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 2550 aaronmk
import copy
8 1014 aaronmk
import csv
9 1714 aaronmk
import itertools
10 53 aaronmk
import os.path
11
import sys
12 299 aaronmk
import xml.dom.minidom as minidom
13 53 aaronmk
14 266 aaronmk
sys.path.append(os.path.dirname(__file__)+"/../lib")
15 53 aaronmk
16 1389 aaronmk
import csvs
17 2040 aaronmk
import db_xml
18 344 aaronmk
import exc
19 1714 aaronmk
import iters
20 1705 aaronmk
import maps
21 64 aaronmk
import opts
22 2035 aaronmk
import parallelproc
23 281 aaronmk
import Parser
24 982 aaronmk
import profiling
25 131 aaronmk
import sql
26 2288 aaronmk
import sql_gen
27 3103 aaronmk
import sql_io
28 1758 aaronmk
import streams
29 715 aaronmk
import strings
30 828 aaronmk
import term
31 310 aaronmk
import util
32 1014 aaronmk
import xpath
33 133 aaronmk
import xml_dom
34 86 aaronmk
import xml_func
35 1713 aaronmk
import xml_parse
36 53 aaronmk
37 1404 aaronmk
def get_with_prefix(map_, prefixes, key):
38 2040 aaronmk
    '''Gets all entries for the given key with any of the given prefixes
39
    @return tuple(found_key, found_value)
40
    '''
41 1484 aaronmk
    values = []
42 1681 aaronmk
    for key_ in strings.with_prefixes(['']+prefixes, key): # also with no prefix
43
        try: value = map_[key_]
44 1484 aaronmk
        except KeyError, e: continue # keep going
45 2040 aaronmk
        values.append((key_, value))
46 1484 aaronmk
47
    if values != []: return values
48
    else: raise e # re-raise last KeyError
49 1404 aaronmk
50 1018 aaronmk
def metadata_value(name): return None # this feature has been removed
51 84 aaronmk
52 1360 aaronmk
def cleanup(val):
53
    if val == None: return val
54 1374 aaronmk
    return util.none_if(strings.cleanup(strings.ustr(val)), u'', u'\\N')
55 1360 aaronmk
56 847 aaronmk
def main_():
57 131 aaronmk
    env_names = []
58
    def usage_err():
59 944 aaronmk
        raise SystemExit('Usage: '+opts.env_usage(env_names, True)+' '
60 1945 aaronmk
            +sys.argv[0]+' [map_path...] [<input] [>output]\n'
61 1946 aaronmk
            'Note: Row #s start with 1')
62 838 aaronmk
63 1570 aaronmk
    ## Get config from env vars
64 838 aaronmk
65 1570 aaronmk
    # Modes
66 946 aaronmk
    test = opts.env_flag('test', False, env_names)
67 947 aaronmk
    commit = opts.env_flag('commit', False, env_names) and not test
68 944 aaronmk
        # never commit in test mode
69 947 aaronmk
    redo = opts.env_flag('redo', test, env_names) and not commit
70 2977 aaronmk
        # never redo in commit mode (run `make schemas/reinstall` instead)
71 1570 aaronmk
72
    # Ranges
73 1946 aaronmk
    start = util.cast(int, opts.get_env_var('start', 1, env_names)) # 1-based
74
    # Make start interally 0-based.
75
    # It's 1-based to the user to match up with the staging table row #s.
76
    start -= 1
77 1945 aaronmk
    if test: n_default = 1
78
    else: n_default = None
79
    n = util.cast(int, util.none_if(opts.get_env_var('n', n_default, env_names),
80
        u''))
81
    end = n
82 1570 aaronmk
    if end != None: end += start
83
84
    # Debugging
85 3132 aaronmk
    verbosity = util.cast(float, opts.get_env_var('verbosity', None, 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 3132 aaronmk
    # Set default verbosity. Must happen after by_col is set.
108
    if verbosity == None:
109
        if test: verbosity = 0.5 # automated tests should not be verbose
110
        elif by_col: verbosity = 3 # show all queries to assist profiling
111
        else: verbosity = 1.1 # just show row progress
112
113 1570 aaronmk
    ##
114
115 838 aaronmk
    # Logging
116 2457 aaronmk
    verbose_errors = test and verbosity > 0
117 2449 aaronmk
    debug = verbosity > 1
118 2439 aaronmk
    def log(msg, level=1):
119
        '''Higher level -> more verbose'''
120 2452 aaronmk
        if level <= verbosity:
121 2490 aaronmk
            if verbosity <= 2:
122
                if level == 1.5: msg = '# '+msg # msg is Redmine list item
123
                elif msg.startswith('DB query:'): # remove extra debug info
124
                    first_line, nl, msg = msg.partition('\n')
125
            elif level > 1: msg = '['+str(level)+'] '+msg # include level in msg
126
127 2883 aaronmk
            sys.stderr.write(strings.to_raw_str(msg.rstrip('\n')+'\n'))
128 2439 aaronmk
    if debug: log_debug = lambda msg, level=2: log(msg, level)
129 1901 aaronmk
    else: log_debug = sql.log_debug_none
130 662 aaronmk
131 53 aaronmk
    # Parse args
132 510 aaronmk
    map_paths = sys.argv[1:]
133 512 aaronmk
    if map_paths == []:
134
        if in_is_db or not out_is_db: usage_err()
135
        else: map_paths = [None]
136 53 aaronmk
137 646 aaronmk
    def connect_db(db_config):
138 1901 aaronmk
        log('Connecting to '+sql.db_config_str(db_config))
139 2920 aaronmk
        return sql.connect(db_config, caching=cache_sql, autocommit=commit,
140 2916 aaronmk
            debug_temp=verbosity > 3 and commit, log_debug=log_debug)
141 646 aaronmk
142 1945 aaronmk
    if end != None: end_str = str(end-1) # end is one past the last #
143 1573 aaronmk
    else: end_str = 'end'
144 1901 aaronmk
    log('Processing input rows '+str(start)+'-'+end_str)
145 1573 aaronmk
146 1014 aaronmk
    ex_tracker = exc.ExPercentTracker(iter_text='row')
147
    profiler = profiling.ItersProfiler(start_now=True, iter_text='row')
148
149 1856 aaronmk
    # Parallel processing
150 2035 aaronmk
    pool = parallelproc.MultiProducerPool(cpus)
151 1901 aaronmk
    log('Using '+str(pool.process_ct)+' parallel CPUs')
152 1846 aaronmk
153 1014 aaronmk
    doc = xml_dom.create_doc()
154
    root = doc.documentElement
155 751 aaronmk
    out_is_xml_ref = [False]
156 1014 aaronmk
    in_label_ref = [None]
157
    def update_in_label():
158
        if in_label_ref[0] != None:
159
            xpath.get(root, '/_ignore/inLabel="'+in_label_ref[0]+'"', True)
160
    def prep_root():
161
        root.clear()
162
        update_in_label()
163
    prep_root()
164 751 aaronmk
165 1991 aaronmk
    # Define before the out_is_db section because it's used by by_col
166
    row_ins_ct_ref = [0]
167
168 2601 aaronmk
    if out_is_db:
169
        out_db = connect_db(out_db_config)
170 2602 aaronmk
        rel_funcs = set(sql.tables(out_db, schema_like='%',
171 2601 aaronmk
            table_like=r'\__%'))
172
173 838 aaronmk
    def process_input(root, row_ready, map_path):
174 512 aaronmk
        '''Inputs datasource to XML tree, mapping if needed'''
175
        # Load map header
176
        in_is_xpaths = True
177 751 aaronmk
        out_is_xpaths = True
178 512 aaronmk
        out_label = None
179
        if map_path != None:
180
            metadata = []
181
            mappings = []
182
            stream = open(map_path, 'rb')
183
            reader = csv.reader(stream)
184
            in_label, out_label = reader.next()[:2]
185 1402 aaronmk
186 512 aaronmk
            def split_col_name(name):
187 1402 aaronmk
                label, sep, root = name.partition(':')
188
                label, sep2, prefixes_str = label.partition('[')
189
                prefixes_str = strings.remove_suffix(']', prefixes_str)
190
                prefixes = strings.split(',', prefixes_str)
191
                return label, sep != '', root, prefixes
192 1198 aaronmk
                    # extract datasrc from "datasrc[data_format]"
193 1402 aaronmk
194 1705 aaronmk
            in_label, in_root, prefixes = maps.col_info(in_label)
195
            in_is_xpaths = in_root != None
196 1014 aaronmk
            in_label_ref[0] = in_label
197
            update_in_label()
198 1705 aaronmk
            out_label, out_root = maps.col_info(out_label)[:2]
199
            out_is_xpaths = out_root != None
200 1841 aaronmk
            if out_is_xpaths: has_types = out_root.find('/*s/') >= 0
201 1705 aaronmk
                # outer elements are types
202 1402 aaronmk
203 512 aaronmk
            for row in reader:
204
                in_, out = row[:2]
205 2029 aaronmk
                if out != '': mappings.append([in_, out_root+out])
206 1402 aaronmk
207 512 aaronmk
            stream.close()
208
209
            root.ownerDocument.documentElement.tagName = out_label
210
        in_is_xml = in_is_xpaths and not in_is_db
211 751 aaronmk
        out_is_xml_ref[0] = out_is_xpaths and not out_is_db
212 56 aaronmk
213 1897 aaronmk
        def process_rows(process_row, rows, rows_start=0):
214
            '''Processes input rows
215 838 aaronmk
            @param process_row(in_row, i)
216 1945 aaronmk
            @rows_start The (0-based) row # of the first row in rows. Set this
217
                only if the pre-start rows have already been skipped.
218 297 aaronmk
            '''
219 1897 aaronmk
            rows = iter(rows)
220
221
            if end != None: row_nums = xrange(rows_start, end)
222
            else: row_nums = itertools.count(rows_start)
223 2038 aaronmk
            i = -1
224 1897 aaronmk
            for i in row_nums:
225 1718 aaronmk
                try: row = rows.next()
226 2038 aaronmk
                except StopIteration:
227
                    i -= 1 # last row # didn't count
228
                    break # no more rows
229 1718 aaronmk
                if i < start: continue # not at start row yet
230
231 2881 aaronmk
                # Row # is interally 0-based, but 1-based to the user
232
                log('Processing input row #'+str(i+1), level=1.1)
233 838 aaronmk
                process_row(row, i)
234
                row_ready(i, row)
235 2033 aaronmk
            row_ct = i-start+1
236 982 aaronmk
            return row_ct
237 838 aaronmk
238 1898 aaronmk
        def map_rows(get_value, rows, **kw_args):
239 838 aaronmk
            '''Maps input rows
240
            @param get_value(in_, row):str
241
            '''
242 2030 aaronmk
            # Prevent collisions if multiple inputs mapping to same output
243
            outputs_idxs = dict()
244
            for i, mapping in enumerate(mappings):
245
                in_, out = mapping
246
                default = util.NamedTuple(count=1, first=i)
247
                idxs = outputs_idxs.setdefault(out, default)
248
                if idxs is not default: # key existed, so there was a collision
249
                    if idxs.count == 1: # first key does not yet have /_alt/#
250
                        mappings[idxs.first][1] += '/_alt/0'
251
                    mappings[i][1] += '/_alt/'+str(idxs.count)
252
                    idxs.count += 1
253
254 2026 aaronmk
            id_node = None
255
            if out_is_db:
256
                for i, mapping in enumerate(mappings):
257
                    in_, out = mapping
258
                    # All put_obj()s should return the same id_node
259
                    nodes, id_node = xpath.put_obj(root, out, '-1', has_types,
260
                        '$'+str(in_)) # value is placeholder that documents name
261 2032 aaronmk
                    mappings[i] = [in_, nodes]
262
                assert id_node != None
263 2026 aaronmk
264 2119 aaronmk
                if debug: # only calc if debug
265 2026 aaronmk
                    log_debug('Put template:\n'+str(root))
266
267 838 aaronmk
            def process_row(row, i):
268 316 aaronmk
                row_id = str(i)
269 2032 aaronmk
                if id_node != None: xml_dom.set_value(id_node, row_id)
270 316 aaronmk
                for in_, out in mappings:
271 2027 aaronmk
                    log_debug('Getting '+str(in_))
272 316 aaronmk
                    value = metadata_value(in_)
273 2027 aaronmk
                    if value == None: value = cleanup(get_value(in_, row))
274
                    log_debug('Putting '+repr(value)+' to '+str(out))
275 2032 aaronmk
                    if out_is_db: # out is list of XML nodes
276
                        for node in out: xml_dom.set_value(node, value)
277
                    elif value != None: # out is XPath
278 1360 aaronmk
                        xpath.put_obj(root, out, row_id, has_types, value)
279 1898 aaronmk
            return process_rows(process_row, rows, **kw_args)
280 297 aaronmk
281 1898 aaronmk
        def map_table(col_names, rows, **kw_args):
282 1416 aaronmk
            col_names_ct = len(col_names)
283 1403 aaronmk
            col_idxs = util.list_flip(col_names)
284
285 2029 aaronmk
            # Resolve prefixes
286 2025 aaronmk
            mappings_orig = mappings[:] # save a copy
287
            mappings[:] = [] # empty existing elements
288
            for in_, out in mappings_orig:
289 1403 aaronmk
                if metadata_value(in_) == None:
290 2040 aaronmk
                    try: cols = get_with_prefix(col_idxs, prefixes, in_)
291 2025 aaronmk
                    except KeyError: pass
292 2040 aaronmk
                    else: mappings[len(mappings):] = [[db_xml.ColRef(*col), out]
293
                        for col in cols] # can't use += because that uses =
294 1403 aaronmk
295 2040 aaronmk
            def get_value(in_, row): return row.list[in_.idx]
296 1416 aaronmk
            def wrap_row(row):
297
                return util.ListDict(util.list_as_length(row, col_names_ct),
298
                    col_names, col_idxs) # handle CSV rows of different lengths
299 1403 aaronmk
300 1898 aaronmk
            return map_rows(get_value, util.WrapIter(wrap_row, rows), **kw_args)
301 1403 aaronmk
302 1700 aaronmk
        if in_is_db:
303 2809 aaronmk
            def on_error(e): ex_tracker.track(e)
304
305 1982 aaronmk
            in_db = connect_db(in_db_config)
306 126 aaronmk
307 1982 aaronmk
            # Get table and schema name
308
            schema = in_schema # modified, so can't have same name as outer var
309
            table = in_table # modified, so can't have same name as outer var
310
            if table == None:
311
                assert in_is_xpaths
312
                schema, sep, table = in_root.partition('.')
313
                if sep == '': # only the table name was specified
314
                    table = schema
315
                    schema = None
316 2313 aaronmk
            table = sql_gen.Table(table, schema)
317 1982 aaronmk
318 1991 aaronmk
            # Fetch rows
319
            if by_col: limit = 0 # only fetch column names
320
            else: limit = n
321 2313 aaronmk
            cur = sql.select(in_db, table, limit=limit, start=start,
322
                cacheable=False)
323 1991 aaronmk
            col_names = list(sql.col_names(cur))
324
325 1989 aaronmk
            if by_col:
326 2042 aaronmk
                map_table(col_names, []) # just create the template
327 2550 aaronmk
328 2734 aaronmk
                if n == None: # doing full import
329
                    log('Clearing errors table')
330 3103 aaronmk
                    sql.truncate(in_db, sql_io.errors_table(in_db, table))
331 2734 aaronmk
332 2550 aaronmk
                # Strip XML functions not in the DB
333 2602 aaronmk
                special_funcs = db_xml.put_table_special_funcs | rel_funcs
334
                xml_func.process(root, rel_funcs=special_funcs)
335 2103 aaronmk
                if debug: log_debug('Putting stripped:\n'+str(root))
336 2119 aaronmk
                    # only calc if debug
337 2550 aaronmk
338
                # Import rows
339 2422 aaronmk
                in_row_ct_ref = [0]
340 2928 aaronmk
                db_xml.put_table(in_db, root.firstChild, table, in_row_ct_ref,
341
                    row_ins_ct_ref, n, start, on_error)
342 2422 aaronmk
                row_ct = in_row_ct_ref[0]
343 1984 aaronmk
            else:
344
                # Use normal by-row method
345 1991 aaronmk
                row_ct = map_table(col_names, sql.rows(cur), rows_start=start)
346
                    # rows_start: pre-start rows have been skipped
347 1136 aaronmk
348 1849 aaronmk
            in_db.db.close()
349 161 aaronmk
        elif in_is_xml:
350 2809 aaronmk
            stdin = streams.LineCountStream(sys.stdin)
351
            def on_error(e):
352
                exc.add_msg(e, term.emph('input line #:')+' '
353
                    +str(stdin.line_num))
354
                ex_tracker.track(e)
355
356 1715 aaronmk
            def get_rows(doc2rows):
357 1758 aaronmk
                return iters.flatten(itertools.imap(doc2rows,
358
                    xml_parse.docs_iter(stdin, on_error)))
359 1715 aaronmk
360 1714 aaronmk
            if map_path == None:
361 1715 aaronmk
                def doc2rows(in_xml_root):
362 1701 aaronmk
                    iter_ = xml_dom.NodeElemIter(in_xml_root)
363
                    util.skip(iter_, xml_dom.is_text) # skip metadata
364 1715 aaronmk
                    return iter_
365
366
                row_ct = process_rows(lambda row, i: root.appendChild(row),
367
                    get_rows(doc2rows))
368 1714 aaronmk
            else:
369 1715 aaronmk
                def doc2rows(in_xml_root):
370 1701 aaronmk
                    rows = xpath.get(in_xml_root, in_root, limit=end)
371 1714 aaronmk
                    if rows == []: raise SystemExit('Map error: Root "'
372
                        +in_root+'" not found in input')
373
                    return rows
374
375
                def get_value(in_, row):
376
                    in_ = './{'+(','.join(strings.with_prefixes(
377
                        ['']+prefixes, in_)))+'}' # also with no prefix
378
                    nodes = xpath.get(row, in_, allow_rooted=False)
379
                    if nodes != []: return xml_dom.value(nodes[0])
380
                    else: return None
381
382 1715 aaronmk
                row_ct = map_rows(get_value, get_rows(doc2rows))
383 56 aaronmk
        else: # input is CSV
384 133 aaronmk
            map_ = dict(mappings)
385 1389 aaronmk
            reader, col_names = csvs.reader_and_header(sys.stdin)
386 1403 aaronmk
            row_ct = map_table(col_names, reader)
387 982 aaronmk
388
        return row_ct
389 53 aaronmk
390 838 aaronmk
    def process_inputs(root, row_ready):
391 982 aaronmk
        row_ct = 0
392
        for map_path in map_paths:
393
            row_ct += process_input(root, row_ready, map_path)
394
        return row_ct
395 512 aaronmk
396 1886 aaronmk
    pool.share_vars(locals())
397 130 aaronmk
    if out_is_db:
398 53 aaronmk
        try:
399 947 aaronmk
            if redo: sql.empty_db(out_db)
400 1886 aaronmk
            pool.share_vars(locals())
401 449 aaronmk
402 838 aaronmk
            def row_ready(row_num, input_row):
403 2119 aaronmk
                row_str_ = [None]
404
                def row_str():
405
                    if row_str_[0] == None:
406
                        # Row # is interally 0-based, but 1-based to the user
407
                        row_str_[0] = (term.emph('row #:')+' '+str(row_num+1)
408
                            +'\n'+term.emph('input row:')+'\n'+str(input_row))
409
                        if verbose_errors: row_str_[0] += ('\n'
410
                            +term.emph('output row:')+'\n'+str(root))
411
                    return row_str_[0]
412
413
                if debug: log_debug(row_str()) # only calc if debug
414
415 452 aaronmk
                def on_error(e):
416 2119 aaronmk
                    exc.add_msg(e, row_str())
417 2046 aaronmk
                    ex_tracker.track(e, row_num, detail=verbose_errors)
418 1886 aaronmk
                pool.share_vars(locals())
419 452 aaronmk
420 2032 aaronmk
                row_root = root.cloneNode(True) # deep copy so don't modify root
421 2639 aaronmk
                xml_func.process(row_root, on_error, rel_funcs, out_db)
422 2032 aaronmk
                if not xml_dom.is_empty(row_root):
423
                    assert xml_dom.has_one_child(row_root)
424 442 aaronmk
                    try:
425 982 aaronmk
                        sql.with_savepoint(out_db,
426 2032 aaronmk
                            lambda: db_xml.put(out_db, row_root.firstChild,
427 1850 aaronmk
                                row_ins_ct_ref, on_error))
428 449 aaronmk
                    except sql.DatabaseErrors, e: on_error(e)
429
430 982 aaronmk
            row_ct = process_inputs(root, row_ready)
431
            sys.stdout.write('Inserted '+str(row_ins_ct_ref[0])+
432 460 aaronmk
                ' new rows into database\n')
433 1868 aaronmk
434
            # Consume asynchronous tasks
435
            pool.main_loop()
436 3117 aaronmk
        finally: out_db.close()
437 751 aaronmk
    else:
438 759 aaronmk
        def on_error(e): ex_tracker.track(e)
439 838 aaronmk
        def row_ready(row_num, input_row): pass
440 982 aaronmk
        row_ct = process_inputs(root, row_ready)
441 759 aaronmk
        xml_func.process(root, on_error)
442 751 aaronmk
        if out_is_xml_ref[0]:
443
            doc.writexml(sys.stdout, **xml_dom.prettyxml_config)
444
        else: # output is CSV
445
            raise NotImplementedError('CSV output not supported yet')
446 985 aaronmk
447 1868 aaronmk
    # Consume any asynchronous tasks not already consumed above
448 1862 aaronmk
    pool.main_loop()
449
450 982 aaronmk
    profiler.stop(row_ct)
451
    ex_tracker.add_iters(row_ct)
452 2439 aaronmk
    log('Processed '+str(row_ct)+' input rows')
453
    log(profiler.msg())
454
    log(ex_tracker.msg())
455 985 aaronmk
    ex_tracker.exit()
456 53 aaronmk
457 847 aaronmk
def main():
458
    try: main_()
459 1719 aaronmk
    except Parser.SyntaxError, e: raise SystemExit(str(e))
460 847 aaronmk
461 846 aaronmk
if __name__ == '__main__':
462 847 aaronmk
    profile_to = opts.get_env_var('profile_to', None)
463
    if profile_to != None:
464
        import cProfile
465 1584 aaronmk
        sys.stderr.write('Profiling to '+profile_to+'\n')
466 847 aaronmk
        cProfile.run(main.func_code, profile_to)
467
    else: main()