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aaronmk
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#!/usr/bin/env python
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# Maps one datasource to another, using a map spreadsheet if needed
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# For outputting an XML file to a PostgreSQL database, use the general format of
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# http://vegbank.org/vegdocs/xml/vegbank_example_ver1.0.2.xml
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import os.path
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import sys
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import xml.dom.minidom
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sys.path.append(os.path.dirname(__file__)+"/../lib")
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import opts
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from Parser import SyntaxException
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import sql
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import xml_dom
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import xml_func
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def metadata_value(name):
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if type(name) == str and name.startswith(':'): return name[1:]
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else: return None
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def main():
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env_names = []
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def usage_err():
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raise SystemExit('Usage: '+opts.env_usage(env_names, True)
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+' [commit=1] '+sys.argv[0]+' [map_path] [<input] [>output]')
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limit = opts.get_env_var('n', None, env_names)
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if limit != None: limit = int(limit)
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commit = opts.env_flag('commit')
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# Get db config from env vars
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db_config_names = ['engine', 'host', 'user', 'password', 'database']
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def get_db_config(prefix):
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return opts.get_env_vars(db_config_names, prefix, env_names)
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in_db_config = get_db_config('in')
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out_db_config = get_db_config('out')
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in_is_db = 'engine' in in_db_config
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out_is_db = 'engine' in out_db_config
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# Parse args
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map_path = None
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try: _prog_name, map_path = sys.argv
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except ValueError:
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if in_is_db: usage_err()
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# Load map header
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in_is_xpaths = True
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if map_path != None:
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import copy
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import csv
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import xpath
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metadata = []
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mappings = []
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stream = open(map_path, 'rb')
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reader = csv.reader(stream)
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in_label, out_label = reader.next()[:2]
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def split_col_name(name):
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name, sep, root = name.partition(':')
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return name, sep != '', root
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in_label, in_is_xpaths, in_root = split_col_name(in_label)
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out_label, out_is_xpaths, out_root = split_col_name(out_label)
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assert out_is_xpaths # CSV output not supported yet
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has_types = out_root.startswith('/*s/') # outer elements are types
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for row in reader:
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in_, out = row[:2]
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if out != '':
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if out_is_xpaths: out = out_root+out
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mappings.append((in_, out))
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stream.close()
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in_is_xml = in_is_xpaths and not in_is_db
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# Input datasource to XML tree, mapping if needed
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if in_is_xml:
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doc0 = xml.dom.minidom.parse(sys.stdin)
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if map_path != None:
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doc1 = xml_dom.create_doc(out_label)
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root = doc1.documentElement
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if in_is_db:
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assert in_is_xpaths
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import db_xml
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in_root_xml = xpath.path2xml(in_root)
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for i, mapping in enumerate(mappings):
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in_, out = mapping
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if metadata_value(in_) == None:
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mappings[i] = (xpath.path2xml(in_root+'/'+in_), out)
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in_db = sql.connect(in_db_config)
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in_pkeys = {}
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for row_idx, row in enumerate(sql.rows(db_xml.get(in_db,
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in_root_xml, in_pkeys, limit))):
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row_id = str(row_idx)
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pkey, = row
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for in_, out in mappings:
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value = metadata_value(in_)
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if value == None:
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in_ = in_.cloneNode(True) # don't modify orig value!
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xml_dom.set_id(xpath.get(in_, in_root), pkey)
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value = sql.value_or_none(db_xml.get(in_db, in_,
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in_pkeys))
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if value != None:
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xpath.put_obj(root, out, row_id, has_types, str(value))
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in_db.close()
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elif in_is_xml:
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row = xpath.get(doc0.documentElement, in_root)
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for row_idx, row in enumerate(xml_dom.NodeElemIter(row.parentNode)):
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if not (limit == None or row_idx < limit): break
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row_id = str(row_idx)
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for in_, out in mappings:
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value = metadata_value(in_)
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if value == None:
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node = xpath.get(row, in_)
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if node != None: value = xml_dom.value(node)
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if value != None:
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xpath.put_obj(root, out, row_id, has_types, value)
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else: # input is CSV
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map_ = dict(mappings)
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reader = csv.reader(sys.stdin)
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cols = reader.next()
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col_idxs = dict([(value, idx) for idx, value in enumerate(cols)])
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for i, mapping in enumerate(mappings):
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in_, out = mapping
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if metadata_value(in_) == None:
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try: mappings[i] = (col_idxs[in_], out)
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except KeyError: pass
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for row_idx, row in enumerate(reader):
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if not (limit == None or row_idx < limit): break
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row_id = str(row_idx)
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for in_, out in mappings:
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value = metadata_value(in_)
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if value == None:
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value = row[in_]
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if value == '': value = None
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if value != None:
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xpath.put_obj(root, out, row_id, has_types, value)
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xml_func.process(root)
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else: doc1 = doc0
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# Output XML tree
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if out_is_db:
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from psycopg2.extensions import ISOLATION_LEVEL_SERIALIZABLE
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import db_xml
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out_db = sql.connect(out_db_config)
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out_db.set_isolation_level(ISOLATION_LEVEL_SERIALIZABLE)
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try:
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row_ct_ref = [0]
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db_xml.xml2db(out_db, doc1.documentElement, row_ct_ref)
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print 'Inserted '+str(row_ct_ref[0])+' rows'
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if commit: out_db.commit()
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finally:
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out_db.rollback()
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out_db.close()
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else: xml_dom.writexml(sys.stdout, doc1) # output is XML
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try: main()
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except SyntaxException, ex: raise SystemExit(str(ex))
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