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 2040 aaronmk
import db_xml
17 344 aaronmk
import exc
18 1714 aaronmk
import iters
19 1705 aaronmk
import maps
20 64 aaronmk
import opts
21 2035 aaronmk
import parallelproc
22 281 aaronmk
import Parser
23 982 aaronmk
import profiling
24 131 aaronmk
import sql
25 1758 aaronmk
import streams
26 715 aaronmk
import strings
27 828 aaronmk
import term
28 310 aaronmk
import util
29 1014 aaronmk
import xpath
30 133 aaronmk
import xml_dom
31 86 aaronmk
import xml_func
32 1713 aaronmk
import xml_parse
33 53 aaronmk
34 1404 aaronmk
def get_with_prefix(map_, prefixes, key):
35 2040 aaronmk
    '''Gets all entries for the given key with any of the given prefixes
36
    @return tuple(found_key, found_value)
37
    '''
38 1484 aaronmk
    values = []
39 1681 aaronmk
    for key_ in strings.with_prefixes(['']+prefixes, key): # also with no prefix
40
        try: value = map_[key_]
41 1484 aaronmk
        except KeyError, e: continue # keep going
42 2040 aaronmk
        values.append((key_, value))
43 1484 aaronmk
44
    if values != []: return values
45
    else: raise e # re-raise last KeyError
46 1404 aaronmk
47 1018 aaronmk
def metadata_value(name): return None # this feature has been removed
48 84 aaronmk
49 1360 aaronmk
def cleanup(val):
50
    if val == None: return val
51 1374 aaronmk
    return util.none_if(strings.cleanup(strings.ustr(val)), u'', u'\\N')
52 1360 aaronmk
53 847 aaronmk
def main_():
54 131 aaronmk
    env_names = []
55
    def usage_err():
56 944 aaronmk
        raise SystemExit('Usage: '+opts.env_usage(env_names, True)+' '
57 1945 aaronmk
            +sys.argv[0]+' [map_path...] [<input] [>output]\n'
58 1946 aaronmk
            'Note: Row #s start with 1')
59 838 aaronmk
60 1570 aaronmk
    ## Get config from env vars
61 838 aaronmk
62 1570 aaronmk
    # Modes
63 946 aaronmk
    test = opts.env_flag('test', False, env_names)
64 947 aaronmk
    commit = opts.env_flag('commit', False, env_names) and not test
65 944 aaronmk
        # never commit in test mode
66 947 aaronmk
    redo = opts.env_flag('redo', test, env_names) and not commit
67
        # never redo in commit mode (manually run `make empty_db` instead)
68 1570 aaronmk
69
    # Ranges
70 1946 aaronmk
    start = util.cast(int, opts.get_env_var('start', 1, env_names)) # 1-based
71
    # Make start interally 0-based.
72
    # It's 1-based to the user to match up with the staging table row #s.
73
    start -= 1
74 1945 aaronmk
    if test: n_default = 1
75
    else: n_default = None
76
    n = util.cast(int, util.none_if(opts.get_env_var('n', n_default, env_names),
77
        u''))
78
    end = n
79 1570 aaronmk
    if end != None: end += start
80
81
    # Debugging
82 946 aaronmk
    debug = opts.env_flag('debug', False, env_names)
83 859 aaronmk
    sql.run_raw_query.debug = debug
84 1574 aaronmk
    verbose = debug or opts.env_flag('verbose', not test, env_names)
85 2118 aaronmk
    verbose_errors = opts.env_flag('verbose_errors', test or debug, env_names)
86 944 aaronmk
    opts.get_env_var('profile_to', None, env_names) # add to env_names
87 131 aaronmk
88 1570 aaronmk
    # DB
89
    def get_db_config(prefix):
90 1926 aaronmk
        return opts.get_env_vars(sql.db_config_names, prefix, env_names)
91 1570 aaronmk
    in_db_config = get_db_config('in')
92
    out_db_config = get_db_config('out')
93
    in_is_db = 'engine' in in_db_config
94
    out_is_db = 'engine' in out_db_config
95 1982 aaronmk
    in_schema = opts.get_env_var('in_schema', None, env_names)
96
    in_table = opts.get_env_var('in_table', None, env_names)
97 1570 aaronmk
98 1989 aaronmk
    # Optimization
99 2050 aaronmk
    cache_sql = opts.env_flag('cache_sql', True, env_names)
100 1989 aaronmk
    by_col = in_db_config == out_db_config and opts.env_flag('by_col', False,
101
        env_names) # by-column optimization only applies if mapping to same DB
102
    if test: cpus_default = 0
103 2044 aaronmk
    else: cpus_default = 0 # or None to use parallel processing by default
104 1989 aaronmk
    cpus = util.cast(int, util.none_if(opts.get_env_var('cpus', cpus_default,
105
        env_names), u''))
106
107 1570 aaronmk
    ##
108
109 838 aaronmk
    # Logging
110 662 aaronmk
    def log(msg, on=verbose):
111 1901 aaronmk
        if on: sys.stderr.write(msg+'\n')
112
    if debug: log_debug = lambda msg: log(msg, debug)
113
    else: log_debug = sql.log_debug_none
114 662 aaronmk
115 53 aaronmk
    # Parse args
116 510 aaronmk
    map_paths = sys.argv[1:]
117 512 aaronmk
    if map_paths == []:
118
        if in_is_db or not out_is_db: usage_err()
119
        else: map_paths = [None]
120 53 aaronmk
121 646 aaronmk
    def connect_db(db_config):
122 1901 aaronmk
        log('Connecting to '+sql.db_config_str(db_config))
123 2192 aaronmk
        return sql.connect(db_config, caching=cache_sql,
124
            autocommit=debug and commit, log_debug=log_debug)
125 646 aaronmk
126 1945 aaronmk
    if end != None: end_str = str(end-1) # end is one past the last #
127 1573 aaronmk
    else: end_str = 'end'
128 1901 aaronmk
    log('Processing input rows '+str(start)+'-'+end_str)
129 1573 aaronmk
130 1014 aaronmk
    ex_tracker = exc.ExPercentTracker(iter_text='row')
131
    profiler = profiling.ItersProfiler(start_now=True, iter_text='row')
132
133 1856 aaronmk
    # Parallel processing
134 2035 aaronmk
    pool = parallelproc.MultiProducerPool(cpus)
135 1901 aaronmk
    log('Using '+str(pool.process_ct)+' parallel CPUs')
136 1846 aaronmk
137 1014 aaronmk
    doc = xml_dom.create_doc()
138
    root = doc.documentElement
139 751 aaronmk
    out_is_xml_ref = [False]
140 1014 aaronmk
    in_label_ref = [None]
141
    def update_in_label():
142
        if in_label_ref[0] != None:
143
            xpath.get(root, '/_ignore/inLabel="'+in_label_ref[0]+'"', True)
144
    def prep_root():
145
        root.clear()
146
        update_in_label()
147
    prep_root()
148 751 aaronmk
149 1991 aaronmk
    # Define before the out_is_db section because it's used by by_col
150
    row_ins_ct_ref = [0]
151
152 838 aaronmk
    def process_input(root, row_ready, map_path):
153 512 aaronmk
        '''Inputs datasource to XML tree, mapping if needed'''
154
        # Load map header
155
        in_is_xpaths = True
156 751 aaronmk
        out_is_xpaths = True
157 512 aaronmk
        out_label = None
158
        if map_path != None:
159
            metadata = []
160
            mappings = []
161
            stream = open(map_path, 'rb')
162
            reader = csv.reader(stream)
163
            in_label, out_label = reader.next()[:2]
164 1402 aaronmk
165 512 aaronmk
            def split_col_name(name):
166 1402 aaronmk
                label, sep, root = name.partition(':')
167
                label, sep2, prefixes_str = label.partition('[')
168
                prefixes_str = strings.remove_suffix(']', prefixes_str)
169
                prefixes = strings.split(',', prefixes_str)
170
                return label, sep != '', root, prefixes
171 1198 aaronmk
                    # extract datasrc from "datasrc[data_format]"
172 1402 aaronmk
173 1705 aaronmk
            in_label, in_root, prefixes = maps.col_info(in_label)
174
            in_is_xpaths = in_root != None
175 1014 aaronmk
            in_label_ref[0] = in_label
176
            update_in_label()
177 1705 aaronmk
            out_label, out_root = maps.col_info(out_label)[:2]
178
            out_is_xpaths = out_root != None
179 1841 aaronmk
            if out_is_xpaths: has_types = out_root.find('/*s/') >= 0
180 1705 aaronmk
                # outer elements are types
181 1402 aaronmk
182 512 aaronmk
            for row in reader:
183
                in_, out = row[:2]
184 2029 aaronmk
                if out != '': mappings.append([in_, out_root+out])
185 1402 aaronmk
186 512 aaronmk
            stream.close()
187
188
            root.ownerDocument.documentElement.tagName = out_label
189
        in_is_xml = in_is_xpaths and not in_is_db
190 751 aaronmk
        out_is_xml_ref[0] = out_is_xpaths and not out_is_db
191 56 aaronmk
192 1897 aaronmk
        def process_rows(process_row, rows, rows_start=0):
193
            '''Processes input rows
194 838 aaronmk
            @param process_row(in_row, i)
195 1945 aaronmk
            @rows_start The (0-based) row # of the first row in rows. Set this
196
                only if the pre-start rows have already been skipped.
197 297 aaronmk
            '''
198 1897 aaronmk
            rows = iter(rows)
199
200
            if end != None: row_nums = xrange(rows_start, end)
201
            else: row_nums = itertools.count(rows_start)
202 2038 aaronmk
            i = -1
203 1897 aaronmk
            for i in row_nums:
204 1718 aaronmk
                try: row = rows.next()
205 2038 aaronmk
                except StopIteration:
206
                    i -= 1 # last row # didn't count
207
                    break # no more rows
208 1718 aaronmk
                if i < start: continue # not at start row yet
209
210 838 aaronmk
                process_row(row, i)
211
                row_ready(i, row)
212 2033 aaronmk
            row_ct = i-start+1
213 982 aaronmk
            return row_ct
214 838 aaronmk
215 1898 aaronmk
        def map_rows(get_value, rows, **kw_args):
216 838 aaronmk
            '''Maps input rows
217
            @param get_value(in_, row):str
218
            '''
219 2030 aaronmk
            # Prevent collisions if multiple inputs mapping to same output
220
            outputs_idxs = dict()
221
            for i, mapping in enumerate(mappings):
222
                in_, out = mapping
223
                default = util.NamedTuple(count=1, first=i)
224
                idxs = outputs_idxs.setdefault(out, default)
225
                if idxs is not default: # key existed, so there was a collision
226
                    if idxs.count == 1: # first key does not yet have /_alt/#
227
                        mappings[idxs.first][1] += '/_alt/0'
228
                    mappings[i][1] += '/_alt/'+str(idxs.count)
229
                    idxs.count += 1
230
231 2026 aaronmk
            id_node = None
232
            if out_is_db:
233
                for i, mapping in enumerate(mappings):
234
                    in_, out = mapping
235
                    # All put_obj()s should return the same id_node
236
                    nodes, id_node = xpath.put_obj(root, out, '-1', has_types,
237
                        '$'+str(in_)) # value is placeholder that documents name
238 2032 aaronmk
                    mappings[i] = [in_, nodes]
239
                assert id_node != None
240 2026 aaronmk
241 2119 aaronmk
                if debug: # only calc if debug
242 2026 aaronmk
                    log_debug('Put template:\n'+str(root))
243
244 838 aaronmk
            def process_row(row, i):
245 316 aaronmk
                row_id = str(i)
246 2032 aaronmk
                if id_node != None: xml_dom.set_value(id_node, row_id)
247 316 aaronmk
                for in_, out in mappings:
248 2027 aaronmk
                    log_debug('Getting '+str(in_))
249 316 aaronmk
                    value = metadata_value(in_)
250 2027 aaronmk
                    if value == None: value = cleanup(get_value(in_, row))
251
                    log_debug('Putting '+repr(value)+' to '+str(out))
252 2032 aaronmk
                    if out_is_db: # out is list of XML nodes
253
                        for node in out: xml_dom.set_value(node, value)
254
                    elif value != None: # out is XPath
255 1360 aaronmk
                        xpath.put_obj(root, out, row_id, has_types, value)
256 1898 aaronmk
            return process_rows(process_row, rows, **kw_args)
257 297 aaronmk
258 1898 aaronmk
        def map_table(col_names, rows, **kw_args):
259 1416 aaronmk
            col_names_ct = len(col_names)
260 1403 aaronmk
            col_idxs = util.list_flip(col_names)
261
262 2029 aaronmk
            # Resolve prefixes
263 2025 aaronmk
            mappings_orig = mappings[:] # save a copy
264
            mappings[:] = [] # empty existing elements
265
            for in_, out in mappings_orig:
266 1403 aaronmk
                if metadata_value(in_) == None:
267 2040 aaronmk
                    try: cols = get_with_prefix(col_idxs, prefixes, in_)
268 2025 aaronmk
                    except KeyError: pass
269 2040 aaronmk
                    else: mappings[len(mappings):] = [[db_xml.ColRef(*col), out]
270
                        for col in cols] # can't use += because that uses =
271 1403 aaronmk
272 2040 aaronmk
            def get_value(in_, row): return row.list[in_.idx]
273 1416 aaronmk
            def wrap_row(row):
274
                return util.ListDict(util.list_as_length(row, col_names_ct),
275
                    col_names, col_idxs) # handle CSV rows of different lengths
276 1403 aaronmk
277 1898 aaronmk
            return map_rows(get_value, util.WrapIter(wrap_row, rows), **kw_args)
278 1403 aaronmk
279 1758 aaronmk
        stdin = streams.LineCountStream(sys.stdin)
280
        def on_error(e):
281
            exc.add_msg(e, term.emph('input line #:')+' '+str(stdin.line_num))
282
            ex_tracker.track(e)
283
284 1700 aaronmk
        if in_is_db:
285 1982 aaronmk
            in_db = connect_db(in_db_config)
286 126 aaronmk
287 1982 aaronmk
            # Get table and schema name
288
            schema = in_schema # modified, so can't have same name as outer var
289
            table = in_table # modified, so can't have same name as outer var
290
            if table == None:
291
                assert in_is_xpaths
292
                schema, sep, table = in_root.partition('.')
293
                if sep == '': # only the table name was specified
294
                    table = schema
295
                    schema = None
296
297 1991 aaronmk
            # Fetch rows
298
            if by_col: limit = 0 # only fetch column names
299
            else: limit = n
300 2053 aaronmk
            cur = sql.select(in_db, sql.qual_name(in_db, schema, table),
301
                limit=limit, start=start, cacheable=False, table_is_esc=True)
302 1991 aaronmk
            col_names = list(sql.col_names(cur))
303
304 1989 aaronmk
            if by_col:
305 2042 aaronmk
                map_table(col_names, []) # just create the template
306 1993 aaronmk
                xml_func.strip(root)
307 2103 aaronmk
                if debug: log_debug('Putting stripped:\n'+str(root))
308 2119 aaronmk
                    # only calc if debug
309 2052 aaronmk
                db_xml.put_table(in_db, root.firstChild, table, schema, commit,
310
                    row_ins_ct_ref)
311 2174 aaronmk
                row_ct = 0 # unknown for now
312 1984 aaronmk
            else:
313
                # Use normal by-row method
314 1991 aaronmk
                row_ct = map_table(col_names, sql.rows(cur), rows_start=start)
315
                    # rows_start: pre-start rows have been skipped
316 1136 aaronmk
317 1849 aaronmk
            in_db.db.close()
318 161 aaronmk
        elif in_is_xml:
319 1715 aaronmk
            def get_rows(doc2rows):
320 1758 aaronmk
                return iters.flatten(itertools.imap(doc2rows,
321
                    xml_parse.docs_iter(stdin, on_error)))
322 1715 aaronmk
323 1714 aaronmk
            if map_path == None:
324 1715 aaronmk
                def doc2rows(in_xml_root):
325 1701 aaronmk
                    iter_ = xml_dom.NodeElemIter(in_xml_root)
326
                    util.skip(iter_, xml_dom.is_text) # skip metadata
327 1715 aaronmk
                    return iter_
328
329
                row_ct = process_rows(lambda row, i: root.appendChild(row),
330
                    get_rows(doc2rows))
331 1714 aaronmk
            else:
332 1715 aaronmk
                def doc2rows(in_xml_root):
333 1701 aaronmk
                    rows = xpath.get(in_xml_root, in_root, limit=end)
334 1714 aaronmk
                    if rows == []: raise SystemExit('Map error: Root "'
335
                        +in_root+'" not found in input')
336
                    return rows
337
338
                def get_value(in_, row):
339
                    in_ = './{'+(','.join(strings.with_prefixes(
340
                        ['']+prefixes, in_)))+'}' # also with no prefix
341
                    nodes = xpath.get(row, in_, allow_rooted=False)
342
                    if nodes != []: return xml_dom.value(nodes[0])
343
                    else: return None
344
345 1715 aaronmk
                row_ct = map_rows(get_value, get_rows(doc2rows))
346 56 aaronmk
        else: # input is CSV
347 133 aaronmk
            map_ = dict(mappings)
348 1389 aaronmk
            reader, col_names = csvs.reader_and_header(sys.stdin)
349 1403 aaronmk
            row_ct = map_table(col_names, reader)
350 982 aaronmk
351
        return row_ct
352 53 aaronmk
353 838 aaronmk
    def process_inputs(root, row_ready):
354 982 aaronmk
        row_ct = 0
355
        for map_path in map_paths:
356
            row_ct += process_input(root, row_ready, map_path)
357
        return row_ct
358 512 aaronmk
359 1886 aaronmk
    pool.share_vars(locals())
360 130 aaronmk
    if out_is_db:
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 2119 aaronmk
                row_str_ = [None]
368
                def row_str():
369
                    if row_str_[0] == None:
370
                        # Row # is interally 0-based, but 1-based to the user
371
                        row_str_[0] = (term.emph('row #:')+' '+str(row_num+1)
372
                            +'\n'+term.emph('input row:')+'\n'+str(input_row))
373
                        if verbose_errors: row_str_[0] += ('\n'
374
                            +term.emph('output row:')+'\n'+str(root))
375
                    return row_str_[0]
376
377
                if debug: log_debug(row_str()) # only calc if debug
378
379 452 aaronmk
                def on_error(e):
380 2119 aaronmk
                    exc.add_msg(e, row_str())
381 2046 aaronmk
                    ex_tracker.track(e, row_num, detail=verbose_errors)
382 1886 aaronmk
                pool.share_vars(locals())
383 452 aaronmk
384 2032 aaronmk
                row_root = root.cloneNode(True) # deep copy so don't modify root
385 2106 aaronmk
                xml_func.process(row_root, on_error, out_db)
386 2032 aaronmk
                if not xml_dom.is_empty(row_root):
387
                    assert xml_dom.has_one_child(row_root)
388 442 aaronmk
                    try:
389 982 aaronmk
                        sql.with_savepoint(out_db,
390 2032 aaronmk
                            lambda: db_xml.put(out_db, row_root.firstChild,
391 1850 aaronmk
                                row_ins_ct_ref, on_error))
392 1849 aaronmk
                        if commit: out_db.db.commit()
393 449 aaronmk
                    except sql.DatabaseErrors, e: on_error(e)
394
395 982 aaronmk
            row_ct = process_inputs(root, row_ready)
396
            sys.stdout.write('Inserted '+str(row_ins_ct_ref[0])+
397 460 aaronmk
                ' new rows into database\n')
398 1868 aaronmk
399
            # Consume asynchronous tasks
400
            pool.main_loop()
401 53 aaronmk
        finally:
402 2166 aaronmk
            if out_db.connected():
403
                out_db.db.rollback()
404
                out_db.db.close()
405 751 aaronmk
    else:
406 759 aaronmk
        def on_error(e): ex_tracker.track(e)
407 838 aaronmk
        def row_ready(row_num, input_row): pass
408 982 aaronmk
        row_ct = process_inputs(root, row_ready)
409 759 aaronmk
        xml_func.process(root, on_error)
410 751 aaronmk
        if out_is_xml_ref[0]:
411
            doc.writexml(sys.stdout, **xml_dom.prettyxml_config)
412
        else: # output is CSV
413
            raise NotImplementedError('CSV output not supported yet')
414 985 aaronmk
415 1868 aaronmk
    # Consume any asynchronous tasks not already consumed above
416 1862 aaronmk
    pool.main_loop()
417
418 982 aaronmk
    profiler.stop(row_ct)
419
    ex_tracker.add_iters(row_ct)
420 990 aaronmk
    if verbose:
421
        sys.stderr.write('Processed '+str(row_ct)+' input rows\n')
422
        sys.stderr.write(profiler.msg()+'\n')
423
        sys.stderr.write(ex_tracker.msg()+'\n')
424 985 aaronmk
    ex_tracker.exit()
425 53 aaronmk
426 847 aaronmk
def main():
427
    try: main_()
428 1719 aaronmk
    except Parser.SyntaxError, e: raise SystemExit(str(e))
429 847 aaronmk
430 846 aaronmk
if __name__ == '__main__':
431 847 aaronmk
    profile_to = opts.get_env_var('profile_to', None)
432
    if profile_to != None:
433
        import cProfile
434 1584 aaronmk
        sys.stderr.write('Profiling to '+profile_to+'\n')
435 847 aaronmk
        cProfile.run(main.func_code, profile_to)
436
    else: main()