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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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986
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# Exit status is the # of errors in the import, up to the maximum exit status
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53
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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 csv
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import itertools
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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 csvs
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import exc
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1714
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import iters
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import maps
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import opts
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import Parser
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import profiling
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import sql
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import streams
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715
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import strings
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import term
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import util
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1014
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import xpath
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import xml_dom
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86
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import xml_func
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1713
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import xml_parse
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class Pool:
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def apply_async(func, args=None, kw_args=None, callback=None):
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if args == None: args = ()
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if kwds == None: kwds = {}
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if callback == None: callback = lambda v: None
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callback(func(*args, **kw_args))
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1404
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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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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(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 metadata_value(name): return None # this feature has been removed
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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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847
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+sys.argv[0]+' [map_path...] [<input] [>output]')
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838
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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', test, env_names) and not commit
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# never redo in commit mode (manually run `make empty_db` instead)
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# Ranges
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start = util.cast(int, opts.get_env_var('start', '0', env_names))
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if test: end_default = 1
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else: end_default = None
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end = util.cast(int, util.none_if(
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opts.get_env_var('n', end_default, env_names), u''))
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if end != None: end += start
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# Optimization
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1851
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if test: cpus_default = 0
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else: cpus_default = None
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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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1846
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1570
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# Debugging
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debug = opts.env_flag('debug', False, env_names)
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859
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sql.run_raw_query.debug = debug
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verbose = debug or opts.env_flag('verbose', not test, env_names)
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opts.get_env_var('profile_to', None, env_names) # add to env_names
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1570
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# DB
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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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##
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838
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# Logging
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662
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def log(msg, on=verbose):
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if on: sys.stderr.write(msg)
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859
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def log_start(action, on=verbose): log(action+'...\n', on)
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662
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53
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# Parse args
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510
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map_paths = sys.argv[1:]
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512
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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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646
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def connect_db(db_config):
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662
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log_start('Connecting to '+sql.db_config_str(db_config))
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return sql.connect(db_config)
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646
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1573
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if end != None: end_str = str(end-1)
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else: end_str = 'end'
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log_start('Processing input rows '+str(start)+'-'+end_str)
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1014
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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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1856
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# Parallel processing
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try:
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if cpus == 0: raise ImportError('Parallel processing turned off')
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import multiprocessing
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import multiprocessing.pool
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except ImportError, e:
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log_start('Not using parallel processing: '+str(e))
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job_server = Pool()
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else:
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if cpus == None: cpus = multiprocessing.cpu_count()
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log_start('Using '+str(cpus)+' CPUs')
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job_server = multiprocessing.pool.Pool(processes=cpus)
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137 |
1846
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aaronmk
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138 |
1014
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aaronmk
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doc = xml_dom.create_doc()
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root = doc.documentElement
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140 |
751
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aaronmk
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out_is_xml_ref = [False]
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1014
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aaronmk
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in_label_ref = [None]
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def update_in_label():
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if in_label_ref[0] != None:
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xpath.get(root, '/_ignore/inLabel="'+in_label_ref[0]+'"', True)
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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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149 |
751
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aaronmk
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150 |
838
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aaronmk
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def process_input(root, row_ready, map_path):
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151 |
512
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aaronmk
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'''Inputs datasource to XML tree, mapping if needed'''
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152 |
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# Load map header
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153 |
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in_is_xpaths = True
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154 |
751
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aaronmk
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out_is_xpaths = True
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155 |
512
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aaronmk
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out_label = None
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156 |
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if map_path != None:
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metadata = []
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158 |
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mappings = []
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159 |
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stream = open(map_path, 'rb')
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160 |
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reader = csv.reader(stream)
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161 |
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in_label, out_label = reader.next()[:2]
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162 |
1402
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aaronmk
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163 |
512
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aaronmk
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def split_col_name(name):
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164 |
1402
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aaronmk
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label, sep, root = name.partition(':')
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165 |
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label, sep2, prefixes_str = label.partition('[')
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166 |
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prefixes_str = strings.remove_suffix(']', prefixes_str)
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167 |
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prefixes = strings.split(',', prefixes_str)
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168 |
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return label, sep != '', root, prefixes
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169 |
1198
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aaronmk
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# extract datasrc from "datasrc[data_format]"
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170 |
1402
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aaronmk
|
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171 |
1705
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aaronmk
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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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173 |
1014
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aaronmk
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in_label_ref[0] = in_label
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174 |
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update_in_label()
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175 |
1705
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aaronmk
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out_label, out_root = maps.col_info(out_label)[:2]
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176 |
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out_is_xpaths = out_root != None
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177 |
1841
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aaronmk
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if out_is_xpaths: has_types = out_root.find('/*s/') >= 0
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178 |
1705
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aaronmk
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# outer elements are types
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179 |
1402
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aaronmk
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|
180 |
512
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aaronmk
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for row in reader:
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in_, out = row[:2]
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182 |
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if out != '':
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183 |
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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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185 |
1402
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aaronmk
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|
186 |
512
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aaronmk
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stream.close()
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187 |
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188 |
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root.ownerDocument.documentElement.tagName = out_label
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189 |
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in_is_xml = in_is_xpaths and not in_is_db
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190 |
751
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aaronmk
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out_is_xml_ref[0] = out_is_xpaths and not out_is_db
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191 |
56
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aaronmk
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192 |
1148
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aaronmk
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def process_rows(process_row, rows):
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193 |
838
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aaronmk
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'''Processes input rows
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194 |
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@param process_row(in_row, i)
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195 |
297
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aaronmk
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'''
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196 |
1718
|
aaronmk
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i = 0
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197 |
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while end == None or i < end:
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198 |
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try: row = rows.next()
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199 |
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except StopIteration: break # no more rows
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200 |
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if i < start: continue # not at start row yet
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201 |
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|
202 |
838
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aaronmk
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process_row(row, i)
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203 |
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row_ready(i, row)
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204 |
1718
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aaronmk
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i += 1
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205 |
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row_ct = i-start
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206 |
982
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aaronmk
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return row_ct
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207 |
838
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aaronmk
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208 |
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def map_rows(get_value, rows):
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209 |
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'''Maps input rows
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210 |
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@param get_value(in_, row):str
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211 |
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'''
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212 |
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def process_row(row, i):
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213 |
316
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aaronmk
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row_id = str(i)
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214 |
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for in_, out in mappings:
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215 |
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value = metadata_value(in_)
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216 |
662
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aaronmk
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if value == None:
|
217 |
857
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aaronmk
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log_start('Getting '+str(in_), debug)
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218 |
1360
|
aaronmk
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value = cleanup(get_value(in_, row))
|
219 |
1348
|
aaronmk
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if value != None:
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220 |
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log_start('Putting '+str(out), debug)
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221 |
1360
|
aaronmk
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xpath.put_obj(root, out, row_id, has_types, value)
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222 |
982
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aaronmk
|
return process_rows(process_row, rows)
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223 |
297
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aaronmk
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|
224 |
1403
|
aaronmk
|
def map_table(col_names, rows):
|
225 |
1416
|
aaronmk
|
col_names_ct = len(col_names)
|
226 |
1403
|
aaronmk
|
col_idxs = util.list_flip(col_names)
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227 |
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228 |
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i = 0
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229 |
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while i < len(mappings): # mappings len changes in loop
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230 |
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in_, out = mappings[i]
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231 |
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if metadata_value(in_) == None:
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232 |
1404
|
aaronmk
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try: mappings[i] = (
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233 |
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get_with_prefix(col_idxs, prefixes, in_), out)
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234 |
|
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except KeyError:
|
235 |
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del mappings[i]
|
236 |
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continue # keep i the same
|
237 |
1403
|
aaronmk
|
i += 1
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238 |
|
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|
239 |
|
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def get_value(in_, row):
|
240 |
1484
|
aaronmk
|
return util.coalesce(*util.list_subset(row.list, in_))
|
241 |
1416
|
aaronmk
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def wrap_row(row):
|
242 |
|
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return util.ListDict(util.list_as_length(row, col_names_ct),
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243 |
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col_names, col_idxs) # handle CSV rows of different lengths
|
244 |
1403
|
aaronmk
|
|
245 |
|
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return map_rows(get_value, util.WrapIter(wrap_row, rows))
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246 |
|
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|
247 |
1758
|
aaronmk
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stdin = streams.LineCountStream(sys.stdin)
|
248 |
|
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def on_error(e):
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249 |
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exc.add_msg(e, term.emph('input line #:')+' '+str(stdin.line_num))
|
250 |
|
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ex_tracker.track(e)
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251 |
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|
252 |
1700
|
aaronmk
|
if in_is_db:
|
253 |
130
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aaronmk
|
assert in_is_xpaths
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254 |
126
|
aaronmk
|
|
255 |
1136
|
aaronmk
|
in_db = connect_db(in_db_config)
|
256 |
|
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cur = sql.select(in_db, table=in_root, fields=None, conds=None,
|
257 |
|
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limit=end, start=0)
|
258 |
1403
|
aaronmk
|
row_ct = map_table(list(sql.col_names(cur)), sql.rows(cur))
|
259 |
1136
|
aaronmk
|
|
260 |
1849
|
aaronmk
|
in_db.db.close()
|
261 |
161
|
aaronmk
|
elif in_is_xml:
|
262 |
1715
|
aaronmk
|
def get_rows(doc2rows):
|
263 |
1758
|
aaronmk
|
return iters.flatten(itertools.imap(doc2rows,
|
264 |
|
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xml_parse.docs_iter(stdin, on_error)))
|
265 |
1715
|
aaronmk
|
|
266 |
1714
|
aaronmk
|
if map_path == None:
|
267 |
1715
|
aaronmk
|
def doc2rows(in_xml_root):
|
268 |
1701
|
aaronmk
|
iter_ = xml_dom.NodeElemIter(in_xml_root)
|
269 |
|
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util.skip(iter_, xml_dom.is_text) # skip metadata
|
270 |
1715
|
aaronmk
|
return iter_
|
271 |
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|
272 |
|
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row_ct = process_rows(lambda row, i: root.appendChild(row),
|
273 |
|
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get_rows(doc2rows))
|
274 |
1714
|
aaronmk
|
else:
|
275 |
1715
|
aaronmk
|
def doc2rows(in_xml_root):
|
276 |
1701
|
aaronmk
|
rows = xpath.get(in_xml_root, in_root, limit=end)
|
277 |
1714
|
aaronmk
|
if rows == []: raise SystemExit('Map error: Root "'
|
278 |
|
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+in_root+'" not found in input')
|
279 |
|
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return rows
|
280 |
|
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|
281 |
|
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def get_value(in_, row):
|
282 |
|
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in_ = './{'+(','.join(strings.with_prefixes(
|
283 |
|
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['']+prefixes, in_)))+'}' # also with no prefix
|
284 |
|
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nodes = xpath.get(row, in_, allow_rooted=False)
|
285 |
|
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if nodes != []: return xml_dom.value(nodes[0])
|
286 |
|
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else: return None
|
287 |
|
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|
288 |
1715
|
aaronmk
|
row_ct = map_rows(get_value, get_rows(doc2rows))
|
289 |
56
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aaronmk
|
else: # input is CSV
|
290 |
133
|
aaronmk
|
map_ = dict(mappings)
|
291 |
1389
|
aaronmk
|
reader, col_names = csvs.reader_and_header(sys.stdin)
|
292 |
1403
|
aaronmk
|
row_ct = map_table(col_names, reader)
|
293 |
982
|
aaronmk
|
|
294 |
|
|
return row_ct
|
295 |
53
|
aaronmk
|
|
296 |
838
|
aaronmk
|
def process_inputs(root, row_ready):
|
297 |
982
|
aaronmk
|
row_ct = 0
|
298 |
|
|
for map_path in map_paths:
|
299 |
|
|
row_ct += process_input(root, row_ready, map_path)
|
300 |
|
|
return row_ct
|
301 |
512
|
aaronmk
|
|
302 |
130
|
aaronmk
|
if out_is_db:
|
303 |
53
|
aaronmk
|
import db_xml
|
304 |
|
|
|
305 |
646
|
aaronmk
|
out_db = connect_db(out_db_config)
|
306 |
53
|
aaronmk
|
try:
|
307 |
947
|
aaronmk
|
if redo: sql.empty_db(out_db)
|
308 |
982
|
aaronmk
|
row_ins_ct_ref = [0]
|
309 |
449
|
aaronmk
|
|
310 |
838
|
aaronmk
|
def row_ready(row_num, input_row):
|
311 |
452
|
aaronmk
|
def on_error(e):
|
312 |
835
|
aaronmk
|
exc.add_msg(e, term.emph('row #:')+' '+str(row_num))
|
313 |
828
|
aaronmk
|
exc.add_msg(e, term.emph('input row:')+'\n'+str(input_row))
|
314 |
|
|
exc.add_msg(e, term.emph('output row:')+'\n'+str(root))
|
315 |
1617
|
aaronmk
|
ex_tracker.track(e, row_num)
|
316 |
452
|
aaronmk
|
|
317 |
449
|
aaronmk
|
xml_func.process(root, on_error)
|
318 |
442
|
aaronmk
|
if not xml_dom.is_empty(root):
|
319 |
|
|
assert xml_dom.has_one_child(root)
|
320 |
|
|
try:
|
321 |
982
|
aaronmk
|
sql.with_savepoint(out_db,
|
322 |
|
|
lambda: db_xml.put(out_db, root.firstChild,
|
323 |
1850
|
aaronmk
|
row_ins_ct_ref, on_error))
|
324 |
1849
|
aaronmk
|
if commit: out_db.db.commit()
|
325 |
449
|
aaronmk
|
except sql.DatabaseErrors, e: on_error(e)
|
326 |
1010
|
aaronmk
|
prep_root()
|
327 |
449
|
aaronmk
|
|
328 |
982
|
aaronmk
|
row_ct = process_inputs(root, row_ready)
|
329 |
|
|
sys.stdout.write('Inserted '+str(row_ins_ct_ref[0])+
|
330 |
460
|
aaronmk
|
' new rows into database\n')
|
331 |
53
|
aaronmk
|
finally:
|
332 |
1849
|
aaronmk
|
out_db.db.rollback()
|
333 |
|
|
out_db.db.close()
|
334 |
751
|
aaronmk
|
else:
|
335 |
759
|
aaronmk
|
def on_error(e): ex_tracker.track(e)
|
336 |
838
|
aaronmk
|
def row_ready(row_num, input_row): pass
|
337 |
982
|
aaronmk
|
row_ct = process_inputs(root, row_ready)
|
338 |
759
|
aaronmk
|
xml_func.process(root, on_error)
|
339 |
751
|
aaronmk
|
if out_is_xml_ref[0]:
|
340 |
|
|
doc.writexml(sys.stdout, **xml_dom.prettyxml_config)
|
341 |
|
|
else: # output is CSV
|
342 |
|
|
raise NotImplementedError('CSV output not supported yet')
|
343 |
985
|
aaronmk
|
|
344 |
982
|
aaronmk
|
profiler.stop(row_ct)
|
345 |
|
|
ex_tracker.add_iters(row_ct)
|
346 |
990
|
aaronmk
|
if verbose:
|
347 |
|
|
sys.stderr.write('Processed '+str(row_ct)+' input rows\n')
|
348 |
|
|
sys.stderr.write(profiler.msg()+'\n')
|
349 |
|
|
sys.stderr.write(ex_tracker.msg()+'\n')
|
350 |
985
|
aaronmk
|
ex_tracker.exit()
|
351 |
53
|
aaronmk
|
|
352 |
847
|
aaronmk
|
def main():
|
353 |
|
|
try: main_()
|
354 |
1719
|
aaronmk
|
except Parser.SyntaxError, e: raise SystemExit(str(e))
|
355 |
847
|
aaronmk
|
|
356 |
846
|
aaronmk
|
if __name__ == '__main__':
|
357 |
847
|
aaronmk
|
profile_to = opts.get_env_var('profile_to', None)
|
358 |
|
|
if profile_to != None:
|
359 |
|
|
import cProfile
|
360 |
1584
|
aaronmk
|
sys.stderr.write('Profiling to '+profile_to+'\n')
|
361 |
847
|
aaronmk
|
cProfile.run(main.func_code, profile_to)
|
362 |
|
|
else: main()
|