-
Notifications
You must be signed in to change notification settings - Fork 18
2200 lines (1625 loc) · 78.9 KB
/
build.yml
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
name: Build
on:
schedule:
- cron: '0 10 * * *' # every day at 10am
push:
tags:
- 'v*.*.*'
pull_request:
branches:
- main
merge_group:
permissions: read-all
jobs:
fmt:
runs-on: ubuntu-24.04
steps:
- name: Setup Clojure
uses: DeLaGuardo/setup-clojure@94d767dbb80ae5c637d0f1ad70b75fa2b00495cd # 13.0
with:
cljfmt: 0.13.0
- name: Check out Git repository
uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4
- name: Check Formatting
run: make fmt
lint:
runs-on: ubuntu-24.04
steps:
- name: Setup Clojure
uses: DeLaGuardo/setup-clojure@94d767dbb80ae5c637d0f1ad70b75fa2b00495cd # 13.0
with:
clj-kondo: '2024.09.27'
- name: Check out Git repository
uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4
- name: Lint
run: make lint
job-ig:
runs-on: ubuntu-24.04
steps:
- name: Setup Node
uses: actions/setup-node@39370e3970a6d050c480ffad4ff0ed4d3fdee5af # v4
with:
node-version: 21
- name: Check out Git repository
uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4
- name: Build
working-directory: job-ig
run: make build
- name: Validate
working-directory: job-ig
run: make validate
- name: Upload Profiles
uses: actions/upload-artifact@b4b15b8c7c6ac21ea08fcf65892d2ee8f75cf882 # v4
with:
name: job-ig-profiles
path: job-ig/fsh-generated/resources/*.json
test:
strategy:
matrix:
module:
- admin-api
- anomaly
- async
- byte-buffer
- byte-string
- cache-collector
- cassandra
- coll
- cql
- db
- db-resource-store
- db-resource-store-cassandra
- db-tx-log
- db-tx-log-kafka
- executor
- extern-terminology-service
- fhir-client
- fhir-path
- fhir-structure
- http-client
- interaction
- jepsen
- job-async-interaction
- job-re-index
- job-scheduler
- job-util
- kv
- luid
- metrics
- module-base
- openid-auth
- operation-graphql
- operation-measure-evaluate-measure
- operation-patient-everything
- operation-patient-purge
- operation-totals
- page-id-cipher
- page-store
- page-store-cassandra
- rest-api
- rest-util
- rocksdb
- scheduler
- server
- thread-pool-executor-collector
java-version:
- '17'
- '21'
exclude:
- module: jepsen
java-version: '17'
needs: job-ig
runs-on: ubuntu-24.04
steps:
- name: Setup Java
uses: actions/setup-java@8df1039502a15bceb9433410b1a100fbe190c53b # v4
with:
distribution: 'temurin'
java-version: ${{ matrix.java-version }}
- name: Setup Clojure
uses: DeLaGuardo/setup-clojure@94d767dbb80ae5c637d0f1ad70b75fa2b00495cd # 13.0
with:
cli: '1.12.0.1479'
- name: Check out Git repository
uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4
- name: Cache Local Maven Repo
uses: actions/cache@6849a6489940f00c2f30c0fb92c6274307ccb58a # v4
with:
path: ~/.m2/repository
key: ${{ runner.os }}-temurin-${{ matrix.java-version }}-maven-${{ matrix.module }}-${{ hashFiles(format('modules/{0}/deps.edn', matrix.module)) }}
- name: Download Job IG Profiles
uses: actions/download-artifact@fa0a91b85d4f404e444e00e005971372dc801d16 # v4
with:
name: job-ig-profiles
path: job-ig/fsh-generated/resources
- name: Test
run: make -C modules/${{ matrix.module }} test
- name: Test Coverage
if: ${{ matrix.java-version == '21' && matrix.module != 'db' && matrix.module != 'jepsen' }}
run: make -C modules/${{ matrix.module }} test-coverage
- name: Upload Coverage Report
if: ${{ matrix.java-version == '21' && matrix.module != 'db' && matrix.module != 'jepsen' }}
uses: actions/upload-artifact@b4b15b8c7c6ac21ea08fcf65892d2ee8f75cf882 # v4
with:
name: coverage-report-${{ matrix.module }}
path: modules/${{ matrix.module }}/target/coverage/codecov.json
# Special treatment, because it runs much longer as the other modules.
test-coverage-db:
needs: job-ig
runs-on: ubuntu-24.04
steps:
- name: Setup Java
uses: actions/setup-java@8df1039502a15bceb9433410b1a100fbe190c53b # v4
with:
distribution: 'temurin'
java-version: '21'
- name: Setup Clojure
uses: DeLaGuardo/setup-clojure@94d767dbb80ae5c637d0f1ad70b75fa2b00495cd # 13.0
with:
cli: '1.12.0.1479'
- name: Check out Git repository
uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4
- name: Cache Local Maven Repo
uses: actions/cache@6849a6489940f00c2f30c0fb92c6274307ccb58a # v4
with:
path: ~/.m2/repository
key: ${{ runner.os }}-temurin-21-maven-db-coverage-${{ hashFiles('modules/db/deps.edn') }}
- name: Download Job IG Profiles
uses: actions/download-artifact@fa0a91b85d4f404e444e00e005971372dc801d16 # v4
with:
name: job-ig-profiles
path: job-ig/fsh-generated/resources
- name: Test Coverage
run: make -C modules/db test-coverage
- name: Upload Coverage Report
uses: actions/upload-artifact@b4b15b8c7c6ac21ea08fcf65892d2ee8f75cf882 # v4
with:
name: coverage-report-db
path: modules/db/target/coverage/codecov.json
test-root:
strategy:
matrix:
java-version:
- '17'
- '21'
needs: job-ig
runs-on: ubuntu-24.04
steps:
- name: Setup Java
uses: actions/setup-java@8df1039502a15bceb9433410b1a100fbe190c53b # v4
with:
distribution: 'temurin'
java-version: ${{ matrix.java-version }}
- name: Setup Clojure
uses: DeLaGuardo/setup-clojure@94d767dbb80ae5c637d0f1ad70b75fa2b00495cd # 13.0
with:
cli: '1.12.0.1479'
- name: Check out Git repository
uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4
- name: Cache Local Maven Repo
uses: actions/cache@6849a6489940f00c2f30c0fb92c6274307ccb58a # v4
with:
path: ~/.m2/repository
key: ${{ runner.os }}-temurin-${{ matrix.java-version }}-maven-${{ hashFiles('deps.edn') }}
- name: Download Job IG Profiles
uses: actions/download-artifact@fa0a91b85d4f404e444e00e005971372dc801d16 # v4
with:
name: job-ig-profiles
path: job-ig/fsh-generated/resources
- name: Test
run: make test-root
upload-coverage:
needs: [ test, test-coverage-db ]
runs-on: ubuntu-24.04
steps:
- name: Download Coverage Reports
uses: actions/download-artifact@fa0a91b85d4f404e444e00e005971372dc801d16 # v4
with:
pattern: coverage-report-*
- name: Codecov Upload
uses: codecov/codecov-action@b9fd7d16f6d7d1b5d2bec1a2887e65ceed900238 # v4
with:
name: codecov-umbrella
token: ${{ secrets.CODECOV_TOKEN }}
fail_ci_if_error: true
build:
needs: job-ig
runs-on: ubuntu-24.04
steps:
- name: Setup Java
uses: actions/setup-java@8df1039502a15bceb9433410b1a100fbe190c53b # v4
with:
distribution: 'temurin'
java-version: '21'
- name: Setup Clojure
uses: DeLaGuardo/setup-clojure@94d767dbb80ae5c637d0f1ad70b75fa2b00495cd # 13.0
with:
cli: '1.12.0.1479'
- name: Check out Git repository
uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4
- name: Cache Local Maven Repo
uses: actions/cache@6849a6489940f00c2f30c0fb92c6274307ccb58a # v4
with:
path: ~/.m2/repository
key: ${{ runner.os }}-temurin-21-maven-build-${{ hashFiles('**/deps.edn') }}
- name: Download Job IG Profiles
uses: actions/download-artifact@fa0a91b85d4f404e444e00e005971372dc801d16 # v4
with:
name: job-ig-profiles
path: job-ig/fsh-generated/resources
- name: Build Uberjar
run: make uberjar
- name: Upload Blaze Uberjar
uses: actions/upload-artifact@b4b15b8c7c6ac21ea08fcf65892d2ee8f75cf882 # v4
with:
name: blaze-uberjar
path: target/blaze-*-standalone.jar
- name: Set up Docker Buildx
uses: docker/setup-buildx-action@c47758b77c9736f4b2ef4073d4d51994fabfe349 # v3
- name: Build and Export to Docker
uses: docker/build-push-action@4f58ea79222b3b9dc2c8bbdd6debcef730109a75 # v6
with:
context: .
tags: blaze:latest
outputs: type=docker,dest=/tmp/blaze.tar
- name: Upload Blaze Image
uses: actions/upload-artifact@b4b15b8c7c6ac21ea08fcf65892d2ee8f75cf882 # v4
with:
name: blaze-image
path: /tmp/blaze.tar
build-frontend:
runs-on: ubuntu-24.04
steps:
- name: Check out Git repository
uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4
- name: Setup Node
uses: actions/setup-node@39370e3970a6d050c480ffad4ff0ed4d3fdee5af # v4
with:
node-version: 21
- name: Build Frontend
run: make build-frontend
- name: Set up Docker Buildx
uses: docker/setup-buildx-action@c47758b77c9736f4b2ef4073d4d51994fabfe349 # v3
- name: Build and Export to Docker
uses: docker/build-push-action@4f58ea79222b3b9dc2c8bbdd6debcef730109a75 # v6
with:
context: modules/frontend
tags: blaze-frontend:latest
outputs: type=docker,dest=/tmp/blaze-frontend.tar
- name: Upload Blaze Image
uses: actions/upload-artifact@b4b15b8c7c6ac21ea08fcf65892d2ee8f75cf882 # v4
with:
name: blaze-frontend-image
path: /tmp/blaze-frontend.tar
image-scan:
needs: [ build, build-frontend ]
runs-on: ubuntu-24.04
permissions:
security-events: write
strategy:
matrix:
image:
- blaze
- blaze-frontend
steps:
- name: Download Image
uses: actions/download-artifact@fa0a91b85d4f404e444e00e005971372dc801d16 # v4
with:
name: ${{ matrix.image }}-image
path: /tmp
- name: Load Image
run: docker load --input /tmp/${{ matrix.image }}.tar
- name: Check out Git repository
uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4
- name: Run Trivy Vulnerability Scanner
uses: aquasecurity/trivy-action@18f2510ee396bbf400402947b394f2dd8c87dbb0 # 0.29.0
with:
image-ref: ${{ matrix.image }}:latest
format: sarif
output: trivy-results.sarif
severity: 'CRITICAL,HIGH'
timeout: '15m0s'
env:
TRIVY_DB_REPOSITORY: public.ecr.aws/aquasecurity/trivy-db:2
TRIVY_JAVA_DB_REPOSITORY: public.ecr.aws/aquasecurity/trivy-java-db:1
- name: Upload Trivy Scan Results to GitHub Security Tab
if: ${{ (github.repository_owner == 'samply') || (vars.IMAGE_SCAN_UPLOAD == 'true') }}
uses: github/codeql-action/upload-sarif@ea9e4e37992a54ee68a9622e985e60c8e8f12d9f # v3
with:
sarif_file: trivy-results.sarif
cql-expr-cache-test:
needs: build
runs-on: ubuntu-24.04
steps:
- name: Check out Git repository
uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4
- name: Install Blazectl
run: .github/scripts/install-blazectl.sh
- name: Download Blaze Image
uses: actions/download-artifact@fa0a91b85d4f404e444e00e005971372dc801d16 # v4
with:
name: blaze-image
path: /tmp
- name: Load Blaze Image
run: docker load --input /tmp/blaze.tar
- name: Run Blaze
run: docker run --name blaze -d -e JAVA_TOOL_OPTIONS=-Xmx2g -e ENABLE_ADMIN_API=true -e CQL_EXPR_CACHE_SIZE=1000 -p 8080:8080 -p 8081:8081 -v blaze-data:/app/data blaze:latest
- name: Wait for Blaze
run: .github/scripts/wait-for-url.sh http://localhost:8080/health
- name: Docker Logs
run: docker logs blaze
- name: Check Capability Statement
run: .github/scripts/check-capability-statement.sh
- name: Ensure that the State of PatientLastChange Index is Current
run: .github/scripts/check-patient-last-change-index-state.sh current
- name: Load Data
run: blazectl --no-progress --server http://localhost:8080/fhir upload .github/test-data/synthea
- name: Prometheus Metrics
run: .github/scripts/test-cql-expr-cache-metrics.sh
- name: Check Total-Number of Resources are 92114
run: .github/scripts/check-total-number-of-resources.sh 92114
- name: Evaluate CQL Query 1
run: .github/scripts/evaluate-measure.sh q1 56
- name: Evaluate CQL Query 1 using Blazectl
run: .github/scripts/evaluate-measure-blazectl.sh q1 56
- name: Evaluate CQL Query 1 - Subject List
run: .github/scripts/evaluate-measure-subject-list.sh q1 56
- name: Evaluate CQL Query 1 on Individual Patients
run: .github/scripts/evaluate-patient-q1-measure.sh
- name: Evaluate CQL Query 2
run: .github/scripts/evaluate-measure.sh q2 42
- name: Evaluate CQL Query 2 using Blazectl
run: .github/scripts/evaluate-measure-blazectl.sh q2 42
- name: Evaluate CQL Query 2 - Subject List
run: .github/scripts/evaluate-measure-subject-list.sh q2 42
- name: Evaluate CQL Query 4
run: .github/scripts/evaluate-measure.sh q4 0
- name: Evaluate CQL Query 4 using Blazectl
run: .github/scripts/evaluate-measure-blazectl.sh q4 0
- name: Evaluate CQL Query 4 - Subject List
run: .github/scripts/evaluate-measure-subject-list.sh q4 0
- name: Evaluate CQL Query 7
run: .github/scripts/evaluate-measure.sh q7 81
- name: Evaluate CQL Query 7 using Blazectl
run: .github/scripts/evaluate-measure-blazectl.sh q7 81
- name: Evaluate CQL Query 7 - Subject List
run: .github/scripts/evaluate-measure-subject-list.sh q7 81
- name: Evaluate CQL Query 14
run: .github/scripts/evaluate-measure.sh q14 96
- name: Check Bloom Filter
run: .github/scripts/check-bloom-filter.sh a08d0235112a8033c36c5d33564aaa00f4190281e4db8f7ec1d8d55cd7f4c56f 96
- name: Evaluate CQL Query 14 using Blazectl
run: .github/scripts/evaluate-measure-blazectl.sh q14 96
- name: Evaluate CQL Query 14 - Subject List
run: .github/scripts/evaluate-measure-subject-list.sh q14 96
- name: Evaluate CQL Query 17
run: .github/scripts/evaluate-measure.sh q17 120
- name: Evaluate CQL Query 17 using Blazectl
run: .github/scripts/evaluate-measure-blazectl.sh q17 120
- name: Evaluate CQL Query 17 - Subject List
run: .github/scripts/evaluate-measure-subject-list.sh q17 120
- name: Evaluate CQL Query 20 using Blazectl
run: .github/scripts/evaluate-measure-blazectl-stratifier.sh q20-stratifier-city 120
- name: Evaluate CQL Query 21 using Blazectl
run: .github/scripts/evaluate-measure-blazectl-stratifier.sh q21-stratifier-city-of-only-women 64
- name: Evaluate CQL Query 26 using Blazectl
run: .github/scripts/evaluate-measure-blazectl-stratifier.sh q26-stratifier-bmi 120
- name: Evaluate CQL Query 27 using Blazectl
run: .github/scripts/evaluate-measure-blazectl-stratifier.sh q27-stratifier-calculated-bmi 120
- name: Evaluate CQL Query 32 using Blazectl
run: .github/scripts/evaluate-measure-blazectl-stratifier.sh q32-stratifier-underweight 120
- name: Evaluate CQL Query 36
run: .github/scripts/evaluate-measure.sh q36-parameter 86
- name: Check Bloom Filter
run: .github/scripts/check-bloom-filter.sh fbb79d85457069c8e1926c949690deecd60d751942d5b0cd0b61c08e6029224c 86
- name: Evaluate CQL Query 36 - Subject List
run: .github/scripts/evaluate-measure-subject-list.sh q36-parameter 86
- name: Evaluate CQL Query 37
run: .github/scripts/evaluate-measure.sh q37-overlaps 24
- name: Check Bloom Filter
run: .github/scripts/check-bloom-filter.sh 9fe779d821d7647831331b490939aa0cdf314d76c9b2a9518ffaf559353db043 24
- name: Evaluate CQL Query 37 using Blazectl
run: .github/scripts/evaluate-measure-blazectl.sh q37-overlaps 24
- name: Evaluate CQL Query 37 - Subject List
run: .github/scripts/evaluate-measure-subject-list.sh q37-overlaps 24
- name: Evaluate CQL Query 46
run: .github/scripts/evaluate-measure.sh q46-between-date 19
- name: Check Bloom Filter
run: .github/scripts/check-bloom-filter.sh 237bcfac3e879272f508e143095e4a0025e1b54505bbb2cf36fbda83dec237f2 19
- name: Evaluate CQL Query 46 using Blazectl
run: .github/scripts/evaluate-measure-blazectl.sh q46-between-date 19
integration-test:
needs: build
runs-on: ubuntu-24.04
strategy:
matrix:
variant:
- standalone
- distributed
steps:
- name: Check out Git repository
uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4
- name: Install Blazectl
run: .github/scripts/install-blazectl.sh
- name: Download Blaze Image
uses: actions/download-artifact@fa0a91b85d4f404e444e00e005971372dc801d16 # v4
with:
name: blaze-image
path: /tmp
- name: Load Blaze Image
run: docker load --input /tmp/blaze.tar
- name: Run Blaze
run: docker run --name blaze -d -e JAVA_TOOL_OPTIONS=-Xmx2g -e ALLOW_MULTIPLE_DELETE=true -e ENABLE_INTERACTION_DELETE_HISTORY=true -e ENABLE_OPERATION_PATIENT_PURGE=true -p 8080:8080 -p 8081:8081 --read-only --tmpfs /tmp:exec -v blaze-data:/app/data blaze:latest
if: ${{ matrix.variant == 'standalone' }}
- name: Run Kafka, Cassandra and Blaze
run: docker compose -f .github/distributed-test/docker-compose.yml up -d
if: ${{ matrix.variant == 'distributed' }}
- name: Wait for Blaze
run: .github/scripts/wait-for-url.sh http://localhost:8080/health
if: ${{ matrix.variant == 'standalone' }}
- name: Wait for Blaze 1
run: .github/scripts/wait-for-url.sh http://localhost:8081/metrics
if: ${{ matrix.variant == 'distributed' }}
- name: Wait for Blaze 2
run: .github/scripts/wait-for-url.sh http://localhost:8082/metrics
if: ${{ matrix.variant == 'distributed' }}
- name: Docker Logs
run: docker logs blaze
if: ${{ matrix.variant == 'standalone' }}
- name: Docker Logs Kafka
run: docker compose -f .github/distributed-test/docker-compose.yml logs kafka
if: ${{ matrix.variant == 'distributed' }}
- name: Docker Logs Cassandra 1
run: docker compose -f .github/distributed-test/docker-compose.yml logs cassandra-1
if: ${{ matrix.variant == 'distributed' }}
- name: Docker Logs Cassandra 2
run: docker compose -f .github/distributed-test/docker-compose.yml logs cassandra-2
if: ${{ matrix.variant == 'distributed' }}
- name: Docker Logs Blaze 1
run: docker compose -f .github/distributed-test/docker-compose.yml logs blaze-1
if: ${{ matrix.variant == 'distributed' }}
- name: Docker Logs Blaze 2
run: docker compose -f .github/distributed-test/docker-compose.yml logs blaze-2
if: ${{ matrix.variant == 'distributed' }}
- name: Docker Stats
run: docker stats --no-stream
- name: Check Capability Statement
run: .github/scripts/check-capability-statement.sh
- name: Check Capability Statement Filtered by _elements
run: .github/scripts/check-capability-statement-filtered.sh
- name: Check Capability Statement Caching
run: .github/scripts/check-capability-statement-caching.sh
- name: Check Referential Integrity Enforced
run: .github/scripts/check-referential-integrity-enforced.sh
- name: Load Data
run: blazectl --no-progress --server http://localhost:8080/fhir upload .github/test-data/synthea
- name: Check Total-Number of Resources are 92114
run: .github/scripts/check-total-number-of-resources.sh 92114
- name: Check Resource Totals
run: .github/scripts/check-resource-totals.sh
- name: Count Resources
run: blazectl count-resources --server http://localhost:8080/fhir
- name: Download All Resources
run: .github/scripts/download-all-resources.sh
- name: Download Patient Resources
run: .github/scripts/download-resources.sh Patient
- name: Download Male Patient Resources
run: .github/scripts/download-resources-query.sh Patient "gender=male" 56
- name: Download Female Patient Resources
run: .github/scripts/download-resources-query.sh Patient "gender=female" 64
- name: Download Patient Resources - Including Observation, Condition, Encounter and Procedure
run: .github/scripts/revinclude.sh
- name: Download Observation Resources
run: .github/scripts/download-resources.sh Observation
- name: Download Observation Resources with special LOINC Codes
run: .github/scripts/download-resources-query.sh Observation "code=http://loinc.org|10230-1,http://loinc.org|10480-2,http://loinc.org|10834-0,http://loinc.org|14804-9,http://loinc.org|14959-1,http://loinc.org|1742-6,http://loinc.org|1751-7,http://loinc.org|17861-6,http://loinc.org|18262-6,http://loinc.org|19123-9" 2399
- name: Download Observation Resources with all LOINC Codes
run: .github/scripts/download-resources-query.sh Observation "_count=500&code=http://loinc.org|10230-1,http://loinc.org|10480-2,http://loinc.org|10834-0,http://loinc.org|14804-9,http://loinc.org|14959-1,http://loinc.org|1742-6,http://loinc.org|1751-7,http://loinc.org|17861-6,http://loinc.org|18262-6,http://loinc.org|19123-9,http://loinc.org|1920-8,http://loinc.org|1960-4,http://loinc.org|1975-2,http://loinc.org|1988-5,http://loinc.org|19926-5,http://loinc.org|19994-3,http://loinc.org|2019-8,http://loinc.org|2028-9,http://loinc.org|20454-5,http://loinc.org|20505-4,http://loinc.org|20565-8,http://loinc.org|20570-8,http://loinc.org|2069-3,http://loinc.org|2075-0,http://loinc.org|2085-9,http://loinc.org|2093-3,http://loinc.org|21000-5,http://loinc.org|2157-6,http://loinc.org|2160-0,http://loinc.org|21905-5,http://loinc.org|21906-3,http://loinc.org|21907-1,http://loinc.org|21908-9,http://loinc.org|2276-4,http://loinc.org|2339-0,http://loinc.org|2345-7,http://loinc.org|2498-4,http://loinc.org|2500-7,http://loinc.org|2502-3,http://loinc.org|2514-8,http://loinc.org|2532-0,http://loinc.org|25428-4,http://loinc.org|2571-8,http://loinc.org|26881-3,http://loinc.org|2703-7,http://loinc.org|2708-6,http://loinc.org|2713-6,http://loinc.org|2744-1,http://loinc.org|2823-3,http://loinc.org|28245-9,http://loinc.org|2857-1,http://loinc.org|2885-2,http://loinc.org|29463-7,http://loinc.org|2947-0,http://loinc.org|2951-2,http://loinc.org|3094-0,http://loinc.org|32167-9,http://loinc.org|32207-3,http://loinc.org|32465-7,http://loinc.org|32623-1,http://loinc.org|33728-7,http://loinc.org|33756-8,http://loinc.org|33762-6,http://loinc.org|33914-3,http://loinc.org|33959-8,http://loinc.org|38208-5,http://loinc.org|38265-5,http://loinc.org|38483-4,http://loinc.org|39156-5,http://loinc.org|44667-4,http://loinc.org|44963-7,http://loinc.org|4544-3,http://loinc.org|4548-4,http://loinc.org|46240-8,http://loinc.org|46288-7,http://loinc.org|48065-7,http://loinc.org|49765-1,http://loinc.org|55277-8,http://loinc.org|5767-9,http://loinc.org|5770-3,http://loinc.org|5778-6,http://loinc.org|57905-2,http://loinc.org|5792-7,http://loinc.org|5794-3,http://loinc.org|5797-6,http://loinc.org|5799-2,http://loinc.org|5802-4,http://loinc.org|5803-2,http://loinc.org|5804-0,http://loinc.org|5811-5,http://loinc.org|5902-2,http://loinc.org|59032-3,http://loinc.org|5905-5,http://loinc.org|59408-5,http://loinc.org|59557-9,http://loinc.org|59576-9,http://loinc.org|6075-6,http://loinc.org|6082-2,http://loinc.org|6085-5,http://loinc.org|6095-4,http://loinc.org|6106-9,http://loinc.org|6158-0,http://loinc.org|6189-5,http://loinc.org|6206-7,http://loinc.org|6246-3,http://loinc.org|6248-9,http://loinc.org|6273-7,http://loinc.org|6276-0,http://loinc.org|6298-4,http://loinc.org|6299-2,http://loinc.org|6301-6,http://loinc.org|63513-6,http://loinc.org|65750-2,http://loinc.org|66519-0,http://loinc.org|66524-0,http://loinc.org|66529-9,http://loinc.org|66534-9,http://loinc.org|6690-2,http://loinc.org|6768-6,http://loinc.org|6833-8,http://loinc.org|6844-5,http://loinc.org|69453-9,http://loinc.org|704-7,http://loinc.org|706-2,http://loinc.org|711-2,http://loinc.org|713-8,http://loinc.org|718-7,http://loinc.org|71802-3,http://loinc.org|72106-8,http://loinc.org|72166-2,http://loinc.org|72514-3,http://loinc.org|7258-7,http://loinc.org|731-0,http://loinc.org|736-9,http://loinc.org|742-7,http://loinc.org|751-8,http://loinc.org|75325-1,http://loinc.org|76690-7,http://loinc.org|770-8,http://loinc.org|77606-2,http://loinc.org|777-3,http://loinc.org|785-6,http://loinc.org|786-4,http://loinc.org|787-2,http://loinc.org|788-0,http://loinc.org|789-8,http://loinc.org|80382-5,http://loinc.org|80383-3,http://loinc.org|8302-2,http://loinc.org|8310-5,http://loinc.org|8331-1,http://loinc.org|8478-0,http://loinc.org|85318-4,http://loinc.org|85319-2,http://loinc.org|85337-4,http://loinc.org|85339-0,http://loinc.org|85352-3,http://loinc.org|85354-9,http://loinc.org|88020-3,http://loinc.org|88021-1,http://loinc.org|88040-1,http://loinc.org|88262-1,http://loinc.org|8867-4,http://loinc.org|89579-7,http://loinc.org|91148-7,http://loinc.org|92130-4,http://loinc.org|92131-2,http://loinc.org|92134-6,http://loinc.org|92138-7,http://loinc.org|92139-5,http://loinc.org|92140-3,http://loinc.org|92141-1,http://loinc.org|92142-9,http://loinc.org|9279-1,http://loinc.org|94040-3,http://loinc.org|94531-1,http://loinc.org|9843-4,http://loinc.org|99999-0" 42929
- name: Download Observation Resources of male Patients
run: .github/scripts/download-resources-query.sh Observation "patient.gender=male" 20466
- name: Download Observation Resources of male Patients Sorted by ID
run: .github/scripts/download-resources-query-sort.sh Observation "patient.gender=male" "_id" 20466
- name: Download Observation Resources of male Patients Sorted Ascending by Last Updated
run: .github/scripts/download-resources-query-sort.sh Observation "patient.gender=male" "_lastUpdated" 20466
- name: Download Observation Resources of male Patients Sorted Descending by Last Updated
run: .github/scripts/download-resources-query-sort.sh Observation "patient.gender=male" "-_lastUpdated" 20466
- name: Download Laboratory Observation Resources Sorted by ID
run: .github/scripts/download-resources-query-sort.sh Observation "category=laboratory" "_id" 29206
- name: Download Laboratory Observation Resources Sorted Ascending by Last Updated
run: .github/scripts/download-resources-query-sort.sh Observation "category=laboratory" "_lastUpdated" 29206
- name: Download Observation Resources of female Patients
run: .github/scripts/download-resources-query.sh Observation "_count=500&patient.gender=female" 22463
- name: Download Observation Resources of the year 1970
run: .github/scripts/download-resources-query.sh Observation "date=1970" 59
- name: Download Observation Resources of the year 1970 Sorted by ID
run: .github/scripts/download-resources-query-sort.sh Observation "date=1970" "_id" 59
- name: Download Observation Resources of the year 1980
run: .github/scripts/download-resources-query.sh Observation "date=1980" 0
- name: Download Observation Resources of the year 1980 Sorted by ID
run: .github/scripts/download-resources-query-sort.sh Observation "date=1980" "_id" 0
- name: Download Observation Resources of the year 1990
run: .github/scripts/download-resources-query.sh Observation "date=1990" 19
- name: Download Observation Resources of the year 2000
run: .github/scripts/download-resources-query.sh Observation "date=2000" 101
- name: Download Observation Resources of the year 2010
run: .github/scripts/download-resources-query.sh Observation "date=2010" 995
- name: Download Observation Resources of the year 2020
run: .github/scripts/download-resources-query.sh Observation "date=2020" 17419
- name: Download Observation Resources of the year 2020 Sorted by ID
run: .github/scripts/download-resources-query-sort.sh Observation "date=2020" "_id" 17419
- name: Download Observation Resources not of the year 2020
run: .github/scripts/download-resources-query.sh Observation "date=ne2020" 25510
- name: Download Observation Resources not of the year 2020 Sorted by ID
run: .github/scripts/download-resources-query-sort.sh Observation "date=ne2020" "_id" 25510
- name: Download Observation Resources greater than the year 2010
run: .github/scripts/download-resources-query.sh Observation "date=gt2010" 38486
- name: Download Observation Resources greater than the year 2020
run: .github/scripts/download-resources-query.sh Observation "date=gt2020" 983
- name: Download Observation Resources less than the year 2010
run: .github/scripts/download-resources-query.sh Observation "date=lt2010" 3448
- name: Download Observation Resources less than the year 2020
run: .github/scripts/download-resources-query.sh Observation "date=lt2020" 24527
- name: Download Observation Resources greater equal the year 2010
run: .github/scripts/download-resources-query.sh Observation "date=ge2010" 39481
- name: Download Observation Resources greater equal the year 2020
run: .github/scripts/download-resources-query.sh Observation "date=ge2020" 18402
- name: Download Observation Resources less equal the year 2010
run: .github/scripts/download-resources-query.sh Observation "date=le2010" 4443
- name: Download Observation Resources less equal the year 2020
run: .github/scripts/download-resources-query.sh Observation "date=le2020" 41946
- name: Download Observation Resources that start after the year 2010
run: .github/scripts/download-resources-query.sh Observation "date=sa2010" 38486
- name: Download Observation Resources that start after the year 2020
run: .github/scripts/download-resources-query.sh Observation "date=sa2020" 983
- name: Download Observation Resources that end before the year 2010
run: .github/scripts/download-resources-query.sh Observation "date=eb2010" 3448
- name: Download Observation Resources that end before the year 2020
run: .github/scripts/download-resources-query.sh Observation "date=eb2020" 24527
- name: Check Observation Date Search
run: .github/scripts/check-date-search.sh "Observation"
- name: Check Encounter Date Search
run: .github/scripts/check-date-search.sh "Encounter"
- name: Check DiagnosticReport Date Search
run: .github/scripts/check-date-search.sh "DiagnosticReport"
- name: Download Observation Resources of female Patients Sorted Ascending
run: .github/scripts/download-resources-query-sort.sh Observation "patient.gender=female" "_lastUpdated" 22463
- name: Download Observation Resources of female Patients Sorted Descending
run: .github/scripts/download-resources-query-sort.sh Observation "patient.gender=female" "-_lastUpdated" 22463
- name: Download Observation Resources - Including Patients
run: blazectl --no-progress --server http://localhost:8080/fhir download Observation -q '_include=Observation:patient' -o Observation-Patient.ndjson
- name: Download Observation Resources - Including Encounters and Patients
run: blazectl --no-progress --server http://localhost:8080/fhir download Observation -q '_include=Observation:encounter&_include=Observation:patient' -o Observation-Encounter-Patient.ndjson
- name: Download Observation Resources - Including Encounters and Encounter Patients
run: blazectl --no-progress --server http://localhost:8080/fhir download Observation -q '_include=Observation:encounter&_include:iterate=Encounter:patient' -o Observation-Encounter-Encounter-Patient.ndjson
- name: Download Condition Resources
run: .github/scripts/download-resources.sh Condition
- name: Download Condition Resources - Including Subjects
run: blazectl --no-progress --server http://localhost:8080/fhir download Condition -q '_include=Condition:subject' -o Condition-Subject.ndjson
- name: Download Condition Resources - Including Encounters
run: blazectl --no-progress --server http://localhost:8080/fhir download Condition -q '_include=Condition:encounter' -o Condition-Encounter.ndjson
- name: Download DiagnosticReport Resources
run: .github/scripts/download-resources.sh DiagnosticReport
- name: Download MedicationRequest Resources of Medications with code 854235
run: .github/scripts/download-resources-query.sh MedicationRequest "medication.code=1736854" 112
- name: Download MedicationRequest Resources of Medications with code 854235 Sorted Ascending
run: .github/scripts/download-resources-query-sort.sh MedicationRequest "medication.code=1736854" "_lastUpdated" 112
- name: Download MedicationRequest Resources of Medications with code 854235 Sorted Descending
run: .github/scripts/download-resources-query-sort.sh MedicationRequest "medication.code=1736854" "-_lastUpdated" 112
- name: Download MedicationRequest Resources - Including Medications
run: blazectl --no-progress --server http://localhost:8080/fhir download MedicationRequest -q '_include=MedicationRequest:medication' -o MedicationRequest.ndjson
- name: Download male Patient Resources having inpatient Encounters in 2010
run: .github/scripts/download-resources-query.sh Patient "gender=male&_has:Encounter:patient:class=IMP&_has:Encounter:patient:date=2010" 8
- name: Download female Patient Resources having inpatient Encounters in 2010
run: .github/scripts/download-resources-query.sh Patient "gender=female&_has:Encounter:patient:class=IMP&_has:Encounter:patient:date=2010" 11
- name: Download Observations using _elements=subject
run: .github/scripts/download-observations-elements.sh
- name: Download Observations of all Encounters using ID's
run: .github/scripts/download-observations-of-all-encounters.sh
- name: Search Observation _lastUpdated
run: .github/scripts/search-patient-last-updated.sh
- name: Search Observation _profile
run: .github/scripts/search-observation-profile.sh
- name: Search Compartment
run: .github/scripts/search-compartment.sh
- name: Evaluate CQL Query 1
run: .github/scripts/evaluate-measure.sh q1 56
- name: Evaluate CQL Query 1 as Batch
run: .github/scripts/evaluate-measure-as-batch.sh q1 56
- name: Evaluate CQL Query 1 async
run: .github/scripts/evaluate-measure-async.sh q1 56
- name: Evaluate CQL Query 1 using Blazectl
run: .github/scripts/evaluate-measure-blazectl.sh q1 56
- name: Evaluate CQL Query 1 - Subject List
run: .github/scripts/evaluate-measure-subject-list.sh q1 56
- name: Evaluate CQL Query 1 - Subject List as Batch
run: .github/scripts/evaluate-measure-subject-list-as-batch.sh q1 56
- name: Evaluate CQL Query 1 on Individual Patients
run: .github/scripts/evaluate-patient-q1-measure.sh
- name: Evaluate CQL Query 2
run: .github/scripts/evaluate-measure.sh q2 42
- name: Evaluate CQL Query 2 as Batch
run: .github/scripts/evaluate-measure-as-batch.sh q2 42
- name: Evaluate CQL Query 2 using Blazectl
run: .github/scripts/evaluate-measure-blazectl.sh q2 42
- name: Evaluate CQL Query 2 - Subject List
run: .github/scripts/evaluate-measure-subject-list.sh q2 42
- name: Evaluate CQL Query 2 - Subject List as Batch
run: .github/scripts/evaluate-measure-subject-list-as-batch.sh q2 42
- name: Evaluate CQL Query 4
run: .github/scripts/evaluate-measure.sh q4 0
- name: Evaluate CQL Query 4 using Blazectl
run: .github/scripts/evaluate-measure-blazectl.sh q4 0
- name: Evaluate CQL Query 4 - Subject List
run: .github/scripts/evaluate-measure-subject-list.sh q4 0
- name: Evaluate CQL Query 7
run: .github/scripts/evaluate-measure.sh q7 81
- name: Evaluate CQL Query 7 using Blazectl
run: .github/scripts/evaluate-measure-blazectl.sh q7 81
- name: Evaluate CQL Query 7 - Subject List
run: .github/scripts/evaluate-measure-subject-list.sh q7 81
- name: Evaluate CQL Query 14
run: .github/scripts/evaluate-measure.sh q14 96
- name: Evaluate CQL Query 14 using Blazectl
run: .github/scripts/evaluate-measure-blazectl.sh q14 96
- name: Evaluate CQL Query 14 - Subject List
run: .github/scripts/evaluate-measure-subject-list.sh q14 96
- name: Evaluate CQL Query 15 using Blazectl
run: .github/scripts/evaluate-measure.sh q15 31
- name: Evaluate CQL Query 17
run: .github/scripts/evaluate-measure.sh q17 120
- name: Evaluate CQL Query 17 using Blazectl
run: .github/scripts/evaluate-measure-blazectl.sh q17 120
- name: Evaluate CQL Query 17 - Subject List
run: .github/scripts/evaluate-measure-subject-list.sh q17 120
- name: Evaluate CQL Query 20 using Blazectl
run: .github/scripts/evaluate-measure-blazectl-stratifier.sh q20-stratifier-city 120
- name: Evaluate CQL Query 21 using Blazectl
run: .github/scripts/evaluate-measure-blazectl-stratifier.sh q21-stratifier-city-of-only-women 64
- name: Evaluate CQL Query 26 using Blazectl
run: .github/scripts/evaluate-measure-blazectl-stratifier.sh q26-stratifier-bmi 120
- name: Evaluate CQL Query 27 using Blazectl
run: .github/scripts/evaluate-measure-blazectl-stratifier.sh q27-stratifier-calculated-bmi 120
- name: Evaluate CQL Query 32 using Blazectl
run: .github/scripts/evaluate-measure-blazectl-stratifier.sh q32-stratifier-underweight 120
- name: Evaluate CQL Query 36
run: .github/scripts/evaluate-measure.sh q36-parameter 86
- name: Evaluate CQL Query 36 - Subject List
run: .github/scripts/evaluate-measure-subject-list.sh q36-parameter 86
- name: Evaluate CQL Query 34
run: .github/scripts/evaluate-measure.sh q37-overlaps 24
- name: Evaluate CQL Query 34 using Blazectl
run: .github/scripts/evaluate-measure-blazectl.sh q37-overlaps 24
- name: Evaluate CQL Query 34 - Subject List
run: .github/scripts/evaluate-measure-subject-list.sh q37-overlaps 24
- name: Evaluate CQL Query 46
run: .github/scripts/evaluate-measure.sh q46-between-date 19
- name: Evaluate CQL Query 46 using Blazectl
run: .github/scripts/evaluate-measure-blazectl.sh q46-between-date 19
- name: Forwarded Header HTTPS
run: .github/scripts/forwarded-header.sh https
- name: Forwarded Header HTTP
run: .github/scripts/forwarded-header.sh http
- name: X-Forwarded Headers HTTPS
run: .github/scripts/x-forwarded-headers.sh https
- name: X-Forwarded Headers HTTP
run: .github/scripts/x-forwarded-headers.sh http
- name: Delete
run: .github/scripts/delete.sh
- name: Delete Violating Referential Integrity
run: .github/scripts/check-referential-integrity-for-delete.sh 409
- name: Delete After Referring Resource is Deleted Succeeds
run: .github/scripts/check-delete-succeeds-after-referring-resource-is-deleted.sh
- name: Batch
run: .github/scripts/batch.sh
- name: Batch Metadata
run: .github/scripts/batch-metadata.sh
- name: Transaction
run: .github/scripts/transaction.sh
- name: Transaction Read/Write
run: .github/scripts/transaction-rw.sh
- name: Transactional Delete Preserving Referential Integrity
run: .github/scripts/transactional-delete.sh
- name: Transaction with Invalid (Null) Resource
run: .github/scripts/transaction-null-resource.sh
- name: OPTIONS
run: curl -f -XOPTIONS http://localhost:8080/fhir/metadata
- name: Health
run: curl -f http://localhost:8080/health
- name: Health - HEAD
run: curl -f --head http://localhost:8080/health
- name: Not Acceptable
run: .github/scripts/not-acceptable.sh
- name: Conditional Update If-None-Match
run: .github/scripts/conditional-update-if-none-match.sh
- name: GraphQL Patient
run: .github/scripts/graphql.sh Patient
- name: GraphQL Observation
run: .github/scripts/graphql.sh Observation