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 1846 aaronmk
    # Optimization
79 1851 aaronmk
    if test: cpus_default = 0
80
    else: cpus_default = None
81 1856 aaronmk
    cpus = util.cast(int, util.none_if(opts.get_env_var('cpus', cpus_default,
82
        env_names), u''))
83 1846 aaronmk
84 1570 aaronmk
    # Debugging
85 946 aaronmk
    debug = opts.env_flag('debug', False, env_names)
86 859 aaronmk
    sql.run_raw_query.debug = debug
87 1574 aaronmk
    verbose = debug or opts.env_flag('verbose', not test, env_names)
88 944 aaronmk
    opts.get_env_var('profile_to', None, env_names) # add to env_names
89 131 aaronmk
90 1570 aaronmk
    # DB
91
    def get_db_config(prefix):
92 1926 aaronmk
        return opts.get_env_vars(sql.db_config_names, prefix, env_names)
93 1570 aaronmk
    in_db_config = get_db_config('in')
94
    out_db_config = get_db_config('out')
95
    in_is_db = 'engine' in in_db_config
96
    out_is_db = 'engine' in out_db_config
97 1982 aaronmk
    in_schema = opts.get_env_var('in_schema', None, env_names)
98
    in_table = opts.get_env_var('in_table', None, env_names)
99 1570 aaronmk
100
    ##
101
102 838 aaronmk
    # Logging
103 662 aaronmk
    def log(msg, on=verbose):
104 1901 aaronmk
        if on: sys.stderr.write(msg+'\n')
105
    if debug: log_debug = lambda msg: log(msg, debug)
106
    else: log_debug = sql.log_debug_none
107 662 aaronmk
108 53 aaronmk
    # Parse args
109 510 aaronmk
    map_paths = sys.argv[1:]
110 512 aaronmk
    if map_paths == []:
111
        if in_is_db or not out_is_db: usage_err()
112
        else: map_paths = [None]
113 53 aaronmk
114 646 aaronmk
    def connect_db(db_config):
115 1901 aaronmk
        log('Connecting to '+sql.db_config_str(db_config))
116
        return sql.connect(db_config, log_debug=log_debug)
117 646 aaronmk
118 1945 aaronmk
    if end != None: end_str = str(end-1) # end is one past the last #
119 1573 aaronmk
    else: end_str = 'end'
120 1901 aaronmk
    log('Processing input rows '+str(start)+'-'+end_str)
121 1573 aaronmk
122 1014 aaronmk
    ex_tracker = exc.ExPercentTracker(iter_text='row')
123
    profiler = profiling.ItersProfiler(start_now=True, iter_text='row')
124
125 1856 aaronmk
    # Parallel processing
126 1862 aaronmk
    pool = parallel.MultiProducerPool(cpus)
127 1901 aaronmk
    log('Using '+str(pool.process_ct)+' parallel CPUs')
128 1846 aaronmk
129 1014 aaronmk
    doc = xml_dom.create_doc()
130
    root = doc.documentElement
131 751 aaronmk
    out_is_xml_ref = [False]
132 1014 aaronmk
    in_label_ref = [None]
133
    def update_in_label():
134
        if in_label_ref[0] != None:
135
            xpath.get(root, '/_ignore/inLabel="'+in_label_ref[0]+'"', True)
136
    def prep_root():
137
        root.clear()
138
        update_in_label()
139
    prep_root()
140 751 aaronmk
141 838 aaronmk
    def process_input(root, row_ready, map_path):
142 512 aaronmk
        '''Inputs datasource to XML tree, mapping if needed'''
143
        # Load map header
144
        in_is_xpaths = True
145 751 aaronmk
        out_is_xpaths = True
146 512 aaronmk
        out_label = None
147
        if map_path != None:
148
            metadata = []
149
            mappings = []
150
            stream = open(map_path, 'rb')
151
            reader = csv.reader(stream)
152
            in_label, out_label = reader.next()[:2]
153 1402 aaronmk
154 512 aaronmk
            def split_col_name(name):
155 1402 aaronmk
                label, sep, root = name.partition(':')
156
                label, sep2, prefixes_str = label.partition('[')
157
                prefixes_str = strings.remove_suffix(']', prefixes_str)
158
                prefixes = strings.split(',', prefixes_str)
159
                return label, sep != '', root, prefixes
160 1198 aaronmk
                    # extract datasrc from "datasrc[data_format]"
161 1402 aaronmk
162 1705 aaronmk
            in_label, in_root, prefixes = maps.col_info(in_label)
163
            in_is_xpaths = in_root != None
164 1014 aaronmk
            in_label_ref[0] = in_label
165
            update_in_label()
166 1705 aaronmk
            out_label, out_root = maps.col_info(out_label)[:2]
167
            out_is_xpaths = out_root != None
168 1841 aaronmk
            if out_is_xpaths: has_types = out_root.find('/*s/') >= 0
169 1705 aaronmk
                # outer elements are types
170 1402 aaronmk
171 512 aaronmk
            for row in reader:
172
                in_, out = row[:2]
173
                if out != '':
174
                    if out_is_xpaths: out = xpath.parse(out_root+out)
175
                    mappings.append((in_, out))
176 1402 aaronmk
177 512 aaronmk
            stream.close()
178
179
            root.ownerDocument.documentElement.tagName = out_label
180
        in_is_xml = in_is_xpaths and not in_is_db
181 751 aaronmk
        out_is_xml_ref[0] = out_is_xpaths and not out_is_db
182 56 aaronmk
183 1897 aaronmk
        def process_rows(process_row, rows, rows_start=0):
184
            '''Processes input rows
185 838 aaronmk
            @param process_row(in_row, i)
186 1945 aaronmk
            @rows_start The (0-based) row # of the first row in rows. Set this
187
                only if the pre-start rows have already been skipped.
188 297 aaronmk
            '''
189 1897 aaronmk
            rows = iter(rows)
190
191
            if end != None: row_nums = xrange(rows_start, end)
192
            else: row_nums = itertools.count(rows_start)
193
            for i in row_nums:
194 1718 aaronmk
                try: row = rows.next()
195
                except StopIteration: break # no more rows
196
                if i < start: continue # not at start row yet
197
198 838 aaronmk
                process_row(row, i)
199
                row_ready(i, row)
200 1718 aaronmk
            row_ct = i-start
201 982 aaronmk
            return row_ct
202 838 aaronmk
203 1898 aaronmk
        def map_rows(get_value, rows, **kw_args):
204 838 aaronmk
            '''Maps input rows
205
            @param get_value(in_, row):str
206
            '''
207
            def process_row(row, i):
208 316 aaronmk
                row_id = str(i)
209
                for in_, out in mappings:
210
                    value = metadata_value(in_)
211 662 aaronmk
                    if value == None:
212 1901 aaronmk
                        log_debug('Getting '+str(in_))
213 1360 aaronmk
                        value = cleanup(get_value(in_, row))
214 1348 aaronmk
                    if value != None:
215 1901 aaronmk
                        log_debug('Putting '+str(out))
216 1360 aaronmk
                        xpath.put_obj(root, out, row_id, has_types, value)
217 1898 aaronmk
            return process_rows(process_row, rows, **kw_args)
218 297 aaronmk
219 1898 aaronmk
        def map_table(col_names, rows, **kw_args):
220 1416 aaronmk
            col_names_ct = len(col_names)
221 1403 aaronmk
            col_idxs = util.list_flip(col_names)
222
223
            i = 0
224
            while i < len(mappings): # mappings len changes in loop
225
                in_, out = mappings[i]
226
                if metadata_value(in_) == None:
227 1404 aaronmk
                    try: mappings[i] = (
228
                        get_with_prefix(col_idxs, prefixes, in_), out)
229
                    except KeyError:
230
                        del mappings[i]
231
                        continue # keep i the same
232 1403 aaronmk
                i += 1
233
234
            def get_value(in_, row):
235 1484 aaronmk
                return util.coalesce(*util.list_subset(row.list, in_))
236 1416 aaronmk
            def wrap_row(row):
237
                return util.ListDict(util.list_as_length(row, col_names_ct),
238
                    col_names, col_idxs) # handle CSV rows of different lengths
239 1403 aaronmk
240 1898 aaronmk
            return map_rows(get_value, util.WrapIter(wrap_row, rows), **kw_args)
241 1403 aaronmk
242 1758 aaronmk
        stdin = streams.LineCountStream(sys.stdin)
243
        def on_error(e):
244
            exc.add_msg(e, term.emph('input line #:')+' '+str(stdin.line_num))
245
            ex_tracker.track(e)
246
247 1700 aaronmk
        if in_is_db:
248 1982 aaronmk
            in_db = connect_db(in_db_config)
249 126 aaronmk
250 1982 aaronmk
            # Get table and schema name
251
            schema = in_schema # modified, so can't have same name as outer var
252
            table = in_table # modified, so can't have same name as outer var
253
            if table == None:
254
                assert in_is_xpaths
255
                schema, sep, table = in_root.partition('.')
256
                if sep == '': # only the table name was specified
257
                    table = schema
258
                    schema = None
259
            table_is_esc = False
260
            if schema != None:
261
                table = sql.qual_name(in_db, schema, table)
262
                table_is_esc = True
263
264
            cur = sql.select(in_db, table, limit=n, start=start,
265
                table_is_esc=table_is_esc)
266 1898 aaronmk
            row_ct = map_table(list(sql.col_names(cur)), sql.rows(cur),
267
                rows_start=start) # rows_start: pre-start rows have been skipped
268 1136 aaronmk
269 1849 aaronmk
            in_db.db.close()
270 161 aaronmk
        elif in_is_xml:
271 1715 aaronmk
            def get_rows(doc2rows):
272 1758 aaronmk
                return iters.flatten(itertools.imap(doc2rows,
273
                    xml_parse.docs_iter(stdin, on_error)))
274 1715 aaronmk
275 1714 aaronmk
            if map_path == None:
276 1715 aaronmk
                def doc2rows(in_xml_root):
277 1701 aaronmk
                    iter_ = xml_dom.NodeElemIter(in_xml_root)
278
                    util.skip(iter_, xml_dom.is_text) # skip metadata
279 1715 aaronmk
                    return iter_
280
281
                row_ct = process_rows(lambda row, i: root.appendChild(row),
282
                    get_rows(doc2rows))
283 1714 aaronmk
            else:
284 1715 aaronmk
                def doc2rows(in_xml_root):
285 1701 aaronmk
                    rows = xpath.get(in_xml_root, in_root, limit=end)
286 1714 aaronmk
                    if rows == []: raise SystemExit('Map error: Root "'
287
                        +in_root+'" not found in input')
288
                    return rows
289
290
                def get_value(in_, row):
291
                    in_ = './{'+(','.join(strings.with_prefixes(
292
                        ['']+prefixes, in_)))+'}' # also with no prefix
293
                    nodes = xpath.get(row, in_, allow_rooted=False)
294
                    if nodes != []: return xml_dom.value(nodes[0])
295
                    else: return None
296
297 1715 aaronmk
                row_ct = map_rows(get_value, get_rows(doc2rows))
298 56 aaronmk
        else: # input is CSV
299 133 aaronmk
            map_ = dict(mappings)
300 1389 aaronmk
            reader, col_names = csvs.reader_and_header(sys.stdin)
301 1403 aaronmk
            row_ct = map_table(col_names, reader)
302 982 aaronmk
303
        return row_ct
304 53 aaronmk
305 838 aaronmk
    def process_inputs(root, row_ready):
306 982 aaronmk
        row_ct = 0
307
        for map_path in map_paths:
308
            row_ct += process_input(root, row_ready, map_path)
309
        return row_ct
310 512 aaronmk
311 1886 aaronmk
    pool.share_vars(locals())
312 130 aaronmk
    if out_is_db:
313 53 aaronmk
        import db_xml
314
315 646 aaronmk
        out_db = connect_db(out_db_config)
316 53 aaronmk
        try:
317 947 aaronmk
            if redo: sql.empty_db(out_db)
318 982 aaronmk
            row_ins_ct_ref = [0]
319 1886 aaronmk
            pool.share_vars(locals())
320 449 aaronmk
321 838 aaronmk
            def row_ready(row_num, input_row):
322 452 aaronmk
                def on_error(e):
323 1946 aaronmk
                    exc.add_msg(e, term.emph('row #:')+' '+str(row_num+1))
324
                        # row # is interally 0-based, but 1-based to the user
325 828 aaronmk
                    exc.add_msg(e, term.emph('input row:')+'\n'+str(input_row))
326
                    exc.add_msg(e, term.emph('output row:')+'\n'+str(root))
327 1617 aaronmk
                    ex_tracker.track(e, row_num)
328 1886 aaronmk
                pool.share_vars(locals())
329 452 aaronmk
330 449 aaronmk
                xml_func.process(root, on_error)
331 442 aaronmk
                if not xml_dom.is_empty(root):
332
                    assert xml_dom.has_one_child(root)
333
                    try:
334 982 aaronmk
                        sql.with_savepoint(out_db,
335
                            lambda: db_xml.put(out_db, root.firstChild,
336 1850 aaronmk
                                row_ins_ct_ref, on_error))
337 1849 aaronmk
                        if commit: out_db.db.commit()
338 449 aaronmk
                    except sql.DatabaseErrors, e: on_error(e)
339 1010 aaronmk
                prep_root()
340 449 aaronmk
341 982 aaronmk
            row_ct = process_inputs(root, row_ready)
342
            sys.stdout.write('Inserted '+str(row_ins_ct_ref[0])+
343 460 aaronmk
                ' new rows into database\n')
344 1868 aaronmk
345
            # Consume asynchronous tasks
346
            pool.main_loop()
347 53 aaronmk
        finally:
348 1849 aaronmk
            out_db.db.rollback()
349
            out_db.db.close()
350 751 aaronmk
    else:
351 759 aaronmk
        def on_error(e): ex_tracker.track(e)
352 838 aaronmk
        def row_ready(row_num, input_row): pass
353 982 aaronmk
        row_ct = process_inputs(root, row_ready)
354 759 aaronmk
        xml_func.process(root, on_error)
355 751 aaronmk
        if out_is_xml_ref[0]:
356
            doc.writexml(sys.stdout, **xml_dom.prettyxml_config)
357
        else: # output is CSV
358
            raise NotImplementedError('CSV output not supported yet')
359 985 aaronmk
360 1868 aaronmk
    # Consume any asynchronous tasks not already consumed above
361 1862 aaronmk
    pool.main_loop()
362
363 982 aaronmk
    profiler.stop(row_ct)
364
    ex_tracker.add_iters(row_ct)
365 990 aaronmk
    if verbose:
366
        sys.stderr.write('Processed '+str(row_ct)+' input rows\n')
367
        sys.stderr.write(profiler.msg()+'\n')
368
        sys.stderr.write(ex_tracker.msg()+'\n')
369 985 aaronmk
    ex_tracker.exit()
370 53 aaronmk
371 847 aaronmk
def main():
372
    try: main_()
373 1719 aaronmk
    except Parser.SyntaxError, e: raise SystemExit(str(e))
374 847 aaronmk
375 846 aaronmk
if __name__ == '__main__':
376 847 aaronmk
    profile_to = opts.get_env_var('profile_to', None)
377
    if profile_to != None:
378
        import cProfile
379 1584 aaronmk
        sys.stderr.write('Profiling to '+profile_to+'\n')
380 847 aaronmk
        cProfile.run(main.func_code, profile_to)
381
    else: main()