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 53 aaronmk
import os.path
9
import sys
10 299 aaronmk
import xml.dom.minidom as minidom
11 53 aaronmk
12 266 aaronmk
sys.path.append(os.path.dirname(__file__)+"/../lib")
13 53 aaronmk
14 344 aaronmk
import exc
15 64 aaronmk
import opts
16 281 aaronmk
import Parser
17 982 aaronmk
import profiling
18 131 aaronmk
import sql
19 715 aaronmk
import strings
20 828 aaronmk
import term
21 310 aaronmk
import util
22 1014 aaronmk
import xpath
23 133 aaronmk
import xml_dom
24 86 aaronmk
import xml_func
25 53 aaronmk
26 1018 aaronmk
def metadata_value(name): return None # this feature has been removed
27 84 aaronmk
28 847 aaronmk
def main_():
29 131 aaronmk
    env_names = []
30
    def usage_err():
31 944 aaronmk
        raise SystemExit('Usage: '+opts.env_usage(env_names, True)+' '
32 847 aaronmk
            +sys.argv[0]+' [map_path...] [<input] [>output]')
33 838 aaronmk
34
    # Get db config from env vars
35
    db_config_names = ['engine', 'host', 'user', 'password', 'database']
36
    def get_db_config(prefix):
37
        return opts.get_env_vars(db_config_names, prefix, env_names)
38
    in_db_config = get_db_config('in')
39
    out_db_config = get_db_config('out')
40
    in_is_db = 'engine' in in_db_config
41
    out_is_db = 'engine' in out_db_config
42
43
    # Get other config from env vars
44
    end = util.cast(int, opts.get_env_var('n', None, env_names))
45
    start = util.cast(int, opts.get_env_var('start', '0', env_names))
46
    if end != None: end += start
47 946 aaronmk
    test = opts.env_flag('test', False, env_names)
48 947 aaronmk
    commit = opts.env_flag('commit', False, env_names) and not test
49 944 aaronmk
        # never commit in test mode
50 947 aaronmk
    redo = opts.env_flag('redo', test, env_names) and not commit
51
        # never redo in commit mode (manually run `make empty_db` instead)
52 946 aaronmk
    debug = opts.env_flag('debug', False, env_names)
53 859 aaronmk
    sql.run_raw_query.debug = debug
54 946 aaronmk
    verbose = debug or opts.env_flag('verbose', False, env_names)
55 944 aaronmk
    opts.get_env_var('profile_to', None, env_names) # add to env_names
56 131 aaronmk
57 838 aaronmk
    # Logging
58 662 aaronmk
    def log(msg, on=verbose):
59
        if on: sys.stderr.write(msg)
60 859 aaronmk
    def log_start(action, on=verbose): log(action+'...\n', on)
61 662 aaronmk
62 53 aaronmk
    # Parse args
63 510 aaronmk
    map_paths = sys.argv[1:]
64 512 aaronmk
    if map_paths == []:
65
        if in_is_db or not out_is_db: usage_err()
66
        else: map_paths = [None]
67 53 aaronmk
68 646 aaronmk
    def connect_db(db_config):
69 662 aaronmk
        log_start('Connecting to '+sql.db_config_str(db_config))
70 1014 aaronmk
        return sql.connect(db_config)
71 646 aaronmk
72 1014 aaronmk
    ex_tracker = exc.ExPercentTracker(iter_text='row')
73
    profiler = profiling.ItersProfiler(start_now=True, iter_text='row')
74
75
    doc = xml_dom.create_doc()
76
    root = doc.documentElement
77 751 aaronmk
    out_is_xml_ref = [False]
78 1014 aaronmk
    in_label_ref = [None]
79
    def update_in_label():
80
        if in_label_ref[0] != None:
81
            xpath.get(root, '/_ignore/inLabel="'+in_label_ref[0]+'"', True)
82
    def prep_root():
83
        root.clear()
84
        update_in_label()
85
    prep_root()
86 751 aaronmk
87 838 aaronmk
    def process_input(root, row_ready, map_path):
88 512 aaronmk
        '''Inputs datasource to XML tree, mapping if needed'''
89
        # Load map header
90
        in_is_xpaths = True
91 751 aaronmk
        out_is_xpaths = True
92 512 aaronmk
        out_label = None
93
        if map_path != None:
94
            metadata = []
95
            mappings = []
96
            stream = open(map_path, 'rb')
97
            reader = csv.reader(stream)
98
            in_label, out_label = reader.next()[:2]
99
            def split_col_name(name):
100
                name, sep, root = name.partition(':')
101 1122 aaronmk
                return name.partition('-')[0], sep != '', root
102
                    # extract datasrc from "datasrc-data_format"
103 512 aaronmk
            in_label, in_is_xpaths, in_root = split_col_name(in_label)
104 1014 aaronmk
            in_label_ref[0] = in_label
105
            update_in_label()
106 512 aaronmk
            out_label, out_is_xpaths, out_root = split_col_name(out_label)
107
            has_types = out_root.startswith('/*s/') # outer elements are types
108
            for row in reader:
109
                in_, out = row[:2]
110
                if out != '':
111
                    if out_is_xpaths: out = xpath.parse(out_root+out)
112
                    mappings.append((in_, out))
113
            stream.close()
114
115
            root.ownerDocument.documentElement.tagName = out_label
116
        in_is_xml = in_is_xpaths and not in_is_db
117 751 aaronmk
        out_is_xml_ref[0] = out_is_xpaths and not out_is_db
118 56 aaronmk
119 512 aaronmk
        if in_is_xml:
120
            doc0 = minidom.parse(sys.stdin)
121 1006 aaronmk
            doc0_root = doc0.documentElement
122
            if out_label == None: out_label = doc0_root.tagName
123 53 aaronmk
124 838 aaronmk
        def process_rows(process_row, rows):
125
            '''Processes input rows
126
            @param process_row(in_row, i)
127 297 aaronmk
            '''
128 838 aaronmk
            i = -1 # in case for loop does not execute
129 314 aaronmk
            for i, row in enumerate(rows):
130 838 aaronmk
                if i < start: continue
131
                if end != None and i >= end: break
132
                process_row(row, i)
133
                row_ready(i, row)
134 978 aaronmk
            row_ct = i-start+1
135 982 aaronmk
            return row_ct
136 838 aaronmk
137
        def map_rows(get_value, rows):
138
            '''Maps input rows
139
            @param get_value(in_, row):str
140
            '''
141
            def process_row(row, i):
142 316 aaronmk
                row_id = str(i)
143
                for in_, out in mappings:
144
                    value = metadata_value(in_)
145 662 aaronmk
                    if value == None:
146 857 aaronmk
                        log_start('Getting '+str(in_), debug)
147 662 aaronmk
                        value = get_value(in_, row)
148 715 aaronmk
                    if value != None: xpath.put_obj(root, out, row_id,
149
                        has_types, strings.cleanup(value))
150 982 aaronmk
            return process_rows(process_row, rows)
151 297 aaronmk
152 310 aaronmk
        if map_path == None:
153 1006 aaronmk
            iter_ = xml_dom.NodeElemIter(doc0_root)
154 310 aaronmk
            util.skip(iter_, xml_dom.is_text) # skip metadata
155 982 aaronmk
            row_ct = process_rows(lambda row, i: root.appendChild(row), iter_)
156 309 aaronmk
        elif in_is_db:
157 130 aaronmk
            assert in_is_xpaths
158 126 aaronmk
159 117 aaronmk
            import db_xml
160
161 161 aaronmk
            in_root_xml = xpath.path2xml(in_root)
162 164 aaronmk
            for i, mapping in enumerate(mappings):
163
                in_, out = mapping
164
                if metadata_value(in_) == None:
165 168 aaronmk
                    mappings[i] = (xpath.path2xml(in_root+'/'+in_), out)
166 126 aaronmk
167 646 aaronmk
            in_db = connect_db(in_db_config)
168 133 aaronmk
            in_pkeys = {}
169 297 aaronmk
            def get_value(in_, row):
170 167 aaronmk
                pkey, = row
171 297 aaronmk
                in_ = in_.cloneNode(True) # don't modify orig value!
172 886 aaronmk
                xml_dom.set_id(xpath.get(in_, in_root)[0], pkey)
173 297 aaronmk
                value = sql.value_or_none(db_xml.get(in_db, in_, in_pkeys))
174
                if value != None: return str(value)
175
                else: return None
176 982 aaronmk
            row_ct = map_rows(get_value, sql.rows(db_xml.get(in_db, in_root_xml,
177 865 aaronmk
                in_pkeys, end, 0)))
178 117 aaronmk
            in_db.close()
179 161 aaronmk
        elif in_is_xml:
180 297 aaronmk
            def get_value(in_, row):
181 1005 aaronmk
                nodes = xpath.get(row, in_, allow_rooted=False)
182 886 aaronmk
                if nodes != []: return xml_dom.value(nodes[0])
183 297 aaronmk
                else: return None
184 1006 aaronmk
            rows = xpath.get(doc0_root, in_root, limit=end)
185 886 aaronmk
            if rows == []: raise SystemExit('Map error: Root "'+in_root
186 883 aaronmk
                +'" not found in input')
187 982 aaronmk
            row_ct = map_rows(get_value, rows)
188 56 aaronmk
        else: # input is CSV
189 133 aaronmk
            map_ = dict(mappings)
190 59 aaronmk
            reader = csv.reader(sys.stdin)
191 84 aaronmk
            cols = reader.next()
192 162 aaronmk
            col_idxs = dict([(value, idx) for idx, value in enumerate(cols)])
193 164 aaronmk
            for i, mapping in enumerate(mappings):
194
                in_, out = mapping
195
                if metadata_value(in_) == None:
196
                    try: mappings[i] = (col_idxs[in_], out)
197
                    except KeyError: pass
198 162 aaronmk
199 297 aaronmk
            def get_value(in_, row):
200 1133 aaronmk
                try: value = row[in_]
201
                except KeyError: pass
202 297 aaronmk
                if value != '': return value
203
                else: return None
204 982 aaronmk
            row_ct = map_rows(get_value, reader)
205
206
        return row_ct
207 53 aaronmk
208 838 aaronmk
    def process_inputs(root, row_ready):
209 982 aaronmk
        row_ct = 0
210
        for map_path in map_paths:
211
            row_ct += process_input(root, row_ready, map_path)
212
        return row_ct
213 512 aaronmk
214 130 aaronmk
    if out_is_db:
215 53 aaronmk
        import db_xml
216
217 646 aaronmk
        out_db = connect_db(out_db_config)
218 310 aaronmk
        out_pkeys = {}
219 53 aaronmk
        try:
220 947 aaronmk
            if redo: sql.empty_db(out_db)
221 982 aaronmk
            row_ins_ct_ref = [0]
222 449 aaronmk
223 838 aaronmk
            def row_ready(row_num, input_row):
224 452 aaronmk
                def on_error(e):
225 835 aaronmk
                    exc.add_msg(e, term.emph('row #:')+' '+str(row_num))
226 828 aaronmk
                    exc.add_msg(e, term.emph('input row:')+'\n'+str(input_row))
227
                    exc.add_msg(e, term.emph('output row:')+'\n'+str(root))
228 452 aaronmk
                    ex_tracker.track(e)
229
230 449 aaronmk
                xml_func.process(root, on_error)
231 442 aaronmk
                if not xml_dom.is_empty(root):
232
                    assert xml_dom.has_one_child(root)
233
                    try:
234 982 aaronmk
                        sql.with_savepoint(out_db,
235
                            lambda: db_xml.put(out_db, root.firstChild,
236
                                out_pkeys, row_ins_ct_ref, on_error))
237 442 aaronmk
                        if commit: out_db.commit()
238 449 aaronmk
                    except sql.DatabaseErrors, e: on_error(e)
239 1010 aaronmk
                prep_root()
240 449 aaronmk
241 982 aaronmk
            row_ct = process_inputs(root, row_ready)
242
            sys.stdout.write('Inserted '+str(row_ins_ct_ref[0])+
243 460 aaronmk
                ' new rows into database\n')
244 53 aaronmk
        finally:
245 133 aaronmk
            out_db.rollback()
246
            out_db.close()
247 751 aaronmk
    else:
248 759 aaronmk
        def on_error(e): ex_tracker.track(e)
249 838 aaronmk
        def row_ready(row_num, input_row): pass
250 982 aaronmk
        row_ct = process_inputs(root, row_ready)
251 759 aaronmk
        xml_func.process(root, on_error)
252 751 aaronmk
        if out_is_xml_ref[0]:
253
            doc.writexml(sys.stdout, **xml_dom.prettyxml_config)
254
        else: # output is CSV
255
            raise NotImplementedError('CSV output not supported yet')
256 985 aaronmk
257 982 aaronmk
    profiler.stop(row_ct)
258
    ex_tracker.add_iters(row_ct)
259 990 aaronmk
    if verbose:
260
        sys.stderr.write('Processed '+str(row_ct)+' input rows\n')
261
        sys.stderr.write(profiler.msg()+'\n')
262
        sys.stderr.write(ex_tracker.msg()+'\n')
263 985 aaronmk
    ex_tracker.exit()
264 53 aaronmk
265 847 aaronmk
def main():
266
    try: main_()
267
    except Parser.SyntaxException, e: raise SystemExit(str(e))
268
269 846 aaronmk
if __name__ == '__main__':
270 847 aaronmk
    profile_to = opts.get_env_var('profile_to', None)
271
    if profile_to != None:
272
        import cProfile
273
        cProfile.run(main.func_code, profile_to)
274
    else: main()