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Revision 73

Added by Aaron Marcuse-Kubitza almost 13 years ago

map: Fixed bugs to enable mapping straight from CSV to a database. Still need a way to set plot.authorPlotCode for specimens data.

View differences:

map
22 22 
    out_db_config = get_db_config('out')
23 23 
    in_is_db = in_db_config != None
24 24 
    out_is_db = out_db_config != None
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    uses_map = in_is_db or not out_is_db
26 25
27 26 
    # Parse args
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    map_path = None
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    try: _prog_name, map_path = sys.argv
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    except ValueError:
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        if uses_map: raise SystemExit('Usage: '+opts.env_usage(env_names, True)
31 
            +' [commit=1] '+sys.argv[0]+' [map_path] [<input] [>output]')
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        if in_is_db or not out_is_db: raise SystemExit('Usage: '
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            +opts.env_usage(env_names, True)+' [commit=1] '+sys.argv[0]
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            +' [map_path] [<input] [>output]')
32 33 
    commit = opts.env_flag('commit')
33 34
34 35 
    # Load map header
35 36 
    in_is_xml = True
36 
    if uses_map:
37 
    if map_path != None:
37 38 
        import copy
38 39 
        import csv
39 40
40 41 
        import xpath
41 42
42 
        map_stream = open(map_path, 'rb')
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        map_reader = csv.reader(map_stream)
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        src, dest = map_reader.next()[:2]
43 
        mappings = []
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        stream = open(map_path, 'rb')
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        reader = csv.reader(stream)
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        src, dest = reader.next()[:2]
45 47 
        def split_col_name(name):
46 48 
            name, sep, root = name.partition(':')
47 49 
            return name, sep != '', root
......
49 51 
        dest, out_is_xml, dest_root = split_col_name(dest)
50 52 
        assert out_is_xml
51 53 
        has_types = dest_root.startswith('/*s/') # outer elements are types
54 
        for row in reader:
55 
            in_, out = row[:2]
56 
            if out != '':
57 
                try: out = xpath.parse(dest_root+out)
58 
                except SyntaxException, ex: raise SystemExit(str(ex))
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                mappings.append((in_, out))
60 
        stream.close()
52 61
53 62 
    # Input datasource to XML tree, mapping if needed
54 63 
    if in_is_xml: doc = xml.dom.minidom.parse(sys.stdin)
55 
    if uses_map:
64 
    if map_path != None:
56 65 
        from Parser import SyntaxException
57 66 
        import xml_xpath
58 67
59 
        map_ = {}
60 
        for row in map_reader:
61 
            in_, out = row[:2]
62 
            if out != '':
63 
                try: out = xpath.parse(dest_root+out)
64 
                except SyntaxException, ex: raise SystemExit(str(ex))
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                if in_is_xml: pass # TODO: process the mapping
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                elif in_is_db: pass # TODO: process the mapping
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                else: map_[in_] = out
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        map_stream.close()
69
70 68 
        out_doc = xml.dom.minidom.getDOMImplementation().createDocument(None,
71 69 
            dest, None)
72 70 
        if in_is_xml: raise Exception('XML-XML mapping not supported yet')
71 
        elif in_is_db: raise Exception('DB-XML mapping not supported yet')
73 72 
        else: # input is CSV
73 
            map_ = dict(mappings)
74 74 
            reader = csv.reader(sys.stdin)
75 75 
            fieldnames = reader.next()
76 76 
            row_idx = 0

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