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 2035 aaronmk
import parallelproc
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 2035 aaronmk
    pool = parallelproc.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 1991 aaronmk
    # Define before the out_is_db section because it's used by by_col
144
    row_ins_ct_ref = [0]
145
146 838 aaronmk
    def process_input(root, row_ready, map_path):
147 512 aaronmk
        '''Inputs datasource to XML tree, mapping if needed'''
148
        # Load map header
149
        in_is_xpaths = True
150 751 aaronmk
        out_is_xpaths = True
151 512 aaronmk
        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 1402 aaronmk
159 512 aaronmk
            def split_col_name(name):
160 1402 aaronmk
                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 1198 aaronmk
                    # extract datasrc from "datasrc[data_format]"
166 1402 aaronmk
167 1705 aaronmk
            in_label, in_root, prefixes = maps.col_info(in_label)
168
            in_is_xpaths = in_root != None
169 1014 aaronmk
            in_label_ref[0] = in_label
170
            update_in_label()
171 1705 aaronmk
            out_label, out_root = maps.col_info(out_label)[:2]
172
            out_is_xpaths = out_root != None
173 1841 aaronmk
            if out_is_xpaths: has_types = out_root.find('/*s/') >= 0
174 1705 aaronmk
                # outer elements are types
175 1402 aaronmk
176 512 aaronmk
            for row in reader:
177
                in_, out = row[:2]
178 2029 aaronmk
                if out != '': mappings.append([in_, out_root+out])
179 1402 aaronmk
180 512 aaronmk
            stream.close()
181
182
            root.ownerDocument.documentElement.tagName = out_label
183
        in_is_xml = in_is_xpaths and not in_is_db
184 751 aaronmk
        out_is_xml_ref[0] = out_is_xpaths and not out_is_db
185 56 aaronmk
186 1897 aaronmk
        def process_rows(process_row, rows, rows_start=0):
187
            '''Processes input rows
188 838 aaronmk
            @param process_row(in_row, i)
189 1945 aaronmk
            @rows_start The (0-based) row # of the first row in rows. Set this
190
                only if the pre-start rows have already been skipped.
191 297 aaronmk
            '''
192 1897 aaronmk
            rows = iter(rows)
193
194
            if end != None: row_nums = xrange(rows_start, end)
195
            else: row_nums = itertools.count(rows_start)
196 2038 aaronmk
            i = -1
197 1897 aaronmk
            for i in row_nums:
198 1718 aaronmk
                try: row = rows.next()
199 2038 aaronmk
                except StopIteration:
200
                    i -= 1 # last row # didn't count
201
                    break # no more rows
202 1718 aaronmk
                if i < start: continue # not at start row yet
203
204 838 aaronmk
                process_row(row, i)
205
                row_ready(i, row)
206 2033 aaronmk
            row_ct = i-start+1
207 982 aaronmk
            return row_ct
208 838 aaronmk
209 1898 aaronmk
        def map_rows(get_value, rows, **kw_args):
210 838 aaronmk
            '''Maps input rows
211
            @param get_value(in_, row):str
212
            '''
213 2030 aaronmk
            # Prevent collisions if multiple inputs mapping to same output
214
            outputs_idxs = dict()
215
            for i, mapping in enumerate(mappings):
216
                in_, out = mapping
217
                default = util.NamedTuple(count=1, first=i)
218
                idxs = outputs_idxs.setdefault(out, default)
219
                if idxs is not default: # key existed, so there was a collision
220
                    if idxs.count == 1: # first key does not yet have /_alt/#
221
                        mappings[idxs.first][1] += '/_alt/0'
222
                    mappings[i][1] += '/_alt/'+str(idxs.count)
223
                    idxs.count += 1
224
225 2026 aaronmk
            id_node = None
226
            if out_is_db:
227
                for i, mapping in enumerate(mappings):
228
                    in_, out = mapping
229
                    # All put_obj()s should return the same id_node
230
                    nodes, id_node = xpath.put_obj(root, out, '-1', has_types,
231
                        '$'+str(in_)) # value is placeholder that documents name
232 2032 aaronmk
                    mappings[i] = [in_, nodes]
233
                assert id_node != None
234 2026 aaronmk
235
                if debug: # only str() if debug
236
                    log_debug('Put template:\n'+str(root))
237
238 838 aaronmk
            def process_row(row, i):
239 316 aaronmk
                row_id = str(i)
240 2032 aaronmk
                if id_node != None: xml_dom.set_value(id_node, row_id)
241 316 aaronmk
                for in_, out in mappings:
242 2027 aaronmk
                    log_debug('Getting '+str(in_))
243 316 aaronmk
                    value = metadata_value(in_)
244 2027 aaronmk
                    if value == None: value = cleanup(get_value(in_, row))
245
                    log_debug('Putting '+repr(value)+' to '+str(out))
246 2032 aaronmk
                    if out_is_db: # out is list of XML nodes
247
                        for node in out: xml_dom.set_value(node, value)
248
                    elif value != None: # out is XPath
249 1360 aaronmk
                        xpath.put_obj(root, out, row_id, has_types, value)
250 2027 aaronmk
                if debug: log_debug('Putting:\n'+str(root))# only str() if debug
251 1898 aaronmk
            return process_rows(process_row, rows, **kw_args)
252 297 aaronmk
253 1898 aaronmk
        def map_table(col_names, rows, **kw_args):
254 1416 aaronmk
            col_names_ct = len(col_names)
255 1403 aaronmk
            col_idxs = util.list_flip(col_names)
256
257 2029 aaronmk
            # Resolve prefixes
258 2025 aaronmk
            mappings_orig = mappings[:] # save a copy
259
            mappings[:] = [] # empty existing elements
260
            for in_, out in mappings_orig:
261 1403 aaronmk
                if metadata_value(in_) == None:
262 2025 aaronmk
                    try: names = get_with_prefix(col_idxs, prefixes, in_)
263
                    except KeyError: pass
264 2031 aaronmk
                    else: mappings[len(mappings):] = [[v, out] for v in names]
265
                        # can't use += because that uses assignment
266 1403 aaronmk
267 2031 aaronmk
            def get_value(in_, row): return row.list[in_]
268 1416 aaronmk
            def wrap_row(row):
269
                return util.ListDict(util.list_as_length(row, col_names_ct),
270
                    col_names, col_idxs) # handle CSV rows of different lengths
271 1403 aaronmk
272 1898 aaronmk
            return map_rows(get_value, util.WrapIter(wrap_row, rows), **kw_args)
273 1403 aaronmk
274 1758 aaronmk
        stdin = streams.LineCountStream(sys.stdin)
275
        def on_error(e):
276
            exc.add_msg(e, term.emph('input line #:')+' '+str(stdin.line_num))
277
            ex_tracker.track(e)
278
279 1700 aaronmk
        if in_is_db:
280 1982 aaronmk
            in_db = connect_db(in_db_config)
281 126 aaronmk
282 1982 aaronmk
            # Get table and schema name
283
            schema = in_schema # modified, so can't have same name as outer var
284
            table = in_table # modified, so can't have same name as outer var
285
            if table == None:
286
                assert in_is_xpaths
287
                schema, sep, table = in_root.partition('.')
288
                if sep == '': # only the table name was specified
289
                    table = schema
290
                    schema = None
291
            table_is_esc = False
292
            if schema != None:
293
                table = sql.qual_name(in_db, schema, table)
294
                table_is_esc = True
295
296 1991 aaronmk
            # Fetch rows
297
            if by_col: limit = 0 # only fetch column names
298
            else: limit = n
299
            cur = sql.select(in_db, table, limit=limit, start=start,
300
                table_is_esc=table_is_esc)
301
            col_names = list(sql.col_names(cur))
302
303 1989 aaronmk
            if by_col:
304 1991 aaronmk
                row_ready = lambda row_num, input_row: None# disable row_ready()
305 1994 aaronmk
                row = ['$'+v for v in col_names] # values are the column names
306
                map_table(col_names, [row]) # map just the sample row
307 1993 aaronmk
                xml_func.strip(root)
308 1998 aaronmk
                db_xml.put_table(in_db, root.firstChild, table, commit,
309
                    row_ins_ct_ref, table_is_esc)
310 1984 aaronmk
            else:
311
                # Use normal by-row method
312 1991 aaronmk
                row_ct = map_table(col_names, sql.rows(cur), rows_start=start)
313
                    # rows_start: pre-start rows have been skipped
314 1136 aaronmk
315 1849 aaronmk
            in_db.db.close()
316 161 aaronmk
        elif in_is_xml:
317 1715 aaronmk
            def get_rows(doc2rows):
318 1758 aaronmk
                return iters.flatten(itertools.imap(doc2rows,
319
                    xml_parse.docs_iter(stdin, on_error)))
320 1715 aaronmk
321 1714 aaronmk
            if map_path == None:
322 1715 aaronmk
                def doc2rows(in_xml_root):
323 1701 aaronmk
                    iter_ = xml_dom.NodeElemIter(in_xml_root)
324
                    util.skip(iter_, xml_dom.is_text) # skip metadata
325 1715 aaronmk
                    return iter_
326
327
                row_ct = process_rows(lambda row, i: root.appendChild(row),
328
                    get_rows(doc2rows))
329 1714 aaronmk
            else:
330 1715 aaronmk
                def doc2rows(in_xml_root):
331 1701 aaronmk
                    rows = xpath.get(in_xml_root, in_root, limit=end)
332 1714 aaronmk
                    if rows == []: raise SystemExit('Map error: Root "'
333
                        +in_root+'" not found in input')
334
                    return rows
335
336
                def get_value(in_, row):
337
                    in_ = './{'+(','.join(strings.with_prefixes(
338
                        ['']+prefixes, in_)))+'}' # also with no prefix
339
                    nodes = xpath.get(row, in_, allow_rooted=False)
340
                    if nodes != []: return xml_dom.value(nodes[0])
341
                    else: return None
342
343 1715 aaronmk
                row_ct = map_rows(get_value, get_rows(doc2rows))
344 56 aaronmk
        else: # input is CSV
345 133 aaronmk
            map_ = dict(mappings)
346 1389 aaronmk
            reader, col_names = csvs.reader_and_header(sys.stdin)
347 1403 aaronmk
            row_ct = map_table(col_names, reader)
348 982 aaronmk
349
        return row_ct
350 53 aaronmk
351 838 aaronmk
    def process_inputs(root, row_ready):
352 982 aaronmk
        row_ct = 0
353
        for map_path in map_paths:
354
            row_ct += process_input(root, row_ready, map_path)
355
        return row_ct
356 512 aaronmk
357 1886 aaronmk
    pool.share_vars(locals())
358 130 aaronmk
    if out_is_db:
359 53 aaronmk
        import db_xml
360
361 646 aaronmk
        out_db = connect_db(out_db_config)
362 53 aaronmk
        try:
363 947 aaronmk
            if redo: sql.empty_db(out_db)
364 1886 aaronmk
            pool.share_vars(locals())
365 449 aaronmk
366 838 aaronmk
            def row_ready(row_num, input_row):
367 452 aaronmk
                def on_error(e):
368 1946 aaronmk
                    exc.add_msg(e, term.emph('row #:')+' '+str(row_num+1))
369
                        # row # is interally 0-based, but 1-based to the user
370 828 aaronmk
                    exc.add_msg(e, term.emph('input row:')+'\n'+str(input_row))
371
                    exc.add_msg(e, term.emph('output row:')+'\n'+str(root))
372 1617 aaronmk
                    ex_tracker.track(e, row_num)
373 1886 aaronmk
                pool.share_vars(locals())
374 452 aaronmk
375 2032 aaronmk
                row_root = root.cloneNode(True) # deep copy so don't modify root
376
                xml_func.process(row_root, on_error)
377
                if not xml_dom.is_empty(row_root):
378
                    assert xml_dom.has_one_child(row_root)
379 442 aaronmk
                    try:
380 982 aaronmk
                        sql.with_savepoint(out_db,
381 2032 aaronmk
                            lambda: db_xml.put(out_db, row_root.firstChild,
382 1850 aaronmk
                                row_ins_ct_ref, on_error))
383 1849 aaronmk
                        if commit: out_db.db.commit()
384 449 aaronmk
                    except sql.DatabaseErrors, e: on_error(e)
385
386 982 aaronmk
            row_ct = process_inputs(root, row_ready)
387
            sys.stdout.write('Inserted '+str(row_ins_ct_ref[0])+
388 460 aaronmk
                ' new rows into database\n')
389 1868 aaronmk
390
            # Consume asynchronous tasks
391
            pool.main_loop()
392 53 aaronmk
        finally:
393 1849 aaronmk
            out_db.db.rollback()
394
            out_db.db.close()
395 751 aaronmk
    else:
396 759 aaronmk
        def on_error(e): ex_tracker.track(e)
397 838 aaronmk
        def row_ready(row_num, input_row): pass
398 982 aaronmk
        row_ct = process_inputs(root, row_ready)
399 759 aaronmk
        xml_func.process(root, on_error)
400 751 aaronmk
        if out_is_xml_ref[0]:
401
            doc.writexml(sys.stdout, **xml_dom.prettyxml_config)
402
        else: # output is CSV
403
            raise NotImplementedError('CSV output not supported yet')
404 985 aaronmk
405 1868 aaronmk
    # Consume any asynchronous tasks not already consumed above
406 1862 aaronmk
    pool.main_loop()
407
408 982 aaronmk
    profiler.stop(row_ct)
409
    ex_tracker.add_iters(row_ct)
410 990 aaronmk
    if verbose:
411
        sys.stderr.write('Processed '+str(row_ct)+' input rows\n')
412
        sys.stderr.write(profiler.msg()+'\n')
413
        sys.stderr.write(ex_tracker.msg()+'\n')
414 985 aaronmk
    ex_tracker.exit()
415 53 aaronmk
416 847 aaronmk
def main():
417
    try: main_()
418 1719 aaronmk
    except Parser.SyntaxError, e: raise SystemExit(str(e))
419 847 aaronmk
420 846 aaronmk
if __name__ == '__main__':
421 847 aaronmk
    profile_to = opts.get_env_var('profile_to', None)
422
    if profile_to != None:
423
        import cProfile
424 1584 aaronmk
        sys.stderr.write('Profiling to '+profile_to+'\n')
425 847 aaronmk
        cProfile.run(main.func_code, profile_to)
426
    else: main()