-
Notifications
You must be signed in to change notification settings - Fork 0
/
athena_template.yaml
1186 lines (1152 loc) · 36.9 KB
/
athena_template.yaml
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
249
250
251
252
253
254
255
256
257
258
259
260
261
262
263
264
265
266
267
268
269
270
271
272
273
274
275
276
277
278
279
280
281
282
283
284
285
286
287
288
289
290
291
292
293
294
295
296
297
298
299
300
301
302
303
304
305
306
307
308
309
310
311
312
313
314
315
316
317
318
319
320
321
322
323
324
325
326
327
328
329
330
331
332
333
334
335
336
337
338
339
340
341
342
343
344
345
346
347
348
349
350
351
352
353
354
355
356
357
358
359
360
361
362
363
364
365
366
367
368
369
370
371
372
373
374
375
376
377
378
379
380
381
382
383
384
385
386
387
388
389
390
391
392
393
394
395
396
397
398
399
400
401
402
403
404
405
406
407
408
409
410
411
412
413
414
415
416
417
418
419
420
421
422
423
424
425
426
427
428
429
430
431
432
433
434
435
436
437
438
439
440
441
442
443
444
445
446
447
448
449
450
451
452
453
454
455
456
457
458
459
460
461
462
463
464
465
466
467
468
469
470
471
472
473
474
475
476
477
478
479
480
481
482
483
484
485
486
487
488
489
490
491
492
493
494
495
496
497
498
499
500
501
502
503
504
505
506
507
508
509
510
511
512
513
514
515
516
517
518
519
520
521
522
523
524
525
526
527
528
529
530
531
532
533
534
535
536
537
538
539
540
541
542
543
544
545
546
547
548
549
550
551
552
553
554
555
556
557
558
559
560
561
562
563
564
565
566
567
568
569
570
571
572
573
574
575
576
577
578
579
580
581
582
583
584
585
586
587
588
589
590
591
592
593
594
595
596
597
598
599
600
601
602
603
604
605
606
607
608
609
610
611
612
613
614
615
616
617
618
619
620
621
622
623
624
625
626
627
628
629
630
631
632
633
634
635
636
637
638
639
640
641
642
643
644
645
646
647
648
649
650
651
652
653
654
655
656
657
658
659
660
661
662
663
664
665
666
667
668
669
670
671
672
673
674
675
676
677
678
679
680
681
682
683
684
685
686
687
688
689
690
691
692
693
694
695
696
697
698
699
700
701
702
703
704
705
706
707
708
709
710
711
712
713
714
715
716
717
718
719
720
721
722
723
724
725
726
727
728
729
730
731
732
733
734
735
736
737
738
739
740
741
742
743
744
745
746
747
748
749
750
751
752
753
754
755
756
757
758
759
760
761
762
763
764
765
766
767
768
769
770
771
772
773
774
775
776
777
778
779
780
781
782
783
784
785
786
787
788
789
790
791
792
793
794
795
796
797
798
799
800
801
802
803
804
805
806
807
808
809
810
811
812
813
814
815
816
817
818
819
820
821
822
823
824
825
826
827
828
829
830
831
832
833
834
835
836
837
838
839
840
841
842
843
844
845
846
847
848
849
850
851
852
853
854
855
856
857
858
859
860
861
862
863
864
865
866
867
868
869
870
871
872
873
874
875
876
877
878
879
880
881
882
883
884
885
886
887
888
889
890
891
892
893
894
895
896
897
898
899
900
901
902
903
904
905
906
907
908
909
910
911
912
913
914
915
916
917
918
919
920
921
922
923
924
925
926
927
928
929
930
931
932
933
934
935
936
937
938
939
940
941
942
943
944
945
946
947
948
949
950
951
952
953
954
955
956
957
958
959
960
961
962
963
964
965
966
967
968
969
970
971
972
973
974
975
976
977
978
979
980
981
982
983
984
985
986
987
988
989
990
991
992
993
994
995
996
997
998
999
1000
# Copyright 2019 Amazon.com, Inc. or its affiliates. All Rights Reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License"). You may not use this file except in compliance with the License.
# A copy of the License is located at
# http://aws.amazon.com/apache2.0/
# or in the "license" file accompanying this file. This file is distributed on an "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND,
# either express or implied. See the License for the specific language governing permissions and limitations under the License.
# modified so that this template from https://aws.amazon.com/blogs/big-data/perform-biomedical-informatics-without-a-database-using-mimic-iii-data-and-amazon-athena/
# can be used to just create the athena database for quries via a local copy in my own aws account.
AWSTemplateFormatVersion: '2010-09-09'
Description: This CloudFormation Template deploys a Glue Catalog entry for the MIMIC-III dataset in the AWS Open Data Registry.
Resources:
MIMICDatabase:
Type: "AWS::Glue::Database"
Properties:
DatabaseInput:
Description: MIMIC-III Database in Parquet format
Name: "###DBNAME###"
CatalogId: !Ref AWS::AccountId
admissionsTable:
Type: "AWS::Glue::Table"
Properties:
TableInput:
Name: admissions
StorageDescriptor:
InputFormat: org.apache.hadoop.hive.ql.io.parquet.MapredParquetInputFormat
OutputFormat: org.apache.hadoop.hive.ql.io.parquet.MapredParquetOutputFormat
StoredAsSubDirectories: False
Location: ###LOCATION###parquet/ADMISSIONS/
SerdeInfo:
SerializationLibrary: org.apache.hadoop.hive.ql.io.parquet.serde.ParquetHiveSerDe
Columns:
- Name: row_id
Type: int
- Name: subject_id
Type: int
- Name: hadm_id
Type: int
- Name: admittime
Type: timestamp
- Name: dischtime
Type: timestamp
- Name: deathtime
Type: timestamp
- Name: admission_type
Type: string
- Name: admission_location
Type: string
- Name: discharge_location
Type: string
- Name: insurance
Type: string
- Name: language
Type: string
- Name: religion
Type: string
- Name: marital_status
Type: string
- Name: ethnicity
Type: string
- Name: edregtime
Type: timestamp
- Name: edouttime
Type: timestamp
- Name: diagnosis
Type: string
- Name: hospital_expire_flag
Type: smallint
- Name: has_chartevents_data
Type: smallint
DatabaseName: !Ref MIMICDatabase
CatalogId: !Ref AWS::AccountId
calloutTable:
Type: "AWS::Glue::Table"
Properties:
TableInput:
Name: callout
StorageDescriptor:
InputFormat: org.apache.hadoop.hive.ql.io.parquet.MapredParquetInputFormat
OutputFormat: org.apache.hadoop.hive.ql.io.parquet.MapredParquetOutputFormat
StoredAsSubDirectories: False
Location: ###LOCATION###parquet/CALLOUT/
SerdeInfo:
SerializationLibrary: org.apache.hadoop.hive.ql.io.parquet.serde.ParquetHiveSerDe
Columns:
- Name: row_id
Type: int
- Name: subject_id
Type: int
- Name: hadm_id
Type: int
- Name: submit_wardid
Type: int
- Name: submit_careunit
Type: string
- Name: curr_wardid
Type: int
- Name: curr_careunit
Type: string
- Name: callout_wardid
Type: int
- Name: callout_service
Type: string
- Name: request_tele
Type: smallint
- Name: request_resp
Type: smallint
- Name: request_cdiff
Type: smallint
- Name: request_mrsa
Type: smallint
- Name: request_vre
Type: smallint
- Name: callout_status
Type: string
- Name: callout_outcome
Type: string
- Name: discharge_wardid
Type: int
- Name: acknowledge_status
Type: string
- Name: createtime
Type: timestamp
- Name: updatetime
Type: timestamp
- Name: acknowledgetime
Type: timestamp
- Name: outcometime
Type: timestamp
- Name: firstreservationtime
Type: timestamp
- Name: currentreservationtime
Type: timestamp
DatabaseName: !Ref MIMICDatabase
CatalogId: !Ref AWS::AccountId
caregiversTable:
Type: "AWS::Glue::Table"
Properties:
TableInput:
Name: caregivers
StorageDescriptor:
InputFormat: org.apache.hadoop.hive.ql.io.parquet.MapredParquetInputFormat
OutputFormat: org.apache.hadoop.hive.ql.io.parquet.MapredParquetOutputFormat
StoredAsSubDirectories: False
Location: ###LOCATION###parquet/CAREGIVERS/
SerdeInfo:
SerializationLibrary: org.apache.hadoop.hive.ql.io.parquet.serde.ParquetHiveSerDe
Columns:
- Name: row_id
Type: int
- Name: cgid
Type: int
- Name: label
Type: string
- Name: description
Type: string
DatabaseName: !Ref MIMICDatabase
CatalogId: !Ref AWS::AccountId
charteventsTable:
Type: "AWS::Glue::Table"
Properties:
TableInput:
Name: chartevents
StorageDescriptor:
InputFormat: org.apache.hadoop.hive.ql.io.parquet.MapredParquetInputFormat
OutputFormat: org.apache.hadoop.hive.ql.io.parquet.MapredParquetOutputFormat
StoredAsSubDirectories: False
Location: ###LOCATION###parquet/CHARTEVENTS/
SerdeInfo:
SerializationLibrary: org.apache.hadoop.hive.ql.io.parquet.serde.ParquetHiveSerDe
Columns:
- Name: row_id
Type: int
- Name: subject_id
Type: int
- Name: hadm_id
Type: int
- Name: icustay_id
Type: int
- Name: itemid
Type: int
- Name: charttime
Type: timestamp
- Name: storetime
Type: timestamp
- Name: cgid
Type: int
- Name: value
Type: string
- Name: valuenum
Type: double
- Name: valueuom
Type: string
- Name: warning
Type: int
- Name: error
Type: int
- Name: resultstatus
Type: string
- Name: stopped
Type: string
DatabaseName: !Ref MIMICDatabase
CatalogId: !Ref AWS::AccountId
cpteventsTable:
Type: "AWS::Glue::Table"
Properties:
TableInput:
Name: cptevents
StorageDescriptor:
InputFormat: org.apache.hadoop.hive.ql.io.parquet.MapredParquetInputFormat
OutputFormat: org.apache.hadoop.hive.ql.io.parquet.MapredParquetOutputFormat
StoredAsSubDirectories: False
Location: ###LOCATION###parquet/CPTEVENTS/
SerdeInfo:
SerializationLibrary: org.apache.hadoop.hive.ql.io.parquet.serde.ParquetHiveSerDe
Columns:
- Name: row_id
Type: int
- Name: subject_id
Type: int
- Name: hadm_id
Type: int
- Name: costcenter
Type: string
- Name: chartdate
Type: timestamp
- Name: cpt_cd
Type: string
- Name: cpt_number
Type: int
- Name: cpt_suffix
Type: string
- Name: ticket_id_seq
Type: int
- Name: sectionheader
Type: string
- Name: subsectionheader
Type: string
- Name: description
Type: string
DatabaseName: !Ref MIMICDatabase
CatalogId: !Ref AWS::AccountId
dcptTable:
Type: "AWS::Glue::Table"
Properties:
TableInput:
Name: d_cpt
StorageDescriptor:
InputFormat: org.apache.hadoop.hive.ql.io.parquet.MapredParquetInputFormat
OutputFormat: org.apache.hadoop.hive.ql.io.parquet.MapredParquetOutputFormat
StoredAsSubDirectories: False
Location: ###LOCATION###parquet/D_CPT/
SerdeInfo:
SerializationLibrary: org.apache.hadoop.hive.ql.io.parquet.serde.ParquetHiveSerDe
Columns:
- Name: row_id
Type: int
- Name: category
Type: smallint
- Name: sectionrange
Type: string
- Name: sectionheader
Type: string
- Name: subsectionrange
Type: string
- Name: subsectionheader
Type: string
- Name: codesuffix
Type: string
- Name: mincodeinsubsection
Type: int
- Name: maxcodeinsubsection
Type: int
DatabaseName: !Ref MIMICDatabase
CatalogId: !Ref AWS::AccountId
dicddiagnosesTable:
Type: "AWS::Glue::Table"
Properties:
TableInput:
Name: d_icd_diagnoses
StorageDescriptor:
InputFormat: org.apache.hadoop.hive.ql.io.parquet.MapredParquetInputFormat
OutputFormat: org.apache.hadoop.hive.ql.io.parquet.MapredParquetOutputFormat
StoredAsSubDirectories: False
Location: ###LOCATION###parquet/D_ICD_DIAGNOSES/
SerdeInfo:
SerializationLibrary: org.apache.hadoop.hive.ql.io.parquet.serde.ParquetHiveSerDe
Columns:
- Name: row_id
Type: int
- Name: icd9_code
Type: string
- Name: short_title
Type: string
- Name: long_title
Type: string
DatabaseName: !Ref MIMICDatabase
CatalogId: !Ref AWS::AccountId
dicdproceduresTable:
Type: "AWS::Glue::Table"
Properties:
TableInput:
Name: d_icd_procedures
StorageDescriptor:
InputFormat: org.apache.hadoop.hive.ql.io.parquet.MapredParquetInputFormat
OutputFormat: org.apache.hadoop.hive.ql.io.parquet.MapredParquetOutputFormat
StoredAsSubDirectories: False
Location: ###LOCATION###parquet/D_ICD_PROCEDURES/
SerdeInfo:
SerializationLibrary: org.apache.hadoop.hive.ql.io.parquet.serde.ParquetHiveSerDe
Columns:
- Name: row_id
Type: int
- Name: icd9_code
Type: string
- Name: short_title
Type: string
- Name: long_title
Type: string
DatabaseName: !Ref MIMICDatabase
CatalogId: !Ref AWS::AccountId
ditemsTable:
Type: "AWS::Glue::Table"
Properties:
TableInput:
Name: d_items
StorageDescriptor:
InputFormat: org.apache.hadoop.hive.ql.io.parquet.MapredParquetInputFormat
OutputFormat: org.apache.hadoop.hive.ql.io.parquet.MapredParquetOutputFormat
StoredAsSubDirectories: False
Location: ###LOCATION###parquet/D_ITEMS/
SerdeInfo:
SerializationLibrary: org.apache.hadoop.hive.ql.io.parquet.serde.ParquetHiveSerDe
Columns:
- Name: row_id
Type: int
- Name: itemid
Type: int
- Name: label
Type: string
- Name: abbreviation
Type: string
- Name: dbsource
Type: string
- Name: linksto
Type: string
- Name: category
Type: string
- Name: unitname
Type: string
- Name: param_type
Type: string
- Name: conceptid
Type: int
DatabaseName: !Ref MIMICDatabase
CatalogId: !Ref AWS::AccountId
dlabitemsTable:
Type: "AWS::Glue::Table"
Properties:
TableInput:
Name: d_labitems
StorageDescriptor:
InputFormat: org.apache.hadoop.hive.ql.io.parquet.MapredParquetInputFormat
OutputFormat: org.apache.hadoop.hive.ql.io.parquet.MapredParquetOutputFormat
StoredAsSubDirectories: False
Location: ###LOCATION###parquet/D_LABITEMS/
SerdeInfo:
SerializationLibrary: org.apache.hadoop.hive.ql.io.parquet.serde.ParquetHiveSerDe
Columns:
- Name: row_id
Type: int
- Name: itemid
Type: int
- Name: label
Type: string
- Name: fluid
Type: string
- Name: category
Type: string
- Name: loinc_code
Type: string
DatabaseName: !Ref MIMICDatabase
CatalogId: !Ref AWS::AccountId
datetimeeventsTable:
Type: "AWS::Glue::Table"
Properties:
TableInput:
Name: datetimeevents
StorageDescriptor:
InputFormat: org.apache.hadoop.hive.ql.io.parquet.MapredParquetInputFormat
OutputFormat: org.apache.hadoop.hive.ql.io.parquet.MapredParquetOutputFormat
StoredAsSubDirectories: False
Location: ###LOCATION###parquet/DATETIMEEVENTS/
SerdeInfo:
SerializationLibrary: org.apache.hadoop.hive.ql.io.parquet.serde.ParquetHiveSerDe
Columns:
- Name: row_id
Type: int
- Name: subject_id
Type: int
- Name: hadm_id
Type: int
- Name: icustay_id
Type: int
- Name: itemid
Type: int
- Name: charttime
Type: timestamp
- Name: storetime
Type: timestamp
- Name: cgid
Type: int
- Name: value
Type: string
- Name: valueuom
Type: string
- Name: warning
Type: int
- Name: error
Type: int
- Name: resultstatus
Type: string
- Name: stopped
Type: string
DatabaseName: !Ref MIMICDatabase
CatalogId: !Ref AWS::AccountId
diagnosesicdTable:
Type: "AWS::Glue::Table"
Properties:
TableInput:
Name: diagnoses_icd
StorageDescriptor:
InputFormat: org.apache.hadoop.hive.ql.io.parquet.MapredParquetInputFormat
OutputFormat: org.apache.hadoop.hive.ql.io.parquet.MapredParquetOutputFormat
StoredAsSubDirectories: False
Location: ###LOCATION###parquet/DIAGNOSES_ICD/
SerdeInfo:
SerializationLibrary: org.apache.hadoop.hive.ql.io.parquet.serde.ParquetHiveSerDe
Columns:
- Name: row_id
Type: int
- Name: subject_id
Type: int
- Name: hadm_id
Type: int
- Name: seq_num
Type: int
- Name: icd9_code
Type: string
DatabaseName: !Ref MIMICDatabase
CatalogId: !Ref AWS::AccountId
drgcodesTable:
Type: "AWS::Glue::Table"
Properties:
TableInput:
Name: drgcodes
StorageDescriptor:
InputFormat: org.apache.hadoop.hive.ql.io.parquet.MapredParquetInputFormat
OutputFormat: org.apache.hadoop.hive.ql.io.parquet.MapredParquetOutputFormat
StoredAsSubDirectories: False
Location: ###LOCATION###parquet/DRGCODES/
SerdeInfo:
SerializationLibrary: org.apache.hadoop.hive.ql.io.parquet.serde.ParquetHiveSerDe
Columns:
- Name: row_id
Type: int
- Name: subject_id
Type: int
- Name: hadm_id
Type: int
- Name: drg_type
Type: string
- Name: drg_code
Type: string
- Name: description
Type: string
- Name: drg_severity
Type: smallint
- Name: drg_mortality
Type: smallint
DatabaseName: !Ref MIMICDatabase
CatalogId: !Ref AWS::AccountId
icustaysTable:
Type: "AWS::Glue::Table"
Properties:
TableInput:
Name: icustays
StorageDescriptor:
InputFormat: org.apache.hadoop.hive.ql.io.parquet.MapredParquetInputFormat
OutputFormat: org.apache.hadoop.hive.ql.io.parquet.MapredParquetOutputFormat
StoredAsSubDirectories: False
Location: ###LOCATION###parquet/ICUSTAYS/
SerdeInfo:
SerializationLibrary: org.apache.hadoop.hive.ql.io.parquet.serde.ParquetHiveSerDe
Columns:
- Name: row_id
Type: int
- Name: subject_id
Type: int
- Name: hadm_id
Type: int
- Name: icustay_id
Type: int
- Name: dbsource
Type: string
- Name: first_careunit
Type: string
- Name: last_careunit
Type: string
- Name: first_wardid
Type: smallint
- Name: last_wardid
Type: smallint
- Name: intime
Type: timestamp
- Name: outtime
Type: timestamp
- Name: los
Type: double
DatabaseName: !Ref MIMICDatabase
CatalogId: !Ref AWS::AccountId
icustaysTable:
Type: "AWS::Glue::Table"
Properties:
TableInput:
Name: icustays
StorageDescriptor:
InputFormat: org.apache.hadoop.hive.ql.io.parquet.MapredParquetInputFormat
OutputFormat: org.apache.hadoop.hive.ql.io.parquet.MapredParquetOutputFormat
StoredAsSubDirectories: False
Location: ###LOCATION###parquet/ICUSTAYS/
SerdeInfo:
SerializationLibrary: org.apache.hadoop.hive.ql.io.parquet.serde.ParquetHiveSerDe
Columns:
- Name: row_id
Type: int
- Name: subject_id
Type: int
- Name: hadm_id
Type: int
- Name: icustay_id
Type: int
- Name: dbsource
Type: string
- Name: first_careunit
Type: string
- Name: last_careunit
Type: string
- Name: first_wardid
Type: smallint
- Name: last_wardid
Type: smallint
- Name: intime
Type: timestamp
- Name: outtime
Type: timestamp
- Name: los
Type: double
DatabaseName: !Ref MIMICDatabase
CatalogId: !Ref AWS::AccountId
inputeventscvTable:
Type: "AWS::Glue::Table"
Properties:
TableInput:
Name: inputevents_cv
StorageDescriptor:
InputFormat: org.apache.hadoop.hive.ql.io.parquet.MapredParquetInputFormat
OutputFormat: org.apache.hadoop.hive.ql.io.parquet.MapredParquetOutputFormat
StoredAsSubDirectories: False
Location: ###LOCATION###parquet/INPUTEVENTS_CV/
SerdeInfo:
SerializationLibrary: org.apache.hadoop.hive.ql.io.parquet.serde.ParquetHiveSerDe
Columns:
- Name: row_id
Type: int
- Name: subject_id
Type: int
- Name: hadm_id
Type: int
- Name: icustay_id
Type: int
- Name: charttime
Type: timestamp
- Name: itemid
Type: int
- Name: amount
Type: double
- Name: amountuom
Type: string
- Name: rate
Type: double
- Name: rateuom
Type: string
- Name: storetime
Type: timestamp
- Name: cgid
Type: int
- Name: orderid
Type: int
- Name: linkorderid
Type: int
- Name: stopped
Type: string
- Name: newbottle
Type: int
- Name: originalamount
Type: double
- Name: originalamountuom
Type: string
- Name: originalroute
Type: string
- Name: originalrate
Type: double
- Name: originalrateuom
Type: string
- Name: originalsite
Type: string
DatabaseName: !Ref MIMICDatabase
CatalogId: !Ref AWS::AccountId
inputeventsmvTable:
Type: "AWS::Glue::Table"
Properties:
TableInput:
Name: inputevents_mv
StorageDescriptor:
InputFormat: org.apache.hadoop.hive.ql.io.parquet.MapredParquetInputFormat
OutputFormat: org.apache.hadoop.hive.ql.io.parquet.MapredParquetOutputFormat
StoredAsSubDirectories: False
Location: ###LOCATION###parquet/INPUTEVENTS_MV/
SerdeInfo:
SerializationLibrary: org.apache.hadoop.hive.ql.io.parquet.serde.ParquetHiveSerDe
Columns:
- Name: row_id
Type: int
- Name: subject_id
Type: int
- Name: hadm_id
Type: int
- Name: icustay_id
Type: int
- Name: starttime
Type: timestamp
- Name: endtime
Type: timestamp
- Name: itemid
Type: int
- Name: amount
Type: double
- Name: amountuom
Type: string
- Name: rate
Type: double
- Name: rateuom
Type: string
- Name: storetime
Type: timestamp
- Name: cgid
Type: int
- Name: orderid
Type: int
- Name: linkorderid
Type: int
- Name: ordercategoryname
Type: string
- Name: secondaryordercategoryname
Type: string
- Name: ordercomponenttypedescription
Type: string
- Name: ordercategorydescription
Type: string
- Name: patientweight
Type: double
- Name: totalamount
Type: double
- Name: totalamountuom
Type: string
- Name: isopenbag
Type: smallint
- Name: continueinnextdept
Type: smallint
- Name: cancelreason
Type: smallint
- Name: statusdescription
Type: string
- Name: comments_editedby
Type: string
- Name: comments_canceledby
Type: string
- Name: comments_date
Type: timestamp
- Name: originalamount
Type: double
- Name: originalrate
Type: double
DatabaseName: !Ref MIMICDatabase
CatalogId: !Ref AWS::AccountId
labeventsTable:
Type: "AWS::Glue::Table"
Properties:
TableInput:
Name: labevents
StorageDescriptor:
InputFormat: org.apache.hadoop.hive.ql.io.parquet.MapredParquetInputFormat
OutputFormat: org.apache.hadoop.hive.ql.io.parquet.MapredParquetOutputFormat
StoredAsSubDirectories: False
Location: ###LOCATION###parquet/LABEVENTS/
SerdeInfo:
SerializationLibrary: org.apache.hadoop.hive.ql.io.parquet.serde.ParquetHiveSerDe
Columns:
- Name: row_id
Type: int
- Name: subject_id
Type: int
- Name: hadm_id
Type: int
- Name: itemid
Type: int
- Name: charttime
Type: timestamp
- Name: value
Type: string
- Name: valuenum
Type: double
- Name: valueuom
Type: string
- Name: flag
Type: string
DatabaseName: !Ref MIMICDatabase
CatalogId: !Ref AWS::AccountId
microbiologyeventsTable:
Type: "AWS::Glue::Table"
Properties:
TableInput:
Name: microbiologyevents
StorageDescriptor:
InputFormat: org.apache.hadoop.hive.ql.io.parquet.MapredParquetInputFormat
OutputFormat: org.apache.hadoop.hive.ql.io.parquet.MapredParquetOutputFormat
StoredAsSubDirectories: False
Location: ###LOCATION###parquet/MICROBIOLOGYEVENTS/
SerdeInfo:
SerializationLibrary: org.apache.hadoop.hive.ql.io.parquet.serde.ParquetHiveSerDe
Columns:
- Name: row_id
Type: int
- Name: subject_id
Type: int
- Name: hadm_id
Type: int
- Name: chartdate
Type: timestamp
- Name: charttime
Type: timestamp
- Name: spec_itemid
Type: int
- Name: spec_type_desc
Type: string
- Name: org_itemid
Type: int
- Name: org_name
Type: string
- Name: isolate_num
Type: smallint
- Name: ab_itemid
Type: int
- Name: ab_name
Type: string
- Name: dilution_text
Type: string
- Name: dilution_comparison
Type: string
- Name: dilution_value
Type: double
- Name: interpretation
Type: string
DatabaseName: !Ref MIMICDatabase
CatalogId: !Ref AWS::AccountId
noteeventsTable:
Type: "AWS::Glue::Table"
Properties:
TableInput:
Name: noteevents
StorageDescriptor:
InputFormat: org.apache.hadoop.hive.ql.io.parquet.MapredParquetInputFormat
OutputFormat: org.apache.hadoop.hive.ql.io.parquet.MapredParquetOutputFormat
StoredAsSubDirectories: False
Location: ###LOCATION###parquet/NOTEEVENTS/
SerdeInfo:
SerializationLibrary: org.apache.hadoop.hive.ql.io.parquet.serde.ParquetHiveSerDe
Columns:
- Name: row_id
Type: int
- Name: subject_id
Type: int
- Name: hadm_id
Type: int
- Name: chartdate
Type: timestamp
- Name: charttime
Type: timestamp
- Name: storetime
Type: timestamp
- Name: category
Type: string
- Name: description
Type: string
- Name: cgid
Type: int
- Name: iserror
Type: string
- Name: text
Type: string
DatabaseName: !Ref MIMICDatabase
CatalogId: !Ref AWS::AccountId
outputeventsTable:
Type: "AWS::Glue::Table"
Properties:
TableInput:
Name: outputevents
StorageDescriptor:
InputFormat: org.apache.hadoop.hive.ql.io.parquet.MapredParquetInputFormat
OutputFormat: org.apache.hadoop.hive.ql.io.parquet.MapredParquetOutputFormat
StoredAsSubDirectories: False
Location: ###LOCATION###parquet/OUTPUTEVENTS/
SerdeInfo:
SerializationLibrary: org.apache.hadoop.hive.ql.io.parquet.serde.ParquetHiveSerDe
Columns:
- Name: row_id
Type: int
- Name: subject_id
Type: int
- Name: hadm_id
Type: int
- Name: icustay_id
Type: int
- Name: charttime
Type: timestamp
- Name: itemid
Type: int
- Name: value
Type: double
- Name: valueuom
Type: string
- Name: storetime
Type: timestamp
- Name: cgid
Type: int
- Name: stopped
Type: string
- Name: newbottle
Type: string
- Name: iserror
Type: int
DatabaseName: !Ref MIMICDatabase
CatalogId: !Ref AWS::AccountId
patientsTable:
Type: "AWS::Glue::Table"
Properties:
TableInput:
Name: patients
StorageDescriptor:
InputFormat: org.apache.hadoop.hive.ql.io.parquet.MapredParquetInputFormat
OutputFormat: org.apache.hadoop.hive.ql.io.parquet.MapredParquetOutputFormat
StoredAsSubDirectories: False
Location: ###LOCATION###parquet/PATIENTS/
SerdeInfo:
SerializationLibrary: org.apache.hadoop.hive.ql.io.parquet.serde.ParquetHiveSerDe
Columns:
- Name: row_id
Type: int
- Name: subject_id
Type: int
- Name: gender
Type: string
- Name: dob
Type: timestamp
- Name: dod
Type: timestamp
- Name: dod_hosp
Type: timestamp
- Name: dod_ssn
Type: timestamp
- Name: expire_flag
Type: int
DatabaseName: !Ref MIMICDatabase
CatalogId: !Ref AWS::AccountId
prescriptionsTable:
Type: "AWS::Glue::Table"
Properties:
TableInput:
Name: prescriptions
StorageDescriptor:
InputFormat: org.apache.hadoop.hive.ql.io.parquet.MapredParquetInputFormat
OutputFormat: org.apache.hadoop.hive.ql.io.parquet.MapredParquetOutputFormat
StoredAsSubDirectories: False
Location: ###LOCATION###parquet/PRESCRIPTIONS/
SerdeInfo:
SerializationLibrary: org.apache.hadoop.hive.ql.io.parquet.serde.ParquetHiveSerDe
Columns:
- Name: row_id
Type: int
- Name: subject_id
Type: int
- Name: hadm_id
Type: int
- Name: icustay_id
Type: int
- Name: startdate
Type: timestamp
- Name: enddate
Type: timestamp
- Name: drug_type
Type: string
- Name: drug
Type: string
- Name: drug_name_poe
Type: string
- Name: drug_name_generic
Type: string
- Name: formulary_drug_cd
Type: string
- Name: gsn
Type: string
- Name: ndc
Type: string
- Name: prod_strength
Type: string
- Name: dose_val_rx
Type: string
- Name: dose_unit_rx
Type: string
- Name: form_val_disp
Type: string
- Name: form_unit_disp
Type: string
- Name: route
Type: string
DatabaseName: !Ref MIMICDatabase
CatalogId: !Ref AWS::AccountId
prescriptionsTable:
Type: "AWS::Glue::Table"
Properties:
TableInput:
Name: prescriptions
StorageDescriptor:
InputFormat: org.apache.hadoop.hive.ql.io.parquet.MapredParquetInputFormat
OutputFormat: org.apache.hadoop.hive.ql.io.parquet.MapredParquetOutputFormat
StoredAsSubDirectories: False
Location: ###LOCATION###parquet/PRESCRIPTIONS/
SerdeInfo:
SerializationLibrary: org.apache.hadoop.hive.ql.io.parquet.serde.ParquetHiveSerDe
Columns:
- Name: row_id
Type: int
- Name: subject_id
Type: int
- Name: hadm_id
Type: int
- Name: icustay_id
Type: int
- Name: startdate
Type: timestamp
- Name: enddate
Type: timestamp
- Name: drug_type
Type: string
- Name: drug
Type: string
- Name: drug_name_poe
Type: string
- Name: drug_name_generic
Type: string
- Name: formulary_drug_cd