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aaronmk
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#!/usr/bin/env python
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# Maps one datasource to another, using a map spreadsheet if needed
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# For outputting an XML file to a PostgreSQL database, use the general format of
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# http://vegbank.org/vegdocs/xml/vegbank_example_ver1.0.2.xml
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import os.path
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import sys
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import xml.dom.minidom as minidom
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sys.path.append(os.path.dirname(__file__)+"/../lib")
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import exc
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import opts
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import Parser
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import sql
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import strings
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import term
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import util
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import xml_dom
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import xml_func
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def metadata_value(name):
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if type(name) == str and name.startswith(':'): return name[1:]
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else: return None
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def main():
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ex_tracker = exc.ExTracker()
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env_names = []
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def usage_err():
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raise SystemExit('Usage: ' + opts.env_usage(env_names, True)
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+' [commit=1] [test=1] [verbose=1] [debug=1] '+sys.argv[0]
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+' [map_path...] [<input] [>output]')
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limit = opts.get_env_var('n', None, env_names)
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if limit != None: limit = int(limit)
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test = opts.env_flag('test')
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commit = not test and opts.env_flag('commit') # never commit in test mode
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debug = opts.env_flag('debug')
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verbose = debug or opts.env_flag('verbose')
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def log(msg, on=verbose):
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if on: sys.stderr.write(msg)
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def log_start(action, on=verbose): log(action+'...', on)
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def log_done(on=verbose): log('Done\n', on)
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# Get db config from env vars
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db_config_names = ['engine', 'host', 'user', 'password', 'database']
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def get_db_config(prefix):
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return opts.get_env_vars(db_config_names, prefix, env_names)
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in_db_config = get_db_config('in')
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out_db_config = get_db_config('out')
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in_is_db = 'engine' in in_db_config
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out_is_db = 'engine' in out_db_config
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# Parse args
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map_paths = sys.argv[1:]
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if map_paths == []:
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if in_is_db or not out_is_db: usage_err()
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else: map_paths = [None]
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def connect_db(db_config):
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log_start('Connecting to '+sql.db_config_str(db_config))
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db = sql.connect(db_config)
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log_done()
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return db
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out_is_xml_ref = [False]
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def process_input(root, process_row, map_path):
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'''Inputs datasource to XML tree, mapping if needed'''
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# Load map header
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in_is_xpaths = True
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out_is_xpaths = True
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out_label = None
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if map_path != None:
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import copy
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import csv
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import xpath
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metadata = []
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mappings = []
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stream = open(map_path, 'rb')
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reader = csv.reader(stream)
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in_label, out_label = reader.next()[:2]
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def split_col_name(name):
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name, sep, root = name.partition(':')
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return name, sep != '', root
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in_label, in_is_xpaths, in_root = split_col_name(in_label)
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out_label, out_is_xpaths, out_root = split_col_name(out_label)
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has_types = out_root.startswith('/*s/') # outer elements are types
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for row in reader:
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in_, out = row[:2]
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if out != '':
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if out_is_xpaths: out = xpath.parse(out_root+out)
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mappings.append((in_, out))
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stream.close()
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root.ownerDocument.documentElement.tagName = out_label
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in_is_xml = in_is_xpaths and not in_is_db
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out_is_xml_ref[0] = out_is_xpaths and not out_is_db
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if in_is_xml:
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doc0 = minidom.parse(sys.stdin)
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if out_label == None: out_label = doc0.documentElement.tagName
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def process_rows(get_value, rows):
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'''Processes input values
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@param get_value f(in_, row):str
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'''
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for i, row in enumerate(rows):
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if not (limit == None or i < limit): break
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row_id = str(i)
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for in_, out in mappings:
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value = metadata_value(in_)
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if value == None:
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log_start('Getting '+str(in_), debug)
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value = get_value(in_, row)
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log_done(debug)
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if value != None: xpath.put_obj(root, out, row_id,
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has_types, strings.cleanup(value))
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process_row(row)
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sys.stderr.write('Processed '+str(i+1)+' input rows\n')
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if map_path == None:
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iter_ = xml_dom.NodeElemIter(doc0.documentElement)
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util.skip(iter_, xml_dom.is_text) # skip metadata
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for child in iter_:
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root.appendChild(child)
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process_row(child)
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elif in_is_db:
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assert in_is_xpaths
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import db_xml
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in_root_xml = xpath.path2xml(in_root)
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for i, mapping in enumerate(mappings):
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in_, out = mapping
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if metadata_value(in_) == None:
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mappings[i] = (xpath.path2xml(in_root+'/'+in_), out)
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in_db = connect_db(in_db_config)
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in_pkeys = {}
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def get_value(in_, row):
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pkey, = row
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in_ = in_.cloneNode(True) # don't modify orig value!
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xml_dom.set_id(xpath.get(in_, in_root), pkey)
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value = sql.value_or_none(db_xml.get(in_db, in_, in_pkeys))
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if value != None: return str(value)
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else: return None
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process_rows(get_value, sql.rows(db_xml.get(in_db, in_root_xml,
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in_pkeys, limit)))
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in_db.close()
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elif in_is_xml:
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def get_value(in_, row):
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node = xpath.get(row, in_)
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if node != None: return xml_dom.value(node)
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else: return None
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row0 = xpath.get(doc0.documentElement, in_root)
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process_rows(get_value, xml_dom.NodeElemIter(row0.parentNode))
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else: # input is CSV
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map_ = dict(mappings)
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reader = csv.reader(sys.stdin)
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cols = reader.next()
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col_idxs = dict([(value, idx) for idx, value in enumerate(cols)])
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for i, mapping in enumerate(mappings):
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in_, out = mapping
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if metadata_value(in_) == None:
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try: mappings[i] = (col_idxs[in_], out)
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except KeyError: pass
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def get_value(in_, row):
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value = row[in_]
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if value != '': return value
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else: return None
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process_rows(get_value, reader)
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def process_inputs(root, process_row):
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for map_path in map_paths: process_input(root, process_row, map_path)
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# Output XML tree
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doc = xml_dom.create_doc()
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root = doc.documentElement
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if out_is_db:
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import db_xml
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out_db = connect_db(out_db_config)
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out_pkeys = {}
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try:
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if test: sql.empty_db(out_db)
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row_ct_ref = [0]
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def process_row(input_row):
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def on_error(e):
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exc.add_msg(e, term.emph('input row:')+'\n'+str(input_row))
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exc.add_msg(e, term.emph('output row:')+'\n'+str(root))
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ex_tracker.track(e)
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xml_func.process(root, on_error)
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if not xml_dom.is_empty(root):
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assert xml_dom.has_one_child(root)
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try:
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sql.with_savepoint(out_db, lambda: db_xml.put(out_db,
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root.firstChild, out_pkeys, row_ct_ref, on_error))
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if commit: out_db.commit()
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except sql.DatabaseErrors, e: on_error(e)
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root.clear()
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process_inputs(root, process_row)
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sys.stdout.write('Inserted '+str(row_ct_ref[0])+
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' new rows into database\n')
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finally:
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out_db.rollback()
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out_db.close()
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else:
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def on_error(e): ex_tracker.track(e)
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452
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def process_row(input_row): pass
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process_inputs(root, process_row)
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759
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xml_func.process(root, on_error)
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if out_is_xml_ref[0]:
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doc.writexml(sys.stdout, **xml_dom.prettyxml_config)
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else: # output is CSV
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raise NotImplementedError('CSV output not supported yet')
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try: main()
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except Parser.SyntaxException, e: raise SystemExit(str(e))
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