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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
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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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aaronmk
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import opts
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import xml_func
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def metadata_value(name):
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if name.startswith(':'): return name[1:]
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else: return None
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def main():
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# Get db config from env vars
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db_config_names = ['host', 'user', 'password', 'database']
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env_names = []
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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 = in_db_config != None
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out_is_db = out_db_config != None
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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 or not out_is_db: raise SystemExit('Usage: '
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+opts.env_usage(env_names, True)+' [commit=1] '+sys.argv[0]
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+' [map_path] [<input] [>output]')
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commit = opts.env_flag('commit')
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# Load map header
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in_is_xml = 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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from Parser import SyntaxException
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import xpath
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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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src, dest = 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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src, in_is_xml, src_root = split_col_name(src)
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dest, out_is_xml, dest_root = split_col_name(dest)
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assert out_is_xml
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has_types = dest_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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try: mappings.append((in_, xpath.parse(dest_root+out)))
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except SyntaxException, ex: raise SystemExit(str(ex))
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stream.close()
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# Input datasource to XML tree, mapping if needed
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if in_is_xml: doc0 = xml.dom.minidom.parse(sys.stdin)
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if map_path != None:
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doc1 = xml.dom.minidom.getDOMImplementation().createDocument(None,
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dest, None)
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if in_is_db:
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assert in_is_xml
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import psycopg2
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import db_xml
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try: src_root = xpath.parse(src_root)
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except SyntaxException, ex: raise SystemExit(str(ex))
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in_db = psycopg2.connect(**in_db_config)
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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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raise SystemExit('DB-XML mapping not supported yet')
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in_db.close()
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elif in_is_xml: raise SystemExit('XML-XML mapping not supported yet')
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else: # input is CSV
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metadata = []
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map_ = {}
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for in_, out in mappings:
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value = metadata_value(in_)
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if value != None: metadata.append((value, out))
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else: map_[in_] = out
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reader = csv.reader(sys.stdin)
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cols = reader.next()
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for row_idx, row in enumerate(reader):
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row_id = str(row_idx)
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def put_col(path, value):
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xpath.put_obj(doc1, path, row_id, has_types, value)
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for value, out in metadata: put_col(out, value)
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for i, col in enumerate(cols):
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if row[i] != '' and col in map_: put_col(map_[col], row[i])
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xml_func.process(doc1)
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else: doc1 = doc0
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aaronmk
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# Output XML tree
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if out_db_config != None: # output is database
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aaronmk
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import psycopg2
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from psycopg2.extensions import ISOLATION_LEVEL_SERIALIZABLE
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import db_xml
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aaronmk
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db = psycopg2.connect(**out_db_config)
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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(db, doc1.documentElement, row_ct_ref)
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aaronmk
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print 'Inserted '+str(row_ct_ref[0])+' rows'
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if commit: db.commit()
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finally:
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db.rollback()
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db.close()
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else: doc1.writexml(sys.stdout, addindent=' ', newl='\n') # output is XML
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aaronmk
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main()
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