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refine.py
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#!/usr/bin/env python
"""
Client library to communicate with a Refine server.
"""
# Copyright (c) 2011 Paul Makepeace, Real Programmers. All rights reserved.
# This program is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later version.
# This program is distributed in the hope that it will be useful,
# but WITHOUT ANY WARRANTY; without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
# GNU General Public License for more details.
# You should have received a copy of the GNU General Public License
# along with this program. If not, see <http://www.gnu.org/licenses/>
import csv
import json
import gzip
import os
import re
import StringIO
import time
import urllib
import urllib2_file
import urllib2
import urlparse
from google.refine import facet
from google.refine import history
REFINE_HOST = os.environ.get('OPENREFINE_HOST', os.environ.get('GOOGLE_REFINE_HOST', '127.0.0.1'))
REFINE_PORT = os.environ.get('OPENREFINE_PORT', os.environ.get('GOOGLE_REFINE_PORT', '3333'))
class RefineServer(object):
"""Communicate with a Refine server."""
@staticmethod
def url():
"""Return the URL to the Refine server."""
server = 'http://' + REFINE_HOST
if REFINE_PORT != '80':
server += ':' + REFINE_PORT
return server
def __init__(self, server=None):
if server is None:
server = self.url()
self.server = server[:-1] if server.endswith('/') else server
self.__version = None # see version @property below
self.token = None # CSRF token introduced in OpenRefine 3.3
self.get_csrf_token()
def get_csrf_token(self):
"""Return csrf token."""
try:
url = self.server + '/command/core/get-csrf-token'
response = json.loads(urllib2.urlopen(url).read())
self.token = response['token']
return self.token
except:
pass # fail silently to not disturb usage of OpenRefine <3.3
def urlopen(self, command, data=None, params=None, project_id=None):
"""Open a Refine URL and with optional query params and POST data.
data: POST data dict
param: query params dict
project_id: project ID as string
Returns urllib2.urlopen iterable."""
url = self.server + '/command/core/' + command
if data is None:
data = {}
if params is None:
params = {}
if project_id:
# XXX haven't figured out pattern on qs v body
if 'delete' in command or data:
data['project'] = project_id
else:
params['project'] = project_id
# be lazy and send the token for each API call (even when not needed)
if self.token:
params['csrf_token'] = self.token
if params:
url += '?' + urllib.urlencode(params)
req = urllib2.Request(url)
if data:
req.add_data(data) # data = urllib.urlencode(data)
#req.add_header('Accept-Encoding', 'gzip')
try:
response = urllib2.urlopen(req)
except urllib2.HTTPError as e:
if 'Missing or invalid csrf_token parameter' == e.msg:
self.get_csrf_token()
params['csrf_token'] = self.token
response = urllib2.urlopen(req)
else:
raise Exception('HTTP %d "%s" for %s\n\t%s' % (e.code, e.msg, e.geturl(), data))
except urllib2.URLError as e:
raise urllib2.URLError(
'%s for %s. No Refine server reachable/running; ENV set?' %
(e.reason, self.server))
if response.info().get('Content-Encoding', None) == 'gzip':
# Need a seekable filestream for gzip
gzip_fp = gzip.GzipFile(fileobj=StringIO.StringIO(response.read()))
# XXX Monkey patch response's filehandle. Better way?
urllib.addbase.__init__(response, gzip_fp)
return response
def urlopen_json(self, *args, **kwargs):
"""Open a Refine URL, optionally POST data, and return parsed JSON."""
response = json.loads(self.urlopen(*args, **kwargs).read())
if 'code' in response and response['code'] not in ('ok', 'pending'):
error_message = ('server ' + response['code'] + ': ' +
response.get('message', response.get('stack', response)))
raise Exception(error_message)
return response
def get_version(self):
"""Return version data.
{"revision":"r1836","full_version":"2.0 [r1836]",
"full_name":"Google Refine 2.0 [r1836]","version":"2.0"}"""
return self.urlopen_json('get-version')
@property
def version(self):
if self.__version is None:
self.__version = self.get_version()['version']
return self.__version
class Refine:
"""Class representing a connection to a Refine server."""
def __init__(self, server):
if isinstance(server, RefineServer):
self.server = server
else:
self.server = RefineServer(server)
def list_projects(self):
"""Return a dict of projects indexed by id.
{u'1877818633188': {
'id': u'1877818633188', u'name': u'akg',
u'modified': u'2011-04-07T12:30:07Z',
u'created': u'2011-04-07T12:30:07Z'
},
"""
# It's tempting to add in an index by name but there can be
# projects with the same name.
return self.server.urlopen_json('get-all-project-metadata')['projects']
def get_project_name(self, project_id):
"""Returns project name given project_id."""
projects = self.list_projects()
return projects[project_id]['name']
def open_project(self, project_id):
"""Open a Refine project."""
return RefineProject(self.server, project_id)
# These aren't used yet but are included for reference
new_project_defaults = {
'text/line-based/*sv': {
'encoding': '',
'separator': ',',
'ignore_lines': -1,
'header_lines': 1,
'skip_data_lines': 0,
'limit': -1,
'store_blank_rows': True,
'guess_cell_value_types': True,
'process_quotes': True,
'store_blank_cells_as_nulls': True,
'include_file_sources': False},
'text/line-based': {
'encoding': '',
'lines_per_row': 1,
'ignore_lines': -1,
'limit': -1,
'skip_data_lines': -1,
'store_blank_rows': True,
'store_blank_cells_as_nulls': True,
'include_file_sources': False},
'text/line-based/fixed-width': {
'encoding': '',
'column_widths': [20],
'ignore_lines': -1,
'header_lines': 0,
'skip_data_lines': 0,
'limit': -1,
'guess_cell_value_types': False,
'store_blank_rows': True,
'store_blank_cells_as_nulls': True,
'include_file_sources': False},
'text/line-based/pc-axis': {
'encoding': '',
'limit': -1,
'skip_data_lines': -1,
'include_file_sources': False},
'text/rdf+n3': {'encoding': ''},
'text/xml/ods': {
'sheets': [],
'ignore_lines': -1,
'header_lines': 1,
'skip_data_lines': 0,
'limit': -1,
'store_blank_rows': True,
'store_blank_cells_as_nulls': True,
'include_file_sources': False},
'binary/xls': {
'xml_based': False,
'sheets': [],
'ignore_lines': -1,
'header_lines': 1,
'skip_data_lines': 0,
'limit': -1,
'store_blank_rows': True,
'store_blank_cells_as_nulls': True,
'include_file_sources': False}
}
def new_project(self, project_file=None, project_url=None, project_name=None, project_format='text/line-based/*sv',
encoding='',
separator=',',
ignore_lines=-1,
header_lines=1,
skip_data_lines=0,
limit=-1,
store_blank_rows=True,
guess_cell_value_types=False,
process_quotes=True,
store_blank_cells_as_nulls=True,
include_file_sources=False,
**opts):
if (project_file and project_url) or (not project_file and not project_url):
raise ValueError('One (only) of project_file and project_url must be set')
def s(opt):
if isinstance(opt, bool):
return 'true' if opt else 'false'
if opt is None:
return ''
return str(opt)
# the new APIs requires a json in the 'option' POST or GET argument
# POST is broken at the moment, so we send it in the URL
new_style_options = dict(opts, **{
'encoding': s(encoding),
'separator': s(separator)
})
params = {
'options': json.dumps(new_style_options),
}
# old style options
options = {
'format': project_format,
'ignore-lines': s(ignore_lines),
'header-lines': s(header_lines),
'skip-data-lines': s(skip_data_lines),
'limit': s(limit),
'guess-value-type': s(guess_cell_value_types),
'process-quotes': s(process_quotes),
'store-blank-rows': s(store_blank_rows),
'store-blank-cells-as-nulls': s(store_blank_cells_as_nulls),
'include-file-sources': s(include_file_sources)
}
if project_url is not None:
options['url'] = project_url
elif project_file is not None:
options['project-file'] = {
'fd': open(project_file),
'filename': project_file,
}
if project_name is None:
# make a name for itself by stripping extension and directories
project_name = (project_file or 'New project').rsplit('.', 1)[0]
project_name = os.path.basename(project_name)
options['project-name'] = project_name
response = self.server.urlopen(
'create-project-from-upload', options, params
)
# expecting a redirect to the new project containing the id in the url
url_params = urlparse.parse_qs(
urlparse.urlparse(response.geturl()).query)
if 'project' in url_params:
project_id = url_params['project'][0]
return RefineProject(self.server, project_id)
else:
raise Exception('Project not created')
def RowsResponseFactory(column_index):
"""Factory for the parsing the output from get_rows().
Uses the project's model's row cell index so that a row can be used
as a dict by column name."""
class RowsResponse(object):
class RefineRows(object):
class RefineRow(object):
def __init__(self, row_response):
self.flagged = row_response['flagged']
self.starred = row_response['starred']
self.index = row_response['i']
self.row = [c['v'] if c else None
for c in row_response['cells']]
def __getitem__(self, column):
# Trailing nulls seem to be stripped from row data
try:
return self.row[column_index[column]]
except IndexError:
return None
def __init__(self, rows_response):
self.rows_response = rows_response
def __iter__(self):
for row_response in self.rows_response:
yield self.RefineRow(row_response)
def __getitem__(self, index):
return self.RefineRow(self.rows_response[index])
def __len__(self):
return len(self.rows_response)
def __init__(self, response):
self.mode = response['mode']
self.filtered = response['filtered']
self.start = response['start']
self.limit = response['limit']
self.total = response['total']
self.rows = self.RefineRows(response['rows'])
return RowsResponse
class RefineProject:
"""An OpenRefine project."""
def __init__(self, server, project_id=None):
if not isinstance(server, RefineServer):
if '/project?project=' in server:
server, project_id = server.split('/project?project=')
server = RefineServer(server)
elif re.match(r'\d+$', server): # just digits => project ID
server, project_id = RefineServer(), server
else:
server = RefineServer(server)
self.server = server
if not project_id:
raise Exception('Missing Refine project ID')
self.project_id = project_id
self.engine = facet.Engine()
self.sorting = facet.Sorting()
self.history_entry = None
# following filled in by get_models()
self.key_column = None
self.has_records = False
self.columns = None
self.column_order = {} # map of column names to order in UI
self.rows_response_factory = None # for parsing get_rows()
self.get_models()
# following filled in by get_reconciliation_services
self.recon_services = None
def project_name(self):
return Refine(self.server).get_project_name(self.project_id)
def project_url(self):
"""Return a URL to the project."""
return '%s/project?project=%s' % (self.server.server, self.project_id)
def do_raw(self, command, data):
"""Issue a command to the server & return a response object."""
return self.server.urlopen(command, project_id=self.project_id,
data=data)
def do_json(self, command, data=None, include_engine=True):
"""Issue a command to the server, parse & return decoded JSON."""
if include_engine:
if data is None:
data = {}
data['engine'] = self.engine.as_json()
response = self.server.urlopen_json(command,
project_id=self.project_id,
data=data)
if 'historyEntry' in response:
# **response['historyEntry'] won't work as keys are unicode :-/
he = response['historyEntry']
self.history_entry = history.HistoryEntry(he['id'], he['time'],
he['description'])
return response
def get_models(self):
"""Fill out column metadata.
Column structure is a list of columns in their order.
The cellIndex is an index for that column's data into the list returned
from get_rows()."""
response = self.do_json('get-models', include_engine=False)
column_model = response['columnModel']
column_index = {} # map of column name to index into get_rows() data
self.columns = [column['name'] for column in column_model['columns']]
for i, column in enumerate(column_model['columns']):
name = column['name']
self.column_order[name] = i
try:
column_index[name] = column['cellIndex']
except KeyError:
column_index[name] = i
self.key_column = column_model['keyColumnName']
self.has_records = response['recordModel'].get('hasRecords', False)
self.rows_response_factory = RowsResponseFactory(column_index)
# TODO: implement rest
return response
def get_preference(self, name):
"""Returns the (JSON) value of a given preference setting."""
response = self.server.urlopen_json('get-preference',
params={'name': name})
return json.loads(response['value'])
def wait_until_idle(self, polling_delay=0.5):
while True:
response = self.do_json('get-processes', include_engine=False)
if 'processes' in response and len(response['processes']) > 0:
time.sleep(polling_delay)
else:
return
def apply_operations(self, file_path, wait=True):
json_data = open(file_path).read()
response_json = self.do_json('apply-operations', {'operations': json_data})
if response_json['code'] == 'pending' and wait:
self.wait_until_idle()
return 'ok'
return response_json['code'] # can be 'ok' or 'pending'
def export(self, encoding=None, export_format='tsv'):
"""Return a fileobject of a project's data."""
url = ('export-rows/' +
urllib.quote(self.project_name().encode('utf8')) +
'.' + export_format)
data = {'format': export_format}
if encoding:
data['encoding'] = encoding
return self.do_raw(url, data)
def export_templating(self, encoding=None, engine='', prefix='',
template='', rowSeparator='\n', suffix=''):
"""Return a fileobject of a project's data in templating mode."""
url = ('export-rows/' +
urllib.quote(self.project_name().encode('utf8')) +
'.' + 'txt')
data = {'format': 'template',
'template': template,
'engine': engine,
'prefix': prefix,
'suffix': suffix,
'separator': rowSeparator}
if encoding:
data['encoding'] = encoding
return self.do_raw(url, data)
def export_rows(self, **kwargs):
"""Return an iterable of parsed rows of a project's data."""
return csv.reader(self.export(**kwargs), dialect='excel-tab')
def delete(self):
response_json = self.do_json('delete-project', include_engine=False)
return 'code' in response_json and response_json['code'] == 'ok'
def compute_facets(self, facets=None):
"""Compute facets as per the project's engine.
The response object has two attributes, mode & facets. mode is one of
'row-based' or 'record-based'. facets is a magic list of facets in the
same order as they were specified in the Engine. Magic allows the
original Engine's facet as index into the response, e.g.,
name_facet = TextFacet('name')
response = project.compute_facets(name_facet)
response.facets[name_facet] # same as response.facets[0]
"""
if facets:
self.engine.set_facets(facets)
response = self.do_json('compute-facets')
return self.engine.facets_response(response)
def get_rows(self, facets=None, sort_by=None, start=0, limit=10):
if facets:
self.engine.set_facets(facets)
if sort_by is not None:
self.sorting = facet.Sorting(sort_by)
response = self.do_json('get-rows', {'sorting': self.sorting.as_json(),
'start': start, 'limit': limit})
return self.rows_response_factory(response)
def reorder_rows(self, sort_by=None):
if sort_by is not None:
self.sorting = facet.Sorting(sort_by)
response = self.do_json('reorder-rows',
{'sorting': self.sorting.as_json()})
# clear sorting
self.sorting = facet.Sorting()
return response
def remove_rows(self, facets=None):
if facets:
self.engine.set_facets(facets)
return self.do_json('remove-rows')
def text_transform(self, column, expression, on_error='set-to-blank',
repeat=False, repeat_count=10):
response = self.do_json('text-transform', {
'columnName': column, 'expression': expression,
'onError': on_error, 'repeat': repeat,
'repeatCount': repeat_count})
return response
def edit(self, column, edit_from, edit_to):
edits = [{'from': [edit_from], 'to': edit_to}]
return self.mass_edit(column, edits)
def mass_edit(self, column, edits, expression='value'):
"""edits is [{'from': ['foo'], 'to': 'bar'}, {...}]"""
edits = json.dumps(edits)
response = self.do_json('mass-edit', {
'columnName': column, 'expression': expression, 'edits': edits})
return response
clusterer_defaults = {
'binning': {
'type': 'binning',
'function': 'fingerprint',
'params': {},
},
'knn': {
'type': 'knn',
'function': 'levenshtein',
'params': {
'radius': 1,
'blocking-ngram-size': 6,
},
},
}
def compute_clusters(self, column, clusterer_type='binning',
function=None, params=None):
"""Returns a list of clusters of {'value': ..., 'count': ...}."""
clusterer = self.clusterer_defaults[clusterer_type]
if params is not None:
clusterer['params'] = params
if function is not None:
clusterer['function'] = function
clusterer['column'] = column
response = self.do_json('compute-clusters', {
'clusterer': json.dumps(clusterer)})
return [[{'value': x['v'], 'count': x['c']} for x in cluster]
for cluster in response]
def annotate_one_row(self, row, annotation, state=True):
if annotation not in ('starred', 'flagged'):
raise ValueError('annotation must be one of starred or flagged')
state = 'true' if state is True else 'false'
return self.do_json('annotate-one-row', {'row': row.index,
annotation: state})
def flag_row(self, row, flagged=True):
return self.annotate_one_row(row, 'flagged', flagged)
def star_row(self, row, starred=True):
return self.annotate_one_row(row, 'starred', starred)
def add_column(self, column, new_column, expression='value',
column_insert_index=None, on_error='set-to-blank'):
if column_insert_index is None:
column_insert_index = self.column_order[column] + 1
response = self.do_json('add-column', {
'baseColumnName': column, 'newColumnName': new_column,
'expression': expression, 'columnInsertIndex': column_insert_index,
'onError': on_error})
self.get_models()
return response
def split_column(self, column, separator=',', mode='separator',
regex=False, guess_cell_type=True,
remove_original_column=True):
response = self.do_json('split-column', {
'columnName': column, 'separator': separator, 'mode': mode,
'regex': regex, 'guessCellType': guess_cell_type,
'removeOriginalColumn': remove_original_column})
self.get_models()
return response
def rename_column(self, column, new_column):
response = self.do_json('rename-column', {'oldColumnName': column,
'newColumnName': new_column})
self.get_models()
return response
def reorder_columns(self, new_column_order):
"""Takes an array of column names in the new order."""
response = self.do_json('reorder-columns', {
'columnNames': new_column_order})
self.get_models()
return response
def move_column(self, column, index):
"""Move column to a new position."""
if index == 'end':
index = len(self.columns) - 1
response = self.do_json('move-column', {'columnName': column,
'index': index})
self.get_models()
return response
def blank_down(self, column):
response = self.do_json('blank-down', {'columnName': column})
self.get_models()
return response
def fill_down(self, column):
response = self.do_json('fill-down', {'columnName': column})
self.get_models()
return response
def transpose_columns_into_rows(
self, start_column, column_count,
combined_column_name, separator=':', prepend_column_name=True,
ignore_blank_cells=True):
response = self.do_json('transpose-columns-into-rows', {
'startColumnName': start_column, 'columnCount': column_count,
'combinedColumnName': combined_column_name,
'prependColumnName': prepend_column_name,
'separator': separator, 'ignoreBlankCells': ignore_blank_cells})
self.get_models()
return response
def transpose_rows_into_columns(self, column, row_count):
response = self.do_json('transpose-rows-into-columns', {
'columnName': column, 'rowCount': row_count})
self.get_models()
return response
# Reconciliation
# http://code.google.com/p/google-refine/wiki/ReconciliationServiceApi
def guess_types_of_column(self, column, service):
"""Query the reconciliation service for what it thinks this column is.
service: reconciliation endpoint URL
Returns [
{"id":"/domain/type","name":"Type Name","score":10.2,"count":18},
...
]
"""
response = self.do_json('guess-types-of-column', {
'columnName': column, 'service': service}, include_engine=False)
return response['types']
def get_reconciliation_services(self):
response = self.get_preference('reconciliation.standardServices')
self.recon_services = response
return response
def get_reconciliation_service_by_name_or_url(self, name):
recon_services = self.get_reconciliation_services()
for recon_service in recon_services:
if recon_service['name'] == name or recon_service['url'] == name:
return recon_service
return None
def reconcile(self, column, service, reconciliation_type=None,
reconciliation_config=None):
"""Perform a reconciliation asynchronously.
config: {
"mode": "standard-service",
"service": "http://.../reconcile/",
"identifierSpace": "http://.../ns/authority",
"schemaSpace": "http://.../ns/type",
"type": {
"id": "/domain/type",
"name": "Type Name"
},
"autoMatch": true,
"columnDetails": []
}
Returns typically {'code': 'pending'}; call wait_until_idle() to wait
for reconciliation to complete.
"""
# Create a reconciliation config by looking up recon service info
if reconciliation_config is None:
service = self.get_reconciliation_service_by_name_or_url(service)
if reconciliation_type is None:
raise ValueError('Must have at least one of config or type')
reconciliation_config = {
'mode': 'standard-service',
'service': service['url'],
'identifierSpace': service['identifierSpace'],
'schemaSpace': service['schemaSpace'],
'type': {
'id': reconciliation_type['id'],
'name': reconciliation_type['name'],
},
'autoMatch': True,
'columnDetails': [],
}
return self.do_json('reconcile', {
'columnName': column, 'config': json.dumps(reconciliation_config)})