Project

General

Profile

1
#!/usr/bin/env python
2
# Maps one datasource to another, using a map spreadsheet if needed
3
# For outputting an XML file to a PostgreSQL database, use the general format of
4
# http://vegbank.org/vegdocs/xml/vegbank_example_ver1.0.2.xml
5

    
6
import os.path
7
import sys
8
import xml.dom.minidom as minidom
9

    
10
sys.path.append(os.path.dirname(__file__)+"/../lib")
11

    
12
import exc
13
import opts
14
import Parser
15
import sql
16
import strings
17
import util
18
import xml_dom
19
import xml_func
20

    
21
def metadata_value(name):
22
    if type(name) == str and name.startswith(':'): return name[1:]
23
    else: return None
24

    
25
def main():
26
    ex_tracker = exc.ExTracker()
27
    
28
    env_names = []
29
    def usage_err():
30
        raise SystemExit('Usage: ' + opts.env_usage(env_names, True)
31
            +' [commit=1] [test=1] [verbose=1] [debug=1] '+sys.argv[0]
32
            +' [map_path...] [<input] [>output]')
33
    limit = opts.get_env_var('n', None, env_names)
34
    if limit != None: limit = int(limit)
35
    test = opts.env_flag('test')
36
    commit = not test and opts.env_flag('commit') # never commit in test mode
37
    debug = opts.env_flag('debug')
38
    verbose = debug or opts.env_flag('verbose')
39
    
40
    def log(msg, on=verbose):
41
        if on: sys.stderr.write(msg)
42
    def log_start(action, on=verbose): log(action+'...', on)
43
    def log_done(on=verbose): log('Done\n', on)
44
    
45
    # Get db config from env vars
46
    db_config_names = ['engine', 'host', 'user', 'password', 'database']
47
    def get_db_config(prefix):
48
        return opts.get_env_vars(db_config_names, prefix, env_names)
49
    in_db_config = get_db_config('in')
50
    out_db_config = get_db_config('out')
51
    in_is_db = 'engine' in in_db_config
52
    out_is_db = 'engine' in out_db_config
53
    
54
    # Parse args
55
    map_paths = sys.argv[1:]
56
    if map_paths == []:
57
        if in_is_db or not out_is_db: usage_err()
58
        else: map_paths = [None]
59
    
60
    def connect_db(db_config):
61
        log_start('Connecting to '+sql.db_config_str(db_config))
62
        db = sql.connect(db_config)
63
        log_done()
64
        return db
65
    
66
    def process_input(root, process_row, map_path):
67
        '''Inputs datasource to XML tree, mapping if needed'''
68
        # Load map header
69
        in_is_xpaths = True
70
        out_label = None
71
        if map_path != None:
72
            import copy
73
            import csv
74
            
75
            import xpath
76
            
77
            metadata = []
78
            mappings = []
79
            stream = open(map_path, 'rb')
80
            reader = csv.reader(stream)
81
            in_label, out_label = reader.next()[:2]
82
            def split_col_name(name):
83
                name, sep, root = name.partition(':')
84
                return name, sep != '', root
85
            in_label, in_is_xpaths, in_root = split_col_name(in_label)
86
            out_label, out_is_xpaths, out_root = split_col_name(out_label)
87
            assert out_is_xpaths # CSV output not supported yet
88
            has_types = out_root.startswith('/*s/') # outer elements are types
89
            for row in reader:
90
                in_, out = row[:2]
91
                if out != '':
92
                    if out_is_xpaths: out = xpath.parse(out_root+out)
93
                    mappings.append((in_, out))
94
            stream.close()
95
            
96
            root.ownerDocument.documentElement.tagName = out_label
97
        in_is_xml = in_is_xpaths and not in_is_db
98
        
99
        if in_is_xml:
100
            doc0 = minidom.parse(sys.stdin)
101
            if out_label == None: out_label = doc0.documentElement.tagName
102
        
103
        def process_rows(get_value, rows):
104
            '''Processes input values
105
            @param get_value f(in_, row):str
106
            '''
107
            for i, row in enumerate(rows):
108
                if not (limit == None or i < limit): break
109
                row_id = str(i)
110
                for in_, out in mappings:
111
                    value = metadata_value(in_)
112
                    if value == None:
113
                        log_start('Getting '+str(in_), debug)
114
                        value = get_value(in_, row)
115
                        log_done(debug)
116
                    if value != None: xpath.put_obj(root, out, row_id,
117
                        has_types, strings.cleanup(value))
118
                process_row(row)
119
            sys.stderr.write('Processed '+str(i+1)+' input rows\n')
120
        
121
        if map_path == None:
122
            iter_ = xml_dom.NodeElemIter(doc0.documentElement)
123
            util.skip(iter_, xml_dom.is_text) # skip metadata
124
            for child in iter_:
125
                root.appendChild(child)
126
                process_row(child)
127
        elif in_is_db:
128
            assert in_is_xpaths
129
            
130
            import db_xml
131
            
132
            in_root_xml = xpath.path2xml(in_root)
133
            for i, mapping in enumerate(mappings):
134
                in_, out = mapping
135
                if metadata_value(in_) == None:
136
                    mappings[i] = (xpath.path2xml(in_root+'/'+in_), out)
137
            
138
            in_db = connect_db(in_db_config)
139
            in_pkeys = {}
140
            def get_value(in_, row):
141
                pkey, = row
142
                in_ = in_.cloneNode(True) # don't modify orig value!
143
                xml_dom.set_id(xpath.get(in_, in_root), pkey)
144
                value = sql.value_or_none(db_xml.get(in_db, in_, in_pkeys))
145
                if value != None: return str(value)
146
                else: return None
147
            process_rows(get_value, sql.rows(db_xml.get(in_db, in_root_xml,
148
                in_pkeys, limit)))
149
            in_db.close()
150
        elif in_is_xml:
151
            def get_value(in_, row):
152
                node = xpath.get(row, in_)
153
                if node != None: return xml_dom.value(node)
154
                else: return None
155
            row0 = xpath.get(doc0.documentElement, in_root)
156
            process_rows(get_value, xml_dom.NodeElemIter(row0.parentNode))
157
        else: # input is CSV
158
            map_ = dict(mappings)
159
            reader = csv.reader(sys.stdin)
160
            cols = reader.next()
161
            col_idxs = dict([(value, idx) for idx, value in enumerate(cols)])
162
            for i, mapping in enumerate(mappings):
163
                in_, out = mapping
164
                if metadata_value(in_) == None:
165
                    try: mappings[i] = (col_idxs[in_], out)
166
                    except KeyError: pass
167
            
168
            def get_value(in_, row):
169
                value = row[in_]
170
                if value != '': return value
171
                else: return None
172
            process_rows(get_value, reader)
173
    
174
    def process_inputs(root, process_row):
175
        for map_path in map_paths: process_input(root, process_row, map_path)
176
    
177
    # Output XML tree
178
    doc = xml_dom.create_doc()
179
    root = doc.documentElement
180
    if out_is_db:
181
        import db_xml
182
        
183
        out_db = connect_db(out_db_config)
184
        out_pkeys = {}
185
        try:
186
            if test: sql.empty_db(out_db)
187
            row_ct_ref = [0]
188
            
189
            def process_row(input_row):
190
                def on_error(e):
191
                    exc.add_msg(e, 'output row:\n'+str(root))
192
                    exc.add_msg(e, 'input row:\n'+str(input_row))
193
                    ex_tracker.track(e)
194
                
195
                xml_func.process(root, on_error)
196
                if not xml_dom.is_empty(root):
197
                    assert xml_dom.has_one_child(root)
198
                    try:
199
                        sql.with_savepoint(out_db, lambda: db_xml.put(out_db,
200
                            root.firstChild, out_pkeys, row_ct_ref, on_error))
201
                        if commit: out_db.commit()
202
                    except sql.DatabaseErrors, e: on_error(e)
203
                root.clear()
204
            
205
            process_inputs(root, process_row)
206
            sys.stdout.write('Inserted '+str(row_ct_ref[0])+
207
                ' new rows into database\n')
208
        finally:
209
            out_db.rollback()
210
            out_db.close()
211
    else: # output is XML
212
        def process_row(input_row): pass
213
        process_inputs(root, process_row)
214
        xml_func.process(root)
215
        doc.writexml(sys.stdout, **xml_dom.prettyxml_config)
216

    
217
try: main()
218
except Parser.SyntaxException, e: raise SystemExit(str(e))
(9-9/17)