1
|
|
|
#pylint: disable=W0223 |
2
|
1 |
|
import os |
3
|
|
|
|
4
|
1 |
|
import logging |
5
|
1 |
|
import datetime |
6
|
|
|
|
7
|
1 |
|
from collections import Counter, OrderedDict |
8
|
|
|
|
9
|
1 |
|
import pandas as pd |
10
|
|
|
|
11
|
1 |
|
from crowdtruth.models.worker import Worker |
12
|
1 |
|
from crowdtruth.models.unit import Unit |
13
|
1 |
|
from crowdtruth.models.job import Job |
14
|
1 |
|
from crowdtruth.configuration import DefaultConfig |
15
|
|
|
|
16
|
|
|
|
17
|
|
|
|
18
|
|
|
|
19
|
|
|
# create an ordered counter so that we can maintain |
20
|
|
|
# the position of tags in the order they were annotated |
21
|
1 |
|
class OrderedCounter(Counter, OrderedDict): |
22
|
|
|
""" ordered counter """ |
23
|
1 |
|
pass |
24
|
|
|
|
25
|
1 |
|
def create_ordered_counter(ordered_counter, annotation_vector): |
26
|
|
|
""" ordered counter """ |
27
|
1 |
|
for relation in annotation_vector: |
28
|
1 |
|
if relation not in ordered_counter: |
29
|
1 |
|
ordered_counter.update({relation: 0}) |
30
|
1 |
|
return ordered_counter |
31
|
|
|
|
32
|
|
|
|
33
|
1 |
|
class Found(Exception): |
34
|
|
|
""" Exception """ |
35
|
1 |
|
pass |
36
|
|
|
|
37
|
1 |
|
def validate_timestamp_field(date_string, date_format): |
38
|
|
|
""" function to validate time columns in input files """ |
39
|
|
|
|
40
|
|
|
try: |
41
|
|
|
date_obj = datetime.datetime.strptime(date_string, date_format) |
42
|
|
|
print(date_obj) |
43
|
|
|
except ValueError: |
44
|
|
|
raise ValueError('Incorrect date format') |
45
|
|
|
|
46
|
1 |
|
def get_file_list(directory): |
47
|
|
|
""" return list of documents in folder """ |
48
|
|
|
filelist = [] |
49
|
|
|
|
50
|
|
|
# go through all files in this folder |
51
|
|
|
for file in os.listdir(directory): |
52
|
|
|
# if it is a folder scan it |
53
|
|
|
if os.path.isdir(directory+'/'+file): |
54
|
|
|
sublist = get_file_list(directory+'/'+file) |
55
|
|
|
sublist_length = len(sublist) |
56
|
|
|
if sublist_length: |
57
|
|
|
filelist.append(sublist) |
58
|
|
|
|
59
|
|
|
# if it is a csv file open it |
60
|
|
|
elif file.endswith('.csv') and file != 'groundtruth.csv': |
61
|
|
|
filelist.append(file) |
62
|
|
|
return filelist |
63
|
|
|
|
64
|
1 |
|
def load(**kwargs): |
65
|
|
|
""" Load judgment files """ |
66
|
|
|
# placeholder for aggregated results |
67
|
1 |
|
results = { |
68
|
|
|
'jobs' : [], |
69
|
|
|
'units' : [], |
70
|
|
|
'workers' : [], |
71
|
|
|
'judgments' : [], |
72
|
|
|
'annotations' : [] |
73
|
|
|
} |
74
|
|
|
|
75
|
|
|
|
76
|
1 |
|
if 'config' not in kwargs: |
77
|
|
|
config = DefaultConfig() |
78
|
|
|
else: |
79
|
1 |
|
logging.info('Config loaded') |
80
|
1 |
|
config = kwargs['config'] |
81
|
|
|
|
82
|
|
|
# check if files is a single file or folder |
83
|
1 |
|
if 'file' in kwargs and kwargs['file'].endswith('.csv'): |
84
|
1 |
|
files = [kwargs['file']] |
85
|
|
|
elif 'directory' in kwargs: |
86
|
|
|
directory = kwargs['directory'] |
87
|
|
|
files = get_file_list(directory) |
88
|
|
|
logging.info('Found ' + str(len(files)) + ' files') |
89
|
|
|
else: |
90
|
|
|
raise ValueError('No input was provided') |
91
|
|
|
|
92
|
|
|
|
93
|
1 |
|
for file in files: |
94
|
1 |
|
if 'directory' in locals(): |
95
|
|
|
logging.info("Processing " + file) |
96
|
|
|
file = directory + "/" + file |
97
|
1 |
|
res, config = process_file(file, config) |
98
|
1 |
|
for value in res: |
99
|
1 |
|
results[value].append(res[value]) |
100
|
|
|
|
101
|
1 |
|
for value in results: |
102
|
1 |
|
results[value] = pd.concat(results[value]) |
103
|
|
|
|
104
|
|
|
|
105
|
|
|
# workers and annotations can appear across jobs, so we have to aggregate those extra |
106
|
1 |
|
results['workers'] = results['workers'].groupby(results['workers'].index).agg({ |
107
|
|
|
'unit' : 'sum', |
108
|
|
|
'judgment' : 'sum', |
109
|
|
|
'job' : 'count', |
110
|
|
|
'duration' : 'mean' |
111
|
|
|
}) |
112
|
|
|
|
113
|
|
|
# aggregate annotations |
114
|
1 |
|
results['annotations'] = results['annotations'].groupby(results['annotations'].index).sum() |
115
|
|
|
|
116
|
1 |
|
return results, config |
117
|
|
|
|
118
|
1 |
|
def remove_empty_rows(config, judgments): |
119
|
|
|
""" remove rows where the worker did not give an answer (AMT issue) """ |
120
|
1 |
|
empty_rows = set() |
121
|
1 |
|
for col in config.outputColumns: |
122
|
1 |
|
empty_rows = empty_rows.union(judgments[pd.isnull(judgments[col]) == True].index) |
123
|
1 |
|
for col in config.outputColumns: |
124
|
1 |
|
judgments = judgments[pd.isnull(judgments[col]) == False] |
125
|
1 |
|
judgments = judgments.reset_index(drop=True) |
126
|
1 |
|
count_empty_rows = len(empty_rows) |
127
|
1 |
|
if count_empty_rows > 0: |
128
|
|
|
if count_empty_rows == 1: |
129
|
|
|
logging.warning(str(count_empty_rows) + " row with incomplete information in " |
130
|
|
|
"output columns was removed.") |
131
|
|
|
else: |
132
|
|
|
logging.warning(str(count_empty_rows) + " rows with incomplete information in " |
133
|
|
|
"output columns were removed.") |
134
|
1 |
|
return judgments |
135
|
|
|
|
136
|
1 |
|
def remove_single_judgment_units(judgments): |
137
|
|
|
""" remove units with just 1 judgment """ |
138
|
1 |
|
units_1work = judgments.groupby('unit').filter(lambda x: len(x) == 1)["unit"] |
139
|
1 |
|
judgments = judgments[~judgments['unit'].isin(units_1work)] |
140
|
1 |
|
judgments = judgments.reset_index(drop=True) |
141
|
1 |
|
no_units_1work = len(units_1work) |
142
|
1 |
|
if no_units_1work > 0: |
143
|
|
|
if no_units_1work == 1: |
144
|
|
|
logging.warning(str(no_units_1work) + " Media Unit that was annotated by only" |
145
|
|
|
" 1 Worker was omitted, since agreement cannot be calculated.") |
146
|
|
|
else: |
147
|
|
|
logging.warning(str(no_units_1work) + " Media Units that were annotated by only" |
148
|
|
|
" 1 Worker were omitted, since agreement cannot be calculated.") |
149
|
1 |
|
return judgments |
150
|
|
|
|
151
|
1 |
|
def make_output_cols_safe_keys(config, judgments): |
152
|
|
|
""" make output values safe keys """ |
153
|
1 |
|
for col in config.output.values(): |
154
|
1 |
|
if isinstance(judgments[col].iloc[0], dict): |
155
|
|
|
logging.info("Values stored as dictionary") |
156
|
|
|
if config.open_ended_task: |
157
|
|
|
judgments[col] = judgments[col].apply(lambda x: OrderedCounter(x)) |
158
|
|
|
else: |
159
|
|
|
judgments[col] = judgments[col].apply(lambda x: create_ordered_counter( \ |
160
|
|
|
OrderedCounter(x), config.annotation_vector)) |
161
|
|
|
else: |
162
|
1 |
|
logging.info("Values not stored as dictionary") |
163
|
1 |
|
if config.open_ended_task: |
164
|
1 |
|
judgments[col] = judgments[col].apply(lambda x: OrderedCounter( \ |
165
|
|
|
x.split(config.annotation_separator))) |
166
|
|
|
else: |
167
|
1 |
|
judgments[col] = judgments[col].apply(lambda x: create_ordered_counter( \ |
168
|
|
|
OrderedCounter(x.split(config.annotation_separator)), \ |
169
|
|
|
config.annotation_vector)) |
170
|
1 |
|
return judgments |
171
|
|
|
|
172
|
1 |
|
def process_file(filename, config): |
173
|
|
|
""" process input files with the given configuration""" |
174
|
|
|
|
175
|
1 |
|
judgments = pd.read_csv(filename)#, encoding=result['encoding']) |
176
|
|
|
|
177
|
1 |
|
platform = get_platform(judgments) |
178
|
|
|
|
179
|
1 |
|
if platform is False: |
180
|
|
|
logging.info("Custom crowdsourcing platform!") |
181
|
|
|
no_of_columns = len(config.customPlatformColumns) |
182
|
|
|
if no_of_columns != 5: |
183
|
|
|
logging.warning("The following column names are required: judgment id, " |
184
|
|
|
"unit id, worker id, start time, submit time") |
185
|
|
|
raise ValueError('No custom platform configuration was provided') |
186
|
|
|
else: |
187
|
|
|
|
188
|
|
|
platform = { |
189
|
|
|
#'id' : 'custom', |
190
|
|
|
config.customPlatformColumns[0] : 'judgment', |
191
|
|
|
config.customPlatformColumns[1] : 'unit', |
192
|
|
|
config.customPlatformColumns[2] : 'worker', |
193
|
|
|
config.customPlatformColumns[3] : 'started', |
194
|
|
|
config.customPlatformColumns[4] : 'submitted' |
195
|
|
|
} |
196
|
|
|
|
197
|
|
|
|
198
|
|
|
# we must establish which fields were part of the input data and which are output judgments |
199
|
|
|
# if there is a config, check if there is a definition of which fields to use |
200
|
|
|
#config = [] |
201
|
|
|
# else use the default and select them automatically |
202
|
1 |
|
config = get_column_types(judgments, config) |
203
|
|
|
|
204
|
1 |
|
judgments = remove_empty_rows(config, judgments) |
205
|
|
|
# allow customization of the judgments |
206
|
1 |
|
judgments = config.processJudgments(judgments) |
207
|
|
|
|
208
|
|
|
# update the config after the preprocessing of judgments |
209
|
1 |
|
config = get_column_types(judgments, config) |
210
|
|
|
|
211
|
1 |
|
all_columns = dict(list(config.input.items()) + list(config.output.items()) \ |
212
|
|
|
+ list(platform.items())) |
213
|
|
|
# allColumns = dict(config.input.items() | config.output.items() | platform.items()) |
214
|
1 |
|
judgments = judgments.rename(columns=all_columns) |
215
|
|
|
|
216
|
|
|
# remove columns we don't care about |
217
|
1 |
|
judgments = judgments[list(all_columns.values())] |
218
|
|
|
|
219
|
1 |
|
judgments['job'] = filename.split('.csv')[0] |
220
|
|
|
|
221
|
|
|
# make output values safe keys |
222
|
1 |
|
judgments = make_output_cols_safe_keys(config, judgments) |
223
|
|
|
|
224
|
1 |
|
judgments['started'] = judgments['started'].apply(lambda x: pd.to_datetime(str(x))) |
225
|
1 |
|
judgments['submitted'] = judgments['submitted'].apply(lambda x: pd.to_datetime(str(x))) |
226
|
1 |
|
judgments['duration'] = judgments.apply(lambda row: (row['submitted'] - row['started']).seconds, |
227
|
|
|
axis=1) |
228
|
|
|
|
229
|
|
|
# remove units with just 1 judgment |
230
|
1 |
|
judgments = remove_single_judgment_units(judgments) |
231
|
|
|
|
232
|
|
|
# |
233
|
|
|
# aggregate units |
234
|
|
|
# |
235
|
1 |
|
units = Unit.aggregate(judgments, config) |
236
|
|
|
|
237
|
1 |
|
for col in config.output.values(): |
238
|
1 |
|
judgments[col+'.count'] = judgments[col].apply(lambda x: sum(x.values())) |
239
|
1 |
|
judgments[col+'.unique'] = judgments[col].apply(lambda x: len(x)) |
240
|
|
|
|
241
|
|
|
|
242
|
|
|
# |
243
|
|
|
# aggregate workers |
244
|
|
|
# |
245
|
1 |
|
workers = Worker.aggregate(judgments, config) |
246
|
|
|
|
247
|
|
|
|
248
|
|
|
# |
249
|
|
|
# aggregate annotations |
250
|
|
|
# i.e. output columns |
251
|
|
|
# |
252
|
1 |
|
annotations = pd.DataFrame() |
253
|
1 |
|
for col in config.output.values(): |
254
|
1 |
|
res = pd.DataFrame(judgments[col].apply(lambda x: \ |
255
|
|
|
pd.Series(list(x.keys())).value_counts()).sum(), columns=[col]) |
256
|
1 |
|
annotations = pd.concat([annotations, res], axis=0) |
257
|
|
|
|
258
|
|
|
# |
259
|
|
|
# aggregate job |
260
|
|
|
# |
261
|
1 |
|
job = Job.aggregate(units, judgments, config) |
262
|
|
|
|
263
|
|
|
# Clean up judgments |
264
|
|
|
# remove input columns from judgments |
265
|
1 |
|
output_cols = [col for col in judgments.columns.values \ |
266
|
|
|
if col.startswith('output') or col.startswith('metric')] |
267
|
1 |
|
judgments = judgments[output_cols + list(platform.values()) + ['duration', 'job']] |
268
|
|
|
|
269
|
|
|
# set judgment id as index |
270
|
1 |
|
judgments.set_index('judgment', inplace=True) |
271
|
|
|
|
272
|
|
|
# add missing vector values if closed task |
273
|
1 |
|
for col in config.output.values(): |
274
|
1 |
|
try: |
275
|
|
|
# openended = config.open_ended_task |
276
|
1 |
|
for idx in list(units.index): |
277
|
1 |
|
for relation in config.annotation_vector: |
278
|
1 |
|
if relation not in units[col][idx]: |
279
|
1 |
|
units[col][idx].update({relation : 0}) |
280
|
|
|
except AttributeError: |
281
|
|
|
continue |
282
|
|
|
|
283
|
1 |
|
return { |
284
|
|
|
'jobs' : job, |
285
|
|
|
'units' : units, |
286
|
|
|
'workers' : workers, |
287
|
|
|
'judgments' : judgments, |
288
|
|
|
'annotations' : annotations, |
289
|
|
|
}, config |
290
|
|
|
|
291
|
|
|
|
292
|
1 |
|
def get_platform(dframe): |
293
|
|
|
""" Get the crowdsourcing platform this file originates to """ |
294
|
|
|
|
295
|
1 |
|
if dframe.columns.values[0] == '_unit_id': |
296
|
|
|
# CrowdFlower |
297
|
1 |
|
return { |
298
|
|
|
#'_platform' : 'cf', |
299
|
|
|
'_id' : 'judgment', |
300
|
|
|
'_unit_id' : 'unit', |
301
|
|
|
'_worker_id' : 'worker', |
302
|
|
|
'_started_at' : 'started', |
303
|
|
|
'_created_at' : 'submitted' |
304
|
|
|
} |
305
|
|
|
elif dframe.columns.values[0] == 'HITId': |
306
|
|
|
# Mturk |
307
|
|
|
return { |
308
|
|
|
#'id' : 'amt', |
309
|
|
|
'AssignmentId' : 'judgment', |
310
|
|
|
'HITId' : 'unit', |
311
|
|
|
'WorkerId' : 'worker', |
312
|
|
|
'AcceptTime' : 'started', |
313
|
|
|
'SubmitTime' : 'submitted' |
314
|
|
|
} |
315
|
|
|
return False |
316
|
|
|
|
317
|
|
|
|
318
|
1 |
|
def get_column_types(dframe, config): |
319
|
|
|
""" return input and output columns """ |
320
|
|
|
# returns a list of columns that contain are input content |
321
|
1 |
|
config.input = {} |
322
|
1 |
|
config.output = {} |
323
|
|
|
|
324
|
|
|
# get a dict of the columns with input content and the columns with output judgments |
325
|
|
|
# each entry matches [original column name]:[safestring column name] |
326
|
1 |
|
if dframe.columns.values[0] == 'HITId': |
327
|
|
|
# Mturk |
328
|
|
|
# if config is specified, use those columns |
329
|
|
|
if config.inputColumns: |
330
|
|
|
config.input = {c: 'input.'+c.replace('Input.', '') |
331
|
|
|
for c in dframe.columns.values if c in config.inputColumns} |
332
|
|
|
else: |
333
|
|
|
config.input = {c: 'input.'+c.replace('Input.', '') |
334
|
|
|
for c in dframe.columns.values if c.startswith('Input.')} |
335
|
|
|
|
336
|
|
|
# if config is specified, use those columns |
337
|
|
|
if config.outputColumns: |
338
|
|
|
config.output = {c: 'output.'+c.replace('Answer.', '') |
339
|
|
|
for c in dframe.columns.values if c in config.outputColumns} |
340
|
|
|
else: |
341
|
|
|
config.output = {c: 'output.'+c.replace('Answer.', '') |
342
|
|
|
for c in dframe.columns.values if c.startswith('Answer.')} |
343
|
|
|
return config |
344
|
|
|
|
345
|
1 |
|
elif dframe.columns.values[0] == '_unit_id': |
346
|
|
|
|
347
|
|
|
# if a config is specified, use those columns |
348
|
1 |
|
if config.inputColumns: |
349
|
1 |
|
config.input = {c: 'input.'+c for c in dframe.columns.values \ |
350
|
|
|
if c in config.inputColumns} |
351
|
1 |
|
if config.outputColumns: |
352
|
1 |
|
config.output = {c: 'output.'+c for c in dframe.columns.values \ |
353
|
|
|
if c in config.outputColumns} |
354
|
|
|
# if there is a config for both input and output columns, we can return those |
355
|
1 |
|
if config.inputColumns and config.outputColumns: |
356
|
1 |
|
return config |
357
|
|
|
|
358
|
|
|
# try to identify the input and output columns |
359
|
|
|
# this is the case if all the values in the column are identical |
360
|
|
|
# this is not failsafe but should give decent results without settings |
361
|
|
|
# it is best to make a settings.py file for a collection |
362
|
|
|
|
363
|
|
|
units = dframe.groupby('_unit_id') |
364
|
|
|
columns = [c for c in dframe.columns.values if c != 'clustering' and not c.startswith('_') |
365
|
|
|
and not c.startswith('e_') and not c.endswith('_gold') |
366
|
|
|
and not c.endswith('_reason') and not c.endswith('browser')] |
367
|
|
|
for colname in columns: |
368
|
|
|
try: |
369
|
|
|
for _, unit in units: |
370
|
|
|
unique = unit[colname].nunique() |
371
|
|
|
if unique != 1 and unique != 0: |
372
|
|
|
raise Found |
373
|
|
|
if not config.inputColumns: |
374
|
|
|
config.input[colname] = 'input.'+colname |
375
|
|
|
|
376
|
|
|
except Found: |
377
|
|
|
if not config.outputColumns: |
378
|
|
|
config.output[colname] = 'output.'+colname |
379
|
|
|
|
380
|
|
|
return config |
381
|
|
|
else: |
382
|
|
|
# unknown platform type |
383
|
|
|
|
384
|
|
|
# if a config is specified, use those columns |
385
|
|
|
if config.inputColumns: |
386
|
|
|
config.input = {c: 'input.'+c for c in dframe.columns.values \ |
387
|
|
|
if c in config.inputColumns} |
388
|
|
|
if config.outputColumns: |
389
|
|
|
config.output = {c: 'output.'+c for c in dframe.columns.values \ |
390
|
|
|
if c in config.outputColumns} |
391
|
|
|
# if there is a config for both input and output columns, we can return those |
392
|
|
|
if config.inputColumns and config.outputColumns: |
393
|
|
|
return config |
394
|
|
|
|