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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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# Exit status is the # of errors in the import, up to the maximum exit status
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# Multi-safe (supports an input appearing multiple times).
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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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# Duplicate-column safe (supports multiple columns of the same name, which will
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# be combined)
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# Case- and punctuation-insensitive.
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import copy
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import csv
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import itertools
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import os.path
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import warnings
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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 csvs
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import db_xml
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import exc
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import ints
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import iters
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import maps
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import opts
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import parallelproc
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import Parser
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import profiling
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import sql
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import sql_gen
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import sql_io
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import streams
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import strings
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import term
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import util
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import xpath
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import xml_dom
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import xml_func
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import xml_parse
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metadata_prefix = ':'
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collision_suffix = '/_alt/'
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def get_with_prefix(map_, prefixes, key):
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'''Gets all entries for the given key with any of the given prefixes
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@return tuple(found_key, found_value)
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'''
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values = []
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for key_ in strings.with_prefixes(['']+prefixes, key): # also with no prefix
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try: value = map_[key_]
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except KeyError, e: continue # keep going
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values.append((key_, value))
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if values != []: return values
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else: raise e # re-raise last KeyError
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def is_metadata(str_): return str_.startswith(metadata_prefix)
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def metadata_value(name):
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removed_ref = [False]
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name = strings.remove_prefix(metadata_prefix, name, removed_ref)
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if removed_ref[0]: return name
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else: return None
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def cleanup(val):
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if val == None: return val
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return util.none_if(strings.cleanup(strings.ustr(val)), u'', u'\\N')
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def main_():
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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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+sys.argv[0]+' [map_path...] [<input] [>output]\n'
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'Note: Row #s start with 1')
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## Get config from env vars
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# Modes
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test = opts.env_flag('test', False, env_names)
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commit = opts.env_flag('commit', False, env_names) and not test
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# never commit in test mode
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redo = opts.env_flag('redo', False, env_names) and not commit
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# never redo in commit mode (run `make schemas/reinstall` instead)
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# Ranges
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start = util.cast(int, opts.get_env_var('start', 1, env_names)) # 1-based
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# Make start interally 0-based.
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# It's 1-based to the user to match up with the staging table row #s.
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start -= 1
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if test: n_default = 1
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else: n_default = None
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n = util.cast(int, util.none_if(opts.get_env_var('n', n_default, env_names),
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u''))
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end = n
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if end != None: end += start
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# Debugging
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verbosity = util.cast(float, opts.get_env_var('verbosity', None, env_names))
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opts.get_env_var('profile_to', None, env_names) # add to env_names
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# DB
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def get_db_config(prefix):
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return opts.get_env_vars(sql.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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in_schema = opts.get_env_var('in_schema', None, env_names)
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in_table = opts.get_env_var('in_table', None, env_names)
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if in_schema != None:
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for config in [in_db_config, out_db_config]:
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config['schemas'] += ','+in_schema
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# Optimization
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cache_sql = opts.env_flag('cache_sql', True, env_names)
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by_col = in_db_config == out_db_config and opts.env_flag('by_col', False,
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env_names) # by-column optimization only applies if mapping to same DB
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if test: cpus_default = 0
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else: cpus_default = 0 # or None to use parallel processing by default
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cpus = util.cast(int, util.none_if(opts.get_env_var('cpus', cpus_default,
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env_names), u''))
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# Set default verbosity. Must happen after by_col is set.
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if verbosity == None:
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if test: verbosity = 0.5 # automated tests should not be verbose
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elif by_col: verbosity = 3 # show all queries to assist debugging
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else: verbosity = 1.1 # just show row progress
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# fix verbosity
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if by_col and not test: verbosity = ints.set_min(verbosity, 2)
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# live column-based import MUST be run with verbosity 2+ (3 preferred)
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# to provide debugging information for often-complex errors.
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# without this, debugging is effectively impossible.
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# automated tests are exempt from this because they output to the screen
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##
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# Logging
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verbose_errors = test and verbosity > 0
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debug = verbosity >= 1.5
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def log(msg, level=1):
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'''Higher level -> more verbose'''
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if level <= verbosity:
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if verbosity <= 2:
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if level == 1.5: msg = '# '+msg # msg is Redmine list item
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elif msg.startswith('DB query:'): # remove extra debug info
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first_line, nl, msg = msg.partition('\n')
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elif level > 1: msg = '['+str(level)+'] '+msg # include level in msg
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sys.stderr.write(strings.to_raw_str(msg.rstrip('\n')+'\n'))
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if debug: log_debug = lambda msg, level=2: log(msg, level)
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else: log_debug = sql.log_debug_none
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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('Connecting to '+sql.db_config_str(db_config))
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return sql.connect(db_config, caching=cache_sql, autocommit=commit,
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debug_temp=verbosity > 3 and commit, log_debug=log_debug)
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if end != None: end_str = str(end-1) # end is one past the last #
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else: end_str = 'end'
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log('Processing input rows '+str(start)+'-'+end_str)
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ex_tracker = exc.ExPercentTracker(iter_text='row')
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profiler = profiling.ItersProfiler(start_now=True, iter_text='row')
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# Parallel processing
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pool = parallelproc.MultiProducerPool(cpus)
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log('Using '+str(pool.process_ct)+' parallel CPUs')
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# Set up DB access
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row_ins_ct_ref = [0]
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if out_is_db:
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out_db = connect_db(out_db_config)
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def is_rel_func(name):
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return (name in db_xml.put_special_funcs
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or sql.function_exists(out_db, sql_gen.Function(name)))
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doc = xml_dom.create_doc()
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root = doc.documentElement
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out_is_xml_ref = [False]
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in_label_ref = [None]
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col_defaults = {}
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def update_in_label():
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if in_schema != None: os.environ['source'] = in_schema
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elif in_label_ref[0] != None: os.environ['source'] = in_label_ref[0]
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def prep_root():
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root.clear()
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update_in_label()
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prep_root()
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def process_input(root, row_ready, 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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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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label, sep, root = name.partition(':')
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return label, sep != '', root, []
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in_label, in_root, prefixes = maps.col_info(in_label)
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in_is_xpaths = in_root != None
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in_label_ref[0] = in_label
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update_in_label()
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out_label, out_root = maps.col_info(out_label)[:2]
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out_is_xpaths = out_root != None
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if out_is_xpaths: has_types = out_root.find('/*s/') >= 0
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# 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 != '': mappings.append([in_, out_root+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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def process_rows(process_row, rows, rows_start=0):
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'''Processes input rows
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@param process_row(in_row, i)
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@rows_start The (0-based) row # of the first row in rows. Set this
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only if the pre-start rows have already been skipped.
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'''
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rows = iter(rows)
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if end != None: row_nums = xrange(rows_start, end)
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else: row_nums = itertools.count(rows_start)
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i = -1
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for i in row_nums:
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try: row = rows.next()
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except StopIteration:
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i -= 1 # last row # didn't count
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break # no more rows
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if i < start: continue # not at start row yet
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# Row # is interally 0-based, but 1-based to the user
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log('Processing input row #'+str(i+1), level=1.1)
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process_row(row, i)
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row_ready(i, row)
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row_ct = i-start+1
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return row_ct
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def map_rows(get_value, rows, **kw_args):
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'''Maps input rows
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@param get_value(in_, row):str
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'''
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# Prevent collisions if multiple inputs mapping to same output
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outputs_idxs = dict()
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for i, mapping in enumerate(mappings):
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in_, out = mapping
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default = util.NamedTuple(count=1, first=i)
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idxs = outputs_idxs.setdefault(out, default)
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if idxs is not default: # key existed, so there was a collision
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if idxs.count == 1: # first key does not yet have suffix
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mappings[idxs.first][1] += collision_suffix+'0'
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mappings[i][1] += collision_suffix+str(idxs.count)
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idxs.count += 1
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id_node = None
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if out_is_db:
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mappings_orig = mappings[:] # save a copy
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mappings[:] = [] # empty existing elements
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for in_, out in mappings_orig:
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in_str = strings.ustr(in_)
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is_metadata_ = is_metadata(in_str)
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if is_metadata_: value = metadata_value(in_str)
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else: value = '$'+in_str # mark as name
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# All put_obj()s should return the same id_node
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nodes, id_node = xpath.put_obj(root, out, '-1', has_types,
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value) # value is placeholder that documents name
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if not is_metadata_: mappings.append([in_, nodes])
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if id_node == None:
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warnings.warn(UserWarning('Map warning: No mappings or no '
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'column name matches. Are you importing the correct '
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'input table?'))
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xml_func.simplify(root)
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sys.stdout.write(strings.to_raw_str('Put template:\n'
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+strings.ustr(root)))
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sys.stdout.flush()
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def process_row(row, i):
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row_id = str(i)
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if id_node != None: xml_dom.set_value(id_node, row_id)
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for in_, out in mappings:
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log_debug('Getting '+strings.ustr(in_))
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value = cleanup(get_value(in_, row))
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log_debug('Putting '+strings.urepr(value)+' to '
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+strings.ustr(out))
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if out_is_db: # out is list of XML nodes
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for node in out: xml_dom.set_value(node, value)
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elif value != None: # out is XPath
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xpath.put_obj(root, out, row_id, has_types, value)
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return process_rows(process_row, rows, **kw_args)
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def map_table(col_names, rows, **kw_args):
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col_names_ct = len(col_names)
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col_idxs = util.list_flip(col_names)
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col_names_map = dict(zip(col_names, col_names))
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prefixes_simp = map(maps.simplify, prefixes)
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# Resolve prefixes
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mappings_orig = mappings[:] # save a copy
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mappings[:] = [] # empty existing elements
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for in_, out in mappings_orig:
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if is_metadata(in_): mappings.append([in_, out])
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else:
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try:
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cols = get_with_prefix(col_names_map, prefixes_simp,
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in_)
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except KeyError: pass
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else:
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cols = [(orig, col_idxs[orig]) for simp, orig in cols]
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mappings[len(mappings):] = [[db_xml.ColRef(*col), out]
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for col in cols] # can't use += because that uses =
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def get_value(in_, row): return row.list[in_.idx]
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def wrap_row(row):
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return util.ListDict(util.list_as_length(row, col_names_ct),
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col_names, col_idxs) # handle CSV rows of different lengths
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return map_rows(get_value, util.WrapIter(wrap_row, rows), **kw_args)
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if in_is_db:
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def on_error(e): ex_tracker.track(e)
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if by_col: in_db = out_db
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else: in_db = connect_db(in_db_config)
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# Get table and schema name
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schema = in_schema # modified, so can't have same name as outer var
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table = in_table # modified, so can't have same name as outer var
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if table == None:
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assert in_is_xpaths
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schema, sep, table = in_root.partition('.')
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if sep == '': # only the table name was specified
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table = schema
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schema = None
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table = sql_gen.Table(table, schema)
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# Fetch rows
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if by_col: limit = 0 # only fetch column names
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else: limit = n
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try:
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cur = sql.select(in_db, table, limit=limit, start=start,
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recover=True, cacheable=False)
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except sql.DoesNotExistException:
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table = None
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col_names = []
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rows = []
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else:
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col_names = list(sql.col_names(cur))
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rows = sql.rows(cur)
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if by_col:
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map_table(col_names, []) # just create the template
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if table != None and start == 0 and n == None: # full re-import
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log('Clearing errors table')
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errors_table_ = sql_io.errors_table(in_db, table)
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if errors_table_ != None:
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sql.drop_table(in_db, errors_table_)
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# Strip XML functions not in the DB
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xml_func.process(root, is_rel_func=is_rel_func)
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if debug: log_debug('Putting stripped:\n'+strings.ustr(root))
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# only calc if debug
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# Import rows
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in_row_ct_ref = [0]
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db_xml.put_table(in_db, root.firstChild, table, in_row_ct_ref,
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row_ins_ct_ref, n, start, on_error, col_defaults)
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row_ct = in_row_ct_ref[0]
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else:
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# Use normal by-row method
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row_ct = map_table(col_names, rows, rows_start=start)
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# rows_start: pre-start rows have been skipped
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in_db.db.close()
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elif in_is_xml:
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stdin = streams.LineCountStream(sys.stdin)
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def on_error(e):
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exc.add_msg(e, term.emph('input line #:')+' '
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403
|
+str(stdin.line_num))
|
404
|
ex_tracker.track(e)
|
405
|
|
406
|
def get_rows(doc2rows):
|
407
|
return iters.flatten(itertools.imap(doc2rows,
|
408
|
xml_parse.docs_iter(stdin, on_error)))
|
409
|
|
410
|
if map_path == None:
|
411
|
def doc2rows(in_xml_root):
|
412
|
iter_ = xml_dom.NodeElemIter(in_xml_root)
|
413
|
util.skip(iter_, xml_dom.is_text) # skip metadata
|
414
|
return iter_
|
415
|
|
416
|
row_ct = process_rows(lambda row, i: root.appendChild(row),
|
417
|
get_rows(doc2rows))
|
418
|
else:
|
419
|
def doc2rows(in_xml_root):
|
420
|
rows = xpath.get(in_xml_root, in_root, limit=end)
|
421
|
if rows == []: warnings.warn(UserWarning('Map warning: '
|
422
|
'Root "'+in_root+'" not found in input'))
|
423
|
return rows
|
424
|
|
425
|
def get_value(in_, row):
|
426
|
in_ = './{'+(','.join(strings.with_prefixes(
|
427
|
['']+prefixes, in_)))+'}' # also with no prefix
|
428
|
nodes = xpath.get(row, in_, allow_rooted=False)
|
429
|
if nodes != []: return xml_dom.value(nodes[0])
|
430
|
else: return None
|
431
|
|
432
|
row_ct = map_rows(get_value, get_rows(doc2rows))
|
433
|
else: # input is CSV
|
434
|
reader, col_names = csvs.reader_and_header(sys.stdin)
|
435
|
row_ct = map_table(col_names, reader)
|
436
|
|
437
|
return row_ct
|
438
|
|
439
|
def process_inputs(root, row_ready):
|
440
|
row_ct = 0
|
441
|
for map_path in map_paths:
|
442
|
row_ct += process_input(root, row_ready, map_path)
|
443
|
return row_ct
|
444
|
|
445
|
pool.share_vars(locals())
|
446
|
if out_is_db:
|
447
|
try:
|
448
|
if redo: sql.empty_db(out_db)
|
449
|
pool.share_vars(locals())
|
450
|
|
451
|
def row_ready(row_num, input_row):
|
452
|
row_str_ = [None]
|
453
|
def row_str():
|
454
|
if row_str_[0] == None:
|
455
|
# Row # is interally 0-based, but 1-based to the user
|
456
|
row_str_[0] = (term.emph('row #:')+' '+str(row_num+1)
|
457
|
+'\n'+term.emph('input row:')+'\n'
|
458
|
+strings.ustr(input_row))
|
459
|
if verbose_errors: row_str_[0] += ('\n'
|
460
|
+term.emph('output row:')+'\n'+strings.ustr(root))
|
461
|
return row_str_[0]
|
462
|
|
463
|
if debug: log_debug(row_str()) # only calc if debug
|
464
|
|
465
|
def on_error(e):
|
466
|
exc.add_msg(e, row_str())
|
467
|
ex_tracker.track(e, row_num, detail=verbose_errors)
|
468
|
pool.share_vars(locals())
|
469
|
|
470
|
row_root = root.cloneNode(True) # deep copy so don't modify root
|
471
|
xml_func.process(row_root, on_error, is_rel_func, out_db)
|
472
|
if debug: log_debug('Putting processed:\n'
|
473
|
+strings.ustr(row_root)) # only calc if debug
|
474
|
if not xml_dom.is_empty(row_root):
|
475
|
assert xml_dom.has_one_child(row_root)
|
476
|
try:
|
477
|
sql.with_savepoint(out_db,
|
478
|
lambda: db_xml.put(out_db, row_root.firstChild,
|
479
|
row_ins_ct_ref, on_error, col_defaults))
|
480
|
except sql.DatabaseErrors, e: on_error(e)
|
481
|
|
482
|
row_ct = process_inputs(root, row_ready)
|
483
|
sys.stdout.write('Inserted '+str(row_ins_ct_ref[0])+
|
484
|
' new rows into database\n')
|
485
|
sys.stdout.flush()
|
486
|
|
487
|
# Consume asynchronous tasks
|
488
|
pool.main_loop()
|
489
|
finally: out_db.close()
|
490
|
else:
|
491
|
def on_error(e): ex_tracker.track(e)
|
492
|
def row_ready(row_num, input_row): pass
|
493
|
row_ct = process_inputs(root, row_ready)
|
494
|
xml_func.process(root, on_error)
|
495
|
if out_is_xml_ref[0]:
|
496
|
doc.writexml(sys.stdout, **xml_dom.prettyxml_config)
|
497
|
else: # output is CSV
|
498
|
raise NotImplementedError('CSV output not supported yet')
|
499
|
|
500
|
# Consume any asynchronous tasks not already consumed above
|
501
|
pool.main_loop()
|
502
|
|
503
|
profiler.stop(row_ct)
|
504
|
if not by_col: ex_tracker.add_iters(row_ct) # only if errors are done by row
|
505
|
log('Processed '+str(row_ct)+' input rows')
|
506
|
log(profiler.msg())
|
507
|
log(ex_tracker.msg())
|
508
|
ex_tracker.exit()
|
509
|
|
510
|
def main():
|
511
|
try: main_()
|
512
|
except Parser.SyntaxError, e: raise SystemExit(strings.ustr(e))
|
513
|
|
514
|
if __name__ == '__main__':
|
515
|
profile_to = opts.get_env_var('profile_to', None)
|
516
|
if profile_to != None:
|
517
|
import cProfile
|
518
|
sys.stderr.write('Profiling to '+profile_to+'\n')
|
519
|
cProfile.run(main.func_code, profile_to)
|
520
|
else: main()
|