big_recordlink.py

#!/usr/bin/env python
# -*- coding: utf-8 -*-

import os
import csv
import tempfile
import time
import logging
import optparse
import itertools

import dj_database_url
import psycopg2
import psycopg2.extras

import dedupe


class Database(object):
    def __init__(self, *args, **kwargs):
        self.con = kwargs.pop('connection')
        super().__init__(*args, **kwargs)
    
    def match(self, data_1, data_2, threshold=0.5):

        blocked_pairs = self._blockData(data_1, data_2)
        return self.matchBlocks(blocked_pairs, threshold)

    def _blockData(self, data_1, data_2):
        cur = self.con.cursor()
        

        if not self.loaded_indices:
             self.blocker.indexAll(data_2)

        cur.execute("DROP TABLE IF EXISTS block")
        cur.execute("""CREATE TABLE block
                       (block_key VARCHAR(200), record_id INTEGER)""")

        self.con.commit()
             
        for block_key, record_id in self.blocker(data_2.items(), target=True):
            cur.execute("INSERT INTO block VALUES (%s, %s)",
                        (block_key, record_id))

        cur.execute("CREATE INDEX ON block (block_key)")
        self.con.commit()

        for each in self._blockGenerator(data_1, data_2):
            yield each

        cur.close()

    def _blockGenerator(self, data_1, data_2):

        cur = self.con.cursor()

        block_groups = itertools.groupby(self.blocker(data_1.items()),
                                         lambda x: x[1])
        i = 0

        for record_id, blocks in block_groups:
            A = [(record_id, data_1[record_id], set())]

            block_keys, _ = list(zip(*blocks))
            cur.execute("""
                SELECT DISTINCT record_id 
                FROM block
                WHERE block_key IN %s""", (block_keys,))

            match_ids = (row['record_id'] for row in cur.fetchall())
            
            B = [(record_id, data_2[record_id], set())
                 for record_id in match_ids]

            i += 1

            if i % 10000 == 0:
                print(i, "records")
                print(time.time() - start_time, "seconds")

            if B:
                yield (A, B)

        cur.close()


class RecordLink(Database, dedupe.RecordLink):
    pass


class StaticRecordLink(Database, dedupe.StaticRecordLink):
    pass


## Logging

# Dedupe uses Python logging to show or suppress verbose output. Added
# for convenience.  To enable verbose output, run `python
# pgsql_big_dedupe_example.py -v`
optp = optparse.OptionParser()
optp.add_option('-v', '--verbose', dest='verbose', action='count',
                help='Increase verbosity (specify multiple times for more)'
                )
(opts, args) = optp.parse_args()
log_level = logging.WARNING
if opts.verbose:
    if opts.verbose == 1:
        log_level = logging.INFO
    elif opts.verbose >= 2:
        log_level = logging.DEBUG
logging.getLogger().setLevel(log_level)

# ## Setup; change these names if you screw up earlier settings/trainings
settings_file = 'fig_reclink_settings'
training_file = 'fig_reclink_training.json'

start_time = time.time()

# Set the database connection from environment variable using
# [dj_database_url](https://github.com/kennethreitz/dj-database-url)
# For example:
#   export DATABASE_URL=postgres://user:password@host/mydatabase
db_conf = dj_database_url.config()

if not db_conf:
    raise Exception(
        'set DATABASE_URL environment variable with your connection, e.g. '
        'export DATABASE_URL=postgres://user:password@host/mydatabase'
    )

con = psycopg2.connect(database=db_conf['NAME'],
                       user=db_conf['USER'],
                       password=db_conf['PASSWORD'],
                       host=db_conf['HOST'],
                       cursor_factory=psycopg2.extras.RealDictCursor)

c = con.cursor()


con.commit()

CROSS_MATCH = """
    CREATE TABLE IF NOT EXISTS cross_match_exact AS
    SELECT source.donor_id AS source,
           target.donor_id AS target
    FROM data_a AS source
    INNER JOIN data_b AS target
    USING({fields})"""

c.execute(CROSS_MATCH.format(fields=FIELDS))

c.execute("CREATE INDEX IF NOT EXISTS source_idx ON cross_match_exact (source)")
c.execute("CREATE INDEX IF NOT EXISTS target_idx ON cross_match_exact (target)")

con.commit()

B_SELECT = """
    SELECT data_a.*
    FROM data_a 
    LEFT JOIN cross_match_exact
    ON donor_id = source
    WHERE target IS NULL"""

M8_SELECT = """
    SELECT data_b.* 
    FROM data_b
    LEFT JOIN cross_match_exact
    ON donor_id = target
    WHERE source IS NULL"""


if os.path.exists(settings_file):
    print('reading from ', settings_file)
    with open(settings_file, 'rb') as sf:
        deduper = StaticRecordLink(sf, num_cores=4, connection=con)
else:

    # Define the fields dedupe will pay attention to
    #
    # The address, city, and zip fields are often missing, so we'll
    # tell dedupe that, and we'll learn a model that take that into
    # account
    fields = [
        {'field': 'bpcounty', 'type': 'Exact'},
        {'field': 'age', 'type': 'Price'},
        {'field': 'bpparish', 'type': 'String', 'crf': True}
        ]

    # Create a new deduper object and pass our data model to it.
    deduper = RecordLink(fields, num_cores=4, connection=con)

    # Named cursor runs server side with psycopg2
    with con.cursor('donor_select') as cur:

        cur.execute(B_SELECT)
        temp_d = {i: row for i, row in enumerate(cur)}

    with con.cursor('tower_select') as cur:
        cur.execute(M8_SELECT)
        temp_z = {i: row for i, row in enumerate(cur)}

    deduper.sample(temp_d, temp_z)

    # If we have training data saved from a previous run of dedupe,
    # look for it an load it in.
    #
    # __Note:__ if you want to train from
    # scratch, delete the training_file
    if os.path.exists(training_file):
        print('reading labeled examples from ', training_file)
        with open(training_file) as tf:
            deduper.readTraining(tf)

    # ## Active learning

    print('starting active labeling...')
    # Starts the training loop. Dedupe will find the next pair of records
    # it is least certain about and ask you to label them as duplicates
    # or not.

    # use 'y', 'n' and 'u' keys to flag duplicates
    # press 'f' when you are finished
    dedupe.convenience.consoleLabel(deduper)
    # When finished, save our labeled, training pairs to disk
    with open(training_file, 'w') as tf:
        deduper.writeTraining(tf)

    # Notice our argument here
    #
    # `recall` is the proportion of true dupes pairs that the learned
    # rules must cover. You may want to reduce this if your are making
    # too many blocks and too many comparisons.
    deduper.train(recall=0.90)

    with open(settings_file, 'wb') as sf:
        deduper.writeSettings(sf)

    # We can now remove some of the memory hogging objects we used
    # for training
    deduper.cleanupTraining()


with con.cursor('donor_select') as cur:
    cur.execute(B_SELECT)
    data_1 = {row['donor_id']: row for row in cur}

with con.cursor('tower_select') as cur:
    cur.execute(M8_SELECT)
    data_2 = {row['donor_id']: row for row in cur}

clustered_dupes = deduper.match(data_1, data_2, threshold=0.0)

# Writing out results

c.execute("DROP TABLE IF EXISTS cross_match_fuzzy")

print('creating cross_match_fuzzy database')
c.execute("CREATE TABLE cross_match_fuzzy "
          "(source INTEGER, target INTEGER, "
          " score FLOAT)")


csv_file = tempfile.NamedTemporaryFile(prefix='cross_match_fuzzy_', delete=False,
                                       mode='w')
csv_writer = csv.writer(csv_file)

for (source, target), score in clustered_dupes:
    csv_writer.writerow((source, target, score))

csv_file.close()

with open(csv_file.name, 'r') as f:
    c.copy_expert("COPY cross_match_fuzzy FROM STDIN CSV", f)

os.remove(csv_file.name)

con.commit()

c.close()
con.close()

Great example however what is FIELDS (on line 151) supposed to be? in the example above it is missing. I tried to pass in an array/set/tuple of the field names in my dataset, but it will not use that data. Could you provide an example?

the script is failing @ clustered_dupes = deduper.match(data_1, data_2, threshold=0.0) with error
return self.matchBlocks(blocked_pairs, threshold)
AttributeError: 'StaticRecordLink' object has no attribute 'matchBlocks'

Seconding @ohenrik. FIELDS is undefined and I'm not sure what it's meant to be.