aaronmk
import xml_parse
32 53 aaronmk
33 1404 aaronmk
def get_with_prefix(map_, prefixes, key):
34 1484 aaronmk
    '''Gets all entries for the given key with any of the given prefixes'''
35
    values = []
36 1681 aaronmk
    for key_ in strings.with_prefixes(['']+prefixes, key): # also with no prefix
37
        try: value = map_[key_]
38 1484 aaronmk
        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 1404 aaronmk
44 1018 aaronmk
def metadata_value(name): return None # this feature has been removed
45 84 aaronmk
46 1360 aaronmk
def cleanup(val):
47
    if val == None: return val
48 1374 aaronmk
    return util.none_if(strings.cleanup(strings.ustr(val)), u'', u'\\N')
49 1360 aaronmk
50 847 aaronmk
def main_():
51 131 aaronmk
    env_names = []
52
    def usage_err():
53 944 aaronmk
        raise SystemExit('Usage: '+opts.env_usage(env_names, True)+' '
54 1945 aaronmk
            +sys.argv[0]+' [map_path...] [<input] [>output]\n'
55 1946 aaronmk
            'Note: Row #s start with 1')
56 838 aaronmk
57 1570 aaronmk
    ## Get config from env vars
58 838 aaronmk
59 1570 aaronmk
    # Modes
60 946 aaronmk
    test = opts.env_flag('test', False, env_names)
61 947 aaronmk
    commit = opts.env_flag('commit', False, env_names) and not test
62 944 aaronmk
        # never commit in test mode
63 947 aaronmk
    redo = opts.env_flag('redo', test, env_names) and not commit
64
        # never redo in commit mode (manually run `make empty_db` instead)
65 1570 aaronmk
66
    # Ranges
67 1946 aaronmk
    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 1945 aaronmk
    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 1570 aaronmk
    if end != None: end += start
77
78
    # Debugging
79 946 aaronmk
    debug = opts.env_flag('debug', False, env_names)
80 859 aaronmk
    sql.run_raw_query.debug = debug
81 1574 aaronmk
    verbose = debug or opts.env_flag('verbose', not test, env_names)
82 944 aaronmk
    opts.get_env_var('profile_to', None, env_names) # add to env_names
83 131 aaronmk
84 1570 aaronmk
    # DB
85
    def get_db_config(prefix):
86 1926 aaronmk
        return opts.get_env_vars(sql.db_config_names, prefix, env_names)
87 1570 aaronmk
    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 1982 aaronmk
    in_schema = opts.get_env_var('in_schema', None, env_names)
92
    in_table = opts.get_env_var('in_table', None, env_names)
93 1570 aaronmk
94 1989 aaronmk
    # 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 1570 aaronmk
    ##
103
104 838 aaronmk
    # Logging
105 662 aaronmk
    def log(msg, on=verbose):
106 1901 aaronmk
        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
109 662 aaronmk
110 53 aaronmk
    # Parse args
111 510 aaronmk
    map_paths = sys.argv[1:]
112 512 aaronmk
    if map_paths == []:
113
        if in_is_db or not out_is_db: usage_err()
114
        else: map_paths = [None]
115 53 aaronmk
116 646 aaronmk
    def connect_db(db_config):
117 1901 aaronmk
        log('Connecting to '+sql.db_config_str(db_config))
118
        return sql.connect(db_config, log_debug=log_debug)
119 646 aaronmk
120 1945 aaronmk
    if end != None: end_str = str(end-1) # end is one past the last #
121 1573 aaronmk
    else: end_str = 'end'
122 1901 aaronmk
    log('Processing input rows '+str(start)+'-'+end_str)
123 1573 aaronmk
124 1014 aaronmk
    ex_tracker = exc.ExPercentTracker(iter_text='row')
125
    profiler = profiling.ItersProfiler(start_now=True, iter_text='row')
126
127 1856 aaronmk
    # Parallel processing
128 1862 aaronmk
    pool = parallel.MultiProducerPool(cpus)
129 1901 aaronmk
    log('Using '+str(pool.process_ct)+' parallel CPUs')
130 1846 aaronmk
131 1014 aaronmk
    doc = xml_dom.create_doc()
132
    root = doc.documentElement
133 751 aaronmk
    out_is_xml_ref = [False]
134 1014 aaronmk
    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()
142 751 aaronmk
143 838 aaronmk
    def process_input(root, row_ready, map_path):
144 512 aaronmk
        '''Inputs datasource to XML tree, mapping if needed'''
145
        # Load map header
146
        in_is_xpaths = True
147 751 aaronmk
        out_is_xpaths = True
148 512 aaronmk
        out_label = None
149
        if map_path != None:
150
            metadata = []
151
            mappings = []
152
            stream = open(map_path, 'rb')
153
            reader = csv.reader(stream)
154
            in_label, out_label = reader.next()[:2]
155 1402 aaronmk
156 512 aaronmk
            def split_col_name(name):
157 1402 aaronmk
                label, sep, root = name.partition(':')
158
                label, sep2, prefixes_str = label.partition('[')
159
                prefixes_str = strings.remove_suffix(']', prefixes_str)
160
                prefixes = strings.split(',', prefixes_str)
161
                return label, sep != '', root, prefixes
162 1198 aaronmk
                    # extract datasrc from "datasrc[data_format]"
163 1402 aaronmk
164 1705 aaronmk
            in_label, in_root, prefixes = maps.col_info(in_label)
165
            in_is_xpaths = in_root != None
166 1014 aaronmk
            in_label_ref[0] = in_label
167
            update_in_label()
168 1705 aaronmk
            out_label, out_root = maps.col_info(out_label)[:2]
169
            out_is_xpaths = out_root != None
170 1841 aaronmk
            if out_is_xpaths: has_types = out_root.find('/*s/') >= 0
171 1705 aaronmk
                # outer elements are types
172 1402 aaronmk
173 512 aaronmk
            for row in reader:
174
                in_, out = row[:2]
175
                if out != '':
176
                    if out_is_xpaths: out = xpath.parse(out_root+out)
177
                    mappings.append((in_, out))
178 1402 aaronmk
179 512 aaronmk
            stream.close()
180
181
            root.ownerDocument.documentElement.tagName = out_label
182
        in_is_xml = in_is_xpaths and not in_is_db
183 751 aaronmk
        out_is_xml_ref[0] = out_is_xpaths and not out_is_db
184 56 aaronmk
185 1897 aaronmk
        def process_rows(process_row, rows, rows_start=0):
186
            '''Processes input rows
187 838 aaronmk
            @param process_row(in_row, i)
188 1945 aaronmk
            @rows_start The (0-based) row # of the first row in rows. Set this
189
                only if the pre-start rows have already been skipped.
190 297 aaronmk
            '''
191 1897 aaronmk
            rows = iter(rows)
192
193
            if end != None: row_nums = xrange(rows_start, end)
194
            else: row_nums = itertools.count(rows_start)
195
            for i in row_nums:
196 1718 aaronmk
                try: row = rows.next()
197
                except StopIteration: break # no more rows
198
                if i < start: continue # not at start row yet
199
200 838 aaronmk
                process_row(row, i)
201
                row_ready(i, row)
202 1718 aaronmk
            row_ct = i-start
203 982 aaronmk
            return row_ct
204 838 aaronmk
205 1898 aaronmk
        def map_rows(get_value, rows, **kw_args):
206 838 aaronmk
            '''Maps input rows
207
            @param get_value(in_, row):str
208
            '''
209
            def process_row(row, i):
210 316 aaronmk
                row_id = str(i)
211
                for in_, out in mappings:
212
                    value = metadata_value(in_)
213 662 aaronmk
                    if value == None:
214 1901 aaronmk
                        log_debug('Getting '+str(in_))
215 1360 aaronmk
                        value = cleanup(get_value(in_, row))
216 1348 aaronmk
                    if value != None:
217 1901 aaronmk
                        log_debug('Putting '+str(out))
218 1360 aaronmk
                        xpath.put_obj(root, out, row_id, has_types, value)
219 1898 aaronmk
            return process_rows(process_row, rows, **kw_args)
220 297 aaronmk
221 1898 aaronmk
        def map_table(col_names, rows, **kw_args):
222 1416 aaronmk
            col_names_ct = len(col_names)
223 1403 aaronmk
            col_idxs = util.list_flip(col_names)
224
225
            i = 0
226
            while i < len(mappings): # mappings len changes in loop
227
                in_, out = mappings[i]
228
                if metadata_value(in_) == None:
229 1404 aaronmk
                    try: mappings[i] = (
230
                        get_with_prefix(col_idxs, prefixes, in_), out)
231
                    except KeyError:
232
                        del mappings[i]
233
                        continue # keep i the same
234 1403 aaronmk
                i += 1
235
236
            def get_value(in_, row):
237 1484 aaronmk
                return util.coalesce(*util.list_subset(row.list, in_))
238 1416 aaronmk
            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 1403 aaronmk
242 1898 aaronmk
            return map_rows(get_value, util.WrapIter(wrap_row, rows), **kw_args)
243 1403 aaronmk
244 1758 aaronmk
        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 1700 aaronmk
        if in_is_db:
250 1982 aaronmk
            in_db = connect_db(in_db_config)
251 126 aaronmk
252 1982 aaronmk
            # 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 1989 aaronmk
            if by_col:
267 1985 aaronmk
                # Mapping to same DB and by-column optimization enabled
268 1984 aaronmk
                raise NotImplementedError(
269
                    'By-column optimization not available yet')
270
            else:
271
                # Use normal by-row method
272
                cur = sql.select(in_db, table, limit=n, start=start,
273
                    table_is_esc=table_is_esc)
274
                row_ct = map_table(list(sql.col_names(cur)), sql.rows(cur),
275
                    rows_start=start) # rows_start: pre-start rows were skipped
276 1136 aaronmk
277 1849 aaronmk
            in_db.db.close()
278 161 aaronmk
        elif in_is_xml:
279 1715 aaronmk
            def get_rows(doc2rows):
280 1758 aaronmk
                return iters.flatten(itertools.imap(doc2rows,
281
                    xml_parse.docs_iter(stdin, on_error)))
282 1715 aaronmk
283 1714 aaronmk
            if map_path == None:
284 1715 aaronmk
                def doc2rows(in_xml_root):
285 1701 aaronmk
                    iter_ = xml_dom.NodeElemIter(in_xml_root)
286
                    util.skip(iter_, xml_dom.is_text) # skip metadata
287 1715 aaronmk
                    return iter_
288
289
                row_ct = process_rows(lambda row, i: root.appendChild(row),
290
                    get_rows(doc2rows))
291 1714 aaronmk
            else:
292 1715 aaronmk
                def doc2rows(in_xml_root):
293 1701 aaronmk
                    rows = xpath.get(in_xml_root, in_root, limit=end)
294 1714 aaronmk
                    if rows == []: raise SystemExit('Map error: Root "'
295
                        +in_root+'" not found in input')
296
                    return rows
297
298
                def get_value(in_, row):
299
                    in_ = './{'+(','.join(strings.with_prefixes(
300
                        ['']+prefixes, in_)))+'}' # also with no prefix
301
                    nodes = xpath.get(row, in_, allow_rooted=False)
302
                    if nodes != []: return xml_dom.value(nodes[0])
303
                    else: return None
304
305 1715 aaronmk
                row_ct = map_rows(get_value, get_rows(doc2rows))
306 56 aaronmk
        else: # input is CSV
307 133 aaronmk
            map_ = dict(mappings)
308 1389 aaronmk
            reader, col_names = csvs.reader_and_header(sys.stdin)
309 1403 aaronmk
            row_ct = map_table(col_names, reader)
310 982 aaronmk
311
        return row_ct
312 53 aaronmk
313 838 aaronmk
    def process_inputs(root, row_ready):
314 982 aaronmk
        row_ct = 0
315
        for map_path in map_paths:
316
            row_ct += process_input(root, row_ready, map_path)
317
        return row_ct
318 512 aaronmk
319 1886 aaronmk
    pool.share_vars(locals())
320 130 aaronmk
    if out_is_db:
321 53 aaronmk
        import db_xml
322
323 646 aaronmk
        out_db = connect_db(out_db_config)
324 53 aaronmk
        try:
325 947 aaronmk
            if redo: sql.empty_db(out_db)
326 982 aaronmk
            row_ins_ct_ref = [0]
327 1886 aaronmk
            pool.share_vars(locals())
328 449 aaronmk
329 838 aaronmk
            def row_ready(row_num, input_row):
330 452 aaronmk
                def on_error(e):
331 1946 aaronmk
                    exc.add_msg(e, term.emph('row #:')+' '+str(row_num+1))
332
                        # row # is interally 0-based, but 1-based to the user
333 828 aaronmk
                    exc.add_msg(e, term.emph('input row:')+'\n'+str(input_row))
334
                    exc.add_msg(e, term.emph('output row:')+'\n'+str(root))
335 1617 aaronmk
                    ex_tracker.track(e, row_num)
336 1886 aaronmk
                pool.share_vars(locals())
337 452 aaronmk
338 449 aaronmk
                xml_func.process(root, on_error)
339 442 aaronmk
                if not xml_dom.is_empty(root):
340
                    assert xml_dom.has_one_child(root)
341
                    try:
342 982 aaronmk
                        sql.with_savepoint(out_db,
343
                            lambda: db_xml.put(out_db, root.firstChild,
344 1850 aaronmk
                                row_ins_ct_ref, on_error))
345 1849 aaronmk
                        if commit: out_db.db.commit()
346 449 aaronmk
                    except sql.DatabaseErrors, e: on_error(e)
347 1010 aaronmk
                prep_root()
348 449 aaronmk
349 982 aaronmk
            row_ct = process_inputs(root, row_ready)
350
            sys.stdout.write('Inserted '+str(row_ins_ct_ref[0])+
351 460 aaronmk
                ' new rows into database\n')
352 1868 aaronmk
353
            # Consume asynchronous tasks
354
            pool.main_loop()
355 53 aaronmk
        finally:
356 1849 aaronmk
            out_db.db.rollback()
357
            out_db.db.close()
358 751 aaronmk
    else:
359 759 aaronmk
        def on_error(e): ex_tracker.track(e)
360 838 aaronmk
        def row_ready(row_num, input_row): pass
361 982 aaronmk
        row_ct = process_inputs(root, row_ready)
362 759 aaronmk
        xml_func.process(root, on_error)
363 751 aaronmk
        if out_is_xml_ref[0]:
364
            doc.writexml(sys.stdout, **xml_dom.prettyxml_config)
365
        else: # output is CSV
366
            raise NotImplementedError('CSV output not supported yet')
367 985 aaronmk
368 1868 aaronmk
    # Consume any asynchronous tasks not already consumed above
369 1862 aaronmk
    pool.main_loop()
370
371 982 aaronmk
    profiler.stop(row_ct)
372
    ex_tracker.add_iters(row_ct)
373 990 aaronmk
    if verbose:
374
        sys.stderr.write('Processed '+str(row_ct)+' input rows\n')
375
        sys.stderr.write(profiler.msg()+'\n')
376
        sys.stderr.write(ex_tracker.msg()+'\n')
377 985 aaronmk
    ex_tracker.exit()
378 53 aaronmk
379 847 aaronmk
def main():
380
    try: main_()
381 1719 aaronmk
    except Parser.SyntaxError, e: raise SystemExit(str(e))
382 847 aaronmk
383 846 aaronmk
if __name__ == '__main__':
384 847 aaronmk
    profile_to = opts.get_env_var('profile_to', None)
385
    if profile_to != None:
386
        import cProfile
387 1584 aaronmk
        sys.stderr.write('Profiling to '+profile_to+'\n')
388 847 aaronmk
        cProfile.run(main.func_code, profile_to)
389
    else: main()