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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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aaronmk
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# Exit status is the # of errors in the import, up to the maximum exit status
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3768
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aaronmk
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# Multi-safe (supports an input appearing multiple times).
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53
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aaronmk
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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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4213
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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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4505
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aaronmk
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# Case- and punctuation-insensitive.
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53
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aaronmk
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2550
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aaronmk
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import copy
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1014
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aaronmk
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import csv
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1714
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import itertools
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53
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import os.path
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3577
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import warnings
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53
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aaronmk
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import sys
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299
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aaronmk
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import xml.dom.minidom as minidom
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53
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aaronmk
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266
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sys.path.append(os.path.dirname(__file__)+"/../lib")
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53
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aaronmk
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1389
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import csvs
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2040
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aaronmk
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import db_xml
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344
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import exc
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9455
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import ints
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1714
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aaronmk
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import iters
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1705
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aaronmk
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import maps
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64
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import opts
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2035
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import parallelproc
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281
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import Parser
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982
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import profiling
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131
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import sql
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2288
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import sql_gen
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3103
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import sql_io
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1758
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import streams
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715
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aaronmk
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import strings
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828
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import term
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310
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import util
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1014
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import xpath
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133
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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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53
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5911
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metadata_prefix = ':'
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collision_suffix = '/_alt/'
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4047
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1404
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def get_with_prefix(map_, prefixes, key):
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2040
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aaronmk
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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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1484
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aaronmk
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except KeyError, e: continue # keep going
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2040
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values.append((key_, value))
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1484
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if values != []: return values
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else: raise e # re-raise last KeyError
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1404
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aaronmk
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5927
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def is_metadata(str_): return str_.startswith(metadata_prefix)
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5911
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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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84
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aaronmk
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1360
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def cleanup(val):
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if val == None: return val
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1374
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return util.none_if(strings.cleanup(strings.ustr(val)), u'', u'\\N')
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1360
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847
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def main_():
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env_names = []
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def usage_err():
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944
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raise SystemExit('Usage: '+opts.env_usage(env_names, True)+' '
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1945
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aaronmk
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+sys.argv[0]+' [map_path...] [<input] [>output]\n'
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1946
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aaronmk
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'Note: Row #s start with 1')
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838
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aaronmk
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1570
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## Get config from env vars
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838
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1570
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aaronmk
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# Modes
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946
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test = opts.env_flag('test', False, env_names)
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947
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commit = opts.env_flag('commit', False, env_names) and not test
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944
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# never commit in test mode
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7122
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redo = opts.env_flag('redo', False, env_names) and not commit
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2977
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# never redo in commit mode (run `make schemas/reinstall` instead)
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1570
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aaronmk
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# Ranges
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1946
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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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1945
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aaronmk
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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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1570
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aaronmk
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if end != None: end += start
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# Debugging
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3132
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verbosity = util.cast(float, opts.get_env_var('verbosity', None, env_names))
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944
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aaronmk
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opts.get_env_var('profile_to', None, env_names) # add to env_names
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131
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aaronmk
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1570
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aaronmk
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# DB
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def get_db_config(prefix):
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1926
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return opts.get_env_vars(sql.db_config_names, prefix, env_names)
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1570
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aaronmk
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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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1982
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aaronmk
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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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3339
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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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1570
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aaronmk
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116 |
1989
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aaronmk
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# Optimization
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2050
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aaronmk
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cache_sql = opts.env_flag('cache_sql', True, env_names)
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1989
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aaronmk
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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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2044
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aaronmk
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else: cpus_default = 0 # or None to use parallel processing by default
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1989
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aaronmk
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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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125 |
3132
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aaronmk
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# Set default verbosity. Must happen after by_col is set.
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4026
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aaronmk
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if verbosity == None:
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3132
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aaronmk
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if test: verbosity = 0.5 # automated tests should not be verbose
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9453
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aaronmk
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elif by_col: verbosity = 3 # show all queries to assist debugging
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3132
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aaronmk
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else: verbosity = 1.1 # just show row progress
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131 |
9455
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aaronmk
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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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137 |
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138 |
1570
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aaronmk
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##
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139 |
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140 |
838
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aaronmk
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# Logging
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141 |
2457
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aaronmk
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verbose_errors = test and verbosity > 0
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142 |
3243
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aaronmk
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debug = verbosity >= 1.5
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143 |
2439
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aaronmk
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def log(msg, level=1):
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144 |
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'''Higher level -> more verbose'''
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145 |
2452
|
aaronmk
|
if level <= verbosity:
|
146 |
2490
|
aaronmk
|
if verbosity <= 2:
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147 |
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if level == 1.5: msg = '# '+msg # msg is Redmine list item
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148 |
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elif msg.startswith('DB query:'): # remove extra debug info
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149 |
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first_line, nl, msg = msg.partition('\n')
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150 |
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elif level > 1: msg = '['+str(level)+'] '+msg # include level in msg
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151 |
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152 |
2883
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aaronmk
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sys.stderr.write(strings.to_raw_str(msg.rstrip('\n')+'\n'))
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153 |
2439
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aaronmk
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if debug: log_debug = lambda msg, level=2: log(msg, level)
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154 |
1901
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aaronmk
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else: log_debug = sql.log_debug_none
|
155 |
662
|
aaronmk
|
|
156 |
53
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aaronmk
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# Parse args
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157 |
510
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aaronmk
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map_paths = sys.argv[1:]
|
158 |
512
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aaronmk
|
if map_paths == []:
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159 |
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if in_is_db or not out_is_db: usage_err()
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160 |
|
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else: map_paths = [None]
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161 |
53
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aaronmk
|
|
162 |
646
|
aaronmk
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def connect_db(db_config):
|
163 |
1901
|
aaronmk
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log('Connecting to '+sql.db_config_str(db_config))
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164 |
2920
|
aaronmk
|
return sql.connect(db_config, caching=cache_sql, autocommit=commit,
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165 |
2916
|
aaronmk
|
debug_temp=verbosity > 3 and commit, log_debug=log_debug)
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166 |
646
|
aaronmk
|
|
167 |
1945
|
aaronmk
|
if end != None: end_str = str(end-1) # end is one past the last #
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168 |
1573
|
aaronmk
|
else: end_str = 'end'
|
169 |
1901
|
aaronmk
|
log('Processing input rows '+str(start)+'-'+end_str)
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170 |
1573
|
aaronmk
|
|
171 |
1014
|
aaronmk
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ex_tracker = exc.ExPercentTracker(iter_text='row')
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172 |
|
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profiler = profiling.ItersProfiler(start_now=True, iter_text='row')
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173 |
|
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|
174 |
1856
|
aaronmk
|
# Parallel processing
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175 |
2035
|
aaronmk
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pool = parallelproc.MultiProducerPool(cpus)
|
176 |
1901
|
aaronmk
|
log('Using '+str(pool.process_ct)+' parallel CPUs')
|
177 |
1846
|
aaronmk
|
|
178 |
3661
|
aaronmk
|
# Set up DB access
|
179 |
|
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row_ins_ct_ref = [0]
|
180 |
|
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if out_is_db:
|
181 |
|
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out_db = connect_db(out_db_config)
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182 |
3689
|
aaronmk
|
def is_rel_func(name):
|
183 |
|
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return (name in db_xml.put_special_funcs
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184 |
|
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or sql.function_exists(out_db, sql_gen.Function(name)))
|
185 |
3661
|
aaronmk
|
|
186 |
1014
|
aaronmk
|
doc = xml_dom.create_doc()
|
187 |
|
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root = doc.documentElement
|
188 |
751
|
aaronmk
|
out_is_xml_ref = [False]
|
189 |
3653
|
aaronmk
|
|
190 |
1014
|
aaronmk
|
in_label_ref = [None]
|
191 |
3653
|
aaronmk
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col_defaults = {}
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192 |
1014
|
aaronmk
|
def update_in_label():
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193 |
10114
|
aaronmk
|
if in_schema != None: os.environ['source'] = in_schema
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194 |
|
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elif in_label_ref[0] != None: os.environ['source'] = in_label_ref[0]
|
195 |
3653
|
aaronmk
|
|
196 |
1014
|
aaronmk
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def prep_root():
|
197 |
|
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root.clear()
|
198 |
|
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update_in_label()
|
199 |
|
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prep_root()
|
200 |
751
|
aaronmk
|
|
201 |
838
|
aaronmk
|
def process_input(root, row_ready, map_path):
|
202 |
512
|
aaronmk
|
'''Inputs datasource to XML tree, mapping if needed'''
|
203 |
|
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# Load map header
|
204 |
|
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in_is_xpaths = True
|
205 |
751
|
aaronmk
|
out_is_xpaths = True
|
206 |
512
|
aaronmk
|
out_label = None
|
207 |
|
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if map_path != None:
|
208 |
|
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metadata = []
|
209 |
|
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mappings = []
|
210 |
|
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stream = open(map_path, 'rb')
|
211 |
|
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reader = csv.reader(stream)
|
212 |
|
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in_label, out_label = reader.next()[:2]
|
213 |
1402
|
aaronmk
|
|
214 |
512
|
aaronmk
|
def split_col_name(name):
|
215 |
1402
|
aaronmk
|
label, sep, root = name.partition(':')
|
216 |
4652
|
aaronmk
|
return label, sep != '', root, []
|
217 |
1402
|
aaronmk
|
|
218 |
1705
|
aaronmk
|
in_label, in_root, prefixes = maps.col_info(in_label)
|
219 |
|
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in_is_xpaths = in_root != None
|
220 |
1014
|
aaronmk
|
in_label_ref[0] = in_label
|
221 |
|
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update_in_label()
|
222 |
1705
|
aaronmk
|
out_label, out_root = maps.col_info(out_label)[:2]
|
223 |
|
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out_is_xpaths = out_root != None
|
224 |
1841
|
aaronmk
|
if out_is_xpaths: has_types = out_root.find('/*s/') >= 0
|
225 |
1705
|
aaronmk
|
# outer elements are types
|
226 |
1402
|
aaronmk
|
|
227 |
512
|
aaronmk
|
for row in reader:
|
228 |
|
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in_, out = row[:2]
|
229 |
2029
|
aaronmk
|
if out != '': mappings.append([in_, out_root+out])
|
230 |
1402
|
aaronmk
|
|
231 |
512
|
aaronmk
|
stream.close()
|
232 |
|
|
|
233 |
|
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root.ownerDocument.documentElement.tagName = out_label
|
234 |
|
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in_is_xml = in_is_xpaths and not in_is_db
|
235 |
751
|
aaronmk
|
out_is_xml_ref[0] = out_is_xpaths and not out_is_db
|
236 |
56
|
aaronmk
|
|
237 |
1897
|
aaronmk
|
def process_rows(process_row, rows, rows_start=0):
|
238 |
4026
|
aaronmk
|
'''Processes input rows
|
239 |
838
|
aaronmk
|
@param process_row(in_row, i)
|
240 |
1945
|
aaronmk
|
@rows_start The (0-based) row # of the first row in rows. Set this
|
241 |
|
|
only if the pre-start rows have already been skipped.
|
242 |
297
|
aaronmk
|
'''
|
243 |
1897
|
aaronmk
|
rows = iter(rows)
|
244 |
|
|
|
245 |
|
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if end != None: row_nums = xrange(rows_start, end)
|
246 |
|
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else: row_nums = itertools.count(rows_start)
|
247 |
2038
|
aaronmk
|
i = -1
|
248 |
1897
|
aaronmk
|
for i in row_nums:
|
249 |
1718
|
aaronmk
|
try: row = rows.next()
|
250 |
2038
|
aaronmk
|
except StopIteration:
|
251 |
|
|
i -= 1 # last row # didn't count
|
252 |
|
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break # no more rows
|
253 |
1718
|
aaronmk
|
if i < start: continue # not at start row yet
|
254 |
|
|
|
255 |
2881
|
aaronmk
|
# Row # is interally 0-based, but 1-based to the user
|
256 |
|
|
log('Processing input row #'+str(i+1), level=1.1)
|
257 |
838
|
aaronmk
|
process_row(row, i)
|
258 |
|
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row_ready(i, row)
|
259 |
2033
|
aaronmk
|
row_ct = i-start+1
|
260 |
982
|
aaronmk
|
return row_ct
|
261 |
838
|
aaronmk
|
|
262 |
1898
|
aaronmk
|
def map_rows(get_value, rows, **kw_args):
|
263 |
838
|
aaronmk
|
'''Maps input rows
|
264 |
|
|
@param get_value(in_, row):str
|
265 |
|
|
'''
|
266 |
2030
|
aaronmk
|
# Prevent collisions if multiple inputs mapping to same output
|
267 |
|
|
outputs_idxs = dict()
|
268 |
|
|
for i, mapping in enumerate(mappings):
|
269 |
|
|
in_, out = mapping
|
270 |
|
|
default = util.NamedTuple(count=1, first=i)
|
271 |
|
|
idxs = outputs_idxs.setdefault(out, default)
|
272 |
|
|
if idxs is not default: # key existed, so there was a collision
|
273 |
4048
|
aaronmk
|
if idxs.count == 1: # first key does not yet have suffix
|
274 |
4047
|
aaronmk
|
mappings[idxs.first][1] += collision_suffix+'0'
|
275 |
|
|
mappings[i][1] += collision_suffix+str(idxs.count)
|
276 |
2030
|
aaronmk
|
idxs.count += 1
|
277 |
|
|
|
278 |
2026
|
aaronmk
|
id_node = None
|
279 |
|
|
if out_is_db:
|
280 |
5927
|
aaronmk
|
mappings_orig = mappings[:] # save a copy
|
281 |
|
|
mappings[:] = [] # empty existing elements
|
282 |
|
|
for in_, out in mappings_orig:
|
283 |
|
|
in_str = strings.ustr(in_)
|
284 |
|
|
is_metadata_ = is_metadata(in_str)
|
285 |
|
|
if is_metadata_: value = metadata_value(in_str)
|
286 |
|
|
else: value = '$'+in_str # mark as name
|
287 |
|
|
|
288 |
2026
|
aaronmk
|
# All put_obj()s should return the same id_node
|
289 |
|
|
nodes, id_node = xpath.put_obj(root, out, '-1', has_types,
|
290 |
5927
|
aaronmk
|
value) # value is placeholder that documents name
|
291 |
|
|
if not is_metadata_: mappings.append([in_, nodes])
|
292 |
3580
|
aaronmk
|
if id_node == None:
|
293 |
8075
|
aaronmk
|
warnings.warn(UserWarning('Map warning: No mappings or no '
|
294 |
|
|
'column name matches. Are you importing the correct '
|
295 |
|
|
'input table?'))
|
296 |
4042
|
aaronmk
|
xml_func.simplify(root)
|
297 |
4491
|
aaronmk
|
sys.stdout.write(strings.to_raw_str('Put template:\n'
|
298 |
|
|
+strings.ustr(root)))
|
299 |
3669
|
aaronmk
|
sys.stdout.flush()
|
300 |
2026
|
aaronmk
|
|
301 |
838
|
aaronmk
|
def process_row(row, i):
|
302 |
316
|
aaronmk
|
row_id = str(i)
|
303 |
2032
|
aaronmk
|
if id_node != None: xml_dom.set_value(id_node, row_id)
|
304 |
316
|
aaronmk
|
for in_, out in mappings:
|
305 |
4491
|
aaronmk
|
log_debug('Getting '+strings.ustr(in_))
|
306 |
5927
|
aaronmk
|
value = cleanup(get_value(in_, row))
|
307 |
4492
|
aaronmk
|
log_debug('Putting '+strings.urepr(value)+' to '
|
308 |
|
|
+strings.ustr(out))
|
309 |
2032
|
aaronmk
|
if out_is_db: # out is list of XML nodes
|
310 |
|
|
for node in out: xml_dom.set_value(node, value)
|
311 |
|
|
elif value != None: # out is XPath
|
312 |
1360
|
aaronmk
|
xpath.put_obj(root, out, row_id, has_types, value)
|
313 |
1898
|
aaronmk
|
return process_rows(process_row, rows, **kw_args)
|
314 |
297
|
aaronmk
|
|
315 |
1898
|
aaronmk
|
def map_table(col_names, rows, **kw_args):
|
316 |
1416
|
aaronmk
|
col_names_ct = len(col_names)
|
317 |
1403
|
aaronmk
|
col_idxs = util.list_flip(col_names)
|
318 |
6740
|
aaronmk
|
col_names_map = dict(zip(col_names, col_names))
|
319 |
4503
|
aaronmk
|
prefixes_simp = map(maps.simplify, prefixes)
|
320 |
1403
|
aaronmk
|
|
321 |
2029
|
aaronmk
|
# Resolve prefixes
|
322 |
2025
|
aaronmk
|
mappings_orig = mappings[:] # save a copy
|
323 |
|
|
mappings[:] = [] # empty existing elements
|
324 |
|
|
for in_, out in mappings_orig:
|
325 |
7148
|
aaronmk
|
if is_metadata(in_): mappings.append([in_, out])
|
326 |
5928
|
aaronmk
|
else:
|
327 |
4503
|
aaronmk
|
try:
|
328 |
4505
|
aaronmk
|
cols = get_with_prefix(col_names_map, prefixes_simp,
|
329 |
6740
|
aaronmk
|
in_)
|
330 |
2025
|
aaronmk
|
except KeyError: pass
|
331 |
4503
|
aaronmk
|
else:
|
332 |
4505
|
aaronmk
|
cols = [(orig, col_idxs[orig]) for simp, orig in cols]
|
333 |
4503
|
aaronmk
|
mappings[len(mappings):] = [[db_xml.ColRef(*col), out]
|
334 |
|
|
for col in cols] # can't use += because that uses =
|
335 |
1403
|
aaronmk
|
|
336 |
2040
|
aaronmk
|
def get_value(in_, row): return row.list[in_.idx]
|
337 |
1416
|
aaronmk
|
def wrap_row(row):
|
338 |
|
|
return util.ListDict(util.list_as_length(row, col_names_ct),
|
339 |
|
|
col_names, col_idxs) # handle CSV rows of different lengths
|
340 |
1403
|
aaronmk
|
|
341 |
1898
|
aaronmk
|
return map_rows(get_value, util.WrapIter(wrap_row, rows), **kw_args)
|
342 |
1403
|
aaronmk
|
|
343 |
1700
|
aaronmk
|
if in_is_db:
|
344 |
2809
|
aaronmk
|
def on_error(e): ex_tracker.track(e)
|
345 |
|
|
|
346 |
3186
|
aaronmk
|
if by_col: in_db = out_db
|
347 |
|
|
else: in_db = connect_db(in_db_config)
|
348 |
126
|
aaronmk
|
|
349 |
1982
|
aaronmk
|
# Get table and schema name
|
350 |
|
|
schema = in_schema # modified, so can't have same name as outer var
|
351 |
|
|
table = in_table # modified, so can't have same name as outer var
|
352 |
|
|
if table == None:
|
353 |
|
|
assert in_is_xpaths
|
354 |
|
|
schema, sep, table = in_root.partition('.')
|
355 |
|
|
if sep == '': # only the table name was specified
|
356 |
|
|
table = schema
|
357 |
|
|
schema = None
|
358 |
2313
|
aaronmk
|
table = sql_gen.Table(table, schema)
|
359 |
1982
|
aaronmk
|
|
360 |
1991
|
aaronmk
|
# Fetch rows
|
361 |
|
|
if by_col: limit = 0 # only fetch column names
|
362 |
|
|
else: limit = n
|
363 |
6385
|
aaronmk
|
try:
|
364 |
|
|
cur = sql.select(in_db, table, limit=limit, start=start,
|
365 |
|
|
recover=True, cacheable=False)
|
366 |
|
|
except sql.DoesNotExistException:
|
367 |
6445
|
aaronmk
|
table = None
|
368 |
6385
|
aaronmk
|
col_names = []
|
369 |
|
|
rows = []
|
370 |
|
|
else:
|
371 |
|
|
col_names = list(sql.col_names(cur))
|
372 |
|
|
rows = sql.rows(cur)
|
373 |
1991
|
aaronmk
|
|
374 |
1989
|
aaronmk
|
if by_col:
|
375 |
2042
|
aaronmk
|
map_table(col_names, []) # just create the template
|
376 |
2550
|
aaronmk
|
|
377 |
6454
|
aaronmk
|
if table != None and start == 0 and n == None: # full re-import
|
378 |
2734
|
aaronmk
|
log('Clearing errors table')
|
379 |
4474
|
aaronmk
|
errors_table_ = sql_io.errors_table(in_db, table)
|
380 |
|
|
if errors_table_ != None:
|
381 |
|
|
sql.drop_table(in_db, errors_table_)
|
382 |
2734
|
aaronmk
|
|
383 |
2550
|
aaronmk
|
# Strip XML functions not in the DB
|
384 |
3427
|
aaronmk
|
xml_func.process(root, is_rel_func=is_rel_func)
|
385 |
4491
|
aaronmk
|
if debug: log_debug('Putting stripped:\n'+strings.ustr(root))
|
386 |
2119
|
aaronmk
|
# only calc if debug
|
387 |
2550
|
aaronmk
|
|
388 |
|
|
# Import rows
|
389 |
2422
|
aaronmk
|
in_row_ct_ref = [0]
|
390 |
2928
|
aaronmk
|
db_xml.put_table(in_db, root.firstChild, table, in_row_ct_ref,
|
391 |
3627
|
aaronmk
|
row_ins_ct_ref, n, start, on_error, col_defaults)
|
392 |
2422
|
aaronmk
|
row_ct = in_row_ct_ref[0]
|
393 |
1984
|
aaronmk
|
else:
|
394 |
|
|
# Use normal by-row method
|
395 |
6385
|
aaronmk
|
row_ct = map_table(col_names, rows, rows_start=start)
|
396 |
1991
|
aaronmk
|
# rows_start: pre-start rows have been skipped
|
397 |
3186
|
aaronmk
|
|
398 |
|
|
in_db.db.close()
|
399 |
161
|
aaronmk
|
elif in_is_xml:
|
400 |
2809
|
aaronmk
|
stdin = streams.LineCountStream(sys.stdin)
|
401 |
|
|
def on_error(e):
|
402 |
|
|
exc.add_msg(e, term.emph('input line #:')+' '
|
403 |
|
|
+str(stdin.line_num))
|
404 |
|
|
ex_tracker.track(e)
|
405 |
|
|
|
406 |
1715
|
aaronmk
|
def get_rows(doc2rows):
|
407 |
1758
|
aaronmk
|
return iters.flatten(itertools.imap(doc2rows,
|
408 |
|
|
xml_parse.docs_iter(stdin, on_error)))
|
409 |
1715
|
aaronmk
|
|
410 |
1714
|
aaronmk
|
if map_path == None:
|
411 |
1715
|
aaronmk
|
def doc2rows(in_xml_root):
|
412 |
1701
|
aaronmk
|
iter_ = xml_dom.NodeElemIter(in_xml_root)
|
413 |
|
|
util.skip(iter_, xml_dom.is_text) # skip metadata
|
414 |
1715
|
aaronmk
|
return iter_
|
415 |
|
|
|
416 |
|
|
row_ct = process_rows(lambda row, i: root.appendChild(row),
|
417 |
|
|
get_rows(doc2rows))
|
418 |
1714
|
aaronmk
|
else:
|
419 |
1715
|
aaronmk
|
def doc2rows(in_xml_root):
|
420 |
1701
|
aaronmk
|
rows = xpath.get(in_xml_root, in_root, limit=end)
|
421 |
3581
|
aaronmk
|
if rows == []: warnings.warn(UserWarning('Map warning: '
|
422 |
|
|
'Root "'+in_root+'" not found in input'))
|
423 |
1714
|
aaronmk
|
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 |
1715
|
aaronmk
|
row_ct = map_rows(get_value, get_rows(doc2rows))
|
433 |
56
|
aaronmk
|
else: # input is CSV
|
434 |
1389
|
aaronmk
|
reader, col_names = csvs.reader_and_header(sys.stdin)
|
435 |
1403
|
aaronmk
|
row_ct = map_table(col_names, reader)
|
436 |
982
|
aaronmk
|
|
437 |
|
|
return row_ct
|
438 |
53
|
aaronmk
|
|
439 |
838
|
aaronmk
|
def process_inputs(root, row_ready):
|
440 |
982
|
aaronmk
|
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 |
512
|
aaronmk
|
|
445 |
1886
|
aaronmk
|
pool.share_vars(locals())
|
446 |
130
|
aaronmk
|
if out_is_db:
|
447 |
53
|
aaronmk
|
try:
|
448 |
947
|
aaronmk
|
if redo: sql.empty_db(out_db)
|
449 |
1886
|
aaronmk
|
pool.share_vars(locals())
|
450 |
449
|
aaronmk
|
|
451 |
838
|
aaronmk
|
def row_ready(row_num, input_row):
|
452 |
2119
|
aaronmk
|
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 |
4491
|
aaronmk
|
+'\n'+term.emph('input row:')+'\n'
|
458 |
|
|
+strings.ustr(input_row))
|
459 |
2119
|
aaronmk
|
if verbose_errors: row_str_[0] += ('\n'
|
460 |
4491
|
aaronmk
|
+term.emph('output row:')+'\n'+strings.ustr(root))
|
461 |
2119
|
aaronmk
|
return row_str_[0]
|
462 |
|
|
|
463 |
|
|
if debug: log_debug(row_str()) # only calc if debug
|
464 |
|
|
|
465 |
452
|
aaronmk
|
def on_error(e):
|
466 |
2119
|
aaronmk
|
exc.add_msg(e, row_str())
|
467 |
2046
|
aaronmk
|
ex_tracker.track(e, row_num, detail=verbose_errors)
|
468 |
1886
|
aaronmk
|
pool.share_vars(locals())
|
469 |
452
|
aaronmk
|
|
470 |
2032
|
aaronmk
|
row_root = root.cloneNode(True) # deep copy so don't modify root
|
471 |
3689
|
aaronmk
|
xml_func.process(row_root, on_error, is_rel_func, out_db)
|
472 |
4491
|
aaronmk
|
if debug: log_debug('Putting processed:\n'
|
473 |
|
|
+strings.ustr(row_root)) # only calc if debug
|
474 |
2032
|
aaronmk
|
if not xml_dom.is_empty(row_root):
|
475 |
|
|
assert xml_dom.has_one_child(row_root)
|
476 |
442
|
aaronmk
|
try:
|
477 |
982
|
aaronmk
|
sql.with_savepoint(out_db,
|
478 |
2032
|
aaronmk
|
lambda: db_xml.put(out_db, row_root.firstChild,
|
479 |
3653
|
aaronmk
|
row_ins_ct_ref, on_error, col_defaults))
|
480 |
449
|
aaronmk
|
except sql.DatabaseErrors, e: on_error(e)
|
481 |
|
|
|
482 |
982
|
aaronmk
|
row_ct = process_inputs(root, row_ready)
|
483 |
|
|
sys.stdout.write('Inserted '+str(row_ins_ct_ref[0])+
|
484 |
460
|
aaronmk
|
' new rows into database\n')
|
485 |
3669
|
aaronmk
|
sys.stdout.flush()
|
486 |
1868
|
aaronmk
|
|
487 |
|
|
# Consume asynchronous tasks
|
488 |
|
|
pool.main_loop()
|
489 |
3117
|
aaronmk
|
finally: out_db.close()
|
490 |
751
|
aaronmk
|
else:
|
491 |
759
|
aaronmk
|
def on_error(e): ex_tracker.track(e)
|
492 |
838
|
aaronmk
|
def row_ready(row_num, input_row): pass
|
493 |
982
|
aaronmk
|
row_ct = process_inputs(root, row_ready)
|
494 |
759
|
aaronmk
|
xml_func.process(root, on_error)
|
495 |
751
|
aaronmk
|
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 |
985
|
aaronmk
|
|
500 |
1868
|
aaronmk
|
# Consume any asynchronous tasks not already consumed above
|
501 |
1862
|
aaronmk
|
pool.main_loop()
|
502 |
|
|
|
503 |
982
|
aaronmk
|
profiler.stop(row_ct)
|
504 |
3324
|
aaronmk
|
if not by_col: ex_tracker.add_iters(row_ct) # only if errors are done by row
|
505 |
2439
|
aaronmk
|
log('Processed '+str(row_ct)+' input rows')
|
506 |
|
|
log(profiler.msg())
|
507 |
|
|
log(ex_tracker.msg())
|
508 |
985
|
aaronmk
|
ex_tracker.exit()
|
509 |
53
|
aaronmk
|
|
510 |
847
|
aaronmk
|
def main():
|
511 |
|
|
try: main_()
|
512 |
4491
|
aaronmk
|
except Parser.SyntaxError, e: raise SystemExit(strings.ustr(e))
|
513 |
847
|
aaronmk
|
|
514 |
846
|
aaronmk
|
if __name__ == '__main__':
|
515 |
847
|
aaronmk
|
profile_to = opts.get_env_var('profile_to', None)
|
516 |
|
|
if profile_to != None:
|
517 |
|
|
import cProfile
|
518 |
1584
|
aaronmk
|
sys.stderr.write('Profiling to '+profile_to+'\n')
|
519 |
847
|
aaronmk
|
cProfile.run(main.func_code, profile_to)
|
520 |
|
|
else: main()
|